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Paredes-Martínez F, Eixerés L, Zamora-Caballero S, Casino P. Structural and functional insights underlying recognition of histidine phosphotransfer protein in fungal phosphorelay systems. Commun Biol 2024; 7:814. [PMID: 38965424 PMCID: PMC11224324 DOI: 10.1038/s42003-024-06459-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 06/14/2024] [Indexed: 07/06/2024] Open
Abstract
In human pathogenic fungi, receiver domains from hybrid histidine kinases (hHK) have to recognize one HPt. To understand the recognition mechanism, we have assessed phosphorelay from receiver domains of five hHKs of group III, IV, V, VI, and XI to HPt from Chaetomium thermophilum and obtained the structures of Ct_HPt alone and in complex with the receiver domain of hHK group VI. Our data indicate that receiver domains phosphotransfer to Ct_HPt, show a low affinity for complex formation, and prevent a Leu-Thr switch to stabilize phosphoryl groups, also derived from the structures of the receiver domains of hHK group III and Candida albicans Sln1. Moreover, we have elucidated the envelope structure of C. albicans Ypd1 using small-angle X-ray scattering which reveals an extended flexible conformation of the long loop αD-αE which is not involved in phosphotransfer. Finally, we have analyzed the role of salt bridges in the structure of Ct_HPt alone.
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Affiliation(s)
- Francisco Paredes-Martínez
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain
- Instituto Universitario en Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Lluís Eixerés
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain
- Instituto Universitario en Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Sara Zamora-Caballero
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Patricia Casino
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain.
- Instituto Universitario en Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain.
- CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain.
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2
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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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3
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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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4
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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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5
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Qadir M, Wang X, Shah SRU, Zhou XR, Shi J, Wang H. Molecular Network for Regulation of Ovule Number in Plants. Int J Mol Sci 2021; 22:ijms222312965. [PMID: 34884791 PMCID: PMC8657818 DOI: 10.3390/ijms222312965] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022] Open
Abstract
In seed-bearing plants, the ovule ("small egg") is the organ within the gynoecium that develops into a seed after fertilization. The gynoecium located in the inner compartment of the flower turns into a fruit. The number of ovules in the ovary determines the upper limit or the potential of seed number per fruit in plants, greatly affecting the final seed yield. Ovule number is an important adaptive characteristic for plant evolution and an agronomic trait for crop improvement. Therefore, understanding the mechanism and pathways of ovule number regulation becomes a significant research aspect in plant science. This review summarizes the ovule number regulators and their regulatory mechanisms and pathways. Specially, an integrated molecular network for ovule number regulation is constructed, in which phytohormones played a central role, followed by transcription factors, enzymes, other protein and micro-RNA. Of them, AUX, BR and CK are positive regulator of ovule number, whereas GA acts negatively on it. Interestingly, many ovule number regulators have conserved functions across several plant taxa, which should be the targets of genetic improvement via breeding or gene editing. Many ovule number regulators identified to date are involved in the diverse biological process, such as ovule primordia formation, ovule initiation, patterning, and morphogenesis. The relations between ovule number and related characteristics/traits especially of gynoecium/fruit size, ovule fertility, and final seed number, as well as upcoming research questions, are also discussed. In summary, this review provides a general overview of the present finding in ovule number regulation, which represents a more comprehensive and in-depth cognition on it.
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Affiliation(s)
- Muslim Qadir
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chines Academy of Agricultural Sciences, Wuhan 430062, China; (M.Q.); (X.W.)
- Department of Plant Breeding and Genetics, Faculty of Agriculture, Lasbela University of Agriculture Water and Marine Sciences (LUAWMS), Lasbela 74200, Pakistan;
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chines Academy of Agricultural Sciences, Wuhan 430062, China; (M.Q.); (X.W.)
| | - Syed Rehmat Ullah Shah
- Department of Plant Breeding and Genetics, Faculty of Agriculture, Lasbela University of Agriculture Water and Marine Sciences (LUAWMS), Lasbela 74200, Pakistan;
- Department of Soil and Environment, Swedish University of Agricultural Sciences, P.O. Box 7080, SE-75007 Uppsala, Sweden
| | - Xue-Rong Zhou
- Commonwealth Scientific Industrial Research Organization (CSIRO) Agriculture Food, Canberra, ACT 2601, Australia;
| | - Jiaqin Shi
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chines Academy of Agricultural Sciences, Wuhan 430062, China; (M.Q.); (X.W.)
