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Plant Proteomic Research 4.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 43893

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Department of Biology, University of Mississippi, Oxford, MS 38677, USA
Interests: disease triangle; guard cells; glucosinolates; proteomics; metabolomics; mass spectrometry
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Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our 2016 Special Issue, "Plant Proteomic Research" (https://www.mdpi.com/journal/ijms/special_issues/plant-proteomic), “Plant Proteomic Research 2.0” (https://www.mdpi.com/journal/ijms/special_issues/plant-proteomic_2) and “Plant Proteomic Research 3.0” (https://www.mdpi.com/journal/ijms/special_issues/plant-proteomic_3).

Advancement in high-throughput “Omics” techniques has revolutionized plant molecular biology research. Proteomics offers one of the best approach for the functional analysis of the genome, generating detailed information that can be integrated with those obtained by other classic and -omics approaches. It thus provides a deep knowledge and understanding of the diverse proteoforms and different plant processes. Several different generations of proteomics platforms (e.g., gel-based, gel free, isotope-labeling, label free, data-dependent and data-independent) have appeared in the past twenty years. They have been exploited in describing protein profiles, posttranslational modifications, protein turnover, protein complex and interactions, subcellular proteomes, single cell and single-cell type proteomes. Nevertheless, the ultimate success of any proteomic strategy lies in the various factors, including isolation of full component of proteins, separation, visualization and their accurate characterization. Despite recent advancements, more emphasis needs to be given to the protein sample preparation protocols, especially for very low-abundant, hydrophobic, and large molecular weight. Thus, the amalgamation of diverse MS techniques, complemented with genome-sequence data and modern bioinformatics analysis with improved sample preparation and fractionation strategies, offer a powerful tool to identify and characterize novel proteins/proteoforms in spatial and temporal resolution and under different environmental conditions. Furthermore, post-translational modifications and protein–protein interactions provide deep insight into protein molecular function. Authors are welcome to submit original research articles and reviews addressing recent advancements, as well as limitations of current proteomic techniques and their diverse applications to gain new insights into plant molecular responses to various biotic and abiotic stressors and the molecular bases of other processes. Proteomics focus is also related to translational purposes, including food traceability and allergen detection. In addition, bioinformatic techniques are needed for more confident identification, quantitation, data analysis, networking and multi-omics, especially with non-model, orphan, plants, including medicinal, meditational plants and forest tree species.

Prof. Dr. Sixue Chen
Prof. Dr. Setsuko Komatsu
Guest Editors

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Keywords

  • plant proteomic research
  • methods, techniques and protocols of plant proteomics
  • applications of plant proteomics

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Published Papers (13 papers)

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Editorial

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5 pages, 214 KiB  
Editorial
Plant Proteomic Research 4.0: Frontiers in Stress Resilience
by Sixue Chen and Setsuko Komatsu
Int. J. Mol. Sci. 2021, 22(24), 13362; https://doi.org/10.3390/ijms222413362 - 12 Dec 2021
Cited by 2 | Viewed by 2155
Abstract
Large-scale high-throughput multi-omics technologies are indispensable components of systems biology in terms of discovering and defining parts of the system [...] Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)

