Special Issue "Plant Proteomics 2017"

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (30 June 2017)

Special Issue Editors

Guest Editor
Dr. Véronique Santoni

Biochimie et Physiologie Moléculaire des Plantes, INRA/CNRS/SupAgro/UM2, UMR 5004, Montpellier Cedex 1, France
Website | E-Mail
Interests: aquaporin; phosphorylation; plant membrane; quantitative proteomics
Guest Editor
Dr. Elisabeth Jamet

Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borderouge-Auzeville, BP42617, Castanet-Tolosan 31326, France
Website | E-Mail
Interests: plant; cell wall biology; development; evolution; proteomics; post-translational modification; cell wall architecture; protein/protein; protein/polysaccharide interaction

Special Issue Information

Dear Colleagues,

During recent years, proteomics has become the key to understand physiological processes involving the regulation of expression of many genes from transcription to production of metabolites. Each of these steps is part of the overall mechanisms tightly coordinated to allow organisms to develop or adapt to their environment. Plant proteomics has been dramatically expanding since the beginning of the 2000s thanks to major advances in the development of three technological tools. It started with the sequencing of full genomes and collection of expressed sequence tags or RNAs. The release of the Arabidopsis thaliana genome in 2000 has allowed this plant to become a pioneer model for dicots, and particularly for proteomics studies. More than 650 articles have been published in this field since 2000. A. thaliana has been quickly followed by Brachypodium distachyon as a model for monocots and by plants of agronomical interest such as rice, maize, sugarcane, alfalfa, tomato or flax. Apart from these plants, others for which sequencing data were not available could be studied as well, thanks to the possibility to work with heterologous data. In addition, over the last decade, remarkable technological advances have been achieved due to improvements in mass spectrometry which allowed refining the coverage of total proteomes and sub-proteomes from small amounts of starting material and characterizing post-translational modifications and protein-protein interactions. Furthermore, quantitative proteomics now provides detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during the plant life cycle. Finally, the development of computational tools allows managing the tremendous amount of data generated by mass spectrometers to deliver relevant biological information. Thus, powerful mass spectrometry-based technologies now provide unprecedented insights into the composition, structure, function and control of the proteome, shedding light on complex biological processes and phenotypes.

This Special issue of Proteomes welcomes submissions of original research or review articles aiming at deciphering physiological processes with the use of proteomics tools. Contributions will deal with the dynamics of proteins in their native and modified forms, with the combination of several “omics” approaches in contrasted physiological situations as well as with technical advances in the proteomic field.

Dr. Elisabeth Jamet
Dr. Véronique Santoni
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 papers will be 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. Proteomes is an international peer-reviewed open access quarterly 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 350 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

  • Omics data integration
  • Plant development
  • Plant interactions with their environment
  • Plant proteomics
  • Quantitative proteomics

Published Papers (5 papers)

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Research

Open AccessArticle A Proteomic Approach to Investigate the Drought Response in the Orphan Crop Eragrostis tef
Proteomes 2017, 5(4), 32; doi:10.3390/proteomes5040032
Received: 22 June 2017 / Revised: 20 October 2017 / Accepted: 10 November 2017 / Published: 15 November 2017
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Abstract
The orphan crop, Eragrostis tef, was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50%
[...] Read more.
The orphan crop, Eragrostis tef, was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions. Validation of the iTRAQ dataset was done with selected stress-related proteins, fructose-bisphosphate aldolase (FBA) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX). Western blot analyses confirmed protein presence and showed increased protein abundance levels during water deficit while enzymatic activity for FBA, MDHAR and POX increased at selected RWC points. Gene ontology (GO)-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in tef upregulated proteins, while terms linked to reactive oxygen species (ROS)-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in tef downregulated proteins. Full article
(This article belongs to the Special Issue Plant Proteomics 2017)
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Open AccessArticle Proteomic Investigations of Proteases Involved in Cotyledon Senescence: A Model to Explore the Genotypic Variability of Proteolysis Machinery Associated with Nitrogen Remobilization Efficiency during the Leaf Senescence of Oilseed Rape
Proteomes 2017, 5(4), 29; doi:10.3390/proteomes5040029
Received: 29 August 2017 / Revised: 23 October 2017 / Accepted: 24 October 2017 / Published: 2 November 2017
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Abstract
Oilseed rape is characterized by a low nitrogen remobilization efficiency during leaf senescence, mainly due to a lack of proteolysis. Because cotyledons are subjected to senescence, it was hypothesized that contrasting protease activities between genotypes may be distinguishable early in the senescence of
[...] Read more.
Oilseed rape is characterized by a low nitrogen remobilization efficiency during leaf senescence, mainly due to a lack of proteolysis. Because cotyledons are subjected to senescence, it was hypothesized that contrasting protease activities between genotypes may be distinguishable early in the senescence of cotyledons. To verify this assumption, our goals were to (i) characterize protease activities in cotyledons between two genotypes with contrasting nitrogen remobilization efficiency (Ténor and Samouraï) under limiting or ample nitrate supply; and (ii) test the role of salicylic acid (SA) and abscisic acid (ABA) in proteolysis regulation. Protease activities were measured and identified by a proteomics approach combining activity-based protein profiling with LC-MS/MS. As in senescing leaves, chlorophyll and protein contents decrease in senescing cotyledons and are correlated with an increase in serine and cysteine protease activities. Two RD21-like and SAG-12 proteases previously associated with an efficient proteolysis in senescing leaves of Ténor are also detected in senescing cotyledons. The infiltration of ABA and SA provokes the induction of senescence and several cysteine and serine protease activities. The study of protease activities during the senescence of cotyledons seems to be a promising experimental model to investigate the regulation and genotypic variability of proteolysis associated with efficient N remobilization. Full article
(This article belongs to the Special Issue Plant Proteomics 2017)
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Open AccessArticle A Microsomal Proteomics View of H2O2- and ABA-Dependent Responses
Proteomes 2017, 5(3), 22; doi:10.3390/proteomes5030022
Received: 18 May 2017 / Revised: 28 July 2017 / Accepted: 16 August 2017 / Published: 18 August 2017
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Abstract
The plant hormone abscisic acid (ABA) modulates a number of plant developmental processes and responses to stress. In planta, ABA has been shown to induce reactive oxygen species (ROS) production through the action of plasma membrane-associated nicotinamide adenine dinucleotide phosphate (NADPH)-oxidases. Although quantitative
[...] Read more.
The plant hormone abscisic acid (ABA) modulates a number of plant developmental processes and responses to stress. In planta, ABA has been shown to induce reactive oxygen species (ROS) production through the action of plasma membrane-associated nicotinamide adenine dinucleotide phosphate (NADPH)-oxidases. Although quantitative proteomics studies have been performed to identify ABA- or hydrogen peroxide (H2O2)-dependent proteins, little is known about the ABA- and H2O2-dependent microsomal proteome changes. Here, we examined the effect of 50 µM of either H2O2 or ABA on the Arabidopsis microsomal proteome using tandem mass spectrometry and identified 86 specifically H2O2-dependent, and 52 specifically ABA-dependent proteins that are differentially expressed. We observed differential accumulation of proteins involved in the tricarboxylic acid (TCA) cycle notably in response to H2O2. Of these, aconitase 3 responded to both H2O2 and ABA. Additionally, over 30 proteins linked to RNA biology responded significantly to both treatments. Gene ontology categories such as ‘response to stress’ and ‘transport’ were enriched, suggesting that H2O2 or ABA directly and/or indirectly cause complex and partly overlapping cellular responses. Data are available via ProteomeXchange with identifier PXD006513. Full article
