International Journal of Molecular Sciences

Editorial

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3 pages, 151 KiB

Open AccessEditorial

Preface—Plant Proteomic Research

by Setsuko Komatsu and Zahed Hossain

Int. J. Mol. Sci. 2017, 18(1), 88; https://doi.org/10.3390/ijms18010088 - 4 Jan 2017

Cited by 9 | Viewed by 5527

Abstract

Plants, being sessile in nature, are constantly exposed to environmental challenges resulting in substantial yield loss[...] Full article

(This article belongs to the Special Issue Plant Proteomic Research)

Research

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16 pages, 3028 KiB

Open AccessArticle

The Cannabis Proteome Draft Map Project

by Conor Jenkins and Benjamin Orsburn

Int. J. Mol. Sci. 2020, 21(3), 965; https://doi.org/10.3390/ijms21030965 - 31 Jan 2020

Cited by 18 | Viewed by 5241

Abstract

Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant [...] Read more.

Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated protein FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources developed from our proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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24 pages, 2220 KiB

Open AccessArticle

Proteomic Analysis of Quercetin-Treated K562 Cells

by Fabrizia Brisdelli, Laura Di Francesco, Alessandra Giorgi, Anna Rita Lizzi, Carla Luzi, Giuseppina Mignogna, Argante Bozzi and M. Eugenia Schininà

Int. J. Mol. Sci. 2020, 21(1), 32; https://doi.org/10.3390/ijms21010032 - 19 Dec 2019

Cited by 8 | Viewed by 4663

Abstract

Among natural products under investigation for their additive potential in cancer prevention and treatment, the flavonoid quercetin has received attention for its effects on the cell cycle arrest and apoptosis. In the past, we addressed this issue in K562 cells, a cellular model [...] Read more.

Among natural products under investigation for their additive potential in cancer prevention and treatment, the flavonoid quercetin has received attention for its effects on the cell cycle arrest and apoptosis. In the past, we addressed this issue in K562 cells, a cellular model of the human chronic myeloid leukemia. Here, we applied stable isotope labeling by amino acids in cell culture (SILAC) proteomics with the aim to increase knowledge on the regulative and metabolic pathways modulated by quercetin in these cells. After 24 h of quercetin treatment, we observed that apoptosis was not completely established, thus we selected this time range to capture quantitative data. As a result, we were able to achieve a robust identification of 1703 proteins, and to measure fold changes between quercetin-treated and untreated cells for 1206 proteins. Through a bioinformatics functional analysis on a subset of 112 proteins, we propose that the apoptotic phenotype of K562 cells entails a significant modulation of the translational machinery, RNA metabolism, antioxidant defense systems, and enzymes involved in lipid metabolism. Finally, we selected eight differentially expressed proteins, validated their modulated expression in quercetin-treated K562 cells, and discussed their possible role in flavonoid cytotoxicity. This quantitative profiling, performed for the first time on this type of tumor cells upon treatment with a flavonoid, will contribute to revealing the molecular basis of the multiplicity of the effects selectively exerted by quercetin on K562 cells. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 1726 KiB

Open AccessArticle

Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis

by Yusuke Kawashima, Eiichiro Watanabe, Taichi Umeyama, Daisuke Nakajima, Masahira Hattori, Kenya Honda and Osamu Ohara

Int. J. Mol. Sci. 2019, 20(23), 5932; https://doi.org/10.3390/ijms20235932 - 26 Nov 2019

Cited by 85 | Viewed by 9768

Abstract

Data-independent acquisition (DIA)-mass spectrometry (MS)-based proteomic analysis overtop the existing data-dependent acquisition (DDA)-MS-based proteomic analysis to enable deep proteome coverage and precise relative quantitative analysis in single-shot liquid chromatography (LC)-MS/MS. However, DIA-MS-based proteomic analysis has not yet been optimized in terms of system [...] Read more.

Data-independent acquisition (DIA)-mass spectrometry (MS)-based proteomic analysis overtop the existing data-dependent acquisition (DDA)-MS-based proteomic analysis to enable deep proteome coverage and precise relative quantitative analysis in single-shot liquid chromatography (LC)-MS/MS. However, DIA-MS-based proteomic analysis has not yet been optimized in terms of system robustness and throughput, particularly for its practical applications. We established a single-shot LC-MS/MS system with an MS measurement time of 90 min for a highly sensitive and deep proteomic analysis by optimizing the conditions of DIA and nanoLC. We identified 7020 and 4068 proteins from 200 ng and 10 ng, respectively, of tryptic floating human embryonic kidney cells 293 (HEK293F) cell digest by performing the constructed LC-MS method with a protein sequence database search. The numbers of identified proteins from 200 ng and 10 ng of tryptic HEK293F increased to 8509 and 5706, respectively, by searching the chromatogram library created by gas-phase fractionated DIA. Moreover, DIA protein quantification was highly reproducible, with median coefficients of variation of 4.3% in eight replicate analyses. We could demonstrate the power of this system by applying the proteomic analysis to detect subtle changes in protein profiles between cerebrums in germ-free and specific pathogen-free mice, which successfully showed that >40 proteins were differentially produced between the cerebrums in the presence or absence of bacteria. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 3064 KiB

Open AccessArticle

Interpretation of Fiber Supplementation on Offspring Testicular Development in a Pregnant Sow Model from a Proteomics Perspective

by Yan Lin, Lujie Li, Yang Li, Ke Wang, Dongqin Wei, Shengyu Xu, Bin Feng, Lianqiang Che, Zhengfeng Fang, Jian Li, Yong Zhuo and De Wu

Int. J. Mol. Sci. 2019, 20(18), 4549; https://doi.org/10.3390/ijms20184549 - 13 Sep 2019

Cited by 9 | Viewed by 3339

Abstract

To study the effects of maternal fiber supplementation during pregnancy on the testicular development of male offspring and its possible mechanisms, 36 sows (Landrace × Yorkshire) were allocated to either a control diet (n = 18) or a fiber diet (the control [...] Read more.

To study the effects of maternal fiber supplementation during pregnancy on the testicular development of male offspring and its possible mechanisms, 36 sows (Landrace × Yorkshire) were allocated to either a control diet (n = 18) or a fiber diet (the control diet supplemented with 22.60 g/kg inulin and 181.60 g/kg cellulosic; n = 18) during pregnancy. The body and testes weight of the offspring, 7-day-old piglets, was recorded. Testes were collected for further analyses. Results showed that the testicular organ index and the number of spermatogonia in single seminiferous tubule were higher in piglets from the fiber group than from the control group (p < 0.05). In addition, a significant increase in the concentration of glucose, lactate, and lipids in the testes was found in the fiber group (p < 0.05). Proteomic analysis suggested that there were notable differences in glucolipid transport and metabolism, oxidation, and male reproduction-related proteins expression between the two groups (p < 0.05). Results revealed that the most enriched signaling pathways in the fiber group testes included starch and sucrose metabolism, fatty acid metabolism, glutathione metabolism, and the renin-angiotensin system. mRNA expression analyzes further confirmed the importance of some signaling pathways in maternal fiber nutrition regulating offspring testicular development. Our results shed new light on the underlying molecular mechanisms of maternal fiber nutrition on offspring testicular development and provided a valuable insight for future explorations of the effect of maternal fiber nutrition on man reproduction. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 2979 KiB

Open AccessArticle

Proteomics Approach for the Discovery of Rheumatoid Arthritis Biomarkers Using Mass Spectrometry

by Sora Mun, Jiyeong Lee, Arum Park, Hyo-Jin Kim, Yoo-Jin Lee, Hyunsong Son, Miji Shin, Mi-Kyoung Lim and Hee-Gyoo Kang

Int. J. Mol. Sci. 2019, 20(18), 4368; https://doi.org/10.3390/ijms20184368 - 5 Sep 2019

Cited by 38 | Viewed by 5651

Abstract

Rheumatoid arthritis is an autoimmune disease that causes serious functional loss in patients. Early and accurate diagnosis of rheumatoid arthritis may attenuate its severity. Despite a diagnosis guideline in the 2010 American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) classification criteria for [...] Read more.

Rheumatoid arthritis is an autoimmune disease that causes serious functional loss in patients. Early and accurate diagnosis of rheumatoid arthritis may attenuate its severity. Despite a diagnosis guideline in the 2010 American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) classification criteria for rheumatoid arthritis, the practical difficulties in its diagnosis highlight the need of developing new methods for diagnosing rheumatoid arthritis. The current study aimed to identify rheumatoid arthritis diagnostic biomarkers by using a proteomics approach. Serum protein profiling was conducted using mass spectrometry, and five distinguishable biomarkers were identified therefrom. In the validation study, the five biomarkers were quantitatively verified by multiple reaction monitoring (MRM) analysis. Two proteins, namely serum amyloid A4 and vitamin D binding protein, showed high performance in distinguishing patients with rheumatoid arthritis from healthy controls. Logistic analysis was conducted to evaluate how accurately the two biomarkers distinguish patients with rheumatoid arthritis from healthy controls. The classification accuracy was 86.0% and 81.4% in patients with rheumatoid arthritis and in healthy controls, respectively. Serum amyloid A4 and vitamin D binding protein could be potential biomarkers related to the inflammatory response and joint destruction that accompany rheumatoid arthritis. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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19 pages, 6918 KiB

Open AccessArticle

An Insight into the Proteome of Uveal Melanoma-Derived Ectosomes Reveals the Presence of Potentially Useful Biomarkers

by Magdalena Surman, Dorota Hoja-Łukowicz, Sabina Szwed, Sylwia Kędracka-Krok, Urszula Jankowska, Magdalena Kurtyka, Anna Drożdż, Anna Lityńska, Ewa Stępień and Małgorzata Przybyło

Int. J. Mol. Sci. 2019, 20(15), 3789; https://doi.org/10.3390/ijms20153789 - 2 Aug 2019

Cited by 34 | Viewed by 4379

Abstract

Cancer cells are known to release extracellular vesicles that often promote disease development and progression. The present study investigated the protein content and glycosylation pattern of ectosomes released in vitro by a human primary uveal melanoma Mel202 cell line. Ectosomes released by Mel202 [...] Read more.

Cancer cells are known to release extracellular vesicles that often promote disease development and progression. The present study investigated the protein content and glycosylation pattern of ectosomes released in vitro by a human primary uveal melanoma Mel202 cell line. Ectosomes released by Mel202 cells were isolated from conditioned media using sequential centrifugation, and a nano-LC-MS/MS approach was used to determine their protein content. Subsequently, proteins from ectosomes, the whole cell extracts, and the membrane fractions were probed with a panel of lectins using Western blotting and flow cytometry to reveal characteristic glycan structures. As many as 2527 unique proteins were identified, and many of them are known to be involved in cancer cell proliferation and altered metabolism, tumor invasion, metastasis, or drug resistance. Lectin-based studies revealed a distinct glycosylation pattern between Mel202-derived ectosomes and the parental cell membranes. Selective enrichment of ectosomal proteins with bisected complex type N-glycans and α2,6-linked sialic acids may be significant for ectosome formation and sequestration. Differences in the surface glycosylation of Mel202 cells and ectosomes supports recent findings that the budding of ectosomes occurs within strictly determined fragments of the plasma membrane, and thus ectosomes contain a unique protein and glycan composition. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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22 pages, 3737 KiB

Open AccessArticle

Proteomic Analysis of Morphologically Changed Tissues after Prolonged Dexamethasone Treatment

by Abeer K. Malkawi, Afshan Masood, Zakia Shinwari, Minnie Jacob, Hicham Benabdelkamel, Goran Matic, Falah Almuhanna, Majed Dasouki, Ayodele A. Alaiya and Anas M. Abdel Rahman

Int. J. Mol. Sci. 2019, 20(13), 3122; https://doi.org/10.3390/ijms20133122 - 26 Jun 2019

Cited by 19 | Viewed by 5344

Abstract

Prolonged dexamethasone (Dex) administration leads to serious adverse and decrease brain and heart size, muscular atrophy, hemorrhagic liver, and presence of kidney cysts. Herein, we used an untargeted proteomic approach using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for simultaneous identification of changes in proteomes [...] Read more.

Prolonged dexamethasone (Dex) administration leads to serious adverse and decrease brain and heart size, muscular atrophy, hemorrhagic liver, and presence of kidney cysts. Herein, we used an untargeted proteomic approach using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for simultaneous identification of changes in proteomes of the major organs in Sprague–Dawley (SD rats post Dex treatment. The comparative and quantitative proteomic analysis of the brain, heart, muscle, liver, and kidney tissues revealed differential expression of proteins (n = 190, 193, 39, 230, and 53, respectively) between Dex-treated and control rats. Functional network analysis using ingenuity pathway analysis (IPA revealed significant differences in regulation of metabolic pathways within the morphologically changed organs that related to: (i) brain—cell morphology, nervous system development, and function and neurological disease; (ii) heart—cellular development, cellular function and maintenance, connective tissue development and function; (iii) skeletal muscle—nucleic acid metabolism, and small molecule biochemical pathways; (iv) liver—lipid metabolism, small molecular biochemistry, and nucleic acid metabolism; and (v) kidney—drug metabolism, organism injury and abnormalities, and renal damage. Our study provides a comprehensive description of the organ-specific proteomic profilesand differentially altered biochemical pathways, after prolonged Dex treatement to understand the molecular basis for development of side effects. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 1840 KiB

Open AccessArticle

Rapid Detection and Identification of Antimicrobial Peptide Fingerprints of Nasal Fluid by Mesoporous Silica Particles and MALDI-TOF/TOF Mass Spectrometry: From the Analytical Approach to the Diagnostic Applicability in Precision Medicine

by Mariaimmacolata Preianò, Giuseppina Maggisano, Maria Stella Murfuni, Chiara Villella, Carmela Colica, Annalisa Fregola, Corrado Pelaia, Nicola Lombardo, Girolamo Pelaia, Rocco Savino and Rosa Terracciano

Int. J. Mol. Sci. 2018, 19(12), 4005; https://doi.org/10.3390/ijms19124005 - 12 Dec 2018

Cited by 13 | Viewed by 4640

Abstract

Background: Antimicrobial peptides (AMP) play a pivotal role in innate host defense and in immune response. The delineation of new MS-based profiling tools, which are able to produce panels of AMP of the nasal fluid (NF), may be attractive for the discovery of [...] Read more.

Background: Antimicrobial peptides (AMP) play a pivotal role in innate host defense and in immune response. The delineation of new MS-based profiling tools, which are able to produce panels of AMP of the nasal fluid (NF), may be attractive for the discovery of new potential diagnostic markers of respiratory disorders. Methods: Swabs collected NF from healthy patients and from patients with respiratory disorders. We used a fast procedure based on mesoporous silica particles (MPS) to enrich NF in its AMP component in combination with MALDI-TOF/TOF MS as a key tool for rapidly analyzing clinical samples. Results: Reproducible MS peptide fingerprints were generated for each subject and several AMP were detected including (Human Neutrophil Peptides) HNPs, Statherin, Thymosin-β4, Peptide P-D, II-2, β-MSP, SLPI, Lysozyme-C, and their proteo-forms. In particular, Statherin, Thymosin-β4, and Peptide P-D were accurately identified by direct MS/MS sequencing. Examples of applicability of this tool are shown. AMP fingerprints were obtained before and after a nasal polypectomy as well as before and post-treatment with azelastine/fluticasone in one case of allergic rhinitis. Conclusion: The potential of our platform to be implemented by new mesoporous materials for capturing a wider picture of AMP might offer an amazing opportunity for diagnostic clinical studies on individual and population scales. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 2636 KiB

Open AccessCommunication

Label-Free Quantitative Proteomics in a Methylmalonyl-CoA Mutase-Silenced Neuroblastoma Cell Line

by Michele Costanzo, Armando Cevenini, Emanuela Marchese, Esther Imperlini, Maddalena Raia, Luigi Del Vecchio, Marianna Caterino and Margherita Ruoppolo

Int. J. Mol. Sci. 2018, 19(11), 3580; https://doi.org/10.3390/ijms19113580 - 13 Nov 2018

Cited by 32 | Viewed by 4239

Abstract

Methylmalonic acidemias (MMAs) are inborn errors of metabolism due to the deficient activity of methylmalonyl-CoA mutase (MUT). MUT catalyzes the formation of succinyl-CoA from methylmalonyl-CoA, produced from propionyl-CoA catabolism and derived from odd chain fatty acids β-oxidation, cholesterol, and branched-chain amino acids degradation. [...] Read more.

Methylmalonic acidemias (MMAs) are inborn errors of metabolism due to the deficient activity of methylmalonyl-CoA mutase (MUT). MUT catalyzes the formation of succinyl-CoA from methylmalonyl-CoA, produced from propionyl-CoA catabolism and derived from odd chain fatty acids β-oxidation, cholesterol, and branched-chain amino acids degradation. Increased methylmalonyl-CoA levels allow for the presymptomatic diagnosis of the disease, even though no approved therapies exist. MMA patients show hyperammonemia, ketoacidosis, lethargy, respiratory distress, cognitive impairment, and hepatomegaly. The long-term consequences concern neurologic damage and terminal kidney failure, with little chance of survival. The cellular pathways affected by MUT deficiency were investigated using a quantitative proteomics approach on a cellular model of MUT knockdown. Currently, a consistent reduction of the MUT protein expression was obtained in the neuroblastoma cell line (SH-SY5Y) by using small-interfering RNA (siRNA) directed against an MUT transcript (MUT siRNA). The MUT absence did not affect the cell viability and apoptotic process in SH-SY5Y. In the present study, we evaluate and quantify the alterations in the protein expression profile as a consequence of MUT-silencing by a mass spectrometry-based label-free quantitative analysis, using two different quantitative strategies. Both quantitative methods allowed us to observe that the expression of the proteins involved in mitochondrial oxido-reductive homeostasis balance was affected by MUT deficiency. The alterated functional mitochondrial activity was observed in siRNA_MUT cells cultured with a propionate-supplemented medium. Finally, alterations in the levels of proteins involved in the metabolic pathways, like carbohydrate metabolism and lipid metabolism, were found. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 2837 KiB

Open AccessArticle

Proteomic Analysis of Plasma Membrane Proteins of Antler Stem Cells Using Label-Free LC–MS/MS

by Datao Wang, Hengxing Ba, Chenguang Li, Quanmin Zhao and Chunyi Li

Int. J. Mol. Sci. 2018, 19(11), 3477; https://doi.org/10.3390/ijms19113477 - 5 Nov 2018

Cited by 11 | Viewed by 5253

Abstract

Deer antlers are unusual mammalian organs that can fully regenerate after annual shedding. Stem cells resident in the pedicle periosteum (PPCs) provide the main cell source for antler regeneration. Central to various cellular processes are plasma membrane proteins, but the expression of these [...] Read more.

Deer antlers are unusual mammalian organs that can fully regenerate after annual shedding. Stem cells resident in the pedicle periosteum (PPCs) provide the main cell source for antler regeneration. Central to various cellular processes are plasma membrane proteins, but the expression of these proteins has not been well documented in antler regeneration. In the present study, plasma membrane proteins of PPCs and facial periosteal cells (FPCs) were analyzed using label-free liquid chromatography–mass spetrometry (LC–MS/MS). A total of 1739 proteins were identified. Of these proteins, 53 were found solely in the PPCs, 100 solely in the FPCs, and 1576 co-existed in both PPCs and FPCs; and 39 were significantly up-regulated in PPCs and 49 up-regulated in FPCs. In total, 226 gene ontology (GO) terms were significantly enriched from the differentially expressed proteins (DEPs). Five clusters of biological processes from these GO terms comprised responses to external stimuli, signal transduction, membrane transport, regulation of tissue regeneration, and protein modification processes. Further studies are required to demonstrate the relevancy of these DEPs in antler stem cell biology and antler regeneration. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 4529 KiB

Open AccessArticle

IL-18 and S100A12 Are Upregulated in Experimental Central Retinal Vein Occlusion

by Lasse Jørgensen Cehofski, Anders Kruse, Svend Kirkeby, Alexander Nørgård Alsing, Jonas Ellegaard Nielsen, Kentaro Kojima, Bent Honoré and Henrik Vorum

Int. J. Mol. Sci. 2018, 19(11), 3328; https://doi.org/10.3390/ijms19113328 - 25 Oct 2018

Cited by 19 | Viewed by 4674

Abstract

Retinal vein occlusion (RVO) is a common retinal vascular disease. RVO may be complicated by pronounced ischemia that often leads to severe loss of visual function. The present work aimed at studying the retinal proteome of RVO complicated by ischemia. In six Danish [...] Read more.

Retinal vein occlusion (RVO) is a common retinal vascular disease. RVO may be complicated by pronounced ischemia that often leads to severe loss of visual function. The present work aimed at studying the retinal proteome of RVO complicated by ischemia. In six Danish Landrace pigs RVO was induced with argon laser in the right eye of each animal. As four retinal veins were occluded, the RVO best corresponded to a central retinal vein occlusion (CRVO). Left control eyes received a similar laser treatment without inducing occlusion. RVO and retinal ischemia were verified by angiography. The retinas were collected 15 days after RVO for proteomic analysis. RVO resulted in a downregulation of proteins involved in visual perception, including rhodopsin, transducin alpha chain, and peripherin-2. RVO also caused a downregulation of proteins involved in neurotransmitter transport, including glutamate decarboxylase 1 (GAD1), glutamate decarboxylase 2 (GAD2), and complexins 2–4. RVO lead to increased contents of proteins involved in inflammation, including interleukin-18 (IL-18), S100A12, and annexin A1 (ANXA1). Immunohistochemistry revealed a general retinal upregulation of IL-18 and ANXA1 while S100A12 was highly abundant in retinal ganglion cells in RVO. IL-18 and S100A12 are likely to be driving forces in the inflammatory response of RVO complicated by ischemia. Our findings also suggest that RVO results in compromised neurotransmission and a downregulation of proteins involved in visual perception. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 11726 KiB

Open AccessArticle

Quiescin Sulfhydryl Oxidase 1 (QSOX1) Secreted by Lung Cancer Cells Promotes Cancer Metastasis

by Hye-Jin Sung, Jung-Mo Ahn, Yeon-Hee Yoon, Sang-Su Na, Young-Jin Choi, Yong-In Kim, Soo-Youn Lee, Eung-Bae Lee, Sukki Cho and Je-Yoel Cho

Int. J. Mol. Sci. 2018, 19(10), 3213; https://doi.org/10.3390/ijms19103213 - 17 Oct 2018

Cited by 36 | Viewed by 5562

Abstract

As lung cancer shows the highest mortality in cancer-related death, serum biomarkers are demanded for lung cancer diagnosis and its treatment. To discover lung cancer protein biomarkers, secreted proteins from primary cultured lung cancer and adjacent normal tissues from patients were subjected to [...] Read more.

As lung cancer shows the highest mortality in cancer-related death, serum biomarkers are demanded for lung cancer diagnosis and its treatment. To discover lung cancer protein biomarkers, secreted proteins from primary cultured lung cancer and adjacent normal tissues from patients were subjected to LC/MS–MS proteomic analysis. Quiescin sulfhydryl oxidase (QSOX1) was selected as a biomarker candidate from the enriched proteins in the secretion of lung cancer cells. QSOX1 levels were higher in 82% (51 of 62 tissues) of lung cancer tissues compared to adjacent normal tissues. Importantly, QSOX1 serum levels were significantly higher in cancer patients (p < 0.05, Area Under curve (AUC) = 0.89) when measured by multiple reaction monitoring (MRM). Higher levels of QSOX1 were also uniquely detected in lung cancer tissues, among several other solid cancers, by immunohistochemistry. QSOX1-knock-downed Lewis lung cancer (LLC) cells were less viable from oxidative stress and reduced migration and invasion. In addition, LLC mouse models with QSOX1 knock-down also proved that QSOX1 functions in promoting cancer metastasis. In conclusion, QSOX1 might be a lung cancer tissue-derived biomarker and be involved in the promotion of lung cancers, and thus can be a therapeutic target for lung cancers. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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12 pages, 2948 KiB

Open AccessArticle

Elucidating Functions of FleQ in Xanthomonas oryzae pv. oryzae by Comparative Proteomic and Phenotypic Analyses

by Nahee Bae, Hye-Jee Park, Hanbi Park, Minyoung Kim, Eunsoo Do and Sang-Wook Han

Int. J. Mol. Sci. 2018, 19(10), 3038; https://doi.org/10.3390/ijms19103038 - 5 Oct 2018

Cited by 15 | Viewed by 4051

Abstract

To acclimate to different environments, gene expression has to be controlled using diverse transcriptional activators. FleQ activates σ⁵⁴-dependent transcription initiation and regulates flagellar biosynthesis and other mechanisms in several bacteria. Xanthomonas oryzae pv. oryzae (Xoo), which is a causal [...] Read more.

To acclimate to different environments, gene expression has to be controlled using diverse transcriptional activators. FleQ activates σ⁵⁴-dependent transcription initiation and regulates flagellar biosynthesis and other mechanisms in several bacteria. Xanthomonas oryzae pv. oryzae (Xoo), which is a causal agent of bacterial leaf blight on rice, lacking FleQ loses swimming motility and virulence is not altered. However, other biological mechanisms related with FleQ in Xoo are unknown. In this study, we generated the FleQ-overexpressing strain, Xoo(FleQ), and knockout mutant, XooΔfleQ. To predict the mechanisms affected by FleQ, label-free shotgun comparative proteomics was carried out. Based on proteomic results, we performed diverse phenotypic assays. Xoo(FleQ) had reduced ability to elicit disease symptoms and exopolysaccharide production. Additionally, the ability of XooΔfleQ(EV) (empty vector) and Xoo(FleQ) to form biofilm was decreased. Swarming motility of XooΔfleQ(EV) was abolished, but was only reduced for Xoo(FleQ). Additionally, abnormal twitching motility was observed in both strains. Siderophore production of Xoo(FleQ) was enhanced in iron-rich conditions. The proteomic and phenotypic analyses revealed that FleQ is involved in flagellar-dependent motility and other mechanisms, including symptom development, twitching motility, exopolysaccharide production, biofilm formation, and siderophore production. Thus, this study provides fundamental information about a σ⁵⁴-dependent transcription activator in Xoo. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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13 pages, 2826 KiB

Open AccessArticle

Evaluation of the Use of TRIzol-Based Protein Extraction Approach for Gel-Based Proteomic Analysis of Dried Seafood Products and Chinese Tonic Foods

by Kin-Ka Chan, Celia Sze-Nga Kwok, Eric Tung-Po Sze and Fred Wang-Fat Lee

Int. J. Mol. Sci. 2018, 19(7), 1998; https://doi.org/10.3390/ijms19071998 - 9 Jul 2018

Cited by 10 | Viewed by 5252

Abstract

Although the emergence of gel-free approaches has greatly enhanced proteomic studies, two-dimensional gel electrophoresis (2-DE) remains one of the most widely used proteomic techniques for its high resolving power, relatively low cost, robustness, and high resolution. Preparation of high-quality protein samples remains the [...] Read more.

Although the emergence of gel-free approaches has greatly enhanced proteomic studies, two-dimensional gel electrophoresis (2-DE) remains one of the most widely used proteomic techniques for its high resolving power, relatively low cost, robustness, and high resolution. Preparation of high-quality protein samples remains the key in high-quality 2-DE for proteomic analysis. Samples with high endogenous levels of interfering molecules, such as salts, nucleic acids, lipids, and polysaccharides, would yield a low-quality 2-DE gel and hinder the analysis. Recently, a TRIzol-based protein extraction method has gained prominence and has attracted attention due to its promising performance in high-quality 2-DE. The authors evaluate the use of this approach for four valuable dried food products, namely two dried seafood products (abalone slices and whelk slices) and two traditional Chinese tonic foods (ganoderma and caterpillar fungus). The results indicate that 2-DE gels obtained through the TRIzol-based method are of high-quality and are comparable to those obtained through the trichloroacetic acid–acetone method in terms of spot number, spot intensity, and resolution. The TRIzol-based method is generally applicable to dried food samples and is simple and fast, which greatly streamlines the protein extraction procedure. Additionally, it enables the concurrent extraction and analysis of RNA, DNA, and protein from the same sample. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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24 pages, 3856 KiB

Open AccessArticle

Mechanism of Salt-Induced Self-Compatibility Dissected by Comparative Proteomic Analysis in Brassica napus L.

by Yong Yang, Zhiquan Liu, Tong Zhang, Guilong Zhou, Zhiqiang Duan, Bing Li, Shengwei Dou, Xiaomei Liang, Jinxing Tu, Jinxiong Shen, Bin Yi, Tingdong Fu, Cheng Dai and Chaozhi Ma

Int. J. Mol. Sci. 2018, 19(6), 1652; https://doi.org/10.3390/ijms19061652 - 3 Jun 2018

Cited by 18 | Viewed by 6328

Abstract

Self-incompatibility (SI) in plants genetically prevents self-fertilization to promote outcrossing and genetic diversity. Its hybrids in Brassica have been widely cultivated due to the propagation of SI lines by spraying a salt solution. We demonstrated that suppression of Brassica napus SI from edible [...] Read more.

