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Wu J, Song Y, Zhang ZS, Wang JX, Zhang X, Zang JY, Bai MY, Yu LH, Xiang CB. GAF domain is essential for nitrate-dependent AtNLP7 function. BMC PLANT BIOLOGY 2022; 22:366. [PMID: 35871642 PMCID: PMC9310391 DOI: 10.1186/s12870-022-03755-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Nitrate is an essential nutrient and an important signaling molecule in plants. However, the molecular mechanisms by which plants perceive nitrate deficiency signaling are still not well understood. Here we report that AtNLP7 protein transport from the nucleus to the cytoplasm in response to nitrate deficiency is dependent on the N-terminal GAF domain. With the deletion of the GAF domain, AtNLP7ΔGAF always remains in the nucleus regardless of nitrate availability. AtNLP7 ΔGAF also shows reduced activation of nitrate-induced genes due to its impaired binding to the nitrate-responsive cis-element (NRE) as well as decreased growth like nlp7-1 mutant. In addition, AtNLP7ΔGAF is unable to mediate the reduction of reactive oxygen species (ROS) accumulation upon nitrate treatment. Our investigation shows that the GAF domain of AtNLP7 plays a critical role in the sensing of nitrate deficiency signal and in the nitrate-triggered ROS signaling process.
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Affiliation(s)
- Jie Wu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical 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, 230027, Anhui Province, China.
| | - Ying Song
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical 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, 230027, Anhui Province, China
| | - Zi-Sheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical 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, 230027, Anhui Province, China
| | - Jing-Xian Wang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical 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, 230027, Anhui Province, China
| | - Xuan Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical 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, 230027, Anhui Province, China
| | - Jian-Ye Zang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical 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, 230027, Anhui Province, China
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, Shandong Province, China
| | - Lin-Hui Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Cheng-Bin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical 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, 230027, Anhui Province, China.
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Sakuraba Y, Zhuo M, Yanagisawa S. RWP-RK domain-containing transcription factors in the Viridiplantae: biology and phylogenetic relationships. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4323-4337. [PMID: 35605260 DOI: 10.1093/jxb/erac229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The RWP-RK protein family is a group of transcription factors containing the RWP-RK DNA-binding domain. This domain is an ancient motif that emerged before the establishment of the Viridiplantae-the green plants, consisting of green algae and land plants. The domain is mostly absent in other kingdoms but widely distributed in Viridiplantae. In green algae, a liverwort, and several angiosperms, RWP-RK proteins play essential roles in nitrogen responses and sexual reproduction-associated processes, which are seemingly unrelated phenomena but possibly interdependent in autotrophs. Consistent with related but diversified roles of the RWP-RK proteins in these organisms, the RWP-RK protein family appears to have expanded intensively, but independently, in the algal and land plant lineages. Thus, bryophyte RWP-RK proteins occupy a unique position in the evolutionary process of establishing the RWP-RK protein family. In this review, we summarize current knowledge of the RWP-RK protein family in the Viridiplantae, and discuss the significance of bryophyte RWP-RK proteins in clarifying the relationship between diversification in the RWP-RK protein family and procurement of sophisticated mechanisms for adaptation to the terrestrial environment.
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Affiliation(s)
- Yasuhito Sakuraba
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mengna Zhuo
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shuichi Yanagisawa
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Zhou Z, Zhang L, Shu J, Wang M, Li H, Shu H, Wang X, Sun Q, Zhang S. Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple. PLANTS (BASEL, SWITZERLAND) 2022; 11:1408. [PMID: 35684181 PMCID: PMC9182997 DOI: 10.3390/plants11111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, and research on root architecture has progressed slowly. This paper describes ideas for the precise breeding and domestication of wild apple resources and the application of key genes. The primary goal of this research is to combine the existing rootstock resources with molecular breeding and summarize the methods of precision breeding. Here, we reviewed the existing rootstock germplasm, high-quality genome, and genetic resources available to explain how wild resources might be used in modern breeding. In particular, we proposed the 'from genotype to phenotype' theory and summarized the difficulties in future breeding processes. Lastly, the genetics governing root diversity and associated regulatory mechanisms were elaborated on to optimize the precise breeding of rootstocks.
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Affiliation(s)
- Zhou Zhou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Lei Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Jing Shu
- College of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
| | - Mengyu Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Han Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Huairui Shu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Xiaoyun Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Qinghua Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
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54
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Molecular mechanisms underlying nitrate responses in plants. Curr Biol 2022; 32:R433-R439. [DOI: 10.1016/j.cub.2022.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Liao HS, Chung YH, Hsieh MH. Glutamate: A multifunctional amino acid in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 318:111238. [PMID: 35351313 DOI: 10.1016/j.plantsci.2022.111238] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Glutamate (Glu) is a versatile metabolite and a signaling molecule in plants. Glu biosynthesis is associated with the primary nitrogen assimilation pathway. The conversion between Glu and 2-oxoglutarate connects Glu metabolism to the tricarboxylic acid cycle, carbon metabolism, and energy production. Glu is the predominant amino donor for transamination reactions in the cell. In addition to protein synthesis, Glu is a building block for tetrapyrroles, glutathione, and folate. Glu is the precursor of γ-aminobutyric acid that plays an important role in balancing carbon/nitrogen metabolism and various cellular processes. Glu can conjugate to the major auxin indole 3-acetic acid (IAA), and IAA-Glu is destined for oxidative degradation. Glu also conjugates with isochorismate for the production of salicylic acid. Accumulating evidence indicates that Glu functions as a signaling molecule to regulate plant growth, development, and defense responses. The ligand-gated Glu receptor-like proteins (GLRs) mediate some of these responses. However, many of the Glu signaling events are GLR-independent. The receptor perceiving extracellular Glu as a danger signal is still unknown. In addition to GLRs, Glu may act on receptor-like kinases or receptor-like proteins to trigger immune responses. Glu metabolism and Glu signaling may entwine to regulate growth, development, and defense responses in plants.
