1
|
Miao F, Wang Y, Haq NU, Lyu MJA, Zhu XG. Rewiring of primary metabolism for ammonium recycling under short-term low CO 2 treatment - its implication for C 4 evolution. FRONTIERS IN PLANT SCIENCE 2024; 15:1322261. [PMID: 39148616 PMCID: PMC11324553 DOI: 10.3389/fpls.2024.1322261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 07/04/2024] [Indexed: 08/17/2024]
Abstract
The dramatic decrease in atmospheric CO2 concentration during Oligocene was proposed as directly linked to C4 evolution. However, it remains unclear how the decreased CO2 concentration directly facilitate C4 evolution, besides its role as a selection pressure. We conducted a systematic transcriptomics and metabolomics analysis under short-term low CO2 condition and found that Arabidopsis grown under this condition showed 1) increased expression of most genes encoding C4-related enzymes and transporters; 2) increased expression of genes involved in photorespiration and pathways related to carbon skeleton generation for ammonium refixation; 3) increased expression of genes directly involved in ammonium refixation. Furthermore, we found that in vitro treatment of leaves with NH4 + induced a similar pattern of changes in C4 related genes and genes involved in ammonium refixation. These data support the view that Arabidopsis grown under short-term low CO2 conditions rewired its metabolism to supply carbon skeleton for ammonium recycling, during which process the expression of C4 genes were up-regulated as a result of a hitchhiking process. This study provides new insights into the adaptation of the C3 model plant Arabidopsis under low CO2 conditions and suggests that low CO2 can facilitate the evolution of C4 photosynthesis beyond the commonly assumed role of being a selection pressure.
Collapse
Affiliation(s)
- Fenfen Miao
- University of Chinese Academy of Sciences (UCAS), Beijing, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ying Wang
- University of Chinese Academy of Sciences (UCAS), Beijing, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Noor Ui Haq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Ming-Ju Amy Lyu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xin-Guang Zhu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| |
Collapse
|
2
|
Zhao H, Ge M, Zhang F, Du D, Zhao Z, Shen C, Hao Q, Xiao M, Shi X, Wang J, Fan M. Integrated morphological, physiological and transcriptomic analyses reveal the responses of Toona sinensis seedlings to low-nitrogen stress. Genomics 2024; 116:110899. [PMID: 39047875 DOI: 10.1016/j.ygeno.2024.110899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 07/03/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
Nitrogen is one of the most essential elements for plant growth and development. In this study, the growth, physiology, and transcriptome of Toona sinensis (A. Juss) Roem seedlings were compared between low-nitrogen (LN) and normal-nitrogen (NN) conditions. These results indicate that LN stress adversely influences T. sinensis seedling growth. The activities of key enzymes related to nitrogen assimilation and phytohormone contents were altered by LN stress. A total of 2828 differentially expressed genes (DEGs) in roots and 1547 in leaves were identified between the LN and NN treatments. A differential enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that nitrogen and sugar metabolism, flavonoid biosynthesis, plant hormone signal transduction, and ABC transporters, were strongly affected by LN stress. In summary, this research provides information for further understanding the response of T. sinensis to LN stress.
Collapse
Affiliation(s)
- Hu Zhao
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China.
| | - Miaomiao Ge
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Fengzhe Zhang
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Didi Du
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Zilu Zhao
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Cheng Shen
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Qingping Hao
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Min Xiao
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Xiaopu Shi
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China.
| | - Juan Wang
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Mingqin Fan
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| |
Collapse
|
3
|
Shanks CM, Rothkegel K, Brooks MD, Cheng CY, Alvarez JM, Ruffel S, Krouk G, Gutiérrez RA, Coruzzi GM. Nitrogen sensing and regulatory networks: it's about time and space. THE PLANT CELL 2024; 36:1482-1503. [PMID: 38366121 PMCID: PMC11062454 DOI: 10.1093/plcell/koae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.
Collapse
Affiliation(s)
- Carly M Shanks
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Karin Rothkegel
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Matthew D Brooks
- Global Change and Photosynthesis Research Unit, USDA-ARS, Urbana, IL 61801, USA
| | - Chia-Yi Cheng
- Department of Life Science, National Taiwan University, Taipei 10663, Taiwan
| | - José M Alvarez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias, Universidad Andrés Bello, 8370035 Santiago, Chile
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Gabriel Krouk
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Rodrigo A Gutiérrez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Gloria M Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| |
Collapse
|
4
|
Xu Y, Qi S, Wang Y, Jia J. Integration of nitrate and abscisic acid signaling in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024:erae128. [PMID: 38661493 DOI: 10.1093/jxb/erae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/19/2024] [Indexed: 04/26/2024]
Abstract
To meet the demands of the new Green Revolution and sustainable agriculture, it is important to develop crop varieties with improved yield, nitrogen use efficiency, and stress resistance. Nitrate is the major form of inorganic nitrogen available for plant growth in many well-aerated agricultural soils, and acts as a signaling molecule regulating plant development, growth, and stress responses. Abscisic acid (ABA), an important phytohormone, plays vital roles in integrating extrinsic and intrinsic responses and mediating plant growth and development in response to biotic and abiotic stresses. Therefore, elucidating the interplay between nitrate and ABA can contribute to crop breeding and sustainable agriculture. Here, we review studies that have investigated the interplay between nitrate and ABA in root growth modulation, nitrate and ABA transport processes, seed germination regulation, and drought responses. We also focus on nitrate and ABA interplay in several reported omics analyses with some important nodes in the crosstalk between nitrate and ABA. Through these insights, we proposed some research perspectives that could help to develop crop varieties adapted to a changing environment and to improve crop yield with high nitrogen use efficiency and strong stress resistance.
Collapse
Affiliation(s)
- Yiran Xu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shengdong Qi
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yong Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Jingbo Jia
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| |
Collapse
|
5
|
Huang Y, Ji Z, Zhang S, Li S. Function of hormone signaling in regulating nitrogen-use efficiency in plants. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154191. [PMID: 38335845 DOI: 10.1016/j.jplph.2024.154191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Nitrogen (N) is one of the most important nutrients for crop plant performance, however, the excessive application of nitrogenous fertilizers in agriculture significantly increases production costs and causes severe environmental problems. Therefore, comprehensively understanding the molecular mechanisms of N-use efficiency (NUE) with the aim of developing new crop varieties that combine high yields with improved NUE is an urgent goal for achieving more sustainable agriculture. Plant NUE is a complex trait that is affected by multiple factors, of which hormones are known to play pivotal roles. In this review, we focus on the interaction between the biosynthesis and signaling pathways of plant hormones with N metabolism, and summarize recent studies on the interplay between hormones and N, including how N regulates multiple hormone biosynthesis, transport and signaling and how hormones modulate root system architecture (RSA) in response to external N sources. Finally, we explore potential strategies for promoting crop NUE by modulating hormone synthesis, transport and signaling. This provides insights for future breeding of N-efficient crop varieties and the advancement of sustainable agriculture.
Collapse
Affiliation(s)
- Yunzhi Huang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhe Ji
- Department of Biology, University of Oxford, Oxford, UK
| | - Siyu Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Shan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
6
|
Buoso S, Lodovici A, Salvatori N, Tomasi N, Arkoun M, Maillard A, Marroni F, Alberti G, Peressotti A, Pinton R, Zanin L. Nitrogen nutrition and xylem sap composition in Zea mays: effect of urea, ammonium and nitrate on ionomic and metabolic profiles. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111825. [PMID: 37572967 DOI: 10.1016/j.plantsci.2023.111825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
In plants the communication between organs is mainly carried out via the xylem and phloem. The concentration and the molecular species of some phytohormones, assimilates and inorganic ions that are translocated in the xylem vessel play a key role in the systemic nutritional signaling in plants. In this work the composition of the xylem sap of maize was investigated at the metabolic and ionomic level depending on the N form available in the nutrient solution. Plants were grown up to 7 days in hydroponic system under N-free nutrient solution or nutrient solution containing N in form of nitrate, urea, ammonium or a combination of urea and ammonium. For the first time this work provides evidence that the ureic nutrition reduced the water translocation in maize plants more than mineral N forms. This result correlates with those obtained from the analyses of photosynthetic parameters (stomatal conductance and transpiration rate) suggesting a parsimonious use of water by maize plants under urea nutrition. A peculiar composition in amino acids and phytohormones (i.e. S, Gln, Pro, ABA) of the xylem sap under urea nutrition could explain differences in xylem sap exudation in comparison to plants treated with mineral N forms. The knowledge improvement of urea nutrition will allow to further perform good agronomic strategies to improve the resilience of maize crop to water stress.
