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Busoms S, Pérez-Martín L, Terés J, Huang XY, Yant L, Tolrà R, Salt DE, Poschenrieder C. Combined genomics to discover genes associated with tolerance to soil carbonate. Plant Cell Environ 2023; 46:3986-3998. [PMID: 37565316 DOI: 10.1111/pce.14691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Carbonate-rich soils limit plant performance and crop production. Previously, local adaptation to carbonated soils was detected in wild Arabidopsis thaliana accessions, allowing the selection of two demes with contrasting phenotypes: A1 (carbonate tolerant, c+) and T6 (carbonate sensitive, c-). Here, A1(c+) and T6(c - ) seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO3 , pH 8.3) to obtain ionomic profiles and conduct transcriptomic analysis. In parallel, A1(c+) and T6(c - ) parental lines and their progeny were cultivated on carbonated soil to evaluate fitness and segregation patterns. To understand the genetic architecture beyond the contrasted phenotypes, a bulk segregant analysis sequencing (BSA-Seq) was performed. Transcriptomics revealed 208 root and 2503 leaf differentially expressed genes in A1(c+) versus T6(c - ) comparison under bicarbonate stress, mainly involved in iron, nitrogen and carbon metabolism, hormones and glycosylates biosynthesis. Based on A1(c+) and T6(c - ) genome contrasts and BSA-Seq analysis, 69 genes were associated with carbonate tolerance. Comparative analysis of genomics and transcriptomics discovered a final set of 18 genes involved in bicarbonate stress responses that may have relevant roles in soil carbonate tolerance.
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Affiliation(s)
- Silvia Busoms
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Pérez-Martín
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joana Terés
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Levi Yant
- Future Food Beacon of Excellence & School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Roser Tolrà
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton, UK
| | - Charlotte Poschenrieder
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
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2
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Gao YQ, Huang JQ, Reyt G, Song T, Love A, Tiemessen D, Xue PY, Wu WK, George MW, Chen XY, Chao DY, Castrillo G, Salt DE. A dirigent protein complex directs lignin polymerization and assembly of the root diffusion barrier. Science 2023; 382:464-471. [PMID: 37883539 DOI: 10.1126/science.adi5032] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023]
Abstract
Functionally similar to the tight junctions present in animal guts, plant roots have evolved a lignified Casparian strip as an extracellular diffusion barrier in the endodermis to seal the root apoplast and maintain nutrient homeostasis. How this diffusion barrier is structured has been partially defined, but its lignin polymerization and assembly steps remain elusive. Here, we characterize a family of dirigent proteins (DPs) essential for both the localized polymerization of lignin required for Casparian strip biogenesis in the cell wall and for attachment of the strip to the plasma membrane to seal the apoplast. We reveal a Casparian strip lignification mechanism that requires cooperation between DPs and the Schengen pathway. Furthermore, we demonstrate that DPs directly mediate lignin polymerization as part of this mechanism.
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Affiliation(s)
- Yi-Qun Gao
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Jin-Quan Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guilhem Reyt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Tao Song
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ashley Love
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - David Tiemessen
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Pei-Ying Xue
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Farmland Eco-environment of Hebei Province, College of Resources and Environmental Sciences, Hebei Agricultural University, Hebei, Baoding 071000, China
| | - Wen-Kai Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Gabriel Castrillo
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
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3
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Song T, Tian YQ, Liu CB, Gao YQ, Wang YL, Zhang J, Su Y, Xu LN, Han ML, Salt DE, Chao DY. A new family of proteins is required for tethering of Casparian strip membrane domain and nutrient homoeostasis in rice. Nat Plants 2023; 9:1749-1759. [PMID: 37653341 DOI: 10.1038/s41477-023-01503-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/01/2023] [Indexed: 09/01/2023]
Abstract
Cell-cell junctions are essential for multicellular organisms to maintain nutrient homoeostasis. A plant-type tight junction, the Casparian strip (CS)-Casparian strip membrane domain (CSD) that seals the paracellular space between adjacent endodermal cells, has been known for more than one hundred years. However, the molecular basis of this structure remains unknown. Here we report that a new family of proteins containing a glycine/alanine/proline-rich domain, a lectin domain and a secretory signal peptide (GAPLESS) mediates tethering of the plasma membrane to the CS in rice. The GAPLESS proteins are specifically localized in the CS of root endodermal cells, and loss of their functions results in a disabled cell-cell junction and disrupted nutrient homoeostasis. The GAPLESS protein forms a tight complex with OsCASP1 in the plasma membrane, thereby mediating the CS-CSD junction. This study provides valuable insights into the junctional complex of plant endodermal cells, shedding light on our understanding of nutrient homoeostasis in crops and the cell junctions of eukaryotes.
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Affiliation(s)
- Tao Song
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Qi Tian
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chu-Bin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi-Qun Gao
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Nottingham, UK
| | - Ya-Ling Wang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Su
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Na Xu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mei-Ling Han
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - David E Salt
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Nottingham, UK
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
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4
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Giehl RFH, Flis P, Fuchs J, Gao Y, Salt DE, von Wirén N. Cell type-specific mapping of ion distribution in Arabidopsis thaliana roots. Nat Commun 2023; 14:3351. [PMID: 37311779 DOI: 10.1038/s41467-023-38880-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/16/2023] [Indexed: 06/15/2023] Open
Abstract
Cell type-specific mapping of element distribution is critical to fully understand how roots partition nutrients and toxic elements with aboveground parts. In this study, we developed a method that combines fluorescence-activated cell sorting (FACS) with inductively coupled plasma mass spectrometry (ICP-MS) to assess the ionome of different cell populations within Arabidopsis thaliana roots. The method reveals that most elements exhibit a radial concentration gradient increasing from the rhizodermis to inner cell layers, and detected previously unknown ionomic changes resulting from perturbed xylem loading processes. With this approach, we also identify a strong accumulation of manganese in trichoblasts of iron-deficient roots. We demonstrate that confining manganese sequestration in trichoblasts but not in endodermal cells efficiently retains manganese in roots, therefore preventing toxicity in shoots. These results indicate the existence of cell type-specific constraints for efficient metal sequestration in roots. Thus, our approach opens an avenue to investigate element compartmentation and transport pathways in plants.
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Affiliation(s)
- Ricardo F H Giehl
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, 06466, Seeland, Germany.
| | - Paulina Flis
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jörg Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, 06466, Seeland, Germany
| | - Yiqun Gao
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Nicolaus von Wirén
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, 06466, Seeland, Germany.
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5
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Gonin M, Salas-González I, Gopaulchan D, Frene JP, Roden S, Van de Poel B, Salt DE, Castrillo G. Plant microbiota controls an alternative root branching regulatory mechanism in plants. Proc Natl Acad Sci U S A 2023; 120:e2301054120. [PMID: 37011213 PMCID: PMC10104509 DOI: 10.1073/pnas.2301054120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
The establishment of beneficial interactions with microbes has helped plants to modulate root branching plasticity in response to environmental cues. However, how the plant microbiota harmonizes with plant roots to control their branching is unknown. Here, we show that the plant microbiota influences root branching in the model plant Arabidopsis thaliana. We define that the microbiota's ability to control some stages in root branching can be independent of the phytohormone auxin that directs lateral root development under axenic conditions. In addition, we revealed a microbiota-driven mechanism controlling lateral root development that requires the induction of ethylene response pathways. We show that the microbial effects on root branching can be relevant for plant responses to environmental stresses. Thus, we discovered a microbiota-driven regulatory pathway controlling root branching plasticity that could contribute to plant adaptation to different ecosystems.
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Affiliation(s)
- Mathieu Gonin
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
| | - Isai Salas-González
- Center for Genomics Sciences, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - David Gopaulchan
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
| | - Juan P Frene
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
- Future Food Beacon of Excellence, University of Nottingham, LE12 5RD, United Kingdom
| | - Stijn Roden
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Bram Van de Poel
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
- Leuven Plant Institute, KU Leuven, 3001 Leuven, Belgium
| | - David E Salt
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
- Future Food Beacon of Excellence, University of Nottingham, LE12 5RD, United Kingdom
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
- Future Food Beacon of Excellence, University of Nottingham, LE12 5RD, United Kingdom
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6
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. Plant Cell 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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7
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Salt DE. GMO or non-GMO? That is the question. New Phytol 2023; 237:7-8. [PMID: 36102015 DOI: 10.1111/nph.18399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
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8
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Fischer S, Flis P, Zhao FJ, Salt DE. Transcriptional network underpinning ploidy-related elevated leaf potassium in neo-tetraploids. Plant Physiol 2022; 190:1715-1730. [PMID: 35929797 PMCID: PMC9614460 DOI: 10.1093/plphys/kiac360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Whole-genome duplication generates a tetraploid from a diploid. Newly created tetraploids (neo-tetraploids) of Arabidopsis (Arabidopsis thaliana) have elevated leaf potassium (K), compared to their diploid progenitor. Micro-grafting has previously established that this elevated leaf K is driven by processes within the root. Here, mutational analysis revealed that the K+-uptake transporters K+ TRANSPORTER 1 (AKT1) and HIGH AFFINITY K+ TRANSPORTER 5 (HAK5) are not necessary for the difference in leaf K caused by whole-genome duplication. However, the endodermis and salt overly sensitive and abscisic acid-related signaling were necessary for the elevated leaf K in neo-tetraploids. Contrasting the root transcriptomes of neo-tetraploid and diploid wild-type and mutants that suppress the neo-tetraploid elevated leaf K phenotype allowed us to identify a core set of 92 differentially expressed genes associated with the difference in leaf K between neo-tetraploids and their diploid progenitor. This core set of genes connected whole-genome duplication with the difference in leaf K between neo-tetraploids and their diploid progenitors. The set of genes is enriched in functions such as cell wall and Casparian strip development and ion transport in the endodermis, root hairs, and procambium. This gene set provides tools to test the intriguing idea of recreating the physiological effects of whole-genome duplication within a diploid genome.
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Affiliation(s)
- Sina Fischer
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - 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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9
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Wang Y, Salt DE, Koornneef M, Aarts MGM. Construction and analysis of a Noccaea caerulescens TILLING population. BMC Plant Biol 2022; 22:360. [PMID: 35869423 PMCID: PMC9308233 DOI: 10.1186/s12870-022-03739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/27/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Metals such as Zn or Cd are toxic to plant and humans when they are exposed in high quantities through contaminated soil or food. Noccaea caerulescens, an extraordinary Zn/Cd/Ni hyperaccumulating species, is used as a model plant for metal hyperaccumulation and phytoremediation studies. Current reverse genetic techniques to generate mutants based on transgenesis is cumbersome due to the low transformation efficiency of this species. We aimed to establish a mutant library for functional genomics by a non-transgenic approach, to identify mutants with an altered mineral profiling, and to screen for mutations in bZIP19, a regulator of Zn homeostasis in N. caerulescens. RESULTS To generate the N. caerulescens mutant library, 3000 and 5000 seeds from two sister plants of a single-seed recurrent inbred descendant of the southern French accession Saint-Félix-de-Pallières (SF) were mutagenized respectively by 0.3 or 0.4% ethyl methane sulfonate (EMS). Two subpopulations of 5000 and 7000 M2 plants were obtained after 0.3 or 0.4% EMS treatment. The 0.4% EMS treatment population had a higher mutant frequency and was used for TILLING. A High Resolution Melting curve analysis (HRM) mutation screening platform was optimized and successfully applied to detect mutations for NcbZIP19, encoding a transcription factor controlling Zn homeostasis. Of four identified point mutations in NcbZIP19, two caused non-synonymous substitutions, however, these two mutations did not alter the ionome profile compared to the wild type. Forward screening of the 0.4% EMS treatment population by mineral concentration analysis (ionomics) in leaf material of each M2 plant revealed putative mutants affected in the concentration of one or more of the 20 trace elements tested. Several of the low-Zn mutants identified in the ionomic screen did not give progeny, illustrating the importance of Zn for the species. The mutant frequency of the population was evaluated based on an average of 2.3 knockout mutants per tested monogenic locus. CONCLUSIONS The 0.4% EMS treatment population is effectively mutagenized suitable for forward mutant screens and TILLING. Difficulties in seed production in low Zn mutants, obtained by both forward and reverse genetic approach, hampered further analysis of the nature of the low Zn phenotypes.
