Comprehensive Analysis of Mitochondria in Roots and Hypocotyls of Soybean under Flooding Stress using Proteomics and Metabolomics Techniques

Komatsu, Setsuko; Yamamoto, Akifumi; Nakamura, Takuji; Nouri, Mohammad‐Zaman; Nanjo, Yohei; Nishizawa, Keito; Furukawa, Kiyoshi

doi:10.1021/pr2001918

Cited by 134 publications

(123 citation statements)

References 52 publications

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“…4, Table 2). In our previous report 22 , the expression of the TCA cycle-related proteins malate dehydrogenase, aconitase, isocitrate dehydrogenase, and 2-oxoglutarate dehydrogenase were upregulated by flooding stress in to study the activity and expression of the enzymes related to Ala and GABA metabolism.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Metabolite Alteration under Flooding Stress in Soybeans

Nakamura¹,

Yamamoto²,

Hiraga³

et al. 2012

JARQ

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Soybean is a crop known to be susceptible to flooding and enhancing flooding tolerance may be a workable strategy to improve soybean production. To elucidate the effects of flooding on soybean metabolism, metabolite alterations in seedlings during flooding treatment were identified using capillary electrophoresis-mass spectrometry (CE/MS). The principal component analysis (PCA) of soybean seedlings revealed that the first component accounted for 62.2% of total variance, and the alteration of metabolites in control and flooding treatments appears to be separated by this component. Furthermore, comparison of the metabolic loading scores in the first component of PCA show that the significant metabolites for the first component were alanine (Ala), gamma-aminobutyric acid (GABA), citrate, fumarate and malate. Quantitative analysis revealed that the total soluble sugar content of seedlings in both control and flooding treatments had declined and was lower in the latter than the former. Phosphoenolpyruvate, pyruvate and lactate, which belong to glycolytic and fermentation pathways, increased transiently, but decreased 3 to 4 days after treatment. Citrate, 2-oxoglutarate, succinate, fumarate, Ala, and GABA, which are related to the TCA cycle and amino acid metabolism, accumulated during flooding treatment. These results suggest that metabolism associated with the TCA cycle, the Ala synthetic pathway, and the GABA shunt may be strongly influenced by flooding during soybean germination.Discipline: Agricultural environment / Soil fertilizers and plant nutrition Additional key words: capillary electrophoresis -mass spectrometry (CE/MS), flooding, metabolomic analysis, soybean seedlings Present address:

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Section: Discussionmentioning

confidence: 99%

Evaluation of Metabolite Alteration under Flooding Stress in Soybeans

Nakamura¹,

Yamamoto²,

Hiraga³

et al. 2012

JARQ

Self Cite

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“…In addition to these allosteric changes, some of the enzymes of the TCA cycle are regulated at the level of protein abundance-for example, in response to oxidative or flooding stress or during the diel cycle (179,193,341,342). Similarly, they are potentially regulated by a wide number of post-translational modifications such as phosphorylation, Trx-mediated redox status regulation, and lysine acetylation (21, 89, 134).…”

Section: Mitochondrial Contribution To Energy Metabolism-respirationmentioning

confidence: 99%

Metabolic Control of Redox and Redox Control of Metabolism in Plants

Geigenberger

Fernie

2014

Antioxidants & Redox Signaling

139

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Significance: Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression. Recent Advances: The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels. Critical Issues: It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter-and intracellular levels. Future Directions: Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.

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“…Biological multivariate data generated from metabolomic studies are commonly analyzed using principal component analysis (PCA) [202], partial least square (PLS) [203], and orthogonal projections to latent structures (O-PLS) [203,204]. Numerous metabolomic studies have been done on crops under stress, including: salinity [215][216][217], drought [218][219][220][221], flooding [222], ozone treatment [223], fungal infections [224][225][226], bacterial infections [217,227], other infections [228], and multiple stresses [229,230].…”

Section: Phenomementioning

confidence: 99%

“…Eighty-one mitochondria-related metabolites were identified and quantified with reference to the commercially available standards [226]. There was an accumulation of TCA cycle-related metabolites, including citrate, succinate, and aconitate, but a reduction in ATP in flood-stressed plants, which can be explained by the arrest of aerobic respiration due to anoxia [222]. Following a similar logic, the accumulation of antimicrobial compounds, such as caffeic acid, phytoalexins, glycoalkaloids, and other polyphenolic compounds, are common in pathogen-infected crops compared to their uninfected counterparts [224][225][226]228].…”

Section: Phenomementioning

confidence: 99%

Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research

Li¹,

Qi²,

Ni³

et al. 2016

Crop Breeding

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Abiotic and biotic stresses lead to massive reprogramming of different life processes and are the major limiting factors hampering crop productivity. Omics-based research platforms allow for a holistic and comprehensive survey on crop stress responses and hence may bring forth better crop improvement strategies. Since high-throughput approaches generate considerable amounts of data, bioinformatics tools will play an essential role in storing, retrieving, sharing, processing, and analyzing them. Genomic and functional genomic studies in crops still lag far behind similar studies in humans and other animals. In this review, we summarize some useful genomics and bioinformatics resources available to crop scientists. In addition, we also discuss the major challenges and advancements in the "-omics" studies, with an emphasis on their possible impacts on crop stress research and crop improvement.

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Comprehensive Analysis of Mitochondria in Roots and Hypocotyls of Soybean under Flooding Stress using Proteomics and Metabolomics Techniques

Cited by 134 publications

References 52 publications

Evaluation of Metabolite Alteration under Flooding Stress in Soybeans

Evaluation of Metabolite Alteration under Flooding Stress in Soybeans

Metabolic Control of Redox and Redox Control of Metabolism in Plants

Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research

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