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Williamson G, Bizior A, Harris T, Pritchard L, Hoskisson P, Javelle A. Biological ammonium transporters from the Amt/Mep/Rh superfamily: mechanism, energetics, and technical limitations. Biosci Rep 2024; 44:BSR20211209. [PMID: 38131184 PMCID: PMC10794816 DOI: 10.1042/bsr20211209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Abstract
The exchange of ammonium across cellular membranes is a fundamental process in all domains of life and is facilitated by the ubiquitous Amt/Mep/Rh transporter superfamily. Remarkably, despite a high structural conservation in all domains of life, these proteins have gained various biological functions during evolution. It is tempting to hypothesise that the physiological functions gained by these proteins may be explained at least in part by differences in the energetics of their translocation mechanisms. Therefore, in this review, we will explore our current knowledge of energetics of the Amt/Mep/Rh family, discuss variations in observations between different organisms, and highlight some technical drawbacks which have hampered effects at mechanistic characterisation. Through the review, we aim to provide a comprehensive overview of current understanding of the mechanism of transport of this unique and extraordinary Amt/Mep/Rh superfamily of ammonium transporters.
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Affiliation(s)
- Gordon Williamson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, U.K
| | - Adriana Bizior
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, U.K
| | - Thomas Harris
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, U.K
| | - Leighton Pritchard
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, U.K
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, U.K
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, U.K
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2
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Liao Z, Xia X, Zhang Z, Nong B, Guo H, Feng R, Chen C, Xiong F, Qiu Y, Li D, Yang X. Genome-wide association study using specific-locus amplified fragment sequencing identifies new genes influencing nitrogen use efficiency in rice landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1126254. [PMID: 37521918 PMCID: PMC10375723 DOI: 10.3389/fpls.2023.1126254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/28/2023] [Indexed: 08/01/2023]
Abstract
Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10-7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10-6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.
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Affiliation(s)
- Zuyu Liao
- College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hui Guo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rui Feng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Can Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Faqian Xiong
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yongfu Qiu
- College of Agriculture, Guangxi University, Nanning, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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3
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Chew J, Joseph S, Chen G, Zhang Y, Zhu L, Liu M, Taherymoosavi S, Munroe P, Mitchell DRG, Pan G, Li L, Bian R, Fan X. Biochar-based fertiliser enhances nutrient uptake and transport in rice seedlings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154174. [PMID: 35231505 DOI: 10.1016/j.scitotenv.2022.154174] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/14/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Biochar-based compound fertilisers (BCF) are gaining increasing attention as they are cost-effectiveness and improve soil fertility and crop yield. However, little is known about the mechanisms by which micron-size BCF particles enhance crop growth. In the present study, Wuyunjing7 rice seedlings were exposed to micron-size particles of wheat straw-based BCF (mBCF) diffused through a 25-μm nylon mesh. The control was fertilised with urea, diammonium phosphate, and potassium chloride to ensure that both treatments received comparables level of N, P, and K. The effects of mBCF on rice seedling growth were evaluated by determining the changes in nitrogen uptake and utilisation via nitrogen content measurements, short-term 15N-NH4+ influx assays, and analyses of transcript-level nutrient transporter gene expression. The shoot biomass of rice seedling treated with mBCF at the rate of 5 mg/ g soil was 33% greater than that for the control. Root and shoot 15N accumulation rates were 44% and 14% higher, respectively, in the mBCF-treated than the control. The mBCF-treated rice seedlings had higher phosphorus, potassium, and iron content than the control. Moreover, the treatments significantly differed in terms of their nutrient transporter gene expression levels. Spectroscopy and microscopy were used to visualise nutrient distributions across transverse root sections. There were relatively higher iron oxide nanoparticle and silicon-based compound concentrations in the roots of the mBCF-treated rice seedlings than in those of the control. The foregoing difference might account for the fact that the growth of the mBCF-treated rice was superior to that of the control. We demonstrated that the mBCF treatment created a more negative electrical potential at the root epidermal cell layer (~ - 160 mV) than the root surface. This potential difference may have been the driving force for mineral nutrient absorption.
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Affiliation(s)
- JinKiat Chew
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Stephen Joseph
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; School of Materials Science and Engineering, University of NSW, Sydney, NSW 2052, Australia; Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - Guanhong Chen
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Yuyue Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Longlong Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Minglong Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Paul Munroe
- School of Materials Science and Engineering, University of NSW, Sydney, NSW 2052, Australia
| | - David R G Mitchell
- Electron Microscopy Centre, AIIM Building, Innovation Campus, University of Wollongong, North Wollongong, NSW 2517, Australia
| | - Genxing Pan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianqing Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongjun Bian
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaorong Fan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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4
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Yan Z, Yang MY, Zhao BG, Li G, Chao Q, Tian F, Gao G, Wang BC. OsAPL controls the nutrient transport systems in the leaf of rice (Oryza sativa L.). PLANTA 2022; 256:11. [PMID: 35699777 DOI: 10.1007/s00425-022-03913-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
OsAPL positively controls the seedling growth and grain size in rice by targeting the plasma membrane H+-ATPase-encoding gene, OsRHA1, as well as drastically affects genes encoding H+-coupled secondary active transporters. Nutrient transport is a key component of both plant growth and environmental adaptation. Photosynthates and nutrients produced in the source organs (e.g., leaves) need to be transported to the sink organs (e.g., seeds). In rice, the unloading of nutrients occurs through apoplastic transport (i.e., across the membrane via transporters) and is dependent on the efficiency and number of transporters embedded in the cell membrane. However, the genetic mechanisms underlying the regulation of these transporters remain to be determined. Here we show that rice (Oryza sativa L., Kitaake) ALTERED PHLOEM DEVELOPMENT (OsAPL), homologous to a MYB family transcription factor promoting phloem development in Arabidopsis thaliana, regulates the number of transporters in rice. Overexpression of OsAPL leads to a 10% increase in grain yield at the heading stage. OsAPL acts as a transcriptional activator of OsRHA1, which encodes a subunit of the plasma membrane H+-ATPase (primary transporter). In addition, OsAPL strongly affects the expression of genes encoding H+-coupled secondary active transporters. Decreased expression of OsAPL leads to a decreased expression level of nutrient transporter genes. Taken together, our findings suggest the involvement of OsAPL in nutrients transport and crop yield accumulation in rice.
