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Phosphorylation-dependent derepression by the response regulator HnoC in the Shewanella oneidensis nitric oxide signaling network. Proc Natl Acad Sci U S A 2013; 110:E4648-57. [PMID: 24218564 DOI: 10.1073/pnas.1318128110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitric oxide (NO) is an important signaling molecule that regulates diverse physiological processes in all domains of life. In many gammaproteobacteria, NO controls behavioral responses through a complex signaling network involving heme-nitric oxide/oxygen binding (H-NOX) domains as selective NO sensors. In Shewanella oneidensis, H-NOX-mediated NO sensing increases biofilm formation, which is thought to serve as a protective mechanism against NO cytotoxicity. The H-NOX/NO-responsive (hno) signaling network involves H-NOX-dependent control of HnoK autophosphorylation and phosphotransfer from HnoK to three response regulators. Two of these response regulators, HnoB and HnoD, regulate cyclic-di-GMP levels and influence biofilm formation. However, the role of the third response regulator in the signaling network, HnoC, has not been determined. Here we describe a role for HnoC as a transcriptional repressor for the signaling genes in the hno network. The genes controlled by HnoC were identified by microarray analysis, and its function as a repressor was confirmed in vivo. HnoC belongs to an uncharacterized family of DNA-binding response regulators. Binding of HnoC to its promoter targets was characterized in vitro, revealing an unprecedented regulation mechanism, which further extends the functional capabilities of DNA-binding response regulators. In the unphosphorylated state HnoC forms a tetramer, which tightly binds to an inverted-repeat target sequence overlapping with the promoter regions. Phosphorylation of HnoC induces dissociation of the response regulator tetramer and detachment of subunits from the promoter DNA, which subsequently leads to transcriptional derepression.
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52
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Luo SC, Lou YC, Rajasekaran M, Chang YW, Hsiao CD, Chen C. Structural basis of a physical blockage mechanism for the interaction of response regulator PmrA with connector protein PmrD from Klebsiella pneumoniae. J Biol Chem 2013; 288:25551-25561. [PMID: 23861396 PMCID: PMC3757216 DOI: 10.1074/jbc.m113.481978] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In bacteria, the two-component system is the most prevalent for sensing and transducing environmental signals into the cell. The PmrA-PmrB two-component system, responsible for sensing external stimuli of high Fe(3+) and mild acidic conditions, can control the genes involved in lipopolysaccharide modification and polymyxin resistance in pathogens. In Klebsiella pneumoniae, the small basic connector protein PmrD protects phospho-PmrA and prolongs the expression of PmrA-activated genes. We previously determined the phospho-PmrA recognition mode of PmrD. However, how PmrA interacts with PmrD and prevents its dephosphorylation remains unknown. To address this question, we solved the x-ray crystal structure of the N-terminal receiver domain of BeF3(-)-activated PmrA (PmrA(N)) at 1.70 Å. With this structure, we applied the data-driven docking method based on NMR chemical shift perturbation to generate the complex model of PmrD-PmrA(N), which was further validated by site-directed spin labeling experiments. In the complex model, PmrD may act as a blockade to prevent phosphatase from contacting with the phosphorylation site on PmrA.
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Affiliation(s)
| | | | | | - Yi-Wei Chang
- Molecular Biology, Academia Sinica, Taipei 115, Taiwan and
| | | | - Chinpan Chen
- From the Institutes of Biomedical Sciences and ,Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, To whom correspondence should be addressed: Institute of Biomedical Sciences, Academia Sinica, 128 Academia Rd., Section 2, Taipei 115, Taiwan. Tel.: 886-2-2652-3035; Fax: 886-2-2788-7641; E-mail:
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53
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Barbieri CM, Wu T, Stock AM. Comprehensive analysis of OmpR phosphorylation, dimerization, and DNA binding supports a canonical model for activation. J Mol Biol 2013; 425:1612-26. [PMID: 23399542 DOI: 10.1016/j.jmb.2013.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 01/22/2013] [Accepted: 02/02/2013] [Indexed: 11/16/2022]
Abstract
The OmpR/PhoB family of response regulators (RRs) is the largest class of two-component system signal transduction proteins. Extensive biochemical and structural characterization of these transcription factors has provided insights into their activation and DNA-binding mechanisms. For the most part, OmpR/PhoB family proteins are thought to become activated through phosphorylation from their cognate histidine kinase partners, which in turn facilitates an allosteric change in the RR, enabling homodimerization and subsequently enhanced DNA binding. Incongruently, it has been suggested that OmpR, the eponymous member of this RR family, becomes activated via different mechanisms, whereby DNA binding plays a central role in facilitating dimerization and phosphorylation. Characterization of the rate and extent of the phosphorylation of OmpR and OmpR DNA-binding mutants following activation of the EnvZ/OmpR two-component system shows that DNA binding is not essential for phosphorylation of OmpR in vivo. In addition, detailed analyses of the energetics of DNA binding and dimerization of OmpR in both its unphosphorylated and phosphorylated state indicate that phosphorylation enhances OmpR dimerization and that this dimerization enhancement is the energetic driving force for phosphorylation-mediated regulation of OmpR-DNA binding. These findings suggest that OmpR phosphorylation-mediated activation follows the same paradigm as the other members of the OmpR/PhoB family of RRs in contrast to previously proposed models of OmpR activation.
