1
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Wang J, Zhu R, Meng Q, Qin H, Quan R, Wei P, Li X, Jiang L, Huang R. A natural variation in OsDSK2a modulates plant growth and salt tolerance through phosphorylation by SnRK1A in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1881-1896. [PMID: 38346083 PMCID: PMC11182596 DOI: 10.1111/pbi.14308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 12/11/2023] [Accepted: 01/29/2024] [Indexed: 06/19/2024]
Abstract
Plants grow rapidly for maximal production under optimal conditions; however, they adopt a slower growth strategy to maintain survival when facing environmental stresses. As salt stress restricts crop architecture and grain yield, identifying genetic variations associated with growth and yield responses to salinity is critical for breeding optimal crop varieties. OsDSK2a is a pivotal modulator of plant growth and salt tolerance via the modulation of gibberellic acid (GA) metabolism; however, its regulation remains unclear. Here, we showed that OsDSK2a can be phosphorylated at the second amino acid (S2) to maintain its stability. The gene-edited mutant osdsk2aS2G showed decreased plant height and enhanced salt tolerance. SnRK1A modulated OsDSK2a-S2 phosphorylation and played a substantial role in GA metabolism. Genetic analysis indicated that SnRK1A functions upstream of OsDSK2a and affects plant growth and salt tolerance. Moreover, SnRK1A activity was suppressed under salt stress, resulting in decreased phosphorylation and abundance of OsDSK2a. Thus, SnRK1A preserves the stability of OsDSK2a to maintain plant growth under normal conditions, and reduces the abundance of OsDSK2a to limit growth under salt stress. Haplotype analysis using 3 K-RG data identified a natural variation in OsDSK2a-S2. The allele of OsDSK2a-G downregulates plant height and improves salt-inhibited grain yield. Thus, our findings revealed a new mechanism for OsDSK2a stability and provided a valuable target for crop breeding to overcome yield limitations under salinity stress.
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Affiliation(s)
- Juan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Key Facility of Crop Gene Resources and Genetic ImprovementBeijingChina
| | - Rui Zhu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Qingshi Meng
- Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hua Qin
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Key Facility of Crop Gene Resources and Genetic ImprovementBeijingChina
| | - Ruidang Quan
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Key Facility of Crop Gene Resources and Genetic ImprovementBeijingChina
| | - Pengcheng Wei
- College of AgronomyAnhui Agricultural UniversityHefeiChina
| | - Xiaoying Li
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Lei Jiang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Rongfeng Huang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Key Facility of Crop Gene Resources and Genetic ImprovementBeijingChina
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2
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Li G, Zhao Y. The critical roles of three sugar-related proteins (HXK, SnRK1, TOR) in regulating plant growth and stress responses. HORTICULTURE RESEARCH 2024; 11:uhae099. [PMID: 38863993 PMCID: PMC11165164 DOI: 10.1093/hr/uhae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/25/2024] [Indexed: 06/13/2024]
Abstract
Sugar signaling is one of the most critical regulatory signals in plants, and its metabolic network contains multiple regulatory factors. Sugar signal molecules regulate cellular activities and organism development by combining with other intrinsic regulatory factors and environmental inputs. HXK, SnRK1, and TOR are three fundamental proteins that have a pivotal role in the metabolism of sugars in plants. HXK, being the initial glucose sensor discovered in plants, is renowned for its multifaceted characteristics. Recent investigations have unveiled that HXK additionally assumes a significant role in plant hormonal signaling and abiotic stress. SnRK1 serves as a vital regulator of growth under energy-depleted circumstances, whereas TOR, a large protein, acts as a central integrator of signaling pathways that govern cell metabolism, organ development, and transcriptome reprogramming in response to diverse stimuli. Together, these two proteins work to sense upstream signals and modulate downstream signals to regulate cell growth and proliferation. In recent years, there has been an increasing amount of research on these three proteins, particularly on TOR and SnRK1. Furthermore, studies have found that these three proteins not only regulate sugar signaling but also exhibit certain signal crosstalk in regulating plant growth and development. This review provides a comprehensive overview and summary of the basic functions and regulatory networks of these three proteins. It aims to serve as a reference for further exploration of the interactions between these three proteins and their involvement in co-regulatory networks.
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Affiliation(s)
- Guangshuo Li
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark
| | - Ying Zhao
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
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3
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Wang Z, Wang P, Cao H, Liu M, Kong L, Wang H, Ren W, Fu Q, Ma W. Genome-wide identification of bZIP transcription factors and their expression analysis in Platycodon grandiflorus under abiotic stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1403220. [PMID: 38863542 PMCID: PMC11165138 DOI: 10.3389/fpls.2024.1403220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
The Basic Leucine Zipper (bZIP) transcription factors (TFs) family is among of the largest and most diverse gene families found in plant species, and members of the bZIP TFs family perform important functions in plant developmental processes and stress response. To date, bZIP genes in Platycodon grandiflorus have not been characterized. In this work, a number of 47 PgbZIP genes were identified from the genome of P. grandiflorus, divided into 11 subfamilies. The distribution of these PgbZIP genes on the chromosome and gene replication events were analyzed. The motif, gene structure, cis-elements, and collinearity relationships of the PgbZIP genes were simultaneously analyzed. In addition, gene expression pattern analysis identified ten candidate genes involved in the developmental process of different tissue parts of P. grandiflorus. Among them, Four genes (PgbZIP5, PgbZIP21, PgbZIP25 and PgbZIP28) responded to drought and salt stress, which may have potential biological roles in P. grandiflorus development under salt and drought stress. Four hub genes (PgbZIP13, PgbZIP30, PgbZIP32 and PgbZIP45) mined in correlation network analysis, suggesting that these PgbZIP genes may form a regulatory network with other transcription factors to participate in regulating the growth and development of P. grandiflorus. This study provides new insights regarding the understanding of the comprehensive characterization of the PgbZIP TFs for further exploration of the functions of growth and developmental regulation in P. grandiflorus and the mechanisms for coping with abiotic stress response.
