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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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Shekhawat PK, Goyal A, Akhatar J, Sharma S, Kaur N, Bharti B, Mittal M, Sardana VK, Chhuneja P, Banga SS, Atri C. Genetic analysis of the variation for mineral accumulation in the leaves and seeds of natural germplasm of Brassica rapa L. (AA) and the its derived forms extracted from an allotetraploid B.juncea L.(AABB). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108084. [PMID: 37832370 DOI: 10.1016/j.plaphy.2023.108084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/16/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
Brassica rapa L. (2n = 20; AA) is a vegetable and oilseed crop that is grown all over the world. Its leaves, shoots, and seeds store significant amounts of minerals. We used inductively coupled plasma-optical emission spectroscopy (ICP-OES) to determine the concentrations of eleven minerals in the leaves and seeds of 195 advanced generation inbred lines, of which 92 represented natural (NR) B. rapa and the remaining 103 were derived (DR) from a set of mother genotypes originally extracted from an allotetraploid B. juncea (2n = 36; AABB). The inbred lines differed for the composition of leaf and seed minerals. Leaf concentrations of N, K, Zn, and Se were higher in the DR subpanel as compared to NR subpanel, along with high seed accumulations of K and Se. DArT genotyping and genome wide association mapping led to the identification of SNPs associated with leaf and seed mineral compositions. Chromosomes A03, A05, and A10 harboured the most associated loci. Annotations of the regions adjacent to respective GWAS peaks allowed prediction of genes known for acquisition, transport, and accumulation of minerals and heavy metal detoxification. Transcriptome analysis revealed differential expression patterns of the predicted candidates, with most genes either down-regulated in derived genotypes relative to natural forms or their expression being comparable between the two. General downregulation may be a consequence of extracting B. rapa from allotetraploid B. juncea through genome resection. Some of the identified SNPs may be used as DNA markers for breeding programmes designed to modify the leaf and seed mineral compositions.
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Affiliation(s)
- Pooja Kanwar Shekhawat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sanjula Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Baudh Bharti
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - V K Sardana
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
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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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Chen Q, Yu L, Chao W, Xiang J, Yang X, Ye J, Liao X, Zhou X, Rao S, Cheng S, Cong X, Xiao B, Xu F. Comparative physiological and transcriptome analysis reveals the potential mechanism of selenium accumulation and tolerance to selenate toxicity of Broussonetia papyrifera. TREE PHYSIOLOGY 2022; 42:2578-2595. [PMID: 35899437 DOI: 10.1093/treephys/tpac095] [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: 02/28/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Broussonetia papyrifera is an important fodder tree that is widely distributed in China. Enhancing the selenium (Se) content in B. papyrifera may help to improve the nutritional value of the feed. In this study, sodium selenite and selenate were foliar applied to investigate the mechanisms of Se tolerance and accumulation in B. papyrifera. The results showed that both Se forms significantly increased the total Se content, and the proportion of organic Se was significantly higher in the sodium selenite treatment than in the control. In addition, the soluble sugar, phenolic acid and flavonoid contents and antioxidant enzyme activities were increased by exogenous Se. The de novo RNA sequencing results showed that 644 and 1804 differentially expressed genes were identified in the selenite and selenate comparison groups, respectively. Pathway enrichment analysis demonstrated that 24 of the 108 pathways were significantly enriched, of which sulfur assimilation genes in the sodium selenite-treated groups were upregulated, whereas Se conjugation and transporter genes, such as SBP1, PCS, GSTs, ABCs and GPX, were significantly induced under selenate treatment. The hub genes identified by weighted-gene co-expression network analysis further confirmed that sulfur assimilation, conjugation and transporter genes might play a vital role in Se assimilation and tolerance. From this, a model of Se metabolism in B. papyrifera was proposed based on the above physiological and RNA sequencing data. This study is the first study to report that B. papyrifera has a strong ability to accumulate and tolerate exogenous Se, thereby providing a foundation for further characterization of the accumulation and tolerance mechanism of B. papyrifera. Our findings can provide technical support for producing Se-enriched fodder.