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Affiliation(s)
- Christopher M Barbieri
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 679 Hoes Lane West, Piscataway, NJ 08854, USA
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Micevski D, Dougan DA. Proteolytic regulation of stress response pathways in Escherichia coli. Subcell Biochem 2013; 66:105-28. [PMID: 23479439 DOI: 10.1007/978-94-007-5940-4_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Maintaining correct cellular function is a fundamental biological process for all forms of life. A critical aspect of this process is the maintenance of protein homeostasis (proteostasis) in the cell, which is largely performed by a group of proteins, referred to as the protein quality control (PQC) network. This network of proteins, comprised of chaperones and proteases, is critical for maintaining proteostasis not only during favourable growth conditions, but also in response to stress. Indeed proteases play a crucial role in the clearance of unwanted proteins that accumulate during stress, but more importantly, in the activation of various different stress response pathways. In bacteria, the cells response to stress is usually orchestrated by a specific transcription factor (sigma factor). In Escherichia coli there are seven different sigma factors, each of which responds to a particular stress, resulting in the rapid expression of a specific set of genes. The cellular concentration of each transcription factor is tightly controlled, at the level of transcription, translation and protein stability. Here we will focus on the proteolytic regulation of two sigma factors (σ(32) and σ(S)), which control the heat and general stress response pathways, respectively. This review will also briefly discuss the role proteolytic systems play in the clearance of unwanted proteins that accumulate during stress.
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Affiliation(s)
- Dimce Micevski
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, 3086, Australia
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55
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Martin B, Soulet AL, Mirouze N, Prudhomme M, Mortier-Barrière I, Granadel C, Noirot-Gros MF, Noirot P, Polard P, Claverys JP. ComE/ComE~P interplay dictates activation or extinction status of pneumococcal X-state (competence). Mol Microbiol 2012; 87:394-411. [PMID: 23216914 DOI: 10.1111/mmi.12104] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2012] [Indexed: 01/29/2023]
Abstract
Since 1996, induction of competence for genetic transformation of Streptococcus pneumoniae is known to be controlled by the ComD/ComE two-component regulatory system. The mechanism of induction is generally described as involving ComD autophosphorylation, transphosphorylation of ComE and transcriptional activation by ComE~P of the early competence (com) genes, including comX which encodes the competence-specific σ(X) . However, none of these features has been experimentally established. Here we document the autokinase activity of ComD proteins in vitro, and provide an estimate of the stoichiometry of ComD and ComE in vivo. We report that a phosphorylmimetic mutant, ComE(D58E), constructed because of the failure to detect transphosphorylation of purified ComE in vitro, displays full spontaneous competence in ΔcomD cells, an that in vitro ComE(D58E) exhibits significantly improved binding affinity for P(comCDE). We also provide evidence for a differential transcriptional activation and repression of P(comCDE) and P(comX). Altogether, these data support the model of ComE~P-dependent activation of transcription. Finally, we establish that ComE antagonizes expression of the early com genes and propose that the rapid deceleration of transcription from P(comCDE) observed even in cells lacking σ(X) is due to the progressive accumulation of ComE, which outcompetes ComE~P.
