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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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Phosphoproteomics of Mycobacterium-host interaction and inspirations for novel measures against tuberculosis. Cell Signal 2022; 91:110238. [PMID: 34986388 DOI: 10.1016/j.cellsig.2021.110238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/19/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (Mtb) remains a tremendous global public health concern. Deciphering the biology of the pathogen and its interaction with host can inspire new measures against tuberculosis. Phosphorylation plays versatile and important role in the pathogen and host physiology, such as virulence, signaling and immune response. Proteome-wide phosphorylation of Mtb and its infected host cells, namely phosphoproteome, can inform the post-translational modification of the interaction network between the pathogen and the host, key targets for novel antibiotics. We summarized the phosphoproteome of Mtb, as well as the host, focusing on potential application for new measures against tuberculosis.
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Bourret RB, Kennedy EN, Foster CA, Sepúlveda VE, Goldman WE. A Radical Reimagining of Fungal Two-Component Regulatory Systems. Trends Microbiol 2021; 29:883-893. [PMID: 33853736 DOI: 10.1016/j.tim.2021.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/17/2022]
Abstract
Bacterial two-component regulatory systems (TCSs) mediate signal transduction by transferring phosphoryl groups between sensor kinase and response regulator proteins, sometimes using intermediary histidine-phosphotransferase (Hpt) domains to form multistep phosphorelays. Because (i) almost all known fungal sensor kinases exhibit a domain architecture characteristic of bacterial TCS phosphorelays, (ii) all known fungal Hpts are stand-alone proteins suited to shuttle between cytoplasm and nucleus, and (iii) the best-characterized fungal TCS is a canonical phosphorelay, it is widely assumed that most or all fungal TCSs function via phosphorelays. However, fungi generally encode more sensor kinases than Hpts or response regulators, leading to a disparity between putative phosphorelay inputs and outputs. The simplest resolution of this paradox is to hypothesize that most fungal sensor kinases do not participate in phosphorelays. Reimagining how fungal TCSs might function leads to multiple testable predictions.
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Affiliation(s)
- Robert B Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA.
| | - Emily N Kennedy
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
| | - Clay A Foster
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
| | - Victoria E Sepúlveda
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
| | - William E Goldman
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
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Modulation of Response Regulator CheY Reaction Kinetics by Two Variable Residues That Affect Conformation. J Bacteriol 2020; 202:JB.00089-20. [PMID: 32424010 DOI: 10.1128/jb.00089-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/09/2020] [Indexed: 01/16/2023] Open
Abstract
Microorganisms and plants utilize two-component systems to regulate adaptive responses to changing environmental conditions. Sensor kinases detect stimuli and alter their autophosphorylation activity accordingly. Signal propagation occurs via the transfer of phosphoryl groups from upstream kinases to downstream response regulator proteins. Removal of phosphoryl groups from the response regulator typically resets the system. Members of the same protein family may catalyze phosphorylation and dephosphorylation reactions with different efficiencies, exhibiting rate constants spanning many orders of magnitude to accommodate response time scales from milliseconds to days. We previously found that variable positions one or two residues to the C-terminal side of the conserved Asp phosphorylation site (D+2) or Thr/Ser (T+1/T+2) in response regulators alter reaction kinetics by direct interaction with phosphodonor or phosphoacceptor molecules. Here, we explore the kinetic effects of amino acid substitutions at the two positions immediately C-terminal to the conserved Lys (K+1/K+2) in the model Escherichia coli response regulator CheY. We measured CheY autophosphorylation and autodephosphorylation rate constants for 27 pairs of K+1/K+2 residues that represent 84% of naturally occurring response regulators. Effects on autodephosphorylation were modest, but autophosphorylation rate constants varied by 2 orders of magnitude, suggesting that the K+1/K+2 positions influence reaction kinetics by altering the conformational spectrum sampled by CheY at equilibrium. Additional evidence supporting this indirect mechanism includes the following: the effect on autophosphorylation rate constants is independent of the phosphodonor, the autophosphorylation rate constants and dissociation constants for the phosphoryl group analog BeF3 - are inversely correlated, and the K+1/K+2 positions are distant from the phosphorylation site.IMPORTANCE We have identified five variable positions in response regulators that allow the rate constants of autophosphorylation and autodephosporylation reactions each to be altered over 3 orders of magnitude in CheY. The distributions of variable residue combinations across response regulator subfamilies suggest that distinct mechanisms associated with different variable positions allow reaction rates to be tuned independently during evolution for diverse biological purposes. This knowledge could be used in synthetic-biology applications to adjust the properties (e.g., background noise and response duration) of biosensors and may allow prediction of response regulator reaction kinetics from the primary amino acid sequence.
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Bourret RB, Silversmith RE. Measuring the Activities of Two-Component Regulatory System Phosphatases. Methods Enzymol 2018; 607:321-351. [PMID: 30149864 DOI: 10.1016/bs.mie.2018.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Two-component regulatory systems (TCSs) are used for signal transduction by organisms from all three phylogenetic domains of the living world. TCSs use transient protein phosphorylation and dephosphorylation reactions to convert stimuli into appropriate responses to changing environmental conditions. Phosphoryl groups flow from ATP to sensor kinases (which detect stimuli) to response regulators (which implement responses) to inorganic phosphate (Pi). The phosphorylation state of response regulators controls their output activity. The rate at which phosphoryl groups are removed from response regulators correlates with the timescale of the corresponding biological function. Dephosphorylation reactions are fastest in chemotaxis TCS and slower in other TCS. Response regulators catalyze their own dephosphorylation, but at least five types of phosphatases are known to enhance dephosphorylation of response regulators. In each case, the phosphatases are believed to stimulate the intrinsic autodephosphorylation reaction. We discuss in depth the properties of TCS (particularly the differences between chemotaxis and nonchemotaxis TCS) relevant to designing in vitro assays for TCS phosphatases. We describe detailed assay methods for chemotaxis TCS phosphatases using loss of 32P, change in intrinsic fluorescence as a result of dephosphorylation, or release of Pi. The phosphatase activities of nonchemotaxis TCS phosphatases are less well characterized. We consider how the properties of nonchemotaxis TCS affect assay design and suggest suitable modifications for phosphatases from nonchemotaxis TCS, with an emphasis on the Pi release method.
