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Huang F, He Y. Epigenetic control of gene expression by cellular metabolisms in plants. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102572. [PMID: 38875845 DOI: 10.1016/j.pbi.2024.102572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/09/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
Covalent modifications on DNA and histones can regulate eukaryotic gene expression and are often referred to as epigenetic modifications. These chemical reactions require various metabolites as donors or co-substrates, such as acetyl coenzyme A, S-adenosyl-l-methionine, and α-ketoglutarate. Metabolic processes that take place in the cytoplasm, nucleus, or other cellular compartments may impact epigenetic modifications in the nucleus. Here, we review recent advances on metabolic control of chromatin modifications and thus gene expression in plants, with a focus on the functions of nuclear compartmentalization of metabolic processes and enzymes in DNA and histone modifications. Furthermore, we discuss the functions of cellular metabolisms in fine-tuning gene expression to facilitate the responses or adaptation to environmental changes in plants.
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Affiliation(s)
- Fei Huang
- Peking-Tsinghua Center for Life Sciences & National Key Laboratory of Wheat Improvement, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yuehui He
- Peking-Tsinghua Center for Life Sciences & National Key Laboratory of Wheat Improvement, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China.
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Li L, Lu X, Dai P, Ma H. DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages. Int J Mol Sci 2024; 25:2964. [PMID: 38474210 DOI: 10.3390/ijms25052964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.
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Affiliation(s)
- Lijie Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaochen Lu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Ping Dai
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Huaiyu Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
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Yu A, Zhou Z, Chen Y, Sun J, Li P, Gu X, Liu A. Functional Genome Analyses Reveal the Molecular Basis of Oil Accumulation in Developing Seeds of Castor Beans. Int J Mol Sci 2023; 25:92. [PMID: 38203263 PMCID: PMC10778879 DOI: 10.3390/ijms25010092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Castor (Ricinus communis L.) seeds produce abundant ricinoleic acid during seed maturation, which is important for plant development and human demands. Ricinoleic acid, as a unique hydroxy fatty acid (HFA), possesses a distinct bond structure that could be used as a substitute for fossil fuels. Here, we identified all homologous genes related to glycolysis, hydroxy fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in castor seeds. Furthermore, we investigated their expression patterns globally during five seed development stages. We characterized a total of 66 genes involved in the glycolysis pathway, with the majority exhibiting higher expression levels during the early stage of castor bean seed development. This metabolic process provided abundant acetyl-CoA for fatty acid (FA) biosynthesis. Subsequently, we identified 82 genes involved in the processes of de novo FA biosynthesis and TAG assembly, with the majority exhibiting high expression levels during the middle or late stages. In addition, we examined the expression patterns of the transcription factors involved in carbohydrate and oil metabolism. For instance, RcMYB73 and RcERF72 exhibited high expression levels during the early stage, whereas RcWRI1, RcABI3, and RcbZIP67 showed relatively higher expression levels during the middle and late stages, indicating their crucial roles in seed development and oil accumulation. Our study suggests that the high HFA production in castor seeds is attributed to the interaction of multiple genes from sugar transportation to lipid droplet packaging. Therefore, this research comprehensively characterizes all the genes related to glycolysis, fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in the castor and provides novel insight into exploring the genetic mechanisms underlying seed oil accumulation in the endosperm of castor beans.
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Affiliation(s)
| | | | | | | | | | | | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (A.Y.); (Z.Z.); (Y.C.); (J.S.); (P.L.); (X.G.)
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Caldana C, Carrari F, Fernie AR, Sampathkumar A. How metabolism and development are intertwined in space and time. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:347-359. [PMID: 37433681 DOI: 10.1111/tpj.16391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
Developmental transitions, occurring throughout the life cycle of plants, require precise regulation of metabolic processes to generate the energy and resources necessary for the committed growth processes. In parallel, the establishment of new cells, tissues, and even organs, alongside their differentiation provoke profound changes in metabolism. It is increasingly being recognized that there is a certain degree of feedback regulation between the components and products of metabolic pathways and developmental regulators. The generation of large-scale metabolomics datasets during developmental transitions, in combination with molecular genetic approaches has helped to further our knowledge on the functional importance of metabolic regulation of development. In this perspective article, we provide insights into studies that elucidate interactions between metabolism and development at the temporal and spatial scales. We additionally discuss how this influences cell growth-related processes. We also highlight how metabolic intermediates function as signaling molecules to direct plant development in response to changing internal and external conditions.
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Affiliation(s)
- Camila Caldana
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Fernando Carrari
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arun Sampathkumar
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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Zhou M, Yuan Y, Lin J, Lin L, Zhou J, Li Z. γ-Aminobutyric Acid Priming Alleviates Acid-Aluminum Toxicity to Creeping Bentgrass by Regulating Metabolic Homeostasis. Int J Mol Sci 2023; 24:14309. [PMID: 37762612 PMCID: PMC10532299 DOI: 10.3390/ijms241814309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Aluminum (Al) toxicity is a major limiting factor for plant growth and crop production in acidic soils. This study aims to investigate the effects of γ-aminobutyric acid (GABA) priming on mitigating acid-Al toxicity to creeping bentgrass (Agrostis stolonifera) associated with changes in plant growth, photosynthetic parameters, antioxidant defense, key metabolites, and genes related to organic acids metabolism. Thirty-seven-old plants were primed with or without 0.5 mM GABA for three days and then subjected to acid-Al stress (5 mmol/L AlCl3·6H2O, pH 4.35) for fifteen days. The results showed that acid-Al stress significantly increased the accumulation of Al and also restricted aboveground and underground growths, photosynthesis, photochemical efficiency, and osmotic balance, which could be effectively alleviated by GABA priming. The application of GABA significantly activated antioxidant enzymes, including superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase, to reduce oxidative damage to cells under acid-Al stress. Metabolomics analysis demonstrated that the GABA pretreatment significantly induced the accumulation of many metabolites such as quinic acid, pyruvic acid, shikimic acid, glycine, threonine, erythrose, glucose-6-phosphate, galactose, kestose, threitol, ribitol, glycerol, putrescine, galactinol, and myo-inositol associated with osmotic, antioxidant, and metabolic homeostases under acid-Al stress. In addition, the GABA priming significantly up-regulated genes related to the transportation of malic acid and citric acid in leaves in response to acid-Al stress. Current findings indicated GABA-induced tolerance to acid-Al stress in relation to scavenging of reactive oxygen species, osmotic adjustment, and accumulation and transport of organic metabolites in leaves. Exogenous GABA priming could improve the phytoremediation potential of perennial creeping bentgrass for the restoration of Al-contaminated soils.
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Affiliation(s)
| | | | | | | | | | - Zhou Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.Z.); (Y.Y.); (L.L.); (J.Z.)
