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Kopriva S, Rahimzadeh Karvansara P, Takahashi H. Adaptive modifications in plant sulfur metabolism over evolutionary time. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4697-4711. [PMID: 38841807 PMCID: PMC11350084 DOI: 10.1093/jxb/erae252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024]
Abstract
Sulfur (S) is an essential element for life on Earth. Plants are able to take up and utilize sulfate (SO42-), the most oxidized inorganic form of S compounds on Earth, through the reductive S assimilatory pathway that couples with photosynthetic energy conversion. Organic S compounds are subsequently synthesized in plants and made accessible to animals, primarily as the amino acid methionine. Thus, plant S metabolism clearly has nutritional importance in the global food chain. S metabolites may be part of redox regulation and drivers of essential metabolic pathways as cofactors and prosthetic groups, such as Fe-S centers, CoA, thiamine, and lipoic acid. The evolution of the S metabolic pathways and enzymes reflects the critical importance of functional innovation and diversifications. Here we review the major evolutionary alterations that took place in S metabolism across different scales and outline research directions that may take advantage of understanding the evolutionary adaptations.
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Affiliation(s)
- Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, D-50674 Cologne, Germany
| | - Parisa Rahimzadeh Karvansara
- Institute of Molecular Photosynthesis, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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2
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de Jager N, Shukla V, Koprivova A, Lyčka M, Bilalli L, You Y, Zeier J, Kopriva S, Ristova D. Traits linked to natural variation of sulfur content in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1036-1050. [PMID: 37831920 PMCID: PMC10837017 DOI: 10.1093/jxb/erad401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 10/15/2023]
Abstract
Sulfur (S) is an essential mineral nutrient for plant growth and development; it is important for primary and specialized plant metabolites that are crucial for biotic and abiotic interactions. Foliar S content varies up to 6-fold under a controlled environment, suggesting an adaptive value under certain natural environmental conditions. However, a major quantitative regulator of S content in Arabidopsis thaliana has not been identified yet, pointing to the existence of either additional genetic factors controlling sulfate/S content or of many minor quantitative regulators. Here, we use overlapping information of two separate ionomics studies to select groups of accessions with low, mid, and high foliar S content. We quantify series of metabolites, including anions (sulfate, phosphate, and nitrate), thiols (cysteine and glutathione), and seven glucosinolates, gene expression of 20 genes, sulfate uptake, and three biotic traits. Our results suggest that S content is tightly connected with sulfate uptake, the concentration of sulfate and phosphate anions, and glucosinolate and glutathione synthesis. Additionally, our results indicate that the growth of pathogenic bacteria is enhanced in the A. thaliana accessions containing higher S in their leaves, suggesting a complex regulation between S homeostasis, primary and secondary metabolism, and biotic pressures.
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Affiliation(s)
- Nicholas de Jager
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, D-50674 Cologne, Germany
| | - Varsa Shukla
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, D-50674 Cologne, Germany
| | - Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, D-50674 Cologne, Germany
| | - Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Lorina Bilalli
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, D-50674 Cologne, Germany
| | - Yanrong You
- Institute for Molecular Ecophysiology of Plants, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Jürgen Zeier
- Institute for Molecular Ecophysiology of Plants, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, D-50674 Cologne, Germany
| | - Daniela Ristova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, D-50674 Cologne, Germany
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3
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Study on ZmRPN10 Regulating Leaf Angle in Maize by RNA-Seq. Int J Mol Sci 2022; 24:ijms24010189. [PMID: 36613631 PMCID: PMC9820655 DOI: 10.3390/ijms24010189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin/proteasome-mediated proteolysis (UPP) plays a crucial role in almost all aspects of plant growth and development, proteasome subunit RPN10 mediates ubiquitination substrate recognition in the UPP process. The recognition pathway of ubiquitinated UPP substrate is different in different species, which indicates that the mechanism and function of RPN10 are different in different species. However, the homologous ZmRPN10 in maize has not been studied. In this study, the changing of leaf angle and gene expression in leaves in maize wild-type B73 and mutant rpn10 under exogenous brassinosteroids (BRs) were investigated. The regulation effect of BR on the leaf angle of rpn10 was significantly stronger than that of B73. Transcriptome analysis showed that among the differentially expressed genes, CRE1, A-ARR and SnRK2 were significantly up-regulated, and PP2C, BRI1 AUX/IAA, JAZ and MYC2 were significantly down-regulated. This study revealed the regulation mechanism of ZmRPN10 on maize leaf angle and provided a promising gene resource for maize breeding.
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Koprivova A, Elkatmis B, Gerlich SC, Trick M, Harper AL, Bancroft I, Kopriva S. Natural Variation in OASC Gene for Mitochondrial O-Acetylserine Thiollyase Affects Sulfate Levels in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2022; 12:35. [PMID: 36616163 PMCID: PMC9824738 DOI: 10.3390/plants12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Sulfur plays a vital role in the primary and secondary metabolism of plants, and carries an important function in a large number of different compounds. Despite this importance, compared to other mineral nutrients, relatively little is known about sulfur sensing and signalling, as well as about the mechanisms controlling sulfur metabolism and homeostasis. Sulfur contents in plants vary largely not only among different species, but also among accessions of the same species. We previously used associative transcriptomics to identify several genes potentially controlling variation in sulfate content in the leaves of Brassica napus, including an OASC gene for mitochondrial O-acetylserine thiollyase (OAS-TL), an enzyme involved in cysteine synthesis. Here, we show that loss of OASC in Arabidopsis thaliana lowers not only sulfate, but also glutathione levels in the leaves. The reduced accumulation is caused by lower sulfate uptake and translocation to the shoots; however, the flux through the pathway is not affected. In addition, we identified a single nucleotide polymorphism in the OASC gene among A. thaliana accessions that is linked to variation in sulfate content. Both genetic and transgenic complementation confirmed that the exchange of arginine at position 81 for lysine in numerous accessions resulted in a less active OASC and a lower sulfate content in the leaves. The mitochondrial isoform of OAS-TL is, thus, after the ATPS1 isoform of sulfurylase and the APR2 form of APS reductase 2, the next metabolic enzyme with a role in regulation of sulfate content in Arabidopsis.
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Affiliation(s)
- Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Büsra Elkatmis
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Silke C. Gerlich
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Andrea L. Harper
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
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5
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Yin H, Yan Y, Hu W, Liu G, Zeng H, Wei Y, Shi H. Genome-wide association studies reveal genetic basis of ionomic variation in cassava. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1212-1223. [PMID: 36239073 DOI: 10.1111/tpj.16006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
As one of the most important food crops, cassava (Manihot esculenta) is the main dietary source of micronutrients for about 1 billion people. However, the ionomic variation in cassava and the underlying genetic mechanisms remain unclear so far. Herein, genome-wide association studies were performed to reveal the specific single nucleotide polymorphisms (SNPs) that affect the ionomic variation in cassava. We identified 164 SNPs with P-values lower than the threshold located in 88 loci associated with divergent ionomic variations. Among them, 13 SNPs are related to both calcium (Ca) and magnesium (Mg), and many loci for different ionomic traits seem to be clustered on specific chromosome regions. Moreover, we identified the peak SNPs in the promoter regions of Sc10g003170 (encoding methionyl-tRNA synthetase [MetRS]) and Sc18g015190 (encoding the transcriptional regulatory protein AlgP) for nitrogen (N) and phosphorus (P) accumulation, respectively. Notably, these two SNPs (chr10_32807962 and chr18_31343738) were directly correlated with the transcript levels of Sc10g003170 (MetRS) and Sc18g015190 (AlgP), which positively modulated N accumulation and P concentration in cassava, respectively. Taken together, this study provides important insight into the genetic basis of cassava natural ionomic variation, which will promote genetic breeding to improve nutrient use and accumulation of elements in cassava.