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Affiliation(s)
- Qiangwen Chen
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Li Yu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Wei Chao
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Juan Xiang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Xiaoli Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Xian Zhou
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Shen Rao
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, Hubei, China
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, Hubei, China
| | - Shuiyuan Cheng
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, Hubei, China
- National Selenium Rich Product Quality Supervision and Inspection Center, Enshi 445000, Hubei, China
| | - Xin Cong
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, Hubei, China
- Enshi Se-Run Material Engineering Technology Co., Ltd, Enshi, 445000, China
| | - Bo Xiao
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
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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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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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7
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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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Campos ACAL, van Dijk WFA, Ramakrishna P, Giles T, Korte P, Douglas A, Smith P, Salt DE. 1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:536-554. [PMID: 33506585 DOI: 10.1111/tpj.15177] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/07/2021] [Accepted: 01/20/2021] [Indexed: 05/06/2023]
Abstract
Soil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the 'ionome', of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.
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Affiliation(s)
- Ana Carolina A L Campos
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - William F A van Dijk
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Priya Ramakrishna
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Tom Giles
- Digital Research Service and Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Pamela Korte
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
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9
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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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Wang C, Zheng L, Tang Z, Sun S, Ma JF, Huang XY, Zhao FJ. OASTL-A1 functions as a cytosolic cysteine synthase and affects arsenic tolerance in rice. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3678-3689. [PMID: 32129444 DOI: 10.1093/jxb/eraa113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
Arsenic (As) contamination in paddy soil can cause phytotoxicity and elevated As accumulation in rice grains. Arsenic detoxification is closely linked to sulfur assimilation, but the genes involved have not been described in rice. In this study, we characterize the function of OASTL-A1, an O-acetylserine(thiol) lyase, in cysteine biosynthesis and detoxification of As in rice. Tissue expression analysis revealed that OsOASTL-A1 is mainly expressed in roots at the vegetative growth stage and in nodes at the reproductive stage. Furthermore, the expression of OsOASTL-A1 in roots was strongly induced by As exposure. Transgenic rice plants expressing pOsOASTL-A1::GUS (β-glucuronidase) indicated that OsOASTL-A1 was strongly expressed in the outer cortex and the vascular cylinder in the root mature zone. Subcellular localization using OsOASTL-A1:eGFP (enhanced green fluorescent protein) fusion protein showed that OsOASTL-A1 was localized to the cytosol. In vivo and in vitro enzyme activity assays showed that OsOASTL-A1 possessed the O-acetylserine(thiol) lyase activity. Knockout of OsOASTL-A1 led to significantly lower levels of cysteine, glutathione, and phytochelatins in roots and increased sensitivity to arsenate stress. Furthermore, the osoastl-a1 knockout mutants reduced As accumulation in the roots, but increased As accumulation in shoots. We conclude that OsOASTL-A1 is the cytosolic O-acetylserine(thiol) lyase that plays an important role in non-protein thiol biosynthesis in roots for As detoxification.