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Affiliation(s)
- Hong-Sheng Liao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hsin Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan.
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56
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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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Feng ZQ, Li T, Wang X, Sun WJ, Zhang TT, You CX, Wang XF. Identification and characterization of apple MdNLP7 transcription factor in the nitrate response. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111158. [PMID: 35151440 DOI: 10.1016/j.plantsci.2021.111158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/02/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Nitrogen is an essential nutrient for plant growth and development. Low utilization of nitrogen fertilizer during agricultural production causes a series of environmental problems, such as water eutrophication, soil acidity, and air pollution. Investigating the patterns and mechanisms of crop NO3- absorption and utilization therefore key to fully improving crop nitrogen utilization rates and promoting sustainable agricultural development. Apple is one of the most important horticultural crops in the world. Its nitrogen demand by apple during the growth period is very high, but few studies have been performed on apple genes, that regulate the NO3- response. Here, we found that the apple transcription factor MdNLP7 promoted nitrogen absorption and assimilation by activating the expression of MdNIA2 and MdNRT1.1. MdNLP7 also regulated H2O2 content by increasing catalase activity, which may also influence nitrate utilization. Our findings provide insight into the mechanisms by which MdNLP7 controls nitrate utilization in apple.
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Affiliation(s)
- Zi-Quan Feng
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Tong Li
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xun Wang
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Wei-Jian Sun
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Ting-Ting Zhang
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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58
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Schmitz RJ, Grotewold E, Stam M. Cis-regulatory sequences in plants: Their importance, discovery, and future challenges. THE PLANT CELL 2022; 34:718-741. [PMID: 34918159 PMCID: PMC8824567 DOI: 10.1093/plcell/koab281] [Citation(s) in RCA: 125] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 05/19/2023]
Abstract
The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.
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Affiliation(s)
- Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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Swift J, Greenham K, Ecker JR, Coruzzi GM, McClung CR. The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:764-778. [PMID: 34797944 PMCID: PMC9215356 DOI: 10.1111/tpj.15589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 05/26/2023]
Abstract
As sessile organisms, plants are finely tuned to respond dynamically to developmental, circadian and environmental cues. Genome-wide studies investigating these types of cues have uncovered the intrinsically different ways they can impact gene expression over time. Recent advances in single-cell sequencing and time-based bioinformatic algorithms are now beginning to reveal the dynamics of these time-based responses within individual cells and plant tissues. Here, we review what these techniques have revealed about the spatiotemporal nature of gene regulation, paying particular attention to the three distinct ways in which plant tissues are time sensitive. (i) First, we discuss how studying plant cell identity can reveal developmental trajectories hidden in pseudotime. (ii) Next, we present evidence that indicates that plant cell types keep their own local time through tissue-specific regulation of the circadian clock. (iii) Finally, we review what determines the speed of environmental signaling responses, and how they can be contingent on developmental and circadian time. By these means, this review sheds light on how these different scales of time-based responses can act with tissue and cell-type specificity to elicit changes in whole plant systems.
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Affiliation(s)
- Joseph Swift
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Kathleen Greenham
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Gloria M. Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, NY, USA
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Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate. Proc Natl Acad Sci U S A 2022; 119:2107879119. [PMID: 35046022 PMCID: PMC8794810 DOI: 10.1073/pnas.2107879119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/24/2022] Open
Abstract
Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type-specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.
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61
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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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Jia Z, Giehl RFH, von Wirén N. Nutrient-hormone relations: Driving root plasticity in plants. MOLECULAR PLANT 2022; 15:86-103. [PMID: 34920172 DOI: 10.1016/j.molp.2021.12.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/04/2021] [Accepted: 12/14/2021] [Indexed: 05/25/2023]
Abstract
Optimal plant development requires root uptake of 14 essential mineral elements from the soil. Since the bioavailability of these nutrients underlies large variation in space and time, plants must dynamically adjust their root architecture to optimize nutrient access and acquisition. The information on external nutrient availability and whole-plant demand is translated into cellular signals that often involve phytohormones as intermediates to trigger a systemic or locally restricted developmental response. Timing and extent of such local root responses depend on the overall nutritional status of the plant that is transmitted from shoots to roots in the form of phytohormones or other systemic long-distance signals. The integration of these systemic and local signals then determines cell division or elongation rates in primary and lateral roots, the initiation, emergence, or elongation of lateral roots, as well as the formation of root hairs. Here, we review the cascades of nutrient-related sensing and signaling events that involve hormones and highlight nutrient-hormone relations that coordinate root developmental plasticity in plants.
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Affiliation(s)
- Zhongtao Jia
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Ricardo F H Giehl
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland, OT Gatersleben, Germany.
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63
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Guedes JG, Leitão C, Meireles C, Duarte P, Sottomayor M. TARGETing Transcriptional Regulation in the Medicinal Plant Catharanthus roseus. Methods Mol Biol 2022; 2505:191-202. [PMID: 35732946 DOI: 10.1007/978-1-0716-2349-7_14] [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] [Indexed: 06/15/2023]
Abstract
Transcriptional regulation is a central piece of the highly valuable monoterpenoid indole alkaloid pathway of C. roseus , and the ultimate tool for its understanding and manipulation. Here, we describe the adaptation of the TARGET methodology to identify specific and genome-wide leaf targets of C. roseus candidate transcription factors (TFs).
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Affiliation(s)
- Joana G Guedes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vila do Conde, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Catarina Leitão
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Catarina Meireles
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Patrícia Duarte
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Mariana Sottomayor
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vila do Conde, Portugal.
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vila do Conde, Portugal.
