Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ

Molnar, Kathleen S.; Bonomi, Massimiliano; Pellarin, Riccardo; Clinthorne, Graham D.; González, Gabriel; Goldberg, Shalom D.; Goulian, Mark; Šali, Andrej; DeGrado, William F.

doi:10.1016/j.str.2014.04.019

Cited by 107 publications

(138 citation statements)

References 66 publications

(108 reference statements)

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“…Whereas these models are in most cases predicted from isolated domains, cysteine crosslinking in PhoQ (24) and water accessibility studies on DcuS (43) directly probe the TM segments. Bayesian modeling based on cross-linking data suggests a scissoring movement of TM helices for PhoQ, whereas water accessibility of both states of DcuS is in favor of a piston-type pull.…”

Section: Discussionmentioning

confidence: 99%

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Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

Salvi

Schomburg

Giller

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Bacteria use membrane-integral sensor histidine kinases (HK) to perceive stimuli and transduce signals from the environment to the cytosol. Information on how the signal is transmitted across the membrane by HKs is still scarce. Combining both liquid-and solid-state NMR, we demonstrate that structural rearrangements in the extracytoplasmic, citrate-sensing Per-Arnt-Sim (PAS) domain of HK CitA are identical for the isolated domain in solution and in a longer construct containing the membrane-embedded HK and lacking only the kinase core. We show that upon citrate binding, the PAS domain contracts, resulting in a shortening of the C-terminal β-strand. We demonstrate that this contraction of the PAS domain, which is well characterized for the isolated domain, is the signal transmitted to the transmembrane (TM) helices in a CitA construct in liposomes. Putting the extracytoplasmic PAS domain into context of the membrane-embedded CitA construct slows down citrate-binding kinetics by at least a factor of 60, confirming that TM helix motions are linked to the citrate-binding event. Our results are confirmation of a hallmark of the HK signal transduction mechanism with atomic resolution on a full-length construct lacking only the kinase core domain.transmembrane receptors | solid-state NMR spectroscopy | transmembrane signaling | integrated structural biology | histidine sensor kinase H istidine kinases (HKs) are key players in prokaryotic signaling and the primary means of processing extracellular stimuli (1-6). Due to their modular organization, HKs can relay a multitude of different input stimuli, including sensing of nutrients, light, physicochemical parameters (e.g., metal ions, ions gradient), temperature, oxygen, and molecules reporting cell density, to accomplish diverse responses. Over the last decade, various structures have been solved for the cytosolic kinase core and a number of signaling domains and more recently even for the complete cytoplasmic region (7-13), but the transmembrane (TM) signaling mechanism itself remains challenging to decipher. Structural information on individual stimulus-receiving domains therefore provides an important tool to identify TM signal transduction schemes.Because extracytoplasmic receiver domains are generally directly connected to TM helices, structural rearrangements within these motifs can be correlated with the TM-signaling mechanism. Different receiver domains have been characterized with and without their ligands and reveal structural differences between the two states that impose restraints on possible motions of the TM helices. Based on such structures, a symmetry-to-asymmetry switch has been postulated for KinB (14), TorT/TorS (15), and LuxPQ (16), implying a possible tilt of TM helices (17). For chemotaxis sensor Tar and for HK NarX a piston movement of the second TM helix has been postulated as a consequence of receiver domain motions (9,(18)(19)(20).Among receiver domains, PAS domains stand out by being able to process diverse input signals, which is reflected by...

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Section: Discussionmentioning

confidence: 99%

“…Depending on their ligands, PAS domains have been associated with a piston-type motion (21-23) or a scissorslike displacement of TM helices (24) for signaling across the membrane. However, structures of full-length HKs including TM regions are so far not available.…”

mentioning

confidence: 99%

Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

Salvi

Schomburg

Giller

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Signal transduction between the perception and the enzymatic domains of sensor kinases generally involves combinations of rotation, scissor, or piston movements of coiled-coil regions (40)(41)(42)(43)(44)(45)(46)(47)(48)(49). A simple model is that a sensor kinase populates two thermodynamically stable structural states.…”

Section: Discussionmentioning

confidence: 99%

“…A simple model is that a sensor kinase populates two thermodynamically stable structural states. Stimulus perception shifts this equilibrium, and the transition of one domain changes the probability for the next domain to shift to the alternative state (46). In BvgS, kinase activity at the basal state is characterized by clamshell motions of the VFT1 domains and by considerable dynamics of linker 2, which precedes the enzymatic moiety (7,29).…”