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Affiliation(s)
- Chengcheng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lihua Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shengkai Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Chuo, Kurashiki, Japan
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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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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Kopriva S, Malagoli M, Takahashi H. Sulfur nutrition: impacts on plant development, metabolism, and stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4069-4073. [PMID: 31423538 DOI: 10.1093/jxb/erz319] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Stanislav Kopriva
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Mario Malagoli
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padua, Legnaro, Italy
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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13
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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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14
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Luo T, Li S, Han D, Guo X, Shuai L, Wu Z. The effect of desulfurization on the postharvest quality and sulfite metabolism in pulp of sulfitated "Feizixiao" Litchi ( Litchi chinensis Sonn.) fruits. Food Sci Nutr 2019; 7:1715-1726. [PMID: 31139384 PMCID: PMC6526637 DOI: 10.1002/fsn3.1008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/25/2019] [Accepted: 03/02/2019] [Indexed: 01/02/2023] Open
Abstract
The residual sulfite caused by sulfur fumigation (SF) is a hazard to health and influenced the export trade of litchi. Desulfurization (DS) is a valid chemical method to reduce the residual sulfite. However, the effect of DS on fumigated litchi has not been studied at physiological and molecular level. This study was aimed to evaluate the effect of DS (SF plus 3% desulfurizer) on the postharvest quality, sulfite residue, and the sulfite metabolism in sulfitated "Feizixiao" litchi during the 4°C storage. Results indicated that the DS promoted the color recovery of sulfitated litchi and achieved an effect similar to SF on controlling rot and browning. DS recovered the water content and respiration rate of sulfitated litchi pericarp. Thus, DS improves commodity properties of sulfitated litchi. Moreover, DS greatly reduced sulfite residue especially in pulp and ensured the edible safety of sulfitated litchi. The activities of sulfite oxidase, sulfite reductase, serine acetyltransferase, and O-acetylserine(thiol) lyase in pulp increased after SF but fell down after DS while the expressions of their encoding genes decreased after SF but then rallied after DS. These results indicated the key role of these enzymes in sulfite metabolism after SF and DS changed the sulfite metabolism at both enzymatic and transcriptional level. It could be concluded that DS used in this study was an effective method for improving the color recovery and ensuring the edible safety of sulfitated litchi by not only chemical reaction but also both of enzymatic and transcriptional regulation.
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Affiliation(s)
- Tao Luo
- College of Horticulture, South China Agricultural University/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South ChinaMinistry of EducationGuangzhouP.R. China
| | - Shuangshuang Li
- College of Horticulture, South China Agricultural University/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South ChinaMinistry of EducationGuangzhouP.R. China
| | - Dongmei Han
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences/Key Laboratory of South Subtropical Fruit Biology and Genetic Resource UtilizationMinistry of AgricultureGuangzhouP.R. China
| | - Xiaomeng Guo
- College of Horticulture, South China Agricultural University/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South ChinaMinistry of EducationGuangzhouP.R. China
| | - Liang Shuai
- College of Food and Biological Engineering/Institute of Food Science and Engineering TechnologyHezhou UniversityHezhouP.R. China
| | - Zhenxian Wu
- College of Horticulture, South China Agricultural University/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South ChinaMinistry of EducationGuangzhouP.R. China
- Guangdong Litchi Engineering Research Center/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China) of Ministry of AgricultureGuangzhouP.R. China
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15
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Nyikó T, Auber A, Bucher E. Functional and molecular characterization of the conserved Arabidopsis PUMILIO protein, APUM9. PLANT MOLECULAR BIOLOGY 2019; 100:199-214. [PMID: 30868544 PMCID: PMC6513901 DOI: 10.1007/s11103-019-00853-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 03/01/2019] [Indexed: 05/08/2023]
Abstract
Here we demonstrate that the APUM9 RNA-binding protein and its co-factors play a role in mRNA destabilization and how this activity might regulate early plant development. APUM9 is a conserved PUF RNA-binding protein (RBP) under complex transcriptional control mediated by a transposable element (TE) that restricts its expression in Arabidopsis. Currently, little is known about the functional and mechanistic details of the plant PUF regulatory system and the biological relevance of the TE-mediated repression of APUM9 in plant development and stress responses. By combining a range of transient assays, we show here, that APUM9 binding to target transcripts can trigger their rapid decay via its conserved C-terminal RNA-binding domain. APUM9 directly interacts with DCP2, the catalytic subunit of the decapping complex and DCP2 overexpression induces rapid decay of APUM9 targeted mRNAs. We show that APUM9 negatively regulates the expression of ABA signaling genes during seed imbibition, and thereby might contribute to the switch from dormant stage to seed germination. By contrast, strong TE-mediated repression of APUM9 is important for normal plant growth in the later developmental stages. Finally, APUM9 overexpression plants show slightly enhanced heat tolerance suggesting that TE-mediated control of APUM9, might have a role not only in embryonic development, but also in plant adaptation to heat stress conditions.