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Affiliation(s)
- Zhen Yan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- College of Life Sciences, National Demonstration Center for Experimental Biology Education, Sichuan University, Chengdu, 610064, China
| | - Man-Yu Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Biligen-Gaowa Zhao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guo Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100039, China
| | - Feng Tian
- Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG) and Biomedical Pioneering Innovation Center (BIOPIC), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ge Gao
- Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100039, China.
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5
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Genome-Wide Identification and Expression Analysis of AMT Gene Family in Apple (Malus domestica Borkh.). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050457] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ammonium is one of the prevalent nitrogen sources for growth and development of higher plants. Ammonium acquisition from soil is facilitated by ammonium transporters (AMTs), which are plasma membrane proteins that exclusively transport ammonium/ammonia. However, the functional characteristics and molecular mechanisms of AMTs in apple remain unclear. In this work, 15 putative AMT genes were identified and classified into four clusters (AMT1–AMT4) in apple. According to expression analysis, these AMTs had varying expressions in roots, leaves, stems, flowers and fruits. Some of them were strongly affected by diurnal cycles. AMT genes showed multiple transcript patterns to N regimes and were quite responsive to osmotic stress. In addition, phosphorylation analysis revealed that there were some conserved phosphorylation residues within the C-terminal of AMT proteins. Furthermore, detailed research was conducted on AMT1;2 functioning by heterologous expression in yeast. The present study is expected to provide basic bioinformatic information and expression profiles for the apple AMT family and to lay a basis for exploring the functional roles and regulation mechanisms of AMTs in apple.
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6
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Sathee L, Krishna GK, Adavi SB, Jha SK, Jain V. Role of protein phosphatases in the regulation of nitrogen nutrition in plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2911-2922. [PMID: 35035144 PMCID: PMC8720119 DOI: 10.1007/s12298-021-01115-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/18/2021] [Accepted: 12/07/2021] [Indexed: 05/20/2023]
Abstract
The reversible protein phosphorylation and dephosphorylation mediated by protein kinases and phosphatases regulate different biological processes and their response to environmental cues, including nitrogen (N) availability. Nitrate assimilation is under the strict control of phosphorylation-dephosphorylation mediated post-translational regulation. The protein phosphatase family with approximately 150 members in Arabidopsis and around 130 members in rice is a promising player in N uptake and assimilation pathways. Protein phosphatase 2A (PP2A) enhances the activation of nitrate reductase (NR) by deactivating SnRK1 and reduces the binding of inhibitory 14-3-3 proteins on NR. The functioning of nitrate transporter NPF6.3 is regulated by phosphorylation of CBL9 (Calcineurin B like protein 9) and CIPK23 (CBL interacting protein kinase 23) module. Phosphorylation by CIPK23 inhibits the activity of NPF6.3, whereas protein phosphatases (PP2C) enhance the NPF6.3-dependent nitrate sensing. PP2Cs and CIPK23 also regulate ammonium transporters (AMTs). Under either moderate ammonium supply or high N demand, CIPK23 is bound and inactivated by PP2Cs. Ammonium uptake is mediated by nonphosphorylated and active AMT1s. Whereas, under high ammonium availability, CIPK23 gets activated and phosphorylate AMT1;1 and AMT1;2 rendering them inactive. Recent reports suggest the critical role of protein phosphatases in regulating N use efficiency (NUE). In rice, PP2C9 regulates NUE by improving N uptake and assimilation. Comparative leaf proteome of wild type and PP2C9 over-expressing transgenic rice lines showed 30 differentially expressed proteins under low N level. These proteins are involved in photosynthesis, N metabolism, signalling, and defence.
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Affiliation(s)
- Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - G. K. Krishna
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Thrissur, 680 656 India
| | - Sandeep B. Adavi
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Shailendra K. Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Vanita Jain
- Agricultural Education Division, ICAR, KAB-II, New Delhi, 110 012 India
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7
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Konishi N, Ma JF. Three polarly localized ammonium transporter 1 members are cooperatively responsible for ammonium uptake in rice under low ammonium condition. THE NEW PHYTOLOGIST 2021; 232:1778-1792. [PMID: 34392543 DOI: 10.1111/nph.17679] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Ammonium is a preferential nitrogen form for rice (Oryza sativa) grown in paddy field, but the molecular mechanisms for ammonium uptake have not been well understood. We functionally characterized three members belonging to ammonium transporter 1 (AMT1) and investigated their contributions to ammonium uptake. Spatial expression analysis showed that the upregulated expression of OsAMT1;1 and OsAMT1;2 and downregulated expression of OsAMT1;3 by ammonium were higher in the root mature region than in the root tips. All OsAMT1 members were polarly localized at the distal side of exodermis in the mature region of crown roots and lateral roots. Upon exposure to ammonium, localization of OsAMT1;1 and OsAMT1;2 was also observed in the endoplasmic reticulum, but their abundance in the plasma membrane was not changed. Single knockout of either gene did not affect ammonium uptake, but knockout of all three genes resulted in 95% reduction of ammonium uptake. However, the nitrogen uptake did not differ between the wild-type rice and triple mutants at high ammonium and nitrate supply. Our results indicate that three OsAMT1 members are cooperatively required for uptake of low ammonium in rice roots and that they undergo a distinct regulatory mechanism in response to ammonium.
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Affiliation(s)
- Noriyuki Konishi
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan
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8
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Wang W, Li A, Zhang Z, Chu C. Posttranslational Modifications: Regulation of Nitrogen Utilization and Signaling. PLANT & CELL PHYSIOLOGY 2021; 62:543-552. [PMID: 33493288 PMCID: PMC8462382 DOI: 10.1093/pcp/pcab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/07/2021] [Indexed: 05/08/2023]
Abstract
Nitrogen is the most important macroelement required for the composition of key molecules, such as nucleic acids, proteins and other organic compounds. As sessile organisms, plants have evolved sophisticated mechanisms to acquire nitrogen for their normal growth and development. Besides the transcriptional and translational regulation of nitrogen uptake, assimilation, remobilization and signal transduction, posttranslational modifications (PTMs) are shown to participate in these processes in plants. In addition to alterations in protein abundance, PTMs may dramatically increase the complexity of the proteome without the concomitant changes in gene transcription and have emerged as an important type of protein regulation in terms of protein function, subcellular localization and protein activity and stability. Herein, we briefly summarize recent advances on the posttranslational regulation of nitrogen uptake, assimilation, remobilization and nitrogen signaling and discuss the underlying mechanisms of PTMs as well as the signal output of such PTMs. Understanding these regulation mechanisms will provide novel insights for improving the nitrogen use efficiency of plants.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Aifu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihua Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Chengcai Chu
- * Corresponding author: E-mail, ; Fax, +86-10-64806608
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9
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Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L.). Transgenic Res 2021; 31:23-42. [PMID: 34524604 DOI: 10.1007/s11248-021-00284-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/06/2021] [Indexed: 12/18/2022]
Abstract
Nitrogen (N) as a macronutrient is an important determinant of plant growth. The excessive usage of chemical fertilizers is increasing environmental pollution; hence, the improvement of crop's nitrogen use efficiency (NUE) is imperative for sustainable agriculture. N uptake, transportation, assimilation, and remobilization are four important determinants of plant NUE. Oryza sativa L. (rice) is a staple food for approximately half of the human population, around the globe and improvement in rice yield is pivotal for rice breeders. The N transporters, enzymes indulged in N assimilation, and several transcription factors affect the rice NUE and subsequent yield. Although, a couple of improvements have been made regarding rice NUE, the knowledge about regulatory mechanisms operating NUE is scarce. The current review provides a precise knowledge of how rice plants detect soil N and how this detection is translated into the language of responses that regulate the growth. Additionally, the transcription factors that control N-associated genes in rice are discussed in detail. This mechanistic insight will help the researchers to improve rice yield with minimized use of chemical fertilizers.
