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Mendieta JP, Tu X, Jiang D, Yan H, Zhang X, Marand AP, Zhong S, Schmitz RJ. Investigating the cis-Regulatory Basis of C 3 and C 4 Photosynthesis in Grasses at Single-Cell Resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574340. [PMID: 38405933 PMCID: PMC10888913 DOI: 10.1101/2024.01.05.574340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
While considerable knowledge exists about the enzymes pivotal for C4 photosynthesis, much less is known about the cis-regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C4 enzymes for five different grass species. This study spans four C4 species, covering three distinct photosynthetic subtypes: Zea mays and Sorghum bicolor (NADP-ME), Panicum miliaceum (NAD-ME), Urochloa fusca (PEPCK), along with the C3 outgroup Oryza sativa. We studied the cis-regulatory landscape of enzymes essential across all C4 species and those unique to C4 subtypes, measuring cell-type-specific biases for C4 enzymes using chromatin accessibility data. Integrating these data with phylogenetics revealed diverse co-option of gene family members between species, showcasing the various paths of C4 evolution. Besides promoter proximal ACRs, we found that, on average, C4 genes have two to three distal cell-type-specific ACRs, highlighting the complexity and divergent nature of C4 evolution. Examining the evolutionary history of these cell-type-specific ACRs revealed a spectrum of conserved and novel ACRs, even among closely related species, indicating ongoing evolution of cis-regulation at these C4 loci. This study illuminates the dynamic and complex nature of CRE evolution in C4 photosynthesis, particularly highlighting the intricate cis-regulatory evolution of key loci. Our findings offer a valuable resource for future investigations, potentially aiding in the optimization of C3 crop performance under changing climatic conditions.
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Affiliation(s)
| | - Xiaoyu Tu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daiquan Jiang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong
| | - Haidong Yan
- Department of Genetics, University of Georgia
| | - Xuan Zhang
- Department of Genetics, University of Georgia
| | - Alexandre P Marand
- Department of Genetics, University of Georgia
- Department of Molecular, Cellular, and Development Biology, University of Michigan
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong
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2
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Zou C, Li L, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Jia W, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable PS, Chang Y, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK, Zhang H. The genome of broomcorn millet. Nat Commun 2019; 10:436. [PMID: 30683860 PMCID: PMC6347628 DOI: 10.1038/s41467-019-08409-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/04/2018] [Indexed: 01/05/2023] Open
Abstract
Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology.
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Affiliation(s)
- Changsong Zou
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, 475001, Kaifeng, Henan, China
| | - Leiting Li
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Delin Li
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- China Agricultural University, 100193, Beijing, China
| | - Qiming Tang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Lihong Xiao
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | | | - Ping Deng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Wei Jia
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Ru Huang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Meiling Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Yidan Sun
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Jiamin Hu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Patrick S Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- China Agricultural University, 100193, Beijing, China
- Department of Agronomy, Iowa State University, Ames, IA, 50011-3650, USA
| | - Yuxiao Chang
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Feng Li
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Hui Zhang
- Key Laboratory of Plant Stress Research, Shandong Normal University, No. 88 Wenhua East Rd, Jinan, 250014, Shandong, China
| | - Baili Feng
- School of Agronomy, Northwest Agriculture & Forestry University, 3 Weihui Rd, 712100, Yangling, China
| | - Xinguang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, 200032, Shanghai, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - James C Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
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Offermann S, Friso G, Doroshenk KA, Sun Q, Sharpe RM, Okita TW, Wimmer D, Edwards GE, van Wijk KJ. Developmental and Subcellular Organization of Single-Cell C₄ Photosynthesis in Bienertia sinuspersici Determined by Large-Scale Proteomics and cDNA Assembly from 454 DNA Sequencing. J Proteome Res 2015; 14:2090-108. [PMID: 25772754 DOI: 10.1021/pr5011907] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Kranz C4 species strictly depend on separation of primary and secondary carbon fixation reactions in different cell types. In contrast, the single-cell C4 (SCC4) species Bienertia sinuspersici utilizes intracellular compartmentation including two physiologically and biochemically different chloroplast types; however, information on identity, localization, and induction of proteins required for this SCC4 system is currently very limited. In this study, we determined the distribution of photosynthesis-related proteins and the induction of the C4 system during development by label-free proteomics of subcellular fractions and leaves of different developmental stages. This was enabled by inferring a protein sequence database from 454 sequencing of Bienertia cDNAs. Large-scale proteome rearrangements were observed as C4 photosynthesis developed during leaf maturation. The proteomes of the two chloroplasts are different with differential accumulation of linear and cyclic electron transport components, primary and secondary carbon fixation reactions, and a triose-phosphate shuttle that is shared between the two chloroplast types. This differential protein distribution pattern suggests the presence of a mRNA or protein-sorting mechanism for nuclear-encoded, chloroplast-targeted proteins in SCC4 species. The combined information was used to provide a comprehensive model for NAD-ME type carbon fixation in SCC4 species.
