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1.
Proc Natl Acad Sci U S A ; 121(14): e2312064121, 2024 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-38530894

RESUMEN

Motile bacteria use large receptor arrays to detect chemical and physical stimuli in their environment, process this complex information, and accordingly bias their swimming in a direction they deem favorable. The chemoreceptor molecules form tripod-like trimers of receptor dimers through direct contacts between their cytoplasmic tips. A pair of trimers, together with a dedicated kinase enzyme, form a core signaling complex. Hundreds of core complexes network to form extended arrays. While considerable progress has been made in revealing the hierarchical structure of the array, the molecular properties underlying signal processing in these structures remain largely unclear. Here we analyzed the signaling properties of nonnetworked core complexes in live cells by following both conformational and kinase control responses to attractant stimuli and to output-biasing lesions at various locations in the receptor molecule. Contrary to the prevailing view that individual receptors are binary two-state devices, we demonstrate that conformational coupling between the ligand binding and the kinase-control receptor domains is, in fact, only moderate. In addition, we demonstrate communication between neighboring receptors through their trimer-contact domains that biases them to adopt similar signaling states. Taken together, these data suggest a view of signaling in receptor trimers that allows significant signal integration to occur within individual core complexes.


Asunto(s)
Proteínas de Escherichia coli , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Células Quimiorreceptoras/metabolismo , Proteínas Portadoras/metabolismo , Quimiotaxis/fisiología , Proteínas Bacterianas/metabolismo , Histidina Quinasa/metabolismo
2.
mBio ; 14(5): e0079323, 2023 Oct 31.
Artículo en Inglés | MEDLINE | ID: mdl-37772839

RESUMEN

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.


Asunto(s)
Quimiotaxis , Proteínas de Escherichia coli , Escherichia coli/genética , Escherichia coli/química , Proteínas Quimiotácticas Aceptoras de Metilo/química , Transducción de Señal , Proteínas de Escherichia coli/química , Proteínas Bacterianas/química
3.
J Bacteriol ; 204(12): e0027822, 2022 12 20.
Artículo en Inglés | MEDLINE | ID: mdl-36448786

RESUMEN

In isotropic environments, an Escherichia coli cell exhibits coordinated rotational switching of its flagellar motors, produced by fluctuations in the intracellular concentration of phosphorylated CheY (CheY-P) emanating from chemoreceptor signaling arrays. In this study, we show that these CheY-P fluctuations arise through modifications of chemoreceptors by two sensory adaptation enzymes: the methyltransferase CheR and the methylesterase CheB. A cell containing CheR, CheB, and the serine chemoreceptor Tsr exhibited motor synchrony, whereas a cell lacking CheR and CheB or containing enzymatically inactive forms did not. Tsr variants with different combinations of methylation-mimicking Q residues at the adaptation sites also failed to show coordinated motor switching in cells lacking CheR and CheB. Cells containing CheR, CheB, and Tsr [NDND], a variant in which the adaptation site residues are not substrates for CheR or CheB modifications, also lacked motor synchrony. TsrΔNWETF, which lacks a C-terminal pentapeptide-binding site for CheR and CheB, and the ribose-galactose receptor Trg, which natively lacks this motif, failed to produce coordinated motor switching, despite the presence of CheR and CheB. However, addition of the NWETF sequence to Trg enabled Trg-NWETF to produce motor synchrony, as the sole receptor type in cells containing CheR and CheB. Finally, CheBc, the catalytic domain of CheB, supported motor coordination in combination with CheR and Tsr. These results indicate that the coordination of motor switching requires CheR/CheB-mediated changes in receptor modification state. We conclude that the opposing receptor substrate-site preferences of CheR and CheB produce spontaneous blinking of the chemoreceptor array's output activity. IMPORTANCE Under steady-state conditions with no external stimuli, an Escherichia coli cell coordinately switches the rotational direction of its flagellar motors. Here, we demonstrate that the CheR and CheB enzymes of the chemoreceptor sensory adaptation system mediate this coordination. Stochastic fluctuations in receptor adaptation states trigger changes in signal output from the receptor array, and this array blinking generates fluctuations in CheY-P concentration that coordinate directional switching of the flagellar motors. Thus, in the absence of chemoeffector gradients, the sensory adaptation system controls run-tumble swimming of the cell, its optimal foraging strategy.