Collapse
Affiliation(s)
- Sara Buoso
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Arianna Lodovici
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Nicole Salvatori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy; Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Nicola Tomasi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Mustapha Arkoun
- Laboratoire de Nutrition Végétale, Agro Innovation International-TIMAC AGRO, Saint-Malo 35400, France
| | - Anne Maillard
- Laboratoire de Nutrition Végétale, Agro Innovation International-TIMAC AGRO, Saint-Malo 35400, France
| | - Fabio Marroni
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Giorgio Alberti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Alessandro Peressotti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Roberto Pinton
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Laura Zanin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.
| |
Collapse
|
7
|
Crabos A, Huang Y, Boursat T, Maurel C, Ruffel S, Krouk G, Boursiac Y. Distinct early transcriptional regulations by turgor and osmotic potential in the roots of Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5917-5930. [PMID: 37603421 DOI: 10.1093/jxb/erad307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/28/2023] [Indexed: 08/23/2023]
Abstract
In a context of climate change, deciphering signaling pathways driving plant adaptation to drought, changes in water availability, and salt is key. A crossing point of these plant stresses is their impact on plant water potential (Ψ), a composite physico-chemical variable reflecting the availability of water for biological processes such as plant growth and stomatal aperture. The Ψ of plant cells is mainly driven by their turgor and osmotic pressures. Here we investigated the effect of a variety of osmotic treatments on the roots of Arabidopsis plants grown in hydroponics. We used, among others, a permeating solute as a way to differentiate variations on turgor from variations in osmotic pressure. Measurement of cortical cell turgor pressure with a cell pressure probe allowed us to monitor the intensity of the treatments and thereby preserve the cortex from plasmolysis. Transcriptome analyses at an early time point (15 min) showed specific and quantitative transcriptomic responses to both osmotic and turgor pressure variations. Our results highlight how water-related biophysical parameters can shape the transcriptome of roots under stress and provide putative candidates to explore further the early perception of water stress in plants.
Collapse
Affiliation(s)
- Amandine Crabos
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Yunji Huang
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Thomas Boursat
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
- Laboratoire de Mécanique et Génie Civil (LMGC), Univ Montpellier, CNRS, Montpellier, France
| | - Christophe Maurel
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Gabriel Krouk
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Yann Boursiac
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| |
Collapse
|
8
|
Abualia R, Riegler S, Benkova E. Nitrate, Auxin and Cytokinin-A Trio to Tango. Cells 2023; 12:1613. [PMID: 37371083 DOI: 10.3390/cells12121613] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links.
Collapse
Affiliation(s)
- Rashed Abualia
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Stefan Riegler
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Eva Benkova
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| |
Collapse
|
9
|
Transcriptome and Metabolome Reveal the Molecular Mechanism of Barley Genotypes Underlying the Response to Low Nitrogen and Resupply. Int J Mol Sci 2023; 24:ijms24054706. [PMID: 36902137 PMCID: PMC10003240 DOI: 10.3390/ijms24054706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Nitrogen is one of the most important mineral elements for plant growth and development. Excessive nitrogen application not only pollutes the environment, but also reduces the quality of crops. However, are few studies on the mechanism of barley tolerance to low nitrogen at both the transcriptome and metabolomics levels. In this study, the nitrogen-efficient genotype (W26) and the nitrogen-sensitive genotype (W20) of barley were treated with low nitrogen (LN) for 3 days and 18 days, then treated with resupplied nitrogen (RN) from 18 to 21 days. Later, the biomass and the nitrogen content were measured, and RNA-seq and metabolites were analyzed. The nitrogen use efficiency (NUE) of W26 and W20 treated with LN for 21 days was estimated by nitrogen content and dry weight, and the values were 87.54% and 61.74%, respectively. It turned out to have a significant difference in the two genotypes under the LN condition. According to the transcriptome analysis, 7926 differentially expressed genes (DEGs) and 7537 DEGs were identified in the leaves of W26 and W20, respectively, and 6579 DEGs and 7128 DEGs were found in the roots of W26 and W20, respectively. After analysis of the metabolites, 458 differentially expressed metabolites (DAMs) and 425 DAMs were found in the leaves of W26 and W20, respectively, and 486 DAMs and 368 DAMs were found in the roots of W26 and W20, respectively. According to the KEGG joint analysis of DEGs and DAMs, it was discovered that glutathione (GSH) metabolism was the pathway of significant enrichment in the leaves of both W26 and W20. In this study, the metabolic pathways of nitrogen metabolism and GSH metabolism of barley under nitrogen were constructed based on the related DAMs and DEGs. In leaves, GSH, amino acids, and amides were the main identified DAMs, while in roots, GSH, amino acids, and phenylpropanes were mainly found DAMs. Finally, some nitrogen-efficient candidate genes and metabolites were selected based on the results of this study. The responses of W26 and W20 to low nitrogen stress were significantly different at the transcriptional and metabolic levels. The candidate genes that have been screened will be verified in future. These data not only provide new insights into how barley responds to LN, but also provide new directions for studying the molecular mechanisms of barley under abiotic stress.
Collapse
|
10
|
Xing J, Cao X, Zhang M, Wei X, Zhang J, Wan X. Plant nitrogen availability and crosstalk with phytohormones signallings and their biotechnology breeding application in crops. PLANT BIOTECHNOLOGY JOURNAL 2022. [PMID: 36435985 DOI: 10.1111/pbi.13971] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/27/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen (N), one of the most important nutrients, limits plant growth and crop yields in sustainable agriculture system, in which phytohormones are known to play essential roles in N availability. Hence, it is not surprising that massive studies about the crosstalk between N and phytohormones have been constantly emerging. In this review, with the intellectual landscape of N and phytohormones crosstalk provided by the bibliometric analysis, we trace the research story of best-known crosstalk between N and various phytohormones over the last 20 years. Then, we discuss how N regulates various phytohormones biosynthesis and transport in plants. In reverse, we also summarize how phytohormones signallings modulate root system architecture (RSA) in response to N availability. Besides, we expand to outline how phytohormones signallings regulate uptake, transport, and assimilation of N in plants. Further, we conclude advanced biotechnology strategies, explain their application, and provide potential phytohormones-regulated N use efficiency (NUE) targets in crops. Collectively, this review provides not only a better understanding on the recent progress of crosstalk between N and phytohormones, but also targeted strategies for improvement of NUE to increase crop yields in future biotechnology breeding of crops.
Collapse
Affiliation(s)
- Jiapeng Xing
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing, China
| | - Xiaocong Cao
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing, China
| | - Mingcai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xun Wei
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing, China
| | - Juan Zhang
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing, China
| | - Xiangyuan Wan
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing, China
| |
Collapse
|
11
|
Wang Q, Ou EL, Wang PC, Chen Y, Wang ZY, Wang ZW, Fang XW, Zhang JL. Bacillus amyloliquefaciens GB03 augmented tall fescue growth by regulating phytohormone and nutrient homeostasis under nitrogen deficiency. FRONTIERS IN PLANT SCIENCE 2022; 13:979883. [PMID: 36275534 PMCID: PMC9582836 DOI: 10.3389/fpls.2022.979883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen is an important nutrient for plant growth and development. Soil microorganisms have been used to curb the imbalance between the limited content of natural environmental nitrogen and the pollution caused by increasing nitrogen fertilizer use in ecologically fragile areas. Bacillus amyloliquefaciens GB03 has been shown to confer growth promotion and abiotic stress tolerance in Arabidopsis thaliana. This study provided a new insight into the role of the plant growth-promoting rhizobacterium B. amyloliquefaciens GB03 as an initiator of defense against nitrogen deficiency in non-leguminous grass tall fescue (Festuca arundinacea). Two-week-old seedlings of tall fescue were grown with or without GB03 for 4 weeks under total nitrogen (3.75 mM NO3 -) or low nitrogen (0.25 mM NO3 -) treatment. Growth parameters, chlorophyll content, endogenous total nitrogen, total phosphorus content, and phytohormone content, including those of auxin indole-3-acetic acid, cytokinin, gibberellic acid, and abscisic acid, were determined at the time of harvest. Tall fescue grown in GB03-inoculated soil was more robust than the non-inoculated controls with respect to plant height, root length, plant biomass, chlorophyll concentration, and nutrient (total nitrogen and total phosphorus) contents under total nitrogen treatment. GB03 increased indole acetic acid content by 24.7%, whereas decreased cytokinin and abscisic acid contents by 28.4% and 26.9%, respectively, under a total nitrogen level. Remarkably, GB03 increased indole acetic acid content by more than 80% and inhibited abscisic acid production by nearly 70% under a low nitrogen level. These results showed, for the first time, that GB03 played a crucial role in mediating NO3 -dependent regulation of tall fescue growth and development, especially revealing the mechanism of soil bacteria improve resistance to nitrogen deficiency stress in non-nitrogen-fixing species.
Collapse
Affiliation(s)
- Qian Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Er-Ling Ou
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Pu-Chang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Ying Chen
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Zi-Yuan Wang
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Zhi-Wei Wang
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xiang-Wen Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jin-Lin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| |
Collapse
|
12
|
Chai S, Chen J, Yue X, Li C, Zhang Q, de Dios VR, Yao Y, Tan W. Interaction of BES1 and LBD37 transcription factors modulates brassinosteroid-regulated root forging response under low nitrogen in arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:998961. [PMID: 36247555 PMCID: PMC9555238 DOI: 10.3389/fpls.2022.998961] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Brassinosteriod (BR) plays important roles in regulation of plant growth, development and environmental responses. BR signaling regulates multiple biological processes through controlling the activity of BES1/BZR1 regulators. Apart from the roles in the promotion of plant growth, BR is also involved in regulation of the root foraging response under low nitrogen, however how BR signaling regulate this process remains unclear. Here we show that BES1 and LBD37 antagonistically regulate root foraging response under low nitrogen conditions. Both the transcriptional level and dephosphorylated level of BES1, is significant induced by low nitrogen, predominantly in root. Phenotypic analysis showed that BES1 gain-of-function mutant or BES1 overexpression transgenic plants exhibits progressive outgrowth of lateral root in response to low nitrogen and BES1 negatively regulates repressors of nitrate signaling pathway and positively regulates several key genes required for NO3 - uptake and signaling. In contrast, BES1 knock-down mutant BES1-RNAi exhibited a dramatical reduction of lateral root elongation in response to low N. Furthermore, we identified a BES1 interacting protein, LBD37, which is a negative repressor of N availability signals. Our results showed that BES1 can inhibit LBD37 transcriptional repression on N-responsive genes. Our results thus demonstrated that BES1-LBD37 module acts critical nodes to integrate BR signaling and nitrogen signaling to modulate the root forging response at LN condition.