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Affiliation(s)
- Sascha Offermann
- †Institute of Botany, Leibniz University, Herrenhaeuser Strasse 2, Hannover 30419, Germany
| | - Giulia Friso
- ‡Department of Plant Biology, Cornell University, 332 Emerson Hall, Ithaca, New York 14853, United States
| | - Kelly A Doroshenk
- §Institute of Biological Chemistry, Washington State University, 299 Clark Hall, Pullman, Washington 99164, United States
| | - Qi Sun
- ∥Computational Biology Service Unit, Cornell University, 618 Rhodes Hall, Ithaca, New York 14853, United States
| | - Richard M Sharpe
- ⊥School of Biological Science, Washington State University, 303 Heald Hall, Pullman, Washington 99164, United States
| | - Thomas W Okita
- §Institute of Biological Chemistry, Washington State University, 299 Clark Hall, Pullman, Washington 99164, United States
| | - Diana Wimmer
- †Institute of Botany, Leibniz University, Herrenhaeuser Strasse 2, Hannover 30419, Germany
| | - Gerald E Edwards
- ⊥School of Biological Science, Washington State University, 303 Heald Hall, Pullman, Washington 99164, United States
| | - Klaas J van Wijk
- ‡Department of Plant Biology, Cornell University, 332 Emerson Hall, Ithaca, New York 14853, United States
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Goron TL, Raizada MN. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution. FRONTIERS IN PLANT SCIENCE 2015; 6:157. [PMID: 25852710 PMCID: PMC4371761 DOI: 10.3389/fpls.2015.00157] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 02/27/2015] [Indexed: 05/20/2023]
Abstract
Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed "orphan cereals." Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.
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Affiliation(s)
| | - Manish N. Raizada
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
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5
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Lin Q, Li S, Dong W, Feng C, Yin X, Xu C, Sun C, Chen K. Involvement of CitCHX and CitDIC in developmental-related and postharvest-hot-air driven citrate degradation in citrus fruits. PLoS One 2015; 10:e0119410. [PMID: 25738939 PMCID: PMC4349887 DOI: 10.1371/journal.pone.0119410] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/13/2015] [Indexed: 01/08/2023] Open
Abstract
Citrate is the predominant organic acid associated with taste in citrus fruit. Although citrate metabolism has been widely studied in recent years, the potential contributions of transport proteins to citrate content remain unclear. In the present study, high-acid citrus fruit Gaocheng ('GC', Citrus sp.) and low-acid citrus fruit Satsuma mandarin ('SM', Citrus unshiu Marc.) were selected for study, and the degradation of citrate was deduced to be the main cause of the difference in acidity in fully mature fruits. RNA-seq analysis was carried out on 'GC' and 'SM' fruit samples over the same time course, and the results indicated that citrate degradation occurred mainly through the glutamine pathway, catalyzed by CitAco3-CitGS2-CitGDU1, and also two transport-related genes, CitCHX and CitDIC, were shown to be associated with citrate degradation. These results were confirmed by real-time PCR. In postharvest 'GC' fruit, the expressions of these two transport-related genes were induced by 2-fold under hot air treatment, accompanied by a reduction of 7%-9% in total acid degradation. Transient expression of CitCHX and CitDIC in tobacco leaves was performed, and the citrate content was reduced by 62%, 75% and 78% following CitCHX, CitDIC and CitCHX plus CitDIC treatments, respectively, as compared with expression of an empty vector. Overall, these data indicated that two transport proteins, CitCHX and CitDIC, are not only involved in citrate degradation during fruit development, but also involved in postharvest hot air triggered citrate reduction.