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Affiliation(s)
- Tünde Nyikó
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS-INRA), 42 rue Georges Morel, 24, 49071, Beaucouzé, France
- Agricultural Biotechnology Institute, Szent-Györgyi Albert 4, Gödöllő, 2100, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Györgyi Albert 4, Gödöllő, 2100, Hungary
| | - Etienne Bucher
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS-INRA), 42 rue Georges Morel, 24, 49071, Beaucouzé, France.
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16
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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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17
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Lima LW, Pilon-Smits EAH, Schiavon M. Mechanisms of selenium hyperaccumulation in plants: A survey of molecular, biochemical and ecological cues. Biochim Biophys Acta Gen Subj 2018; 1862:2343-2353. [PMID: 29626605 DOI: 10.1016/j.bbagen.2018.03.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/20/2018] [Accepted: 03/25/2018] [Indexed: 12/01/2022]
Abstract
BACKGROUND Selenium (Se) is a micronutrient required for many life forms, but toxic at higher concentration. Plants do not have a Se requirement, but can benefit from Se via enhanced antioxidant activity. Some plant species can accumulate Se to concentrations above 0.1% of dry weight and seem to possess mechanisms that distinguish Se from its analog sulfur (S). Research on these so-called Se hyperaccumulators aims to identify key genes for this remarkable trait and to understand ecological implications. SCOPE OF REVIEW This review gives a broad overview of the current knowledge about Se uptake and metabolism in plants, with a special emphasis on hypothesized mechanisms of Se hyperaccumulation. The role of Se in plant defense responses and the associated ecological implications are discussed. MAJOR CONCLUSIONS Hyperaccumulators have enhanced expression of S transport and assimilation genes, and may possess transporters with higher specificity for selenate over sulfate. Genes involved in antioxidant reactions and biotic stress resistance are also upregulated. Key regulators in these processes appear to be the growth regulators jasmonic acid, salicylic acid and ethylene. Hyperaccumulation may have evolved owing to associated ecological benefits, particularly protection against pathogens and herbivores, and as a form of elemental allelopathy. GENERAL SIGNIFICANCE Understanding plant Se uptake and metabolism in hyperaccumulators has broad relevance for the environment, agriculture and human and animal nutrition and may help generate crops with selenate-specific uptake and high capacity to convert selenate to less toxic, anticarcinogenic, organic Se compounds.
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Affiliation(s)
| | | | - Michela Schiavon
- DAFNAE, University of Padova, Agripolis, 35020 Legnaro, PD, Italy.
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18
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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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19
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Zhou Y, Tang Q, Wu M, Mou D, Liu H, Wang S, Zhang C, Ding L, Luo J. Comparative transcriptomics provides novel insights into the mechanisms of selenium tolerance in the hyperaccumulator plant Cardamine hupingshanensis. Sci Rep 2018; 8:2789. [PMID: 29434336 PMCID: PMC5809607 DOI: 10.1038/s41598-018-21268-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
Selenium (Se) is an essential mineral element for animals and humans. Cardamine hupingshanensis (Brassicaceae), found in the Wuling mountain area of China, has been identified as a novel Se hyperaccumulator plant. However, the mechanism for selenium tolerance in Cardamine plants remains unknown. In this study, two cDNA libraries were constructed from seedlings of C. hupingshanensis treated with selenite. Approximately 100 million clean sequencing reads were de novo assembled into 48,989 unigenes, of which 39,579 and 33,510 were expressed in the roots and leaves, respectively. Biological pathways and candidate genes involved in selenium tolerance mechanisms were identified. Differential expression analysis identified 25 genes located in four pathways that were significantly responsive to selenite in C. hupingshanensis seedlings. The results of RNA sequencing (RNA-Seq) and quantitative real-time PCR (RT-qPCR) confirmed that storage function, oxidation, transamination and selenation play very important roles in the selenium tolerance in C. hupingshanensis. Furthermore, a different degradation pathway synthesizing malformed or deformed selenoproteins increased selenium tolerance at different selenite concentrations. This study provides novel insights into the mechanisms of selenium tolerance in a hyperaccumulator plant, and should serve as a rich gene resource for C. hupingshanensis.