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10
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Molecular Regulatory Networks for Improving Nitrogen Use Efficiency in Rice. Int J Mol Sci 2021; 22:ijms22169040. [PMID: 34445746 PMCID: PMC8396546 DOI: 10.3390/ijms22169040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022] Open
Abstract
Nitrogen is an important factor limiting the growth and yield of rice. However, the excessive application of nitrogen will lead to water eutrophication and economic costs. To create rice varieties with high nitrogen use efficiency (NUE) has always been an arduous task in rice breeding. The processes for improving NUE include nitrogen uptake, nitrogen transport from root to shoot, nitrogen assimilation, and nitrogen redistribution, with each step being indispensable to the improvement of NUE. Here, we summarize the effects of absorption, transport, and metabolism of nitrate, ammonium, and amino acids on NUE, as well as the role of hormones in improving rice NUE. Our discussion provide insight for further research in the future.
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11
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Islam S, Zhang J, Zhao Y, She M, Ma W. Genetic regulation of the traits contributing to wheat nitrogen use efficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110759. [PMID: 33487345 DOI: 10.1016/j.plantsci.2020.110759] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 05/25/2023]
Abstract
High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.
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Affiliation(s)
- Shahidul Islam
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Jingjuan Zhang
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Yun Zhao
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Maoyun She
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Wujun Ma
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia.
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12
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Thi Nong H, Tateishi R, Suriyasak C, Kobayashi T, Oyama Y, Chen WJ, Matsumoto R, Hamaoka N, Iwaya-Inoue M, Ishibashi Y. Effect of Seedling Nitrogen Condition on Subsequent Vegetative Growth Stages and Its Relationship to the Expression of Nitrogen Transporter Genes in Rice. PLANTS (BASEL, SWITZERLAND) 2020; 9:E861. [PMID: 32646051 PMCID: PMC7412562 DOI: 10.3390/plants9070861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/23/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022]
Abstract
Nitrogen (N) deficiency is one of the most common problems in soils, limiting crop growth and production. However, the effects of N limitation in seedlings on vegetative growth remain poorly understood. Here, we show that N limitation in rice seedlings restricted vegetative growth but not yield. Aboveground parts were affected mainly during the period of tillering, but belowground parts were sensitive throughout vegetative growth, especially during panicle development. At the tillering stage, N-limited plants had a significantly lower N content in shoots, but not in roots. On the other hand, N content in roots during the panicle development stage was significantly lower in N-limited plants. This distinct response was driven by significant changes in expression of N transporter genes during growth. Under N limitation, N translocation from roots to shoots was greatly sped up by systemic expression of N transporter genes to obtain balanced growth. N limitation during the seedling stage did not reduce any yield components. We conclude that the N condition during the seedling stage affects physiological responses such as N translocation through the expression of N transporter genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yushi Ishibashi
- Graduate school of Bioresource and Bioenviromental Sciences, Kyushu University, Mootoka 774, Fukuoka 819–0395, Japan; (H.T.N.); (R.T.); (C.S.); (T.K.); (Y.O.); (W.J.C.); (R.M.); (N.H.); (M.I.-I.)
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13
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Hao DL, Zhou JY, Yang SY, Huang YN, Su YH. Functional and Regulatory Characterization of Three AMTs in Maize Roots. FRONTIERS IN PLANT SCIENCE 2020; 11:884. [PMID: 32676086 PMCID: PMC7333355 DOI: 10.3389/fpls.2020.00884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Maize grows in nitrate-dominated dryland soils, but shortly upon localized dressing of nitrogen fertilizers, ammonium is retained as a noticeable form of nitrogen source available to roots. Thus in addition to nitrate, the absorption of ammonium can be an important strategy that promotes rapid plant growth at strong nitrogen demanding stages. The present study reports the functional characterization of three root-expressed ammonium transporters (AMTs), aiming at finding out functional and regulatory properties that correlate with efficient nitrogen acquisition of maize. Using a stable electrophysiological recording method we previously established in Xenopus laevis oocytes that integrates the capture of currents in response to voltage ramps with onsite stability controls, we demonstrate that all three ZmAMT1s engage NH4 + uniporting as ammonium uptake mechanisms. The K m value for ZmAMT1.1a, 1.1b, or ZmAMT1.3 is, respectively, 9.9, 15.6, or 18.6 μM, indicating a typical high-affinity transport of NH4 + ions. Importantly, the uptake currents of these ZmAMT1s are markedly amplified upon extracellular acidification. A pH drop from 7.4 to 5.4 results in a 140.8%, 64.1% or a 120.7% increase of ammonium uptake activity through ZmAMT1.1a, 1.1b, or ZmAMT1.3. Since ammonium uptake by plant roots accompanies a spontaneous acidification to the root medium, the functional promotion of ZmAMT1.1a, 1.1b, and ZmAMT1.3 by low pH is in line with the facilitated ammonium uptake activity in maize roots. Furthermore, the expression of the three ZmAMT1 genes is induced under ammonium-dominated conditions. Thus we describe a facilitated ammonium uptake strategy in maize roots by functional and expression regulations of ZmAMT1 transporters that may coordinate with efficient acquisition of this form of nitrogen source when available.
