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Article ; Online: A nonequilibrium allosteric model for receptor-kinase complexes: The role of energy dissipation in chemotaxis signaling.

Hathcock, David / Yu, Qiwei / Mello, Bernardo A / Amin, Divya N / Hazelbauer, Gerald L / Tu, Yuhai

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 42, Page(s) e2303115120

Abstract: ... ...

Abstract	The
MeSH term(s)	Chemotaxis/physiology ; Methyl-Accepting Chemotaxis Proteins/metabolism ; Escherichia coli Proteins/metabolism ; Ligands ; Histidine Kinase/metabolism ; Escherichia coli/metabolism ; Signal Transduction/physiology ; Bacterial Proteins/metabolism
Chemical Substances	Methyl-Accepting Chemotaxis Proteins ; Escherichia coli Proteins ; Ligands ; Histidine Kinase (EC 2.7.13.1) ; Bacterial Proteins
Language	English
Publishing date	2023-10-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2303115120
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Article ; Online: Resolving the binding-kinase discrepancy in bacterial chemotaxis: A nonequilibrium allosteric model and the role of energy dissipation.

Hathcock, David / Yu, Qiwei / Mello, Bernardo A / Amin, Divya N / Hazelbauer, Gerald L / Tu, Yuhai

ArXiv

2023

Abstract: The Escherichia coli chemotaxis signaling pathway has served as a model system for studying the adaptive sensing of environmental signals by large protein complexes. The chemoreceptors control the kinase activity of CheA in response to the extracellular ... ...

Abstract	The Escherichia coli chemotaxis signaling pathway has served as a model system for studying the adaptive sensing of environmental signals by large protein complexes. The chemoreceptors control the kinase activity of CheA in response to the extracellular ligand concentration and adapt across a wide concentration range by undergoing methylation and demethylation. Methylation shifts the kinase response curve by orders of magnitude in ligand concentration while incurring a much smaller change in the ligand binding curve. Here, we show that this asymmetric shift in binding and kinase response is inconsistent with equilibrium allosteric models regardless of parameter choices. To resolve this inconsistency, we present a nonequilibrium allosteric model that explicitly includes the dissipative reaction cycles driven by ATP hydrolysis. The model successfully explains all existing measurements for both aspartate and serine receptors. Our results suggest that while ligand binding controls the equilibrium balance between the ON and OFF states of the kinase, receptor methylation modulates the kinetic properties (e.g., the phosphorylation rate) of the ON state. Furthermore, sufficient energy dissipation is necessary for maintaining and enhancing the sensitivity range and amplitude of the kinase response. We demonstrate that the nonequilibrium allosteric model is broadly applicable to other sensor-kinase systems by successfully fitting previously unexplained data from the DosP bacterial oxygen-sensing system. Overall, this work provides a new perspective on cooperative sensing by large protein complexes and opens up new research directions for understanding their microscopic mechanisms through simultaneous measurements and modeling of ligand binding and downstream responses.
Language	English
Publishing date	2023-02-23
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
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Article ; Online: Methyltransferase CheR binds to its chemoreceptor substrates independent of their signaling conformation yet modifies them differentially.

Li, Mingshan / Hazelbauer, Gerald L

Protein science : a publication of the Protein Society

2019 Volume 29, Issue 2, Page(s) 443–454

Abstract: Methylation of specific chemoreceptor glutamyl residues by methyltransferase CheR mediates sensory adaptation and gradient sensing in bacterial chemotaxis. Enzyme action is a function of chemoreceptor signaling conformation: kinase-off receptors are more ...