- Correspondence: (J.S.); (H.W.)
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chines Academy of Agricultural Sciences, Wuhan 430062, China; (M.Q.); (X.W.)
- Correspondence: (J.S.); (H.W.)
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6
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Patel R, Mehta K, Goswami D, Saraf M. An Anecdote on Prospective Protein Targets for Developing Novel Plant Growth Regulators. Mol Biotechnol 2021; 64:109-129. [PMID: 34561838 DOI: 10.1007/s12033-021-00404-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/15/2021] [Indexed: 11/28/2022]
Abstract
Phytohormones are the main regulatory molecules of core signalling networks associated with plant life cycle regulation. Manipulation of hormone signalling cascade enables the control over physiological traits of plant, which has major applications in field of agriculture and food sustainability. Hence, stable analogues of these hormones are long sought after and many of them are currently known, but the quest for more effective, stable and economically viable analogues is still going on. This search has been further strengthened by the identification of the components of signalling cascade such as receptors, downstream cascade members and transcription factors. Furthermore, many proteins of phytohormone cascades are available in crystallized forms. Such crystallized structures can provide the basis for identification of novel interacting compounds using in silico approach. Plenty of computational tools and bioinformatics software are now available that can aid in this process. Here, the metadata of all the major phytohormone signalling cascades are presented along with discussion on major protein-ligand interactions and protein components that may act as a potential target for manipulation of phytohormone signalling cascade. Furthermore, structural aspects of phytohormones and their known analogues are also discussed that can provide the basis for the synthesis of novel analogues.
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Affiliation(s)
- Rohit Patel
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Krina Mehta
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
| | - Meenu Saraf
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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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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Chen SK, Guan HH, Wu PH, Lin LT, Wu MC, Chang HY, Chen NC, Lin CC, Chuankhayan P, Huang YC, Lin PJ, Chen CJ. Structural insights into the histidine-containing phospho-transfer protein and receiver domain of sensor histidine kinase suggest a complex model in the two-component regulatory system in Pseudomonas aeruginosa. IUCRJ 2020; 7:934-948. [PMID: 32939285 PMCID: PMC7467158 DOI: 10.1107/s2052252520009665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
In Pseudomonas aeruginosa, an important opportunistic pathogen that causes numerous acute and chronic infections, the hybrid two-component system (TCS) regulates the swarming ability and biofilm formation with a multistep phospho-relay, and consists of hybrid-sensor histidine kinase (HK), histidine-containing phospho-transfer protein (Hpt) and response regulator (RR). In this work, two crystal structures of HptB and the receiver domain of HK PA1611 (PA1611REC) of P. aeruginosa have been determined in order to elucidate their interactions for the transfer of the phospho-ryl group. The structure of HptB folds into an elongated four-helix bundle - helices α2, α3, α4 and α5, covered by the short N-terminal helix α1. The imidazole side chain of the conserved active-site histidine residue His57, located near the middle of helix α3, protrudes from the bundle and is exposed to solvent. The structure of PA1611REC possesses a conventional (β/α)5 topology with five-stranded parallel β-sheets folded in the central region, surrounded by five α-helices. The divalent Mg2+ ion is located in the negatively charged active-site cleft and interacts with Asp522, Asp565 and Arg567. The HptB-PA1611REC complex is further modeled to analyze the binding surface and interactions between the two proteins. The model shows a shape complementarity between the convex surface of PA1611REC and the kidney-shaped HptB with fewer residues and a different network involved in interactions compared with other TCS complexes, such as SLN1-R1/YPD1 from Saccharomyces cerevisiae and AHK5RD/AHP1 from Arabidopsis thaliana. These structural results provide a better understanding of the TCS in P. aeruginosa and could potentially lead to the discovery of a new treatment for infection.