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Affiliation(s)
- Zhen Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Panpan Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Huiyan Cao
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Meiqi Liu
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lingyang Kong
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Honggang Wang
- Research Office of Development and Utilization of Medicinal Plants, Heilongjiang Academy of Forestry, Yichun, China
| | - Weichao Ren
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Qifeng Fu
- Experimental Teaching and Practical Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Ma
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
- Experimental Teaching and Practical Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
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4
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Morales-Herrera S, Paul MJ, Van Dijck P, Beeckman T. SnRK1/TOR/T6P: three musketeers guarding energy for root growth. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00062-1. [PMID: 38580543 DOI: 10.1016/j.tplants.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Abstract
Sugars derived from photosynthesis, specifically sucrose, are the primary source of plant energy. Sucrose is produced in leaves and transported to the roots through the phloem, serving as a vital energy source. Environmental conditions can result in higher or lower photosynthesis, promoting anabolism or catabolism, respectively, thereby influencing the sucrose budget available for roots. Plants can adjust their root system to optimize the search for soil resources and to ensure the plant's adaptability to diverse environmental conditions. Recently, emerging research indicates that SNF1-RELATED PROTEIN KINASE 1 (SnRK1), trehalose 6-phosphate (T6P), and TARGET OF RAPAMYCIN (TOR) collectively serve as fundamental regulators of root development, together forming a signaling module to interpret the nutritional status of the plant and translate this to growth adjustments in the below ground parts.
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Affiliation(s)
- S Morales-Herrera
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark Arenberg, Leuven, Belgium
| | - M J Paul
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - P Van Dijck
- Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark Arenberg, Leuven, Belgium; KU Leuven Plant Institute (LPI), Leuven, Belgium
| | - T Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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5
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Cayuela A, Villasante-Fernández A, Corbalán-Acedo A, Baena-González E, Ferrando A, Belda-Palazón B. An Escherichia coli-Based Phosphorylation System for Efficient Screening of Kinase Substrates. Int J Mol Sci 2024; 25:3813. [PMID: 38612623 PMCID: PMC11011427 DOI: 10.3390/ijms25073813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/29/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Posttranslational modifications (PTMs), particularly phosphorylation, play a pivotal role in expanding the complexity of the proteome and regulating diverse cellular processes. In this study, we present an efficient Escherichia coli phosphorylation system designed to streamline the evaluation of potential substrates for Arabidopsis thaliana plant kinases, although the technology is amenable to any. The methodology involves the use of IPTG-inducible vectors for co-expressing kinases and substrates, eliminating the need for radioactive isotopes and prior protein purification. We validated the system's efficacy by assessing the phosphorylation of well-established substrates of the plant kinase SnRK1, including the rat ACETYL-COA CARBOXYLASE 1 (ACC1) and FYVE1/FREE1 proteins. The results demonstrated the specificity and reliability of the system in studying kinase-substrate interactions. Furthermore, we applied the system to investigate the phosphorylation cascade involving the A. thaliana MKK3-MPK2 kinase module. The activation of MPK2 by MKK3 was demonstrated to phosphorylate the Myelin Basic Protein (MBP), confirming the system's ability to unravel sequential enzymatic steps in phosphorylation cascades. Overall, this E. coli phosphorylation system offers a rapid, cost-effective, and reliable approach for screening potential kinase substrates, presenting a valuable tool to complement the current portfolio of molecular techniques for advancing our understanding of kinase functions and their roles in cellular signaling pathways.
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Affiliation(s)
- Andrés Cayuela
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
| | - Adela Villasante-Fernández
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
| | - Antonio Corbalán-Acedo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
| | | | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
| | - Borja Belda-Palazón
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
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6
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Kreisz P, Hellens AM, Fröschel C, Krischke M, Maag D, Feil R, Wildenhain T, Draken J, Braune G, Erdelitsch L, Cecchino L, Wagner TC, Ache P, Mueller MJ, Becker D, Lunn JE, Hanson J, Beveridge CA, Fichtner F, Barbier FF, Weiste C. S 1 basic leucine zipper transcription factors shape plant architecture by controlling C/N partitioning to apical and lateral organs. Proc Natl Acad Sci U S A 2024; 121:e2313343121. [PMID: 38315839 PMCID: PMC10873608 DOI: 10.1073/pnas.2313343121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/21/2023] [Indexed: 02/07/2024] Open
Abstract
Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant's nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.
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Affiliation(s)
- Philipp Kreisz
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Alicia M. Hellens
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
| | - Christian Fröschel
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Markus Krischke
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Daniel Maag
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Regina Feil
- Group System Regulation, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm14476, Germany
| | - Theresa Wildenhain
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Jan Draken
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Gabriel Braune
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Leon Erdelitsch
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Laura Cecchino
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Tobias C. Wagner
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Peter Ache
- Department of Molecular Plant Physiology and Biophysics, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Martin J. Mueller
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Dirk Becker
- Department of Molecular Plant Physiology and Biophysics, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - John E. Lunn
- Group System Regulation, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm14476, Germany
| | - Johannes Hanson
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, UmeåSE-901 87, Sweden
| | - Christine A. Beveridge
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
| | - Franziska Fichtner
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- Department of Plant Biochemistry, Institute for Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Francois F. Barbier
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- Institute for Plant Sciences of Montpellier, University of Montpellier, CNRS, INRAe, Institut Agro, Montpellier34060, France
| | - Christoph Weiste
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
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7
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Göbel M, Fichtner F. Functions of sucrose and trehalose 6-phosphate in controlling plant development. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154140. [PMID: 38007969 DOI: 10.1016/j.jplph.2023.154140] [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: 07/23/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/28/2023]
Abstract
Plants exhibit enormous plasticity in regulating their architecture to be able to adapt to a constantly changing environment and carry out vital functions such as photosynthesis, anchoring, and nutrient uptake. Phytohormones play a role in regulating these responses, but sugar signalling mechanisms are also crucial. Sucrose is not only an important source of carbon and energy fuelling plant growth, but it also functions as a signalling molecule that influences various developmental processes. Trehalose 6-phosphate (Tre6P), a sucrose-specific signalling metabolite, is emerging as an important regulator in plant metabolism and development. Key players involved in sucrose and Tre6P signalling pathways, including MAX2, SnRK1, bZIP11, and TOR, have been implicated in processes such as flowering, branching, and root growth. We will summarize our current knowledge of how these pathways shape shoot and root architecture and highlight how sucrose and Tre6P signalling are integrated with known signalling networks in shaping plant growth.
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Affiliation(s)
- Moritz Göbel
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Plant Biochemistry, Germany; Cluster of Excellences on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Germany
| | - Franziska Fichtner
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Plant Biochemistry, Germany; Cluster of Excellences on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Germany.
