Crystal structures of the receiver domain of the response regulator PhoP from Escherichia coli in the absence and presence of the phosphoryl analog beryllofluoride

Crystal structure of receiver domain of putative NarL family response regulator spr1814 from Streptococcus pneumoniae in the absence and presence of the phosphoryl analog beryllofluoride

Spr1814 of Streptococcus pneumoniae is a putative response regulator (RR) that has four-helix helix-turn-helix DNA-binding domain and belongs to the NarL family. The prototypical RR contains two domains, an N-terminal receiver domain linked to a variable effector domain. The receiver domain functions as a phosphorylation-activated switch and contains the typical doubly wound five-stranded α/β fold. Here, we report the crystal structure of the receiver domain of spr1814 (spr1814(R)) determined in the absence and presence of beryllofluoride as a phosphoryl analog. Based on the overall structure, spr1814(R) was shown to contain the typical fold similar with other structures of the receiver domain; however, an additional linker region connecting the receiver and DNA-binding domain was inserted into the dimer interface of spr1814(R), resulting in the formation of unique dimer interface. Upon phosphorylation, the conformational change of the linker region was observed and this suggests that domain rearrangement between the receiver domain and effector domain could occur in full-length spr1814.

The promoter architectural landscape of the Salmonella PhoP regulon

The DNA-binding protein PhoP controls virulence and Mg²⁺ homeostasis in the Gram-negative pathogen Salmonella enterica serovar Typhimurium. PhoP regulates expression of a large number of genes that differ both in their ancestry and in the biochemical functions and physiological roles of the encoded products. This suggests that PhoP-regulated genes are differentially expressed. To understand how a bacterial activator might generate varied gene expression behaviour, we investigated the cis-acting promoter features (i.e. the number of PhoP binding sites, as well as their orientation and location with respect to the sites bound by RNA polymerase and the sequences that constitute the PhoP binding sites) in 23 PhoP-activated promoters. Our results show that natural PhoP-activated promoters utilize only a limited number of combinations of cis-acting features – or promoter architectures. We determine that PhoP activates transcription by different mechanisms, and that ancestral and horizontally acquired PhoP-activated genes have distinct promoter architectures.

Inhibition of bacterial virulence: drug-like molecules targeting the Salmonella enterica PhoP response regulator

Two-component signal transduction (TCST) is the predominant signaling scheme used in bacteria to sense and respond to environmental changes in order to survive and thrive. A typical TCST system consists of a sensor histidine kinase to detect external signals and an effector response regulator to respond to external changes. In the signaling scheme, the histidine kinase phosphorylates and activates the response regulator, which functions as a transcription factor to modulate gene expression. One promising strategy toward antibacterial development is to target TCST regulatory systems, specifically the response regulators to disrupt the expression of genes important for virulence. In Salmonella enterica, the PhoQ/PhoP signal transduction system is used to sense and respond to low magnesium levels and regulates the expression for over 40 genes necessary for growth under these conditions, and more interestingly, genes that are important for virulence. In this study, a hybrid approach coupling computational and experimental methods was applied to identify drug-like compounds to target the PhoP response regulator. A computational approach of structure-based virtual screening combined with a series of biochemical and biophysical assays was used to test the predictability of the computational strategy and to characterize the mode of action of the compounds. Eight compounds from virtual screening inhibit the formation of the PhoP-DNA complex necessary for virulence gene regulation. This investigation served as an initial case study for targeting TCST response regulators to modulate the gene expression of a signal transduction pathway important for bacterial virulence. With the increasing resistance of pathogenic bacteria to current antibiotics, targeting TCST response regulators that control virulence is a viable strategy for the development of antimicrobial therapeutics with novel modes of action.