Asunto(s)
Proteínas de Escherichia coli , Escherichia coli , Escherichia coli/genética , Escherichia coli/metabolismo , Quimiotaxis , Proteínas Bacterianas/genética , Proteínas Bacterianas/química , Células Quimiorreceptoras , Proteínas de Escherichia coli/metabolismo , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo
4.
Proc Natl Acad Sci U S A ; 119(28): e2204161119, 2022 07 12.
Artículo en Inglés | MEDLINE | ID: mdl-35787052

RESUMEN

The chemotaxis machinery of Escherichia coli has served as a model for exploring the molecular signaling mechanisms of transmembrane chemoreceptors known as methyl-accepting chemotaxis proteins (MCPs). Yet, fundamental questions about signal transmission through MCP molecules remain unanswered. Our work with the E. coli serine chemoreceptor Tsr has developed in vivo reporters that distinguish kinase-OFF and kinase-ON structures in the cytoplasmic methylation helix (MH) cap, which receives stimulus signals from an adjoining, membrane-proximal histidine kinase, adenylyl cyclases, MCPs, and phosphatases (HAMP) domain. The cytoplasmic helices of the Tsr homodimer interact mainly through packing interactions of hydrophobic residues at a and d heptad positions. We investigated the in vivo crosslinking properties of Tsr molecules bearing cysteine replacements at functionally tolerant g heptad positions in the N-terminal and C-terminal cap helices. Upon treatment of cells with bismaleimidoethane (BMOE), a bifunctional thiol-reagent, Tsr-G273C/Q504C readily formed a doubly crosslinked product in the presence of serine but not in its absence. Moreover, a serine stimulus combined with BMOE treatment during in vivo Förster resonance energy transfer-based kinase assays locked Tsr-G273C/Q504C in kinase-OFF output. An OFF-shifting lesion in MH1 (D269P) promoted the formation of the doubly crosslinked species in the absence of serine, whereas an ON-shifting lesion (G268P) suppressed the formation of the doubly crosslinked species. Tsr-G273C/Q504C also showed output-dependent crosslinking patterns in combination with ON-shifting and OFF-shifting adaptational modifications. Our results are consistent with a helix breathing-axial rotation-bundle repacking signaling mechanism and imply that in vivo crosslinking tools could serve to probe helix-packing transitions and their output consequences in other regions of the receptor molecule.


Asunto(s)
Escherichia coli , Proteínas Quimiotácticas Aceptoras de Metilo/química , Escherichia coli/metabolismo , Proteínas de la Membrana/metabolismo , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo , Modelos Moleculares , Serina/metabolismo
5.
Sci Signal ; 15(718): eabj1737, 2022 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-35077199

RESUMEN

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.


Asunto(s)
Proteínas de Escherichia coli , Escherichia coli , Quimiotaxis , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Histidina Quinasa/metabolismo , Proteínas Quimiotácticas Aceptoras de Metilo/genética
6.
Nat Commun ; 11(1): 743, 2020 02 06.
Artículo en Inglés | MEDLINE | ID: mdl-32029744

RESUMEN

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.


Asunto(s)
Proteínas de Escherichia coli/química , Escherichia coli/química , Proteínas Quimiotácticas Aceptoras de Metilo/química , Microscopía por Crioelectrón , Tomografía con Microscopio Electrónico , Escherichia coli/genética , Escherichia coli/ultraestructura , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/ultraestructura , Histidina Quinasa/química , Histidina Quinasa/genética , Histidina Quinasa/ultraestructura , Proteínas Quimiotácticas Aceptoras de Metilo/genética , Proteínas Quimiotácticas Aceptoras de Metilo/ultraestructura , Modelos Moleculares , Complejos Multiproteicos/química , Complejos Multiproteicos/genética , Complejos Multiproteicos/ultraestructura
7.
Commun Biol ; 3(1): 24, 2020 01 10.
Artículo en Inglés | MEDLINE | ID: mdl-31925330

RESUMEN

To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism.