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Camut L, Gallova B, Jilli L, Sirlin-Josserand M, Carrera E, Sakvarelidze-Achard L, Ruffel S, Krouk G, Thomas SG, Hedden P, Phillips AL, Davière JM, Achard P. Nitrate signaling promotes plant growth by upregulating gibberellin biosynthesis and destabilization of DELLA proteins. Curr Biol 2021; 31:4971-4982.e4. [PMID: 34614391 DOI: 10.1016/j.cub.2021.09.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 08/13/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Nitrate, one of the main nitrogen (N) sources for crops, acts as a nutrient and key signaling molecule coordinating gene expression, metabolism, and various growth processes throughout the plant life cycle. It is widely accepted that nitrate-triggered developmental programs cooperate with hormone synthesis and transport to finely adapt plant architecture to N availability. Here, we report that nitrate, acting through its signaling pathway, promotes growth in Arabidopsis and wheat, in part by modulating the accumulation of gibberellin (GA)-regulated DELLA growth repressors. We show that nitrate reduces the abundance of DELLAs by increasing GA contents through activation of GA metabolism gene expression. Consistently, the growth restraint conferred by nitrate deficiency is partially rescued in global-DELLA mutant that lacks all DELLAs. At the cellular level, we show that nitrate enhances both cell proliferation and elongation in a DELLA-dependent and -independent manner, respectively. Our findings establish a connection between nitrate and GA signaling pathways that allow plants to adapt their growth to nitrate availability.
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Affiliation(s)
- Lucie Camut
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Barbora Gallova
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Lucas Jilli
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Mathilde Sirlin-Josserand
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, 46022 Valencia, Spain
| | - Lali Sakvarelidze-Achard
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Stephen G Thomas
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Peter Hedden
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK; Laboratory of Growth Regulators, Institute of Experimental Botany and Palacky University, 78371 Olomouc, Czech Republic
| | - Andrew L Phillips
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Jean-Michel Davière
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Patrick Achard
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France.
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Pélissier PM, Motte H, Beeckman T. Lateral root formation and nutrients: nitrogen in the spotlight. PLANT PHYSIOLOGY 2021; 187:1104-1116. [PMID: 33768243 PMCID: PMC8566224 DOI: 10.1093/plphys/kiab145] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/12/2021] [Indexed: 05/08/2023]
Abstract
Lateral roots are important to forage for nutrients due to their ability to increase the uptake area of a root system. Hence, it comes as no surprise that lateral root formation is affected by nutrients or nutrient starvation, and as such contributes to the root system plasticity. Understanding the molecular mechanisms regulating root adaptation dynamics toward nutrient availability is useful to optimize plant nutrient use efficiency. There is at present a profound, though still evolving, knowledge on lateral root pathways. Here, we aimed to review the intersection with nutrient signaling pathways to give an update on the regulation of lateral root development by nutrients, with a particular focus on nitrogen. Remarkably, it is for most nutrients not clear how lateral root formation is controlled. Only for nitrogen, one of the most dominant nutrients in the control of lateral root formation, the crosstalk with multiple key signals determining lateral root development is clearly shown. In this update, we first present a general overview of the current knowledge of how nutrients affect lateral root formation, followed by a deeper discussion on how nitrogen signaling pathways act on different lateral root-mediating mechanisms for which multiple recent studies yield insights.
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Affiliation(s)
- Pierre-Mathieu Pélissier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent 9052, Belgium
- Author for communication:
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Jiang S, Jardinaud MF, Gao J, Pecrix Y, Wen J, Mysore K, Xu P, Sanchez-Canizares C, Ruan Y, Li Q, Zhu M, Li F, Wang E, Poole PS, Gamas P, Murray JD. NIN-like protein transcription factors regulate leghemoglobin genes in legume nodules. Science 2021; 374:625-628. [PMID: 34709882 DOI: 10.1126/science.abg5945] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Suyu Jiang
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences, Shanghai, China
| | | | - Jinpeng Gao
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences, Shanghai, China
| | - Yann Pecrix
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.,CIRAD, UMR PVBMT, Pôle de Protection des Plantes, Saint-Pierre 97410, France
| | - Jiangqi Wen
- Noble Research Institute, Ardmore, OK 73401, USA
| | | | - Ping Xu
- Shanghai Engineering Research Center of Plant Germplasm Resource, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | | | - Yiting Ruan
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences, Shanghai, China
| | - Qiujiu Li
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences, Shanghai, China
| | - Meijun Zhu
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences, Shanghai, China
| | - Fuyu Li
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences, Shanghai, China
| | - Ertao Wang
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences, Shanghai, China
| | - Phillip S Poole
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Pascal Gamas
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jeremy D Murray
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences, Shanghai, China.,John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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67
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Chu X, Wang JG, Li M, Zhang S, Gao Y, Fan M, Han C, Xiang F, Li G, Wang Y, Yu X, Xiang CB, Bai MY. HBI transcription factor-mediated ROS homeostasis regulates nitrate signal transduction. THE PLANT CELL 2021; 33:3004-3021. [PMID: 34129038 PMCID: PMC8462818 DOI: 10.1093/plcell/koab165] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/09/2021] [Indexed: 05/20/2023]
Abstract
Nitrate is both an important nutrient and a critical signaling molecule that regulates plant metabolism, growth, and development. Although several components of the nitrate signaling pathway have been identified, the molecular mechanism of nitrate signaling remains unclear. Here, we showed that the growth-related transcription factors HOMOLOG OF BRASSINOSTEROID ENHANCED EXPRESSION2 INTERACTING WITH IBH1 (HBI1) and its three closest homologs (HBIs) positively regulate nitrate signaling in Arabidopsis thaliana. HBI1 is rapidly induced by nitrate through NLP6 and NLP7, which are master regulators of nitrate signaling. Mutations in HBIs result in the reduced effects of nitrate on plant growth and ∼22% nitrate-responsive genes no longer to be regulated by nitrate. HBIs increase the expression levels of a set of antioxidant genes to reduce the accumulation of reactive oxygen species (ROS) in plants. Nitrate treatment induces the nuclear localization of NLP7, whereas such promoting effects of nitrate are significantly impaired in the hbi-q and cat2 cat3 mutants, which accumulate high levels of H2O2. These results demonstrate that HBI-mediated ROS homeostasis regulates nitrate signal transduction through modulating the nucleocytoplasmic shuttling of NLP7. Overall, our findings reveal that nitrate treatment reduces the accumulation of H2O2, and H2O2 inhibits nitrate signaling, thereby forming a feedback regulatory loop to regulate plant growth and development.