Collapse
Affiliation(s)
- Shuli Chai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Junhua Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Xiaolan Yue
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Chenlin Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Qiang Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Víctor Resco de Dios
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
- Department of Crop and Forest Sciences & Agrotecnio Center, Universitat de Lleida, Leida, Spain
| | - Yinan Yao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Wenrong Tan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| |
Collapse
|
13
|
Chen S, Yang D, Wang Q, Huang X, Ren H, Xu K. Study on the advanced nitrogen removal under low temperature by biofilm on weak magnetic carriers. BIORESOURCE TECHNOLOGY 2022; 360:127580. [PMID: 35798170 DOI: 10.1016/j.biortech.2022.127580] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/26/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
The advanced nitrogen removal under low temperature is inhibited because of reduction of the microbial activity. Packed bed reactors filled with different magnetic carriers (0, 0.3, 0.6, 0.9 mT) were constructed to enhance advanced denitrification under low temperature (5 ℃). Results showed that 0.3 and 0.9 mT carriers significantly improved denitrification, indicating the "window" effect. Total nitrogen removals were increased by 6.96% and 8.25%, and NO2- accumulation decreased by 25.70% and 13.90% in 0.3 and 0.9 mT reactors, respectively. Analysis of enzyme activity and electron transport chain showed that 0.3 mT carrier mainly increased NIR activity by improving compound III and cytC abundance while 0.9 mT carrier mainly increased NAR activity by improving compound I and NADH abundance, indicating different pathways. Similar microbial community in 0.3 and 0.9 mT reactors were revealed. Overall, weak magnetic carriers can be used to enhance advanced nitrogen removal under low temperature.
Collapse
Affiliation(s)
- Sien Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Dongli Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qingxin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xueying Huang
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ke Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| |
Collapse
|
14
|
Geem KR, Kim J, Bae W, Jee MG, Yu J, Jang I, Lee DY, Hong CP, Shim D, Ryu H. Nitrate enhances the secondary growth of storage roots in Panax ginseng. J Ginseng Res 2022; 47:469-478. [DOI: 10.1016/j.jgr.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022] Open
|
15
|
Abstract
As sessile organisms, plants have developed sophisticated mechanism to sense and utilize nutrients from the environment, and modulate their growth and development according to the nutrient availability. Research in the past two decades revealed that nutrient assimilation is not occurring spontaneously, but nutrient signaling networks are complexly regulated and integrate sensing and signaling, gene expression, and metabolism to ensure homeostasis and coordination with plant energy conversion and other processes. Here, we review the importance of the macronutrient sulfur (S) and compare the knowledge of S signaling with other important macronutrients, such as nitrogen (N) and phosphorus (P). We focus on key advances in understanding sulfur sensing and signaling, uptake and assimilation, and we provide new analysis of published literature, to identify core genes regulated by the key transcriptional factor in S starvation response, SLIM1/EIL3, and compare the impact on other nutrient deficiency and stresses on S-related genes.
Collapse
Affiliation(s)
- Daniela Ristova
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Stanislav Kopriva
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Zülpicher Str. 47b, 50674 Cologne, Germany
| |
Collapse
|
16
|
Liu Y, Maniero RA, Giehl RFH, Melzer M, Steensma P, Krouk G, Fitzpatrick TB, von Wirén N. PDX1.1-dependent biosynthesis of vitamin B 6 protects roots from ammonium-induced oxidative stress. MOLECULAR PLANT 2022; 15:820-839. [PMID: 35063660 DOI: 10.1016/j.molp.2022.01.012] [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: 06/02/2021] [Revised: 11/05/2021] [Accepted: 01/17/2022] [Indexed: 05/10/2023]
Abstract
Despite serving as a major inorganic nitrogen source for plants, ammonium causes toxicity at elevated concentrations, inhibiting root elongation early on. While previous studies have shown that ammonium-inhibited root development relates to ammonium uptake and formation of reactive oxygen species (ROS) in roots, it remains unclear about the mechanisms underlying the repression of root growth and how plants cope with this inhibitory effect of ammonium. In this study, we demonstrate that ammonium-induced apoplastic acidification co-localizes with Fe precipitation and hydrogen peroxide (H2O2) accumulation along the stele of the elongation and differentiation zone in root tips, indicating Fe-dependent ROS formation. By screening ammonium sensitivity in T-DNA insertion lines of ammonium-responsive genes, we identified PDX1.1, which is upregulated by ammonium in the root stele and whose product catalyzes de novo biosynthesis of vitamin B6. Root growth of pdx1.1 mutants is hypersensitive to ammonium, while chemical complementation or overexpression of PDX1.1 restores root elongation. This salvage strategy requires non-phosphorylated forms of vitamin B6 that are able to quench ROS and rescue root growth from ammonium inhibition. Collectively, these results suggest that PDX1.1-mediated synthesis of non-phosphorylated B6 vitamers acts as a primary strategy to protect roots from ammonium-dependent ROS formation.
Collapse
Affiliation(s)
- Ying Liu
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Rodolfo A Maniero
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Ricardo F H Giehl
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Michael Melzer
- Structural Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Priscille Steensma
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Gabriel Krouk
- BPMP, Université de Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany.
| |
Collapse
|
17
|
Liu L, Wang X, Lai Y, He G, Wen S, He H, Li Z, Zhang B, Zhang D. Transcriptomic analysis reveals the significant effects of fertilization on the biosynthesis of sesquiterpenes in Phoebe bournei. Genomics 2022; 114:110375. [PMID: 35490893 DOI: 10.1016/j.ygeno.2022.110375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/02/2022] [Accepted: 04/24/2022] [Indexed: 01/14/2023]
Abstract
Phoebe bournei is a potential medicinal plant. Its essential oils (Eos) are mainly composed of sesquiterpenes that has potential activities of anti-bacteria and anti-tumors. In this study, we evaluated the effects of compost and compound fertilizer on the total amount and main components of Eos in P. bournei, we also studied the molecular mechanism undergoing this process by deep sequencing the genes involved in the biosynthesis of sesquiterpenes. Fertilization enhanced the total amount of main components in Eos from both leaves and twigs. Bicyclogermacrene, the primary sesquiterpene in the leaf EO, was significantly increased under compost treatment, while bicyclogermacrene and δ-cadinene (the second most abundant sesquiterpene) were decreased under compound fertilizer treatment. The two fertilizers had no significant effect on the abundance of the primary (+) - δ-cadinene in the twig EO, but had a positive effect on the second most abundant sesquiterpene copaene. Significant differences were observed in the number of differentially expressed genes (DEGs) with the leaves showing greater number of DEGs as compared to the twigs after compost treatment. Terpenoid backbone biosynthesis (TBB) is a key pathway of sesquiterpenes synthesis. The expression of genes regulating several important enzymes in TBB was altered after fertilization. After the compost treatment, the expression of the leaf DXS gene (ACQ66107.1), being closely related to the sesquiterpene biosynthesis in P. bournei leaves, was decreased. Compost and compound fertilizer altered the expression of the two important branch-point enzymes (FPPS and GGPPS) genes (ART33314.1 and ATT59265.1), which contributed to the changes of the total amount and components of P. bournei sesquiterpenes. This study provides a new insight into the future use of P. bournei for Eos.
Collapse
Affiliation(s)
- Li Liu
- School of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xu Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China
| | - Yong Lai
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Gongxiu He
- School of Forestry, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Shizhi Wen
- School of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Hanjie He
- School of Life Sciences and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Zhenshan Li
- School of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | - Dangquan Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
| |
Collapse
|
18
|
Li Y, Wang M, Teng K, Dong D, Liu Z, Zhang T, Han L. Transcriptome profiling revealed candidate genes, pathways and transcription factors related to nitrogen utilization and excessive nitrogen stress in perennial ryegrass. Sci Rep 2022; 12:3353. [PMID: 35233054 PMCID: PMC8888628 DOI: 10.1038/s41598-022-07329-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 02/10/2022] [Indexed: 11/09/2022] Open
Abstract
Ryegrass (Lolium perenne L.), a high-quality forage grass, is a good nutrient source for herbivorous livestock. However, improving nitrogen use efficiency and avoiding nitrate toxicity caused by excessive nitrogen are continual challenges in ryegrass production. The molecular mechanism underlying the response of ryegrass to nitrogen, especially excessive nitrogen, remains unclear. In this study, the transcriptomic changes under different nitrogen levels were investigated in perennial ryegrass by high-throughput next-generation RNA sequencing. Phenotypic characterization showed that treatment with half of the standard N concentration (N0.5) led to a better growth state than the other three treatments. The treatments with the standard N concentration (N1) and treatments with ten times higher than the standard N concentration (N10) contained excessive nitrogen, which placed stress on plant growth. Analysis of differentially expressed genes indicated that 345 and 104 genes are involved in the regulation of nitrogen utilization and excessive nitrogen stress, respectively. KEGG enrichment analysis suggested that "photosynthesis-antenna proteins" may respond positively to appropriate nitrogen conditions, whereas "steroid biosynthesis", "carotenoid biosynthesis" and "C5-branched dibasic acid metabolism" were identified as the top significantly enriched pathways in response to excessive nitrogen. Additionally, 21 transcription factors (TFs) related to nitrogen utilization were classified into 10 families, especially the AP2-EREBP and MYB TF families. Four TFs related to excessive nitrogen stress were identified, including LOBs, NACs, AP2-EREBPs and HBs. The expression patterns of these selected genes were also analyzed. These results provide new insight into the regulatory mechanism of ryegrass in response to nitrogen utilization and excessive nitrogen stress.