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Chen J, Cao J, Bian Y, Zhang H, Li X, Wu Z, Guo G, Lv G. Identification of Genetic Variations and Candidate Genes Responsible for Stalk Sugar Content and Agronomic Traits in Fresh Corn via GWAS across Multiple Environments. Int J Mol Sci 2022; 23:ijms232113490. [PMID: 36362278 PMCID: PMC9655584 DOI: 10.3390/ijms232113490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/10/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
The stem and leaves of fresh corn plants can be used as green silage or can be converted to biofuels, and the stalk sugar content and yield directly determine the application value of fresh corn. To identify the genetic variations and candidate genes responsible for the related traits in fresh corn, the genome-wide scan and genome-wide association analysis (GWAS) were performed. A total of 32 selective regions containing 172 genes were detected between sweet and waxy corns. Using the stalk sugar content and seven other agronomic traits measured in four seasons over two years, the GWAS identified ninety-two significant single nucleotide polymorphisms (SNPs). Most importantly, seven SNPs associated with the stalk sugar content were detected across multiple environments, which could explain 13.68–17.82% of the phenotypic variation. Accessions differing in genotype for certain significant SNPs showed significant variation in the stalk sugar content and other agronomic traits, and the expression levels of six important candidate genes were significantly different between two materials with different stalk sugar content. The genetic variations and candidate genes provide valuable resources for future studies of the molecular mechanism of the stalk sugar content and establish the foundation for molecular marker-assisted breeding of fresh corn.
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Affiliation(s)
- Jianjian Chen
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
| | - Jinming Cao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yunlong Bian
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Hui Zhang
- Zhejiang Agricultural Technology Extension Center, Hangzhou 310004, China
| | - Xiangnan Li
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
| | - Zhenxing Wu
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
| | - Guojin Guo
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
| | - Guihua Lv
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
- Correspondence: ; Tel.: +86-013454997051
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Yuan J, Cheng L, Li H, An C, Wang Y, Zhang F. Physiological and protein profiling analysis provides insight into the underlying molecular mechanism of potato tuber development regulated by jasmonic acid in vitro. BMC PLANT BIOLOGY 2022; 22:481. [PMID: 36210448 PMCID: PMC9549635 DOI: 10.1186/s12870-022-03852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Jasmonates (JAs) are one of important phytohormones regulating potato tuber development. It is a complex process and the underlying molecular mechanism regulating tuber development by JAs is still limited. This study attempted to illuminate it through the potential proteomic dynamics information about tuber development in vitro regulated by exogenous JA. RESULTS A combined analysis of physiological and iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic approach was performed in tuber development in vitro under exogenous JA treatments (0, 0.5, 5 and 50 μΜ). Physiological results indicated that low JA concentration (especially 5 μM) promoted tuber development, whereas higher JA concentration (50 μM) showed inhibition effect. A total of 257 differentially expressed proteins (DEPs) were identified by iTRAQ, which provided a comprehensive overview on the functional protein profile changes of tuber development regulated by JA. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that low JA concentration (especially 5 μM) exhibited the promotion effects on tuber development in various cellular processes. Some cell wall polysaccharide synthesis and cytoskeleton formation-related proteins were up-regulated by JA to promote tuber cell expansion. Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development. CONCLUSIONS This study is the first to integrate physiological and proteomic data to provide useful information about the JA-signaling response mechanism of potato tuber development in vitro. The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA.
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Affiliation(s)
- Jianlong Yuan
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lixiang Cheng
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Huijun Li
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Congcong An
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Feng Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
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Lee CP, Elsässer M, Fuchs P, Fenske R, Schwarzländer M, Millar AH. The versatility of plant organic acid metabolism in leaves is underpinned by mitochondrial malate-citrate exchange. THE PLANT CELL 2021; 33:3700-3720. [PMID: 34498076 PMCID: PMC8643697 DOI: 10.1093/plcell/koab223] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/31/2021] [Indexed: 05/07/2023]
Abstract
Malate and citrate underpin the characteristic flexibility of central plant metabolism by linking mitochondrial respiratory metabolism with cytosolic biosynthetic pathways. However, the identity of mitochondrial carrier proteins that influence both processes has remained elusive. Here we show by a systems approach that DICARBOXYLATE CARRIER 2 (DIC2) facilitates mitochondrial malate-citrate exchange in vivo in Arabidopsis thaliana. DIC2 knockout (dic2-1) retards growth of vegetative tissues. In vitro and in organello analyses demonstrate that DIC2 preferentially imports malate against citrate export, which is consistent with altered malate and citrate utilization in response to prolonged darkness of dic2-1 plants or a sudden shift to darkness of dic2-1 leaves. Furthermore, isotopic glucose tracing reveals a reduced flux towards citrate in dic2-1, which results in a metabolic diversion towards amino acid synthesis. These observations reveal the physiological function of DIC2 in mediating the flow of malate and citrate between the mitochondrial matrix and other cell compartments.
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Affiliation(s)
- Chun Pong Lee
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Marlene Elsässer
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Philippe Fuchs
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
- Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
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Du W, Zhang Y, Si J, Zhang Y, Fan S, Xia H, Kong L. Nitrate alleviates ammonium toxicity in wheat ( Triticum aestivum L.) by regulating tricarboxylic acid cycle and reducing rhizospheric acidification and oxidative damage. PLANT SIGNALING & BEHAVIOR 2021; 16:1991687. [PMID: 34753392 PMCID: PMC9208799 DOI: 10.1080/15592324.2021.1991687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Ammonium (NH4+) is one of the most important nutrients required by plants. However, a high concentration of NH4+ as the sole nitrogen source suppresses plant growth. Although nitrate (NO3-) can alleviate NH4+ toxicity, the mechanisms underlying this ability have not been fully elucidated. In this study, wheat plants were cultivated in hydroponic solution with 7.5 mM NO3- (control), 7.5 mM NH4+ (sole ammonium, SA) or 7.5 mM NH4+ plus 1.0 mM NO3- (ammonium and nitrate, AN). The results showed that compared with the control, the SA treatment significantly decreased root growth, protein content and the concentrations of most intermediates and the activity of enzymes from the tricarboxylic acid (TCA) cycle. Moreover, increased the activity of plasma membrane H+-ATPase and the rate of H+ efflux along roots, caused solution acidification, and increased the activity of mitochondrial respiratory chain complexes I-IV and the contents of protein-bound carbonyls and malondialdehyde in roots. SA treatment induced ultrastructure disruption and reduced the viability of root cells. Compared with the SA treatment, the AN treatment increased root growth, protein content, the concentrations of most intermediates and the activity of enzymes from the TCA cycle. Furthermore, AN treatment decreased the rate of H+ efflux, retarded medium acidification, decreased protein carbonylation and lipid peroxidation in roots and relieved ultrastructure disruption and increased the viability of root cells. Taken together, these results indicate that NO3--dependent alleviation of NH4+ toxicity in wheat seedlings is closely associated with physiological processes that mediate TCA cycle, relieve rhizospheric acidification and decrease the production of ROS and oxidative damage.
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Affiliation(s)
- Wanying Du
- College of Life Science, Shandong Normal University, Jinan, China
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunxiu Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jisheng Si
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yan Zhang
- College of Life Science, Shandong Normal University, Jinan, China
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shoujin Fan
- College of Life Science, Shandong Normal University, Jinan, China
| | - Haiyong Xia
- College of Life Science, Shandong Normal University, Jinan, China
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lingan Kong
- College of Life Science, Shandong Normal University, Jinan, China
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- CONTACT Lingan Kong Crop Research Institute, Shandong Academy of Agricultural Sciences , 202Gongyebei Road, Jinan250100, China
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Le XH, Lee CP, Millar AH. The mitochondrial pyruvate carrier (MPC) complex mediates one of three pyruvate-supplying pathways that sustain Arabidopsis respiratory metabolism. THE PLANT CELL 2021; 33:2776-2793. [PMID: 34137858 PMCID: PMC8408480 DOI: 10.1093/plcell/koab148] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/19/2021] [Indexed: 05/03/2023]
Abstract
Malate oxidation by plant mitochondria enables the generation of both oxaloacetate and pyruvate for tricarboxylic acid (TCA) cycle function, potentially eliminating the need for pyruvate transport into mitochondria in plants. Here, we show that the absence of the mitochondrial pyruvate carrier 1 (MPC1) causes the co-commitment loss of its putative orthologs, MPC3/MPC4, and eliminates pyruvate transport into Arabidopsis thaliana mitochondria, proving it is essential for MPC complex function. While the loss of either MPC or mitochondrial pyruvate-generating NAD-malic enzyme (NAD-ME) did not cause vegetative phenotypes, the lack of both reduced plant growth and caused an increase in cellular pyruvate levels, indicating a block in respiratory metabolism, and elevated the levels of branched-chain amino acids at night, a sign of alterative substrate provision for respiration. 13C-pyruvate feeding of leaves lacking MPC showed metabolic homeostasis was largely maintained except for alanine and glutamate, indicating that transamination contributes to the restoration of the metabolic network to an operating equilibrium by delivering pyruvate independently of MPC into the matrix. Inhibition of alanine aminotransferases when MPC1 is absent resulted in extremely retarded phenotypes in Arabidopsis, suggesting all pyruvate-supplying enzymes work synergistically to support the TCA cycle for sustained plant growth.
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Affiliation(s)
- Xuyen H. Le
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Chun-Pong Lee
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - A. Harvey Millar
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
- Author for correspondence:
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Moseler A, Kruse I, Maclean AE, Pedroletti L, Franceschetti M, Wagner S, Wehler R, Fischer-Schrader K, Poschet G, Wirtz M, Dörmann P, Hildebrandt TM, Hell R, Schwarzländer M, Balk J, Meyer AJ. The function of glutaredoxin GRXS15 is required for lipoyl-dependent dehydrogenases in mitochondria. PLANT PHYSIOLOGY 2021; 186:1507-1525. [PMID: 33856472 PMCID: PMC8260144 DOI: 10.1093/plphys/kiab172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/02/2021] [Indexed: 05/02/2023]
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors in all life and are used in a wide array of diverse biological processes, including electron transfer chains and several metabolic pathways. Biosynthesis machineries for Fe-S clusters exist in plastids, the cytosol, and mitochondria. A single monothiol glutaredoxin (GRX) is involved in Fe-S cluster assembly in mitochondria of yeast and mammals. In plants, the role of the mitochondrial homolog GRXS15 has only partially been characterized. Arabidopsis (Arabidopsis thaliana) grxs15 null mutants are not viable, but mutants complemented with the variant GRXS15 K83A develop with a dwarf phenotype similar to the knockdown line GRXS15amiR. In an in-depth metabolic analysis of the variant and knockdown GRXS15 lines, we show that most Fe-S cluster-dependent processes are not affected, including biotin biosynthesis, molybdenum cofactor biosynthesis, the electron transport chain, and aconitase in the tricarboxylic acid (TCA) cycle. Instead, we observed an increase in most TCA cycle intermediates and amino acids, especially pyruvate, glycine, and branched-chain amino acids (BCAAs). Additionally, we found an accumulation of branched-chain α-keto acids (BCKAs), the first degradation products resulting from transamination of BCAAs. In wild-type plants, pyruvate, glycine, and BCKAs are all metabolized through decarboxylation by mitochondrial lipoyl cofactor (LC)-dependent dehydrogenase complexes. These enzyme complexes are very abundant, comprising a major sink for LC. Because biosynthesis of LC depends on continuous Fe-S cluster supply to lipoyl synthase, this could explain why LC-dependent processes are most sensitive to restricted Fe-S supply in grxs15 mutants.
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Affiliation(s)
- Anna Moseler
- Institute of Crop Science and Resource Conservation (INRES)—Chemical Signalling, University of Bonn, 53113 Bonn, Germany
- Université de Lorraine, INRAE, IAM, Nancy 54000, France
| | - Inga Kruse
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
- Present address: Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G1 1XQ, UK
| | - Andrew E Maclean
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
- Present address: Wellcome Trust Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8TA, UK
| | - Luca Pedroletti
- Institute of Crop Science and Resource Conservation (INRES)—Chemical Signalling, University of Bonn, 53113 Bonn, Germany
| | | | - Stephan Wagner
- Institute of Crop Science and Resource Conservation (INRES)—Chemical Signalling, University of Bonn, 53113 Bonn, Germany
| | - Regina Wehler
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, 53115 Bonn, Germany
| | - Katrin Fischer-Schrader
- Department of Chemistry, Institute for Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Gernot Poschet
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, 53115 Bonn, Germany
| | | | - Rüdiger Hell
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP)—Plant Energy Biology, University of Münster, 48143 Münster, Germany
| | - Janneke Balk
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES)—Chemical Signalling, University of Bonn, 53113 Bonn, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich, 52425 Jülich, Germany
- Author for communication:
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12
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Zhang Y, Giese J, Kerbler SM, Siemiatkowska B, Perez de Souza L, Alpers J, Medeiros DB, Hincha DK, Daloso DM, Stitt M, Finkemeier I, Fernie AR. Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis. MOLECULAR PLANT 2021; 14:1104-1118. [PMID: 33798747 DOI: 10.1016/j.molp.2021.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/26/2021] [Accepted: 03/29/2021] [Indexed: 05/22/2023]
Abstract
Protein phosphorylation is a well-established post-translational mechanism that regulates protein functions and metabolic pathways. It is known that several plant mitochondrial proteins are phosphorylated in a reversible manner. However, the identities of the protein kinases/phosphatases involved in this mechanism and their roles in the regulation of the tricarboxylic acid (TCA) cycle remain unclear. In this study, we isolated and characterized plants lacking two mitochondrially targeted phosphatases (Sal2 and PP2c63) along with pyruvate dehydrogenase kinase (PDK). Protein-protein interaction analysis, quantitative phosphoproteomics, and enzymatic analyses revealed that PDK specifically regulates pyruvate dehydrogenase complex (PDC), while PP2c63 nonspecifically regulates PDC. When recombinant PP2c63 and Sal2 proteins were added to mitochondria isolated from mutant plants, protein-protein interaction and enzymatic analyses showed that PP2c63 directly phosphorylates and modulates the activity of PDC, while Sal2 only indirectly affects TCA cycle enzymes. Characterization of steady-state metabolite levels and fluxes in the mutant lines further revealed that these phosphatases regulate flux through the TCA cycle, and that altered metabolism in the sal2 pp2c63 double mutant compromises plant growth. These results are discussed in the context of current models of the control of respiration in plants.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Jonas Giese
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, 48149 Muenster, Germany
| | - Sandra M Kerbler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beata Siemiatkowska
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Leonardo Perez de Souza
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jessica Alpers
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - David Barbosa Medeiros
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Danilo M Daloso
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brasil
| | - Mark Stitt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, 48149 Muenster, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
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13
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Wang J, Liang C, Yang S, Song J, Li X, Dai X, Wang F, Juntawong N, Tan F, Zhang X, Jiao C, Zou X, Chen W. iTRAQ-based quantitative proteomic analysis of heat stress-induced mechanisms in pepper seedlings. PeerJ 2021; 9:e11509. [PMID: 34141478 PMCID: PMC8180192 DOI: 10.7717/peerj.11509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 05/03/2021] [Indexed: 11/30/2022] Open
Abstract
Background As one of the most important vegetable crops, pepper has rich nutritional value and high economic value. Increasing heat stress due to the global warming has a negative impact on the growth and yield of pepper. Methods To understand the heat stress response mechanism of pepper, an iTRAQ-based quantitative proteomic analysis was employed to identify possible heat-responsive proteins and metabolic pathways in 17CL30 and 05S180 pepper seedlings under heat stress. Result In the present study, we investigated the changes of phenotype, physiology, and proteome in heat-tolerant (17CL30) and heat-sensitive (05S180) pepper cultivars in response to heat stress. Phenotypic and physiological changes showed that 17CL30 had a stronger ability to resist heat stress compared with 05S180. In proteomic analysis, a total of 3,874 proteins were identified, and 1,591 proteins were considered to participate in the process of heat stress response. According to bioinformatic analysis of heat-responsive proteins, the heat tolerance of 17CL30 might be related to a higher ROS scavenging, photosynthesis, signal transduction, carbohydrate metabolism, and stress defense, compared with 05S180.
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Affiliation(s)
- Jing Wang
- Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China.,Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Chengliang Liang
- Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Sha Yang
- Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jingshuang Song
- Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xuefeng Li
- Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiongze Dai
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
| | - Fei Wang
- Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Niran Juntawong
- Faculty of Science, Department of Botany, Kasetsart University, Bangkok, Thailand
| | - Fangjun Tan
- Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xilu Zhang
- Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Chunhai Jiao
- Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Xuexiao Zou
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
| | - Wenchao Chen
- Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
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14
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Tisdale RH, Zobel RW, Burkey KO. Tropospheric ozone rapidly decreases root growth by altering carbon metabolism and detoxification capability in growing soybean roots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:144292. [PMID: 33418251 DOI: 10.1016/j.scitotenv.2020.144292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
High tropospheric ozone (O3) concentrations lead to significant global soybean (Glycine max) yield reductions. Research concerning O3 impacts on soybean has focused on the contributions of above-ground tissues. In this study, Mandarin (Ottawa) (O3-sensitive) and Fiskeby III (O3-tolerant) soybean genotypes provide contrasting materials to investigate O3 effects on root growth. We compared root morphological and proteomic changes when 16-day-old plants were treated with charcoal-filtered (CF) air or elevated O3 (80 ppb O3 for 7 h/day) in continuously stirred-tank reactors (CSTR) for 7 days. Our results showed that in Mandarin (Ottawa), decreased expression of enzymes involved in the tricarboxylic acid (TCA) cycle contributes to reduction of root biomass and diameter under elevated O3. In contrast, O3 tolerance in Fiskeby III roots was associated with O3-dependent induction of enzymes involved in glycolysis and O3-independent expression of enzymes involved in the ascorbate-glutathione cycle. We conclude that a decreased abundance of key redox enzymes in roots due to limited carbon availability rapidly alters root growth under O3 stress. However, maintaining a high abundance of enzymes associated with redox status and detoxification capability contributes to overall O3 tolerance in roots.
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Affiliation(s)
- Ripley H Tisdale
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA.
| | - Richard W Zobel
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA
| | - Kent O Burkey
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA
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15
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Zhang L, Feng P, Deng Y, Yin W, Wan Y, Lei T, He G, Wang N. Decreased Vascular Bundle 1 affects mitochondrial and plant development in rice. RICE (NEW YORK, N.Y.) 2021; 14:13. [PMID: 33492479 PMCID: PMC7835275 DOI: 10.1186/s12284-021-00454-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Mitochondria are vital regulators of plant growth and development, constitute the predominant source of ATP, and participate in multiple anabolic and catabolic metabolic pathways. But the mechanism by which dysfunctional mitochondria affect plant growth remains unknown, and more mitochondria-defective mutants need to be identified. RESULTS A mitochondria-defective mutant decreased vascular bundle 1 (dvb1) was isolated from rice mutant library mutagenized by EMS (ethylmethane sulfonate), which shows dwarfism, narrow leaves, short branches, few vascular bundles, and low fertility. Map-based cloning, genetic complementation, and phylogenetic analysis revealed that DVB1 encodes a structural protein classified in the Mic10 family and is required for the formation of cristae in mitochondria, and was primarily expressed in vascular bundles. The DVB1 protein is partially localized in the mitochondria and capable of forming dimers and polymers. Comparing with the wild type, disruption of amino acid metabolism and increased auxin synthesis were observed in dvb1 mutant which also showed increased sensitivity to the mitochondrial electron transport inhibitors. CONCLUSIONS DVB1 belongs to Mic10 family and DVB1 is partially localized in the mitochondria. Further studies indicated that DVB1 is important for mitochondrial and plant development in rice.
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Affiliation(s)
- Lisha Zhang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ping Feng
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yao Deng
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Wuzhong Yin
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yingchun Wan
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ting Lei
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guanghua He
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
| | - Nan Wang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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16
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Han HL, Liu J, Feng XJ, Zhang M, Lin QF, Wang T, Qi SL, Xu T, Hua XJ. SSR1 is involved in maintaining the function of mitochondria electron transport chain and iron homeostasis upon proline treatment in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2021; 256:153325. [PMID: 33271443 DOI: 10.1016/j.jplph.2020.153325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Although increasing intracellular proline under stressed condition could help the plants survive, treating plant with high level of proline under normal condition could be inhibitory to plant growth. Among other possible mechanisms, proline-induced mitochondrial reactive oxygen species (ROS) production due to electron overflow in mitochondria electron transport chain (mETC) caused by elevated proline degradation may contribute to the proline toxicity. However, direct evidences are still elusive. Here, we reported a functional characterization of SSR1, encoding a protein localized in mitochondria matrix, in maintaining the function of mETC through analyzing the proline hypersensitive phenotype of an Arabidopsis mutant ssr1-1 with a truncated SSR1 protein. Our analysis demonstrated that upon proline treatment, there were higher mitochondrial ROS, lower ATP content, reduced activity of mETC complex I and II, and reduced iron content in ssr1-1, in comparison to the wild type. Therefore, SSR1 is involved in maintaining normal capacity of mETC in transporting electrons in a way that related to iron homeostasis. Our results also supported that normal mETC activity is required for alleviating the proline toxicity.
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Affiliation(s)
- Hui Ling Han
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jie Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuan Jun Feng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Min Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Qing Fang Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Ting Wang
- College of Life Sciences, Shangrao Normal University, Shangrao, Jiangxi, 334001, China.
| | - Shi Lian Qi
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Tao Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.
| | - Xue Jun Hua
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.
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17
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Foong SL, Paek KH. Capsicum annum Hsp26.5 promotes defense responses against RNA viruses via ATAF2 but is hijacked as a chaperone for tobamovirus movement protein. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6142-6158. [PMID: 32640023 DOI: 10.1093/jxb/eraa320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
The expression of Capsicum annuum HEAT SHOCK PROTEIN 26.5 (CaHsp26.5) was triggered by the inoculation of Tobacco mosaic virus pathotype P0 (TMV-P0) but its function in the defense response of plants is unknown. We used gene silencing and overexpression approaches to investigate the effect of CaHsp26.5 expression on different plant RNA viruses. Moreover, we performed protein-protein and protein-RNA interaction assays to study the mechanism of CaHsp26.5 function. CaHsp26.5 binding to a short poly-cytosine motif in the 3'-untranslated region of the genome of some viruses triggers the expression of several defense-related genes such as PATHOGENESIS-RELATED GENE 1 with the help of a transcription factor, NAC DOMAIN-CONTAINING PROTEIN 81 (ATAF2). Thus, an elevated CaHsp26.5 level was accompanied by increased plant resistance against plant viruses such as Cucumber mosaic virus strain Korea. However, the movement proteins of Pepper mild mottle virus pathotype P1,2,3 and TMV-P0 were shown to be able to interact with CaHsp26.5 to maintain the integrity of their proteins. Our work shows CaHsp26.5 as a positive player in the plant defense response against several plant RNA viruses. However, some tobamoviruses can hijack CaHsp26.5's chaperone activity for their own benefit.
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Affiliation(s)
- Siew-Liang Foong
- Department of Life Sciences, Korea University, Seoul, Republic of Korea
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18
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Turk H, Genisel M. Melatonin-related mitochondrial respiration responses are associated with growth promotion and cold tolerance in plants. Cryobiology 2019; 92:76-85. [PMID: 31758919 DOI: 10.1016/j.cryobiol.2019.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/10/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Abstract
Melatonin has the ability to improve plant growth and strengthened plant tolerance to environmental stresses; however, the effects of melatonin on mitochondrial respiration in plants and the underlying biochemical and molecular mechanisms are still unclear. The objective of the study is to determine possible effects of melatonin on mitochondrial respiration and energy efficiency in maize leaves grown under optimum temperature and cold stress and to reveal the relationship between melatonin-induced possible alterations in mitochondrial respiration and cold tolerance. Melatonin and cold stress, alone and in combination, caused significant increases in activities and gene expressions of pyruvate dehydrogenase, citrate synthase, and malate dehydrogenase, indicating an acceleration in the rate of tricarboxylic acid cycle. Total mitochondrial respiration rate, cytochrome pathway rate, and alternative respiration rate were increased by the application of melatonin and/or cold stress. Similarly, gene expression and protein levels of cytochrome oxidase and alternative oxidase were also enhanced by melatonin and/or cold stress. The highest values for all these parameters were obtained from the seedlings treated with the combined application of melatonin and cold stress. The activity and gene expression of ATP synthase and ATP concentration were augmented by melatonin under control and cold stress. On the other hand, cold stress reduced markedly plant growth parameters, including root length, plant height, leaf surface area, and chlorophyll content and increased the content of reactive oxygen species (ROS), including superoxide anion and hydrogen peroxide and oxidative damage, including malondialdehyde content and electrolyte leakage level; however, melatonin significantly promoted the plant growth parameters and reduced ROS content and oxidative damage under control and cold stress. These data revealed that melatonin-induced growth promotion and cold tolerance in maize is associated with its modulating effect on mitochondrial respiration.
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Affiliation(s)
- Hulya Turk
- East Anatolian High Technology Application and Research Center, Ataturk University, Erzurum, Turkey.
| | - Mucip Genisel
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Agri Ibrahim Cecen University, Agri, Turkey
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19
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Launay A, Cabassa-Hourton C, Eubel H, Maldiney R, Guivarc’h A, Crilat E, Planchais S, Lacoste J, Bordenave-Jacquemin M, Clément G, Richard L, Carol P, Braun HP, Lebreton S, Savouré A. Proline oxidation fuels mitochondrial respiration during dark-induced leaf senescence in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6203-6214. [PMID: 31504781 PMCID: PMC6859731 DOI: 10.1093/jxb/erz351] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
Leaf senescence is a form of developmentally programmed cell death that allows the remobilization of nutrients and cellular materials from leaves to sink tissues and organs. Among the catabolic reactions that occur upon senescence, little is known about the role of proline catabolism. In this study, the involvement in dark-induced senescence of proline dehydrogenases (ProDHs), which catalyse the first and rate-limiting step of proline oxidation in mitochondria, was investigated using prodh single- and double-mutants with the help of biochemical, proteomic, and metabolomic approaches. The presence of ProDH2 in mitochondria was confirmed by mass spectrometry and immunogold labelling in dark-induced leaves of Arabidopsis. The prodh1 prodh2 mutant exhibited enhanced levels of most tricarboxylic acid cycle intermediates and free amino acids, demonstrating a role of ProDH in mitochondrial metabolism. We also found evidence of the involvement and the importance of ProDH in respiration, with proline as an alternative substrate, and in remobilization of proline during senescence to generate glutamate and energy that can then be exported to sink tissues and organs.
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Affiliation(s)
- Alban Launay
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Cécile Cabassa-Hourton
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Holger Eubel
- Institute of Plant Genetics, Plant Proteomics, Leibniz University Hannover, Hannover, Germany
| | - Régis Maldiney
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Anne Guivarc’h
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Emilie Crilat
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Séverine Planchais
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Jérôme Lacoste
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
- Present address: Sorbonne Université, CNRS, Institut de Biologie Paris Seine, IBPS, F-75005 Paris, France
| | - Marianne Bordenave-Jacquemin
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, UMR 1318, INRA-AgroParisTech, Centre INRA Versailles, Versailles Cedex, France
| | - Luc Richard
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Pierre Carol
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Hans-Peter Braun
- Institute of Plant Genetics, Plant Proteomics, Leibniz University Hannover, Hannover, Germany
| | - Sandrine Lebreton
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
- Correspondence: or
| | - Arnould Savouré
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
- Correspondence: or
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20
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Comparative analysis of proteomic and metabolomic profiles of different species of Paris. J Proteomics 2019; 200:11-27. [PMID: 30890455 DOI: 10.1016/j.jprot.2019.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/12/2019] [Accepted: 02/01/2019] [Indexed: 02/08/2023]
Abstract
An extract prepared from species of Paris is the most widely consumed herbal product in China. The genus Paris includes a variety of genotypes with different medicinal component contents but only two are defined as official sources. Closely related species have different medicinal properties because of differential expression of proteins and metabolites. To better understand the molecular basis of these differences, we examined proteomic and metabolomic changes in rhizomes of P. polyphylla var. chinensis, P. polyphylla var. yunnanensis, and P. fargesii var. fargesii using a technique known as sequential window acquisition of all theoretical mass spectra as well as gas chromatography-time-of-flight mass spectrometry. In total, 419 proteins showed significant abundance changes, and 33 metabolites could be used to discriminate Paris species. A complex analysis of proteomic and metabolomic data revealed a higher efficiency of sucrose utilization and an elevated protein abundance in the sugar metabolic pathway of P. polyphylla var. chinensis. The pyruvate content and efficiency of acetyl-CoA-utilization in saponin biosynthesis were also higher in P. polyphylla var. chinensis than in the other two species. The results expand our understanding of the proteome and metabolome of Paris and offer new insights into the species-specific traits of these herbaceous plants. SIGNIFICANCE: The traditional Chinese medicine Paris is the most widely consumed herbal product for the treatment of joint pain, rheumatoid arthritis and antineoplastic. All Paris species have roughly the same morphological characteristics; however, different members have different medicinal compound contents. Efficient exploitation of genetic diversity is a key factor in the development of rare medicinal plants with improved agronomic traits and malleability to challenging environmental conditions. Nevertheless, only a partial understanding of physiological and molecular mechanisms of different plants of Paris can be achieved without proteomics. To better understand the molecular basis of these differences and facilitate the use of other Paris species, we examine proteomic metabolomic changes in rhizomes of Paris using the technique known as SWATH-MS and GC/TOF-MS. Our research has provided information that can be used in other studies to compare metabolic traits in different Paris species. Our findings can also serve as a theoretical basis for the selection and cultivation of other Paris species with a higher medicinal value.
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21
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Fan X, Xu J, Lavoie M, Peijnenburg WJGM, Zhu Y, Lu T, Fu Z, Zhu T, Qian H. Multiwall carbon nanotubes modulate paraquat toxicity in Arabidopsis thaliana. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 233:633-641. [PMID: 29107903 DOI: 10.1016/j.envpol.2017.10.116] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/05/2017] [Accepted: 10/28/2017] [Indexed: 05/21/2023]
Abstract
Carbon nanotubes can be either toxic or beneficial to plant growth and can also modulate toxicity of organic contaminants through surface sorption. The complex interacting toxic effects of carbon nanotubes and organic contaminants in plants have received little attention in the literature to date. In this study, the toxicity of multiwall carbon nanotubes (MWCNT, 50 mg/L) and paraquat (MV, 0.82 mg/L), separately or in combination, were evaluated at the physiological and the proteomic level in Arabidopsis thaliana for 7-14 days. The results revealed that the exposure to MWCNT had no inhibitory effect on the growth of shoots and leaves. Rather, MWCNT stimulated the relative electron transport rate and the effective photochemical quantum yield of PSII value as compared to the control by around 12% and lateral root production up to nearly 4-fold as compared to the control. The protective effect of MWCNT on MV toxicity on the root surface area could be quantitatively explained by the extent of MV adsorption on MWCNT and was related to stimulation of photosynthesis, antioxidant protection and number and area of lateral roots which in turn helped nutrient assimilation. The influence of MWCNT and MV on photosynthesis and oxidative stress at the physiological level was consistent with the proteomics analysis, with various over-expressed photosynthesis-related proteins (by more than 2 folds) and various under-expressed oxidative stress related proteins (by about 2-3 folds). This study brings new insights into the interactive effects of two xenobiotics (MWCNT and MV) on the physiology of a model plant.
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Affiliation(s)
- Xiaoji Fan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Jiahui Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Michel Lavoie
- Quebec-Ocean and Takuvik Joint International Research Unit, Université Laval, Québec, Canada
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA, Leiden, The Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, The Netherlands
| | - Youchao Zhu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tingheng Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
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22
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Proteomics reveals key proteins participating in growth difference between fall dormant and non-dormant alfalfa in terminal buds. J Proteomics 2017; 173:126-138. [PMID: 29229487 DOI: 10.1016/j.jprot.2017.11.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/18/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022]
Abstract
To explore the molecular mechanism of growth differences between fall dormant (FD) and non-FD alfalfa, we conducted iTRAQ-based quantitative proteomics on terminal buds of Maverick (FD) and Cuf101 (non-FD) cultivars, identified differential abundance protein species (DAPS) and verified expression profiling of certain corresponding mRNA by qRT-PCR. A total of 3872 protein species were annotated. Of the 90 DAPS, 56 and 34 were respectively up- and down-accumulated in Maverick, compared to Cuf101. They were grouped into 35 functional categories and enriched in seven pathways. Of which, auxin polar transport was up-regulated, while phenylpropanoid biosynthesis, pyruvate metabolism and transportation, vitamin B1 synthesis process and flavonoid biosynthesis were down-regulated in Maverick, comparing with Cuf101. In Maverick, mRNA abundances of l-asparaginase, chalcone and stilbene synthase family protein, cinnamyl alcohol dehydrogenase-like protein, thiazole biosynthetic enzyme, pyruvate dehydrogenase E1 beta subunit, and aldo/keto reductase family oxidoreductase were significantly lower at FD than at other stages, and lower than in Cuf101. We also observed opposite mRNA profiles of thiazole biosynthetic enzyme, chalcone and stilbene synthase family protein, pyruvate dehydrogenase E1 beta subunit in both cultivars from summer to autumn. Our results suggest that these DAPS could play important roles in growth difference between FD and non-FD alfalfa. BIOLOGICAL SIGNIFICANCE Up to now, as far as we know, currently the proteins related with the growth differences between FD and non-FD alfalfa cultivars in autumn have not yet been identified in terminal buds. This study identified the protein species expressed in alfalfa terminal buds, selected differentially abundant protein species in terminal buds between Maverick (FD) and Cuf101 (non-FD) cultivars in autumn and identified the important protein species participated in the growth differences. This study lays a foundation for further investigation of the molecular mechanism of the growth differences between FD and non-FD alfalfa and the cultivation of advanced alfalfa cultivars.
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23
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Che-Othman MH, Millar AH, Taylor NL. Connecting salt stress signalling pathways with salinity-induced changes in mitochondrial metabolic processes in C3 plants. PLANT, CELL & ENVIRONMENT 2017; 40:2875-2905. [PMID: 28741669 DOI: 10.1111/pce.13034] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/26/2017] [Accepted: 07/09/2017] [Indexed: 05/12/2023]
Abstract
Salinity exerts a severe detrimental effect on crop yields globally. Growth of plants in saline soils results in physiological stress, which disrupts the essential biochemical processes of respiration, photosynthesis, and transpiration. Understanding the molecular responses of plants exposed to salinity stress can inform future strategies to reduce agricultural losses due to salinity; however, it is imperative that signalling and functional response processes are connected to tailor these strategies. Previous research has revealed the important role that plant mitochondria play in the salinity response of plants. Review of this literature shows that 2 biochemical processes required for respiratory function are affected under salinity stress: the tricarboxylic acid cycle and the transport of metabolites across the inner mitochondrial membrane. However, the mechanisms by which components of these processes are affected or react to salinity stress are still far from understood. Here, we examine recent findings on the signal transduction pathways that lead to adaptive responses of plants to salinity and discuss how they can be involved in and be affected by modulation of the machinery of energy metabolism with attention to the role of the tricarboxylic acid cycle enzymes and mitochondrial membrane transporters in this process.
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Affiliation(s)
- M Hafiz Che-Othman
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
- School of Bioscience and Biotechnology, Faculty of Science and Technology, National University of Malaysia, Bangi, Selangor, 43600, Malaysia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Nicolas L Taylor
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
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24
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Shen JL, Li CL, Wang M, He LL, Lin MY, Chen DH, Zhang W. Mitochondrial pyruvate carrier 1 mediates abscisic acid-regulated stomatal closure and the drought response by affecting cellular pyruvate content in Arabidopsis thaliana. BMC PLANT BIOLOGY 2017; 17:217. [PMID: 29166881 PMCID: PMC5700692 DOI: 10.1186/s12870-017-1175-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/13/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Stomata are micropores surrounded by pairs of guard cells, and their opening is finely controlled to balance water vapor loss as transpiration and CO2 absorption for photosynthesis. The regulatory signaling network for stomatal movement is complicated, and increasing numbers of new genes have been shown to be involved in this process. Our previous study indicated that a member of the plant putative mitochondrial pyruvate carrier (MPC) family, NRGA1, is a negative regulator of guard cell abscisic acid (ABA) signaling. In this study, we identified novel physiological roles of pyruvate and MPC1, another member of the MPC family, in the regulation of stomatal closure in Arabidopsis. RESULTS Loss-of-function mutants of MPC1 (mpc1) were hypersensitive to ABA-induced stomatal closure and ABA-activated guard cell slow-type anion currents, and showed a reduced rate of water loss upon drought treatment compared with wild-type plants. In contrast, plants overexpressing MPC1 showed a hyposensitive ABA response and increased sensitivity to drought stress. In addition, mpc1 mutants accumulated more pyruvate after drought or ABA treatment. The increased pyruvate content also induced stomatal closure and activated the slow-type anion channels of guard cells, and this process was dependent on the function of RbohD/F NADPH oxidases and reactive oxygen species concentrations in guard cells. CONCLUSIONS Our findings revealed the essential roles of MPC1 and pyruvate in stomatal movement and plant drought resistance.
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Affiliation(s)
- Jian-Lin Shen
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100 China
| | - Chun-Long Li
- College of Life Science, Jiangsu Normal University, Xuzhou, 221116 China
| | - Mei Wang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100 China
| | - Li-Long He
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100 China
| | - Min-Yan Lin
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100 China
| | - Dong-Hua Chen
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100 China
| | - Wei Zhang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100 China
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25
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Silva AT, Ligterink W, Hilhorst HWM. Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2017; 95:481-496. [PMID: 29046998 PMCID: PMC5688192 DOI: 10.1007/s11103-017-0665-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 10/04/2017] [Indexed: 05/02/2023]
Abstract
Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational. The transition involves several developmental stages from seed germination to seedling establishment, i.e. between imbibition of the mature dry seed and opening of the cotyledons, the final stage of seedling establishment. We hypothesized that the advancement of growth is associated with certain signature metabolite profiles. Metabolite-metabolite correlation analysis underlined two specific profiles which appear to be involved in the metabolic preparation for seed germination and efficient seedling establishment, respectively. Metabolite profiles were also compared to transcript profiles and although transcriptional changes did not always equate to a proportional metabolic response, in depth correlation analysis identified several transcripts that may directly influence the flux through metabolic pathways during the seed-to-seedling transition. This correlation analysis also pinpointed metabolic pathways which are significant for the seed-to-seedling transition, and metabolite contents that appeared to be controlled directly by transcript abundance. This global view of the transcriptional and metabolic changes during the seed-to-seedling transition in Arabidopsis opens up new perspectives for understanding the complex regulatory mechanism underlying this transition.
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Affiliation(s)
- Anderson Tadeu Silva
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA.
| | - Wilco Ligterink
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Henk W M Hilhorst
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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26
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Gipson AB, Morton KJ, Rhee RJ, Simo S, Clayton JA, Perrett ME, Binkley CG, Jensen EL, Oakes DL, Rouhier MF, Rouhier KA. Disruptions in valine degradation affect seed development and germination in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1029-1039. [PMID: 28321931 PMCID: PMC5461199 DOI: 10.1111/tpj.13538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 03/07/2017] [Accepted: 03/10/2017] [Indexed: 05/20/2023]
Abstract
We have functionally characterized the role of two putative mitochondrial enzymes in valine degradation using insertional mutants. Prior to this study, the relationship between branched-chain amino acid degradation (named for leucine, valine and isoleucine) and seed development was limited to leucine catabolism. Using a reverse genetics approach, we show that disruptions in the mitochondrial valine degradation pathway affect seed development and germination in Arabidopsis thaliana. A null mutant of 3-hydroxyisobutyryl-CoA hydrolase (CHY4, At4g31810) resulted in an embryo lethal phenotype, while a null mutant of methylmalonate semialdehyde dehydrogenase (MMSD, At2g14170) resulted in seeds with wrinkled coats, decreased storage reserves, elevated valine and leucine, and reduced germination rates. These data highlight the unique contributions CHY4 and MMSD make to the overall growth and viability of plants. It also increases our knowledge of the role branched-chain amino acid catabolism plays in seed development and amino acid homeostasis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Kerry A. Rouhier
- Kenyon College 200 N. College Rd, Gambier, OH 43022
- Doan University 1014 Boswell Ave, Crete, NE 68333
- Corresponding author: Kerry A. Rouhier, 200 N. College Rd, Gambier, OH 43022, USA tel: (740) 427-5359, fax: (740) 427-5731,
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27
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Van Dingenen J, Blomme J, Gonzalez N, Inzé D. Plants grow with a little help from their organelle friends. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6267-6281. [PMID: 27815330 DOI: 10.1093/jxb/erw399] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chloroplasts and mitochondria are indispensable for plant development. They not only provide energy and carbon sources to cells, but also have evolved to become major players in a variety of processes such as amino acid metabolism, hormone biosynthesis and cellular signalling. As semi-autonomous organelles, they contain a small genome that relies largely on nuclear factors for its maintenance and expression. An intensive crosstalk between the nucleus and the organelles is therefore essential to ensure proper functioning, and the nuclear genes encoding organellar proteins involved in photosynthesis and oxidative phosphorylation are obviously crucial for plant growth. Organ growth is determined by two main cellular processes: cell proliferation and cell expansion. Here, we review how plant growth is affected in mutants of organellar proteins that are differentially expressed during leaf and root development. Our findings indicate a clear role for organellar proteins in plant organ growth, primarily during cell proliferation. However, to date, the role of the nuclear-encoded organellar proteins in the cellular processes driving organ growth has not been investigated in much detail. We therefore encourage researchers to extend their phenotypic characterization beyond macroscopic features in order to get a better view on how chloroplasts and mitochondria regulate the basic processes of cell proliferation and cell expansion, essential to driving growth.
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Affiliation(s)
- Judith Van Dingenen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jonas Blomme
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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28
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Ma X, Xu Q, Meyer WA, Huang B. Hormone regulation of rhizome development in tall fescue (Festuca arundinacea) associated with proteomic changes controlling respiratory and amino acid metabolism. ANNALS OF BOTANY 2016; 118:481-94. [PMID: 27443301 PMCID: PMC4998981 DOI: 10.1093/aob/mcw120] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/17/2016] [Accepted: 04/18/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Rhizomes are underground stems with meristematic tissues capable of generating shoots and roots. However, mechanisms controlling rhizome formation and growth are yet to be completely understood. The objectives of this study were to investigate whether rhizome development could be regulated by cytokinins (CKs) and gibberellic acids (GAs), and determine underlying mechanisms of regulation of rhizome formation and growth of tall fescue (Festuca arundinacea) by a CK or GA through proteomic and transcript analysis. METHODS A rhizomatous genotype of tall fescue ('BR') plants were treated with 6-benzylaminopurine (BAP, a synthetic cytokinin) or GA3 in hydroponic culture in growth chambers. Furthermore, comparative proteomic analysis of two-dimensional electrophoresis and mass spectrometry were performed to investigate proteins and associated metabolic pathways imparting increased rhizome number by BAP and rhizome elongation by GA3 KEY RESULTS: BAP stimulated rhizome formation while GA3 promoted rhizome elongation. Proteomic analysis identified 76 differentially expressed proteins (DEPs) due to BAP treatment and 37 DEPs due to GA3 treatment. Cytokinin-related genes and cell division-related genes were upregulated in the rhizome node by BAP and gibberellin-related and cell growth-related genes in the rhizome by GA3 CONCLUSIONS: Most of the BAP- or GA-responsive DEPs were involved in respiratory metabolism and amino acid metabolism. Transcription analysis demonstrated that genes involved in hormone metabolism, signalling pathways, cell division and cell-wall loosening were upregulated by BAP or GA3 The CK and GA promoted rhizome formation and growth, respectively, by activating metabolic pathways that supply energy and amino acids to support cell division and expansion during rhizome initiation and elongation in tall fescue.
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Affiliation(s)
- Xiqing Ma
- College of Agro-grassland Science Nanjing Agricultural University, Nanjing 210095, PR China Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Qian Xu
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, PR China
| | - William A Meyer
- Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
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29
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Song L, Liu D. Mutations in the three Arabidopsis genes that encode the E2 subunit of the mitochondrial pyruvate dehydrogenase complex differentially affect enzymatic activity and plant growth. PLANT CELL REPORTS 2015; 34:1919-26. [PMID: 26194327 DOI: 10.1007/s00299-015-1838-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/23/2015] [Accepted: 07/01/2015] [Indexed: 05/24/2023]
Abstract
Three members of the E2 subunit of the Arabidopsis mitochondrial pyruvate dehydrogenase (mtPDC) complex differentially affect mtPDC activity and plant growth. In all organisms, the mitochondrial pyruvate dehydrogenase complex (mtPDC) consists of three components: E1, E2, and E3. In this multi-enzyme complex, the E2 subunits form the core structure. In Arabidopsis, the E2 subunits are encoded by three genes: mtE2-1, mtE2-2, and mtE2-3. The contribution of each mtE2 gene to total mtPDC activity, however, is unknown. In this study, we show that knockdown of the expression of the mtE2-1 gene to 17% of that in the wild type has only a slight effect on plant growth whereas knockout of mtE2-2 leads to an embryo-lethal phenotype. The nearly null mutation of mtE2-3 does not cause any developmental abnormality. Based on these results, we conclude that mtE2-2 plays a major role in determining the total activity of the mtPDC in Arabidopsis while mtE2-1 and mtE2-3 are more or less functionally redundant with mtE2-2 under normal growth condition. Our results provide genetic evidence for a recently proposed novel mechanism that regulates plant mtPDC activity.
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Affiliation(s)
- Li Song
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Dong Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, People's Republic of China.
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30
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Schertl P, Braun HP. Respiratory electron transfer pathways in plant mitochondria. FRONTIERS IN PLANT SCIENCE 2014; 5:163. [PMID: 24808901 PMCID: PMC4010797 DOI: 10.3389/fpls.2014.00163] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/07/2014] [Indexed: 05/18/2023]
Abstract
The respiratory electron transport chain (ETC) couples electron transfer from organic substrates onto molecular oxygen with proton translocation across the inner mitochondrial membrane. The resulting proton gradient is used by the ATP synthase complex for ATP formation. In plants, the ETC is especially intricate. Besides the "classical" oxidoreductase complexes (complex I-IV) and the mobile electron transporters cytochrome c and ubiquinone, it comprises numerous "alternative oxidoreductases." Furthermore, several dehydrogenases localized in the mitochondrial matrix and the mitochondrial intermembrane space directly or indirectly provide electrons for the ETC. Entry of electrons into the system occurs via numerous pathways which are dynamically regulated in response to the metabolic state of a plant cell as well as environmental factors. This mini review aims to summarize recent findings on respiratory electron transfer pathways in plants and on the involved components and supramolecular assemblies.
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Affiliation(s)
| | - Hans-Peter Braun
- Abteilung Pflanzenproteomik, Institut für Pflanzengenetik, Leibniz Universität HannoverHannover, Germany
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31
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Nägele T, Mair A, Sun X, Fragner L, Teige M, Weckwerth W. Solving the differential biochemical Jacobian from metabolomics covariance data. PLoS One 2014; 9:e92299. [PMID: 24695071 PMCID: PMC3977476 DOI: 10.1371/journal.pone.0092299] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 02/20/2014] [Indexed: 11/19/2022] Open
Abstract
High-throughput molecular analysis has become an integral part in organismal systems biology. In contrast, due to a missing systematic linkage of the data with functional and predictive theoretical models of the underlying metabolic network the understanding of the resulting complex data sets is lacking far behind. Here, we present a biomathematical method addressing this problem by using metabolomics data for the inverse calculation of a biochemical Jacobian matrix, thereby linking computer-based genome-scale metabolic reconstruction and in vivo metabolic dynamics. The incongruity of metabolome coverage by typical metabolite profiling approaches and genome-scale metabolic reconstruction was solved by the design of superpathways to define a metabolic interaction matrix. A differential biochemical Jacobian was calculated using an approach which links this metabolic interaction matrix and the covariance of metabolomics data satisfying a Lyapunov equation. The predictions of the differential Jacobian from real metabolomic data were found to be correct by testing the corresponding enzymatic activities. Moreover it is demonstrated that the predictions of the biochemical Jacobian matrix allow for the design of parameter optimization strategies for ODE-based kinetic models of the system. The presented concept combines dynamic modelling strategies with large-scale steady state profiling approaches without the explicit knowledge of individual kinetic parameters. In summary, the presented strategy allows for the identification of regulatory key processes in the biochemical network directly from metabolomics data and is a fundamental achievement for the functional interpretation of metabolomics data.
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Affiliation(s)
- Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Andrea Mair
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Xiaoliang Sun
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Lena Fragner
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Markus Teige
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- * E-mail:
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32
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Nunes-Nesi A, Araújo WL, Obata T, Fernie AR. Regulation of the mitochondrial tricarboxylic acid cycle. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:335-43. [PMID: 23462640 DOI: 10.1016/j.pbi.2013.01.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 01/24/2013] [Accepted: 01/26/2013] [Indexed: 05/04/2023]
Abstract
Recent years have seen considerable advances in our understanding of the particular physiological roles of the constituent enzymes of the tricarboxylic acid (TCA) cycle. Despite acquiring a fairly comprehensive overview of the functional importance of these proteins relatively little is known concerning how this important pathway is regulated. In this review we concentrate on the mitochondrial reactions since this organelle is the only one in which a full cycle can, at least theoretically, operate. We summarize what is known about the regulation of the enzymes of the pathway both from historical kinetic studies as well as discussing more recent transcriptional and proteomic studies and our enhanced understanding of subcellular compartmentation within the context of metabolic regulation.
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Affiliation(s)
- Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-000 Viçosa, Minas Gerais, Brazil
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