Research

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17 pages, 2934 KiB  
Article
Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling
by Kibrom B. Abreha, Erik Alexandersson, Svante Resjö, Åsa Lankinen, Daniela Sueldo, Farnusch Kaschani, Markus Kaiser, Renier A. L. van der Hoorn, Fredrik Levander and Erik Andreasson
Int. J. Mol. Sci. 2021, 22(21), 12033; https://doi.org/10.3390/ijms222112033 - 6 Nov 2021
Cited by 2 | Viewed by 2685
Abstract
Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, [...] Read more.
Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June–August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June–August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July–August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and β-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and β-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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23 pages, 21235 KiB  
Article
Comparative Phosphoproteomic Analysis Reveals the Response of Starch Metabolism to High-Temperature Stress in Rice Endosperm
by Yuehan Pang, Yaqi Hu and Jinsong Bao
Int. J. Mol. Sci. 2021, 22(19), 10546; https://doi.org/10.3390/ijms221910546 - 29 Sep 2021
Cited by 15 | Viewed by 2891
Abstract
High-temperature stress severely affects rice grain quality. While extensive research has been conducted at the physiological, transcriptional, and protein levels, it is still unknown how protein phosphorylation regulates seed development in high-temperature environments. Here, we explore the impact of high-temperature stress on the [...] Read more.
High-temperature stress severely affects rice grain quality. While extensive research has been conducted at the physiological, transcriptional, and protein levels, it is still unknown how protein phosphorylation regulates seed development in high-temperature environments. Here, we explore the impact of high-temperature stress on the phosphoproteome of developing grains from two indica rice varieties, 9311 and Guangluai4 (GLA4), with different starch qualities. A total of 9994 phosphosites from 3216 phosphoproteins were identified in all endosperm samples. We identified several consensus phosphorylation motifs ([sP], [LxRxxs], [Rxxs], [tP]) induced by high-temperature treatment and revealed a core set of protein kinases, splicing factors, and regulatory factors in response to high-temperature stress, especially those involved in starch metabolism. A detailed phosphorylation scenario in the regulation of starch biosynthesis (AGPase, GBSSI, SSIIa, SSIIIa, BEI, BEIIb, ISA1, PUL, PHO1, PTST) in rice endosperm was proposed. Furthermore, the dynamic changes in phosphorylated enzymes related to starch synthesis (SSIIIa-Ser94, BEI-Ser562, BEI-Ser620, BEI-Ser821, BEIIb-Ser685, BEIIb-Ser715) were confirmed by Western blot analysis, which revealed that phosphorylation might play specific roles in amylopectin biosynthesis in response to high-temperature stress. The link between phosphorylation-mediated regulation and starch metabolism will provide new insights into the mechanism underlying grain quality development in response to high-temperature stress. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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15 pages, 2143 KiB  
Article
Proteomic and Biochemical Analyses of the Mechanism of Tolerance in Mutant Soybean Responding to Flooding Stress
by Setsuko Komatsu, Hisateru Yamaguchi, Keisuke Hitachi, Kunihiro Tsuchida, Yuhi Kono and Minoru Nishimura
Int. J. Mol. Sci. 2021, 22(16), 9046; https://doi.org/10.3390/ijms22169046 - 22 Aug 2021
Cited by 13 | Viewed by 3465
Abstract
To investigate the mechanism of flooding tolerance of soybean, flooding-tolerant mutants derived from gamma-ray irradiated soybean were crossed with parent cultivar Enrei for removal of other factors besides the genes related to flooding tolerance in primary generated mutant soybean. Although the growth of [...] Read more.
To investigate the mechanism of flooding tolerance of soybean, flooding-tolerant mutants derived from gamma-ray irradiated soybean were crossed with parent cultivar Enrei for removal of other factors besides the genes related to flooding tolerance in primary generated mutant soybean. Although the growth of the wild type was significantly suppressed by flooding compared with the non-flooding condition, that of the mutant lines was better than that of the wild type even if it was treated with flooding. A two-day-old mutant line was subjected to flooding for 2 days and proteins were analyzed using a gel-free/label-free proteomic technique. Oppositely changed proteins in abundance between the wild type and mutant line under flooding stress were associated in endoplasmic reticulum according to gene-ontology categorization. Immunoblot analysis confirmed that calnexin accumulation increased in both the wild type and mutant line; however, calreticulin accumulated in only the mutant line under flooding stress. Furthermore, although glycoproteins in the wild type decreased by flooding compared with the non-flooding condition, those in the mutant line increased even if it was under flooding stress. Alcohol dehydrogenase accumulated in the wild type and mutant line; however, this enzyme activity significantly increased and mildly increased in the wild type and mutant line, respectively, under flooding stress compared with the non-flooding condition. Cell death increased and decreased in the wild type and mutant line, respectively, by flooding stress. These results suggest that the regulation of cell death through the fermentation system and glycoprotein folding might be an important factor for the acquisition of flooding tolerance in mutant soybean. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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19 pages, 3319 KiB  
Article
DIA-Based Quantitative Proteomics Reveals the Protein Regulatory Networks of Floral Thermogenesis in Nelumbo nucifera
by Yueyang Sun, Yu Zou, Jing Jin, Hao Chen, Zhiying Liu, Qinru Zi, Zeyang Xiong, Ying Wang, Qian Li, Jing Peng and Yi Ding
Int. J. Mol. Sci. 2021, 22(15), 8251; https://doi.org/10.3390/ijms22158251 - 31 Jul 2021
Cited by 7 | Viewed by 2853
Abstract
The sacred lotus (Nelumbo nucifera) can maintain a stable floral chamber temperature between 30 and 35 °C when blooming despite fluctuations in ambient temperatures between about 8 and 45 °C, but the regulatory mechanism of floral thermogenesis remains unclear. Here, we [...] Read more.
The sacred lotus (Nelumbo nucifera) can maintain a stable floral chamber temperature between 30 and 35 °C when blooming despite fluctuations in ambient temperatures between about 8 and 45 °C, but the regulatory mechanism of floral thermogenesis remains unclear. Here, we obtained comprehensive protein profiles from receptacle tissue at five developmental stages using data-independent acquisition (DIA)-based quantitative proteomics technology to reveal the molecular basis of floral thermogenesis of N. nucifera. A total of 6913 proteins were identified and quantified, of which 3513 differentially abundant proteins (DAPs) were screened. Among them, 640 highly abundant proteins during the thermogenic stages were mainly involved in carbon metabolism processes such as the tricarboxylic acid (TCA) cycle. Citrate synthase was identified as the most connected protein in the protein-protein interaction (PPI) network. Next, the content of alternative oxidase (AOX) and plant uncoupling protein (pUCP) in different tissues indicated that AOX was specifically abundant in the receptacles. Subsequently, a protein module highly related to the thermogenic phenotype was identified by the weighted gene co-expression network analysis (WGCNA). In summary, the regulation mechanism of floral thermogenesis in N. nucifera involves complex regulatory networks, including TCA cycle metabolism, starch and sucrose metabolism, fatty acid degradation, and ubiquinone synthesis, etc. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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28 pages, 16159 KiB  
Article
Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins
by Orarat Ginsawaeng, Michal Gorka, Alexander Erban, Carolin Heise, Franziska Brueckner, Rainer Hoefgen, Joachim Kopka, Aleksandra Skirycz, Dirk K. Hincha and Ellen Zuther
Int. J. Mol. Sci. 2021, 22(15), 8172; https://doi.org/10.3390/ijms22158172 - 29 Jul 2021
Cited by 11 | Viewed by 3567
Abstract
During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the [...] Read more.
During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes in primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome, a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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17 pages, 7203 KiB  
Article
Proteomics of Homeobox7 Enhanced Salt Tolerance in Mesembryanthemum crystallinum
by Xuemei Zhang, Bowen Tan, Dan Zhu, Daniel Dufresne, Tingbo Jiang and Sixue Chen
Int. J. Mol. Sci. 2021, 22(12), 6390; https://doi.org/10.3390/ijms22126390 - 15 Jun 2021
Cited by 14 | Viewed by 2477
Abstract
Mesembryanthemum crystallinum (common ice plant) is a halophyte species that has adapted to extreme conditions. In this study, we cloned a McHB7 transcription factor gene from the ice plant. The expression of McHB7 was significantly induced by 500 mM NaCl and it reached [...] Read more.
Mesembryanthemum crystallinum (common ice plant) is a halophyte species that has adapted to extreme conditions. In this study, we cloned a McHB7 transcription factor gene from the ice plant. The expression of McHB7 was significantly induced by 500 mM NaCl and it reached the peak under salt treatment for 7 days. The McHB7 protein was targeted to the nucleus. McHB7-overexpressing in ice plant leaves through Agrobacterium-mediated transformation led to 25 times more McHB7 transcripts than the non-transformed wild type (WT). After 500 mM NaCl treatment for 7 days, the activities of superoxide dismutase (SOD) and peroxidase (POD) and water content of the transgenic plants were higher than the WT, while malondialdehyde (MDA) was decreased in the transgenic plants. A total of 1082 and 1072 proteins were profiled by proteomics under control and salt treatment, respectively, with 22 and 11 proteins uniquely identified under control and salt stress, respectively. Among the 11 proteins, 7 were increased and 4 were decreased after salt treatment. Most of the proteins whose expression increased in the McHB7 overexpression (OE) ice plants under high salinity were involved in transport regulation, catalytic activities, biosynthesis of secondary metabolites, and response to stimulus. The results demonstrate that the McHB7 transcription factor plays a positive role in improving plant salt tolerance. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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16 pages, 2469 KiB  
Article
Endoplasmic Reticulum Subproteome Analysis Reveals Underlying Defense Mechanisms of Wheat Seedling Leaves under Salt Stress
by Junwei Zhang, Dongmiao Liu, Dong Zhu, Nannan Liu and Yueming Yan
Int. J. Mol. Sci. 2021, 22(9), 4840; https://doi.org/10.3390/ijms22094840 - 3 May 2021
Cited by 15 | Viewed by 2975
Abstract
Salt stress is the second most important abiotic stress factor in the world, which seriously affects crop growth, development and grain production. In this study, we performed the first integrated physiological and endoplasmic reticulum (ER) proteome analysis of wheat seedling leaves under salt [...] Read more.