Collapse
Affiliation(s)
- Yinruizhi Li
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Mengdi Wang
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Ke Teng
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Di Dong
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Zhuocheng Liu
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Tiejun Zhang
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Liebao Han
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China.
| |
Collapse
|
19
|
Xie H, Zhao W, Li W, Zhang Y, Hajný J, Han H. Small signaling peptides mediate plant adaptions to abiotic environmental stress. PLANTA 2022; 255:72. [PMID: 35218440 DOI: 10.1007/s00425-022-03859-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/14/2022] [Indexed: 05/27/2023]
Abstract
Peptide-receptor complexes activate distinct downstream regulatory networks to mediate plant adaptions to abiotic environmental stress. Plants are constantly exposed to various adverse environmental factors; thus they must adjust their growth accordingly. Plants recruit small secretory peptides to adapt to these detrimental environments. These small peptides, which are perceived by their corresponding receptors and/or co-receptors, act as local- or long-distance mobile signaling molecules to establish cell-to-cell regulatory networks, resulting in optimal cellular and physiological outputs. In this review, we highlight recent advances on the regulatory role of small peptides in plant abiotic responses and nutrients signaling.
Collapse
Affiliation(s)
- Heping Xie
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
| | - Wen Zhao
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
| | - Weilin Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
| | - Yuzhou Zhang
- College of Life Science, Northwest A&F University, Shaanxi, 712100, Yangling, China
| | - Jakub Hajný
- Laboratory of Growth Regulators, Institute of Experimental Botany and Palacký University, The Czech Academy of Sciences, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Huibin Han
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China.
| |
Collapse
|
20
|
Siqueira JA, Otoni WC, Araújo WL. The hidden half comes into the spotlight: Peeking inside the black box of root developmental phases. PLANT COMMUNICATIONS 2022; 3:100246. [PMID: 35059627 PMCID: PMC8760039 DOI: 10.1016/j.xplc.2021.100246] [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: 03/29/2021] [Revised: 08/13/2021] [Accepted: 09/18/2021] [Indexed: 05/30/2023]
Abstract
Efficient use of natural resources (e.g., light, water, and nutrients) can be improved with a tailored developmental program that maximizes the lifetime and fitness of plants. In plant shoots, a developmental phase represents a time window in which the meristem triggers the development of unique morphological and physiological traits, leading to the emergence of leaves, flowers, and fruits. Whereas developmental phases in plant shoots have been shown to enhance food production in crops, this phenomenon has remained poorly investigated in roots. In light of recent advances, we suggest that root development occurs in three main phases: root apical meristem appearance, foraging, and senescence. We provide compelling evidence suggesting that these phases are regulated by at least four developmental pathways: autonomous, non-autonomous, hormonal, and periodic. Root developmental pathways differentially coordinate organ plasticity, promoting morphological alterations, tissue regeneration, and cell death regulation. Furthermore, we suggest how nutritional checkpoints may allow progression through the developmental phases, thus completing the root life cycle. These insights highlight novel and exciting advances in root biology that may help maximize the productivity of crops through more sustainable agriculture and the reduced use of chemical fertilizers.
Collapse
|
21
|
Zoghbi-Rodríguez NM, Gamboa-Tuz SD, Pereira-Santana A, Rodríguez-Zapata LC, Sánchez-Teyer LF, Echevarría-Machado I. Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants. Int J Mol Sci 2021; 22:13036. [PMID: 34884876 PMCID: PMC8658032 DOI: 10.3390/ijms222313036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/29/2022] Open
Abstract
Nitrate transporter 2 (NRT2) and NRT3 or nitrate-assimilation-related 2 (NAR2) proteins families form a two-component, high-affinity nitrate transport system, which is essential for the acquisition of nitrate from soils with low N availability. An extensive phylogenomic analysis across land plants for these families has not been performed. In this study, we performed a microsynteny and orthology analysis on the NRT2 and NRT3 genes families across 132 plants (Sensu lato) to decipher their evolutionary history. We identified significant differences in the number of sequences per taxonomic group and different genomic contexts within the NRT2 family that might have contributed to N acquisition by the plants. We hypothesized that the greater losses of NRT2 sequences correlate with specialized ecological adaptations, such as aquatic, epiphytic, and carnivory lifestyles. We also detected expansion on the NRT2 family in specific lineages that could be a source of key innovations for colonizing contrasting niches in N availability. Microsyntenic analysis on NRT3 family showed a deep conservation on land plants, suggesting a high evolutionary constraint to preserve their function. Our study provides novel information that could be used as guide for functional characterization of these gene families across plant lineages.
Collapse
Affiliation(s)
- Normig M. Zoghbi-Rodríguez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico;
| | - Samuel David Gamboa-Tuz
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico; (S.D.G.-T.); (L.C.R.-Z.)
| | - Alejandro Pereira-Santana
- Conacyt-Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara 44270, Mexico;
| | - Luis C. Rodríguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico; (S.D.G.-T.); (L.C.R.-Z.)
| | - Lorenzo Felipe Sánchez-Teyer
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico; (S.D.G.-T.); (L.C.R.-Z.)
| | - Ileana Echevarría-Machado
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico;
| |
Collapse
|
22
|
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.
Collapse
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:
| |
Collapse
|
23
|
Buoso S, Tomasi N, Arkoun M, Maillard A, Jing L, Marroni F, Pluchon S, Pinton R, Zanin L. Transcriptomic and metabolomic profiles of Zea mays fed with urea and ammonium. PHYSIOLOGIA PLANTARUM 2021; 173:935-953. [PMID: 34245168 PMCID: PMC8597056 DOI: 10.1111/ppl.13493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
The simultaneous presence of different N-forms in the rhizosphere leads to beneficial effects on nitrogen (N) nutrition in plants. Although widely used as fertilizers, the occurrence of cross connection between urea and ammonium nutrition has been scarcely studied in plants. Maize fed with a mixture of urea and ammonium displayed a better N-uptake efficiency than ammonium- or urea-fed plants (Buoso et al., Plant Physiol Biochem, 2021a; 162: 613-623). Through multiomic approaches, we provide the molecular characterization of maize response to urea and ammonium nutrition. Several transporters and enzymes involved in N-nutrition were upregulated by all three N-treatments (urea, ammonium, or urea and ammonium). Already after 1 day of treatment, the availability of different N-forms induced specific transcriptomic and metabolomic responses. The combination of urea and ammonium induced a prompt assimilation of N, characterized by high levels of some amino acids in shoots. Moreover, ZmAMT1.1a, ZmGLN1;2, ZmGLN1;5, ZmGOT1, and ZmGOT3, as well transcripts involved in glycolysis-TCA cycle were induced in roots by urea and ammonium mixture. Depending on N-form, even changes in the composition of phytohormones were observed in maize. This study paves the way to formulate guidelines for the optimization of N fertilization to improve N-use efficiency in maize and therefore limit N-losses in the environment.
Collapse
Affiliation(s)
- Sara Buoso
- Department of Agricultural, Food, Environmental, and Animal SciencesUniversity of UdineUdine
| | - Nicola Tomasi
- Department of Agricultural, Food, Environmental, and Animal SciencesUniversity of UdineUdine
| | - Mustapha Arkoun
- Laboratoire de Nutrition Végétale, Agroinnovation International—TIMAC AGROSaint‐MaloFrance
| | - Anne Maillard
- Laboratoire de Nutrition Végétale, Agroinnovation International—TIMAC AGROSaint‐MaloFrance
| | - Lun Jing
- Laboratoire de Nutrition Végétale, Agroinnovation International—TIMAC AGROSaint‐MaloFrance
| | - Fabio Marroni
- Department of Agricultural, Food, Environmental, and Animal SciencesUniversity of UdineUdine
| | - Sylvain Pluchon
- Laboratoire de Nutrition Végétale, Agroinnovation International—TIMAC AGROSaint‐MaloFrance
| | - Roberto Pinton
- Department of Agricultural, Food, Environmental, and Animal SciencesUniversity of UdineUdine
| | - Laura Zanin
- Department of Agricultural, Food, Environmental, and Animal SciencesUniversity of UdineUdine
| |
Collapse
|
24
|
Liu L, Gao H, Li S, Han Z, Li B. Calcium signaling networks mediate nitrate sensing and responses in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2021; 16:1938441. [PMID: 34180337 PMCID: PMC8330996 DOI: 10.1080/15592324.2021.1938441] [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: 04/05/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 05/31/2023]
Abstract
Nitrate signaling integrates and coordinates the expression of a wide range of genes, metabolic pathways and ultimately, plant growth and development. Calcium signaling is proved to be involved in the primary nitrate response pathway. However, it is much less understood how calcium signaling mediates nitrate sensing and responses from the extracellular space to cytoplasm, then to the nucleus. In this review, we describe how transceptor-channel complex (cyclic nucleotide-gated channel protein 15 interacting with nitrate transceptor, CNGC15-NRT1.1), calcineurin B-like proteins (CBLs, CBL1, CBL9), CBL-interacting protein kinases (CIPKs), phospholipase C (PLC) and calcium-dependent protein kinases (CDPKs, also CPKs), acting as key players, complete a potential backbone of the nitrate-signaling pathway, from the plasma membrane to the nucleus. NRT1.1 together with CBL1/9-CIPK23 and CBL-CIPK8 links the NO3- signaling to cytoplasmic and nuclear regulators and triggers downstream NO3- responses. PLCs and inositol 1, 4, 5-triphosphate (IP3) connect NO3- signaling and cytoplasmic Ca2+ signature. CPK10/30/32 fill the gap between NRT1.1 and NIN-like protein (NLP) transcription factors. The arabidopsis nitrate regulated1 (ANR1) is induced from the endosome by the Ca2+-CPKs-NLPs signaling pathway activated by the unphosphorylated form of NRT1.1 (NRT1.1 T101A) at high nitrate condition. Understanding how calcium signaling interconnects the upstream nitrate sensor complex with downstream multiple sensors of the nitrate-signaling pathway is key to completing the nutrient-growth regulatory networks.