Asunto(s)
Tomografía con Microscopio Electrónico , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/ultraestructura , Conformación Molecular , Simulación de Dinámica Molecular , Proteínas Adaptadoras Transductoras de Señales , Quimiotaxis , Escherichia coli
8.
J Bacteriol ; 202(1)2019 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-31611290

RESUMEN

In Escherichia coli and Salmonella, the c-di-GMP effector YcgR inhibits flagellar motility by interacting directly with the motor to alter both its bias and speed. Here, we demonstrate that in both of these bacteria, YcgR acts sequentially, altering motor bias first and then decreasing motor speed. We show that when c-di-GMP levels are high, deletion of ycgR restores wild-type motor behavior in E. coli, indicating that YcgR is the only motor effector in this bacterium. Yet, motility and chemotaxis in soft agar do not return to normal, suggesting that there is a second mechanism that inhibits motility under these conditions. In Salmonella, c-di-GMP-induced synthesis of extracellular cellulose has been reported to entrap flagella and to be responsible for the YcgR-independent motility defect. We found that this is not the case in E. coli Instead, we found through reversion analysis that deletion of rssB, which codes for a response regulator/adaptor protein that normally directs ClpXP protease to target σS for degradation, restored wild-type motility in the ycgR mutant. Our data suggest that high c-di-GMP levels may promote altered interactions between these proteins to downregulate flagellar gene expression.IMPORTANCE Flagellum-driven motility has been studied in E. coli and Salmonella for nearly half a century. Over 60 genes control flagellar assembly and function. The expression of these genes is regulated at multiple levels in response to a variety of environmental signals. Cues that elevate c-di-GMP levels, however, inhibit motility by direct binding of the effector YcgR to the flagellar motor. In this study conducted mainly in E. coli, we show that YcgR is the only effector of motor control and tease out the order of YcgR-mediated events. In addition, we find that the σS regulator protein RssB contributes to negative regulation of flagellar gene expression when c-di-GMP levels are elevated.


Asunto(s)
GMP Cíclico/análogos & derivados , Proteínas de Unión al ADN/fisiología , Proteínas de Escherichia coli/fisiología , Escherichia coli/genética , Flagelos/fisiología , Regulón/fisiología , Factores de Transcripción/fisiología , GMP Cíclico/fisiología , Escherichia coli/fisiología , Regulación Bacteriana de la Expresión Génica
9.
J Bacteriol ; 201(23)2019 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-31501279

RESUMEN

Escherichia coli chemotaxis relies on control of the autophosphorylation activity of the histidine kinase CheA by transmembrane chemoreceptors. Core signaling units contain two receptor trimers of dimers, one CheA homodimer, and two monomeric CheW proteins that couple CheA activity to receptor control. Core signaling units appear to operate as two-state devices, with distinct kinase-on and kinase-off CheA output states whose structural nature is poorly understood. A recent all-atom molecular dynamic simulation of a receptor core unit revealed two alternative conformations, "dipped" and "undipped," for the ATP-binding CheA.P4 domain that could be related to kinase activity states. To explore possible signaling roles for the dipped CheA.P4 conformation, we created CheA mutants with amino acid replacements at residues (R265, E368, and D372) implicated in promoting the dipped conformation and examined their signaling consequences with in vivo Förster resonance energy transfer (FRET)-based kinase assays. We used cysteine-directed in vivo cross-linking reporters for the dipped and undipped conformations to assess mutant proteins for these distinct CheA.P4 domain configurations. Phenotypic suppression analyses revealed functional interactions among the conformation-controlling residues. We found that structural interactions between R265, located at the N terminus of the CheA.P3 dimerization domain, and E368/D372 in the CheA.P4 domain played a critical role in stabilizing the dipped conformation and in producing kinase-on output. Charge reversal replacements at any of these residues abrogated the dipped cross-linking signal, CheA kinase activity, and chemotactic ability. We conclude that the dipped conformation of the CheA.P4 domain is critical to the kinase-active state in core signaling units.IMPORTANCE Regulation of CheA kinase in chemoreceptor arrays is critical for Escherichia coli chemotaxis. However, to date, little is known about the CheA conformations that lead to the kinase-on or kinase-off states. Here, we explore the signaling roles of a distinct conformation of the ATP-binding CheA.P4 domain identified by all-atom molecular dynamics simulation. Amino acid replacements at residues predicted to stabilize the so-called "dipped" CheA.P4 conformation abolished the kinase activity of CheA and its ability to support chemotaxis. Our findings indicate that the dipped conformation of the CheA.P4 domain is critical for reaching the kinase-active state in chemoreceptor signaling arrays.


