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Zhou CM, Li JX, Zhang TQ, Xu ZG, Ma ML, Zhang P, Wang JW. The structure of B-ARR reveals the molecular basis of transcriptional activation by cytokinin. Proc Natl Acad Sci U S A 2024; 121:e2319335121. [PMID: 38198526 PMCID: PMC10801921 DOI: 10.1073/pnas.2319335121] [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: 11/04/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
The phytohormone cytokinin has various roles in plant development, including meristem maintenance, vascular differentiation, leaf senescence, and regeneration. Prior investigations have revealed that cytokinin acts via a phosphorelay similar to the two-component system by which bacteria sense and respond to external stimuli. The eventual targets of this phosphorelay are type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs), containing the conserved N-terminal receiver domain (RD), middle DNA binding domain (DBD), and C-terminal transactivation domain. While it has been established for two decades that the phosphoryl transfer from a specific histidyl residue in ARABIDOPSIS HIS PHOSPHOTRANSFER PROTEINS (AHPs) to an aspartyl residue in the RD of B-ARRs results in a rapid transcriptional response to cytokinin, the underlying molecular basis remains unclear. In this work, we determine the crystal structures of the RD-DBD of ARR1 (ARR1RD-DBD) as well as the ARR1DBD-DNA complex from Arabidopsis. Analyses of the ARR1DBD-DNA complex have revealed the structural basis for sequence-specific recognition of the GAT trinucleotide by ARR1. In particular, comparing the ARR1RD-DBD and ARR1DBD-DNA structures reveals that unphosphorylated ARR1RD-DBD exists in a closed conformation with extensive contacts between the RD and DBD. In vitro and vivo functional assays have further suggested that phosphorylation of the RD weakens its interaction with DBD, subsequently permits the DNA binding capacity of DBD, and promotes the transcriptional activity of ARR1. Our findings thus provide mechanistic insights into phosphorelay activation of gene transcription in response to cytokinin.
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Affiliation(s)
- Chuan-Miao Zhou
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Jian-Xu Li
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai201602, China
| | - Tian-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Miao-Lian Ma
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
- Key Laboratory of Plant Carbon Capture, Chinese Academy of Sciences, Shanghai200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
- Key Laboratory of Plant Carbon Capture, Chinese Academy of Sciences, Shanghai200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
- New Cornerstone Science Laboratory, Shanghai200032, China
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Arkhipov DV, Lomin SN, Romanov GA. A Model of the Full-Length Cytokinin Receptor: New Insights and Prospects. Int J Mol Sci 2023; 25:73. [PMID: 38203244 PMCID: PMC10779265 DOI: 10.3390/ijms25010073] [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: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Cytokinins (CK) are one of the most important classes of phytohormones that regulate a wide range of processes in plants. A CK receptor, a sensor hybrid histidine kinase, was discovered more than 20 years ago, but the structural basis for its signaling is still a challenge for plant biologists. To date, only two fragments of the CK receptor structure, the sensory module and the receiver domain, were experimentally resolved. Some other regions were built up by molecular modeling based on structures of proteins homologous to CK receptors. However, in the long term, these data have proven insufficient for solving the structure of the full-sized CK receptor. The functional unit of CK receptor is the receptor dimer. In this article, a molecular structure of the dimeric form of the full-length CK receptor based on AlphaFold Multimer and ColabFold modeling is presented for the first time. Structural changes of the receptor upon interacting with phosphotransfer protein are visualized. According to mathematical simulation and available data, both types of dimeric receptor complexes with hormones, either half- or fully liganded, appear to be active in triggering signals. In addition, the prospects of using this and similar models to address remaining fundamental problems of CK signaling were outlined.
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Affiliation(s)
| | | | - Georgy A. Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia; (D.V.A.); (S.N.L.)
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3
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Rieger J, Fitz M, Fischer SM, Wallmeroth N, Flores-Romero H, Fischer NM, Brand LH, García-Sáez AJ, Berendzen KW, Mira-Rodado V. Exploring the Binding Affinity of the ARR2 GARP DNA Binding Domain via Comparative Methods. Genes (Basel) 2023; 14:1638. [PMID: 37628689 PMCID: PMC10454580 DOI: 10.3390/genes14081638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Plants have evolved signaling mechanisms such as the multi-step phosphorelay (MSP) to respond to different internal and external stimuli. MSP responses often result in gene transcription regulation that is modulated through transcription factors such as B-type Arabidopsis response regulator (ARR) proteins. Among these proteins, ARR2 is a key component that is expressed ubiquitously and is involved in many aspects of plant development. Although it has been noted that B-type ARRs bind to their cognate genes through a DNA-binding domain termed the GARP domain, little is known about the structure and function of this type of DNA-binding domain; thus, how ARRs bind to DNA at a structural level is still poorly understood. In order to understand how the MSP functions in planta, it is crucial to unravel both the kinetics as well as the structural identity of the components involved in such interactions. For this reason, this work focusses on resolving how the GARP domain of ARR2 (GARP2) binds to the promoter region of ARR5, one of its native target genes in cytokinin signaling. We have established that GARP2 specifically binds to the ARR5 promoter with three different bi-molecular interaction systems-qDPI-ELISA, FCS, and MST-and we also determined the KD of this interaction. In addition, structural modeling of the GARP2 domain confirms that GARP2 entails a HTH motif, and that protein-DNA interaction most likely occurs via the α3-helix and the N-terminal arm of this domain since mutations in this region hinder ARR2's ability to activate transcription.