Abstract	Methylation of specific chemoreceptor glutamyl residues by methyltransferase CheR mediates sensory adaptation and gradient sensing in bacterial chemotaxis. Enzyme action is a function of chemoreceptor signaling conformation: kinase-off receptors are more readily methylated than kinase-on, a feature central to adaptational and gradient-sensing mechanisms. Differential enzyme action could reflect differential binding, catalysis or both. We investigated by measuring CheR binding to kinase-off and kinase-on forms of Escherichia coli aspartate receptor Tar deleted of its CheR-tethering, carboxyl terminus pentapeptide. This allowed characterization of the low-affinity binding of enzyme to the substrate receptor body, otherwise masked by high-affinity interaction with pentapeptide. We quantified the low-affinity protein-protein interactions by determining kinetic rate constants of association and dissociation using bio-layer interferometry and from those values calculating equilibrium constants. Whether Tar signaling conformations were shifted by ligand occupancy or adaptational modification, there was little or no difference between the two signaling conformations in kinetic or equilibrium parameters of enzyme-receptor binding. Thus, differential methyltransferase action does not reflect differential binding. Instead, the predominant determinants of binding must be common to different signaling conformations. Characterization of the dependence of association rate constants on Deybe length, a measure of the influence of electrostatics, implicated electrostatic interactions as a common binding determinant. Taken together, our observations indicate that differential action of methyltransferase on kinase-off and kinase-on chemoreceptors is not the result of differential binding and suggest it reflects differential catalytic propensity. Differential catalysis rather than binding could well be central to other enzymes distinguishing alternative conformations of protein substrates.
MeSH term(s)	Escherichia coli/chemistry ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Kinetics ; Methyltransferases/chemistry ; Methyltransferases/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Receptors, Cell Surface/chemistry ; Receptors, Cell Surface/metabolism ; Substrate Specificity
Chemical Substances	Escherichia coli Proteins ; Receptors, Cell Surface ; Tar protein, E coli ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2019-11-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3760
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Article ; Online: ATP Binding as a Key Target for Control of the Chemotaxis Kinase.

Jun, Se-Young / Pan, Wenlin / Hazelbauer, Gerald L

Journal of bacteriology

2020 Volume 202, Issue 13

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 ... ...

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.
MeSH term(s)	Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Binding Sites ; Chemotaxis ; Escherichia coli/chemistry ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli/physiology ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Histidine Kinase/chemistry ; Histidine Kinase/genetics ; Histidine Kinase/metabolism ; Kinetics ; Methyl-Accepting Chemotaxis Proteins/chemistry ; Methyl-Accepting Chemotaxis Proteins/genetics ; Methyl-Accepting Chemotaxis Proteins/metabolism ; Models, Molecular
Chemical Substances	Escherichia coli Proteins ; Methyl-Accepting Chemotaxis Proteins ; Adenosine Diphosphate (61D2G4IYVH) ; Adenosine Triphosphate (8L70Q75FXE) ; Histidine Kinase (EC 2.7.13.1) ; cheA protein, E coli (EC 2.7.13.3)
Language	English
Publishing date	2020-06-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00095-20
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Article ; Online: A Selective Tether Recruits Activated Response Regulator CheB to Its Chemoreceptor Substrate.

Li, Mingshan / Xu, Xianjin / Zou, Xiaoqin / Hazelbauer, Gerald L

mBio

2021 Volume 12, Issue 6, Page(s) e0310621

Abstract: Methylesterase/deamidase CheB is a key component of bacterial chemotaxis systems. It is also a prominent example of a two-component response regulator in which the effector domain is an enzyme. Like other response regulators, CheB is activated by ... ...

Abstract	Methylesterase/deamidase CheB is a key component of bacterial chemotaxis systems. It is also a prominent example of a two-component response regulator in which the effector domain is an enzyme. Like other response regulators, CheB is activated by phosphorylation of an aspartyl residue in its regulatory domain, creating an open conformation between its two domains. Studies of CheB in Escherichia coli and related organisms have shown that its enzymatic action is also enhanced by a pentapeptide-binding site for the enzyme at the chemoreceptor carboxyl terminus. Related carboxyl-terminal pentapeptides are found on >25,000 chemoreceptor sequences distributed across 11 bacterial phyla and many bacterial species, in which they presumably play similar roles. Yet, little is known about the interrelationship of CheB phosphorylation, pentapeptide binding, and interactions with its substrate methylesters and amides on the body of the chemoreceptor. We investigated by characterizing the binding kinetics of CheB to Nanodisc-inserted chemoreceptor dimers. The resulting kinetic and thermodynamic constants revealed a synergy between CheB phosphorylation and pentapeptide binding in which a phosphorylation mimic enhanced pentapeptide binding, and the pentapeptide served not only as a high-affinity tether for CheB but also selected the activated conformation of the enzyme. The basis of this selection was revealed by molecular modeling that predicted a pentapeptide-binding site on CheB which existed only in the open, activated enzyme. Recruitment of activated enzyme by selective tethering represents a previously unappreciated strategy for regulating response regulator action, one that may well occur in other two-component systems.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Binding Sites ; Carboxylic Ester Hydrolases/chemistry ; Carboxylic Ester Hydrolases/genetics ; Carboxylic Ester Hydrolases/metabolism ; Chemotaxis ; Dimerization ; Escherichia coli/chemistry ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Kinetics ; Peptides/chemistry ; Peptides/metabolism ; Phosphorylation ; Protein Binding ; Protein Domains ; Receptors, Cell Surface/chemistry ; Receptors, Cell Surface/genetics ; Receptors, Cell Surface/metabolism ; Salmonella typhimurium/chemistry ; Salmonella typhimurium/enzymology ; Salmonella typhimurium/genetics
Chemical Substances	Bacterial Proteins ; Escherichia coli Proteins ; Peptides ; Receptors, Cell Surface ; Tar protein, E coli ; Carboxylic Ester Hydrolases (EC 3.1.1.-) ; chemotactic protein methylesterase (EC 3.1.1.-)
Language	English
Publishing date	2021-11-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.03106-21
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Article ; Online: Microbiology: Adaptation by target remodelling.