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Affiliation(s)
- Hongyan Yin
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
| | - Yu Yan
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Hainan Province, Haikou, Xueyuan Road 4, China
| | - Guoyin Liu
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Hongqiu Zeng
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Yunxie Wei
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Haitao Shi
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
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6
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Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice. Int J Mol Sci 2022; 23:ijms23116203. [PMID: 35682882 PMCID: PMC9181796 DOI: 10.3390/ijms23116203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022] Open
Abstract
Sulfur (S) is an essential mineral nutrient required for plant growth and development. Plants usually face temporal and spatial variation in sulfur availability, including the heterogeneous sulfate content in soils. As sessile organisms, plants have evolved sophisticated mechanisms to modify their gene expression and physiological processes in order to optimize S acquisition and usage. Such plasticity relies on a complicated network to locally sense S availability and systemically respond to S status, which remains poorly understood. Here, we took advantage of a split-root system and performed transcriptome-wide gene expression analysis on rice plants in S deficiency followed by sulfate resupply. S deficiency altered the expressions of 6749 and 1589 genes in roots and shoots, respectively, accounting for 18.07% and 4.28% of total transcripts detected. Homogeneous sulfate resupply in both split-root halves recovered the expression of 27.06% of S-deficiency-responsive genes in shoots, while 20.76% of S-deficiency-responsive genes were recovered by heterogeneous sulfate resupply with only one split-root half being resupplied with sulfate. The local sulfate resupply response genes with expressions only recovered in the split-root half resupplied with sulfate but not in the other half remained in S deficiency were identified in roots, which were mainly enriched in cellular amino acid metabolic process and root growth and development. Several systemic response genes were also identified in roots, whose expressions remained unchanged in the split-root half resupplied with sulfate but were recovered in the other split-root half without sulfate resupply. The systemic response genes were mainly related to calcium signaling and auxin and ABA signaling. In addition, a large number of S-deficiency-responsive genes exhibited simultaneous local and systemic responses to sulfate resupply, such as the sulfate transporter gene OsSULTR1;1 and the O-acetylserine (thiol) lyase gene, highlighting the existence of a systemic regulation of sulfate uptake and assimilation in S deficiency plants followed by sulfate resupply. Our studies provided a comprehensive transcriptome-wide picture of a local and systemic response to heterogeneous sulfate resupply, which will facilitate an understanding of the systemic regulation of S homeostasis in rice.
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7
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Günal S, Kopriva S. Measurement of flux through sulfate assimilation using [35S]sulfate. Methods Enzymol 2022; 676:197-209. [DOI: 10.1016/bs.mie.2022.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Jiang L, Wang Y, Xia A, Wang Q, Zhang X, Jez JM, Li Z, Tan W, He Y. A natural single-nucleotide polymorphism variant in sulfite reductase influences sulfur assimilation in maize. THE NEW PHYTOLOGIST 2021; 232:692-704. [PMID: 34254312 DOI: 10.1111/nph.17616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Plants absorb sulfur from the environment and assimilate it into suitable forms for the biosynthesis of a broad range of molecules. Although the biochemical pathway of sulfur assimilation is known, how genetic differences contribute to natural variation in sulfur assimilation remains poorly understood. Here, using a genome-wide association study, we uncovered a single-nucleotide polymorphism (SNP) variant in the sulfite reductase (SiR) gene that was significantly associated with SiR protein abundance in a maize natural association population. We also demonstrated that the synonymous C to G base change at SNP69 may repress translational activity by altering messenger RNA secondary structure, which leads to reduction in ZmSiR protein abundance and sulfur assimilation activity. Population genetic analyses showed that the SNP69C allele was likely a variant occurring after the initial maize domestication and accumulated with the spread of maize cultivation from tropical to temperate regions. This study provides the first evidence that genetic polymorphisms in the exon of ZmSiR could influence the protein abundance through a posttranscriptional mechanism and in part contribute to natural variation in sulfur assimilation. These findings provide a prospective target to improve maize varieties with proper sulfur nutrient levels assisted by molecular breeding and engineering.
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Affiliation(s)
- Luguang Jiang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Yan Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Aiai Xia
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Qi Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Xiaolei Zhang
- Safety and Quality Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Weiming Tan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Yan He
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
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9
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Ali S, Tyagi A, Bae H. Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants. Int J Mol Sci 2021; 22:7182. [PMID: 34281232 PMCID: PMC8267685 DOI: 10.3390/ijms22137182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
| | - Anshika Tyagi
- National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
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Henriet C, Balliau T, Aimé D, Le Signor C, Kreplak J, Zivy M, Gallardo K, Vernoud V. Proteomics of developing pea seeds reveals a complex antioxidant network underlying the response to sulfur deficiency and water stress. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2611-2626. [PMID: 33558872 DOI: 10.1093/jxb/eraa571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/19/2021] [Indexed: 05/17/2023]
Abstract
Pea is a legume crop producing protein-rich seeds and is increasingly in demand for human consumption and animal feed. The aim of this study was to explore the proteome of developing pea seeds at three key stages covering embryogenesis, the transition to seed-filling, and the beginning of storage-protein synthesis, and to investigate how the proteome was influenced by S deficiency and water stress, applied either separately or combined. Of the 3184 proteins quantified by shotgun proteomics, 2473 accumulated at particular stages, thus providing insights into the proteome dynamics at these stages. Differential analyses in response to the stresses and inference of a protein network using the whole proteomics dataset identified a cluster of antioxidant proteins (including a glutathione S-transferase, a methionine sulfoxide reductase, and a thioredoxin) possibly involved in maintaining redox homeostasis during early seed development and preventing cellular damage under stress conditions. Integration of the proteomics data with previously obtained transcriptomics data at the transition to seed-filling revealed the transcriptional events associated with the accumulation of the stress-regulated antioxidant proteins. This transcriptional defense response involves genes of sulfate homeostasis and assimilation, thus providing candidates for targeted studies aimed at dissecting the signaling cascade linking S metabolism to antioxidant processes in developing seeds.
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Affiliation(s)
- Charlotte Henriet
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Thierry Balliau
- Plateforme d'Analyse de Protéomique Paris Sud-Ouest (PAPPSO), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR Génétique Quantitative et Évolution-Le Moulon, Gif-sur-Yvette, France
| | - Delphine Aimé
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Michel Zivy
- Plateforme d'Analyse de Protéomique Paris Sud-Ouest (PAPPSO), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR Génétique Quantitative et Évolution-Le Moulon, Gif-sur-Yvette, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Vanessa Vernoud
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
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11
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Dietzen C, Koprivova A, Whitcomb SJ, Langen G, Jobe TO, Hoefgen R, Kopriva S. The Transcription Factor EIL1 Participates in the Regulation of Sulfur-Deficiency Response. PLANT PHYSIOLOGY 2020; 184:2120-2136. [PMID: 33060195 PMCID: PMC7723090 DOI: 10.1104/pp.20.01192] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/07/2020] [Indexed: 06/08/2023]
Abstract
Sulfur, an indispensable constituent of many cellular components, is a growth-limiting macronutrient for plants. Thus, to successfully adapt to changing sulfur availability and environmental stress, a sulfur-deficiency response helps plants to cope with the limited supply. On the transcriptional level, this response is controlled by SULFUR LIMITATION1 (SLIM1), a member of the ETHYLENE-INSENSITIVE3-LIKE (EIL) transcription factor family. In this study, we identified EIL1 as a second transcriptional activator regulating the sulfur-deficiency response, subordinate to SLIM1/EIL3. Our comprehensive RNA sequencing analysis in Arabidopsis (Arabidopsis thaliana) allowed us to obtain a complete picture of the sulfur-deficiency response and quantify the contributions of these two transcription factors. We confirmed the key role of SLIM1/EIL3 in controlling the response, particularly in the roots, but showed that in leaves more than 50% of the response is independent of SLIM1/EIL3 and EIL1. RNA sequencing showed an additive contribution of EIL1 to the regulation of the sulfur-deficiency response but also identified genes specifically regulated through EIL1. SLIM1/EIL3 seems to have further functions (e.g. in the regulation of genes responsive to hypoxia or mediating defense at both low and normal sulfur supply). These results contribute to the dissection of mechanisms of the sulfur-deficiency response and provide additional possibilities to improve adaptation to sulfur-deficiency conditions.
