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Cassidy CK, Qin Z, Frosio T, Gosink K, Yang Z, Sansom MSP, Stansfeld PJ, Parkinson JS, Zhang P. Structure of the native chemotaxis core signaling unit from phage E-protein lysed E. coli cells. mBio 2023; 14:e0079323. [PMID: 37772839 PMCID: PMC10653900 DOI: 10.1128/mbio.00793-23] [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: 03/28/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Bacterial chemotaxis is a ubiquitous behavior that enables cell movement toward or away from specific chemicals. It serves as an important model for understanding cell sensory signal transduction and motility. Characterization of the molecular mechanisms underlying chemotaxis is of fundamental interest and requires a high-resolution structural picture of the sensing machinery, the chemosensory array. In this study, we combine cryo-electron tomography and molecular simulation to present the complete structure of the core signaling unit, the basic building block of chemosensory arrays, from Escherichia coli. Our results provide new insight into previously poorly-resolved regions of the complex and offer a structural basis for designing new experiments to test mechanistic hypotheses.
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Affiliation(s)
- C. Keith Cassidy
- Diamond Light Source, Didcot, United Kingdom
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri, USA
| | - Zhuan Qin
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Khoosheh Gosink
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - John S. Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Peijun Zhang
- Diamond Light Source, Didcot, United Kingdom
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
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Tran T, Karunanayake Mudiyanselage APKK, Eyles SJ, Thompson LK. Bacterial chemoreceptor signaling complexes control kinase activity by stabilizing the catalytic domain of CheA. Proc Natl Acad Sci U S A 2023; 120:e2218467120. [PMID: 37523532 PMCID: PMC10410752 DOI: 10.1073/pnas.2218467120] [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: 10/28/2022] [Accepted: 07/10/2023] [Indexed: 08/02/2023] Open
Abstract
Motile bacteria have a chemotaxis system that enables them to sense their environment and direct their swimming toward favorable conditions. Chemotaxis involves a signaling process in which ligand binding to the extracellular domain of the chemoreceptor alters the activity of the histidine kinase, CheA, bound ~300 Å away to the distal cytoplasmic tip of the receptor, to initiate a phosphorylation cascade that controls flagellar rotation. The cytoplasmic domain of the receptor is thought to propagate this signal via changes in dynamics and/or stability, but it is unclear how these changes modulate the kinase activity of CheA. To address this question, we have used hydrogen deuterium exchange mass spectrometry to probe the structure and dynamics of CheA within functional signaling complexes of the Escherichia coli aspartate receptor cytoplasmic fragment, CheA, and CheW. Our results reveal that stabilization of the P4 catalytic domain of CheA correlates with kinase activation. Furthermore, differences in activation of the kinase that occur during sensory adaptation depend on receptor destabilization of the P3 dimerization domain of CheA. Finally, hydrogen exchange properties of the P1 domain that bears the phosphorylated histidine identify the dimer interface of P1/P1' in the CheA dimer and support an ordered sequential binding mechanism of catalysis, in which dimeric P1/P1' has productive interactions with P4 only upon nucleotide binding. Thus stabilization/destabilization of domains is a key element of the mechanism of modulating CheA kinase activity in chemotaxis, and may play a role in the control of other kinases.
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Affiliation(s)
- Thomas Tran
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA01003
| | | | - Stephen J. Eyles
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA01003
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA01003
| | - Lynmarie K. Thompson
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA01003
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Hadjidemetriou K, Kaur S, Cassidy CK, Zhang P. Mechanisms of E. coli chemotaxis signaling pathways visualized using cryoET and computational approaches. Biochem Soc Trans 2022; 50:1595-1605. [PMID: 36421737 PMCID: PMC9788364 DOI: 10.1042/bst20220191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022]
Abstract
Chemotaxis signaling pathways enable bacteria to sense and respond to their chemical environment and, in some species, are critical for lifestyle processes such as biofilm formation and pathogenesis. The signal transduction underlying chemotaxis behavior is mediated by large, highly ordered protein complexes known as chemosensory arrays. For nearly two decades, cryo-electron tomography (cryoET) has been used to image chemosensory arrays, providing an increasingly detailed understanding of their structure and function. In this mini-review, we provide an overview of the use of cryoET to study chemosensory arrays, including imaging strategies, key results, and outstanding questions. We further discuss the application of molecular modeling and simulation techniques to complement structure determination efforts and provide insight into signaling mechanisms. We close the review with a brief outlook, highlighting promising future directions for the field.
