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Rodrigues WFC, Lisboa ABP, Lima JE, Ricachenevsky FK, Del-Bem LE. Ferrous iron uptake via IRT1/ZIP evolved at least twice in green plants. THE NEW PHYTOLOGIST 2023; 237:1951-1961. [PMID: 36626937 DOI: 10.1111/nph.18661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Iron (Fe) is essential for virtually all organisms, being irreplaceable because of its electrochemical properties that enable many biochemical processes, including photosynthesis. Besides its abundance, Fe is generally found in the poorly soluble form of ferric iron (Fe3+ ), while most plants uptake the soluble form Fe2+ . The model angiosperm Arabidopsis thaliana, for example, captures Fe through a mechanism that lowers rhizosphere pH through proton pumping that increases Fe3+ solubility, which is then reduced by a membrane-bound reductase and transported into the cell by the zinc-regulated, iron-regulated transporter-like protein (ZIP) family protein AtIRT1. ZIP proteins are transmembrane transporters of divalent metals such as Fe2+ , Zn2+ , Mn2+ , and Cd2+ . In this work, we investigated the evolution of functional homologs of IRON-REGULATED TRANSPORTER 1/ZIP in the supergroup Archaeplastida (Viridiplantae + Rhodophyta + Glaucophyta) using 51 genomes of diverse lineages. Our analyses suggest that Fe is acquired through deeply divergent ZIP proteins in land plants and chlorophyte green algae, indicating that Fe2+ uptake by ZIP proteins evolved independently at least twice throughout green plant evolution. Our results indicate that the archetypical IRON-REGULATED TRANSPORTER (IRT) proteins from angiosperms likely emerged before the origin of land plants during early streptophyte algae terrestrialization, a process that required the evolution of Fe acquisition in terrestrial subaerial settings.
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Affiliation(s)
- Wenderson Felipe Costa Rodrigues
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), 31270-901, Belo Horizonte, Brazil
- Graduate Program in Plant Biology, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), 31270-901, Belo Horizonte, Brazil
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), 31270-901, Belo Horizonte, Brazil
| | - Ayrton Breno P Lisboa
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), 31270-901, Belo Horizonte, Brazil
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), 31270-901, Belo Horizonte, Brazil
| | - Joni Esrom Lima
- Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), 31270-901, Belo Horizonte, Brazil
| | - Felipe Klein Ricachenevsky
- Department of Botany, Institute of Biosciences (IB), Federal University of Rio Grande do Sul (UFRGS), 91501-900, Porto Alegre, Brazil
- Graduate Program in Cellular and Molecular Biology, Center for Biotechnology, Federal University of Rio Grande do Sul (UFRGS), 91501-900, Porto Alegre, Brazil
| | - Luiz-Eduardo Del-Bem
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), 31270-901, Belo Horizonte, Brazil
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), 31270-901, Belo Horizonte, Brazil
- Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), 31270-901, Belo Horizonte, Brazil
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
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Gu TY, Qi ZA, Chen SY, Yan J, Fang ZJ, Wang JM, Gong JM. Dual-function DEFENSIN 8 mediates phloem cadmium unloading and accumulation in rice grains. PLANT PHYSIOLOGY 2023; 191:515-527. [PMID: 36087013 PMCID: PMC9806624 DOI: 10.1093/plphys/kiac423] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/15/2022] [Indexed: 06/01/2023]
Abstract
Grain cadmium (Cd) is translocated from source to sink tissues exclusively via phloem, though the phloem Cd unloading transporter has not been identified yet. Here, we isolated and functionally characterized a defensin-like gene DEFENSIN 8 (DEF8) highly expressed in rice (Oryza sativa) grains and induced by Cd exposure in seedling roots. Histochemical analysis and subcellular localization detected DEF8 expression preferentially in pericycle cells and phloem of seedling roots, as well as in phloem of grain vasculatures. Further analysis demonstrated that DEF8 is secreted into extracellular spaces possibly by vesicle trafficking. DEF8 bound to Cd in vitro, and Cd efflux from protoplasts as well as loading into xylem vessels decreased in the def8 mutant seedlings compared with the wild type. At maturity, significantly less Cd accumulation was observed in the mutant grains. These results suggest that DEF8 is a dual function protein that facilitates Cd loading into xylem and unloading from phloem, thus mediating Cd translocation from roots to shoots and further allocation to grains, representing a phloem Cd unloading regulator. Moreover, essential mineral nutrient accumulation as well as important agronomic traits were not affected in the def8 mutants, suggesting DEF8 is an ideal target for breeding low grain Cd rice.