Self-incompatibility (SI) in plants genetically prevents self-fertilization to promote outcrossing and genetic diversity. Its hybrids in Brassica have been widely cultivated due to the propagation of SI lines by spraying a salt solution. We demonstrated that suppression of Brassica napus SI from edible salt solution treatment was ascribed to sodium chloride and independent of S haplotypes, but it did not obviously change the expression of SI-related genes. Using the isobaric tags for relative and absolute quantitation (iTRAQ) technique, we identified 885 differentially accumulated proteins (DAPs) in Brassica napus stigmas of un-pollinated (UP), pollinated with compatible pollen (PC), pollinated with incompatible pollen (PI), and pollinated with incompatible pollen after edible salt solution treatment (NA). Of the 307 DAPs in NA/UP, 134 were unique and 94 were shared only with PC/UP. In PC and NA, some salt stress protein species, such as glyoxalase I, were induced, and these protein species were likely to participate in the self-compatibility (SC) pathway. Most of the identified protein species were related to metabolic pathways, biosynthesis of secondary metabolites, ribosome, and so on. A systematic analysis implied that salt treatment-overcoming SI in B. napus was likely conferred by at least five different physiological mechanisms: (i) the use of Ca²⁺ as signal molecule; (ii) loosening of the cell wall to allow pollen tube penetration; (iii) synthesis of compatibility factor protein species for pollen tube growth; (iv) depolymerization of microtubule networks to facilitate pollen tube movement; and (v) inhibition of protein degradation pathways to restrain the SI response. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 6901 KiB

Open AccessArticle

Proteomic Analysis of Various Rat Ocular Tissues after Ischemia–Reperfusion Injury and Possible Relevance to Acute Glaucoma

by Hsin-Yi Chen, Hsiu-Chuan Chou, Shing-Jyh Chang, En-Chi Liao, Yi-Ting Tsai, Yu-Shan Wei, Ji-Min Li, Li-Hsun Lin, Meng-Wei Lin, Ying-Jen Chen, Yu-Sheng Chen, Chih-Chun Lin, Yi-Shiuan Wang, Mei-Lan Ko and Hong-Lin Chan

Int. J. Mol. Sci. 2017, 18(2), 334; https://doi.org/10.3390/ijms18020334 - 5 Feb 2017

Cited by 14 | Viewed by 5746

Abstract

Glaucoma is a group of eye diseases that can cause vision loss and optical nerve damage. To investigate the protein expression alterations in various intraocular tissues (i.e., the cornea, conjunctiva, uvea, retina, and sclera) during ischemia–reperfusion (IR) injury, this study performed a proteomic [...] Read more.

Glaucoma is a group of eye diseases that can cause vision loss and optical nerve damage. To investigate the protein expression alterations in various intraocular tissues (i.e., the cornea, conjunctiva, uvea, retina, and sclera) during ischemia–reperfusion (IR) injury, this study performed a proteomic analysis to qualitatively investigate such alterations resulting from acute glaucoma. The IR injury model combined with the proteomic analysis approach of two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to monitor the protein expression alterations in two groups of specimens (an IR injury group and a control group). The analysis results revealed 221 unique differentially expressed proteins of a total of 1481 proteins in the cornea between the two groups. In addition, 97 of 1206 conjunctival proteins, 90 of 1354 uveal proteins, 61 of 1180 scleral proteins, and 37 of 1204 retinal proteins were differentially expressed. These findings imply that different ocular tissues have different tolerances against IR injury. To sum up, this study utilized the acute glaucoma model combined with 2D-DIGE and MALDI-TOF MS to investigate the IR injury affected protein expression on various ocular tissues, and based on the ratio of protein expression alterations, the alterations in the ocular tissues were in the following order: the cornea, conjunctiva, uvea, sclera, and retina. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 1955 KiB

Open AccessArticle

LC-MS/MS Analysis Unravels Deep Oxidation of Manganese Superoxide Dismutase in Kidney Cancer

by Zuohui Zhao, Kazem M. Azadzoi, Han-Pil Choi, Ruirui Jing, Xin Lu, Cuiling Li, Fengqin Wang, Jiaju Lu and Jing-Hua Yang

Int. J. Mol. Sci. 2017, 18(2), 319; https://doi.org/10.3390/ijms18020319 - 4 Feb 2017

Cited by 15 | Viewed by 6445

Abstract

Manganese superoxide dismutase (MNSOD) is one of the major scavengers of reactive oxygen species (ROS) in mitochondria with pivotal regulatory role in ischemic disorders, inflammation and cancer. Here we report oxidative modification of MNSOD in human renal cell carcinoma (RCC) by the shotgun [...] Read more.

Manganese superoxide dismutase (MNSOD) is one of the major scavengers of reactive oxygen species (ROS) in mitochondria with pivotal regulatory role in ischemic disorders, inflammation and cancer. Here we report oxidative modification of MNSOD in human renal cell carcinoma (RCC) by the shotgun method using data-dependent liquid chromatography tandem mass spectrometry (LC-MS/MS). While 5816 and 5571 proteins were identified in cancer and adjacent tissues, respectively, 208 proteins were found to be up- or down-regulated (p < 0.05). Ontological category, interaction network and Western blotting suggested a close correlation between RCC-mediated proteins and oxidoreductases such as MNSOD. Markedly, oxidative modifications of MNSOD were identified at histidine (H⁵⁴ and H⁵⁵), tyrosine (Y⁵⁸), tryptophan (W¹⁴⁷, W¹⁴⁹, W²⁰⁵ and W²¹⁰) and asparagine (N²⁰⁶ and N²⁰⁹) residues additional to methionine. These oxidative insults were located at three hotspots near the hydrophobic pocket of the manganese binding site, of which the oxidation of Y⁵⁸, W¹⁴⁷ and W¹⁴⁹ was up-regulated around three folds and the oxidation of H⁵⁴ and H⁵⁵ was detected in the cancer tissues only (p < 0.05). When normalized to MNSOD expression levels, relative MNSOD enzymatic activity was decreased in cancer tissues, suggesting impairment of MNSOD enzymatic activity in kidney cancer due to modifications. Thus, LC-MS/MS analysis revealed multiple oxidative modifications of MNSOD at different amino acid residues that might mediate the regulation of the superoxide radicals, mitochondrial ROS scavenging and MNSOD activity in kidney cancer. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 4302 KiB

Open AccessArticle

Histone H3 Methyltransferase Suv39h1 Prevents Myogenic Terminal Differentiation by Repressing MEF2 Activity in Muscle Cells

by Wei Jin, Yangyang Shang, Jian Peng and Siwen Jiang

Int. J. Mol. Sci. 2016, 17(12), 1908; https://doi.org/10.3390/ijms17121908 - 28 Nov 2016

Cited by 8 | Viewed by 6930

Abstract

The myogenic regulatory factors (MRFs) and myocyte enhancer factor 2 (MEF2) transcription factors have been extensively studied as key transcription factors that regulate myogenic gene expression. However, few reports on the molecular mechanism that modulates chromatin remodeling during skeletal muscle differentiation are available. [...] Read more.

The myogenic regulatory factors (MRFs) and myocyte enhancer factor 2 (MEF2) transcription factors have been extensively studied as key transcription factors that regulate myogenic gene expression. However, few reports on the molecular mechanism that modulates chromatin remodeling during skeletal muscle differentiation are available. We reported here that the expression of the H3-K9 methyltransferase Suv39h1 was decreased during myoblast differentiation. Ectopic expression of Suv39h1 could inhibit myoblast differentiation, increasing H3-K9 methylation levels, whereas knockdown of Suv39h1 stimulated myoblast differentiation. Furthermore, Suv39h1 interacted with MEF2C directly and inhibited MEF2 transcription activity in a dose-dependent manner. Together, our studies revealed a molecular mechanism wherein Suv39h1 modulated myogenic gene expression and activation during skeletal muscle differentiation. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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24 pages, 3849 KiB

Open AccessArticle

Comparative Proteomic and Physiological Analysis Reveals the Variation Mechanisms of Leaf Coloration and Carbon Fixation in a Xantha Mutant of Ginkgo biloba L.

by Xinliang Liu, Wanwen Yu, Guibin Wang, Fuliang Cao, Jinfeng Cai and Huanli Wang

Int. J. Mol. Sci. 2016, 17(11), 1794; https://doi.org/10.3390/ijms17111794 - 27 Oct 2016

Cited by 34 | Viewed by 7968

Abstract

Yellow-green leaf mutants are common in higher plants, and these non-lethal chlorophyll-deficient mutants are ideal materials for research on photosynthesis and plant development. A novel xantha mutant of Ginkgo biloba displaying yellow-colour leaves (YL) and green-colour leaves (GL) was identified in this study. [...] Read more.

Yellow-green leaf mutants are common in higher plants, and these non-lethal chlorophyll-deficient mutants are ideal materials for research on photosynthesis and plant development. A novel xantha mutant of Ginkgo biloba displaying yellow-colour leaves (YL) and green-colour leaves (GL) was identified in this study. The chlorophyll content of YL was remarkably lower than that in GL. The chloroplast ultrastructure revealed that YL had less dense thylakoid lamellae, a looser structure and fewer starch grains than GL. Analysis of the photosynthetic characteristics revealed that YL had decreased photosynthetic activity with significantly high nonphotochemical quenching. To explain these phenomena, we analysed the proteomic differences in leaves and chloroplasts between YL and GL of ginkgo using two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF MS. In total, 89 differential proteins were successfully identified, 82 of which were assigned functions in nine metabolic pathways and cellular processes. Among them, proteins involved in photosynthesis, carbon fixation in photosynthetic organisms, carbohydrate/energy metabolism, amino acid metabolism, and protein metabolism were greatly enriched, indicating a good correlation between differentially accumulated proteins and physiological changes in leaves. The identifications of these differentially accumulated proteins indicates the presence of a specific different metabolic network in YL and suggests that YL possess slower chloroplast development, weaker photosynthesis, and a less abundant energy supply than GL. These studies provide insights into the mechanism of molecular regulation of leaf colour variation in YL mutants. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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13 pages, 5434 KiB

Open AccessArticle

iTRAQ-Based Quantitative Proteomic Analysis of the Potentiated and Dormant Antler Stem Cells

by Zhen Dong, Hengxing Ba, Wei Zhang, Dawn Coates and Chunyi Li

Int. J. Mol. Sci. 2016, 17(11), 1778; https://doi.org/10.3390/ijms17111778 - 25 Oct 2016

Cited by 23 | Viewed by 6249

Abstract

As the only known organ that can completely regenerate in mammals, deer antler is of real significance in the field of regenerative medicine. Recent studies have shown that the regenerative capacity of the antlers comes from the pedicle periosteum and the cells resident [...] Read more.

As the only known organ that can completely regenerate in mammals, deer antler is of real significance in the field of regenerative medicine. Recent studies have shown that the regenerative capacity of the antlers comes from the pedicle periosteum and the cells resident in the periosteum possess the attributes of stem cells. Currently, the molecular mechanism of antler regeneration remains unclear. In the present study, we compared the potentiated and dormant antler stem cells using isobaric tags for the relative and absolute quantification (iTRAQ) labeling of the peptides, coupled with two-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS) to compare the proteome profiles. Proteins were identified by searching against the NCBI nr database and our own Cervine transcriptome database, and bioinformatics analysis was conducted to identify the differentially expressed proteins. Based on this searching strategy, we identified 169 differentially expressed proteins in total, consisting of 70 up- and 99 down-regulated in the potentiated vs. dormant antler stem cells. Reliability of the iTRAQ was confirmed via quantitative real-time polymerase chain reaction (qRT-PCR) to measure the expression of selected genes. We identified transduction pathways through the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, such as HIF-1 and PI3K-AKT signaling pathways that play important roles in regulating the regeneration of antlers. In summary, the initiation stage of antler regeneration, a process from dormant to potentiated states in antler stem cells, is regulated by multiple proteins and complicated signal networks. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 4024 KiB

Open AccessArticle

iTRAQ-Based Proteomics Analysis of Serum Proteins in Wistar Rats Treated with Sodium Fluoride: Insight into the Potential Mechanism and Candidate Biomarkers of Fluorosis

by Yan Wei, Beibei Zeng, Hua Zhang, Cheng Chen, Yanli Wu, Nanlan Wang, Yanqiu Wu and Liming Shen

Int. J. Mol. Sci. 2016, 17(10), 1644; https://doi.org/10.3390/ijms17101644 - 28 Sep 2016

Cited by 22 | Viewed by 7386

Abstract

Fluorosis induced by exposure to high level fluoride is quite widespread in the world. The manifestations of fluorosis include dental mottling, bone damage, and impaired malfunction of soft tissues. However, the molecular mechanism of fluorosis has not been clarified until now. To explore [...] Read more.

Fluorosis induced by exposure to high level fluoride is quite widespread in the world. The manifestations of fluorosis include dental mottling, bone damage, and impaired malfunction of soft tissues. However, the molecular mechanism of fluorosis has not been clarified until now. To explore the underlying mechanisms of fluorosis and screen out serum biomarkers, we carried out a quantitative proteomics study to identify differentially expressed serum proteins in Wistar rats treated with sodium fluoride (NaF) by using a proteomics approach of isobaric tagging for relative and absolute quantitation (iTRAQ). We fed Wistar rats drinking water that had 50, 150, and 250 mg/L of dissolved NaF for 24 weeks. For the experimental duration, each rat was given an examination of the lower incisors to check for the condition of dental fluorosis (DF). By the end of the treatment, fluoride ion concentration in serum and lower incisors were detected. The results showed that NaF treatment can induce rat fluorosis. By iTRAQ analysis, a total of 37 differentially expressed serum proteins were identified between NaF-treated and control rats. These proteins were further analyzed by bioinformatics, out of which two proteins were validated by enzyme-linked immunoadsorbent assays (ELISA). The major proteins were involved in complement and coagulation cascade, inflammatory response, complement activation, defense response, and wound response, suggesting that inflammation and immune reactions may play a key role in fluorosis pathogenesis. These proteins may contribute to the understanding of the mechanism of fluoride toxicity, and may serve as potential biomarkers for fluorosis. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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13 pages, 1209 KiB

Open AccessArticle

Proteomic Analysis of Hylocereus polyrhizus Reveals Metabolic Pathway Changes

by Qingzhu Hua, Qianjun Zhou, Susheng Gan, Jingyu Wu, Canbin Chen, Jiaqiang Li, Yaoxiong Ye, Jietang Zhao, Guibing Hu and Yonghua Qin

Int. J. Mol. Sci. 2016, 17(10), 1606; https://doi.org/10.3390/ijms17101606 - 28 Sep 2016

Cited by 20 | Viewed by 7704

Abstract

Red dragon fruit or red pitaya (Hylocereus polyrhizus) is the only edible fruit that contains betalains. The color of betalains ranges from red and violet to yellow in plants. Betalains may also serve as an important component of health-promoting and disease-preventing [...] Read more.

Red dragon fruit or red pitaya (Hylocereus polyrhizus) is the only edible fruit that contains betalains. The color of betalains ranges from red and violet to yellow in plants. Betalains may also serve as an important component of health-promoting and disease-preventing functional food. Currently, the biosynthetic and regulatory pathways for betalain production remain to be fully deciphered. In this study, isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analyses were used to reveal the molecular mechanism of betalain biosynthesis in H. polyrhizus fruits at white and red pulp stages, respectively. A total of 1946 proteins were identified as the differentially expressed between the two samples, and 936 of them were significantly highly expressed at the red pulp stage of H. polyrhizus. RNA-seq and iTRAQ analyses showed that some transcripts and proteins were positively correlated; they belonged to “phenylpropanoid biosynthesis”, “tyrosine metabolism”, “flavonoid biosynthesis”, “ascorbate and aldarate metabolism”, “betalains biosynthesis” and “anthocyanin biosynthesis”. In betalains biosynthesis pathway, several proteins/enzymes such as polyphenol oxidase, CYP76AD3 and 4,5-dihydroxy-phenylalanine (DOPA) dioxygenase extradiol-like protein were identified. The present study provides a new insight into the molecular mechanism of the betalain biosynthesis at the posttranscriptional level. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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19 pages, 7991 KiB

Open AccessArticle

Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)-Based Comparative Proteome Analysis of the Response of Ramie under Drought Stress

by Xia An, Jingyu Zhang, Lunjin Dai, Gang Deng, Yiwen Liao, Lijun Liu, Bo Wang and Dingxiang Peng

Int. J. Mol. Sci. 2016, 17(10), 1607; https://doi.org/10.3390/ijms17101607 - 27 Sep 2016

Cited by 19 | Viewed by 6485

Abstract

In this study, we conducted the first isobaric tags for relative and absolute quantitation (isobaric tags for relative and absolute quantitation (iTRAQ))-based comparative proteomic analysis of ramie plantlets after 0 (minor drought stress), 24 (moderate drought stress), and 72 h (severe drought [...] Read more.

In this study, we conducted the first isobaric tags for relative and absolute quantitation (isobaric tags for relative and absolute quantitation (iTRAQ))-based comparative proteomic analysis of ramie plantlets after 0 (minor drought stress), 24 (moderate drought stress), and 72 h (severe drought stress) of treatment with 15% (w/v) poly (ethylene glycol)6000 (PEG6000) to simulate drought stress. In our study, the association analysis of proteins and transcript expression revealed 1244 and 968 associated proteins identified in leaves and roots, respectively. L1, L2, and L3 are leaf samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups, a total of 118, 216, and 433 unique proteins were identified as differentially expressed during L1 vs. L2, L2 vs. L3, and L1 vs. L3, respectively. R1, R2, and R3 are root samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups，a total of 124, 27, and 240 unique proteins were identified as differentially expressed during R1 vs. R2, R2 vs. R3, and R1 vs. R3, respectively. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was significantly upregulated in roots in response to drought stress. This enhancement may result in more glycolytically generated adenosine triphosphate (ATP) in roots to adapt to adverse environmental conditions. To obtain complementary information related to iTRAQ data, the mRNA levels of 12 proteins related to glycolysis/gluconeogenesis in leaves and 7 in roots were further analyzed by qPCR. Most of their expression levels were higher in R3 than R1 and R2, suggesting that these compounds may promote drought tolerance by modulating the production of available energy. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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17 pages, 10133 KiB

Open AccessArticle

Comparative Proteomic Analysis of Mature Pollen in Triploid and Diploid Populus deltoides

by Xiao-Ling Zhang, Jin Zhang, Ying-Hua Guo, Pei Sun, Hui-Xia Jia, Wei Fan, Meng-Zhu Lu and Jian-Jun Hu

Int. J. Mol. Sci. 2016, 17(9), 1475; https://doi.org/10.3390/ijms17091475 - 3 Sep 2016

Cited by 10 | Viewed by 6658

Abstract

Ploidy affects plant growth vigor and cell size, but the relative effects of pollen fertility and allergenicity between triploid and diploid have not been systematically examined. Here we performed comparative analyses of fertility, proteome, and abundances of putative allergenic proteins of pollen in [...] Read more.

Ploidy affects plant growth vigor and cell size, but the relative effects of pollen fertility and allergenicity between triploid and diploid have not been systematically examined. Here we performed comparative analyses of fertility, proteome, and abundances of putative allergenic proteins of pollen in triploid poplar ‘ZhongHuai1’ (‘ZH1’, triploid) and ‘ZhongHuai2’ (‘ZH2’, diploid) generated from the same parents. The mature pollen was sterile in triploid poplar ‘ZH1’. By applying two-dimensional gel electrophoresis (2-DE), a total of 72 differentially expressed protein spots (DEPs) were detected in triploid poplar pollen. Among them, 24 upregulated and 43 downregulated proteins were identified in triploid poplar pollen using matrix-assisted laser desorption/ionisation coupled with time of-flight tandem mass spectrometer analysis (MALDI-TOF/TOF MS/MS). The main functions of these DEPs were related with “S-adenosylmethionine metabolism”, “actin cytoskeleton organization”, or “translational elongation”. The infertility of triploid poplar pollen might be related to its abnormal cytoskeletal system. In addition, the abundances of previously identified 28 putative allergenic proteins were compared among three poplar varieties (‘ZH1’, ‘ZH2’, and ‘2KEN8‘). Most putative allergenic proteins were downregulated in triploid poplar pollen. This work provides an insight into understanding the protein regulation mechanism of pollen infertility and low allergenicity in triploid poplar, and gives a clue to improving poplar polyploidy breeding and decreasing the pollen allergenicity. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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20 pages, 2692 KiB

Open AccessArticle

Quantitative Proteomic Analysis of Escherichia coli Heat-Labile Toxin B Subunit (LTB) with Enterovirus 71 (EV71) Subunit VP1

by Lin Liu, Yongping Ma, Huicong Zhou and Mingjun Wu

Int. J. Mol. Sci. 2016, 17(9), 1419; https://doi.org/10.3390/ijms17091419 - 27 Aug 2016

Cited by 5 | Viewed by 6120

Abstract

The nontoxic heat-labile toxin (LT) B subunit (LTB) was used as mucosal adjuvant experimentally. However, the mechanism of LTB adjuvant was still unclear. The LTB and enterovirus 71 (EV71) VP1 subunit (EVP1) were constructed in pET32 and expressed in E. coli BL21, respectively. [...] Read more.

The nontoxic heat-labile toxin (LT) B subunit (LTB) was used as mucosal adjuvant experimentally. However, the mechanism of LTB adjuvant was still unclear. The LTB and enterovirus 71 (EV71) VP1 subunit (EVP1) were constructed in pET32 and expressed in E. coli BL21, respectively. The immunogenicity of purified EVP1 and the adjuvanticity of LTB were evaluated via intranasal immunization EVP1 plus LTB in Balb/c mice. In order to elucidate the proteome change triggered by the adjuvant of LTB, the proteomic profiles of LTB, EVP1, and LTB plus EVP1 were quantitatively analyzed by iTRAQ-LC-MS/MS (isobaric tags for relative and absolute quantitation; liquid chromatography-tandem mass spectrometry) in murine macrophage RAW264.7. The proteomic data were analyzed by bioinformatics and validated by western blot analysis. The predicted protein interactions were confirmed using LTB pull-down and the LTB processing pathway was validated by confocal microscopy. The results showed that LTB significantly boosted EVP1 specific systematic and mucosal antibodies. A total of 3666 differential proteins were identified in the three groups. Pathway enrichment of proteomic data predicted that LTB upregulated the specific and dominant MAPK (mitogen-activated protein kinase) signaling pathway and the protein processing in endoplasmic reticulum (PPER) pathway, whereas LTB or EVP1 did not significantly upregulate these two signaling pathways. Confocal microscopy and LTB pull-down assays confirmed that the LTB adjuvant was endocytosed and processed through endocytosis (ENS)-lysosomal-endoplasmic reticulum (ER) system. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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18 pages, 1681 KiB

Open AccessArticle

Drought-Induced Leaf Proteome Changes in Switchgrass Seedlings

by Zhujia Ye, Sasikiran Sangireddy, Ikenna Okekeogbu, Suping Zhou, Chih-Li Yu, Dafeng Hui, Kevin J. Howe, Tara Fish and Theodore W. Thannhauser

Int. J. Mol. Sci. 2016, 17(8), 1251; https://doi.org/10.3390/ijms17081251 - 2 Aug 2016

Cited by 16 | Viewed by 7615

Abstract

Switchgrass (Panicum virgatum) is a perennial crop producing deep roots and thus highly tolerant to soil water deficit conditions. However, seedling establishment in the field is very susceptible to prolonged and periodic drought stress. In this study, a “sandwich” system simulating [...] Read more.

Switchgrass (Panicum virgatum) is a perennial crop producing deep roots and thus highly tolerant to soil water deficit conditions. However, seedling establishment in the field is very susceptible to prolonged and periodic drought stress. In this study, a “sandwich” system simulating a gradual water deletion process was developed. Switchgrass seedlings were subjected to a 20-day gradual drought treatment process when soil water tension was increased to 0.05 MPa (moderate drought stress) and leaf physiological properties had expressed significant alteration. Drought-induced changes in leaf proteomes were identified using the isobaric tags for relative and absolute quantitation (iTRAQ) labeling method followed by nano-scale liquid chromatography mass spectrometry (nano-LC-MS/MS) analysis. Additionally, total leaf proteins were processed using a combinatorial library of peptide ligands to enrich for lower abundance proteins. Both total proteins and those enriched samples were analyzed to increase the coverage of the quantitative proteomics analysis. A total of 7006 leaf proteins were identified, and 257 (4% of the leaf proteome) expressed a significant difference (p < 0.05, fold change <0.6 or >1.7) from the non-treated control to drought-treated conditions. These proteins are involved in the regulation of transcription and translation, cell division, cell wall modification, phyto-hormone metabolism and signaling transduction pathways, and metabolic pathways of carbohydrates, amino acids, and fatty acids. A scheme of abscisic acid (ABA)-biosynthesis and ABA responsive signal transduction pathway was reconstructed using these drought-induced significant proteins, showing systemic regulation at protein level to deploy the respective mechanism. Results from this study, in addition to revealing molecular responses to drought stress, provide a large number of proteins (candidate genes) that can be employed to improve switchgrass seedling growth and establishment under soil drought conditions (Data are available via ProteomeXchange with identifier PXD004675). Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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19 pages, 573 KiB

Open AccessArticle

Aluminum Toxicity-Induced Alterations of Leaf Proteome in Two Citrus Species Differing in Aluminum Tolerance

by Huan Li, Lin-Tong Yang, Yi-Ping Qi, Peng Guo, Yi-Bin Lu and Li-Song Chen

Int. J. Mol. Sci. 2016, 17(7), 1180; https://doi.org/10.3390/ijms17071180 - 21 Jul 2016

Cited by 44 | Viewed by 7632

Abstract

Seedlings of aluminum-tolerant ‘Xuegan’ (Citrus sinensis) and Al-intolerant ‘sour pummelo’ (Citrus grandis) were fertigated for 18 weeks with nutrient solution containing 0 and 1.2 mM AlCl₃·6H₂O. Al toxicity-induced inhibition of photosynthesis and the decrease of [...] Read more.

Seedlings of aluminum-tolerant ‘Xuegan’ (Citrus sinensis) and Al-intolerant ‘sour pummelo’ (Citrus grandis) were fertigated for 18 weeks with nutrient solution containing 0 and 1.2 mM AlCl₃·6H₂O. Al toxicity-induced inhibition of photosynthesis and the decrease of total soluble protein only occurred in C. grandis leaves, demonstrating that C. sinensis had higher Al tolerance than C. grandis. Using isobaric tags for relative and absolute quantification (iTRAQ), we obtained more Al toxicity-responsive proteins from C. sinensis than from C. grandis leaves, which might be responsible for the higher Al tolerance of C. sinensis. The following aspects might contribute to the Al tolerance of C. sinensis: (a) better maintenance of photosynthesis and energy balance via inducing photosynthesis and energy-related proteins; (b) less increased requirement for the detoxification of reactive oxygen species and other toxic compounds, such as aldehydes, and great improvement of the total ability of detoxification; and (c) upregulation of low-phosphorus-responsive proteins. Al toxicity-responsive proteins related to RNA regulation, protein metabolism, cellular transport and signal transduction might also play key roles in the higher Al tolerance of C. sinensis. We present the global picture of Al toxicity-induced alterations of protein profiles in citrus leaves, and identify some new Al toxicity-responsive proteins related to various biological processes. Our results provide some novel clues about plant Al tolerance. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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15 pages, 2916 KiB

Open AccessArticle

Comprehensive and Quantitative Proteomic Analysis of Metamorphosis-Related Proteins in the Veined Rapa Whelk, Rapana venosa

by Hao Song, Hai-Yan Wang and Tao Zhang

Int. J. Mol. Sci. 2016, 17(6), 924; https://doi.org/10.3390/ijms17060924 - 15 Jun 2016

Cited by 20 | Viewed by 6913

Abstract

Larval metamorphosis of the veined rapa whelk (Rapana venosa) is a pelagic to benthic transition that involves considerable structural and physiological changes. Because metamorphosis plays a pivotal role in R. venosa commercial breeding and natural populations, the endogenous proteins that drive [...] Read more.

