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Life
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Plant Proteomics
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Plant Proteomics

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 27475

Special Issue Editors

Dr. Claudius Marondedze

E-Mail Website
Guest Editor
1. Rijk Zwaan, De Lier 2678 ZG, Netherlands
2. Department of Biochemistry, Midlands State University, P Bag 9055 Gweru, Zimbabwe
Interests: plant biology; seed and flower development; abiotic stress; RNA-binding proteins; developmental genetics; molecular biology; proteomics; post-translational modifications; post-transcriptional gene regulation
Dr. Marco Chiapello

E-Mail Website1 Website2
Guest Editor
Institute for Sustainable Plant Protection, National Research Council, Strada delle cacce 73, Turin, Italy
Dr. Nino Nikolovski

E-Mail
Guest Editor
ETH Zurich, Zurich, Switzland

Special Issue Information

Dear Colleagues,

Globally, proteomics has become an important tool to understand diverse physiological and biochemical processes essential in gene regulation from the genesis of genes to biosynthesis of metabolites. In simple terms, the transcriptional, post-transcriptional, translational, and post-translational regulation of gene expression contributes to proteome dynamics at a given time and space. As in other biological systems, plants proteomics has unveiled interesting insights into the mechanisms associated with growth, development, and responses to extreme environmental cues, with more possible insights through targeted proteomics approaches that have enabled the discovery of the diversity of protein functions at organ, tissue or cell level, as well as their role in RNA processing and modification. The field of proteomics has been growing rapidly for the past two decades thanks to advances in technology, including mass spectrometry and the availability of various fully sequenced and well-annotated genomes. In addition to classical quantitative proteomics, it is now possible to characterize post-translational modifications via enrichment techniques combined with tandem mass spectrometry and protein–protein interactions via, for example, chemical crosslinking mass spectrometry. Nonetheless, comprehensive subcellular targeted proteomics and multi-protein–protein interaction complexes studies are still lagging behind. Such analyses would provide insights into organelle communications and networks, which are important to understand cellular signaling events during development and stress responses.

This Special issue of Plant Proteomics welcomes submissions of original research, review or perspective articles addressing current technical advances in plant proteomic methodologies aimed at dissecting plant physiological processes, protein dynamics during development, during abiotic and biotic stresses and post-transcriptional regulation. Contributions highlighting applications of proteomics in plant research and outlining challenges for future applications are also welcome.

Dr. Claudius Marondedze
Dr. Marco Chiapello
Dr. Nino Nikolovski
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • organelle proteomics
  • plant–environment interactions
  • plant proteomics
  • post-transcriptional gene regulation
  • post-translational modification
  • quantitative proteomics
  • systems analysis

Published Papers (10 papers)