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Affiliation(s)
- Xiaoqian Chu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jia-Gang Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Mingzhe Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Shujuan Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an 271018, China
| | - Min Fan
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Chao Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an 271018, China
| | - Xiang Yu
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, 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, Hefei 230027, China
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
- Author for correspondence:
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Gómez-Saldivar G, Glauser DA, Meister P. Tissue-specific DamID protocol using nanopore sequencing. J Biol Methods 2021; 8:e152. [PMID: 34514013 PMCID: PMC8411031 DOI: 10.14440/jbm.2021.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
DNA adenine methylation identification (DamID) is a powerful method to determine DNA binding profiles of proteins at a genomic scale. The method leverages the fusion between a protein of interest and the Dam methyltransferase of E. coli, which methylates proximal DNA in vivo. Here, we present an optimized procedure, which was developed for tissue-specific analyses in Caenorhabditis elegans and successfully used to footprint genes actively transcribed by RNA polymerases and to map transcription factor binding in gene regulatory regions. The present protocol details C. elegans-specific steps involved in the preparation of transgenic lines and genomic DNA samples, as well as broadly applicable steps for the DamID procedure, including the isolation of methylated DNA fragments, the preparation of multiplexed libraries, Nanopore sequencing, and data analysis. Two distinctive features of the approach are (i) the use of an efficient recombination-based strategy to selectively analyze rare cell types and (ii) the use of Nanopore sequencing, which streamlines the process. The method allows researchers to go from genomic DNA samples to sequencing results in less than a week, while being sensitive enough to report reliable DNA footprints in cell types as rare as 2 cells per animal.
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Affiliation(s)
| | | | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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69
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Varshney RK, Barmukh R, Roorkiwal M, Qi Y, Kholova J, Tuberosa R, Reynolds MP, Tardieu F, Siddique KHM. Breeding custom-designed crops for improved drought adaptation. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e202100017. [PMID: 36620433 PMCID: PMC9744523 DOI: 10.1002/ggn2.202100017] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 01/11/2023]
Abstract
The current pace of crop improvement is inadequate to feed the burgeoning human population by 2050. Higher, more stable, and sustainable crop production is required against a backdrop of drought stress, which causes significant losses in crop yields. Tailoring crops for drought adaptation may hold the key to address these challenges and provide resilient production systems for future harvests. Understanding the genetic and molecular landscape of the functionality of alleles associated with adaptive traits will make designer crop breeding the prospective approach for crop improvement. Here, we highlight the potential of genomics technologies combined with crop physiology for high-throughput identification of the genetic architecture of key drought-adaptive traits and explore innovative genomic breeding strategies for designing future crops.
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Affiliation(s)
- Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- State Agricultural Biotechnology Centre, Centre for Crop and Food InnovationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Roberto Tuberosa
- Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | | | - Francois Tardieu
- Université de Montpellier, INRAE, Laboratoire d'Ecophysiologie des Plantes sous Stress, EnvironnementauxMontpellierFrance
| | - Kadambot H. M. Siddique
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
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Nishida H, Nosaki S, Suzuki T, Ito M, Miyakawa T, Nomoto M, Tada Y, Miura K, Tanokura M, Kawaguchi M, Suzaki T. Different DNA-binding specificities of NLP and NIN transcription factors underlie nitrate-induced control of root nodulation. THE PLANT CELL 2021; 33:2340-2359. [PMID: 33826745 PMCID: PMC8364233 DOI: 10.1093/plcell/koab103] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/03/2021] [Indexed: 05/20/2023]
Abstract
Leguminous plants produce nodules for nitrogen fixation; however, nodule production incurs an energy cost. Therefore, as an adaptive strategy, leguminous plants halt root nodule development when sufficient amounts of nitrogen nutrients, such as nitrate, are present in the environment. Although legume NODULE INCEPTION (NIN)-LIKE PROTEIN (NLP) transcription factors have recently been identified, understanding how nodulation is controlled by nitrate, a fundamental question for nitrate-mediated transcriptional regulation of symbiotic genes, remains elusive. Here, we show that two Lotus japonicus NLPs, NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1)/LjNLP4 and NRSYM2/LjNLP1, have overlapping functions in the nitrate-induced control of nodulation and act as master regulators for nitrate-dependent gene expression. We further identify candidate target genes of LjNLP4 by combining transcriptome analysis with a DNA affinity purification-seq approach. We then demonstrate that LjNLP4 and LjNIN, a key nodulation-specific regulator and paralog of LjNLP4, have different DNA-binding specificities. Moreover, LjNLP4-LjNIN dimerization underlies LjNLP4-mediated bifunctional transcriptional regulation. These data provide a basic principle for how nitrate controls nodulation through positive and negative regulation of symbiotic genes.
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Affiliation(s)
- Hanna Nishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shohei Nosaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Momoyo Ito
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takuya Miyakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
| | - Kenji Miura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masaru Tanokura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, Japan
| | - Takuya Suzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Author for correspondence:
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Vega A, Fredes I, O'Brien J, Shen Z, Ötvös K, Abualia R, Benkova E, Briggs SP, Gutiérrez RA. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Rep 2021; 22:e51813. [PMID: 34357701 PMCID: PMC8447600 DOI: 10.15252/embr.202051813] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/13/2021] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Nitrate commands genome‐wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild‐type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post‐translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.