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Affiliation(s)
- Yifeng Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.,Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China.,Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Qiaoyu Tang
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China
| | - Meiru Wu
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China
| | - Di Mou
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China
| | - Hui Liu
- Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chi Zhang
- Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Li Ding
- Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
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21
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Selenium and Sulfur to Produce Allium Functional Crops. Molecules 2017; 22:molecules22040558. [PMID: 28358332 PMCID: PMC6154330 DOI: 10.3390/molecules22040558] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 12/20/2022] Open
Abstract
Selenium is an element that must be considered in the nutrition of certain crops since its use allows the obtaining of biofortified crops with a positive impact on human health. The objective of this review is to present the information on the use of Se and S in the cultivation of plants of the genus Allium. The main proposal is to use Allium as specialist plants for biofortification with Se and S, considering the natural ability to accumulate both elements in different phytochemicals, which promotes the functional value of Allium. In spite of this, in the agricultural production of these species, the addition of sulfur is not realized to obtain functional foods and plants more resistant; it is only sought to cover the necessary requirements for growth. On the other hand, selenium does not appear in the agronomic management plans of most of the producers. Including S and Se fertilization as part of agronomic management can substantially improve Allium crop production. Allium species may be suitable to carry out biofortification with Se; this practice can be combined with the intensive use of S to obtain crops with higher production and sensory, nutritional, and functional quality.
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22
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Thomas CL, Alcock TD, Graham NS, Hayden R, Matterson S, Wilson L, Young SD, Dupuy LX, White PJ, Hammond JP, Danku JMC, Salt DE, Sweeney A, Bancroft I, Broadley MR. Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit. BMC PLANT BIOLOGY 2016; 16:214. [PMID: 27716103 PMCID: PMC5050600 DOI: 10.1186/s12870-016-0902-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/25/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Mineral nutrient uptake and utilisation by plants are controlled by many traits relating to root morphology, ion transport, sequestration and translocation. The aims of this study were to determine the phenotypic diversity in root morphology and leaf and seed mineral composition of a polyploid crop species, Brassica napus L., and how these traits relate to crop habit. Traits were quantified in a diversity panel of up to 387 genotypes: 163 winter, 127 spring, and seven semiwinter oilseed rape (OSR) habits, 35 swede, 15 winter fodder, and 40 exotic/unspecified habits. Root traits of 14 d old seedlings were measured in a 'pouch and wick' system (n = ~24 replicates per genotype). The mineral composition of 3-6 rosette-stage leaves, and mature seeds, was determined on compost-grown plants from a designed experiment (n = 5) by inductively coupled plasma-mass spectrometry (ICP-MS). RESULTS Seed size explained a large proportion of the variation in root length. Winter OSR and fodder habits had longer primary and lateral roots than spring OSR habits, with generally lower mineral concentrations. A comparison of the ratios of elements in leaf and seed parts revealed differences in translocation processes between crop habits, including those likely to be associated with crop-selection for OSR seeds with lower sulphur-containing glucosinolates. Combining root, leaf and seed traits in a discriminant analysis provided the most accurate characterisation of crop habit, illustrating the interdependence of plant tissues. CONCLUSIONS High-throughput morphological and composition phenotyping reveals complex interrelationships between mineral acquisition and accumulation linked to genetic control within and between crop types (habits) in B. napus. Despite its recent genetic ancestry (<10 ky), root morphology, and leaf and seed composition traits could potentially be used in crop improvement, if suitable markers can be identified and if these correspond with suitable agronomy and quality traits.