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Research

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24 pages, 3783 KiB  
Article
A Label-Free Proteomic and Complementary Metabolomic Analysis of Leaves of the Resurrection Plant Xerophyta schlechteri during Dehydration
by Hawwa Gabier, David L. Tabb, Jill M. Farrant and Mohamed Suhail Rafudeen
Life 2021, 11(11), 1242; https://doi.org/10.3390/life11111242 - 16 Nov 2021
Cited by 2 | Viewed by 1902
Abstract
Vegetative desiccation tolerance, or the ability to survive the loss of ~95% relative water content (RWC), is rare in angiosperms, with these being commonly called resurrection plants. It is a complex multigenic and multi-factorial trait, with its understanding requiring a comprehensive systems biology [...] Read more.
Vegetative desiccation tolerance, or the ability to survive the loss of ~95% relative water content (RWC), is rare in angiosperms, with these being commonly called resurrection plants. It is a complex multigenic and multi-factorial trait, with its understanding requiring a comprehensive systems biology approach. The aim of the current study was to conduct a label-free proteomic analysis of leaves of the resurrection plant Xerophyta schlechteri in response to desiccation. A targeted metabolomics approach was validated and correlated to the proteomics, contributing the missing link in studies on this species. Three physiological stages were identified: an early response to drying, during which the leaf tissues declined from full turgor to a RWC of ~80–70%, a mid-response in which the RWC declined to 40% and a late response where the tissues declined to 10% RWC. We identified 517 distinct proteins that were differentially expressed, of which 253 proteins were upregulated and 264 were downregulated in response to the three drying stages. Metabolomics analyses, which included monitoring the levels of a selection of phytohormones, amino acids, sugars, sugar alcohols, fatty acids and organic acids in response to dehydration, correlated with some of the proteomic differences, giving insight into the biological processes apparently involved in desiccation tolerance in this species. Full article
(This article belongs to the Special Issue Plant Proteomics)
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13 pages, 2258 KiB  
Article
Narrow Precursor Mass Range for DIA–MS Enhances Protein Identification and Quantification in Arabidopsis
by Huoming Zhang and Dalila Bensaddek
Life 2021, 11(9), 982; https://doi.org/10.3390/life11090982 - 18 Sep 2021
Cited by 8 | Viewed by 2835
Abstract
Data independent acquisition–mass spectrometry (DIA–MS) is becoming widely utilised for robust and accurate quantification of samples in quantitative proteomics. Here, we describe the systematic evaluation of the effects of DIA precursor mass range on total protein identification and quantification. We show that a [...] Read more.
Data independent acquisition–mass spectrometry (DIA–MS) is becoming widely utilised for robust and accurate quantification of samples in quantitative proteomics. Here, we describe the systematic evaluation of the effects of DIA precursor mass range on total protein identification and quantification. We show that a narrow mass range of precursors (~250 m/z) for DIA–MS enables a higher number of protein identifications. Subsequent application of DIA with narrow precursor range (from 400 to 650 m/z) on an Arabidopsis sample with spike-in known proteins identified 34.7% more proteins than in conventional DIA (cDIA) with a wide precursor range of 400–1200 m/z. When combining several DIA–MS analyses with narrow precursor ranges (i.e., 400–650, 650–900 and 900–1200 m/z), we were able to quantify 10,099 protein groups with a median coefficient of variation of <6%. These findings represent a 54.7% increase in the number of proteins quantified than with cDIA analysis. This is particularly important for low abundance proteins, as exemplified by the six-protein mix spike-in. In cDIA only five out of the six-protein mix were quantified while our approach allowed accurate quantitation of all six proteins. Full article
(This article belongs to the Special Issue Plant Proteomics)
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17 pages, 12350 KiB  
Article
Color-Specific Recovery to Extreme High-Light Stress in Plants
by Débora Parrine, Todd M. Greco, Bilal Muhammad, Bo-Sen Wu, Xin Zhao and Mark Lefsrud
Life 2021, 11(8), 812; https://doi.org/10.3390/life11080812 - 10 Aug 2021
Cited by 3 | Viewed by 2218
Abstract
Plants pigments, such as chlorophyll and carotenoids, absorb light within specific wavelength ranges, impacting their response to environmental light changes. Although the color-specific response of plants to natural levels of light is well described, extreme high-light stress is still being discussed as a [...] Read more.