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Affiliation(s)
- Shao-Kang Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City 701, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Pei-Hsun Wu
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Li-Ting Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Meng-Chun Wu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City 701, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Hwan-You Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Nai-Chi Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Chien-Chih Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yen-Chieh Huang
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Pei-Ju Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chun-Jung Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City 701, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan
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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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Hofmann A, Müller S, Drechsler T, Berleth M, Caesar K, Rohr L, Harter K, Groth G. High-Level Expression, Purification and Initial Characterization of Recombinant Arabidopsis Histidine Kinase AHK1. PLANTS 2020; 9:plants9030304. [PMID: 32121559 PMCID: PMC7154865 DOI: 10.3390/plants9030304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 01/16/2023]
Abstract
Plants employ a number of phosphorylation cascades in response to a wide range of environmental stimuli. Previous studies in Arabidopsis and yeast indicate that histidine kinase AHK1 is a positive regulator of drought and osmotic stress responses. Based on these studies AHK1 was proposed a plant osmosensor, although the molecular basis of plant osmosensing still remains unknown. To understand the molecular role and signaling mechanism of AHK1 in osmotic stress, we have expressed and purified full-length AHK1 from Arabidopsis in a bacterial host to allow for studies on the isolated transmembrane receptor. Purification of the recombinant protein solubilized from the host membranes was achieved in a single step by metal-affinity chromatography. Analysis of the purified AHK1 by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting show a single band indicating that the preparation is highly pure and devoid of contaminants or degradation products. In addition, gel filtration experiments indicate that the preparation is homogenous and monodisperse. Finally, CD-spectroscopy, phosphorylation activity, dimerization studies, and protein–protein interaction with plant phosphorylation targeting AHP2 demonstrate that the purified protein is functionally folded and acts as phospho-His or phospho-Asp phosphatase. Hence, the expression and purification of recombinant AHK1 reported here provide a basis for further detailed functional and structural studies of the receptor, which might help to understand plant osmosensing and osmosignaling on the molecular level.
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Affiliation(s)
- Alexander Hofmann
- Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf 40225, Germany; (A.H.); (S.M.); (M.B.)
| | - Sophia Müller
- Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf 40225, Germany; (A.H.); (S.M.); (M.B.)
| | - Thomas Drechsler
- Center for Plant Molecular Biology (ZMBP), Eberhard Karls Universität Tübingen, Tübingen 72076, Germany; (T.D.); (K.C.); (L.R.); (K.H.)
| | - Mareike Berleth
- Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf 40225, Germany; (A.H.); (S.M.); (M.B.)
| | - Katharina Caesar
- Center for Plant Molecular Biology (ZMBP), Eberhard Karls Universität Tübingen, Tübingen 72076, Germany; (T.D.); (K.C.); (L.R.); (K.H.)
| | - Leander Rohr
- Center for Plant Molecular Biology (ZMBP), Eberhard Karls Universität Tübingen, Tübingen 72076, Germany; (T.D.); (K.C.); (L.R.); (K.H.)
| | - Klaus Harter
- Center for Plant Molecular Biology (ZMBP), Eberhard Karls Universität Tübingen, Tübingen 72076, Germany; (T.D.); (K.C.); (L.R.); (K.H.)
| | - Georg Groth
- Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf 40225, Germany; (A.H.); (S.M.); (M.B.)
- Correspondence: ; Tel.: +49-211-811-2822
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11
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Trajtenberg F, Buschiazzo A. Protein Dynamics in Phosphoryl-Transfer Signaling Mediated by Two-Component Systems. Methods Mol Biol 2020; 2077:1-18. [PMID: 31707648 DOI: 10.1007/978-1-4939-9884-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The ability to perceive the environment, an essential attribute in living organisms, is linked to the evolution of signaling proteins that recognize specific signals and execute predetermined responses. Such proteins constitute concerted systems that can be as simple as a unique protein, able to recognize a ligand and exert a phenotypic change, or extremely complex pathways engaging dozens of different proteins which act in coordination with feedback loops and signal modulation. To understand how cells sense their surroundings and mount specific adaptive responses, we need to decipher the molecular workings of signal recognition, internalization, transfer, and conversion into chemical changes inside the cell. Protein allostery and dynamics play a central role. Here, we review recent progress on the study of two-component systems, important signaling machineries of prokaryotes and lower eukaryotes. Such systems implicate a sensory histidine kinase and a separate response regulator protein. Both components exploit protein flexibility to effect specific conformational rearrangements, modulating protein-protein interactions, and ultimately transmitting information accurately. Recent work has revealed how histidine kinases switch between discrete functional states according to the presence or absence of the signal, shifting key amino acid positions that define their catalytic activity. In concert with the cognate response regulator's allosteric changes, the phosphoryl-transfer flow during the signaling process is exquisitely fine-tuned for proper specificity, efficiency and directionality.
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Affiliation(s)
- Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Département de Microbiologie, Institut Pasteur, Paris, France.
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12
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Abstract
Signal transduction systems configured around a core phosphotransfer step between a histidine kinase and a cognate response regulator protein occur in organisms from all domains of life. These systems, termed two-component systems, constitute the majority of multi-component signaling pathways in Bacteria but are less prevalent in Archaea and Eukarya. The core signaling domains are modular, allowing versatility in configuration of components into single-step phosphotransfer and multi-step phosphorelay pathways, the former being predominant in bacteria and the latter in eukaryotes. Two-component systems regulate key cellular regulatory processes that provide adaptive responses to environmental stimuli and are of interest for the development of antimicrobial therapeutics, biotechnology applications, and biosensor engineering. In bacteria, two-component systems have been found to mediate responses to an extremely broad array of extracellular and intracellular chemical and physical stimuli, whereas in archaea and eukaryotes, the use of two-component systems is more limited. This review summarizes recent advances in exploring the repertoire of sensor histidine kinases in the Archaea and Eukarya domains of life.
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Affiliation(s)
- Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), SFR ICAT 4208, UNIV Angers, UNIV Brest, Angers, France
| | - Ann M Stock
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
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13
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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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14
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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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15
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Shimagaki K, Weigt M. Selection of sequence motifs and generative Hopfield-Potts models for protein families. Phys Rev E 2019; 100:032128. [PMID: 31639992 DOI: 10.1103/physreve.100.032128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 06/10/2023]
Abstract
Statistical models for families of evolutionary related proteins have recently gained interest: In particular, pairwise Potts models as those inferred by the direct-coupling analysis have been able to extract information about the three-dimensional structure of folded proteins and about the effect of amino acid substitutions in proteins. These models are typically requested to reproduce the one- and two-point statistics of the amino acid usage in a protein family, i.e., to capture the so-called residue conservation and covariation statistics of proteins of common evolutionary origin. Pairwise Potts models are the maximum-entropy models achieving this. Although being successful, these models depend on huge numbers of ad hoc introduced parameters, which have to be estimated from finite amounts of data and whose biophysical interpretation remains unclear. Here, we propose an approach to parameter reduction, which is based on selecting collective sequence motifs. It naturally leads to the formulation of statistical sequence models in terms of Hopfield-Potts models. These models can be accurately inferred using a mapping to restricted Boltzmann machines and persistent contrastive divergence. We show that, when applied to protein data, even 20-40 patterns are sufficient to obtain statistically close-to-generative models. The Hopfield patterns form interpretable sequence motifs and may be used to clusterize amino acid sequences into functional subfamilies. However, the distributed collective nature of these motifs intrinsically limits the ability of Hopfield-Potts models in predicting contact maps, showing the necessity of developing models going beyond the Hopfield-Potts models discussed here.
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Affiliation(s)
- Kai Shimagaki
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie Computationnelle et Quantitative-LCQB, Paris, France
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie Computationnelle et Quantitative-LCQB, Paris, France
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16
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Millar AJ, Urquiza U, Freeman PL, Hume A, Plotkin GD, Sorokina O, Zardilis A, Zielinski T. Practical steps to digital organism models, from laboratory model species to 'Crops in silico. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2403-2418. [PMID: 30615184 DOI: 10.1093/jxb/ery435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/28/2018] [Indexed: 05/20/2023]
Abstract
A recent initiative named 'Crops in silico' proposes that multi-scale models 'have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts' in plant science, particularly directed to crop species. To that end, the group called for 'a paradigm shift in plant modelling, from largely isolated efforts to a connected community'. 'Wet' (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community. Parts of this community invested in 'dry' (theoretical) research, under the rubric of Systems Biology. Our past research combined concepts from Systems Biology and crop modelling. Here we outline the approaches that seem most relevant to connected, 'digital organism' initiatives. We illustrate the scale of experimental research required, by collecting the kinetic parameter values that are required for a quantitative, dynamic model of a gene regulatory network. By comparison with the Systems Biology Markup Language (SBML) community, we note computational resources and community structures that will help to realize the potential for plant Systems Biology to connect with a broader crop science community.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Uriel Urquiza
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- EPCC, Bayes Centre, University of Edinburgh, Edinburgh, UK
| | - Gordon D Plotkin
- Laboratory for the Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Oxana Sorokina
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Argyris Zardilis
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tomasz Zielinski
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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17
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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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18
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Upton EC, Maciunas LJ, Loll PJ. Vancomycin does not affect the enzymatic activities of purified VanSA. PLoS One 2019; 14:e0210627. [PMID: 30677074 PMCID: PMC6345502 DOI: 10.1371/journal.pone.0210627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 12/29/2018] [Indexed: 11/18/2022] Open
Abstract
VanS is a membrane-bound sensor histidine kinase responsible for sensing vancomycin and activating transcription of vancomycin-resistance genes. In the presence of vancomycin, VanS phosphorylates the transcription factor VanR, converting it to its transcriptionally active form. In the absence of vancomycin, VanS dephosphorylates VanR, thereby maintaining it in a transcriptionally inactive state. To date, the mechanistic details of how vancomycin modulates VanS activity have remained elusive. We have therefore studied these details in an in vitro system, using the full-length VanS and VanR proteins responsible for type-A vancomycin resistance in enterococci. Both detergent- and amphipol-solubilized VanSA display all the enzymatic activities expected for a sensor histidine kinase, with amphipol reconstitution providing a marked boost in overall activity relative to detergent solubilization. A putative constitutively activated VanSA mutant (T168K) was constructed and purified, and was found to exhibit the expected reduction in phosphatase activity, providing confidence that detergent-solubilized VanSA behaves in a physiologically relevant manner. In both detergent and amphipol solutions, VanSA’s enzymatic activities were found to be insensitive to vancomycin, even at levels many times higher than the antibiotic’s minimum inhibitory concentration. This result argues against direct activation of VanSA via formation of a binary antibiotic-kinase complex, suggesting instead that either additional factors are required to form a functional signaling complex, or that activation does not require direct interaction with the antibiotic.
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Affiliation(s)
- Elizabeth C. Upton
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Lina J. Maciunas
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Patrick J. Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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19
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Kennedy EN, Hebdon SD, Menon SK, Foster CA, Copeland DM, Xu Q, Janiak-Spens F, West AH. Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins. BMC BIOCHEMISTRY 2019; 20:1. [PMID: 30665347 PMCID: PMC6341664 DOI: 10.1186/s12858-019-0104-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/07/2019] [Indexed: 11/29/2022]
Abstract
Background Many bacteria and certain eukaryotes utilize multi-step His-to-Asp phosphorelays for adaptive responses to their extracellular environments. Histidine phosphotransfer (HPt) proteins function as key components of these pathways. HPt proteins are genetically diverse, but share a common tertiary fold with conserved residues near the active site. A surface-exposed glycine at the H + 4 position relative to the phosphorylatable histidine is found in a significant number of annotated HPt protein sequences. Previous reports demonstrated that substitutions at this position result in diminished phosphotransfer activity between HPt proteins and their cognate signaling partners. Results We report the analysis of partner binding interactions and phosphotransfer activity of the prototypical HPt protein Ypd1 from Saccharomyces cerevisiae using a set of H + 4 (G68) substituted proteins. Substitutions at this position with large, hydrophobic, or charged amino acids nearly abolished phospho-acceptance from the receiver domain of its upstream signaling partner, Sln1 (Sln1-R1). An in vitro binding assay indicated that G68 substitutions caused only modest decreases in affinity between Ypd1 and Sln1-R1, and these differences did not appear to be large enough to account for the observed decrease in phosphotransfer activity. The crystal structure of one of these H + 4 mutants, Ypd1-G68Q, which exhibited a diminished ability to participate in phosphotransfer, shows a similar overall structure to that of wild-type. Molecular modelling suggests that the highly conserved active site residues within the receiver domain of Sln1 must undergo rearrangement to accommodate larger H + 4 substitutions in Ypd1. Conclusions Phosphotransfer reactions require precise arrangement of active site elements to align the donor-acceptor atoms and stabilize the transition state during the reaction. Any changes likely result in an inability to form a viable transition state during phosphotransfer. Our data suggest that the high degree of evolutionary conservation of residues with small side chains at the H + 4 position in HPt proteins is required for optimal activity and that the presence of larger residues at the H + 4 position would cause alterations in the positioning of active site residues in the partner response regulator. Electronic supplementary material The online version of this article (10.1186/s12858-019-0104-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emily N Kennedy
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.,Present Address: University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Skyler D Hebdon
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Smita K Menon
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Clay A Foster
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.,Present Address: University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel M Copeland
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.,Present Address: Pacira Pharmaceuticals, San Diego, CA, 92121, USA
| | - Qingping Xu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.,Present Address: GMCA at Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Fabiola Janiak-Spens
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Ann H West
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
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20
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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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21
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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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22
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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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23
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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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24
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Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Sci Rep 2017; 7:9747. [PMID: 28852026 PMCID: PMC5575035 DOI: 10.1038/s41598-017-09617-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/21/2017] [Indexed: 12/13/2022] Open
Abstract
A time-course transcriptome analysis of two cassava varieties that are either resistant or susceptible to cassava brown streak disease (CBSD) was conducted using RNASeq, after graft inoculation with Ugandan cassava brown streak virus (UCBSV). From approximately 1.92 billion short reads, the largest number of differentially expressed genes (DEGs) was obtained in the resistant (Namikonga) variety at 2 days after grafting (dag) (3887 DEGs) and 5 dag (4911 DEGs). At the same time points, several defense response genes (encoding LRR-containing, NBARC-containing, pathogenesis-related, late embryogenesis abundant, selected transcription factors, chaperones, and heat shock proteins) were highly expressed in Namikonga. Also, defense-related GO terms of 'translational elongation', 'translation factor activity', 'ribosomal subunit' and 'phosphorelay signal transduction', were overrepresented in Namikonga at these time points. More reads corresponding to UCBSV sequences were recovered from the susceptible variety (Albert) (733 and 1660 read counts per million (cpm)) at 45 dag and 54 dag compared to Namikonga (10 and 117 cpm respectively). These findings suggest that Namikonga's resistance involves restriction of multiplication of UCBSV within the host. These findings can be used with other sources of evidence to identify candidate genes and biomarkers that would contribute substantially to knowledge-based resistance breeding.
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Affiliation(s)
- T Amuge
- National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - D K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - M S Katari
- Center for Genomics and Systems Biology, New York University, New York, USA
| | - A A Myburg
- Genetics Department, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - S L Goldman
- Center for Genomics and Systems Biology, New York University, New York, USA
| | - M E Ferguson
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya.
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25
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Trajtenberg F, Imelio JA, Machado MR, Larrieux N, Marti MA, Obal G, Mechaly AE, Buschiazzo A. Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action. eLife 2016; 5:e21422. [PMID: 27938660 PMCID: PMC5231405 DOI: 10.7554/elife.21422] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/09/2016] [Indexed: 01/19/2023] Open
Abstract
Two-component systems (TCS) are protein machineries that enable cells to respond to input signals. Histidine kinases (HK) are the sensory component, transferring information toward downstream response regulators (RR). HKs transfer phosphoryl groups to their specific RRs, but also dephosphorylate them, overall ensuring proper signaling. The mechanisms by which HKs discriminate between such disparate directions, are yet unknown. We now disclose crystal structures of the HK:RR complex DesK:DesR from Bacillus subtilis, comprising snapshots of the phosphotransfer and the dephosphorylation reactions. The HK dictates the reactional outcome through conformational rearrangements that include the reactive histidine. The phosphotransfer center is asymmetric, poised for dissociative nucleophilic substitution. The structural bases of HK phosphatase/phosphotransferase control are uncovered, and the unexpected discovery of a dissociative reactional center, sheds light on the evolution of TCS phosphotransfer reversibility. Our findings should be applicable to a broad range of signaling systems and instrumental in synthetic TCS rewiring.
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Affiliation(s)
- Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Juan A Imelio
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Matías R Machado
- Biomolecular Simulations, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Nicole Larrieux
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcelo A Marti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gonzalo Obal
- Protein Biophysics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Ariel E Mechaly
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Département de Microbiologie, Institut Pasteur, Paris, France
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26
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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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27
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Immormino RM, Silversmith RE, Bourret RB. A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation. Biochemistry 2016; 55:5595-5609. [PMID: 27589219 PMCID: PMC5050157 DOI: 10.1021/acs.biochem.6b00645] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Two-component regulatory systems, minimally composed of a sensor kinase and a response regulator protein, are common mediators of signal transduction in microorganisms. All response regulators contain a receiver domain with conserved active site residues that catalyze the signal activating and deactivating phosphorylation and dephosphorylation reactions. We explored the impact of variable active site position T+1 (one residue C-terminal to the conserved Thr/Ser) on reaction kinetics and signaling fidelity, using wild type and mutant Escherichia coli CheY, CheB, and NarL to represent the three major sequence classes observed across response regulators: Ala/Gly, Ser/Thr, and Val/Ile/Met, respectively, at T+1. Biochemical and structural data together suggested that different amino acids at T+1 impacted reaction kinetics by altering access to the active site while not perturbing overall protein structure. A given amino acid at position T+1 had similar effects on autodephosphorylation in each protein background tested, likely by modulating access of the attacking water molecule to the active site. Similarly, rate constants for CheY autophosphorylation with three different small molecule phosphodonors were consistent with the steric constraints on access to the phosphorylation site arising from combination of specific phosphodonors with particular amino acids at T+1. Because other variable active site residues also influence response regulator phosphorylation biochemistry, we began to explore how context (here, the amino acid at T+2) affected the influence of position T+1 on CheY autocatalytic reactions. Finally, position T+1 affected the fidelity and kinetics of phosphotransfer between sensor kinases and response regulators but was not a primary determinant of their interaction.
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Affiliation(s)
| | - Ruth E. Silversmith
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599-7290, United States
| | - Robert B. Bourret
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599-7290, United States
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28
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Hörnschemeyer P, Liss V, Heermann R, Jung K, Hunke S. Interaction Analysis of a Two-Component System Using Nanodiscs. PLoS One 2016; 11:e0149187. [PMID: 26882435 PMCID: PMC4755656 DOI: 10.1371/journal.pone.0149187] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/28/2016] [Indexed: 11/25/2022] Open
Abstract
Two-component systems are the major means by which bacteria couple adaptation to environmental changes. All utilize a phosphorylation cascade from a histidine kinase to a response regulator, and some also employ an accessory protein. The system-wide signaling fidelity of two-component systems is based on preferential binding between the signaling proteins. However, information on the interaction kinetics between membrane embedded histidine kinase and its partner proteins is lacking. Here, we report the first analysis of the interactions between the full-length membrane-bound histidine kinase CpxA, which was reconstituted in nanodiscs, and its cognate response regulator CpxR and accessory protein CpxP. Using surface plasmon resonance spectroscopy in combination with interaction map analysis, the affinity of membrane-embedded CpxA for CpxR was quantified, and found to increase by tenfold in the presence of ATP, suggesting that a considerable portion of phosphorylated CpxR might be stably associated with CpxA in vivo. Using microscale thermophoresis, the affinity between CpxA in nanodiscs and CpxP was determined to be substantially lower than that between CpxA and CpxR. Taken together, the quantitative interaction data extend our understanding of the signal transduction mechanism used by two-component systems.
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Affiliation(s)
- Patrick Hörnschemeyer
- Fachbereich Biologie/Chemie, Mikrobiologie, Universität Osnabrück, Barbarastrasse 11, D-49076, Osnabrück, Germany
| | - Viktoria Liss
- Fachbereich Biologie/Chemie, Mikrobiologie, Universität Osnabrück, Barbarastrasse 11, D-49076, Osnabrück, Germany
| | - Ralf Heermann
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, 82152, Martinsried, Germany
| | - Kirsten Jung
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, 82152, Martinsried, Germany
| | - Sabine Hunke
- Fachbereich Biologie/Chemie, Mikrobiologie, Universität Osnabrück, Barbarastrasse 11, D-49076, Osnabrück, Germany
- * E-mail:
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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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30
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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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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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Zhang J, Yu J, Wen CK. An alternate route of ethylene receptor signaling. FRONTIERS IN PLANT SCIENCE 2014; 5:648. [PMID: 25477894 PMCID: PMC4238421 DOI: 10.3389/fpls.2014.00648] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/03/2014] [Indexed: 05/29/2023]
Abstract
The gaseous plant hormone ethylene is perceived by a family of ethylene receptors and mediates an array of ethylene responses. In the absence of ethylene, receptor signaling is conveyed via the C-terminal histidine kinase domain to the N-terminus of the CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) protein kinase, which represses ethylene signaling mediated by ETHYLENE INSENSITIVE2 (EIN2) followed by EIN3. In the presence of ethylene, the receptors are inactivated when ethylene binds to their N-terminal domain, and consequently CTR1 is inactive, allowing EIN2 and EIN3 to activate ethylene signaling. Recent findings have shown that the ethylene receptor N-terminal portion can conditionally mediate the receptor signal output in mutants lacking CTR1, thus providing evidence of an alternative pathway from the ethylene receptors not involving CTR1. Here we highlight the evidence for receptor signaling to an alternative pathway and suggest that receptor signaling is coordinated via the N- and C-termini, as we address the biological significance of the negative regulation of ethylene signaling by the two pathways.