Second monomer binding is the rate-limiting step in the formation of the dimeric PhoP-DNA complex

PhoP, the response regulator of the PhoP/PhoQ system, regulates Mg(2+) homeostasis in Salmonella typhimurium. Dimerization of PhoP on the DNA is necessary for its regulatory function, and PhoP regulates the expression of genes in a phosphorylation-dependent manner. Higher PhoP concentrations, however, can activate PhoP and substitute for phosphorylation-dependent gene regulation. Activation of PhoP by phosphorylation is explained by self-assembly of phosphorylated PhoP (PhoP-p) in solution and binding of the PhoP-p dimer to the promoter. To understand the mechanism of PhoP dimerization on the DNA, we examined the interactions of PhoP with double-stranded DNAs containing the canonical PhoP box (PB). We present results from multiple biophysical methods, demonstrating that PhoP is a monomer in solution over a range of concentrations and binds to PB in a stepwise manner with a second PhoP molecule binding weakly. The affinity for the binding of the first PhoP molecule to PB is more than ∼17-fold higher than the affinity of the second PhoP monomer for PB. Kinetic analyses of PhoP binding reveal that the on rate of the second PhoP monomer binding is the rate-limiting step during the formation of the (PhoP)(2)-DNA complex. Results show that a moderate increase in PhoP concentration can promote dimerization of PhoP on the DNA, which otherwise could be achieved by PhoP-p at much lower protein concentrations. Detailed analyses of PhoP-DNA interactions have revealed the existence of a kinetic barrier that is the key for specificity in the formation of the productive (PhoP)(2)-DNA complex.

The atypical response regulator protein ChxR has structural characteristics and dimer interface interactions that are unique within the OmpR/PhoB subfamily

Typically as a result of phosphorylation, OmpR/PhoB response regulators form homodimers through a receiver domain as an integral step in transcriptional activation. Phosphorylation stabilizes the ionic and hydrophobic interactions between monomers. Recent studies have shown that some response regulators retain functional activity in the absence of phosphorylation and are termed atypical response regulators. The two currently available receiver domain structures of atypical response regulators are very similar to their phospho-accepting homologs, and their propensity to form homodimers is generally retained. An atypical response regulator, ChxR, from Chlamydia trachomatis, was previously reported to form homodimers; however, the residues critical to this interaction have not been elucidated. We hypothesize that the intra- and intermolecular interactions involved in forming a transcriptionally competent ChxR are distinct from the canonical phosphorylation (activation) paradigm in the OmpR/PhoB response regulator subfamily. To test this hypothesis, structural and functional studies were performed on the receiver domain of ChxR. Two crystal structures of the receiver domain were solved with the recently developed method using triiodo compound I3C. These structures revealed many characteristics unique to OmpR/PhoB subfamily members: typical or atypical. Included was the absence of two α-helices present in all other OmpR/PhoB response regulators. Functional studies on various dimer interface residues demonstrated that ChxR forms relatively stable homodimers through hydrophobic interactions, and disruption of these can be accomplished with the introduction of a charged residue within the dimer interface. A gel shift study with monomeric ChxR supports that dimerization through the receiver domain is critical for interaction with DNA.

Structure of the response regulator PhoP from Mycobacterium tuberculosis reveals a dimer through the receiver domain

The PhoP protein from Mycobacterium tuberculosis is a response regulator of the OmpR/PhoB subfamily, whose structure consists of an N-terminal receiver domain and a C-terminal DNA-binding domain. How the DNA-binding activities are regulated by phosphorylation of the receiver domain remains unclear due to a lack of structural information on the full-length proteins. Here we report the crystal structure of the full-length PhoP of M. tuberculosis. Unlike other known structures of full-length proteins of the same subfamily, PhoP forms a dimer through its receiver domain with the dimer interface involving α4-β5-α5, a common interface for activated receiver domain dimers. However, the switch residues, Thr99 and Tyr118, are in a conformation resembling those of nonactivated receiver domains. The Tyr118 side chain is involved in the dimer interface interactions. The receiver domain is tethered to the DNA-binding domain through a flexible linker and does not impose structural constraints on the DNA-binding domain. This structure suggests that phosphorylation likely facilitates/stabilizes receiver domain dimerization, bringing the DNA-binding domains to close proximity, thereby increasing their binding affinity for direct repeat DNA sequences.