Salt stress is the second most important abiotic stress factor in the world, which seriously affects crop growth, development and grain production. In this study, we performed the first integrated physiological and endoplasmic reticulum (ER) proteome analysis of wheat seedling leaves under salt stress using a label-free-based quantitative proteomic approach. Salt stress caused significant decrease in seedling height, root length, relative water content and chlorophyll content of wheat seedling leaves, indicating that wheat seedling growth was significantly inhibited under salt stress. The ER proteome analysis identified 233 ER-localized differentially accumulated proteins (DAPs) in response to salt stress, including 202 upregulated and 31 downregulated proteins. The upregulated proteins were mainly involved in the oxidation-reduction process, transmembrane transport, the carboxylic acid metabolic process, stress response, the arbohydrate metabolic process and proteolysis, while the downregulated proteins mainly participated in the metabolic process, biological regulation and the cellular process. In particular, salt stress induced significant upregulation of protein disulfide isomerase-like proteins and heat shock proteins and significant downregulation of ribosomal protein abundance. Further transcript expression analysis revealed that half of the detected DAP genes showed a consistent pattern with their protein levels under salt stress. A putative metabolic pathway of ER subproteome of wheat seedling leaves in response to salt stress was proposed, which reveals the potential roles of wheat ER proteome in salt stress response and defense. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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28 pages, 8857 KiB  
Article
Quantitative Proteomics Reveals the Dynamic Regulation of the Tomato Proteome in Response to Phytophthora infestans
by Kai-Ting Fan, Yang Hsu, Ching-Fang Yeh, Chi-Hsin Chang, Wei-Hung Chang and Yet-Ran Chen
Int. J. Mol. Sci. 2021, 22(8), 4174; https://doi.org/10.3390/ijms22084174 - 17 Apr 2021
Cited by 8 | Viewed by 4241
Abstract
Late blight (LB) disease is a major threat to potato and tomato production. It is caused by the hemibiotrophic pathogen, Phytophthora infestans. P. infestans can destroy all of the major organs in plants of susceptible crops and result in a total loss [...] Read more.
Late blight (LB) disease is a major threat to potato and tomato production. It is caused by the hemibiotrophic pathogen, Phytophthora infestans. P. infestans can destroy all of the major organs in plants of susceptible crops and result in a total loss of productivity. At the early pathogenesis stage, this hemibiotrophic oomycete pathogen causes an asymptomatic biotrophic infection in hosts, which then progresses to a necrotrophic phase at the later infection stage. In this study, to examine how the tomato proteome is regulated by P. infestans at different stages of pathogenesis, a data-independent acquisition (DIA) proteomics approach was used to trace the dynamics of the protein regulation. A comprehensive picture of the regulation of tomato proteins functioning in the immunity, signaling, defense, and metabolism pathways at different stages of P. infestans infection is revealed. Among the regulated proteins, several involved in mediating plant defense responses were found to be differentially regulated at the transcriptional or translational levels across different pathogenesis phases. This study increases understanding of the pathogenesis of P. infestans in tomato and also identifies key transcriptional and translational events possibly targeted by the pathogen during different phases of its life cycle, thus providing novel insights for developing a new strategy towards better control of LB disease in tomato. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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17 pages, 2351 KiB  
Article
Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for Quercus ilex
by Bonoso San-Eufrasio, Ezequiel Darío Bigatton, Victor M. Guerrero-Sánchez, Palak Chaturvedi, Jesús V. Jorrín-Novo, María-Dolores Rey and María Ángeles Castillejo
Int. J. Mol. Sci. 2021, 22(6), 3191; https://doi.org/10.3390/ijms22063191 - 21 Mar 2021
Cited by 13 | Viewed by 3239
Abstract
Drought is one of the main causes of mortality in holm oak (Quercus ilex) seedlings used in reforestation programs. Although this species shows high adaptability to the extreme climate conditions prevailing in Southern Spain, its intrinsic genetic variability may play a [...] Read more.
Drought is one of the main causes of mortality in holm oak (Quercus ilex) seedlings used in reforestation programs. Although this species shows high adaptability to the extreme climate conditions prevailing in Southern Spain, its intrinsic genetic variability may play a role in the differential response of some populations and individuals. The aim of this work was to identify proteins and derived proteotypic peptides potentially useful as putative markers for drought tolerance in holm oak by using a targeted post-acquisition proteomics approach. For this purpose, we used a set of proteins identified by shotgun (LC-MSMS) analysis in a drought experiment on Q. ilex seedlings from four different provenances (viz. the Andalusian provinces Granada, Huelva, Cadiz and Seville). A double strategy involving the quantification of proteins and target peptides by shotgun analysis and post-acquisition data analysis based on proteotypic peptides was used. To this end, an initial list of proteotypic peptides from proteins highly represented under drought conditions was compiled that was used in combination with the raw files from the shotgun experiment to quantify the relative abundance of the fragment’s ion peaks with the software Skyline. The most abundant peptides under drought conditions in at least two populations were selected as putative markers of drought tolerance. A total of 30 proteins and 46 derived peptides belonging to the redox, stress-related, synthesis,-folding and degradation, and primary and secondary metabolism functional groups were thus identified. Two proteins (viz., subtilisin and chaperone GrpE protein) were found at increased levels in three populations, which make them especially interesting for validation drought tolerance markers in subsequent experiments. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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Review