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Affiliation(s)
- Andrea Vega
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Isabel Fredes
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - José O'Brien
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Fruticultura y Enología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Zhouxin Shen
- Cell and Developmental Biology, University of California San Diego. San Diego, CA, USA
| | - Krisztina Ötvös
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria.,Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Rashed Abualia
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Eva Benkova
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Steven P Briggs
- Cell and Developmental Biology, University of California San Diego. San Diego, CA, USA
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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72
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Abstract
Nutrients are vital to life through intertwined sensing, signaling, and metabolic processes. Emerging research focuses on how distinct nutrient signaling networks integrate and coordinate gene expression, metabolism, growth, and survival. We review the multifaceted roles of sugars, nitrate, and phosphate as essential plant nutrients in controlling complex molecular and cellular mechanisms of dynamic signaling networks. Key advances in central sugar and energy signaling mechanisms mediated by the evolutionarily conserved master regulators HEXOKINASE1 (HXK1), TARGET OF RAPAMYCIN (TOR), and SNF1-RELATED PROTEIN KINASE1 (SNRK1) are discussed. Significant progress in primary nitrate sensing, calcium signaling, transcriptome analysis, and root-shoot communication to shape plant biomass and architecture are elaborated. Discoveries on intracellular and extracellular phosphate signaling and the intimate connections with nitrate and sugar signaling are examined. This review highlights the dynamic nutrient, energy, growth, and stress signaling networks that orchestrate systemwide transcriptional, translational, and metabolic reprogramming, modulate growth and developmental programs, and respond to environmental cues. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lei Li
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; ,
| | - Kun-Hsiang Liu
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; , .,State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, and Institute of Future Agriculture, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Jen Sheen
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; ,
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73
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Konishi M, Okitsu T, Yanagisawa S. Nitrate-responsive NIN-like protein transcription factors perform unique and redundant roles in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5735-5750. [PMID: 34050740 DOI: 10.1093/jxb/erab246] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Upon sensing nitrate, NODULE INCEPTION (NIN)-like protein (NLP) transcription factors alter gene expression to promote nitrate uptake and utilization. Of the nine NLPs in Arabidopsis, the physiological roles of only three NLPs (NLP6-NLP8) have been characterized to date. To evaluate the unique and redundant roles of Arabidopsis NLPs, we assessed the phenotypes of single and higher order nlp mutants. Unlike other nlp single mutants, nlp2 and nlp7 single mutants showed a reduction in shoot fresh weight when grown in the presence of nitrate as the sole nitrogen source, indicating that NLP2, like NLP7, plays a major role in vegetative growth. Interestingly, the growth defect of nlp7 recovered upon the supply of ammonium or glutamine, whereas that of nlp2 did not. Furthermore, complementation assays using chimeric constructs revealed that the coding sequence, but not the promoter region, of NLP genes was responsible for the differences between nlp2 and nlp7 single mutant phenotypes, suggesting differences in protein function. Importantly, nitrate utilization was almost completely abolished in the nlp septuple mutant (nlp2 nlp4 nlp5 nlp6 nlp7 nlp8 nlp9), suggesting that NLPs other than NLP2 and NLP7 also assist in the regulation of nitrate-inducible gene expression and nitrate-dependent promotion of vegetative growth in Arabidopsis.
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Affiliation(s)
- Mineko Konishi
- Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Tokyo, Japan
| | - Takayuki Okitsu
- Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Tokyo, Japan
| | - Shuichi Yanagisawa
- Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Tokyo, Japan
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74
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Alvarez JM, Brooks MD, Swift J, Coruzzi GM. Time-Based Systems Biology Approaches to Capture and Model Dynamic Gene Regulatory Networks. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:105-131. [PMID: 33667112 PMCID: PMC9312366 DOI: 10.1146/annurev-arplant-081320-090914] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
All aspects of transcription and its regulation involve dynamic events. However, capturing these dynamic events in gene regulatory networks (GRNs) offers both a promise and a challenge. The promise is that capturing and modeling the dynamic changes in GRNs will allow us to understand how organisms adapt to a changing environment. The ability to mount a rapid transcriptional response to environmental changes is especially important in nonmotile organisms such as plants. The challenge is to capture these dynamic, genome-wide events and model them in GRNs. In this review, we cover recent progress in capturing dynamic interactions of transcription factors with their targets-at both the local and genome-wide levels-and how they are used to learn how GRNs operate as a function of time. We also discuss recent advances that employ time-based machine learning approaches to forecast gene expression at future time points, a key goal of systems biology.