Regulation of response regulator autophosphorylation through interdomain contacts

DNA-binding response regulators (RRs) of the OmpR/PhoB subfamily alternate between inactive and active conformational states, with the latter having enhanced DNA-binding affinity. Phosphorylation of an aspartate residue in the receiver domain, usually via phosphotransfer from a cognate histidine kinase, stabilizes the active conformation. Many of the available structures of inactive OmpR/PhoB family proteins exhibit extensive interfaces between the N-terminal receiver and C-terminal DNA-binding domains. These interfaces invariably involve the α4-β5-α5 face of the receiver domain, the locus of the largest differences between inactive and active conformations and the surface that mediates dimerization of receiver domains in the active state. Structures of receiver domain dimers of DrrB, DrrD, and MtrA have been determined, and phosphorylation kinetics were analyzed. Analysis of phosphotransfer from small molecule phosphodonors has revealed large differences in autophosphorylation rates among OmpR/PhoB RRs. RRs with substantial domain interfaces exhibit slow rates of phosphorylation. Rates are greatly increased in isolated receiver domain constructs. Such differences are not observed between autophosphorylation rates of full-length and isolated receiver domains of a RR that lacks interdomain interfaces, and they are not observed in histidine kinase-mediated phosphotransfer. These findings suggest that domain interfaces restrict receiver domain conformational dynamics, stabilizing an inactive conformation that is catalytically incompetent for phosphotransfer from small molecule phosphodonors. Inhibition of phosphotransfer by domain interfaces provides an explanation for the observation that some RRs cannot be phosphorylated by small molecule phosphodonors in vitro and provides a potential mechanism for insulating some RRs from small molecule-mediated phosphorylation in vivo.

Molecular strategies for phosphorylation-mediated regulation of response regulator activity

Response regulator (RR) proteins exploit different molecular surfaces in their inactive and active conformations for a variety of regulatory intramolecular and/or intermolecular protein-protein interactions that either inhibit or activate effector domain activities. This versatile strategy enables numerous regulatory mechanisms among RRs. The recent accumulation of structures of inactive and active forms of multidomain RRs and RR complexes has revealed many different domain arrangements that have provided insight into regulatory mechanisms. Although diversity is the rule, even among subfamily members containing homologous domains, several structural modes of interaction and mechanisms of regulation recur frequently. These themes involve interactions at the alpha4-beta5-alpha5 face of the receiver domain, modes of dimerization of receiver domains, and inhibitory or activating heterodomain interactions.

Structural and mechanistic determinants of c-di-GMP signalling

Bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) is a ubiquitous second messenger that regulates cell surface-associated traits in bacteria. Components of this regulatory network include GGDEF and EAL domain-containing proteins that determine the cellular concentrations of c-di-GMP by mediating its synthesis and degradation, respectively. Crystal structure analyses in combination with functional studies have revealed the catalytic mechanisms and regulatory principles involved. Downstream, c-di-GMP is recognized by PilZ domain-containing receptors that can undergo large-scale domain rearrangements on ligand binding. Here, we review recent data on the structure and functional properties of the protein families that are involved in c-di-GMP signalling and discuss the mechanistic implications.

Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB

Structural analysis of the Escherichia coli response regulator transcription factor PhoB indicates that the protein dimerizes in two different orientations that are both mediated by the receiver domain. The two dimers exhibit 2-fold rotational symmetry: one involves the alpha 4-beta 5-alpha 5 surface and the other involves the alpha1/alpha 5 surface. The alpha 4-beta 5-alpha 5 dimer is observed when the protein is crystallized in the presence of the phosphoryl analog BeF(3)(-), while the alpha1/alpha 5 dimer is observed in its absence. From these studies, a model of the inactive and active states of PhoB has been proposed that involves the formation of two distinct dimers. In order to gain further insight into the roles of these dimers, we have engineered a series of mutations in PhoB intended to perturb each of them selectively. Our results indicate that perturbation of the alpha 4-beta 5-alpha 5 surface disrupts phosphorylation-dependent dimerization and DNA binding as well as PhoB-mediated transcriptional activation of phoA, while perturbations to the alpha1/alpha 5 surface do not. Furthermore, experiments with a GCN4 leucine zipper/PhoB chimera protein indicate that PhoB is activated through an intermolecular mechanism. Together, these results support a model of activation of PhoB in which phosphorylation promotes dimerization via the alpha 4-beta 5-alpha 5 face, which enhances DNA binding and thus the ability of PhoB to regulate transcription.