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Affiliation(s)
- Janine Rieger
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Michael Fitz
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Stefan Markus Fischer
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Niklas Wallmeroth
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Hector Flores-Romero
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | - Nina Monika Fischer
- Institute for Bioinformatics and Medical Informatics, Tübingen University, 72076 Tübingen, Germany
| | - Luise Helene Brand
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Ana J. García-Sáez
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | | | - Virtudes Mira-Rodado
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
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4
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Ha CV, Mostofa MG, Nguyen KH, Tran CD, Watanabe Y, Li W, Osakabe Y, Sato M, Toyooka K, Tanaka M, Seki M, Burritt DJ, Anderson CM, Zhang R, Nguyen HM, Le VP, Bui HT, Mochida K, Tran LSP. The histidine phosphotransfer AHP4 plays a negative role in Arabidopsis plant response to drought. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1732-1752. [PMID: 35883014 DOI: 10.1111/tpj.15920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Cytokinin plays an important role in plant stress responses via a multistep signaling pathway, involving the histidine phosphotransfer proteins (HPs). In Arabidopsis thaliana, the AHP2, AHP3 and AHP5 proteins are known to affect drought responses; however, the role of AHP4 in drought adaptation remains undetermined. In the present study, using a loss-of-function approach we showed that AHP4 possesses an important role in the response of Arabidopsis to drought. This is evidenced by the higher survival rates of ahp4 than wild-type (WT) plants under drought conditions, which is accompanied by the downregulated AHP4 expression in WT during periods of dehydration. Comparative transcriptome analysis of ahp4 and WT plants revealed AHP4-mediated expression of several dehydration- and/or abscisic acid-responsive genes involved in modulation of various physiological and biochemical processes important for plant drought acclimation. In comparison with WT, ahp4 plants showed increased wax crystal accumulation in stems, thicker cuticles in leaves, greater sensitivity to exogenous abscisic acid at germination, narrow stomatal apertures, heightened leaf temperatures during dehydration, and longer root length under osmotic stress. In addition, ahp4 plants showed greater photosynthetic efficiency, lower levels of reactive oxygen species, reduced electrolyte leakage and lipid peroxidation, and increased anthocyanin contents under drought, when compared with WT. These differences displayed in ahp4 plants are likely due to upregulation of genes that encode enzymes involved in reactive oxygen species scavenging and non-enzymatic antioxidant metabolism. Overall, our findings suggest that AHP4 plays a crucial role in plant drought adaptation.
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Affiliation(s)
- Chien Van Ha
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Donald Danforth Plant Science Center, 975 N Warson Rd, Saint Louis, Missouri, 63132, USA
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
| | - Mohammad Golam Mostofa
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
| | - Kien Huu Nguyen
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, 100000, Vietnam
| | - Cuong Duy Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, 100000, Vietnam
| | - Yasuko Watanabe
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Weiqiang Li
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Jilin Da'an Agro-ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Yuriko Osakabe
- School of Life Science and Technology, Tokyo Institute of Technology, J2-12, 4259 Nagatsuda-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Mayuko Sato
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Kiminori Toyooka
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - David J Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | | | - Ru Zhang
- Donald Danforth Plant Science Center, 975 N Warson Rd, Saint Louis, Missouri, 63132, USA
| | - Huong Mai Nguyen
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
| | - Vy Phuong Le
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
| | - Hien Thuy Bui
- Division of Plant Science and Technology, Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Keiichi Mochida
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- School of Information and Data Science, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan
| | - Lam-Son Phan Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
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5
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Diurnal control of intracellular distributions of PAS-Histidine kinase 1 and its interactions with partner proteins in the moss Physcomitrium patens. Biochem Biophys Res Commun 2022; 616:1-7. [DOI: 10.1016/j.bbrc.2022.05.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 11/20/2022]
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6
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Del Rosario Cárdenas-Aquino M, Sarria-Guzmán Y, Martínez-Antonio A. Review: Isoprenoid and aromatic cytokinins in shoot branching. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111240. [PMID: 35487650 DOI: 10.1016/j.plantsci.2022.111240] [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: 11/16/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Shoot branching is an important event of plant development that defines growth and reproduction. The BRANCHED1 gene (BRC1/TB1/FC1) is crucial for this process. Within the phytohormones, cytokinins directly activate axillary buds to promote shoot branching. In addition, strigolactones and auxins inhibit bud outgrowth. This review addresses the involvement of aromatic and isoprenoid cytokinins in shoot branching. And how auxins and strigolactones contribute to regulating this process also. The results obtained by others and our working group with lemongrass (Cymbopogon citratus) show that cytokinins affect both shoot and root apical meristem development, consistent with other plant species. However, many questions remain about how cytokinins and strigolactones antagonistically regulate BRC1 gene expression. Additionally, many details of the interaction among cytokinins, auxins, and strigolactones need to be clarified. We will gain a more comprehensive scheme of bud outgrowth with these details.
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Affiliation(s)
| | - Yohanna Sarria-Guzmán
- Facultad de Ingeniería y Ciencias Básicas, Fundación Universitaria del Área Andina, Transv 22 Bis #4-105, Valledupar 200005, Cesar, Colombia
| | - Agustino Martínez-Antonio
- Biological Engineering Laboratory, Cinvestav Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Gto, México.