Plants pigments, such as chlorophyll and carotenoids, absorb light within specific wavelength ranges, impacting their response to environmental light changes. Although the color-specific response of plants to natural levels of light is well described, extreme high-light stress is still being discussed as a general response, without considering the impact of wavelengths in particular response processes. In this study, we explored how the plant proteome coordinated the response and recovery to extreme light conditions (21,000 µmol m−2 s−1) under different wavelengths. Changes at the protein and mRNA levels were measured, together with the photosynthetic parameters of plants under extreme high-light conditions. The changes in abundance of four proteins involved in photoinhibition, and in the biosynthesis/assembly of PSII (PsbS, PsbH, PsbR, and Psb28) in both light treatments were measured. The blue-light treatment presented a three-fold higher non-photochemical quenching and did not change the level of the oxygen-evolving complex (OEC) or the photosystem II (PSII) complex components when compared to the control, but significantly increased psbS transcripts. The red-light treatment caused a higher abundance of PSII and OEC proteins but kept the level of psbS transcripts the same as the control. Interestingly, the blue light stimulated a more efficient energy dissipation mechanism when compared to the red light. In addition, extreme high-light stress mechanisms activated by blue light involve the role of OEC through increasing PsbS transcript levels. In the proteomics spatial analysis, we report disparate activation of multiple stress pathways under three differently damaged zones as the enriched function of light stress only found in the medium-damaged zone of the red LED treatment. The results indicate that the impact of extreme high-light stress on the proteomic level is wavelength-dependent. Full article
(This article belongs to the Special Issue Plant Proteomics)
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15 pages, 1516 KiB  
Communication
Proteomic Insight into the Symbiotic Relationship of Pinus massoniana Lamb and Suillus luteus towards Developing Al-Stress Resistance
by Haiyan Liu, Houying Chen, Guijie Ding, Kuaifen Li and Yao Wang
Life 2021, 11(2), 177; https://doi.org/10.3390/life11020177 - 23 Feb 2021
Cited by 5 | Viewed by 2175
Abstract
Global warming significantly impacts forest range areas by increasing soil acidification or aluminum toxicity. Aluminum (Al) toxicity retards plant growth by inhibiting the root development process, hindering water uptake, and limiting the bioavailability of other essential micronutrients. Pinus massoniana (masson pine), globally recognized [...] Read more.
Global warming significantly impacts forest range areas by increasing soil acidification or aluminum toxicity. Aluminum (Al) toxicity retards plant growth by inhibiting the root development process, hindering water uptake, and limiting the bioavailability of other essential micronutrients. Pinus massoniana (masson pine), globally recognized as a reforestation plant, is resistant to stress conditions including biotic and abiotic stresses. This resistance is linked to the symbiotic relationship with diverse ectomycorrhizal fungal species. In the present study, we investigated the genetic regulators as expressed proteins, conferring a symbiotic relationship between Al-stress resistance and Suillus luteus in masson pine. Multi-treatment trials resulted in the identification of 12 core Al-stress responsive proteins conserved between Al stress conditions with or without S. luteus inoculation. These proteins are involved in chaperonin CPN60-2, protein refolding and ATP-binding, Cu-Zn-superoxide dismutase precursor, oxidation-reduction process, and metal ion binding, phosphoglycerate kinase 1, glycolytic process, and metabolic process. Furthermore, 198 Al responsive proteins were identified specifically under S. luteus-inoculation and are involved in gene regulation, metabolic process, oxidation-reduction process, hydrolase activity, and peptide activity. Chlorophyll a-b binding protein, endoglucanase, putative spermidine synthase, NADH dehydrogenase, and glutathione-S-transferase were found with a significant positive expression under a combined Al and S. luteus treatment, further supported by the up-regulation of their corresponding genes. This study provides a theoretical foundation for exploiting the regulatory role of ectomycorrhizal inoculation and associated genetic changes in resistance against Al stress in masson pine. Full article
(This article belongs to the Special Issue Plant Proteomics)
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13 pages, 1592 KiB  
Article
Arabidopsis Plant Natriuretic Peptide Is a Novel Interactor of Rubisco Activase
by Ilona Turek, Chris Gehring and Helen Irving
Life 2021, 11(1), 21; https://doi.org/10.3390/life11010021 - 31 Dec 2020
Cited by 4 | Viewed by 2739
Abstract
Plant natriuretic peptides (PNPs) are a group of systemically acting peptidic hormones affecting solute and solvent homeostasis and responses to biotrophic pathogens. Although an increasing body of evidence suggests PNPs modulate plant responses to biotic and abiotic stress, which could lead to their [...] Read more.