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Affiliation(s)
- Bernard Martin
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France
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56
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Chim N, Owens CP, Contreras H, Goulding CW. Withdrawn. Infect Disord Drug Targets 2012:CDTID-EPUB-20121116-2. [PMID: 23167715 PMCID: PMC3695056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Withdrawn by the publisher.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Cedric P. Owens
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Heidi Contreras
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine CA 92697, USA
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57
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Thanikkal EJ, Mangu JCK, Francis MS. Interactions of the CpxA sensor kinase and cognate CpxR response regulator from Yersinia pseudotuberculosis. BMC Res Notes 2012; 5:536. [PMID: 23013530 PMCID: PMC3517363 DOI: 10.1186/1756-0500-5-536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 09/22/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The CpxA sensor kinase-CpxR response regulator two-component regulatory system is a sentinel of bacterial envelope integrity. Integrating diverse signals, it can alter the expression of a wide array of components that serve to shield the envelope from damage and to promote bacterial survival. In bacterial pathogens such as Yersinia pseudotuberculosis, this also extends to pathogenesis. CpxR is thought to dimerize upon phosphorylation by the sensor kinase CpxA. This phosphorylation enables CpxR binding to specific DNA sequences where it acts on gene transcription. As Cpx pathway activation is dependent on protein-protein interactions, we performed an interaction analysis of CpxR and CpxA from Y. pseudotuberculosis. RESULTS CpxR full-length and truncated versions that either contained or lacked a putative internal linker were all assessed for their ability to homodimerize and interact with CpxA. Using an adenylate cyclase-based bacterial two hybrid approach, full-length CpxR readily engaged with CpxA. The CpxR N-terminus could also homodimerize with itself and with a full-length CpxR. A second homodimerization assay based upon the λcI repressor also demonstrated that the CpxR C-terminus could homodimerize. While the linker was not specifically required, it enhanced CpxR homodimerization. Mutagenesis of cpxR identified the aspartate at residue 51, putative N-terminal coiled-coil and C-terminal winged-helix-turn-helix domains as mediators of CpxR homodimerization. Scrutiny of CpxA full-length and truncated versions revealed that dimerization involved the N-terminus and an internal dimerization and histidine phosphotransfer domain. CONCLUSIONS This interaction analysis mapped regions of CpxR and CpxA that were responsible for interactions with self or with each other. When combined with other physiological and biochemical tests both hybrid-based assays can be useful in dissecting molecular contacts that may underpin Cpx pathway activation and repression.
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Affiliation(s)
- Edvin J Thanikkal
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
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58
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Structural insights into the regulatory mechanism of the response regulator RocR from Pseudomonas aeruginosa in cyclic Di-GMP signaling. J Bacteriol 2012; 194:4837-46. [PMID: 22753070 DOI: 10.1128/jb.00560-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleotide messenger cyclic di-GMP (c-di-GMP) plays a central role in the regulation of motility, virulence, and biofilm formation in many pathogenic bacteria. EAL domain-containing phosphodiesterases are the major signaling proteins responsible for the degradation of c-di-GMP and maintenance of its cellular level. We determined the crystal structure of a single mutant (R286W) of the response regulator RocR from Pseudomonas aeruginosa to show that RocR exhibits a highly unusual tetrameric structure arranged around a single dyad, with the four subunits adopting two distinctly different conformations. Subunits A and B adopt a conformation with the REC domain located above the c-di-GMP binding pocket, whereas subunits C and D adopt an open conformation with the REC domain swung to the side of the EAL domain. Remarkably, the access to the substrate-binding pockets of the EAL domains of the open subunits C and D are blocked in trans by the REC domains of subunits A and B, indicating that only two of the four active sites are engaged in the degradation of c-di-GMP. In conjunction with biochemical and biophysical data, we propose that the structural changes within the REC domains triggered by the phosphorylation are transmitted to the EAL domain active sites through a pathway that traverses the dimerization interfaces composed of a conserved regulatory loop and the neighboring motifs. This exquisite mechanism reinforces the crucial role of the regulatory loop and suggests that similar regulatory mechanisms may be operational in many EAL domain proteins, considering the preservation of the dimerization interface and the spatial arrangement of the regulatory domains.
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59
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Krasteva PV, Giglio KM, Sondermann H. Sensing the messenger: the diverse ways that bacteria signal through c-di-GMP. Protein Sci 2012; 21:929-48. [PMID: 22593024 DOI: 10.1002/pro.2093] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 05/04/2012] [Indexed: 11/11/2022]
Abstract
An intracellular second messenger unique to bacteria, c-di-GMP, has gained appreciation as a key player in adaptation and virulence strategies, such as biofilm formation, persistence, and cytotoxicity. Diguanylate cyclases containing GGDEF domains and phosphodiesterases containing either EAL or HD-GYP domains have been identified as the enzymes controlling intracellular c-di-GMP levels, yet little is known regarding signal transmission and the sensory targets for this signaling molecule. Although limited in number, identified c-di-GMP receptors in bacteria are characterized by prominent diversity and multilevel impact. In addition, c-di-GMP has been shown to have immunomodulatory effects in mammals and several eukaryotic c-di-GMP sensors have been proposed. The structural biology of c-di-GMP receptors is a rapidly developing field of research, which holds promise for the development of novel therapeutics against bacterial infections. In this review, we highlight recent advances in identifying bacterial and eukaryotic c-di-GMP signaling mechanisms and emphasize the need for mechanistic structure-function studies on confirmed signaling targets.