Asunto(s)
Quimiotaxis/genética , Proteínas de Escherichia coli/química , Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Histidina Quinasa/química , Proteínas Quimiotácticas Aceptoras de Metilo/química , Transducción de Señal/genética , Secuencias de Aminoácidos , Sustitución de Aminoácidos , Sitios de Unión , Escherichia coli/enzimología , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Histidina Quinasa/genética , Histidina Quinasa/metabolismo , Proteínas Quimiotácticas Aceptoras de Metilo/genética , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Mutación , Fosforilación , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Multimerización de Proteína , Electricidad Estática
10.
Proc Natl Acad Sci U S A ; 116(31): 15651-15660, 2019 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-31315979

RESUMEN

Motile Escherichia coli cells use chemoreceptor signaling arrays to track chemical gradients with exquisite precision. Highly conserved residues in the cytoplasmic hairpin tip of chemoreceptor molecules promote assembly of trimer-based signaling complexes and modulate the activity of their CheA kinase partners. To explore hairpin tip output states in the serine receptor Tsr, we characterized the signaling consequences of amino acid replacements at the salt-bridge residue pair E385-R388. All mutant receptors assembled trimers and signaling complexes, but most failed to support serine chemotaxis in soft agar assays. Small side-chain replacements at either residue produced OFF- or ON-shifted outputs that responded to serine stimuli in wild-type fashion, suggesting that these receptors, like the wild-type, operate as two-state signaling devices. Larger aliphatic or aromatic side chains caused slow or partial kinase control responses that proved dependent on the connections between core signaling units that promote array cooperativity. In a mutant lacking one of two key adapter-kinase contacts (interface 2), those mutant receptors exhibited more wild-type behaviors. Lastly, mutant receptors with charged amino acid replacements assembled signaling complexes that were locked in kinase-ON (E385K|R) or kinase-OFF (R388D|E) output. The hairpin tips of mutant receptors with these more aberrant signaling properties probably have nonnative structures or dynamic behaviors. Our results suggest that chemoeffector stimuli and adaptational modifications influence the cooperative connections between core signaling units. This array remodeling process may involve activity-dependent changes in the relative strengths of interface 1 and 2 interactions between the CheW and CheA.P5 components of receptor core signaling complexes.


Asunto(s)
Proteínas de Escherichia coli/química , Escherichia coli/enzimología , Histidina Quinasa/química , Proteínas Quimiotácticas Aceptoras de Metilo/química , Mutación , Transducción de Señal , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Histidina Quinasa/genética , Histidina Quinasa/metabolismo , Proteínas Quimiotácticas Aceptoras de Metilo/genética , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo , Estructura Secundaria de Proteína
11.
mBio ; 10(4)2019 07 02.
Artículo en Inglés | MEDLINE | ID: mdl-31266867

RESUMEN

Tsr, the serine chemoreceptor in Escherichia coli, transduces signals from a periplasmic ligand-binding site to its cytoplasmic tip, where it controls the activity of the CheA kinase. To function, Tsr forms trimers of homodimers (TODs), which associate in vivo with the CheA kinase and CheW coupling protein. Together, these proteins assemble into extended hexagonal arrays. Here, we use cryo-electron tomography and molecular dynamics simulation to study Tsr in the context of a near-native array, characterizing its signaling-related conformational changes at both the individual dimer and the trimer level. In particular, we show that individual Tsr dimers within a trimer exhibit asymmetric flexibilities that are a function of the signaling state, highlighting the effect of their different protein interactions at the receptor tips. We further reveal that the dimer compactness of the Tsr trimer changes between signaling states, transitioning at the glycine hinge from a compact conformation in the kinase-OFF state to an expanded conformation in the kinase-ON state. Hence, our results support a crucial role for the glycine hinge: to allow the receptor flexibility necessary to achieve different signaling states while also maintaining structural constraints imposed by the membrane and extended array architecture.IMPORTANCE In Escherichia coli, membrane-bound chemoreceptors, the histidine kinase CheA, and coupling protein CheW form highly ordered chemosensory arrays. In core signaling complexes, chemoreceptor trimers of dimers undergo conformational changes, induced by ligand binding and sensory adaptation, which regulate kinase activation. Here, we characterize by cryo-electron tomography the kinase-ON and kinase-OFF conformations of the E. coli serine receptor in its native array context. We found distinctive structural differences between the members of a receptor trimer, which contact different partners in the signaling unit, and structural differences between the ON and OFF signaling complexes. Our results provide new insights into the signaling mechanism of chemoreceptor arrays and suggest an important functional role for a previously postulated flexible region and glycine hinge in the receptor molecule.