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Affiliation(s)
- Yanli Wang
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- College of Horticulture Science & Technology, Hebei Normal University of Science & Technology, No 360, West of HeBei street, Qinhuang Dao, China
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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10
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Alcock TD, Salt DE, Wilson P, Ramsden SJ. More sustainable vegetable oil: Balancing productivity with carbon storage opportunities. Sci Total Environ 2022; 829:154539. [PMID: 35302036 DOI: 10.1016/j.scitotenv.2022.154539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Intensive cultivation and post-harvest vegetable oil production stages are major sources of greenhouse gas (GHG) emissions. Variation between production systems and reporting disparity have resulted in discordance in previous emissions estimates. The aim of this study was to assess global systems-wide variation in GHG emissions resulting from palm, soybean, rapeseed and sunflower oil production. Such an analysis is critical to understand the implications of meeting increasing edible oil demand. To achieve this, we performed a unified re-analysis of life cycle input data from diverse palm, soybean, rapeseed, and sunflower oil production systems, from a saturating search of published literature. The resulting dataset reflects almost 6000 producers in 38 countries, and is representative of over 71% of global vegetable oil production. Across all oil crop systems, median GHG emissions were 3.81 kg CO2e per kg refined oil. Crop specific median emissions ranged from 2.49 kg CO2e for rapeseed oil to 4.25 kg CO2e for soybean oil per kg refined oil. Determination of the carbon cost of agricultural land occupation revealed that carbon storage potential in native compared to agricultural land cover drives variation in production GHG emissions, and indicates that expansion of production in low carbon storage potential land, whilst reforesting areas of high carbon storage potential, could reduce net GHG emissions whilst boosting productivity. Nevertheless, there remains considerable scope to improve sustainability within current production systems, including through increasing yields whilst limiting application of inputs with high carbon footprints, and in the case of palm oil through more widespread adoption of methane capture technologies in processing stages.
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Affiliation(s)
- Thomas D Alcock
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK; Crop Physiology, School of Life Sciences - Weihenstephan, Technical University of Munich, 85354 Freising, Germany.
| | - David E Salt
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK; School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
| | - Paul Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
| | - Stephen J Ramsden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
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11
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Tergemina E, Elfarargi AF, Flis P, Fulgione A, Göktay M, Neto C, Scholle M, Flood PJ, Xerri SA, Zicola J, Döring N, Dinis H, Krämer U, Salt DE, Hancock AM. A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment. Sci Adv 2022; 8:eabm9385. [PMID: 35584228 PMCID: PMC9116884 DOI: 10.1126/sciadv.abm9385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Most well-characterized cases of adaptation involve single genetic loci. Theory suggests that multilocus adaptive walks should be common, but these are challenging to identify in natural populations. Here, we combine trait mapping with population genetic modeling to show that a two-step process rewired nutrient homeostasis in a population of Arabidopsis as it colonized the base of an active stratovolcano characterized by extremely low soil manganese (Mn). First, a variant that disrupted the primary iron (Fe) uptake transporter gene (IRT1) swept quickly to fixation in a hard selective sweep, increasing Mn but limiting Fe in the leaves. Second, multiple independent tandem duplications occurred at NRAMP1 and together rose to near fixation in the island population, compensating the loss of IRT1 by improving Fe homeostasis. This study provides a clear case of a multilocus adaptive walk and reveals how genetic variants reshaped a phenotype and spread over space and time.
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Affiliation(s)
- Emmanuel Tergemina
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ahmed F. Elfarargi
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough, LE12 5RD Nottingham, UK
| | - Andrea Fulgione
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Mehmet Göktay
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Célia Neto
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Marleen Scholle
- Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Pádraic J. Flood
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Sophie-Asako Xerri
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Johan Zicola
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Nina Döring
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Herculano Dinis
- Parque Natural do Fogo, Direção Nacional do Ambiente, 115 Chã d’Areia, Praia, Santiago, Cabo Verde, Africa
- Associação Projecto Vitó, 8234, Xaguate, Cidade de São Filipe, Fogo, Cabo Verde, Africa
| | - Ute Krämer
- Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - David E. Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough, LE12 5RD Nottingham, UK
| | - Angela M. Hancock
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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12
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Gorelova V, Colinas M, Dell’Aglio E, Flis P, Salt DE, Fitzpatrick TB. Phosphorylated B6 vitamer deficiency in SALT OVERLY SENSITIVE 4 mutants compromises shoot and root development. Plant Physiol 2022; 188:220-240. [PMID: 34730814 PMCID: PMC8774746 DOI: 10.1093/plphys/kiab475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/05/2021] [Indexed: 05/31/2023]
Abstract
Stunted growth in saline conditions is a signature phenotype of the Arabidopsis SALT OVERLY SENSITIVE mutants (sos1-5) affected in pathways regulating the salt stress response. One of the mutants isolated, sos4, encodes a kinase that phosphorylates pyridoxal (PL), a B6 vitamer, forming the important coenzyme pyridoxal 5'-phosphate (PLP). Here, we show that sos4-1 and more recently isolated alleles are deficient in phosphorylated B6 vitamers including PLP. This deficit is concomitant with a lowered PL level. Ionomic profiling of plants under standard laboratory conditions (without salt stress) reveals that sos4 mutants are perturbed in mineral nutrient homeostasis, with a hyperaccumulation of transition metal micronutrients particularly in the root, accounting for stress sensitivity. This is coincident with the accumulation of reactive oxygen species, as well as enhanced lignification and suberization of the endodermis, although the Casparian strip is intact and functional. Further, micrografting shows that SOS4 activity in the shoot is necessary for proper root development. Growth under very low light alleviates the impairments, including salt sensitivity, suggesting that SOS4 is important for developmental processes under moderate light intensities. Our study provides a basis for the integration of SOS4 derived B6 vitamers into plant health and fitness.
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Affiliation(s)
- Vera Gorelova
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Maite Colinas
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Elisa Dell’Aglio
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Paulina Flis
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, UK
| | - David E Salt
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, UK
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
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13
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Calvo‐Polanco M, Ribeyre Z, Dauzat M, Reyt G, Hidalgo‐Shrestha C, Diehl P, Frenger M, Simonneau T, Muller B, Salt DE, Franke RB, Maurel C, Boursiac Y. Physiological roles of Casparian strips and suberin in the transport of water and solutes. New Phytol 2021; 232:2295-2307. [PMID: 34617285 PMCID: PMC9298204 DOI: 10.1111/nph.17765] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/02/2021] [Indexed: 05/09/2023]
Abstract
The formation of Casparian strips (CS) and the deposition of suberin at the endodermis of plant roots are thought to limit the apoplastic transport of water and ions. We investigated the specific role of each of these apoplastic barriers in the control of hydro-mineral transport by roots and the consequences on shoot growth. A collection of Arabidopsis thaliana mutants defective in suberin deposition and/or CS development was characterized under standard conditions using a hydroponic system and the Phenopsis platform. Mutants altered in suberin deposition had enhanced root hydraulic conductivity, indicating a restrictive role for this compound in water transport. In contrast, defective CS directly increased solute leakage and indirectly reduced root hydraulic conductivity. Defective CS also led to a reduction in rosette growth, which was partly dependent on the hydro-mineral status of the plant. Ectopic suberin was shown to partially compensate for defective CS phenotypes. Altogether, our work shows that the functionality of the root apoplastic diffusion barriers greatly influences the plant physiology, and that their integrity is tightly surveyed.
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Affiliation(s)
- Monica Calvo‐Polanco
- BPMPUniv MontpellierCNRSINRAEInstitut Agro34060MontpellierFrance
- Excellence Unit AGRIENVIRONMENTCIALEUniversity of Salamanca37185SalamancaSpain
| | - Zoe Ribeyre
- LEPSEUniv MontpellierINRAEInstitut Agro34060MontpellierFrance
| | - Myriam Dauzat
- LEPSEUniv MontpellierINRAEInstitut Agro34060MontpellierFrance
| | - Guilhem Reyt
- Future Food Beacon of Excellence and the School of BiosciencesUniversity of NottinghamNottinghamLE12 5RDUK
| | | | - Patrick Diehl
- Institute of Cellular and Molecular BotanyUniversity of Bonn53115BonnGermany
| | - Marc Frenger
- Institute of Cellular and Molecular BotanyUniversity of Bonn53115BonnGermany
| | | | - Bertrand Muller
- LEPSEUniv MontpellierINRAEInstitut Agro34060MontpellierFrance
| | - David E. Salt
- Future Food Beacon of Excellence and the School of BiosciencesUniversity of NottinghamNottinghamLE12 5RDUK
| | - Rochus B. Franke
- Institute of Cellular and Molecular BotanyUniversity of Bonn53115BonnGermany
| | | | - Yann Boursiac
- BPMPUniv MontpellierCNRSINRAEInstitut Agro34060MontpellierFrance
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14
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Lee S, Lee J, Ricachenevsky FK, Punshon T, Tappero R, Salt DE, Guerinot ML. Redundant roles of four ZIP family members in zinc homeostasis and seed development in Arabidopsis thaliana. Plant J 2021; 108:1162-1173. [PMID: 34559918 PMCID: PMC8613002 DOI: 10.1111/tpj.15506] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/29/2021] [Accepted: 09/08/2021] [Indexed: 05/28/2023]
Abstract
Zinc (Zn) is essential for normal plant growth and development. The Zn-regulated transporter, iron-regulated transporter (IRT)-like protein (ZIP) family members are involved in Zn transport and cellular Zn homeostasis throughout the domains of life. In this study, we have characterized four ZIP transporters from Arabidopsis thaliana (IRT3, ZIP4, ZIP6, and ZIP9) to better understand their functional roles. The four ZIP proteins can restore the growth defect of a yeast Zn uptake mutant and are upregulated under Zn deficiency. Single and double mutants show no phenotypes under Zn-sufficient or Zn-limited growth conditions. In contrast, triple and quadruple mutants show impaired growth irrespective of external Zn supply due to reduced Zn translocation from root to shoot. All four ZIP genes are highly expressed during seed development, and siliques from all single and higher-order mutants exhibited an increased number of abnormal seeds and decreased Zn levels in mature seeds relative to wild type. The seed phenotypes could be reversed by supplementing the soil with Zn. Our data demonstrate that IRT3, ZIP4, ZIP6, and ZIP9 function redundantly in maintaining Zn homeostasis and seed development in A. thaliana.
