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Plant Proteomic Research 5.0: From Data to Insights

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 2022) | Viewed by 20078

Special Issue Editors


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Guest Editor

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Guest Editor
1. CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD 4053, Australia
2. School of Science, Edith Cowan University, 270 Joondalup Rd, Joondalup, WA 6027, Australia
Interests: proteins; peptides; proteomics; allergy; food intolerance; alternative proteins; sustainable food production
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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

Plant Proteomic Research 3.0” (https://www.mdpi.com/journal/ijms/special_issues/plant-proteomic_3)

Plant Proteomic Research 4.0” (https://www.mdpi.com/journal/ijms/special_issues/plant-proteomic_4)

Proteomics offers one of the best approaches for the functional analysis of the genome, generating detailed information that can be integrated with that obtained by other classic and omics approaches. It thus provides deep knowledge and an understanding of the diverse proteoforms and different plant processes. Several different generations of proteomics platforms have appeared in the past twenty years. They have been exploited for describing protein profiles, post-translational modifications, protein turnover, protein complexes and interactions, subcellular proteomes, single cells and single-cell-type proteomes. Nevertheless, the ultimate success of any proteomic strategy lies in the various factors, including the isolation of all the components 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 cases with very low abundance, hydrophobicity, and a 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 functions. Authors are welcome to submit original research articles and reviews addressing the 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 a 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. Setsuko Komatsu
Prof. Dr. Michelle Colgrave
Guest Editors

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Keywords

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

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Published Papers (9 papers)

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Editorial

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3 pages, 192 KiB  
Editorial
Plant Proteomic Research 5.0: From Data to Insights
by Setsuko Komatsu and Michelle L. Colgrave
Int. J. Mol. Sci. 2023, 24(1), 258; https://doi.org/10.3390/ijms24010258 - 23 Dec 2022
Viewed by 965
Abstract
Proteomics offers one of the best approaches for the functional analysis of the genome, generating detailed information that can be integrated with that obtained by other classic and omics approaches [...] Full article
(This article belongs to the Special Issue Plant Proteomic Research 5.0: From Data to Insights)

Research

Jump to: Editorial

20 pages, 5220 KiB  
Article
Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome
by Markéta Luklová, Jan Novák, Romana Kopecká, Michaela Kameniarová, Vladěna Gibasová, Břetislav Brzobohatý and Martin Černý
Int. J. Mol. Sci. 2022, 23(22), 14134; https://doi.org/10.3390/ijms232214134 - 16 Nov 2022
Cited by 3 | Viewed by 1629
Abstract
Plants are sessile organisms forced to adapt to environmental variations recurring in a day–night cycle. Extensive research has uncovered the transcriptional control of plants’ inner clock and has revealed at least some part of the intricate and elaborate regulatory mechanisms that govern plant [...] Read more.
Plants are sessile organisms forced to adapt to environmental variations recurring in a day–night cycle. Extensive research has uncovered the transcriptional control of plants’ inner clock and has revealed at least some part of the intricate and elaborate regulatory mechanisms that govern plant diel responses and provide adaptation to the ever-changing environment. Here, we analyzed the proteome of the Arabidopsis thaliana mutant genotypes collected in the middle of the day and the middle of the night, including four mutants in the phytochrome (phyA, phyB, phyC, and phyD) and the circadian clock protein LHY. Our approach provided a novel insight into the diel regulations, identifying 640 significant changes in the night–day protein abundance. The comparison with previous studies confirmed that a large portion of identified proteins was a known target of diurnal regulation. However, more than 300 were novel oscillations hidden under standard growth chamber conditions or not manifested in the wild type. Our results indicated a prominent role for ROS metabolism and phytohormone cytokinin in the observed regulations, and the consecutive analyses confirmed that. The cytokinin signaling significantly increased at night, and in the mutants, the hydrogen peroxide content was lower, and the night–day variation seemed to be lost in the phyD genotype. Furthermore, regulations in the lhy and phyB mutants were partially similar to those found in the catalase mutant cat2, indicating shared ROS-mediated signaling pathways. Our data also shed light on the role of the relatively poorly characterized Phytochrome D, pointing to its connection to glutathione metabolism and the regulation of glutathione S-transferases. Full article
(This article belongs to the Special Issue Plant Proteomic Research 5.0: From Data to Insights)
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17 pages, 2469 KiB  
Article
Proteomic and Biochemical Approaches Elucidate the Role of Millimeter-Wave Irradiation in Wheat Growth under Flooding Stress
by Setsuko Komatsu, Yoshie Tsutsui, Takashi Furuya, Hisateru Yamaguchi, Keisuke Hitachi, Kunihiro Tsuchida and Masahiko Tani
Int. J. Mol. Sci. 2022, 23(18), 10360; https://doi.org/10.3390/ijms231810360 - 08 Sep 2022
Cited by 3 | Viewed by 1363
Abstract
Flooding impairs wheat growth and considerably affects yield productivity worldwide. On the other hand, irradiation with millimeter waves enhanced the growth of chickpea and soybean under flooding stress. In the current work, millimeter-wave irradiation notably enhanced wheat growth, even under flooding stress. To [...] Read more.
Flooding impairs wheat growth and considerably affects yield productivity worldwide. On the other hand, irradiation with millimeter waves enhanced the growth of chickpea and soybean under flooding stress. In the current work, millimeter-wave irradiation notably enhanced wheat growth, even under flooding stress. To explore the protective mechanisms of millimeter-wave irradiation on wheat under flooding, quantitative proteomics was performed. According to functional categorization, proteins whose abundances were changed significantly with and without irradiation under flooding stress were correlated to glycolysis, reactive-oxygen species scavenging, cell organization, and hormonal metabolism. Immunoblot analysis confirmed that fructose-bisphosphate aldolase and β tubulin accumulated in root and leaf under flooding; however, even in such condition, their accumulations were recovered to the control level in irradiated wheat. The abundance of ascorbate peroxidase increased in leaf under flooding and recovered to the control level in irradiated wheat. Because the abundance of auxin-related proteins changed with millimeter-wave irradiation, auxin was applied to wheat under flooding, resulting in the application of auxin improving its growth, even in such condition. These results suggest that millimeter-wave irradiation on wheat seeds improves the recovery of plant growth from flooding via the regulation of glycolysis, reactive-oxygen species scavenging, and cell organization. Additionally, millimeter-wave irradiation could promote tolerance against flooding through the regulation of auxin contents in wheat. Full article
(This article belongs to the Special Issue Plant Proteomic Research 5.0: From Data to Insights)
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19 pages, 2518 KiB  
Article
Cottonseed Meal Protein Isolate as a New Source of Alternative Proteins: A Proteomics Perspective
by Chee Fan Tan, Soon Hong Kwan, Chun Shing Lee, Yan Ni Annie Soh, Ying Swan Ho and Xuezhi Bi
Int. J. Mol. Sci. 2022, 23(17), 10105; https://doi.org/10.3390/ijms231710105 - 03 Sep 2022
Cited by 7 | Viewed by 3103
Abstract
Cottonseed meal (CSM) is a good source of dietary proteins but is unsuitable for human consumption due to its gossypol content. To unlock its potential, we developed a protein extraction process with a gossypol removal treatment to generate CSM protein isolate (CSMPI) with [...] Read more.
