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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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Maki T, Kusaka H, Matsumoto Y, Yamazaki A, Yamaoka S, Ohno S, Doi M, Tanaka Y. The mutation of CaCKI1 causes seedless fruits in chili pepper (Capsicum annuum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:85. [PMID: 36964815 DOI: 10.1007/s00122-023-04342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
The seedless mutant tn-1 in chili pepper is caused by a mutation in CaCKI1 (CA12g21620), which encodes histidine kinase involving female gametophyte development. An amino acid insertion in the receiver domain of CaCKI1 may be the mutation responsible for tn-1. Seedlessness is a desirable trait in fruit crops because the removal of seeds is a troublesome step for consumers and processing industries. However, little knowledge is available to develop seedless chili peppers. In a previous study, a chili pepper mutant tn-1, which stably produces seedless fruits, was isolated. In this study, we report characterization of tn-1 and identification of the causative gene. Although pollen germination was normal, confocal laser microscopy observations revealed deficiency in embryo sac development in tn-1. By marker analysis, the tn-1 locus was narrowed down to a 313 kb region on chromosome 12. Further analysis combined with mapping-by-sequencing identified CA12g21620, which encodes histidine kinase as a candidate gene. Phylogenetic analysis revealed CA12g21620 was the homolog of Arabidopsis CKI1 (Cytokinin Independent 1), which plays an important role in female gametophyte development, and CA12g21620 was designated as CaCKI1. Sequence analysis revealed that tn-1 has a 3-bp insertion in the 6th exon resulting in one lysine (K) residue insertion in receiver domain of CaCKI1, and the sequence nearby the insertion is widely conserved among CKI1 orthologs in various plants. This suggested that one K residue insertion may reduce the phosphorylation relay downstream of CaCKI1 and impair normal development of female gametophyte, resulting in seedless fruits production in tn-1. Furthermore, we demonstrated that virus-induced gene silencing of CaCKI1 reduced normally developed female gametophyte in chili pepper. This study describes the significant role of CaCKI1 in seed development in chili pepper and the possibility of developing seedless cultivars using its mutation.
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Affiliation(s)
- Takahiro Maki
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Hirokazu Kusaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yuki Matsumoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Akira Yamazaki
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
- Faculty of Agriculture, Kindai University, Naka Machi, Nara, 631-8505, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Sho Ohno
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Motoaki Doi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan.
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4
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Dutt M, Mahmoud LM, Nehela Y, Grosser JW, Killiny N. The Citrus sinensis TILLER ANGLE CONTROL 1 (CsTAC1) gene regulates tree architecture in sweet oranges by modulating the endogenous hormone content. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111401. [PMID: 35905898 DOI: 10.1016/j.plantsci.2022.111401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Citrus is a major fruit crop cultivated on a global scale. Citrus trees are long lived perennials with a large canopy. Understanding the genetic control of tree architecture could provide tools for breeding and selection of citrus cultivars suitable for high density planting with improved light exposure. Tree architecture is modulated by the TILLER ANGLE CONTROL 1 (TAC1) gene which plays an important role in the regulation of the shoot angle. Herein, we used CRISPR/Cas9 technology to knockout the CsTAC1 gene for the biochemical and molecular analysis of its function. Nine transgenic lines were obtained, and five edited plants were confirmed based on T7EI mismatch detection assay and Sanger sequencing. The transgenic citrus lines exhibited pleiotropic phenotypes, including differences in branch angle and stem growth. Additionally, silencing CsTAC1 led to enhanced CsLAZY1 transcript levels in the tested lines. Analysis of the phytohormonal profile revealed that TAC1-edited plants exhibited lower auxin contents and increased cytokinin levels in the leaves compared to the wild-type plants. The GA7 gibberellin level was enhanced in most of the edited lines. Collectively, TAC1 affects branch angle in association with hormone signals in citrus.
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Affiliation(s)
- Manjul Dutt
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA.
| | - Lamiaa M Mahmoud
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA; Pomology Department, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt
| | - Yasser Nehela
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA; Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31512, Egypt
| | - Jude W Grosser
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA
| | - Nabil Killiny
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA
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5
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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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6
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Tran LH, Urbanowicz A, Jasiński M, Jaskolski M, Ruszkowski M. 3D Domain Swapping Dimerization of the Receiver Domain of Cytokinin Receptor CRE1 From Arabidopsis thaliana and Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:756341. [PMID: 34630499 PMCID: PMC8498639 DOI: 10.3389/fpls.2021.756341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Cytokinins are phytohormones regulating many biological processes that are vital to plants. CYTOKININ RESPONSE1 (CRE1), the main cytokinin receptor, has a modular architecture composed of a cytokinin-binding CHASE (Cyclases/Histidine kinases Associated Sensory Extracellular) domain, followed by a transmembrane fragment, an intracellular histidine kinase (HK) domain, and a receiver domain (REC). Perception of cytokinin signaling involves (i) a hormone molecule binding to the CHASE domain, (ii) CRE1 autophosphorylation at a conserved His residue in the HK domain, followed by a phosphorelay to (iii) a conserved Asp residue in the REC domain, (iv) a histidine-containing phosphotransfer protein (HPt), and (v) a response regulator (RR). This work focuses on the crystal structures of the REC domain of CRE1 from the model plant Arabidopsis thaliana and from the model legume Medicago truncatula. Both REC domains form tight 3D-domain-swapped dimers. Dimerization of the REC domain agrees with the quaternary assembly of the entire CRE1 but is incompatible with a model of its complex with HPt, suggesting that a considerable conformational change should occur to enable the signal transduction. Indeed, phosphorylation of the REC domain can change the HPt-binding properties of CRE1, as shown by functional studies.
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Affiliation(s)
- Linh H. Tran
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Michał Jasiński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Poznań, Poland
| | - Mariusz Jaskolski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznań, Poland
| | - Milosz Ruszkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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7
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Hoang XLT, Prerostova S, Thu NBA, Thao NP, Vankova R, Tran LSP. Histidine Kinases: Diverse Functions in Plant Development and Responses to Environmental Conditions. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:297-323. [PMID: 34143645 DOI: 10.1146/annurev-arplant-080720-093057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The two-component system (TCS), which is one of the most evolutionarily conserved signaling pathway systems, has been known to regulate multiple biological activities and environmental responses in plants. Significant progress has been made in characterizing the biological functions of the TCS components, including signal receptor histidine kinase (HK) proteins, signal transducer histidine-containing phosphotransfer proteins, and effector response regulator proteins. In this review, our scope is focused on the diverse structure, subcellular localization, and interactions of the HK proteins, as well as their signaling functions during development and environmental responses across different plant species. Based on data collected from scientific studies, knowledge about acting mechanisms and regulatory roles of HK proteins is presented. This comprehensive summary ofthe HK-related network provides a panorama of sophisticated modulating activities of HK members and gaps in understanding these activities, as well as the basis for developing biotechnological strategies to enhance the quality of crop plants.