Larval metamorphosis of the veined rapa whelk (Rapana venosa) is a pelagic to benthic transition that involves considerable structural and physiological changes. Because metamorphosis plays a pivotal role in R. venosa commercial breeding and natural populations, the endogenous proteins that drive this transition attract considerable interest. This study is the first to perform a comprehensive and quantitative proteomic analysis related to metamorphosis in a marine gastropod. We analyzed the proteomes of competent R. venosa larvae and post-larvae, resulting in the identification of 5312 proteins, including 470 that were downregulated and 668 that were upregulated after metamorphosis. The differentially expressed proteins reflected multiple processes involved in metamorphosis, including cytoskeleton and cell adhesion, ingestion and digestion, stress response and immunity, as well as specific tissue development. Our data improve understanding of the physiological traits controlling R. venosa metamorphosis and provide a solid basis for further study. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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11 pages, 1147 KiB

Open AccessCommunication

Changes in the Arabidopsis thaliana Proteome Implicate cAMP in Biotic and Abiotic Stress Responses and Changes in Energy Metabolism

by May Alqurashi, Chris Gehring and Claudius Marondedze

Int. J. Mol. Sci. 2016, 17(6), 852; https://doi.org/10.3390/ijms17060852 - 1 Jun 2016

Cited by 35 | Viewed by 7960

Abstract

The second messenger 3′,5′-cyclic adenosine monophosphate (cAMP) is increasingly recognized as having many different roles in plant responses to environmental stimuli. To gain further insights into these roles, Arabidopsis thaliana cell suspension culture was treated with 100 nM of cell permeant 8-bromo-cAMP for [...] Read more.

The second messenger 3′,5′-cyclic adenosine monophosphate (cAMP) is increasingly recognized as having many different roles in plant responses to environmental stimuli. To gain further insights into these roles, Arabidopsis thaliana cell suspension culture was treated with 100 nM of cell permeant 8-bromo-cAMP for 5 or 10 min. Here, applying mass spectrometry and comparative proteomics, 20 proteins were identified as differentially expressed and we noted a specific bias in proteins with a role in abiotic stress, particularly cold and salinity, biotic stress as well as proteins with a role in glycolysis. These findings suggest that cAMP is sufficient to elicit specific stress responses that may in turn induce complex changes to cellular energy homeostasis. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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24 pages, 9256 KiB

Open AccessArticle

Chronic Heat Stress Induces Immune Response, Oxidative Stress Response, and Apoptosis of Finishing Pig Liver: A Proteomic Approach

by Yanjun Cui, Yue Hao, Jielei Li, Weiguang Bao, Gan Li, Yanli Gao and Xianhong Gu

Int. J. Mol. Sci. 2016, 17(5), 393; https://doi.org/10.3390/ijms17050393 - 11 May 2016

Cited by 91 | Viewed by 11499

Abstract

Heat stress (HS) negatively affects human health, animal welfare, and livestock production. We analyzed the hepatic proteomes of finishing pigs subjected to chronic heat stress (HS), thermal neutral (TN), and restricted feed intake conditions, identifying differences between direct and indirect (via reduced feed [...] Read more.

Heat stress (HS) negatively affects human health, animal welfare, and livestock production. We analyzed the hepatic proteomes of finishing pigs subjected to chronic heat stress (HS), thermal neutral (TN), and restricted feed intake conditions, identifying differences between direct and indirect (via reduced feed intake) HS. Twenty-four castrated male pigs were randomly allocated to three treatments for three weeks: (1) thermal neutral (TN) (22 °C) with ad libitum feeding; (2) chronic HS (30 °C) with ad libitum feeding; and (3) TN, pair-fed to HS intake (PF). Hepatic proteome analysis was conducted using two-dimensional gel electrophoresis and mass spectrometry. Both HS and PF significantly reduced liver weight (p < 0.05). Forty-five hepatic proteins were differentially abundant when comparing HS with TN (37), PF with TN (29), and HS with PF (16). These proteins are involved in heat shock response and immune defense, oxidative stress response, cellular apoptosis, metabolism, signal transduction, and cytoskeleton. We also observed increased abundance of proteins and enzymes associated with heat shock response and immune defense, reduced the redox state, enhanced multiple antioxidant abilities, and increased apoptosis in HS liver. Heat-load, independent of reduced feed intake, induced an innate immune response, while food restriction caused stress and cellular apoptosis. Our results provide novel insights into the effects of chronic HS on liver. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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20 pages, 6152 KiB

Open AccessArticle

Proteome Profile and Quantitative Proteomic Analysis of Buffalo (Bubalusbubalis) Follicular Fluid during Follicle Development

by Qiang Fu, Yulin Huang, Zhiqiang Wang, Fumei Chen, Delun Huang, Yangqing Lu, Xianwei Liang and Ming Zhang

Int. J. Mol. Sci. 2016, 17(5), 618; https://doi.org/10.3390/ijms17050618 - 29 Apr 2016

Cited by 40 | Viewed by 8647

Abstract

Follicular fluid (FF) accumulates in the antrum of the ovarian follicle and provides the microenvironment for oocyte development. FF plays an important role in follicle growth and oocyte maturation. The FF provides a unique window to investigate the processes occurring during buffalo follicular [...] Read more.

Follicular fluid (FF) accumulates in the antrum of the ovarian follicle and provides the microenvironment for oocyte development. FF plays an important role in follicle growth and oocyte maturation. The FF provides a unique window to investigate the processes occurring during buffalo follicular development. The observed low quality of buffalo oocytes may arise from the poor follicular microenvironment. Investigating proteins found in buffalo FF (BFF) should provide insight into follicular development processes and provide further understanding of intra-follicular maturation and oocytes quality. Here, a proteomic-based approach was used to analyze the proteome of BFF. SDS-PAGE separation combined with mass spectrometry was used to generate the proteomic dataset. In total, 363 proteins were identified and classified by Gene Ontology terms. The proteins were assigned to 153 pathways, including signaling pathways. To evaluate difference in proteins expressed between BFF with different follicle size (small, <4 mm; and large, >8 mm), a quantitative proteomic analysis based on multi-dimensional liquid chromatography pre-fractionation tandem Orbitrap mass spectrometry identification was performed. Eleven differentially expressed proteins (six downregulated and five upregulated in large BFF) were identified and assigned to a variety of functional processes, including serine protease inhibition, oxidation protection and the complement cascade system. Three differentially expressed proteins, Vimentin, Peroxiredoxin-1 and SERPIND1, were verified by Western blotting, consistent with the quantitative proteomics results. Our datasets offers new information about proteins present in BFF and should facilitate the development of new biomarkers. These differentially expressed proteins illuminate the size-dependent protein changes in follicle microenvironment. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 2809 KiB

Open AccessArticle

Redox Proteomic Profiling of Specifically Carbonylated Proteins in the Serum of Triple Transgenic Alzheimer’s Disease Mice

by Liming Shen, Youjiao Chen, Aochu Yang, Cheng Chen, Liping Liao, Shuiming Li, Ming Ying, Jing Tian, Qiong Liu and Jiazuan Ni

Int. J. Mol. Sci. 2016, 17(4), 469; https://doi.org/10.3390/ijms17040469 - 12 Apr 2016

Cited by 21 | Viewed by 7796

Abstract

Oxidative stress is a key event in the onset and progression of neurodegenerative diseases, including Alzheimer’s disease (AD). To investigate the role of oxidative stress in AD and to search for potential biomarkers in peripheral blood, serums were collected in this study from [...] Read more.

Oxidative stress is a key event in the onset and progression of neurodegenerative diseases, including Alzheimer’s disease (AD). To investigate the role of oxidative stress in AD and to search for potential biomarkers in peripheral blood, serums were collected in this study from the 3-, 6-, and 12-month-old triple transgenic AD mice (3×Tg-AD mice) and the age- and sex-matched non-transgenic (non-Tg) littermates. The serum oxidized proteins were quantified by slot-blot analysis and enzyme-linked immunosorbent assay (ELISA) to investigate the total levels of serum protein carbonyl groups. Western blotting, in conjunction with two-dimensional gel electrophoresis (2D-Oxyblot), was employed to identify and quantify the specifically-carbonylated proteins in the serum of 3×Tg-AD mice. The results showed that the levels of serum protein carbonyls were increased in the three month old 3×Tg-AD mice compared with the non-Tg control mice, whereas no significant differences were observed in the six and 12 months old AD mice, suggesting that oxidative stress is an early event in AD progression. With the application of 2D-Oxyblot analysis, (immunoglobin) Ig gamma-2B chain C region (IGH-3), Ig lambda-2 chain C region (IGLC2), Ig kappa chain C region (IGKC), and Ig kappa chain V-V region HP R16.7 were identified as significantly oxidized proteins compared with the control. Among them IGH-3 and IGKC were validated via immunoprecipitation and Western blot analysis. Identification of oxidized proteins in the serums of 3×Tg-AD mice can not only reveal potential roles of those proteins in the pathogenesis of AD but also provide potential biomarkers of AD at the early stage. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 4082 KiB

Open AccessArticle

A Proteomic Approach for the Identification of Up-Regulated Proteins Involved in the Metabolic Process of the Leiomyoma

by Blendi Ura, Federica Scrimin, Giorgio Arrigoni, Cinzia Franchin, Lorenzo Monasta and Giuseppe Ricci

Int. J. Mol. Sci. 2016, 17(4), 540; https://doi.org/10.3390/ijms17040540 - 9 Apr 2016

Cited by 12 | Viewed by 6493

Abstract

Uterine leiomyoma is the most common benign smooth muscle cell tumor of the uterus. Proteomics is a powerful tool for the analysis of complex mixtures of proteins. In our study, we focused on proteins that were upregulated in the leiomyoma compared to the [...] Read more.

Uterine leiomyoma is the most common benign smooth muscle cell tumor of the uterus. Proteomics is a powerful tool for the analysis of complex mixtures of proteins. In our study, we focused on proteins that were upregulated in the leiomyoma compared to the myometrium. Paired samples of eight leiomyomas and adjacent myometrium were obtained and submitted to two-dimensional gel electrophoresis (2-DE) and mass spectrometry for protein identification and to Western blotting for 2-DE data validation. The comparison between the patterns revealed 24 significantly upregulated (p < 0.05) protein spots, 12 of which were found to be associated with the metabolic processes of the leiomyoma and not with the normal myometrium. The overexpression of seven proteins involved in the metabolic processes of the leiomyoma was further validated by Western blotting and 2D Western blotting. Four of these proteins have never been associated with the leiomyoma before. The 2-DE approach coupled with mass spectrometry, which is among the methods of choice for comparative proteomic studies, identified a number of proteins overexpressed in the leiomyoma and involved in several biological processes, including metabolic processes. A better understanding of the mechanism underlying the overexpression of these proteins may be important for therapeutic purposes. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 3147 KiB

Open AccessArticle

The Expression Profile of Complement Components in Podocytes

by Xuejuan Li, Fangrui Ding, Xiaoyan Zhang, Baihong Li and Jie Ding

Int. J. Mol. Sci. 2016, 17(4), 471; https://doi.org/10.3390/ijms17040471 - 30 Mar 2016

Cited by 39 | Viewed by 7403

Abstract

Podocytes are critical for maintaining the glomerular filtration barrier and are injured in many renal diseases, especially proteinuric kidney diseases. Recently, reports suggested that podocytes are among the renal cells that synthesize complement components that mediate glomerular diseases. Nevertheless, the profile and extent [...] Read more.

Podocytes are critical for maintaining the glomerular filtration barrier and are injured in many renal diseases, especially proteinuric kidney diseases. Recently, reports suggested that podocytes are among the renal cells that synthesize complement components that mediate glomerular diseases. Nevertheless, the profile and extent of complement component expression in podocytes remain unclear. This study examined the expression profile of complement in podocytes under physiological conditions and in abnormal podocytes induced by multiple stimuli. In total, 23/32 complement component components were detected in podocyte by conventional RT-PCR. Both primary cultured podocytes and immortalized podocytes expressed the complement factors C1q, C1r, C2, C3, C7, MASP, CFI, DAF, CD59, C4bp, CD46, Protein S, CR2, C1qR, C3aR, C5aR, and Crry (17/32), whereas C4, CFB, CFD, C5, C6, C8, C9, MBL1, and MBL2 (9/32) complement factors were not expressed. C3, Crry, and C1q-binding protein were detected by tandem mass spectrometry. Podocyte complement gene expression was affected by several factors (puromycin aminonucleoside (PAN), angiotensin II (Ang II), interleukin-6 (IL-6), and transforming growth factor-β (TGF-β)). Representative complement components were detected using fluorescence confocal microscopy. In conclusion, primary podocytes express various complement components at the mRNA and protein levels. The complement gene expressions were affected by several podocyte injury factors. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 2714 KiB

Open AccessArticle

Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods

by Mike Buckley

Int. J. Mol. Sci. 2016, 17(4), 445; https://doi.org/10.3390/ijms17040445 - 24 Mar 2016

Cited by 61 | Viewed by 10249

Abstract

Collagen is one of the most ubiquitous proteins in the animal kingdom and the dominant protein in extracellular tissues such as bone, skin and other connective tissues in which it acts primarily as a supporting scaffold. It has been widely investigated scientifically, not [...] Read more.

Collagen is one of the most ubiquitous proteins in the animal kingdom and the dominant protein in extracellular tissues such as bone, skin and other connective tissues in which it acts primarily as a supporting scaffold. It has been widely investigated scientifically, not only as a biomedical material for regenerative medicine, but also for its role as a food source for both humans and livestock. Due to the long-term stability of collagen, as well as its abundance in bone, it has been proposed as a source of biomarkers for species identification not only for heat- and pressure-rendered animal feed but also in ancient archaeological and palaeontological specimens, typically carried out by peptide mass fingerprinting (PMF) as well as in-depth liquid chromatography (LC)-based tandem mass spectrometric methods. Through the analysis of the three most common domesticates species, cow, sheep, and pig, this research investigates the advantages of each approach over the other, investigating sites of sequence variation with known functional properties of the collagen molecule. Results indicate that the previously identified species biomarkers through PMF analysis are not among the most variable type 1 collagen peptides present in these tissues, the latter of which can be detected by LC-based methods. However, it is clear that the highly repetitive sequence motif of collagen throughout the molecule, combined with the variability of the sites and relative abundance levels of hydroxylation, can result in high scoring false positive peptide matches using these LC-based methods. Additionally, the greater alpha 2(I) chain sequence variation, in comparison to the alpha 1(I) chain, did not appear to be specific to any particular functional properties, implying that intra-chain functional constraints on sequence variation are not as great as inter-chain constraints. However, although some of the most variable peptides were only observed in LC-based methods, until the range of publicly available collagen sequences improves, the simplicity of the PMF approach and suitable range of peptide sequence variation observed makes it the ideal method for initial taxonomic identification prior to further analysis by LC-based methods only when required. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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26 pages, 17102 KiB

Open AccessArticle

Proteomic Analysis Reveals the Leaf Color Regulation Mechanism in Chimera Hosta “Gold Standard” Leaves

by Juanjuan Yu, Jinzheng Zhang, Qi Zhao, Yuelu Liu, Sixue Chen, Hongliang Guo, Lei Shi and Shaojun Dai

Int. J. Mol. Sci. 2016, 17(3), 346; https://doi.org/10.3390/ijms17030346 - 8 Mar 2016

Cited by 11 | Viewed by 9302

Abstract

Leaf color change of variegated leaves from chimera species is regulated by fine-tuned molecular mechanisms. Hosta “Gold Standard” is a typical chimera Hosta species with golden-green variegated leaves, which is an ideal material to investigate the molecular mechanisms of leaf variegation. In this [...] Read more.

Leaf color change of variegated leaves from chimera species is regulated by fine-tuned molecular mechanisms. Hosta “Gold Standard” is a typical chimera Hosta species with golden-green variegated leaves, which is an ideal material to investigate the molecular mechanisms of leaf variegation. In this study, the margin and center regions of young and mature leaves from Hosta “Gold Standard”, as well as the leaves from plants after excess nitrogen fertilization were studied using physiological and comparative proteomic approaches. We identified 31 differentially expressed proteins in various regions and development stages of variegated leaves. Some of them may be related to the leaf color regulation in Hosta “Gold Standard”. For example, cytosolic glutamine synthetase (GS1), heat shock protein 70 (Hsp70), and chloroplastic elongation factor G (cpEF-G) were involved in pigment-related nitrogen synthesis as well as protein synthesis and processing. By integrating the proteomics data with physiological results, we revealed the metabolic patterns of nitrogen metabolism, photosynthesis, energy supply, as well as chloroplast protein synthesis, import and processing in various leaf regions at different development stages. Additionally, chloroplast-localized proteoforms involved in nitrogen metabolism, photosynthesis and protein processing implied that post-translational modifications were crucial for leaf color regulation. These results provide new clues toward understanding the mechanisms of leaf color regulation in variegated leaves. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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13 pages, 875 KiB

Open AccessArticle

Understanding the Heat Shock Response in the Sea Cucumber Apostichopus japonicus, Using iTRAQ-Based Proteomics

by Dongxue Xu, Lina Sun, Shilin Liu, Libin Zhang and Hongsheng Yang

Int. J. Mol. Sci. 2016, 17(2), 150; https://doi.org/10.3390/ijms17020150 - 4 Feb 2016

Cited by 48 | Viewed by 6374

Abstract

The sea cucumber Apostichopus japonicus is exploited as a commercial species owing to their high nutritive and medicinal value. Recent high summer temperatures have caused high mortality rates in A. japonicus. In this study, we applied the isobaric tag for relative and [...] Read more.

The sea cucumber Apostichopus japonicus is exploited as a commercial species owing to their high nutritive and medicinal value. Recent high summer temperatures have caused high mortality rates in A. japonicus. In this study, we applied the isobaric tag for relative and absolute quantitation (iTRAQ) technique to investigate the global protein expression profile under an acute short-term (48 h) heat stress. In total, 3432 proteins were identified, and 127 proteins showed significant heat stress responses, with 61 upregulated proteins and 66 downregulated proteins. Our results suggest that heat stress influenced the expression of proteins involved in various biological processes, such as tissue protection and detoxification, lipid and amino acid metabolism, energy production and usage, transcription and translation, cell apoptosis, and cell proliferation. These findings provide a better understanding about the response and thermo-tolerance mechanisms of A. japonicus under heat stress. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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10 pages, 3699 KiB

Open AccessCommunication

Comparative Proteomic Analysis of Mature and Immature Oocytes of the Swamp Buffalo (Bubalus bubalis)

by Qiang Fu, Zhen-Fang Liu, Yu-Lin Huang, Yang-Qing Lu and Ming Zhang

Int. J. Mol. Sci. 2016, 17(1), 94; https://doi.org/10.3390/ijms17010094 - 14 Jan 2016

Cited by 8 | Viewed by 5800

Abstract

Maternal protein components change markedly during mammalian oogenesis. Many of these proteins have yet to be characterized and verified. In this study, a proteomics approach was used to evaluate changes in proteins during oogenesis in the Swamp Buffalo (Bubalus bubalis). Proteins [...] Read more.

Maternal protein components change markedly during mammalian oogenesis. Many of these proteins have yet to be characterized and verified. In this study, a proteomics approach was used to evaluate changes in proteins during oogenesis in the Swamp Buffalo (Bubalus bubalis). Proteins from 500 immature oocytes and 500 in vitro matured oocytes were subjected to two-dimensional electrophoresis, and more than 400 spots were detected. Image analysis indicated that 17 proteins were differentially expressed between the two groups. Eight proteins were identified by mass spectrometry. In mature oocytes, three proteins were down-regulated: major vault protein (MVP), N-acetyllactosaminide β-1,6-N-acetylglucosaminyl-transferase (GCNT-2), and gem-associated protein (GEMIN)8, whereas five other proteins, heat shock protein (HSP)60, Ras-responsive element-binding protein 1 (RREB-1), heat shock cognate 71 kDa protein (HSC71), hemoglobin subunit α (HBA), and BMP-2-inducible protein kinase (BMP-2K), were up-regulated. The expression profiles of HSP60 and GEMIN8 were further verified by Western blotting. The changes in HSP60 protein expression demonstrate the increasing need for mitochondrial protein importation to facilitate macromolecular assembly during oocyte maturation. The down-regulation of GEMIN8 production implies that RNA splicing is impaired in mature oocytes. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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9 pages, 2198 KiB

Open AccessArticle

Stable Expression of Basic Fibroblast Growth Factor in Chloroplasts of Tobacco

by Yun-Peng Wang, Zheng-Yi Wei, Xiao-Fang Zhong, Chun-Jing Lin, Yu-Hong Cai, Jian Ma, Yu-Ying Zhang, Yan-Zhi Liu and Shao-Chen Xing

Int. J. Mol. Sci. 2016, 17(1), 19; https://doi.org/10.3390/ijms17010019 - 23 Dec 2015

Cited by 43 | Viewed by 7217

Abstract

Basic fibroblast growth factor (bFGF) is a multifunctional factor in acceleration of cell proliferation, differentiation and transference, and therefore widely used in clinical applications. In this study, expression vector pWX-Nt03 harboring a codon-optimized bFGF gene was constructed and introduced into the tobacco chloroplasts [...] Read more.

Basic fibroblast growth factor (bFGF) is a multifunctional factor in acceleration of cell proliferation, differentiation and transference, and therefore widely used in clinical applications. In this study, expression vector pWX-Nt03 harboring a codon-optimized bFGF gene was constructed and introduced into the tobacco chloroplasts by particle bombardment. After four rounds of selection, bFGF was proved to integrate into the chloroplast genome of regenerated plants and two of four transgenic plants were confirmed to be homoplastomic by PCR and Southern hybridization. ELISA assay indicated that bFGF represented approximately 0.1% of total soluble protein in the leaves of transplastomic tobacco plants. This is the first report of bFGF expression via chloroplast transformation in model plant, providing an additional option for the production of chloroplast-produced therapeutic proteins. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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12 pages, 1469 KiB

Open AccessArticle

A Combined Metabolomic and Proteomic Analysis of Gestational Diabetes Mellitus

by Joanna Hajduk, Agnieszka Klupczynska, Paweł Dereziński, Jan Matysiak, Piotr Kokot, Dorota M. Nowak, Marzena Gajęcka, Ewa Nowak-Markwitz and Zenon J. Kokot

Int. J. Mol. Sci. 2015, 16(12), 30034-30045; https://doi.org/10.3390/ijms161226133 - 16 Dec 2015

Cited by 24 | Viewed by 8113

Abstract

The aim of this pilot study was to apply a novel combined metabolomic and proteomic approach in analysis of gestational diabetes mellitus. The investigation was performed with plasma samples derived from pregnant women with diagnosed gestational diabetes mellitus (n = 18) and [...] Read more.

The aim of this pilot study was to apply a novel combined metabolomic and proteomic approach in analysis of gestational diabetes mellitus. The investigation was performed with plasma samples derived from pregnant women with diagnosed gestational diabetes mellitus (n = 18) and a matched control group (n = 13). The mass spectrometry-based analyses allowed to determine 42 free amino acids and low molecular-weight peptide profiles. Different expressions of several peptides and altered amino acid profiles were observed in the analyzed groups. The combination of proteomic and metabolomic data allowed obtaining the model with a high discriminatory power, where amino acids ethanolamine, l-citrulline, l-asparagine, and peptide ions with m/z 1488.59; 4111.89 and 2913.15 had the highest contribution to the model. The sensitivity (94.44%) and specificity (84.62%), as well as the total group membership classification value (90.32%) calculated from the post hoc classification matrix of a joint model were the highest when compared with a single analysis of either amino acid levels or peptide ion intensities. The obtained results indicated a high potential of integration of proteomic and metabolomics analysis regardless the sample size. This promising approach together with clinical evaluation of the subjects can also be used in the study of other diseases. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 9553 KiB

Open AccessArticle

Microtubule-Associated Protein SBgLR Facilitates Storage Protein Deposition and Its Expression Leads to Lysine Content Increase in Transgenic Maize Endosperm

by Chen Liu, Shixue Li, Jing Yue, Wenhan Xiao, Qian Zhao, Dengyun Zhu and Jingjuan Yu

Int. J. Mol. Sci. 2015, 16(12), 29772-29786; https://doi.org/10.3390/ijms161226199 - 12 Dec 2015

Cited by 8 | Viewed by 7372

Abstract

Maize (Zea mays) seed is deficient in protein and lysine content. Many studies have been made to improve the nutritional quality of maize seeds. Previously, we reported the role of a natural lysine-rich protein gene SBgLR in increasing protein and lysine [...] Read more.

Maize (Zea mays) seed is deficient in protein and lysine content. Many studies have been made to improve the nutritional quality of maize seeds. Previously, we reported the role of a natural lysine-rich protein gene SBgLR in increasing protein and lysine content. However, how the SBgLR improves lysine and protein content remains unclear. Here, the reasons and possible mechanism for SBgLR in protein and lysine improvement have been analyzed and discussed. Through seed-specific expression of SBgLR, we obtained transgenic maize with the simultaneously increased lysine and protein contents. High-protein and high-lysine characters were stably inherited across generations. The expression of SBgLR in maize kernels increased the accumulation of both zeins and non-zein proteins. Transmission electron microscopy showed that the number of protein bodies (PBs) was increased obviously in SBgLR transgenic immature endosperms with the morphology and structure of PBs unchanged. The proteinaceous matrix was more abundant in transgenic mature endosperms under scanning electron microscopy. The stabilities of zein and lysine-rich non-zein genes were also increased in transgenic endosperms. Finally, the potential application of SBgLR in maize nutrient improvement was evaluated. This study shows that a cytoskeleton-associated protein has potential applicable value in crop nutrient improving, and provided a feasible strategy for improvement of maize grain quality. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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17 pages, 1903 KiB

Open AccessArticle

Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza A Virus (H7N9)

by Ningning Sun, Wanchun Sun, Shuiming Li, Jingbo Yang, Longfei Yang, Guihua Quan, Xiang Gao, Zijian Wang, Xin Cheng, Zehui Li, Qisheng Peng and Ning Liu

Int. J. Mol. Sci. 2015, 16(11), 25982-25998; https://doi.org/10.3390/ijms161125934 - 30 Oct 2015

Cited by 36 | Viewed by 7819

Abstract

Avian influenza A viruses are serious veterinary pathogens that normally circulate among avian populations, causing substantial economic impacts. Some strains of avian influenza A viruses, such as H5N1, H9N2, and recently reported H7N9, have been occasionally found to adapt to humans from other [...] Read more.

Avian influenza A viruses are serious veterinary pathogens that normally circulate among avian populations, causing substantial economic impacts. Some strains of avian influenza A viruses, such as H5N1, H9N2, and recently reported H7N9, have been occasionally found to adapt to humans from other species. In order to replicate efficiently in the new host, influenza viruses have to interact with a variety of host factors. In the present study, H7N9 nucleoprotein was transfected into human HEK293T cells, followed by immunoprecipitated and analyzed by proteomics approaches. A series of host proteins co-immunoprecipitated were identified with high confidence, some of which were found to be acetylated at their lysine residues. Bioinformatics analysis revealed that spliceosome might be the most relevant pathway involved in host response to nucleoprotein expression, increasing our emerging knowledge of host proteins that might be involved in influenza virus replication activities. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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21 pages, 4294 KiB

Open AccessArticle

Quantitative Proteomics Analysis of Herbaceous Peony in Response to Paclobutrazol Inhibition of Lateral Branching

by Daqiu Zhao, Saijie Gong, Zhaojun Hao, Jiasong Meng and Jun Tao

Int. J. Mol. Sci. 2015, 16(10), 24332-24352; https://doi.org/10.3390/ijms161024332 - 14 Oct 2015

Cited by 13 | Viewed by 7226

Abstract

Herbaceous peony (Paeonia lactiflora Pall.) is an emerging high-grade cut flower worldwide, which is usually used in wedding bouquets and known as the “wedding flower”. However, abundant lateral branches appear frequently in some excellent cultivars, and a lack of a method to [...] Read more.

Herbaceous peony (Paeonia lactiflora Pall.) is an emerging high-grade cut flower worldwide, which is usually used in wedding bouquets and known as the “wedding flower”. However, abundant lateral branches appear frequently in some excellent cultivars, and a lack of a method to remove Paeonia lactiflora lateral branches other than inefficient artificial methods is an obstacle for improving the quality of its cut flowers. In this study, paclobutrazol (PBZ) application was found to inhibit the growth of lateral branches in Paeonia lactiflora for the first time, including 96.82% decreased lateral bud number per branch, 77.79% and 42.31% decreased length and diameter of lateral branches, respectively, declined cell wall materials and changed microstructures. Subsequently, isobaric tag for relative and absolute quantitation (iTRAQ) technology was used for quantitative proteomics analysis of lateral branches under PBZ application and control. The results indicated that 178 differentially expressed proteins (DEPs) successfully obtained, 98 DEPs were up-regulated and 80 DEPs were down-regulated. Thereafter, 34 candidate DEPs associated with the inhibited growth of lateral branches were screened according to their function and classification. These PBZ-stress responsive candidate DEPs were involved in eight biological processes, which played a very important role in the growth and development of lateral branches together with the response to PBZ stress. These results provide a better understanding of the molecular theoretical basis for removing Paeonia lactiflora lateral branches using PBZ application. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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32 pages, 2208 KiB

Open AccessArticle

The Proteome Profiles of the Cerebellum of Juvenile, Adult and Aged Rats—An Ontogenetic Study

by Michael Wille, Antje Schümann, Andreas Wree, Michael Kreutzer, Michael O. Glocker, Grit Mutzbauer and Oliver Schmitt

Int. J. Mol. Sci. 2015, 16(9), 21454-21485; https://doi.org/10.3390/ijms160921454 - 7 Sep 2015

Cited by 4 | Viewed by 7437

Abstract

In this study, we searched for proteins that change their expression in the cerebellum (Ce) of rats during ontogenesis. This study focuses on the question of whether specific proteins exist which are differentially expressed with regard to postnatal stages of development. A better [...] Read more.