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Affiliation(s)
- Christof Dietzen
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Sarah J Whitcomb
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Gregor Langen
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Timothy O Jobe
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
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12
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Whitt L, Ricachenevsky FK, Ziegler GZ, Clemens S, Walker E, Maathuis FJM, Kear P, Baxter I. A curated list of genes that affect the plant ionome. PLANT DIRECT 2020; 4:e00272. [PMID: 33103043 PMCID: PMC7576880 DOI: 10.1002/pld3.272] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 05/07/2023]
Abstract
Understanding the mechanisms underlying plants' adaptation to their environment will require knowledge of the genes and alleles underlying elemental composition. Modern genetics is capable of quickly, and cheaply indicating which regions of DNA are associated with particular phenotypes in question, but most genes remain poorly annotated, hindering the identification of candidate genes. To help identify candidate genes underlying elemental accumulations, we have created the known ionome gene (KIG) list: a curated collection of genes experimentally shown to change uptake, accumulation, and distribution of elements. We have also created an automated computational pipeline to generate lists of KIG orthologs in other plant species using the PhytoMine database. The current version of KIG consists of 176 known genes covering 5 species, 23 elements, and their 1588 orthologs in 10 species. Analysis of the known genes demonstrated that most were identified in the model plant Arabidopsis thaliana, and that transporter coding genes and genes altering the accumulation of iron and zinc are overrepresented in the current list.
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Affiliation(s)
- Lauren Whitt
- Donald Danforth Plant Science CenterSaint LouisMOUSA
| | - Felipe Klein Ricachenevsky
- Departamento de Botânica Programa de Pós‐Graduação em Biologia Celular e MolecularUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | | | | | | | | | | | - Ivan Baxter
- Donald Danforth Plant Science CenterSaint LouisMOUSA
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Giovannetti M, Göschl C, Dietzen C, Andersen SU, Kopriva S, Busch W. Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content. PLoS Genet 2019; 15:e1008126. [PMID: 31856195 PMCID: PMC6941899 DOI: 10.1371/journal.pgen.1008126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 01/03/2020] [Accepted: 11/21/2019] [Indexed: 12/12/2022] Open
Abstract
Phosphate represents a major limiting factor for plant productivity. Plants have evolved different solutions to adapt to phosphate limitation ranging from a profound tuning of their root system architecture and metabolic profile to the evolution of widespread mutualistic interactions. Here we elucidated plant responses and their genetic basis to different phosphate levels in a plant species that is widely used as a model for AM symbiosis: Lotus japonicus. Rather than focussing on a single model strain, we measured root growth and anion content in response to different levels of phosphate in 130 Lotus natural accessions. This allowed us not only to uncover common as well as divergent responses within this species, but also enabled Genome Wide Association Studies by which we identified new genes regulating phosphate homeostasis in Lotus. Among them, we showed that insertional mutants of a cytochrome B5 reductase and a Leucine-Rich-Repeat receptor showed different phosphate concentration in plants grown under phosphate sufficient condition. Under low phosphate conditions, we found a correlation between plant biomass and the decrease of plant phosphate concentration in plant tissues, representing a dilution effect. Altogether our data of the genetic and phenotypic variation within a species capable of AM complements studies that have been conducted in Arabidopsis, and advances our understanding of the continuum of genotype by phosphate level interaction existing throughout dicot plants.
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Affiliation(s)
- Marco Giovannetti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Christian Göschl
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Christof Dietzen
- University of Cologne, Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Stanislav Kopriva
- University of Cologne, Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory, La Jolla, California, United States of America
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El-Soda M, Neris Moreira C, Goredema-Matongera N, Jamar D, Koornneef M, Aarts MGM. QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana. BMC PLANT BIOLOGY 2019; 19:410. [PMID: 31533608 PMCID: PMC6751748 DOI: 10.1186/s12870-019-1996-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 08/29/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability. RESULTS Recombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions of Arabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped to PP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other to SIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found in SULTR2;1, encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped to FMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of the SUL2 locus. CONCLUSION We identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .
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Affiliation(s)
- Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613 Egypt
| | - Charles Neris Moreira
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Nakai Goredema-Matongera
- Department of Research and Specialist Services, Maize Breeding Programme, Crop Breeding Institute, P. O. Box CY550 Causeway, Harare, Zimbabwe
| | - Diaan Jamar
- Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Mark G. M. Aarts
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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15
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Jez JM. Structural biology of plant sulfur metabolism: from sulfate to glutathione. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4089-4103. [PMID: 30825314 DOI: 10.1093/jxb/erz094] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
Sulfur is an essential element for all organisms. Plants must assimilate this nutrient from the environment and convert it into metabolically useful forms for the biosynthesis of a wide range of compounds, including cysteine and glutathione. This review summarizes structural biology studies on the enzymes involved in plant sulfur assimilation [ATP sulfurylase, adenosine-5'-phosphate (APS) reductase, and sulfite reductase], cysteine biosynthesis (serine acetyltransferase and O-acetylserine sulfhydrylase), and glutathione biosynthesis (glutamate-cysteine ligase and glutathione synthetase) pathways. Overall, X-ray crystal structures of enzymes in these core pathways provide molecular-level information on the chemical events that allow plants to incorporate sulfur into essential metabolites and revealed new biochemical regulatory mechanisms, such as structural rearrangements, protein-protein interactions, and thiol-based redox switches, for controlling different steps in these pathways.
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Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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16
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Abstract
Sulfur is present in the amino acids cysteine and methionine and in a large range of essential coenzymes and cofactors and is therefore essential for all organisms. It is also a constituent of sulfate esters in proteins, carbohydrates, and numerous cellular metabolites. The sulfation and desulfation reactions modifying a variety of different substrates are commonly known as sulfation pathways. Although relatively little is known about the function of most sulfated metabolites, the synthesis of activated sulfate used in sulfation pathways is essential in both animal and plant kingdoms. In humans, mutations in the genes encoding the sulfation pathway enzymes underlie a number of developmental aberrations, and in flies and worms, their loss-of-function is fatal. In plants, a lower capacity for synthesizing activated sulfate for sulfation reactions results in dwarfism, and a complete loss of activated sulfate synthesis is also lethal. Here, we review the similarities and differences in sulfation pathways and associated processes in animals and plants, and we point out how they diverge from bacteria and yeast. We highlight the open questions concerning localization, regulation, and importance of sulfation pathways in both kingdoms and the ways in which findings from these "red" and "green" experimental systems may help reciprocally address questions specific to each of the systems.
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Affiliation(s)
- Süleyman Günal
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany
| | - Rebecca Hardman
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany.
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham B15 2TH, United Kingdom.
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Takou M, Wieters B, Kopriva S, Coupland G, Linstädter A, De Meaux J. Linking genes with ecological strategies in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1141-1151. [PMID: 30561727 PMCID: PMC6382341 DOI: 10.1093/jxb/ery447] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 05/22/2023]
Abstract
Arabidopsis thaliana is the most prominent model system in plant molecular biology and genetics. Although its ecology was initially neglected, collections of various genotypes revealed a complex population structure, with high levels of genetic diversity and substantial levels of phenotypic variation. This helped identify the genes and gene pathways mediating phenotypic change. Population genetics studies further demonstrated that this variation generally contributes to local adaptation. Here, we review evidence showing that traits affecting plant life history, growth rate, and stress reactions are not only locally adapted, they also often co-vary. Co-variation between these traits indicates that they evolve as trait syndromes, and reveals the ecological diversification that took place within A. thaliana. We argue that examining traits and the gene that control them within the context of global summary schemes that describe major ecological strategies will contribute to resolve important questions in both molecular biology and ecology.
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Affiliation(s)
| | | | | | - George Coupland
- Max Planck Institute of Plant Breeding Research, Cologne, Germany
| | - Anja Linstädter
- Institute of Botany, University of Cologne, Germany
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Germany
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Joshi NC, Meyer AJ, Bangash SAK, Zheng ZL, Leustek T. Arabidopsis γ-glutamylcyclotransferase affects glutathione content and root system architecture during sulfur starvation. THE NEW PHYTOLOGIST 2019; 221:1387-1397. [PMID: 30368820 DOI: 10.1111/nph.15466] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
γ-Glutamylcyclotransferase initiates glutathione degradation to component amino acids l-glutamate, l-cysteine and l-glycine. The enzyme is encoded by three genes in Arabidopsis thaliana, one of which (GGCT2;1) is transcriptionally upregulated by starvation for the essential macronutrient sulfur (S). Regulation by S-starvation suggests that GGCT2;1 mobilizes l-cysteine from glutathione when there is insufficient sulfate for de novo l-cysteine synthesis. The response of wild-type seedlings to S-starvation was compared to ggct2;1 null mutants. S-starvation causes glutathione depletion in S-starved wild-type seedlings, but higher glutathione is maintained in the primary root tip than in other seedling tissues. Although GGCT2;1 is induced throughout seedlings, its expression is concentrated in the primary root tip where it activates the γ-glutamyl cycle. S-starved wild-type plants also produce longer primary roots, and lateral root growth is suppressed. While glutathione is also rapidly depleted in ggct2;1 null seedlings, much higher glutathione is maintained in the primary root tip compared to the wild-type. S-starved ggct2;1 primary roots grow longer than the wild-type, and lateral root growth is not suppressed. These results point to a role for GGCT2;1 in S-starvation-response changes to root system architecture through activity of the γ-glutamyl cycle in the primary root tip. l-Cysteine mobilization from glutathione is not solely a function of GGCT2;1.