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Affiliation(s)
- C. L. Thomas
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - T. D. Alcock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - N. S. Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - R. Hayden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - S. Matterson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - L. Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - S. D. Young
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - L. X. Dupuy
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - P. J. White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, 11451 Kingdom of Saudi Arabia
| | - J. P. Hammond
- School of Agriculture, Policy and Development and the Centre for Food Security, University of Reading, Whiteknights, PO Box 237, Reading, RG6 6AR UK
| | - J. M. C. Danku
- University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU UK
| | - D. E. Salt
- University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU UK
| | - A. Sweeney
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - I. Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - M. R. Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
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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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24
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Koprivova A, Kopriva S. Hormonal control of sulfate uptake and assimilation. PLANT MOLECULAR BIOLOGY 2016; 91:617-27. [PMID: 26810064 DOI: 10.1007/s11103-016-0438-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/11/2016] [Indexed: 05/23/2023]
Abstract
Plant hormones have a plethora of functions in control of plant development, stress response, and primary metabolism, including nutrient homeostasis. In the plant nutrition, the interplay of hormones with responses to nitrate and phosphate deficiency is well described, but relatively little is known about the interaction between phytohormones and regulation of sulfur metabolism. As for other nutrients, sulfate deficiency results in modulation of root architecture, where hormones are expected to play an important role. Accordingly, sulfate deficiency induces genes involved in metabolism of tryptophane and auxin. Also jasmonate biosynthesis is induced, pointing to the need of increase the defense capabilities of the plants when sulfur is limiting. However, hormones affect also sulfate uptake and assimilation. The pathway is coordinately induced by jasmonate and the key enzyme, adenosine 5'-phosphosulfate reductase, is additionally regulated by ethylene, abscisic acid, nitric oxid, and other phytohormones. Perhaps the most intriguing link between hormones and sulfate assimilation is the fact that the main regulator of the response to sulfate starvation, SULFATE LIMITATION1 (SLIM1) belongs to the family of ethylene related transcription factors. We will review the current knowledge of interplay between phytohormones and control of sulfur metabolism and discuss the main open questions.
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Affiliation(s)
- Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
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25
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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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26
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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: 35] [Impact Index Per Article: 4.4] [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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27
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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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28
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Fine mapping and candidate gene analysis of an anthocyanin-rich gene, BnaA.PL1, conferring purple leaves in Brassica napus L. Mol Genet Genomics 2016; 291:1523-34. [PMID: 27003438 DOI: 10.1007/s00438-016-1199-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 03/12/2016] [Indexed: 10/22/2022]
Abstract
Because of the advantages of anthocyanins, the genetics and breeding of crops rich in anthocyanins has become a hot research topic. However, due to the lack of anthocyanin-related mutants, no regulatory genes have been mapped in Brassica napus. In this study, we first report the characterization of a B. napus line with purple leaves and the fine mapping and candidate screening of the BnaA.PL1 gene. The amount of anthocyanins in the purple leaf line was six times higher than that in a green leaf line. A genetic analysis indicated that the purple character was controlled by an incomplete dominant gene. Through map-based cloning, we localized the BnaA.PL1 gene to a 99-kb region at the end of B. napus chromosome A03. Transcriptional analysis of 11 genes located in the target region revealed that the expression level of only the BnAPR2 gene in seedling leaves decreased from purple to reddish green to green individuals, a finding that was consistent with the measured anthocyanin accumulation levels. Molecular cloning and sequence analysis of BnAPR2 showed that the purple individual-derived allele contained 17 variants. Markers co-segregating with BnaA.PL1 were developed from the sequence of BnAPR2 and were validated in the BC4P2 population. These results suggested that BnAPR2, which encodes adenosine 5'-phosphosulfate reductase, is likely to be a valuable candidate gene. This work may lay the foundation for the marker-assisted selection of B. napus vegetables that are rich in anthocyanins and for an improved understanding of the molecular mechanisms controlling anthocyanin accumulation in Brassica.