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8
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Morales-Herrera S, Jourquin J, Coppé F, Lopez-Galvis L, De Smet T, Safi A, Njo M, Griffiths CA, Sidda JD, Mccullagh JSO, Xue X, Davis BG, Van der Eycken J, Paul MJ, Van Dijck P, Beeckman T. Trehalose-6-phosphate signaling regulates lateral root formation in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2023; 120:e2302996120. [PMID: 37748053 PMCID: PMC10556606 DOI: 10.1073/pnas.2302996120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/08/2023] [Indexed: 09/27/2023] Open
Abstract
Plant roots explore the soil for water and nutrients, thereby determining plant fitness and agricultural yield, as well as determining ground substructure, water levels, and global carbon sequestration. The colonization of the soil requires investment of carbon and energy, but how sugar and energy signaling are integrated with root branching is unknown. Here, we show through combined genetic and chemical modulation of signaling pathways that the sugar small-molecule signal, trehalose-6-phosphate (T6P) regulates root branching through master kinases SNF1-related kinase-1 (SnRK1) and Target of Rapamycin (TOR) and with the involvement of the plant hormone auxin. Increase of T6P levels both via genetic targeting in lateral root (LR) founder cells and through light-activated release of the presignaling T6P-precursor reveals that T6P increases root branching through coordinated inhibition of SnRK1 and activation of TOR. Auxin, the master regulator of LR formation, impacts this T6P function by transcriptionally down-regulating the T6P-degrader trehalose phosphate phosphatase B in LR cells. Our results reveal a regulatory energy-balance network for LR formation that links the 'sugar signal' T6P to both SnRK1 and TOR downstream of auxin.
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Affiliation(s)
- Stefania Morales-Herrera
- Department of Plant Biotechnology and Bioinformatics Ghent University, GhentB-9052, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, GhentB-9052, Belgium
- Laboratory of Molecular Cell Biology, Katholieke Universiteit Leuven, LeuvenB3001, Belgium
- Vlaams Instituut voor Biotechnologie-Katholieke Universiteit Leuven Center for Microbiology, LeuvenB3001, Belgium
| | - Joris Jourquin
- Department of Plant Biotechnology and Bioinformatics Ghent University, GhentB-9052, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, GhentB-9052, Belgium
| | - Frederic Coppé
- Department of Plant Biotechnology and Bioinformatics Ghent University, GhentB-9052, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, GhentB-9052, Belgium
| | - Lorena Lopez-Galvis
- Department of Plant Biotechnology and Bioinformatics Ghent University, GhentB-9052, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, GhentB-9052, Belgium
- Laboratory of Molecular Cell Biology, Katholieke Universiteit Leuven, LeuvenB3001, Belgium
- Vlaams Instituut voor Biotechnologie-Katholieke Universiteit Leuven Center for Microbiology, LeuvenB3001, Belgium
| | - Tom De Smet
- Department of Organic and Macromolecular Chemistry, Laboratory for Organic and Bio-Organic Synthesis, Ghent University, GhentB-9000, Belgium
| | - Alaeddine Safi
- Department of Plant Biotechnology and Bioinformatics Ghent University, GhentB-9052, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, GhentB-9052, Belgium
| | - Maria Njo
- Department of Plant Biotechnology and Bioinformatics Ghent University, GhentB-9052, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, GhentB-9052, Belgium
| | - Cara A. Griffiths
- Department of Sustainable Soils and Crops, Rothamsted Research, HarpendenAL5 2JQ, United Kingdom
| | - John D. Sidda
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, OxfordOX1 3TA, United Kingdom
| | - James S. O. Mccullagh
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, OxfordOX1 3TA, United Kingdom
| | - Xiaochao Xue
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, OxfordOX1 3TA, United Kingdom
| | - Benjamin G. Davis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, OxfordOX1 3TA, United Kingdom
- Next Generation Chemistry, The Rosalind Franklin Institute, DidcotOX1 3TA, United Kingdom
- Department of Pharmacology, University of Oxford, OxfordOX1 3TA, United Kingdom
| | - Johan Van der Eycken
- Department of Organic and Macromolecular Chemistry, Laboratory for Organic and Bio-Organic Synthesis, Ghent University, GhentB-9000, Belgium
| | - Matthew J. Paul
- Department of Sustainable Soils and Crops, Rothamsted Research, HarpendenAL5 2JQ, United Kingdom
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Katholieke Universiteit Leuven, LeuvenB3001, Belgium
- Vlaams Instituut voor Biotechnologie-Katholieke Universiteit Leuven Center for Microbiology, LeuvenB3001, Belgium
- Katholieke Universiteit Leuven Plant Institute, Katholieke Universiteit Leuven, LeuvenB3001, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics Ghent University, GhentB-9052, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, GhentB-9052, Belgium
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9
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Robinson D. OPT-ing out: Root-shoot dynamics are caused by local resource capture and biomass allocation, not optimal partitioning. PLANT, CELL & ENVIRONMENT 2023; 46:3023-3039. [PMID: 36285352 DOI: 10.1111/pce.14470] [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: 06/16/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Combining plant growth analysis with a simple model of local resource capture and biomass allocation applied to exemplary experimental data, showed that dynamic changes in allocation to roots when nutrients are scarce is caused by disparities in growth rates between roots and shoots. Whole-plant growth rates also change but are not caused by an adaptive allocation response. Allocation and whole-plant growth rate are interdependent, not independent, traits. Following a switch in nutrient availability or partial biomass removal, convergence of allocation and growth rate trajectories does not reflect goal-seeking behaviour, but the constraints imposed by finite resource availability. Optimal root-shoot allocations are unnecessary to maximise whole-plant growth rate. Similar growth rates are attainable with different allocations. Changes in allocation cannot maintain or restore a superior whole-plant growth rate. Roots and shoots do not have to be tightly coordinated but can operate semiautonomously, as their modular construction permits. These findings question the plausibility of the prevailing general explanation of plants' root-shoot allocation responses, 'optimal partitioning theory' (OPT). Local allocation models, not OPT, explain the origins of variability in root-shoot trade-offs in individuals, the allocation of biomass at global and ecosystem scales and inform selection for allocation plasticity in crop breeding.
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Affiliation(s)
- David Robinson
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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10
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Safi A, Smagghe W, Gonçalves A, Wang Q, Xu K, Fernandez AI, Cappe B, Riquet FB, Mylle E, Eeckhout D, De Winne N, Van De Slijke E, Persyn F, Persiau G, Van Damme D, Geelen D, De Jaeger G, Beeckman T, Van Leene J, Vanneste S. Phase separation-based visualization of protein-protein interactions and kinase activities in plants. THE PLANT CELL 2023; 35:3280-3302. [PMID: 37378595 PMCID: PMC10473206 DOI: 10.1093/plcell/koad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/23/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
Protein activities depend heavily on protein complex formation and dynamic posttranslational modifications, such as phosphorylation. The dynamic nature of protein complex formation and posttranslational modifications is notoriously difficult to monitor in planta at cellular resolution, often requiring extensive optimization. Here, we generated and exploited the SYnthetic Multivalency in PLants (SYMPL)-vector set to assay protein-protein interactions (PPIs) (separation of phases-based protein interaction reporter) and kinase activities (separation of phases-based activity reporter of kinase) in planta, based on phase separation. This technology enabled easy detection of inducible, binary and ternary PPIs among cytoplasmic and nuclear proteins in plant cells via a robust image-based readout. Moreover, we applied the SYMPL toolbox to develop an in vivo reporter for SNF1-related kinase 1 activity, allowing us to visualize tissue-specific, dynamic SnRK1 activity in stable transgenic Arabidopsis (Arabidopsis thaliana) plants. The SYMPL cloning toolbox provides a means to explore PPIs, phosphorylation, and other posttranslational modifications with unprecedented ease and sensitivity.