Collapse
Affiliation(s)
- Li Liu
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, P.R. China
| | - Huanhuan Gao
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, P.R. China
| | - Shaoxuan Li
- Fruit & Tea Research Institute, Qingdao Academy of Agricultural Sciences, Qingdao, China
| | - Zhen Han
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, P.R. China
| | - Bo Li
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, P.R. China
| |
Collapse
|
25
|
He L, Teng L, Tang X, Long W, Wang Z, Wu Y, Liao L. Agro-morphological and metabolomics analysis of low nitrogen stress response in Axonopus compressus. AOB PLANTS 2021; 13:plab022. [PMID: 34234932 PMCID: PMC8256886 DOI: 10.1093/aobpla/plab022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 05/14/2023]
Abstract
Axonopus compressus also known as carpet grass is a robust, stoloniferous grass that can grow in minimal fertilization and resists well to abiotic and biotic stresses including low nitrogen (LN) stress. This study aimed at characterizing the agro-morphological and metabolome responses to LN in carpet grass leaves. Under LN stress, carpet grass increased yellowness of leaves and root dry matter while reduced turf quality and shoot dry weight. The metabolome comparison between samples from optimum and LN conditions indicated 304 differentially accumulated metabolites (DAMs), which could be classified into 12 major and 31 subclasses. The results revealed that the leaf tissues accumulated more anthocyanins and other flavonoid metabolites under LN stress. Conversely, amino acids, nucleic acids and their derivatives were reduced in response to LN stress. The overall evaluation of individual metabolites and pathways, and previous studies on metabolomes indicated that carpet grass reduced its energy consumption in leaves and increased the level of organic acid metabolism and secondary metabolism in order to resist LN stress conditions.
Collapse
Affiliation(s)
- Li He
- College of Life Science, Jinggangshan University, Ji’an, Jiangxi 343009, China
| | - Li Teng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Xiaomin Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Wanwan Long
- College of Life Science, Jinggangshan University, Ji’an, Jiangxi 343009, China
| | - Zhiyong Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Yang Wu
- College of Life Science, Jinggangshan University, Ji’an, Jiangxi 343009, China
| | - Li Liao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan 570228, China
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Ötvös K, Marconi M, Vega A, O’Brien J, Johnson A, Abualia R, Antonielli L, Montesinos JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik K, Benková E. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO J 2021; 40:e106862. [PMID: 33399250 PMCID: PMC7849315 DOI: 10.15252/embj.2020106862] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023] Open
Abstract
Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate-dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.
Collapse
Affiliation(s)
- Krisztina Ötvös
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
- Bioresources UnitCenter for Health & BioresourcesAIT Austrian Institute of Technology GmbHTullnAustria
| | - Marco Marconi
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM‐INIA) Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
| | - Andrea Vega
- Pontifical Catholic University of ChileSantiagoChile
| | - Jose O’Brien
- Pontifical Catholic University of ChileSantiagoChile
| | - Alexander Johnson
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Rashed Abualia
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Livio Antonielli
- Bioresources UnitCenter for Health & BioresourcesAIT Austrian Institute of Technology GmbHTullnAustria
| | | | - Yuzhou Zhang
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Shutang Tan
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Candela Cuesta
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Christina Artner
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | | | - Alain Gojon
- BPMPCNRSINRAEInstitut AgroUniv MontpellierMontpellierFrance
| | - Jirí Friml
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | | | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM‐INIA) Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
| | - Eva Benková
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| |
Collapse
|
28
|
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.
Collapse
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,
| |
Collapse
|
29
|
Lee WJ, Truong HA, Trịnh CS, Kim JH, Lee S, Hong SW, Lee H. NITROGEN RESPONSE DEFICIENCY 1-mediated CHL1 induction contributes to optimized growth performance during altered nitrate availability in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1382-1398. [PMID: 33048402 DOI: 10.1111/tpj.15007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Plants cannot fix nitrogen directly; they must absorb it from the soil through their roots, or in rare cases, form associations with nitrogen-fixing bacteria. The efficiency of nitrogen use in most domesticated crops is low, and more than half of the available nitrogen in the soil can leach into the environment. Understanding the nitrogen signaling pathways is essential for maximizing the efficiency of nitrogen use in crops. In the present study, we characterized the Myeloblastosis (Myb)-like gene NITROGEN RESPONSE DEFICIENCY 1 (NID1). We observed that the growth performance of nid1 knockout (KO) mutant Arabidopsis plants was better than that of wild-type Col-0 plants under very low-nitrate conditions, leading to improved growth performance in the nid1 KO plants. The results of chromatin immunoprecipitation and electrophoretic mobility shift assays indicated that NID1 binds to the promoter of the NITRATE TRANSPORTER (NRT)1.1 gene. Furthermore, nid1 KO plants exhibited similar growth performance to the nid1 KO/chl1-5 (nrt1.1 KO) double mutant and chl1-5 (nrt1.1 KO) plants in response to low-nitrate conditions. We suggest that NID1 plays a crucial role as a transcription factor in optimizing plant growth by modulating the transcript abundance of the nitrate transceptor CHL1, leading to enhanced ABA accumulation in low-nitrate conditions.
Collapse
Affiliation(s)
- Won J Lee
- College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea
| | - Hai A Truong
- College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Cao S Trịnh
- College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jun H Kim
- College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Seokjin Lee
- College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Suk-Whan Hong
- Department of Molecular Biotechnology, College of Agriculture and Life Sciences, Bioenergy Research Center, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hojoung Lee
- College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea
| |
Collapse
|
30
|
Luo J, Havé M, Clément G, Tellier F, Balliau T, Launay-Avon A, Guérard F, Zivy M, Masclaux-Daubresse C. Integrating multiple omics to identify common and specific molecular changes occurring in Arabidopsis under chronic nitrate and sulfate limitations. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6471-6490. [PMID: 32687580 DOI: 10.1093/jxb/eraa337] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Plants have fundamental dependences on nitrogen and sulfur and frequently have to cope with chronic limitations when their supply is sub-optimal. This study aimed at characterizing the metabolomic, proteomic, and transcriptomic changes occurring in Arabidopsis leaves under chronic nitrate (Low-N) and chronic sulfate (Low-S) limitations in order to compare their effects, determine interconnections, and examine strategies of adaptation. Metabolite profiling globally revealed opposite effects of Low-S and Low-N on carbohydrate and amino acid accumulations, whilst proteomic data showed that both treatments resulted in increases in catabolic processes, stimulation of mitochondrial and cytosolic metabolism, and decreases in chloroplast metabolism. Lower abundances of ribosomal proteins and translation factors under Low-N and Low-S corresponded with growth limitation. At the transcript level, the major and specific effect of Low-N was the enhancement of expression of defence and immunity genes. The main effect of chronic Low-S was a decrease in transcripts of genes involved in cell division, DNA replication, and cytoskeleton, and an increase in the expression of autophagy genes. This was consistent with a role of target-of-rapamycin kinase in the control of plant metabolism and cell growth and division under chronic Low-S. In addition, Low-S decreased the expression of several NLP transcription factors, which are master actors in nitrate sensing. Finally, both the transcriptome and proteome data indicated that Low-S repressed glucosinolate synthesis, and that Low-N exacerbated glucosinolate degradation. This showed the importance of glucosinolate as buffering molecules for N and S management.
Collapse
Affiliation(s)
- Jie Luo
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- College of Horticulture and Forestry Sciences, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China
| | - Marien Havé
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Frédérique Tellier
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Thierry Balliau
- UMR GQE- le Moulon, INRAE, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Florence Guérard
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Michel Zivy
- UMR GQE- le Moulon, INRAE, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | | |
Collapse
|
31
|
Krouk G, Kiba T. Nitrogen and Phosphorus interactions in plants: from agronomic to physiological and molecular insights. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:104-109. [PMID: 32882570 DOI: 10.1016/j.pbi.2020.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) and Phosphorus (P) are the two most essential nutrients ensuring food production and security. The ever growing population demands more N and P-based fertilizers. Even though the N provision to the agricultural system is virtually infinite (Haber and Bosch process) it triggers pollution when it is not used by the plant and leaks into the environment. On the other hand, P is predicted to be a limited source worldwide. P use is also responsible for water eutrophication. Thus understanding plant response to combinations of N and P has clear implications for sustainable human development. Recent works have shed new light on how N and P closely interact to control plant responses. Several molecular actors have been revealed controlling the molecular interaction between these two essential elements drafting a working model of N and P interactions. We summarize here these new findings as well as several previous lines of evidence in agronomy and physiology studies preceding this new trend of investigation in the molecular world.
Collapse
Affiliation(s)
- Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France.
| | - Takatoshi Kiba
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
| |
Collapse
|
32
|
Liu KH, Diener A, Lin Z, Liu C, Sheen J. Primary nitrate responses mediated by calcium signalling and diverse protein phosphorylation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4428-4441. [PMID: 31985788 PMCID: PMC7382375 DOI: 10.1093/jxb/eraa047] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/24/2020] [Indexed: 05/04/2023]
Abstract
Nitrate, the major source of inorganic nitrogen for plants, is a critical signal controlling nutrient transport and assimilation and adaptive growth responses throughout the plant. Understanding how plants perceive nitrate and how this perception is transduced into responses that optimize growth are important for the rational improvement of crop productivity and for mitigating pollution from the use of fertilizers. This review highlights recent findings that reveal key roles of cytosolic-nuclear calcium signalling and dynamic protein phosphorylation via diverse mechanisms in the primary nitrate response (PNR). Nitrate-triggered calcium signatures as well as the critical functions of subgroup III calcium-sensor protein kinases, a specific protein phosphatase 2C, and RNA polymerase II C-terminal domain phosphatase-like 3 are discussed. Moreover, genome-wide meta-analysis of nitrate-regulated genes encoding candidate protein kinases and phosphatases for modulating critical phosphorylation events in the PNR are elaborated. We also consider how phosphoproteomics approaches can contribute to the identification of putative regulatory protein kinases in the PNR. Exploring and integrating experimental strategies, new methodologies, and comprehensive datasets will further advance our understanding of the molecular and cellular mechanisms underlying the complex regulatory processes in the PNR.
Collapse
Affiliation(s)
- Kun-Hsiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
- Correspondence:
| | - Andrew Diener
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ziwei Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Cong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
33
|
Araus V, Swift J, Alvarez JM, Henry A, Coruzzi GM. A balancing act: how plants integrate nitrogen and water signals. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4442-4451. [PMID: 31990028 PMCID: PMC7382378 DOI: 10.1093/jxb/eraa054] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/24/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen (N) and water (W) are crucial inputs for plant survival as well as costly resources for agriculture. Given their importance, the molecular mechanisms that plants rely on to signal changes in either N or W status have been under intense scrutiny. However, how plants sense and respond to the combination of N and W signals at the molecular level has received scant attention. The purpose of this review is to shed light on what is currently known about how plant responses to N are impacted by W status. We review classic studies which detail how N and W combinations have both synergistic and antagonistic effects on key plant traits, such as root architecture and stomatal aperture. Recent molecular studies of N and W interactions show that mutations in genes involved in N metabolism affect drought responses, and vice versa. Specifically, perturbing key N signaling genes may lead to changes in drought-responsive gene expression programs, which is supported by a meta-analysis we conduct on available transcriptomic data. Additionally, we cite studies that show how combinatorial transcriptional responses to N and W status might drive crop phenotypes. Through these insights, we suggest research strategies that could help to develop crops adapted to marginal soils depleted in both N and W, an important task in the face of climate change.
Collapse
Affiliation(s)
- Viviana Araus
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Joseph Swift
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Jose 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
| | - Amelia Henry
- International Rice Research Institute, Metro Manila, Philippines
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Correspondence:
| |
Collapse
|
34
|
Asim M, Ullah Z, Xu F, An L, Aluko OO, Wang Q, Liu H. Nitrate Signaling, Functions, and Regulation of Root System Architecture: Insights from Arabidopsis thaliana. Genes (Basel) 2020; 11:E633. [PMID: 32526869 PMCID: PMC7348705 DOI: 10.3390/genes11060633] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 01/07/2023] Open
Abstract
Root system architecture (RSA) is required for the acquisition of water and mineral nutrients from the soil. One of the essential nutrients, nitrate (NO3-), is sensed and transported by nitrate transporters NRT1.1 and NRT2.1 in the plants. Nitrate transporter 1.1 (NRT1.1) is a dual-affinity nitrate transporter phosphorylated at the T101 residue by calcineurin B-like interacting protein kinase (CIPKs); it also regulates the expression of other key nitrate assimilatory genes. The differential phosphorylation (phosphorylation and dephosphorylation) strategies and underlying Ca2+ signaling mechanism of NRT1.1 stimulate lateral root growth by activating the auxin transport activity and Ca2+-ANR1 signaling at the plasma membrane and the endosomes, respectively. NO3- additionally functions as a signal molecule that forms a signaling system, which consists of a vast array of transcription factors that control root system architecture that either stimulate or inhibit lateral and primary root development in response to localized and high nitrate (NO3-), respectively. This review elucidates the so-far identified nitrate transporters, nitrate sensing, signal transduction, and the key roles of nitrate transporters and its downstream transcriptional regulatory network in the primary and lateral root development in Arabidopsis thaliana under stress conditions.
Collapse
Affiliation(s)
- Muhammad Asim
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Zia Ullah
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Fangzheng Xu
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Lulu An
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Oluwaseun Olayemi Aluko
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Qian Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Haobao Liu
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
| |
Collapse
|
35
|
Joshi V, Joshi M, Penalosa A. Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea). PLoS One 2020; 15:e0232011. [PMID: 32374731 PMCID: PMC7202632 DOI: 10.1371/journal.pone.0232011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/05/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrogen (N) is critical to the growth and productivity of crops. To understand the molecular mechanisms influenced by N stress, we used RNA-Sequencing (RNA-Seq) to analyze differentially expressed genes (DEGs) in root and leaf tissues of spinach. N stress negatively influenced photosynthesis, biomass accumulation, amino acid profiles, and partitioning of N across tissues. RNA-seq analysis revealed that N stress caused most transcriptomic changes in roots, identifying 1,346 DEGs. High-affinity nitrate transporters (NRT2.1, NRT2.5) and glutamine amidotransferase (GAT1) genes were strongly induced in roots in response to N deplete and replete conditions, respectively. GO and KEGG analyses revealed that the functions associated with metabolic pathways and nutrient reservoir activity were enriched due to N stress. Whereas KEGG pathway enrichment analysis indicated the upregulation of DEGs associated with DNA replication, pyrimidine, and purine metabolism in the presence of high N in leaf tissue. A subset of transcription factors comprising bHLH, MYB, WRKY, and AP2/ERF family members was over-represented in both tissues in response to N perturbation. Interesting DEGs associated with N uptake, amino acid metabolism, hormonal pathway, carbon metabolism, along with transcription factors, were highlighted. The results provide valuable information about the underlying molecular processes in response to N stress in spinach and; could serve as a resource for functional analysis of candidate genes/pathways and enhancement of nitrogen use efficiency.
Collapse
Affiliation(s)
- Vijay Joshi
- Texas A&M AgriLife Research and Extension Center, Uvalde, Texas, United States of America
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Madhumita Joshi
- Texas A&M AgriLife Research and Extension Center, Uvalde, Texas, United States of America
| | - Arianne Penalosa
- College of Science, University of Texas, Arlington, Texas, United States of America
| |
Collapse
|
36
|
Asim M, Ullah Z, Oluwaseun A, Wang Q, Liu H. Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana. Int J Mol Sci 2020; 21:E2880. [PMID: 32326090 PMCID: PMC7215989 DOI: 10.3390/ijms21082880] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 11/17/2022] Open
Abstract
Nitrate (NO3-) and auxin are key regulators of root growth and development, modulating the signalling cascades in auxin-induced lateral root formation. Auxin biosynthesis, transport, and transduction are significantly altered by nitrate. A decrease in nitrate (NO3-) supply tends to promote auxin translocation from shoots to roots and vice-versa. This nitrate mediated auxin biosynthesis regulating lateral roots growth is induced by the nitrate transporters and its downstream transcription factors. Most nitrate responsive genes (short-term and long-term) are involved in signalling overlap between nitrate and auxin, thereby inducing lateral roots initiation, emergence, and development. Moreover, in the auxin signalling pathway, the varying nitrate supply regulates lateral roots development by modulating the auxin accumulation in the roots. Here, we focus on the roles of nitrate responsive genes in mediating auxin biosynthesis in Arabidopsis root, and the mechanism involved in the transport of auxin at different nitrate levels. In addition, this review also provides an insight into the significance of nitrate responsive regulatory module and their downstream transcription factors in root system architecture in the model plant Arabidopsis thaliana.
Collapse
Affiliation(s)
- Muhammad Asim
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zia Ullah
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Aluko Oluwaseun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qian Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
| | - Haobao Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
| |
Collapse
|
37
|
Saiz-Fernández I, Lacuesta M, Pérez-López U, Sampedro MC, Barrio RJ, De Diego N. Interplay between 1-aminocyclopropane-1-carboxylic acid, γ-aminobutyrate and D-glucose in the regulation of high nitrate-induced root growth inhibition in maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110418. [PMID: 32081267 DOI: 10.1016/j.plantsci.2020.110418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/30/2019] [Accepted: 01/18/2020] [Indexed: 06/10/2023]
Abstract
Nitrogen is one of the main factors that affect plant growth and development. However, high nitrogen concentrations can inhibit both shoot and root growth, even though the processes involved in this inhibition are still unknown. The aim of this work was to identify the metabolic alterations that induce the inhibition of root growth caused by high nitrate supply, when the whole plant growth is also reduced. High nitrate altered nitrogen and carbon metabolism, reducing the content of sugars and inducing the accumulation of Ca2+ and amino acids, such as glutamate, alanine and γ-aminobutyrate (GABA), that could act to replenish the succinate pool in the tricarboxylic acid cycle and maintain its activity. Other metabolic alterations found were the accumulation of the polyamines spermidine and spermine, and the reduction of jasmonic acid (JA) and the ethylene precursor aminocyclopropane-1-carboxylic acid (ACC). These results indicate that the growth root inhibition by high NO3- is a complex metabolic response that involves GABA as a key link between C and N metabolism which, together with plant growth regulators such as auxins, cytokinins, abscisic acid, JA, and the ethylene precursor ACC, is able to regulate the metabolic response of root grown under high nitrate concentrations.
Collapse
Affiliation(s)
- Iñigo Saiz-Fernández
- Department of Plant Biology and Ecology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, E-01006, Vitoria-Gasteiz, Spain; Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic.
| | - Maite Lacuesta
- Department of Plant Biology and Ecology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, E-01006, Vitoria-Gasteiz, Spain.
| | - Usue Pérez-López
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, E-48080, Bilbao, Spain.
| | - M Carmen Sampedro
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Basque Country UPV/EHU, E-01006, Vitoria-Gasteiz, Spain.
| | - Ramon J Barrio
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Basque Country UPV/EHU, E-01006, Vitoria-Gasteiz, Spain.
| | - Nuria De Diego
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic.
| |
Collapse
|
38
|
Vega A, O'Brien JA, Gutiérrez RA. Nitrate and hormonal signaling crosstalk for plant growth and development. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:155-163. [PMID: 31726384 DOI: 10.1016/j.pbi.2019.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 05/22/2023]
Abstract
Nitrate is an essential macronutrient for plants, a primary nitrogen source in natural and human-made ecosystems. Nitrate can also act as a signaling molecule that directs genome-wide gene expression changes with an impact on plant metabolism, physiology, growth and development. Nitrate and phytohormone signaling pathways crosstalk to modulate growth and developmental programs in a multifactorial manner. Nitrate-signaling controls plant growth and development using molecular mechanisms that involve phytohormone-signaling pathways. In contrast, many phytohormones modulate or impact nitrate signaling in interconnected pathways. In this review, we explore recent progress in our understanding of well-documented connections between nitrate and phytohormones such as auxin, cytokinin and abscisic acid. We also discuss recent studies connecting nitrate to other phytohormones such as ethylene, salicylic acid, gibberellins and brassinosteroids. While many molecular details remain to be elucidated, a number of core signaling components at the intersection between nitrate and the major hormonal pathways have been described. We focus on established interactions of nitrate and different hormonal pathways to bring about cellular, growth and developmental processes in Arabidopsis thaliana.
Collapse
Affiliation(s)
- Andrea Vega
- FONDAP Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), Chile; Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile
| | - José Antonio O'Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile; Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), Chile; Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile.
| |
Collapse
|
39
|
Vidotti MS, Lyra DH, Morosini JS, Granato ÍSC, Quecine MC, de Azevedo JL, Fritsche-Neto R. Additive and heterozygous (dis)advantage GWAS models reveal candidate genes involved in the genotypic variation of maize hybrids to Azospirillum brasilense. PLoS One 2019; 14:e0222788. [PMID: 31536609 PMCID: PMC6752820 DOI: 10.1371/journal.pone.0222788] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/07/2019] [Indexed: 11/18/2022] Open
Abstract
Maize genotypes can show different responsiveness to inoculation with Azospirillum brasilense and an intriguing issue is which genes of the plant are involved in the recognition and growth promotion by these Plant Growth-Promoting Bacteria (PGPB). We conducted Genome-Wide Association Studies (GWAS) using additive and heterozygous (dis)advantage models to find candidate genes for root and shoot traits under nitrogen (N) stress and N stress plus A. brasilense. A total of 52,215 Single Nucleotide Polymorphism (SNP) markers were used for GWAS analyses. For the six root traits with significant inoculation effect, the GWAS analyses revealed 25 significant SNPs for the N stress plus A. brasilense treatment, in which only two were overlapped with the 22 found for N stress only. Most were found by the heterozygous (dis)advantage model and were more related to exclusive gene ontology terms. Interestingly, the candidate genes around the significant SNPs found for the maize-A. brasilense association were involved in different functions previously described for PGPB in plants (e.g. signaling pathways of the plant's defense system and phytohormone biosynthesis). Our findings are a benchmark in the understanding of the genetic variation among maize hybrids for the association with A. brasilense and reveal the potential for further enhancement of maize through this association.
Collapse
Affiliation(s)
- Miriam Suzane Vidotti
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Júlia Silva Morosini
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - João Lúcio de Azevedo
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Roberto Fritsche-Neto
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| |
Collapse
|
40
|
Marshall-Colón A, Kliebenstein DJ. Plant Networks as Traits and Hypotheses: Moving Beyond Description. TRENDS IN PLANT SCIENCE 2019; 24:840-852. [PMID: 31300195 DOI: 10.1016/j.tplants.2019.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Biology relies on the central thesis that the genes in an organism encode molecular mechanisms that combine with stimuli and raw materials from the environment to create a final phenotypic expression representative of the genomic programming. While conceptually simple, the genotype-to-phenotype linkage in a eukaryotic organism relies on the interactions of thousands of genes and an environment with a potentially unknowable level of complexity. Modern biology has moved to the use of networks in systems biology to try to simplify this complexity to decode how an organism's genome works. Previously, biological networks were basic ways to organize, simplify, and analyze data. However, recent advances are allowing networks to move beyond description and become phenotypes or hypotheses in their own right. This review discusses these efforts, like mapping responses across biological scales, including relationships among cellular entities, and the direct use of networks as traits or hypotheses.
Collapse
Affiliation(s)
- Amy Marshall-Colón
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA; DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
| |
Collapse
|
41
|
Ueda Y, Yanagisawa S. Perception, transduction, and integration of nitrogen and phosphorus nutritional signals in the transcriptional regulatory network in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3709-3717. [PMID: 30949701 DOI: 10.1093/jxb/erz148] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/19/2019] [Indexed: 05/20/2023]
Abstract
Nitrate and phosphate ions are major sources of nitrogen and phosphorus for plants. In addition to their vital roles as indispensable macronutrients, these ions function as signalling molecules and induce a variety of responses. Plants adapt to different levels of nutrients by altering their gene expression profile and subsequent physiological and morphological responses. Advances made in recent years have provided novel insights into plant nutrient sensing and modulation of gene expression. Key breakthroughs include elucidation of the mechanisms underlying post-translational regulation of NIN-LIKE PROTEIN (NLP) and PHOSPHATE STARVATION RESPONSE (PHR) family transcription factors, which function as master regulators of responses to nitrate and phosphate starvation, respectively. Determination of the mechanisms whereby these nutrient signals are integrated through NIGT1/HHO family proteins has likewise represented important progress. Further studies have revealed novel roles in nutrient signalling of transcription factors that have previously been shown to be associated with other signals, such as light and phytohormones. Nitrate and phosphate signals are thus transmitted through an intricate gene regulatory network with the help of various positive and negative transcriptional regulators. These complex regulatory patterns enable plants to integrate input signals from various environmental factors and trigger appropriate responses, as exemplified by the regulatory module involving NIGT1/HHO family proteins. These mechanisms collectively support nutrient homeostasis in plants.
Collapse
Affiliation(s)
- Yoshiaki Ueda
- Biotechnology Research Center, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo
| | - Shuichi Yanagisawa
- Biotechnology Research Center, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo
| |
Collapse
|
42
|
Colchado-López J, Cervantes RC, Rosas U. A Linear Model to Describe Branching and Allometry in Root Architecture. PLANTS (BASEL, SWITZERLAND) 2019; 8:plants8070218. [PMID: 31336829 PMCID: PMC6681317 DOI: 10.3390/plants8070218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 05/31/2023]
Abstract
Root architecture is a complex structure that comprises multiple traits of the root phenotype. Novel platforms and models have been developed to better understand root architecture. In this methods paper, we introduce a novel allometric model, named rhizochron index (m), which describes lateral root (LR) branching and elongation patterns across the primary root (PR). To test our model, we obtained data from 16 natural accessions of Arabidopsis thaliana at three stages of early root development to measure conventional traits of root architecture (e.g., PR and LR length), and extracted the rhizochron index (m). In addition, we tested previously published datasets to assess the utility of the rhizochron index (m) to distinguish mutants and environmental effects on root architecture. Our results indicate that rhizochron index (m) is useful to distinguish the natural variations of root architecture between A. thaliana accessions, but not across early stages of root development. Correlation analyses in these accessions showed that m is a novel trait that partially captures information from other root architecture traits such as total lateral root length, and the ratio between lateral root and primary root lengths. Moreover, we found that the rhizochron index was useful to distinguish ABA effect on root architecture, as well as the mutant pho1 phenotype. We propose the rhizochron index (m) as a new feature of the root architectural system to be considered, in addition to conventional traits in future investigations.