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Hao DL, Zhou JY, Yang SY, Qi W, Yang KJ, Su YH. Function and Regulation of Ammonium Transporters in Plants. Int J Mol Sci 2020; 21:E3557. [PMID: 32443561 PMCID: PMC7279009 DOI: 10.3390/ijms21103557] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023] Open
Abstract
Ammonium transporter (AMT)-mediated acquisition of ammonium nitrogen from soils is essential for the nitrogen demand of plants, especially for those plants growing in flooded or acidic soils where ammonium is dominant. Recent advances show that AMTs additionally participate in many other physiological processes such as transporting ammonium from symbiotic fungi to plants, transporting ammonium from roots to shoots, transferring ammonium in leaves and reproductive organs, or facilitating resistance to plant diseases via ammonium transport. Besides being a transporter, several AMTs are required for the root development upon ammonium exposure. To avoid the adverse effects of inadequate or excessive intake of ammonium nitrogen on plant growth and development, activities of AMTs are fine-tuned not only at the transcriptional level by the participation of at least four transcription factors, but also at protein level by phosphorylation, pH, endocytosis, and heterotrimerization. Despite these progresses, it is worth noting that stronger growth inhibition, not facilitation, unfortunately occurs when AMT overexpression lines are exposed to optimal or slightly excessive ammonium. This implies that a long road remains towards overcoming potential limiting factors and achieving AMT-facilitated yield increase to accomplish the goal of persistent yield increase under the present high nitrogen input mode in agriculture.
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Affiliation(s)
- Dong-Li Hao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (D.-L.H.); (J.-Y.Z.); (S.-Y.Y.)
| | - Jin-Yan Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (D.-L.H.); (J.-Y.Z.); (S.-Y.Y.)
| | - Shun-Ying Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (D.-L.H.); (J.-Y.Z.); (S.-Y.Y.)
| | - Wei Qi
- College of Resources and Environment, Shandong Agricultural University, Taian 271018, China;
| | - Ke-Jun Yang
- Agro-Tech Extension and Service Center, Zhucheng 262200, China;
| | - Yan-Hua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (D.-L.H.); (J.-Y.Z.); (S.-Y.Y.)
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15
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Yang X, Xia X, Zeng Y, Nong B, Zhang Z, Wu Y, Tian Q, Zeng W, Gao J, Zhou W, Liang H, Li D, Deng G. Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency. BMC PLANT BIOLOGY 2020; 20:193. [PMID: 32375632 PMCID: PMC7203820 DOI: 10.1186/s12870-020-02419-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/29/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family may involve in nitrate uptake and transport. Here, we identified PTR gene family in rice and analyzed their expression profile in near-isogenic lines. RESULTS We identified 96, 85 and 78 PTR genes in Nipponbare, R498 and Oryza glaberrima, and the phylogenetic trees were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanut (125) and soybean (127). The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and their distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. The PTR genes in rice have 0-11 introns and 1-12 exons, and 16 of them have the NPF (NRT1/PTR family) domain. The results of RNA-seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 at three stages were 928, 1467, and 1586, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one module, and obtained 25 target modules. Among these modules, three modules may be involved in rice N uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism. CONCLUSIONS In this study, we comprehensively analyzed the PTR gene family in rice. 96 PTR genes were identified in Nippobare genome and 25 of them were located on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had undergone positive selection. The RNA-seq results showed that many PTR genes were involved in rice nitrogen use efficiency (NUE), and protein kinases might play an important role in this process. These results provide a fundamental basis to improve the rice NUE via molecular breeding.
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Affiliation(s)
- Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.
| | - Xiuzhong Xia
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Yu Zeng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Baoxuan Nong
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Zongqiong Zhang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Yanyan Wu
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Qinglan Tian
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Weiying Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Ju Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Weiyong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Danting Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.
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16
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Zhang Z, Gao S, Chu C. Improvement of nutrient use efficiency in rice: current toolbox and future perspectives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1365-1384. [PMID: 31919537 DOI: 10.1007/s00122-019-03527-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/24/2019] [Indexed: 05/03/2023]
Abstract
Modern agriculture relies heavily on chemical fertilizers, especially in terms of cereal production. The excess application of fertilizers not only increases production cost, but also causes severe environmental problems. As one of the major cereal crops, rice (Oryza sativa L.) provides the staple food for nearly half of population worldwide, especially in developing countries. Therefore, improving rice yield is always the priority for rice breeding. Macronutrients, especially nitrogen (N) and phosphorus (P), are two most important players for the grain yield of rice. However, with economic development and improved living standard, improving nutritional quality such as micronutrient contents in grains has become a new goal in order to solve the "hidden hunger." Micronutrients, such as iron (Fe), zinc (Zn), and selenium (Se), are critical nutritional elements for human health. Therefore, breeding the rice varieties with improved nutrient use efficiency (NUE) is thought to be one of the most feasible ways to increase both grain yield and nutritional quality with limited fertilizer input. In this review, we summarized the progresses in molecular dissection of genes for NUE by reverse genetics on macronutrients (N and P) and micronutrients (Fe, Zn, and Se), exploring natural variations for improving NUE in rice; and also, the current genetic toolbox and future perspectives for improving rice NUE are discussed.
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Affiliation(s)
- Zhihua Zhang
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaopei Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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17
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Yang S, Hao D, Jin M, Li Y, Liu Z, Huang Y, Chen T, Su Y. Internal ammonium excess induces ROS-mediated reactions and causes carbon scarcity in rice. BMC PLANT BIOLOGY 2020; 20:143. [PMID: 32264840 PMCID: PMC7140567 DOI: 10.1186/s12870-020-02363-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/25/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND Overuse of nitrogen fertilizers is often a major practice to ensure sufficient nitrogen demand of high-yielding rice, leading to persistent NH4+ excess in the plant. However, this excessive portion of nitrogen nutrient does not correspond to further increase in grain yields. For finding out the main constraints related to this phenomenon, the performance of NH4+ excess in rice plant needs to be clearly addressed beyond the well-defined root growth adjustment. The present work isolates an acute NH4+ excess condition in rice plant from causing any measurable growth change and analyses the initial performance of such internal NH4+ excess. RESULTS We demonstrate that the acute internal NH4+ excess in rice plant accompanies readily with a burst of reactive oxygen species (ROS) and initiates the downstream reactions. At the headstream of carbon production, photon caption genes and the activity of primary CO2 fixation enzymes (Rubisco) are evidently suppressed, indicating a reduction in photosynthetic carbon income. Next, the vigorous induction of glutathione transferase (GST) genes and enzyme activities along with the rise of glutathione (GSH) production suggest the activation of GSH cycling for ROS cleavage. Third, as indicated by strong induction of glycolysis / glycogen breakdown related genes in shoots, carbohydrate metabolisms are redirected to enhance the production of energy and carbon skeletons for the cost of ROS scavenging. As the result of the development of these defensive reactions, a carbon scarcity would accumulatively occur and lead to a growth inhibition. Finally, a sucrose feeding cancels the ROS burst, restores the activity of Rubisco and alleviates the demand for the activation of GSH cycling. CONCLUSION Our results demonstrate that acute NH4+ excess accompanies with a spontaneous ROS burst and causes carbon scarcity in rice plant. Therefore, under overuse of N fertilizers carbon scarcity is probably a major constraint in rice plant that limits the performance of nitrogen.