(This article belongs to the Special Issue Plant Proteomics 2017)
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Open AccessArticle A Combination of Histological, Physiological, and Proteomic Approaches Shed Light on Seed Desiccation Tolerance of the Basal Angiosperm Amborella trichopoda
Proteomes 2017, 5(3), 19; doi:10.3390/proteomes5030019
Received: 30 June 2017 / Revised: 22 July 2017 / Accepted: 25 July 2017 / Published: 28 July 2017
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Abstract
Desiccation tolerance allows plant seeds to remain viable in a dry state for years and even centuries. To reveal potential evolutionary processes of this trait, we have conducted a shotgun proteomic analysis of isolated embryo and endosperm from mature seeds of Amborella trichopoda
[...] Read more.
Desiccation tolerance allows plant seeds to remain viable in a dry state for years and even centuries. To reveal potential evolutionary processes of this trait, we have conducted a shotgun proteomic analysis of isolated embryo and endosperm from mature seeds of Amborella trichopoda, an understory shrub endemic to New Caledonia that is considered to be the basal extant angiosperm. The present analysis led to the characterization of 415 and 69 proteins from the isolated embryo and endosperm tissues, respectively. The role of these proteins is discussed in terms of protein evolution and physiological properties of the rudimentary, underdeveloped, Amborella embryos, notably considering that the acquisition of desiccation tolerance corresponds to the final developmental stage of mature seeds possessing large embryos. Full article
(This article belongs to the Special Issue Plant Proteomics 2017)
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Open AccessArticle Exogenous Auxin Elicits Changes in the Arabidopsis thaliana Root Proteome in a Time-Dependent Manner
Proteomes 2017, 5(3), 16; doi:10.3390/proteomes5030016
Received: 26 April 2017 / Revised: 27 June 2017 / Accepted: 4 July 2017 / Published: 10 July 2017
PDF Full-text (1299 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Auxin is involved in many aspects of root development and physiology, including the formation of lateral roots. Improving our understanding of how the auxin response is mediated at the protein level over time can aid in developing a more complete molecular framework of
[...] Read more.
Auxin is involved in many aspects of root development and physiology, including the formation of lateral roots. Improving our understanding of how the auxin response is mediated at the protein level over time can aid in developing a more complete molecular framework of the process. This study evaluates the effects of exogenous auxin treatment on the Arabidopsis root proteome after exposure of young seedlings to auxin for 8, 12, and 24 h, a timeframe permitting the initiation and full maturation of individual lateral roots. Root protein extracts were processed to peptides, fractionated using off-line strong-cation exchange, and analyzed using ultra-performance liquid chromatography and data independent acquisition-based mass spectrometry. Protein abundances were then tabulated using label-free techniques and evaluated for significant changes. Approximately 2000 proteins were identified during the time course experiment, with the number of differences between the treated and control roots increasing over the 24 h time period, with more proteins found at higher abundance with exposure to auxin than at reduced abundance. Although the proteins identified and changing in levels at each time point represented similar biological processes, each time point represented a distinct snapshot of the response. Auxin coordinately regulates many physiological events in roots and does so by influencing the accumulation and loss of distinct proteins in a time-dependent manner. Data are available via ProteomeXchange with the identifier PXD001400. Full article
(This article belongs to the Special Issue Plant Proteomics 2017)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Proteome analysis of the specific proteins produced in each organ of the Japanese white birch plantlet No.8 treated with azelaic acid
Author: Shinso Yokota
Affiliation: Faculty of Agriculture, Utsunomiya University
Abstract: In order to clarify resistance mechanisms induced by azelaic acid (AZA) signaling and AZA signal transduction pathways in the Japanese white birch plantlet No. 8, the present study identified the specific proteins produced in each organ, the 3rd internode, stalk and petiole, leaf, and root, of the plantlet treated with AZA by proteomic approach. The numbers of specifically expressed protein spots in the two-dimensional electrophoresis gels from the 3rd internode, stalk and petiole, leaf, and root of the AZA-treated plantlet were 5, 3, 3, and 2, respectively. These specific proteins were identified by sequence tag method using LC/MS/MS. It was suggested that AZA signaling in the birch plantlet functions in the upstream of systemic acquired resistance (SAR) to induce the proteins involved in the SAR induction, and that AZA serves as a long distance signal.

Title: Revealing the rice cytosolic proteome
Author: Joshua Heazlewood
Affiliation:
Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
Abstract:
The cytosol plays a central role in plant metabolism being location of numerous biochemical processes such as glycolysis and gluconeogenesis. While numerous subcellular proteomic studies have been conducted in plants, few attempts have been made to characterize this important compartment. Much attention in this area has focused on the reference plant Arabidopsis with numerous organelle surveys. In important crop species such as rice (Oryza sativa), few such surveys have been conducted and in particular no analysis has been undertaken to define the rice cytosol. To that effect, this study focused on the enrichment of the cytosolic fraction of rice suspension cell cultures and its characterization by shotgun proteomics to better define proteins found in this compartment. A gentle disruption approach was developed for the rice suspension cell cultures to eliminate contamination. In total, around 1000 proteins were reproducibly identified from the rice cytosol after manual curation of known contaminants. The location of a subset of these proteins were selected and their localization verified by fluorescent-tags. These data provide additional insight into the role of the cytosol within plants with a specific focus on grasses. The data have been deposited in the ProteomeXchange with the identifier PXD001116.

Title: Aluminum-induced proteome expression in switchgrass roots
Authors: Mahesh Rangu, Zhujia Ye, Sarabjit Bhatti, Suping Zhou*, Yang Yong, Tara Fish, Theodore Thannhauser*
Abstract: Aluminum (Al) stress causes significant reduction in plant growth when grown in acidic soil. The most noticeable symptom of Al toxicity is the development of stunted root systems on sensitive plants. Switchgrass plants were grown hydroponically in Al-treated and control cultures. After a month of aluminum treatment plants started showing physiological stresses such as declining photosynthetic activities, from this roots were harvested. Root-tip and root-elongation zone tissues were separately analyzed using TMT-MS quantitative proteomics analysis. A total of 256 proteins (approximately 3% of total proteins) showed significant differences between control and treated samples with significant fold change, (p<0.05, FDR<0.05 [201 proteins up-regulated, 55 proteins down regulated]). MapMan software was used for the functional classification of significantly different proteins. The expressed proteins were involved in different biological pathways including; cell cycle and cell division, transcription, protein synthesis, protein degradation, stress related pathways. The highest numbers of proteins expressed were from enzyme families (22), protein synthesis (23), protein degradation (16) and stress related enzymes (26). Proteins like the germin-like proteins and peroxidase superfamily protein were down-regulated while glutathione S-transferase, phosphate transporter and histone superfamily protein were up-regulated. Various transcription factors were identified and found to be both repressed or induced depending upon their functional context.
Keywords: TMT-MS analysis, Proteomic analysis, MapMan software, significant proteins

Title: Phytase immobilized enzymatic nano-reactor liberating phytate-protein complexes for complementary proteomic profiling of maize embryo
Authors: Wenzhong Zhang1, Jun Yao2*, Fang Xu1,2*, Pengyuan Yang2
Affiliations:
1 School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China. Email: ;
2 Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China. Email:
3 Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27599-7431,USA

A simple, robust and reliable sample pre-treatment method is indispensable for complementary proteomic profiling of plant samples. Traditional water soluble protein extraction has been an option but which might lose certain protein information because of abundant phytate co-existing in plant samples. For example, maize embryo contains up to 1 wt% of phytate, and the polyanionic phytate molecule with its six phosphate groups can bind to specific proteins thus forming insoluble complexes. Also multivalent metal ions interact with phytate and protein to form ternary complexes. The binding nature is related to type, solubility and conformational characteristics of the proteins. The formation of phytate-protein complexes occurs as water-insoluble and subsequently leading to failure of the complementary proteomic identification of plant samples.

In our recent study, enzyme phytase was innovatively considered to overcome the problem of phytate-protein complexes throughout water-soluble protein extraction of plant samples, because phytase could decompose its substrate phytate into inositol phosphates and inorganic phosphate

Being compatible with mass spectrometry, hybrid phytase immobilized enzymatic nano-reactor (PIENR) was designed by us to resolve the interference of phytate through soluble protein extraction of maize embryo. After proteomic analysis, 422 proteins were identified under PIENR-assisted conditions in comparison to 256 proteins using traditional sample extraction protocol. The identified proteins in both methods were correspondently discussed with regards to isoelectric point, amino acid distributions as well as potential copper ion binding nature. PIENAR-assisted strategy exhibited its advantage for complementary proteomic profiling of maize embryos and its real application could be further extended to wider scope of plant proteomics.

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