Asunto(s)
Escherichia coli/enzimología , Proteínas Quimiotácticas Aceptoras de Metilo/química , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo , Multimerización de Proteína , Microscopía por Crioelectrón , Tomografía con Microscopio Electrónico , Escherichia coli/fisiología , Simulación de Dinámica Molecular , Conformación Proteica , Transducción de Señal
12.
Proc Natl Acad Sci U S A ; 115(15): E3519-E3528, 2018 04 10.
Artículo en Inglés | MEDLINE | ID: mdl-29581254

RESUMEN

Environmental awareness is an essential attribute for all organisms. The chemotaxis system of Escherichia coli provides a powerful experimental model for the investigation of stimulus detection and signaling mechanisms at the molecular level. These bacteria sense chemical gradients with transmembrane proteins [methyl-accepting chemotaxis proteins (MCPs)] that have an extracellular ligand-binding domain and intracellular histidine kinases, adenylate cyclases, methyl-accepting proteins, and phosphatases (HAMP) and signaling domains that govern locomotor behavior. HAMP domains are versatile input-output elements that operate in a variety of bacterial signaling proteins, including the sensor kinases of two-component regulatory systems. The MCP HAMP domain receives stimulus information and in turn modulates output signaling activity. This study describes mutants of the Escherichia coli serine chemoreceptor, Tsr, that identify a heptad-repeat structural motif (LLF) at the membrane-proximal end of the receptor signaling domain that is critical for HAMP output control. The homodimeric Tsr signaling domain is an extended, antiparallel, four-helix bundle that controls the activity of an associated kinase. The N terminus of each subunit adjoins the HAMP domain; the LLF residues lie at the C terminus of the methylation-helix bundle. We found, by using in vivo Förster resonance energy transfer kinase assays, that most amino acid replacements at any of the LLF residues abrogate chemotactic responses to serine and lock Tsr output in a kinase-active state, impervious to HAMP-mediated down-regulation. We present evidence that the LLF residues may function like a leucine zipper to promote stable association of the C-terminal signaling helices, thereby creating a metastable helix-packing platform for the N-terminal signaling helices that facilitates conformational control by the HAMP domains in MCP-family chemoreceptors.


Asunto(s)
Células Quimiorreceptoras/metabolismo , Células Quimiorreceptoras/fisiología , Quimiotaxis/fisiología , Escherichia coli/genética , Escherichia coli/metabolismo , Adenilil Ciclasas/genética , Adenilil Ciclasas/metabolismo , Secuencias de Aminoácidos , Proteínas Bacterianas/metabolismo , Escherichia coli/enzimología , Proteínas de Escherichia coli/metabolismo , Histidina Quinasa/genética , Histidina Quinasa/metabolismo , Proteínas de la Membrana/metabolismo , Proteínas Quimiotácticas Aceptoras de Metilo/genética , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo , Modelos Moleculares , Monoéster Fosfórico Hidrolasas/genética , Monoéster Fosfórico Hidrolasas/metabolismo , Dominios Proteicos , Serina/metabolismo , Transducción de Señal
13.
Methods Mol Biol ; 1729: 79-85, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29429084

RESUMEN

The technique of all-codon mutagenesis can generate mutants that represent all possible amino acid replacements at any particular residue in a protein. It is thus a powerful tool to probe structure-function relationships in proteins of interest. In this chapter, we describe how we used all-codon mutagenesis to obtain mutants of the Escherichia coli serine receptor Tsr with amino acid replacements at residue F373, a functionally important site in this protein. We provide general protocols for mutagenesis of a target codon in a plasmid-borne gene and for the selection and screening of the resultant mutants. These techniques should be adaptable for the study of a variety of bacterial proteins.