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Affiliation(s)
- Jose M Alvarez
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Matthew D Brooks
- Global Change and Photosynthesis Research Unit, US Department of Agriculture Agricultural Research Service, Urbana, Illinois 61801, USA
| | - Joseph Swift
- Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA;
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75
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Xin W, Wang J, Li J, Zhao H, Liu H, Zheng H, Yang L, Wang C, Yang F, Chen J, Zou D. Candidate Gene Analysis for Nitrogen Absorption and Utilization in Japonica Rice at the Seedling Stage Based on a Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2021; 12:670861. [PMID: 34149769 PMCID: PMC8212024 DOI: 10.3389/fpls.2021.670861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Over-application of nitrogen (N) fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high N use efficiency (NUE) reduce fertilizer requirements, enabling sustainable agriculture. Genome-wide association study (GWAS) analysis of N absorption and utilization traits under low and high N conditions was performed to obtain 12 quantitative trait loci (QTLs) based on genotypic data including 151,202 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 267 japonica rice varieties. Eighteen candidate genes were obtained by integrating GWAS and transcriptome analyses; among them, the functions of OsNRT2.4, OsAMT1.2, and OsAlaAT genes in N transport and assimilation have been identified, and OsJAZ12 and OsJAZ13 also play important roles in rice adaptation to abiotic stresses. A NUE-related candidate gene, OsNAC68, was identified by quantitative real-time PCR (qRT-PCR) analyses. OsNAC68 encodes a NAC transcription factor and has been shown to be a positive regulator of the drought stress response in rice. Overexpression of OsNAC68 significantly increased rice NUE and grain yield under deficient N conditions, but the difference was not significant under sufficient N conditions. NUE and grain yield significantly decreased under both N supply conditions in the osbnac68 mutant. This study provides crucial insights into the genetic basis of N absorption and utilization in rice, and a NUE-related gene, OsNAC68, was cloned to provide important resources for rice breeding with high NUE and grain yield.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
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76
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Safi A, Medici A, Szponarski W, Martin F, Clément-Vidal A, Marshall-Colon A, Ruffel S, Gaymard F, Rouached H, Leclercq J, Coruzzi G, Lacombe B, Krouk G. GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3881-3901. [PMID: 33758916 PMCID: PMC8096604 DOI: 10.1093/jxb/erab114] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/22/2021] [Indexed: 05/04/2023]
Abstract
Plants need to cope with strong variations of nitrogen availability in the soil. Although many molecular players are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of nitrogen. Following nitrogen removal, plants activate their nitrogen starvation response (NSR), which is characterized by the activation of very high-affinity nitrate transport systems (NRT2.4 and NRT2.5) and other sentinel genes involved in N remobilization such as GDH3. Using a combination of functional genomics via transcription factor perturbation and molecular physiology studies, we show that the transcription factors belonging to the HHO subfamily are important regulators of NSR through two potential mechanisms. First, HHOs directly repress the high-affinity nitrate transporters, NRT2.4 and NRT2.5. hho mutants display increased high-affinity nitrate transport activity, opening up promising perspectives for biotechnological applications. Second, we show that reactive oxygen species (ROS) are important to control NSR in wild-type plants and that HRS1 and HHO1 overexpressors and mutants are affected in their ROS content, defining a potential feed-forward branch of the signaling pathway. Taken together, our results define the relationships of two types of molecular players controlling the NSR, namely ROS and the HHO transcription factors. This work (i) up opens perspectives on a poorly understood nutrient-related signaling pathway and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.
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Affiliation(s)
- Alaeddine Safi
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Correspondence: or
| | - Anna Medici
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | | | - Florence Martin
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Anne Clément-Vidal
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Amy Marshall-Colon
- New York University, Department of Biology, Center for Genomics & Systems Biology, New York, NY, USA
- Present address: Department of Plant Biology, University of Illinois at Urbana -Champaign, Urbana, IL, USA
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Frédéric Gaymard
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Hatem Rouached
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Department of Plant, Soil, and Microbial Sciences, and Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Julie Leclercq
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gloria Coruzzi
- New York University, Department of Biology, Center for Genomics & Systems Biology, New York, NY, USA
| | - Benoît Lacombe
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Correspondence: or
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77
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Wang G, Li X, An Y, Zhang J, Li H. Transient ChIP-Seq for Genome-wide In Vivo DNA Binding Landscape. TRENDS IN PLANT SCIENCE 2021; 26:524-525. [PMID: 33397601 DOI: 10.1016/j.tplants.2020.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Affiliation(s)
- Guanqun Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xiaozheng Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yunyun An
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Haoxuan Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong.
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78
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Liu C, Wu Q, Sun L, You X, Ye X, Wan Y, Wu X, Jiang L, Zhao G, Xiang D, Zou L. Nitrate dose-responsive transcriptome analysis identifies transcription factors and small secreted peptides involved in nitrogen response in Tartary buckwheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:1-13. [PMID: 33652200 DOI: 10.1016/j.plaphy.2021.02.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an economically important pseudocereal crop, which can adapt well to extreme environments, including low nitrogen (LN) stress. However, little is known regarding the associated molecular mechanisms. In this study, the molecular mechanism of Tartary buckwheat roots in response to different doses of nitrate was investigated by combining physiological changes with transcriptional regulatory network. LN improved elongation and branching of lateral roots, indicating that the plasticity of lateral roots drives the adaption of Tartary buckwheat under LN condition. The roots of the seedlings that were cultivated under four N conditions were selected for RNA-Seq analysis. In total 1686 nitrate dose-responsive genes were identified. Of these genes, 16 genes encoding N transporters showed response to N availability, and they may play important roles in N transport and root system architecture in Tartary buckwheat roots. 108 transcription factors (TFs) showed dose-response to N availability, and they may regulate N response and root growth under varied N conditions by modulating the expression of N transporters. A NIN-like protein, FtNLP7, was identified and it may contribute to the transcriptional regulation of N transporters. Furthermore, 81 N-responsive genes were identified as the small secreted peptides (SSPs). 48 N-responsive SSPs were annotated as hypothetical proteins and they may be the species-specific proteins of Tartary buckwheat. This paper provides useful information for further investigation of the mechanisms underlying the adaptation of Tartary buckwheat under N-deficient condition.
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Affiliation(s)
- Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China
| | - Lu Sun
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China
| | - Xiaoqing You
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China
| | - Xueling Ye
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China
| | - Xiaoyong Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China
| | - Liangzhen Jiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China.
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China.
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79
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Fichtner F, Dissanayake IM, Lacombe B, Barbier F. Sugar and Nitrate Sensing: A Multi-Billion-Year Story. TRENDS IN PLANT SCIENCE 2021; 26:352-374. [PMID: 33281060 DOI: 10.1016/j.tplants.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/23/2020] [Accepted: 11/04/2020] [Indexed: 05/03/2023]
Abstract
Sugars and nitrate play a major role in providing carbon and nitrogen in plants. Understanding how plants sense these nutrients is crucial, most notably for crop improvement. The mechanisms underlying sugar and nitrate sensing are complex and involve moonlighting proteins such as the nitrate transporter NRT1.1/NFP6.3 or the glycolytic enzyme HXK1. Major components of nutrient signaling, such as SnRK1, TOR, and HXK1, are relatively well conserved across eukaryotes, and the diversification of components such as the NRT1 family and the SWEET sugar transporters correlates with plant terrestrialization. In plants, Tre6P plays a hormone-like role in plant development. In addition, nutrient signaling has evolved to interact with the more recent hormone signaling, allowing fine-tuning of physiological and developmental responses.