In this study, we searched for proteins that change their expression in the cerebellum (Ce) of rats during ontogenesis. This study focuses on the question of whether specific proteins exist which are differentially expressed with regard to postnatal stages of development. A better characterization of the microenvironment and its development may result from these study findings. A differential two-dimensional polyacrylamide gel electrophoresis (2DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of the samples revealed that the number of proteins of the functional classes differed depending on the developmental stages. Especially members of the functional classes of biosynthesis, regulatory proteins, chaperones and structural proteins show the highest differential expression within the analyzed stages of development. Therefore, members of these functional protein groups seem to be involved in the development and differentiation of the Ce within the analyzed development stages. In this study, changes in the expression of proteins in the Ce at different postnatal developmental stages (postnatal days (P) 7, 90, and 637) could be observed. At the same time, an identification of proteins which are involved in cell migration and differentiation was possible. Especially proteins involved in processes of the biosynthesis and regulation, the dynamic organization of the cytoskeleton as well as chaperones showed a high amount of differentially expressed proteins between the analyzed dates. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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21 pages, 1170 KiB

Open AccessArticle

Identification of Proteins Modulated in the Date Palm Stem Infested with Red Palm Weevil (Rhynchophorus ferrugineus Oliv.) Using Two Dimensional Differential Gel Electrophoresis and Mass Spectrometry

by Khawaja Ghulam Rasool, Muhammad Altaf Khan, Abdulrahman Saad Aldawood, Muhammad Tufail, Muhammad Mukhtar and Makio Takeda

Int. J. Mol. Sci. 2015, 16(8), 19326-19346; https://doi.org/10.3390/ijms160819326 - 17 Aug 2015

Cited by 20 | Viewed by 8250

Abstract

A state of the art proteomic methodology using Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI TOF) has been employed to characterize peptides modulated in the date palm stem subsequent to infestation with red palm weevil (RPW). Our analyses revealed 32 differentially expressed peptides [...] Read more.

A state of the art proteomic methodology using Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI TOF) has been employed to characterize peptides modulated in the date palm stem subsequent to infestation with red palm weevil (RPW). Our analyses revealed 32 differentially expressed peptides associated with RPW infestation in date palm stem. To identify RPW infestation associated peptides (I), artificially wounded plants (W) were used as additional control beside uninfested plants, a conventional control (C). A constant unique pattern of differential expression in infested (I), wounded (W) stem samples compared to control (C) was observed. The upregulated proteins showed relative fold intensity in order of I > W and downregulated spots trend as W > I, a quite interesting pattern. This study also reveals that artificially wounding of date palm stem affects almost the same proteins as infestation; however, relative intensity is quite lower than in infested samples both in up and downregulated spots. All 32 differentially expressed spots were subjected to MALDI-TOF analysis for their identification and we were able to match 21 proteins in the already existing databases. Relatively significant modulated expression pattern of a number of peptides in infested plants predicts the possibility of developing a quick and reliable molecular methodology for detecting plants infested with date palm. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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23 pages, 2432 KiB

Open AccessArticle

Proteomic Identification of Target Proteins of Thiodigalactoside in White Adipose Tissue from Diet-Induced Obese Rats

by Hilal Ahmad Parray and Jong Won Yun

Int. J. Mol. Sci. 2015, 16(7), 14441-14463; https://doi.org/10.3390/ijms160714441 - 25 Jun 2015

Cited by 17 | Viewed by 7319

Abstract

Previously, galectin-1 (GAL1) was found to be up-regulated in obesity-prone subjects, suggesting that use of a GAL1 inhibitor could be a novel therapeutic approach for treatment of obesity. We evaluated thiodigalactoside (TDG) as a potent inhibitor of GAL1 and identified target proteins of [...] Read more.

Previously, galectin-1 (GAL1) was found to be up-regulated in obesity-prone subjects, suggesting that use of a GAL1 inhibitor could be a novel therapeutic approach for treatment of obesity. We evaluated thiodigalactoside (TDG) as a potent inhibitor of GAL1 and identified target proteins of TDG by performing comparative proteome analysis of white adipose tissue (WAT) from control and TDG-treated rats fed a high fat diet (HFD) using two dimensional gel electrophoresis (2-DE) combined with MALDI-TOF-MS. Thirty-two spots from a total of 356 matched spots showed differential expression between control and TDG-treated rats, as identified by peptide mass fingerprinting. These proteins were categorized into groups such as carbohydrate metabolism, tricarboxylic acid (TCA) cycle, signal transduction, cytoskeletal, and mitochondrial proteins based on functional analysis using Protein Annotation Through Evolutionary Relationship (PANTHER) and Database for Annotation, Visualization, Integrated Discovery (DAVID) classification. One of the most striking findings of this study was significant changes in Carbonic anhydrase 3 (CA3), Voltage-dependent anion channel 1 (VDAC1), phosphatidylethanolamine-binding protein 1 (PEBP1), annexin A2 (ANXA2) and lactate dehydrogenase A chain (LDHA) protein levels between WAT from control and TDG-treated groups. In addition, we confirmed increased expression of thermogenic proteins as well as reduced expression of lipogenic proteins in response to TDG treatment. These results suggest that TDG may effectively prevent obesity, and TDG-responsive proteins can be used as novel target proteins for obesity treatment. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 2787 KiB

Open AccessArticle

Atrazine Triggers DNA Damage Response and Induces DNA Double-Strand Breaks in MCF-10A Cells

by Peixin Huang, John Yang, Jie Ning, Michael Wang and Qisheng Song

Int. J. Mol. Sci. 2015, 16(7), 14353-14368; https://doi.org/10.3390/ijms160714353 - 24 Jun 2015

Cited by 24 | Viewed by 6899

Abstract

Atrazine, a pre-emergent herbicide in the chloro-s-triazine family, has been widely used in crop lands and often detected in agriculture watersheds, which is considered as a potential threat to human health. Although atrazine and its metabolites showed an elevated incidence of [...] Read more.

Atrazine, a pre-emergent herbicide in the chloro-s-triazine family, has been widely used in crop lands and often detected in agriculture watersheds, which is considered as a potential threat to human health. Although atrazine and its metabolites showed an elevated incidence of mammary tumors in female Sprague–Dawley (SD) rats, no molecular evidence was found relevant to its carcinogenesis in humans. This study aims to determine whether atrazine could induce the expression of DNA damage response-related proteins in normal human breast epithelial cells (MCF-10A) and to examine the cytotoxicity of atrazine at a molecular level. Our results indicate that a short-term exposure of MCF-10A to an environmentally-detectable concentration of atrazine (0.1 µg/mL) significantly increased the expression of tumor necrosis factor receptor-1 (TNFR1) and phosphorylated Rad17 in the cells. Atrazine treatment increased H2AX phosphorylation (γH2AX) and the formation of γH2AX foci in the nuclei of MCF-10A cells. Atrazine also sequentially elevated DNA damage checkpoint proteins of ATM- and RAD3-related (ATR), ATRIP and phospho-Chk1, suggesting that atrazine could induce DNA double-strand breaks and trigger the DNA damage response ATR-Chk1 pathway in MCF-10A cells. Further investigations are needed to determine whether atrazine-triggered DNA double-strand breaks and DNA damage response ATR-Chk1 pathway occur in vivo. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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32 pages, 2154 KiB

Open AccessArticle

A Comparative Proteomic Analysis of the Buds and the Young Expanding Leaves of the Tea Plant (Camellia sinensis L.)

by Qin Li, Juan Li, Shuoqian Liu, Jianan Huang, Haiyan Lin, Kunbo Wang, Xiaomei Cheng and Zhonghua Liu

Int. J. Mol. Sci. 2015, 16(6), 14007-14038; https://doi.org/10.3390/ijms160614007 - 18 Jun 2015

Cited by 27 | Viewed by 9778

Abstract

Tea (Camellia sinensis L.) is a perennial woody plant that is widely cultivated to produce a popular non-alcoholic beverage; this beverage has received much attention due to its pleasant flavor and bioactive ingredients, particularly several important secondary metabolites. Due to the significant [...] Read more.

Tea (Camellia sinensis L.) is a perennial woody plant that is widely cultivated to produce a popular non-alcoholic beverage; this beverage has received much attention due to its pleasant flavor and bioactive ingredients, particularly several important secondary metabolites. Due to the significant changes in the metabolite contents of the buds and the young expanding leaves of tea plants, high-performance liquid chromatography (HPLC) analysis and isobaric tags for relative and absolute quantitation (iTRAQ) analysis were performed. A total of 233 differentially expressed proteins were identified. Among these, 116 proteins were up-regulated and 117 proteins were down-regulated in the young expanding leaves compared with the buds. A large array of diverse functions was revealed, including roles in energy and carbohydrate metabolism, secondary metabolite metabolism, nucleic acid and protein metabolism, and photosynthesis- and defense-related processes. These results suggest that polyphenol biosynthesis- and photosynthesis-related proteins regulate the secondary metabolite content of tea plants. The energy and antioxidant metabolism-related proteins may promote tea leaf development. However, reverse transcription quantitative real-time PCR (RT-qPCR) showed that the protein expression levels were not well correlated with the gene expression levels. These findings improve our understanding of the molecular mechanism of the changes in the metabolite content of the buds and the young expanding leaves of tea plants. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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22 pages, 2416 KiB

Open AccessArticle

Proteomic Analysis of Immature Fraxinus mandshurica Cotyledon Tissues during Somatic Embryogenesis: Effects of Explant Browning on Somatic Embryogenesis

by Chun-Ping Liu, Ling Yang and Hai-Long Shen

Int. J. Mol. Sci. 2015, 16(6), 13692-13713; https://doi.org/10.3390/ijms160613692 - 15 Jun 2015

Cited by 18 | Viewed by 6059

Abstract

Manchurian ash (Fraxinus mandshurica Rupr.) is a valuable hardwood species in Northeast China. In cultures of F. mandshurica, somatic embryos were produced mainly on browned explants. Therefore, we studied the mechanism of explant browning and its relationship with somatic embryogenesis (SE). [...] Read more.

Manchurian ash (Fraxinus mandshurica Rupr.) is a valuable hardwood species in Northeast China. In cultures of F. mandshurica, somatic embryos were produced mainly on browned explants. Therefore, we studied the mechanism of explant browning and its relationship with somatic embryogenesis (SE). We used explants derived from F. mandshurica immature zygotic embryo cotyledons as materials. Proteins were extracted from browned embryogenic explants, browned non-embryogenic explants, and non-brown explants, and then separated by 2-dimensional electrophoresis. Differentially and specifically expressed proteins were analyzed by mass spectrometry to identify proteins involved in the browning of explants and SE. Some stress response and defense proteins such as chitinases, peroxidases, aspartic proteinases, and an osmotin-like protein played important roles during SE of F. mandshurica. Our results indicated that explant browning might not be caused by the accumulation and oxidation of polyphenols only, but also by some stress-related processes, which were involved in programmed cell death (PCD), and then induced SE. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 577 KiB

Open AccessArticle

Identification of Site-Specific Stroke Biomarker Candidates by Laser Capture Microdissection and Labeled Reference Peptide

by Tingting Lian, Daixin Qu, Xu Zhao, Lixia Yu and Bing Gao

Int. J. Mol. Sci. 2015, 16(6), 13427-13441; https://doi.org/10.3390/ijms160613427 - 11 Jun 2015

Cited by 16 | Viewed by 7114

Abstract

The search to date for accurate protein biomarkers in acute ischemic stroke has taken into consideration the stage and/or the size of infarction, but has not accounted for the site of stroke. In the present study, multiple reaction monitoring using labeled reference peptide [...] Read more.

The search to date for accurate protein biomarkers in acute ischemic stroke has taken into consideration the stage and/or the size of infarction, but has not accounted for the site of stroke. In the present study, multiple reaction monitoring using labeled reference peptide (LRP) following laser capture microdissection (LCM) is used to identify site-specific protein biomarker candidates. In middle cerebral artery occlusion (MCAO) rat models, both intact and infarcted brain tissue was collected by LCM, followed by on-film digestion and semi-quantification using triple-quadrupole mass spectrometry. Thirty-four unique peptides were detected for the verification of 12 proteins in both tissue homogenates and LCM-captured samples. Six insoluble proteins, including neurofilament light polypeptide (NEFL), alpha-internexin (INA), microtubule-associated protein 2 (MAP2), myelin basic protein (MBP), myelin proteolipid protein (PLP) and 2′,3′-cyclic-nucleotide 3′-phosphodiesterase (CNP), were found to be site-specific. Soluble proteins, such as neuron-specific enolase (NSE) and ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1), and some insoluble proteins, including neurofilament heavy polypeptide (NEFH), glial fibrillary acidic protein (GFAP), microtubule-associated protein tau (MAPT) and tubulin β-3 chain (TUBB3), were found to be evenly distributed in the brain. Therefore, we conclude that some insoluble protein biomarkers for stroke are site-specific, and would make excellent candidates for the design and analysis of relevant clinical studies in the future. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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29 pages, 1244 KiB

Open AccessArticle

Proteomic Insights into Sulfur Metabolism in the Hydrogen-Producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1

by Yoon-Jung Moon, Joseph Kwon, Sung-Ho Yun, Hye Li Lim, Jonghyun Kim, Soo Jung Kim, Sung Gyun Kang, Jung-Hyun Lee, Seung Il Kim and Young-Ho Chung

Int. J. Mol. Sci. 2015, 16(5), 9167-9195; https://doi.org/10.3390/ijms16059167 - 23 Apr 2015

Cited by 10 | Viewed by 7971

Abstract

The hyperthermophilic archaeon Thermococcus onnurineus NA1 has been shown to produce H₂ when using CO, formate, or starch as a growth substrate. This strain can also utilize elemental sulfur as a terminal electron acceptor for heterotrophic growth. To gain insight into sulfur [...] Read more.

The hyperthermophilic archaeon Thermococcus onnurineus NA1 has been shown to produce H₂ when using CO, formate, or starch as a growth substrate. This strain can also utilize elemental sulfur as a terminal electron acceptor for heterotrophic growth. To gain insight into sulfur metabolism, the proteome of T. onnurineus NA1 cells grown under sulfur culture conditions was quantified and compared with those grown under H₂-evolving substrate culture conditions. Using label-free nano-UPLC-MS^E-based comparative proteomic analysis, approximately 38.4% of the total identified proteome (589 proteins) was found to be significantly up-regulated (≥1.5-fold) under sulfur culture conditions. Many of these proteins were functionally associated with carbon fixation, Fe–S cluster biogenesis, ATP synthesis, sulfur reduction, protein glycosylation, protein translocation, and formate oxidation. Based on the abundances of the identified proteins in this and other genomic studies, the pathways associated with reductive sulfur metabolism, H₂-metabolism, and oxidative stress defense were proposed. The results also revealed markedly lower expression levels of enzymes involved in the sulfur assimilation pathway, as well as cysteine desulfurase, under sulfur culture condition. The present results provide the first global atlas of proteome changes triggered by sulfur, and may facilitate an understanding of how hyperthermophilic archaea adapt to sulfur-rich, extreme environments. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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18 pages, 6710 KiB

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Proteome Analysis of Dormancy-Released Seeds of Fraxinus mandshurica Rupr. in Response to Re-Dehydration under Different Conditions

by Peng Zhang, Di Liu, Hailong Shen, Yuhua Li and Yuzhe Nie

Int. J. Mol. Sci. 2015, 16(3), 4713-4730; https://doi.org/10.3390/ijms16034713 - 2 Mar 2015

Cited by 8 | Viewed by 7000

Abstract

Desiccation tolerance is the ability of orthodox seeds to achieve equilibrium with atmospheric relative humidity and to survive in this state. Understanding how orthodox seeds respond to dehydration is important for improving quality and long-term storage of seeds under low temperature and drought [...] Read more.

Desiccation tolerance is the ability of orthodox seeds to achieve equilibrium with atmospheric relative humidity and to survive in this state. Understanding how orthodox seeds respond to dehydration is important for improving quality and long-term storage of seeds under low temperature and drought stress conditions. Long-term storage of seeds is an artificial situation, because in most natural situations a seed that has been shed may not remain in a desiccated state for very long, and if dormant it may undergo repeated cycles of hydration. Different types of seeds are differentially sensitive to desiccation and this directly affects long-term storage. For these reasons, many researchers are investigating loss of desiccation tolerance during orthodox seed development to understand how it is acquired. In this study, the orthodox seed proteome response of Fraxinus mandshurica Rupr. to dehydration (to a relative water content of 10%, which mimics seed dehydration) was investigated under four different conditions viz. 20 °C; 20 °C with silica gel; 1 °C; and 1 °C after pretreatment with Ca²⁺. Proteins from seeds dehydrated under different conditions were extracted and separated by two-dimensional difference gel electrophoresis (2D-DIGE). A total of 2919 protein spots were detected, and high-resolution 2D-DIGE indicated there were 27 differentially expressed. Seven of these were identified using MALDI TOF/TOF mass spectrometry. Inferences from bioinformatics annotations of these proteins established the possible involvement of detoxifying enzymes, transport proteins, and nucleotide metabolism enzymes in response to dehydration. Of the seven differentially abundant proteins, the amounts of six were down-regulated and one was up-regulated. Also, a putative acyl-coenzyme A oxidase of the glyoxylate cycle increased in abundance. In particular, the presence of kinesin-1, a protein important for regulation and cargo interaction, was up-regulated in seeds exposed to low temperature dehydration. Kinesin-1 is present in all major lineages, but it is rarely detected in seed desiccation tolerance of woody species. These observations provide new insight into the proteome of seeds in deep dormancy under different desiccation conditions. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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20 pages, 4344 KiB

Open AccessArticle

Analysis of Dermal Papilla Cell Interactome Using STRING Database to Profile the ex Vivo Hair Growth Inhibition Effect of a Vinca Alkaloid Drug, Colchicine

by Ching-Wu Hsia, Ming-Yi Ho, Hao-Ai Shui, Chong-Bin Tsai and Min-Jen Tseng

Int. J. Mol. Sci. 2015, 16(2), 3579-3598; https://doi.org/10.3390/ijms16023579 - 5 Feb 2015

Cited by 27 | Viewed by 8576

Abstract

Dermal papillae (DPs) control the formation of hair shafts. In clinical settings, colchicine (CLC) induces patients’ hair shedding. Compared to the control, the ex vivo hair fiber elongation of organ cultured vibrissa hair follicles (HFs) declined significantly after seven days of CLC treatment. [...] Read more.

Dermal papillae (DPs) control the formation of hair shafts. In clinical settings, colchicine (CLC) induces patients’ hair shedding. Compared to the control, the ex vivo hair fiber elongation of organ cultured vibrissa hair follicles (HFs) declined significantly after seven days of CLC treatment. The cultured DP cells (DPCs) were used as the experimental model to study the influence of CLC on the protein dynamics of DPs. CLC could alter the morphology and down-regulate the expression of alkaline phosphatase (ALP), the marker of DPC activity, and induce IκBα phosphorylation of DPCs. The proteomic results showed that CLC modulated the expression patterns (fold > 2) of 24 identified proteins, seven down-regulated and 17 up-regulated. Most of these proteins were presumably associated with protein turnover, metabolism, structure and signal transduction. Protein-protein interactions (PPI) among these proteins, established by Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, revealed that they participate in protein metabolic process, translation, and energy production. Furthermore, ubiquitin C (UbC) was predicted to be the controlling hub, suggesting the involvement of ubiquitin-proteasome system in modulating the pathogenic effect of CLC on DPC. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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20 pages, 1333 KiB

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Activation of the Ubiquitin Proteasome Pathway by Silk Fibroin Modified Chitosan Nanoparticles in Hepatic Cancer Cells

by Ming-Hui Yang, Tze-Wen Chung, Yi-Shan Lu, Yi-Ling Chen, Wan-Chi Tsai, Shiang-Bin Jong, Shyng-Shiou Yuan, Pao-Chi Liao, Po-Chiao Lin and Yu-Chang Tyan

Int. J. Mol. Sci. 2015, 16(1), 1657-1676; https://doi.org/10.3390/ijms16011657 - 12 Jan 2015

Cited by 11 | Viewed by 9025

Abstract

Silk fibroin (SF) is a protein with bulky hydrophobic domains and can be easily purified as sericin-free silk-based biomaterial. Silk fibroin modified chitosan nanoparticle (SF-CSNP), a biocompatible material, has been widely used as a potential drug delivery system. Our current investigation studied the [...] Read more.

Silk fibroin (SF) is a protein with bulky hydrophobic domains and can be easily purified as sericin-free silk-based biomaterial. Silk fibroin modified chitosan nanoparticle (SF-CSNP), a biocompatible material, has been widely used as a potential drug delivery system. Our current investigation studied the bio-effects of the SF-CSNP uptake by liver cells. In this experiment, the characterizations of SF-CSNPs were measured by particle size analysis and protein assay. The average size of the SF-CSNP was 311.9 ± 10.7 nm, and the average zeta potential was +13.33 ± 0.3 mV. The SF coating on the SF-CSNP was 6.27 ± 0.17 μg/mL. Moreover, using proteomic approaches, several proteins involved in the ubiquitin proteasome pathway were identified by analysis of differential protein expressions of HepG2 cell uptake the SF-CSNP. Our experimental results have demonstrated that the SF-CSNP may be involved in liver cancer cell survival and proliferation. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 1228 KiB

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Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

by Claudius Marondedze, Aloysius Wong, Arnoud Groen, Natalia Serrano, Boris Jankovic, Kathryn Lilley, Christoph Gehring and Ludivine Thomas

Int. J. Mol. Sci. 2015, 16(1), 857-870; https://doi.org/10.3390/ijms16010857 - 31 Dec 2014

Cited by 9 | Viewed by 7629

Abstract

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, [...] Read more.

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 1911 KiB

Open AccessArticle

Identification of Biomarkers in Cerebrospinal Fluid and Serum of Multiple Sclerosis Patients by Immunoproteomics Approach

by Paolo Colomba, Simona Fontana, Giuseppe Salemi, Marilisa Barranca, Claudia Lo Sicco, Maria Antonietta Mazzola, Paolo Ragonese, Giovanni Savettieri, Giacomo De Leo, Riccardo Alessandro and Giovanni Duro

Int. J. Mol. Sci. 2014, 15(12), 23269-23282; https://doi.org/10.3390/ijms151223269 - 15 Dec 2014

Cited by 11 | Viewed by 6277

Abstract

Multiple sclerosis (MS) is an autoimmune inflammatory demyelinating disease of the central nervous system. At present, the molecular mechanisms causing the initiation, development and progression of MS are poorly understood, and no reliable proteinaceous disease markers are available. In this study, we used [...] Read more.

Multiple sclerosis (MS) is an autoimmune inflammatory demyelinating disease of the central nervous system. At present, the molecular mechanisms causing the initiation, development and progression of MS are poorly understood, and no reliable proteinaceous disease markers are available. In this study, we used an immunoproteomics approach to identify autoreactive antibodies in the cerebrospinal fluid of MS patients to use as candidate markers with potential diagnostic value. We identified an autoreactive anti-transferrin antibody that may have a potential link with the development and progression of MS. We found this antibody at high levels also in the serum of MS patients and created an immunoenzymatic assay to detect it. Because of the complexity and heterogeneity of multiple sclerosis, it is difficult to find a single marker for all of the processes involved in the origin and progression of the disease, so the development of a panel of biomarkers is desirable, and anti-transferrin antibody could be one of these. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 1440 KiB

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Crosstalk between Edc4 and Mammalian Target of Rapamycin Complex 1 (mTORC1) Signaling in mRNA Decapping

by Hazir Rahman, Muhammad Qasim, Michael Oellerich and Abdul R. Asif

Int. J. Mol. Sci. 2014, 15(12), 23179-23195; https://doi.org/10.3390/ijms151223179 - 12 Dec 2014

Cited by 6 | Viewed by 8180

Abstract

The mammalian target of rapamycin complex 1 (mTORC1) is involved in the cellular transcription and translation processes. The undertaken study characterized the enhancer of mRNA decapping protein 4 (Edc4) as mTORC1 interacting protein. Human T lymphoblast (CCRF-CEM) cells were used for mTORC1 purification. [...] Read more.

The mammalian target of rapamycin complex 1 (mTORC1) is involved in the cellular transcription and translation processes. The undertaken study characterized the enhancer of mRNA decapping protein 4 (Edc4) as mTORC1 interacting protein. Human T lymphoblast (CCRF-CEM) cells were used for mTORC1 purification. Co-immunoprecipitation coupled with immunoblotting analysis was used to confirm the interaction of Edc4 in mTORC1 specific purifications. Further assays were incorporated to conclude the role of mTORC1 in mRNA decapping via Edc4. Edc4 was identified as a new interacting protein with mTORC1 in both the endogenous and myc-tag raptor component mTORC1 specific purifications. Quantitative co-localization using confocal microscopy demonstrated that raptor component of mTORC1 coexists with Edc4 in processing (P) bodies, a site for mRNA degradation. Incubation of cells with rapamycin, a known inhibitor of mTOR kinase activity, increased the total Edc4 protein expression but at the same time decreased the Edc4 interaction with mTORC1. Moreover, rapamycin treatment resulted in a significant decrease in total serine phosphorylated Edc4 protein signal and the total 5'-capped mRNA. These findings provide the first evidence for the pivotal role of mTORC1 in Edc4 regulation. Further in-depth studies are required to get a complete understanding of molecular crosstalk between mTORC1 signaling and mRNA decapping pathway. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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21 pages, 2425 KiB

Open AccessArticle

Comparative Proteomic Analysis of Labellum and Inner Lateral Petals in Cymbidium ensifolium Flowers

by Xiaobai Li, Weiwei Xu, Moytri Roy Chowdhury and Feng Jin

Int. J. Mol. Sci. 2014, 15(11), 19877-19897; https://doi.org/10.3390/ijms151119877 - 31 Oct 2014

Cited by 19 | Viewed by 6825

Abstract

The labellum in orchids shares homology with the inner lateral petals of the flower. The labellum is a modified petal and often distinguished from other petals and sepals due to its large size and irregular shape. Herein, we combined two-dimensional gel electrophoresis (2-DE) [...] Read more.

The labellum in orchids shares homology with the inner lateral petals of the flower. The labellum is a modified petal and often distinguished from other petals and sepals due to its large size and irregular shape. Herein, we combined two-dimensional gel electrophoresis (2-DE) and matrix assisted laser desorption/ionization time of flight/time of flight (MALDI-TOF/TOF) approaches to identify the differentially expressed proteome between labellum and inner lateral petal in one of Orchid species (C. ensifolium). A total of 30 protein spots were identified, which showed more than a two-fold significant difference (p < 0.05) in their expression. Compared with C. ensifolium transcriptome (sequenced in house), 21 proteins matched the translated nucleotide. The proteins identified were classified into 48 categories according to gene ontology (GO). Additionally, these proteins were involved in 18 pathways and 9 possible protein-protein interactions. Serine carboxypeptidase and beta-glucosidase were involved in the phenylpropanoid pathway, which could regulate biosynthesis of floral scent components. Malate dehydrogenase (maeB) and triosephosphate isomerase (TPI) in carbon fixation pathway could regulate the energy metabolism. Xyloglucan endotransglucosylase/hydrolase (XET/XTH) could promote cell wall formation and aid the petal’s morphogenesis. The identification of such differentially expressed proteins provides new targets for future studies; these will assess the proteins’ physiological roles and significance in labellum and inner lateral petals. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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23 pages, 2180 KiB

Open AccessArticle

Differential Proteomics Analysis of Bacillus amyloliquefaciens and Its Genome-Shuffled Mutant for Improving Surfactin Production

by Junfeng Zhao, Lin Cao, Chong Zhang, Lei Zhong, Jing Lu and Zhaoxin Lu

Int. J. Mol. Sci. 2014, 15(11), 19847-19869; https://doi.org/10.3390/ijms151119847 - 31 Oct 2014

Cited by 14 | Viewed by 6686

Abstract

Genome shuffling technology was used as a novel whole-genome engineering approach to rapidly improve the antimicrobial lipopeptide yield of Bacillus amyloliquefaciens. Comparative proteomic analysis of the parental ES-2-4 and genome-shuffled FMB38 strains was conducted to examine the differentially expressed proteins. The proteome [...] Read more.