Plant natriuretic peptides (PNPs) are a group of systemically acting peptidic hormones affecting solute and solvent homeostasis and responses to biotrophic pathogens. Although an increasing body of evidence suggests PNPs modulate plant responses to biotic and abiotic stress, which could lead to their potential biotechnological application by conferring increased stress tolerance to plants, the exact mode of PNPs action is still elusive. In order to gain insight into PNP-dependent signalling, we set out to identify interactors of PNP present in the model plant Arabidopsis thaliana, termed AtPNP-A. Here, we report identification of rubisco activase (RCA), a central regulator of photosynthesis converting Rubisco catalytic sites from a closed to an open conformation, as an interactor of AtPNP-A through affinity isolation followed by mass spectrometric identification. Surface plasmon resonance (SPR) analyses reveals that the full-length recombinant AtPNP-A and the biologically active fragment of AtPNP-A bind specifically to RCA, whereas a biologically inactive scrambled peptide fails to bind. These results are considered in the light of known functions of PNPs, PNP-like proteins, and RCA in biotic and abiotic stress responses. Full article
(This article belongs to the Special Issue Plant Proteomics)
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21 pages, 4136 KiB  
Article
Comparative Proteomic Analysis of Walnut (Juglans regia L.) Pellicle Tissues Reveals the Regulation of Nut Quality Attributes
by Paulo A. Zaini, Noah G. Feinberg, Filipa S. Grilo, Houston J. Saxe, Michelle R. Salemi, Brett S. Phinney, Carlos H. Crisosto and Abhaya M. Dandekar
Life 2020, 10(12), 314; https://doi.org/10.3390/life10120314 - 27 Nov 2020
Cited by 8 | Viewed by 2630
Abstract
Walnuts (Juglans regia L.) are a valuable dietary source of polyphenols and lipids, with increasing worldwide consumption. California is a major producer, with ’Chandler’ and ’Tulare’ among the cultivars more widely grown. ’Chandler’ produces kernels with extra light color at a higher [...] Read more.
Walnuts (Juglans regia L.) are a valuable dietary source of polyphenols and lipids, with increasing worldwide consumption. California is a major producer, with ’Chandler’ and ’Tulare’ among the cultivars more widely grown. ’Chandler’ produces kernels with extra light color at a higher frequency than other cultivars, gaining preference by growers and consumers. Here we performed a deep comparative proteome analysis of kernel pellicle tissue from these two valued genotypes at three harvest maturities, detecting a total of 4937 J. regia proteins. Late and early maturity stages were compared for each cultivar, revealing many developmental responses common or specific for each cultivar. Top protein biomarkers for each developmental stage were also selected based on larger fold-change differences and lower variance among replicates, including proteins for biosynthesis of lipids and phenols, defense-related proteins and desiccation stress-related proteins. Comparison between the genotypes also revealed the common and specific protein repertoires, totaling 321 pellicle proteins with differential abundance at harvest stage. The proteomics data provides clues on antioxidant, secondary, and hormonal metabolism that could be involved in the loss of quality in the pellicles during processing for commercialization. Full article
(This article belongs to the Special Issue Plant Proteomics)
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18 pages, 7131 KiB  
Article
Erythromycin Treatment of Brassica campestris Seedlings Impacts the Photosynthetic and Protein Synthesis Pathways
by Young-Eun Yoon, Hyun Min Cho, Dong-won Bae, Sung Joong Lee, Hyeonji Choe, Min Chul Kim, Mi Sun Cheong and Yong Bok Lee
Life 2020, 10(12), 311; https://doi.org/10.3390/life10120311 - 26 Nov 2020
Cited by 6 | Viewed by 2145
Abstract
Erythromycin (Ery) is a commonly used veterinary drug that prevents infections and promotes the growth of farm animals. Ery is often detected in agricultural fields due to the effects of manure application in the ecosystem. However, there is a lack of information on [...] Read more.
Erythromycin (Ery) is a commonly used veterinary drug that prevents infections and promotes the growth of farm animals. Ery is often detected in agricultural fields due to the effects of manure application in the ecosystem. However, there is a lack of information on Ery toxicity in crops. In this study, we performed a comparative proteomic analysis to identify the molecular mechanisms of Ery toxicity during seedling growth based on our observation of a decrease in chlorophyll (Chl) contents using Brassica campestris. A total of 452 differentially abundant proteins (DAPs) were identified including a ribulose-1,5-bisphosphate carboxylase (RuBisCO). The proteomic analysis according to gene ontology (GO) classification revealed that many of these DAPs responding to Ery treatment functioned in a cellular process and a metabolic process. The molecular function analysis showed that DAPs classified within catalytic activity were predominantly changed by Ery, including metabolite interconversion enzyme and protein modifying enzyme. An analysis of functional pathways using MapMan revealed that many photosynthesis components were downregulated, whereas many protein biosynthesis components were upregulated. A good relationship was observed between protein and transcript abundance in a photosynthetic pathway, as determined by qPCR analysis. These combined results suggest that Ery affects plant physiological activity by downregulating protein abundance in the photosynthetic pathway. Full article
(This article belongs to the Special Issue Plant Proteomics)
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Review