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Affiliation(s)
- Qiong Lin
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Shaojia Li
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Wencheng Dong
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Chao Feng
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xueren Yin
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Changjie Xu
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Chongde Sun
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, P. R. China
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6
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Goron TL, Raizada MN. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 25852710 DOI: 10.3389/fpl.2015.00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed "orphan cereals." Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.
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Affiliation(s)
- Travis L Goron
- Department of Plant Agriculture, University of Guelph Guelph, ON, Canada
| | - Manish N Raizada
- Department of Plant Agriculture, University of Guelph Guelph, ON, Canada
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7
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Weber APM, Bräutigam A. The role of membrane transport in metabolic engineering of plant primary metabolism. Curr Opin Biotechnol 2012; 24:256-62. [PMID: 23040411 DOI: 10.1016/j.copbio.2012.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/18/2012] [Accepted: 09/18/2012] [Indexed: 11/29/2022]
Abstract
Plant cells are highly compartmentalized and so is their metabolism. Most metabolic pathways are distributed across several cellular compartments, which requires the activities of membrane transporters to catalyze the flux of precursors, intermediates, and end products between compartments. Metabolites such as sucrose and amino acids have to be transported between cells and tissues to supply, for example, metabolism in developing seeds or fruits with precursors and energy. Thus, rational engineering of plant primary metabolism requires a detailed and molecular understanding of the membrane transporters. This knowledge however still lags behind that of soluble enzymes. Recent advances include the molecular identification of pyruvate transporters at the chloroplast and mitochondrial membranes and of a new class of transporters called SWEET that are involved in the release of sugars to the apoplast.
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Affiliation(s)
- Andreas P M Weber
- Institute for Plant Biochemistry and Center of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Geb. 26.03.01, Universitätsstrasse 1, D-40225 Düsseldorf, Germany.
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8
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Sobhanian H, Motamed N, Jazii FR, Nakamura T, Komatsu S. Salt stress induced differential proteome and metabolome response in the shoots of Aeluropus lagopoides (Poaceae), a halophyte C(4) plant. J Proteome Res 2010; 9:2882-97. [PMID: 20397718 DOI: 10.1021/pr900974k] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A proteomic approach was used to identify proteins affected by salt in the halophyte C(4) plant Aeluropus lagopoides (Poaceae) in an attempt to understand the mechanism of salt tolerance. Plants were treated with 450 mM NaCl for 10 days, and proteins were then extracted from the shoots and separated by two-dimensional polyacrylamide gel electrophoresis. A total of 1805 protein spots were detected, of which 39 were up-regulated and 44 were down-regulated by treatment with NaCl. Metabolism-related proteins were up-regulated, whereas photosynthesis-related proteins were down-regulated. Dose-dependence studies showed that the up-regulation continued at NaCl concentrations above 450 mM for defense-related proteins alone. Western blot analysis confirmed the down-regulation of RuBisCO LSU and RuBisCO SSU and severe down-regulation of RuBisCO activase. The activity of glyoxalase I increased with increasing NaCl concentration. Metabolome studies indicated up-regulation of amino acids and down-regulation of tricarboxylic acid cycle-related metabolites. These studies suggest that up-regulation of energy formation, amino acid biosynthesis, C(4) photosynthesis, and detoxification are the main strategies for salt tolerance in A. lagopoides.