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Affiliation(s)
- Petya Violinova Krasteva
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
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60
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Insights into the mechanism of activation of the phosphorylation-independent response regulator NblR. Role of residues Cys69 and Cys96. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:382-90. [DOI: 10.1016/j.bbagrm.2012.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 01/12/2012] [Accepted: 01/13/2012] [Indexed: 12/22/2022]
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61
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Hooghe B, Broos S, van Roy F, De Bleser P. A flexible integrative approach based on random forest improves prediction of transcription factor binding sites. Nucleic Acids Res 2012; 40:e106. [PMID: 22492513 PMCID: PMC3413102 DOI: 10.1093/nar/gks283] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Transcription factor binding sites (TFBSs) are DNA sequences of 6–15 base pairs. Interaction of these TFBSs with transcription factors (TFs) is largely responsible for most spatiotemporal gene expression patterns. Here, we evaluate to what extent sequence-based prediction of TFBSs can be improved by taking into account the positional dependencies of nucleotides (NPDs) and the nucleotide sequence-dependent structure of DNA. We make use of the random forest algorithm to flexibly exploit both types of information. Results in this study show that both the structural method and the NPD method can be valuable for the prediction of TFBSs. Moreover, their predictive values seem to be complementary, even to the widely used position weight matrix (PWM) method. This led us to combine all three methods. Results obtained for five eukaryotic TFs with different DNA-binding domains show that our method improves classification accuracy for all five eukaryotic TFs compared with other approaches. Additionally, we contrast the results of seven smaller prokaryotic sets with high-quality data and show that with the use of high-quality data we can significantly improve prediction performance. Models developed in this study can be of great use for gaining insight into the mechanisms of TF binding.
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Affiliation(s)
- Bart Hooghe
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
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62
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Tang YT, Gao R, Havranek JJ, Groisman EA, Stock AM, Marshall GR. Inhibition of bacterial virulence: drug-like molecules targeting the Salmonella enterica PhoP response regulator. Chem Biol Drug Des 2012; 79:1007-17. [PMID: 22339993 PMCID: PMC3445336 DOI: 10.1111/j.1747-0285.2012.01362.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
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.
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Affiliation(s)
- Yat T Tang
- Center for Computational Biology, Department of Biochemistry and Molecular Biophysics, Washington University School of MedicineSt. Louis, MO 63110, USA
| | - Rong Gao
- Howard Hughes Medical Institute, Center for Advanced Biotechnology and Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical SchoolPiscataway, NJ 08854, USA
| | - James J Havranek
- Department of Genetics, Washington University School of MedicineSt. Louis, MO 63110, USA
| | - Eduardo A Groisman
- Howard Hughes Medical Institute, Department of Molecular Microbiology, Washington University School of MedicineSt. Louis, MO 63110, USA
| | - Ann M Stock
- Howard Hughes Medical Institute, Center for Advanced Biotechnology and Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical SchoolPiscataway, NJ 08854, USA
| | - Garland R Marshall
- Center for Computational Biology, Department of Biochemistry and Molecular Biophysics, Washington University School of MedicineSt. Louis, MO 63110, USA
- *Corresponding author: Garland R. Marshall,
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63
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Singh V, Ekka MK, Kumaran S. Second monomer binding is the rate-limiting step in the formation of the dimeric PhoP-DNA complex. Biochemistry 2012; 51:1346-56. [PMID: 22268791 DOI: 10.1021/bi201257d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Vijay Singh
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
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64
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Sinorhizobium meliloti CheA complexed with CheS exhibits enhanced binding to CheY1, resulting in accelerated CheY1 dephosphorylation. J Bacteriol 2011; 194:1075-87. [PMID: 22194454 DOI: 10.1128/jb.06505-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Retrophosphorylation of the histidine kinase CheA in the chemosensory transduction chain is a widespread mechanism for efficient dephosphorylation of the activated response regulator. First discovered in Sinorhizobium meliloti, the main response regulator CheY2-P shuttles its phosphoryl group back to CheA, while a second response regulator, CheY1, serves as a sink for surplus phosphoryl groups from CheA-P. We have identified a new component in this phospho-relay system, a small 97-amino-acid protein named CheS. CheS has no counterpart in enteric bacteria but revealed distinct similarities to proteins of unknown function in other members of the α subgroup of proteobacteria. Deletion of cheS causes a phenotype similar to that of a cheY1 deletion strain. Fluorescence microscopy revealed that CheS is part of the polar chemosensory cluster and that its cellular localization is dependent on the presence of CheA. In vitro binding, as well as coexpression and copurification studies, gave evidence of CheA/CheS complex formation. Using limited proteolysis coupled with mass spectrometric analyses, we defined CheA(163-256) to be the CheS binding domain, which overlaps with the N-terminal part of the CheY2 binding domain (CheA(174-316)). Phosphotransfer experiments using isolated CheA-P showed that dephosphorylation of CheY1-P but not CheY2-P is increased in the presence of CheS. As determined by surface plasmon resonance spectroscopy, CheY1 binds ∼100-fold more strongly to CheA/CheS than to CheA. We propose that CheS facilitates signal termination by enhancing the interaction of CheY1 and CheA, thereby promoting CheY1-P dephosphorylation, which results in a more efficient drainage of the phosphate sink.