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13 pages, 938 KiB  
Review
A Decade of Pollen Phosphoproteomics
by Božena Klodová and Jan Fíla
Int. J. Mol. Sci. 2021, 22(22), 12212; https://doi.org/10.3390/ijms222212212 - 11 Nov 2021
Cited by 4 | Viewed by 2217
Abstract
Angiosperm mature pollen represents a quiescent stage with a desiccated cytoplasm surrounded by a tough cell wall, which is resistant to the suboptimal environmental conditions and carries the genetic information in an intact stage to the female gametophyte. Post pollination, pollen grains are [...] Read more.
Angiosperm mature pollen represents a quiescent stage with a desiccated cytoplasm surrounded by a tough cell wall, which is resistant to the suboptimal environmental conditions and carries the genetic information in an intact stage to the female gametophyte. Post pollination, pollen grains are rehydrated, activated, and a rapid pollen tube growth starts, which is accompanied by a notable metabolic activity, synthesis of novel proteins, and a mutual communication with female reproductive tissues. Several angiosperm species (Arabidopsis thaliana, tobacco, maize, and kiwifruit) were subjected to phosphoproteomic studies of their male gametophyte developmental stages, mostly mature pollen grains. The aim of this review is to compare the available phosphoproteomic studies and to highlight the common phosphoproteins and regulatory trends in the studied species. Moreover, the pollen phosphoproteome was compared with root hair phosphoproteome to pinpoint the common proteins taking part in their tip growth, which share the same cellular mechanisms. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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25 pages, 7958 KiB  
Review
Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice
by Piengtawan Tappiban, Yining Ying, Feifei Xu and Jinsong Bao
Int. J. Mol. Sci. 2021, 22(11), 5901; https://doi.org/10.3390/ijms22115901 - 31 May 2021
Cited by 21 | Viewed by 3686
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world’s population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect [...] Read more.
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world’s population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6–20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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24 pages, 1333 KiB  
Review
Posttranslational Modification of Waxy to Genetically Improve Starch Quality in Rice Grain
by Tosin Victor Adegoke, Yifeng Wang, Lijuan Chen, Huimei Wang, Wanning Liu, Xingyong Liu, Yi-Chen Cheng, Xiaohong Tong, Jiezheng Ying and Jian Zhang
Int. J. Mol. Sci. 2021, 22(9), 4845; https://doi.org/10.3390/ijms22094845 - 3 May 2021
Cited by 14 | Viewed by 4898
Abstract
The waxy (Wx) gene, encoding the granule-bound starch synthase (GBSS), is responsible for amylose biosynthesis and plays a crucial role in defining eating and cooking quality. The waxy locus controls both the non-waxy and waxy rice phenotypes. Rice starch can be [...] Read more.
The waxy (Wx) gene, encoding the granule-bound starch synthase (GBSS), is responsible for amylose biosynthesis and plays a crucial role in defining eating and cooking quality. The waxy locus controls both the non-waxy and waxy rice phenotypes. Rice starch can be altered into various forms by either reducing or increasing the amylose content, depending on consumer preference and region. Low-amylose rice is preferred by consumers because of its softness and sticky appearance. A better way of improving crops other than downregulation and overexpression of a gene or genes may be achieved through the posttranslational modification of sites or regulatory enzymes that regulate them because of their significance. The impact of posttranslational GBSSI modifications on extra-long unit chains (ELCs) remains largely unknown. Numerous studies have been reported on different crops, such as wheat, maize, and barley, but the rice starch granule proteome remains largely unknown. There is a need to improve the yield of low-amylose rice by employing posttranslational modification of Wx, since the market demand is increasing every day in order to meet the market demand for low-amylose rice in the regional area that prefers low-amylose rice, particularly in China. In this review, we have conducted an in-depth review of waxy rice, starch properties, starch biosynthesis, and posttranslational modification of waxy protein to genetically improve starch quality in rice grains. Full article
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
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