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Affiliation(s)
- Robert B Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States.
| | - Ruth E Silversmith
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States
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Silversmith RE, Bourret RB. Fluorescence Measurement of Kinetics of CheY Autophosphorylation with Small Molecule Phosphodonors. Methods Mol Biol 2018; 1729:321-335. [PMID: 29429101 DOI: 10.1007/978-1-4939-7577-8_25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The Escherichia coli chemotaxis protein CheY is a model receiver domain containing a native tryptophan residue that serves as a fluorescent probe for CheY autophosphorylation with small molecule phosphodonors. Here we describe fluorescence measurement of apparent bimolecular rate constants for reaction of wild type and mutant CheY with phosphodonors acetyl phosphate, phosphoramidate, or monophosphoimidazole. Step-by-step protocols to synthesize phosphoramidate (K+ salt) and monophosphoimidazole (Na+ salt), which are not commercially available, are provided. Key factors to consider in developing autophosphorylation assays for other response regulators are also discussed.
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Affiliation(s)
- Ruth E Silversmith
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Robert B Bourret
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
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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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Experimental Analysis of Functional Variation within Protein Families: Receiver Domain Autodephosphorylation Kinetics. J Bacteriol 2016; 198:2483-93. [PMID: 27381915 DOI: 10.1128/jb.00853-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 06/28/2016] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED Plants and microorganisms use two-component signal transduction systems (TCSs) to mediate responses to environmental stimuli. TCSs mediate responses through phosphotransfer from a conserved histidine on a sensor kinase to a conserved aspartate on the receiver domain of a response regulator. Typically, signal termination occurs through dephosphorylation of the receiver domain, which can catalyze its own dephosphorylation. Despite strong structural conservation between receiver domains, reported autodephosphorylation rate constants (kdephos) span a millionfold range. Variable receiver domain active-site residues D + 2 and T + 2 (two amino acids C terminal to conserved phosphorylation site and Thr/Ser, respectively) influence kdephos values, but the extent and mechanism of influence are unclear. We used sequence analysis of a large database of naturally occurring receiver domains to design mutant receiver domains for experimental analysis of autodephosphorylation kinetics. When combined with previous analyses, kdephos values were obtained for CheY variants that contained D + 2/T + 2 pairs found in 54% of receiver domain sequences. Tested pairs of amino acids at D + 2/T + 2 generally had similar effects on kdephos in CheY, PhoBN, or Spo0F. Acid or amide residues at D + 2/T + 2 enhanced kdephos CheY variants altered at D + 2/T + 2 exhibited rate constants for autophosphorylation with phosphoramidates and autodephosphorylation that were inversely correlated, suggesting that D + 2/T + 2 residues interact with aspects of the ground or transition states that differ between the two reactions. kdephos of CheY variants altered at D + 2/T + 2 correlated significantly with kdephos of wild-type receiver domains containing the same D + 2/T + 2 pair. Additionally, particular D + 2/T + 2 pairs were enriched in different response regulator subfamilies, suggesting functional significance. IMPORTANCE One protein family, defined by a conserved domain, can include hundreds of thousands of known members. Characterizing conserved residues within a conserved domain can identify functions shared by all family members. However, a general strategy to assess features that differ between members of a family is lacking. Fully exploring the impact of just two variable positions within a conserved domain could require assessment of 400 (i.e., 20 × 20) variants. Instead, we created and analyzed a nonredundant database of receiver domain sequences. Five percent of D + 2/T + 2 pairs were sufficient to represent 50% of receiver domain sequences. Using protein sequence analysis to prioritize mutant choice made it experimentally feasible to extensively probe the influence of positions D + 2 and T + 2 on receiver domain autodephosphorylation kinetics.
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Allen KN, Dunaway-Mariano D. Catalytic scaffolds for phosphoryl group transfer. Curr Opin Struct Biol 2016; 41:172-179. [PMID: 27526404 DOI: 10.1016/j.sbi.2016.07.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022]
Abstract
A single genome encodes a large number of phosphoryl hydrolases for the purposes of phosphate recycling, primary and secondary metabolism, signal transduction and regulation, and protection from xenobiotics. Phosphate monoester hydrolysis faces a high kinetic barrier, yet there are multiple solutions to the problem both in terms of catalytic mechanisms and three-dimensional structure of the hydrolases. Recent structural and mechanistic findings highlight the trigonal-bipyramidal nature of the transition state for enzyme promoted phosphate monoester hydrolysis and the evolution and role of inserted loops/domains in governing substrate specificity and promiscuity. Important questions remain as to how electrostatics modulate water networks and critical proton-transfer events. How substrate targeting and catalysis is achieved by the independently evolved catalytic platforms is compared and contrasted in this article.
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Affiliation(s)
- Karen N Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215-2521, USA.
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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