KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Plant proteome changes under abiotic stress--contribution of proteomics studies to understanding plant stress response

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Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes. Bioinformatics platforms and their associated databases are also essential for the effective design of approaches making the best use of genomic resources, including resource integration. We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology.

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Genomics and bioinformatics resources for crop improvement.

Proteomic analyses of soybean seedlings responding to flooding were conducted to identify proteins involved in such response. Soybean was germinated for 48 h and then subjected to flooding stress for 6−48 h. Proteomic analysis of hypocotyl and root was used in a time-dependent manner, and altered proteins were identified using soybean protein data file constructed for this research. Under flooding stress, 35 proteins were up-regulated, whereas 16 proteins were down-regulated at a 24-h time point. Changes in energy generation was recognized because several glycolytic enzymes were up-regulated. General stress response was also shown to occur as various reactive oxygen species scavengers were up-regulated. Other identified proteins with diverse functional categories suggest that flooding stress includes not only hypoxic stress, but also other stresses such as weak light, disease, and water stresses. In addition, proteins with unknown functions were shown to be positioned as hubs which activate other proteins...

Proteome analysis of early-stage soybean seedlings under flooding stress.

Alcohol dehydrogenase (Adh) is the key enzyme in alcohol fermentation. We analyzed Adh expression in order to clarify the role of Adh of soybeans (Glycine max) to flooding stress. Proteome analysis confirmed that expression of Adh is significantly upregulated in 4-day-old soybean seedlings subjected to 2 days of flooding. Southern hybridization analysis and soybean genome database search revealed that soybean has at least 6 Adh genes. The GmAdh2 gene that responded to flooding was isolated from soybean cultivar Enrei. Adh2 expression was markedly increased 6 h after flooding and decreased 24 h after floodwater drainage. In situ hybridization and Western blot indicated that flooding strongly induces Adh2 expression in RNA and protein levels in the root apical meristem. Osmotic, cold, or drought stress did not induce expression of Adh2. These results indicate that Adh2 is a flooding-response specific soybean gene expressed in root tissue.

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Characterization of a novel flooding stress-responsive alcohol dehydrogenase expressed in soybean roots

The Soybean Proteome Database aims to be a data repository for functional analyses of soybean responses to flooding injury, recognized as a major constraint for establishment and production of this plant. The current release contains 21 reference maps of soybean (Glycine max cv. Enrei) proteins electrophoresed on two-dimensional polyacrylamide gels of which the samples were collected from several organs, tissues and organelles. These reference maps include 7311 detected proteins and 532 identified proteins, or proteins for which a sequence or peptide peak has been determined. The database is searchable by protein properties such as accession number, description and isoelectric point and molecular weight range. The Soybean Proteome Database also integrates multiple "omes". An omics table reveals relationships among 106 mRNAs, 51 proteins and 89 metabolites that vary over time under flooding stress. The tabulated metabolites are anchored to a metabolome network. A unified temporal-profile tag attached to the mRNAs, proteins and metabolites facilitates retrieval of the data based on the temporal expression profiles. A graphical user interface based on dynamic HTML facilitates viewing the metabolome network as well as the profiles of multiple omes in a uniform manner. The entire database is available at http://proteome.dc.affrc.go.jp/Soybean/.

Soybean proteome database: a data resource for plant differential omics.

Abstract Abiotic stress caused by global climate change varies widely, which negatively affect crops growth and productivity throughout the world. Environmental changes can alter plant’s physiological state and trigger several signaling pathways for adaptation to unfavorable conditions. Plant response to abiotic stress includes changes in protein expression and post-translational modification of proteins to activate their defense system against the challenges. Research on plant proteomes has provided beneficial information for a comprehensive understanding of the protein networks in plants in response to external stimuli. Large-scale proteomics is a powerful approach for studies of complex biological processes in which a number of proteins take part; proteome analysis of sub-cellular structures and modified proteins has enabled identification of novel components of plant stress responses that had not previously been discovered. In this review, we have discussed the recent developments of crop proteomics in the context of several climatic factors including photosynthetic stress, air pollutants, thermal stress including heat and cold, and osmotic stress, including drought, salt, and flooding stress, and metal stress. The aim of this review is to take a snapshot of several proteomic approaches in crop plants that provide a comprehensive list of components affected by certain abiotic stresses in climate. The biological relevance of these proteins in regard to plant stress tolerance will be described as well.

Proteomics application of crops in the context of climatic changes. Food Res Int

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.

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Akiko Hashiguchi

Papers

Proteome analysis of early-stage soybean seedlings under flooding stress.

Characterization of a novel flooding stress-responsive alcohol dehydrogenase expressed in soybean roots

Soybean proteome database: a data resource for plant differential omics.

Proteomics application of crops in the context of climatic changes. Food Res Int

Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress.