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Zheng X, Duan Y, Zheng H, Tang H, Zheng L, Yu X. Genome-Wide Identification and Characterization of the RWP-RK Proteins in Zanthoxylum armatum. Genes (Basel) 2024; 15:665. [PMID: 38927601 PMCID: PMC11202622 DOI: 10.3390/genes15060665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Apomixis is a common reproductive characteristic of Zanthoxylum plants, and RWP-RKs are plant-specific transcription factors known to regulate embryonic development. However, the genome-wide analysis and function prediction of RWP-RK family genes in Z. armatum are unclear. In this study, 36 ZaRWP-RK transcription factors were identified in the genome of Z. armatum, among which 15 genes belonged to the RKD subfamily and 21 belonged to the NLP subfamily. Duplication events of ZaRWP-RK genes were mainly segmental duplication, and synteny analysis revealed a close phylogenetic relationship between Z. armatum and Arabidopsis. The analysis of cis-elements indicated that ZaRWP-RK genes may be involved in the regulation of the embryonic development of Z. armatum by responding to plant hormones such as abscisic acid, auxin, and gibberellin. Results of a real-time PCR showed that the expression levels of most ZaRWP-RK genes were significantly increased from flowers to young fruits. Protein-protein interaction network analysis further revealed the potential roles of the ZaRWP-RK proteins in apomixis. Collectively, this study is expected to improve our understanding of ZaRWP-RK transcription factors and provide a theoretical basis for future investigations into the ZaRWP-RK genes and their regulatory mechanisms in the apomixis process of Z. armatum.
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Affiliation(s)
| | | | | | | | | | - Xiaobo Yu
- Southwest Research Center for Cross Breeding of Special Economic Plants, School of Life Science, Leshan Normal University, Leshan 614000, China; (X.Z.); (Y.D.); (H.Z.); (H.T.); (L.Z.)
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2
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Apodiakou A, Alseekh S, Hoefgen R, Whitcomb SJ. Overexpression of SLIM1 transcription factor accelerates vegetative development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2024; 15:1327152. [PMID: 38571711 PMCID: PMC10988502 DOI: 10.3389/fpls.2024.1327152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
The transcription factor Sulfur Limitation 1 (SLIM1) belongs to the plant-specific Ethylene Insenstive3-Like transcription factor family and is known to coordinate gene expression in response to sulfur deficiency. However, the roles of SLIM1 in nutrient-sufficient conditions have not been characterized. Employing constitutive SLIM1 overexpression (35S::SLIM1) and CRISPR/Cas9 mutant plants (slim1-cr), we identified several distinct phenotypes in nutrient-sufficient conditions in Arabidopsis thaliana. Overexpression of SLIM1 results in plants with approximately twofold greater rosette area throughout vegetative development. 35S::SLIM1 plants also bolt earlier and exhibit earlier downregulation of photosynthesis-associated genes and earlier upregulation of senescence-associated genes than Col-0 and slim1-cr plants. This suggests that overexpression of SLIM1 accelerates development in A. thaliana. Genome-wide differential gene expression analysis relative to Col-0 at three time points with slim1-cr and two 35S::SLIM1 lines allowed us to identify 1,731 genes regulated directly or indirectly by SLIM1 in vivo.
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Affiliation(s)
- Anastasia Apodiakou
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Saleh Alseekh
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Rainer Hoefgen
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Sarah J. Whitcomb
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- Cereal Crops Research Unit, United States Department of Agriculture - Agricultural Research Service, Madison, WI, United States
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Adavi SB, Sathee L. Calcium regulates primary nitrate response associated gene transcription in a time- and dose-dependent manner. PROTOPLASMA 2024; 261:257-269. [PMID: 37770644 DOI: 10.1007/s00709-023-01893-z] [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: 03/16/2023] [Accepted: 09/16/2023] [Indexed: 09/30/2023]
Abstract
Nitrate (NO3-) is the primary source of nitrogen preferred by most arable crops, including wheat. The pioneering experiment on primary nitrate response (PNR) was carried out three decades ago. Since then, much research has been carried out to understand the NO3- signaling. Nitrate is sensed by the dual affinity NO3- transceptor NPF6.3, which further relays the information to a master regulator NIN-like protein 7 (NLP7) through calcium-dependent protein kinases (CPK10, CPK30, CPK32), highlighting the importance of calcium ion (Ca2+) as one of the important secondary messengers in relaying the NO3- signaling in Arabidopsis. In a previous study, we found that Ca2+ regulates nitrogen starvation response in wheat. In this study, 10 days old NO3--starved wheat seedlings were exposed to various treatments. Our study on time course changes in expression of PNR sentinel genes; NPF6.1, NPF6.2, NRT2.1, NRT2.3, NR, and NIR in wheat manifest the highest level of expression at 30 min after NO3- exposure. The use of Ca2+ chelator EGTA confirmed the involvement of Ca2+ in the regulation of transcription of NPFs and NRTs as well the NO3- uptake. We also observed the NO3- dose-dependent and tissue-specific regulation of nitrate reductase activity involving Ca2+ as a mediator. The participation of Ca2+ in the PNR and NO3- signaling in wheat is confirmed by pharmacological analysis, physiological evidences, and protoplast-based Ca2+ localization.
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Affiliation(s)
- Sandeep B Adavi
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012.
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Zhang Z, Diao R, Sun J, Liu Y, Zhao M, Wang Q, Xu Z, Zhong B. Diversified molecular adaptations of inorganic nitrogen assimilation and signaling machineries in plants. THE NEW PHYTOLOGIST 2024; 241:2108-2123. [PMID: 38155438 DOI: 10.1111/nph.19508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Plants evolved sophisticated machineries to monitor levels of external nitrogen supply, respond to nitrogen demand from different tissues and integrate this information for coordinating its assimilation. Although roles of inorganic nitrogen in orchestrating developments have been studied in model plants and crops, systematic understanding of the origin and evolution of its assimilation and signaling machineries remains largely unknown. We expanded taxon samplings of algae and early-diverging land plants, covering all main lineages of Archaeplastida, and reconstructed the evolutionary history of core components involved in inorganic nitrogen assimilation and signaling. Most components associated with inorganic nitrogen assimilation were derived from the ancestral Archaeplastida. Improvements of assimilation machineries by gene duplications and horizontal gene transfers were evident during plant terrestrialization. Clusterization of genes encoding nitrate assimilation proteins might be an adaptive strategy for algae to cope with changeable nitrate availability in different habitats. Green plants evolved complex nitrate signaling machinery that was stepwise improved by domains shuffling and regulation co-option. Our study highlights innovations in inorganic nitrogen assimilation and signaling machineries, ranging from molecular modifications of proteins to genomic rearrangements, which shaped developmental and metabolic adaptations of plants to changeable nutrient availability in environments.
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Affiliation(s)
- Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Runjie Diao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengru Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zilong Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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Wu J, Sun LQ, Song Y, Bai Y, Wan GY, Wang JX, Xia JQ, Zhang ZY, Zhang ZS, Zhao Z, Xiang CB. The OsNLP3/4-OsRFL module regulates nitrogen-promoted panicle architecture in rice. THE NEW PHYTOLOGIST 2023; 240:2404-2418. [PMID: 37845836 DOI: 10.1111/nph.19318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/16/2023] [Indexed: 10/18/2023]
Abstract
Rice panicles, a major component of yield, are regulated by phytohormones and nutrients. How mineral nutrients promote panicle architecture remains largely unknown. Here, we report that NIN-LIKE PROTEIN3 and 4 (OsNLP3/4) are crucial positive regulators of rice panicle architecture in response to nitrogen (N). Loss-of-function mutants of either OsNLP3 or OsNLP4 produced smaller panicles with reduced primary and secondary branches and fewer grains than wild-type, whereas their overexpression plants showed the opposite phenotypes. The OsNLP3/4-regulated panicle architecture was positively correlated with N availability. OsNLP3/4 directly bind to the promoter of OsRFL and activate its expression to promote inflorescence meristem development. Furthermore, OsRFL activates OsMOC1 expression by binding to its promoter. Our findings reveal the novel N-responsive OsNLP3/4-OsRFL-OsMOC1 module that integrates N availability to regulate panicle architecture, shedding light on how N nutrient signals regulate panicle architecture and providing candidate targets for the improvement of crop yield.
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Affiliation(s)
- Jie Wu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Liang-Qi Sun
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Ying Song
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Yu Bai
- Experimental Center of Engineering and Materials Science, University of Science and Technology of China, Hefei, 230027, China
| | - Guang-Yu Wan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Jing-Xian Wang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Jin-Qiu Xia
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Zheng-Yi Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Zi-Sheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Zhong Zhao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Cheng-Bin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
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6
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Yan D, Nambara E. Conserved and unique functions of NIN-like proteins in nitrate sensing and signaling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111842. [PMID: 37633494 DOI: 10.1016/j.plantsci.2023.111842] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Nitrogen is the most abundant element in the atmosphere and serves as the foundation block of life, including plants on earth. Unlike carbon fixation through photosynthesis, plants rely heavily on external supports to acquire nitrogen. To this end, plants have adapted various strategies such as forming mutualistic relationships with nitrogen-fixing bacteria and evolving a large regulatory network that includes multiple transporters, sensors, and transcription factors for fine-tuning nitrate sensing and signaling. Nodule Inception (NIN) and NIN-like protein (NLP) are central in this network by executing multiple functions such as initiating and regulating the nodule symbiosis for nitrogen fixation, acting as the intracellular sensor to monitor the nitrate fluctuations in the environment, and activating the transcription of nitrate-responsive genes for optimal nitrogen uptake, assimilation, and usage. The involvement of NLPs in intracellular nitrate binding and early nitrate responses highlight their pivotal role in the primary nitrate response (PNR). Genome-wide reprogramming in response to nitrate by NLP is highly transient and rapid, requiring regulation in a precise and dynamic manner. This review aims to summarize recent progress in the study of NIN/NLP for a better understanding of the molecular basis of their roles and regulations in nitrate sensing and signaling, with the hope of shedding light on increasing biological nitrogen fixation and improving nitrogen use efficiency (NUE) to minimize fertilizer input in agriculture.
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Affiliation(s)
- Dawei Yan
- Department of Cell & Systems Biology, University of Toronto, Toronto M5S3B2, Ontario, Canada.
| | - Eiji Nambara
- Department of Cell & Systems Biology, University of Toronto, Toronto M5S3B2, Ontario, Canada
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Jin Y, Luo J, Yang Y, Jia J, Sun M, Wang X, Khan I, Huang D, Huang L. The evolution and expansion of RWP-RK gene family improve the heat adaptability of elephant grass (Pennisetum purpureum Schum.). BMC Genomics 2023; 24:510. [PMID: 37653366 PMCID: PMC10472707 DOI: 10.1186/s12864-023-09550-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 08/02/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Along with global warming, resulting in crop production, exacerbating the global food crisis. Therefore, it is urgent to study the mechanism of plant heat resistance. However, crop resistance genes were lost due to long-term artificial domestication. By analyzing the potential heat tolerance genes and molecular mechanisms in other wild materials, more genetic resources can be provided for improving the heat tolerance of crops. Elephant grass (Pennisetum purpureum Schum.) has strong adaptability to heat stress and contains abundant heat-resistant gene resources. RESULTS Through sequence structure analysis, a total of 36 RWP-RK members were identified in elephant grass. Functional analysis revealed their close association with heat stress. Four randomly selected RKDs (RKD1.1, RKD4.3, RKD6.6, and RKD8.1) were analyzed for expression, and the results showed upregulation under high temperature conditions, suggesting their active role in response to heat stress. The members of RWP-RK gene family (36 genes) in elephant grass were 2.4 times higher than that of related tropical crops, rice (15 genes) and sorghum (15 genes). The 36 RWPs of elephant grass contain 15 NLPs and 21 RKDs, and 73% of RWPs are related to WGD. Among them, combined with the DAP-seq results, it was found that RWP-RK gene family expansion could improve the heat adaptability of elephant grass by enhancing nitrogen use efficiency and peroxidase gene expression. CONCLUSIONS RWP-RK gene family expansion in elephant grass is closely related to thermal adaptation evolution and speciation. The RKD subgroup showed a higher responsiveness than the NLP subgroup when exposed to high temperature stress. The promoter region of the RKD subgroup contains a significant number of MeJA and ABA responsive elements, which may contribute to their positive response to heat stress. These results provided a scientific basis for analyzing the heat adaptation mechanism of elephant grass and improving the heat tolerance of other crops.
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Affiliation(s)
- Yarong Jin
- Herbivorous Livestock Research Institute, Chongqing Academy of Animal Sciences, Chongqing, 402460, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinchan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuchen Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiyuan Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Imran Khan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Dejun Huang
- Herbivorous Livestock Research Institute, Chongqing Academy of Animal Sciences, Chongqing, 402460, China.
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Lin C, Guo X, Yu X, Li S, Li W, Yu X, An F, Zhao P, Ruan M. Genome-Wide Survey of the RWP-RK Gene Family in Cassava ( Manihot esculenta Crantz) and Functional Analysis. Int J Mol Sci 2023; 24:12925. [PMID: 37629106 PMCID: PMC10454212 DOI: 10.3390/ijms241612925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The plant-specific RWP-RK transcription factor family plays a central role in the regulation of nitrogen response and gametophyte development. However, little information is available regarding the evolutionary relationships and characteristics of the RWP-RK family genes in cassava, an important tropical crop. Herein, 13 RWP-RK proteins identified in cassava were unevenly distributed across 9 of the 18 chromosomes (Chr), and these proteins were divided into two clusters based on their phylogenetic distance. The NLP subfamily contained seven cassava proteins including GAF, RWP-RK, and PB1 domains; the RKD subfamily contained six cassava proteins including the RWP-RK domain. Genes of the NLP subfamily had a longer sequence and more introns than the RKD subfamily. A large number of hormone- and stress-related cis-acting elements were found in the analysis of RWP-RK promoters. Real-time quantitative PCR revealed that all MeNLP1-7 and MeRKD1/3/5 genes responded to different abiotic stressors (water deficit, cold temperature, mannitol, polyethylene glycol, NaCl, and H2O2), hormonal treatments (abscisic acid and methyl jasmonate), and nitrogen starvation. MeNLP3/4/5/6/7 and MeRKD3/5, which can quickly and efficiently respond to different stresses, were found to be important candidate genes for further functional assays in cassava. The MeRKD5 and MeNLP6 proteins were localized to the cell nucleus in tobacco leaf. Five and one candidate proteins interacting with MeRKD5 and MeNLP6, respectively, were screened from the cassava nitrogen starvation library, including agamous-like mads-box protein AGL14, metallothionein 2, Zine finger FYVE domain containing protein, glyceraldehyde-3-phosphate dehydrogenase, E3 Ubiquitin-protein ligase HUWE1, and PPR repeat family protein. These results provided a solid basis to understand abiotic stress responses and signal transduction mediated by RWP-RK genes in cassava.
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Affiliation(s)
- Chenyu Lin
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (C.L.); (X.G.); (X.Y.)
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Xin Guo
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (C.L.); (X.G.); (X.Y.)
| | - Xiaohui Yu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (C.L.); (X.G.); (X.Y.)
| | - Shuxia Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Wenbin Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Xiaoling Yu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Feng An
- Hainan Danzhou Agro-Ecosystem National Observation and Research Station, Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China;
| | - Pingjuan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Mengbin Ruan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
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9
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Wu Y, Su SX, Wang T, Peng GH, He L, Long C, Li W. Identification and expression characteristics of NLP (NIN-like protein) gene family in pepper (Capsicum annuum L.). Mol Biol Rep 2023; 50:6655-6668. [PMID: 37358766 DOI: 10.1007/s11033-023-08587-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND Pepper (Capsicum annum L.) is the main crop in the vegetable industry. The growth and development of peppers are regulated by nitrate, but there is limited research on the molecular mechanisms of nitrate absorption and assimilation in peppers. A plant specific transcription factor NLP plays an important role in nitrate signal transduction. METHODS AND RESULTS In this study, a total of 7 NLP members were identified based on pepper genome data. Two nitrogen transport elements (GCN4) were found in the CaNLP5 promoter. In the phylogenetic tree, CaNLP members are divided into three branches, with pepper NLP and tomato NLP having the closest genetic relationship. The expression levels of CaNLP1, CaNLP3, and CaNLP4 are relatively high in the roots, stems, and leaves. The expression level of CaNLP7 gene is relatively high during the 5-7 days of pepper fruit color transformation. After various non-Biotic stress and hormone treatments, the expression of CaNLP1 was at a high level. The expression of CaNLP3 and CaNLP4 was down regulated in leaves, but up regulated in roots. Under conditions of nitrogen deficiency and sufficient nitrate, the expression patterns of NLP genes in pepper leaves and roots were determined. CONCLUSION These results provide important insights into the multiple functions of CaNLPs in regulating nitrate absorption and transport.
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Affiliation(s)
- Yuan Wu
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Industry Technology Research Academy of Pepper, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Shi-Xian Su
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Tao Wang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Industry Technology Research Academy of Pepper, Guizhou University, Guiyang, 550025, China
| | - Gui-Hua Peng
- Research Institute of Pepper, Zunyi, 563000, Guizhou Province, China
| | - Lei He
- Research Institute of Pepper, Zunyi, 563000, Guizhou Province, China
| | - Cha Long
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Wei Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China.
- Industry Technology Research Academy of Pepper, Guizhou University, Guiyang, 550025, China.
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China.
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10
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Yu J, Yuan Y, Dong L, Cui G. Genome-wide investigation of NLP gene family members in alfalfa (Medicago sativa L.): evolution and expression profiles during development and stress. BMC Genomics 2023; 24:320. [PMID: 37312045 DOI: 10.1186/s12864-023-09418-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND NIN-like protein (NLP) transcription factors (TFs) compose a plant-specific gene family whose members play vital roles in plant physiological processes, especially in the regulation of plant growth and the response to nitrate-nitrogen. However, no systematic identification or analysis of the NLP gene family has been reported in alfalfa. The recently completed whole-genome sequence of alfalfa has allowed us to investigate genome-wide characteristics and expression profiles. RESULTS 53 MsNLP genes were identified from alfalfa and renamed according to their respective chromosome distributions. Phylogenetic analysis demonstrated that these MsNLPs can be classified into three groups on the basis of their conserved domains. Gene structure and protein motif analyses showed that closely clustered MsNLP genes were relatively conserved within each subgroup. Synteny analysis revealed four fragment duplication events of MsNLPs in alfalfa. The ratios of nonsynonymous (Ka) and synonymous (Ks) substitution rates of gene pairs indicated that the MsNLP genes underwent purifying selection during evolution. Examination of the expression patterns of different tissues revealed specific expression patterns of the MsNLP genes in the leaves, indicating that these genes are involved in plant functional development. Prediction of cis-acting regulatory elements and expression profiles further demonstrated that the MsNLP genes might play important roles in the response to abiotic stress and in phytohormone signal transduction processes. CONCLUSION This study represents the first genome-wide characterization of MsNLP in alfalfa. Most MsNLPs are expressed mainly in leaves and respond positively to abiotic stresses and hormonal treatments. These results provide a valuable resource for an improved understanding of the characteristics and biological roles of the MsNLP genes in alfalfa.
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Affiliation(s)
- Jinqiu Yu
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Yuying Yuan
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Linling Dong
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Guowen Cui
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China.
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11
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Durand M, Brehaut V, Clement G, Kelemen Z, Macé J, Feil R, Duville G, Launay-Avon A, Roux CPL, Lunn JE, Roudier F, Krapp A. The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply. THE PLANT CELL 2023; 35:1429-1454. [PMID: 36752317 PMCID: PMC10118280 DOI: 10.1093/plcell/koad025] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Nitrate signaling improves plant growth under limited nitrate availability and, hence, optimal resource use for crop production. Whereas several transcriptional regulators of nitrate signaling have been identified, including the Arabidopsis thaliana transcription factor NIN-LIKE PROTEIN7 (NLP7), additional regulators are expected to fine-tune this pivotal physiological response. Here, we characterized Arabidopsis NLP2 as a top-tier transcriptional regulator of the early nitrate response gene regulatory network. NLP2 interacts with NLP7 in vivo and shares key molecular features such as nitrate-dependent nuclear localization, DNA-binding motif, and some target genes with NLP7. Genetic, genomic, and metabolic approaches revealed a specific role for NLP2 in the nitrate-dependent regulation of carbon and energy-related processes that likely influence plant growth under distinct nitrogen environments. Our findings highlight the complementarity and specificity of NLP2 and NLP7 in orchestrating a multitiered nitrate regulatory network that links nitrate assimilation with carbon and energy metabolism for efficient nitrogen use and biomass production.
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Affiliation(s)
- Mickaël Durand
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
- UMR CNRS 7267, EBI Ecologie et Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Virginie Brehaut
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Gilles Clement
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Zsolt Kelemen
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Julien Macé
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm D-14476, Germany
| | - Garry Duville
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
| | - Christine Paysant-Le Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm D-14476, Germany
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Anne Krapp
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
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12
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Amin N, Ahmad N, Khalifa MAS, Du Y, Mandozai A, Khattak AN, Piwu W. Identification and Molecular Characterization of RWP-RK Transcription Factors in Soybean. Genes (Basel) 2023; 14:genes14020369. [PMID: 36833296 PMCID: PMC9956977 DOI: 10.3390/genes14020369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
The RWP-RK is a small family of plant-specific transcription factors that are mainly involved in nitrate starvation responses, gametogenesis, and root nodulation. To date, the molecular mechanisms underpinning nitrate-regulated gene expression in many plant species have been extensively studied. However, the regulation of nodulation-specific NIN proteins during nodulation and rhizobial infection under nitrogen starvation in soybean still remain unclear. Here, we investigated the genome-wide identification of RWP-RK transcription factors and their essential role in nitrate-inducible and stress-responsive gene expression in soybean. In total, 28 RWP-RK genes were identified from the soybean genome, which were unevenly distributed on 20 chromosomes from 5 distinct groups during phylogeny classification. The conserved topology of RWP-RK protein motifs, cis-acting elements, and functional annotation has led to their potential as key regulators during plant growth, development, and diverse stress responses. The RNA-seq data revealed that the up-regulation of GmRWP-RK genes in the nodules indicated that these genes might play crucial roles during root nodulation in soybean. Furthermore, qRT-PCR analysis revealed that most GmRWP-RK genes under Phytophthora sojae infection and diverse environmental conditions (such as heat, nitrogen, and salt) were significantly induced, thus opening a new window of possibilities into their regulatory roles in adaptation mechanisms that allow soybean to tolerate biotic and abiotic stress. In addition, the dual luciferase assay indicated that GmRWP-RK1 and GmRWP-RK2 efficiently bind to the promoters of GmYUC2, GmSPL9, and GmNIN, highlighting their possible involvement in nodule formation. Together, our findings provide novel insights into the functional role of the RWP-RK family during defense responses and root nodulation in soybean.
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Affiliation(s)
- Nooral Amin
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mohamed A. S. Khalifa
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Yeyao Du
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Ajmal Mandozai
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Aimal Nawaz Khattak
- Institute of Crop Science Chinese Academy of Agriculture Sciences, Beijing 100000, China
| | - Wang Piwu
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence:
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13
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Han X, Wang J, Zhang Y, Kong Y, Dong H, Feng X, Li T, Zhou C, Yu J, Xin D, Chen Q, Qi Z. Changes in the m6A RNA methylome accompany the promotion of soybean root growth by rhizobia under cadmium stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129843. [PMID: 36113351 DOI: 10.1016/j.jhazmat.2022.129843] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/13/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) is the most widely distributed heavy metal pollutant in soil and has significant negative effects on crop yields and human health. Rhizobia can enhance soybean growth in the presence of heavy metals, and the legume-rhizobia symbiosis has been used to promote heavy-metal phytoremediation, but much remains to be learned about the molecular networks that underlie these effects. Here, we demonstrated that soybean root growth was strongly suppressed after seven days of Cd exposure but that the presence of rhizobia largely eliminated this effect, even prior to nodule development. Moreover, rhizobia did not appear to promote root growth by limiting plant Cd uptake: seedlings with and without rhizobia had similar root Cd concentrations. Previous studies have demonstrated a role for m6A RNA methylation in the response of rice and barley to Cd stress. We therefore performed transcriptome-wide m6A methylation profiling to investigate changes in the soybean RNA methylome in response to Cd with and without rhizobia. Here, we provide some of the first data on transcriptome-wide m6a RNA methylation patterns in soybean; m6A modifications were concentrated at the 3' UTR of transcripts and showed a positive relationship with transcript abundance. Transcriptome-wide m6A RNA methylation peaks increased in the presence of Cd, and the integration of m6A methylome and transcriptome results enabled us to identify 154 genes whose transcripts were both differentially methylated and differentially expressed in response to Cd stress. Annotation results suggested that these genes were associated with Ca2+ homeostasis, ROS pathways, polyamine metabolism, MAPK signaling, hormones, and biotic stress responses. There were 176 differentially methylated and expressed transcripts under Cd stress in the presence of rhizobia. In contrast to the Cd-only gene set, they were also enriched in genes related to auxin, jasmonic acid, and brassinosteroids, as well as abiotic stress tolerance. They contained fewer genes related to Ca2+ homeostasis and also included candidates with known functions in the legume-rhizobia symbiosis. These findings offer new insights into how rhizobia promote soybean root growth under Cd stress; they provide candidate genes for research on plant heavy metal responses and for the use of legumes in phytoremediation.
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Affiliation(s)
- Xue Han
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Jialin Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Yu Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Youlin Kong
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Huiying Dong
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Xuezhen Feng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Tianshu Li
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Changjun Zhou
- Daqing Branch, Heilongjiang Academy of Agricultural Sciences, Daqing 163316, Heilongjiang, People's Republic of China
| | - Jidong Yu
- Daqing Branch, Heilongjiang Academy of Agricultural Sciences, Daqing 163316, Heilongjiang, People's Republic of China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China.
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China.
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14
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Kasemsap P, Bloom AJ. Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 12:85. [PMID: 36616214 PMCID: PMC9823454 DOI: 10.3390/plants12010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.
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15
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Parakkunnel R, Naik K B, Vanishree G, C S, Purru S, Bhaskar K U, Bhat KV, Kumar S. Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome. FRONTIERS IN PLANT SCIENCE 2022; 13:1076229. [PMID: 36618639 PMCID: PMC9817154 DOI: 10.3389/fpls.2022.1076229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Susmita C
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
| | - Supriya Purru
- ICAR- National Academy of Agricultural Research Management, Hyderabad, Telengana, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - KV. Bhat
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
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16
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Gao Y, Qi S, Wang Y. Nitrate signaling and use efficiency in crops. PLANT COMMUNICATIONS 2022; 3:100353. [PMID: 35754172 PMCID: PMC9483113 DOI: 10.1016/j.xplc.2022.100353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Nitrate (NO3-) is not only an essential nutrient but also an important signaling molecule for plant growth. Low nitrogen use efficiency (NUE) of crops is causing increasingly serious environmental and ecological problems. Understanding the molecular mechanisms of NO3- regulation in crops is crucial for NUE improvement in agriculture. During the last several years, significant progress has been made in understanding the regulation of NO3- signaling in crops, and some key NO3- signaling factors have been shown to play important roles in NO3- utilization. However, no detailed reviews have yet summarized these advances. Here, we focus mainly on recent advances in crop NO3- signaling, including short-term signaling, long-term signaling, and the impact of environmental factors. We also review the regulation of crop NUE by crucial genes involved in NO3- signaling. This review provides useful information for further research on NO3- signaling in crops and a theoretical basis for breeding new crop varieties with high NUE, which has great significance for sustainable agriculture.
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Affiliation(s)
- Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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17
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Mathesius U. Are legumes different? Origins and consequences of evolving nitrogen fixing symbioses. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153765. [PMID: 35952452 DOI: 10.1016/j.jplph.2022.153765] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 05/14/2023]
Abstract
Nitrogen fixing symbioses between plants and bacteria are ancient and, while not numerous, are formed in diverse lineages of plants ranging from microalgae to angiosperms. One symbiosis stands out as the most widespread one is that between legumes and rhizobia, leading to the formation of nitrogen-fixing nodules. The legume family is one of the largest and most diverse group of plants and legumes have been used by humans since the beginning of agriculture, both as high nitrogen food, as well as pastures and rotation crops. One open question is whether their ability to form a nitrogen-fixing symbiosis has contributed to legumes' success, and whether legumes have any unique characteristics that have made them more diverse and widespread than other groups of plants. This review examines the evolutionary journey that has led to the diversification of legumes, in particular its nitrogen-fixing symbiosis, and asks four questions to investigate which legume traits might have contributed to their success: 1. In what ways do legumes differ from other plant groups that have evolved nitrogen-fixing symbioses? In order to answer this question, the characteristics of the symbioses, and efficiencies of nitrogen fixation are compared between different groups of nitrogen fixing plants. 2. Could certain unique features of legumes be a reason for their success? This section examines the manifestations and possible benefits of a nitrogen-rich 'lifestyle' in legumes. 3. If nitrogen fixation was a reason for such a success, why have some species lost the symbiosis? Formation of symbioses has trade-offs, and while these are less well known for non-legumes, there are known energetic and ecological reasons for loss of symbiotic potential in legumes. 4. What can we learn from the unique traits of legumes for future crop improvements? While exploiting some of the physiological properties of legumes could be used to improve legume breeding, our increasing molecular understanding of the essential regulators of root nodule symbioses raise hope of creating new nitrogen fixing symbioses in other crop species.
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Affiliation(s)
- Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, The Australian National University, 134 Linnaeus Way, Canberra, ACT, 2601, Australia.
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18
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Wu Z, Chen H, Pan Y, Feng H, Fang D, Yang J, Wang Y, Yang J, Sahu SK, Liu J, Xing Y, Wang X, Liu M, Luo X, Gao P, Li L, Liu Z, Yang H, Liu X, Xu X, Liu H, Wang E. Genome of Hippophae rhamnoides provides insights into a conserved molecular mechanism in actinorhizal and rhizobial symbioses. THE NEW PHYTOLOGIST 2022; 235:276-291. [PMID: 35118662 DOI: 10.1111/nph.18017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Sea buckthorn (Hippophae rhamnoides), a horticulturally multipurpose species in the family Elaeagnaceae, can build associations with Frankia actinomycetes to enable symbiotic nitrogen-fixing. Currently, no high-quality reference genome is available for an actinorhizal plant, which greatly hinders the study of actinorhizal symbiotic nodulation. Here, by combining short-read, long-read and Hi-C sequencing technologies, we generated a chromosome-level reference genome of H. rhamnoides (scaffold N50: 65 Mb, and genome size: 730 Mb) and predicted 30 812 protein-coding genes mainly on 12 pseudochromosomes. Hippophae rhamnoides was found to share a high proportion of symbiotic nodulation genes with Medicago truncatula, implying a shared molecular mechanism between actinorhizal and rhizobial symbioses. Phylogenetic analysis clustered the three paralogous NODULE INCEPTION (NIN) genes of H. rhamnoides with those of other nodulating species, forming the NIN group that most likely evolved from the ancestral NLP group. The genome of H. rhamnoides will help us to decipher the underlying genetic programming of actinorhizal symbiosis, and our high-quality genome and transcriptomic resources will make H. rhamnoides a new excellent model plant for actinorhizal symbiosis research.
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Affiliation(s)
- Zefeng Wu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Hongyun Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Ya Pan
- Jinzhong Institute of Forestry, Jinzhong, Shanxi, 030600, China
| | - Huan Feng
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jun Yang
- Shanghai Chenshan Plant Science Research Center (CAS), Shanghai, 210602, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jianling Liu
- Jinzhong Institute of Forestry, Jinzhong, Shanxi, 030600, China
| | - Yu'e Xing
- Jinzhong Institute of Forestry, Jinzhong, Shanxi, 030600, China
| | - Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xinyue Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Peng Gao
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Lifeng Li
- Jinzhong Municipal Planning and Natural Resources Bureau, Jinzhong, Shanxi, 030600, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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Guo S, Arshad A, Yang L, Qin Y, Mu X, Mi G. Comparative Transcriptome Analysis Reveals Common and Developmental Stage-Specific Genes That Respond to Low Nitrogen in Maize Leaves. PLANTS 2022; 11:plants11121550. [PMID: 35736701 PMCID: PMC9230787 DOI: 10.3390/plants11121550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/04/2022] [Accepted: 06/04/2022] [Indexed: 11/16/2022]
Abstract
A growing leaf can be divided into three sections: division zone, elongation zone, and maturation zone. In previous studies, low nitrogen (LN) inhibited maize growth and development, especially leaf growth; however, the gene expression in response to LN in different regions in leaf were not clear. Here, using hydroponics and a transcriptome approach, we systematically analyzed the molecular responses of those zones and differentially expressed genes (DEG) in response to LN supply. Developmental stage-specific genes (SGs) were highly stage-specific and involved in distinct biological processes. SGs from division (SGs–DZ) and elongation zones (SGs–EZ) were more related to developmentally dependent processes, whereas SGs of the maturation zone (SGs–MZ) were more related to metabolic processes. The common genes (CGs) were overrepresented in carbon and N metabolism, suggesting that rebalancing carbon and N metabolism in maize leaves under LN condition was independent of developmental stage. Coexpression modules (CMs) were also constructed in our experiment and a total of eight CMs were detected. Most of SGs–DZ and SGs–EZ were classified into a set termed CM turquoise, which was mainly enriched in ribosome and DNA replication, whereas several genes from SGs–MZ and CGs were clustered into CM blue, which mainly focused on photosynthesis and carbon metabolism. Finally, a comprehensive coexpression network was extracted from CM blue, and several maize CONSTANS-LIKE(ZmCOL) genes seemed to participate in regulating photosynthesis in maize leaves under LN condition in a developmental stage-specific manner. With this study, we uncovered the LN-responsive CGs and SGs that are important for promoting plant growth and development under insufficient nitrogen supply.
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Affiliation(s)
- Song Guo
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (S.G.); (Y.Q.)
| | - Adnan Arshad
- College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China;
- PODA Organization, Islamabad 44000, Pakistan
| | - Lan Yang
- College of Resources and Environmental, Hunan Agricultural University, Changsha 410128, China;
| | - Yusheng Qin
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (S.G.); (Y.Q.)
| | - Xiaohuan Mu
- Synergetic Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China;
| | - Guohua Mi
- College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China;
- National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing 100193, China
- Correspondence: ; Tel.: +86-10-62734454
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20
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Zhang ZS, Xia JQ, Alfatih A, Song Y, Huang YJ, Sun LQ, Wan GY, Wang SM, Wang YP, Hu BH, Zhang GH, Qin P, Li SG, Yu LH, Wu J, Xiang CB. Rice NIN-LIKE PROTEIN 3 modulates nitrogen use efficiency and grain yield under nitrate-sufficient conditions. PLANT, CELL & ENVIRONMENT 2022; 45:1520-1536. [PMID: 35150141 DOI: 10.1111/pce.14294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen (N) is an essential macronutrient for crop growth and yield. Improving the N use efficiency (NUE) of crops is important to agriculture. However, the molecular mechanisms underlying NUE regulation remain largely elusive. Here we report that the OsNLP3 (NIN-like protein 3) regulates NUE and grain yield in rice under N sufficient conditions. OsNLP3 transcript level is significantly induced by N starvation and its protein nucleocytosolic shuttling is specifically regulated by nitrate. Loss-of-function of OsNLP3 reduces plant growth, grain yield, and NUE under sufficient nitrate conditions, whereas under low nitrate or different ammonium conditions, osnlp3 mutants show no clear difference from the wild type. Importantly, under sufficient N conditions in the field, OsNLP3 overexpression lines display improved grain yield and NUE compared with the wild type. OsNLP3 orchestrates the expression of multiple N uptake and assimilation genes by directly binding to the nitrate-responsive cis-elements in their promoters. Overall, our study demonstrates that OsNLP3, together with OsNLP1 and OsNLP4, plays overlapping and differential roles in N acquisition and NUE, and modulates NUE and the grain yield increase promoted by N fertilizer. Therefore, OsNLP3 is a promising candidate gene for the genetic improvement of grain yield and NUE in rice.
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Affiliation(s)
- Zi-Sheng Zhang
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Jin-Qiu Xia
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Alamin Alfatih
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Ying Song
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yi-Jie Huang
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Liang-Qi Sun
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Guang-Yu Wan
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Shi-Mei Wang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yu-Ping Wang
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Bin-Hua Hu
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Guo-Hua Zhang
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Peng Qin
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Shi-Gui Li
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Lin-Hui Yu
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shanxi, China
| | - Jie Wu
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Cheng-Bin Xiang
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
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Hernández-Reyes C, Lichtenberg E, Keller J, Delaux PM, Ott T, Schenk ST. NIN-Like Proteins: Interesting Players in Rhizobia-Induced Nitrate Signaling Response During Interaction with Non-Legume Host Arabidopsis thaliana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:230-243. [PMID: 34813707 DOI: 10.1094/mpmi-10-21-0261-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nitrogen is an essential macronutrient and a key cellular messenger. Plants have evolved refined molecular systems to sense the cellular nitrogen status. This is exemplified by the root nodule symbiosis between legumes and symbiotic rhizobia, where nitrate availability inhibits this mutualistic interaction. Additionally, nitrate also functions as a metabolic messenger, resulting in nitrate signaling cascades which intensively crosstalk with other physiological pathways. Nodule inception-like proteins (NLPs) are key players in nitrate signaling and regulate nitrate-dependent transcription during legume-rhizobia interactions. Nevertheless, the coordinated interplay between nitrate signaling pathways and rhizobacteria-induced responses remains to be elucidated. In our study, we investigated rhizobia-induced changes in the root system architecture of the non-legume host arabidopsis under different nitrate conditions. We demonstrate that rhizobium-induced lateral root growth and increased root hair length and density are regulated by a nitrate-related signaling pathway. Key players in this process are AtNLP4 and AtNLP5, because the corresponding mutants failed to respond to rhizobia. At the cellular level, AtNLP4 and AtNLP5 control a rhizobia-induced decrease in cell elongation rates, while additional cell divisions occurred independently of AtNLP4. In summary, our data suggest that root morphological responses to rhizobia are coordinated by a newly considered nitrate-related NLP pathway that is evolutionarily linked to regulatory circuits described in legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Casandra Hernández-Reyes
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS-Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | | | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, INP Toulouse, 31326 Castanet Tolosan, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, INP Toulouse, 31326 Castanet Tolosan, France
| | - Thomas Ott
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS-Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Sebastian T Schenk
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
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22
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Gu B, Chen Y, Xie F, Murray JD, Miller AJ. Inorganic Nitrogen Transport and Assimilation in Pea ( Pisum sativum). Genes (Basel) 2022; 13:158. [PMID: 35052498 PMCID: PMC8774688 DOI: 10.3390/genes13010158] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
The genome sequences of several legume species are now available allowing the comparison of the nitrogen (N) transporter inventories with non-legume species. A survey of the genes encoding inorganic N transporters and the sensing and assimilatory families in pea, revealed similar numbers of genes encoding the primary N assimilatory enzymes to those in other types of plants. Interestingly, we find that pea and Medicago truncatula have fewer members of the NRT2 nitrate transporter family. We suggest that this difference may result from a decreased dependency on soil nitrate acquisition, as legumes have the capacity to derive N from a symbiotic relationship with diazotrophs. Comparison with M. truncatula, indicates that only one of three NRT2s in pea is likely to be functional, possibly indicating less N uptake before nodule formation and N-fixation starts. Pea seeds are large, containing generous amounts of N-rich storage proteins providing a reserve that helps seedling establishment and this may also explain why fewer high affinity nitrate transporters are required. The capacity for nitrate accumulation in the vacuole is another component of assimilation, as it can provide a storage reservoir that supplies the plant when soil N is depleted. Comparing published pea tissue nitrate concentrations with other plants, we find that there is less accumulation of nitrate, even in non-nodulated plants, and that suggests a lower capacity for vacuolar storage. The long-distance transported form of organic N in the phloem is known to be specialized in legumes, with increased amounts of organic N molecules transported, like ureides, allantoin, asparagine and amides in pea. We suggest that, in general, the lower tissue and phloem nitrate levels compared with non-legumes may also result in less requirement for high affinity nitrate transporters. The pattern of N transporter and assimilatory enzyme distribution in pea is discussed and compared with non-legumes with the aim of identifying future breeding targets.
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Affiliation(s)
- Benguo Gu
- Biochemistry & Metabolism Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (B.G.); (Y.C.)
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
| | - Yi Chen
- Biochemistry & Metabolism Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (B.G.); (Y.C.)
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
| | - Jeremy D. Murray
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
| | - Anthony J. Miller
- Biochemistry & Metabolism Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (B.G.); (Y.C.)
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
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23
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Liu M, Zhi X, Wang Y, Wang Y. Genome-wide survey and expression analysis of NIN-like Protein (NLP) genes reveals its potential roles in the response to nitrate signaling in tomato. BMC PLANT BIOLOGY 2021; 21:347. [PMID: 34301191 PMCID: PMC8299697 DOI: 10.1186/s12870-021-03116-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/29/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Tomato (Solanum lycopersicum) is one of the most important horticultural crops, with a marked preference for nitrate as an inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in nitrate signaling. RESULTS In this study, genome-wide analysis identified six NLP members in tomato genome. These members were clustered into three clades in a phylogenetic tree. Comparative genomic analysis showed that SlNLP genes exhibited collinear relationships to NLPs in Arabidopsis, canola, maize and rice, and that the expansion of the SlNLP family mainly resulted from segmental duplications in the tomato genome. Tissue-specific expression analysis showed that one of the close homologs of AtNLP6/7, SlNLP3, was strongly expressed in roots during both the seedling and flowering stages, that SlNLP4 and SlNLP6 exhibited preferential expression in stems and leaves and that SlNLP6 was expressed at high levels in fruits. Furthermore, the nitrate uptake in tomato roots and the expression patterns of SlNLP genes were measured under nitrogen deficiency and nitrate resupply conditions. Four SlNLPs, SlNLP1, SlNLP2, SlNLP4 and SlNLP6, were upregulated after nitrogen starvation. And SlNLP1 and SlNLP5 were induced rapidly and temporally by nitrate. CONCLUSIONS These results provide significant insights into the potential diverse functions of SlNLPs to regulate nitrate uptake.
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Affiliation(s)
- Mengyuan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaona Zhi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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24
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Xu P, Chen H, Hu J, Cai W. Potential evidence for transgenerational epigenetic memory in Arabidopsis thaliana following spaceflight. Commun Biol 2021; 4:835. [PMID: 34215844 PMCID: PMC8253727 DOI: 10.1038/s42003-021-02342-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/28/2021] [Indexed: 11/12/2022] Open
Abstract
Plants grown in spaceflight exhibited differential methylation responses and this is important because plants are sessile, they are constantly exposed to a variety of environmental pressures and respond to them in many ways. We previously showed that the Arabidopsis genome exhibited lower methylation level after spaceflight for 60 h in orbit. Here, using the offspring of the seedlings grown in microgravity environment in the SJ-10 satellite for 11 days and returned to Earth, we systematically studied the potential effects of spaceflight on DNA methylation, transcriptome, and phenotype in the offspring. Whole-genome methylation analysis in the first generation of offspring (F1) showed that, although there was no significant difference in methylation level as had previously been observed in the parent plants, some residual imprints of DNA methylation differences were detected. Combined DNA methylation and RNA-sequencing analysis indicated that expression of many pathways, such as the abscisic acid-activated pathway, protein phosphorylation, and nitrate signaling pathway, etc. were enriched in the F1 population. As some phenotypic differences still existed in the F2 generation, it was suggested that these epigenetic DNA methylation modifications were partially retained, resulting in phenotypic differences in the offspring. Furthermore, some of the spaceflight-induced heritable differentially methylated regions (DMRs) were retained. Changes in epigenetic modifications caused by spaceflight affected the growth of two future seed generations. Altogether, our research is helpful in better understanding the adaptation mechanism of plants to the spaceflight environment. In order to investigate whether the effects of spaceflight on plants persist in future generations, Xu et al studied the offspring of Arabidopsis thaliana seedlings that had been grown in a microgravity environment for 11 days. They found that epigenetic modifications caused by spaceflight potentially affected the growth of two future seed generations, shedding light on the longevity of the effects of spaceflight on plants.
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Affiliation(s)
- Peipei Xu
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Haiying Chen
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jinbo Hu
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weiming Cai
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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25
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Hsin KT, Yang TJ, Lee YH, Cheng YS. Phylogenetic and Structural Analysis of NIN-Like Proteins With a Type I/II PB1 Domain That Regulates Oligomerization for Nitrate Response. FRONTIERS IN PLANT SCIENCE 2021; 12:672035. [PMID: 34135927 PMCID: PMC8200828 DOI: 10.3389/fpls.2021.672035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Absorption of macronutrients such as nitrogen is a critical process for land plants. There is little information available on the correlation between the root evolution of land plants and the protein regulation of nitrogen absorption and responses. NIN-like protein (NLP) transcription factors contain a Phox and Bem1 (PB1) domain, which may regulate nitrate-response genes and seem to be involved in the adaptation to growing on land in terms of plant root development. In this report, we reveal the NLP phylogeny in land plants and the origin of NLP genes that may be involved in the nitrate-signaling pathway. Our NLP phylogeny showed that duplication of NLP genes occurred before divergence of chlorophyte and land plants. Duplicated NLP genes may lost in most chlorophyte lineages. The NLP genes of bryophytes were initially monophyletic, but this was followed by divergence of lycophyte NLP genes and then angiosperm NLP genes. Among those identified NLP genes, PB1, a protein-protein interaction domain was identified across our phylogeny. To understand how protein-protein interaction mediate via PB1 domain, we examined the PB1 domain of Arabidopsis thaliana NLP7 (AtNLP7) in terms of its molecular oligomerization and function as representative. Based on the structure of the PB1 domain, determined using small-angle x-ray scattering (SAXS) and site-directed mutagenesis, we found that the NLP7 PB1 protein forms oligomers and that several key residues (K867 and D909/D911/E913/D922 in the OPCA motif) play a pivotal role in the oligomerization of NLP7 proteins. The fact that these residues are all conserved across land plant lineages means that this oligomerization may have evolved after the common ancestor of extant land plants colonized the land. It would then have rapidly become established across land-plant lineages in order to mediate protein-protein interactions in the nitrate-signaling pathway.
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Affiliation(s)
- Kuan-Ting Hsin
- Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Tzu-Jing Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Hsuan Lee
- Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yi-Sheng Cheng
- Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan
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26
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Lin Z, Guo C, Lou S, Jin S, Zeng W, Guo Y, Fang J, Xu Z, Zuo Z, Ma L. Functional analyses unveil the involvement of moso bamboo (Phyllostachys edulis) group I and II NIN-LIKE PROTEINS in nitrate signaling regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 306:110862. [PMID: 33775367 DOI: 10.1016/j.plantsci.2021.110862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
For rapid growth, moso bamboo (Phyllostachys edulis) requires large amounts of nutrients. Nitrate is an indispensable molecular signal to regulate nitrogen absorption and assimilation, which are regulated by group III NIN-LIKE PROTEINs (NLPs). However, no Phyllostachys edulis NLP (PeNLP) has been characterized. Here, eight PeNLPs were identified, which showed dynamic expression patterns in bamboo tissues. Nitrate did not affect PeNLP mRNA levels, and PeNLP1, -2, -5, -6, -7, and -8 successfully restored nitrate signaling in Arabidopsis atnlp7-1 protoplasts through recovering AtNiR and AtNRT2.1 expression. Four group I and II PeNLPs (PeNLP1, -2, -5, and -8) interacted with the nitrate-responsive cis-element of PeNiR. Moreover, nitrate triggered the nuclear retention of PeNLP8. PeNLP8 overexpression in Arabidopsis significantly increased the primary root length, lateral root number, leaf area, and dry and wet weight of the transgenic plants, and PeNLP8 expression rescued the root architectural defect phenotype of atnlp7-1 mutants. Interestingly, PeNLP8 overexpression dramatically reduced nitrate content but elevated total amino acid content in Arabidopsis. Overall, the present study unveiled the potential involvement of group I and II NLPs in nitrate signaling regulation and provided genetic resources for engineering plants with high nitrogen use efficiency.
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Affiliation(s)
- Zezhong Lin
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cuiting Guo
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuaitong Lou
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Songsong Jin
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Weike Zeng
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanan Guo
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jun Fang
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agriculture Sciences, Shanghai, 201403, China
| | - Zhenguo Xu
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002, China
| | - Zecheng Zuo
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Liuyin Ma
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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27
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Lv X, Ding Y, Long M, Liang W, Gu X, Liu Y, Wen X. Effect of Foliar Application of Various Nitrogen Forms on Starch Accumulation and Grain Filling of Wheat ( Triticum aestivum L.) Under Drought Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:645379. [PMID: 33841473 PMCID: PMC8030621 DOI: 10.3389/fpls.2021.645379] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Foliar nitrogen (N) fertilizer application at later stages of wheat (Triticum aestivum L.) growth is an effective method of attenuating drought stress and improving grain filling. The influences or modes of action of foliar application of various nitrogen forms on wheat growth and grain filling need further research. The objective of this study was to examine the regulatory effects of various forms of foliar nitrogen [NO3 -, NH4 +, and CO(NH2)2] on wheat grain filling under drought stress and to elucidate their underlying mechanisms. The relative effects of each nitrogen source differed in promoting grain filling. Foliar NH4 +-N application notably prolonged the grain filling period. In contrast, foliar application of CO(NH2)2 and NO3 --N accelerated the grain filling rate and regulated levels of abscisic acid (ABA), z-riboside (ZR), and ethylene (ETH) in wheat grains. Analysis of gene expression revealed that CO(NH2)2 and NO3 --N upregulated the genes involved in the sucrose-starch conversion pathway, promoting the remobilization of carbohydrates and starch synthesis in the grains. Besides, activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were increased, whereas the content of malondialdehyde (MDA) declined under foliar nitrogen application (especially NH4 +-N). Under drought stress, enhancement of carbohydrate remobilization and sink strength became key factors in grain filling, and the relative differences in the effects of three N forms became more evident. In conclusion, NH4 +-N application improved the antioxidant enzyme system and delayed photoassimilate transportation. On the other hand, foliar applications of NO3 --N and CO(NH2)2 enhanced sink capacity and alleviated drought stress injury in wheat.
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Wu J, Zhang Z, Xia J, Alfatih A, Song Y, Huang Y, Wan G, Sun L, Tang H, Liu Y, Wang S, Zhu Q, Qin P, Wang Y, Li S, Mao C, Zhang G, Chu C, Yu L, Xiang C. Rice NIN-LIKE PROTEIN 4 plays a pivotal role in nitrogen use efficiency. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:448-461. [PMID: 32876985 PMCID: PMC7955889 DOI: 10.1111/pbi.13475] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 08/08/2020] [Accepted: 08/20/2020] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is one of the key essential macronutrients that affects rice growth and yield. Inorganic N fertilizers are excessively used to boost yield and generate serious collateral environmental pollution. Therefore, improving crop N use efficiency (NUE) is highly desirable and has been a major endeavour in crop improvement. However, only a few regulators have been identified that can be used to improve NUE in rice to date. Here we show that the rice NIN-like protein 4 (OsNLP4) significantly improves the rice NUE and yield. Field trials consistently showed that loss-of-OsNLP4 dramatically reduced yield and NUE compared with wild type under different N regimes. In contrast, the OsNLP4 overexpression lines remarkably increased yield by 30% and NUE by 47% under moderate N level compared with wild type. Transcriptomic analyses revealed that OsNLP4 orchestrates the expression of a majority of known N uptake, assimilation and signalling genes by directly binding to the nitrate-responsive cis-element in their promoters to regulate their expression. Moreover, overexpression of OsNLP4 can recover the phenotype of Arabidopsis nlp7 mutant and enhance its biomass. Our results demonstrate that OsNLP4 plays a pivotal role in rice NUE and sheds light on crop NUE improvement.
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Affiliation(s)
- Jie Wu
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Zi‐Sheng Zhang
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Jin‐Qiu Xia
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Alamin Alfatih
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Ying Song
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Yi‐Jie Huang
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Guang‐Yu Wan
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Liang‐Qi Sun
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Hui Tang
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Yang Liu
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
| | - Shi‐Mei Wang
- Rice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Qi‐Sheng Zhu
- Rice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Peng Qin
- Rice Research InstituteState Key Laboratory of Hybrid RiceSichuan Agricultural UniversityChengduSichuanChina
| | - Yu‐Ping Wang
- Rice Research InstituteState Key Laboratory of Hybrid RiceSichuan Agricultural UniversityChengduSichuanChina
| | - Shi‐Gui Li
- Rice Research InstituteState Key Laboratory of Hybrid RiceSichuan Agricultural UniversityChengduSichuanChina
| | - Chuan‐Zao Mao
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Gui‐Quan Zhang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing)Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Lin‐Hui Yu
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
- Present address:
Biology DepartmentBrookhaven National LaboratoryUpton, New YorkNYUSA
| | - Cheng‐Bin Xiang
- School of Life Sciences and Division of Molecular & Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui ProvinceChina
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Ma Y, Chen R. Nitrogen and Phosphorus Signaling and Transport During Legume-Rhizobium Symbiosis. FRONTIERS IN PLANT SCIENCE 2021; 12:683601. [PMID: 34239527 PMCID: PMC8258413 DOI: 10.3389/fpls.2021.683601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/25/2021] [Indexed: 05/11/2023]
Abstract
Nitrogen (N) and phosphorus (P) are the two predominant mineral elements, which are not only essential for plant growth and development in general but also play a key role in symbiotic N fixation in legumes. Legume plants have evolved complex signaling networks to respond to both external and internal levels of these macronutrients to optimize symbiotic N fixation in nodules. Inorganic phosphate (Pi) and nitrate (NO3 -) are the two major forms of P and N elements utilized by plants, respectively. Pi starvation and NO3 - application both reduce symbiotic N fixation via similar changes in the nodule gene expression and invoke local and long-distance, systemic responses, of which N-compound feedback regulation of rhizobial nitrogenase activity appears to operate under both conditions. Most of the N and P signaling and transport processes have been investigated in model organisms, such as Medicago truncatula, Lotus japonicus, Glycine max, Phaseolus vulgaris, Arabidopsis thaliana, Oryza sativa, etc. We attempted to discuss some of these processes wherever appropriate, to serve as references for a better understanding of the N and P signaling and transport during symbiosis.
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Affiliation(s)
- Yanlin Ma
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Rujin Chen
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
- School of Life Sciences, Lanzhou University, Lanzhou, China
- *Correspondence: Rujin Chen,
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30
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Maurya J, Bandyopadhyay T, Prasad M. Transcriptional regulators of nitrate metabolism: Key players in improving nitrogen use in crops. J Biotechnol 2020; 324:121-133. [PMID: 33031844 DOI: 10.1016/j.jbiotec.2020.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/19/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
Abstract
Green revolution has boosted crop yields by the development of varieties which rely on high fertilizer application. Since then, higher productivity has largely witnessed excessive nitrogen (N) fertilizer application resulting in many environmentally and agronomically unsustainable consequences. One possible solution to this problem is to develop varieties with efficient N use endowed with genetically superior N metabolizing machinery, thereby significantly reducing N loss in soil and facilitating gainful yield performance at lower N conditions. Nitrate (NO3-) is the major form of N acquired by plants in aerobic soils. Hence, its efficient acquisition, transport, assimilation into complex organic compounds, and overall homeostasis is crucial to ensure productivity under optimal and suboptimal N conditions. Transcription factors are prime regulators of these processes, and insights into their mechanism of action and the resultant effect on N metabolism are crucial to generating crops with efficient and durable nitrogen use efficiency. The present review, therefore, presents a comprehensive updated account of major N responsive transcription factor families, their cross-talk with other growth factors, and explores existing and potential areas of their biotechnological application to maximize crop yields.
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Affiliation(s)
- Jyoti Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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31
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Luo J, Havé M, Clément G, Tellier F, Balliau T, Launay-Avon A, Guérard F, Zivy M, Masclaux-Daubresse C. Integrating multiple omics to identify common and specific molecular changes occurring in Arabidopsis under chronic nitrate and sulfate limitations. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6471-6490. [PMID: 32687580 DOI: 10.1093/jxb/eraa337] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Plants have fundamental dependences on nitrogen and sulfur and frequently have to cope with chronic limitations when their supply is sub-optimal. This study aimed at characterizing the metabolomic, proteomic, and transcriptomic changes occurring in Arabidopsis leaves under chronic nitrate (Low-N) and chronic sulfate (Low-S) limitations in order to compare their effects, determine interconnections, and examine strategies of adaptation. Metabolite profiling globally revealed opposite effects of Low-S and Low-N on carbohydrate and amino acid accumulations, whilst proteomic data showed that both treatments resulted in increases in catabolic processes, stimulation of mitochondrial and cytosolic metabolism, and decreases in chloroplast metabolism. Lower abundances of ribosomal proteins and translation factors under Low-N and Low-S corresponded with growth limitation. At the transcript level, the major and specific effect of Low-N was the enhancement of expression of defence and immunity genes. The main effect of chronic Low-S was a decrease in transcripts of genes involved in cell division, DNA replication, and cytoskeleton, and an increase in the expression of autophagy genes. This was consistent with a role of target-of-rapamycin kinase in the control of plant metabolism and cell growth and division under chronic Low-S. In addition, Low-S decreased the expression of several NLP transcription factors, which are master actors in nitrate sensing. Finally, both the transcriptome and proteome data indicated that Low-S repressed glucosinolate synthesis, and that Low-N exacerbated glucosinolate degradation. This showed the importance of glucosinolate as buffering molecules for N and S management.
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Affiliation(s)
- Jie Luo
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- College of Horticulture and Forestry Sciences, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China
| | - Marien Havé
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Frédérique Tellier
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Thierry Balliau
- UMR GQE- le Moulon, INRAE, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Florence Guérard
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Michel Zivy
- UMR GQE- le Moulon, INRAE, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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32
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Alfatih A, Wu J, Zhang ZS, Xia JQ, Jan SU, Yu LH, Xiang CB. Rice NIN-LIKE PROTEIN 1 rapidly responds to nitrogen deficiency and improves yield and nitrogen use efficiency. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6032-6042. [PMID: 32585013 DOI: 10.1093/jxb/eraa292] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/17/2020] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is indispensable for crop growth and yield, but excessive agricultural application of nitrogenous fertilizers has generated severe environmental problems. A desirable and economical solution to cope with these issues is to improve crop nitrogen use efficiency (NUE). Plant NUE has been a focal point of intensive research worldwide, yet much still has to be learned about its genetic determinants and regulation. Here, we show that rice (Oryza sativa L.) NIN-LIKE PROTEIN 1 (OsNLP1) plays a fundamental role in N utilization. OsNLP1 protein localizes in the nucleus and its transcript level is rapidly induced by N starvation. Overexpression of OsNLP1 improves plant growth, grain yield, and NUE under different N conditions, while knockout of OsNLP1 impairs grain yield and NUE under N-limiting conditions. OsNLP1 regulates nitrate and ammonium utilization by cooperatively orchestrating multiple N uptake and assimilation genes. Chromatin immunoprecipitation and yeast one-hybrid assays showed that OsNLP1 can directly bind to the promoter of these genes to activate their expression. Therefore, our results demonstrate that OsNLP1 is a key regulator of N utilization and represents a potential target for improving NUE and yield in rice.
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Affiliation(s)
- Alamin Alfatih
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Jie Wu
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Zi-Sheng Zhang
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Jin-Qiu Xia
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Sami Ullah Jan
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Lin-Hui Yu
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Cheng-Bin Xiang
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
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33
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Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea. Int J Genomics 2020; 2020:2568640. [PMID: 32908854 PMCID: PMC7474775 DOI: 10.1155/2020/2568640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/30/2020] [Accepted: 08/07/2020] [Indexed: 11/17/2022] Open
Abstract
RWP-RK proteins are important factors involved in nitrate response and gametophyte development in plants, and the functions of RWP-RK proteins have been analyzed in many species. However, the characterization of peanut RWP-RK proteins is limited. In this study, we identified 16, 19, and 32 RWP-RK members from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively, and investigated their evolution relationships. The RWP-RK proteins were classified into two groups, RWP-RK domain proteins and NODULE-INCEPTION-like proteins. Chromosomal distributions, gene structures, and conserved motifs of RWP-RK genes were compared among wild and cultivated peanuts. In addition, we identified 12 orthologous gene pairs from the two wild peanut species, 13 from A. duranensis and A. hypogaea, and 13 from A. ipaensis and A. hypogaea. One, one, and seventeen duplicated gene pairs were identified within the A. duranensis, A. ipaensis, and A. hypogaea genomes, respectively. Moreover, different numbers of cis-acting elements in the RWP-RK promoters were found in wild and cultivated species (87 in A. duranensis, 89 in A. ipaensis, and 92 in A. hypogaea), and as a result, many RWP-RK genes showed distinct expression patterns in different tissues. Our study will provide useful information for further functional and evolutionary analysis of the RWP-RK genes.
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34
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Yin M, Zhang Z, Xuan M, Feng H, Ye W, Zheng X, Wang Y. Conserved Subgroups of the Plant-Specific RWP-RK Transcription Factor Family Are Present in Oomycete Pathogens. Front Microbiol 2020; 11:1724. [PMID: 32849368 PMCID: PMC7399023 DOI: 10.3389/fmicb.2020.01724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Nitrogen is a major constituent of proteins, chlorophyll, nucleotides, and hormones and has profound effects on plant growth and productivity. RWP-RK family transcription factors (TFs) are key regulators that bind to cis-acting elements in the promoter regions of nitrogen use efficiency-related genes and genes responsible for gametogenesis and embryogenesis. The proteins share a conserved RWPxRK motif; have been found in all vascular plants, green algae, and slime molds; and are considered to be a plant-specific TF family. In this study, we show that RWP-RK proteins are also widely present in the Stramenopila kingdom, particularly among the oomycetes, with 12-15 members per species. These proteins form three distinct phylogenetic subgroups, two of which are relatively closely related to the nodule inception (NIN)-like protein (NLP) or the RWP-RK domain protein (RKD) subfamilies of plant RWP-RK proteins. The donor for horizontal gene transfer of RWP-RK domains to slime molds is likely to have been among the Stramenopila, predating the divide between brown algae and oomycetes. The RWP-RK domain has secondary structures that are conserved across plants and oomycetes, but several amino acids that may affect DNA-binding affinity differ. The transcriptional activities of orthologous RWP-RK genes were found to be conserved in oomycetes. Our results demonstrate that RWP-RK family TF genes are present in the oomycetes and form specific subgroups with functions that are likely conserved. Our results provide new insights for further understanding the evolution and function of this TF family in specific eukaryotic organisms.
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Affiliation(s)
- Maozhu Yin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Mingrun Xuan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Hui Feng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
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35
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Liu B, Wu J, Yang S, Schiefelbein J, Gan Y. Nitrate regulation of lateral root and root hair development in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4405-4414. [PMID: 31796961 PMCID: PMC7382377 DOI: 10.1093/jxb/erz536] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/03/2019] [Indexed: 05/16/2023]
Abstract
Nitrogen (N) is one of the most important macronutrients for plant growth and development. However, the concentration and distribution of N varies in soil due to a variety of environmental factors. In response, higher plants have evolved a developmentally flexible root system to efficiently take up N under N-limited conditions. Over the past decade, significant progress has been made in understanding this form of plant 'root-foraging' behavior, which is controlled by both a local and a long-distance systemic nitrate signaling pathway. In this review, we focus on the key components of nitrate perception, signaling, and transduction and its role in lateral root development. We also highlight recent findings on the molecular mechanisms of the nitrate systemic signaling pathway, including small signaling peptides involved in long-distance shoot-root communication. Furthermore, we summarize the transcription factor networks responsible for nitrate-dependent lateral root and root hair development.
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Affiliation(s)
- Bohan Liu
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Junyu Wu
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuaiqi Yang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Correspondence: or
| | - Yinbo Gan
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Correspondence: or
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36
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Liu J, Bisseling T. Evolution of NIN and NIN-like Genes in Relation to Nodule Symbiosis. Genes (Basel) 2020; 11:E777. [PMID: 32664480 PMCID: PMC7397163 DOI: 10.3390/genes11070777] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/26/2020] [Accepted: 07/09/2020] [Indexed: 01/06/2023] Open
Abstract
Legumes and actinorhizal plants are capable of forming root nodules symbiosis with rhizobia and Frankia bacteria. All these nodulating species belong to the nitrogen fixation clade. Most likely, nodulation evolved once in the last common ancestor of this clade. NIN (NODULE INCEPTION) is a transcription factor that is essential for nodulation in all studied species. Therefore, it seems probable that it was recruited at the start when nodulation evolved. NIN is the founding member of the NIN-like protein (NLP) family. It arose by duplication, and this occurred before nodulation evolved. Therefore, several plant species outside the nitrogen fixation clade have NLP(s), which is orthologous to NIN. In this review, we discuss how NIN has diverged from the ancestral NLP, what minimal changes would have been essential for it to become a key transcription controlling nodulation, and which adaptations might have evolved later.
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Affiliation(s)
- Jieyu Liu
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands;
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands;
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
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37
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Genome wide analysis of NLP transcription factors reveals their role in nitrogen stress tolerance of rice. Sci Rep 2020; 10:9368. [PMID: 32523127 PMCID: PMC7287097 DOI: 10.1038/s41598-020-66338-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/14/2020] [Indexed: 02/08/2023] Open
Abstract
The NIN-LIKE PROTEIN (NLP) family of transcription factors were identified as nitrate-responsive cis-element (NRE)-binding proteins, which function as transcriptional activators in the nitrate-regulated expression of downstream genes. This study was aimed at genome-wide analysis of NLP gene family in rice and the expression profiling of NLPs in response to nitrogen (N) supply and deficiency in rice genotypes with contrasting N use efficiency (NUE). Based on in silico analysis, 6 NLP genes (including alternative splice forms 11 NLPs) were identified from rice. Expression of NLPs was promoted by nitrate supply as well as N deficiency (NLP1, NLP3, NLP4 and NLP5). Four rice genotypes APO (high NUE under sufficient N), IR83929-B-B-291-3-1-1 (IR-3-1-1), Nerica-L-42 (NL-42) (High NUE at low N), and Pusa Basmati 1 (PB1, low NUE) to correlate traits governing NUE and expression of NLPs. Analysis of rate of nitrate uptake and expression of N assimilatory and uptake genes established that IR-3-1-1 has high uptake and assimilation efficiency, translating into high NUE, whereas PB1 is efficient in uptake only when N availability is high. Along with the transcriptional upregulation of NLPs, genotype IR-3-1-1, displayed highest expression of OsNRT1.1B gene, the closest rice homologue of nitrate transceptor AtNRT1.1 and plays major role in nitrate uptake, translocation and signaling in rice. The results showed that high NUE rice genotypes has both high Nitrogen uptake efficiency (NUpE) and Nitrogen utilization efficiency (NUtE), resulting from the effective and coordinated signal transduction network involving the rice homologue of nitrate transceptor OsNRT1.1B, the probable primary nitrate response (PNR) regulator OsNLP1 and the master response regulator OsNLP3, a homologue of AtNLP6/7.
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Mutte SK, Weijers D. Deep Evolutionary History of the Phox and Bem1 (PB1) Domain Across Eukaryotes. Sci Rep 2020; 10:3797. [PMID: 32123237 PMCID: PMC7051960 DOI: 10.1038/s41598-020-60733-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/14/2020] [Indexed: 01/01/2023] Open
Abstract
Protein oligomerization is a fundamental process to build complex functional modules. Domains that facilitate the oligomerization process are diverse and widespread in nature across all kingdoms of life. One such domain is the Phox and Bem1 (PB1) domain, which is functionally well-studied in the animal kingdom. However, beyond animals, neither the origin nor the evolutionary patterns of PB1-containing proteins are understood. While PB1 domain proteins have been found in other kingdoms including plants, it is unclear how these relate to animal PB1 proteins. To address this question, we utilized large transcriptome datasets along with the proteomes of a broad range of species. We discovered eight PB1 domain-containing protein families in plants, along with four each in Protozoa and Fungi and three families in Chromista. Studying the deep evolutionary history of PB1 domains throughout eukaryotes revealed the presence of at least two, but likely three, ancestral PB1 copies in the Last Eukaryotic Common Ancestor (LECA). These three ancestral copies gave rise to multiple orthologues later in evolution. Analyzing the sequence and secondary structure properties of plant PB1 domains from all the eight families showed their common ubiquitin β-grasp fold, despite poor sequence identity. Tertiary structural models of these plant PB1 families, combined with Random Forest based classification, indicated family-specific differences attributed to the length of PB1 domain and the proportion of β-sheets. Thus, this study not only identifies novel PB1 families, but also provides an evolutionary basis to understand their diverse functional interactions.
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Affiliation(s)
- Sumanth Kumar Mutte
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, the Netherlands.
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Huisman R, Geurts R. A Roadmap toward Engineered Nitrogen-Fixing Nodule Symbiosis. PLANT COMMUNICATIONS 2020; 1:100019. [PMID: 33404552 PMCID: PMC7748023 DOI: 10.1016/j.xplc.2019.100019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/06/2019] [Accepted: 12/27/2019] [Indexed: 05/26/2023]
Abstract
In the late 19th century, it was discovered that legumes can establish a root nodule endosymbiosis with nitrogen-fixing rhizobia. Soon after, the question was raised whether it is possible to transfer this trait to non-leguminous crops. In the past century, an ever-increasing amount of knowledge provided unique insights into the cellular, molecular, and genetic processes controlling this endosymbiosis. In addition, recent phylogenomic studies uncovered several genes that evolved to function specifically to control nodule formation and bacterial infection. However, despite this massive body of knowledge, the long-standing objective to engineer the nitrogen-fixing nodulation trait on non-leguminous crop plants has not been achieved yet. In this review, the unsolved questions and engineering strategies toward nitrogen-fixing nodulation in non-legume plants are discussed and highlighted.
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Affiliation(s)
- Rik Huisman
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Rene Geurts
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
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Fan H, Quan S, Qi S, Xu N, Wang Y. Novel Aspects of Nitrate Regulation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:574246. [PMID: 33362808 PMCID: PMC7758431 DOI: 10.3389/fpls.2020.574246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Nitrogen (N) is one of the most essential macronutrients for plant growth and development. Nitrate (NO3 -), the major form of N that plants uptake from the soil, acts as an important signaling molecule in addition to its nutritional function. Over the past decade, significant progress has been made in identifying new components involved in NO3 - regulation and starting to unravel the NO3 - regulatory network. Great reviews have been made recently by scientists on the key regulators in NO3 - signaling, NO3 - effects on plant development, and its crosstalk with phosphorus (P), potassium (K), hormones, and calcium signaling. However, several novel aspects of NO3 - regulation have not been previously reviewed in detail. Here, we mainly focused on the recent advances of post-transcriptional regulation and non-coding RNA (ncRNAs) in NO3 - signaling, and NO3 - regulation on leaf senescence and the circadian clock. It will help us to extend the general picture of NO3 - regulation and provide a basis for further exploration of NO3 - regulatory network.
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Affiliation(s)
- Hongmei Fan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Na Xu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yong Wang,
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The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants. Int J Mol Sci 2019; 20:ijms20246343. [PMID: 31888214 PMCID: PMC6941117 DOI: 10.3390/ijms20246343] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/16/2022] Open
Abstract
Auxin plays essential roles in plant normal growth and development. The auxin signaling pathway relies on the auxin gradient within tissues and cells, which is facilitated by both local auxin biosynthesis and polar auxin transport (PAT). The TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA)/YUCCA (YUC) pathway is the most important and well-characterized pathway that plants deploy to produce auxin. YUCs function as flavin-containing monooxygenases (FMO) catalyzing the rate-limiting irreversible oxidative decarboxylation of indole-3-pyruvate acid (IPyA) to form indole-3-acetic acid (IAA). The spatiotemporal dynamic expression of different YUC gene members finely tunes the local auxin biosynthesis in plants, which contributes to plant development as well as environmental responses. In this review, the recent advances in the identification, evolution, molecular structures, and functions in plant development and stress response regarding the YUC gene family are addressed.
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Physiological and Transcriptomic Changes during the Early Phases of Adventitious Root Formation in Mulberry Stem Hardwood Cuttings. Int J Mol Sci 2019; 20:ijms20153707. [PMID: 31362363 PMCID: PMC6696018 DOI: 10.3390/ijms20153707] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023] Open
Abstract
The initiation and induction of root primordia are of great importance for adventitious root (AR) formation in cutting propagation of horticultural and forestry crops. However, the underlying mechanisms orchestrating these early phases of AR formation remain largely unexplored. Here, we investigated the physiological and transcriptomic changes during the early AR phases in mulberry stem hardwood cuttings. The results showed that the concentrations of soluble proteins increased, whereas concentrations of soluble sugars and starch were decreased. Indole-3-acetic acid (IAA) and zeatin had a rapid transit peak at 6 h after planting (hAP) and declined thereafter. The activities of peroxidase and catalase persistently increased and indole-3-acetic acid oxidase was maintained at a higher stable level from 0 hAP, while the activities of polyphenol oxidase fluctuated with soluble phenolics and IAA levels. The comparative transcriptome identified 4276 common genes that were differentially regulated at −6, 0 and 54 hAP. They were separated into five clusters with distinct biological functions such as defense response and photosynthesis. Considerable common genes were assigned to pathways of sugar metabolism, mitogen-activated protein kinase, and circadian rhythm. The gene co-expression network analysis revealed three major co-expressed modules involved in stress responses, hormone signaling, energy metabolism, starch metabolism, and circadian rhythm. These findings demonstrate the positive effect of auxin on AR induction, and uncovered the crucial roles of stress responses, hormone signaling and circadian rhythm in coordinating the physiological changes during the early phases of AR formation in mulberry stem hardwood cuttings.
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