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7
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Djeghdir I, Chefdor F, Bertheau L, Koudounas K, Carqueijeiro I, Lemos Cruz P, Courdavault V, Depierreux C, Larcher M, Lamblin F, Héricourt F, Glévarec G, Oudin A, Carpin S. Evaluation of type-B RR dimerization in poplar: A mechanism to preserve signaling specificity? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111068. [PMID: 34763861 DOI: 10.1016/j.plantsci.2021.111068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Plants possess specific signaling pathways, such as the MultiStep Phosphorelay (MSP), which is involved in cytokinin and ethylene sensing, and light, drought or osmotic stress sensing. These MSP comprise histidine-aspartate kinases (HKs) as receptors, histidine phosphotransfer (HPts) proteins acting as phosphorelay proteins, and response regulators (RRs), some of which act as transcription factors (type-B RRs). In previous studies, we identified partners of the poplar osmosensing signaling pathway, composed of two HKs, three main HPts, and six type-B RRs. To date, it is unresolved as to how cytokinin or osmotic stress signal specificity is achieved in the MSP in order to generate specific responses. Here, we present a large-scale interaction study of poplar type-B RR dimerization. Using the two-hybrid assay, we were able to show the homodimerization of type-B RRs, the heterodimerization of duplicated type-B RRs, and surprisingly, a lack of interaction between some type-B RRs belonging to different duplicates. The lack of interaction of the duplicates RR12-14 and RR18-19, which are involved in the osmosensing pathway has been confirmed by BiFC experiments. This study reveals, for the first time, an overview of type-B RR dimerization in poplar and makes way for the hypothesis that signal specificity for cytokinin or osmotic stress could be in part due to the fact that it is impossible for specific type-B RRs to heterodimerize.
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Affiliation(s)
- I Djeghdir
- LBLGC, Université d'Orléans, INRAE, USC1328, 45067, Orléans, Cedex 2, France
| | - F Chefdor
- LBLGC, Université d'Orléans, INRAE, USC1328, 45067, Orléans, Cedex 2, France
| | - L Bertheau
- LBLGC, Université d'Orléans, INRAE, USC1328, 45067, Orléans, Cedex 2, France
| | - K Koudounas
- Biomolécules et Biotechnologies Végétales (BBV), EA 2106, Université de Tours, 31 Avenue Monge, 37200, Tours, France
| | - I Carqueijeiro
- Biomolécules et Biotechnologies Végétales (BBV), EA 2106, Université de Tours, 31 Avenue Monge, 37200, Tours, France
| | - P Lemos Cruz
- Biomolécules et Biotechnologies Végétales (BBV), EA 2106, Université de Tours, 31 Avenue Monge, 37200, Tours, France
| | - V Courdavault
- Biomolécules et Biotechnologies Végétales (BBV), EA 2106, Université de Tours, 31 Avenue Monge, 37200, Tours, France
| | - C Depierreux
- LBLGC, Université d'Orléans, INRAE, USC1328, 45067, Orléans, Cedex 2, France
| | - M Larcher
- LBLGC, Université d'Orléans, INRAE, USC1328, 45067, Orléans, Cedex 2, France
| | - F Lamblin
- LBLGC, Université d'Orléans, INRAE, USC1328, 45067, Orléans, Cedex 2, France
| | - F Héricourt
- LBLGC, Université d'Orléans, INRAE, USC1328, 45067, Orléans, Cedex 2, France
| | - G Glévarec
- Biomolécules et Biotechnologies Végétales (BBV), EA 2106, Université de Tours, 31 Avenue Monge, 37200, Tours, France
| | - A Oudin
- Biomolécules et Biotechnologies Végétales (BBV), EA 2106, Université de Tours, 31 Avenue Monge, 37200, Tours, France
| | - S Carpin
- LBLGC, Université d'Orléans, INRAE, USC1328, 45067, Orléans, Cedex 2, France.
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8
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Anami S, Yamashino T, Suzuki R, Nakai K, Sato K, Wu B, Ryo M, Sugita M, Aoki S. Red light-regulated interaction of Per-Arnt-Sim histidine kinases with partner histidine-containing phosphotransfer proteins in Physcomitrium patens. Genes Cells 2021; 26:698-713. [PMID: 34086383 DOI: 10.1111/gtc.12878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022]
Abstract
Multi-step phosphorelay (MSP) is a broadly distributed signaling system in organisms. In MSP, histidine kinases (HKs) receive various environmental signals and transmit them by autophosphorylation followed by phosphotransfer to partner histidine-containing phosphotransfer proteins (HPts). Previously, we reported that Per-Arnt-Sim (PAS) domain-containing HK1 (PHK1) and PHK2 of the moss Physcomitrium (Physcomitrella) patens repressed red light-induced protonema branching, a critical step in the moss life cycle. In plants, PHK homolog-encoding genes are conserved only in early-diverging lineages such as bryophytes and lycophytes. PHKs-mediated signaling machineries attract attention especially from an evolutionary viewpoint, but they remain uninvestigated. Here, we studied the P. patens PHKs focusing on their subcellular patterns of localization and interaction with HPts. Yeast two-hybrid analysis, a localization assay with a green fluorescent protein, and a bimolecular fluorescence complementation analysis together showed that PHKs are localized and interact with partner HPts mostly in the nucleus, as unprecedented features for plant HKs. Additionally, red light triggered the interactions between PHKs and HPts in the cytoplasm, and light co-repressed the expression of PHK1 and PHK2 as well as genes encoding their partner HPts. Our results emphasize the uniqueness of PHKs-mediated signaling machineries, and functional implications of this uniqueness are discussed.