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Affiliation(s)
| | - Satinder Kaur
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - C. Keith Cassidy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Peijun Zhang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, U.K
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Maschmann Z, Chandrasekaran S, Chua TK, Crane BR. Interdomain Linkers Regulate Histidine Kinase Activity by Controlling Subunit Interactions. Biochemistry 2022; 61:2672-2686. [PMID: 36321948 PMCID: PMC10134573 DOI: 10.1021/acs.biochem.2c00326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Bacterial chemoreceptors regulate the cytosolic multidomain histidine kinase CheA through largely unknown mechanisms. Residue substitutions in the peptide linkers that connect the P4 kinase domain to the P3 dimerization and P5 regulatory domain affect CheA basal activity and activation. To understand the role that these linkers play in CheA activity, the P3-to-P4 linker (L3) and P4-to-P5 linker (L4) were extended and altered in variants of Thermotoga maritima (Tm) CheA. Flexible extensions of the L3 and L4 linkers in CheA-LV1 (linker variant 1) allowed for a well-folded kinase domain that retained wild-type (WT)-like binding affinities for nucleotide and normal interactions with the receptor-coupling protein CheW. However, CheA-LV1 autophosphorylation activity registered ∼50-fold lower compared to WT. Neither a WT nor LV1 dimer containing a single P4 domain could autophosphorylate the P1 substrate domain. Autophosphorylation activity was rescued in variants with extended L3 and L4 linkers that favor helical structure and heptad spacing. Autophosphorylation depended on linker spacing and flexibility and not on sequence. Pulse-dipolar electron-spin resonance (ESR) measurements with spin-labeled adenosine 5'-triphosphate (ATP) analogues indicated that CheA autophosphorylation activity inversely correlated with the proximity of the P4 domains within the dimers of the variants. Despite their separation in primary sequence and space, the L3 and L4 linkers also influence the mobility of the P1 substrate domains. In all, interactions of the P4 domains, as modulated by the L3 and L4 linkers, affect domain dynamics and autophosphorylation of CheA, thereby providing potential mechanisms for receptors to regulate the kinase.
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Affiliation(s)
- Zachary Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
| | - Siddarth Chandrasekaran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
- National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca NY 1485
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
- National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca NY 1485
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Piñas GE, DeSantis MD, Cassidy CK, Parkinson JS. Hexameric rings of the scaffolding protein CheW enhance response sensitivity and cooperativity in Escherichia coli chemoreceptor arrays. Sci Signal 2022; 15:eabj1737. [PMID: 35077199 DOI: 10.1126/scisignal.abj1737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Escherichia coli chemoreceptor array is a supramolecular assembly that enables cells to respond to extracellular cues dynamically and with great precision and sensitivity. In the array, transmembrane receptors organized as trimers of dimers are connected at their cytoplasmic tips by hexameric rings of alternating subunits of the kinase CheA and the scaffolding protein CheW (CheA-CheW rings). Interactions of CheW molecules with the members of receptor trimers not directly bound to CheA-CheW rings may lead to the formation of hexameric CheW rings in the chemoreceptor array. Here, we detected such CheW rings with a cellular cysteine-directed cross-linking assay and explored the requirements for their formation and their participation in array assembly. We found that CheW ring formation varied with cellular CheW abundance, depended on the presence of receptors capable of a trimer-of-dimers arrangement, and did not require CheA. Cross-linking studies of a CheA~CheW fusion protein incapable of forming homomeric CheW oligomers demonstrated that CheW rings were not essential for the assembly of CheA-containing arrays. Förster resonance energy transfer (FRET)-based kinase assays of arrays containing variable amounts of CheW rings revealed that CheW rings enhanced the cooperativity and the sensitivity of the responses to attractants. We propose that six-membered CheW rings provide the additional interconnectivity required for optimal signaling and gradient tracking performance by chemosensory arrays.
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Affiliation(s)
- Germán E Piñas
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D DeSantis
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - John S Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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Muok AR, Chua TK, Srivastava M, Yang W, Maschmann Z, Borbat PP, Chong J, Zhang S, Freed JH, Briegel A, Crane BR. Engineered chemotaxis core signaling units indicate a constrained kinase-off state. Sci Signal 2020; 13:13/657/eabc1328. [PMID: 33172954 DOI: 10.1126/scisignal.abc1328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacterial chemoreceptors, the histidine kinase CheA, and the coupling protein CheW form transmembrane molecular arrays with remarkable sensing properties. The receptors inhibit or stimulate CheA kinase activity depending on the presence of attractants or repellants, respectively. We engineered chemoreceptor cytoplasmic regions to assume a trimer of receptor dimers configuration that formed well-defined complexes with CheA and CheW and promoted a CheA kinase-off state. These mimics of core signaling units were assembled to homogeneity and investigated by site-directed spin-labeling with pulse-dipolar electron-spin resonance spectroscopy (PDS), small-angle x-ray scattering, targeted protein cross-linking, and cryo-electron microscopy. The kinase-off state was especially stable, had relatively low domain mobility, and associated the histidine substrate and docking domains with the kinase core, thus preventing catalytic activity. Together, these data provide an experimentally restrained model for the inhibited state of the core signaling unit and suggest that chemoreceptors indirectly sequester the kinase and substrate domains to limit histidine autophosphorylation.
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Affiliation(s)
- Alise R Muok
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Wen Yang
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Zach Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Petr P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Jenna Chong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Sheng Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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Jun SY, Pan W, Hazelbauer GL. ATP Binding as a Key Target for Control of the Chemotaxis Kinase. J Bacteriol 2020; 202:e00095-20. [PMID: 32341073 PMCID: PMC7283602 DOI: 10.1128/jb.00095-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
In bacterial chemotaxis, chemoreceptors in signaling complexes modulate the activity of two-component histidine kinase CheA in response to chemical stimuli. CheA catalyzes phosphoryl transfer from ATP to a histidinyl residue of its P1 domain. That phosphoryl group is transferred to two response regulators. Receptor control is almost exclusively at autophosphorylation, but the aspect of enzyme action on which that control acts is unclear. We investigated this by a kinetic analysis of activated kinase in signaling complexes. We found that phosphoryl transfer from ATP to P1 is an ordered sequential reaction in which the binding of ATP to CheA is the necessary first step; the second substrate, the CheA P1 domain, binds only to an ATP-occupied enzyme; and phosphorylated P1 is released prior to the second product, namely, ADP. We confirmed the crucial features of this kinetically deduced ordered mechanism by assaying P1 binding to the enzyme. In the absence of a bound nucleotide, there was no physiologically significant binding, but the enzyme occupied with a nonhydrolyzable ATP analog bound P1. Previous structural and computational analyses indicated that ATP binding creates the P1-binding site by ordering the "ATP lid." This process identifies the structural basis for the ordered kinetic mechanism. Recent mathematical modeling of kinetic data identified ATP binding as a focus of receptor-mediated kinase control. The ordered kinetic mechanism provides the biochemical logic of that control. We conclude that chemoreceptors modulate kinase by controlling ATP binding. Structural similarities among two-component kinases, particularly the ATP lid, suggest that ordered mechanisms and control of ATP binding are general features of two-component signaling.IMPORTANCE Our work provides important new insights into the action of the chemotaxis signaling kinase CheA by identifying the kinetic mechanism of its autophosphorylation as an ordered sequential reaction, in which the required first step is binding of ATP. These insights provide a framework for integrating previous kinetic, mathematical modeling, structural, simulation, and docking observations to conclude that chemoreceptors control the activity of the chemotaxis kinase by regulating binding of the autophosphorylation substrate ATP. Previously observed conformational changes in the ATP lid of the enzyme active site provide a structural basis for the ordered mechanism. Such lids are characteristic of two-component histidine kinases in general, suggesting that ordered sequential mechanisms and regulation by controlling ATP binding are common features of these kinases.
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Affiliation(s)
- Se-Young Jun
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Wenlin Pan
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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8
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Burt A, Cassidy CK, Ames P, Bacia-Verloop M, Baulard M, Huard K, Luthey-Schulten Z, Desfosses A, Stansfeld PJ, Margolin W, Parkinson JS, Gutsche I. Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain. Nat Commun 2020; 11:743. [PMID: 32029744 PMCID: PMC7005262 DOI: 10.1038/s41467-020-14350-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/21/2019] [Indexed: 12/01/2022] Open
Abstract
Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays. Understanding stimulus detection and transmission at the molecular level requires precise structural characterisation of the array building block known as a core signalling unit. Here we introduce an Escherichia coli strain that forms small minicells possessing extended and highly ordered chemosensory arrays. We use cryo-electron tomography and subtomogram averaging to provide a three-dimensional map of a complete core signalling unit, with visible densities corresponding to the HAMP and periplasmic domains. This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields a molecular model of the transmembrane core signalling unit and enables spatial localisation of its individual domains. Our work thus offers a solid structural basis for the interpretation of a wide range of existing data and the design of further experiments to elucidate signalling mechanisms within the core signalling unit and larger array.
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Affiliation(s)
- Alister Burt
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter Ames
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Megghane Baulard
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Karine Huard
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - William Margolin
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - John S Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
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