Section: Discussionmentioning

confidence: 99%

Conformational Changes of an Interdomain Linker Mediate Mechanical Signal Transmission in Sensor Kinase BvgS

et al. 2017

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The whooping cough agent, Bordetella pertussis, controls the expression of its large virulence regulon in a coordinated manner through the two-component system BvgAS. BvgS is a dimeric, multidomain sensor kinase. Each monomer comprises, in succession, tandem periplasmic Venus flytrap (VFT) domains, a transmembrane segment, a cytoplasmic Per-Arnt-Sim (PAS) domain, a kinase module, and additional phosphorelay domains. BvgS shifts between kinase and phosphatase modes of activity in response to chemical modulators that modify the clamshell motions of the VFT domains. We have shown previously that this regulation involves a shift between distinct states of conformation and dynamics of the two-helix coiled-coil linker preceding the enzymatic module. In this work, we determined the mechanism of signal transduction across the membrane via a first linker, which connects the VFT and PAS domains of BvgS, using extensive cysteine cross-linking analyses and other approaches. Modulator perception by the periplasmic domains appears to trigger a small, symmetrical motion of the transmembrane segments toward the periplasm, causing rearrangements of the noncanonical cytoplasmic coiled coil that follows. As a consequence, the interface of the PAS domains is modified, which affects the second linker and eventually causes the shift of enzymatic activity. The major features of this first linker are well conserved among BvgS homologs, indicating that the mechanism of signal transduction unveiled here is likely to be generally relevant for this family of sensor kinases.IMPORTANCE Bordetella pertussis produces virulence factors coordinately regulated by the two-component system BvgAS. BvgS is a sensor kinase, and BvgA is a response regulator that activates gene transcription when phosphorylated by BvgS. Sensor kinases homologous to BvgS are also found in other pathogens. Our goal is to decipher the mechanisms of BvgS signaling, since these sensor kinases may represent new targets for antibacterial agents. Signal perception by the sensor domains of BvgS triggers small motions of the helical linker region underneath. The protein domain that follows this linker undergoes a large conformational change that amplifies the initial signal, causing a shift of activity from kinase to phosphatase. Because BvgS homologs harbor similar regions, these signaling mechanisms are likely to apply generally to that family of sensor kinases.

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“…The approach is extensively described elsewhere (44,45,49,50). Briefly, using Bayes' theorem, we estimate the posterior probability p…”

Section: Determining the Structures Of C3(h 2 O) C3 C3b With Integrmentioning

confidence: 99%

Structure of complement C3(H₂O) revealed by quantitative cross-linking/mass spectrometry and modeling

Chen

Pellarin²,

Fischer

et al. 2016

Preprint

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The slow but spontaneous and ubiquitous formation of C3(H 2 O), the hydrolytic and conformationally rearranged product of C3, initiates antibody-independent activation of the complement system that is a key first line of antimicrobial defense. The structure of C3(H 2 O) has not been determined. Here we subjected C3(H 2 O) to quantitative cross-linking/mass spectrometry (QCLMS). This revealed details of the structural differences and similarities between C3(H 2 O) and C3, as well as between C3(H 2 O) and its pivotal proteolytic cleavage product, C3b, which shares functionally similarity with C3(H 2 O). Considered in combination with the crystal structures of C3 and C3b, the QCMLS data suggest that C3(H 2 O) generation is accompanied by the migration of the thioester-containing domain of C3 from one end of the molecule to the other. This creates a stable C3b-like platform able to bind the zymogen, factor B, or the regulator, factor H. Integration of available crystallographic and QCLMS data allowed the determination of a 3D model of the C3(H 2 O) domain architecture. The unique arrangement of domains thus observed in C3(H 2 O), which retains the anaphylatoxin domain (that is excised when C3 is enzymatically activated to C3b), can be used to rationalize observed differences between C3(H 2 O) and C3b in terms of complement activation and regulation. Molecular & Cellular Proteomics

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Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ

Cited by 107 publications

References 66 publications

Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

Conformational Changes of an Interdomain Linker Mediate Mechanical Signal Transmission in Sensor Kinase BvgS

Structure of complement C3(H₂O) revealed by quantitative cross-linking/mass spectrometry and modeling

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Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ

Cited by 107 publications

References 66 publications

Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

Conformational Changes of an Interdomain Linker Mediate Mechanical Signal Transmission in Sensor Kinase BvgS

Structure of complement C3(H2O) revealed by quantitative cross-linking/mass spectrometry and modeling

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Structure of complement C3(H₂O) revealed by quantitative cross-linking/mass spectrometry and modeling