Collapse
Affiliation(s)
- Joel Colchado-López
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - R Cristian Cervantes
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Ulises Rosas
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico.
| |
Collapse
|
43
|
Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions. Nat Commun 2019; 10:1569. [PMID: 30952851 PMCID: PMC6451032 DOI: 10.1038/s41467-019-09522-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 03/15/2019] [Indexed: 12/21/2022] Open
Abstract
Charting a temporal path in gene networks requires linking early transcription factor (TF)-triggered events to downstream effects. We scale-up a cell-based TF-perturbation assay to identify direct regulated targets of 33 nitrogen (N)-early response TFs encompassing 88% of N-responsive Arabidopsis genes. We uncover a duality where each TF is an inducer and repressor, and in vitro cis-motifs are typically specific to regulation directionality. Validated TF-targets (71,836) are used to refine precision of a time-inferred root network, connecting 145 N-responsive TFs and 311 targets. These data are used to chart network paths from direct TF1-regulated targets identified in cells to indirect targets responding only in planta via Network Walking. We uncover network paths from TGA1 and CRF4 to direct TF2 targets, which in turn regulate 76% and 87% of TF1 indirect targets in planta, respectively. These results have implications for N-use and the approach can reveal temporal networks for any biological system. Temporal control of transcriptional networks enables organisms to adapt to changing environment. Here, the authors use a scaled-up cell-based assay to identify direct targets of nitrogen-early responsive transcription factors and validate a network path mediating dynamic nitrogen signaling in Arabidopsis.
Collapse
|
44
|
Swift J, Adame M, Tranchina D, Henry A, Coruzzi GM. Water impacts nutrient dose responses genome-wide to affect crop production. Nat Commun 2019; 10:1374. [PMID: 30914651 PMCID: PMC6435674 DOI: 10.1038/s41467-019-09287-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 02/26/2019] [Indexed: 01/20/2023] Open
Abstract
Changes in nutrient dose have dramatic effects on gene expression and development. One outstanding question is whether organisms respond to changes in absolute nutrient amount (moles) vs. its concentration in water (molarity). This question is particularly relevant to plants, as soil drying can alter nutrient concentration, without changing its absolute amount. To compare the effects of amount vs. concentration, we expose rice to a factorial matrix varying the dose of nitrogen (N) and water (W) over a range of combinations, and quantify transcriptome and phenotype responses. Using linear models, we identify distinct dose responses to either N-moles, W-volume, N-molarity (N/W), or their synergistic interaction (N×W). Importantly, genes whose expression patterns are best explained by N-dose and W interactions (N/W or N×W) in seedlings are associated with crop outcomes in replicated field trials. Such N-by-W responsive genes may assist future efforts to develop crops resilient to increasingly arid, low nutrient soils.
Collapse
Affiliation(s)
- Joseph Swift
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, 10003, NY, USA
| | - Mark Adame
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, 10003, NY, USA
| | - Daniel Tranchina
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, 10003, NY, USA
- Courant Institute for Mathematical Sciences, New York University, New York, 10012, NY, USA
| | - Amelia Henry
- International Rice Research Institute, Los Banos, 4031, Laguna, Philippines
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, 10003, NY, USA.
| |
Collapse
|
45
|
|
46
|
Gaudinier A, Rodriguez-Medina J, Zhang L, Olson A, Liseron-Monfils C, Bågman AM, Foret J, Abbitt S, Tang M, Li B, Runcie DE, Kliebenstein DJ, Shen B, Frank MJ, Ware D, Brady SM. Transcriptional regulation of nitrogen-associated metabolism and growth. Nature 2018; 563:259-264. [PMID: 30356219 DOI: 10.1038/s41586-018-0656-3] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 08/22/2018] [Indexed: 11/09/2022]
Abstract
Nitrogen is an essential macronutrient for plant growth and basic metabolic processes. The application of nitrogen-containing fertilizer increases yield, which has been a substantial factor in the green revolution1. Ecologically, however, excessive application of fertilizer has disastrous effects such as eutrophication2. A better understanding of how plants regulate nitrogen metabolism is critical to increase plant yield and reduce fertilizer overuse. Here we present a transcriptional regulatory network and twenty-one transcription factors that regulate the architecture of root and shoot systems in response to changes in nitrogen availability. Genetic perturbation of a subset of these transcription factors revealed coordinate transcriptional regulation of enzymes involved in nitrogen metabolism. Transcriptional regulators in the network are transcriptionally modified by feedback via genetic perturbation of nitrogen metabolism. The network, genes and gene-regulatory modules identified here will prove critical to increasing agricultural productivity.
Collapse
Affiliation(s)
- Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Joel Rodriguez-Medina
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA
| | | | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Jessica Foret
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Michelle Tang
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.,Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA.,DynaMo Center of Excellence, University of Copenhagen, Frederiksberg C, Denmark
| | - Bo Shen
- DuPont Pioneer, Johnston, IA, USA
| | | | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA.,US Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.
| |
Collapse
|
47
|
Ristova D, Giovannetti M, Metesch K, Busch W. Natural genetic variation shapes root system responses to phytohormones in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:468-481. [PMID: 30030851 PMCID: PMC6220887 DOI: 10.1111/tpj.14034] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/13/2018] [Accepted: 07/02/2018] [Indexed: 05/21/2023]
Abstract
Plants adjust their architecture by modulating organ growth. This ability is largely dependent on phytohormones. While responses to phytohormones have been studied extensively, it remains unclear to which extent and how these responses are modulated in non-reference strains. Here, we assess variation of root traits upon treatment with auxin, cytokinin and abscisic acid (ABA) in 192 Arabidopsis accessions. We identify common response patterns, uncover the extent of their modulation by specific genotypes, and find that the Col-0 reference accession is not a good representative of the species in this regard. We conduct genome-wide association studies and identify 114 significant associations, most of them relating to ABA treatment. The numerous ABA candidate genes are not enriched for known ABA-associated genes, indicating that we largely uncovered unknown players. Overall, our study provides a comprehensive view of the diversity of hormone responses in the Arabidopsis thaliana species, and shows that variation of genes that are yet mostly not associated with such a role to determine natural variation of the response to phytohormones.
Collapse
Affiliation(s)
- Daniela Ristova
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Marco Giovannetti
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Kristina Metesch
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
- Salk Institute for Biological StudiesPlant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory10010 N Torrey Pines RdLa JollaCA92037USA
| |
Collapse
|
48
|
Ruffel S. Nutrient-Related Long-Distance Signals: Common Players and Possible Cross-Talk. PLANT & CELL PHYSIOLOGY 2018; 59:1723-1732. [PMID: 30085239 DOI: 10.1093/pcp/pcy152] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/19/2018] [Indexed: 05/20/2023]
Abstract
Nutrient fluctuations are more a rule rather than an exception in the life of sessile organisms such as plants. Despite this constraint that adds up to abiotic and biotic stresses, plants are able to accomplish their life cycle thanks to an efficient signaling network that reciprocally controls nutrient acquisition and use with growth and development. The majority of nutrients are acquired by the root system where multiple local signaling pathways that rely on nutrient-sensing systems are implemented to direct root growth toward soil resources. Moreover, long-distance signaling plays an essential role in integrating nutrient availability at the whole-plant level and adjusting nutrient acquisition to plant growth requirements. By studying the signaling network for single mineral nutrients, several long-distance signals traveling between roots and shoots and taking a diversity of forms have been identified and are summarized here. However, the nutritional environment is multifactorial, adding a tremendous complexity for our understanding of the nutrient signaling network as a unique system. For instance, long-distance signals are expected to support this nutrient cross-talk in part, but the mechanisms are still largely unknown. Therefore, the involvement of possible long-distance signals as conveyers of nutrient cross-talk is discussed here together with approaches and strategies that are now considered to build a picture from the nutrient signaling puzzle.
Collapse
Affiliation(s)
- Sandrine Ruffel
- BPMP, INRA, CNRS, Universit� de Montpellier, Montpellier SupAgro, Montpellier, France
| |
Collapse
|
49
|
Weber K, Burow M. Nitrogen - essential macronutrient and signal controlling flowering time. PHYSIOLOGIA PLANTARUM 2018; 162:251-260. [PMID: 29095491 DOI: 10.1111/ppl.12664] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 10/10/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen, as limiting nutrient for plant growth and crop yield, is a main component of fertilizers and heavily used in modern agriculture. Early reports from over-application of fertilizers in crop production have shown to repress the transition from vegetative to reproductive phase. For the model plant Arabidopsis thaliana, there is evidence that low nitrogen conditions promote early flowering, while high nitrogen as well as nitrogen starvation conditions display the opposite effect. To gain a better understanding of how nitrogen affects the onset of flowering, we reviewed the existing literature for A. thaliana and carried out a meta-analysis on available transcriptomics data, seeking for potential genes and pathways involved in both nitrogen responses and flowering time control. With this strategy, we aimed at identifying potential gateways for integration of nitrogen signaling and potential regulators that might link the regulatory networks controlling nitrogen and flowering in A. thaliana. We found that photoperiodic pathway genes have high potential to be involved in nitrogen-dependent flowering.
Collapse
Affiliation(s)
- Konrad Weber
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
50
|
Herrera Paredes S, Gao T, Law TF, Finkel OM, Mucyn T, Teixeira PJPL, Salas González I, Feltcher ME, Powers MJ, Shank EA, Jones CD, Jojic V, Dangl JL, Castrillo G. Design of synthetic bacterial communities for predictable plant phenotypes. PLoS Biol 2018; 16:e2003962. [PMID: 29462153 PMCID: PMC5819758 DOI: 10.1371/journal.pbio.2003962] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/17/2018] [Indexed: 01/01/2023] Open
Abstract
Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant-bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation-responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.
Collapse
Affiliation(s)
- Sur Herrera Paredes
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tianxiang Gao
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Theresa F. Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Omri M. Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tatiana Mucyn
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isaí Salas González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Meghan E. Feltcher
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Matthew J. Powers
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elizabeth A. Shank
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| |
Collapse
|