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65
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Hickey JM, Lovell S, Battaile KP, Hu L, Middaugh CR, Hefty PS. The atypical response regulator protein ChxR has structural characteristics and dimer interface interactions that are unique within the OmpR/PhoB subfamily. J Biol Chem 2011; 286:32606-16. [PMID: 21775428 PMCID: PMC3173177 DOI: 10.1074/jbc.m111.220574] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 07/06/2011] [Indexed: 02/03/2023] Open
Abstract
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.
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Affiliation(s)
| | - Scott Lovell
- the Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, and
| | - Kevin P. Battaile
- the Hauptman-Woodward Medical Research Institute, IMCA-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439
| | - Lei Hu
- Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045
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66
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Menon S, Wang S. Structure of the response regulator PhoP from Mycobacterium tuberculosis reveals a dimer through the receiver domain. Biochemistry 2011; 50:5948-57. [PMID: 21634789 DOI: 10.1021/bi2005575] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
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.
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Affiliation(s)
- Smita Menon
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
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Barbieri CM, Mack TR, Robinson VL, Miller MT, Stock AM. Regulation of response regulator autophosphorylation through interdomain contacts. J Biol Chem 2010; 285:32325-35. [PMID: 20702407 PMCID: PMC2952233 DOI: 10.1074/jbc.m110.157164] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 07/29/2010] [Indexed: 11/17/2022] Open
Abstract
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.
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Affiliation(s)
- Christopher M. Barbieri
- From the Center for Advanced Biotechnology and Medicine
- the Department of Biochemistry
- the Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635 and
| | - Timothy R. Mack
- From the Center for Advanced Biotechnology and Medicine
- the Department of Biochemistry
- the Graduate School of Biomedical Sciences, and
| | - Victoria L. Robinson
- From the Center for Advanced Biotechnology and Medicine
- the Department of Biochemistry
- the Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635 and
| | - Matthew T. Miller
- From the Center for Advanced Biotechnology and Medicine
- the Department of Chemistry, Rutgers University, Piscataway, New Jersey 08854-8066
| | - Ann M. Stock
- From the Center for Advanced Biotechnology and Medicine
- the Department of Biochemistry
- the Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635 and
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68
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Le Gac M, Doebeli M. Epistasis and frequency dependence influence the fitness of an adaptive mutation in a diversifying lineage. Mol Ecol 2010; 19:2430-8. [PMID: 20497320 DOI: 10.1111/j.1365-294x.2010.04664.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The opportunity for a mutation to invade a population can dramatically vary depending on the context in which this mutation occurs. Such context dependence is difficult to document as it requires the ability to measure how a mutation affects phenotypes and fitness and to manipulate the context in which the mutation occurs. We identified a mutation in a gene encoding a global regulator in one of two ecotypes that diverged from a common ancestor during 1200 generations of experimental evolution. We replaced the ancestral allele by the mutant allele, and vice versa, in several clones isolated during the time course of the evolution experiment, and compared the phenotype and fitness of clones isogenic except for the focal mutation. We show that the fitness and phenotype of the mutation are strongly affected by epistatic interactions between genes in the same genome, as well as by frequency dependent selection resulting from biotic interactions between individuals in the same population. We conclude that amongst the replicate population in which it spread, the mutation we identified is only adaptive when occurring in specific genomes and competing with specific individuals. This study thus demonstrates that the opportunity for an adaptive mutation to spread in an evolutionary lineage can only be understood in the light of its genomic and competitive environments.
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Affiliation(s)
- Mickael Le Gac
- Department of Zoology, University of British Columbia, Vancouver, BC V6T1Z4, Canada.