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Affiliation(s)
- Alaeddine Safi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Wouter Smagghe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Amanda Gonçalves
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- VIB, Bioimaging Core, B-9052 Ghent, Belgium
| | - Qing Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ke Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ana Ibis Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Benjamin Cappe
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
| | - Franck B Riquet
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Freya Persyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
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11
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Yuan P, Liu H, Wang X, Hammond JP, Shi L. Genome-wide association study reveals candidate genes controlling root system architecture under low phosphorus supply at seedling stage in Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:63. [PMID: 37521313 PMCID: PMC10382450 DOI: 10.1007/s11032-023-01411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/18/2023] [Indexed: 08/01/2023]
Abstract
Optimal root system architecture (RSA) is essential for vigorous growth and yield in crops. Plants have evolved adaptive mechanisms in response to low phosphorus (LP) stress, and one of those is changes in RSA. Here, more than five million single-nucleotide polymorphisms (SNPs) obtained from whole-genome re-sequencing data (WGR) of an association panel of 370 oilseed rape (Brassica napus L.) were used to conduct a genome-wide association study (GWAS) of RSA traits of the panel at LP in "pouch and wick" system. Fifty-two SNPs were forcefully associated with lateral root length (LRL), total root length (TRL), lateral root density (LRD), lateral root number (LRN), mean lateral root length (MLRL), and root dry weight (RDW) at LP. There were significant correlations between phenotypic variation and the number of favorable alleles of the associated loci on chromosomes A06 (chrA06_20030601), C03 (chrC03_3535483), and C07 (chrC07_42348561), respectively. Three candidate genes (BnaA06g29270D, BnaC03g07130D, and BnaC07g43230D) were detected by combining transcriptome, candidate gene association analysis, and haplotype analysis. Cultivar carrying "CCGC" at BnaA06g29270DHap1, "CAAT" at BnaC03g07130DHap1, and "ATC" at BnaC07g43230DHap1 had greater LRL, LRN, and RDW than lines carrying other haplotypes at LP supply. The RSA of a cultivar harboring the three favorable haplotypes was further confirmed by solution culture experiments. These findings define exquisite insights into genetic architectures underlying B. napus RSA at LP and provide valuable gene resources for root breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01411-2.
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Affiliation(s)
- Pan Yuan
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
| | - Haijiang Liu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiaohua Wang
- College of Agriculture and Forestry Science, Linyi University, Linyi, 276000 China
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR UK
| | - Lei Shi
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
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12
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Li H, Duijts K, Pasini C, van Santen JE, Lamers J, de Zeeuw T, Verstappen F, Wang N, Zeeman SC, Santelia D, Zhang Y, Testerink C. Effective root responses to salinity stress include maintained cell expansion and carbon allocation. THE NEW PHYTOLOGIST 2023; 238:1942-1956. [PMID: 36908088 DOI: 10.1111/nph.18873] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/25/2023] [Indexed: 05/04/2023]
Abstract
Acclimation of root growth is vital for plants to survive salt stress. Halophytes are great examples of plants that thrive even under severe salinity, but their salt tolerance mechanisms, especially those mediated by root responses, are still largely unknown. We compared root growth responses of the halophyte Schrenkiella parvula with its glycophytic relative species Arabidopsis thaliana under salt stress and performed transcriptomic analysis of S. parvula roots to identify possible gene regulatory networks underlying their physiological responses. Schrenkiella parvula roots do not avoid salt and experience less growth inhibition under salt stress. Salt-induced abscisic acid levels were higher in S. parvula roots compared with Arabidopsis. Root transcriptomic analysis of S. parvula revealed the induction of sugar transporters and genes regulating cell expansion and suberization under salt stress. 14 C-labeled carbon partitioning analyses showed that S. parvula continued allocating carbon to roots from shoots under salt stress while carbon barely allocated to Arabidopsis roots. Further physiological investigation revealed that S. parvula roots maintained root cell expansion and enhanced suberization under severe salt stress. In summary, roots of S. parvula deploy multiple physiological and developmental adjustments under salt stress to maintain growth, providing new avenues to improve salt tolerance of plants using root-specific strategies.
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Affiliation(s)
- Hongfei Li
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Kilian Duijts
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Carlo Pasini
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Joyce E van Santen
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Jasper Lamers
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Thijs de Zeeuw
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Francel Verstappen
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Nan Wang
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Diana Santelia
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Yanxia Zhang
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
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13
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Kircher S, Schopfer P. Photosynthetic sucrose drives the lateral root clock in Arabidopsis seedlings. Curr Biol 2023:S0960-9822(23)00543-2. [PMID: 37207646 DOI: 10.1016/j.cub.2023.04.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/20/2022] [Accepted: 04/25/2023] [Indexed: 05/21/2023]
Abstract
The development of plant roots is subject to control by light. Here, we show that, similar to monotonous root elongation, the periodic induction of lateral roots (LRs) depends on the activation by light of photomorphogenic and photosynthetic photoreceptors in the shoot in a hierarchical order. The prevailing belief is that the plant hormone auxin serves as a mobile signal transmitter, responsible for interorgan communication, including light-controlled shoot-to-root connections. Alternatively, it has been proposed that the transcription factor HY5 assumes the role as a mobile shoot-to-root signal transmitter. Here, we provide evidence that photosynthetic sucrose produced in the shoot acts as the long-distance signal carrier regulating the local, tryptophan-based biosynthesis of auxin in the LR generation zone of the primary root tip, where the LR clock controls the pace of LR initiation in an auxin-tunable manner. Synchronization of LR formation with primary root elongation allows the adjustment of overall root growth to the photosynthetic performance of the shoot and the maintenance of a constant LR density during light-dark changes in a variable light environment.