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29
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White PJ. Selenium accumulation by plants. ANNALS OF BOTANY 2016; 117:217-35. [PMID: 26718221 PMCID: PMC4724052 DOI: 10.1093/aob/mcv180] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/09/2015] [Accepted: 10/19/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Selenium (Se) is an essential mineral element for animals and humans, which they acquire largely from plants. The Se concentration in edible plants is determined by the Se phytoavailability in soils. Selenium is not an essential element for plants, but excessive Se can be toxic. Thus, soil Se phytoavailability determines the ecology of plants. Most plants cannot grow on seleniferous soils. Most plants that grow on seleniferous soils accumulate <100 mg Se kg(-1) dry matter and cannot tolerate greater tissue Se concentrations. However, some plant species have evolved tolerance to Se, and commonly accumulate tissue Se concentrations >100 mg Se kg(-1) dry matter. These plants are considered to be Se accumulators. Some species can even accumulate Se concentrations of 1000-15 000 mg Se kg(-1 )dry matter and are called Se hyperaccumulators. SCOPE This article provides an overview of Se uptake, translocation and metabolism in plants and highlights the possible genetic basis of differences in these between and within plant species. The review focuses initially on adaptations allowing plants to tolerate large Se concentrations in their tissues and the evolutionary origin of species that hyperaccumulate Se. It then describes the variation in tissue Se concentrations between and within angiosperm species and identifies genes encoding enzymes limiting the rates of incorporation of Se into organic compounds and chromosomal loci that might enable the development of crops with greater Se concentrations in their edible portions. Finally, it discusses transgenic approaches enabling plants to tolerate greater Se concentrations in the rhizosphere and in their tissues. CONCLUSIONS The trait of Se hyperaccumulation has evolved several times in separate angiosperm clades. The ability to tolerate large tissue Se concentrations is primarily related to the ability to divert Se away from the accumulation of selenocysteine and selenomethionine, which might be incorporated into non-functional proteins, through the synthesis of less toxic Se metabilites. There is potential to breed or select crops with greater Se concentrations in their edible tissues, which might be used to increase dietary Se intakes of animals and humans.
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Affiliation(s)
- Philip J White
- Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK and Distinguished Scientist Fellowship Program, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
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30
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Kopriva S, Talukdar D, Takahashi H, Hell R, Sirko A, D'Souza SF, Talukdar T. Editorial: Frontiers of Sulfur Metabolism in Plant Growth, Development, and Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 6:1220. [PMID: 26793206 PMCID: PMC4709830 DOI: 10.3389/fpls.2015.01220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/17/2015] [Indexed: 05/29/2023]
Affiliation(s)
- Stanislav Kopriva
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of CologneCologne, Germany
| | - Dibyendu Talukdar
- Department of Botany, Raja Peary Mohan College, University of CalcuttaUttarpara, India
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Rüdiger Hell
- Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Agnieszka Sirko
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | | | - Tulika Talukdar
- Department of Botany, Acharya Prafulla Chandra Roy Government CollegeSiliguri, India
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31
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Chen X, Yuan L, Ludewig U. Natural Genetic Variation of Seed Micronutrients of Arabidopsis thaliana Grown in Zinc-Deficient and Zinc-Amended Soil. FRONTIERS IN PLANT SCIENCE 2016; 7:1070. [PMID: 27507976 PMCID: PMC4960235 DOI: 10.3389/fpls.2016.01070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/07/2016] [Indexed: 05/03/2023]
Abstract
The quality of edible seeds for human and animal nutrition is crucially dependent on high zinc (Zn) and iron (Fe) seed concentrations. The micronutrient bioavailability is strongly reduced by seed phytate that forms complexes with seed cations. Superior genotypes with increased seed Zn concentrations had been identified, but low micronutrient seed levels often prevail when the plants are grown in Zn-deficient soils, which are globally widespread and correlate with human Zn-deficiency. Here, seed Zn concentrations of Arabidopsis accessions grown in Zn-deficient and Zn-amended conditions were measured together with seed Fe and manganese (Mn), in a panel of 108 accessions. By applying genome-wide association, de novo candidate genes potentially involved in the seed micronutrient accumulation were identified. However, a candidate inositol 1,3,4-trisphosphate 5/6-kinase 3 gene (ITPK3), located close to a significant nucleotide polymorphism associated with relative Zn seed concentrations, was dispensable for seed micronutrients accumulation in Col-0. Loss of this gene in itpk3-1 did neither affect phytate seed levels, nor seed Zn, Fe, and Mn. It is concluded that large natural variance of micronutrient seed levels is identified in the population and several accessions maintain high seed Zn despite growth in Zn-deficient conditions.