Cottonseed meal (CSM) is a good source of dietary proteins but is unsuitable for human consumption due to its gossypol content. To unlock its potential, we developed a protein extraction process with a gossypol removal treatment to generate CSM protein isolate (CSMPI) with ultra-low gossypol content. This process successfully reduced the free and total gossypol content to 4.8 ppm and 147.2 ppm, respectively, far below the US FDA limit. In addition, the functional characterisation of CSMPI revealed a better oil absorption capacity and water solubility than pea protein isolate. Proteome profiling showed that the treatment improved protein identification, while SDS-PAGE analysis indicated that the treatment did not induce protein degradation. Amino acid analysis revealed that post-treated CSMPI was rich in branched-chain amino acids (BCAAs). Mass spectrometry analysis of various protein fractions obtained from an in vitro digestibility assay helped to establish the digestibility profile of CSM proteins. Several potential allergens in CSMPI were also found using allergenic prediction software, but further evaluation based on their digestibility profiles and literature reviews suggests that the likelihood of CSMPI allergenicity remains low. Overall, our results help to navigate and direct the application of CSMPIs as alternative proteins toward nutritive human food application. Full article
(This article belongs to the Special Issue Plant Proteomic Research 5.0: From Data to Insights)
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15 pages, 2718 KiB  
Article
Overexpression of McHB7 Transcription Factor from Mesembryanthemum crystallinum Improves Plant Salt Tolerance
by Xuemei Zhang, Bowen Tan, Zihan Cheng, Dan Zhu, Tingbo Jiang and Sixue Chen
Int. J. Mol. Sci. 2022, 23(14), 7879; https://doi.org/10.3390/ijms23147879 - 17 Jul 2022
Cited by 5 | Viewed by 1725
Abstract
Mesembryanthemum crystallinum (common ice plant) is one of the facultative halophyte plants, and it serves as a model for investigating the molecular mechanisms underlying its salt stress response and tolerance. Here we cloned one of the homeobox transcription factor (TF) genes, McHB7, [...] Read more.
Mesembryanthemum crystallinum (common ice plant) is one of the facultative halophyte plants, and it serves as a model for investigating the molecular mechanisms underlying its salt stress response and tolerance. Here we cloned one of the homeobox transcription factor (TF) genes, McHB7, from the ice plant, which has 60% similarity with the Arabidopsis AtHB7. Overexpression of the McHB7 in Arabidopsis (OE) showed that the plants had significantly elevated relative water content (RWC), chlorophyll content, superoxide dismutase (SOD), and peroxidase (POD) activities after salt stress treatment. Our proteomic analysis identified 145 proteins to be significantly changed in abundance, and 66 were exclusively increased in the OE plants compared to the wild type (WT). After salt treatment, 979 and 959 metabolites were significantly increased and decreased, respectively, in the OE plants compared to the WT. The results demonstrate that the McHB7 can improve photosynthesis, increase the leaf chlorophyll content, and affect the TCA cycle by regulating metabolites (e.g., pyruvate) and proteins (e.g., citrate synthase). Moreover, McHB7 modulates the expression of stress-related proteins (e.g., superoxide dismutase, dehydroascorbate reductase, and pyrroline-5-carboxylate synthase B) to scavenge reactive oxygen species and enhance plant salt tolerance. Full article
(This article belongs to the Special Issue Plant Proteomic Research 5.0: From Data to Insights)
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18 pages, 22396 KiB  
Article
Integrative Proteome and Phosphoproteome Profiling of Early Cold Response in Maize Seedlings
by Jiayun Xing, Jinjuan Tan, Hanqian Feng, Zhongjing Zhou, Min Deng, Hongbing Luo and Zhiping Deng
Int. J. Mol. Sci. 2022, 23(12), 6493; https://doi.org/10.3390/ijms23126493 - 10 Jun 2022
Cited by 7 | Viewed by 1923
Abstract
Cold limits the growth and yield of maize in temperate regions, but the molecular mechanism of cold adaptation remains largely unexplored in maize. To identify early molecular events during cold shock, maize seedlings were treated under 4 °C for 30 min and 2 [...] Read more.
Cold limits the growth and yield of maize in temperate regions, but the molecular mechanism of cold adaptation remains largely unexplored in maize. To identify early molecular events during cold shock, maize seedlings were treated under 4 °C for 30 min and 2 h, and analyzed at both the proteome and phosphoproteome levels. Over 8500 proteins and 19,300 phosphopeptides were quantified. About 660 and 620 proteins were cold responsive at protein abundance or site-specific phosphorylation levels, but only 65 proteins were shared between them. Functional enrichment analysis of cold-responsive proteins and phosphoproteins revealed that early cold response in maize is associated with photosynthesis light reaction, spliceosome, endocytosis, and defense response, consistent with similar studies in Arabidopsis. Thirty-two photosynthesis proteins were down-regulated at protein levels, and 48 spliceosome proteins were altered at site-specific phosphorylation levels. Thirty-one kinases and 33 transcriptional factors were cold responsive at protein, phosphopeptide, or site-specific phosphorylation levels. Our results showed that maize seedlings respond to cold shock rapidly, at both the proteome and phosphoproteome levels. This study provides a comprehensive landscape at the cold-responsive proteome and phosphoproteome in maize seedlings that can be a significant resource to understand how C4 plants respond to a sudden temperature drop. Full article
(This article belongs to the Special Issue Plant Proteomic Research 5.0: From Data to Insights)
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21 pages, 15215 KiB  
Article
Effects of Fe and Mn Deficiencies on the Root Protein Profiles of Tomato (Solanum lycopersicum) Using Two-Dimensional Electrophoresis and Label-Free Shotgun Analyses
by Laura Ceballos-Laita, Daisuke Takahashi, Matsuo Uemura, Javier Abadía, Ana Flor López-Millán and Jorge Rodríguez-Celma
Int. J. Mol. Sci. 2022, 23(7), 3719; https://doi.org/10.3390/ijms23073719 - 28 Mar 2022
Cited by 5 | Viewed by 2177
Abstract
