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Special Issue "Plant Proteomic Research 3.0"

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: 30 September 2020.

Special Issue Editors

Prof. Dr. Jesus V. Jorrin-Novo
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Guest Editor
Agroforestry and Plant biochemistry, Proteomics, and Systems Biology. Dpt. Of Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain

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) and “Plant Proteomic Research 2.0” (https://www.mdpi.com/journal/ijms/special_issues/plant-proteomic_2)

Advancement in high-throughput “Omics” techniques has revolutionized plant molecular biology research. Proteomics offer one of the best options for the functional analysis of the genome, generating detailed information that integrated with that obtained by other classic and -omics approaches will provided a deeper knowledge of the different plant processes Up to six different generations of proteomics platforms (gel, label, gel free/label free, targeted) have appeared in the last twenty years which are being exploited in describing protein profiles, PTMs and interactions. 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 identification. Despite recent advancements, more emphasis needs to be given to the protein extraction protocols, especially for very low-abundant, hydrophobic, and large molecular weight. Thus, 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 and to follow temporal changes in protein relative abundances under different environmental conditions. Furthermore, post-translational modifications and protein-protein interactions provide deeper 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 get new insights of 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 a more confident identification, quantitation, data analysis and networking, especially with non-model, orphan, plants, including medicinal, and meditational plants as well as forest tree species.

Prof. Dr. Setsuko Komatsu
Prof. Dr. Jesus V. Jorrin-Novo
Guest Editors

Manuscript Submission Information

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Keywords

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

Published Papers (4 papers)