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Affiliation(s)
- Shunying Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008, China
| | - Dongli Hao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008, China
| | - Man Jin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zengtai Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanan Huang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tianxiang Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008, China.
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Zhang F, Wang L, Bai P, Wei K, Zhang Y, Ruan L, Wu L, Cheng H. Identification of Regulatory Networks and Hub Genes Controlling Nitrogen Uptake in Tea Plants [ Camellia sinensis (L.) O. Kuntze]. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2445-2456. [PMID: 31899627 DOI: 10.1021/acs.jafc.9b06427] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nitrogen (N) uptake, as the first step of N metabolism, is a key limiting factor for plant growth. To understand the gene expression networks that control N absorption and metabolism in tea plants, we analyzed transcriptomes in the young roots of two groups of tea plants with significantly different growth rates under different N treatments (0, 0.2, and 2 mM). Using pairwise comparisons and weighted gene co-expression network analyses (WGCNA), we successfully constructed 16 co-expression modules. Among them, a specific module (turquoise) that substantially responded to the low N treatment was identified. Based on KEGG analysis, the relative genes that enriched in the "N metabolism" pathways were used to construct gene co-expression networks of N metabolism. Finally, a high-affinity ammonium (NH4+) transporter designated CsAMT1.2 was identified as a hub gene in the N metabolism network in tea plant roots and the gene expression could be highly induced by N resupply. The gene functional analysis revealed that CsAMT1.2 could make functional complementation of MEP1, MEP2, and MEP3 genes in 31019b yeast cells and improve NH4+ uptake rate in 31019b at low NH4+ level. Thus, CsAMT1.2 was a key gene controlling N uptake in tea plants and might play a vital role in promoting NH4+ uptake from the environment in tea roots. This study provided a useful foundation for improving the NUE in tea plantations.
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Affiliation(s)
- Fen Zhang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Liyuan Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Peixian Bai
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Kang Wei
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Yazhen Zhang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Li Ruan
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Liyun Wu
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Hao Cheng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
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Hao DL, Yang SY, Liu SX, Zhou JY, Huang YN, Véry AA, Sentenac H, Su YH. Functional Characterization of the Arabidopsis Ammonium Transporter AtAMT1;3 With the Emphasis on Structural Determinants of Substrate Binding and Permeation Properties. FRONTIERS IN PLANT SCIENCE 2020; 11:571. [PMID: 32528489 PMCID: PMC7256485 DOI: 10.3389/fpls.2020.00571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/17/2020] [Indexed: 05/13/2023]
Abstract
AtAMT1;3 is a major contributor to high-affinity ammonium uptake in Arabidopsis roots. Using a stable electrophysiological recording strategy, we demonstrate in Xenopus laevis oocytes that AtAMT1;3 functions as a typical high-affinity NH4 + uniporter independent of protons and Ca2+. The findings that AtAMT1;3 transports methylammonium (MeA+, a chemical analog of NH4 +) with extremely low affinity (K m in the range of 2.9-6.1 mM) led to investigate the mechanisms underlying substrate binding. Homologous modeling and substrate docking analyses predicted that the deduced substrate binding motif of AtAMT1;3 facilitates the binding of NH4 + ions but loosely accommodates the binding of MeA+ to a more superficial location of the permeation pathway. Amongst point mutations tested based on this analysis, P181A resulted in both significantly increased current amplitudes and substrate binding affinity, whereas F178I led to opposite effects. Thus these 2 residues, which flank W179, a major structural component of the binding site, are also important determinants of AtAMT1;3 transport capacity by being involved in substrate binding. The Q365K mutation neighboring the histidine residue H378, which confines the substrate permeation tunnel, affected only the current amplitudes but not the binding affinities, providing evidence that Q365 mainly controls the substrate diffusion rate within the permeation pathway.
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Affiliation(s)
- Dong-Li Hao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shun-Ying Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shu-Xia Liu
- Department of Computational Biology, Beijing Computing Center, Beijing, China
| | - Jin-Yan Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ya-Nan Huang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Anne-Aliénor Véry
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Hervé Sentenac
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
- *Correspondence: Hervé Sentenac,
| | - Yan-Hua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- Yan-Hua Su,
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20
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Meyer RC, Gryczka C, Neitsch C, Müller M, Bräutigam A, Schlereth A, Schön H, Weigelt-Fischer K, Altmann T. Genetic diversity for nitrogen use efficiency in Arabidopsis thaliana. PLANTA 2019; 250:41-57. [PMID: 30904943 DOI: 10.1007/s00425-019-03140-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The plasticity of plant growth response to differing nitrate availability renders the identification of biomarkers difficult, but allows access to genetic factors as tools to modulate root systems to a wide range of soil conditions. Nitrogen availability is a major determinant of crop yield. While the application of fertiliser substantially increases the yield on poor soils, it also causes nitrate pollution of water resources and high costs for farmers. Increasing nitrogen use efficiency in crop plants is a necessary step to implement low-input agricultural systems. We exploited the genetic diversity present in the worldwide Arabidopsis thaliana population to study adaptive growth patterns and changes in gene expression associated with chronic low nitrate stress, to identify biomarkers associated with good plant performance under low nitrate availability. Arabidopsis accessions were grown on agar plates with limited and sufficient supply of nitrate to measure root system architecture as well as shoot and root fresh weight. Differential gene expression was determined using Affymetrix ATH1 arrays. We show that the response to differing nitrate availability is highly variable in Arabidopsis accessions. Analyses of vegetative shoot growth and root system architecture identified accession-specific reaction modes to cope with limited nitrate availability. Transcription and epigenetic factors were identified as important players in the adaption to limited nitrogen in a global gene expression analysis. Five nitrate-responsive genes emerged as possible biomarkers for NUE in Arabidopsis. The plasticity of plant growth in response to differing nitrate availability in the substrate renders the identification of morphological and molecular features as biomarkers difficult, but at the same time allows access to a multitude of genetic factors which can be used as tools to modulate and adjust root systems to a wide range of soil conditions.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
| | - Corina Gryczka
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Cathleen Neitsch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
- IDT Biologika GmbH, Magdeburg, Germany
| | - Margarete Müller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
