Special Issue "Proteomics in Plant–Environment Interactions"

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

Deadline for manuscript submissions: closed (31 May 2017)

Special Issue Editors

Guest Editor
Prof. Dr. M. Margarida Oliveira

Plant Functional Genomics Lab, GPlantS Unit, Instituto de Tecnologia Química e Biológica, Av. da República, 2780-157 Oeiras, Portugal
Website | E-Mail
Interests: plant–environment interactions; regulation of plant development; plant stress response; model plants and crops
Guest Editor
Dr. Isabel A. Abreu

Proteome Regulation in Plants Lab, GPlantS Unit, Instituto de Tecnologia Química e Biológica, Av. da República, 2780-157 Oeiras, Portugal
Website | E-Mail
Interests: plant response to environmental changes; post-translational modifications; model plants and crops; photosynthesis, quantitative proteomics; mass spectrometry

Special Issue Information

Dear Colleagues,

 

The regulation of plant development is greatly influenced by the environment (biotic and abiotic factors). More and more, erratic climate conditions affect plant development and productivity, posing increasing challenges to breeders and producers and threatening natural environments. The understanding of the processes of perceiving and adjusting to the environment extend from the genomic to the phenotypic level.

Correlations between genome and phenotype have been widely used in plant breeding programs. This approach has proven very useful, but it is somewhat limiting. A single gene does not often result in a single protein. Several key regulatory processes occur at the post-transcriptional and post-translational levels, exponentially increasing the complexity of the cell proteome and undoubtedly impacting the plant phenotype.

Proteomics allow looking directly at the cell proteome, and the recent developments in mass spectrometry allow discrimination of protein isoforms and identification and quantification of post-translational modifications. This makes proteomics a very powerful approach to study the molecular responses of plants to environmental factors.

For this Special Issue on “Proteomics in Plant-Environment Interactions”, we welcome submissions of revision and original research articles focusing on all aspects of plant interaction with the environment, making use of proteomics as a central tool.

We have particular interest in proteomic contributions to uncover:

-       how plants deal with pests and pathogens, or with symbiotic organisms,
-       how plants modify development for better adaptation to stressful conditions,
-       how efficiently plants manage to use light and nutrients to maximize growth

This Special Issue will allow understanding how seriously proteome regulation can impact plant yield and production, and what tools are at our reach to modulate plant growth and adaptation.

Prof. Dr. M. Margarida Oliveira
Dr. Isabel A. Abreu
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 550 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

  • plant proteomics
  • plant–environment interactions
  • regulation of plant development

Published Papers (5 papers)

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Research

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Open AccessFeature PaperArticle Comparison between Proteome and Transcriptome Response in Potato (Solanum tuberosum L.) Leaves Following Potato Virus Y (PVY) Infection
Received: 4 May 2017 / Revised: 27 June 2017 / Accepted: 1 July 2017 / Published: 6 July 2017
Cited by 5 | PDF Full-text (1380 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Plant diseases caused by viral infection are affecting all major crops. Being an obligate intracellular organisms, chemical control of these pathogens is so far not applied in the field except to control the insect vectors of the viruses. Understanding of molecular responses of [...] Read more.
Plant diseases caused by viral infection are affecting all major crops. Being an obligate intracellular organisms, chemical control of these pathogens is so far not applied in the field except to control the insect vectors of the viruses. Understanding of molecular responses of plant immunity is therefore economically important, guiding the enforcement of crop resistance. To disentangle complex regulatory mechanisms of the plant immune responses, understanding system as a whole is a must. However, integrating data from different molecular analysis (transcriptomics, proteomics, metabolomics, smallRNA regulation etc.) is not straightforward. We evaluated the response of potato (Solanum tuberosum L.) following the infection with potato virus Y (PVY). The response has been analyzed on two molecular levels, with microarray transcriptome analysis and mass spectroscopy-based proteomics. Within this report, we performed detailed analysis of the results on both levels and compared two different approaches for analysis of proteomic data (spectral count versus MaxQuant). To link the data on different molecular levels, each protein was mapped to the corresponding potato transcript according to StNIB paralogue grouping. Only 33% of the proteins mapped to microarray probes in a one-to-one relation and additionally many showed discordance in detected levels of proteins with corresponding transcripts. We discussed functional importance of true biological differences between both levels and showed that the reason for the discordance between transcript and protein abundance lies partly in complexity and structure of biological regulation of proteome and transcriptome and partly in technical issues contributing to it. Full article
(This article belongs to the Special Issue Proteomics in Plant–Environment Interactions)
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Open AccessArticle Effects of Al3+ and La3+ Trivalent Metal Ions on Tomato Fruit Proteomes
Received: 21 November 2016 / Revised: 26 January 2017 / Accepted: 7 February 2017 / Published: 11 February 2017
Cited by 1 | PDF Full-text (1847 KB) | HTML Full-text | XML Full-text
Abstract
The tomato (Solanum lycopersicum) ripening process from mature green (MG) to turning and then to red stages is accompanied by the occurrences of physiological and biochemical reactions, which ultimately result in the formation of the flavor, color and texture of ripe [...] Read more.
The tomato (Solanum lycopersicum) ripening process from mature green (MG) to turning and then to red stages is accompanied by the occurrences of physiological and biochemical reactions, which ultimately result in the formation of the flavor, color and texture of ripe fruits. The two trivalent metal ions Al3+ and La3+ are known to induce different levels of phytotoxicity in suppressing root growth. This paper aims to understand the impacts of these two metal ions on tomato fruit proteomes. Tomato ‘Micro-Tom’ plants were grown in a hydroponic culture system supplemented with 50 μM aluminum sulfate (Al2 (SO4)3.18H2O) for Al3+ or La2(SO4)3 for La3+. Quantitative proteomics analysis, using isobaric tags for relative and absolute quantitation, were performed for fruits at MG, turning and red stages. Results show that in MG tomatoes, proteins involved in protein biosynthesis, photosynthesis and primary carbohydrate metabolisms were at a significantly lower level in Al-treated compared to La-treated plants. For the turning and red tomatoes, only a few proteins of significant differences between the two metal treatments were identified. Results from this study indicate that compared to La3+, Al3+ had a greater influence on the basic biological activities in green tomatoes, but such an impact became indistinguishable as tomatoes matured into the late ripening stages. Full article
(This article belongs to the Special Issue Proteomics in Plant–Environment Interactions)
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Review