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Affiliation(s)
- Naveen C Joshi
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Andreas J Meyer
- INRES - Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Sajid A K Bangash
- INRES - Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Zhi-Liang Zheng
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, 10468, USA
| | - Thomas Leustek
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
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Boldrin PF, Faquin V, Clemente ADCS, de Andrade T, Guilherme LRG. Genotypic Variation and Biofortification with Selenium in Brazilian Wheat Cultivars. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1371-1379. [PMID: 30512055 DOI: 10.2134/jeq2018.01.0045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Selenium is essential to human and animal health, as it regulates glutathione peroxidase activity. Although not considered essential to plants, it may be beneficial to plant growth and development at low concentrations. This study evaluated the effect of selenate application on Se biofortification, macro- and micronutrient content, and the expression of genes involved in Se uptake and assimilation in 12 Brazilian wheat ( L.) cultivars. This nutrient-solution experiment was performed in a greenhouse and consisted of a complete 12 × 2 factorial randomized design, with 12 wheat cultivars in the absence or presence of Se in solution (13 μmol), with three replicates. The presence of Se in solution did not affect growth and yield of wheat cultivars. Selenium content and accumulation in the grain varied significantly among the different cultivars. The presence of Se affected macronutrient content more than micronutrient content, and selenate application increased S content in the shoots of eight cultivars and in the grains of five cultivars. Examination of gene expression did not allow identification of responses within the two groups of cultivars-with high or low Se contents-after selenate application. Our findings are relevant to the design of Se biofortification strategies for wheat in tropical and subtropical agroecosystems.
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Chen ZR, Kuang L, Gao YQ, Wang YL, Salt DE, Chao DY. AtHMA4 Drives Natural Variation in Leaf Zn Concentration of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:270. [PMID: 29545819 PMCID: PMC5839161 DOI: 10.3389/fpls.2018.00270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/15/2018] [Indexed: 05/22/2023]
Abstract
Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in Heavy Metal-ATPase 4 (HMA4) controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 Arabidopsis thaliana wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0. Both quantitative trait loci (QTL) analysis and bulked segregant analysis (BSA) identified HMA4 as a strong candidate accounting for this variation in leaf Zn concentration. Genetic complementation experiments confirmed this hypothesis. Sequence analysis revealed that a 1-bp deletion in the third exon of HMA4 from Fab-2 is responsible for the lose of function of HMA4 driving the low Zn observed in Fab-2. Unlike in Fab-2 polymorphisms in the promoter region were found to be responsible for the weak function of HMA4 in Van-0. This is supported by both an expression analysis of HMA4 in Van-0 and through a series of T-DNA insertion mutants which generate truncated HMA4 promoters in the Col-0 background. In addition, we also observed that Fab-2, Van-0 and the hma4-2 null mutant in the Col-0 background show enhanced resistance to a combination of high Zn and high Cd in the growth medium, raising the possibility that variation at HMA4 may play a role in environmental adaptation.
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Affiliation(s)
- Zi-Ru Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Kuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yi-Qun Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - David E. Salt
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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21
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Qiao L, Cao M, Zheng J, Zhao Y, Zheng ZL. Gene coexpression network analysis of fruit transcriptomes uncovers a possible mechanistically distinct class of sugar/acid ratio-associated genes in sweet orange. BMC PLANT BIOLOGY 2017; 17:186. [PMID: 29084509 PMCID: PMC5663102 DOI: 10.1186/s12870-017-1138-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/22/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND The ratio of sugars to organic acids, two of the major metabolites in fleshy fruits, has been considered the most important contributor to fruit sweetness. Although accumulation of sugars and acids have been extensively studied, whether plants evolve a mechanism to maintain, sense or respond to the fruit sugar/acid ratio remains a mystery. In a prior study, we used an integrated systems biology tool to identify a group of 39 acid-associated genes from the fruit transcriptomes in four sweet orange varieties (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). RESULTS We reanalyzed the prior sweet orange fruit transcriptome data, leading to the identification of 72 genes highly correlated with the fruit sugar/acid ratio. The majority of these sugar/acid ratio-related genes are predicted to be involved in regulatory functions such as transport, signaling and transcription or encode enzymes involved in metabolism. Surprisingly, only three of these sugar/acid ratio-correlated genes are weakly correlated with sugar level and none of them overlaps with the acid-associated genes. Weighted Gene Coexpression Network Analysis (WGCNA) has revealed that these genes belong to four modules, Blue, Grey, Brown and Turquoise, with the former two modules being unique to the sugar/acid ratio control. CONCLUSION Our results indicate that orange fruits contain a possible mechanistically distinct class of genes that may potentially be involved in maintaining fruit sugar/acid ratios and/or responding to the cellular sugar/acid ratio status. Therefore, our analysis of orange transcriptomes provides an intriguing insight into the potentially novel genetic or molecular mechanisms controlling the sugar/acid ratio in fruits.
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Affiliation(s)
- Liang Qiao
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Minghao Cao
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Jian Zheng
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Yihong Zhao
- Division of Biostatistics, Department of Child and Adolescent Psychiatry, New York University Langone Medical Center, New York, NY 10016 USA
| | - Zhi-Liang Zheng
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY 10468 USA
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22
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Khare R, Kumar S, Shukla T, Ranjan A, Trivedi PK. Differential sulphur assimilation mechanism regulates response of Arabidopsis thaliana natural variation towards arsenic stress under limiting sulphur condition. JOURNAL OF HAZARDOUS MATERIALS 2017; 337:198-207. [PMID: 28525880 DOI: 10.1016/j.jhazmat.2017.05.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 06/07/2023]
Abstract
Arsenic (As) is a ubiquitous element, which imposes threat to crops productivity and human health through contaminated food chain. As a part of detoxification mechanism, As is chelated and sequestered into the vacuoles via sulphur containing compounds glutathione (GSH) and phytochelatins (PCs). Under limiting sulphur (LS) conditions, exposure of As leads to enhanced toxic effects in plants. Therefore, it is a prerequisite to understand molecular mechanisms involved in As stress response under sulphur deficiency conditions in plants. In recent years, natural variation has been utilized to explore the genetic determinants linked to plant development and stress response. In this study, natural variation in Arabidopsis has been utilized to understand the molecular mechanisms underlying LS and As(III) stress response. Analysis of different accession of Arabidopsis led to the identification of Koz2-2 and Ri-0 as the most tolerant and sensitive accessions, respectively, towards As(III) and LS+As(III) stress. Biochemical analysis and expression profiling of the genes responsible for sulphur transport and assimilation as well as metal detoxification and accumulation revealed significantly enhanced sulphur assimilation mechanism in Koz2-2 as compared to Ri-0. Analyses suggest that genetic variation regulates differential response of accessions towards As(III) under LS condition.
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Affiliation(s)
- Ria Khare
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226 001, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India
| | - Smita Kumar
- Centre of Bio-Medical Research (CBMR), Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Raibareli Road, Lucknow, 226014, India.
| | - Tapsi Shukla
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226 001, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India
| | - Avriti Ranjan
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226 001, India
| | - Prabodh Kumar Trivedi
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226 001, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India.