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Affiliation(s)
- Stefan Kircher
- Department of Molecular Plant Physiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
| | - Peter Schopfer
- Department of Molecular Plant Physiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
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14
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Avidan O, Moraes TA, Mengin V, Feil R, Rolland F, Stitt M, Lunn JE. In vivo protein kinase activity of SnRK1 fluctuates in Arabidopsis rosettes during light-dark cycles. PLANT PHYSIOLOGY 2023; 192:387-408. [PMID: 36725081 PMCID: PMC10152665 DOI: 10.1093/plphys/kiad066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/12/2022] [Accepted: 01/09/2023] [Indexed: 05/03/2023]
Abstract
Sucrose-nonfermenting 1 (SNF1)-related kinase 1 (SnRK1) is a central hub in carbon and energy signaling in plants, and is orthologous with SNF1 in yeast and the AMP-activated protein kinase (AMPK) in animals. Previous studies of SnRK1 relied on in vitro activity assays or monitoring of putative marker gene expression. Neither approach gives unambiguous information about in vivo SnRK1 activity. We have monitored in vivo SnRK1 activity using Arabidopsis (Arabidopsis thaliana) reporter lines that express a chimeric polypeptide with an SNF1/SnRK1/AMPK-specific phosphorylation site. We investigated responses during an equinoctial diel cycle and after perturbing this cycle. As expected, in vivo SnRK1 activity rose toward the end of the night and rose even further when the night was extended. Unexpectedly, although sugars rose after dawn, SnRK1 activity did not decline until about 12 h into the light period. The sucrose signal metabolite, trehalose 6-phosphate (Tre6P), has been shown to inhibit SnRK1 in vitro. We introduced the SnRK1 reporter into lines that harbored an inducible trehalose-6-phosphate synthase construct. Elevated Tre6P decreased in vivo SnRK1 activity in the light period, but not at the end of the night. Reporter polypeptide phosphorylation was sometimes negatively correlated with Tre6P, but a stronger and more widespread negative correlation was observed with glucose-6-phosphate. We propose that SnRK1 operates within a network that controls carbon utilization and maintains diel sugar homeostasis, that SnRK1 activity is regulated in a context-dependent manner by Tre6P, probably interacting with further inputs including hexose phosphates and the circadian clock, and that SnRK1 signaling is modulated by factors that act downstream of SnRK1.
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Affiliation(s)
- Omri Avidan
- Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Thiago A Moraes
- Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Virginie Mengin
- Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Regina Feil
- Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Filip Rolland
- Laboratory of Molecular Plant Biology, KU Leuven, B-3001 Leuven, Belgium
- KU Leuven Plant Institute (LPI), B-3001 Leuven, Belgium
| | - Mark Stitt
- Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - John E Lunn
- Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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15
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Huang J, Zhao J, Wang X, Ma L, Ma Z, Meng X, Fan H. SnRK1 signaling regulates cucumber growth and resistance to Corynespora cassiicola. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 332:111716. [PMID: 37086974 DOI: 10.1016/j.plantsci.2023.111716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
Energy metabolism is one of the key factors determining the growth and development of plants and the response to biotic and abiotic stresses. Sucrose non-fermentation 1 related protein kinase 1 (SnRK1) is an important energy-sensitive regulator that plays a key role in the overall control of carbohydrate metabolism. However, little is known about the function of SnRK1 in cucumber. In this study, metformin (an SnRK1 activator) and trehalose (an SnRK1 inhibitor) were used to investigate the role of SnRK1 signaling in cucumber. The results showed that SnRK1 activation could inhibit the growth of cucumber, slow down the net photosynthetic rate (Pn), reduce the contents of photosynthetic pigments and soluble sugars, and suppress the expression of genes related to sucrose metabolism. By contrast, SnRK1 inhibition yielded opposite results. Furthermore, SnRK1 activation and CsSnRK1 over-expression improved cucumber resistance to Corynespora cassiicola. While, SnRK1 inhibition and CsSnRK1 silencing reduced the resistance of cucumber to C. cassiicola. The results indicated that CsSnRK1 gene can positively regulate the resistance of cucumber to C. cassiicola. We conclude that CsSnRK1 signaling plays an important role in balancing the growth and immune response of cucumber. These results can be applied to the improvement of disease-resistant cucumber varieties.
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Affiliation(s)
- Jingnan Huang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Juyong Zhao
- Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning 110161, China
| | - Xue Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Lifeng Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Zhangtong Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Xiangnan Meng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
| | - Haiyan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
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16
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Retzer K, Weckwerth W. Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems. FRONTIERS IN PLANT SCIENCE 2023; 14:1154088. [PMID: 37008498 PMCID: PMC10060999 DOI: 10.3389/fpls.2023.1154088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Roots are sensors evolved to simultaneously respond to manifold signals, which allow the plant to survive. Root growth responses, including the modulation of directional root growth, were shown to be differently regulated when the root is exposed to a combination of exogenous stimuli compared to an individual stress trigger. Several studies pointed especially to the impact of the negative phototropic response of roots, which interferes with the adaptation of directional root growth upon additional gravitropic, halotropic or mechanical triggers. This review will provide a general overview of known cellular, molecular and signalling mechanisms involved in directional root growth regulation upon exogenous stimuli. Furthermore, we summarise recent experimental approaches to dissect which root growth responses are regulated upon which individual trigger. Finally, we provide a general overview of how to implement the knowledge gained to improve plant breeding.
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Affiliation(s)
- Katarzyna Retzer
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Molecular Systems Biology (MoSys), University of Vienna, Wien, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Wien, Austria
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17
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Zhang W, Fang D, Dong K, Hu F, Ye Z, Cao J. Insights into the environmental factors shaping lateral root development. PHYSIOLOGIA PLANTARUM 2023; 175:e13878. [PMID: 36808102 DOI: 10.1111/ppl.13878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/07/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Roots are important organs of plants. Plants rely on roots for water, nutrients, and organic salts. In the whole root system, lateral roots (LRs) account for a large proportion and are critical to the development of the plant. Many environmental factors affect LR development. Therefore, a systematic understanding of these factors can provide a theoretical basis for creating optimal growth conditions for plants. In this paper, the factors affecting LR development are systematically and comprehensively summarized, and the molecular mechanism and regulatory network of LR development are described. Changes in the external environment not only lead to hormone homeostasis in plants but also affect the composition and activity of rhizosphere microbial communities, which in turn affect plants' nitrogen and phosphorus uptake and growth dynamics. LR development is influenced by hormone levels and external environment. In particular, auxin and abscisic acid coordinate with each other to maintain normal LR development. Of course, changes in the external environment are also important for root development, and they affect the intrinsic hormone levels of plants by affecting the accumulation and transport of hormones. For example, nitrogen, phosphorus, reactive oxygen species, nitric oxide, water, drought, light, and rhizosphere microorganisms affect LR development and plant tolerance in a variety of ways, including regulating hormone levels. This review summarizes the factors affecting LR development and the regulatory network and points out the direction for future research.