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Affiliation(s)
| | | | - Si-Ying Chen
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Yan
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Zi-Jun Fang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun-Min Wang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Liu B, Yu H, Yang Q, Ding L, Sun F, Qu J, Feng W, Yang Q, Li W, Fu F. Zinc Transporter ZmLAZ1-4 Modulates Zinc Homeostasis on Plasma and Vacuolar Membrane in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:881055. [PMID: 35586216 PMCID: PMC9108671 DOI: 10.3389/fpls.2022.881055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Zinc is an essential micronutrient for plant growth and development, and functions as a cofactor for hundreds of transcription factors and enzymes in numerous biological processes. Zinc deficiency is common abiotic stress resulting in yield loss and quality deterioration of crops, but zinc excess causes toxicity for biological systems. In plants, zinc homeostasis is tightly modulated by zinc transporters and binding compounds that uptake/release, transport, localize, and store zinc, as well as their upstream regulators. Lazarus 1 (LAZ1), a member of DUF300 protein family, functions as transmembrane organic solute transporter in vertebrates. However, the function of LAZ1 in plants is still obscure. In the present study, the ZmLAZ1-4 protein was confirmed to bind to zinc ions by bioinformatic prediction and thermal shift assay. Heterologous expression of ZmLAZ1-4 in the zinc-sensitive yeast mutant, Arabidopsis, and maize significantly facilitated the accumulation of Zn2+ in transgenic lines, respectively. The result of subcellular localization exhibited that ZmLAZ1-4 was localized on the plasma and vacuolar membrane, as well as chloroplast. Moreover, the ZmLAZ1-4 gene was negatively co-expressed with ZmBES1/BZR1-11 gene through co-expression and real-time quantitative PCR analysis. The results of yeast one-hybrid and dual-luciferase assay suggested that ZmBES1/BZR1-11 could bind to ZmLAZ1-4 promoter to inhibit its transcription. All results indicated that ZmLAZ1-4 was a novel zinc transporter on plasma and vacuolar membrane, and transported zinc under negative regulation of the ZmBES1/BZR1-11 transcription factor. The study provides insights into further underlying the mechanism of ZmLAZ1-4 regulating zinc homeostasis.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wanchen Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Fengling Fu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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Zhao FJ, Tang Z, Song JJ, Huang XY, Wang P. Toxic metals and metalloids: Uptake, transport, detoxification, phytoremediation, and crop improvement for safer food. MOLECULAR PLANT 2022; 15:27-44. [PMID: 34619329 DOI: 10.1016/j.molp.2021.09.016] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 05/20/2023]
Abstract
Agricultural soils are under threat of toxic metal/metalloid contamination from anthropogenic activities, leading to excessive accumulation of arsenic (As), cadmium (Cd), lead (Pb), and mercury (Hg) in food crops that poses significant risks to human health. Understanding how these toxic metals and their methylated species are taken up, translocated, and detoxified is prerequisite to developing strategies to limit their accumulation for safer food. Toxic metals are taken up and transported across different cellular compartments and plant tissues via various transporters for essential or beneficial nutrients, e.g. As by phosphate and silicon transporters, and Cd by manganese (Mn), zinc (Zn), and iron (Fe) transporters. These transport processes are subjected to interactions with nutrients and the regulation at the transcriptional and post-translational levels. Complexation with thiol-rich compounds, such as phytochelatins, and sequestration in the vacuoles are the common mechanisms for detoxification and for limiting their translocation. A number of genes involved in toxic metal uptake, transport, and detoxification have been identified, offering targets for genetic manipulation via gene editing or transgenic technologies. Natural variations in toxic metal accumulation exist within crop germplasm, and some of the quantitative trait loci underlying these variations have been cloned, paving the way for marker-assisted breeding of low metal accumulation crops. Using plants to extract and remove toxic metals from soil is also possible, but this phytoremediation approach requires metal hyperaccumulation for efficiency. Knowledge gaps and future research needs are also discussed.