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69
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Tiwari N, Woods L, Haley R, Kight A, Goforth R, Clark K, Ataai M, Henry R, Beitle R. Identification and characterization of native proteins of Escherichia coli BL-21 that display affinity towards Immobilized Metal Affinity Chromatography and Hydrophobic Interaction Chromatography Matrices. Protein Expr Purif 2010; 70:191-5. [DOI: 10.1016/j.pep.2009.10.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 10/28/2009] [Accepted: 10/29/2009] [Indexed: 10/20/2022]
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70
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Novel antibacterial compounds specifically targeting the essential WalR response regulator. J Antibiot (Tokyo) 2010; 63:127-34. [PMID: 20111065 DOI: 10.1038/ja.2010.4] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The WalK/WalR (YycG/YycF) two-component system, which is essential for cell viability, is highly conserved and specific to low-GC percentage of Gram-positive bacteria, making it an attractive target for novel antimicrobial compounds. Recent work has shown that WalK/WalR exerts an effect as a master regulatory system in controlling and coordinating cell wall metabolism with cell division in Bacillus subtilis and Staphylococcus aureus. In this paper, we develop a high-throughput screening system for WalR inhibitors and identify two novel inhibitors targeting the WalR response regulator (RR): walrycin A (4-methoxy-1-naphthol) and walrycin B (1,6-dimethyl-3-[4-(trifluoromethyl)phenyl]pyrimido[5,4-e][1,2,4]triazine-5,7-dione). Addition of these compounds simultaneously affects the expression of WalR regulon genes, leading to phenotypes consistent with those of cells starved for the WalK/WalR system and having a bactericidal effect. B. subtilis cells form extremely long aseptate filaments and S. aureus cells form large aggregates under these conditions. These results show that walrycins A and B are the first antibacterial agents targeting WalR in B. subtilis and S. aureus.
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71
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Gao R, Stock AM. Molecular strategies for phosphorylation-mediated regulation of response regulator activity. Curr Opin Microbiol 2010; 13:160-7. [PMID: 20080056 DOI: 10.1016/j.mib.2009.12.009] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 12/21/2009] [Accepted: 12/23/2009] [Indexed: 10/20/2022]
Abstract
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.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, UMDNJ-Robert Wood Johnson, Medical School and Howard Hughes Medical Institute, Piscataway, NJ, USA
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72
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Mycobacterium tuberculosis PhoP recognizes two adjacent direct-repeat sequences to form head-to-head dimers. J Bacteriol 2009; 191:7466-76. [PMID: 19820095 DOI: 10.1128/jb.00669-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium tuberculosis PhoP of the PhoP-PhoR two-component signaling system orchestrates a complex transcription program and is essential for the growth and virulence of the tubercle bacillus. PhoP comprises a phosphorylation domain at the amino-terminal half and a DNA-binding domain in the carboxy-terminal half of the protein. We show here that the protein recognizes a 23-bp sequence of the phoP upstream region comprising two adjacent direct repeat motifs believed to promote transcription regulation. DNA binding, which involves the recruitment of two monomeric PhoP molecules, was dependent on conserved adenines of the repeat sequences and the orientation of the repeat motifs relative to each other. Although response regulators such as PhoB and FixJ dimerize upon phosphorylation, we demonstrate here that PhoP dimerization can also be stimulated by DNA binding. Using the established asymmetric tandem binding model by members of the OmpR/PhoB protein family as a guide, we set out to examine intermolecular interactions between PhoP dimers by protein cross-linking. Our results are consistent with a model in which two PhoP protomers bind the duplex DNA with a symmetric head-to-head orientation to project their N termini toward one another, arguing against previously proposed head-to-tail tandem dimer formation for members of the OmpR/PhoB protein subfamily.
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73
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CtrA, a global response regulator, uses a distinct second category of weak DNA binding sites for cell cycle transcription control in Caulobacter crescentus. J Bacteriol 2009; 191:5458-70. [PMID: 19542275 DOI: 10.1128/jb.00355-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CtrA controls cell cycle programs of chromosome replication and genetic transcription. Phosphorylated CtrA approximately P exhibits high affinity (dissociation constant [K(d)], <10 nM) for consensus TTAA-N7-TTAA binding sites with "typical" (N = 7) spacing. We show here that ctrA promoters P1 and P2 use low-affinity (K(d), >500 nM) CtrA binding sites with "atypical" (N not equal 7) spacing. Footprints demonstrated that phosphorylated CtrA approximately P does not exhibit increased affinity for "atypical" sites, as it does for sites in the replication origin. Instead, high levels of CtrA (>10 microM) accumulate, which can drive CtrA binding to "atypical" sites. In vivo cross-linking showed that when the stable CtrADelta3 protein persists during the cell cycle, the "atypical" sites at ctrA and motB are persistently bound. Interestingly, the cell cycle timing of ctrA P1 and P2 transcription is not altered by persistent CtrADelta3 binding. Therefore, operator DNA occupancy is not sufficient for regulation, and it is the cell cycle variation of CtrA approximately P phosphorylation that provides the dominant "activation" signal. Protein dimerization is one potential means of "activation." The glutathione S-transferase (GST) protein dimerizes, and fusion with CtrA (GST-CtrA) creates a stable dimer with enhanced affinity for TTAA motifs. Electrophoretic mobility shift assays with GST-CtrA revealed cooperative modes of binding that further distinguish the "atypical" sites. GST-CtrA also binds a single TTAA motif in ctrA P1 aided by DNA in the extended TTAACCAT motif. We discuss how "atypical" sites are a common yet distinct category of CtrA regulatory sites and new implications for the working and evolution of cell cycle control networks.