Asunto(s)
Sustitución de Aminoácidos , Escherichia coli/fisiología , Proteínas Quimiotácticas Aceptoras de Metilo/genética , Quimiotaxis , Codón , Escherichia coli/genética , Proteínas Quimiotácticas Aceptoras de Metilo/química , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo , Mutagénesis Sitio-Dirigida , Transducción de Señal
14.
Methods Mol Biol ; 1729: 127-135, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29429088

RESUMEN

Bacteria use two-component signal transduction systems to elicit adaptive responses to environmental changes. The simplest of these systems comprises a transmembrane sensor with histidine kinase activity and its cytoplasmic response regulator partner. Stimulus-response studies of two-component signaling systems typically employ expression reporters, such as ß-galactosidase, that operate with relatively slow kinetics and low precision. In this chapter, we illustrate a new strategy for directly measuring the signaling activities of two-component sensor kinases in vivo. Our method exploits recent work that defines the recognition determinants for sensor-response regulator signaling transactions, which enabled us to couple histidine kinases to a FRET-based assay that uses signaling components of the E. coli chemotaxis system. We demonstrate the approach with NarX, a nitrate/nitrite sensor kinase, but the method should be applicable to other two-component sensor kinases.


Asunto(s)
Proteínas de Escherichia coli/metabolismo , Escherichia coli/fisiología , Histidina Quinasa/metabolismo , Proteínas Quinasas/metabolismo , Adaptación Fisiológica , Quimiotaxis , Citoplasma/metabolismo , Transferencia Resonante de Energía de Fluorescencia , Genes Reporteros , Fosforilación , Transducción de Señal
15.
J Mol Biol ; 430(7): 1051-1064, 2018 03 30.
Artículo en Inglés | MEDLINE | ID: mdl-29453948

RESUMEN

In Escherichia coli chemosensory arrays, transmembrane receptors, a histidine autokinase CheA, and a scaffolding protein CheW interact to form an extended hexagonal lattice of signaling complexes. One interaction, previously assigned a crucial signaling role, occurs between chemoreceptors and the CheW-binding P5 domain of CheA. Structural studies showed a receptor helix fitting into a hydrophobic cleft at the boundary between P5 subdomains. Our work aimed to elucidate the in vivo roles of the receptor-P5 interface, employing as a model the interaction between E. coli CheA and Tsr, the serine chemoreceptor. Crosslinking assays confirmed P5 and Tsr contacts in vivo and their strict dependence on CheW. Moreover, the P5 domain only mediated CheA recruitment to polar receptor clusters if CheW was also present. Amino acid replacements at CheA.P5 cleft residues reduced CheA kinase activity, lowered serine response cooperativity, and partially impaired chemotaxis. Pseudoreversion studies identified suppressors of P5 cleft defects at other P5 groove residues or at surface-exposed residues in P5 subdomain 1, which interacts with CheW in signaling complexes. Our results indicate that a high-affinity P5-receptor binding interaction is not essential for core complex function. Rather, P5 groove residues are probably required for proper cleft structure and/or dynamic behavior, which likely impact conformational communication between P5 subdomains and the strong binding interaction with CheW that is necessary for kinase activation. We propose a model for signal transmission in chemotaxis signaling complexes in which the CheW-receptor interface plays the key role in conveying signaling-related conformational changes from receptors to the CheA kinase.


Asunto(s)
Proteínas de Escherichia coli/química , Histidina Quinasa/química , Proteínas Quimiotácticas Aceptoras de Metilo/química , Transducción de Señal , Quimiotaxis , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Histidina Quinasa/genética , Histidina Quinasa/metabolismo , Proteínas Quimiotácticas Aceptoras de Metilo/genética , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo , Modelos Moleculares , Mutación
16.
Proc Natl Acad Sci U S A ; 114(36): E7583-E7591, 2017 09 05.
Artículo en Inglés | MEDLINE | ID: mdl-28827352

RESUMEN

A sensory adaptation system that tunes chemoreceptor sensitivity enables motile Escherichia coli cells to track chemical gradients with high sensitivity over a wide dynamic range. Sensory adaptation involves feedback control of covalent receptor modifications by two enzymes: CheR, a methyltransferase, and CheB, a methylesterase. This study describes a CheR function that opposes the signaling consequences of its catalytic activity. In the presence of CheR, a variety of mutant serine chemoreceptors displayed up to 40-fold enhanced detection sensitivity to chemoeffector stimuli. This response enhancement effect did not require the known catalytic activity of CheR, but did involve a binding interaction between CheR and receptor molecules. Response enhancement was maximal at low CheR:receptor stoichiometry and quantitative analyses argued against a reversible binding interaction that simply shifts the ON-OFF equilibrium of receptor signaling complexes. Rather, a short-lived CheR binding interaction appears to promote a long-lasting change in receptor molecules, either a covalent modification or conformation that enhances their response to attractant ligands.