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Affiliation(s)
- Weimeng Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Da Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Kui Dong
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Fei Hu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ziyi Ye
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
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18
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Zhang M, Chen Y, Xing H, Ke W, Shi Y, Sui Z, Xu R, Gao L, Guo G, Li J, Xing J, Zhang Y. Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:772-790. [PMID: 36354146 DOI: 10.1111/jipb.13408] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Lateral roots play essential roles in drought tolerance in maize (Zea mays L.). However, the genetic basis for the variation in the number of lateral roots in maize remains elusive. Here, we identified a major quantitative trait locus (QTL), qLRT5-1, controlling lateral root number using a recombinant inbred population from a cross between the maize lines Zong3 (with many lateral roots) and 87-1 (with few lateral roots). Fine-mapping and functional analysis determined that the candidate gene for qLRT5-1, ZmLRT, expresses the primary transcript for the microRNA miR166a. ZmLRT was highly expressed in root tips and lateral root primordia, and knockout and overexpression of ZmLRT increased and decreased lateral root number, respectively. Compared with 87-1, the ZmLRT gene model of Zong3 lacked the second and third exons and contained a 14 bp deletion at the junction between the first exon and intron, which altered the splicing site. In addition, ZmLRT expression was significantly lower in Zong3 than in 87-1, which might be attributed to the insertions of a transposon and over large DNA fragments in the Zong3 ZmLRT promoter region. These mutations decreased the abundance of mature miR166a in Zong3, resulting in increased lateral roots at the seedling stage. Furthermore, miR166a post-transcriptionally repressed five development-related class-III homeodomain-leucine zipper genes. Moreover, knockout of ZmLRT enhanced drought tolerance of maize seedlings. Our study furthers our understanding of the genetic basis of lateral root number variation in maize and highlights ZmLRT as a target for improving drought tolerance in maize.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yanhong Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Agronomy College of Shandong Agricultural University, Taian, 271018, China
| | - Hongyan Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yunlu Shi
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Yantai Science and Technology Innovation Promotion Center, Yantai, 264003, China
| | - Ruibin Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lulu Gao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ganggang Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yirong Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
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19
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Son S, Im JH, Ko J, Han K. SNF1-related protein kinase 1 represses Arabidopsis growth through post-translational modification of E2Fa in response to energy stress. THE NEW PHYTOLOGIST 2023; 237:823-839. [PMID: 36478538 PMCID: PMC10107498 DOI: 10.1111/nph.18597] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/08/2022] [Indexed: 06/01/2023]
Abstract
Cellular sugar starvation and/or energy deprivation serves as an important signaling cue for the live cells to trigger the necessary stress adaptation response. When exposed to cellular energy stress (ES) conditions, the plants reconfigure metabolic pathways and rebalance energy status while restricting vegetative organ growth. Despite the vital importance of this ES-induced growth restriction, the regulatory mechanism underlying the response remains largely elusive in plants. Using plant cell- and whole plant-based functional analyses coupled with extended genetic validation, we show that cellular ES-activated SNF1-related protein kinase 1 (SnRK1.1) directly interacts with and phosphorylates E2Fa transcription factor, a critical cell cycle regulator. Phosphorylation of E2Fa by SnRK1.1 leads to its proteasome-mediated protein degradation, resulting in S-phase repression and organ growth restriction. Our findings show that ES-dependently activated SnRK1.1 adjusts cell proliferation and vegetative growth for plants to cope with constantly fluctuating environments.
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Affiliation(s)
- Seungmin Son
- Department of Life SciencesKorea University145 Anamro, Sungbuk‐guSeoul02841Korea
- National Institute of Agricultural Sciences, Rural Development AdministrationJeonju54874Korea
| | - Jong Hee Im
- Department of Life SciencesKorea University145 Anamro, Sungbuk‐guSeoul02841Korea
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
| | - Jae‐Heung Ko
- Department of Plant & Environmental New Resources, College of Life Science and Graduate School of BiotechnologyKyung Hee UniversityYongin‐siGyeonggi‐do17104Korea
| | - Kyung‐Hwan Han
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
- Department of ForestryMichigan State UniversityEast LansingMI48824USA
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20
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Gao S, Li C, Chen X, Li S, Liang N, Wang H, Zhan Y, Zeng F. Basic helix-loop-helix transcription factor PxbHLH02 enhances drought tolerance in Populus (Populus simonii × P. nigra). TREE PHYSIOLOGY 2023; 43:185-202. [PMID: 36054366 DOI: 10.1093/treephys/tpac107] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
The basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in plant morphogenesis and various abiotic and biotic stress responses. However, further exploration is required of drought-responsive bHLH family members and their detailed regulatory mechanisms in Populus. Two bHLH TF genes, PxbHLH01/02, were identified in Populus simonii × P. nigra and cloned. The aim of this study was to examine the role of bHLH TFs in drought tolerance in P. simonii × P. nigra. The results showed that the amino acid sequences of the two genes were homologous to Arabidopsis thaliana UPBEAT1 (AtUPB1) and overexpression of PxbHLH01/02 restored normal root length in the AtUPB1 insertional mutant (upb1-1). The PxbHLH01/02 gene promoter activity analysis suggested that they were involved in stress responses and hormone signaling. Furthermore, Arabidopsis transgenic lines overexpressing PxbHLH01/02 exhibited higher stress tolerance compared with the wild-type. Populus simonii × P. nigra overexpressing PxbHLH02 increased drought tolerance and exhibited higher superoxide dismutase and peroxidase activities, lower H2O2 and malondialdehyde content, and lower relative conductivity. The results of transcriptome sequencing (RNA-seq) and quantitative real-time PCR suggested that the response of PxbHLH02 to drought stress was related to abscisic acid (ABA) signal transduction. Overall, the findings of this study suggest that PxbHLH02 from P. simonii × P. nigra functions as a positive regulator of drought stress responses by regulating stomatal aperture and promoting ABA signal transduction.
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Affiliation(s)
- Shangzhu Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Caihua Li
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050041, China
| | - Xiaohui Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Sida Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Nansong Liang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Hengtao Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yaguang Zhan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fansuo Zeng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
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21
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Liu Y, Cao L, Wu X, Wang S, Zhang P, Li M, Jiang J, Ding X, Cao X. Functional characterization of wild soybean (Glycine soja) GsSnRK1.1 protein kinase in plant resistance to abiotic stresses. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153881. [PMID: 36463657 DOI: 10.1016/j.jplph.2022.153881] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Protein kinases play crucial roles in the regulation of plant resistance to various stresses. In this work, we determined that GsSnRK1.1 was actively responsive to saline-alkali, drought, and abscisic acid (ABA) stresses by histochemical staining and qRT-PCR analyses. The wild-type GsSnRK1.1 but not the kinase-dead mutant, GsSnRK1.1(K49M), demonstrated in vitro kinase activity by phosphorylating GsABF2. Intriguingly, we found that GsSnRK1.1 could complement the loss of SNF1 kinase in yeast Msy1193 (-snf1) mutant, rescue growth defects of yeast cells on medium with glycerol as a carbon resource, and promote yeast resistance to NaCl or NaHCO3. To further elucidate GsSnRK1.1 function in planta, we knocked out SnRK1.1 gene from the Arabidopsis genome by the CRISPR/Cas9 approach, and then expressed GsSnRK1.1 and a series of mutants into snrk1.1-null lines. The transgenic Arabidopsis lines were subjected to various abiotic stress treatments. The results showed that GsSnRK1.1(T176E) mutant with enhanced protein kinase activity significantly promoted, but GsSnRK1.1(K49M) and GsSnRK1.1(T176A) mutants with disrupted protein kinase activity abrogated, plant stomatal closure and tolerance to abiotic stresses. In conclusion, this study provides the molecular clues to fully understand the physiological functions of plant SnRK1 protein kinases.
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Affiliation(s)
- Yuanming Liu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Lei Cao
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Xuan Wu
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Sai Wang
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Pengmin Zhang
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Minglong Li
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Jihong Jiang
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Xiaodong Ding
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China.
| | - Xiaoying Cao
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China.
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22
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Feng X, Meng Q, Zeng J, Yu Q, Xu D, Dai X, Ge L, Ma W, Liu W. Genome-wide identification of sucrose non-fermenting-1-related protein kinase genes in maize and their responses to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1087839. [PMID: 36618673 PMCID: PMC9815513 DOI: 10.3389/fpls.2022.1087839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Protein kinases play an important role in plants in response to environmental changes through signal transduction. As a large family of protein kinases, sucrose non-fermenting-1 (SNF1)-related kinases (SnRKs) were found and functionally verified in many plants. Nevertheless, little is known about the SnRK family of Zea mays. METHODS Evolutionary relationships, chromosome locations, gene structures, conserved motifs, and cis-elements in promoter regions were systematically analyzed. Besides, tissue-specific and stress-induced expression patterns of ZmSnRKs were determined. Finally, functional regulatory networks between ZmSnRKs and other proteins or miRNAs were constructed. RESULTS AND DISCUSSION In total, 60 SnRK genes located on 10 chromosomes were discovered in maize. ZmSnRKs were classified into three subfamilies (ZmSnRK1, ZmSnRK2, and ZmSnRK3), consisting of 4, 14, and 42 genes, respectively. Gene structure analysis showed that 33 of the 42 ZmSnRK3 genes contained only one exon. Most ZmSnRK genes contained at least one ABRE, MBS, and LTR cis-element and a few ZmSnRK genes had AuxRR-core, P-box, MBSI, and SARE ciselements in their promoter regions. The Ka:Ks ratio of 22 paralogous ZmSnRK gene pairs revealed that the ZmSnRK gene family had experienced a purifying selection. Meanwhile, we analyzed the expression profiles of ZmSnRKs, and they exhibited significant differences in various tissues and abiotic stresses. In addition, A total of eight ZmPP2Cs, which can interact with ZmSnRK proteins, and 46 miRNAs, which can target 24 ZmSnRKs, were identified. Generally, these results provide valuable information for further function verification of ZmSnRKs, and improve our understanding of the role of ZmSnRKs in the climate resilience of maize.
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Affiliation(s)
- Xue Feng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Quan Meng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Qian Yu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Xuehuan Dai
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Lei Ge
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Wenxing Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
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23
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Van Leene J, Eeckhout D, Gadeyne A, Matthijs C, Han C, De Winne N, Persiau G, Van De Slijke E, Persyn F, Mertens T, Smagghe W, Crepin N, Broucke E, Van Damme D, Pleskot R, Rolland F, De Jaeger G. Mapping of the plant SnRK1 kinase signalling network reveals a key regulatory role for the class II T6P synthase-like proteins. NATURE PLANTS 2022; 8:1245-1261. [PMID: 36376753 DOI: 10.1038/s41477-022-01269-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
The central metabolic regulator SnRK1 controls plant growth and survival upon activation by energy depletion, but detailed molecular insight into its regulation and downstream targets is limited. Here we used phosphoproteomics to infer the sucrose-dependent processes targeted upon starvation by kinases as SnRK1, corroborating the relation of SnRK1 with metabolic enzymes and transcriptional regulators, while also pointing to SnRK1 control of intracellular trafficking. Next, we integrated affinity purification, proximity labelling and crosslinking mass spectrometry to map the protein interaction landscape, composition and structure of the SnRK1 heterotrimer, providing insight in its plant-specific regulation. At the intersection of this multi-dimensional interactome, we discovered a strong association of SnRK1 with class II T6P synthase (TPS)-like proteins. Biochemical and cellular assays show that TPS-like proteins function as negative regulators of SnRK1. Next to stable interactions with the TPS-like proteins, similar intricate connections were found with known regulators, suggesting that plants utilize an extended kinase complex to fine-tune SnRK1 activity for optimal responses to metabolic stress.