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Affiliation(s)
- Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jia-Jun Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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5
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Stanton C, Sanders D, Krämer U, Podar D. Zinc in plants: Integrating homeostasis and biofortification. MOLECULAR PLANT 2022; 15:65-85. [PMID: 34952215 DOI: 10.1016/j.molp.2021.12.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 05/24/2023]
Abstract
Zinc plays many essential roles in life. As a strong Lewis acid that lacks redox activity under environmental and cellular conditions, the Zn2+ cation is central in determining protein structure and catalytic function of nearly 10% of most eukaryotic proteomes. While specific functions of zinc have been elucidated at a molecular level in a number of plant proteins, wider issues abound with respect to the acquisition and distribution of zinc by plants. An important challenge is to understand how plants balance between Zn supply in soil and their own nutritional requirement for zinc, particularly where edaphic factors lead to a lack of bioavailable zinc or, conversely, an excess of zinc that bears a major risk of phytotoxicity. Plants are the ultimate source of zinc in the human diet, and human Zn deficiency accounts for over 400 000 deaths annually. Here, we review the current understanding of zinc homeostasis in plants from the molecular and physiological perspectives. We provide an overview of approaches pursued so far in Zn biofortification of crops. Finally, we outline a "push-pull" model of zinc nutrition in plants as a simplifying concept. In summary, this review discusses avenues that can potentially deliver wider benefits for both plant and human Zn nutrition.
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Affiliation(s)
| | - Dale Sanders
- John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Dorina Podar
- Department of Molecular Biology and Biotechnology and Centre for Systems Biology, Biodiversity and Bioresources, Babes-Bolyai University, 400084 Cluj-Napoca, Romania.
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Nag A, Gupta K, Dubey N, Mishra SK, Panigrahi J. Genomic characterization of ZIP genes in pigeonpea ( CcZIP) and their expression analysis among the genotypes with contrasting host response to pod borer. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2787-2804. [PMID: 35035136 PMCID: PMC8720128 DOI: 10.1007/s12298-021-01111-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Zinc (Zn) is a vital micronutrient from the perspective of biofortification and biotic stress endurance in pigeonpea. The ZIP transporters with domain (Pfam: PF02535) regulate uptake and transport of metal ions, including Zn, in consonance with plant metal homeostasis. Genome-wide analysis in pigeonpea identified 19 non-redundant members of ZIP family (CcZIP) that were analyzed for gene structure, conserved motifs and homology besides other structural and biochemical parameters. Intra-specific as well as the inter-specific phylogenetic relationships of these 19 CcZIPs were elucidated by comparison with ZIP proteins of Arabidopsis thaliana, Medicago truncatula, Phaseolus vulgaris and Glycine max. In addition to gene structure, the cis-regulatory elements (CREs) in the promoter region were also identified. It revealed several stress responsive CREs that might be regulatory for differential expression of CcZIP proteins. Expression analysis showed that both CcZIP3 and CcZIP15, having zinc deficiency responsive element, up-regulated in the reproductive leaf tissues and down-regulated in matured green pods of the pod borer resistant genotypes with higher zinc content. Alternately, the expression of CcZIP6 and CcZIP13 was higher in matured green pods than reproductive leaves of the resistant genotypes. These findings on differential expression indicate the possible role of these CcZIPs on the mobilization of Zn from leaves to pods, phloem loading and unloading, and higher accumulation of seed zinc in pod borer resistant genotypes used in this study. Further functional characterization of CcZIP genes could shed light on their role in bio-fortification and genetic improvement to inhibit the pod borer herbivory in pigeonpea. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01111-1.