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10
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11
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Deng W, Luo K, Li Z, Yang Y. Molecular cloning and characterization of a mitochondrial dicarboxylate/tricarboxylate transporter gene inCitrus junosresponse to aluminum stress. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/19401730802351012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Miller G, Stein H, Honig A, Kapulnik Y, Zilberstein A. Responsive modes of Medicago sativa proline dehydrogenase genes during salt stress and recovery dictate free proline accumulation. PLANTA 2005. [PMID: 15809861 DOI: 10.1007/s00425-005-1518-1514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Free proline accumulation is an innate response of many plants to osmotic stress. To characterize transcriptional regulation of the key proline cycle enzymes in alfalfa (Medicago sativa), two proline dehydrogenase (MsPDH) genes and a partial sequence of Delta (1) -pyrroline-5-carboxylate dehydrogenase (MsP5CDH) gene were identified and cloned. The two MsPDH genes share a high nucleotide sequence homology and a similar exon/intron structure. Estimation of transcript levels during salt stress and recovery revealed that proline accumulation during stress was linearly correlated with a strong decline in MsPDH transcript levels, while Delta (1) -pyrroline-5-carboxylate synthetase (MsP5CS) and MsP5CDH steady-state transcript levels remained essentially unchanged. MsPDH transcript levels dramatically decreased in a fast, salt concentration-dependent manner. The extent of salt-induced proline accumulation also correlated with salt concentrations. Salt-induced repression of MsPDH1 promoter linked to the GUS reporter gene confirmed that the decline in MsPDH transcript levels was due to less transcription initiation. Contrary to the salt-dependent repression, a rapid induction of MsPDH transcription occurred at a very early stage of the recovery process, independently of earlier salt treatments. Hence our results suggest the existence of two different regulatory modes of MsPDH expression; the repressing mode that quantifies salt concentration in an as yet unknown mechanism and the "rehydration"-enhancing mode that responds to stress relief in a maximal induction of MsPDH transcription. As yet the components of salt sensing as well as those that might interact with MsPDH promoter to reduce transcription are still unknown.
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MESH Headings
- Abscisic Acid/pharmacology
- DNA, Complementary/genetics
- Gene Expression Regulation, Enzymologic/drug effects
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant/genetics
- Medicago sativa/drug effects
- Medicago sativa/enzymology
- Medicago sativa/genetics
- Medicago sativa/metabolism
- Molecular Sequence Data
- Plant Leaves/enzymology
- Plant Roots/enzymology
- Proline/metabolism
- Proline Oxidase/genetics
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Sodium Chloride/pharmacology
- Transcription, Genetic/genetics
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Affiliation(s)
- Gadi Miller
- Department of Plant Science, Tel Aviv University, Tel-Aviv 69978, Israel
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13
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Miller G, Stein H, Honig A, Kapulnik Y, Zilberstein A. Responsive modes of Medicago sativa proline dehydrogenase genes during salt stress and recovery dictate free proline accumulation. PLANTA 2005; 222:70-79. [PMID: 15809861 DOI: 10.1007/s00425-005-1518-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Accepted: 01/24/2005] [Indexed: 05/24/2023]
Abstract
Free proline accumulation is an innate response of many plants to osmotic stress. To characterize transcriptional regulation of the key proline cycle enzymes in alfalfa (Medicago sativa), two proline dehydrogenase (MsPDH) genes and a partial sequence of Delta (1) -pyrroline-5-carboxylate dehydrogenase (MsP5CDH) gene were identified and cloned. The two MsPDH genes share a high nucleotide sequence homology and a similar exon/intron structure. Estimation of transcript levels during salt stress and recovery revealed that proline accumulation during stress was linearly correlated with a strong decline in MsPDH transcript levels, while Delta (1) -pyrroline-5-carboxylate synthetase (MsP5CS) and MsP5CDH steady-state transcript levels remained essentially unchanged. MsPDH transcript levels dramatically decreased in a fast, salt concentration-dependent manner. The extent of salt-induced proline accumulation also correlated with salt concentrations. Salt-induced repression of MsPDH1 promoter linked to the GUS reporter gene confirmed that the decline in MsPDH transcript levels was due to less transcription initiation. Contrary to the salt-dependent repression, a rapid induction of MsPDH transcription occurred at a very early stage of the recovery process, independently of earlier salt treatments. Hence our results suggest the existence of two different regulatory modes of MsPDH expression; the repressing mode that quantifies salt concentration in an as yet unknown mechanism and the "rehydration"-enhancing mode that responds to stress relief in a maximal induction of MsPDH transcription. As yet the components of salt sensing as well as those that might interact with MsPDH promoter to reduce transcription are still unknown.