Asunto(s)
Adaptación Biológica/fisiología , Células Quimiorreceptoras/metabolismo , Proteínas Bacterianas/metabolismo , Catálisis , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Ligandos , Proteínas de la Membrana/metabolismo , Metiltransferasas/metabolismo , Serina/metabolismo , Transducción de Señal/fisiología
18.
J Mol Biol ; 429(6): 823-835, 2017 03 24.
Artículo en Inglés | MEDLINE | ID: mdl-28215934

RESUMEN

Residues E402 and R404 of the Escherichia coli serine chemoreceptor, Tsr, appear to form a salt bridge that spans the interfaces between neighboring dimers in the Tsr trimer of dimers, a key structural component of receptor core signaling complexes. To assess their functional roles, we constructed full sets of single amino acid replacement mutants at E402 and R404 and characterized their signaling behaviors with a suite of in vivo assays. Our results indicate that the E402 and R404 residues of Tsr play their most critical signaling roles at their inner locations near the trimer axis where they likely participate in stabilizing the trimer-of-dimer packing and the kinase-ON state of core signaling complexes. Mutant receptors with a variety of side-chain replacements still accessed both the ON and OFF signaling states, suggesting that core signaling complexes produce kinase activity over a range of receptor conformations and dynamic motions. Similarly, the kinase-OFF state may not be a discrete conformation but rather a range of structures outside the range of those suitable for kinase activation. Consistent with this idea, some structural lesions at both E402 and R404 produced signaling behaviors that are not compatible with discrete two-state models of core complex signaling states. Those lesions might stabilize intermediate receptor conformations along the OFF-ON energy landscape. Amino acid replacements produced different constellations of signaling defects at each residue, indicating that they play distinct structure-function roles. R404, but not E402, was critical for high signal cooperativity in the receptor array.


Asunto(s)
Escherichia coli/genética , Escherichia coli/fisiología , Proteínas Quimiotácticas Aceptoras de Metilo/genética , Proteínas Quimiotácticas Aceptoras de Metilo/metabolismo , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Transducción de Señal , Sustitución de Aminoácidos , Análisis Mutacional de ADN , Mutagénesis Sitio-Dirigida , Fosforilación , Multimerización de Proteína , Procesamiento Proteico-Postraduccional
19.
mBio ; 7(6)2016 12 20.
Artículo en Inglés | MEDLINE | ID: mdl-27999161

RESUMEN

Motile bacteria use large receptor arrays to detect and follow chemical gradients in their environment. Extended receptor arrays, composed of networked signaling complexes, promote cooperative stimulus control of their associated signaling kinases. Here, we used structural lesions at the communication interface between core complexes to create an Escherichia coli strain with functional but dispersed signaling complexes. This strain allowed us to directly study how networking of signaling complexes affects chemotactic signaling and gradient-tracking performance. We demonstrate that networking of receptor complexes provides bacterial cells with about 10-fold-heightened detection sensitivity to attractants while maintaining a wide dynamic range over which receptor adaptational modifications can tune response sensitivity. These advantages proved especially critical for chemotaxis toward an attractant source under conditions in which bacteria are unable to alter the attractant gradient. IMPORTANCE: Chemoreceptor arrays are found in many motile bacteria. However, although our understanding of bacterial chemotaxis is quite detailed, the signaling and behavioral advantages of networked receptor arrays had not been directly studied in cells. We have recently shown that lesions in a key interface of the E. coli receptor array diminish physical connections and functional coupling between core signaling complexes while maintaining their basic signaling capacity. In this study, we exploited an interface 2 mutant to show, for the first time, that coupling between core complexes substantially enhances stimulus detection and chemotaxis performance.


Asunto(s)
Células Quimiorreceptoras/fisiología , Quimiotaxis , Proteínas de Escherichia coli/fisiología , Escherichia coli/fisiología , Quimiotaxis/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Mutación , Transducción de Señal/genética
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