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Affiliation(s)
- Xuan Lan Thi Hoang
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; , ,
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Sylva Prerostova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
| | - Nguyen Binh Anh Thu
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; , ,
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Phuong Thao
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; , ,
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79409, USA;
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
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8
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Terceros GC, Resentini F, Cucinotta M, Manrique S, Colombo L, Mendes MA. The Importance of Cytokinins during Reproductive Development in Arabidopsis and Beyond. Int J Mol Sci 2020; 21:ijms21218161. [PMID: 33142827 PMCID: PMC7662338 DOI: 10.3390/ijms21218161] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
Fertilization and seed formation are fundamental events in the life cycle of flowering plants. The seed is a functional unit whose main purpose is to propagate the plant. The first step in seed development is the formation of male and female gametophytes and subsequent steps culminate in successful fertilization. The detailed study of this process is highly relevant because it directly impacts human needs, such as protecting biodiversity and ensuring sustainable agriculture to feed the increasing world population. Cytokinins comprise a class of phytohormones that play many important roles during plant growth and development and in recent years, the role of this class of phytohormones during reproduction has become clear. Here, we review the role of cytokinins during ovule, pollen and seed formation at the genetic and molecular levels. The expansion of knowledge concerning the molecular mechanisms that control plant reproduction is extremely important to optimise seed production.
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9
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Huo R, Liu Z, Yu X, Li Z. The Interaction Network and Signaling Specificity of Two-Component System in Arabidopsis. Int J Mol Sci 2020; 21:ijms21144898. [PMID: 32664520 PMCID: PMC7402358 DOI: 10.3390/ijms21144898] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 01/25/2023] Open
Abstract
Two-component systems (TCS) in plants have evolved into a more complicated multi-step phosphorelay (MSP) pathway, which employs histidine kinases (HKs), histidine-containing phosphotransfer proteins (HPts), and response regulators (RRs) to regulate various aspects of plant growth and development. How plants perceive the external signals, then integrate and transduce the secondary signals specifically to the desired destination, is a fundamental characteristic of the MSP signaling network. The TCS elements involved in the MSP pathway and molecular mechanisms of signal transduction have been best understood in the model plant Arabidopsis thaliana. In this review, we focus on updated knowledge on TCS signal transduction in Arabidopsis. We first present a brief description of the TCS elements; then, the protein–protein interaction network is established. Finally, we discuss the possible molecular mechanisms involved in the specificity of the MSP signaling at the mRNA and protein levels.
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Affiliation(s)
- Ruxue Huo
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China;
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China
| | - Zhenning Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China
- Correspondence: (Z.L.); (Z.L.)
| | - Xiaolin Yu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China;
- Correspondence: (Z.L.); (Z.L.)
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10
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Hater F, Nakel T, Groß-Hardt R. Reproductive Multitasking: The Female Gametophyte. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:517-546. [PMID: 32442389 DOI: 10.1146/annurev-arplant-081519-035943] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fertilization of flowering plants requires the organization of complex tasks, many of which become integrated by the female gametophyte (FG). The FG is a few-celled haploid structure that orchestrates division of labor to coordinate successful interaction with the sperm cells and their transport vehicle, the pollen tube. As reproductive outcome is directly coupled to evolutionary success, the underlying mechanisms are under robust molecular control, including integrity check and repair mechanisms. Here, we review progress on understanding the development and function of the FG, starting with the functional megaspore, which represents the haploid founder cell of the FG. We highlight recent achievements that have greatly advanced our understanding of pollen tube attraction strategies and the mechanisms that regulate plant hybridization and gamete fusion. In addition, we discuss novel insights into plant polyploidization strategies that expand current concepts on the evolution of flowering plants.
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Affiliation(s)
- Friederike Hater
- Centre for Biomolecular Interactions, University of Bremen, 28359 Bremen, Germany;
| | - Thomas Nakel
- Centre for Biomolecular Interactions, University of Bremen, 28359 Bremen, Germany;
| | - Rita Groß-Hardt
- Centre for Biomolecular Interactions, University of Bremen, 28359 Bremen, Germany;
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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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13
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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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14
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Tao Y, Chen D, Zou T, Zeng J, Gao F, He Z, Zhou D, He Z, Yuan G, Liu M, Zhao H, Deng Q, Wang S, Zheng A, Zhu J, Liang Y, Wang L, Li P, Li S. Defective Leptotene Chromosome 1 (DLC1) encodes a type-B response regulator and is required for rice meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:556-570. [PMID: 31004552 DOI: 10.1111/tpj.14344] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/09/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Meiosis is critical for sexual reproduction and the generation of new allelic variations in most eukaryotes. In this study, we report the isolation of a meiotic gene, DLC1, using a map-based cloning strategy. The dlc1 mutant is sterile in both male and female gametophytes due to an earlier defect in the leptotene chromosome and subsequent abnormalities at later stages. DLC1 is strongly expressed in the pollen mother cells (PMCs) and tapetum and encodes a nucleus-located rice type-B response regulator (RR) with transcriptional activity. Further investigations showed that DLC1 interacts with all five putative rice histidine phosphotransfer proteins (HPs) in yeast and planta cells, suggesting a possible participation of the two-component signalling systems (TCS) in rice meiosis. Our results demonstrated that DLC1 is required for rice meiosis and fertility, providing useful information for the role of TCS in rice meiosis.
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Affiliation(s)
- Yang Tao
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dan Chen
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Zou
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Jing Zeng
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fengyan Gao
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongshan He
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dan Zhou
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhiyuan He
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoqiang Yuan
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Miaomiao Liu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongfeng Zhao
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Aiping Zheng
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- State Key Laboratory of crop gene exploitation and utilization in southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yueyang Liang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lingxia Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- State Key Laboratory of crop gene exploitation and utilization in southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuangcheng Li
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- State Key Laboratory of crop gene exploitation and utilization in southwest China, Sichuan Agricultural University, Chengdu, 611130, China
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15
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Tan S, Debellé F, Gamas P, Frugier F, Brault M. Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes. BMC Genomics 2019; 20:373. [PMID: 31088345 PMCID: PMC6518804 DOI: 10.1186/s12864-019-5724-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/22/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering root cortical cell divisions at the onset of nodule initiation. Cytokinin signaling is based on a Two-Component System (TCS) phosphorelay cascade, involving successively Cytokinin-binding Histidine Kinase receptors, phosphorelay proteins shuttling between the cytoplasm and the nucleus, and Type-B Response Regulator (RRB) transcription factors activating the expression of cytokinin primary response genes. Among those, Type-A Response Regulators (RRA) exert a negative feedback on the TCS signaling. To determine whether the legume plant nodulation capacity is linked to specific features of TCS proteins, a genome-wide identification was performed in six legume genomes (Cajanus cajan, pigeonpea; Cicer arietinum, chickpea; Glycine max, soybean; Phaseolus vulgaris, common bean; Lotus japonicus; Medicago truncatula). The diversity of legume TCS proteins was compared to the one found in two non-nodulating species, Arabidopsis thaliana and Vitis vinifera, which are references for functional analyses of TCS components and phylogenetic analyses, respectively. RESULTS A striking expansion of non-canonical RRBs was identified, notably leading to the emergence of proteins where the conserved phosphor-accepting aspartate residue is replaced by a glutamate or an asparagine. M. truncatula genome-wide expression datasets additionally revealed that only a limited subset of cytokinin-related TCS genes is highly expressed in different organs, namely MtCHK1/MtCRE1, MtHPT1, and MtRRB3, suggesting that this "core" module potentially acts in most plant organs including nodules. CONCLUSIONS Further functional analyses are required to determine the relevance of these numerous non-canonical TCS RRBs in symbiotic nodulation, as well as of canonical MtHPT1 and MtRRB3 core signaling elements.