Genome shuffling technology was used as a novel whole-genome engineering approach to rapidly improve the antimicrobial lipopeptide yield of Bacillus amyloliquefaciens. Comparative proteomic analysis of the parental ES-2-4 and genome-shuffled FMB38 strains was conducted to examine the differentially expressed proteins. The proteome was separated by 2-DE (two dimensional electrophoresis) and analyzed by MS (mass spectrum). In the shuffled strain FMB38, 51 differentially expressed protein spots with higher than two-fold spot density were detected by gel image comparison. Forty-six protein spots were detectable by silver staining and further MS analysis. The results demonstrated that among the 46 protein spots expressed particularly induced in the genome-shuffled mutant, 15 were related to metabolism, five to DNA replication, recombination and repair, six to translation and post-translational modifications, one to cell secretion and signal transduction mechanisms, three to surfactin synthesis, two to energy production and conversion, and 14 to others. All these indicated that the metabolic capability of the mutant was improved by the genome shuffling. The study will enable future detailed investigation of gene expression and function linked with surfactin synthesis. The results of proteome analysis may provide information for metabolic engineering of Bacillus amyloliquefaciens for overproduction of surfactin. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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21 pages, 1901 KiB

Open AccessArticle

Atrazine Affects Phosphoprotein and Protein Expression in MCF-10A Human Breast Epithelial Cells

by Peixin Huang, John Yang and Qisheng Song

Int. J. Mol. Sci. 2014, 15(10), 17806-17826; https://doi.org/10.3390/ijms151017806 - 1 Oct 2014

Cited by 18 | Viewed by 7492

Abstract

Atrazine, a member of the 2-chloro-s-triazine family of herbicides, is the most widely used pesticide in the world and often detected in agriculture watersheds. Although it was generally considered as an endocrine disruptor, posing a potential threat to human health, the molecular mechanisms [...] Read more.

Atrazine, a member of the 2-chloro-s-triazine family of herbicides, is the most widely used pesticide in the world and often detected in agriculture watersheds. Although it was generally considered as an endocrine disruptor, posing a potential threat to human health, the molecular mechanisms of atrazine effects remain unclear. Using two-dimensional gel electrophoresis, we identified a panel of differentially expressed phosphoproteins and total proteins in human breast epithelial MCF-10A cells after being exposed to environmentally relevant concentrations of atrazine. Atrazine treatments for 6 h resulted in differential expression of 4 phosphoproteins and 8 total-proteins as compared to the control cells (>1.5-fold, p < 0.05). MALDI-TOF MS/MS analysis revealed that the differentially expressed proteins belong to various cellular compartments (nucleus, cytosol, membrane) and varied in function, including those regulating the stress response such as peroxiredoxin I, HSP70 and HSP27; structural proteins such as tropomyosin and profilin 1; and oncogenesis proteins such as ANP32A. Six of the 12 identified proteins were verified by quantitative PCR for their transcript levels. The most up-regulated phosphoprotein by atrazine treatment, ANP32A, was further analyzed for its expression, distribution and cellular localization using Western blot and immunocytochemical approaches. The results revealed that ANP32 expression after atrazine treatment increased dose and time dependently and was primarily located in the nucleus. This study may provide new evidence on the potential toxicity of atrazine in human cells. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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23 pages, 2133 KiB

Open AccessArticle

A Proteomic Analysis of Human Follicular Fluid: Comparison between Younger and Older Women with Normal FSH Levels

by Mahmoud Hashemitabar, Maryam Bahmanzadeh, Ali Mostafaie, Mahmoud Orazizadeh, Marzieh Farimani and Roshan Nikbakht

Int. J. Mol. Sci. 2014, 15(10), 17518-17540; https://doi.org/10.3390/ijms151017518 - 29 Sep 2014

Cited by 45 | Viewed by 8457

Abstract

The follicular fluid (FF) is produced during folliculogenesis and contains a variety of proteins that play important roles in follicle development and oocyte maturation. Age-related infertility is usually considered as a problem that can be solved by assisted reproduction technology. Therefore, the identiﬁcation [...] Read more.

The follicular fluid (FF) is produced during folliculogenesis and contains a variety of proteins that play important roles in follicle development and oocyte maturation. Age-related infertility is usually considered as a problem that can be solved by assisted reproduction technology. Therefore, the identiﬁcation of novel biomarkers that are linked to reproductive aging is the subject of this study. FF was obtained from healthy younger (20–32 years old) and older (38–42 years old) women undergoing intracytoplasmic sperm injection (ICSI) due to male factor infertility. The FF was analyzed by two-dimensional gel electrophoresis (2-DE). The power of two-dimensional gel electrophoresis and the identiﬁcation of proteins were exploited using matrix-assisted laser desorption-ionization time-of-flight/time-of-flight (MALDI-TOF-TOF) mass spectrometry. Twenty three protein spots showed reproducible and significant changes in the aged compared to the young group. Of these, 19 protein spots could be identified using MALDI-TOF-TOF-MS. As a result of MASCOT search, five unique downregulated proteins were identified in the older group. These were identified as serotransferrin, hemopexin precursor, complement C3, C4 and kininogen. A number of protein markers were found that may help develop diagnostic methods of infertility. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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26 pages, 1474 KiB

Open AccessArticle

Immunoproteome of Aspergillus fumigatus Using Sera of Patients with Invasive Aspergillosis

by Emylli D. Virginio, Paula H. Kubitschek-Barreira, Marjorie Vieira Batista, Marcelo R. Schirmer, Eliana Abdelhay, Maria A. Shikanai-Yasuda and Leila M. Lopes-Bezerra

Int. J. Mol. Sci. 2014, 15(8), 14505-14530; https://doi.org/10.3390/ijms150814505 - 20 Aug 2014

Cited by 22 | Viewed by 6165

Abstract

Invasive aspergillosis is a life-threatening lung or systemic infection caused by the opportunistic mold Aspergillus fumigatus. The disease affects mainly immunocompromised hosts, and patients with hematological malignances or who have been submitted to stem cell transplantation are at high risk. Despite the current [...] Read more.

Invasive aspergillosis is a life-threatening lung or systemic infection caused by the opportunistic mold Aspergillus fumigatus. The disease affects mainly immunocompromised hosts, and patients with hematological malignances or who have been submitted to stem cell transplantation are at high risk. Despite the current use of Platelia™ Aspergillus as a diagnostic test, the early diagnosis of invasive aspergillosis remains a major challenge in improving the prognosis of the disease. In this study, we used an immunoproteomic approach to identify proteins that could be putative candidates for the early diagnosis of invasive aspergillosis. Antigenic proteins expressed in the first steps of A. fumigatus germination occurring in a human host were revealed using 2-D Western immunoblots with the serum of patients who had previously been classified as probable and proven for invasive aspergillosis. Forty antigenic proteins were identified using mass spectrometry (MS/MS). A BLAST analysis revealed that two of these proteins showed low homology with proteins of either the human host or etiological agents of other invasive fungal infections. To our knowledge, this is the first report describing specific antigenic proteins of A. fumigatus germlings that are recognized by sera of patients with confirmed invasive aspergillosis who were from two separate hospital units. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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10 pages, 3059 KiB

Open AccessArticle

Quantitative Proteomic Analysis of Serum Proteins from Oral Cancer Patients: Comparison of Two Analytical Methods

by Yan Yang, Junwei Huang, Bahareh Rabii, Ramin Rabii and Shen Hu

Int. J. Mol. Sci. 2014, 15(8), 14386-14395; https://doi.org/10.3390/ijms150814386 - 18 Aug 2014

Cited by 14 | Viewed by 6575

Abstract

Serum proteomic analysis can be a valuable approach for the discovery of protein biomarkers for early detection or monitoring of a disease. In this study, two analytical methods were compared for quantification of serum proteins in patients with oral cancer. In the first [...] Read more.

Serum proteomic analysis can be a valuable approach for the discovery of protein biomarkers for early detection or monitoring of a disease. In this study, two analytical methods were compared for quantification of serum proteins in patients with oral cancer. In the first approach, we quantified serum proteins between oral squamous cell carcinoma (OSCC) and healthy control subjects by performing in-solution digestion of serum proteins, isobaric tags for relative and absolute quantification (iTRAQ) labeling of the resulting peptides, strong cation exchange (SCX) fractionation of labeled peptides and finally capillary liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis of the peptides. In the second approach, we first separated serum proteins with SDS-PAGE. The gel-separated proteins were then digested with trypsin and the resulting peptides were labeled with iTRAQ and analyzed with LC-MS/MS for protein quantification. A total of 319 serum proteins were quantified with the first proteomic approach whereas a total of 281 proteins were quantified by the second proteomic approach. Most of the proteins were identified and quantified by both approaches, suggesting that these methods are similarly effective for serum proteome analysis. This study provides compelling evidence that quantitative serum proteomic analysis of OSCC is a valuable approach for identifying differentially expressed proteins in cancer patients’ circulation systems that may be used as potential biomarkers for disease detection. Further validation in large oral cancer patient populations may lead to a simple and low invasive clinical tool for OSCC diagnosis or monitoring. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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29 pages, 1752 KiB

Open AccessArticle

Complete Proteome of a Quinolone-Resistant Salmonella Typhimurium Phage Type DT104B Clinical Strain

by Susana Correia, Júlio D. Nunes-Miranda, Luís Pinto, Hugo M. Santos, María De Toro, Yolanda Sáenz, Carmen Torres, José Luis Capelo, Patrícia Poeta and Gilberto Igrejas

Int. J. Mol. Sci. 2014, 15(8), 14191-14219; https://doi.org/10.3390/ijms150814191 - 15 Aug 2014

Cited by 14 | Viewed by 8857

Abstract

Salmonellosis is one of the most common and widely distributed foodborne diseases. The emergence of Salmonella strains that are resistant to a variety of antimicrobials is a serious global public health concern. Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) is one [...] Read more.

Salmonellosis is one of the most common and widely distributed foodborne diseases. The emergence of Salmonella strains that are resistant to a variety of antimicrobials is a serious global public health concern. Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) is one of these emerging epidemic multidrug resistant strains. Here we collate information from the diverse and comprehensive range of experiments on Salmonella proteomes that have been published. We then present a new study of the proteome of the quinolone-resistant Se20 strain (phage type DT104B), recovered after ciprofloxacin treatment and compared it to the proteome of reference strain SL1344. A total of 186 and 219 protein spots were recovered from Se20 and SL1344 protein extracts, respectively, after two-dimensional gel electrophoresis. The signatures of 94% of the protein spots were successfully identified through matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). Three antimicrobial resistance related proteins, whose genes were previously detected by polymerase chain reaction (PCR), were identified in the clinical strain. The presence of these proteins, dihydropteroate synthase type-2 (sul2 gene), aminoglycoside resistance protein A (strA gene) and aminoglycoside 6'-N-acetyltransferase type Ib-cr4 (aac(6')-Ib-cr4 gene), was confirmed in the DT104B clinical strain. The aac(6')-Ib-cr4 gene is responsible for plasmid-mediated aminoglycoside and quinolone resistance. This is a preliminary analysis of the proteome of these two S. Typhimurium strains and further work is being developed to better understand how antimicrobial resistance is developing in this pathogen. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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12 pages, 957 KiB

Open AccessArticle

Identifying the Subfamilies of Voltage-Gated Potassium Channels Using Feature Selection Technique

by Wei-Xin Liu, En-Ze Deng, Wei Chen and Hao Lin

Int. J. Mol. Sci. 2014, 15(7), 12940-12951; https://doi.org/10.3390/ijms150712940 - 22 Jul 2014

Cited by 33 | Viewed by 7861

Abstract

Voltage-gated K⁺ channel (VKC) plays important roles in biology procession, especially in nervous system. Different subfamilies of VKCs have different biological functions. Thus, knowing VKCs’ subfamilies has become a meaningful job because it can guide the direction for the disease diagnosis and [...] Read more.

Voltage-gated K⁺ channel (VKC) plays important roles in biology procession, especially in nervous system. Different subfamilies of VKCs have different biological functions. Thus, knowing VKCs’ subfamilies has become a meaningful job because it can guide the direction for the disease diagnosis and drug design. However, the traditional wet-experimental methods were costly and time-consuming. It is highly desirable to develop an effective and powerful computational tool for identifying different subfamilies of VKCs. In this study, a predictor, called iVKC-OTC, has been developed by incorporating the optimized tripeptide composition (OTC) generated by feature selection technique into the general form of pseudo-amino acid composition to identify six subfamilies of VKCs. One of the remarkable advantages of introducing the optimized tripeptide composition is being able to avoid the notorious dimension disaster or over fitting problems in statistical predictions. It was observed on a benchmark dataset, by using a jackknife test, that the overall accuracy achieved by iVKC-OTC reaches to 96.77% in identifying the six subfamilies of VKCs, indicating that the new predictor is promising or at least may become a complementary tool to the existing methods in this area. It has not escaped our notice that the optimized tripeptide composition can also be used to investigate other protein classification problems. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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18 pages, 1972 KiB

Open AccessArticle

Proteomic Analyses Reveal that Sky1 Modulates Apoptosis and Mitophagy in Saccharomyces cerevisiae Cells Exposed to Cisplatin

by Silvia Rodríguez-Lombardero, M. Esther Rodríguez-Belmonte, M. Isabel González-Siso, Ángel Vizoso-Vázquez, Vanessa Valdiglesias, Blanca Laffón and M. Esperanza Cerdán

Int. J. Mol. Sci. 2014, 15(7), 12573-12590; https://doi.org/10.3390/ijms150712573 - 15 Jul 2014

Cited by 4 | Viewed by 6502

Abstract

Sky1 is the only member of the SR (Serine–Arginine) protein kinase family in Saccharomyces cerevisiae. When yeast cells are treated with the anti-cancer drug cisplatin, Sky1 kinase activity is necessary to produce the cytotoxic effect. In this study, proteome changes in response to [...] Read more.

Sky1 is the only member of the SR (Serine–Arginine) protein kinase family in Saccharomyces cerevisiae. When yeast cells are treated with the anti-cancer drug cisplatin, Sky1 kinase activity is necessary to produce the cytotoxic effect. In this study, proteome changes in response to this drug and/or SKY1 deletion have been evaluated in order to understand the role of Sky1 in the response of yeast cells to cisplatin. Results reveal differential expression of proteins previously related to the oxidative stress response, DNA damage, apoptosis and mitophagy. With these precedents, the role of Sky1 in apoptosis, necrosis and mitophagy has been evaluated by flow-cytometry, fluorescence microscopy, biosensors and fluorescence techniques. After cisplatin treatment, an apoptotic-like process diminishes in the ∆sky1 strain in comparison to the wild-type. The treatment does not affect mitophagy in the wild-type strain, while an increase is observed in the ∆sky1 strain. The increased resistance to cisplatin observed in the ∆sky1 strain may be attributable to a decrease of apoptosis and an increase of mitophagy. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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24 pages, 1509 KiB

Open AccessArticle

Proteomic Analysis of Embryogenesis and the Acquisition of Seed Dormancy in Norway Maple (Acer platanoides L.)

by Aleksandra Maria Staszak and Tomasz Andrzej Pawłowski

Int. J. Mol. Sci. 2014, 15(6), 10868-10891; https://doi.org/10.3390/ijms150610868 - 17 Jun 2014

Cited by 26 | Viewed by 7803

Abstract

The proteome of zygotic embryos of Acer platanoides L. was analyzed via high-resolution 2D-SDS-PAGE and MS/MS in order to: (1) identify significant physiological processes associated with embryo development; and (2) identify changes in the proteome of the embryo associated with the acquisition of [...] Read more.

The proteome of zygotic embryos of Acer platanoides L. was analyzed via high-resolution 2D-SDS-PAGE and MS/MS in order to: (1) identify significant physiological processes associated with embryo development; and (2) identify changes in the proteome of the embryo associated with the acquisition of seed dormancy. Seventeen spots were identified as associated with morphogenesis at 10 to 13 weeks after flowering (WAF). Thirty-three spots were associated with maturation of the embryo at 14 to 22 WAF. The greatest changes in protein abundance occurred at 22 WAF, when seeds become fully mature. Overall, the stage of morphogenesis was characterized by changes in the abundance of proteins (tubulins and actin) associated with the growth and development of the embryo. Enzymes related to energy supply were especially elevated, most likely due to the energy demand associated with rapid growth and cell division. The stage of maturation is crucial to the establishment of seed dormancy and is associated with a higher abundance of proteins involved in genetic information processing, energy and carbon metabolism and cellular and antioxidant processes. Results indicated that a glycine-rich RNA-binding protein and proteasome proteins may be directly involved in dormancy acquisition control, and future studies are warranted to verify this association. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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18 pages, 1593 KiB

Open AccessArticle

Screening and Functional Analysis of the Peroxiredoxin Specifically Expressed in Bursaphelenchus xylophilus—The Causative Agent of Pine Wilt Disease

by Han-Yu Fu, Jia-Hong Ren, Lin Huang, Hao Li and Jian-Ren Ye

Int. J. Mol. Sci. 2014, 15(6), 10215-10232; https://doi.org/10.3390/ijms150610215 - 10 Jun 2014

Cited by 12 | Viewed by 9859

Abstract

The pine wood nematode, Bursaphelenchus xylophilus, is the causal agent of pine wilt disease. Accurately differentiating B. xylophilus from other nematodes species, especially its related species B. mucronatus, is important for pine wood nematode detection. Thus, we attempted to identify a [...] Read more.

The pine wood nematode, Bursaphelenchus xylophilus, is the causal agent of pine wilt disease. Accurately differentiating B. xylophilus from other nematodes species, especially its related species B. mucronatus, is important for pine wood nematode detection. Thus, we attempted to identify a specific protein in the pine wood nematode using proteomics technology. Here, we compared the proteomes of B. xylophilus and B. mucronatus using Two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization -time-of-flight/time-of-flight (MALDI-TOF/TOF-MS) technologies. In total, 15 highly expressed proteins were identified in B. xylophilus compared with B. mucronatus. Subsequently, the specificity of the proteins identified was confirmed by PCR using the genomic DNA of other nematode species. Finally, a gene encoding a specific protein (Bx-Prx) was obtained. This gene was cloned and expressed in E. coli. The in situ hybridisation pattern of Bx-Prx showed that it was expressed strongly in the tail of B. xylophilus. RNAi was used to assess the function of Bx-Prx, the results indicated that the gene was associated with the reproduction and pathogenicity of B. xylophilus. This discovery provides fundamental information for identifying B. xylophilus via a molecular approach. Moreover, the purified recombinant protein has potential as a candidate diagnostic antigen of pine wilt disease, which may lead to a new immunological detection method for the pine wood nematode. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 995 KiB

Open AccessArticle

Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents

by Hung-Jen Huang, Wei-Yu Chen and Jer-Horng Wu

Int. J. Mol. Sci. 2014, 15(6), 10169-10184; https://doi.org/10.3390/ijms150610169 - 6 Jun 2014

Cited by 19 | Viewed by 11614

Abstract

Protein recovery is crucial for shotgun metaproteomics to study the in situ functionality of microbial populations from complex biofilms but still poorly addressed by far. To fill this knowledge gap, we systematically evaluated the sample preparation with extraction buffers comprising four detergents for [...] Read more.

Protein recovery is crucial for shotgun metaproteomics to study the in situ functionality of microbial populations from complex biofilms but still poorly addressed by far. To fill this knowledge gap, we systematically evaluated the sample preparation with extraction buffers comprising four detergents for the metaproteomics analysis of a terephthalate-degrading methanogenic biofilm using an on-line two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) system. Totally, 1018 non-repeated proteins were identified with the four treatments. On the whole, each treatment could recover the biofilm proteins with specific distributions of molecular weight, hydrophobicity, and isoelectric point. The extraction buffers containing zwitterionic and anionic detergents were found to harvest the proteins with better efficiency and quality, allowing identification up to 76.2% of total identified proteins with the LC-MS/MS analysis. According to the annotation with a relevant metagenomic database, we further observed different taxonomic profiles of bacterial and archaeal members and discriminable patterns of the functional expression among the extraction buffers used. Overall, the finding of the present study provides first insight to the effect of the detergents on the characteristics of extractable proteins from biofilm and the developed protocol combined with nano 2D-LC/MS/MS analysis can improve the metaproteomics studies on microbial functionality of biofilms in the wastewater treatment systems. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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26 pages, 880 KiB

Open AccessArticle

Flowering as the Most Highly Sensitive Period of Grapevine (Vitis vinifera L. cv Mourvèdre) to the Botryosphaeria Dieback Agents Neofusicoccum parvum and Diplodia seriata Infection

by Alessandro Spagnolo, Philippe Larignon, Maryline Magnin-Robert, Agnès Hovasse, Clara Cilindre, Alain Van Dorsselaer, Christophe Clément, Christine Schaeffer-Reiss and Florence Fontaine

Int. J. Mol. Sci. 2014, 15(6), 9644-9669; https://doi.org/10.3390/ijms15069644 - 30 May 2014

Cited by 32 | Viewed by 10570

Abstract

Botryosphaeria dieback is a fungal grapevine trunk disease that currently represents a threat for viticulture worldwide because of the important economical losses due to reduced yield of affected plants and their premature death. Neofusicoccum parvum and Diplodia seriata are among the causal agents. [...] Read more.

Botryosphaeria dieback is a fungal grapevine trunk disease that currently represents a threat for viticulture worldwide because of the important economical losses due to reduced yield of affected plants and their premature death. Neofusicoccum parvum and Diplodia seriata are among the causal agents. Vine green stems were artificially infected with N. parvum or D. seriata at the onset of three different phenological stages (G stage (separated clusters), flowering and veraison). Highest mean lesion lengths were recorded at flowering. Major proteome changes associated to artificial infections during the three different phenological stages were also reported using two dimensional gel electrophoresis (2D)-based analysis. Twenty (G stage), 15 (flowering) and 13 (veraison) differentially expressed protein spots were subjected to nanoLC-MS/MS and a total of 247, 54 and 25 proteins were respectively identified. At flowering, a weaker response to the infection was likely activated as compared to the other stages, and some defense-related proteins were even down regulated (e.g., superoxide dismutase, major latex-like protein, and pathogenesis related protein 10). Globally, the flowering period seemed to represent the period of highest sensitivity of grapevine to Botryosphaeria dieback agent infection, possibly being related to the high metabolic activity in the inflorescences. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 494 KiB

Open AccessArticle

Differential Proteomic Analysis of the Pancreas of Diabetic db/db Mice Reveals the Proteins Involved in the Development of Complications of Diabetes Mellitus

by Victoriano Pérez-Vázquez, Juan M. Guzmán-Flores, Daniela Mares-Álvarez, Magdalena Hernández-Ortiz, Maciste H. Macías-Cervantes, Joel Ramírez-Emiliano and Sergio Encarnación-Guevara

Int. J. Mol. Sci. 2014, 15(6), 9579-9593; https://doi.org/10.3390/ijms15069579 - 30 May 2014

Cited by 18 | Viewed by 9832

Abstract

Type 2 diabetes mellitus is characterized by hyperglycemia and insulin-resistance. Diabetes results from pancreatic inability to secrete the insulin needed to overcome this resistance. We analyzed the protein profile from the pancreas of ten-week old diabetic db/db and wild type mice [...] Read more.

Type 2 diabetes mellitus is characterized by hyperglycemia and insulin-resistance. Diabetes results from pancreatic inability to secrete the insulin needed to overcome this resistance. We analyzed the protein profile from the pancreas of ten-week old diabetic db/db and wild type mice through proteomics. Pancreatic proteins were separated in two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and significant changes in db/db mice respect to wild type mice were observed in 27 proteins. Twenty five proteins were identified by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) and their interactions were analyzed using search tool for the retrieval of interacting genes/proteins (STRING) and database for annotation, visualization and integrated discovery (DAVID). Some of these proteins were Pancreatic α-amylase, Cytochrome b5, Lithostathine-1, Lithostathine-2, Chymotrypsinogen B, Peroxiredoxin-4, Aspartyl aminopeptidase, Endoplasmin, and others, which are involved in the metabolism of carbohydrates and proteins, as well as in oxidative stress, and inflammation. Remarkably, these are mostly endoplasmic reticulum proteins related to peptidase activity, i.e., they are involved in proteolysis, glucose catabolism and in the tumor necrosis factor-mediated signaling pathway. These results suggest mechanisms for insulin resistance, and the chronic inflammatory state observed in diabetes. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 1377 KiB

Open AccessArticle

Proteome Analysis of Subsarcolemmal Cardiomyocyte Mitochondria: A Comparison of Different Analytical Platforms

by Francesco Giorgianni, Diwa Koirala, Karl T. Weber and Sarka Beranova-Giorgianni

Int. J. Mol. Sci. 2014, 15(6), 9285-9301; https://doi.org/10.3390/ijms15069285 - 26 May 2014

Cited by 8 | Viewed by 9957

Abstract

Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents a [...] Read more.

Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents a powerful approach toward system-level insights into disease mechanisms. A crucial aspect in proteomics studies is design of bioanalytical strategies that maximize coverage of the complex repertoire of mitochondrial proteins. In this study, we evaluated the performance of gel-based and gel-free multidimensional platforms for profiling of the proteome in subsarcolemmal mitochondria harvested from rat heart. We compared three different multidimensional proteome fractionation platforms: polymeric reversed-phase liquid chromatography at high pH (PLRP), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and isoelectric focusing (IEF) separations combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), and bioinformatics for protein identification. Across all three platforms, a total of 1043 proteins were identified. Among the three bioanalytical strategies, SDS-PAGE followed by LC-MS/MS provided the best coverage of the mitochondrial proteome. With this platform, 890 proteins with diverse physicochemical characteristics were identified; the mitochondrial protein panel encompassed proteins with various functional roles including bioenergetics, protein import, and mitochondrial fusion. Taken together, results of this study provide a large-scale view of the proteome in subsarcolemmal mitochondria from the rat heart, and aid in the selection of optimal bioanalytical platforms for differential protein expression profiling of mitochondria in health and disease. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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21 pages, 676 KiB

Open AccessArticle

Functional Annotation of Proteomic Data from Chicken Heterophils and Macrophages Induced by Carbon Nanotube Exposure

by Yun-Ze Li, Chung-Shi Cheng, Chao-Jung Chen, Zi-Lin Li, Yao-Tung Lin, Shuen-Ei Chen and San-Yuan Huang

Int. J. Mol. Sci. 2014, 15(5), 8372-8392; https://doi.org/10.3390/ijms15058372 - 12 May 2014

Cited by 6 | Viewed by 7137

Abstract

With the expanding applications of carbon nanotubes (CNT) in biomedicine and agriculture, questions about the toxicity and biocompatibility of CNT in humans and domestic animals are becoming matters of serious concern. This study used proteomic methods to profile gene expression in chicken macrophages [...] Read more.

With the expanding applications of carbon nanotubes (CNT) in biomedicine and agriculture, questions about the toxicity and biocompatibility of CNT in humans and domestic animals are becoming matters of serious concern. This study used proteomic methods to profile gene expression in chicken macrophages and heterophils in response to CNT exposure. Two-dimensional gel electrophoresis identified 12 proteins in macrophages and 15 in heterophils, with differential expression patterns in response to CNT co-incubation (0, 1, 10, and 100 µg/mL of CNT for 6 h) (p < 0.05). Gene ontology analysis showed that most of the differentially expressed proteins are associated with protein interactions, cellular metabolic processes, and cell mobility, suggesting activation of innate immune functions. Western blot analysis with heat shock protein 70, high mobility group protein, and peptidylprolyl isomerase A confirmed the alterations of the profiled proteins. The functional annotations were further confirmed by effective cell migration, promoted interleukin-1β secretion, and more cell death in both macrophages and heterophils exposed to CNT (p < 0.05). In conclusion, results of this study suggest that CNT exposure affects protein expression, leading to activation of macrophages and heterophils, resulting in altered cytoskeleton remodeling, cell migration, and cytokine production, and thereby mediates tissue immune responses. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 1471 KiB

Open AccessArticle

Functional Identification of Proteus mirabilis eptC Gene Encoding a Core Lipopolysaccharide Phosphoethanolamine Transferase

by Eleonora Aquilini, Susana Merino, Yuriy A. Knirel, Miguel Regué and Juan M. Tomás

Int. J. Mol. Sci. 2014, 15(4), 6689-6702; https://doi.org/10.3390/ijms15046689 - 21 Apr 2014

Cited by 17 | Viewed by 7962

Abstract

By comparison of the Proteus mirabilis HI4320 genome with known lipopolysaccharide (LPS) phosphoethanolamine transferases, three putative candidates (PMI3040, PMI3576, and PMI3104) were identified. One of them, eptC (PMI3104) was able to modify the LPS of two defined non-polar core LPS mutants of Klebsiella [...] Read more.

By comparison of the Proteus mirabilis HI4320 genome with known lipopolysaccharide (LPS) phosphoethanolamine transferases, three putative candidates (PMI3040, PMI3576, and PMI3104) were identified. One of them, eptC (PMI3104) was able to modify the LPS of two defined non-polar core LPS mutants of Klebsiella pneumoniae that we use as surrogate substrates. Mass spectrometry and nuclear magnetic resonance showed that eptC directs the incorporation of phosphoethanolamine to the O-6 of l-glycero-d-mano-heptose II. The eptC gene is found in all the P. mirabilis strains analyzed in this study. Putative eptC homologues were found for only two additional genera of the Enterobacteriaceae family, Photobacterium and Providencia. The data obtained in this work supports the role of the eptC (PMI3104) product in the transfer of PEtN to the O-6 of l,d-HepII in P. mirabilis strains. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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13 pages, 2441 KiB

Open AccessArticle

Quality Control and Stability Studies with the Monoclonal Antibody, Trastuzumab: Application of 1D- vs. 2D-Gel Electrophoresis

by Dashnor Nebija, Christian R. Noe, Ernst Urban and Bodo Lachmann

Int. J. Mol. Sci. 2014, 15(4), 6399-6411; https://doi.org/10.3390/ijms15046399 - 15 Apr 2014

Cited by 27 | Viewed by 10163

Abstract

Recombinant monoclonal antibodies (rmAbs) are medicinal products obtained by rDNA technology. Consequently, like other biopharmaceuticals, they require the extensive and rigorous characterization of the quality attributes, such as identity, structural integrity, purity and stability. The aim of this work was to study the [...] Read more.

Recombinant monoclonal antibodies (rmAbs) are medicinal products obtained by rDNA technology. Consequently, like other biopharmaceuticals, they require the extensive and rigorous characterization of the quality attributes, such as identity, structural integrity, purity and stability. The aim of this work was to study the suitability of gel electrophoresis for the assessment of charge heterogeneity, post-translational modifications and the stability of the therapeutic, recombinant monoclonal antibody, trastuzumab. One-dimensional, SDS-PAGE, under reducing and non-reducing conditions, and two-dimensional gel electrophoresis were used for the determination of molecular mass (Mr), the isoelectric point (pI), charge-related isoform patterns and the stability of trastuzumab, subjected to stressed degradation and long-term conditions. For the assessment of the influence of glycosylation in the charge heterogeneity pattern of trastuzumab, an enzymatic deglycosylation study has been performed using N-glycosidase F and sialidase, whereas carboxypeptidase B was used for the lysine truncation study. Experimental data documented that 1D and 2D gel electrophoresis represent fast and easy methods to evaluate the quality of biological medicinal products. Important stability parameters, such as the protein aggregation, can be assessed, as well. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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13 pages, 572 KiB

Open AccessArticle

Cadmium Toxicity Induced Alterations in the Root Proteome of Green Gram in Contrasting Response towards Iron Supplement

by Sowbiya Muneer, Khalid Rehman Hakeem, Rozi Mohamed and Jeong Hyun Lee

Int. J. Mol. Sci. 2014, 15(4), 6343-6355; https://doi.org/10.3390/ijms15046343 - 15 Apr 2014

Cited by 30 | Viewed by 7856

Abstract

Cadmium signifies a severe threat to crop productivity and green gram is a notably iron sensitive plant which shows considerable variation towards cadmium stress. A gel-based proteomics analysis was performed with the roots of green gram exposed to iron and cadmium combined treatments. [...] Read more.

Cadmium signifies a severe threat to crop productivity and green gram is a notably iron sensitive plant which shows considerable variation towards cadmium stress. A gel-based proteomics analysis was performed with the roots of green gram exposed to iron and cadmium combined treatments. The resulting data show that twenty three proteins were down-regulated in iron-deprived roots either in the absence (−Fe/−Cd) or presence (−Fe/+Cd) of cadmium. These down-regulated proteins were however well expressed in roots under iron sufficient conditions, even in the presence of cadmium (+Fe/+Cd). The functional classification of these proteins determined that 21% of the proteins are associated with nutrient metabolism. The other proteins in higher quantities are involved in either transcription or translation regulation, and the rest are involved in biosynthesis metabolism, antioxidant pathways, molecular chaperones and stress response. On the other hand, several protein spots were also absent in roots in response to iron deprivation either in absence (−Fe/−Cd) or presence (−Fe/+Cd) of cadmium but were well expressed in the presence of iron (+Fe/+Cd). Results suggest that green gram plants exposed to cadmium stress are able to change the nutrient metabolic balance in roots, but in the mean time regulate cadmium toxicity through iron supplements. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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24 pages, 6168 KiB

Open AccessArticle

Effect of Wnt3a on Keratinocytes Utilizing in Vitro and Bioinformatics Analysis

by Ju-Suk Nam, Chiranjib Chakraborty, Ashish Ranjan Sharma, Young Her, Kee-Jeong Bae, Garima Sharma, George Priya Doss, Sang-Soo Lee, Myung-Sun Hong and Dong-Keun Song

Int. J. Mol. Sci. 2014, 15(4), 5472-5495; https://doi.org/10.3390/ijms15045472 - 28 Mar 2014

Cited by 4 | Viewed by 8296

Abstract

Wingless-type (Wnt) signaling proteins participate in various cell developmental processes. A suppressive role of Wnt5a on keratinocyte growth has already been observed. However, the role of other Wnt proteins in proliferation and differentiation of keratinocytes remains unknown. Here, we investigated the effects of [...] Read more.

Wingless-type (Wnt) signaling proteins participate in various cell developmental processes. A suppressive role of Wnt5a on keratinocyte growth has already been observed. However, the role of other Wnt proteins in proliferation and differentiation of keratinocytes remains unknown. Here, we investigated the effects of the Wnt ligand, Wnt3a, on proliferation and differentiation of keratinocytes. Keratinocytes from normal human skin were cultured and treated with recombinant Wnt3a alone or in combination with the inflammatory cytokine, tumor necrosis factor α (TNFα). Furthermore, using bioinformatics, we analyzed the biochemical parameters, molecular evolution, and protein–protein interaction network for the Wnt family. Application of recombinant Wnt3a showed an anti-proliferative effect on keratinocytes in a dose-dependent manner. After treatment with TNFα, Wnt3a still demonstrated an anti-proliferative effect on human keratinocytes. Exogenous treatment of Wnt3a was unable to alter mRNA expression of differentiation markers of keratinocytes, whereas an altered expression was observed in TNFα-stimulated keratinocytes. In silico phylogenetic, biochemical, and protein–protein interaction analysis showed several close relationships among the family members of the Wnt family. Moreover, a close phylogenetic and biochemical similarity was observed between Wnt3a and Wnt5a. Finally, we proposed a hypothetical mechanism to illustrate how the Wnt3a protein may inhibit the process of proliferation in keratinocytes, which would be useful for future researchers. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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18 pages, 1285 KiB

Open AccessArticle

Identification of Proteins of Altered Abundance in Oil Palm Infected with Ganoderma boninense

by Jameel R. Al-Obaidi, Yusmin Mohd-Yusuf, Nurhanani Razali, Jaime Jacqueline Jayapalan, Chin-Chong Tey, Normahnani Md-Noh, Sarni Mat Junit, Rofina Yasmin Othman and Onn Haji Hashim

Int. J. Mol. Sci. 2014, 15(3), 5175-5192; https://doi.org/10.3390/ijms15035175 - 24 Mar 2014

Cited by 28 | Viewed by 9364

Abstract

Basal stem rot is a common disease that affects oil palm, causing loss of yield and finally killing the trees. The disease, caused by fungus Ganoderma boninense, devastates thousands of hectares of oil palm plantings in Southeast Asia every year. In the [...] Read more.

Basal stem rot is a common disease that affects oil palm, causing loss of yield and finally killing the trees. The disease, caused by fungus Ganoderma boninense, devastates thousands of hectares of oil palm plantings in Southeast Asia every year. In the present study, root proteins of healthy oil palm seedlings, and those infected with G. boninense, were analyzed by 2-dimensional gel electrophoresis (2-DE). When the 2-DE profiles were analyzed for proteins, which exhibit consistent significant change of abundance upon infection with G. boninense, 21 passed our screening criteria. Subsequent analyses by mass spectrometry and database search identified caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, enolase, fructokinase, cysteine synthase, malate dehydrogenase, and ATP synthase as among proteins of which abundances were markedly altered. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 1522 KiB

Open AccessArticle

Identification of the Novel Interacting Partners of the Mammalian Target of Rapamycin Complex 1 in Human CCRF-CEM and HEK293 Cells

by Hazir Rahman, Muhammad Qasim, Michael Oellerich and Abdul R. Asif

Int. J. Mol. Sci. 2014, 15(3), 4823-4836; https://doi.org/10.3390/ijms15034823 - 18 Mar 2014

Cited by 9 | Viewed by 8737

Abstract

The present study was undertaken to identify proteins that interact with the mammalian target of rapamycin complex 1 (mTORC1) to enable it to carry out its crucial cell signaling functions. Endogenous and myc-tag mTORC1 was purified, in-gel tryptic digested and then identified by [...] Read more.

The present study was undertaken to identify proteins that interact with the mammalian target of rapamycin complex 1 (mTORC1) to enable it to carry out its crucial cell signaling functions. Endogenous and myc-tag mTORC1 was purified, in-gel tryptic digested and then identified by nano-LC ESI Q-TOF MS/MS analysis. A total of nine novel interacting proteins were identified in both endogenous and myc-tag mTORC1 purifications. These new mTORC1 interacting partners include heterogeneous nuclear ribonucleoproteins A2/B1, enhancer of mRNA decapping protein 4, 60S acidic ribosomal protein, P0, nucleolin, dynamin 2, glyceraldehyde 3 phosphate dehydrogenase, 2-oxoglutarate dehydrogenase, glycosyl transferase 25 family member 1 and prohibitin 2. Furthermore hnRNP A2/B1 and dynamin 2 interaction with mTORC1 was confirmed on immunoblotting. The present study has for the first time identified novel interacting partners of mTORC1 in human T lymphoblasts (CCRF-CEM) and human embryonic kidney (HEK293) cells. These new interacting proteins may offer new targets for therapeutic interventions in human diseases caused by perturbed mTORC1 signaling. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 696 KiB

Open AccessArticle

Proteomic Profiling of Cytosolic Glutathione Transferases from Three Bivalve Species: Corbicula fluminea, Mytilus galloprovincialis and Anodonta cygnea

by José Carlos Martins, Alexandre Campos, Hugo Osório, Rute Da Fonseca and Vítor Vasconcelos

Int. J. Mol. Sci. 2014, 15(2), 1887-1900; https://doi.org/10.3390/ijms15021887 - 27 Jan 2014

Cited by 26 | Viewed by 7689

Abstract

Suspension-feeding bivalves are considered efficient toxin vectors with a relative insensitivity to toxicants compared to other aquatic organisms. This fact highlights the potential role of detoxiﬁcation enzymes, such as glutathione transferases (GSTs), in this bivalve resistance. Nevertheless, the GST system has not been [...] Read more.

Suspension-feeding bivalves are considered efficient toxin vectors with a relative insensitivity to toxicants compared to other aquatic organisms. This fact highlights the potential role of detoxiﬁcation enzymes, such as glutathione transferases (GSTs), in this bivalve resistance. Nevertheless, the GST system has not been extensively described in these organisms. In the present study, cytosolic GSTs isoforms (cGST) were surveyed in three bivalves with different habitats and life strategies: Corbicula fluminea, Anodonta cygnea and Mytilus galloprovincialis. GSTs were purified by glutathione-agarose afﬁnity chromatography, and the collection of expressed cGST classes of each bivalve were identified using a proteomic approach. All the purified extracts were also characterized kinetically. Results reveal variations in cGST subunits collection (diversity and properties) between the three tested bivalves. Using proteomics, four pi-class and two sigma-class GST subunits were identified in M. galloprovincialis. C. fluminea also yielded four pi-class and one sigma-class GST subunits. For A. cygnea, two mu-class and one pi-class GST subunits were identified, these being the first record of GSTs from these freshwater mussels. The affinity purified extracts also show differences regarding enzymatic behavior among species. The variations found in cGST collection and kinetics might justify diverse selective advantages for each bivalve organism. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 741 KiB

Open AccessArticle

Optimization and Evaluation of Magnetic Bead Separation Combined with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectroscopy (MALDI-TOF MS) for Proteins Profiling of Peritoneal Dialysis Effluent

by Na Guo, Qiong Wen, Zhi-Jian Li, Ri-Cong Xu, Fen-Fen Peng and Xue-Qing Yu

Int. J. Mol. Sci. 2014, 15(1), 1162-1175; https://doi.org/10.3390/ijms15011162 - 16 Jan 2014

Cited by 7 | Viewed by 7209

Abstract

Peritoneal dialysis effluent (PDE) potentially carries an archive of peptides relevant to pathological processes in abdominal and surrounding tissues. Magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is one such approach that offers a unique tool for profiling of peptides, but this [...] Read more.

Peritoneal dialysis effluent (PDE) potentially carries an archive of peptides relevant to pathological processes in abdominal and surrounding tissues. Magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is one such approach that offers a unique tool for profiling of peptides, but this approach has not been used in the PDE analysis. In this study, we developed a strategy for screening PDE proteins <15 kDa and applied this technique to identify potential biomarkers for peritonitis. We examined four kinds of magnetic beads, including a carbon series (C3, C8), weak cation exchange (WCX) and immobilized metal-affinity chromatography (IMAC-Cu) beads. Samples processed with IMAC-Cu magnetic beads consistently showed more MS signals across all beads within the measured mass range. Moreover, there was no difference in the number and morphology of MS signals between concentrated and unconcentrated samples. The PDE peptidome pattern, based on a panel of 15 peaks, accurately recognized peritonitis PD patients from peritonitis-free patients with sensitivity of 90.5% and specificity of 94.7% respectively. Therefore, IMAC-Cu magnetic beads and unconcentrated samples can be used as a fast and cost-effective approach for sample preparation prior to more in-depth discovery of predictive biomarkers of disease in patients on dialysis. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 1014 KiB

Open AccessArticle

The Effect of 5'-Adenylic Acid on Hepatic Proteome of Mice Radiated by ⁶⁰Co γ-ray

by Cuilin Cheng, Haitian Zhao, Zhenyu Wang, Weihong Lu, Lu Wang, Rongchun Wang and Lei Yao

Int. J. Mol. Sci. 2014, 15(1), 186-202; https://doi.org/10.3390/ijms15010186 - 24 Dec 2013

Cited by 2 | Viewed by 6524

Abstract

Understanding the protection mechanism of 5'-AMP requires comprehensive knowledge of the proteins expressed during the period that the body is exposed to irradiation. Proteomics provides the tools for such analyses. Here, the experimental ICR mice were divided into three groups (normal group, model [...] Read more.

Understanding the protection mechanism of 5'-AMP requires comprehensive knowledge of the proteins expressed during the period that the body is exposed to irradiation. Proteomics provides the tools for such analyses. Here, the experimental ICR mice were divided into three groups (normal group, model group and 5'-AMP + irradiation group). After different treatment, the hepatic total protein of each animal in three groups was separated by two-dimensional gel electrophoresis (2-DE). 2-DE analysis revealed fifty-eight protein spots were differentially expressed in comparison to three groups. From 58 protein spots, we selected nine spots to identify by MALDI-TOF-MS and received credible results. They were determined to be type I arginase, annexin A5, regucalcin, catalase, Tpm3 protein, Pdia4 protein, 14-3-3 protein epsilon, NAD-Malate dehydrogenase and heat shock protein 90. Considering the characteristic of these proteins, we proposed a possible protection pathway. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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18 pages, 4887 KiB

Open AccessArticle

Proteogenomic Characterization of Novel x-Type High Molecular Weight Glutenin Subunit 1Ax1.1

by Miguel Ribeiro, Emmanuelle Bancel, Annie Faye, Mireille Dardevet, Catherine Ravel, Gérard Branlard and Gilberto Igrejas

Int. J. Mol. Sci. 2013, 14(3), 5650-5667; https://doi.org/10.3390/ijms14035650 - 11 Mar 2013

Cited by 21 | Viewed by 11796

Abstract

Analysis of Portuguese wheat (Triticum aestivum L.) landrace ‘Barbela’ revealed the existence of a new x-type high molecular weight-glutenin subunit (HMW-GS) encoded at the Glu-A1 locus, which we named 1Ax1.1. Using one-dimensional and two-dimensional electrophoresis and mass spectrometry, we compared subunit [...] Read more.

Analysis of Portuguese wheat (Triticum aestivum L.) landrace ‘Barbela’ revealed the existence of a new x-type high molecular weight-glutenin subunit (HMW-GS) encoded at the Glu-A1 locus, which we named 1Ax1.1. Using one-dimensional and two-dimensional electrophoresis and mass spectrometry, we compared subunit 1Ax1.1 with other subunits encoded at the Glu-A1 locus. Subunit 1Ax1.1 has a theoretical molecular weight of 93,648 Da (or 91,508 Da for the mature protein) and an isoelectric point (pI) of about 5.7, making it the largest and most acidic HMW-GS known to be encoded at Glu-A1. Specific primers were designed to amplify and sequence 2601 bp of the Glu-A1 locus from the ‘Barbela 28’ wheat genome. A very high level of identity was found between the sequence encoding 1Ax1.1 and those encoding other alleles of the locus. The major difference found was an insertion of 36 amino acids in the central repetitive domain. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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23 pages, 675 KiB

Open AccessArticle

Comparative Proteomic Analysis of Puccinellia tenuiflora Leaves under Na₂CO₃ Stress

by Juanjuan Yu, Sixue Chen, Tai Wang, Guorong Sun and Shaojun Dai

Int. J. Mol. Sci. 2013, 14(1), 1740-1762; https://doi.org/10.3390/ijms14011740 - 15 Jan 2013

Cited by 59 | Viewed by 8486

Abstract

Soil salt-alkalinization is a widespread environmental stress that limits crop growth and agricultural productivity. The influence of soil alkalization caused by Na₂CO₃ on plants is more severe than that of soil salinization. Plants have evolved some unique mechanisms to cope [...] Read more.

Soil salt-alkalinization is a widespread environmental stress that limits crop growth and agricultural productivity. The influence of soil alkalization caused by Na₂CO₃ on plants is more severe than that of soil salinization. Plants have evolved some unique mechanisms to cope with alkali stress; however, the plant alkaline-responsive signaling and molecular pathways are still unknown. In the present study, Na₂CO₃ responsivecharacteristics in leaves from 50-day-old seedlings of halophyte Puccinellia tenuiflora were investigated using physiological and proteomic approaches. Comparative proteomics revealed 43 differentially expressed proteins in P. tenuiflora leaves in response to Na₂CO₃ treatment for seven days. These proteins were mainly involved in photosynthesis, stress and defense, carbohydrate/energy metabolism, protein metabolism, signaling, membrane and transport. By integrating the changes of photosynthesis, ion contents, and stress-related enzyme activities, some unique Na₂CO₃ responsivemechanisms have been discovered in P. tenuiflora. This study provides new molecular information toward improving the alkali tolerance of cereals. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 903 KiB

Open AccessArticle

Interaction of Proteins Identified in Human Thyroid Cells

by Jessica Pietsch, Stefan Riwaldt, Johann Bauer, Albert Sickmann, Gerhard Weber, Jirka Grosse, Manfred Infanger, Christoph Eilles and Daniela Grimm

Int. J. Mol. Sci. 2013, 14(1), 1164-1178; https://doi.org/10.3390/ijms14011164 - 9 Jan 2013

Cited by 33 | Viewed by 8470

Abstract

Influence of gravity forces on the regulation of protein expression by healthy and malignant thyroid cells was studied with the aim to identify protein interactions. Western blot analyses of a limited number of proteins suggested a time-dependent regulation of protein expression by simulated [...] Read more.

Influence of gravity forces on the regulation of protein expression by healthy and malignant thyroid cells was studied with the aim to identify protein interactions. Western blot analyses of a limited number of proteins suggested a time-dependent regulation of protein expression by simulated microgravity. After applying free flow isoelectric focusing and mass spectrometry to search for differently expressed proteins by thyroid cells exposed to simulated microgravity for three days, a considerable number of candidates for gravi-sensitive proteins were detected. In order to show how proteins sensitive to microgravity could directly influence other proteins, we investigated all polypeptide chains identified with Mascot scores above 100, looking for groups of interacting proteins. Hence, UniProtKB entry numbers of all detected proteins were entered into the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and processed. The program indicated that we had detected various groups of interacting proteins in each of the three cell lines studied. The major groups of interacting proteins play a role in pathways of carbohydrate and protein metabolism, regulation of cell growth and cell membrane structuring. Analyzing these groups, networks of interaction could be established which show how a punctual influence of simulated microgravity may propagate via various members of interaction chains. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 583 KiB

Open AccessArticle

Proteome and Peptidome of Human Acquired Enamel Pellicle on Deciduous Teeth

by Jason N. Zimmerman, William Custodio, Sahza Hatibovic-Kofman, Young Ho Lee, Yizhi Xiao and Walter L. Siqueira

Int. J. Mol. Sci. 2013, 14(1), 920-934; https://doi.org/10.3390/ijms14010920 - 7 Jan 2013

Cited by 66 | Viewed by 8795

Abstract

Understanding the composition and structure of the acquired enamel pellicle (AEP) has been a major goal in oral biology. Our lab has conducted studies on the composition of AEP formed on permanent enamel. The exhaustive exploration has provided a comprehensive identification of more [...] Read more.

Understanding the composition and structure of the acquired enamel pellicle (AEP) has been a major goal in oral biology. Our lab has conducted studies on the composition of AEP formed on permanent enamel. The exhaustive exploration has provided a comprehensive identification of more than 100 proteins from AEP formed on permanent enamel. The AEP formed on deciduous enamel has not been subjected to the same biochemical characterization scrutiny as that of permanent enamel, despite the fact that deciduous enamel is structurally different from permanent enamel. We hypothesized that the AEP proteome and peptidome formed on deciduous enamel may also be composed of unique proteins, some of which may not be common with AEP of permanent enamel explored previously. Pellicle material was collected from 10 children (aged 18–54 months) and subjected to mass spectrometry analysis. A total of 76 pellicle proteins were identified from the deciduous pellicle proteome. In addition, 38 natural occurring AEP peptides were identified from 10 proteins, suggesting that primary AEP proteome/peptidome presents a unique proteome composition. This is the first study to provide a comprehensive investigation of in vivo AEP formed on deciduous enamel. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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27 pages, 1644 KiB

Open AccessArticle

Effects of Nickel, Chlorpyrifos and Their Mixture on the Dictyostelium discoideum Proteome

by Lara Boatti, Elisa Robotti, Emilio Marengo, Aldo Viarengo and Francesco Marsano

Int. J. Mol. Sci. 2012, 13(12), 15679-15705; https://doi.org/10.3390/ijms131215679 - 23 Nov 2012

Cited by 9 | Viewed by 6690

Abstract

Mixtures of chemicals can have additive, synergistic or antagonistic interactions. We investigated the effects of the exposure to nickel, the organophosphate insecticide chlorpyrifos at effect concentrations (EC) of 25% and 50% and their binary mixture (Ec25 + EC25) on Dictyostelium discoideum amoebae based [...] Read more.

Mixtures of chemicals can have additive, synergistic or antagonistic interactions. We investigated the effects of the exposure to nickel, the organophosphate insecticide chlorpyrifos at effect concentrations (EC) of 25% and 50% and their binary mixture (Ec25 + EC25) on Dictyostelium discoideum amoebae based on lysosomal membrane stability (LMS). We treated D. discoideum with these compounds under controlled laboratory conditions and evaluated the changes in protein levels using a two-dimensional gel electrophoresis (2DE) proteomic approach. Nickel treatment at EC25 induced changes in 14 protein spots, 12 of which were down-regulated. Treatment with nickel at EC50 resulted in changes in 15 spots, 10 of which were down-regulated. Treatment with chlorpyrifos at EC25 induced changes in six spots, all of which were down-regulated; treatment with chlorpyrifos at EC50 induced changes in 13 spots, five of which were down-regulated. The mixture corresponding to EC25 of each compound induced changes in 19 spots, 13 of which were down-regulated. The data together reveal that a different protein expression signature exists for each treatment, and that only a few proteins are modulated in multiple different treatments. For a simple binary mixture, the proteomic response does not allow for the identification of each toxicant. The protein spots that showed significant differences were identified by mass spectrometry, which revealed modulations of proteins involved in metal detoxification, stress adaptation, the oxidative stress response and other cellular processes. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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29 pages, 2962 KiB

Open AccessArticle

Cancer Cell Response to Anthracyclines Effects: Mysteries of the Hidden Proteins Associated with These Drugs

by Jirina Tyleckova, Rita Hrabakova, Katerina Mairychova, Petr Halada, Lenka Radova, Petr Dzubak, Marian Hajduch, Suresh J. Gadher and Hana Kovarova

Int. J. Mol. Sci. 2012, 13(12), 15536-15564; https://doi.org/10.3390/ijms131215536 - 22 Nov 2012

Cited by 11 | Viewed by 8580

Abstract

A comprehensive proteome map of T-lymphoblastic leukemia cells and its alterations after daunorubicin, doxorubicin and mitoxantrone treatments was monitored and evaluated either by paired comparison with relevant untreated control and using multivariate classification of treated and untreated samples. With the main focus on [...] Read more.

A comprehensive proteome map of T-lymphoblastic leukemia cells and its alterations after daunorubicin, doxorubicin and mitoxantrone treatments was monitored and evaluated either by paired comparison with relevant untreated control and using multivariate classification of treated and untreated samples. With the main focus on early time intervals when the influence of apoptosis is minimized, we found significantly different levels of proteins, which corresponded to 1%–2% of the total amount of protein spots detected. According to Gene Ontology classification of biological processes, the highest representation of identified proteins for all three drugs belong to metabolic processes of proteins and nucleic acids and cellular processes, mainly cytoskeleton organisation and ubiquitin-proteasome pathway. Importantly, we observed significant proportion of changes in proteins involved in the generation of precursor metabolites and energy typical for daunorubicin, transport proteins participating in response to doxorubicin and a group of proteins of immune system characterising response to mitoxantrone. Both a paired comparison and the multivariate evaluation of quantitative data revealed daunorubicin as a distinct member of the group of anthracycline/anthracenedione drugs. A combination of identified drug specific protein changes, which may help to explain anti-cancer activity, together with the benefit of blocking activation of adaptive cancer pathways, presents important approaches to improving treatment outcomes in cancer. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 249 KiB

Open AccessArticle

Nitric Oxide-Dependent Posttranslational Modification in Plants: An Update

by Jeremy Astier and Christian Lindermayr

Int. J. Mol. Sci. 2012, 13(11), 15193-15208; https://doi.org/10.3390/ijms131115193 - 16 Nov 2012

Cited by 188 | Viewed by 11744

Abstract

Nitric oxide (NO) has been demonstrated as an essential regulator of several physiological processes in plants. The understanding of the molecular mechanism underlying its critical role constitutes a major field of research. NO can exert its biological function through different ways, such as [...] Read more.

Nitric oxide (NO) has been demonstrated as an essential regulator of several physiological processes in plants. The understanding of the molecular mechanism underlying its critical role constitutes a major field of research. NO can exert its biological function through different ways, such as the modulation of gene expression, the mobilization of second messengers, or interplays with protein kinases. Besides this signaling events, NO can be responsible of the posttranslational modifications (PTM) of target proteins. Several modifications have been identified so far, whereas metal nitrosylation, the tyrosine nitration and the S-nitrosylation can be considered as the main ones. Recent data demonstrate that these PTM are involved in the control of a wide range of physiological processes in plants, such as the plant immune system. However, a great deal of effort is still necessary to pinpoint the role of each PTM in plant physiology. Taken together, these new advances in proteomic research provide a better comprehension of the role of NO in plant signaling. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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20 pages, 1759 KiB

Open AccessArticle

Profound Re-Organization of Cell Surface Proteome in Equine Retinal Pigment Epithelial Cells in Response to In Vitro Culturing

by Christoph M. Szober, Stefanie M. Hauck, Kerstin N. Euler, Kristina J. H. Fröhlich, Claudia Alge-Priglinger, Marius Ueffing and Cornelia A. Deeg

Int. J. Mol. Sci. 2012, 13(11), 14053-14072; https://doi.org/10.3390/ijms131114053 - 31 Oct 2012

Cited by 8 | Viewed by 7673

Abstract

The purpose of this study was to characterize the cell surface proteome of native compared to cultured equine retinal pigment epithelium (RPE) cells. The RPE plays an essential role in visual function and represents the outer blood-retinal barrier. We are investigating immunopathomechanisms of [...] Read more.