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Research

Open AccessArticle
Label-Free Comparative Proteomic Analysis Combined with Laser-Capture Microdissection Suggests Important Roles of Stress Responses in the Black Layer of Maize Kernels
Int. J. Mol. Sci. 2020, 21(4), 1369; https://doi.org/10.3390/ijms21041369 (registering DOI) - 18 Feb 2020
Abstract
The black layer (BL) is traditionally used as an indicator for kernel harvesting in maize, as it turns visibly dark when the kernel reaches physiological maturity. However, the molecular roles of BL in kernel development have not been fully elucidated. In this work, [...] Read more.
The black layer (BL) is traditionally used as an indicator for kernel harvesting in maize, as it turns visibly dark when the kernel reaches physiological maturity. However, the molecular roles of BL in kernel development have not been fully elucidated. In this work, microscopy images showed that BL began to appear at a growth stage earlier than 10 days after pollination (DAP), and its color gradually deepened to become dark as the development period progressed. Scanning electron microscopy observations revealed that BL is a tissue structure composed of several layers of cells that are gradually squeezed and compressed during kernel development. Laser-capture microdissection (LCM) was used to sample BL and its neighboring inner tissue, basal endosperm transfer layer (BETL), and outer tissue, inner epidermis (IEP), from 20 DAP of kernels. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling (MALDI-TOF MS profiling) detected 41, 104, and 120 proteins from LCM-sampled BL, BETL, and IEP, respectively. Gene ontology (GO) analysis indicated that the 41 BL proteins were primarily involved in the response to stress and stimuli. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that the BL proteins were enriched in several defense pathways, such as the ascorbate and aldarate metabolic pathways. Among the 41 BL proteins, six were BL-specific proteins that were only detected from BL. Annotations of five BL-specific proteins were related to stress responses. During kernel development, transcriptional expression of most BL proteins showed an increase, followed by a decrease, and reached a maximum zero to 20 DAP. These results suggest a role for BL in stress responses for protecting filial tissue against threats from maternal sides, which helps to elucidate the biological functions of BL. Full article
(This article belongs to the Special Issue Plant Proteomic Research 3.0)
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Open AccessArticle
Comparative Analysis of the Effect of Inorganic and Organic Chemicals with Silver Nanoparticles on Soybean under Flooding Stress
Int. J. Mol. Sci. 2020, 21(4), 1300; https://doi.org/10.3390/ijms21041300 (registering DOI) - 14 Feb 2020
Abstract
Extensive utilization of silver nanoparticles (NPs) in agricultural products results in their interaction with other chemicals in the environment. To study the combined effects of silver NPs with nicotinic acid and potassium nitrate (KNO3), a gel-free/label-free proteomic technique was used. Root [...] Read more.
Extensive utilization of silver nanoparticles (NPs) in agricultural products results in their interaction with other chemicals in the environment. To study the combined effects of silver NPs with nicotinic acid and potassium nitrate (KNO3), a gel-free/label-free proteomic technique was used. Root length/weight and hypocotyl length/weight of soybean were enhanced by silver NPs mixed with nicotinic acid and KNO3. Out of a total 6340 identified proteins, 351 proteins were significantly changed, out of which 247 and 104 proteins increased and decreased, respectively. Differentially changed proteins were predominantly associated with protein degradation and synthesis according to the functional categorization. Protein-degradation-related proteins mainly consisted of the proteasome degradation pathway. The cell death was significantly higher in the root tips of soybean under the combined treatment compared to flooding stress. Accumulation of calnexin/calreticulin and glycoproteins was significantly increased under flooding with silver NPs, nicotinic acid, and KNO3. Growth of soybean seedlings with silver NPs, nicotinic acid, and KNO3 was improved under flooding stress. These results suggest that the combined mixture of silver NPs, nicotinic acid, and KNO3 causes positive effects on soybean seedling by regulating the protein quality control for the mis-folded proteins in the endoplasmic reticulum. Therefore, it might improve the growth of soybean under flooding stress. Full article
(This article belongs to the Special Issue Plant Proteomic Research 3.0)
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Open AccessArticle
Comparative Proteomics Profiling Illuminates the Fruitlet Abscission Mechanism of Sweet Cherry as Induced by Embryo Abortion
Int. J. Mol. Sci. 2020, 21(4), 1200; https://doi.org/10.3390/ijms21041200 - 11 Feb 2020
Abstract
Sweet cherry (Prunus avium L.) is a delicious nutrient-rich fruit widely cultivated in countries such as China, America, Chile, and Italy. However, the yield often drops severely due to the frequently-abnormal fruitlet abscission, and few studies on the metabolism during its ripening [...] Read more.
Sweet cherry (Prunus avium L.) is a delicious nutrient-rich fruit widely cultivated in countries such as China, America, Chile, and Italy. However, the yield often drops severely due to the frequently-abnormal fruitlet abscission, and few studies on the metabolism during its ripening process at the proteomic level have been executed so far. To get a better understanding regarding the sweet cherry abscission mechanism, proteomic analysis between the abscising carpopodium and non-abscising carpopodium of sweet cherry was accomplished using a newly developed Liquid chromatography-mass spectrometry/mass spectrometry with Tandem Mass Tag (TMT-LC-MS/MS) methodology. The embryo viability experiments showed that the vigor of the abscission embryos was significantly lower than that of retention embryo. The activity of cell wall degrading enzymes in abscising carpopodium was significantly higher than that in non-abscising carpopodium. The anatomy results suggested that cells in the abscission zone were small and separated. In total, 6280 proteins were identified, among which 5681 were quantified. It has been observed that differentially accumulated proteins (DAPs) influenced several biological functions and various subcellular localizations. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that plenty of metabolic pathways were notably enriched, particularly those involved in phytohormone biosynthesis, cell wall metabolism, and cytoskeletal metabolism, including 1-aminocyclopropane-1-carboxylate oxidase proteins which promote ethylene synthesis, and proteins promoting cell wall degradation, such as endoglucanases, pectinase, and polygalacturonase. Differential expression of proteins concerning phytohormone biosynthesis might activate the shedding regulation signals. Up-regulation of several cell wall degradation-related proteins possibly regulated the shedding of plant organs. Variations of the phytohormone biosynthesis and cell wall degradation-related proteins were explored during the abscission process. Furthermore, changes in cytoskeleton-associated proteins might contribute to the abscission of carpopodium. The current work represented the first study using comparative proteomics between abscising carpopodium and non-abscising carpopodium. These results indicated that embryo abortion might lead to phytohormone synthesis disorder, which effected signal transduction pathways, and hereby controlled genes involved in cell wall degradation and then caused the abscission of fruitlet. Overall, our data may give an intrinsic explanation of the variations in metabolism during the abscission of carpopodium. Full article
(This article belongs to the Special Issue Plant Proteomic Research 3.0)
Open AccessArticle
Integrative Transcriptomic and Proteomic Analyses of Molecular Mechanism Responding to Salt Stress during Seed Germination in Hulless Barley
Int. J. Mol. Sci. 2020, 21(1), 359; https://doi.org/10.3390/ijms21010359 - 06 Jan 2020
Abstract
Hulless barley (Hordeum vulgare L. var. nudum) is one of the most important crops in the Qinghai-Tibet Plateau. Soil salinity seriously affects its cultivation. To investigate the mechanism of salt stress response during seed germination, two contrasting hulless barley genotypes were [...] Read more.
Hulless barley (Hordeum vulgare L. var. nudum) is one of the most important crops in the Qinghai-Tibet Plateau. Soil salinity seriously affects its cultivation. To investigate the mechanism of salt stress response during seed germination, two contrasting hulless barley genotypes were selected to first investigate the molecular mechanism of seed salinity response during the germination stage using RNA-sequencing and isobaric tags for relative and absolute quantitation technologies. Compared to the salt-sensitive landrace lk621, the salt-tolerant one lk573 germinated normally under salt stress. The changes in hormone contents also differed between lk621 and lk573. In lk573, 1597 differentially expressed genes (DEGs) and 171 differentially expressed proteins (DEPs) were specifically detected at 4 h after salt stress, and correspondingly, 2748 and 328 specifically detected at 16 h. Most specific DEGs in lk573 were involved in response to oxidative stress, biosynthetic process, protein localization, and vesicle-mediated transport, and most specific DEPs were assigned to an oxidation-reduction process, carbohydrate metabolic process, and protein phosphorylation. There were 96 genes specifically differentially expressed at both transcriptomic and proteomic levels in lk573. These results revealed the molecular mechanism of salt tolerance and provided candidate genes for further study and salt-tolerant improvement in hulless barley. Full article
(This article belongs to the Special Issue Plant Proteomic Research 3.0)
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