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Affiliation(s)
- Shu Anami
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | | | - Ryo Suzuki
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Kota Nakai
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Kensuke Sato
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Bowen Wu
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Masashi Ryo
- Graduate School of Information Science, Nagoya University, Nagoya, Japan
| | - Mamoru Sugita
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Setsuyuki Aoki
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
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9
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Lomin SN, Myakushina YA, Kolachevskaya OO, Getman IA, Savelieva EM, Arkhipov DV, Deigraf SV, Romanov GA. Global View on the Cytokinin Regulatory System in Potato. FRONTIERS IN PLANT SCIENCE 2020; 11:613624. [PMID: 33408733 PMCID: PMC7779595 DOI: 10.3389/fpls.2020.613624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
Cytokinins (CKs) were earlier shown to promote potato tuberization. Our study aimed to identify and characterize CK-related genes which constitute CK regulatory system in the core potato (Solanum tuberosum) genome. For that, CK-related genes were retrieved from the sequenced genome of the S. tuberosum doubled monoploid (DM) Phureja group, classified and compared with Arabidopsis orthologs. Analysis of selected gene expression was performed with a transcriptome database for the S. tuberosum heterozygous diploid line RH89-039-16. Genes responsible for CK signaling, biosynthesis, transport, and metabolism were categorized in an organ-specific fashion. According to this database, CK receptors StHK2/3 predominate in leaves and flowers, StHK4 in roots. Among phosphotransmitters, StHP1a expression largely predominates. Surprisingly, two pseudo-phosphotransmitters intended to suppress CK effects are hardly expressed in studied organs. Among B-type RR genes, StRR1b, StRR11, and StRR18a are actively expressed, with StRR1b expressing most uniformly in all organs and StRR11 exhibiting the highest expression in roots. By cluster analysis four types of prevailing CK-signaling chains were identified in (1) leaves and flowers, StHK2/3→S t H P1a→StRR1b/+; (2) shoot apical meristems, stolons, and mature tubers, StHK2/4→S t H P1a→StRR1b/+; (3) stems and young tubers, StHK2/4→S t H P1a→StRR1b/11/18a; and (4) roots and tuber sprouts, StHK4→S t H P1a→StRR11/18a. CK synthesis genes StIPT3/5 and StCYP735A are expressed mainly in roots followed by tuber sprouts, but rather weakly in stolons and tubers. By contrast, CK-activation genes StLOGs are active in stolons, and StLOG3b expression is even stolon-confined. Apparently, the main CK effects on tuber initiation are realized via activity of StLOG1/3a/3b/7c/8a genes in stolons. Current advances and future directions in potato research are discussed.
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10
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Oshchepkov MS, Kalistratova AV, Savelieva EM, Romanov GA, Bystrova NA, Kochetkov KA. Natural and synthetic cytokinins and their applications in biotechnology, agrochemistry and medicine. RUSSIAN CHEMICAL REVIEWS 2020. [DOI: 10.1070/rcr4921] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review is devoted to cytokinins — classical plant hormones known for more than six decades. Nevertheless, different aspects of the action of cytokinins are still being investigated. Relevant studies produced interesting, often unexpected, results, which cast doubt on the old paradigms and open new prospects for the use of these phytohormones. Particular attention is given to recent advances in the applications of natural cytokinins and their synthetic analogues in biotechnology, agriculture, medicine and cosmetics. The chemical synthesis, properties and the possible use of artificial cytokinins are considered in detail. The review is aimed at researchers interested in the development and applications of new biologically active compounds with a wide spectrum of action on diverse biological objects, from plants to humans.
The bibliography includes 233 references.
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11
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New Insights into Multistep-Phosphorelay (MSP)/ Two-Component System (TCS) Regulation: Are Plants and Bacteria that Different? PLANTS 2019; 8:plants8120590. [PMID: 31835810 PMCID: PMC6963811 DOI: 10.3390/plants8120590] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/27/2019] [Accepted: 12/07/2019] [Indexed: 12/12/2022]
Abstract
The Arabidopsis multistep-phosphorelay (MSP) is a signaling mechanism based on a phosphorelay that involves three different types of proteins: Histidine kinases, phosphotransfer proteins, and response regulators. Its bacterial equivalent, the two-component system (TCS), is the most predominant device for signal transduction in prokaryotes. The TCS has been extensively studied and is thus generally well-understood. In contrast, the MSP in plants was first described in 1993. Although great advances have been made, MSP is far from being completely comprehended. Focusing on the model organism Arabidopsis thaliana, this review summarized recent studies that have revealed many similarities with bacterial TCSs regarding how TCS/MSP signaling is regulated by protein phosphorylation and dephosphorylation, protein degradation, and dimerization. Thus, comparison with better-understood bacterial systems might be relevant for an improved study of the Arabidopsis MSP.