The purpose of this study was to characterize the cell surface proteome of native compared to cultured equine retinal pigment epithelium (RPE) cells. The RPE plays an essential role in visual function and represents the outer blood-retinal barrier. We are investigating immunopathomechanisms of equine recurrent uveitis, an autoimmune inflammatory disease in horses leading to breakdown of the outer blood-retinal barrier and influx of autoreactive T-cells into affected horses’ vitrei. Cell surface proteins of native and cultured RPE cells from eye-healthy horses were captured by biotinylation, analyzed by high resolution mass spectrometry coupled to liquid chromatography (LC MS/MS), and the most interesting candidates were validated by PCR, immunoblotting and immunocytochemistry. A total of 112 proteins were identified, of which 84% were cell surface membrane proteins. Twenty-three of these proteins were concurrently expressed by both cell states, 28 proteins exclusively by native RPE cells. Among the latter were two RPE markers with highly specialized RPE functions: cellular retinaldehyde-binding protein (CRALBP) and retinal pigment epithelium-specific protein 65kDa (RPE65). Furthermore, 61 proteins were only expressed by cultured RPE cells and absent in native cells. As we believe that initiating events, leading to the breakdown of the outer blood-retinal barrier, take place at the cell surface of RPE cells as a particularly exposed barrier structure, this differential characterization of cell surface proteomes of native and cultured equine RPE cells is a prerequisite for future studies. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 1251 KiB

Open AccessArticle

Profiling the Proteome of Exhaled Breath Condensate in Healthy Smokers and COPD Patients by LC-MS/MS

by Marco Fumagalli, Fabio Ferrari, Maurizio Luisetti, Jan Stolk, Pieter S. Hiemstra, Daniela Capuano, Simona Viglio, Laura Fregonese, Isa Cerveri, Federica Corana, Carmine Tinelli and Paolo Iadarola

Int. J. Mol. Sci. 2012, 13(11), 13894-13910; https://doi.org/10.3390/ijms131113894 - 29 Oct 2012

Cited by 53 | Viewed by 9300

Abstract

Three pools of exhaled breath condensate (EBC) from non-smokers plus healthy smokers (NS + HS, n = 45); chronic obstructive pulmonary disease (COPD) without emphysema (COPD, n = 15) and subjects with pulmonary emphysema associated with α₁-antitrypsin deficiency (AATD, n = [...] Read more.

Three pools of exhaled breath condensate (EBC) from non-smokers plus healthy smokers (NS + HS, n = 45); chronic obstructive pulmonary disease (COPD) without emphysema (COPD, n = 15) and subjects with pulmonary emphysema associated with α₁-antitrypsin deficiency (AATD, n = 23) were used for an exploratory proteomic study aimed at generating fingerprints of these groups that can be used in future pathophysiological and perhaps even clinical research. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was the platform applied for this hypothesis-free investigation. Analysis of pooled specimens resulted in the production of a “fingerprint” made of 44 proteins for NS/HS; 17 for COPD and 15 for the group of AATD subjects. Several inflammatory cytokines (IL-1α, IL-1β, IL-2; IL-12, α and β subunits, IL-15, interferon α and γ, tumor necrosis factor α); Type I and II cytokeratins; two SP-A isoforms; Calgranulin A and B and α1-antitrypsin were detected and validated through the use of surface enhanced laser-desorption ionization mass spectrometry (SELDI-MS) and/or by Western blot (WB) analysis. These results are the prelude of quantitative studies aimed at identifying which of these proteins hold promise as identifiers of differences that could distinguish healthy subjects from patients. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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18 pages, 476 KiB

Open AccessArticle

A Bead-Based Multiplexed Immunoassay to Evaluate Breast Cancer Biomarkers for Early Detection in Pre-Diagnostic Serum

by Annemieke W. J. Opstal-van Winden, Wendy Rodenburg, Jeroen L. A. Pennings, Conny T. M. Van Oostrom, Jos H. Beijnen, Petra H.M. Peeters, Carla H. Van Gils and Annemieke De Vries

Int. J. Mol. Sci. 2012, 13(10), 13587-13604; https://doi.org/10.3390/ijms131013587 - 22 Oct 2012

Cited by 46 | Viewed by 8766

Abstract

This study investigates whether a set of ten potential breast cancer serum biomarkers and cancer antigens (osteopontin (OPN), haptoglobin, cancer antigen 15-3 (CA15-3), carcinoembryonic antigen (CEA), cancer antigen 125 (CA-125), prolactin, cancer antigen 19-9 (CA19-9), α-fetoprotein (AFP), leptin and migration inhibitory factor (MIF)) [...] Read more.

This study investigates whether a set of ten potential breast cancer serum biomarkers and cancer antigens (osteopontin (OPN), haptoglobin, cancer antigen 15-3 (CA15-3), carcinoembryonic antigen (CEA), cancer antigen 125 (CA-125), prolactin, cancer antigen 19-9 (CA19-9), α-fetoprotein (AFP), leptin and migration inhibitory factor (MIF)) can predict early stage breast cancer in samples collected before clinical diagnosis (phase III samples). We performed a nested case-control study within the Prospect-EPIC (European Prospective Investigation into Cancer and nutrition) cohort. We examined to what extent the biomarker panel could discriminate between 68 women diagnosed with breast cancer up to three years after enrollment and 68 matched healthy controls (all 56-64 years at baseline). Using a quantitative bead-based multiplexed assay, we determined protein concentrations in serum samples collected at enrollment. Principal Component Analysis (PCA) and Random Forest (RF) analysis revealed that on the basis of all ten proteins, early cases could not be separated from controls. When we combined serum protein concentrations and subject characteristics related to breast cancer risk in the RF analysis, this did not result in classification accuracy scores that could correctly classify the samples (sensitivity: 50%, specificity: 50%). Our findings indicate that this panel of selected tumor markers cannot be used for diagnosis of early breast cancer. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 2252 KiB

Open AccessArticle

Proteomic Analysis of Albumins and Globulins from Wheat Variety Chinese Spring and Its Fine Deletion Line 3BS-8

by Chao-Ying Ma, Li-Yan Gao, Ning Li, Xiao-Hui Li, Wu-Jun Ma, Rudi Appels and Yue-Ming Yan

Int. J. Mol. Sci. 2012, 13(10), 13398-13413; https://doi.org/10.3390/ijms131013398 - 18 Oct 2012

Cited by 6 | Viewed by 7615

Abstract

The relationship between chromosome deletion in wheat and protein expression were investigated using Chinese Spring and fine deletion line 3BS-8. Through 2-DE (2-D electrophoresis) analysis, no differentially expressed proteins (DEPs) were found in leaf samples; however, 47 DEPs showed at least two-fold abundance [...] Read more.

The relationship between chromosome deletion in wheat and protein expression were investigated using Chinese Spring and fine deletion line 3BS-8. Through 2-DE (2-D electrophoresis) analysis, no differentially expressed proteins (DEPs) were found in leaf samples; however, 47 DEPs showed at least two-fold abundance variation (p < 0.05) in matured wheat grains and 21 spots were identified by tandem MALDI-TOF/TOF-MS. Among the identified spots, four were cultivar-specific, including three (spots B15, B16, and B21) in Chinese Spring and one in 3BS-8 (spot B10). Among variety-different DEPs between Chinese Spring and 3BS-8, most spots showed a higher express profile in CS; only four spots showed up-regulated expression tendency in 3BS-8. An interesting observation was that more than half of the identified protein spots were involved in storage proteins, of which 11 spots were identified as globulins. According to these results, we can presume that the encoded genes of protein spots B15, B16, and B21 were located on the chromosome segment deleted in 3BS-8. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 566 KiB

Open AccessArticle

Use of Biotinylated Ubiquitin for Analysis of Rat Brain Mitochondrial Proteome and Interactome

by Olga A. Buneeva, Marina V. Medvedeva, Arthur T. Kopylov, Victor G. Zgoda and Alexei E. Medvedev

Int. J. Mol. Sci. 2012, 13(9), 11593-11609; https://doi.org/10.3390/ijms130911593 - 14 Sep 2012

Cited by 6 | Viewed by 6669

Abstract

Applicability of in vitro biotinylated ubiquitin for evaluation of endogenous ubiquitin conjugation and analysis of ubiquitin-associated protein-protein interactions has been investigated. Incubation of rat brain mitochondria with biotinylated ubiquitin followed by affinity chromatography on avidin-agarose, intensive washing, tryptic digestion of proteins bound to [...] Read more.

Applicability of in vitro biotinylated ubiquitin for evaluation of endogenous ubiquitin conjugation and analysis of ubiquitin-associated protein-protein interactions has been investigated. Incubation of rat brain mitochondria with biotinylated ubiquitin followed by affinity chromatography on avidin-agarose, intensive washing, tryptic digestion of proteins bound to the affinity sorbent and their mass spectrometry analysis resulted in reliable identification of 50 proteins belonging to mitochondrial and extramitochondrial compartments. Since all these proteins were bound to avidin-agarose only after preincubation of the mitochondrial fraction with biotinylated ubiquitin, they could therefore be referred to as specifically bound proteins. A search for specific ubiquitination signature masses revealed several extramitochondrial and intramitochondrial ubiquitinated proteins representing about 20% of total number of proteins bound to avidin-agarose. The interactome analysis suggests that the identified non-ubiquitinated proteins obviously form tight complexes either with ubiquitinated proteins or with their partners and/or mitochondrial membrane components. Results of the present study demonstrate that the use of biotinylated ubiquitin may be considered as the method of choice for in vitro evaluation of endogenous ubiquitin-conjugating machinery in particular subcellular organelles and changes in ubiquitin/organelle associated interactomes. This may be useful for evaluation of changes in interactomes induced by protein ubiquitination under norm and various brain pathologies. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 439 KiB

Open AccessArticle

Identification of Tillering Node Proteins Differentially Accumulated in Barley Recombinant Inbred Lines with Different Juvenile Growth Habits

by Anetta Kuczyńska, Arkadiusz Kosmala, Maria Surma and Tadeusz Adamski

Int. J. Mol. Sci. 2012, 13(8), 10410-10423; https://doi.org/10.3390/ijms130810410 - 21 Aug 2012

Cited by 8 | Viewed by 6438

Abstract

Barley (Hordeum vulgare L.) is an important cereal crop grown for both the feed and malting industries. The allelic dwarfing gene sdw1/denso has been used throughout the world to develop commercial barley varieties. Proteomic analysis offers a new approach to identify a [...] Read more.

Barley (Hordeum vulgare L.) is an important cereal crop grown for both the feed and malting industries. The allelic dwarfing gene sdw1/denso has been used throughout the world to develop commercial barley varieties. Proteomic analysis offers a new approach to identify a broad spectrum of genes that are expressed in the living system. Two-dimensional electrophoresis and mass spectrometry were applied to investigate changes in protein abundance associated with different juvenile growth habit as effect of the denso locus in barley homozygous lines derived from a Maresi × Pomo cross combination. A total of 31 protein spots were revealed that demonstrate quantitative differences in protein abundance between the analyzed plants with different juvenile growth habit, and these protein spots were selected to be identified by mass spectrometry. Identification was successful for 27 spots, and functional annotations of proteins revealed that most of them are involved in metabolism and disease/defense-related processes. Functions of the identified proteins and their probable influence on the growth habit in barley are discussed. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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20 pages, 1336 KiB

Open AccessArticle

Secretome Survey of Human Plexiform Neurofibroma Derived Schwann Cells Reveals a Secreted form of the RARRES1 Protein

by Hui-Ling Chen, Haeri Seol, Kristy Jean Brown, Heather Gordish-Dressman, Ashley Hill, Vittorio Gallo, Roger Packer and Yetrib Hathout

Int. J. Mol. Sci. 2012, 13(7), 9380-9399; https://doi.org/10.3390/ijms13079380 - 24 Jul 2012

Cited by 8 | Viewed by 8306

Abstract

To bring insights into neurofibroma biochemistry, a comprehensive secretome analysis was performed on cultured human primary Schwann cells isolated from surgically resected plexiform neurofibroma and from normal nerve tissue. Using a combination of SDS-PAGE and high precision LC-MS/MS, 907 proteins were confidently identified [...] Read more.

To bring insights into neurofibroma biochemistry, a comprehensive secretome analysis was performed on cultured human primary Schwann cells isolated from surgically resected plexiform neurofibroma and from normal nerve tissue. Using a combination of SDS-PAGE and high precision LC-MS/MS, 907 proteins were confidently identified in the conditioned media of Schwann cell cultures combined. Label free proteome profiling revealed consistent release of high levels of 22 proteins by the four biological replicates of NF1 Schwann cell cultures relative to the two normal Schwann cell cultures. Inversely, 9 proteins displayed decreased levels in the conditioned media of NF1 relative to normal Schwann cells. The proteins with increased levels included proteins involved in cell growth, angiogenesis and complement pathway while proteins with decreased levels included those involved in cell adhesion, plasminogen pathway and extracellular matrix remodeling. Retinoic acid receptor responder protein-1 (RARRES1), previously described as an integral membrane tumor suppressor, was found exclusively secreted by NF1 Schwann cells but not by normal Schwann cells. All-trans retinoic acid modulated secretion of RARRES1 in a dose dependent manner. This study shows altered secretion of key proteins in NF1 derived Schwann cells. The potential implication of these proteins in neurofibroma biology is discussed. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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18 pages, 412 KiB

Open AccessArticle

Proteomic Analysis of the Organ of Corti Using Nanoscale Liquid Chromatography Coupled with Tandem Mass Spectrometry

by Hong Peng, Miao Liu, Jason Pecka, Kirk W. Beisel and Shi-Jian Ding

Int. J. Mol. Sci. 2012, 13(7), 8171-8188; https://doi.org/10.3390/ijms13078171 - 2 Jul 2012

Cited by 11 | Viewed by 8302

Abstract

The organ of Corti (OC) in the cochlea plays an essential role in auditory signal transduction in the inner ear. For its minute size and trace amount of proteins, the identification of the molecules in pathophysiologic processes in the bone-encapsulated OC requires both [...] Read more.

The organ of Corti (OC) in the cochlea plays an essential role in auditory signal transduction in the inner ear. For its minute size and trace amount of proteins, the identification of the molecules in pathophysiologic processes in the bone-encapsulated OC requires both delicate separation and a highly sensitive analytical tool. Previously, we reported the development of a high resolution metal-free nanoscale liquid chromatography system for highly sensitive phosphoproteomic analysis. Here this system was coupled with a LTQ-Orbitrap XL mass spectrometer to investigate the OC proteome from normal hearing FVB/N male mice. A total of 628 proteins were identified from six replicates of single LC-MS/MS analysis, with a false discovery rate of 1% using the decoy database approach by the OMSSA search engine. This is currently the largest proteome dataset for the OC. A total of 11 proteins, including cochlin, myosin VI, and myosin IX, were identified that when defective are associated with hearing impairment or loss. This study demonstrated the effectiveness of our nanoLC-MS/MS platform for sensitive identification of hearing loss-associated proteins from minute amount of tissue samples. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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Review

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25 pages, 1110 KiB

Open AccessReview

Hidden Relationships between N-Glycosylation and Disulfide Bonds in Individual Proteins

by Tania Bakshi, David Pham, Raminderjeet Kaur and Bingyun Sun

Int. J. Mol. Sci. 2022, 23(7), 3742; https://doi.org/10.3390/ijms23073742 - 29 Mar 2022

Cited by 5 | Viewed by 3945

Abstract

N-Glycosylation (NG) and disulfide bonds (DBs) are two prevalent co/post-translational modifications (PTMs) that are often conserved and coexist in membrane and secreted proteins involved in a large number of diseases. Both in the past and in recent times, the enzymes and chaperones [...] Read more.

N-Glycosylation (NG) and disulfide bonds (DBs) are two prevalent co/post-translational modifications (PTMs) that are often conserved and coexist in membrane and secreted proteins involved in a large number of diseases. Both in the past and in recent times, the enzymes and chaperones regulating these PTMs have been constantly discovered to directly interact with each other or colocalize in the ER. However, beyond a few model proteins, how such cooperation affects N-glycan modification and disulfide bonding at selective sites in individual proteins is largely unknown. Here, we reviewed the literature to discover the current status in understanding the relationships between NG and DBs in individual proteins. Our results showed that more than 2700 human proteins carry both PTMs, and fewer than 2% of them have been investigated in the associations between NG and DBs. We summarized both these proteins with the reported relationships in the two PTMs and the tools used to discover the relationships. We hope that, by exposing this largely understudied field, more investigations can be encouraged to unveil the hidden relationships of NG and DBs in the majority of membranes and secreted proteins for pathophysiological understanding and biotherapeutic development. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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21 pages, 357 KiB

Open AccessReview

Proteomic Research in Peritoneal Dialysis

by Mario Bonomini, Francesc E. Borras, Maribel Troya-Saborido, Laura Carreras-Planella, Lorenzo Di Liberato and Arduino Arduini

Int. J. Mol. Sci. 2020, 21(15), 5489; https://doi.org/10.3390/ijms21155489 - 31 Jul 2020

Cited by 17 | Viewed by 5075

Abstract

Peritoneal dialysis (PD) is an established home care, cost-effective renal replacement therapy (RRT), which offers several advantages over the most used dialysis modality, hemodialysis. Despite its potential benefits, however, PD is an under-prescribed method of treating uremic patients. Infectious complications (primarily peritonitis) and [...] Read more.

Peritoneal dialysis (PD) is an established home care, cost-effective renal replacement therapy (RRT), which offers several advantages over the most used dialysis modality, hemodialysis. Despite its potential benefits, however, PD is an under-prescribed method of treating uremic patients. Infectious complications (primarily peritonitis) and bio-incompatibility of PD solutions are the main contributors to PD drop-out, due to their potential for altering the functional and anatomical integrity of the peritoneal membrane. To improve the clinical outcome of PD, there is a need for biomarkers to identify patients at risk of PD-related complications and to guide personalized interventions. Several recent studies have shown that proteomic investigation may be a powerful tool in the prediction, early diagnosis, prognostic assessment, and therapeutic monitoring of patients on PD. Indeed, analysis of the proteome present in PD effluent has uncovered several proteins involved in inflammation and pro-fibrotic insult, in encapsulating peritoneal sclerosis, or even in detecting early changes before any measurable modifications occur in the traditional clinical parameters used to evaluate PD efficacy. We here review the proteomic studies conducted thus far, addressing the potential use of such omics methodology in identifying potential new biomarkers of the peritoneal membrane welfare in relation to dialytic prescription and adequacy. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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19 pages, 1394 KiB

Open AccessReview

Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics

by Van-An Duong, Jong-Moon Park and Hookeun Lee

Int. J. Mol. Sci. 2020, 21(4), 1524; https://doi.org/10.3390/ijms21041524 - 23 Feb 2020

Cited by 65 | Viewed by 7175

Abstract

Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid [...] Read more.

Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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15 pages, 305 KiB

Open AccessReview

Urinary Peptidomic Biomarkers in Kidney Diseases

by Vittorio Sirolli, Luisa Pieroni, Lorenzo Di Liberato, Andrea Urbani and Mario Bonomini

Int. J. Mol. Sci. 2020, 21(1), 96; https://doi.org/10.3390/ijms21010096 - 21 Dec 2019

Cited by 32 | Viewed by 4921

Abstract

In order to effectively develop personalized medicine for kidney diseases we urgently need to develop highly accurate biomarkers for use in the clinic, since current biomarkers of kidney damage (changes in serum creatinine and/or urine albumin excretion) apply to a later stage of [...] Read more.

In order to effectively develop personalized medicine for kidney diseases we urgently need to develop highly accurate biomarkers for use in the clinic, since current biomarkers of kidney damage (changes in serum creatinine and/or urine albumin excretion) apply to a later stage of disease, lack accuracy, and are not connected with molecular pathophysiology. Analysis of urine peptide content (urinary peptidomics) has emerged as one of the most attractive areas in disease biomarker discovery. Urinary peptidome analysis allows the detection of short and long-term physiological or pathological changes occurring within the kidney. Urinary peptidomics has been applied extensively for several years now in renal patients, and may greatly improve kidney disease management by supporting earlier and more accurate detection, prognostic assessment, and prediction of response to treatment. It also promises better understanding of kidney disease pathophysiology, and has been proposed as a “liquid biopsy” to discriminate various types of renal disorders. Furthermore, proteins being the major drug targets, peptidome analysis may allow one to evaluate the effects of therapies at the protein signaling pathway level. We here review the most recent findings on urinary peptidomics in the setting of the most common kidney diseases. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 1070 KiB

Open AccessReview

Goals and Challenges in Bacterial Phosphoproteomics

by Paula Yagüe, Nathaly Gonzalez-Quiñonez, Gemma Fernández-García, Sergio Alonso-Fernández and Angel Manteca

Int. J. Mol. Sci. 2019, 20(22), 5678; https://doi.org/10.3390/ijms20225678 - 13 Nov 2019

Cited by 27 | Viewed by 4556 | Correction

Abstract

Reversible protein phosphorylation at serine, threonine and tyrosine is a well-known dynamic post-translational modification with stunning regulatory and signalling functions in eukaryotes. Shotgun phosphoproteomic analyses revealed that this post-translational modification is dramatically lower in bacteria than in eukaryotes. However, Ser/Thr/Tyr phosphorylation is present [...] Read more.

Reversible protein phosphorylation at serine, threonine and tyrosine is a well-known dynamic post-translational modification with stunning regulatory and signalling functions in eukaryotes. Shotgun phosphoproteomic analyses revealed that this post-translational modification is dramatically lower in bacteria than in eukaryotes. However, Ser/Thr/Tyr phosphorylation is present in all analysed bacteria (24 eubacteria and 1 archaea). It affects central processes, such as primary and secondary metabolism development, sporulation, pathogenicity, virulence or antibiotic resistance. Twenty-nine phosphoprotein orthologues were systematically identified in bacteria: ribosomal proteins, enzymes from glycolysis and gluconeogenesis, elongation factors, cell division proteins, RNA polymerases, ATP synthases and enzymes from the citrate cycle. While Ser/Thr/Tyr phosphorylation exists in bacteria, there is a consensus that histidine phosphorylation is the most abundant protein phosphorylation in prokaryotes. Unfortunately, histidine shotgun phosphorproteomics is not possible due to the reduced phosphohistidine half-life under the acidic pH conditions used in standard LC-MS/MS analysis. However, considering the fast and continuous advances in LC-MS/MS-based phosphoproteomic methodologies, it is expected that further innovations will allow for the study of His phosphoproteomes and a better coverage of bacterial phosphoproteomes. The characterisation of the biological role of bacterial Ser/Thr/Tyr and His phosphorylations might revolutionise our understanding of prokaryotic physiology. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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11 pages, 380 KiB

Open AccessReview

Current Status of Proteomic Technologies for Discovering and Identifying Gingival Crevicular Fluid Biomarkers for Periodontal Disease

by Sachio Tsuchida, Mamoru Satoh, Masaki Takiwaki and Fumio Nomura

Int. J. Mol. Sci. 2019, 20(1), 86; https://doi.org/10.3390/ijms20010086 - 26 Dec 2018

Cited by 43 | Viewed by 8439

Abstract

Periodontal disease is caused by bacteria in dental biofilms. To eliminate the bacteria, immune system cells release substances that inflame and damage the gums, periodontal ligament, or alveolar bone, leading to swollen bleeding gums, which is a sign of gingivitis. Damage from periodontal [...] Read more.

Periodontal disease is caused by bacteria in dental biofilms. To eliminate the bacteria, immune system cells release substances that inflame and damage the gums, periodontal ligament, or alveolar bone, leading to swollen bleeding gums, which is a sign of gingivitis. Damage from periodontal disease can cause teeth to loosen also. Studies have demonstrated the proteomic approach to be a promising tool for the discovery and identification of biochemical markers of periodontal diseases. Recently, many studies have applied expression proteomics to identify proteins whose expression levels are altered by disease. As a fluid lying in close proximity to the periodontal tissue, the gingival crevicular fluid (GCF) is the principal target in the search for periodontal disease biomarkers because its protein composition may reflect the disease pathophysiology. Biochemical marker analysis of GCF is effective for objective diagnosis in the early and advanced stages of periodontal disease. Periodontal diseases are also promising targets for proteomics, and several groups, including ours, have applied proteomics in the search for GCF biomarkers of periodontal diseases. This search is of continuing interest in the field of experimental and clinical periodontal disease research. In this article, we summarize the current situation of proteomic technologies to discover and identify GCF biomarkers for periodontal diseases. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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30 pages, 2109 KiB

Open AccessReview

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools

by Dana Pascovici, Jemma X. Wu, Matthew J. McKay, Chitra Joseph, Zainab Noor, Karthik Kamath, Yunqi Wu, Shoba Ranganathan, Vivek Gupta and Mehdi Mirzaei

Int. J. Mol. Sci. 2019, 20(1), 16; https://doi.org/10.3390/ijms20010016 - 20 Dec 2018

Cited by 44 | Viewed by 12826

Abstract

Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are [...] Read more.

Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra—many of which likely harbour PTMs—through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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22 pages, 5153 KiB

Open AccessReview

Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification

by Bjoern Titz, Raffaella M. Gadaleta, Giuseppe Lo Sasso, Ashraf Elamin, Kim Ekroos, Nikolai V. Ivanov, Manuel C. Peitsch and Julia Hoeng

Int. J. Mol. Sci. 2018, 19(9), 2775; https://doi.org/10.3390/ijms19092775 - 15 Sep 2018

Cited by 37 | Viewed by 12145

Abstract

Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn′s disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far [...] Read more.

Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn′s disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical “omics” methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD. In this review, we focus on the rapidly evolving proteomics and lipidomics technologies and their broad applicability to IBD studies; these range from investigations of immune-regulatory mechanisms and biomarker discovery to studies dissecting host–microbiome interactions and the role of intestinal epithelial cells. Future studies can leverage recent advances, including improved analytical methodologies, additional relevant sample types, and integrative multi-omics analyses. Proteomics and lipidomics could effectively accelerate the development of novel targeted treatments and the discovery of complementary biomarkers, enabling continuous monitoring of the treatment response of individual patients; this may allow further refinement of treatment and, ultimately, facilitate a personalized medicine approach to IBD. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 1086 KiB

Open AccessReview

Immune Checkpoints as the Immune System Regulators and Potential Biomarkers in HIV-1 Infection

by Maike Sperk, Robert Van Domselaar and Ujjwal Neogi

Int. J. Mol. Sci. 2018, 19(7), 2000; https://doi.org/10.3390/ijms19072000 - 9 Jul 2018

Cited by 32 | Viewed by 5640

Abstract

Immune checkpoints are several co-stimulatory and inhibitory pathways that regulate T cell immune responses. Most of the discoveries about immune checkpoints were made in cancer research where inhibitory immune checkpoints cause immune exhaustion and down-regulate anti-tumor responses. In addition to cancer, immune checkpoints [...] Read more.

Immune checkpoints are several co-stimulatory and inhibitory pathways that regulate T cell immune responses. Most of the discoveries about immune checkpoints were made in cancer research where inhibitory immune checkpoints cause immune exhaustion and down-regulate anti-tumor responses. In addition to cancer, immune checkpoints are exploited in chronic infectious diseases. In human immunodeficiency virus (HIV) infection, the immune checkpoint molecule called programmed cell death protein 1 (PD-1) has been determined as being a major regulatory factor for T cell exhaustion. Recent studies with antibodies blocking either PD-1 ligand 1 (PD-L1) or PD-1 show not only promising results in the enhancement of HIV-specific immune responses but even in reducing the latent HIV reservoir. Apart from the therapeutic target for a functional cure of HIV-1, immune checkpoint molecules might be used as biomarkers for monitoring disease progression and therapeutic response. In this review, we will summarize and discuss the inhibitory immune checkpoint molecules PD-1, cytotoxic T-lymphocyte-associated protein 4 (CTLA4), lymphocyte-activation gene 3 (LAG3), and T cell immunoglobulin and mucin-domain-containing-3 (TIM3) as well as the co-stimulatory molecules CD40L and CD70, including their role in immunity, with a particular focus on HIV infection, and being potential targets for a functional HIV cure. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 1838 KiB

Open AccessReview

The Use of “Omics” in Lactation Research in Dairy Cows

by Shanshan Li, Quanjuan Wang, Xiujuan Lin, Xiaolu Jin, Lan Liu, Caihong Wang, Qiong Chen, Jianxin Liu and Hongyun Liu

Int. J. Mol. Sci. 2017, 18(5), 983; https://doi.org/10.3390/ijms18050983 - 5 May 2017

Cited by 30 | Viewed by 10476

Abstract

“Omics” is the application of genomics, transcriptomics, proteomics, and metabolomics in biological research. Over the years, tremendous amounts of biological information has been gathered regarding the changes in gene, mRNA and protein expressions as well as metabolites in different physiological conditions and regulations, [...] Read more.

“Omics” is the application of genomics, transcriptomics, proteomics, and metabolomics in biological research. Over the years, tremendous amounts of biological information has been gathered regarding the changes in gene, mRNA and protein expressions as well as metabolites in different physiological conditions and regulations, which has greatly advanced our understanding of the regulation of many physiological and pathophysiological processes. The aim of this review is to comprehensively describe the advances in our knowledge regarding lactation mainly in dairy cows that were obtained from the “omics” studies. The “omics” technologies have continuously been preferred as the technical tools in lactation research aiming to develop new nutritional, genetic, and management strategies to improve milk production and milk quality in dairy cows. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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24 pages, 8234 KiB

Open AccessReview

A Review: Proteomics in Retinal Artery Occlusion, Retinal Vein Occlusion, Diabetic Retinopathy and Acquired Macular Disorders

by Lasse Jørgensen Cehofski, Bent Honoré and Henrik Vorum

Int. J. Mol. Sci. 2017, 18(5), 907; https://doi.org/10.3390/ijms18050907 - 28 Apr 2017

Cited by 46 | Viewed by 11186

Abstract

Retinal artery occlusion (RAO), retinal vein occlusion (RVO), diabetic retinopathy (DR) and age-related macular degeneration (AMD) are frequent ocular diseases with potentially sight-threatening outcomes. In the present review we discuss major findings of proteomic studies of RAO, RVO, DR and AMD, including an [...] Read more.

