PlantPReS: A database for plant proteome response to stress

Mousavi, Seyed Ahmad; Pouya, Farhad Movahedi; Ghaffari, Mehdi; Mirzaei, Mehdi; Ghaffari, Akram; Alikhani, Mehdi; Ghareyazie, Mohammad; Komatsu, Setsuko; Haynes, Paul A.; Salekdeh, Ghasem Hosseini

doi:10.1016/j.jprot.2016.03.009

Cited by 38 publications

(15 citation statements)

References 21 publications

(19 reference statements)

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“…For both wet-bench scientists and computational biologists, online databases with user-friendly interfaces are necessary tools to explore the vast amount of data and networks generated by computational modeling. Fortunately, we can now perform comparative network analyses to identify abiotic stress related genes in Arabidopsis ( Landeghem et al, 2016 ), explore uniformly re-processed expression data to query abiotic stress related gene co-expression networks ( Zaag et al, 2015 ), and to search curated databases for published proteins that are related to plant stress response ( Mousavi et al, 2016 ).…”

Section: Modeling Of Plant Abiotic Stress Responsesmentioning

confidence: 99%

Multilevel Regulation of Abiotic Stress Responses in Plants

et al. 2017

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The sessile lifestyle of plants requires them to cope with stresses in situ. Plants overcome abiotic stresses by altering structure/morphology, and in some extreme conditions, by compressing the life cycle to survive the stresses in the form of seeds. Genetic and molecular studies have uncovered complex regulatory processes that coordinate stress adaptation and tolerance in plants, which are integrated at various levels. Investigating natural variation in stress responses has provided important insights into the evolutionary processes that shape the integrated regulation of adaptation and tolerance. This review primarily focuses on the current understanding of how transcriptional, post-transcriptional, post-translational, and epigenetic processes along with genetic variation orchestrate stress responses in plants. We also discuss the current and future development of computational tools to identify biologically meaningful factors from high dimensional, genome-scale data and construct the signaling networks consisting of these components.

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Section: Modeling Of Plant Abiotic Stress Responsesmentioning

confidence: 99%

Multilevel Regulation of Abiotic Stress Responses in Plants

et al. 2017

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“…Protein synthesis and folding may be disturbed and, hence, protein degradation may be activated in plants under stress condition, and previous proteomic studies have identified a large number of drought-corresponsive proteins associated with protein synthesis, folding, and degradation [ 40 ]. In the present study, two DPPs involved in ribosomes and translation, four DPPs related to protein folding, and four DPPs associated with protein degradation were identified, suggesting the important role of protein phosphorylation in regulating protein turnover at the post-transcriptional level.…”

Section: Discussionmentioning

confidence: 99%

Quantitative Phosphoproteomic Analysis Provides Insight into the Response to Short-Term Drought Stress in Ammopiptanthus mongolicus Roots

Sun

Xia

Wang

et al. 2017

IJMS

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Drought is one of the major abiotic stresses that negatively affects plant growth and development. Ammopiptanthus mongolicus is an ecologically important shrub in the mid-Asia desert region and used as a model for abiotic tolerance research in trees. Protein phosphorylation participates in the regulation of various biological processes, however, phosphorylation events associated with drought stress signaling and response in plants is still limited. Here, we conducted a quantitative phosphoproteomic analysis of the response of A. mongolicus roots to short-term drought stress. Data are available via the iProx database with project ID IPX0000971000. In total, 7841 phosphorylation sites were found from the 2019 identified phosphopeptides, corresponding to 1060 phosphoproteins. Drought stress results in significant changes in the abundance of 103 phosphopeptides, corresponding to 90 differentially-phosphorylated phosphoproteins (DPPs). Motif-x analysis identified two motifs, including [pSP] and [RXXpS], from these DPPs. Functional enrichment and protein-protein interaction analysis showed that the DPPs were mainly involved in signal transduction and transcriptional regulation, osmotic adjustment, stress response and defense, RNA splicing and transport, protein synthesis, folding and degradation, and epigenetic regulation. These drought-corresponsive phosphoproteins, and the related signaling and metabolic pathways probably play important roles in drought stress signaling and response in A. mongolicus roots. Our results provide new information for understanding the molecular mechanism of the abiotic stress response in plants at the posttranslational level.

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“…(2) There are numerous rice MS datasets that have not been submitted to public databases. For example, there are more than 30 MS-based studies of rice proteome in PlantPReS (Mousavi et al, 2016); however, only one of these datasets has been submitted to public databases such as PRIDE. We encourage all plant proteomics groups to submit their datasets to public databases and make them available for identification of MPs.…”

Section: Molecular Plantmentioning

confidence: 99%

The Quest for Missing Proteins in Rice

et al. 2019

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Rice (Oryza sativa) is the primary staple food source for more than half of the world's population. Proteins are active macromolecules and central to understanding biological molecular processes. Hence, it is necessary to study all protein forms of plant genes so that their biological functions and roles in regulating important traits such as yield, quality, and responses to environmental stresses can be determined. Although there have been significant advances over the years, a big gap still exists between the number of protein-coding genes (PCGs) and proteins detected with sufficient experimental evidence (Legrain et al., 2011). Therefore, one of the major objectives of proteomics is to detect the proteins without sufficient experimental evidence, also known as the missing proteins (MPs), mainly by using mass spectrometry (MS)-based experimental approaches (Horvatovich et al., 2015).

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PlantPReS: A database for plant proteome response to stress

Cited by 38 publications

References 21 publications

Multilevel Regulation of Abiotic Stress Responses in Plants

Multilevel Regulation of Abiotic Stress Responses in Plants

Quantitative Phosphoproteomic Analysis Provides Insight into the Response to Short-Term Drought Stress in Ammopiptanthus mongolicus Roots

The Quest for Missing Proteins in Rice

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