Transcription factor function and promoter architecture govern the evolution of bacterial regulons

Evolutionary changes in ancestral regulatory circuits can bring about phenotypic differences between related organisms. Studies of regulatory circuits in eukaryotes suggest that these modifications result primarily from changes in cis-regulatory elements (as opposed to alterations in the transcription factors that act upon these sequences). It is presently unclear how the evolution of gene regulatory circuits has proceeded in bacteria, given the rampant effects of horizontal gene transfer, which has significantly altered the composition of bacterial regulons. We now demonstrate that the evolution of the regulons governed by the regulatory protein PhoP in the related human pathogens Salmonella enterica and Yersinia pestis has entailed functional changes in the PhoP protein as well as in the architecture of PhoP-dependent promoters. These changes have resulted in orthologous PhoP proteins that differ both in their ability to promote transcription and in their role as virulence regulators. We posit that these changes allow bacterial transcription factors to incorporate newly acquired genes into ancestral regulatory circuits and yet retain control of the core members of a regulon.

Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics

Single domain response regulators (SD-RRs) are signaling components of two-component phosphorylation pathways that harbor a phosphoryl receiver domain but lack a dedicated output domain. The Escherichia coli protein CheY, the paradigm member of this family, regulates chemotaxis by relaying information between chemoreceptors and the flagellar motor switch. New data provide a more complex picture of CheY-mediated motility control in several bacteria and suggest diverging mechanisms in control of cellular motors. Moreover, advances have been made in understanding cellular functions of SD-RRs beyond chemotaxis. We review recent reports indicating that SD-RRs constitute a family of versatile molecular switches that contribute to cellular organization and dynamics as spatial organizer and/or as allosteric regulators of histidine protein kinases.

Identification of direct residue contacts in protein-protein interaction by message passing

Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes enables various statistical approaches to this problem. In this context covariance-based methods have been used to identify correlation between amino acid positions in interacting proteins. However, these methods have an important shortcoming, in that they cannot distinguish between directly and indirectly correlated residues. We developed a method that combines covariance analysis with global inference analysis, adopted from use in statistical physics. Applied to a set of >2,500 representatives of the bacterial two-component signal transduction system, the combination of covariance with global inference successfully and robustly identified residue pairs that are proximal in space without resorting to ad hoc tuning parameters, both for heterointeractions between sensor kinase (SK) and response regulator (RR) proteins and for homointeractions between RR proteins. The spectacular success of this approach illustrates the effectiveness of the global inference approach in identifying direct interaction based on sequence information alone. We expect this method to be applicable soon to interaction surfaces between proteins present in only 1 copy per genome as the number of sequenced genomes continues to expand. Use of this method could significantly increase the potential targets for therapeutic intervention, shed light on the mechanism of protein-protein interaction, and establish the foundation for the accurate prediction of interacting protein partners.