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MESH Headings
- Abscisic Acid/pharmacology
- DNA, Complementary/genetics
- Gene Expression Regulation, Enzymologic/drug effects
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant/genetics
- Medicago sativa/drug effects
- Medicago sativa/enzymology
- Medicago sativa/genetics
- Medicago sativa/metabolism
- Molecular Sequence Data
- Plant Leaves/enzymology
- Plant Roots/enzymology
- Proline/metabolism
- Proline Oxidase/genetics
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Sodium Chloride/pharmacology
- Transcription, Genetic/genetics
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Affiliation(s)
- Gadi Miller
- Department of Plant Science, Tel Aviv University, Tel-Aviv 69978, Israel
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14
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Taniguchi Y, Nagasaki J, Kawasaki M, Miyake H, Sugiyama T, Taniguchi M. Differentiation of dicarboxylate transporters in mesophyll and bundle sheath chloroplasts of maize. PLANT & CELL PHYSIOLOGY 2004; 45:187-200. [PMID: 14988489 DOI: 10.1093/pcp/pch022] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In NADP-malic enzyme-type C(4) plants such as maize (Zea mays L.), efficient transport of oxaloacetate and malate across the inner envelope membranes of chloroplasts is indispensable. We isolated four maize cDNAs, ZmpOMT1 and ZmpDCT1 to 3, encoding orthologs of plastidic 2-oxoglutarate/malate and general dicarboxylate transporters, respectively. Their transcript levels were upregulated by light in a cell-specific manner; ZmpOMT1 and ZmpDCT1 were expressed in the mesophyll cell (MC) and ZmpDCT2 and 3 were expressed in the bundle sheath cell (BSC). The recombinant ZmpOMT1 protein expressed in yeast could transport malate and 2-oxoglutarate but not glutamate. By contrast, the recombinant ZmpDCT1 and 2 proteins transported 2-oxoglutarate and glutamate at similar affinities in exchange for malate. The recombinant proteins could also transport oxaloacetate at the same binding sites as those for the dicarboxylates. In particular, ZmpOMT1 transported oxaloacetate at a higher efficiency than malate or 2-oxoglutarate. We also compared the activities of oxaloacetate transport between MC and BSC chloroplasts from maize leaves. The K(m) value for oxaloacetate in MC chloroplasts was one order of magnitude lower than that in BSC chloroplasts, and was close to that determined with the recombinant ZmpOMT1 protein. Southern analysis revealed that maize has a single OMT gene. These findings suggest that ZmpOMT1 participates in the import of oxaloacetate into MC chloroplasts in exchange for stromal malate. In BSC chloroplasts, ZmpDCT2 and/or ZmpDCT3 were expected to import malate that is transported from MC.
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Affiliation(s)
- Yojiro Taniguchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601 Japan.
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Renné P, Dressen U, Hebbeker U, Hille D, Flügge UI, Westhoff P, Weber APM. The Arabidopsis mutant dct is deficient in the plastidic glutamate/malate translocator DiT2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 35:316-31. [PMID: 12887583 DOI: 10.1046/j.1365-313x.2003.01806.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The Arabidopsis mutant dicarboxylate transport (dct) is one of the classic mutants in the photorespiratory pathway. It requires high CO2 levels for survival. Physiologic and biochemical characterization of dct indicated that dct is deficient in the transport of dicarboxylates across the chloroplast envelope membrane. Hence, re-assimilation of ammonia generated by the photorespiratory cycle is blocked. However, the defective gene in dct has not been identified at the molecular level. Here, we report on the molecular characterization of the defective gene in dct, on the complementation of the mutant phenotype with a wild-type cDNA, and on the functional characterization of the gene product, DiT2, in a recombinant reconstituted system. Furthermore, we provide the kinetic constants of recombinant DiT1 and DiT2, and we discuss these data with respect to their functions in ammonia assimilation. Moreover, an analysis of the transcript levels of DiT1 and DiT2 in different C3- and C4-type plant species is presented, and we demonstrate that the substrate specificity of DiT2 from the C4-plant Flaveria bidentis is similar to its counterpart from C3 plants.