Retinal artery occlusion (RAO), retinal vein occlusion (RVO), diabetic retinopathy (DR) and age-related macular degeneration (AMD) are frequent ocular diseases with potentially sight-threatening outcomes. In the present review we discuss major findings of proteomic studies of RAO, RVO, DR and AMD, including an overview of ocular proteome changes associated with anti-vascular endothelial growth factor (VEGF) treatments. Despite the severe outcomes of RAO, the proteome of the disease remains largely unstudied. There is also limited knowledge about the proteome of RVO, but proteomic studies suggest that RVO is associated with remodeling of the extracellular matrix and adhesion processes. Proteomic studies of DR have resulted in the identification of potential therapeutic targets such as carbonic anhydrase-I. Proliferative diabetic retinopathy is the most intensively studied stage of DR. Proteomic studies have established VEGF, pigment epithelium-derived factor (PEDF) and complement components as key factors associated with AMD. The aim of this review is to highlight the major milestones in proteomics in RAO, RVO, DR and AMD. Through large-scale protein analyses, proteomics is bringing new important insights into these complex pathological conditions. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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22 pages, 1713 KiB

Open AccessReview

Redox Proteomics and Platelet Activation: Understanding the Redox Proteome to Improve Platelet Quality for Transfusion

by Giona Sonego, Mélanie Abonnenc, Jean-Daniel Tissot, Michel Prudent and Niels Lion

Int. J. Mol. Sci. 2017, 18(2), 387; https://doi.org/10.3390/ijms18020387 - 11 Feb 2017

Cited by 34 | Viewed by 7904

Abstract

Blood banks use pathogen inactivation (PI) technologies to increase the safety of platelet concentrates (PCs). The characteristics of PI-treated PCs slightly differ from those of untreated PCs, but the underlying reasons are not well understood. One possible cause is the generation of oxidative [...] Read more.

Blood banks use pathogen inactivation (PI) technologies to increase the safety of platelet concentrates (PCs). The characteristics of PI-treated PCs slightly differ from those of untreated PCs, but the underlying reasons are not well understood. One possible cause is the generation of oxidative stress during the PI process. This is of great interest since reactive oxygen species (ROS) act as second messengers in platelet functions. Furthermore, there are links between protein oxidation and phosphorylation, another mechanism that is critical for cell regulation. Current research efforts focus on understanding the underlying mechanisms and identifying new target proteins. Proteomics technologies represent powerful tools for investigating signaling pathways involving ROS and post-translational modifications such as phosphorylation, while quantitative techniques enable the comparison of the platelet resting state versus the stimulated state. In particular, redox cysteine is a key player in platelet activation upon stimulation by different agonists. This review highlights the experiments that have provided insights into the roles of ROS in platelet function and the implications for platelet transfusion, and potentially in diseases such as inflammation and platelet hyperactivity. The review also describes the implication of redox mechanism in platelet storage considerations. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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12 pages, 1883 KiB

Open AccessReview

A Proteogenomic Approach to Understanding MYC Function in Metastatic Medulloblastoma Tumors

by Jerome A. Staal, Yanxin Pei and Brian R. Rood

Int. J. Mol. Sci. 2016, 17(10), 1744; https://doi.org/10.3390/ijms17101744 - 19 Oct 2016

Cited by 10 | Viewed by 6681

Abstract

Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. [...] Read more.

Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. Understanding the diverse events driving tumor formation, maintenance, progression, and recurrence is necessary for identifying novel targeted therapeutics and improving survival of patients with this disease. Genomic copy number alteration data, together with clinical studies, identifies c-MYC amplification as an important risk factor associated with the most aggressive forms of medulloblastoma with marked metastatic potential. Yet despite this, very little is known regarding the impact of such genomic abnormalities upon the functional biology of the tumor cell. We discuss here how recent advances in quantitative proteomic techniques are now providing new insights into the functional biology of these aggressive tumors, as illustrated by the use of proteomics to bridge the gap between the genotype and phenotype in the case of c-MYC-amplified/associated medulloblastoma. These integrated proteogenomic approaches now provide a new platform for understanding cancer biology by providing a functional context to frame genomic abnormalities. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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30 pages, 5655 KiB

Open AccessReview

Drought-Responsive Mechanisms in Plant Leaves Revealed by Proteomics

by Xiaoli Wang, Xiaofeng Cai, Chenxi Xu, Quanhua Wang and Shaojun Dai

Int. J. Mol. Sci. 2016, 17(10), 1706; https://doi.org/10.3390/ijms17101706 - 18 Oct 2016

Cited by 208 | Viewed by 13615

Abstract

Plant drought tolerance is a complex trait that requires a global view to understand its underlying mechanism. The proteomic aspects of plant drought response have been extensively investigated in model plants, crops and wood plants. In this review, we summarize recent proteomic studies [...] Read more.

Plant drought tolerance is a complex trait that requires a global view to understand its underlying mechanism. The proteomic aspects of plant drought response have been extensively investigated in model plants, crops and wood plants. In this review, we summarize recent proteomic studies on drought response in leaves to reveal the common and specialized drought-responsive mechanisms in different plants. Although drought-responsive proteins exhibit various patterns depending on plant species, genotypes and stress intensity, proteomic analyses show that dominant changes occurred in sensing and signal transduction, reactive oxygen species scavenging, osmotic regulation, gene expression, protein synthesis/turnover, cell structure modulation, as well as carbohydrate and energy metabolism. In combination with physiological and molecular results, proteomic studies in leaves have helped to discover some potential proteins and/or metabolic pathways for drought tolerance. These findings provide new clues for understanding the molecular basis of plant drought tolerance. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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15 pages, 1970 KiB

Open AccessReview

Using Proteomics to Understand How Leishmania Parasites Survive inside the Host and Establish Infection

by Patrícia Sampaio Tavares Veras and Juliana Perrone Bezerra de Menezes

Int. J. Mol. Sci. 2016, 17(8), 1270; https://doi.org/10.3390/ijms17081270 - 19 Aug 2016

Cited by 32 | Viewed by 10801

Abstract

Leishmania is a protozoan parasite that causes a wide range of different clinical manifestations in mammalian hosts. It is a major public health risk on different continents and represents one of the most important neglected diseases. Due to the high toxicity of the [...] Read more.

Leishmania is a protozoan parasite that causes a wide range of different clinical manifestations in mammalian hosts. It is a major public health risk on different continents and represents one of the most important neglected diseases. Due to the high toxicity of the drugs currently used, and in the light of increasing drug resistance, there is a critical need to develop new drugs and vaccines to control Leishmania infection. Over the past few years, proteomics has become an important tool to understand the underlying biology of Leishmania parasites and host interaction. The large-scale study of proteins, both in parasites and within the host in response to infection, can accelerate the discovery of new therapeutic targets. By studying the proteomes of host cells and tissues infected with Leishmania, as well as changes in protein profiles among promastigotes and amastigotes, scientists hope to better understand the biology involved in the parasite survival and the host-parasite interaction. This review demonstrates the feasibility of proteomics as an approach to identify new proteins involved in Leishmania differentiation and intracellular survival. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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20 pages, 389 KiB

Open AccessReview

Environmental Microbial Community Proteomics: Status, Challenges and Perspectives

by Da-Zhi Wang, Ling-Fen Kong, Yuan-Yuan Li and Zhang-Xian Xie

Int. J. Mol. Sci. 2016, 17(8), 1275; https://doi.org/10.3390/ijms17081275 - 5 Aug 2016

Cited by 69 | Viewed by 9075

Abstract

Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial [...] Read more.

Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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19 pages, 519 KiB

Open AccessReview

Proteomic and Microscopic Strategies towards the Analysis of the Cytoskeletal Networks in Major Neuropsychiatric Disorders

by Joëlle V. F. Coumans, Suresh K. A. Palanisamy, Jim McFarlane and Pierre D. J. Moens

Int. J. Mol. Sci. 2016, 17(4), 581; https://doi.org/10.3390/ijms17040581 - 20 Apr 2016

Cited by 8 | Viewed by 9695

Abstract

Mental health disorders have become worldwide health priorities. It is estimated that in the next 20 years they will account for a 16 trillion United State dollars (US$) loss. Up to now, the underlying pathophysiology of psychiatric disorders remains elusive. Altered cytoskeleton proteins [...] Read more.

Mental health disorders have become worldwide health priorities. It is estimated that in the next 20 years they will account for a 16 trillion United State dollars (US$) loss. Up to now, the underlying pathophysiology of psychiatric disorders remains elusive. Altered cytoskeleton proteins expression that may influence the assembly, organization and maintenance of cytoskeletal integrity has been reported in major depressive disorders, schizophrenia and to some extent bipolar disorders. The use of quantitative proteomics, dynamic microscopy and super-resolution microscopy to investigate disease-specific protein signatures holds great promise to improve our understanding of these disorders. In this review, we present the currently available quantitative proteomic approaches use in neurology, gel-based, stable isotope-labelling and label-free methodologies and evaluate their strengths and limitations. We also reported on enrichment/subfractionation methods that target the cytoskeleton associated proteins and discuss the need of alternative methods for further characterization of the neurocytoskeletal proteome. Finally, we present live cell imaging approaches and emerging dynamic microscopy technology that will provide the tools necessary to investigate protein interactions and their dynamics in the whole cells. While these areas of research are still in their infancy, they offer huge potential towards the understanding of the neuronal network stability and its modification across neuropsychiatric disorders. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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17 pages, 963 KiB

Open AccessReview

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology

by Putty-Reddy Sudhir and Chung-Hsuan Chen

Int. J. Mol. Sci. 2016, 17(3), 432; https://doi.org/10.3390/ijms17030432 - 22 Mar 2016

Cited by 5 | Viewed by 8767

Abstract

A protein complex consists of two or more proteins that are linked together through protein–protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular [...] Read more.

A protein complex consists of two or more proteins that are linked together through protein–protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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14 pages, 392 KiB

Open AccessReview

Proteomic Investigations into Hemodialysis Therapy

by Mario Bonomini, Vittorio Sirolli, Luisa Pieroni, Paolo Felaco, Luigi Amoroso and Andrea Urbani

Int. J. Mol. Sci. 2015, 16(12), 29508-29521; https://doi.org/10.3390/ijms161226189 - 10 Dec 2015

Cited by 20 | Viewed by 6691

Abstract

The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate [...] Read more.

The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane’s performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane’s bio(in)compatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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20 pages, 2119 KiB

Open AccessReview

Maize-Pathogen Interactions: An Ongoing Combat from a Proteomics Perspective

by Olga Pechanova and Tibor Pechan

Int. J. Mol. Sci. 2015, 16(12), 28429-28448; https://doi.org/10.3390/ijms161226106 - 30 Nov 2015

Cited by 66 | Viewed by 12253

Abstract

Maize (Zea mays L.) is a host to numerous pathogenic species that impose serious diseases to its ear and foliage, negatively affecting the yield and the quality of the maize crop. A considerable amount of research has been carried out to elucidate [...] Read more.

Maize (Zea mays L.) is a host to numerous pathogenic species that impose serious diseases to its ear and foliage, negatively affecting the yield and the quality of the maize crop. A considerable amount of research has been carried out to elucidate mechanisms of maize-pathogen interactions with a major goal to identify defense-associated proteins. In this review, we summarize interactions of maize with its agriculturally important pathogens that were assessed at the proteome level. Employing differential analyses, such as the comparison of pathogen-resistant and susceptible maize varieties, as well as changes in maize proteomes after pathogen challenge, numerous proteins were identified as possible candidates in maize resistance. We describe findings of various research groups that used mainly mass spectrometry-based, high through-put proteomic tools to investigate maize interactions with fungal pathogens Aspergillus flavus, Fusarium spp., and Curvularia lunata, and viral agents Rice Black-streaked Dwarf Virus and Sugarcane Mosaic Virus. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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10 pages, 558 KiB

Open AccessReview

Plant Responses to Nanoparticle Stress

by Zahed Hossain, Ghazala Mustafa and Setsuko Komatsu

Int. J. Mol. Sci. 2015, 16(11), 26644-26653; https://doi.org/10.3390/ijms161125980 - 6 Nov 2015

Cited by 226 | Viewed by 14193

Abstract

With the rapid advancement in nanotechnology, release of nanoscale materials into the environment is inevitable. Such contamination may negatively influence the functioning of the ecosystems. Many manufactured nanoparticles (NPs) contain heavy metals, which can cause soil and water contamination. Proteomic techniques have contributed [...] Read more.

With the rapid advancement in nanotechnology, release of nanoscale materials into the environment is inevitable. Such contamination may negatively influence the functioning of the ecosystems. Many manufactured nanoparticles (NPs) contain heavy metals, which can cause soil and water contamination. Proteomic techniques have contributed substantially in understanding the molecular mechanisms of plant responses against various stresses by providing a link between gene expression and cell metabolism. As the coding regions of genome are responsible for plant adaptation to adverse conditions, protein signatures provide insights into the phytotoxicity of NPs at proteome level. This review summarizes the recent contributions of plant proteomic research to elaborate the complex molecular pathways of plant response to NPs stress. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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26 pages, 818 KiB

Open AccessReview

Common Amino Acid Subsequences in a Universal Proteome—Relevance for Food Science

by Piotr Minkiewicz, Małgorzata Darewicz, Anna Iwaniak, Jolanta Sokołowska, Piotr Starowicz, Justyna Bucholska and Monika Hrynkiewicz

Int. J. Mol. Sci. 2015, 16(9), 20748-20773; https://doi.org/10.3390/ijms160920748 - 1 Sep 2015

Cited by 26 | Viewed by 7754

Abstract

A common subsequence is a fragment of the amino acid chain that occurs in more than one protein. Common subsequences may be an object of interest for food scientists as biologically active peptides, epitopes, and/or protein markers that are used in comparative proteomics. [...] Read more.

A common subsequence is a fragment of the amino acid chain that occurs in more than one protein. Common subsequences may be an object of interest for food scientists as biologically active peptides, epitopes, and/or protein markers that are used in comparative proteomics. An individual bioactive fragment, in particular the shortest fragment containing two or three amino acid residues, may occur in many protein sequences. An individual linear epitope may also be present in multiple sequences of precursor proteins. Although recent recommendations for prediction of allergenicity and cross-reactivity include not only sequence identity, but also similarities in secondary and tertiary structures surrounding the common fragment, local sequence identity may be used to screen protein sequence databases for potential allergens in silico. The main weakness of the screening process is that it overlooks allergens and cross-reactivity cases without identical fragments corresponding to linear epitopes. A single peptide may also serve as a marker of a group of allergens that belong to the same family and, possibly, reveal cross-reactivity. This review article discusses the benefits for food scientists that follow from the common subsequences concept. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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25 pages, 1533 KiB

Open AccessReview

Abiotic Stresses: Insight into Gene Regulation and Protein Expression in Photosynthetic Pathways of Plants

by Mohammad-Zaman Nouri, Ali Moumeni and Setsuko Komatsu

Int. J. Mol. Sci. 2015, 16(9), 20392-20416; https://doi.org/10.3390/ijms160920392 - 28 Aug 2015

Cited by 122 | Viewed by 10095

Abstract

Global warming and climate change intensified the occurrence and severity of abiotic stresses that seriously affect the growth and development of plants,especially, plant photosynthesis. The direct impact of abiotic stress on the activity of photosynthesis is disruption of all photosynthesis components such as [...] Read more.

Global warming and climate change intensified the occurrence and severity of abiotic stresses that seriously affect the growth and development of plants,especially, plant photosynthesis. The direct impact of abiotic stress on the activity of photosynthesis is disruption of all photosynthesis components such as photosystem I and II, electron transport, carbon fixation, ATP generating system and stomatal conductance. The photosynthetic system of plants reacts to the stress differently, according to the plant type, photosynthetic systems (C₃ or C₄), type of the stress, time and duration of the occurrence and several other factors. The plant responds to the stresses by a coordinate chloroplast and nuclear gene expression. Chloroplast, thylakoid membrane, and nucleus are the main targets of regulated proteins and metabolites associated with photosynthetic pathways. Rapid responses of plant cell metabolism and adaptation to photosynthetic machinery are key factors for survival of plants in a fluctuating environment. This review gives a comprehensive view of photosynthesis-related alterations at the gene and protein levels for plant adaptation or reaction in response to abiotic stress. Full article

(This article belongs to the Special Issue Plant Proteomic Research)

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34 pages, 775 KiB

Open AccessReview

A Review: Proteomics in Nasopharyngeal Carcinoma

by Ze-Tan Chen, Zhong-Guo Liang and Xiao-Dong Zhu

Int. J. Mol. Sci. 2015, 16(7), 15497-15530; https://doi.org/10.3390/ijms160715497 - 8 Jul 2015

Cited by 36 | Viewed by 8338

Abstract

Although radiotherapy is generally effective in the treatment of major nasopharyngeal carcinoma (NPC), this treatment still makes approximately 20% of patients radioresistant. Therefore, the identification of blood or biopsy biomarkers that can predict the treatment response to radioresistance and that can diagnosis early [...] Read more.

Although radiotherapy is generally effective in the treatment of major nasopharyngeal carcinoma (NPC), this treatment still makes approximately 20% of patients radioresistant. Therefore, the identification of blood or biopsy biomarkers that can predict the treatment response to radioresistance and that can diagnosis early stages of NPC would be highly useful to improve this situation. Proteomics is widely used in NPC for searching biomarkers and comparing differentially expressed proteins. In this review, an overview of proteomics with different samples related to NPC and common proteomics methods was made. In conclusion, identical proteins are sorted as follows: Keratin is ranked the highest followed by such proteins as annexin, heat shock protein, 14-3-3σ, nm-23 protein, cathepsin, heterogeneous nuclear ribonucleoproteins, enolase, triosephosphate isomerase, stathmin, prohibitin, and vimentin. This ranking indicates that these proteins may be NPC-related proteins and have potential value for further studies. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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27 pages, 986 KiB

Open AccessReview

Methodologies and Perspectives of Proteomics Applied to Filamentous Fungi: From Sample Preparation to Secretome Analysis

by Linda Bianco and Gaetano Perrotta

Int. J. Mol. Sci. 2015, 16(3), 5803-5829; https://doi.org/10.3390/ijms16035803 - 12 Mar 2015

Cited by 57 | Viewed by 11097

Abstract

Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic [...] Read more.

Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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19 pages, 699 KiB

Open AccessReview

Recent Advances in Proteomic Studies of Adipose Tissues and Adipocytes

by Eun Young Kim, Won Kon Kim, Kyoung-Jin Oh, Baek Soo Han, Sang Chul Lee and Kwang-Hee Bae

Int. J. Mol. Sci. 2015, 16(3), 4581-4599; https://doi.org/10.3390/ijms16034581 - 27 Feb 2015

Cited by 36 | Viewed by 7832

Abstract

Obesity is a chronic disease that is associated with significantly increased levels of risk of a number of metabolic disorders. Despite these enhanced health risks, the worldwide prevalence of obesity has increased dramatically over the past few decades. Obesity is caused by the [...] Read more.

Obesity is a chronic disease that is associated with significantly increased levels of risk of a number of metabolic disorders. Despite these enhanced health risks, the worldwide prevalence of obesity has increased dramatically over the past few decades. Obesity is caused by the accumulation of an abnormal amount of body fat in adipose tissue, which is composed mostly of adipocytes. Thus, a deeper understanding of the regulation mechanism of adipose tissue and/or adipocytes can provide a clue for overcoming obesity-related metabolic diseases. In this review, we describe recent advances in the study of adipose tissue and/or adipocytes, focusing on proteomic approaches. In addition, we suggest future research directions for proteomic studies which may lead to novel treatments of obesity and obesity-related diseases. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

18 pages, 2120 KiB

Open AccessReview

Anti-Vascular Endothelial Growth Factor Therapy in Breast Cancer

by Tina Bøgelund Kristensen, Malin L. T. Knutsson, Markus Wehland, Britt Elmedal Laursen, Daniela Grimm, Elisabeth Warnke and Nils E. Magnusson

Int. J. Mol. Sci. 2014, 15(12), 23024-23041; https://doi.org/10.3390/ijms151223024 - 11 Dec 2014

Cited by 55 | Viewed by 10210

Abstract

Neo-angiogenesis is a critical process for tumor growth and invasion and has become a promising target in cancer therapy. This manuscript reviews three currently relevant anti-angiogenic agents targeting the vascular endothelial growth factor system: bevacizumab, ramucirumab and sorafenib. The efficacy of anti-angiogenic drugs [...] Read more.

Neo-angiogenesis is a critical process for tumor growth and invasion and has become a promising target in cancer therapy. This manuscript reviews three currently relevant anti-angiogenic agents targeting the vascular endothelial growth factor system: bevacizumab, ramucirumab and sorafenib. The efficacy of anti-angiogenic drugs in adjuvant therapy or as neo-adjuvant treatment has been estimated in clinical trials of advanced breast cancer. To date, the overall observed clinical improvements are unconvincing, and further research is required to demonstrate the efficacy of anti-angiogenic drugs in breast cancer treatments. The outcomes of anti-angiogenic therapy have been highly variable in terms of tumor response. New methods are needed to identify patients who will benefit from this regimen. The development of biomarkers and molecular profiling are relevant research areas that may strengthen the ability to focus anti-angiogenic therapy towards suitable patients, thereby increase the cost-effectiveness, currently estimated to be inadequate. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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16 pages, 790 KiB

Open AccessReview

Farm Animal Serum Proteomics and Impact on Human Health

by Francesco Di Girolamo, Alfonsina D'Amato, Isabella Lante, Fabrizio Signore, Marta Muraca and Lorenza Putignani

Int. J. Mol. Sci. 2014, 15(9), 15396-15411; https://doi.org/10.3390/ijms150915396 - 1 Sep 2014

Cited by 25 | Viewed by 8116

Abstract

Due to the incompleteness of animal genome sequencing, the analysis and characterization of serum proteomes of most farm animals are still in their infancy, compared to the already well-documented human serum proteome. This review focuses on the implications of the farm animal serum [...] Read more.

Due to the incompleteness of animal genome sequencing, the analysis and characterization of serum proteomes of most farm animals are still in their infancy, compared to the already well-documented human serum proteome. This review focuses on the implications of the farm animal serum proteomics in order to identify novel biomarkers for animal welfare, early diagnosis, prognosis and monitoring of infectious disease treatment, and develop new vaccines, aiming at determining the reciprocal benefits for humans and animals. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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18 pages, 835 KiB

Open AccessReview

Biomarkers in Alzheimer’s Disease Analysis by Mass Spectrometry-Based Proteomics

by Yahui Liu, Hong Qing and Yulin Deng

Int. J. Mol. Sci. 2014, 15(5), 7865-7882; https://doi.org/10.3390/ijms15057865 - 6 May 2014

Cited by 42 | Viewed by 10434

Abstract

Alzheimer’s disease (AD) is a common chronic and destructive disease. The early diagnosis of AD is difficult, thus the need for clinically applicable biomarkers development is growing rapidly. There are many methods to biomarker discovery and identification. In this review, we aim to [...] Read more.

Alzheimer’s disease (AD) is a common chronic and destructive disease. The early diagnosis of AD is difficult, thus the need for clinically applicable biomarkers development is growing rapidly. There are many methods to biomarker discovery and identification. In this review, we aim to summarize Mass spectrometry (MS)-based proteomics studies on AD and discuss thoroughly the methods to identify candidate biomarkers in cerebrospinal fluid (CSF) and blood. This review will also discuss the potential research areas on biomarkers. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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25 pages, 1112 KiB

Open AccessReview

Current Status and Future Perspectives of Mass Spectrometry Imaging

by Surendra Nimesh, Susantha Mohottalage, Renaud Vincent and Prem Kumarathasan

Int. J. Mol. Sci. 2013, 14(6), 11277-11301; https://doi.org/10.3390/ijms140611277 - 28 May 2013

Cited by 34 | Viewed by 9959

Abstract

Mass spectrometry imaging is employed for mapping proteins, lipids and metabolites in biological tissues in a morphological context. Although initially developed as a tool for biomarker discovery by imaging the distribution of protein/peptide in tissue sections, the high sensitivity and molecular specificity of [...] Read more.

Mass spectrometry imaging is employed for mapping proteins, lipids and metabolites in biological tissues in a morphological context. Although initially developed as a tool for biomarker discovery by imaging the distribution of protein/peptide in tissue sections, the high sensitivity and molecular specificity of this technique have enabled its application to biomolecules, other than proteins, even in cells, latent finger prints and whole organisms. Relatively simple, with no requirement for labelling, homogenization, extraction or reconstitution, the technique has found a variety of applications in molecular biology, pathology, pharmacology and toxicology. By discriminating the spatial distribution of biomolecules in serial sections of tissues, biomarkers of lesions and the biological responses to stressors or diseases can be better understood in the context of structure and function. In this review, we have discussed the advances in the different aspects of mass spectrometry imaging processes, application towards different disciplines and relevance to the field of toxicology. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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30 pages, 539 KiB

Open AccessReview

Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

by Monica Soldi, Alessandro Cuomo, Michael Bremang and Tiziana Bonaldi

Int. J. Mol. Sci. 2013, 14(3), 5402-5431; https://doi.org/10.3390/ijms14035402 - 6 Mar 2013

Cited by 28 | Viewed by 11127

Abstract

Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce [...] Read more.

Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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23 pages, 877 KiB

Open AccessReview

The Proteomics Big Challenge for Biomarkers and New Drug-Targets Discovery

by Rocco Savino, Sergio Paduano, Mariaimmacolata Preianò and Rosa Terracciano

Int. J. Mol. Sci. 2012, 13(11), 13926-13948; https://doi.org/10.3390/ijms131113926 - 29 Oct 2012

Cited by 63 | Viewed by 12401

Abstract

In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of [...] Read more.

In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on), as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics. Major issues will be presented for proteomic technologies used for the discovery of biomarkers for early disease diagnosis and identification of new drug targets. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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23 pages, 238 KiB

Open AccessReview

Plants versus Fungi and Oomycetes: Pathogenesis, Defense and Counter-Defense in the Proteomics Era

by Abdelbasset El Hadrami, Ahmed F. El-Bebany, Zhen Yao, Lorne R. Adam, Ismail El Hadrami and Fouad Daayf

Int. J. Mol. Sci. 2012, 13(6), 7237-7259; https://doi.org/10.3390/ijms13067237 - 13 Jun 2012

Cited by 13 | Viewed by 8146

Abstract

Plant-fungi and plant-oomycete interactions have been studied at the proteomic level for many decades. However, it is only in the last few years, with the development of new approaches, combined with bioinformatics data mining tools, gel staining, and analytical instruments, such as 2D-PAGE/nanoflow-LC-MS/MS, [...] Read more.

Plant-fungi and plant-oomycete interactions have been studied at the proteomic level for many decades. However, it is only in the last few years, with the development of new approaches, combined with bioinformatics data mining tools, gel staining, and analytical instruments, such as 2D-PAGE/nanoflow-LC-MS/MS, that proteomic approaches thrived. They allow screening and analysis, at the sub-cellular level, of peptides and proteins resulting from plants, pathogens, and their interactions. They also highlight post-translational modifications to proteins, e.g., glycosylation, phosphorylation or cleavage. However, many challenges are encountered during in planta studies aimed at stressing details of host defenses and fungal and oomycete pathogenicity determinants during interactions. Dissecting the mechanisms of such host-pathogen systems, including pathogen counter-defenses, will ensure a step ahead towards understanding current outcomes of interactions from a co-evolutionary point of view, and eventually move a step forward in building more durable strategies for management of diseases caused by fungi and oomycetes. Unraveling intricacies of more complex proteomic interactions that involve additional microbes, i.e., PGPRs and symbiotic fungi, which strengthen plant defenses will generate valuable information on how pathosystems actually function in nature, and thereby provide clues to solving disease problems that engender major losses in crops every year. Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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Open AccessCorrection

Correction: Yagüe, P., et al. Goals and Challenges in Bacterial Phosphoproteomics. Int. J. Mol. Sci. 2019, 20, 5678

by Paula Yagüe, Nathaly Gonzalez-Quiñonez, Gemma Fernández-García, Sergio Alonso-Fernández and Angel Manteca

Int. J. Mol. Sci. 2020, 21(24), 9381; https://doi.org/10.3390/ijms21249381 - 9 Dec 2020

Cited by 1 | Viewed by 1578

Abstract

The authors wish to make the following corrections to this paper [1]:The author name “Gemma Fernánez-García” should be “Gemma Fernández-García” [...] Full article

(This article belongs to the Special Issue Advances in Proteomic Research)

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