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Affiliation(s)
- Atul Nag
- Department of Biosciences and Bioinformatics, Berhampur University, Bhanja Bihar, Berhampur, Odisha 760007 India
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti vihar, Odisha 768019 India
| | - Kapil Gupta
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Rajasthan 305817 India
- Department of Biotechnology, Sidhharth University, Kapilvastu, Siddharth Nagar, UP 272202 India
| | - Neeraj Dubey
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Rajasthan 305817 India
| | - Sujit K. Mishra
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti vihar, Odisha 768019 India
- Department of Zoology, Centurion University of Technology and Management, R. Sitapur, Odisha India
| | - Jogeswar Panigrahi
- Department of Biosciences and Bioinformatics, Berhampur University, Bhanja Bihar, Berhampur, Odisha 760007 India
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti vihar, Odisha 768019 India
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Rajasthan 305817 India
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Ali S, Tyagi A, Bae H. Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants. Int J Mol Sci 2021; 22:7182. [PMID: 34281232 PMCID: PMC8267685 DOI: 10.3390/ijms22137182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
| | - Anshika Tyagi
- National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
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Cardini A, Pellegrino E, White PJ, Mazzolai B, Mascherpa MC, Ercoli L. Transcriptional Regulation of Genes Involved in Zinc Uptake, Sequestration and Redistribution Following Foliar Zinc Application to Medicago sativa. PLANTS (BASEL, SWITZERLAND) 2021; 10:476. [PMID: 33802484 PMCID: PMC7998959 DOI: 10.3390/plants10030476] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/20/2021] [Accepted: 02/25/2021] [Indexed: 11/19/2022]
Abstract
Zinc (Zn) is an essential micronutrient for plants and animals, and Zn deficiency is a widespread problem for agricultural production. Although many studies have been performed on biofortification of staple crops with Zn, few studies have focused on forages. Here, the molecular mechanisms of Zn transport in alfalfa (Medicago sativa L.) were investigated following foliar Zn applications. Zinc uptake and redistribution between shoot and root were determined following application of six Zn doses to leaves. Twelve putative genes encoding proteins involved in Zn transport (MsZIP1-7, MsZIF1, MsMTP1, MsYSL1, MsHMA4, and MsNAS1) were identified and changes in their expression following Zn application were quantified using newly designed RT-qPCR assays. These assays are the first designed specifically for alfalfa and resulted in being more efficient than the ones already available for Medicago truncatula (i.e., MtZIP1-7 and MtMTP1). Shoot and root Zn concentration was increased following foliar Zn applications ≥ 0.1 mg plant-1. Increased expression of MsZIP2, MsHMA4, and MsNAS1 in shoots, and of MsZIP2 and MsHMA4 in roots was observed with the largest Zn dose (10 mg Zn plant-1). By contrast, MsZIP3 was downregulated in shoots at Zn doses ≥ 0.1 mg plant-1. Three functional gene modules, involved in Zn uptake by cells, vacuolar Zn sequestration, and Zn redistribution within the plant, were identified. These results will inform genetic engineering strategies aimed at increasing the efficiency of crop Zn biofortification.
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Affiliation(s)
- Alessio Cardini
- Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy; (A.C.); (L.E.)
| | - Elisa Pellegrino
- Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy; (A.C.); (L.E.)
| | - Philip J. White
- Department of Ecological Science, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK;
| | - Barbara Mazzolai
- Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Pontedera, 56025 Pisa, Italy;
| | - Marco C. Mascherpa
- Istituto di Chimica dei Composti Organo Metallici, National Research Council (CNR), 56124 Pisa, Italy;
| | - Laura Ercoli
- Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy; (A.C.); (L.E.)
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Lu X, Liu S, Zhi S, Chen J, Ye G. Comparative transcriptome profile analysis of rice varieties with different tolerance to zinc deficiency. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:375-390. [PMID: 33296551 DOI: 10.1111/plb.13227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Zinc (Zn) is an indispensable element for rice growth. Zn deficiency results in brown blotches and streaks 2-3 weeks after transplanting, as well as stunting, reduced tillering, and low productivity of rice plants. These processes are controlled by different families of expressed genes. A comparative transcriptome profile analysis was conducted using the roots of two Zn deficiency tolerant varieties (UCP122 and KALIBORO26) and two sensitive varieties (IR26 and IR64) by merging data from untreated control (CK) and Zn deficiency treated samples. Results revealed a total of 4,688 differentially expressed genes (DEGs) between the normal Zn and deficient conditions, with 2,702 and 1,489 unique DEGs upregulated and downregulated, respectively. Functional enrichment analysis identified transcription factors (TFs), such as WRKY, MYB, ERF, and bHLH which are important in the regulation of the Zn deficiency response. Furthermore, chitinases, jasmonic acid, and phenylpropanoid pathways were found to be important in the Zn deficiency response. The metal tolerance protein (MTP) genes also appeared to play an important role in conferring tolerance to Zn deficiency. A heavy metal-associated domain-containing protein 7 was associated with tolerance to Zn deficiency and negatively regulated downstream genes. Collectively, our findings provide valuable expression patterns and candidate genes for the study of molecular mechanisms underlying the response to Zn deficiency and for improvements in breeding for tolerance to Zn deficiency in rice.