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Affiliation(s)
- Jelle Van Leene
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Astrid Gadeyne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Caroline Matthijs
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Han
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Nancy De Winne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert Persiau
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Eveline Van De Slijke
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Freya Persyn
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Toon Mertens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wouter Smagghe
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nathalie Crepin
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Ellen Broucke
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Daniël Van Damme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Roman Pleskot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
| | - Filip Rolland
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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24
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Li R, Radani Y, Ahmad B, Movahedi A, Yang L. Identification and characteristics of SnRK genes and cold stress-induced expression profiles in Liriodendron chinense. BMC Genomics 2022; 23:708. [PMID: 36253733 PMCID: PMC9578244 DOI: 10.1186/s12864-022-08902-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/09/2022] [Indexed: 12/23/2022] Open
Abstract
Background The sucrose non-fermenting 1 (SNF1)-related protein kinases (SnRKs) play a vivid role in regulating plant metabolism and stress response, providing a pathway for regulation between metabolism and stress signals. Conducting identification and stress response studies on SnRKs in plants contributes to the development of strategies for tree species that are more tolerant to stress conditions. Results In the present study, a total of 30 LcSnRKs were identified in Liriodendron chinense (L. chinense) genome, which was distributed across 15 chromosomes and 4 scaffolds. It could be divided into three subfamilies: SnRK1, SnRK2, and SnRK3 based on phylogenetic analysis and domain types. The LcSnRK of the three subfamilies shared the same Ser/Thr kinase structure in gene structure and motif composition, while the functional domains, except for the kinase domain, showed significant differences. A total of 13 collinear gene pairs were detected in L. chinense and Arabidopsis thaliana (A. thaliana), and 18 pairs were detected in L. chinense and rice, suggesting that the LcSnRK family genes may be evolutionarily more closely related to rice. Cis-regulation element analysis showed that LcSnRKs were LTR and TC-rich, which could respond to different environmental stresses. Furthermore, the expression patterns of LcSnRKs are different at different times under low-temperature stress. LcSnRK1s expression tended to be down-regulated under low-temperature stress. The expression of LcSnRK2s tended to be up-regulated under low-temperature stress. The expression trend of LcSnRK3s under low-temperature stress was mainly up-or down-regulated. Conclusion The results of this study will provide valuable information for the functional identification of the LcSnRK gene in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08902-0.
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Affiliation(s)
- Rongxue Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Yasmina Radani
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Baseer Ahmad
- Muhammad Nawaz Sharif University of Agriculture, Multan, Punjab, 25000, Pakistan
| | - Ali Movahedi
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
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25
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Hou H, Kong X, Zhou Y, Yin C, Jiang Y, Qu H, Li T. Genome-wide identification and characterization of bZIP transcription factors in relation to litchi (Litchi chinensis Sonn.) fruit ripening and postharvest storage. Int J Biol Macromol 2022; 222:2176-2189. [DOI: 10.1016/j.ijbiomac.2022.09.292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
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26
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Zhou Y, Li Z, Zhu H, Jiang Y, Jiang G, Qu H. Energy homeostasis mediated by the LcSnRK1α-LcbZIP1/3 signaling pathway modulates litchi fruit senescence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:698-712. [PMID: 35634876 DOI: 10.1111/tpj.15845] [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: 05/14/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Cellular energy status is a key factor deciding the switch-on of the senescence of horticultural crops. Despite the established significance of the conserved energy master regulator sucrose non-fermenting 1 (SNF1)-related protein kinase 1 (SnRK1) in plant development, its working mechanism and related signaling pathway in the regulation of fruit senescence remain enigmatic. Here, we demonstrate that energy deficit accelerates fruit senescence, whereas exogenous ATP treatment delays it. The transient suppression of LcSnRK1α in litchi (Litchi chinensis Sonn.) fruit inhibited the expression of energy metabolism-related genes, while its ectopic expression in tomato (Solanum lycopersicum) promoted ripening and a high energy level. Biochemical analyses revealed that LcSnRK1α interacted with and phosphorylated the transcription factors LcbZIP1 and LcbZIP3, which directly bound to the promoters to activate the expression of DARK-INDUCIBLE 10 (LcDIN10), ASPARAGINE SYNTHASE 1 (LcASN1), and ANTHOCYANIN SYNTHASE (LcANS), thereby fine-tuning the metabolic reprogramming to ensure energy and redox homeostasis. Altogether, these observations reveal a post-translational modification mechanism by which LcSnRK1α-mediated phosphorylation of LcbZIP1 and LcbZIP3 regulates the expression of metabolic reprogramming-related genes, consequently modulating litchi fruit senescence.
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Affiliation(s)
- Yijie Zhou
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhiwei Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hong Zhu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoxiang Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hongxia Qu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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27
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ABA represses TOR and root meristem activity through nuclear exit of the SnRK1 kinase. Proc Natl Acad Sci U S A 2022; 119:e2204862119. [PMID: 35787039 PMCID: PMC9282376 DOI: 10.1073/pnas.2204862119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phytohormone abscisic acid (ABA) promotes plant tolerance to major stresses such as drought, partly by modulating growth through poorly understood mechanisms. Here, we show that ABA-triggered repression of cell proliferation in the Arabidopsis thaliana root meristem relies on the swift subcellular relocalization of SNF1-RELATED KINASE 1 (SnRK1). Under favorable conditions, the SnRK1 catalytic subunit, SnRK1α1, is enriched in the nuclei of root cells, and this is accompanied by normal cell proliferation and meristem size. Depletion of two key drivers of ABA signaling, SnRK2.2 and SnRK2.3, causes constitutive cytoplasmic localization of SnRK1α1 and reduced meristem size, suggesting that, under nonstress conditions, SnRK2s promote growth by retaining SnRK1α1 in the nucleus. In response to ABA, SnRK1α1 translocates to the cytoplasm, and this is accompanied by inhibition of target of rapamycin (TOR), decreased cell proliferation, and reduced meristem size. Blocking nuclear export with leptomycin B abrogates ABA-driven SnRK1α1 relocalization to the cytoplasm and ABA-elicited inhibition of TOR. Furthermore, fusing SnRK1α1 to an SV40 nuclear localization signal leads to defective ABA-dependent TOR repression. Altogether, we demonstrate that SnRK2-dependent changes in SnRK1α1 subcellular localization are crucial for inhibiting TOR and root growth in response to ABA. Rapid relocalization of central regulators such as SnRK1 may represent a general strategy of eukaryotic organisms to respond to environmental changes.
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28
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Chen Q, Zhang J, Li G. Dynamic epigenetic modifications in plant sugar signal transduction. TRENDS IN PLANT SCIENCE 2022; 27:379-390. [PMID: 34865981 DOI: 10.1016/j.tplants.2021.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/28/2021] [Accepted: 10/22/2021] [Indexed: 05/21/2023]
Abstract
In eukaryotes, dynamic chromatin states are closely related to changes in gene expression. Epigenetic modifications help plants adapt to their ever-changing environment by modulating gene expression via covalent modification at specific sites on DNA or histones. Sugars provide energy, but also function as signaling molecules to control plant growth and development. Various epigenetic modifications participate in sensing and transmitting sugar signals. Here we summarize recent progress in uncovering the epigenetic mechanisms involved in sugar signal transduction, including histone acetylation and deacetylation, histone methylation and demethylation, and DNA methylation. We also highlight changes in chromatin marks when crosstalk occurs between sugar signaling and the light, temperature, and phytohormone signaling pathways, and describe potential questions and approaches for future research.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, Shandong, China; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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