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Campos ACAL, Kruijer W, Alexander R, Akkers RC, Danku J, Salt DE, Aarts MGM. Natural variation in Arabidopsis thaliana reveals shoot ionome, biomass, and gene expression changes as biomarkers for zinc deficiency tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3643-3656. [PMID: 28859376 DOI: 10.1093/jxb/erx191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 05/20/2017] [Indexed: 05/12/2023]
Abstract
Zinc (Zn) is an essential nutrient for plants, with a crucial role as a cofactor for many enzymes. Approximately one-third of the global arable land area is Zn deficient, leading to reduced crop yield and quality. To improve crop tolerance to Zn deficiency, it is important to understand the mechanisms plants have adopted to tolerate suboptimal Zn supply. In this study, physiological and molecular aspects of traits related to Zn deficiency tolerance were examined in a panel of 19 Arabidopsis thaliana accessions. Accessions showed a larger variation for shoot biomass than for Zn concentration, indicating that they have different requirements for their minimal Zn concentration required for growth. Accessions with a higher tolerance to Zn deficiency showed an increased expression of the Zn deficiency-responsive genes ZIP4 and IRT3 in comparison with Zn deficiency-sensitive accessions. Changes in the shoot ionome, as a result of the Zn treatment of the plants, were used to build a multinomial logistic regression model able to distinguish plants regarding their Zn nutritional status. This set of biomarkers, reflecting the A. thaliana response to Zn deficiency and Zn deficiency tolerance, can be useful for future studies aiming to improve the performance and Zn status of crop plants grown under suboptimal Zn concentrations.
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Affiliation(s)
- Ana Carolina A L Campos
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, UK
| | - Willem Kruijer
- Biometris, Wageningen University and Research, PO Box 100, 6700AC Wageningen, The Netherlands
| | - Ross Alexander
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- School of Life Sciences, John Muir Building, Heriot Watt University, Edinburgh EH14 4AS, UK
| | - Robert C Akkers
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - John Danku
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, UK
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, UK
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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24
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Grimm DG, Roqueiro D, Salomé PA, Kleeberger S, Greshake B, Zhu W, Liu C, Lippert C, Stegle O, Schölkopf B, Weigel D, Borgwardt KM. easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies. THE PLANT CELL 2017; 29:5-19. [PMID: 27986896 PMCID: PMC5304348 DOI: 10.1105/tpc.16.00551] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 11/28/2016] [Accepted: 12/13/2016] [Indexed: 05/22/2023]
Abstract
The ever-growing availability of high-quality genotypes for a multitude of species has enabled researchers to explore the underlying genetic architecture of complex phenotypes at an unprecedented level of detail using genome-wide association studies (GWAS). The systematic comparison of results obtained from GWAS of different traits opens up new possibilities, including the analysis of pleiotropic effects. Other advantages that result from the integration of multiple GWAS are the ability to replicate GWAS signals and to increase statistical power to detect such signals through meta-analyses. In order to facilitate the simple comparison of GWAS results, we present easyGWAS, a powerful, species-independent online resource for computing, storing, sharing, annotating, and comparing GWAS. The easyGWAS tool supports multiple species, the uploading of private genotype data and summary statistics of existing GWAS, as well as advanced methods for comparing GWAS results across different experiments and data sets in an interactive and user-friendly interface. easyGWAS is also a public data repository for GWAS data and summary statistics and already includes published data and results from several major GWAS. We demonstrate the potential of easyGWAS with a case study of the model organism Arabidopsis thaliana, using flowering and growth-related traits.
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Affiliation(s)
- Dominik G Grimm
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Zentrum für Bioinformatik, Eberhard Karls Universität, 72074 Tübingen, Germany
- Department for Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Damian Roqueiro
- Department for Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Patrice A Salomé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Stefan Kleeberger
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Bastian Greshake
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wangsheng Zhu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Chang Liu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Christoph Lippert
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Oliver Stegle
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Bernhard Schölkopf
- Department of Empirical Inference, Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Karsten M Borgwardt
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Zentrum für Bioinformatik, Eberhard Karls Universität, 72074 Tübingen, Germany
- Department for Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
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25
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Maillard A, Sorin E, Etienne P, Diquélou S, Koprivova A, Kopriva S, Arkoun M, Gallardo K, Turner M, Cruz F, Yvin JC, Ourry A. Non-Specific Root Transport of Nutrient Gives Access to an Early Nutritional Indicator: The Case of Sulfate and Molybdate. PLoS One 2016; 11:e0166910. [PMID: 27870884 PMCID: PMC5117742 DOI: 10.1371/journal.pone.0166910] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/04/2016] [Indexed: 01/08/2023] Open
Abstract
Under sulfur (S) deficiency, crosstalk between nutrients induced accumulation of other nutrients, particularly molybdenum (Mo). This disturbed balanced between S and Mo could provide a way to detect S deficiency and therefore avoid losses in yield and seed quality in cultivated species. Under hydroponic conditions, S deprivation was applied to Brassica napus to determine the precise kinetics of S and Mo uptake and whether sulfate transporters were involved in Mo uptake. Leaf contents of S and Mo were also quantified in a field-grown S deficient oilseed rape crop with different S and N fertilization applications to evaluate the [Mo]:[S] ratio, as an indicator of S nutrition. To test genericity of this indicator, the [Mo]:[S] ratio was also assessed with other cultivated species under different controlled conditions. During S deprivation, Mo uptake was strongly increased in B. napus. This accumulation was not a result of the induction of the molybdate transporters, Mot1 and Asy, but could be a direct consequence of Sultr1.1 and Sultr1.2 inductions. However, analysis of single mutants of these transporters in Arabidopsis thaliana suggested that other sulfate deficiency responsive transporters may be involved. Under field conditions, Mo content was also increased in leaves by a reduction in S fertilization. The [Mo]:[S] ratio significantly discriminated between the plots with different rates of S fertilization. Threshold values were estimated for the hierarchical clustering of commercial crops according to S status. The use of the [Mo]:[S] ratio was also reliable to detect S deficiency for other cultivated species under controlled conditions. The analysis of the leaf [Mo]:[S] ratio seems to be a practical indicator to detect early S deficiency under field conditions and thus improve S fertilization management.
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Affiliation(s)
- Anne Maillard
- Normandie Université, Caen, France
- UNICAEN, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
- INRA, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
| | - Elise Sorin
- Normandie Université, Caen, France
- UNICAEN, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
- INRA, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
- University of Cologne, Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Philippe Etienne
- Normandie Université, Caen, France
- UNICAEN, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
- INRA, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
| | - Sylvain Diquélou
- Normandie Université, Caen, France
- UNICAEN, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
- INRA, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
| | - Anna Koprivova
- University of Cologne, Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Stanislav Kopriva
- University of Cologne, Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Mustapha Arkoun
- Centre Mondial d’Innovation, CMI, Groupe Roullier, Saint-Malo, France
| | | | | | - Florence Cruz
- Centre Mondial d’Innovation, CMI, Groupe Roullier, Saint-Malo, France
| | - Jean-Claude Yvin
- Centre Mondial d’Innovation, CMI, Groupe Roullier, Saint-Malo, France
| | - Alain Ourry
- Normandie Université, Caen, France
- UNICAEN, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
- INRA, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Caen, France
- * E-mail:
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26
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Boldrin PF, de Figueiredo MA, Yang Y, Luo H, Giri S, Hart JJ, Faquin V, Guilherme LRG, Thannhauser TW, Li L. Selenium promotes sulfur accumulation and plant growth in wheat (Triticum aestivum). PHYSIOLOGIA PLANTARUM 2016; 158:80-91. [PMID: 27152969 DOI: 10.1111/ppl.12465] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 03/31/2016] [Indexed: 05/19/2023]
Abstract
Selenium (Se) is an essential micronutrient for animals and humans and a target for biofortification in crops. Sulfur (S) is a crucial nutrient for plant growth. To gain better understanding of Se and S nutrition and interaction in plants, the effects of Se dosages and forms on plant growth as well as on S level in seven wheat lines were examined. Low dosages of both selenate and selenite supplements were found to enhance wheat shoot biomass and show no inhibitory effect on grain production. The stimulation on plant growth was correlated with increased APX antioxidant enzyme activity. Se forms were found to exert different effects on S metabolism in wheat plants. Selenate treatment promoted S accumulation, which was not observed with selenite supplement. An over threefold increase of S levels following selenate treatment at low dosages was observed in shoots of all wheat lines. Analysis of the sulfate transporter gene expression revealed an increased transcription of SULTR1;1, SULTR1;3 and SULTR4;1 in roots following 10 μM Na2 SeO4 treatment. Mass spectrometry-based targeted protein quantification confirmed the gene expression results and showed enhanced protein levels. The results suggest that Se treatment mimics S deficiency to activate specific sulfate transporter expression to stimulate S uptake, resulting in the selenate-induced S accumulation. This study supports that plant growth and nutrition benefit from low dosages of Se fertilization and provides information on the basis underlying Se-induced S accumulation in plants.