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21 pages, 886 KiB  
Review
(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants
by Victor Muleya, L. Maria Lois, Hicham Chahtane, Ludivine Thomas, Marco Chiapello and Claudius Marondedze
Life 2022, 12(2), 324; https://doi.org/10.3390/life12020324 - 21 Feb 2022
Cited by 4 | Viewed by 2365
Abstract
The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics [...] Read more.
The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants. Full article
(This article belongs to the Special Issue Plant Proteomics)
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25 pages, 2054 KiB  
Review
Sorghum’s Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review
by Rudo Ngara, Tatenda Goche, Dirk Z. H. Swanevelder and Stephen Chivasa
Life 2021, 11(7), 704; https://doi.org/10.3390/life11070704 - 17 Jul 2021
Cited by 14 | Viewed by 3564
Abstract
Sorghum is a cereal crop with key agronomic traits of drought and heat stress tolerance, making it an ideal food and industrial commodity for hotter and more arid climates. These stress tolerances also present a useful scientific resource for studying the molecular basis [...] Read more.
Sorghum is a cereal crop with key agronomic traits of drought and heat stress tolerance, making it an ideal food and industrial commodity for hotter and more arid climates. These stress tolerances also present a useful scientific resource for studying the molecular basis for environmental resilience. Here we provide an extensive review of current transcriptome and proteome works conducted with laboratory, greenhouse, or field-grown sorghum plants exposed to drought, osmotic stress, or treated with the drought stress-regulatory phytohormone, abscisic acid. Large datasets from these studies reveal changes in gene/protein expression across diverse signaling and metabolic pathways. Together, the emerging patterns from these datasets reveal that the overall functional classes of stress-responsive genes/proteins within sorghum are similar to those observed in equivalent studies of other drought-sensitive model species. This highlights a monumental challenge of distinguishing key regulatory genes/proteins, with a primary role in sorghum adaptation to drought, from genes/proteins that change in expression because of stress. Finally, we discuss possible options for taking the research forward. Successful exploitation of sorghum research for implementation in other crops may be critical in establishing climate-resilient agriculture for future food security. Full article
(This article belongs to the Special Issue Plant Proteomics)
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8 pages, 555 KiB  
Review
Functional Roles of RNA-Binding Proteins in Plant Signaling
by Victor Muleya and Claudius Marondedze
Life 2020, 10(11), 288; https://doi.org/10.3390/life10110288 - 18 Nov 2020
Cited by 6 | Viewed by 2923
Abstract
RNA-binding proteins (RBPs) are typical proteins that bind RNA through single or multiple RNA-binding domains (RBDs). These proteins have a functional role in determining the fate or function of the bound RNAs. A few hundred RBPs were known through in silico prediction based [...] Read more.
RNA-binding proteins (RBPs) are typical proteins that bind RNA through single or multiple RNA-binding domains (RBDs). These proteins have a functional role in determining the fate or function of the bound RNAs. A few hundred RBPs were known through in silico prediction based on computational assignment informed by structural similarity and the presence of classical RBDs. However, RBPs lacking such conventional RBDs were omitted. Owing to the recent mRNA interactome capture technology based on UV-crosslinking and fixing proteins to their mRNA targets followed by affinity capture purification and identification of RBPs by tandem mass spectrometry, several hundreds of RBPs have recently been discovered. These proteome-wide studies have colossally increased the number of proteins implicated in RNA binding and unearthed hundreds of novel RBPs lacking classical RBDs, such as proteins involved in intermediary metabolism. These discoveries provide wide insights into the post-transcriptional gene regulation players and their role in plant signaling, such as environmental stress conditions. In this review, novel discoveries of RBPs are explored, particularly on the evolving knowledge of their role in stress responses. The molecular functions of these RBPs, particularly focusing on those that do not have classical RBDs, are also elucidated at the systems level. Full article
(This article belongs to the Special Issue Plant Proteomics)
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