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74
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Mack TR, Gao R, Stock AM. Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB. J Mol Biol 2009; 389:349-64. [PMID: 19371748 DOI: 10.1016/j.jmb.2009.04.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Revised: 04/08/2009] [Accepted: 04/08/2009] [Indexed: 12/28/2022]
Abstract
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.
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Affiliation(s)
- Timothy R Mack
- Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854, USA
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75
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Jenal U, Galperin MY. Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics. Curr Opin Microbiol 2009; 12:152-60. [PMID: 19246239 DOI: 10.1016/j.mib.2009.01.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 01/23/2009] [Accepted: 01/26/2009] [Indexed: 11/18/2022]
Abstract
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.
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Affiliation(s)
- Urs Jenal
- Biozentrum, University of Basel, Switzerland.
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76
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Yanover C, Singh M, Zaslavsky E. M are better than one: an ensemble-based motif finder and its application to regulatory element prediction. ACTA ACUST UNITED AC 2009; 25:868-74. [PMID: 19223448 DOI: 10.1093/bioinformatics/btp090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Identifying regulatory elements in genomic sequences is a key component in understanding the control of gene expression. Computationally, this problem is often addressed by motif discovery, where the goal is to find a set of mutually similar subsequences within a collection of input sequences. Though motif discovery is widely studied and many approaches to it have been suggested, it remains a challenging and as yet unresolved problem. RESULTS We introduce SAMF (Solution-Aggregating Motif Finder), a novel approach for motif discovery. SAMF is based on a Markov Random Field formulation, and its key idea is to uncover and aggregate multiple statistically significant solutions to the given motif finding problem. In contrast to many earlier methods, SAMF does not require prior estimates on the number of motif instances present in the data, is not limited by motif length, and allows motifs to overlap. Though SAMF is broadly applicable, these features make it particularly well suited for addressing the challenges of prokaryotic regulatory element detection. We test SAMF's ability to find transcription factor binding sites in an Escherichia coli dataset and show that it outperforms previous methods. Additionally, we uncover a number of previously unidentified binding sites in this data, and provide evidence that they correspond to actual regulatory elements. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chen Yanover
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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77
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Abstract
Two-component signal transduction based on phosphotransfer from a histidine protein kinase to a response regulator protein is a prevalent strategy for coupling environmental stimuli to adaptive responses in bacteria. In both histidine kinases and response regulators, modular domains with conserved structures and biochemical activities adopt different conformational states in the presence of stimuli or upon phosphorylation, enabling a diverse array of regulatory mechanisms based on inhibitory and/or activating protein-protein interactions imparted by different domain arrangements. This review summarizes some of the recent structural work that has provided insight into the functioning of bacterial histidine kinases and response regulators. Particular emphasis is placed on identifying features that are expected to be conserved among different two-component proteins from those that are expected to differ, with the goal of defining the extent to which knowledge of previously characterized two-component proteins can be applied to newly discovered systems.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry, UMDNJ-Robert Wood Johnson Medical School and Howard Hughes Medical Institute, Piscataway, New Jersey 08854-5627
| | - Ann M. Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry, UMDNJ-Robert Wood Johnson Medical School and Howard Hughes Medical Institute, Piscataway, New Jersey 08854-5627
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78
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The HupR Receiver Domain Crystal Structure in its Nonphospho and Inhibitory Phospho States. J Mol Biol 2009; 385:51-64. [DOI: 10.1016/j.jmb.2008.10.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 09/30/2008] [Accepted: 10/08/2008] [Indexed: 11/23/2022]
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79
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Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A 2008; 106:67-72. [PMID: 19116270 DOI: 10.1073/pnas.0805923106] [Citation(s) in RCA: 625] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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80
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Yamada S, Shiro Y. Structural Basis of the Signal Transduction in the Two-Component System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 631:22-39. [DOI: 10.1007/978-0-387-78885-2_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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81
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Ruiz D, Salinas P, Lopez-Redondo ML, Cayuela ML, Marina A, Contreras A. Phosphorylation-independent activation of the atypical response regulator NblR. MICROBIOLOGY-SGM 2008; 154:3002-3015. [PMID: 18832306 DOI: 10.1099/mic.0.2008/020677-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cyanobacteria respond to environmental stress conditions by adjusting their photosynthesis machinery. In Synechococcus sp. PCC 7942, phycobilisome degradation and other acclimation responses after nutrient or high-light stress require activation by the orphan response regulator NblR, a member of the OmpR/PhoB family. Although NblR contains a putative phosphorylatable residue (Asp57), it lacks other conserved residues required to chelate the Mg(2+) necessary for aspartic acid phosphorylation or to transduce the phosphorylation signal. In close agreement with these features, NblR was not phosphorylated in vitro by the low-molecular-mass phosphate donor acetyl phosphate and mutation of Asp57 to Ala had no impact on previously characterized NblR functions in Synechococcus. On the other hand, in vitro and in vivo assays show that the default state of NblR is monomeric, suggesting that, despite input differences, NblR activation could involve the same general mechanism of activation by dimerization present in known members of the OmpR/PhoB family. Structural and functional data indicate that the receiver domain of NblR shares similarities with other phosphorylation-independent response regulators such as FrzS and HP1043. To acknowledge the peculiarities of these atypical 'two-component' regulators with phosphorylation-independent signal transduction mechanisms, we propose the term PIARR, standing for phosphorylation-independent activation of response regulator.
