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      Proteome changes in pepper ( Capsicum annuum L.) leaves induced by the green peach aphid ( Myzus persicae Sulzer)

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          Abstract

          Background

          Aphid attack induces defense responses in plants activating several signaling cascades that led to the production of toxic, repellent or antinutritive compounds and the consequent reorganization of the plant primary metabolism. Pepper ( Capsicum annuum L.) leaf proteomic response against Myzus persicae (Sulzer) has been investigated and analyzed by LC-MS/MS coupled with bioinformatics tools.

          Results

          Infestation with an initially low density (20 aphids/plant) of aphids restricted to a single leaf taking advantage of clip cages resulted in 6 differentially expressed proteins relative to control leaves (3 proteins at 2 days post-infestation and 3 proteins at 4 days post-infestation). Conversely, when plants were infested with a high density of infestation (200 aphids/plant) 140 proteins resulted differentially expressed relative to control leaves (97 proteins at 2 days post-infestation, 112 proteins at 4 days post-infestation and 105 proteins at 7 days post-infestation). The majority of proteins altered by aphid attack were involved in photosynthesis and photorespiration, oxidative stress, translation, protein folding and degradation and amino acid metabolism. Other proteins identified were involved in lipid, carbohydrate and hormone metabolism, transcription, transport, energy production and cell organization. However proteins directly involved in defense were scarce and were mostly downregulated in response to aphids.

          Conclusions

          The unexpectedly very low number of regulated proteins found in the experiment with a low aphid density suggests an active mitigation of plant defensive response by aphids or alternatively an aphid strategy to remain undetected by the plant.

          Under a high density of aphids, pepper leaf proteome however changed significantly revealing nearly all routes of plant primary metabolism being altered. Photosynthesis was so far the process with the highest number of proteins being regulated by the presence of aphids.

          In general, at short times of infestation (2 days) most of the altered proteins were upregulated. However, at longer times of infestation (7 days) the protein downregulation prevailed.

          Proteins involved in plant defense and in hormone signaling were scarce and mostly downregulated.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12870-020-02749-x.

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          Most cited references88

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          The PRIDE database and related tools and resources in 2019: improving support for quantification data

          Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
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            The Perseus computational platform for comprehensive analysis of (prote)omics data.

            A main bottleneck in proteomics is the downstream biological analysis of highly multivariate quantitative protein abundance data generated using mass-spectrometry-based analysis. We developed the Perseus software platform (http://www.perseus-framework.org) to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiple-hypothesis testing. A machine learning module supports the classification and validation of patient groups for diagnosis and prognosis, and it also detects predictive protein signatures. Central to Perseus is a user-friendly, interactive workflow environment that provides complete documentation of computational methods used in a publication. All activities in Perseus are realized as plugins, and users can extend the software by programming their own, which can be shared through a plugin store. We anticipate that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
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              Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response.

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                Author and article information

                Contributors
                victoria.florencio@ua.es
                Journal
                BMC Plant Biol
                BMC Plant Biol
                BMC Plant Biology
                BioMed Central (London )
                1471-2229
                6 January 2021
                6 January 2021
                2021
                : 21
                : 12
                Affiliations
                [1 ]GRID grid.5268.9, ISNI 0000 0001 2168 1800, Unidad Asociada CSIC-UA IPAB. Instituto Universitario de Investigación CIBIO (Centro Iberoamericano de la Biodiversidad), , University of Alicante, ; Carretera de San Vicente del Raspeig, s/n, E-03690 San Vicente del Raspeig, Alicante, Spain
                [2 ]GRID grid.5268.9, ISNI 0000 0001 2168 1800, Genomics and Proteomics Unit, Servicios Técnicos de Investigación, , University of Alicante, ; Carretera de San Vicente del Raspeig, s/n, E-03690 San Vicente del Raspeig, Alicante, Spain
                Author information
                http://orcid.org/0000-0002-1432-1716
                Article
                2749
                10.1186/s12870-020-02749-x
                7788789
                33407137
                d6ae2421-5e41-4a53-b0ce-d44a6bd67016
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 21 February 2020
                : 22 November 2020
                Funding
                Funded by: Ministerio de Economía y Competitividad
                Award ID: Project CGL2016-79054-R
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100009092, Universidad de Alicante;
                Award ID: grant UAFPU2013-5793
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2021

                Plant science & Botany
                plant proteomics,lc-ms/ms,plant defense,biotic stress,plant-aphid interaction

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