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Affiliation(s)
- Xiaochao Chen
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, StuttgartGermany
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interaction, Ministry of Education, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, BeijingChina
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, StuttgartGermany
- *Correspondence: Uwe Ludewig,
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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: 42] [Impact Index Per Article: 4.7] [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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Abstract
Darwin's theory of evolution by natural selection is the foundation of modern biology. However, it has proven remarkably difficult to demonstrate at the genetic, genomic, and population level exactly how wild species adapt to their natural environments. We discuss how one can use large sets of multiple genome sequences from wild populations to understand adaptation, with an emphasis on the small herbaceous plant Arabidopsis thaliana. We present motivation for such studies; summarize progress in describing whole-genome, species-wide sequence variation; and then discuss what insights have emerged from these resources, either based on sequence information alone or in combination with phenotypic data. We conclude with thoughts on opportunities with other plant species and the impact of expected progress in sequencing technology and genome engineering for studying adaptation in nature.
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Affiliation(s)
- Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria;
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35
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Dimkovikj A, Fisher B, Hutchison K, Van Hoewyk D. Stuck between a ROS and a hard place: Analysis of the ubiquitin proteasome pathway in selenocysteine treated Brassica napus reveals different toxicities during selenium assimilation. JOURNAL OF PLANT PHYSIOLOGY 2015; 181:50-4. [PMID: 25974369 DOI: 10.1016/j.jplph.2015.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/13/2015] [Accepted: 04/13/2015] [Indexed: 05/26/2023]
Abstract
During the selenium assimilation pathway, inorganic selenate and selenite are reduced to form selenocysteine (Sec). Tolerance to selenium in plants has long been attributable to minimizing the replacement of cysteine with selenocysteine, which can result in nonspecific selenoproteins that are potentially misfolded. Despite this widely accepted assumption, there is no evidence in higher plants demonstrating that selenocysteine induces toxicity by resulting in malformed proteins. In this study, we use Brassica napus to analyze the ubiquitin-proteasome pathway, which is capable of removing misfolded proteins. Sec rapidly increased proteasome activity and levels of ubiquitinated proteins, strongly indicating that selenocysteine induces protein misfolding. Proteasome inhibition increased the amount of selenium in protein in Sec-treated plants. Collectively, these data provide a mechanism that accounts for Sec toxicity. Additionally, Sec did not cause oxidative stress as judged by examining levels of superoxide using fluorescent microscopy. Therefore, the cellular response to Sec is different compared to selenite, which was recently shown to increase antioxidant metabolism in response to elevated mitochondrial superoxide that ultimately impaired proteasome activity. Therefore, plants must contend with two divergent modes of cytotoxicity during selenium assimilation. Selenite can result in oxidative stress, but increased flux of selenite reduction can yield Sec that in turn can cause protein misfolding.
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Affiliation(s)
| | - Brian Fisher
- Biology Department, Coastal Carolina University, Conway, SC 29526, USA
| | - Kim Hutchison
- Department of Soil Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Doug Van Hoewyk
- Biology Department, Coastal Carolina University, Conway, SC 29526, USA.
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36
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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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37
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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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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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