Iron (Fe) and manganese (Mn) are two essential elements for plants that compete for the same uptake transporters and show conflicting interactions at the regulatory level. In order to understand the differential response to both metal deficiencies in plants, two proteomic techniques (two-dimensional [...] Read more.
Iron (Fe) and manganese (Mn) are two essential elements for plants that compete for the same uptake transporters and show conflicting interactions at the regulatory level. In order to understand the differential response to both metal deficiencies in plants, two proteomic techniques (two-dimensional gel electrophoresis and label-free shotgun) were used to study the proteome profiles of roots from tomato plants grown under Fe or Mn deficiency. A total of 119 proteins changing in relative abundance were confidently quantified and identified, including 35 and 91 in the cases of Fe deficiency and Mn deficiency, respectively, with 7 of them changing in both deficiencies. The identified proteins were categorized according to function, and GO-enrichment analysis was performed. Data showed that both deficiencies provoked a common and intense cell wall remodelling. However, the response observed for Fe and Mn deficiencies differed greatly in relation to oxidative stress, coumarin production, protein, nitrogen, and energy metabolism. Full article
(This article belongs to the Special Issue Plant Proteomic Research 5.0: From Data to Insights)
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18 pages, 3030 KiB  
Article
iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism of Golden-Yellow Leaf Mutant in Hybrid Paper Mulberry
by Fenfen Wang, Naizhi Chen and Shihua Shen
Int. J. Mol. Sci. 2022, 23(1), 127; https://doi.org/10.3390/ijms23010127 - 23 Dec 2021
Cited by 7 | Viewed by 2642
Abstract
Plant growth and development relies on the conversion of light energy into chemical energy, which takes place in the leaves. Chlorophyll mutant variations are important for studying certain physiological processes, including chlorophyll metabolism, chloroplast biogenesis, and photosynthesis. To uncover the mechanisms of the [...] Read more.
Plant growth and development relies on the conversion of light energy into chemical energy, which takes place in the leaves. Chlorophyll mutant variations are important for studying certain physiological processes, including chlorophyll metabolism, chloroplast biogenesis, and photosynthesis. To uncover the mechanisms of the golden-yellow phenotype of the hybrid paper mulberry plant, this study used physiological, cytological, and iTRAQ-based proteomic analyses to compare the green and golden-yellow leaves of hybrid paper mulberry. Physiological results showed that the mutants of hybrid paper mulberry showed golden-yellow leaves, reduced chlorophyll, and carotenoid content, and increased flavonoid content compared with wild-type plants. Cytological observations revealed defective chloroplasts in the mesophyll cells of the mutants. Results demonstrated that 4766 proteins were identified from the hybrid paper mulberry leaves, of which 168 proteins displayed differential accumulations between the green and mutant leaves. The differentially accumulated proteins were primarily involved in chlorophyll synthesis, carotenoid metabolism, and photosynthesis. In addition, differentially accumulated proteins are associated with ribosome pathways and could enable plants to adapt to environmental conditions by regulating the proteome to reduce the impact of chlorophyll reduction on growth and survival. Altogether, this study provides a better understanding of the formation mechanism of the golden-yellow leaf phenotype by combining proteomic approaches. Full article
(This article belongs to the Special Issue Plant Proteomic Research 5.0: From Data to Insights)
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30 pages, 8226 KiB  
Article
Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in Arabidopsis Seedlings upon Cold Exposure
by Jinjuan Tan, Zhongjing Zhou, Hanqian Feng, Jiayun Xing, Yujie Niu and Zhiping Deng
Int. J. Mol. Sci. 2021, 22(23), 12856; https://doi.org/10.3390/ijms222312856 - 27 Nov 2021
Cited by 10 | Viewed by 3144
Abstract
Protein phosphorylation plays an important role in mediating signal transduction in cold response in plants. To better understand how plants sense and respond to the early temperature drop, we performed data-independent acquisition (DIA) method-based mass spectrometry analysis to profile the proteome and phosphoproteome [...] Read more.
Protein phosphorylation plays an important role in mediating signal transduction in cold response in plants. To better understand how plants sense and respond to the early temperature drop, we performed data-independent acquisition (DIA) method-based mass spectrometry analysis to profile the proteome and phosphoproteome of Arabidopsis seedlings upon cold stress in a time-course manner (10, 30 and 120 min of cold treatments). Our results showed the rapid and extensive changes at the phosphopeptide levels, but not at the protein abundance levels, indicating cold-mediated protein phosphorylation and dephosphorylation events. Alteration of over 1200 proteins at phosphopeptide levels were observed within 2 h of cold treatment, including over 140 kinases, over 40 transcriptional factors and over 40 E3 ligases, revealing the complexity of regulation of cold adaption. We summarized cold responsive phosphoproteins involved in phospholipid signaling, cytoskeleton reorganization, calcium signaling, and MAPK cascades. Cold-altered levels of 73 phosphopeptides (mostly novel cold-responsive) representing 62 proteins were validated by parallel reaction monitoring (PRM). In summary, this study furthers our understanding of the molecular mechanisms of cold adaption in plants and strongly supports that DIA coupled with PRM are valuable tools in uncovering early signaling events in plants. Full article
(This article belongs to the Special Issue Plant Proteomic Research 5.0: From Data to Insights)
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