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Affiliation(s)
- Sichul Lee
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
| | - Joohyun Lee
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, 215306, China
| | - Felipe K. Ricachenevsky
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
- Botany Department, Biosciences Institute; and Graduate Program in Cell and Molecular Biology, Biotechnology Center, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Tracy Punshon
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | | | - David E. Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
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15
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Busoms S, Terés J, Yant L, Poschenrieder C, Salt DE. Adaptation to coastal soils through pleiotropic boosting of ion and stress hormone concentrations in wild Arabidopsis thaliana. New Phytol 2021; 232:208-220. [PMID: 34153129 PMCID: PMC8429122 DOI: 10.1111/nph.17569] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/16/2021] [Indexed: 05/05/2023]
Abstract
Local adaptation in coastal areas is driven chiefly by tolerance to salinity stress. To survive high salinity, plants have evolved mechanisms to specifically tolerate sodium. However, the pathways that mediate adaptive changes in these conditions reach well beyond Na+ . Here we perform a high-resolution genetic, ionomic, and functional study of the natural variation in Molybdenum transporter 1 (MOT1) associated with coastal Arabidopsis thaliana accessions. We quantify the fitness benefits of a specific deletion-harbouring allele (MOT1DEL ) present in coastal habitats that is associated with lower transcript expression and molybdenum accumulation. Analysis of the leaf ionome revealed that MOT1DEL plants accumulate more copper (Cu) and less sodium (Na+ ) than plants with the noncoastal MOT1 allele, revealing a complex interdependence in homeostasis of these three elements. Our results indicate that under salinity stress, reduced MOT1 function limits leaf Na+ accumulation through abscisic acid (ABA) signalling. Enhanced ABA biosynthesis requires Cu. This demand is met in Cu deficient coastal soils through MOT1DEL increasing the expression of SPL7 and the copper transport protein COPT6. MOT1DEL is able to deliver a pleiotropic suite of phenotypes that enhance salinity tolerance in coastal soils deficient in Cu. This is achieved by inducing ABA biosynthesis and promoting reduced uptake or better compartmentalization of Na+ , leading to coastal adaptation.
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Affiliation(s)
- Silvia Busoms
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona. Carrer de la Vall Moronta s/n, E-08193 Bellaterra, Barcelona (Spain)
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Joana Terés
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona. Carrer de la Vall Moronta s/n, E-08193 Bellaterra, Barcelona (Spain)
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Charlotte Poschenrieder
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona. Carrer de la Vall Moronta s/n, E-08193 Bellaterra, Barcelona (Spain)
| | - David E Salt
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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16
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Shukla V, Han JP, Cléard F, Lefebvre-Legendre L, Gully K, Flis P, Berhin A, Andersen TG, Salt DE, Nawrath C, Barberon M. Suberin plasticity to developmental and exogenous cues is regulated by a set of MYB transcription factors. Proc Natl Acad Sci U S A 2021. [PMID: 34551972 DOI: 10.1101/2021.01.27.428267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Suberin is a hydrophobic biopolymer that can be deposited at the periphery of cells, forming protective barriers against biotic and abiotic stress. In roots, suberin forms lamellae at the periphery of endodermal cells where it plays crucial roles in the control of water and mineral transport. Suberin formation is highly regulated by developmental and environmental cues. However, the mechanisms controlling its spatiotemporal regulation are poorly understood. Here, we show that endodermal suberin is regulated independently by developmental and exogenous signals to fine-tune suberin deposition in roots. We found a set of four MYB transcription factors (MYB41, MYB53, MYB92, and MYB93), each of which is individually regulated by these two signals and is sufficient to promote endodermal suberin. Mutation of these four transcription factors simultaneously through genome editing leads to a dramatic reduction in suberin formation in response to both developmental and environmental signals. Most suberin mutants analyzed at physiological levels are also affected in another endodermal barrier made of lignin (Casparian strips) through a compensatory mechanism. Through the functional analysis of these four MYBs, we generated plants allowing unbiased investigation of endodermal suberin function, without accounting for confounding effects due to Casparian strip defects, and were able to unravel specific roles of suberin in nutrient homeostasis.
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Affiliation(s)
- Vinay Shukla
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Jian-Pu Han
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Fabienne Cléard
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | | | - Kay Gully
- Department of Molecular Plant Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Paulina Flis
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, NG7 2RD Nottingham, United Kingdom
| | - Alice Berhin
- Department of Molecular Plant Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tonni G Andersen
- Department of Molecular Plant Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - David E Salt
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, NG7 2RD Nottingham, United Kingdom
| | - Christiane Nawrath
- Department of Molecular Plant Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marie Barberon
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland;
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17
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Shukla V, Han JP, Cléard F, Lefebvre-Legendre L, Gully K, Flis P, Berhin A, Andersen TG, Salt DE, Nawrath C, Barberon M. Suberin plasticity to developmental and exogenous cues is regulated by a set of MYB transcription factors. Proc Natl Acad Sci U S A 2021; 118:e2101730118. [PMID: 34551972 PMCID: PMC8488582 DOI: 10.1073/pnas.2101730118] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 11/18/2022] Open
Abstract
Suberin is a hydrophobic biopolymer that can be deposited at the periphery of cells, forming protective barriers against biotic and abiotic stress. In roots, suberin forms lamellae at the periphery of endodermal cells where it plays crucial roles in the control of water and mineral transport. Suberin formation is highly regulated by developmental and environmental cues. However, the mechanisms controlling its spatiotemporal regulation are poorly understood. Here, we show that endodermal suberin is regulated independently by developmental and exogenous signals to fine-tune suberin deposition in roots. We found a set of four MYB transcription factors (MYB41, MYB53, MYB92, and MYB93), each of which is individually regulated by these two signals and is sufficient to promote endodermal suberin. Mutation of these four transcription factors simultaneously through genome editing leads to a dramatic reduction in suberin formation in response to both developmental and environmental signals. Most suberin mutants analyzed at physiological levels are also affected in another endodermal barrier made of lignin (Casparian strips) through a compensatory mechanism. Through the functional analysis of these four MYBs, we generated plants allowing unbiased investigation of endodermal suberin function, without accounting for confounding effects due to Casparian strip defects, and were able to unravel specific roles of suberin in nutrient homeostasis.
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Affiliation(s)
- Vinay Shukla
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Jian-Pu Han
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Fabienne Cléard
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | | | - Kay Gully
- Department of Molecular Plant Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Paulina Flis
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, NG7 2RD Nottingham, United Kingdom
| | - Alice Berhin
- Department of Molecular Plant Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tonni G Andersen
- Department of Molecular Plant Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - David E Salt
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, NG7 2RD Nottingham, United Kingdom
| | - Christiane Nawrath
- Department of Molecular Plant Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marie Barberon
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland;
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18
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Pascut FC, Couvreur V, Dietrich D, Leftley N, Reyt G, Boursiac Y, Calvo-Polanco M, Casimiro I, Maurel C, Salt DE, Draye X, Wells DM, Bennett MJ, Webb KF. Non-invasive hydrodynamic imaging in plant roots at cellular resolution. Nat Commun 2021; 12:4682. [PMID: 34344886 PMCID: PMC8333316 DOI: 10.1038/s41467-021-24913-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022] Open
Abstract
A key impediment to studying water-related mechanisms in plants is the inability to non-invasively image water fluxes in cells at high temporal and spatial resolution. Here, we report that Raman microspectroscopy, complemented by hydrodynamic modelling, can achieve this goal - monitoring hydrodynamics within living root tissues at cell- and sub-second-scale resolutions. Raman imaging of water-transporting xylem vessels in Arabidopsis thaliana mutant roots reveals faster xylem water transport in endodermal diffusion barrier mutants. Furthermore, transverse line scans across the root suggest water transported via the root xylem does not re-enter outer root tissues nor the surrounding soil when en-route to shoot tissues if endodermal diffusion barriers are intact, thereby separating 'two water worlds'.
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Affiliation(s)
- Flavius C Pascut
- Optics & Photonics Research Group, Faculty of Engineering, University of Nottingham, Nottingham, UK.
| | - Valentin Couvreur
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
| | - Daniela Dietrich
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Nicky Leftley
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Guilhem Reyt
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Yann Boursiac
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Monica Calvo-Polanco
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
- Excellence Unit AGRIENVIRONMENT, CIALE, University of Salamanca, Salamanca, Spain
| | - Ilda Casimiro
- Departamento de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, Facultad de Ciencias, Badajoz, Spain
| | - Christophe Maurel
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - David E Salt
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Xavier Draye
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Darren M Wells
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Malcolm J Bennett
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Kevin F Webb
- Optics & Photonics Research Group, Faculty of Engineering, University of Nottingham, Nottingham, UK
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19
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Alcock TD, Thomas CL, Ó Lochlainn S, Pongrac P, Wilson M, Moore C, Reyt G, Vogel-Mikuš K, Kelemen M, Hayden R, Wilson L, Stephenson P, Østergaard L, Irwin JA, Hammond JP, King GJ, Salt DE, Graham NS, White PJ, Broadley MR. Magnesium and calcium overaccumulate in the leaves of a schengen3 mutant of Brassica rapa. Plant Physiol 2021; 186:1616-1631. [PMID: 33831190 PMCID: PMC8260142 DOI: 10.1093/plphys/kiab150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/12/2021] [Indexed: 05/04/2023]
Abstract
Magnesium (Mg) and calcium (Ca) are essential mineral nutrients poorly supplied in many human food systems. In grazing livestock, Mg and Ca deficiencies are costly welfare issues. Here, we report a Brassica rapa loss-of-function schengen3 (sgn3) mutant, braA.sgn3.a-1, which accumulates twice as much Mg and a third more Ca in its leaves. We mapped braA.sgn3.a to a single recessive locus using a forward ionomic screen of chemically mutagenized lines with subsequent backcrossing and linked-read sequencing of second back-crossed, second filial generation (BC2F2) segregants. Confocal imaging revealed a disrupted root endodermal diffusion barrier, consistent with SGN3 encoding a receptor-like kinase required for normal formation of Casparian strips, as reported in thale cress (Arabidopsis thaliana). Analysis of the spatial distribution of elements showed elevated extracellular Mg concentrations in leaves of braA.sgn3.a-1, hypothesized to result from preferential export of excessive Mg from cells to ensure suitable cellular concentrations. This work confirms a conserved role of SGN3 in controlling nutrient homeostasis in B. rapa, and reveals mechanisms by which plants are able to deal with perturbed shoot element concentrations resulting from a "leaky" root endodermal barrier. Characterization of variation in leaf Mg and Ca accumulation across a mutagenized population of B. rapa shows promise for using such populations in breeding programs to increase edible concentrations of essential human and animal nutrients.