Hazelbauer, Gerald L

Nature

2012 Volume 484, Issue 7393, Page(s) 173–175

MeSH term(s)	Adaptation, Biological ; Bacterial Proteins/metabolism ; Chemotaxis ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Membrane Proteins/metabolism ; Methyl-Accepting Chemotaxis Proteins ; Signal Transduction
Chemical Substances	Bacterial Proteins ; Escherichia coli Proteins ; Membrane Proteins ; Methyl-Accepting Chemotaxis Proteins
Language	English
Publishing date	2012-04-11
Publishing country	England
Document type	News ; Comment
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/484173a
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Article ; Online: Bacterial chemotaxis: the early years of molecular studies.

Hazelbauer, Gerald L

Annual review of microbiology

2012 Volume 66, Page(s) 285–303

Abstract: This review focuses on the early years of molecular studies of bacterial chemotaxis and motility, beginning in the 1960s with Julius Adler's pioneering work. It describes key observations that established the field and made bacterial chemotaxis a ... ...

Abstract	This review focuses on the early years of molecular studies of bacterial chemotaxis and motility, beginning in the 1960s with Julius Adler's pioneering work. It describes key observations that established the field and made bacterial chemotaxis a paradigm for the molecular understanding of biological signaling. Consideration of those early years includes aspects of science seldom described in journals: the accidental findings, personal interactions, and scientific culture that often drive scientific progress.
MeSH term(s)	Animals ; Bacterial Physiological Phenomena ; Chemotaxis ; History, 20th Century ; Humans ; Microbiology/history
Language	English
Publishing date	2012-09-06
Publishing country	United States
Document type	Historical Article ; Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	207931-8
ISSN	1545-3251 ; 0066-4227
ISSN (online)	1545-3251
ISSN	0066-4227
DOI	10.1146/annurev-micro-092611-150120
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Book ; Online: Resolving the binding-kinase discrepancy in bacterial chemotaxis

Hathcock, David / Yu, Qiwei / Mello, Bernardo A. / Amin, Divya N. / Hazelbauer, Gerald L. / Tu, Yuhai

A nonequilibrium allosteric model and the role of energy dissipation

2023

Abstract	The Escherichia coli chemotaxis signaling pathway has served as a model system for studying the adaptive sensing of environmental signals by large protein complexes. The chemoreceptors control the kinase activity of CheA in response to the extracellular ligand concentration and adapt across a wide concentration range by undergoing methylation and demethylation. Methylation shifts the kinase response curve by orders of magnitude in ligand concentration while incurring a much smaller change in the ligand binding curve. Here, we show that this asymmetric shift in binding and kinase response is inconsistent with equilibrium allosteric models regardless of parameter choices. To resolve this inconsistency, we present a nonequilibrium allosteric model that explicitly includes the dissipative reaction cycles driven by ATP hydrolysis. The model successfully explains all existing measurements for both aspartate and serine receptors. Our results suggest that while ligand binding controls the equilibrium balance between the ON and OFF states of the kinase, receptor methylation modulates the kinetic properties (e.g., the phosphorylation rate) of the ON state. Furthermore, sufficient energy dissipation is necessary for maintaining and enhancing the sensitivity range and amplitude of the kinase response. We demonstrate that the nonequilibrium allosteric model is broadly applicable to other sensor-kinase systems by successfully fitting previously unexplained data from the DosP bacterial oxygen-sensing system. Overall, this work provides a new perspective on cooperative sensing by large protein complexes and opens up new research directions for understanding their microscopic mechanisms through simultaneous measurements and modeling of ligand binding and downstream responses. Comment: 12 (main text) + 4 (supplemental information) pages, 6+4 figures
Keywords	Physics - Biological Physics ; Condensed Matter - Statistical Mechanics ; Quantitative Biology - Molecular Networks
Subject code	612
Publishing date	2023-02-22
Publishing country	us
Document type	Book ; Online
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Article ; Online: Bacterial Chemoreceptor Dynamics: Helical Stability in the Cytoplasmic Domain Varies with Functional Segment and Adaptational Modification.