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Affiliation(s)
- X Lu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - S Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
| | - S Zhi
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, China
| | - J Chen
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - G Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
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Whitt L, Ricachenevsky FK, Ziegler GZ, Clemens S, Walker E, Maathuis FJM, Kear P, Baxter I. A curated list of genes that affect the plant ionome. PLANT DIRECT 2020; 4:e00272. [PMID: 33103043 PMCID: PMC7576880 DOI: 10.1002/pld3.272] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 05/07/2023]
Abstract
Understanding the mechanisms underlying plants' adaptation to their environment will require knowledge of the genes and alleles underlying elemental composition. Modern genetics is capable of quickly, and cheaply indicating which regions of DNA are associated with particular phenotypes in question, but most genes remain poorly annotated, hindering the identification of candidate genes. To help identify candidate genes underlying elemental accumulations, we have created the known ionome gene (KIG) list: a curated collection of genes experimentally shown to change uptake, accumulation, and distribution of elements. We have also created an automated computational pipeline to generate lists of KIG orthologs in other plant species using the PhytoMine database. The current version of KIG consists of 176 known genes covering 5 species, 23 elements, and their 1588 orthologs in 10 species. Analysis of the known genes demonstrated that most were identified in the model plant Arabidopsis thaliana, and that transporter coding genes and genes altering the accumulation of iron and zinc are overrepresented in the current list.
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Affiliation(s)
- Lauren Whitt
- Donald Danforth Plant Science CenterSaint LouisMOUSA
| | - Felipe Klein Ricachenevsky
- Departamento de Botânica Programa de Pós‐Graduação em Biologia Celular e MolecularUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | | | | | | | | | | | - Ivan Baxter
- Donald Danforth Plant Science CenterSaint LouisMOUSA
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11
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Ecological Stoichiometry Homeostasis of Six Microelements in Leymus chinensis Growing in Soda Saline-Alkali Soil. SUSTAINABILITY 2020. [DOI: 10.3390/su12104226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Soil salinization poses severe threats to grassland ecosystems in various parts of the world, including the Songnen Plain in northeast China. Severe impairment of plant growth in this soil is generally attributed to high soil pH, total alkalinity, and sodium (Na) contents. This paper focuses on the ecological stoichiometry of microelements, which has received much less attention than relations of macroelements, in the soil and plants (specifically Leymus chinensis) growing in it. The results show that the soil’s manganese (Mn), zinc (Zn), iron (Fe), copper (Cu), nickel (Ni) and molybdenum (Mo) contents are lower than average in Chinese soils, but only Mn and Zn are severely deficient in L. chinensis. With increases in soil pH, total alkalinity, and Na, the Mo contents in both soil and L. chinensis slightly increase, while contents of the other microelements decline. Homeostasis indices obtained for the six microelements—and Fe/Zn, Fe/Ni, Fe/Cu, and Cu/Zn ratios—were all between 0.82 and 3.34 (ranging from just below the “plastic” threshold to “weakly homeostatic”). Despite Zn deficiency in the soil, Zn appears to have the highest homeostasis of the six elements in L. chinensis (homeostasis indices of Zn, Cu, Ni, Mn, Fe and Mo were 3.34, 2.54, 1.86, 1.76, 1.52, and 1.33, respectively). In addition, the Cu/Zn ratio had the highest homeostasis index (1.85), followed by Fe/Zn (1.02), Fe/Cu (0.95) and Fe/Ni (0.82). Appropriate application of Mn and Zn fertilizers is recommended to promote the growth and development of L. chinensis in soda saline-alkali soil.
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