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12
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Héricourt F, Larcher M, Chefdor F, Koudounas K, Carqueijeiro I, Lemos Cruz P, Courdavault V, Tanigawa M, Maeda T, Depierreux C, Lamblin F, Glévarec G, Carpin S. New Insight into HPts as Hubs in Poplar Cytokinin and Osmosensing Multistep Phosphorelays: Cytokinin Pathway Uses Specific HPts. PLANTS 2019; 8:plants8120591. [PMID: 31835814 PMCID: PMC6963366 DOI: 10.3390/plants8120591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 02/02/2023]
Abstract
We have previously identified proteins in poplar which belong to an osmosensing (OS) signaling pathway, called a multistep phosphorelay (MSP). The MSP comprises histidine-aspartate kinases (HK), which act as membrane receptors; histidine phosphotransfer (HPt) proteins, which act as phosphorelay proteins; and response regulators (RR), some of which act as transcription factors. In this study, we identified the HK proteins homologous to the Arabidopsis cytokinin (CK) receptors, which are first partners in the poplar cytokinin MSP, and focused on specificity of these two MSPs (CK and OS), which seem to share the same pool of HPt proteins. Firstly, we isolated five CK HKs from poplar which are homologous to Arabidopsis AHK2, AHK3, and AHK4, namely, HK2, HK3a, HK3b, HK4a, HK4b. These HKs were shown to be functional kinases, as observed in a functional complementation of a yeast HK deleted strain. Moreover, one of these HKs, HK4a, was shown to have kinase activity dependent on the presence of CK. Exhaustive interaction tests between these five CK HKs and the 10 HPts characterized in poplar were performed using two-hybrid and BiFC experiments. The resulting partnership was compared to that previously identified between putative osmosensors HK1a/1b and HPt proteins. Finally, in planta coexpression analysis of genes encoding these potential partners revealed that almost all HPts are coexpressed with CK HKs in four different poplar organs. Overall, these results allowed us to unravel the common and specific partnerships existing between OS and CK MSP in Populus.
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Affiliation(s)
- François Héricourt
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Mélanie Larcher
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Françoise Chefdor
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Konstantinos Koudounas
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Inês Carqueijeiro
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Pamela Lemos Cruz
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Vincent Courdavault
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Mirai Tanigawa
- Department of Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (M.T.); (T.M.)
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (M.T.); (T.M.)
| | - Christiane Depierreux
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Frédéric Lamblin
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Gaëlle Glévarec
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Sabine Carpin
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
- Correspondence: ; Tel.: +33-2-3849-4804
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Zdarska M, Cuyacot AR, Tarr PT, Yamoune A, Szmitkowska A, Hrdinová V, Gelová Z, Meyerowitz EM, Hejátko J. ETR1 Integrates Response to Ethylene and Cytokinins into a Single Multistep Phosphorelay Pathway to Control Root Growth. MOLECULAR PLANT 2019; 12:1338-1352. [PMID: 31176773 PMCID: PMC8040967 DOI: 10.1016/j.molp.2019.05.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 04/17/2019] [Accepted: 05/28/2019] [Indexed: 05/18/2023]
Abstract
Cytokinins and ethylene control plant development via sensors from the histidine kinase (HK) family. However, downstream signaling pathways for the key phytohormones are distinct. Here we report that not only cytokinin but also ethylene is able to control root apical meristem (RAM) size through activation of the multistep phosphorelay (MSP) pathway. We found that both cytokinin and ethylene-dependent RAM shortening requires ethylene binding to ETR1 and the HK activity of ETR1. The receiver domain of ETR1 interacts with MSP signaling intermediates acting downstream of cytokinin receptors, further substantiating the role of ETR1 in MSP signaling. We revealed that both cytokinin and ethylene induce the MSP in similar and distinct cell types with ETR1-mediated ethylene signaling controlling MSP output specifically in the root transition zone. We identified members of the MSP pathway specific and common to both hormones and showed that ETR1-regulated ARR3 controls RAM size. ETR1-mediated MSP spatially differs from canonical CTR1/EIN2/EIN3 ethylene signaling and is independent of EIN2, indicating that both pathways can be spatially and functionally separated. Furthermore, we demonstrated that canonical ethylene signaling controls MSP responsiveness to cytokinin specifically in the root transition zone, presumably via regulation of ARR10, one of the positive regulators of MSP signaling in Arabidopsis.
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Affiliation(s)
- Marketa Zdarska
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CETEC-MU, Kamenice 5/A2, 625 00 Brno, Czech Republic; Division of Biology and Biological Engineering 156-29, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
| | - Abigail Rubiato Cuyacot
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CETEC-MU, Kamenice 5/A2, 625 00 Brno, Czech Republic
| | - Paul T Tarr
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering 156-29, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Amel Yamoune
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CETEC-MU, Kamenice 5/A2, 625 00 Brno, Czech Republic
| | - Agnieszka Szmitkowska
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CETEC-MU, Kamenice 5/A2, 625 00 Brno, Czech Republic
| | - Vendula Hrdinová
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CETEC-MU, Kamenice 5/A2, 625 00 Brno, Czech Republic
| | - Zuzana Gelová
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CETEC-MU, Kamenice 5/A2, 625 00 Brno, Czech Republic
| | - Elliot M Meyerowitz
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering 156-29, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jan Hejátko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CETEC-MU, Kamenice 5/A2, 625 00 Brno, Czech Republic.
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Arkhipov DV, Lomin SN, Myakushina YA, Savelieva EM, Osolodkin DI, Romanov GA. Modeling of Protein⁻Protein Interactions in Cytokinin Signal Transduction. Int J Mol Sci 2019; 20:E2096. [PMID: 31035389 PMCID: PMC6539988 DOI: 10.3390/ijms20092096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 01/20/2023] Open
Abstract
The signaling of cytokinins (CKs), classical plant hormones, is based on the interaction of proteins that constitute the multistep phosphorelay system (MSP): catalytic receptors-sensor histidine kinases (HKs), phosphotransmitters (HPts), and transcription factors-response regulators (RRs). Any CK receptor was shown to interact in vivo with any of the studied HPts and vice versa. In addition, both of these proteins tend to form a homodimer or a heterodimeric complex with protein-paralog. Our study was aimed at explaining by molecular modeling the observed features of in planta protein-protein interactions, accompanying CK signaling. For this purpose, models of CK-signaling proteins' structure from Arabidopsis and potato were built. The modeled interaction interfaces were formed by rather conserved areas of protein surfaces, complementary in hydrophobicity and electrostatic potential. Hot spots amino acids, determining specificity and strength of the interaction, were identified. Virtual phosphorylation of conserved Asp or His residues affected this complementation, increasing (Asp-P in HK) or decreasing (His-P in HPt) the affinity of interacting proteins. The HK-HPt and HPt-HPt interfaces overlapped, sharing some of the hot spots. MSP proteins from Arabidopsis and potato exhibited similar properties. The structural features of the modeled protein complexes were consistent with the experimental data.
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Affiliation(s)
- Dmitry V Arkhipov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia.
| | - Sergey N Lomin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia.
| | - Yulia A Myakushina
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia.
| | - Ekaterina M Savelieva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia.
| | - Dmitry I Osolodkin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia.
- FSBSI "Chumakov FSC R&D IBP RAS", Poselok Instituta Poliomelita 8 bd. 1, Poselenie Moskovsky, 108819 Moscow, Russia.
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Trubetskaya ul. 8, 119991 Moscow, Russia.
| | - Georgy A Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia.
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15
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Wallmeroth N, Jeschke D, Slane D, Nägele J, Veerabagu M, Mira-Rodado V, Berendzen KW. ARR22 overexpression can suppress plant Two-Component Regulatory Systems. PLoS One 2019; 14:e0212056. [PMID: 30742656 PMCID: PMC6370222 DOI: 10.1371/journal.pone.0212056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/26/2019] [Indexed: 12/13/2022] Open
Abstract
In plants, several developmental processes are co-coordinated by cytokinins via phosphorylation dependent processes of the Two-Component System (TCS). An outstanding challenge is to track phosphorelay flow from cytokinin perception to its molecular outputs, of which gene activation plays a major role. To address this issue, a kinetic-based reporter system was expounded to track TCS phosphorelay activity in vivo that can distinguish between basal and cytokinin dependent effects of overexpressed TCS members. The TCS phosphorelay can be positively activated by cytokinin and inhibited by pharmaceuticals or naturally interfering components. In this case we took advantage of the phosphohistidine-phosphatase Arabidopsis Response Regulator (ARR) 22 and investigated its phosphocompetition with other TCS members in regulating promoters of ARR5 and WUS in Arabidopsis thaliana cell culture protoplasts. In congruency with the proposed function of ARR22, overexpression of ARR22 blocked the activation of all B-type ARRs in this study in a TCS dependent manner. Furthermore, this effect could not be mimicked by A-type response regulator overexpression or compensated by AHP overexpression. Compared to other reporter assays, ours mimicked effects previously observed only in transgenic plants for all of the TCS proteins studied, suggesting that it is possible to expose phosphocompetition. Thus, our approach can be used to investigate gene signaling networks involving the TCS by leveraging ARR22 as a TCS inhibitor along with B-type ARR overexpression.
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Affiliation(s)
- Niklas Wallmeroth
- Department of Plant Physiology at the Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Daniel Jeschke
- Department of Plant Physiology at the Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Daniel Slane
- Max-Planck Institute for Developmental Biology, Tübingen, Germany
| | - Janine Nägele
- Department of Plant Physiology at the Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Manikandan Veerabagu
- Department of Plant Physiology at the Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Virtudes Mira-Rodado
- Department of Plant Physiology at the Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Kenneth Wayne Berendzen
- Department of Plant Physiology at the Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- Department of the Central Facilities at Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- * E-mail:
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16
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Ryo M, Yamashino T, Nomoto Y, Goto Y, Ichinose M, Sato K, Sugita M, Aoki S. Light-regulated PAS-containing histidine kinases delay gametophore formation in the moss Physcomitrella patens. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4839-4851. [PMID: 29992239 PMCID: PMC6137987 DOI: 10.1093/jxb/ery257] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 07/04/2018] [Indexed: 05/07/2023]
Abstract
Two-component systems (TCSs) are signal transduction mechanisms for responding to various environmental stimuli. In angiosperms, TCSs involved in phytohormone signaling have been intensively studied, whereas there are only a few reports on TCSs in basal land plants. The moss Physcomitrella patens possesses several histidine kinases (HKs) that are lacking in seed plant genomes. Here, we studied two of these unique HKs, PAS-histidine kinase 1 (PHK1) and its paralog PHK2, both of which have PAS (Per-Arnt-Sim) domains, which are known to show versatile functions such as sensing light or molecular oxygen. We found homologs of PHK1 and PHK2 only in early diverged clades such as bryophytes and lycophytes, but not in seed plants. The PAS sequences of PHK1 and PHK2 are more similar to a subset of bacterial PAS sequences than to any angiosperm PAS sequences. Gene disruption lines that lack either PHK1 or PHK2 or both formed gametophores earlier than the wild-type, and consistently, more caulonema side branches were induced in response to light in the disruption lines. Therefore, PHK1 and PHK2 delay the timing of gametophore development, probably by suppressing light-induced caulonema branching. This study provides new insights into the evolution of TCSs in plants.