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Affiliation(s)
- Thomas D Alcock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Catherine L Thomas
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Department of Sustainable Agriculture Sciences, Rothamsted Research, West Common, Hertfordshire AL5 2JQ, UK
| | - Seosamh Ó Lochlainn
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Paula Pongrac
- Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Michael Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Christopher Moore
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Guilhem Reyt
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Katarina Vogel-Mikuš
- Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | | | - Rory Hayden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Lolita Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Pauline Stephenson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Judith A Irwin
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - John P Hammond
- School of Agriculture, Policy and Development and the Centre for Food Security, University of Reading, Whiteknights, P.O. Box 237, Reading RG6 6AR, UK
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia
| | - David E Salt
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Neil S Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Philip J White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh 11451, Saudi Arabia
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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20
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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. Plant J 2021; 106:536-554. [PMID: 33506585 DOI: 10.1111/tpj.15177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Ricachenevsky FK, Punshon T, Salt DE, Fett JP, Guerinot ML. Arabidopsis thaliana zinc accumulation in leaf trichomes is correlated with zinc concentration in leaves. Sci Rep 2021; 11:5278. [PMID: 33674630 PMCID: PMC7935932 DOI: 10.1038/s41598-021-84508-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/17/2021] [Indexed: 11/21/2022] Open
Abstract
Zinc (Zn) is a key micronutrient for plants and animals, and understanding Zn homeostasis in plants can improve both agriculture and human health. While root Zn transporters in plant model species have been characterized in detail, comparatively little is known about shoot processes controlling Zn concentrations and spatial distribution. Previous work showed that Zn hyperaccumulator species such as Arabidopsis halleri accumulate Zn and other metals in leaf trichomes. To date there is no systematic study regarding Zn accumulation in the trichomes of the non-accumulating, genetic model species A. thaliana. Here, we used Synchrotron X-Ray Fluorescence mapping to show that Zn accumulates at the base of trichomes of A. thaliana. Using transgenic and natural accessions of A thaliana that vary in bulk leaf Zn concentration, we demonstrate that higher leaf Zn increases total Zn found at the base of trichome cells. Our data indicates that Zn accumulation in trichomes is a function of the Zn status of the plant, and provides the basis for future studies on a genetically tractable plant species to understand the molecular steps involved in Zn spatial distribution in leaves.
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Affiliation(s)
- Felipe K Ricachenevsky
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande Do Sul, Porto Alegre, Brazil. .,Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, Porto Alegre, RS, 9500, Brazil. .,Department of Biological Sciences, Life Sciences Center, Dartmouth College, 78 College St, Hanover, NH, 03755, USA.
| | - Tracy Punshon
- Department of Biological Sciences, Life Sciences Center, Dartmouth College, 78 College St, Hanover, NH, 03755, USA
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Janette P Fett
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande Do Sul, Porto Alegre, Brazil.,Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, Porto Alegre, RS, 9500, Brazil
| | - Mary Lou Guerinot
- Department of Biological Sciences, Life Sciences Center, Dartmouth College, 78 College St, Hanover, NH, 03755, USA.
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22
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Fischer S, Sánchez-Bermejo E, Xu X, Flis P, Ramakrishna P, Guerinot ML, Zhao FJ, Salt DE. Targeted expression of the arsenate reductase HAC1 identifies cell type specificity of arsenic metabolism and transport in plant roots. J Exp Bot 2021; 72:415-425. [PMID: 33038235 PMCID: PMC7853597 DOI: 10.1093/jxb/eraa465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/05/2020] [Indexed: 05/14/2023]
Abstract
High Arsenic Concentration 1 (HAC1), an Arabidopsis thaliana arsenate reductase, plays a key role in arsenate [As(V)] tolerance. Through conversion of As(V) to arsenite [As(III)], HAC1 enables As(III) export from roots, and restricts translocation of As(V) to shoots. To probe the ability of different root tissues to detoxify As(III) produced by HAC1, we generated A. thaliana lines expressing HAC1 in different cell types. We investigated the As(V) tolerance phenotypes: root growth, As(III) efflux, As translocation, and As chemical speciation. We showed that HAC1 can function in the outer tissues of the root (epidermis, cortex, and endodermis) to confer As(V) tolerance, As(III) efflux, and limit As accumulation in shoots. HAC1 is less effective in the stele at conferring As(V) tolerance phenotypes. The exception is HAC1 activity in the protoxylem, which we found to be sufficient to restrict As translocation, but not to confer As(V) tolerance. In conclusion, we describe cell type-specific functions of HAC1 that spatially separate the control of As(V) tolerance and As translocation. Further, we identify a key function of protoxylem cells in As(V) translocation, consistent with the model where endodermal passage cells, above protoxylem pericycle cells, form a 'funnel' loading nutrients and potentially toxic elements into the vasculature.
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Affiliation(s)
- Sina Fischer
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
| | - Eduardo Sánchez-Bermejo
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
| | - Xuejie Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
| | - Priya Ramakrishna
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
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23
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Liu H, Long SX, Pinson SRM, Tang Z, Guerinot ML, Salt DE, Zhao FJ, Huang XY. Univariate and Multivariate QTL Analyses Reveal Covariance Among Mineral Elements in the Rice Ionome. Front Genet 2021; 12:638555. [PMID: 33569081 PMCID: PMC7868434 DOI: 10.3389/fgene.2021.638555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/06/2021] [Indexed: 11/27/2022] Open
Abstract
Rice provides more than one fifth of daily calories for half of the world’s human population, and is a major dietary source of both essential mineral nutrients and toxic elements. Rice grains are generally poor in some essential nutrients but may contain unsafe levels of some toxic elements under certain conditions. Identification of quantitative trait loci (QTLs) controlling the concentrations of mineral nutrients and toxic trace metals (the ionome) in rice will facilitate development of nutritionally improved rice varieties. However, QTL analyses have traditionally considered each element separately without considering their interrelatedness. In this study, we performed principal component analysis (PCA) and multivariate QTL analyses to identify the genetic loci controlling the covariance among mineral elements in the rice ionome. We resequenced the whole genomes of a rice recombinant inbred line (RIL) population, and performed univariate and multivariate QTL analyses for the concentrations of 16 elements in grains, shoots and roots of the RIL population grown in different conditions. We identified a total of 167 unique elemental QTLs based on analyses of individual elemental concentrations as separate traits, 53 QTLs controlling covariance among elemental concentrations within a single environment/tissue (PC-QTLs), and 152 QTLs which determined covariation among elements across environments/tissues (aPC-QTLs). The candidate genes underlying the QTL clusters with elemental QTLs, PC-QTLs and aPC-QTLs co-localized were identified, including OsHMA4 and OsNRAMP5. The identification of both elemental QTLs and PC QTLs will facilitate the cloning of underlying causal genes and the dissection of the complex regulation of the ionome in rice.
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Affiliation(s)
- Huan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Su-Xian Long
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shannon R M Pinson
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, United States
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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24
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Salas-González I, Reyt G, Flis P, Custódio V, Gopaulchan D, Bakhoum N, Dew TP, Suresh K, Franke RB, Dangl JL, Salt DE, Castrillo G. Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis. Science 2021; 371:science.abd0695. [DOI: 10.1126/science.abd0695] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Isai Salas-González
- Curriculum in Bioinformatics and Computational Biology, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guilhem Reyt
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Paulina Flis
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Valéria Custódio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidad de Nova de Lisboa, Lisboa, Portugal
| | - David Gopaulchan
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Niokhor Bakhoum
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Tristan P. Dew
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Kiran Suresh
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Rochus Benni Franke
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Jeffery L. Dangl
- Curriculum in Bioinformatics and Computational Biology, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David E. Salt
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
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25
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Ruang-Areerate P, Travis AJ, Pinson SRM, Tarpley L, Eizenga GC, Guerinot ML, Salt DE, Douglas A, Price AH, Norton GJ. Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach. Heredity (Edinb) 2020; 126:505-520. [PMID: 33235293 DOI: 10.1038/s41437-020-00390-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 11/09/2022] Open
Abstract
Manganese (Mn) is an essential trace element for plants and commonly contributes to human health; however, the understanding of the genes controlling natural variation in Mn in crop plants is limited. Here, the integration of two of genome-wide association study approaches was used to increase the identification of valuable quantitative trait loci (QTL) and candidate genes responsible for the concentration of grain Mn across 389 diverse rice cultivars grown in Arkansas and Texas, USA, in multiple years. Single-trait analysis was initially performed using three different SNP datasets. As a result, significant loci could be detected using the high-density SNP dataset. Based on the 5.2 M SNP dataset, major QTLs were located on chromosomes 3 and 7 for Mn containing six candidate genes. In addition, the phenotypic data of grain Mn concentration were combined from three flooded-field experiments from the two sites and 3 years using multi-experiment analysis based on the 5.2 M SNP dataset. Two previous QTLs on chromosome 3 were identified across experiments, whereas new Mn QTLs were identified that were not found in individual experiments, on chromosomes 3, 4, 9 and 11. OsMTP8.1 was identified in both approaches and is a good candidate gene that could be controlling grain Mn concentration. This work demonstrates the utilisation of multi-experiment analysis to identify constitutive QTLs and candidate genes associated with the grain Mn concentration. Hence, the approach should be advantageous to facilitate genomic breeding programmes in rice and other crops considering QTLs and genes associated with complex traits in natural populations.
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Affiliation(s)
- Panthita Ruang-Areerate
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK. .,National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Anthony J Travis
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Shannon R M Pinson
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, 72160, USA
| | - Lee Tarpley
- Texas A&M System AgriLife Research Center, Beaumont, TX, 77713, USA
| | - Georgia C Eizenga
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, 72160, USA
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Adam H Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Gareth J Norton
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
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26
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Reyt G, Chao Z, Flis P, Salas-González I, Castrillo G, Chao DY, Salt DE. Uclacyanin Proteins Are Required for Lignified Nanodomain Formation within Casparian Strips. Curr Biol 2020; 30:4103-4111.e6. [PMID: 32857976 PMCID: PMC7575197 DOI: 10.1016/j.cub.2020.07.095] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/14/2020] [Accepted: 07/28/2020] [Indexed: 01/09/2023]
Abstract
Casparian strips (CSs) are cell wall modifications of vascular plants restricting extracellular free diffusion into and out of the vascular system [1]. This barrier plays a critical role in controlling the acquisition of nutrients and water necessary for normal plant development [2-5]. CSs are formed by the precise deposition of a band of lignin approximately 2 μm wide and 150 nm thick spanning the apoplastic space between adjacent endodermal cells [6, 7]. Here, we identified a copper-containing protein, Uclacyanin1 (UCC1), that is sub-compartmentalized within the CS. UCC1 forms a central CS nanodomain in comparison with other CS-located proteins that are found to be mainly accumulated at the periphery of the CS. We found that loss-of-function of two uclacyanins (UCC1 and UCC2) reduces lignification specifically in this central CS nanodomain, revealing a nano-compartmentalized machinery for lignin polymerization. This loss of lignification leads to increased endodermal permeability and, consequently, to a loss of mineral nutrient homeostasis.
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Affiliation(s)
- Guilhem Reyt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Zhenfei Chao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Paulina Flis
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Isai Salas-González
- Curriculum in Bioinformatics and Computational Biology, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriel Castrillo
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences, 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
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK.