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Affiliation(s)
- Paulo F Boldrin
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Department of Soil Science, Federal University of Lavras, Lavras 37200-000, Brazil
| | - Marislaine A de Figueiredo
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Department of Agriculture, Federal University of Lavras, Lavras, Brazil
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Hongmei Luo
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Shree Giri
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Jonathan J Hart
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Valdemar Faquin
- Department of Soil Science, Federal University of Lavras, Lavras 37200-000, Brazil
| | - Luiz R G Guilherme
- Department of Soil Science, Federal University of Lavras, Lavras 37200-000, Brazil
| | - Theorodore W Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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27
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Huang XY, Salt DE. Plant Ionomics: From Elemental Profiling to Environmental Adaptation. MOLECULAR PLANT 2016; 9:787-97. [PMID: 27212388 DOI: 10.1016/j.molp.2016.05.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 05/03/2023]
Abstract
Ionomics is a high-throughput elemental profiling approach to study the molecular mechanistic basis underlying mineral nutrient and trace element composition (also known as the ionome) of living organisms. Since the concept of ionomics was first introduced more than 10 years ago, significant progress has been made in the identification of genes and gene networks that control the ionome. In this update, we summarize the progress made in using the ionomics approach over the last decade, including the identification of genes by forward genetics and the study of natural ionomic variation. We further discuss the potential application of ionomics to the investigation of the ecological functions of ionomic alleles in adaptation to the environment.
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Affiliation(s)
- Xin-Yuan Huang
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK.
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28
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Koprivova A, Kopriva S. Sulfation pathways in plants. Chem Biol Interact 2016; 259:23-30. [PMID: 27206694 DOI: 10.1016/j.cbi.2016.05.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/02/2016] [Accepted: 05/16/2016] [Indexed: 11/27/2022]
Abstract
Plants take up sulfur in the form of sulfate. Sulfate is activated to adenosine 5'-phosphosulfate (APS) and reduced to sulfite and then to sulfide when it is assimilated into amino acid cysteine. Alternatively, APS is phosphorylated to 3'-phosphoadenosine 5'-phosphosulfate (PAPS), and sulfate from PAPS is transferred onto diverse metabolites in its oxidized form. Traditionally, these pathways are referred to as primary and secondary sulfate metabolism, respectively. However, the synthesis of PAPS is essential for plants and even its reduced provision leads to dwarfism. Here the current knowledge of enzymes involved in sulfation pathways of plants will be summarized, the similarities and differences between different kingdoms will be highlighted, and major open questions in the research of plant sulfation will be formulated.
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Affiliation(s)
- Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
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29
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Bohrer AS, Takahashi H. Compartmentalization and Regulation of Sulfate Assimilation Pathways in Plants. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 326:1-31. [PMID: 27572125 DOI: 10.1016/bs.ircmb.2016.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plants utilize sulfate to synthesize primary and secondary sulfur-containing metabolites required for growth and survival in the environment. Sulfate is taken up into roots from the soil and distributed to various organs through the functions of membrane-bound sulfate transporters, while it is utilized as the primary substrate for synthesizing sulfur-containing metabolites in the sulfate assimilation pathways. Transporters and enzymes for the assimilative conversion of sulfate are regulated in highly organized manners depending on changes in sulfate supply from the environment and demand for biosynthesis of reduced sulfur compounds in the plant systems. Over the past few decades, the effect of sulfur nutrition on gene expression of sulfate transporters and assimilatory enzymes has been extensively studied with the aim of understanding the full landscape of regulatory networks.
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Affiliation(s)
- A-S Bohrer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - H Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.
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30
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Aziz M, Nadipalli RK, Xie X, Sun Y, Surowiec K, Zhang JL, Paré PW. Augmenting Sulfur Metabolism and Herbivore Defense in Arabidopsis by Bacterial Volatile Signaling. FRONTIERS IN PLANT SCIENCE 2016; 7:458. [PMID: 27092166 PMCID: PMC4824779 DOI: 10.3389/fpls.2016.00458] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/24/2016] [Indexed: 05/24/2023]
Abstract
Sulfur is an element necessary for the life cycle of higher plants. Its assimilation and reduction into essential biomolecules are pivotal factors determining a plant's growth and vigor as well as resistance to environmental stress. While certain soil microbes can enhance ion solubility via chelating agents or oxidation, microbial regulation of plant-sulfur assimilation has not been reported. With an increasing understanding that soil microbes can activate growth and stress tolerance in plants via chemical signaling, the question arises as to whether such beneficial bacteria also regulate sulfur assimilation. Here we report a previously unidentified mechanism by which the growth-promoting rhizobacterium Bacillus amyloliquefaciens (GB03) transcriptionally activates genes responsible for sulfur assimilation, increasing sulfur uptake and accumulation in Arabidopsis. Transcripts encoding for sulfur-rich aliphatic and indolic glucosinolates are also GB03 induced. As a result, GB03-exposed plants with elevated glucosinolates exhibit greater protection against the generalist herbivore, Spodoptera exigua (beet armyworm, BAW). In contrast, a previously characterized glucosinolate mutant compromised in the production of both aliphatic and indolic glucosinolates is also compromised in terms of GB03-induced protection against insect herbivory. As with in vitro studies, soil-grown plants show enhanced glucosinolate accumulation and protection against BAW feeding with GB03 exposure. These results demonstrate the potential of microbes to enhance plant sulfur assimilation and emphasize the sophisticated integration of microbial signaling in plant defense.
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Affiliation(s)
- Mina Aziz
- Department of Chemistry and Biochemistry, Texas Tech University, LubbockTX, USA
- Center for Plant Lipid Research, University of North Texas, DentonTX, USA
| | | | - Xitao Xie
- Department of Chemistry and Biochemistry, Texas Tech University, LubbockTX, USA
| | - Yan Sun
- Department of Chemistry and Biochemistry, Texas Tech University, LubbockTX, USA
| | - Kazimierz Surowiec
- Department of Chemistry and Biochemistry, Texas Tech University, LubbockTX, USA
| | - Jin-Lin Zhang
- College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Paul W. Paré
- Department of Chemistry and Biochemistry, Texas Tech University, LubbockTX, USA
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31
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Ai Q, Liang G, Zhang H, Yu D. Control of sulfate concentration by miR395-targeted APS genes in Arabidopsis thaliana. PLANT DIVERSITY 2016; 38:92-100. [PMID: 30159453 PMCID: PMC6112208 DOI: 10.1016/j.pld.2015.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/27/2015] [Accepted: 04/27/2015] [Indexed: 05/23/2023]
Abstract
Sulfur nutrition is crucial for plant growth and development, as well as crop yield and quality. Inorganic sulfate in the soil is the major sulfur source for plants. After uptake, sulfate is activated by ATP sulfurylase, and then gets assimilated into sulfur-containing metabolites. However, the mechanism of regulation of sulfate levels by ATP sulfurylase is unclear. Here, we investigated the control of sulfate levels by miR395-mediated regulation of APS1/3/4. Sulfate was over-accumulated in the shoots of miR395 over-expression plants in which the expression of the APS1, APS3, and APS4 genes was suppressed. Accordingly, reduced expression of miR395 caused a decline of sulfate concentration. In agreement with these results, over-expression of the APS1, APS3, and APS4 genes led to the reduction of sulfate levels. Differential expression of these three APS genes in response to sulfate starvation implied that they have different functions. Further investigation revealed that the regulation of sulfate levels mediated by miR395 depends on the repression of its APS targets. Unlike the APS1, APS3, and APS4 genes, which encode plastid-localized ATP sulfurylases, the APS2 gene encodes a cytosolic version of ATP sulfurylase. Genetic analysis indicated that APS2 has no significant effect on sulfate levels. Our data suggest that miR395-targeted APS genes are key regulators of sulfate concentration in leaves.