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Affiliation(s)
- Masashi Ryo
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Takafumi Yamashino
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Correspondence: or
| | - Yuji Nomoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Yuki Goto
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Mizuho Ichinose
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Kensuke Sato
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Setsuyuki Aoki
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Correspondence: or
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Ryo M, Yamashino T, Yamakawa H, Fujita Y, Aoki S. PAS-histidine kinases PHK1 and PHK2 exert oxygen-dependent dual and opposite effects on gametophore formation in the moss Physcomitrella patens. Biochem Biophys Res Commun 2018; 503:2861-2865. [DOI: 10.1016/j.bbrc.2018.08.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 10/28/2022]
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18
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Lomin SN, Myakushina YA, Kolachevskaya OO, Getman IA, Arkhipov DV, Savelieva EM, Osolodkin DI, Romanov GA. Cytokinin perception in potato: new features of canonical players. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3839-3853. [PMID: 29800344 PMCID: PMC6054150 DOI: 10.1093/jxb/ery199] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/15/2018] [Indexed: 05/11/2023]
Abstract
Potato is the most economically important non-cereal food crop. Tuber formation in potato is regulated by phytohormones, cytokinins (CKs) in particular. The present work studied CK signal perception in potato. The sequenced potato genome of doubled monoploid Phureja was used for bioinformatic analysis and as a tool for identification of putative CK receptors from autotetraploid potato cv. Désirée. All basic elements of multistep phosphorelay required for CK signal transduction were identified in the Phureja genome, including three genes orthologous to three CK receptor genes (AHK 2-4) of Arabidopsis. As distinct from Phureja, autotetraploid potato contains at least two allelic isoforms of each receptor type. Putative receptor genes from Désirée plants were cloned, sequenced and expressed, and the main characteristics of encoded proteins were determined, in particular their consensus motifs, modelled structure, ligand-binding properties, and ability to transmit CK signals. In all studied aspects the predicted sensor histidine kinases met the requirements for genuine CK receptors. Expression of potato CK receptors was found to be organ-specific and sensitive to growth conditions, particularly to sucrose content. Our results provide a solid basis for further in-depth study of CK signaling system and biotechnological improvement of potato.
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Affiliation(s)
- Sergey N Lomin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Yulia A Myakushina
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | | | - Irina A Getman
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Arkhipov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina M Savelieva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry I Osolodkin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
- Institute of Poliomyelitis and Viral Encephalitides, FSBSI Chumakov FSC R&D IBP RAS, Poselok Instituta Poliomelita 8 bd 1, Poselenie Moskovsky, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Georgy A Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, Russia
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Liu G, Liu J, Zhang C, You X, Zhao T, Jiang J, Chen X, Zhang H, Yang H, Zhang D, Du C, Li J, Xu X. Physiological and RNA-seq analyses provide insights into the response mechanism of the Cf-10-mediated resistance to Cladosporium fulvum infection in tomato. PLANT MOLECULAR BIOLOGY 2018; 96:403-416. [PMID: 29383477 DOI: 10.1007/s11103-018-0706-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/20/2018] [Indexed: 05/22/2023]
Abstract
Based on the physiological and RNA-seq analysis, some progress has been made in elucidating the Cf-10-mediated resistance responses to C. fulvum infection in tomato. GO and KEGG enrichment analysis revealed that the DEGs were significantly associated with defense-signaling pathways like oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Leaf mold, caused by the fungus Cladosporium fulvum, is one of the most common diseases affecting tomatoes worldwide. Cf series genes including Cf-2, Cf-4, Cf-5, Cf-9 and Cf-10 play very important roles in resisting tomato leaf mold. Understanding the molecular mechanism of Cf gene-mediated resistance is thus the key to facilitating genetic engineering of resistance to C. fulvum infection. Progress has been made in elucidating two Cf genes, Cf -19 and Cf -12, and how they mediate resistance responses to C. fulvum infection in tomato. However, the mechanism of the Cf-10- mediated resistance response is still unclear. In the present study, RNA-seq was used to analyze changes in the transcriptome at different stages of C. fulvum infection. A total of 2,242 differentially expressed genes (DEGs) responsive to C. fulvum between 0 and 16 days post infection (dpi) were identified, including 1,501 upregulated and 741 downregulated genes. The majority of DEGs were associated with defense-signaling pathways including oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Four DEGs associated with plant-pathogen interaction were uniquely activated in Cf-10 tomato and validated by qRT-PCR. In addition, physiological indicators including reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were measured at 0-21 dpi, and hormone expression [Jasmonic acid (JA) and salicylic acid (SA)] was estimated at 0 and 16 dpi to elucidate the mechanism of the Cf-10-mediated resistance response. C. fulvum infection induced the activities of POD, CAT and SOD, and decreased ROS levels. JA was determined to participate in the resistance response to C. fulvum during the initial infection period. The results of this study provide accountable evidence for the physiological and transcriptional regulation of the Cf-10-mediated resistance response to C. fulvum infection, facilitating further understanding of the molecular mechanism of Cf-10-mediated resistance to C. fulvum infection.
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Affiliation(s)
- Guan Liu
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Junfang Liu
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Chunli Zhang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaoqing You
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Tingting Zhao
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Xiuling Chen
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - He Zhang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Huanhuan Yang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Dongye Zhang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Chong Du
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Jingfu Li
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China.