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27
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Houston K, Qiu J, Wege S, Hrmova M, Oakey H, Qu Y, Smith P, Situmorang A, Macaulay M, Flis P, Bayer M, Roy S, Halpin C, Russell J, Schreiber M, Byrt C, Gilliham M, Salt DE, Waugh R. Barley sodium content is regulated by natural variants of the Na + transporter HvHKT1;5. Commun Biol 2020; 3:258. [PMID: 32444849 PMCID: PMC7244711 DOI: 10.1038/s42003-020-0990-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/28/2020] [Indexed: 12/04/2022] Open
Abstract
During plant growth, sodium (Na+) in the soil is transported via the xylem from the root to the shoot. While excess Na+ is toxic to most plants, non-toxic concentrations have been shown to improve crop yields under certain conditions, such as when soil K+ is low. We quantified grain Na+ across a barley genome-wide association study panel grown under non-saline conditions and identified variants of a Class 1 HIGH-AFFINITY-POTASSIUM-TRANSPORTER (HvHKT1;5)-encoding gene responsible for Na+ content variation under these conditions. A leucine to proline substitution at position 189 (L189P) in HvHKT1;5 disturbs its characteristic plasma membrane localisation and disrupts Na+ transport. Under low and moderate soil Na+, genotypes containing HvHKT1:5P189 accumulate high concentrations of Na+ but exhibit no evidence of toxicity. As the frequency of HvHKT1:5P189 increases significantly in cultivated European germplasm, we cautiously speculate that this non-functional variant may enhance yield potential in non-saline environments, possibly by offsetting limitations of low available K+.
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Affiliation(s)
- Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Jiaen Qiu
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Stefanie Wege
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Maria Hrmova
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Life Science, Huaiyin Normal University, 223300, Huaian, China
| | - Helena Oakey
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Yue Qu
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Pauline Smith
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Micha Bayer
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Stuart Roy
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot Dry Climate, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Claire Halpin
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Caitlin Byrt
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- Research School of Biology, 46 Sullivans Creek Road, The Australian National University, Canberra, ACT, 2601, Australia
| | - Matt Gilliham
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK.
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK.
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28
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Chen J, Huang XY, Salt DE, Zhao FJ. Mutation in OsCADT1 enhances cadmium tolerance and enriches selenium in rice grain. New Phytol 2020; 226:838-850. [PMID: 31879959 DOI: 10.1111/nph.16404] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/18/2019] [Indexed: 05/27/2023]
Abstract
How cadmium (Cd) tolerance in rice is regulated remains poorly understood. We used a forward genetic approach to investigate Cd tolerance in rice. Using a root elongation assay, we isolated a rice mutant with enhanced Cd tolerance, cadt1, from an ethyl methanesulphonate (EMS)-mutagenized population of a widely grown Indica cultivar. The mutant accumulated more Cd in roots but not in shoots and grains. Using genomic resequencing and complementation, we identified OsCADT1 as the causal gene for the mutant phenotype, which encodes a putative serine hydroxymethyltransferase. OsCADT1 protein was localized to the nucleus and the OsCADT1 gene was expressed in both roots and shoots. OsCADT1 mutation resulted in higher sulphur and selenium accumulation in the shoots and grains. Selenate influx in cadt1 was 2.4 times that of the wild-type. The mutant showed higher expression of the sulphate/selenate transporter gene OsSULTR1;1 and the sulphur-deficiency-inducible gene OsSDI1. Thiol compounds including cysteine, glutathione and phytochelatins were significantly increased in the mutant, underlying its increased Cd tolerance. Growth and grain biomass were little affected. The results suggest that OsCADT1 acts as a negative regulator of sulphate/selenate uptake and assimilation. OsCADT1 mutation increases Cd tolerance and enriches selenium in rice grains, providing a novel solution for selenium biofortification.
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Affiliation(s)
- Jie Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Pita-Barbosa A, Ricachenevsky FK, Wilson M, Dottorini T, Salt DE. Transcriptional plasticity buffers genetic variation in zinc homeostasis. Sci Rep 2019; 9:19482. [PMID: 31862901 PMCID: PMC6925235 DOI: 10.1038/s41598-019-55736-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/02/2019] [Indexed: 11/08/2022] Open
Abstract
In roots of Arabidopsis thaliana, Zn can be either loaded into the xylem for translocation to the shoot or stored in vacuoles. Vacuolar storage is achieved through the action of the Zn/Cd transporter HMA3 (Heavy Metal Atpase 3). The Col-0 accession has an HMA3 loss-of-function allele resulting in high shoot Cd, when compared to accession CSHL-5 which has a functional allele and low shoot Cd. Interestingly, both Col-0 and CSHL-5 have similar shoot Zn concentrations. We hypothesize that plants sense changes in cytosolic Zn that are due to variation in HMA3 function, and respond by altering expression of genes related to Zn uptake, transport and compartmentalisation, in order to maintain Zn homeostasis. The expression level of genes known to be involved in Zn homeostasis were quantified in both wild-type Col-0 and Col-0::HMA3CSHL-5 plants transformed with the functional CSHL-5 allele of HMA3. We observed significant positive correlations between expression of HMA3 and of genes known to be involved in Zn homeostasis, including ZIP3, ZIP4, MTP1, and bZIP19. The results support our hypothesis that alteration in the level of function of HMA3 is counterbalanced by the fine regulation of the Zn homeostasis gene network in roots of A. thaliana.
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Affiliation(s)
- Alice Pita-Barbosa
- Center for Coastal, Limnology and Marine Studies, Federal University of Rio Grande do Sul, Litoral Norte Campus, Imbé, RS, 95625-000, Brazil
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Felipe K Ricachenevsky
- Biology Department, Center of Natural and Exact Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Michael Wilson
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.
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Zhang L, Wu J, Tang Z, Huang XY, Wang X, Salt DE, Zhao FJ. Variation in the BrHMA3 coding region controls natural variation in cadmium accumulation in Brassica rapa vegetables. J Exp Bot 2019; 70:5865-5878. [PMID: 31367770 PMCID: PMC6812716 DOI: 10.1093/jxb/erz310] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/22/2019] [Indexed: 05/18/2023]
Abstract
Brassica rapa includes several important leafy vegetable crops with the potential for high cadmium (Cd) accumulation, posing a risk to human health. This study aims to understand the genetic basis underlying the variation in Cd accumulation among B. rapa vegetables. Cd uptake and translocation in 64 B. rapa accessions were compared. The role of the heavy metal ATPase gene BrHMA3 in the variation of Cd accumulation was investigated. BrHMA3 encodes a tonoplast-localized Cd transporter. Five full-length and four truncated haplotypes of the BrHMA3 coding sequence were identified, explaining >80% of the variation in the Cd root to shoot translocation among the 64 accessions and in F2 progeny. Truncated BrHMA3 haplotypes had a 2.3 and 9.3 times higher shoot Cd concentration and Cd translocation ratio, respectively, than full-length haplotypes. When expressed in yeast and Arabidopsis thaliana, full-length BrHMA3 showed activity consistent with a Cd transport function, whereas truncated BrHMA3 did not. Variation in the BrHMA3 promoter sequence had little effect on Cd translocation. Variation in the BrHMA3 coding sequence is a key determinant of Cd translocation to and accumulation in the leaves of B. rapa. Strong alleles of BrHMA3 can be used to breed for B. rapa vegetables that are low in Cd in their edible portions.
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Affiliation(s)
- Lingxiao Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - David E Salt
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Loughborough, UK
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Correspondence:
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31
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Chen A, Husted S, Salt DE, Schjoerring JK, Persson DP. The Intensity of Manganese Deficiency Strongly Affects Root Endodermal Suberization and Ion Homeostasis. Plant Physiol 2019; 181:729-742. [PMID: 31399491 PMCID: PMC6776859 DOI: 10.1104/pp.19.00507] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/02/2019] [Indexed: 05/06/2023]
Abstract
Manganese (Mn) deficiency affects various processes in plant shoots. However, the functions of Mn in roots and the processes involved in root adaptation to Mn deficiency are largely unresolved. Here, we show that the suberization of endodermal cells in barley (Hordeum vulgare) roots is altered in response to Mn deficiency, and that the intensity of Mn deficiency ultimately determines whether suberization increases or decreases. Mild Mn deficiency increased the length of the unsuberized zone close to the root tip, and increased the distance from the root tip at which the fully suberized zone developed. By contrast, strong Mn deficiency increased suberization closer to the root tip. Upon Mn resupply, suberization was identical to that seen on Mn-replete plants. Bioimaging and xylem sap analyses suggest that the reduced suberization in mildly Mn-deficient plants promotes radial Mn transport across the endodermis at a greater distance from the root tip. Less suberin also favors the inwards radial transport of calcium and sodium, but negatively affects the potassium concentration in the stele. During strong Mn deficiency, Mn uptake was directed toward the root tip. Enhanced suberization provides a mechanism to prevent absorbed Mn from leaking out of the stele. With more suberin, the inward radial transport of calcium and sodium decreases, whereas that of potassium increases. We conclude that changes in suberization in response to the intensity of Mn deficiency have a strong effect on root ion homeostasis and ion translocation.
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Affiliation(s)
- Anle Chen
- Department of Plant and Environmental Sciences & Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Søren Husted
- Department of Plant and Environmental Sciences & Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham LE12 5RD, United Kingdom
| | - Jan K Schjoerring
- Department of Plant and Environmental Sciences & Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Daniel Pergament Persson
- Department of Plant and Environmental Sciences & Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
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Huang XY, Li M, Luo R, Zhao FJ, Salt DE. Epigenetic regulation of sulfur homeostasis in plants. J Exp Bot 2019; 70:4171-4182. [PMID: 31087073 DOI: 10.1093/jxb/erz218] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/30/2019] [Indexed: 05/21/2023]
Abstract
Plants have evolved sophisticated mechanisms for adaptation to fluctuating availability of nutrients in soil. Such mechanisms are of importance for plants to maintain homeostasis of nutrient elements for their development and growth. The molecular mechanisms controlling the homeostasis of nutrient elements at the genetic level have been gradually revealed, including the identification of regulatory factors and transporters responding to nutrient stresses. Recent studies have suggested that such responses are controlled not only by genetic regulation but also by epigenetic regulation. In this review, we present recent studies on the involvement of DNA methylation, histone modifications, and non-coding RNA-mediated gene silencing in the regulation of sulfur homeostasis and the response to sulfur deficiency. We also discuss the potential effect of sulfur-containing metabolites such as S-adenosylmethionine on the maintenance of DNA and histone methylation.