System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids

Two-component signal transduction, featuring highly conserved histidine kinases (HKs) and response regulators (RRs), is one of the most prevalent signalling schemes in prokaryotes. RRs function as phosphorylation-activated switches to mediate diverse output responses, mostly via transcription regulation. As bacterial genomes typically encode multiple two-component proteins for distinct signalling pathways, the sequence and structural similarities of RR receiver domains create significant challenges to maintain interaction specificity. It is especially demanding for members of the OmpR/PhoB subfamily, the largest RR subfamily, which share a conserved dimerization interface for phosphorylation-mediated transcription regulation. We developed a strategy to investigate RR interaction by analysing Förster resonance energy transfer (FRET) between cyan fluorescent protein (CFP)- and yellow fluorescent protein (YFP)-fused RRs in vitro. Using the Escherichia coli RR PhoB as a model system, we were able to observe phosphorylation-dependent FRET between fluorescent protein (FP)–PhoB proteins and validated the FRET method by determining dimerization affinity and dimerization-coupled phosphorylation kinetics that recapitulated values determined by alternative methods. Further application of the FRET method to all E. coli OmpR/PhoB subfamily RRs revealed that phosphorylation–activated RR interaction is indeed a common theme for OmpR/PhoB subfamily RRs and these RRs display significant interaction specificity. Weak hetero-pair interactions were also identified between several different RRs, suggesting potential cross-regulation between distinct pathways.

The NMR structure of the Staphylococcus aureus response regulator VraR DNA binding domain reveals a dynamic relationship between it and its associated receiver domain

In Staphylococcus aureus, a two-component signaling system consisting of the histidine kinase VraS and the response regulator VraR stimulates gene expression in response to antibiotics that inhibit cell wall formation. With respect to understanding the mechanism of the VraSR response and precise interaction of VraR at promoter sites, the structure of the VraR DNA binding domain (DBD) was determined using NMR methods. The DBD demonstrates a four-helix configuration that is shared with the NarL/FixJ family of response regulators and is monomeric in solution. Unobservable amide resonances in VraR NMR spectra coincided with a set of DNA backbone contact sites predicted from a model of a VraR-DNA complex. This observation suggests that a degree of conformational sampling is required to achieve a high-affinity interaction with DNA. On the basis of chemical shift differences and line broadening, an amino-terminal 3 10 helix and a portion of helix H4 identify a continuous surface that may link the DBD to the receiver domain. The full-length VraR protein thermally denatured with a single transition, suggesting that the receiver domain and DBD were integrated and not simply tethered. Of note, the DBD alone denatured at a temperature that was 21 degrees C higher than that of the full-length protein. Thus, the DBD appears to be thermodynamically and structurally sensitive to state of the receiver domain.

Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog

The crystal structure of the yeast SLN1 response regulator (RR) domain bound to both a phosphoryl analog [beryllium fluoride (BeF(3)(-))] and Mg(2+), in complex with its downstream phosphorelay signaling partner YPD1, has been determined at a resolution of 1.70 A. Comparisons between the BeF(3)(-)-activated complex and the unliganded (or apo) complex determined previously reveal modest but important differences. The SLN1-R1 x Mg(2+) x BeF(3)(-) structure from the complex provides evidence for the first time that the mechanism of phosphorylation-induced activation is highly conserved between bacterial RR domains and this example from a eukaryotic organism. Residues in and around the active site undergo slight rearrangements in order to form bonds with the essential divalent cation and fluorine atoms of BeF(3)(-). Two conserved switch-like residues (Thr1173 and Phe1192) occupy distinctly different positions in the apo versus BeF(3)(-)-bound structures, consistent with the "Y-T" coupling mechanism proposed for the activation of CheY and other bacterial RRs. Several loop regions and the alpha 4-beta 5-alpha 5 surface of the SLN1-R1 domain undergo subtle conformational changes ( approximately 1-3 A displacements relative to the apo structure) that lead to significant changes in terms of contacts that are formed with YPD1. Detailed structural comparisons of protein-protein interactions in the apo and BeF(3)(-)-bound complexes suggest at least a two-state equilibrium model for the formation of a transient encounter complex, in which phosphorylation of the RR promotes the formation of a phosphotransfer-competent complex. In the BeF(3)(-)-activated complex, the position of His64 from YPD1 needs to be within ideal distance of and in near-linear geometry with Asp1144 from the SLN1-R1 domain for phosphotransfer to occur. The ground-state structure presented here suggests that phosphoryl transfer will likely proceed through an associative mechanism involving the formation of a pentacoordinate phosphorus intermediate.