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Affiliation(s)
- Qin Ai
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Gang Liang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Huimin Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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32
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Kopriva S, Calderwood A, Weckopp SC, Koprivova A. Plant sulfur and Big Data. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:1-10. [PMID: 26706053 DOI: 10.1016/j.plantsci.2015.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/26/2015] [Accepted: 09/17/2015] [Indexed: 05/20/2023]
Abstract
Sulfur is an essential mineral nutrient for plants, therefore, the pathways of its uptake and assimilation have been extensively studied. Great progress has been made in elucidation of the individual genes and enzymes and their regulation. Sulfur assimilation has been intensively investigated by -omics technologies and has been target of several genome wide genetic approaches. This brought a significant step in our understanding of the regulation of the pathway and its integration in cellular metabolism. However, the large amount of information derived from other experiments not directly targeting sulfur has also brought new and exciting insights into processes affecting sulfur homeostasis. In this review we will integrate the findings of the targeted experiments with those that brought unintentional progress in sulfur research, and will discuss how to synthesize the large amount of information available in various repositories into a meaningful dissection of the regulation of a specific metabolic pathway. We then speculate how this might be used to further advance knowledge on control of sulfur metabolism and what are the main questions to be answered.
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Affiliation(s)
- Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany.
| | | | - Silke C Weckopp
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
| | - Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
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33
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Forsberg SKG, Andreatta ME, Huang XY, Danku J, Salt DE, Carlborg Ö. The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance. PLoS Genet 2015; 11:e1005648. [PMID: 26599497 PMCID: PMC4657900 DOI: 10.1371/journal.pgen.1005648] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/14/2015] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association (GWA) analyses have generally been used to detect individual loci contributing to the phenotypic diversity in a population by the effects of these loci on the trait mean. More rarely, loci have also been detected based on variance differences between genotypes. Several hypotheses have been proposed to explain the possible genetic mechanisms leading to such variance signals. However, little is known about what causes these signals, or whether this genetic variance-heterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a variance-heterogeneity GWA (vGWA) signal for leaf molybdenum concentrations in Arabidopsis thaliana. Here, fine-mapping of this association reveals that the vGWA emerges from the effects of three independent genetic polymorphisms that all are in strong LD with the markers displaying the genetic variance-heterogeneity. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation or “missing heritability”. Two of the three polymorphisms underlying the genetic variance-heterogeneity are promoter variants for Molybdate transporter 1 (MOT1), and the third a variant located ~25 kb downstream of this gene. A fourth independent association was also detected ~600 kb upstream of MOT1. Use of a T-DNA knockout allele highlights Copper Transporter 6; COPT6 (AT2G26975) as a strong candidate gene for this association. Our results show that an extended LD across a complex locus including multiple functional alleles can lead to a variance-heterogeneity between genotypes in natural populations. Further, they provide novel insights into the genetic regulation of ion homeostasis in A. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations. Most biological traits vary in natural populations, and understanding the genetic basis of this variation remains an important challenge. Genome-wide association (GWA) studies have emerged as a powerful tool to address this challenge by dissecting the genetic architecture of trait variation into the contribution of individual genes. This contribution has traditionally been measured as the difference in the phenotypic means between groups of individuals with alternative genotypes at one, or multiple loci. However, instead of altering the trait mean, certain loci alter the variability of the trait. Here, we describe the genetic dissection of one such variance-controlling locus that drives variation in leaf molybdenum concentrations amongst natural accessions of Arabidopsis thaliana. The variance-controlling locus was found to result from the contributions of multiple alleles at multiple loci that are closely linked on the chromosome and is a major contributor to the “missing heritability” for this trait identified in previous studies. This illustrates that multi-allelic genetic architectures can hide large amounts of additive genetic variation, and that it is possible to uncover this hidden variation using the appropriate experimental designs and statistical methods described here.
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Affiliation(s)
- Simon K. G. Forsberg
- Department of Clinical Sciences, Division of Computational Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Matthew E. Andreatta
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Xin-Yuan Huang
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - John Danku
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - David E. Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Örjan Carlborg
- Department of Clinical Sciences, Division of Computational Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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34
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Real-time fluorescence assays of alkaline phosphatase and ATP sulfurylase activities based on a novel PPi fluorescent probe. Talanta 2015; 137:156-60. [DOI: 10.1016/j.talanta.2015.01.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/17/2015] [Accepted: 01/21/2015] [Indexed: 11/19/2022]
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35
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Kopriva S. Plant sulfur nutrition: From Sachs to Big Data. PLANT SIGNALING & BEHAVIOR 2015; 10:e1055436. [PMID: 26305261 PMCID: PMC4883835 DOI: 10.1080/15592324.2015.1055436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 05/03/2023]
Abstract
Together with water and carbon dioxide plants require 14 essential mineral nutrients to finish their life cycle. The research in plant nutrition can be traced back to Julius Sachs, who was the first to experimentally prove the essentiality of mineral nutrients for plants. Among those elements Sachs showed to be essential is sulfur. Plant sulfur nutrition has been not as extensively studied as the nutrition of nitrogen and phosphate, probably because sulfur was not limiting for agriculture. However, with the reduction of atmospheric sulfur dioxide emissions sulfur deficiency has become common. The research in sulfur nutrition has changed over the years from using yeast and algae as experimental material to adopting Arabidopsis as the plant model as well as from simple biochemical measurements of individual parameters to system biology. Here the evolution of sulfur research from the times of Sachs to the current Big Data is outlined.
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Affiliation(s)
- Stanislav Kopriva
- Botanical Institute; Cluster of Excellence on Plant Sciences; University of Cologne; Cologne, Germany
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Calderwood A, Morris RJ, Kopriva S. Predictive sulfur metabolism - a field in flux. FRONTIERS IN PLANT SCIENCE 2014; 5:646. [PMID: 25477892 PMCID: PMC4235266 DOI: 10.3389/fpls.2014.00646] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/02/2014] [Indexed: 05/08/2023]
Abstract
The key role of sulfur metabolites in response to biotic and abiotic stress in plants, as well as their importance in diet and health has led to a significant interest and effort in trying to understand and manipulate the production of relevant compounds. Metabolic engineering utilizes a set of theoretical tools to help rationally design modifications that enhance the production of a desired metabolite. Such approaches have proven their value in bacterial systems, however, the paucity of success stories to date in plants, suggests that challenges remain. Here, we review the most commonly used methods for understanding metabolic flux, focusing on the sulfur assimilatory pathway. We highlight known issues with both experimental and theoretical approaches, as well as presenting recent methods for integrating different modeling strategies, and progress toward an understanding of flux at the whole plant level.
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Affiliation(s)
| | - Richard J. Morris
- Department of Computational and Systems Biology, John Innes CentreNorwich, UK
| | - Stanislav Kopriva
- Botanical Institute and Cluster of Excellence on Plant Sciences, University of Cologne, Cologne BiocenterCologne, Germany
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Chao DY, Baraniecka P, Danku J, Koprivova A, Lahner B, Luo H, Yakubova E, Dilkes B, Kopriva S, Salt DE. Variation in sulfur and selenium accumulation is controlled by naturally occurring isoforms of the key sulfur assimilation enzyme ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE2 across the Arabidopsis species range. PLANT PHYSIOLOGY 2014; 166:1593-608. [PMID: 25245030 PMCID: PMC4226352 DOI: 10.1104/pp.114.247825] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis (Arabidopsis thaliana) accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction, and its reduced activity in the loss-of-function allele apr2-1 and the two Arabidopsis accessions Hodonín and Shahdara leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Shahdara accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by 4 orders of magnitude across the Arabidopsis species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored.
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Affiliation(s)
- Dai-Yin Chao
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
| | - Patrycja Baraniecka
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
| | - John Danku
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
| | - Anna Koprivova
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
| | - Brett Lahner
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
| | - Hongbing Luo
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
| | - Elena Yakubova
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
| | - Brian Dilkes
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
| | - Stanislav Kopriva
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)
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Koprivova A, Harper AL, Trick M, Bancroft I, Kopriva S. Dissection of the control of anion homeostasis by associative transcriptomics in Brassica napus. PLANT PHYSIOLOGY 2014; 166:442-50. [PMID: 25049360 PMCID: PMC4149728 DOI: 10.1104/pp.114.239947] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
To assess the variation in nutrient homeostasis in oilseed rape and to identify the genes responsible for this variation, we determined foliar anion levels in a diversity panel of Brassica napus accessions, 84 of which had been genotyped previously using messenger RNA sequencing. We applied associative transcriptomics to identify sequence polymorphisms linked to variation in nitrate, phosphate, or sulfate in these accessions. The analysis identified several hundred significant associations for each anion. Using functional annotation of Arabidopsis (Arabidopsis thaliana) homologs and available microarray data, we identified 60 candidate genes for controlling variation in the anion contents. To verify that these genes function in the control of nutrient homeostasis, we obtained Arabidopsis transfer DNA insertion lines for these candidates and tested them for the accumulation of nitrate, phosphate, and sulfate. Fourteen lines differed significantly in levels of the corresponding anions. Several of these genes have been shown previously to affect the accumulation of the corresponding anions in Arabidopsis mutants. These results thus confirm the power of associative transcriptomics in dissection of the genetic control of complex traits and present a set of candidate genes for use in the improvement of efficiency of B. napus mineral nutrition.