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Affiliation(s)
- Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengzhen Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Rongjian Luo
- 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
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
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Terés J, Busoms S, Martín LP, Luís-Villarroya A, Flis P, Álvarez-Fernández A, Tolrà R, Salt DE, Poschenrieder C. Soil carbonate drives local adaptation in Arabidopsis thaliana. Plant Cell Environ 2019; 42:2384-2398. [PMID: 31018012 PMCID: PMC6663613 DOI: 10.1111/pce.13567] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 05/22/2023]
Abstract
High soil carbonate limits crop performance especially in semiarid or arid climates. To understand how plants adapt to such soils, we explored natural variation in tolerance to soil carbonate in small local populations (demes) of Arabidopsis thaliana growing on soils differing in carbonate content. Reciprocal field-based transplants on soils with elevated carbonate (+C) and without carbonate (-C) over several years revealed that demes native to (+C) soils showed higher fitness than those native to (-C) soils when both were grown together on carbonate-rich soil. This supports the role of soil carbonate as a driving factor for local adaptation. Analyses of contrasting demes revealed key mechanisms associated with these fitness differences. Under controlled conditions, plants from the tolerant deme A1(+C) native to (+C) soil were more resistant to both elevated carbonate and iron deficiency than plants from the sensitive T6(-C) deme native to (-C) soil. Resistance of A1(+C) to elevated carbonate was associated with higher root extrusion of both protons and coumarin-type phenolics. Tolerant A1(+C) also had better Ca-exclusion than sensitive T6(-C) . We conclude that Arabidopsis demes are locally adapted in their native habitat to soils with moderately elevated carbonate. This adaptation is associated with both enhanced iron acquisition and calcium exclusion.
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Affiliation(s)
- Joana Terés
- Plant Physiology Lab, Bioscience Faculty, Universidad Autónoma de Barcelona
| | | | - Laura Perez Martín
- Plant Physiology Lab, Bioscience Faculty, Universidad Autónoma de Barcelona
| | | | - Paulina Flis
- Future Food Beacon of Excellence & the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | | | - Roser Tolrà
- Plant Physiology Lab, Bioscience Faculty, Universidad Autónoma de Barcelona
| | - David E Salt
- Future Food Beacon of Excellence & the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
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Huang XY, Liu H, Zhu YF, Pinson SRM, Lin HX, Guerinot ML, Zhao FJ, Salt DE. Natural variation in a molybdate transporter controls grain molybdenum concentration in rice. New Phytol 2019; 221:1983-1997. [PMID: 30339276 DOI: 10.1111/nph.15546] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/07/2018] [Indexed: 05/07/2023]
Abstract
Molybdenum (Mo) is an essential micronutrient for most living organisms, including humans. Cereals such as rice (Oryza sativa) are the major dietary source of Mo. However, little is known about the genetic basis of the variation in Mo content in rice grain. We mapped a quantitative trait locus (QTL) qGMo8 that controls Mo accumulation in rice grain by using a recombinant inbred line population and a backcross introgression line population. We identified a molybdate transporter, OsMOT1;1, as the causal gene for this QTL. OsMOT1;1 exhibits transport activity for molybdate, but not sulfate, when heterogeneously expressed in yeast cells. OsMOT1;1 is mainly expressed in roots and is involved in the uptake and translocation of molybdate under molybdate-limited condition. Knockdown of OsMOT1;1 results in less Mo being translocated to shoots, lower Mo concentration in grains and higher sensitivity to Mo deficiency. We reveal that the natural variation of Mo concentration in rice grains is attributed to the variable expression of OsMOT1;1 due to sequence variation in its promoter. Identification of natural allelic variation in OsMOT1;1 may facilitate the development of rice varieties with Mo-enriched grain for dietary needs and improve Mo nutrition of rice on Mo-deficient soils.
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Affiliation(s)
- Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu-Fei Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shannon R M Pinson
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, 72160, USA
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - David E Salt
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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Yang M, Lu K, Zhao FJ, Xie W, Ramakrishna P, Wang G, Du Q, Liang L, Sun C, Zhao H, Zhang Z, Liu Z, Tian J, Huang XY, Wang W, Dong H, Hu J, Ming L, Xing Y, Wang G, Xiao J, Salt DE, Lian X. Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice. Plant Cell 2018; 30:2720-2740. [PMID: 30373760 PMCID: PMC6305983 DOI: 10.1105/tpc.18.00375] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.
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Affiliation(s)
- Meng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Lu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan 430415, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Priya Ramakrishna
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Guangyuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Du
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Limin Liang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Cuiju Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zonghao Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wensheng Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Huaxia Dong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jintao Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Luchang Ming
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinhua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - David E Salt
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Xingming Lian
- 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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Duan F, Giehl RFH, Geldner N, Salt DE, von Wirén N. Root zone-specific localization of AMTs determines ammonium transport pathways and nitrogen allocation to shoots. PLoS Biol 2018; 16:e2006024. [PMID: 30356235 PMCID: PMC6218093 DOI: 10.1371/journal.pbio.2006024] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 11/05/2018] [Accepted: 10/02/2018] [Indexed: 01/22/2023] Open
Abstract
In plants, nutrient provision of shoots depends on the uptake and transport of nutrients across the root tissue to the vascular system. Nutrient delivery to the vasculature is mediated via the apoplastic transport pathway (ATP), which uses the free space in the cell walls and is controlled by apoplastic barriers and nutrient transporters at the endodermis, or via the symplastic transport pathway (STP). However, the relative importance of these transport routes remains elusive. Here, we show that the STP, mediated by the epidermal ammonium transporter 1;3 (AMT1;3), dominates the radial movement of ammonium across the root tissue when external ammonium is low, whereas apoplastic transport controlled by AMT1;2 at the endodermis prevails at high external ammonium. Then, AMT1;2 favors nitrogen (N) allocation to the shoot, revealing a major importance of the ATP for nutrient partitioning to shoots. When an endodermal bypass was introduced by abolishing Casparian strip (CS) formation, apoplastic ammonium transport decreased. By contrast, symplastic transport was increased, indicating synergism between the STP and the endodermal bypass. We further establish that the formation of apoplastic barriers alters the cell type–specific localization of AMTs and determines STP and ATP contributions. These results show how radial transport pathways vary along the longitudinal gradient of the root axis and contribute to nutrient partitioning between roots and shoots. Radial transport of nutrients from the soil to the vascular system of plant roots occurs via the symplastic transport pathway (STP) and apoplastic transport pathway (ATP). Nutrients move along the STP when crossing the plasma membrane of outer cells and moving to xylem through the cytoplasmic continuum formed by plasmodesmata. Nutrients following the ATP, in turn, initially move passively through the extracellular space but are eventually taken up by endodermal cells, in which Casparian strips (CSs) prevent further apoplastic movement. We assessed the contribution of these transport pathways to radial transport in roots and nutrient provision to shoots by expressing cell type–specific ammonium transporters in a CS-defective mutant. Our study reveals that i) symplastic transport is more efficient at low external ammonium supply; ii) when endodermal cells become sealed by the deposition of suberin lamellae, the expression of ammonium transporters shifts to cortical cells; and iii) apoplastic transport depends on a functional apoplastic barrier at the endodermis, favoring nitrogen (N) partitioning to shoots at high external ammonium.
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Affiliation(s)
- Fengying Duan
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr, Gatersleben, Germany
| | - Ricardo F. H. Giehl
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr, Gatersleben, Germany
| | - Niko Geldner
- Department of Plant Molecular Biology, Biophore, UNIL-Sorge, University of Lausanne, Lausanne, Switzerland
| | - David E. Salt
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr, Gatersleben, Germany
- * E-mail:
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wang C, Na G, Bermejo ES, Chen Y, Banks JA, Salt DE, Zhao FJ. Dissecting the components controlling root-to-shoot arsenic translocation in Arabidopsis thaliana. New Phytol 2018; 217:206-218. [PMID: 28857170 PMCID: PMC6260828 DOI: 10.1111/nph.14761] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/26/2017] [Indexed: 05/25/2023]
Abstract
Arsenic (As) is an important environmental and food-chain toxin. We investigated the key components controlling As accumulation and tolerance in Arabidopsis thaliana. We tested the effects of different combinations of gene knockout, including arsenate reductase (HAC1), γ-glutamyl-cysteine synthetase (γ-ECS), phytochelatin synthase (PCS1) and phosphate effluxer (PHO1), and the heterologous expression of the As-hyperaccumulator Pteris vittata arsenite efflux (PvACR3), on As tolerance, accumulation, translocation and speciation in A. thaliana. Heterologous expression of PvACR3 markedly increased As tolerance and root-to-shoot As translocation in A. thaliana, with PvACR3 being localized to the plasma membrane. Combining PvACR3 expression with HAC1 mutation led to As hyperaccumulation in the shoots, whereas combining HAC1 and PHO1 mutation decreased As accumulation. Mutants of γ-ECS and PCS1 were hypersensitive to As and had higher root-to-shoot As translocation. Combining γ-ECS or PCS1 with HAC1 mutation did not alter As tolerance or accumulation beyond the levels observed in the single mutants. PvACR3 and HAC1 have large effects on root-to-shoot As translocation. Arsenic hyperaccumulation can be engineered in A. thaliana by knocking out the HAC1 gene and expressing PvACR3. PvACR3 and HAC1 also affect As tolerance, but not to the extent of γ-ECS and PCS1.
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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 210095, China
| | - GunNam Na
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Eduardo Sanchez Bermejo
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Yi Chen
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - David E. Salt
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Ricachenevsky FK, Punshon T, Lee S, Oliveira BHN, Trenz TS, Maraschin FDS, Hindt MN, Danku J, Salt DE, Fett JP, Guerinot ML. Elemental Profiling of Rice FOX Lines Leads to Characterization of a New Zn Plasma Membrane Transporter, OsZIP7. Front Plant Sci 2018; 9:865. [PMID: 30018622 PMCID: PMC6037872 DOI: 10.3389/fpls.2018.00865] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/04/2018] [Indexed: 05/07/2023]
Abstract
Iron (Fe) and zinc (Zn) are essential micronutrients required for proper development in both humans and plants. Rice (Oryza sativa L.) grains are the staple food for nearly half of the world's population, but a poor source of metals such as Fe and Zn. Populations that rely on milled cereals are especially prone to Fe and Zn deficiencies, the most prevalent nutritional deficiencies in humans. Biofortification is a cost-effective solution for improvement of the nutritional quality of crops. However, a better understanding of the mechanisms underlying grain accumulation of mineral nutrients is required before this approach can achieve its full potential. Characterization of gene function is more time-consuming in crops than in model species such as Arabidopsis thaliana. Aiming to more quickly characterize rice genes related to metal homeostasis, we applied the concept of high throughput elemental profiling (ionomics) to Arabidopsis lines heterologously expressing rice cDNAs driven by the 35S promoter, named FOX (Full Length Over-eXpressor) lines. We screened lines expressing candidate genes that could be used in the development of biofortified grain. Among the most promising candidates, we identified two lines ovexpressing the metal cation transporter OsZIP7. OsZIP7 expression in Arabidopsis resulted in a 25% increase in shoot Zn concentrations compared to non-transformed plants. We further characterized OsZIP7 and showed that it is localized to the plasma membrane and is able to complement Zn transport defective (but not Fe defective) yeast mutants. Interestingly, we showed that OsZIP7 does not transport Cd, which is commonly transported by ZIP proteins. Importantly, OsZIP7-expressing lines have increased Zn concentrations in their seeds. Our results indicate that OsZIP7 is a good candidate for developing Zn biofortified rice. Moreover, we showed the use of heterologous expression of genes from crops in A. thaliana as a fast method for characterization of crop genes related to the ionome and potentially useful in biofortification strategies.
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Affiliation(s)
- Felipe K. Ricachenevsky
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
- *Correspondence: Felipe K. Ricachenevsky,
| | - Tracy Punshon
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Sichul Lee
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, South Korea
| | - Ben Hur N. Oliveira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thomaz S. Trenz
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Maria N. Hindt
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - John Danku
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - David E. Salt
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Janette P. Fett
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
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Gao YQ, Chen JG, Chen ZR, An D, Lv QY, Han ML, Wang YL, Salt DE, Chao DY. A new vesicle trafficking regulator CTL1 plays a crucial role in ion homeostasis. PLoS Biol 2017; 15:e2002978. [PMID: 29284002 PMCID: PMC5746208 DOI: 10.1371/journal.pbio.2002978] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/21/2017] [Indexed: 11/18/2022] Open
Abstract
Ion homeostasis is essential for plant growth and environmental adaptation, and maintaining ion homeostasis requires the precise regulation of various ion transporters, as well as correct root patterning. However, the mechanisms underlying these processes remain largely elusive. Here, we reported that a choline transporter gene, CTL1, controls ionome homeostasis by regulating the secretory trafficking of proteins required for plasmodesmata (PD) development, as well as the transport of some ion transporters. Map-based cloning studies revealed that CTL1 mutations alter the ion profile of Arabidopsis thaliana. We found that the phenotypes associated with these mutations are caused by a combination of PD defects and ion transporter misregulation. We also established that CTL1 is involved in regulating vesicle trafficking and is thus required for the trafficking of proteins essential for ion transport and PD development. Characterizing choline transporter-like 1 (CTL1) as a new regulator of protein sorting may enable researchers to understand not only ion homeostasis in plants but also vesicle trafficking in general. Ion transporters play a key role in mineral nutrients uptake and transport of plants. Their cellular and subcellular localization is essential for fulfilling their functions and are therefore generally fine-tuned. However, the molecular mechanisms underlying this process remain largely unclear. In this study, we analyze the role of the choline transporter CTL1 in A. thaliana and find that it controls dynamic cell trafficking, a fundamental process that plays vital roles in cell signaling, development, and protein sorting. We also show that CTL1 regulates the expression pattern of different ion transporters through the modulation of vesicle trafficking. These results suggest that CTL1 is a new component of the vesicle trafficking machinery that is also required for ion homeostasis, which link these processes and shed light on the underlying molecular mechanisms.
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Affiliation(s)
- Yi-Qun Gao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences 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
| | - Jiu-Geng Chen
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zi-Ru Chen
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences 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
| | - Dong An
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiao-Yan Lv
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences 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
| | - Mei-Ling Han
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences 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, Chinese Academy of Sciences 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
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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Affiliation(s)
- Ian R Henderson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - David E Salt
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, LE12 5RD, United Kingdom
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Affiliation(s)
- David E Salt
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, LE12 5RD, UK
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Hindt MN, Akmakjian GZ, Pivarski KL, Punshon T, Baxter I, Salt DE, Guerinot ML. BRUTUS and its paralogs, BTS LIKE1 and BTS LIKE2, encode important negative regulators of the iron deficiency response in Arabidopsis thaliana. Metallomics 2017; 9:876-890. [PMID: 28620661 PMCID: PMC5558852 DOI: 10.1039/c7mt00152e] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Iron (Fe) is required for plant health, but it can also be toxic when present in excess. Therefore, Fe levels must be tightly controlled. The Arabidopsis thaliana E3 ligase BRUTUS (BTS) is involved in the negative regulation of the Fe deficiency response and we show here that the two A. thaliana BTS paralogs, BTS LIKE1 (BTSL1) and BTS LIKE2 (BTSL2) encode proteins that act redundantly as negative regulators of the Fe deficiency response. Loss of both of these E3 ligases enhances tolerance to Fe deficiency. We further generated a triple mutant with loss of both BTS paralogs and a partial loss of BTS expression that exhibits even greater tolerance to Fe-deficient conditions and increased Fe accumulation without any resulting Fe toxicity effects. Finally, we identified a mutant carrying a novel missense mutation of BTS that exhibits an Fe deficiency response in the root when grown under both Fe-deficient and Fe-sufficient conditions, leading to Fe toxicity when plants are grown under Fe-sufficient conditions.
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Affiliation(s)
- Maria N Hindt
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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Norton GJ, Travis AJ, Danku JMC, Salt DE, Hossain M, Islam MR, Price AH. Biomass and elemental concentrations of 22 rice cultivars grown under alternate wetting and drying conditions at three field sites in Bangladesh. Food Energy Secur 2017; 6:98-112. [PMID: 28979771 PMCID: PMC5599981 DOI: 10.1002/fes3.110] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 11/13/2022] Open
Abstract
As the global population grows, demand on food production will also rise. For rice, one limiting factor effecting production could be availability of fresh water, hence adoption of techniques that decrease water usage while maintaining or increasing crop yield are needed. Alternative wetting and drying (AWD) is one of these techniques. AWD is a method by which the level of water within a rice field cycles between being flooded and nonflooded during the growth period of the rice crop. The degree to which AWD affects cultivars differently has not been adequately addressed to date. In this study, 22 rice cultivars, mostly landraces of the aus subpopulation, plus some popular improved indica cultivars from Bangladesh, were tested for their response to AWD across three different field sites in Bangladesh. Grain and shoot elemental concentrations were determined at harvest. Overall, AWD slightly increased grain mass and harvest index compared to plants grown under continually flooded (CF) conditions. Plants grown under AWD had decreased concentrations of nitrogen in their straw compared to plants grown under CF. The concentration of elements in the grain were also affected when plants were grown under AWD compared to CF: Nickel, copper, cadmium and iron increased, but sodium, potassium, calcium, cobalt, phosphorus, molybdenum and arsenic decreased in the grains of plants grown under AWD. However, there was some variation in these patterns across different sites. Analysis of variance revealed no significant cultivar × treatment interaction, or site × cultivar × treatment interaction, for any of the plant mass traits. Of the elements analyzed, only grain cadmium concentrations were significantly affected by treatment × cultivar interactions. These data suggest that there is no genetic adaptation amongst the cultivars screened for response to AWD, except for grain cadmium concentration and imply that breeding specifically for AWD is not needed.
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Affiliation(s)
- Gareth J Norton
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen AB24 3UU UK
| | - Anthony J Travis
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen AB24 3UU UK
| | - John M C Danku
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen AB24 3UU UK.,Centre for Plant Integrative Biology School of Biosciences University of Nottingham Sutton Bonington Campus Loughborough LE12 5RD UK
| | - David E Salt
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen AB24 3UU UK.,Centre for Plant Integrative Biology School of Biosciences University of Nottingham Sutton Bonington Campus Loughborough LE12 5RD UK
| | - Mahmud Hossain
- Department of Soil Science Bangladesh Agricultural University Mymensingh Bangladesh
| | - Md Rafiqul Islam
- Department of Soil Science Bangladesh Agricultural University Mymensingh Bangladesh
| | - Adam H Price
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen AB24 3UU UK
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Campos ACAL, Kruijer W, Alexander R, Akkers RC, Danku J, Salt DE, Aarts MGM. Natural variation in Arabidopsis thaliana reveals shoot ionome, biomass, and gene expression changes as biomarkers for zinc deficiency tolerance. J Exp Bot 2017; 68:3643-3656. [PMID: 28859376 DOI: 10.1093/jxb/erx191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 05/20/2017] [Indexed: 05/12/2023]
Abstract
Zinc (Zn) is an essential nutrient for plants, with a crucial role as a cofactor for many enzymes. Approximately one-third of the global arable land area is Zn deficient, leading to reduced crop yield and quality. To improve crop tolerance to Zn deficiency, it is important to understand the mechanisms plants have adopted to tolerate suboptimal Zn supply. In this study, physiological and molecular aspects of traits related to Zn deficiency tolerance were examined in a panel of 19 Arabidopsis thaliana accessions. Accessions showed a larger variation for shoot biomass than for Zn concentration, indicating that they have different requirements for their minimal Zn concentration required for growth. Accessions with a higher tolerance to Zn deficiency showed an increased expression of the Zn deficiency-responsive genes ZIP4 and IRT3 in comparison with Zn deficiency-sensitive accessions. Changes in the shoot ionome, as a result of the Zn treatment of the plants, were used to build a multinomial logistic regression model able to distinguish plants regarding their Zn nutritional status. This set of biomarkers, reflecting the A. thaliana response to Zn deficiency and Zn deficiency tolerance, can be useful for future studies aiming to improve the performance and Zn status of crop plants grown under suboptimal Zn concentrations.
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Affiliation(s)
- Ana Carolina A L Campos
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, UK
| | - Willem Kruijer
- Biometris, Wageningen University and Research, PO Box 100, 6700AC Wageningen, The Netherlands
| | - Ross Alexander
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- School of Life Sciences, John Muir Building, Heriot Watt University, Edinburgh EH14 4AS, UK
| | - Robert C Akkers
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - John Danku
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, UK
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, UK
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Kühnlenz T, Hofmann C, Uraguchi S, Schmidt H, Schempp S, Weber M, Lahner B, Salt DE, Clemens S. Phytochelatin Synthesis Promotes Leaf Zn Accumulation of Arabidopsis thaliana Plants Grown in Soil with Adequate Zn Supply and is Essential for Survival on Zn-Contaminated Soil. Plant Cell Physiol 2016; 57:2342-2352. [PMID: 27694524 DOI: 10.1093/pcp/pcw148] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/10/2016] [Indexed: 06/06/2023]
Abstract
Phytochelatin (PC) synthesis is essential for the detoxification of non-essential metals such as cadmium (Cd). In vitro experiments with Arabidopsis thaliana seedlings had indicated a contribution to zinc (Zn) tolerance as well. We addressed the physiological role of PC synthesis in Zn homeostasis of plants under more natural conditions. Growth responses, PC accumulation and leaf ionomes of wild-type and AtPCS1 mutant plants cultivated in different soils representing adequate Zn supply, Zn deficiency and Zn excess were analyzed. Growth on Zn-contaminated soil triggers PC synthesis and is strongly impaired in PC-deficient mutants. In fact, the contribution of AtPCS1 to tolerating Zn excess is comparable with that of the major Zn tolerance factor MTP1. For plants supplied with a normal level of Zn, a significant reduction in leaf Zn accumulation of AtPCS1 mutants was detected. In contrast, AtPCS1 mutants grown under Zn-limited conditions showed wild-type levels of Zn accumulation, suggesting the operation of distinct Zn translocation pathways. Contrasting phenotypes of the tested AtPCS1 mutant alleles upon growth in Zn- or Cd-contaminated soil indicated differential activation of PC synthesis by these metals. Experiments with truncated versions identified a part of the AtPCS1 protein required for the activation by Zn but not by Cd.
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Affiliation(s)
- Tanja Kühnlenz
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, D-95440 Bayreuth, Germany
| | - Christian Hofmann
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, D-95440 Bayreuth, Germany
| | - Shimpei Uraguchi
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, D-95440 Bayreuth, Germany
- Present address: Department of Public Health, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Holger Schmidt
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, D-95440 Bayreuth, Germany
| | - Stefanie Schempp
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, D-95440 Bayreuth, Germany
| | - Michael Weber
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, D-95440 Bayreuth, Germany
| | - Brett Lahner
- Purdue University, Horticulture and Landscape Architecture, West Lafayette, IN, USA
| | - David E Salt
- Purdue University, Horticulture and Landscape Architecture, West Lafayette, IN, USA
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, D-95440 Bayreuth, Germany stephan.clemens@uni-bayreuth
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Shi S, Wang T, Chen Z, Tang Z, Wu Z, Salt DE, Chao DY, Zhao FJ. OsHAC1;1 and OsHAC1;2 Function as Arsenate Reductases and Regulate Arsenic Accumulation. Plant Physiol 2016; 172:1708-1719. [PMID: 27702843 PMCID: PMC5100750 DOI: 10.1104/pp.16.01332] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/01/2016] [Indexed: 05/18/2023]
Abstract
Rice is a major dietary source of the toxic metalloid arsenic (As). Reducing its accumulation in rice (Oryza sativa) grain is of critical importance to food safety. Rice roots take up arsenate and arsenite depending on the prevailing soil conditions. The first step of arsenate detoxification is its reduction to arsenite, but the enzyme(s) catalyzing this reaction in rice remains unknown. Here, we identify OsHAC1;1 and OsHAC1;2 as arsenate reductases in rice. OsHAC1;1 and OsHAC1;2 are able to complement an Escherichia coli mutant lacking the endogenous arsenate reductase and to reduce arsenate to arsenite. OsHAC1:1 and OsHAC1;2 are predominantly expressed in roots, with OsHAC1;1 being abundant in the epidermis, root hairs, and pericycle cells while OsHAC1;2 is abundant in the epidermis, outer layers of cortex, and endodermis cells. Expression of the two genes was induced by arsenate exposure. Knocking out OsHAC1;1 or OsHAC1;2 decreased the reduction of arsenate to arsenite in roots, reducing arsenite efflux to the external medium. Loss of arsenite efflux was also associated with increased As accumulation in shoots. Greater effects were observed in a double mutant of the two genes. In contrast, overexpression of either OsHAC1;1 or OsHAC1;2 increased arsenite efflux, reduced As accumulation, and enhanced arsenate tolerance. When grown under aerobic soil conditions, overexpression of either OsHAC1;1 or OsHAC1;2 also decreased As accumulation in rice grain, whereas grain As increased in the knockout mutants. We conclude that OsHAC1;1 and OsHAC1;2 are arsenate reductases that play an important role in restricting As accumulation in rice shoots and grain.
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Affiliation(s)
- Shulin Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China (S.S., Z.T., F.-J.Z.)
- 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, 200032, China (T.W., Z.C., D.-Y.C.)
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China (Z.W.)
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom (D.E.S.); and
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (F.-J.Z.)
| | - Tao Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China (S.S., Z.T., F.-J.Z.)
- 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, 200032, China (T.W., Z.C., D.-Y.C.)
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China (Z.W.)
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom (D.E.S.); and
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (F.-J.Z.)
| | - Ziru Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China (S.S., Z.T., F.-J.Z.)
- 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, 200032, China (T.W., Z.C., D.-Y.C.)
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China (Z.W.)
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom (D.E.S.); and
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (F.-J.Z.)
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China (S.S., Z.T., F.-J.Z.)
- 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, 200032, China (T.W., Z.C., D.-Y.C.)
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China (Z.W.)
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom (D.E.S.); and
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (F.-J.Z.)
| | - Zhongchang Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China (S.S., Z.T., F.-J.Z.)
- 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, 200032, China (T.W., Z.C., D.-Y.C.)
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China (Z.W.)
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom (D.E.S.); and
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (F.-J.Z.)
| | - David E Salt
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China (S.S., Z.T., F.-J.Z.)
- 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, 200032, China (T.W., Z.C., D.-Y.C.)
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China (Z.W.)
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom (D.E.S.); and
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (F.-J.Z.)
| | - Dai-Yin Chao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China (S.S., Z.T., F.-J.Z.);
- 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, 200032, China (T.W., Z.C., D.-Y.C.);
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China (Z.W.);
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom (D.E.S.); and
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (F.-J.Z.)
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China (S.S., Z.T., F.-J.Z.);
- 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, 200032, China (T.W., Z.C., D.-Y.C.);
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China (Z.W.);
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom (D.E.S.); and
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (F.-J.Z.)
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Persson DP, Chen A, Aarts MGM, Salt DE, Schjoerring JK, Husted S. Multi-Element Bioimaging of Arabidopsis thaliana Roots. Plant Physiol 2016; 172:835-847. [PMID: 27566167 PMCID: PMC5047091 DOI: 10.1104/pp.16.00770] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/24/2016] [Indexed: 05/06/2023]
Abstract
Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using conventional protocols for microscopy, we observed that diffusible ions such as potassium and sodium were lost during sample dehydration. Thus, we developed a protocol that preserves ions in their native, cellular environment. Briefly, fresh roots are encapsulated in paraffin, cryo-sectioned, and freeze dried. Samples are finally analyzed by laser ablation-inductively coupled plasma-mass spectrometry, utilizing a specially designed internal standard procedure. The method can be further developed to maintain the native composition of proteins, enzymes, RNA, and DNA, making it attractive in combination with other omics techniques. To demonstrate the potential of the method, we analyzed a mutant of Arabidopsis unable to synthesize the metal chelator nicotianamine. The mutant accumulated substantially more zinc and manganese than the wild type in the tissues surrounding the vascular cylinder. For iron, the images looked completely different, with iron bound mainly in the epidermis of the wild-type plants but confined to the cortical cell walls of the mutant. The method offers the power of inductively coupled plasma-mass spectrometry to be fully employed, thereby providing a basis for detailed studies of ion transport in roots. Being applicable to Arabidopsis, the molecular and genetic approaches available in this system can now be fully exploited in order to gain a better mechanistic understanding of these processes.
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Affiliation(s)
- Daniel Pergament Persson
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (D.P.P., A.C., J.K.S., S.H.);Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands (M.G.M.A.); andCentre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom (D.E.S.)
| | - Anle Chen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (D.P.P., A.C., J.K.S., S.H.);Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands (M.G.M.A.); andCentre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom (D.E.S.)
| | - Mark G M Aarts
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (D.P.P., A.C., J.K.S., S.H.);Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands (M.G.M.A.); andCentre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom (D.E.S.)
| | - David E Salt
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (D.P.P., A.C., J.K.S., S.H.);Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands (M.G.M.A.); andCentre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom (D.E.S.)
| | - Jan K Schjoerring
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (D.P.P., A.C., J.K.S., S.H.);Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands (M.G.M.A.); andCentre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom (D.E.S.)
| | - Søren Husted
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (D.P.P., A.C., J.K.S., S.H.);Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands (M.G.M.A.); andCentre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom (D.E.S.)
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49
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Huang XY, Chao DY, Koprivova A, Danku J, Wirtz M, Müller S, Sandoval FJ, Bauwe H, Roje S, Dilkes B, Hell R, Kopriva S, Salt DE. Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006298. [PMID: 27622452 PMCID: PMC5021336 DOI: 10.1371/journal.pgen.1006298] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/12/2016] [Indexed: 12/25/2022] Open
Abstract
Sulphur (S) is an essential element for all living organisms. The uptake, assimilation and metabolism of S in plants are well studied. However, the regulation of S homeostasis remains largely unknown. Here, we report on the identification and characterisation of the more sulphur accumulation1 (msa1-1) mutant. The MSA1 protein is localized to the nucleus and is required for both S-adenosylmethionine (SAM) production and DNA methylation. Loss of function of the nuclear localised MSA1 leads to a reduction in SAM in roots and a strong S-deficiency response even at ample S supply, causing an over-accumulation of sulphate, sulphite, cysteine and glutathione. Supplementation with SAM suppresses this high S phenotype. Furthermore, mutation of MSA1 affects genome-wide DNA methylation, including the methylation of S-deficiency responsive genes. Elevated S accumulation in msa1-1 requires the increased expression of the sulphate transporter genes SULTR1;1 and SULTR1;2 which are also differentially methylated in msa1-1. Our results suggest a novel function for MSA1 in the nucleus in regulating SAM biosynthesis and maintaining S homeostasis epigenetically via DNA methylation. Sulphur is an essential element for all living organisms including plants. Plants take up sulphur from the soil mainly in the form of inorganic sulphate. The uptake of sulphate and assimilation of sulphur have been well studied. However, the regulation of sulphur accumulation in plants remains largely unknown. In this study, we characterize the high leaf sulphur mutant more sulphur accumulation1 (msa1-1) and demonstrate the function of MSA1 in controlling sulphur accumulation in Arabidopsis thaliana. The MSA1 protein is localized to the nucleus and is required for the biosynthesis of S-adenosylmethionine (SAM) which is a universal methyl donor for many methylation reactions, including DNA methylation. Loss of function of MSA1 reduces the SAM level in roots and affects genome-wide DNA methylation, including the methylation of sulphate transporter genes. We show that the high sulphur phenotype of msa1-1 requires elevated expression of the sulphate transporter genes which are differentially methylated in msa1-1. Our results suggest a connection between sulphur homeostasis and DNA methylation that is mediated by MSA1.
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Affiliation(s)
- Xin-Yuan Huang
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Dai-Yin Chao
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - John Danku
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Steffen Müller
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Francisco J. Sandoval
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Hermann Bauwe
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Brian Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Rüdiger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
- * E-mail:
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50
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Yan J, Wang P, Wang P, Yang M, Lian X, Tang Z, Huang CF, Salt DE, Zhao FJ. A loss-of-function allele of OsHMA3 associated with high cadmium accumulation in shoots and grain of Japonica rice cultivars. Plant Cell Environ 2016; 39:1941-54. [PMID: 27038090 DOI: 10.1111/pce.12747] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/20/2016] [Accepted: 03/24/2016] [Indexed: 05/21/2023]
Abstract
Excessive cadmium (Cd) accumulation in rice poses a risk to food safety. OsHMA3 plays an important role in restricting Cd translocation from roots to shoots. A non-functional allele of OsHMA3 has been reported in some Indica rice cultivars with high Cd accumulation, but it is not known if OsHMA3 allelic variation is associated with Cd accumulation in Japonica cultivars. In this study, we identified a Japonica cultivar with consistently high Cd accumulation in shoots and grain in both field and greenhouse experiments. The cultivar possesses an OsHMA3 allele with a predicted amino acid mutation at the 380(th) position from Ser to Arg. The haplotype had no Cd transport activity when the gene was expressed in yeast, and the allele did not complement a known nonfunctional allele of OsHMA3 in F1 test. The allele is present only in temperate Japonica cultivars among diversity panels of 1483 rice cultivars. Different cultivars possessing this allele showed greatly increased root-to-shoot Cd translocation and a shift in root Cd speciation from Cd-S to Cd-O bonding determined by synchrotron X-ray absorption spectroscopy. Our study has identified a new loss-of-function allele of OsHMA3 in Japonica rice cultivars leading to high Cd accumulation in shoots and grain.
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Affiliation(s)
- Jiali Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peitong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Meng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao-Feng Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, UK
| | - Fang Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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