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Affiliation(s)
- Sovanna Tan
- IPS2 (Institute of Plant Sciences Paris-Saclay), CNRS, Université Paris-Sud, Université Paris-Diderot, INRA, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
| | - Frédéric Debellé
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Pascal Gamas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Florian Frugier
- IPS2 (Institute of Plant Sciences Paris-Saclay), CNRS, Université Paris-Sud, Université Paris-Diderot, INRA, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
| | - Mathias Brault
- IPS2 (Institute of Plant Sciences Paris-Saclay), CNRS, Université Paris-Sud, Université Paris-Diderot, INRA, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
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16
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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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17
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Liu Z, Yuan L, Sundaresan V, Yu X. Arabidopsis CKI1 mediated two-component signaling in the specification of female gametophyte. PLANT SIGNALING & BEHAVIOR 2018; 13:e1469360. [PMID: 30148413 PMCID: PMC6204793 DOI: 10.1080/15592324.2018.1469360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/19/2018] [Indexed: 05/30/2023]
Abstract
Cytokinin independent 1 (CKI1) is a histidine kinase involved in the two-component signaling pathway and acts as a master regulator of central cell specification via CKI1-mediated two-component signaling. In this study, the dynamic distribution of two-component system (TCS) signals was primarily investigated during Arabidopsis embryo sac development. TCS signals were stably detected in female gametophytes cells from the megaspore stage all through to the mature embryo sac stage. CKI1 acts as the primary activator of the TCS signaling pathway in embryo sacs. Accordingly, focusing on CKI1, two alternate models are proposed for female gametophyte cell fate specification. In the first model, CKI1 co-determines the central cell fate in combination with a hypothetical X factor at the micropylar pole, and in the alternate model, CKI1 alone determines the central cell fate.
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Affiliation(s)
- Z. Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, China
- Institute of Vegetable Sciences, Zhejiang University, Hangzhou, China
- Department of Plant Biology, University of California, Davis, CA, USA
| | - L. Yuan
- Department of Plant Biology, University of California, Davis, CA, USA
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling, China
| | - V. Sundaresan
- Department of Plant Biology, University of California, Davis, CA, USA
| | - X. Yu
- Institute of Vegetable Sciences, Zhejiang University, Hangzhou, China
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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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19
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Yuan L, Liu Z, Song X, Jernstedt J, Sundaresan V. The gymnosperm ortholog of the angiosperm central cell-specification gene CKI1 provides an essential clue to endosperm origin. THE NEW PHYTOLOGIST 2018; 218:1685-1696. [PMID: 29603241 DOI: 10.1111/nph.15115] [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: 10/10/2017] [Accepted: 02/09/2018] [Indexed: 05/22/2023]
Abstract
A defining feature of angiosperms is double fertilization involving the female gametophyte central cell and formation of a nutrient-storing tissue called endosperm. The route for the evolutionary origin of endosperm from a gymnosperm ancestor, particularly the molecular steps involved, has remained elusive. Recently, the histidine kinase gene Cytokinin-Independent 1 (CKI1), an activator of cytokinin signaling, was described as a key to specification of the endosperm precursor central cell in Arabidopsis. Here, we have investigated the function and expression of a putative ortholog of CKI1 in the gymnosperm Ginkgo biloba. We demonstrate that Ginkgo CKI1 can partially rescue an Arabidopsis cki1 mutant and promote weak activation of the cytokinin signaling pathway in the Arabidopsis embryo sac, but does not confer central cell specification. Ginkgo CKI1 is expressed in both male and female gametophytes of Ginkgo. In the latter, it is expressed in the ventral canal cell, which is sister to the egg cell in the archegonium. As in Arabidopsis, Ginkgo CKI1 is not expressed in the egg cell. The similarities in expression patterns of CKI1 in Ginkgo and Arabidopsis female gametophytes suggest that extant gymnosperms possess an essential component of the molecular machinery required for angiosperm endosperm development, and provide new insights into endosperm origin from a gymnospermous ancestor.
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Affiliation(s)
- Li Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhenning Liu
- College of Agriculture and Forestry Science, Linyi University, Linyi, Shandong, 276000, China
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoya Song
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Judy Jernstedt
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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20
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Pernisova M, Grochova M, Konecny T, Plackova L, Harustiakova D, Kakimoto T, Heisler MG, Novak O, Hejatko J. Cytokinin signalling regulates organ identity via AHK4 receptor in Arabidopsis. Development 2018; 145:dev.163907. [DOI: 10.1242/dev.163907] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/22/2018] [Indexed: 01/19/2023]
Abstract
Mutual interactions of the phytohormones cytokinins and auxin determine root or shoot identity during postembryonic de novo organogenesis in plants. However, our understanding to the role of hormonal metabolism and perception during early stages of cell fate reprograming is still elusive.
In the hypocotyl explant assay, auxin activated root formation while cytokinins mediated early loss of the root identity, primordia disorganization and initiation of shoot development. Exogenous but also endogenous cytokinins influenced the initiation of newly formed organs as well as the pace of organ developmental sequence. The process of de novo shoot apical meristem establishment was accompanied by accumulation of endogenous cytokinins, differential regulation of genes for individual cytokinin receptors, strong activation of AHK4-mediated signalling and induction of shoot-specific homeodomain regulator WUSCHEL. The latter associated with upregulation of isopentenyladenine-type cytokinins, revealing higher shoot-forming potential when compared with trans-zeatin. Moreover, AHK4-controlled cytokinin signalling negatively regulated root stem cell organizer WUSCHEL RELATED HOMEOBOX 5 in the root quiescent centre. We propose an important role of endogenous cytokinin biosynthesis and AHK4-mediated cytokinin signalling in the control of de novo induced organ identity.
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Affiliation(s)
- Marketa Pernisova
- CEITEC - Central European Institute of Technology and Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martina Grochova
- CEITEC - Central European Institute of Technology and Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tomas Konecny
- CEITEC - Central European Institute of Technology and Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Plackova
- Laboratory of Growth Regulators, CRH, Institute of Experimental Botany AS CR and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Danka Harustiakova
- Institute of Biostatistics and Analyses, Faculty of Medicine and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tatsuo Kakimoto
- Department of Biological Science, Graduate School of Science, Osaka University, Osaka, Japan
| | | | - Ondrej Novak
- Laboratory of Growth Regulators, CRH, Institute of Experimental Botany AS CR and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Jan Hejatko
- CEITEC - Central European Institute of Technology and Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
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21
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Lomin SN, Myakushina YA, Arkhipov DV, Leonova OG, Popenko VI, Schmülling T, Romanov GA. Studies of cytokinin receptor-phosphotransmitter interaction provide evidences for the initiation of cytokinin signalling in the endoplasmic reticulum. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:192-202. [PMID: 32291033 DOI: 10.1071/fp16292] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 01/11/2017] [Indexed: 05/06/2023]
Abstract
Cytokinin receptors were shown recently to be localised mainly to the endoplasmic reticulum (ER); however, the activity of ER-located receptors was not proven. We have therefore tested the functionality of ER-located Arabidopsis receptors. The first step of cytokinin signal transduction is the transfer of a phosphoryl group from the activated receptor to a phosphotransfer protein. To determine the subcellular localisation of receptor-phosphotransmitter interaction in planta, BiFC experiments were performed. Receptors ARABIDOPSIS HISTIDINE KINASE 2 (AHK2), AHK3 and AHK4 (CRE1) and phosphotransmitters ARABIDOPSIS HISTIDINE-CONTAINING PHOSPHOTRANSMITTER 1 (AHP1), AHP2 and AHP3 fused to split-eYFP were transiently expressed in Nicotiana benthamiana leaves. Receptor-phosphotransmitter pairs were shown to interact in every possible combination in a pattern reflecting the ER. Receptor dimers, an active form of the receptors, were also detected in the ER. According to BiFC and protease protection data, the catalytic part of AHK3 was located in the cytoplasm whereas the hormone binding module faced the ER lumen. This topology is consistent with receptor signalling from the ER membrane. Finally, the functionality of receptors in different membrane fractions was tested using an in vitro kinase assay visualising the phosphorylation of phosphotransfer proteins. The detected cytokinin-dependent phosphotransfer activity was confined mainly to the ER-enriched fraction. Collectively, our data demonstrate that ER-located cytokinin receptors are active in cytokinin signal transduction. Hence, intracellular cytokinins appear to play an essential role in cytokinin signalling. An updated model for the spatial organisation of cytokinin transport form activation, intracellular trafficking and signalling from the ER is proposed.
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Affiliation(s)
- Sergey N Lomin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
| | - Yulia A Myakushina
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
| | - Dmitry V Arkhipov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
| | - Olga G Leonova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Vladimir I Popenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195 Berlin, Germany
| | - Georgy A Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
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22
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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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23
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Sharan A, Soni P, Nongpiur RC, Singla-Pareek SL, Pareek A. Mapping the 'Two-component system' network in rice. Sci Rep 2017; 7:9287. [PMID: 28839155 PMCID: PMC5571105 DOI: 10.1038/s41598-017-08076-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/06/2017] [Indexed: 01/20/2023] Open
Abstract
Two-component system (TCS) in plants is a histidine to aspartate phosphorelay based signaling system. Rice genome has multifarious TCS signaling machinery comprising of 11 histidine kinases (OsHKs), 5 histidine phosphotransferases (OsHPTs) and 36 response regulators (OsRRs). However, how these TCS members interact with each other and comprehend diverse signaling cascades remains unmapped. Using a highly stringent yeast two-hybrid (Y2H) platform and extensive in planta bimolecular fluorescence complementation (BiFC) assays, distinct arrays of interaction between various TCS proteins have been identified in the present study. Based on these results, an interactome map of TCS proteins has been assembled. This map clearly shows a cross talk in signaling, mediated by different sensory OsHKs. It also highlights OsHPTs as the interaction hubs, which interact with OsRRs, mostly in a redundant fashion. Remarkably, interactions between type-A and type-B OsRRs have also been revealed for the first time. These observations suggest that feedback regulation by type-A OsRRs may also be mediated by interference in signaling at the level of type-B OsRRs, in addition to OsHPTs, as known previously. The interactome map presented here provides a starting point for in-depth molecular investigations for signal(s) transmitted by various TCS modules into diverse biological processes.
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Affiliation(s)
- Ashutosh Sharan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Praveen Soni
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ramsong Chantre Nongpiur
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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24
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Růžička K, Zhang M, Campilho A, Bodi Z, Kashif M, Saleh M, Eeckhout D, El‐Showk S, Li H, Zhong S, De Jaeger G, Mongan NP, Hejátko J, Helariutta Y, Fray RG. Identification of factors required for m 6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. THE NEW PHYTOLOGIST 2017; 215:157-172. [PMID: 28503769 PMCID: PMC5488176 DOI: 10.1111/nph.14586] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/19/2017] [Indexed: 05/04/2023]
Abstract
N6-adenosine methylation (m6 A) of mRNA is an essential process in most eukaryotes, but its role and the status of factors accompanying this modification are still poorly understood. Using combined methods of genetics, proteomics and RNA biochemistry, we identified a core set of mRNA m6 A writer proteins in Arabidopsis thaliana. The components required for m6 A in Arabidopsis included MTA, MTB, FIP37, VIRILIZER and the E3 ubiquitin ligase HAKAI. Downregulation of these proteins led to reduced relative m6 A levels and shared pleiotropic phenotypes, which included aberrant vascular formation in the root, indicating that correct m6 A methylation plays a role in developmental decisions during pattern formation. The conservation of these proteins amongst eukaryotes and the demonstration of a role in writing m6 A for the E3 ubiquitin ligase HAKAI is likely to be of considerable relevance beyond the plant sciences.
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Affiliation(s)
- Kamil Růžička
- Functional Genomics and Proteomics of PlantsCentral European Institute of Technology and National Centre for Biomolecular ResearchMasaryk University62500BrnoCzech Republic
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Mi Zhang
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
| | - Ana Campilho
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
- Research Center in Biodiversity and Genetic ResourcesUniversity of Porto4485‐661 VairãoPortugal
| | - Zsuzsanna Bodi
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
| | - Muhammad Kashif
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Mária Saleh
- Functional Genomics and Proteomics of PlantsCentral European Institute of Technology and National Centre for Biomolecular ResearchMasaryk University62500BrnoCzech Republic
| | - Dominique Eeckhout
- Department of Plant Systems BiologyVIB9052GentBelgium
- Department of Plant Biotechnology and BioinformaticsGhent University9052GentBelgium
| | - Sedeer El‐Showk
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Hongying Li
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess PlateauMinistry of AgricultureTaiyuanShanxi030031China
| | - Silin Zhong
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
- The State Key Laboratory of AgrobiotechnologyThe School of Life SciencesThe Chinese University of Hong KongHong KongChina
| | - Geert De Jaeger
- Department of Plant Systems BiologyVIB9052GentBelgium
- Department of Plant Biotechnology and BioinformaticsGhent University9052GentBelgium
| | - Nigel P. Mongan
- School of Veterinary Medicine and SciencesUniversity of NottinghamSutton BoningtonLoughboroughLE12 5RDUK
| | - Jan Hejátko
- Functional Genomics and Proteomics of PlantsCentral European Institute of Technology and National Centre for Biomolecular ResearchMasaryk University62500BrnoCzech Republic
| | - Ykä Helariutta
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
- Sainsbury LaboratoryUniversity of CambridgeCambridgeCB2 1LRUK
| | - Rupert G. Fray
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
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25
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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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26
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Hung YL, Jiang I, Lee YZ, Wen CK, Sue SC. NMR Study Reveals the Receiver Domain of Arabidopsis ETHYLENE RESPONSE1 Ethylene Receptor as an Atypical Type Response Regulator. PLoS One 2016; 11:e0160598. [PMID: 27486797 PMCID: PMC4972365 DOI: 10.1371/journal.pone.0160598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/21/2016] [Indexed: 11/26/2022] Open
Abstract
The gaseous plant hormone ethylene, recognized by plant ethylene receptors, plays a pivotal role in various aspects of plant growth and development. ETHYLENE RESPONSE1 (ETR1) is an ethylene receptor isolated from Arabidopsis and has a structure characteristic of prokaryotic two-component histidine kinase (HK) and receiver domain (RD), where the RD structurally resembles bacteria response regulators (RRs). The ETR1 HK domain has autophosphorylation activity, and little is known if the HK can transfer the phosphoryl group to the RD for receptor signaling. Unveiling the correlation of the receptor structure and phosphorylation status would advance the studies towards the underlying mechanisms of ETR1 receptor signaling. In this study, using the nuclear magnetic resonance technique, our data suggested that the ETR1-RD is monomeric in solution and the rigid structure of the RD prevents the conserved aspartate residue phosphorylation. Comparing the backbone dynamics with other RRs, we propose that backbone flexibility is critical to the RR phosphorylation. Besides the limited flexibility, ETR1-RD has a unique γ loop conformation of opposite orientation, which makes ETR1-RD unfavorable for phosphorylation. These two features explain why ETR1-RD cannot be phosphorylated and is classified as an atypical type RR. As a control, phosphorylation of the ETR1-RD was also impaired when the sequence was swapped to the fragment of the bacterial typical type RR, CheY. Here, we suggest a molecule insight that the ETR1-RD already exists as an active formation and executes its function through binding with the downstream factors without phosphorylation.
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Affiliation(s)
- Yi-Lin Hung
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Instrumentation Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Ingjye Jiang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chi-Kuang Wen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail:
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27
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Alvarez AF, Barba-Ostria C, Silva-Jiménez H, Georgellis D. Organization and mode of action of two component system signaling circuits from the various kingdoms of life. Environ Microbiol 2016; 18:3210-3226. [DOI: 10.1111/1462-2920.13397] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/17/2016] [Accepted: 05/23/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Adrian F. Alvarez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México; 04510 México City, México
| | - Carlos Barba-Ostria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México; 04510 México City, México
| | - Hortencia Silva-Jiménez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México; 04510 México City, México
| | - Dimitris Georgellis
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México; 04510 México City, México
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28
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Vícha J, Babinský M, Demo G, Otrusinová O, Jansen S, Pekárová B, Žídek L, Munzarová ML. The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations. Proteins 2016; 84:686-99. [PMID: 26879585 DOI: 10.1002/prot.25019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/29/2016] [Accepted: 02/10/2016] [Indexed: 11/09/2022]
Abstract
Sequence dependence of (13) C and (15) N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD , and its complexed form, CKI1RD •Mg(2+), was studied by means of MD/DFT calculations. MD simulations of a 20-ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and its sequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/interior position. Using models covering a 10 and a 15 Å environment of Mg(2+), a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg(2+) binding was described better by the 15 Å as compared to the 10 Å model. Thirteen chemical shifts were analyzed in terms of the effect of Mg(2+) insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg(2+) binding. The strongest individual effects were found for (15) N of D70, S74, and V68, where the electrostatics dominated; for (13) Cβ of D69 and (15) N of K76, where the influences were equal, and for (13) Cα of F72 and (13) Cβ of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed.
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Affiliation(s)
- Jan Vícha
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Martin Babinský
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Olga Otrusinová
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Séverine Jansen
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Blanka Pekárová
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Lukáš Žídek
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Markéta L Munzarová
- Faculty of Science, Department of Chemistry, Masaryk University, Kotlářská 2, Brno, 61137, Czech Republic
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29
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Pekárová B, Szmitkowska A, Dopitová R, Degtjarik O, Žídek L, Hejátko J. Structural Aspects of Multistep Phosphorelay-Mediated Signaling in Plants. MOLECULAR PLANT 2016; 9:71-85. [PMID: 26633861 DOI: 10.1016/j.molp.2015.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 05/16/2023]
Abstract
The multistep phosphorelay (MSP) is a central signaling pathway in plants integrating a wide spectrum of hormonal and environmental inputs and controlling numerous developmental adaptations. For the thorough comprehension of the molecular mechanisms underlying the MSP-mediated signal recognition and transduction, the detailed structural characterization of individual members of the pathway is critical. In this review we describe and discuss the recently known crystal and nuclear magnetic resonance structures of proteins acting in MSP signaling in higher plants, focusing particularly on cytokinin and ethylene signaling in Arabidopsis thaliana. We discuss the range of functional aspects of available structural information including determination of ligand specificity, activation of the receptor via its autophosphorylation, and downstream signal transduction through the phosphorelay. We compare the plant structures with their bacterial counterparts and show that although the overall similarity is high, the differences in structural details are frequent and functionally important. Finally, we discuss emerging knowledge on molecular recognition mechanisms in the MSP, and mention the latest findings regarding structural determinants of signaling specificity in the Arabidopsis MSP that could serve as a general model of this pathway in all higher plants.
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Affiliation(s)
- Blanka Pekárová
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Agnieszka Szmitkowska
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Radka Dopitová
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Oksana Degtjarik
- Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Lukáš Žídek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jan Hejátko
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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Bertheau L, Djeghdir I, Foureau E, Chefdor F, Glevarec G, Oudin A, Depierreux C, Morabito D, Brignolas F, Courdavault V, Héricourt F, Auguin D, Carpin S. Insights into B-type RR members as signaling partners acting downstream of HPt partners of HK1 in the osmotic stress response in Populus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 94:244-252. [PMID: 26126081 DOI: 10.1016/j.plaphy.2015.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/12/2015] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
The B-type response regulators (B-type RRs), final elements of a signaling pathway called "histidine/aspartate phosphorelay system" in plants, are devoted to the regulation of response genes through a transcription factor activity. Signal transduction consists in the transfer of a phosphoryl group from a transmembrane histidine kinase (HK) which recognizes a given stimulus to nuclear RRs via cytosolic shuttle phosphotransfer proteins (HPts). In Arabidopsis, the receptors HK are to date the major characterized candidates to be responsible for initiation of osmotic stress responses. However, little information is available concerning the signaling partners acting downstream of HKs. In Populus, three HPts and five B-type RRs were previously identified as interacting partners of HK1, the Arabidopsis AHK1 homolog. Here, we report the isolation of RR18, a member of the B-type RR family, which shares high sequence similarities with ARR18 characterized to act in the osmosensing signaling pathway in Arabidopsis, from poplar cuttings subjected to osmotic stress conditions. By using yeast and in planta interaction assays, RR18 was further identified as acting downstream of HK1 and its three preferential HPt partners. Besides, our results are in favor of a possible involvement of both RR18 and RR13, the main expressed poplar B-type RR, in the osmotic signaling pathway. Nonetheless, different behaviors of these two B-type RRs in this pathway need to be noted, with one RR, RR13, acting in an early phase, mainly in roots of poplar cuttings, and the other one, RR18, acting in a late phase, mainly in leaves to supply an adequate response.
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Affiliation(s)
- Lucie Bertheau
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067 Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans Cedex 2, France; Université de Toulon, EA 3819, Laboratoire Processus de Transferts et d'Echanges dans l'Environnement (PROTEE), 83957 La Garde Cedex, France
| | - Inès Djeghdir
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067 Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans Cedex 2, France
| | - Emilien Foureau
- Université François Rabelais de Tours, EA 2106, Biomolécules et Biotechnologies Végétales (BBV), 37200 Tours, France
| | - Françoise Chefdor
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067 Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans Cedex 2, France
| | - Gaëlle Glevarec
- Université François Rabelais de Tours, EA 2106, Biomolécules et Biotechnologies Végétales (BBV), 37200 Tours, France
| | - Audrey Oudin
- Université François Rabelais de Tours, EA 2106, Biomolécules et Biotechnologies Végétales (BBV), 37200 Tours, France
| | - Christiane Depierreux
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067 Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans Cedex 2, France
| | - Domenico Morabito
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067 Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans Cedex 2, France
| | - Franck Brignolas
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067 Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans Cedex 2, France
| | - Vincent Courdavault
- Université François Rabelais de Tours, EA 2106, Biomolécules et Biotechnologies Végétales (BBV), 37200 Tours, France
| | - François Héricourt
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067 Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans Cedex 2, France
| | - Daniel Auguin
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067 Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans Cedex 2, France
| | - Sabine Carpin
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067 Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans Cedex 2, France.
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Wang GL, Sun S, Xing GM, Wu XJ, Wang F, Xiong AS. Morphological Characteristics, Anatomical Structure, and Gene Expression: Novel Insights into Cytokinin Accumulation during Carrot Growth and Development. PLoS One 2015. [PMID: 26218147 PMCID: PMC4517795 DOI: 10.1371/journal.pone.0134166] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cytokinins have been implicated in normal plant growth and development. These bioactive molecules are essential for cell production and expansion in higher plants. Carrot is an Apiaceae vegetable with great value and undergoes significant size changes over the process of plant growth. However, cytokinin accumulation and its potential roles in carrot growth have not been elucidated. To address this problem, carrot plants at five stages were collected, and morphological and anatomical characteristics and expression profiles of cytokinin-related genes were determined. During carrot growth and development, cytokinin levels were the highest at the second stage in the roots, whereas relatively stable levels were observed in the petioles and leaves. DcCYP735A2 showed high expression at stage 2 in the roots, which may contribute largely to the higher cytokinin level at this stage. However, expression of most metabolic genes did not follow a pattern similar to that of cytokinin accumulation, indicating that cytokinin biosynthesis was regulated through a complex network. Genes involved in cytokinin signal perception and transduction were also integrated to normal plant growth and development. The results from the present work suggested that cytokinins may regulate plant growth in a stage-dependent manner. Our work would shed novel insights into cytokinin accumulation and its potential roles during carrot growth. Further studies regarding carrot cytokinins may be achieved by modification of the genes involved in cytokinin biosynthesis, inactivation, and perception.
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Affiliation(s)
- Guang-Long Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sheng Sun
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
| | - Guo-Ming Xing
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
| | - Xue-Jun Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- * E-mail:
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Verma V, Sivaraman J, Srivastava AK, Sadanandom A, Kumar PP. Destabilization of interaction between cytokinin signaling intermediates AHP1 and ARR4 modulates Arabidopsis development. THE NEW PHYTOLOGIST 2015; 206:726-737. [PMID: 25643735 DOI: 10.1111/nph.13297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/26/2014] [Indexed: 06/04/2023]
Abstract
Eukaryotic two-component signaling involves the His-Asp-His-Asp multistep phosphorelay (MSP). In Arabidopsis thaliana, cytokinin-mediated MSP signaling intermediates include histidine kinases (HKs), histidine phosphotransfer proteins (Hpts) and response regulators (RRs). The structure-function relationship of interaction between Hpt (e.g. AHP1) and RR (e.g. ARR4) is poorly understood. Using a homology model and yeast two-hybrid analysis, we identified key amino acids of ARR4 at the AHP1-ΔARR4((16-175)) interaction interface. Mutating them in Arabidopsis (arr3,4,5,6,8,9 hextuple mutant background) and performing root length assays provided functional relevance, and coimmunoprecipitation (coIP) assay provided biochemical evidence for the interaction. The homology model mimics crystal structures of Hpt-RR complexes. Mutating selected interface residues of ARR4 either abolished or destabilized the interaction. D45A and Y96A mutations weakened interaction with AHP1, and exhibited weaker rescue of root elongation in the hextuple mutants. CoIP analysis using cytokinin-treated transgenic Arabidopsis seedlings provided biochemical evidence for weakened AHP1-ARR4 interaction. The relevance of the selected residues for the interaction was further validated in two independent pairs of Hpt-RR proteins from Arabidopsis and rice (Oryza sativa). Our data provide evidence of a link between Hpt-RR interaction affinity and regulation of downstream functions of RRs. This establishes a structure-function relationship for the final step of a eukaryotic MSP signal cascade.
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Affiliation(s)
- Vivek Verma
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 117543, Singapore, Singapore
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Zábrady M, Hrdinová V, Müller B, Conrad U, Hejátko J, Janda L. Targeted in vivo inhibition of specific protein-protein interactions using recombinant antibodies. PLoS One 2014; 9:e109875. [PMID: 25299686 PMCID: PMC4192540 DOI: 10.1371/journal.pone.0109875] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 09/04/2014] [Indexed: 11/19/2022] Open
Abstract
With the growing availability of genomic sequence information, there is an increasing need for gene function analysis. Antibody-mediated "silencing" represents an intriguing alternative for the precise inhibition of a particular function of biomolecules. Here, we describe a method for selecting recombinant antibodies with a specific purpose in mind, which is to inhibit intrinsic protein-protein interactions in the cytosol of plant cells. Experimental procedures were designed for conveniently evaluating desired properties of recombinant antibodies in consecutive steps. Our selection method was successfully used to develop a recombinant antibody inhibiting the interaction of ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 3 with such of its upstream interaction partners as the receiver domain of CYTOKININ INDEPENDENT HISTIDINE KINASE 1. The specific down-regulation of the cytokinin signaling pathway in vivo demonstrates the validity of our approach. This selection method can serve as a prototype for developing unique recombinant antibodies able to interfere with virtually any biomolecule in the living cell.
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Affiliation(s)
- Matej Zábrady
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vendula Hrdinová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Bruno Müller
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Udo Conrad
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jan Hejátko
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lubomír Janda
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- * E-mail:
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Borkovcová P, Pekárová B, Válková M, Dopitová R, Brzobohatý B, Janda L, Hejátko J. Antibodies against CKI1RD, a receiver domain of the sensor histidine kinase in Arabidopsis thaliana: from antigen preparation to in planta immunolocalization. PHYTOCHEMISTRY 2014; 100:6-15. [PMID: 24529575 DOI: 10.1016/j.phytochem.2014.01.007] [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: 11/24/2013] [Accepted: 01/17/2014] [Indexed: 06/03/2023]
Abstract
Immunodetection is a powerful tool in functional studies of all organisms. In plants, the gene redundancy and presence of gene families composed of highly homologous members often impedes the unambiguous identification of individual gene products. A family of eight sensor histidine kinases (HKs) mediates the transduction of diverse signals into Arabidopsis thaliana cells, thereby ensuring the initiation of appropriate adaptive responses. Antibodies recognizing specific members of the HK family would be valuable for studying their functions in Arabidopsis and other plant species including important crops. We have focused on developing and applying antibodies against CYTOKININ-INDEPENDENT 1 (CKI1), which encodes a constitutively active membrane-bound sensor HK that regulates the development of female gametophytes and vascular tissue in Arabidopsis. A coding sequence delimiting the C-terminal receiver domain of CKI1 (CKI1(RD)) was expressed in Escherichia coli using the IPTG-inducible expression system and purified to give a highly pure target protein. The purified CKI1(RD) protein was then used as an antigen for anti-CKI1(RD) antibody production. The resulting polyclonal antibodies had a detection limit of 10 ng of target protein at 1:20,000 dilution and were able to specifically distinguish CKI1, both in vitro and in situ, even in a direct comparison with highly homologous members of the same HK family AHK4, CKI2 and ETR1. Finally, anti-CKI1(RD) antibodies were able to selectively bind CKI1-GFP fusion protein in a pull-down assay using crude lysate from an Arabidopsis cell suspension culture. Our results suggest that the receiver domain is a useful target for the functional characterization of sensor HKs in immunological and biochemical studies.
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Affiliation(s)
- Petra Borkovcová
- Functional Genomics and Proteomics of Plants, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, CZ-625 00 Brno, Czech Republic
| | - Blanka Pekárová
- Functional Genomics and Proteomics of Plants, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, CZ-625 00 Brno, Czech Republic
| | - Martina Válková
- Functional Genomics and Proteomics of Plants, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, CZ-625 00 Brno, Czech Republic
| | - Radka Dopitová
- Functional Genomics and Proteomics of Plants, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, CZ-625 00 Brno, Czech Republic
| | - Břetislav Brzobohatý
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic; Department of Molecular Biology and Radiobiology, CEITEC - Central European Institute of Technology, Mendel University of Agriculture and Forestry, Zemědělská 1, CZ-613 00 Brno, Czech Republic
| | - Lubomír Janda
- Functional Genomics and Proteomics of Plants, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, CZ-625 00 Brno, Czech Republic
| | - Jan Hejátko
- Functional Genomics and Proteomics of Plants, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, CZ-625 00 Brno, Czech Republic.
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Immanen J, Nieminen K, Duchens Silva H, Rodríguez Rojas F, Meisel LA, Silva H, Albert VA, Hvidsten TR, Helariutta Y. Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica. BMC Genomics 2013; 14:885. [PMID: 24341635 PMCID: PMC3866579 DOI: 10.1186/1471-2164-14-885] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/27/2013] [Indexed: 01/01/2023] Open
Abstract
Background Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem activity, branching pattern of the shoot, and leaf senescence. These processes influence several traits, including the stem diameter, shoot architecture, and perennial life cycle, which define the development of woody plants. To facilitate research about the role of cytokinin in regulation of woody plant development, we have identified genes associated with cytokinin signaling and homeostasis pathways from two hardwood tree species. Results Taking advantage of the sequenced black cottonwood (Populus trichocarpa) and peach (Prunus persica) genomes, we have compiled a comprehensive list of genes involved in these pathways. We identified genes belonging to the six families of cytokinin oxidases (CKXs), isopentenyl transferases (IPTs), LONELY GUY genes (LOGs), two-component receptors, histidine containing phosphotransmitters (HPts), and response regulators (RRs). All together 85 Populus and 45 Prunus genes were identified, and compared to their Arabidopsis orthologs through phylogenetic analyses. Conclusions In general, when compared to Arabidopsis, differences in gene family structure were often seen in only one of the two tree species. However, one class of genes associated with cytokinin signal transduction, the CKI1-like family of two-component histidine kinases, was larger in both Populus and Prunus than in Arabidopsis.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ykä Helariutta
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland.
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Héricourt F, Chefdor F, Bertheau L, Tanigawa M, Maeda T, Guirimand G, Courdavault V, Larcher M, Depierreux C, Bénédetti H, Morabito D, Brignolas F, Carpin S. Characterization of histidine-aspartate kinase HK1 and identification of histidine phosphotransfer proteins as potential partners in a Populus multistep phosphorelay. PHYSIOLOGIA PLANTARUM 2013; 149:188-199. [PMID: 23330606 DOI: 10.1111/ppl.12024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/18/2012] [Accepted: 12/21/2012] [Indexed: 05/29/2023]
Abstract
In poplar, we identified proteins homologous to yeast proteins involved in osmosensing multistep phosphorelay Sln1p-Ypd1p-Ssk1p. This finding led us to speculate that Populus cells could sense osmotic stress by a similar mechanism. This study focuses on first and second protagonists of this possible pathway: a histidine-aspartate kinase (HK1), putative osmosensor and histidine phosphotransfer proteins (HPt1 to 10), potential partners of this HK. Characterization of HK1 showed its ability to homodimerize in two-hybrid tests and to act as an osmosensor with a kinase activity in yeast, by functional complementation of sln1Δ sho1Δ strain. Moreover, in plant cells, plasma membrane localization of HK1 is shown. Further analysis on HPts allowed us to isolate seven new cDNAs, leading to a total of 10 different HPts identified in poplar. Interaction tests showed that almost all HPts can interact with HK1, but two of them exhibit stronger interactions, suggesting a preferential partnership in poplar. The importance of the phosphorylation status in these interactions has been investigated with two-hybrid tests carried out with mutated HK1 forms. Finally, in planta co-expression analysis of genes encoding these potential partners revealed that only three HPts are co-expressed with HK1 in different poplar organs. This result reinforces the hypothesis of a partnership between HK1 and these three preferential HPts in planta. Taken together, these results shed some light on proteins partnerships that could be involved in the osmosensing pathway in Populus.