Bartelli, Nicholas L / Hazelbauer, Gerald L

Journal of molecular biology

2016 Volume 428, Issue 19, Page(s) 3789–3804

Abstract: Dynamics are thought to be important features of structure and signaling in the cytoplasmic domain of bacterial chemoreceptors. However, little is known about which structural features are dynamic. For this largely helical domain, comprising a four-helix ...

Abstract	Dynamics are thought to be important features of structure and signaling in the cytoplasmic domain of bacterial chemoreceptors. However, little is known about which structural features are dynamic. For this largely helical domain, comprising a four-helix bundle and an extended four-helix coiled coil, functionally important structural dynamics likely involves helical mobility and stability. To investigate, we used continuous wave EPR spectroscopy and site-specific spin labels that directly probed, in essentially physiological conditions, the mobility of helical backbones in the cytoplasmic domain of intact chemoreceptor Tar homodimers inserted into lipid bilayers of Nanodiscs. We observed differences among functional regions, between companion helices in helical hairpins of the coiled coil and between receptor conformational states generated by adaptational modification. Increased adaptational modification decreased helical dynamics while preserving dynamics differences among functional regions and between companion helices. In contrast, receptor ligand occupancy did not have a discernable effect on dynamics to which our approach was sensitive, implying that the two sensory inputs alter different chemoreceptor features. Spectral fitting indicated that differences in helical dynamics we observed for ensemble spin-label mobility reflected differences in proportions of a minority receptor population in which the otherwise helical backbone was essentially disordered. We suggest that our measurements provided site-specific snapshots of equilibria between a majority state of well-ordered helix and a minority state of locally disordered polypeptide backbone. Thus, the proportion of polypeptide chain that is locally and presumably transiently disordered is a structural feature of cytoplasmic domain dynamics that varies with functional region and modification-induced signaling state.
MeSH term(s)	Allosteric Regulation ; Aspartic Acid/metabolism ; Electron Spin Resonance Spectroscopy ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Models, Biological ; Models, Molecular ; Protein Conformation ; Protein Multimerization ; Receptors, Cell Surface/chemistry ; Receptors, Cell Surface/metabolism
Chemical Substances	Escherichia coli Proteins ; Membrane Proteins ; Receptors, Cell Surface ; Tar protein, E coli ; Aspartic Acid (30KYC7MIAI)
Language	English
Publishing date	2016-09-25
Publishing country	England
Document type	Journal Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2016.06.005
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Article ; Online: Spatial Restrictions in Chemotaxis Signaling Arrays: A Role for Chemoreceptor Flexible Hinges across Bacterial Diversity.

Stalla, David / Akkaladevi, Narahari / White, Tommi A / Hazelbauer, Gerald L

International journal of molecular sciences

2019 Volume 20, Issue 12

Abstract: The chemotactic sensory system enables motile bacteria to move toward favorable environments. Throughout bacterial diversity, the chemoreceptors that mediate chemotaxis are clustered into densely packed arrays of signaling complexes. In these arrays, rod- ...

Abstract	The chemotactic sensory system enables motile bacteria to move toward favorable environments. Throughout bacterial diversity, the chemoreceptors that mediate chemotaxis are clustered into densely packed arrays of signaling complexes. In these arrays, rod-shaped receptors are in close proximity, resulting in limited options for orientations. A recent geometric analysis of these limitations in
MeSH term(s)	Bacterial Physiological Phenomena ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Chemotaxis ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Models, Biological ; Protein Binding ; Protein Multimerization ; Signal Transduction ; Structure-Activity Relationship
Chemical Substances	Bacterial Proteins ; Membrane Proteins
Language	English
Publishing date	2019-06-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms20122989
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