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Affiliation(s)
- Petra Renné
- Lehrstuhl Botanik II, Universität zu Köln, Gyrhofstr. 15, D-50931, Köln, Germany
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Spagnoletta A, De Santis A, Palmieri F, Genchi G. Purification and characterization of the reconstitutively active adenine nucleotide carrier from mitochondria of Jerusalem artichoke (Helianthus tuberosus L.) tubers. J Bioenerg Biomembr 2002; 34:465-72. [PMID: 12678438 DOI: 10.1023/a:1022570226209] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The adenine nucleotide carrier from Jerusalem artichoke (Helianthus tuberosus L.) tubers mitochondria was solubilized with Triton X-100 and purified by sequential chromatography on hydroxapatite and Matrex Gel Blue B in the presence of cardiolipin and asolectin. SDS gel electrophoresis of the purified fraction showed a single polypeptide band with an apparent molecular mass of 33 kDa. When reconstituted in liposomes, the adenine nucleotide carrier catalyzed a pyridoxal 5'-phosphate-sensitive ATP/ATP exchange. It was purified 75-fold with a recovery of 15% and a protein yield of 0.18% with respect to the mitochondrial extract. Among the various substrates and inhibitors tested, the reconstituted protein transported only ATP, ADP, and GTP and was inhibited by bongkrekate, phenylisothiocyanate, pyridoxal 5'-phosphate, mersalyl and p-hydroxymercuribenzoate (but not N-ethylmaleimide). Atractyloside and carboxyatractyloside (at concentrations normally inhibitory in animal and plant mitochondria) were without effect in Jerusalem artichoke tubers mitochondria. Vmax of the reconstituted ATP/ATP exchange was determined to be 0.53 micromol/min per mg protein at 25 degrees C. The half-saturation constant Km and the corresponding inhibition constant Ki were 20.4 microM for ATP and 45 microM for ADP. The activation energy of the ATP/ATP exchange was 28 KJ/mol between 5 and 30 degrees C. The N-terminal amino acid partial sequence of the purified protein showed a partial homology with the ANT protein purified from mitochondria of maize shoots.
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Affiliation(s)
- Anna Spagnoletta
- Department of Pharmaco-Biology, University of Calabria, Cosenza, Italy
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Picault N, Palmieri L, Pisano I, Hodges M, Palmieri F. Identification of a novel transporter for dicarboxylates and tricarboxylates in plant mitochondria. Bacterial expression, reconstitution, functional characterization, and tissue distribution. J Biol Chem 2002; 277:24204-11. [PMID: 11978797 DOI: 10.1074/jbc.m202702200] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A cDNA from Arabidopsis thaliana and four related cDNAs from Nicotiana tabacum that we have isolated encode hitherto unidentified members of the mitochondrial carrier family. These proteins have been overexpressed in bacteria and reconstituted into phospholipid vesicles. Their transport properties demonstrate that they are orthologs/isoforms of a novel mitochondrial carrier capable of transporting both dicarboxylates (such as malate, oxaloacetate, oxoglutarate, and maleate) and tricarboxylates (such as citrate, isocitrate, cis-aconitate, and trans-aconitate). The newly identified dicarboxylate-tricarboxylate carrier accepts only the single protonated form of citrate (H-citrate2-) and the unprotonated form of malate (malate2-) and catalyzes obligatory, electroneutral exchanges. Oxoglutarate, citrate, and malate are mutually competitive inhibitors, showing K(i) close to the respective K(m). The carrier is expressed in all plant tissues examined and is largely spread in the plant kingdom. Furthermore, nitrate supply to nitrogen-starved tobacco plants leads to an increase in its mRNA in roots and leaves. The dicarboxylate-tricarboxylate carrier may play a role in important plant metabolic functions requiring organic acid flux to or from the mitochondria, such as nitrogen assimilation, export of reducing equivalents from the mitochondria, and fatty acid elongation.