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Affiliation(s)
- Franziska Fichtner
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Benoit Lacombe
- Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Francois Barbier
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
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80
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Gautrat P, Laffont C, Frugier F, Ruffel S. Nitrogen Systemic Signaling: From Symbiotic Nodulation to Root Acquisition. TRENDS IN PLANT SCIENCE 2021; 26:392-406. [PMID: 33358560 DOI: 10.1016/j.tplants.2020.11.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/30/2020] [Accepted: 11/16/2020] [Indexed: 05/27/2023]
Abstract
Plant nutrient acquisition is tightly regulated by resource availability and metabolic needs, implying the existence of communication between roots and shoots to ensure their integration at the whole-plant level. Here, we focus on systemic signaling pathways controlling nitrogen (N) nutrition, achieved both by the root import of mineral N and, in legume plants, through atmospheric N fixation by symbiotic bacteria inside dedicated root nodules. We explore features conserved between systemic pathways repressing or enhancing symbiotic N fixation and the regulation of mineral N acquisition by roots, as well as their integration with other environmental factors, such as phosphate, light, and CO2 availability.
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Affiliation(s)
- Pierre Gautrat
- IPS2 (Institute of Plant Sciences - Paris Saclay), CNRS, INRAe, Université Paris-Diderot, Université d'Evry, Université Paris-Saclay, Bâtiment 630, Gif-sur-Yvette, France
| | - Carole Laffont
- IPS2 (Institute of Plant Sciences - Paris Saclay), CNRS, INRAe, Université Paris-Diderot, Université d'Evry, Université Paris-Saclay, Bâtiment 630, Gif-sur-Yvette, France
| | - Florian Frugier
- IPS2 (Institute of Plant Sciences - Paris Saclay), CNRS, INRAe, Université Paris-Diderot, Université d'Evry, Université Paris-Saclay, Bâtiment 630, Gif-sur-Yvette, France.
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRAe, Montpellier SupAgro, Montpellier, France.
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81
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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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Brooks MD, Juang CL, Katari MS, Alvarez JM, Pasquino A, Shih HJ, Huang J, Shanks C, Cirrone J, Coruzzi GM. ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks. PLANT PHYSIOLOGY 2021; 185:49-66. [PMID: 33631799 PMCID: PMC8133578 DOI: 10.1093/plphys/kiaa012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/27/2020] [Indexed: 05/08/2023]
Abstract
Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems biology. The promise lies in identifying key transcription factors (TFs) that enable an organism to react to changes in its environment. The challenge lies in validating GRNs that involve hundreds of TFs with hundreds of thousands of interactions with their genome-wide targets experimentally determined by high-throughput sequencing. To address this challenge, we developed ConnecTF, a species-independent, web-based platform that integrates genome-wide studies of TF-target binding, TF-target regulation, and other TF-centric omic datasets and uses these to build and refine validated or inferred GRNs. We demonstrate the functionality of ConnecTF by showing how integration within and across TF-target datasets uncovers biological insights. Case study 1 uses integration of TF-target gene regulation and binding datasets to uncover TF mode-of-action and identify potential TF partners for 14 TFs in abscisic acid signaling. Case study 2 demonstrates how genome-wide TF-target data and automated functions in ConnecTF are used in precision/recall analysis and pruning of an inferred GRN for nitrogen signaling. Case study 3 uses ConnecTF to chart a network path from NLP7, a master TF in nitrogen signaling, to direct secondary TF2s and to its indirect targets in a Network Walking approach. The public version of ConnecTF (https://ConnecTF.org) contains 3,738,278 TF-target interactions for 423 TFs in Arabidopsis, 839,210 TF-target interactions for 139 TFs in maize (Zea mays), and 293,094 TF-target interactions for 26 TFs in rice (Oryza sativa). The database and tools in ConnecTF will advance the exploration of GRNs in plant systems biology applications for model and crop species.
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Affiliation(s)
- Matthew D Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL, USA
| | - Che-Lun Juang
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Manpreet Singh Katari
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - José M Alvarez
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Angelo Pasquino
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Hung-Jui Shih
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Ji Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Carly Shanks
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Jacopo Cirrone
- Courant Institute for Mathematical Sciences, Department of Computer Science, New York University NY, USA
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Author for communication: (G.C.)
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83
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Lu L, Zhang Y, Li L, Yi N, Liu Y, Qaseem MF, Li H, Wu AM. Physiological and Transcriptomic Responses to Nitrogen Deficiency in Neolamarckia cadamba. FRONTIERS IN PLANT SCIENCE 2021; 12:747121. [PMID: 34887886 PMCID: PMC8649893 DOI: 10.3389/fpls.2021.747121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/12/2021] [Indexed: 05/11/2023]
Abstract
Nitrogen (N) is one of the abundant and essential elements for plant growth and development, and N deficiency (ND) affects plants at both physiological and transcriptomic levels. Neolamarckia cadamba is a fast-growing woody plant from the Rubiaceae family. However, the physiological and molecular impacts of ND on this species have not been well investigated. Here, we studied how N. cadamba responds to ND under hydroponic conditions. In a physiological aspect, ND led to a reduction in biomass, chlorophyll content, and photosynthetic capacity. ND also impaired the assimilation of N as the activities of glutamine synthetase (GS) and nitrate reductase (NR) were decreased in the root. Interestingly, the lignin content of stem increased progressively during the ND stress. The main transcription factors, the transcription factors that are important to N regulation has been found to be upregulated, including Nodule inception-like protein 7 (NLP7), TGACG motif-binding factor 1 (TGA1), basic helix-loop-helix protein 45 (BHLH45), NAM, ATAF1,2, CUC2 (NAC) transcription factor 43 (NAC43), and basic leucine zipper pattern 44 (bZIP44). The expression of N transporters, such as nitrate transporter 2.4 (NRT2.4), ammonium transporter 3 (AMT3), and amino acid transporter protein 3 (AAP3), was also upregulated. In addition, phosphorus- and calcium-related genes such as phosphate starvation response 2 (PHR2) and cyclic nucleotide-gated ion channel 15 (CNGC15) were expressed more abundantly in response to ND stress. Our results reveal the physiological and molecular mechanisms by which woody plants respond to ND.