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Affiliation(s)
| | | | - Chi-Kuang Wen
- *Correspondence: Chi-Kuang Wen, National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China 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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Dickson CF, Kumar KK, Jacques DA, Malmirchegini GR, Spirig T, Mackay JP, Clubb RT, Guss JM, Gell DA. Structure of the hemoglobin-IsdH complex reveals the molecular basis of iron capture by Staphylococcus aureus. J Biol Chem 2014; 289:6728-6738. [PMID: 24425866 DOI: 10.1074/jbc.m113.545566] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Staphylococcus aureus causes life-threatening disease in humans. The S. aureus surface protein iron-regulated surface determinant H (IsdH) binds to mammalian hemoglobin (Hb) and extracts heme as a source of iron, which is an essential nutrient for the bacteria. However, the process of heme transfer from Hb is poorly understood. We have determined the structure of IsdH bound to human Hb by x-ray crystallography at 4.2 Å resolution, revealing the structural basis for heme transfer. One IsdH molecule is bound to each α and β Hb subunit, suggesting that the receptor acquires iron from both chains by a similar mechanism. Remarkably, two near iron transporter (NEAT) domains in IsdH perform very different functions. An N-terminal NEAT domain binds α/β globin through a site distant from the globin heme pocket and, via an intervening structural domain, positions the C-terminal heme-binding NEAT domain perfectly for heme transfer. These data, together with a 2.3 Å resolution crystal structure of the isolated N-terminal domain bound to Hb and small-angle x-ray scattering of free IsdH, reveal how multiple domains of IsdH cooperate to strip heme from Hb. Many bacterial pathogens obtain iron from human hemoglobin using proteins that contain multiple NEAT domains and other domains whose functions are poorly understood. Our results suggest that, rather than acting as isolated units, NEAT domains may be integrated into higher order architectures that employ multiple interaction interfaces to efficiently extract heme from host proteins.
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Affiliation(s)
- Claire F Dickson
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Kaavya Krishna Kumar
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales 2006, Australia
| | - David A Jacques
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Thomas Spirig
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Joel P Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - J Mitchell Guss
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales 2006, Australia
| | - David A Gell
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia.
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Lopato S, Borisjuk N, Langridge P, Hrmova M. Endosperm transfer cell-specific genes and proteins: structure, function and applications in biotechnology. FRONTIERS IN PLANT SCIENCE 2014; 5:64. [PMID: 24578704 PMCID: PMC3936200 DOI: 10.3389/fpls.2014.00064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/07/2014] [Indexed: 05/21/2023]
Abstract
Endosperm transfer cells (ETC) are one of four main types of cells in endosperm. A characteristic feature of ETC is the presence of cell wall in-growths that create an enlarged plasma membrane surface area. This specialized cell structure is important for the specific function of ETC, which is to transfer nutrients from maternal vascular tissue to endosperm. ETC-specific genes are of particular interest to plant biotechnologists, who use genetic engineering to improve grain quality and yield characteristics of important field crops. The success of molecular biology-based approaches to manipulating ETC function is dependent on a thorough understanding of the functions of ETC-specific genes and ETC-specific promoters. The aim of this review is to summarize the existing data on structure and function of ETC-specific genes and their products. Potential applications of ETC-specific genes, and in particular their promoters for biotechnology will be discussed.
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Affiliation(s)
- Sergiy Lopato
- *Correspondence: Sergiy Lopato, Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia e-mail:
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