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Otrusinová O, Demo G, Padrta P, Jaseňáková Z, Pekárová B, Gelová Z, Szmitkowska A, Kadeřávek P, Jansen S, Zachrdla M, Klumpler T, Marek J, Hritz J, Janda L, Iwaï H, Wimmerová M, Hejátko J, Žídek L. Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana. J Biol Chem 2017; 292:17525-17540. [PMID: 28860196 DOI: 10.1074/jbc.m117.790212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/28/2017] [Indexed: 11/06/2022] Open
Abstract
Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1RD) from Arabidopsis thaliana We observed that the crystal structures of free, Mg2+-bound, and beryllofluoridated CKI1RD (a stable analogue of the labile phosphorylated form) were identical and similar to the active state of receiver domains of bacterial response regulators. However, the three CKI1RD variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg2+ binding and beryllofluoridation alter the conformational equilibrium of the β3-α3 loop close to the phosphorylation site. Mutations that perturbed the conformational behavior of the β3-α3 loop while keeping the active-site aspartate intact resulted in suppression of CKI1 function. Mechanistically, homology modeling indicated that the β3-α3 loop directly interacts with the ATP-binding site of the CKI1 histidine kinase domain. The functional relevance of the conformational dynamics observed in the β3-α3 loop of CKI1RD was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic β3-α3 loop of CKI1RD, the corresponding loop of the ETR1 receiver domain (ETR1RD) exhibited little conformational exchange and adopted a different orientation in crystals. Biochemical data indicated that ETR1RD is involved in phosphorylation-independent signaling, implying a direct link between conformational behavior and the ability of eukaryotic receiver domains to participate in MSP.
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Affiliation(s)
- Olga Otrusinová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Gabriel Demo
- From the Central European Institute of Technology and
| | - Petr Padrta
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Jaseňáková
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Blanka Pekárová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Gelová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Agnieszka Szmitkowska
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Pavel Kadeřávek
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Séverine Jansen
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Milan Zachrdla
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | | | - Jaromír Marek
- From the Central European Institute of Technology and
| | - Jozef Hritz
- From the Central European Institute of Technology and
| | - Lubomír Janda
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Hideo Iwaï
- the Institute of Biotechnology, University of Helsinki, Viikinkaari 1 (P. O. Box 65), 00014 Helsinki, Finland
| | - Michaela Wimmerová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Jan Hejátko
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Lukáš Žídek
- From the Central European Institute of Technology and .,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
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Kushwah S, Laxmi A. The interaction between glucose and cytokinin signaling in controlling Arabidopsis thaliana seedling root growth and development. PLANT SIGNALING & BEHAVIOR 2017; 12:e1312241. [PMID: 28467152 PMCID: PMC5501229 DOI: 10.1080/15592324.2017.1312241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Cytokinin (CK) and glucose (GLC) control several common responses in plants. There is an extensive overlap between CK and GLC signal transduction pathways in Arabidopsis. Physiologically, both GLC and CK could regulate root length in light. CK interacts with GLC via HXK1 dependent pathway for root length control. Wild-type (WT) roots cannot elongate in the GLC free medium while CK-receptor mutant ARABIDOPSIS HISTIDINE KINASE4 (ahk4) and type B ARR triple mutant ARABIDOPSIS RESPONSE REGULATOR1, 10,11 (arr1, 10,11) roots could elongate even in the absence of GLC as compared with the WT. The root hair initiation was also found defective in CK signaling mutants ahk4, arr1,10,11 and arr3,4,5,6,8,9 on increasing GLC concentration (up to 3%); and lesser number of root hairs were visible even at 5% GLC as compared with the WT. Out of 941 BAP regulated genes, 103 (11%) genes were involved in root growth and development. Out of these 103 genes, 60 (58%) genes were also regulated by GLC. GLC could regulate 5736 genes, which include 327 (6%) genes involved in root growth and development. Out of these 327 genes, 60 (18%) genes were also regulated by BAP. Both GLC and CK signaling cannot alter root length in light in auxin signaling mutant AUXIN RESPONSE3/INDOLE-3-ACETIC ACID17 (axr3/iaa17) suggesting that they may involve auxin signaling component as a nodal point. Therefore CK- and GLC- signaling are involved in controlling different aspects of root growth and development such as root length, with auxin signaling components working as downstream target.
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Affiliation(s)
- Sunita Kushwah
- National Institute of Plant Genome Research, New Delhi, India
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, New Delhi, India
- CONTACT Ashverya Laxmi National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi-110067, India
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Functional Divergence of Poplar Histidine-Aspartate Kinase HK1 Paralogs in Response to Osmotic Stress. Int J Mol Sci 2016; 17:ijms17122061. [PMID: 27941652 PMCID: PMC5187861 DOI: 10.3390/ijms17122061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/01/2016] [Accepted: 12/03/2016] [Indexed: 11/29/2022] Open
Abstract
Previous works have shown the existence of protein partnerships belonging to a MultiStep Phosphorelay (MSP) in Populus putatively involved in osmosensing. This study is focused on the identification of a histidine-aspartate kinase, HK1b, paralog of HK1a. The characterization of HK1b showed its ability to homo- and hetero-dimerize and to interact with a few Histidine-containing Phosphotransfer (HPt) proteins, suggesting a preferential partnership in poplar MSP linked to drought perception. Furthermore, determinants for interaction specificity between HK1a/1b and HPts were studied by mutagenesis analysis, identifying amino acids involved in this specificity. The HK1b expression analysis in different poplar organs revealed its co-expression with three HPts, reinforcing the hypothesis of partnership participation in the MSP in planta. Moreover, HK1b was shown to act as an osmosensor with kinase activity in a functional complementation assay of an osmosensor deficient yeast strain. These results revealed that HK1b showed a different behaviour for canonical phosphorylation of histidine and aspartate residues. These phosphorylation modularities of canonical amino acids could explain the improved osmosensor performances observed in yeast. As conserved duplicates reflect the selective pressures imposed by the environmental requirements on the species, our results emphasize the importance of HK1 gene duplication in poplar adaptation to drought stress.
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