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Affiliation(s)
- Lu Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Yuanyuan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Lu Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Na Yi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Yi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Mirza Faisal Qaseem
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Huiling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
- *Correspondence: Huiling Li,
| | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, China
- Ai-Min Wu,
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84
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Askjaer P, Harr JC. Genetic approaches to revealing the principles of nuclear architecture. Curr Opin Genet Dev 2020; 67:52-60. [PMID: 33338753 DOI: 10.1016/j.gde.2020.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
The spatial organization of chromosomes inside the eukaryotic nucleus is important for DNA replication, repair and gene expression. During development of multicellular organisms, different compendiums of genes are either repressed or activated to produce specific cell types. Genetic manipulation of tractable organisms is invaluable to elucidate chromosome configuration and the underlying mechanisms. Systematic inhibition of genes through RNA interference and, more recently, CRISPR/Cas9-based screens have identified new proteins with significant roles in nuclear organization. Coupling this with advances in imaging techniques, such as multiplexed DNA fluorescence in situ hybridization, and with tissue-specific genome profiling by DNA adenine methylation identification has increased our knowledge about the immense complexity and dynamics of the nucleus.
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Affiliation(s)
- Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville 41013, Spain.
| | - Jennifer C Harr
- Department of Biological Sciences, St. Mary's University, One Camino Santa Maria, San Antonio, TX, 78228, USA.
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Domínguez-Figueroa J, Carrillo L, Renau-Morata B, Yang L, Molina RV, Marino D, Canales J, Weih M, Vicente-Carbajosa J, Nebauer SG, Medina J. The Arabidopsis Transcription Factor CDF3 Is Involved in Nitrogen Responses and Improves Nitrogen Use Efficiency in Tomato. FRONTIERS IN PLANT SCIENCE 2020; 11:601558. [PMID: 33329669 PMCID: PMC7732579 DOI: 10.3389/fpls.2020.601558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/29/2020] [Indexed: 06/12/2023]
Abstract
Nitrate is an essential macronutrient and a signal molecule that regulates the expression of multiple genes involved in plant growth and development. Here, we describe the participation of Arabidopsis DNA binding with one finger (DOF) transcription factor CDF3 in nitrate responses and shows that CDF3 gene is induced under nitrate starvation. Moreover, knockout cdf3 mutant plants exhibit nitrate-dependent lateral and primary root modifications, whereas CDF3 overexpression plants show increased biomass and enhanced root development under both nitrogen poor and rich conditions. Expression analyses of 35S::CDF3 lines reveled that CDF3 regulates the expression of an important set of nitrate responsive genes including, glutamine synthetase-1, glutamate synthase-2, nitrate reductase-1, and nitrate transporters NRT2.1, NRT2.4, and NRT2.5 as well as carbon assimilation genes like PK1 and PEPC1 in response to N availability. Consistently, metabolite profiling disclosed that the total amount of key N metabolites like glutamate, glutamine, and asparagine were higher in CDF3-overexpressing plants, but lower in cdf3-1 in N limiting conditions. Moreover, overexpression of CDF3 in tomato increased N accumulation and yield efficiency under both optimum and limiting N supply. These results highlight CDF3 as an important regulatory factor for the nitrate response, and its potential for improving N use efficiency in crops.
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Affiliation(s)
- José Domínguez-Figueroa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Begoña Renau-Morata
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Valencia, Spain
| | - Lu Yang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Rosa-V Molina
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Valencia, Spain
| | - Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Martin Weih
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Sergio G. Nebauer
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Valencia, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
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Maghiaoui A, Gojon A, Bach L. NRT1.1-centered nitrate signaling in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6226-6237. [PMID: 32870279 DOI: 10.1093/jxb/eraa361] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/14/2020] [Indexed: 05/21/2023]
Abstract
Plants need efficient nitrate (NO3-) sensing systems and sophisticated signaling pathways to develop a wide range of adaptive responses to external fluctuations of NO3- supply. In Arabidopsis thaliana, numerous molecular regulators have been identified to participate in signaling pathways that respond specifically to NO3-. In contrast, only a single NO3- sensing system has been described to date, relying on the NRT1.1 (NPF6.3/CHL1) NO3- transceptor. NRT1.1 governs a wide range of responses to NO3-, from fast reprogramming of genome expression (the primary nitrate response) to longer-term developmental changes (effects on lateral root development). NRT1.1 appears to be at the center of a complex network of signaling pathways, involving numerous molecular players acting downstream and/or upstream of it. Interestingly, some of these regulators are involved in crosstalk with the signaling pathways of other nutrients, such as inorganic phosphate or potassium. Although NRT1.1-mediated NO3- sensing and signaling has mostly been documented in Arabidopsis, recent evidence indicates that similar mechanisms involving NRT1.1 orthologues are operative in rice. This review aims to delineate how the NRT1.1 sensing system and the downstream/upstream transduction cascades are integrated to control both the expression of NO3--responsive genes and the induced plasticity of root development.
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Affiliation(s)
- Amel Maghiaoui
- Biochimie et Physiologie Moléculaire des Plantes (BPMP), UMR 5004 CNRS/INRAE/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, Place Viala, France
| | - Alain Gojon
- Biochimie et Physiologie Moléculaire des Plantes (BPMP), UMR 5004 CNRS/INRAE/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, Place Viala, France
| | - Liên Bach
- Biochimie et Physiologie Moléculaire des Plantes (BPMP), UMR 5004 CNRS/INRAE/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, Place Viala, France
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87
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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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