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Affiliation(s)
- Diego Ruiz
- División de Genética, Universidad de Alicante, Apartado 99, E-03080 Alicante, Spain
| | - Paloma Salinas
- División de Genética, Universidad de Alicante, Apartado 99, E-03080 Alicante, Spain
| | | | - Maria Luisa Cayuela
- División de Genética, Universidad de Alicante, Apartado 99, E-03080 Alicante, Spain
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (CSIC) and CIBERER, 46010 Valencia, Spain
| | - Asunción Contreras
- División de Genética, Universidad de Alicante, Apartado 99, E-03080 Alicante, Spain
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82
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Thomas SA, Brewster JA, Bourret RB. Two variable active site residues modulate response regulator phosphoryl group stability. Mol Microbiol 2008; 69:453-65. [PMID: 18557815 DOI: 10.1111/j.1365-2958.2008.06296.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many signal transduction networks control their output by switching regulatory elements on or off. To synchronize biological response with environmental stimulus, switching kinetics must be faster than changes in input. Two-component regulatory systems (used for signal transduction by bacteria, archaea and eukaryotes) switch via phosphorylation or dephosphorylation of the receiver domain in response regulator proteins. Although receiver domains share conserved active site residues and similar three-dimensional structures, rates of self-catalysed dephosphorylation span a >or= 40,000-fold range in response regulators that control diverse biological processes. For example, autodephosphorylation of the chemotaxis response regulator CheY is 640-fold faster than Spo0F, which controls sporulation. Here we demonstrate that substitutions at two variable active site positions decreased CheY autodephosphorylation up to 40-fold and increased the Spo0F rate up to 110-fold. Particular amino acids had qualitatively similar effects in different response regulators. However, mutant proteins matched to other response regulators at the two key variable positions did not always exhibit similar autodephosphorylation kinetics. Therefore, unknown factors also influence absolute rates. Understanding the effects that particular active site amino acid compositions have on autodephosphorylation rate may allow manipulation of phosphoryl group stability for useful purposes, as well as prediction of signal transduction kinetics from amino acid sequence.
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Affiliation(s)
- Stephanie A Thomas
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
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83
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Wang X, Gao H, Shen Y, Weinstock GM, Zhou J, Palzkill T. A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery. Nucleic Acids Res 2008; 36:4863-71. [PMID: 18653527 PMCID: PMC2528174 DOI: 10.1093/nar/gkn477] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Quantifying the binding energy in DNA–protein interactions is of critical importance to understand transcriptional regulation. Based on a simple computational model, this study describes a high-throughput percentage-of-binding strategy to measure the binding energy in DNA–protein interactions between the Shewanella oneidensis ArcA two-component transcription factor protein and a systematic set of mutants in an ArcA-P (phosphorylated ArcA) binding site. The binding energies corresponding to each of the 4 nt at each position in the 15-bp binding site were used to construct a position-specific energy matrix (PEM) that allowed a reliable prediction of ArcA-P binding sites not only in Shewanella but also in related bacterial genomes.
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Affiliation(s)
- Xiaohu Wang
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
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84
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Gao R, Tao Y, Stock AM. System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids. Mol Microbiol 2008; 69:1358-72. [PMID: 18631241 PMCID: PMC2586830 DOI: 10.1111/j.1365-2958.2008.06355.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
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.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Howard HughesMedical Institute, UMDNJ-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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85
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Rhee JE, Sheng W, Morgan LK, