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Tian J, Zhang F, Zhang G, Li X, Wen C, Li H. A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-L-methionine synthetase. PLANT PHYSIOLOGY 2024; 195:940-957. [PMID: 38417836 PMCID: PMC11142375 DOI: 10.1093/plphys/kiae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 03/01/2024]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in various biological processes. However, the regulatory roles of lncRNAs underlying fruit development have not been extensively studied. The pumpkin (Cucurbita spp.) is a preferred model for understanding the molecular mechanisms regulating fruit development because of its variable shape and size and large inferior ovary. Here, we performed strand-specific transcriptome sequencing on pumpkin (Cucurbita maxima "Rimu") fruits at 6 developmental stages and identified 5,425 reliably expressed lncRNAs. Among the 332 lncRNAs that were differentially expressed during fruit development, the lncRNA MSTRG.44863.1 was identified as a negative regulator of pumpkin fruit development. MSTRG.44863.1 showed a relatively high expression level and an obvious period-specific expression pattern. Transient overexpression and silencing of MSTRG.44863.1 significantly increased and decreased the content of 1-aminocyclopropane carboxylic acid (a precursor of ethylene) and ethylene production, respectively. RNA pull-down and microscale thermophoresis assays further revealed that MSTRG.44863.1 can interact with S-adenosyl-L-methionine synthetase (SAMS), an enzyme in the ethylene synthesis pathway. Considering that ethylene negatively regulates fruit development, these results indicate that MSTRG.44863.1 plays an important role in the regulation of pumpkin fruit development, possibly through interacting with SAMS and affecting ethylene synthesis. Overall, our findings provide a rich resource for further study of fruit-related lncRNAs while offering insights into the regulation of fruit development in plants.
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Affiliation(s)
- Jiaxing Tian
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Guoyu Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaojie Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Haizhen Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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2
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Reyes AV, Shrestha R, Grismer TS, Byun D, Xu SL. Impact of alternative splicing on Arabidopsis proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582853. [PMID: 38496481 PMCID: PMC10942332 DOI: 10.1101/2024.02.29.582853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Alternative splicing is an important regulatory process in eukaryotes. In plants, the major form of alternative splicing is intron retention. Despite its importance, the global impact of AS on the Arabidopsis proteome has not been investigated. In this study, we address this gap by performing a comprehensive integrated analysis of how changes in AS can affect the Arabidopsis proteome using mutants that disrupt ACINUS and PININ, two evolutionarily conserved alternative splicing factors. We used tandem mass tagging (TMT) with real-time search MS3 (RTS-SPS-MS3) coupled with extensive sample fractionations to achieve very high coverage and accurate protein quantification. We then integrated our proteomic data with transcriptomic data to assess how transcript changes and increased intron retention (IIR) affect the proteome. For differentially expressed transcripts, we have observed a weak to moderate correlation between transcript changes and protein changes. Our studies revealed that some IIRs have no effect on either transcript or protein levels, while some IIRs can significantly affect protein levels. Surprisingly, we found that IIRs have a much smaller effect on increasing protein diversity. Notably, the increased intron retention events detected in the double mutant are also detected in the WT under various biotic or abiotic stresses. We further investigated the characteristics of the retained introns. Our extensive proteomic data help to guide the phenotypic analysis and reveal that collective protein changes contribute to the observed phenotypes of the increased anthocyanin, pale green, reduced growth, and short root observed in the acinus pnn double mutant. Overall, our study provides insight into the intricate regulatory mechanism of intron retention and its impact on protein abundance in plants.
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Affiliation(s)
- Andres V Reyes
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - TaraBryn S Grismer
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Danbi Byun
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Shou-Ling Xu
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
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3
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Fuchs P, Feixes-Prats E, Arruda P, Feitosa-Araújo E, Fernie AR, Grefen C, Lichtenauer S, Linka N, de Godoy Maia I, Meyer AJ, Schilasky S, Sweetlove LJ, Wege S, Weber APM, Millar AH, Keech O, Florez-Sarasa I, Barreto P, Schwarzländer M. PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 2 localizes to the Golgi. PLANT PHYSIOLOGY 2024; 194:623-628. [PMID: 37820040 DOI: 10.1093/plphys/kiad540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 10/13/2023]
Abstract
In contrast to its close homolog PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 1 (UCP1), which is an abundant carrier protein in the mitochondria, UCP2 localizes to the Golgi.
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Affiliation(s)
- Philippe Fuchs
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Elisenda Feixes-Prats
- Centre for Research in Agricultural Genomics (CRAG), Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Paulo Arruda
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875 Campinas, Brazil
| | - Elias Feitosa-Araújo
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, D-14476 Postdam-Golm, Germany
| | - Christopher Grefen
- Institute of Molecular and Cellular Botany, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Sophie Lichtenauer
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Ivan de Godoy Maia
- Institute of Biosciences, São Paulo State University (UNESP), 18618-970 Botucatu, Brazil
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Sören Schilasky
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Lee J Sweetlove
- Department of Biology, South Parks Road, University of Oxford, OX1 3RB Oxford, UK
| | - Stefanie Wege
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 6009 Perth, Western Australia, Australia
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden
| | - Igor Florez-Sarasa
- Centre for Research in Agricultural Genomics (CRAG), Campus UAB Bellaterra, 08193 Barcelona, Spain
- Institut de Recerca i Tecnología Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Pedro Barreto
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
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4
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Jiang B, Zhong Z, Gu L, Zhang X, Wei J, Ye C, Lin G, Qu G, Xiang X, Wen C, Hummel M, Bailey-Serres J, Wang Q, He C, Wang X, Lin C. Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis. NATURE PLANTS 2023; 9:2042-2058. [PMID: 38066290 PMCID: PMC10724061 DOI: 10.1038/s41477-023-01580-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023]
Abstract
Light regulates chlorophyll homeostasis and photosynthesis via various molecular mechanisms in plants. The light regulation of transcription and protein stability of nuclear-encoded chloroplast proteins have been extensively studied, but how light regulation of mRNA metabolism affects abundance of nuclear-encoded chloroplast proteins and chlorophyll homeostasis remains poorly understood. Here we show that the blue light receptor cryptochrome 2 (CRY2) and the METTL16-type m6A writer FIONA1 (FIO1) regulate chlorophyll homeostasis in response to blue light. In contrast to the CRY2-mediated photo-condensation of the mRNA adenosine methylase (MTA), photoexcited CRY2 co-condenses FIO1 only in the presence of the CRY2-signalling protein SUPPRESSOR of PHYTOCHROME A (SPA1). CRY2 and SPA1 synergistically or additively activate the RNA methyltransferase activity of FIO1 in vitro, whereas CRY2 and FIO1, but not MTA, are required for the light-induced methylation and translation of the mRNAs encoding multiple chlorophyll homeostasis regulators in vivo. Our study demonstrates that the light-induced liquid-liquid phase separation of the photoreceptor/writer complexes is commonly involved in the regulation of photoresponsive changes of mRNA methylation, whereas the different photo-condensation mechanisms of the CRY/FIO1 and CRY/MTA complexes explain, at least partially, the writer-specific functions in plant photomorphogenesis.
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Affiliation(s)
- Bochen Jiang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China.
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
| | - Zhenhui Zhong
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueyang Zhang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Guifang Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gaoping Qu
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xian Xiang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenjin Wen
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maureen Hummel
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Qin Wang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Xu Wang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China.
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, China.
| | - Chentao Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China.
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
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5
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da Fonseca-Pereira P, Monteiro-Batista RDC, Araújo WL, Nunes-Nesi A. Harnessing enzyme cofactors and plant metabolism: an essential partnership. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1014-1036. [PMID: 36861364 DOI: 10.1111/tpj.16167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/18/2023] [Accepted: 02/25/2023] [Indexed: 05/31/2023]
Abstract
Cofactors are fundamental to the catalytic activity of enzymes. Additionally, because plants are a critical source of several cofactors (i.e., including their vitamin precursors) within the context of human nutrition, there have been several studies aiming to understand the metabolism of coenzymes and vitamins in plants in detail. For example, compelling evidence has been brought forth regarding the role of cofactors in plants; specifically, it is becoming increasingly clear that an adequate supply of cofactors in plants directly affects their development, metabolism, and stress responses. Here, we review the state-of-the-art knowledge on the significance of coenzymes and their precursors with regard to general plant physiology and discuss the emerging functions attributed to them. Furthermore, we discuss how our understanding of the complex relationship between cofactors and plant metabolism can be used for crop improvement.
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Affiliation(s)
- Paula da Fonseca-Pereira
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Rita de Cássia Monteiro-Batista
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
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6
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Yang L, Wang X, Zhao F, Zhang X, Li W, Huang J, Pei X, Ren X, Liu Y, He K, Zhang F, Ma X, Yang D. Roles of S-Adenosylmethionine and Its Derivatives in Salt Tolerance of Cotton. Int J Mol Sci 2023; 24:ijms24119517. [PMID: 37298464 DOI: 10.3390/ijms24119517] [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: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Salinity is a major abiotic stress that restricts cotton growth and affects fiber yield and quality. Although studies on salt tolerance have achieved great progress in cotton since the completion of cotton genome sequencing, knowledge about how cotton copes with salt stress is still scant. S-adenosylmethionine (SAM) plays important roles in many organelles with the help of the SAM transporter, and it is also a synthetic precursor for substances such as ethylene (ET), polyamines (PAs), betaine, and lignin, which often accumulate in plants in response to stresses. This review focused on the biosynthesis and signal transduction pathways of ET and PAs. The current progress of ET and PAs in regulating plant growth and development under salt stress has been summarized. Moreover, we verified the function of a cotton SAM transporter and suggested that it can regulate salt stress response in cotton. At last, an improved regulatory pathway of ET and PAs under salt stress in cotton is proposed for the breeding of salt-tolerant varieties.
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Affiliation(s)
- Li Yang
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Fuyong Zhao
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Xianliang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Junsen Huang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiang Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yangai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Kunlun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Daigang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
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7
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Monné M, Marobbio CMT, Agrimi G, Palmieri L, Palmieri F. Mitochondrial transport and metabolism of the major methyl donor and versatile cofactor S-adenosylmethionine, and related diseases: A review †. IUBMB Life 2022; 74:573-591. [PMID: 35730628 DOI: 10.1002/iub.2658] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/19/2022] [Indexed: 11/08/2022]
Abstract
S-adenosyl-L-methionine (SAM) is a coenzyme and the most commonly used methyl-group donor for the modification of metabolites, DNA, RNA and proteins. SAM biosynthesis and SAM regeneration from the methylation reaction product S-adenosyl-L-homocysteine (SAH) take place in the cytoplasm. Therefore, the intramitochondrial SAM-dependent methyltransferases require the import of SAM and export of SAH for recycling. Orthologous mitochondrial transporters belonging to the mitochondrial carrier family have been identified to catalyze this antiport transport step: Sam5p in yeast, SLC25A26 (SAMC) in humans, and SAMC1-2 in plants. In mitochondria SAM is used by a vast number of enzymes implicated in the following processes: the regulation of replication, transcription, translation, and enzymatic activities; the maturation and assembly of mitochondrial tRNAs, ribosomes and protein complexes; and the biosynthesis of cofactors, such as ubiquinone, lipoate, and molybdopterin. Mutations in SLC25A26 and mitochondrial SAM-dependent enzymes have been found to cause human diseases, which emphasizes the physiological importance of these proteins.
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Affiliation(s)
- Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,Department of Sciences, University of Basilicata, Potenza, Italy
| | - Carlo M T Marobbio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
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8
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Wu D, Li X, Tanaka R, Wood JC, Tibbs-Cortes LE, Magallanes-Lundback M, Bornowski N, Hamilton JP, Vaillancourt B, Diepenbrock CH, Li X, Deason NT, Schoenbaum GR, Yu J, Buell CR, DellaPenna D, Gore MA. Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain. Genetics 2022; 221:6603118. [PMID: 35666198 PMCID: PMC9339294 DOI: 10.1093/genetics/iyac091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/01/2022] [Indexed: 11/20/2022] Open
Abstract
Tocochromanols (tocopherols and tocotrienols, collectively vitamin E) are lipid-soluble antioxidants important for both plant fitness and human health. The main dietary sources of vitamin E are seed oils that often accumulate high levels of tocopherol isoforms with lower vitamin E activity. The tocochromanol biosynthetic pathway is conserved across plant species but an integrated view of the genes and mechanisms underlying natural variation of tocochromanol levels in seed of most cereal crops remains limited. To address this issue, we utilized the high mapping resolution of the maize Ames panel of ∼1,500 inbred lines scored with 12.2 million single-nucleotide polymorphisms to generate metabolomic (mature grain tocochromanols) and transcriptomic (developing grain) data sets for genetic mapping. By combining results from genome- and transcriptome-wide association studies, we identified a total of 13 candidate causal gene loci, including 5 that had not been previously associated with maize grain tocochromanols: 4 biosynthetic genes (arodeH2 paralog, dxs1, vte5, and vte7) and a plastid S-adenosyl methionine transporter (samt1). Expression quantitative trait locus (eQTL) mapping of these 13 gene loci revealed that they are predominantly regulated by cis-eQTL. Through a joint statistical analysis, we implicated cis-acting variants as responsible for colocalized eQTL and GWAS association signals. Our multiomics approach provided increased statistical power and mapping resolution to enable a detailed characterization of the genetic and regulatory architecture underlying tocochromanol accumulation in maize grain and provided insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in maize and other cereals.
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Affiliation(s)
| | | | | | - Joshua C Wood
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | | | - Maria Magallanes-Lundback
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Nolan Bornowski
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - John P Hamilton
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Brieanne Vaillancourt
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | | | - Xianran Li
- United States Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164, USA
| | - Nicholas T Deason
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - C Robin Buell
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Michael A Gore
- Corresponding author: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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9
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Temple H, Phyo P, Yang W, Lyczakowski JJ, Echevarría-Poza A, Yakunin I, Parra-Rojas JP, Terrett OM, Saez-Aguayo S, Dupree R, Orellana A, Hong M, Dupree P. Golgi-localized putative S-adenosyl methionine transporters required for plant cell wall polysaccharide methylation. NATURE PLANTS 2022; 8:656-669. [PMID: 35681018 DOI: 10.1038/s41477-022-01156-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Polysaccharide methylation, especially that of pectin, is a common and important feature of land plant cell walls. Polysaccharide methylation takes place in the Golgi apparatus and therefore relies on the import of S-adenosyl methionine (SAM) from the cytosol into the Golgi. However, so far, no Golgi SAM transporter has been identified in plants. Here we studied major facilitator superfamily members in Arabidopsis that we identified as putative Golgi SAM transporters (GoSAMTs). Knockout of the two most highly expressed GoSAMTs led to a strong reduction in Golgi-synthesized polysaccharide methylation. Furthermore, solid-state NMR experiments revealed that reduced methylation changed cell wall polysaccharide conformations, interactions and mobilities. Notably, NMR revealed the existence of pectin 'egg-box' structures in intact cell walls and showed that their formation is enhanced by reduced methyl esterification. These changes in wall architecture were linked to substantial growth and developmental phenotypes. In particular, anisotropic growth was strongly impaired in the double mutant. The identification of putative transporters involved in import of SAM into the Golgi lumen in plants provides new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.
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Affiliation(s)
- Henry Temple
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pyae Phyo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Weibing Yang
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS) and CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Shanghai, China
| | - Jan J Lyczakowski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Yakunin
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Juan Pablo Parra-Rojas
- Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Susana Saez-Aguayo
- Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry, UK
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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10
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Li W, Liang Q, Mishra RC, Sanchez-Mu�oz R, Wang H, Chen X, Van Der Straeten D, Zhang C, Xiao Y. The 5-formyl-tetrahydrofolate proteome links folates with C/N metabolism and reveals feedback regulation of folate biosynthesis. THE PLANT CELL 2021; 33:3367-3385. [PMID: 34352110 PMCID: PMC8505879 DOI: 10.1093/plcell/koab198] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/23/2021] [Indexed: 05/31/2023]
Abstract
Folates are indispensable for plant development, but their molecular mode of action remains elusive. We synthesized a probe, "5-F-THF-Dayne," comprising 5-formyl-tetrahydrofolate (THF) coupled to a photoaffinity tag. Exploiting this probe in an affinity proteomics study in Arabidopsis thaliana, we retrieved 51 hits. Thirty interactions were independently validated with in vitro expressed proteins to bind 5-F-THF with high or low affinity. Interestingly, the interactors reveal associations beyond one-carbon metabolism, covering also connections to nitrogen (N) metabolism, carbohydrate metabolism/photosynthesis, and proteostasis. Two of the interactions, one with the folate biosynthetic enzyme DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE 1 (AtDHFR-TS1) and another with N metabolism-associated glutamine synthetase 1;4 (AtGLN1;4), were further characterized. In silico and experimental analyses revealed G35/K36 and E330 as key residues for the binding of 5-F-THF in AtDHFR-TS1 and AtGLN1;4, respectively. Site-directed mutagenesis of AtGLN1;4 E330, which co-localizes with the ATP-binding pocket, abolished 5-F-THF binding as well as AtGLN1;4 activity. Furthermore, 5-F-THF was noted to competitively inhibit the activities of AtDHFR-TS1 and AtGLN1;4. In summary, we demonstrated a regulatory role for 5-F-THF in N metabolism, revealed 5-F-THF-mediated feedback regulation of folate biosynthesis, and identified a total of 14 previously unknown high-affinity binding cellular targets of 5-F-THF. Together, this sets a landmark toward understanding the role of folates in plant development.
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Affiliation(s)
- Weichao Li
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ratnesh Chandra Mishra
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, Gent B-9000, Belgium
| | - Raul Sanchez-Mu�oz
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, Gent B-9000, Belgium
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Chen
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, Gent B-9000, Belgium
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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11
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Kloehn J, Lacour CE, Soldati-Favre D. The metabolic pathways and transporters of the plastid organelle in Apicomplexa. Curr Opin Microbiol 2021; 63:250-258. [PMID: 34455306 DOI: 10.1016/j.mib.2021.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/19/2021] [Accepted: 07/24/2021] [Indexed: 11/26/2022]
Abstract
The apicoplast is the relict of a plastid organelle found in several disease-causing apicomplexan parasites such as Plasmodium spp. and Toxoplasma gondii. In these organisms, the organelle has lost its photosynthetic capability but harbours several fitness-conferring or essential metabolic pathways. Although maintaining the apicoplast and fuelling the metabolic pathways within requires the challenging constant import and export of numerous metabolites across its four membranes, only few apicoplast transporters have been identified to date, most of which are orphan transporters. Here we review the roles of metabolic pathways within the apicoplast and what is currently known about the few identified apicoplast metabolite transporters. We discuss what metabolites must get in and out of the apicoplast, the many transporters that are yet to be discovered, and what role these might play in parasite metabolism and as putative drug targets.
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Affiliation(s)
- Joachim Kloehn
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland.
| | - Clément Em Lacour
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland.
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12
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Chen K, Łyskowski A, Jaremko Ł, Jaremko M. Genetic and Molecular Factors Determining Grain Weight in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:605799. [PMID: 34322138 PMCID: PMC8313227 DOI: 10.3389/fpls.2021.605799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 06/22/2021] [Indexed: 05/06/2023]
Abstract
Grain weight is one of the major factors determining single plant yield production of rice and other cereal crops. Research has begun to reveal the regulatory mechanisms underlying grain weight as well as grain size, highlighting the importance of this research for plant molecular biology. The developmental trait of grain weight is affected by multiple molecular and genetic aspects that lead to dynamic changes in cell division, expansion and differentiation. Additionally, several important biological pathways contribute to grain weight, such as ubiquitination, phytohormones, G-proteins, photosynthesis, epigenetic modifications and microRNAs. Our review integrates early and more recent findings, and provides future perspectives for how a more complete understanding of grain weight can optimize strategies for improving yield production. It is surprising that the acquired wealth of knowledge has not revealed more insights into the underlying molecular mechanisms. To accelerating molecular breeding of rice and other cereals is becoming an emergent and critical task for agronomists. Lastly, we highlighted the importance of leveraging gene editing technologies as well as structural studies for future rice breeding applications.
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Affiliation(s)
- Ke Chen
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Andrzej Łyskowski
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Faculty of Chemistry, Rzeszow University of Technology, Rzeszow, Poland
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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13
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Watanabe M, Chiba Y, Hirai MY. Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:643403. [PMID: 34025692 PMCID: PMC8137854 DOI: 10.3389/fpls.2021.643403] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/17/2021] [Indexed: 05/19/2023]
Abstract
The metabolism of an organism is closely related to both its internal and external environments. Metabolites can act as signal molecules that regulate the functions of genes and proteins, reflecting the status of these environments. This review discusses the metabolism and regulatory functions of O-acetylserine (OAS), S-adenosylmethionine (AdoMet), homocysteine (Hcy), and serine (Ser), which are key metabolites related to sulfur (S)-containing amino acids in plant metabolic networks, in comparison to microbial and animal metabolism. Plants are photosynthetic auxotrophs that have evolved a specific metabolic network different from those in other living organisms. Although amino acids are the building blocks of proteins and common metabolites in all living organisms, their metabolism and regulation in plants have specific features that differ from those in animals and bacteria. In plants, cysteine (Cys), an S-containing amino acid, is synthesized from sulfide and OAS derived from Ser. Methionine (Met), another S-containing amino acid, is also closely related to Ser metabolism because of its thiomethyl moiety. Its S atom is derived from Cys and its methyl group from folates, which are involved in one-carbon metabolism with Ser. One-carbon metabolism is also involved in the biosynthesis of AdoMet, which serves as a methyl donor in the methylation reactions of various biomolecules. Ser is synthesized in three pathways: the phosphorylated pathway found in all organisms and the glycolate and the glycerate pathways, which are specific to plants. Ser metabolism is not only important in Ser supply but also involved in many other functions. Among the metabolites in this network, OAS is known to function as a signal molecule to regulate the expression of OAS gene clusters in response to environmental factors. AdoMet regulates amino acid metabolism at enzymatic and translational levels and regulates gene expression as methyl donor in the DNA and histone methylation or after conversion into bioactive molecules such as polyamine and ethylene. Hcy is involved in Met-AdoMet metabolism and can regulate Ser biosynthesis at an enzymatic level. Ser metabolism is involved in development and stress responses. This review aims to summarize the metabolism and regulatory functions of OAS, AdoMet, Hcy, and Ser and compare the available knowledge for plants with that for animals and bacteria and propose a future perspective on plant research.
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Affiliation(s)
- Mutsumi Watanabe
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yukako Chiba
- Graduate School of Life Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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14
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Characterization of In Vivo Function(s) of Members of the Plant Mitochondrial Carrier Family. Biomolecules 2020; 10:biom10091226. [PMID: 32846873 PMCID: PMC7565455 DOI: 10.3390/biom10091226] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023] Open
Abstract
Although structurally related, mitochondrial carrier family (MCF) proteins catalyze the specific transport of a range of diverse substrates including nucleotides, amino acids, dicarboxylates, tricarboxylates, cofactors, vitamins, phosphate and H+. Despite their name, they do not, however, always localize to the mitochondria, with plasma membrane, peroxisomal, chloroplast and thylakoid and endoplasmic reticulum localizations also being reported. The existence of plastid-specific MCF proteins is suggestive that the evolution of these proteins occurred after the separation of the green lineage. That said, plant-specific MCF proteins are not all plastid-localized, with members also situated at the endoplasmic reticulum and plasma membrane. While by no means yet comprehensive, the in vivo function of a wide range of these transporters is carried out here, and we discuss the employment of genetic variants of the MCF as a means to provide insight into their in vivo function complementary to that obtained from studies following their reconstitution into liposomes.
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15
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Alegre S, Pascual J, Trotta A, Angeleri M, Rahikainen M, Brosche M, Moffatt B, Kangasjärvi S. Evolutionary conservation and post-translational control of S-adenosyl-L-homocysteine hydrolase in land plants. PLoS One 2020; 15:e0227466. [PMID: 32678822 PMCID: PMC7367456 DOI: 10.1371/journal.pone.0227466] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/30/2020] [Indexed: 02/01/2023] Open
Abstract
Trans-methylation reactions are intrinsic to cellular metabolism in all living organisms. In land plants, a range of substrate-specific methyltransferases catalyze the methylation of DNA, RNA, proteins, cell wall components and numerous species-specific metabolites, thereby providing means for growth and acclimation in various terrestrial habitats. Trans-methylation reactions consume vast amounts of S-adenosyl-L-methionine (SAM) as a methyl donor in several cellular compartments. The inhibitory reaction by-product, S-adenosyl-L-homocysteine (SAH), is continuously removed by SAH hydrolase (SAHH), which essentially maintains trans-methylation reactions in all living cells. Here we report on the evolutionary conservation and post-translational control of SAHH in land plants. We provide evidence suggesting that SAHH forms oligomeric protein complexes in phylogenetically divergent land plants and that the predominant protein complex is composed by a tetramer of the enzyme. Analysis of light-stress-induced adjustments of SAHH in Arabidopsis thaliana and Physcomitrella patens further suggests that regulatory actions may take place on the levels of protein complex formation and phosphorylation of this metabolically central enzyme. Collectively, these data suggest that plant adaptation to terrestrial environments involved evolution of regulatory mechanisms that adjust the trans-methylation machinery in response to environmental cues.
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Affiliation(s)
- Sara Alegre
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Jesús Pascual
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Andrea Trotta
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
- Institute of Biosciences and Bioresources, National Research Council of Italy, Sesto Fiorentino, Firenze, Italy
| | - Martina Angeleri
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Moona Rahikainen
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Mikael Brosche
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Barbara Moffatt
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Saijaliisa Kangasjärvi
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
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16
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Fernie AR, Cavalcanti JHF, Nunes-Nesi A. Metabolic Roles of Plant Mitochondrial Carriers. Biomolecules 2020; 10:E1013. [PMID: 32650612 PMCID: PMC7408384 DOI: 10.3390/biom10071013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial carriers (MC) are a large family (MCF) of inner membrane transporters displaying diverse, yet often redundant, substrate specificities, as well as differing spatio-temporal patterns of expression; there are even increasing examples of non-mitochondrial subcellular localization. The number of these six trans-membrane domain proteins in sequenced plant genomes ranges from 39 to 141, rendering the size of plant families larger than that found in Saccharomyces cerevisiae and comparable with Homo sapiens. Indeed, comparison of plant MCs with those from these better characterized species has been highly informative. Here, we review the most recent comprehensive studies of plant MCFs, incorporating the torrent of genomic data emanating from next-generation sequencing techniques. As such we present a more current prediction of the substrate specificities of these carriers as well as review the continuing quest to biochemically characterize this feature of the carriers. Taken together, these data provide an important resource to guide direct genetic studies aimed at addressing the relevance of these vital carrier proteins.
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Affiliation(s)
- Alisdair R. Fernie
- Max-Planck-Instiute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany
| | - João Henrique F. Cavalcanti
- Instituto de Educação, Agricultura e Ambiente, Universidade Federal do Amazonas, Humaitá 69800-000, Amazonas, Brazil;
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, Minas Gerais, Brazil
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17
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Markakis K, Lowe PT, Davison‐Gates L, O'Hagan D, Rosser SJ, Elfick A. An Engineered
E. coli
Strain for Direct in Vivo Fluorination. Chembiochem 2020; 21:1856-1860. [DOI: 10.1002/cbic.202000051] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Indexed: 02/04/2023]
Affiliation(s)
- Konstantinos Markakis
- Institute for BioengineeringSchool of EngineeringUniversity of Edinburgh Faraday Building King's Buildings Colin Maclaurin Road Edinburgh EH9 3DW UK
| | - Phillip T. Lowe
- School of ChemistryUniversity of St. Andrews Purdie Building North Haugh St. Andrews KY16 9ST UK
| | - Liam Davison‐Gates
- Institute for BioengineeringSchool of EngineeringUniversity of Edinburgh Faraday Building King's Buildings Colin Maclaurin Road Edinburgh EH9 3DW UK
| | - David O'Hagan
- School of ChemistryUniversity of St. Andrews Purdie Building North Haugh St. Andrews KY16 9ST UK
| | - Susan J. Rosser
- School of Biological SciencesThe University of Edinburgh Roger Land Building The King's Buildings Alexander Crum Brown Road Edinburgh EH9 3FF UK
| | - Alistair Elfick
- Institute for BioengineeringSchool of EngineeringUniversity of Edinburgh Faraday Building King's Buildings Colin Maclaurin Road Edinburgh EH9 3DW UK
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18
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Pinard D, Fierro AC, Marchal K, Myburg AA, Mizrachi E. Organellar carbon metabolism is coordinated with distinct developmental phases of secondary xylem. THE NEW PHYTOLOGIST 2019; 222:1832-1845. [PMID: 30742304 DOI: 10.1111/nph.15739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Subcellular compartmentation of plant biosynthetic pathways in the mitochondria and plastids requires coordinated regulation of nuclear encoded genes, and the role of these genes has been largely ignored by wood researchers. In this study, we constructed a targeted systems genetics coexpression network of xylogenesis in Eucalyptus using plastid and mitochondrial carbon metabolic genes and compared the resulting clusters to the aspen xylem developmental series. The constructed network clusters reveal the organization of transcriptional modules regulating subcellular metabolic functions in plastids and mitochondria. Overlapping genes between the plastid and mitochondrial networks implicate the common transcriptional regulation of carbon metabolism during xylem secondary growth. We show that the central processes of organellar carbon metabolism are distinctly coordinated across the developmental stages of wood formation and are specifically associated with primary growth and secondary cell wall deposition. We also demonstrate that, during xylogenesis, plastid-targeted carbon metabolism is partially regulated by the central clock for carbon allocation towards primary and secondary xylem growth, and we discuss these networks in the context of previously established associations with wood-related complex traits. This study provides a new resolution into the integration and transcriptional regulation of plastid- and mitochondrial-localized carbon metabolism during xylogenesis.
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Affiliation(s)
- Desré Pinard
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Ana Carolina Fierro
- Department of Information Technology, Ghent University - iMinds, Technologiepark 15, Ghent, B-9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, B-9052, Belgium
| | - Kathleen Marchal
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- Department of Information Technology, Ghent University - iMinds, Technologiepark 15, Ghent, B-9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, B-9052, Belgium
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
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19
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Jiang Z, Kempinski C, Kumar S, Kinison S, Linscott K, Nybo E, Janze S, Wood C, Chappell J. Agronomic and chemical performance of field-grown tobacco engineered for triterpene and methylated triterpene metabolism. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1110-1124. [PMID: 29069530 PMCID: PMC5978867 DOI: 10.1111/pbi.12855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/08/2017] [Indexed: 05/13/2023]
Abstract
Squalene is a linear intermediate to nearly all classes of triterpenes and sterols and is itself highly valued for its use in wide range of industrial applications. Another unique linear triterpene is botryococcene and its methylated derivatives generated by the alga Botryococcus braunii race B, which are progenitors to fossil fuel deposits. Production of these linear triterpenes was previously engineered into transgenic tobacco by introducing the key steps of triterpene metabolism into the particular subcellular compartments. In this study, the agronomic characteristics (height, biomass accumulation, leaf area), the photosynthetic capacity (photosynthesis rate, conductance, internal CO2 levels) and triterpene content of select lines grown under field conditions were evaluated for three consecutive growing seasons. We observed that transgenic lines targeting enzymes to the chloroplasts accumulated 50-150 times more squalene than the lines targeting the enzymes to the cytoplasm, without compromising growth or photosynthesis. We also found that the transgenic lines directing botryococcene metabolism to the chloroplast accumulated 10- to 33-fold greater levels than the lines where the same enzymes were targeted to in the cytoplasm. However, growth of these high botryococcene accumulators was highly compromised, yet their photosynthesis rates remained unaffected. In addition, in the transgenic lines targeting a triterpene methyltransferase (TMT) to the chloroplasts of high squalene accumulators, 55%-65% of total squalene was methylated, whereas in the lines expressing a TMT in the cytoplasm, only 6%-13% of squalene was methylated. The growth of these methylated triterpene-accumulating lines was more compromised than that of nonmethylated squalene lines.
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Affiliation(s)
- Zuodong Jiang
- Plant Biology ProgramUniversity of KentuckyLexingtonKYUSA
- Department of Pharmaceutical SciencesUniversity of KentuckyLexingtonKYUSA
| | - Chase Kempinski
- Plant Biology ProgramUniversity of KentuckyLexingtonKYUSA
- Department of Pharmaceutical SciencesUniversity of KentuckyLexingtonKYUSA
| | - Santosh Kumar
- Plant Biology ProgramUniversity of KentuckyLexingtonKYUSA
- Department of Pharmaceutical SciencesUniversity of KentuckyLexingtonKYUSA
| | - Scott Kinison
- Department of Pharmaceutical SciencesUniversity of KentuckyLexingtonKYUSA
| | - Kristin Linscott
- Molecular and Cellular BiochemistryUniversity of KentuckyLexingtonKYUSA
| | - Eric Nybo
- Department of Pharmaceutical SciencesUniversity of KentuckyLexingtonKYUSA
| | - Sarah Janze
- Department of StatisticsUniversity of KentuckyLexingtonKYUSA
| | - Connie Wood
- Department of StatisticsUniversity of KentuckyLexingtonKYUSA
| | - Joe Chappell
- Plant Biology ProgramUniversity of KentuckyLexingtonKYUSA
- Department of Pharmaceutical SciencesUniversity of KentuckyLexingtonKYUSA
- Molecular and Cellular BiochemistryUniversity of KentuckyLexingtonKYUSA
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20
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Rahikainen M, Alegre S, Trotta A, Pascual J, Kangasjärvi S. Trans-methylation reactions in plants: focus on the activated methyl cycle. PHYSIOLOGIA PLANTARUM 2018; 162:162-176. [PMID: 28815615 DOI: 10.1111/ppl.12619] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/02/2017] [Accepted: 08/10/2017] [Indexed: 05/11/2023]
Abstract
Trans-methylation reactions are vital in basic metabolism, epigenetic regulation, RNA metabolism, and posttranslational control of protein function and therefore fundamental in determining the physiological processes in all living organisms. The plant kingdom is additionally characterized by the production of secondary metabolites that undergo specific hydroxylation, oxidation and methylation reactions to obtain a wide array of different chemical structures. Increasing research efforts have started to reveal the enzymatic pathways underlying the biosynthesis of complex metabolites in plants. Further engineering of these enzymatic machineries offers significant possibilities in the development of bio-based technologies, but necessitates deep understanding of their potential metabolic and regulatory interactions. Trans-methylation reactions are tightly coupled with the so-called activated methyl cycle (AMC), an essential metabolic circuit that maintains the trans-methylation capacity in all living cells. Tight regulation of the AMC is crucial in ensuring accurate trans-methylation reactions in different subcellular compartments, cell types, developmental stages and environmental conditions. This review addresses the organization and posttranslational regulation of the AMC and elaborates its critical role in determining metabolic regulation through modulation of methyl utilization in stress-exposed plants.
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Affiliation(s)
- Moona Rahikainen
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Sara Alegre
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Andrea Trotta
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Jesús Pascual
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Saijaliisa Kangasjärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
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21
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Monné M, Daddabbo L, Gagneul D, Obata T, Hielscher B, Palmieri L, Miniero DV, Fernie AR, Weber APM, Palmieri F. Uncoupling proteins 1 and 2 (UCP1 and UCP2) from Arabidopsis thaliana are mitochondrial transporters of aspartate, glutamate, and dicarboxylates. J Biol Chem 2018; 293:4213-4227. [PMID: 29371401 DOI: 10.1074/jbc.ra117.000771] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/15/2018] [Indexed: 12/29/2022] Open
Abstract
The Arabidopsis thaliana genome contains 58 members of the solute carrier family SLC25, also called the mitochondrial carrier family, many of which have been shown to transport specific metabolites, nucleotides, and cofactors across the mitochondrial membrane. Here, two Arabidopsis members of this family, AtUCP1 and AtUCP2, which were previously thought to be uncoupling proteins and hence named UCP1/PUMP1 and UCP2/PUMP2, respectively, are assigned with a novel function. They were expressed in bacteria, purified, and reconstituted in phospholipid vesicles. Their transport properties demonstrate that they transport amino acids (aspartate, glutamate, cysteine sulfinate, and cysteate), dicarboxylates (malate, oxaloacetate, and 2-oxoglutarate), phosphate, sulfate, and thiosulfate. Transport was saturable and inhibited by mercurials and other mitochondrial carrier inhibitors to various degrees. AtUCP1 and AtUCP2 catalyzed a fast counterexchange transport as well as a low uniport of substrates, with transport rates of AtUCP1 being much higher than those of AtUCP2 in both cases. The aspartate/glutamate heteroexchange mediated by AtUCP1 and AtUCP2 is electroneutral, in contrast to that mediated by the mammalian mitochondrial aspartate glutamate carrier. Furthermore, both carriers were found to be targeted to mitochondria. Metabolite profiling of single and double knockouts shows changes in organic acid and amino acid levels. Notably, AtUCP1 and AtUCP2 are the first reported mitochondrial carriers in Arabidopsis to transport aspartate and glutamate. It is proposed that the primary function of AtUCP1 and AtUCP2 is to catalyze an aspartateout/glutamatein exchange across the mitochondrial membrane and thereby contribute to the export of reducing equivalents from the mitochondria in photorespiration.
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Affiliation(s)
- Magnus Monné
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, via Orabona 4, 70125 Bari, Italy.,the Department of Sciences, University of Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy
| | - Lucia Daddabbo
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, via Orabona 4, 70125 Bari, Italy
| | - David Gagneul
- the Cluster of Excellence on Plant Science (CEPLAS), Institute of Plant Biochemistry, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Toshihiro Obata
- the Department Willmitzer, Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany, and
| | - Björn Hielscher
- the Cluster of Excellence on Plant Science (CEPLAS), Institute of Plant Biochemistry, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Luigi Palmieri
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, via Orabona 4, 70125 Bari, Italy.,the Center of Excellence in Comparative Genomics, University of Bari, via Orabona 4, 70125 Bari, Italy
| | - Daniela Valeria Miniero
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, via Orabona 4, 70125 Bari, Italy
| | - Alisdair R Fernie
- the Department Willmitzer, Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany, and
| | - Andreas P M Weber
- the Cluster of Excellence on Plant Science (CEPLAS), Institute of Plant Biochemistry, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Ferdinando Palmieri
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, via Orabona 4, 70125 Bari, Italy, .,the Center of Excellence in Comparative Genomics, University of Bari, via Orabona 4, 70125 Bari, Italy
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Li S, Wei X, Ren Y, Qiu J, Jiao G, Guo X, Tang S, Wan J, Hu P. OsBT1 encodes an ADP-glucose transporter involved in starch synthesis and compound granule formation in rice endosperm. Sci Rep 2017; 7:40124. [PMID: 28054650 PMCID: PMC5215005 DOI: 10.1038/srep40124] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/02/2016] [Indexed: 01/18/2023] Open
Abstract
Starch is the main storage carbohydrate in higher plants. Although several enzymes and regulators for starch biosynthesis have been characterized, a complete regulatory network for starch synthesis in cereal seeds remains elusive. Here, we report the identification and characterization of the rice Brittle1 (OsBT1) gene, which is expressed specifically in the developing endosperm. The osbt1 mutant showed a white-core endosperm and a significantly lower grain weight than the wild-type. The formation and development of compound starch granules in osbt1 was obviously defective: the amyloplast was disintegrated at early developmental stages and the starch granules were disperse and not compound in the endosperm cells in the centre region of osbt1 seeds. The total starch content and amylose content was decreased and the physicochemical properties of starch were altered. Moreover, the degree of polymerization (DP) of amylopectin in osbt1 was remarkably different from that of wild-type. Map-based cloning of OsBT1 indicated that it encodes a putatively ADP-glucose transporter. OsBT1 coded protein localizes in the amyloplast envelope membrane. Furthermore, the expression of starch synthesis related genes was also altered in the osbt1 mutant. These findings indicate that OsBT1 plays an important role in starch synthesis and the formation of compound starch granules.
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Affiliation(s)
- Sanfeng Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yulong Ren
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Jiehua Qiu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiuping Guo
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jianmin Wan
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
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Palmieri F, Monné M. Discoveries, metabolic roles and diseases of mitochondrial carriers: A review. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2362-78. [PMID: 26968366 DOI: 10.1016/j.bbamcr.2016.03.007] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/25/2022]
Abstract
Mitochondrial carriers (MCs) are a superfamily of nuclear-encoded proteins that are mostly localized in the inner mitochondrial membrane and transport numerous metabolites, nucleotides, cofactors and inorganic anions. Their unique sequence features, i.e., a tripartite structure, six transmembrane α-helices and a three-fold repeated signature motif, allow MCs to be easily recognized. This review describes how the functions of MCs from Saccharomyces cerevisiae, Homo sapiens and Arabidopsis thaliana (listed in the first table) were discovered after the genome sequence of S. cerevisiae was determined in 1996. In the genomic era, more than 50 previously unknown MCs from these organisms have been identified and characterized biochemically using a method consisting of gene expression, purification of the recombinant proteins, their reconstitution into liposomes and transport assays (EPRA). Information derived from studies with intact mitochondria, genetic and metabolic evidence, sequence similarity, phylogenetic analysis and complementation of knockout phenotypes have guided the choice of substrates that were tested in the transport assays. In addition, the diseases associated to defects of human MCs have been briefly reviewed. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.
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Affiliation(s)
- Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy.
| | - Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; Department of Sciences, University of Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy
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Jiang Z, Kempinski C, Bush CJ, Nybo SE, Chappell J. Engineering Triterpene and Methylated Triterpene Production in Plants Provides Biochemical and Physiological Insights into Terpene Metabolism. PLANT PHYSIOLOGY 2016; 170:702-16. [PMID: 26603654 PMCID: PMC4734568 DOI: 10.1104/pp.15.01548] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/23/2015] [Indexed: 05/08/2023]
Abstract
Linear, branch-chained triterpenes, including squalene (C30), botryococcene (C30), and their methylated derivatives (C31-C37), generated by the green alga Botryococcus braunii race B have received significant attention because of their utility as chemical and biofuel feedstocks. However, the slow growth habit of B. braunii makes it impractical as a production system. In this study, we evaluated the potential of generating high levels of botryococcene in tobacco (Nicotiana tabacum) plants by diverting carbon flux from the cytosolic mevalonate pathway or the plastidic methylerythritol phosphate pathway by the targeted overexpression of an avian farnesyl diphosphate synthase along with two versions of botryococcene synthases. Up to 544 µg g(-1) fresh weight of botryococcene was achieved when this metabolism was directed to the chloroplasts, which is approximately 90 times greater than that accumulating in plants engineered for cytosolic production. To test if methylated triterpenes could be produced in tobacco, we also engineered triterpene methyltransferases (TMTs) from B. braunii into wild-type plants and transgenic lines selected for high-level triterpene accumulation. Up to 91% of the total triterpene contents could be converted to methylated forms (C31 and C32) by cotargeting the TMTs and triterpene biosynthesis to the chloroplasts, whereas only 4% to 14% of total triterpenes were methylated when this metabolism was directed to the cytoplasm. When the TMTs were overexpressed in the cytoplasm of wild-type plants, up to 72% of the total squalene was methylated, and total triterpene (C30+C31+C32) content was elevated 7-fold. Altogether, these results point to innate mechanisms controlling metabolite fluxes, including a homeostatic role for squalene.
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Affiliation(s)
- Zuodong Jiang
- Plant Biology Program (Z.J., C.K., J.C.) and Department of Pharmaceutical Sciences (C.J.B., S.E.N., J.C.), University of Kentucky, Lexington, Kentucky 40536-0596
| | - Chase Kempinski
- Plant Biology Program (Z.J., C.K., J.C.) and Department of Pharmaceutical Sciences (C.J.B., S.E.N., J.C.), University of Kentucky, Lexington, Kentucky 40536-0596
| | - Caroline J Bush
- Plant Biology Program (Z.J., C.K., J.C.) and Department of Pharmaceutical Sciences (C.J.B., S.E.N., J.C.), University of Kentucky, Lexington, Kentucky 40536-0596
| | - S Eric Nybo
- Plant Biology Program (Z.J., C.K., J.C.) and Department of Pharmaceutical Sciences (C.J.B., S.E.N., J.C.), University of Kentucky, Lexington, Kentucky 40536-0596
| | - Joe Chappell
- Plant Biology Program (Z.J., C.K., J.C.) and Department of Pharmaceutical Sciences (C.J.B., S.E.N., J.C.), University of Kentucky, Lexington, Kentucky 40536-0596
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Mao D, Yu F, Li J, Van de Poel B, Tan D, Li J, Liu Y, Li X, Dong M, Chen L, Li D, Luan S. FERONIA receptor kinase interacts with S-adenosylmethionine synthetase and suppresses S-adenosylmethionine production and ethylene biosynthesis in Arabidopsis. PLANT, CELL & ENVIRONMENT 2015; 38:2566-74. [PMID: 25988356 DOI: 10.1111/pce.12570] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 05/03/2015] [Accepted: 05/07/2015] [Indexed: 05/04/2023]
Abstract
Environmental inputs such as stress can modulate plant cell metabolism, but the detailed mechanism remains unclear. We report here that FERONIA (FER), a plasma membrane receptor-like kinase, may negatively regulate the S-adenosylmethionine (SAM) synthesis by interacting with two S-adenosylmethionine synthases (SAM1 and SAM2). SAM participates in ethylene, nicotianamine and polyamine biosynthetic pathways and provides the methyl group for protein and DNA methylation reactions. The Arabidopsis fer mutants contained a higher level of SAM and ethylene in plant tissues and displayed a dwarf phenotype. Such phenotype in the fer mutants was mimicked by over-expressing the S-adenosylmethionine synthetase in transgenic plants, whereas sam1/2 double mutant showed an opposite phenotype. We propose that FER receptor kinase, in response to environmental stress and plant hormones such as auxin and BR, interacts with SAM synthases and down-regulates ethylene biosynthesis.
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Affiliation(s)
- Dandan Mao
- NJU-NJFU Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Feng Yu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Jian Li
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Bram Van de Poel
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Leuven, 3001, Belgium
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jianglin Li
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yanqionq Liu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xiushang Li
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Mengqiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Liangbi Chen
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Dongping Li
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Sheng Luan
- NJU-NJFU Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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26
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Chatterjee A, Kundu S. Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica. Sci Rep 2015; 5:14975. [PMID: 26443104 PMCID: PMC4595741 DOI: 10.1038/srep14975] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/27/2015] [Indexed: 12/30/2022] Open
Abstract
Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air.
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Affiliation(s)
- Ankita Chatterjee
- 1Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta India
| | - Sudip Kundu
- 1Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta India.,Center of Excellence in Systems Biology and Biomedical Engineering, TEQIP Phase-II, University of Calcutta India
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27
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Molecular cloning and characterization of an S-adenosylmethionine synthetase gene from Chorispora bungeana. Gene 2015. [PMID: 26205258 DOI: 10.1016/j.gene.2015.07.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
S-adenosylmethionine synthetase (SAMS) catalyzes the formation of S-adenosylmethionine (SAM) which is a molecule essential for polyamines and ethylene biosynthesis, methylation modifications of protein, DNA and lipids. SAMS also plays an important role in abiotic stress response. Chorispora bungeana (C. bungeana) is an alpine subnival plant species which possesses strong tolerance to cold stress. Here, we cloned and characterized an S-adenosylmethionine synthetase gene, CbSAMS (C. bungeana S-adenosylmethionine synthetase), from C. bungeana, which encodes a protein of 393 amino acids containing a methionine binding motif GHPDK, an ATP binding motif GAGDQG and a phosphate binding motif GGGAFSGDK. Furthermore, an NES (nuclear export signal) peptide was identified through bioinformatics analysis. To explore the CbSAMS gene expression regulation, we isolated the promoter region of CbSAMS gene 1919bp upstream the ATG start codon, CbSAMSp, and analyzed its cis-acting elements by bioinformatics method. It was revealed that a transcription start site located at 320 bp upstream the ATG start codon and cis-acting elements related to light, ABA, auxin, ethylene, MeJA, low temperature and drought had been found in the CbSAMSp sequence. The gene expression pattern of CbSAMS was then analyzed by TR-qPCR and GUS assay method. The result showed that CbSAMS is expressed in all examined tissues including callus, roots, petioles, leaves, and flowers with a significant higher expression level in roots and flowers. Furthermore, the expression level of CbSAMS was induced by low temperature, ethylene and NaCl. Subcellular localization revealed that CbSAMS was located in the cytoplasm and nucleus but has a significant higher level in the nucleus. These results indicated a potential role of CbSAMS in abiotic stresses and plant growth in C. bungeana.
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Monné M, Miniero DV, Daddabbo L, Palmieri L, Porcelli V, Palmieri F. Mitochondrial transporters for ornithine and related amino acids: a review. Amino Acids 2015; 47:1763-77. [PMID: 26002808 DOI: 10.1007/s00726-015-1990-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/15/2015] [Indexed: 12/18/2022]
Abstract
Among the members of the mitochondrial carrier family, there are transporters that catalyze the translocation of ornithine and related substrates, such as arginine, homoarginine, lysine, histidine, and citrulline, across the inner mitochondrial membrane. The mitochondrial carriers ORC1, ORC2, and SLC25A29 from Homo sapiens, BAC1 and BAC2 from Arabidopsis thaliana, and Ort1p from Saccharomyces cerevisiae have been biochemically characterized by transport assays in liposomes. All of them transport ornithine and amino acids with side chains terminating at least with one amine. There are, however, marked differences in their substrate specificities including their affinity for ornithine (KM values in the mM to μM range). These differences are most likely reflected by minor differences in the substrate binding sites of these carriers. The physiological role of the above-mentioned mitochondrial carriers is to link several metabolic pathways that take place partly in the cytosol and partly in the mitochondrial matrix and to provide basic amino acids for mitochondrial translation. In the liver, human ORC1 catalyzes the citrulline/ornithine exchange across the mitochondrial inner membrane, which is required for the urea cycle. Human ORC1, ORC2, and SLC25A29 are likely to be involved in the biosynthesis and transport of arginine, which can be used as a precursor for the synthesis of NO, agmatine, polyamines, creatine, glutamine, glutamate, and proline, as well as in the degradation of basic amino acids. BAC1 and BAC2 are implicated in some processes similar to those of their human counterparts and in nitrogen and amino acid metabolism linked to stress conditions and the development of plants. Ort1p is involved in the biosynthesis of arginine and polyamines in yeast.
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Affiliation(s)
- Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125, Bari, Italy
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29
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Sang W, Huang ZR, Qi YP, Yang LT, Guo P, Chen LS. An investigation of boron-toxicity in leaves of two citrus species differing in boron-tolerance using comparative proteomics. J Proteomics 2015; 123:128-46. [PMID: 25892131 DOI: 10.1016/j.jprot.2015.04.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 04/02/2015] [Accepted: 04/09/2015] [Indexed: 01/01/2023]
Abstract
UNLABELLED Limited data are available on boron (B)-toxicity-responsive proteins in plants. We first applied 2-dimensional electrophoresis (2-DE) to compare the effects of B-toxicity on leaf protein profiles in B-tolerant Citrus sinensis and B-intolerant Citrus grandis seedlings, and identified 27 (20) protein species with increased abundances and 23 (25) protein species with decreased abundances from the former (latter). Generally speaking, B-toxicity increased the abundances of protein species involved in antioxidation and detoxification, proteolysis, cell transport, and decreased the abundances of protein species involved in protein biosynthesis in the two citrus species. The higher B-tolerance of C. sinensis might include following several aspects: (a) protein species related to photosynthesis and energy metabolism in C. sinensis leaves were more adaptive to B-toxicity than in C. grandis ones, which was responsible for the higher photosynthesis and for the better maintenance of energy homeostasis in the former; and (b) the increased requirement for detoxification of reactive oxygen species and cytotoxic compounds due to decreased photosynthesis was less in B-toxic C. sinensis leaves than in B-toxic C. grandis ones. B-toxicity-responsive protein species involved in coenzyme biosynthesis differed between the two species, which might also contribute to the higher B-tolerance of C. sinensis. BIOLOGICAL SIGNIFICANCE B-toxicity occurs in many regions all over the world, especially in arid and semiarid regions due to the raising of B-rich water tables with high B accumulated in topsoil. In China, B-toxicity often occurs in some citrus orchards. However, the mechanisms of citrus B-tolerance are still not fully understood. Here, we first used 2-DE to identify some new B-toxicity-responsive-proteins involved in carbohydrate and energy metabolism, antioxidation and detoxification, signal transduction and nucleotide metabolism. Our results showed that proteins involved in photosynthesis and energy metabolism displayed more adaptive to B-toxicity in B-tolerant C. sinensis than in B-intolerant C. grandis, which might play a key role in citrus B-tolerance. Therefore, our results reveal some new mechanisms on plant B-response and tolerance.
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Affiliation(s)
- Wen Sang
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeng-Rong Huang
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China
| | - Lin-Tong Yang
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Guo
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li-Song Chen
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Metabolic connectivity as a driver of host and endosymbiont integration. Proc Natl Acad Sci U S A 2015; 112:10208-15. [PMID: 25825767 DOI: 10.1073/pnas.1421375112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The origin of oxygenic photosynthesis in the Archaeplastida common ancestor was foundational for the evolution of multicellular life. It is very likely that the primary endosymbiosis that explains plastid origin relied initially on the establishment of a metabolic connection between the host cell and captured cyanobacterium. We posit that these connections were derived primarily from existing host-derived components. To test this idea, we used phylogenomic and network analysis to infer the phylogenetic origin and evolutionary history of 37 validated plastid innermost membrane (permeome) metabolite transporters from the model plant Arabidopsis thaliana. Our results show that 57% of these transporter genes are of eukaryotic origin and that the captured cyanobacterium made a relatively minor (albeit important) contribution to the process. We also tested the hypothesis that the bacterium-derived hexose-phosphate transporter UhpC might have been the primordial sugar transporter in the Archaeplastida ancestor. Bioinformatic and protein localization studies demonstrate that this protein in the extremophilic red algae Galdieria sulphuraria and Cyanidioschyzon merolae are plastid targeted. Given this protein is also localized in plastids in the glaucophyte alga Cyanophora paradoxa, we suggest it played a crucial role in early plastid endosymbiosis by connecting the endosymbiont and host carbon storage networks. In summary, our work significantly advances understanding of plastid integration and favors a host-centric view of endosymbiosis. Under this view, nuclear genes of either eukaryotic or bacterial (noncyanobacterial) origin provided key elements of the toolkit needed for establishing metabolic connections in the primordial Archaeplastida lineage.
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31
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Monné M, Palmieri F. Antiporters of the mitochondrial carrier family. CURRENT TOPICS IN MEMBRANES 2014; 73:289-320. [PMID: 24745987 DOI: 10.1016/b978-0-12-800223-0.00008-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The eukaryotic transport protein family SLC25 consists of mitochondrial carriers (MCs) that are recognized on the sequence level by a threefold repeated and conserved signature motif. The majority of MCs characterized so far catalyzes strict exchanges of substrates across the mitochondrial inner membrane. The substrates are nucleotides, metabolic intermediates, and cofactors that are required in cytoplasmic and matrix metabolism. This review summarizes and discusses the current knowledge of the antiport mechanism(s) of MCs that has been deduced from determining transport characteristics and by analyzing structural, sequence, and mutagenesis data. The mode of transport varies among different MCs with respect to how the substrate translocation depends on the electrical and pH gradients across the mitochondrial inner membrane, for example, the ADP/ATP carrier is electrogenic (electrophoretic), the GTP/GDP carrier is dependent on the pH gradient, the aspartate/glutamate carrier is dependent on both, and the oxoglutarate/malate carrier is independent of them. The structure of the bovine ADP/ATP carrier consists of a six-transmembrane α-helix bundle with a pseudo-threefold symmetry and a closed matrix gate. By using this structure as a template in homology modeling, residues engaged in substrate binding and the formation of a cytoplasmic gate in MCs have been proposed. The functional importance of the residues of the binding site, the matrix, and the cytoplasmic gates is supported by transport activities of different MCs with single point mutations. Cumulative evidence has been used to postulate a general transport mechanism for MCs.
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Affiliation(s)
- Magnus Monné
- Department of Biosciences, Biotechnology and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, Bari, Italy; Department of Sciences, University of Basilicata, Potenza, Italy
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnology and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, Bari, Italy.
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Eisenhut M, Hocken N, Weber APM. Plastidial metabolite transporters integrate photorespiration with carbon, nitrogen, and sulfur metabolism. Cell Calcium 2014; 58:98-104. [PMID: 25465893 DOI: 10.1016/j.ceca.2014.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 02/08/2023]
Abstract
Plant photorespiration is an essential prerequisite for oxygenic photosynthesis. This metabolic repair pathway bestrides four compartments, which poses the requirement for several metabolites transporters for pathway function. However, in contrast to the well-studied enzymatic steps of the core photorespiratory cycle, only few photorespiratory translocators have been identified to date. In this review, we give an overview of established and unknown plastidic transport proteins involved in photorespiration and intertwined nitrogen and sulfur metabolism, respectively. Furthermore, we discuss the evolutionary origin of the dicarboxylate translocators and the recently identified glycolate glycerate translocator.
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Affiliation(s)
- Marion Eisenhut
- Institute of Plant Biochemistry, Center of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Nadine Hocken
- Institute of Plant Biochemistry, Center of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Center of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225 Düsseldorf, Germany.
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Schmidt R, Waschina S, Boettger-Schmidt D, Kost C, Kaleta C. Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions. ACTA ACUST UNITED AC 2014; 31:373-81. [PMID: 25286919 DOI: 10.1093/bioinformatics/btu658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
MOTIVATION Genome-scale metabolic network reconstructions have been established as a powerful tool for the prediction of cellular phenotypes and metabolic capabilities of organisms. In recent years, the number of network reconstructions has been constantly increasing, mostly because of the availability of novel (semi-)automated procedures, which enabled the reconstruction of metabolic models based on individual genomes and their annotation. The resulting models are widely used in numerous applications. However, the accuracy and predictive power of network reconstructions are commonly limited by inherent inconsistencies and gaps. RESULTS Here we present a novel method to validate metabolic network reconstructions based on the concept of autocatalytic sets. Autocatalytic sets correspond to collections of metabolites that, besides enzymes and a growth medium, are required to produce all biomass components in a metabolic model. These autocatalytic sets are well-conserved across all domains of life, and their identification in specific genome-scale reconstructions allows us to draw conclusions about potential inconsistencies in these models. The method is capable of detecting inconsistencies, which are neglected by other gap-finding methods. We tested our method on the Model SEED, which is the largest repository for automatically generated genome-scale network reconstructions. In this way, we were able to identify a significant number of missing pathways in several of these reconstructions. Hence, the method we report represents a powerful tool to identify inconsistencies in large-scale metabolic networks. AVAILABILITY AND IMPLEMENTATION The method is available as source code on http://users.minet.uni-jena.de/∼m3kach/ASBIG/ASBIG.zip. CONTACT christoph.kaleta@uni-jena.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ralf Schmidt
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Silvio Waschina
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Daniela Boettger-Schmidt
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Christian Kost
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Christoph Kaleta
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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Gutierrez-Carbonell E, Takahashi D, Lattanzio G, Rodríguez-Celma J, Kehr J, Soll J, Philippar K, Uemura M, Abadía J, López-Millán AF. The distinct functional roles of the inner and outer chloroplast envelope of Pea (Pisum sativum) as revealed by proteomic approaches. J Proteome Res 2014; 13:2941-53. [PMID: 24792535 DOI: 10.1021/pr500106s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein profiles of inner (IE) and outer (OE) chloroplast envelope membrane preparations from pea were studied using shotgun nLC-MS/MS and two-dimensional electrophoresis, and 589 protein species (NCBI entries) were identified. The relative enrichment of each protein in the IE/OE pair of membranes was used to provide an integrated picture of the chloroplast envelope. From the 546 proteins identified with shotgun, 321 showed a significant differential distribution, with 180 being enriched in IE and 141 in OE. To avoid redundancy and facilitate in silico localization, Arabidopsis homologues were used to obtain a nonredundant list of 409 envelope proteins, with many showing significant OE or IE enrichment. Functional classification reveals that IE is a selective barrier for transport of many metabolites and plays a major role in controlling protein homeostasis, whereas proteins in OE are more heterogeneous and participate in a wide range of processes. Data support that metabolic processes previously described to occur in the envelope such as chlorophyll and tocopherol biosynthesis can be ascribed to the IE, whereas others such as carotenoid or lipid biosynthesis occur in both membranes. Furthermore, results allow empirical assignation to the IE and/or OE of many proteins previously assigned to the bulk chloroplast envelope proteome.
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Affiliation(s)
- Elain Gutierrez-Carbonell
- Plant Nutrition Department, Aula Dei Experimental Station, CSIC , P.O. Box 13034, 50080 Zaragoza, Spain
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Trono D, Laus MN, Soccio M, Pastore D. Transport pathways--proton motive force interrelationship in durum wheat mitochondria. Int J Mol Sci 2014; 15:8186-215. [PMID: 24821541 PMCID: PMC4057727 DOI: 10.3390/ijms15058186] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/18/2014] [Accepted: 04/24/2014] [Indexed: 12/25/2022] Open
Abstract
In durum wheat mitochondria (DWM) the ATP-inhibited plant mitochondrial potassium channel (PmitoK(ATP)) and the plant uncoupling protein (PUCP) are able to strongly reduce the proton motive force (pmf) to control mitochondrial production of reactive oxygen species; under these conditions, mitochondrial carriers lack the driving force for transport and should be inactive. However, unexpectedly, DWM uncoupling by PmitoK(ATP) neither impairs the exchange of ADP for ATP nor blocks the inward transport of Pi and succinate. This uptake may occur via the plant inner membrane anion channel (PIMAC), which is physiologically inhibited by membrane potential, but unlocks its activity in de-energized mitochondria. Probably, cooperation between PIMAC and carriers may accomplish metabolite movement across the inner membrane under both energized and de-energized conditions. PIMAC may also cooperate with PmitoK(ATP) to transport ammonium salts in DWM. Interestingly, this finding may trouble classical interpretation of in vitro mitochondrial swelling; instead of free passage of ammonia through the inner membrane and proton symport with Pi, that trigger metabolite movements via carriers, transport of ammonium via PmitoK(ATP) and that of the counteranion via PIMAC may occur. Here, we review properties, modulation and function of the above reported DWM channels and carriers to shed new light on the control that they exert on pmf and vice-versa.
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Affiliation(s)
- Daniela Trono
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Centro di Ricerca per la Cerealicoltura, S.S. 673 Km 25, 71122 Foggia, Italy.
| | - Maura N Laus
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università di Foggia, Via Napoli 25, 71122 Foggia, Italy.
| | - Mario Soccio
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università di Foggia, Via Napoli 25, 71122 Foggia, Italy.
| | - Donato Pastore
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università di Foggia, Via Napoli 25, 71122 Foggia, Italy.
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Abstract
Chlorophylls are magnesium-tetrapyrrole molecules that play essential roles in photosynthesis. All chlorophylls have similar five-membered ring structures, with variations in the side chains and/or reduction states. Formyl group substitutions on the side chains of chlorophyll a result in the different absorption properties of chlorophyll b, chlorophyll d, and chlorophyll f. These formyl substitution derivatives exhibit different spectral shifts according to the formyl substitution position. Not only does the presence of various types of chlorophylls allow the photosynthetic organism to harvest sunlight at different wavelengths to enhance light energy input, but the pigment composition of oxygenic photosynthetic organisms also reflects the spectral properties on the surface of the Earth. Two major environmental influencing factors are light and oxygen levels, which may play central roles in the regulatory pathways leading to the different chlorophylls. I review the biochemical processes of chlorophyll biosynthesis and their regulatory mechanisms.
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Affiliation(s)
- Min Chen
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia;
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Teyssier C, Maury S, Beaufour M, Grondin C, Delaunay A, Le Metté C, Ader K, Cadene M, Label P, Lelu-Walter MA. In search of markers for somatic embryo maturation in hybrid larch (Larix × eurolepis): global DNA methylation and proteomic analyses. PHYSIOLOGIA PLANTARUM 2014; 150:271-91. [PMID: 23789891 DOI: 10.1111/ppl.12081] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/08/2013] [Accepted: 05/28/2013] [Indexed: 05/22/2023]
Abstract
A global DNA methylation and proteomics approach was used to investigate somatic embryo maturation in hybrid larch. Each developmental step during somatic embryogenesis was associated with a distinct and significantly different global DNA methylation level: from 45.8% mC for undifferentiated somatic embryos (1-week proliferation) to 61.5% mC for immature somatic embryos (1-week maturation), while maturation was associated with a decrease in DNA methylation to 53.4% for mature cotyledonary somatic embryos (8-weeks maturation). The presence of 5-azacytidine (hypo-methylating agent) or hydroxyurea (hyper-methylating agent) in the maturation medium altered the global DNA methylation status of the embryogenic cultures, and significantly reduced both their relative growth rate and embryogenic potential, suggesting an important role for DNA methylation in embryogenesis. Maturation was also assessed by examining changes in the total protein profile. Storage proteins, identified as legumin- and vicilin-like, appeared at the precotyledonary stage. In the proteomic study, total soluble proteins were extracted from embryos after 1 and 8 weeks of maturation, and separated by two-dimensional gel electrophoresis. There were 147 spots which showed significant differences between the stages of maturation; they were found to be involved mainly in primary metabolism and the stabilization of the resulting metabolites. This indicated that the somatic embryo was still metabolically active at 8 weeks of maturation. This is the first report of analyses of global DNA methylation (including the effects of hyper- and hypo-treatments) and proteome during somatic embryogenesis in hybrid larch, and thus provides novel insights into maturation of conifer somatic embryos.
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Affiliation(s)
- Caroline Teyssier
- INRA, UR 0588, Research Unit for Breeding, Genetics and Physiology of Forest Trees, Orléans, F-45075, France
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Gigolashvili T, Kopriva S. Transporters in plant sulfur metabolism. FRONTIERS IN PLANT SCIENCE 2014; 5:442. [PMID: 25250037 PMCID: PMC4158793 DOI: 10.3389/fpls.2014.00442] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/18/2014] [Indexed: 05/02/2023]
Abstract
Sulfur is an essential nutrient, necessary for synthesis of many metabolites. The uptake of sulfate, primary and secondary assimilation, the biosynthesis, storage, and final utilization of sulfur (S) containing compounds requires a lot of movement between organs, cells, and organelles. Efficient transport systems of S-containing compounds across the internal barriers or the plasma membrane and organellar membranes are therefore required. Here, we review a current state of knowledge of the transport of a range of S-containing metabolites within and between the cells as well as of their long distance transport. An improved understanding of mechanisms and regulation of transport will facilitate successful engineering of the respective pathways, to improve the plant yield, biotic interaction and nutritional properties of crops.
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Affiliation(s)
- Tamara Gigolashvili
- Department of Plant Molecular Physiology, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of CologneCologne Germany
- *Correspondence: Tamara Gigolashvili, Department of Plant Molecular Physiology, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, Zülpicher Street 47 B, 50674 Cologne, Germany e-mail:
| | - Stanislav Kopriva
- Plant Biochemistry Department, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of CologneCologne Germany
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Qiu H, Price DC, Weber APM, Facchinelli F, Yoon HS, Bhattacharya D. Assessing the bacterial contribution to the plastid proteome. TRENDS IN PLANT SCIENCE 2013; 18:680-7. [PMID: 24139901 DOI: 10.1016/j.tplants.2013.09.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/11/2013] [Accepted: 09/18/2013] [Indexed: 05/08/2023]
Abstract
Plastids fulfill a variety of different functions (e.g., photosynthesis and amino acid biosynthesis) that rely on proteins of cyanobacterial (i.e., endosymbiont), noncyanobacterial, and 'host' (eukaryotic) origins. Analysis of plastid proteome data from glaucophytes and green algae allows robust inference of protein origins and organelle protein sharing across the >1 billion years of Archaeplastida evolution. Here, we show that more than one-third of genes encoding plastid proteins lack detectable homologs in Cyanobacteria, underlining the taxonomically broad contributions to plastid functions. Chlamydiae and Proteobacteria are the most significant other bacterial sources of plastid proteins. Mapping of plastid proteins to metabolic pathways shows a core set of anciently derived proteins in Archaeplastida, with many others being lineage specific and derived from independent horizontal gene transfer (HGT) events.
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Affiliation(s)
- Huan Qiu
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08540, USA
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Chen Y, Xu Y, Luo W, Li W, Chen N, Zhang D, Chong K. The F-box protein OsFBK12 targets OsSAMS1 for degradation and affects pleiotropic phenotypes, including leaf senescence, in rice. PLANT PHYSIOLOGY 2013; 163:1673-85. [PMID: 24144792 PMCID: PMC3850201 DOI: 10.1104/pp.113.224527] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/16/2013] [Indexed: 05/18/2023]
Abstract
Leaf senescence is related to the grain-filling rate and grain weight in cereals. Many components involved in senescence regulation at either the genetic or physiological level are known. However, less is known about molecular regulation mechanisms. Here, we report that OsFBK12 (an F-box protein containing a Kelch repeat motif) interacts with S-ADENOSYL-l-METHIONINE SYNTHETASE1 (SAMS1) to regulate leaf senescence and seed size as well as grain number in rice (Oryza sativa). Yeast two-hybrid, pull-down, and bimolecular fluorescence complementation assays indicate that OsFBK12 interacts with Oryza sativa S-PHASE KINASE-ASSOCIATED PROTEIN1-LIKE PROTEIN and with OsSAMS1. Biochemical and physiological data showed that OsFBK12 targets OsSAMS1 for degradation. OsFBK12-RNA interference lines and OsSAMS1 overexpression lines showed increased ethylene levels, while OsFBK12-OX lines and OsSAMS1-RNA interference plants exhibited decreased ethylene. Phenotypically, overexpression of OsFBK12 led to a delay in leaf senescence and germination and increased seed size, whereas knockdown lines of either OsFBK12 or OsSAMS1 promoted the senescence program. Our results suggest that OsFBK12 is involved in the 26S proteasome pathway by interacting with Oryza sativa S-PHASE KINASE-ASSOCIATED PROTEIN1-LIKE PROTEIN and that it targets the substrate OsSAMS1 for degradation, triggering changes in ethylene levels for the regulation of leaf senescence and grain size. These data have potential applications in the molecular breeding of rice.
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The endosymbiont Amoebophilus asiaticus encodes an S-adenosylmethionine carrier that compensates for its missing methylation cycle. J Bacteriol 2013; 195:3183-92. [PMID: 23667233 DOI: 10.1128/jb.00195-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All organisms require S-adenosylmethionine (SAM) as a methyl group donor and cofactor for various biologically important processes. However, certain obligate intracellular parasitic bacteria and also the amoeba symbiont Amoebophilus asiaticus have lost the capacity to synthesize this cofactor and hence rely on its uptake from host cells. Genome analyses revealed that A. asiaticus encodes a putative SAM transporter. The corresponding protein was functionally characterized in Escherichia coli: import studies demonstrated that it is specific for SAM and S-adenosylhomocysteine (SAH), the end product of methylation. SAM transport activity was shown to be highly dependent on the presence of a membrane potential, and by targeted analyses, we obtained direct evidence for a proton-driven SAM/SAH antiport mechanism. Sequence analyses suggest that SAM carriers from Rickettsiales might operate in a similar way, in contrast to chlamydial SAM transporters. SAM/SAH antiport is of high physiological importance, as it allows for compensation for the missing methylation cycle. The identification of a SAM transporter in A. asiaticus belonging to the Bacteroidetes phylum demonstrates that SAM transport is more widely spread than previously assumed and occurs in bacteria belonging to three different phyla (Proteobacteria, Chlamydiae, and Bacteroidetes).
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42
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Facchinelli F, Pribil M, Oster U, Ebert NJ, Bhattacharya D, Leister D, Weber APM. Proteomic analysis of the Cyanophora paradoxa muroplast provides clues on early events in plastid endosymbiosis. PLANTA 2013; 237:637-51. [PMID: 23212214 DOI: 10.1007/s00425-012-1819-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 11/08/2012] [Indexed: 05/06/2023]
Abstract
Glaucophytes represent the first lineage of photosynthetic eukaryotes of primary endosymbiotic origin that diverged after plastid establishment. The muroplast of Cyanophora paradoxa represents a primitive plastid that resembles its cyanobacterial ancestor in pigment composition and the presence of a peptidoglycan wall. To attain insights into the evolutionary history of cyanobiont integration and plastid development, it would thus be highly desirable to obtain knowledge on the composition of the glaucophyte plastid proteome. Here, we provide the first proteomic analysis of the muroplast of C. paradoxa. Mass spectrometric analysis of the muroplast proteome identified 510 proteins with high confidence. The protein repertoire of the muroplast revealed novel paths for reduced carbon flow and export to the cytosol through a sugar phosphate transporter of chlamydial origin. We propose that C. paradoxa possesses a primordial plastid mirroring the situation in the early protoalga.
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Affiliation(s)
- Fabio Facchinelli
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, Universitätsstraße 1, Düsseldorf, Germany
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Rolland N, Curien G, Finazzi G, Kuntz M, Maréchal E, Matringe M, Ravanel S, Seigneurin-Berny D. The Biosynthetic Capacities of the Plastids and Integration Between Cytoplasmic and Chloroplast Processes. Annu Rev Genet 2012; 46:233-64. [DOI: 10.1146/annurev-genet-110410-132544] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Université Joseph Fourier Grenoble I/INRA/CEA, 38054 Grenoble Cedex 9, France; , , , , , , ,
| | - Gilles Curien
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Université Joseph Fourier Grenoble I/INRA/CEA, 38054 Grenoble Cedex 9, France; , , , , , , ,
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Université Joseph Fourier Grenoble I/INRA/CEA, 38054 Grenoble Cedex 9, France; , , , , , , ,
| | - Marcel Kuntz
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Université Joseph Fourier Grenoble I/INRA/CEA, 38054 Grenoble Cedex 9, France; , , , , , , ,
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Université Joseph Fourier Grenoble I/INRA/CEA, 38054 Grenoble Cedex 9, France; , , , , , , ,
| | - Michel Matringe
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Université Joseph Fourier Grenoble I/INRA/CEA, 38054 Grenoble Cedex 9, France; , , , , , , ,
| | - Stéphane Ravanel
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Université Joseph Fourier Grenoble I/INRA/CEA, 38054 Grenoble Cedex 9, France; , , , , , , ,
| | - Daphné Seigneurin-Berny
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Université Joseph Fourier Grenoble I/INRA/CEA, 38054 Grenoble Cedex 9, France; , , , , , , ,
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Gigolashvili T, Geier M, Ashykhmina N, Frerigmann H, Wulfert S, Krueger S, Mugford SG, Kopriva S, Haferkamp I, Flügge UI. The Arabidopsis thylakoid ADP/ATP carrier TAAC has an additional role in supplying plastidic phosphoadenosine 5'-phosphosulfate to the cytosol. THE PLANT CELL 2012; 24:4187-204. [PMID: 23085732 PMCID: PMC3517245 DOI: 10.1105/tpc.112.101964] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 09/03/2012] [Accepted: 09/28/2012] [Indexed: 05/18/2023]
Abstract
3'-Phosphoadenosine 5'-phosphosulfate (PAPS) is the high-energy sulfate donor for sulfation reactions. Plants produce some PAPS in the cytosol, but it is predominantly produced in plastids. Accordingly, PAPS has to be provided by plastids to serve as a substrate for sulfotransferase reactions in the cytosol and the Golgi apparatus. We present several lines of evidence that the recently described Arabidopsis thaliana thylakoid ADP/ATP carrier TAAC transports PAPS across the plastid envelope and thus fulfills an additional function of high physiological relevance. Transport studies using the recombinant protein revealed that it favors PAPS, 3'-phosphoadenosine 5'-phosphate, and ATP as substrates; thus, we named it PAPST1. The protein could be detected both in the plastid envelope membrane and in thylakoids, and it is present in plastids of autotrophic and heterotrophic tissues. TAAC/PAPST1 belongs to the mitochondrial carrier family in contrast with the known animal PAPS transporters, which are members of the nucleotide-sugar transporter family. The expression of the PAPST1 gene is regulated by the same MYB transcription factors also regulating the biosynthesis of sulfated secondary metabolites, glucosinolates. Molecular and physiological analyses of papst1 mutant plants indicate that PAPST1 is involved in several aspects of sulfur metabolism, including the biosynthesis of thiols, glucosinolates, and phytosulfokines.
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Affiliation(s)
- Tamara Gigolashvili
- Botanical Institute, Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, D-50674 Cologne, Germany
| | - Melanie Geier
- Cellular Physiology/Membrane Transport, Technical University of Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Natallia Ashykhmina
- Botanical Institute, Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, D-50674 Cologne, Germany
| | - Henning Frerigmann
- Botanical Institute, Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, D-50674 Cologne, Germany
| | - Sabine Wulfert
- Botanical Institute, Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, D-50674 Cologne, Germany
| | - Stephan Krueger
- Botanical Institute, Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, D-50674 Cologne, Germany
| | - Sarah G. Mugford
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Stanislav Kopriva
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Ilka Haferkamp
- Cellular Physiology/Membrane Transport, Technical University of Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Ulf-Ingo Flügge
- Botanical Institute, Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, D-50674 Cologne, Germany
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Haferkamp I, Linka N. Functional expression and characterisation of membrane transport proteins. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:675-90. [PMID: 22639981 DOI: 10.1111/j.1438-8677.2012.00591.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Membrane transporters set the framework organising the complexity of plant metabolism in cells, tissues and organisms. Their substrate specificity and controlled activity in different cells is a crucial part for plant metabolism to run pathways in concert. Transport proteins catalyse the uptake and exchange of ions, substrates, intermediates, products and cofactors across membranes. Given the large number of metabolites, a wide spectrum of transporters is required. The vast majority of in silico annotated membrane transporters in plant genomes, however, has not yet been functionally characterised. Hence, to understand the metabolic network as a whole, it is important to understand how transporters connect and control the metabolic pathways of plant cells. Heterologous expression and in vitro activity studies of recombinant transport proteins have highly improved their functional analysis in the last two decades. This review provides a comprehensive overview of the recent advances in membrane protein expression and functional characterisation using various host systems and transport assays.
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Affiliation(s)
- I Haferkamp
- Plant Physiology, Technical University of Kaiserslautern, Kaiserslautern, Germany Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - N Linka
- Plant Physiology, Technical University of Kaiserslautern, Kaiserslautern, Germany Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Tan YF, Millar AH, Taylor NL. Components of mitochondrial oxidative phosphorylation vary in abundance following exposure to cold and chemical stresses. J Proteome Res 2012; 11:3860-79. [PMID: 22574745 DOI: 10.1021/pr3003535] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plant mitochondria are highly responsive organelles that vary their metabolism in response to a wide range of chemical and environmental conditions. Quantitative proteomics studies have begun to allow the analysis of these large-scale protein changes in mitochondria. However studies of the integral membrane proteome of plant mitochondria, arguably the site responsible for the most fundamental mitochondrial processes of oxidative phosphorylation, protein import and metabolite transport, remain a technical challenge. Here we have investigated the changes in protein abundance in response to a number of chemical stresses and cold. In addition to refining the subcellular localization of 66 proteins, we have been able to characterize 596 protein × treatment combinations following a range of stresses. To date it has been assumed that the main mitochondrial response to stress involved the induction of alternative respiratory proteins such as AOX, UCPs, and alternative NAD(P)H dehydrogenases; we now provide evidence for a number of very specific protein abundance changes that have not been highlighted previously by transcript studies. This includes both previously characterized stress responsive proteins as well as major components of oxidative phosphorylation, protein import/export, and metabolite transport.
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Affiliation(s)
- Yew-Foon Tan
- ARC Centre of Excellence in Plant Energy Biology, MCS Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
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Huang C, Qian Y, Li Z, Zhou X. Virus-induced gene silencing and its application in plant functional genomics. SCIENCE CHINA-LIFE SCIENCES 2012; 55:99-108. [PMID: 22415680 DOI: 10.1007/s11427-012-4280-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 12/13/2011] [Indexed: 12/13/2022]
Abstract
Virus-induced gene silencing is regarded as a powerful and efficient tool for the analysis of gene function in plants because it is simple, rapid and transformation-free. It has been used to perform both forward and reverse genetics to identify plant functional genes. Many viruses have been developed into virus-induced gene silencing vectors and gene functions involved in development, biotic and abiotic stresses, metabolism, and cellular signaling have been reported. In this review, we discuss the development and application of virus-induced gene silencing in plant functional genomics.
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Affiliation(s)
- Changjun Huang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Lee S, Doxey AC, McConkey BJ, Moffatt BA. Nuclear targeting of methyl-recycling enzymes in Arabidopsis thaliana is mediated by specific protein interactions. MOLECULAR PLANT 2012; 5:231-48. [PMID: 21976714 DOI: 10.1093/mp/ssr083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Numerous transmethylation reactions are required for normal plant growth and development. S-adenosylhomocysteine hydrolase (SAHH) and adenosine kinase (ADK) act coordinately to recycle the by-product of these reactions, S-adenosylhomocysteine (SAH) that would otherwise competitively inhibit methyltransferase (MT) activities. Here, we report on investigations to understand how the SAH produced in the nucleus is metabolized by SAHH and ADK. Localization analyses using green fluorescent fusion proteins demonstrated that both enzymes are capable of localizing to the cytoplasm and the nucleus, although no obvious nuclear localization signal was found in their sequences. Deletion analysis revealed that a 41-amino-acid segment of SAHH (Gly(150)-Lys(190)) is required for nuclear targeting of this enzyme. This segment is surface exposed, shows unique sequence conservation patterns in plant SAHHs, and possesses additional features of protein-protein interaction motifs. ADK and SAHH interact in Arabidopsis via this segment and also interact with an mRNA cap MT. We propose that the targeting of this complex is directed by the nuclear localization signal of the MT; other MTs may similarly target SAHH/ADK to other subcellular compartments to ensure uninterrupted transmethylation.
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Affiliation(s)
- Sanghyun Lee
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
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Haferkamp I, Schmitz-Esser S. The plant mitochondrial carrier family: functional and evolutionary aspects. FRONTIERS IN PLANT SCIENCE 2012; 3:2. [PMID: 22639632 PMCID: PMC3355725 DOI: 10.3389/fpls.2012.00002] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 01/03/2012] [Indexed: 05/19/2023]
Abstract
Mitochondria play a key role in respiration and energy production and are involved in multiple eukaryotic but also in several plant specific metabolic pathways. Solute carriers in the inner mitochondrial membrane connect the internal metabolism with that of the surrounding cell. Because of their common basic structure, these transport proteins affiliate to the mitochondrial carrier family (MCF). Generally, MCF proteins consist of six membrane spanning helices, exhibit typical conserved domains and appear as homodimers in the native membrane. Although structurally related, MCF proteins catalyze the specific transport of various substrates, such as nucleotides, amino acids, dicarboxylates, cofactors, phosphate or H(+). Recent investigations identified MCF proteins also in several other cellular compartments and therefore their localization and physiological function is not only restricted to mitochondria. MCF proteins are a characteristic feature of eukaryotes and bacterial genomes lack corresponding sequences. Therefore, the evolutionary origin of MCF proteins is most likely associated with the establishment of mitochondria. It is not clear whether the host cell, the symbiont, or the chimerical organism invented the ancient MCF sequence. Here, we try to explain the establishment of different MCF proteins and focus on the characteristics of members from plants, in particular from Arabidopsis thaliana.
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Affiliation(s)
- Ilka Haferkamp
- Zelluläre Physiologie/Membrantransport, Technische Universität KaiserslauternKaiserslautern, Germany
- *Correspondence: Ilka Haferkamp, Biologie, Zelluläre Physiologie/Membrantransport, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 22, 67653 Kaiserslautern, Germany. e-mail:
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Linka M, Weber APM. Evolutionary Integration of Chloroplast Metabolism with the Metabolic Networks of the Cells. FUNCTIONAL GENOMICS AND EVOLUTION OF PHOTOSYNTHETIC SYSTEMS 2012. [DOI: 10.1007/978-94-007-1533-2_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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