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Open AccessFeature PaperReview Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress
Received: 29 October 2016 / Revised: 30 November 2016 / Accepted: 16 December 2016 / Published: 21 December 2016
Cited by 4 | PDF Full-text (245 KB) | HTML Full-text | XML Full-text
Abstract
The efficiency of stress-induced adaptive responses of plants depends on intricate coordination of multiple signal transduction pathways that act coordinately or, in some cases, antagonistically. Protein post-translational modifications (PTMs) can regulate protein activity and localization as well as protein–protein interactions in numerous cellular [...] Read more.
The efficiency of stress-induced adaptive responses of plants depends on intricate coordination of multiple signal transduction pathways that act coordinately or, in some cases, antagonistically. Protein post-translational modifications (PTMs) can regulate protein activity and localization as well as protein–protein interactions in numerous cellular processes, thus leading to elaborate regulation of plant responses to various external stimuli. Understanding responses of crop plants under field conditions is crucial to design novel stress-tolerant cultivars that maintain robust homeostasis even under extreme conditions. In this review, proteomic studies of PTMs in crops are summarized. Although the research on the roles of crop PTMs in regulating stress response mechanisms is still in its early stage, several novel insights have been retrieved so far. This review covers techniques for detection of PTMs in plants, representative PTMs in plants under abiotic stress, and how PTMs control functions of representative proteins. In addition, because PTMs under abiotic stresses are well described in soybeans under submergence, recent findings in PTMs of soybean proteins under flooding stress are introduced. This review provides information on advances in PTM study in relation to plant adaptations to abiotic stresses, underlining the importance of PTM study to ensure adequate agricultural production in the future. Full article
(This article belongs to the Special Issue Proteomics in Plant–Environment Interactions)
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Open AccessFeature PaperReview Enzymes and Metabolites in Carbohydrate Metabolism of Desiccation Tolerant Plants
Received: 6 September 2016 / Revised: 1 December 2016 / Accepted: 7 December 2016 / Published: 15 December 2016
Cited by 7 | PDF Full-text (438 KB) | HTML Full-text | XML Full-text
Abstract
Resurrection plants can tolerate extreme water loss. Substantial sugar accumulation is a phenomenon in resurrection plants during dehydration. Sugars have been identified as one important factor contributing to desiccation tolerance. Phylogenetic diversity of resurrection plants reflects the diversity of sugar metabolism in response [...] Read more.
Resurrection plants can tolerate extreme water loss. Substantial sugar accumulation is a phenomenon in resurrection plants during dehydration. Sugars have been identified as one important factor contributing to desiccation tolerance. Phylogenetic diversity of resurrection plants reflects the diversity of sugar metabolism in response to dehydration. Sugars, which accumulate during dehydration, have been shown to protect macromolecules and membranes and to scavenge reactive oxygen species. This review focuses on the performance of enzymes participating in sugar metabolism during dehydration stress. The relation between sugar metabolism and other biochemical activities is discussed and open questions as well as potential experimental approaches are proposed. Full article
(This article belongs to the Special Issue Proteomics in Plant–Environment Interactions)
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Open AccessReview Identification of Abiotic Stress Protein Biomarkers by Proteomic Screening of Crop Cultivar Diversity
Received: 21 June 2016 / Revised: 1 September 2016 / Accepted: 3 September 2016 / Published: 8 September 2016
Cited by 3 | PDF Full-text (241 KB) | HTML Full-text | XML Full-text
Abstract
Modern day agriculture practice is narrowing the genetic diversity in our food supply. This may compromise the ability to obtain high yield under extreme climactic conditions, threatening food security for a rapidly growing world population. To identify genetic diversity, tolerance mechanisms of cultivars, [...] Read more.
Modern day agriculture practice is narrowing the genetic diversity in our food supply. This may compromise the ability to obtain high yield under extreme climactic conditions, threatening food security for a rapidly growing world population. To identify genetic diversity, tolerance mechanisms of cultivars, landraces and wild relatives of major crops can be identified and ultimately exploited for yield improvement. Quantitative proteomics allows for the identification of proteins that may contribute to tolerance mechanisms by directly comparing protein abundance under stress conditions between genotypes differing in their stress responses. In this review, a summary is provided of the data accumulated from quantitative proteomic comparisons of crop genotypes/cultivars which present different stress tolerance responses when exposed to various abiotic stress conditions, including drought, salinity, high/low temperature, nutrient deficiency and UV-B irradiation. This field of research aims to identify molecular features that can be developed as biomarkers for crop improvement, however without accurate phenotyping, careful experimental design, statistical robustness and appropriate biomarker validation and verification it will be challenging to deliver what is promised. Full article
(This article belongs to the Special Issue Proteomics in Plant–Environment Interactions)
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