- Bayer HealthCare Pharmaceuticals, Berlin, Germany
| | - Andrea Bräutigam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Armin Schlereth
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
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21
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Anis GB, Zhang Y, Islam A, Zhang Y, Cao Y, Wu W, Cao L, Cheng S. RDWN6 XB, a major quantitative trait locus positively enhances root system architecture under nitrogen deficiency in rice. BMC PLANT BIOLOGY 2019; 19:12. [PMID: 30621596 PMCID: PMC6325831 DOI: 10.1186/s12870-018-1620-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/27/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Nitrogen (N) is a major input cost in rice production, in addition to causing severe pollution to agricultural and ecological environments. Root dry weight has been considered the most important component related to crop yields than the other root traits. Therefore, development of rice varieties/lines with low input of N fertilizer and higher root traits are essential for sustainable rice production. RESULTS In this context, a main effect quantitative trait locus qRDWN6XB on the long arm of chromosome 6 which positively confers tolerance to N deficiency in the Indica rice variety XieqingzaoB, was identified using a chromosomal segment substitution line (CSSL) population. qRDWN6XB was determined to be located near marker InD90 on chromosome 6 based on association analysis of phenotype data from three N levels and 120 polymorphic molecular markers. The target chromosomal segment substitution line CSSL45, which has the higher root dry weight (RDW) than indica cultivar Zhonghui9308 and carry qRDWN6XB, was selected for further study. A BC5F2:3 population derived from a cross between CSSL45 and Zhonghui9308 was constructed. To fine-map qRDWN6XB, we used the homozygous recombinant plants and ultimately this locus was narrowed to a 52.3-kb between markers ND-4 and RM19771, which contains nine candidate genes in this region. One of these genes, LOC_Os06g15910 as a potassium transporter was considered a strong candidate gene for the RDWN6XB locus. CONCLUSIONS The identification of qRDWN6XB provides a new genetic resource for breeding rice varieties and a starting point to improve grain yield despite the decreased input of N fertilizers. The newly developed and tightly linked InDel marker ND-4 will be useful to improve the root system architecture under low N by marker-assisted selection (MAS) in rice breeding programs.
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Affiliation(s)
- Galal Bakr Anis
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
- Rice Research and Training Center, Field Crops Research Institute, Agriculture Research Center, Kafrelsheikh, 33717 Egypt
| | - Yingxin Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Anowerul Islam
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yue Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yongrun Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Weixun Wu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
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22
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Yao W, Li G, Yu Y, Ouyang Y. funRiceGenes dataset for comprehensive understanding and application of rice functional genes. Gigascience 2018; 7:1-9. [PMID: 29220485 PMCID: PMC5765555 DOI: 10.1093/gigascience/gix119] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 11/22/2017] [Indexed: 12/26/2022] Open
Abstract
Background As a main staple food, rice is also a model plant for functional genomic studies of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement. Findings We built a comprehensive and accurate dataset of ∼2800 functionally characterized rice genes and ∼5000 members of different gene families by integrating data from available databases and reviewing every publication on rice functional genomic studies. The dataset accounts for 19.2% of the 39 045 annotated protein-coding rice genes, which provides the most exhaustive archive for investigating the functions of rice genes. We also constructed 214 gene interaction networks based on 1841 connections between 1310 genes. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. Increasing degree of conservation of the flowering pathway was observed among more closely related plants, implying substantial value of rice genes for future dissection of flowering regulation in other crops. All data are deposited in the funRiceGenes database (https://funricegenes.github.io/). Functionality for advanced search and continuous updating of the database are provided by a Shiny application (http://funricegenes.ncpgr.cn/). Conclusions The funRiceGenes dataset would enable further exploring of the crosslink between gene functions and natural variations in rice, which can also facilitate breeding design to improve target agronomic traits of rice.
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Affiliation(s)
- Wen Yao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Yu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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23
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Guo H, Wang N, McDonald TR, Reinders A, Ward JM. MpAMT1;2 from Marchantia polymorpha is a High-Affinity, Plasma Membrane Ammonium Transporter. PLANT & CELL PHYSIOLOGY 2018; 59:997-1005. [PMID: 29444306 DOI: 10.1093/pcp/pcy038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 02/09/2018] [Indexed: 06/08/2023]
Abstract
Plant ammonium transporters in the AMT/MEP/Rh (ammonium transporter/methylammonium and ammonium permease/Rhesus factor) superfamily have only been previously characterized in flowering plants (angiosperms). Plant AMT1s are electrogenic, while plant AMT2s are electroneutral, and MEP and Rh transporters in other organisms are electroneutral. We analyzed the transport function of MpAMT1;2 from the basal land plant Marchantia polymorpha, a liverwort. MpAMT1;2 was shown to localize to the plasma membrane in Marchantia gametophyte thallus by stable transformation using a C-terminal citrine fusion. MpAMT1;2 expression was studied using quantitative real-time PCR and shown to be higher when plants were N deficient and lower when plants were grown on media containing ammonium, nitrate or the amino acid glutamine. Expression in Xenopus oocytes and analysis by electrophysiology revealed that MpAMT1;2 is an electrogenic ammonium transporter with a very high affinity for ammonium (7 µM at pH 5.6 and a membrane potential of -137 mV). A conserved inhibitory phosphorylation site identified in angiosperm AMT1s is also present in all AMT1s in Marchantia. Here we show that a phosphomimetic mutation T475D in MpAMT1;2 completely inhibits ammonium transport activity. The results indicate that MpAMT1;2 may be important for ammonium uptake into cells in the Marchantia thallus.
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Affiliation(s)
- Hanqing Guo
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, MN, USA
| | - Nu Wang
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, MN, USA
| | - Tami R McDonald
- Biology Department, St. Catherine University, St. Paul, MN, USA
| | - Anke Reinders
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, MN, USA
| | - John M Ward
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, MN, USA
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24
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Li Y, Xiao J, Chen L, Huang X, Cheng Z, Han B, Zhang Q, Wu C. Rice Functional Genomics Research: Past Decade and Future. MOLECULAR PLANT 2018; 11:359-380. [PMID: 29409893 DOI: 10.1016/j.molp.2018.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/15/2018] [Accepted: 01/23/2018] [Indexed: 05/22/2023]
Abstract
Rice (Oryza sativa) is a major staple food crop for more than 3.5 billion people worldwide. Understanding the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledons. Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially characterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.
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Affiliation(s)
- Yan Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lingling Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xuehui Huang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhukuan Cheng
- National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Han
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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25
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Chen L, Liao H. Engineering crop nutrient efficiency for sustainable agriculture. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:710-735. [PMID: 28600834 DOI: 10.1111/jipb.12559] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/21/2023]
Abstract
Increasing crop yields can provide food, animal feed, bioenergy feedstocks and biomaterials to meet increasing global demand; however, the methods used to increase yield can negatively affect sustainability. For example, application of excess fertilizer can generate and maintain high yields but also increases input costs and contributes to environmental damage through eutrophication, soil acidification and air pollution. Improving crop nutrient efficiency can improve agricultural sustainability by increasing yield while decreasing input costs and harmful environmental effects. Here, we review the mechanisms of nutrient efficiency (primarily for nitrogen, phosphorus, potassium and iron) and breeding strategies for improving this trait, along with the role of regulation of gene expression in enhancing crop nutrient efficiency to increase yields. We focus on the importance of root system architecture to improve nutrient acquisition efficiency, as well as the contributions of mineral translocation, remobilization and metabolic efficiency to nutrient utilization efficiency.
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Affiliation(s)
- Liyu Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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26
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Xuan W, Beeckman T, Xu G. Plant nitrogen nutrition: sensing and signaling. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:57-65. [PMID: 28614749 DOI: 10.1016/j.pbi.2017.05.010] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/24/2017] [Accepted: 05/28/2017] [Indexed: 05/26/2023]
Abstract
In response to external fluctuations of nitrogen (N) supplies, plants can activate complex regulatory networks for optimizing N uptake and utilization. In this review, we highlight novel N-responsive sensors, transporters, and signaling molecules recently identified in the dicot Arabidopsis and the monocot rice, and discuss their potential roles in N sensing and signaling. Furthermore, over the last couple of years, N sensing has been shown to be affected by multiple external factors, which act as local signals to trigger systemic signaling coordinated by long-distance mobile signals. Understanding of this complex regulatory network provides a foundation for the development of novel strategies to increase the root N acquisition efficiency under varying N conditions for crop production.
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Affiliation(s)
- Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; VIB-UGent Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, PR China.
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27
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Yamaki T, Otani M, Ono K, Mimura T, Oda K, Minamii T, Matsumoto S, Matsuo Y, Kawamukai M, Akihiro T. Isolation and characterization of rice cesium transporter genes from a rice-transporter-enriched yeast expression library. PHYSIOLOGIA PLANTARUM 2017; 160:425-436. [PMID: 28369958 DOI: 10.1111/ppl.12569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/14/2017] [Accepted: 02/20/2017] [Indexed: 05/02/2023]
Abstract
A considerable portion of agricultural land in central-east Japan has been contaminated by radioactive material, particularly radioactive Cs, due to the industrial accident at the Fukushima Daiichi nuclear power plant. Understanding the mechanism of absorption, translocation and accumulation of Cs+ in plants will greatly assist in developing approaches to help reduce the radioactive contamination of agricultural products. At present, however, little is known regarding the Cs+ transporters in rice. A transporter-enriched yeast expression library was constructed and the library was screened for Cs+ transporter genes. The 1452 full length cDNAs encoding transporter genes were obtained from the Rice Genome Resource Center and 1358 clones of these transporter genes were successively subcloned into yeast expression vectors; which were then transferred into yeast. Using this library, both positive and negative selection screens can be performed, which have not been previously possible. The constructed library is an excellent tool for the isolation of novel transporter genes. This library was screened for clones that were sensitive to Cs+ using a SD-Gal medium containing either 30 or 70 mM CsCl; resulting in the isolation of 13 Cs+ sensitive clones. 137 Cs absorption experiments were conducted and confirmed that all of the identified clones were able to absorb 137 Cs. A total of 3 potassium transporters, 2 ABC transporters and 1 NRAMP transporter were among the 13 identified clones.
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Affiliation(s)
- Tomohiro Yamaki
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Masahiro Otani
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Kohei Ono
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Takuro Mimura
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Koshiro Oda
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Takeshi Minamii
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Shingo Matsumoto
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Yuzy Matsuo
- Microtubule Cytoskeleton Laboratory, Francis Crick Institute Ringgold Standard Institution, London, UK
| | - Makoto Kawamukai
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Takashi Akihiro
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
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28
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Li H, Hu B, Chu C. Nitrogen use efficiency in crops: lessons from Arabidopsis and rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2477-2488. [PMID: 28419301 DOI: 10.1093/jxb/erx101] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Application of chemical fertilizers, especially nitrogen (N), to crops has increased dramatically in the last half century and therefore developing crop varieties with improved N use efficiency (NUE) is urgent for sustainable agriculture. N utilization procedures generally can be divided into uptake, transport, and assimilation. Transporters for nitrate or ammonium acquisition and enzymes for assimilation are among the essential components determining NUE, and many transcription factors also play a pivotal role in regulating N use-associated genes, thereby contributing to NUE. Although some efforts in improving NUE have been made in various plants, the regulatory mechanisms underlying NUE are still elusive, and NUE improvement in crop breeding is very limited. In this review, the crucial components involved in N utilization and the candidates with the potential for NUE improvement in dicot Arabidopsis and monocot rice are summarized. In addition, strategies based on new techniques which can be used for dissecting regulatory mechanisms of NUE and also the possible ways in which NUE can be improved in crops are discussed.
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Affiliation(s)
- Hua Li
- State Key Laboratory of Plant Genomics and CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bin Hu
- State Key Laboratory of Plant Genomics and CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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29
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Yang X, Xia X, Zhang Z, Nong B, Zeng Y, Xiong F, Wu Y, Gao J, Deng G, Li D. QTL Mapping by Whole Genome Re-sequencing and Analysis of Candidate Genes for Nitrogen Use Efficiency in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1634. [PMID: 28983307 PMCID: PMC5613164 DOI: 10.3389/fpls.2017.01634] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/06/2017] [Indexed: 05/22/2023]
Abstract
Nitrogen is a major nutritional element in rice production. However, excessive application of nitrogen fertilizer has caused severe environmental pollution. Therefore, development of rice varieties with improved nitrogen use efficiency (NUE) is urgent for sustainable agriculture. In this study, bulked segregant analysis (BSA) combined with whole genome re-sequencing (WGS) technology was applied to finely map quantitative trait loci (QTL) for NUE. A key QTL, designated as qNUE6 was identified on chromosome 6 and further validated by Insertion/Deletion (InDel) marker-based substitutional mapping in recombinants from F2 population (NIL-13B4 × GH998). Forty-four genes were identified in this 266.5-kb region. According to detection and annotation analysis of variation sites, 39 genes with large-effect single-nucleotide polymorphisms (SNPs) and large-effect InDels were selected as candidates and their expression levels were analyzed by qRT-PCR. Significant differences in the expression levels of LOC_Os06g15370 (peptide transporter PTR2) and LOC_Os06g15420 (asparagine synthetase) were observed between two parents (Y11 and GH998). Phylogenetic analysis in Arabidopsis thaliana identified two closely related homologs, AT1G68570 (AtNPF3.1) and AT5G65010 (ASN2), which share 72.3 and 87.5% amino acid similarity with LOC_Os06g15370 and LOC_Os06g15420, respectively. Taken together, our results suggested that qNUE6 is a possible candidate gene for NUE in rice. The fine mapping and candidate gene analysis of qNUE6 provide the basis of molecular breeding for genetic improvement of rice varieties with high NUE, and lay the foundation for further cloning and functional analysis.
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Affiliation(s)
- Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Xiuzhong Xia
- Rice Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Zongqiong Zhang
- Rice Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Baoxuan Nong
- Rice Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Yu Zeng
- Rice Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Faqian Xiong
- Cash Crops Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Yanyan Wu
- Biotechnology Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Ju Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural SciencesNanning, China
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Danting Li
- Rice Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
- *Correspondence: Danting Li
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30
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Hao D, Yang S, Huang Y, Su Y. Identification of structural elements involved in fine-tuning of the transport activity of the rice ammonium transporter OsAMT1;3. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:99-108. [PMID: 27423220 DOI: 10.1016/j.plaphy.2016.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/01/2016] [Accepted: 07/03/2016] [Indexed: 05/13/2023]
Abstract
Ammonium transporters (AMTs) are major routes for plant uptake of the NH4+-form nitrogen. Plant AMTs mediate predominantly the uptake of NH4+ and to a lesser extent, its organic analog methylammonium (MeA+). Mutagenesis studies on potential phosphorylation residues have achieved solid recognition that alteration of the phosphorylation status can result in allosteric regulation and impair the functionality of plant AMTs. However, molecular insights to the fine-tuning of a functional ammonium transporter remain less clear. In this report, we demonstrate that the rice root expressed OsAMT1;3 (Oryza sativa ammonium transporter 1;3) functions as a typical high-affinity NH4+ transporter and is weakly permeable to MeA+ using growth assays in NH4+ uptake defective yeast cells and electrophysiological measurements in Xenopus oocytes. Upon screening of six point mutations generated with the transporter, we identified two amino acid residues involved in the functional modulation of OsAMT1;3. The H199E mutation caused loss of transport activity whereas other five mutations retained the functionality of OsAMT1;3. Furthermore, the L56F mutation enabled respectively 5- and 3.5 -fold increased capability for NH4+ and MeA+ uptake with several-fold decreased affinity (Km) and accelerated Vmax values. Surprisingly, yeast cells expressing the L56F mutation shown increased Na+ toxicity leading to a speculation that enhanced Na+ permeation occurred with this mutation. The phenomenon was further supported by the observation of significant Na+ uptake current in oocytes. Our results seemingly support a speculation that the L56F mutation of OsAMT1;3 widens the substrate passage tunnel and allows enhanced permeability to NH4+ and larger ions MeA+ and Na+.
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Affiliation(s)
- Dongli Hao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunying Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yanan Huang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanhua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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31
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McDonald TR, Ward JM. Evolution of Electrogenic Ammonium Transporters (AMTs). FRONTIERS IN PLANT SCIENCE 2016; 7:352. [PMID: 27066024 PMCID: PMC4814505 DOI: 10.3389/fpls.2016.00352] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 03/07/2016] [Indexed: 05/05/2023]
Abstract
The ammonium transporter gene family consists of three main clades, AMT, MEP, and Rh. The evolutionary history of the AMT/MEP/Rh gene family is characterized by multiple horizontal gene transfer events, gene family expansion and contraction, and gene loss; thus the gene tree for this family of transporters is unlike the organismal tree. The genomes of angiosperms contain genes for both electrogenic and electroneutral ammonium transporters, but it is not clear how far back in the land plant lineage electrogenic ammonium transporters occur. Here, we place Marchantia polymorpha ammonium transporters in the AMT/MEP/Rh phylogeny and we show that AMTs from the liverwort M. polymorpha are electrogenic. This information suggests that electrogenic ammonium transport evolved at least as early as the divergence of bryophytes in the land plant lineage.
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Affiliation(s)
| | - John M. Ward
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, USA
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32
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Disruption of OsEXO70A1 Causes Irregular Vascular Bundles and Perturbs Mineral Nutrient Assimilation in Rice. Sci Rep 2015; 5:18609. [PMID: 26691393 PMCID: PMC4686888 DOI: 10.1038/srep18609] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/23/2015] [Indexed: 11/08/2022] Open
Abstract
Normal uptake, transportation, and assimilation of primary nutrients are essential to plant growth. Tracheary elements (TEs) are tissues responsible for the transport of water and minerals and characterized by patterned secondary cell wall (SCW) thickening. Exocysts are involved in the regulation of SCW deposition by mediating the targeted transport of materials and enzymes to specific membrane areas. EXO70s are highly duplicated in plants and provide exocysts with functional specificity. In this study, we report the isolation of a rice mutant rapid leaf senescence2 (rls2) that exhibits dwarfism, ferruginous spotted necrotic leaves, decreased hydraulic transport, and disordered primary nutrient assimilation. Histological analysis of rls2-1 mutants has indicated impaired cell expansion, collapsed vascular tissues, and irregular SCW deposition. Map-based cloning has revealed that RLS2 encodes OsEXO70A1, which is one of the 47 members of EXO70s in rice. RLS2 was widely expressed and spatially restricted in vascular bundles. Subcellular localization analysis demonstrated that RLS2 was present on both membrane and nuclear regions. Expression analysis revealed that mutations in rls2 triggers transcriptional fluctuation of orthologous EXO70 genes and affects genes involved in primary nutrient absorption and transport. In brief, our study revealed that RLS2 is required for normal vascular bundle differentiation and primary nutrient assimilation.
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