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Affiliation(s)
- François Héricourt
- Université d'Orléans, UPRES EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), 45067, Orléans Cedex 2, France; INRA, USC1328, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067, Orléans Cedex 2, France
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Verma V, Sivaraman J, Kumar PP. Expression, purification, and characterization of cytokinin signaling intermediates: Arabidopsis histidine phosphotransfer protein 1 (AHP1) and AHP2. PLANT CELL REPORTS 2013; 32:795-805. [PMID: 23525762 DOI: 10.1007/s00299-013-1424-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/05/2013] [Accepted: 03/10/2013] [Indexed: 06/02/2023]
Abstract
We have expressed, purified, and biophysically characterized recombinant AHP1 and AHP2. Also, using computational homology models for AHP1, ARR7, and AHP1–ARR7 complex, we identified threedimensional positioning of key amino acids. Cytokinin signaling involves activation of Arabidopsis Response Regulators (ARRs) by Arabidopsis Histidine Phosphotransfer Proteins (AHPs) by phosphorylation. Type-A ARRs are key regulators of several developmental pathways, but the mechanism underlying this phosphorylation and activation is not known in plants. In this study, we report the successful expression and purification of recombinant AHP1 and AHP2. Biophysical characterization shows that these two recombinant proteins were purified to homogeneity and possess well-defined secondary structures. Brief attempts to purify recombinant ARR7 posed problems during size-exclusion chromatography. Nevertheless, we generated computational homology models for AHP1, ARR7, and AHP1-ARR7 complex using crystal structures of homologous proteins from other organisms. The homology models helped to identify the three-dimensional positioning of the key conserved residues of AHP1 and ARR7 involved in phosphorylation. The similarity in positioning of these residues to other homologous proteins suggests that AHPs and type-A ARRs could be structurally conserved across kingdoms. Thus, our homology models can serve as valuable tools to gain structural insights into the phosphorylation and activation of cytokinin response regulators in plants.
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Affiliation(s)
- Vivek Verma
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
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Bauer J, Reiss K, Veerabagu M, Heunemann M, Harter K, Stehle T. Structure-function analysis of Arabidopsis thaliana histidine kinase AHK5 bound to its cognate phosphotransfer protein AHP1. MOLECULAR PLANT 2013; 6:959-970. [PMID: 23132142 DOI: 10.1093/mp/sss126] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The multi-step phosphorelay (MSP) system defines a key signal transduction pathway in plants and many eukaryotes. In this system, external stimuli first lead to the activation of a histidine kinase, followed by transfer of a phosphoryl group from the receiver domain of the kinase (HK(RD)) to downstream, cytosolic phosphotransfer proteins (HPs). In order to establish the determinants of specificity for this signaling relay system, we have solved the first crystal structure of a plant HK(RD), AHK5(RD), in complex with one of its cognate HPs, AHP1. AHP1 binds AHK5(RD) via a prominent hydrogen bond docking ridge and a hydrophobic patch. These features are conserved among all AHP proteins, but differ significantly from other structurally characterized prokaryotic and eukaryotic HPs. Surface plasmon resonance experiments show that AHK5(RD) binds to AHP1-3 with similar, micromolar affinity, consistent with the transient nature of this signaling complex. Our correlation of structural and functional data provide the first insight, at the atomic level as well as with quantitative affinity data, into the molecular recognition events governing the MSP in plants.
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Affiliation(s)
- Johannes Bauer
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076 Tübingen, Germany
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39
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Kaas Q, Craik DJ. NMR of plant proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:1-34. [PMID: 23611313 DOI: 10.1016/j.pnmrs.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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Degtjarik O, Dopitova R, Puehringer S, Nejedla E, Kuty M, Weiss MS, Hejatko J, Janda L, Kuta Smatanova I. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AHP2, a signal transmitter protein from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:158-61. [PMID: 23385758 PMCID: PMC3564619 DOI: 10.1107/s174430911205186x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 12/25/2012] [Indexed: 02/02/2023]
Abstract
Histidine-containing phosphotransfer proteins from Arabidopsis thaliana (AHP1-5) act as intermediates between sensor histidine kinases and response regulators in a signalling system called multi-step phosphorelay (MSP). AHP proteins mediate and potentially integrate various MSP-based signalling pathways (e.g. cytokinin or osmosensing). However, structural information about AHP proteins and their importance in MSP signalling is still lacking. To obtain a deeper insight into the structural basis of AHP-mediated signal transduction, the three-dimensional structure of AHP2 was determined. The AHP2 coding sequence was cloned into pRSET B expression vector, enabling production of AHP2 fused to an N-terminal His tag. AHP2 was expressed in soluble form in Escherichia coli strain BL21 (DE3) pLysS and then purified to homogeneity using metal chelate affinity chromatography and anion-exchange chromatography under reducing conditions. Successful crystallization in a buffer which was optimized for thermal stability yielded crystals that diffracted to 2.5 Å resolution.
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Affiliation(s)
- Oksana Degtjarik
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and School of Complex Systems, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, 37333 Ceske Budejovice, Czech Republic
| | - Radka Dopitova
- Central European Institute of Technology, Masaryk University, Zerotinovo nam. 9, 60177 Brno, Czech Republic
| | - Sandra Puehringer
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Eliska Nejedla
- Central European Institute of Technology, Masaryk University, Zerotinovo nam. 9, 60177 Brno, Czech Republic
| | - Michal Kuty
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and School of Complex Systems, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic
- Institute of Nanobiology and Structural Biology GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Manfred S. Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Jan Hejatko
- Central European Institute of Technology, Masaryk University, Zerotinovo nam. 9, 60177 Brno, Czech Republic
| | - Lubomir Janda
- Central European Institute of Technology, Masaryk University, Zerotinovo nam. 9, 60177 Brno, Czech Republic
| | - Ivana Kuta Smatanova
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and School of Complex Systems, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic
- Institute of Nanobiology and Structural Biology GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 37333 Nove Hrady, Czech Republic
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