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Affiliation(s)
- Anna Koprivova
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Andrea L Harper
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Stanislav Kopriva
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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Herrmann J, Ravilious GE, McKinney SE, Westfall CS, Lee SG, Baraniecka P, Giovannetti M, Kopriva S, Krishnan HB, Jez JM. Structure and mechanism of soybean ATP sulfurylase and the committed step in plant sulfur assimilation. J Biol Chem 2014; 289:10919-10929. [PMID: 24584934 PMCID: PMC4036203 DOI: 10.1074/jbc.m113.540401] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/27/2014] [Indexed: 11/06/2022] Open
Abstract
Enzymes of the sulfur assimilation pathway are potential targets for improving nutrient content and environmental stress responses in plants. The committed step in this pathway is catalyzed by ATP sulfurylase, which synthesizes adenosine 5'-phosphosulfate (APS) from sulfate and ATP. To better understand the molecular basis of this energetically unfavorable reaction, the x-ray crystal structure of ATP sulfurylase isoform 1 from soybean (Glycine max ATP sulfurylase) in complex with APS was determined. This structure revealed several highly conserved substrate-binding motifs in the active site and a distinct dimerization interface compared with other ATP sulfurylases but was similar to mammalian 3'-phosphoadenosine 5'-phosphosulfate synthetase. Steady-state kinetic analysis of 20 G. max ATP sulfurylase point mutants suggests a reaction mechanism in which nucleophilic attack by sulfate on the α-phosphate of ATP involves transition state stabilization by Arg-248, Asn-249, His-255, and Arg-349. The structure and kinetic analysis suggest that ATP sulfurylase overcomes the energetic barrier of APS synthesis by distorting nucleotide structure and identifies critical residues for catalysis. Mutations that alter sulfate assimilation in Arabidopsis were mapped to the structure, which provides a molecular basis for understanding their effects on the sulfur assimilation pathway.
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Affiliation(s)
- Jonathan Herrmann
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | | | - Samuel E McKinney
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Corey S Westfall
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Soon Goo Lee
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | | | - Marco Giovannetti
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom; Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, I-10125 Torino, Italy
| | - Stanislav Kopriva
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Hari B Krishnan
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri 65211
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130.
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Koprivova A, Calderwood A, Lee BR, Kopriva S. Do PFT1 and HY5 interact in regulation of sulfate assimilation by light in Arabidopsis? FEBS Lett 2014; 588:1116-21. [DOI: 10.1016/j.febslet.2014.02.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 01/10/2023]
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Bohrer AS, Kopriva S, Takahashi H. Plastid-cytosol partitioning and integration of metabolic pathways for APS/PAPS biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2014; 5:751. [PMID: 25657651 PMCID: PMC4302788 DOI: 10.3389/fpls.2014.00751] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 12/08/2014] [Indexed: 05/03/2023]
Abstract
Plants assimilate sulfate from the environment to synthesize biologically active sulfur-containing compounds required for growth and cellular development. The primary steps of sulfur metabolism involve sequential enzymatic reactions synthesizing adenosine 5'-phosphosulfate (APS) and 3'-phosphoadenosine 5'-phosphosulfate (PAPS). Recent finding suggests that an adenosine nucleotide transport system facilitating the exchange of PAPS and 3'-phosphoadenosine 5'-phosphate across the plastid envelope is essential for establishing an intimate connection between the plastidic and cytosolic sulfate assimilation pathways in plants. Subcellular partitioning and integration of metabolic pathways provide focal points for investigating metabolic flux regulations. This perspective article presents an integrative view of sulfur metabolic flux control mechanisms with an emphasis on subcellular partitioning of APS/PAPS biosynthetic pathways in Arabidopsis thaliana.
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Affiliation(s)
- Anne-Sophie Bohrer
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Stanislav Kopriva
- Botanical Institute and Cluster of Excellence on Plant Sciences, University of Cologne, CologneGermany
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
- *Correspondence: Hideki Takahashi, Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, 209 Biochemistry Building, East Lansing, MI 48824, USA e-mail:
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Prioretti L, Gontero B, Hell R, Giordano M. Diversity and regulation of ATP sulfurylase in photosynthetic organisms. FRONTIERS IN PLANT SCIENCE 2014; 5:597. [PMID: 25414712 PMCID: PMC4220642 DOI: 10.3389/fpls.2014.00597] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/13/2014] [Indexed: 05/20/2023]
Abstract
ATP sulfurylase (ATPS) catalyzes the first committed step in the sulfate assimilation pathway, the activation of sulfate prior to its reduction. ATPS has been studied in only a few model organisms and even in these cases to a much smaller extent than the sulfate reduction and cysteine synthesis enzymes. This is possibly because the latter were considered of greater regulatory importance for sulfate assimilation. Recent evidences (reported in this paper) challenge this view and suggest that ATPS may have a crucial regulatory role in sulfate assimilation, at least in algae. In the ensuing text, we summarize the current knowledge on ATPS, with special attention to the processes that control its activity and gene(s) expression in algae. Special attention is given to algae ATPS proteins. The focus on algae is the consequence of the fact that a comprehensive investigation of ATPS revealed that the algal enzymes, especially those that are most likely involved in the pathway of sulfate reduction to cysteine, possess features that are not present in other organisms. Remarkably, algal ATPS proteins show a great diversity of isoforms and a high content of cysteine residues, whose positions are often conserved. According to the occurrence of cysteine residues, the ATPS of eukaryotic algae is closer to that of marine cyanobacteria of the genera Synechococcus and Prochlorococcus and is more distant from that of freshwater cyanobacteria. These characteristics might have evolved in parallel with the radiation of algae in the oceans and the increase of sulfate concentration in seawater.
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Affiliation(s)
- Laura Prioretti
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle MarcheAncona, Italy
| | - Brigitte Gontero
- Aix-Marseille Université Centre National de la Recherche Scientifique, BL' Unité de Bioénergétique et Ingénierie des Protéines UMR 7281Marseille, France
| | - Ruediger Hell
- Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Mario Giordano
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle MarcheAncona, Italy
- Institute of Microbiology Academy of Sciences of the Czech RepublicTrebon, Czech Republic
- *Correspondence: Mario Giordano, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy e-mail:
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Koprivova A, Kopriva S. Molecular mechanisms of regulation of sulfate assimilation: first steps on a long road. FRONTIERS IN PLANT SCIENCE 2014; 5:589. [PMID: 25400653 PMCID: PMC4212615 DOI: 10.3389/fpls.2014.00589] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/10/2014] [Indexed: 05/19/2023]
Abstract
The pathway of sulfate assimilation, which provides plants with the essential nutrient sulfur, is tightly regulated and coordinated with the demand for reduced sulfur. The responses of metabolite concentrations, enzyme activities and mRNA levels to various signals and environmental conditions have been well described for the pathway. However, only little is known about the molecular mechanisms of this regulation. To date, nine transcription factors have been described to control transcription of genes of sulfate uptake and assimilation. In addition, other levels of regulation contribute to the control of sulfur metabolism. Post-transcriptional regulation has been shown for sulfate transporters, adenosine 5'phosphosulfate reductase, and cysteine synthase. Several genes of the pathway are targets of microRNA miR395. In addition, protein-protein interaction is increasingly found in the center of various regulatory circuits. On top of the mechanisms of regulation of single genes, we are starting to learn more about mechanisms of adaptation, due to analyses of natural variation. In this article, the summary of different mechanisms of regulation will be accompanied by identification of the major gaps in knowledge and proposition of possible ways of filling them.
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Affiliation(s)
| | - Stanislav Kopriva
- *Correspondence: Stanislav Kopriva, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany e-mail:
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