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Affiliation(s)
- Nathalie Picault
- Institut de Biotechnologie des Plantes, CNRS UMR8618, Université de Paris Sud, 91405 Orsay, Cedex, France
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Abstract
Nonphotosynthetic plastids are important sites for the biosynthesis of starch, fatty acids, and the assimilation of nitrogen into amino acids in a wide range of plant tissues. Unlike chloroplasts, all the metabolites for these processes have to be imported, or generated by oxidative metabolism within the organelle. The aim of this review is to summarize our present understanding of the anabolic pathways involved, the requirement for import of precursors from the cytosol, the provision of energy for biosynthesis, and the interaction between pathways that share common intermediates. We emphasize the temporal and developmental regulation of events, and the variation in mechanisms employed by different species that produce the same end products.
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Affiliation(s)
- H. E. Neuhaus
- Pflanzenphysiologie, University of Osnabruck, Barbarastrasse 11, D-49069 Osnabruck, Germany;, School of Biological Sciences, University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom; e-mail:
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Abstract
C4 plants, including maize, Flaveria, amaranth, sorghum, and an amphibious sedge Eleocharis vivipara, have been employed to elucidate the molecular mechanisms and signaling pathways that control C4 photosynthesis gene expression. Current evidence suggests that pre-existing genes were recruited for the C4 pathway after acquiring potent and surprisingly diverse regulatory elements. This review emphasizes recent advances in our understanding of the creation of C4 genes, the activities of the C4 gene promoters consisting of synergistic and combinatorial enhancers and silencers, the use of 5' and 3' untranslated regions for transcriptional and posttranscriptional regulations, and the function of novel transcription factors. The research has also revealed new insights into unique or universal mechanisms underlying cell-type specificity, coordinate nuclear-chloroplast actions, hormonal, metabolic, stress and light responses, and the control of enzymatic activities by phosphorylation and reductive processes.
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Affiliation(s)
- Jen Sheen
- Department of Molecular Biology, Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114; e-mail:
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Takabatake R, Hata S, Taniguchi M, Kouchi H, Sugiyama T, Izui K. Isolation and characterization of cDNAs encoding mitochondrial phosphate transporters in soybean, maize, rice, and Arabidopis. PLANT MOLECULAR BIOLOGY 1999; 40:479-86. [PMID: 10437831 DOI: 10.1023/a:1006285009435] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
cDNA clones encoding mitochondrial phosphate transporters were isolated from four herbaceous plants. The cDNAs for the soybean, maize and rice transporters contained entire coding regions, whereas the Arabidopsis cDNA lacked the 5' portion. The hydropathy profiles of the deduced amino acid sequences predicted the existence of six membrane-spanning domains which are highly conserved in the mitochondrial transporter family. In soybeans, the mRNA level for the transporter was high in tissues containing dividing cells. It was suggested that there are multiple copies of transporter genes in both dicots and monocots. The soybean transporter was expressed as inclusion bodies in Escherichia coli, solubilized with detergents, and then reconstituted into liposomes. The resulting proteoliposomes exhibited high phosphate transport activity. The activity was inhibited by N-ethylmaleimide, like those of mammalian phosphate transporters.
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Affiliation(s)
- R Takabatake
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Japan
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Abstract
The purpose of this review is to highlight the unique and common features of splice site selection in plants compared with the better understood yeast and vertebrate systems. A key question in plant splicing is the role of AU sequences and how and at what stage they are involved in spliceosome assembly. Clearly, intronic U- or AU-rich and exonic GC- and AG-rich elements can influence splice site selection and splicing efficiency and are likely to bind proteins. It is becoming clear that splicing of a particular intron depends on a fine balance in the "strength" of the multiple intron signals involved in splice site selection. Individual introns contain varying strengths of signals and what is critical to splicing of one intron may be of less importance to the splicing of another. Thus, small changes to signals may severely disrupt splicing or have little or no effect depending on the overall sequence context of a specific intron/exon organization.
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Affiliation(s)
- J. W. S. Brown
- Department of Cell and Molecular Genetics, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom; e-mail: ;
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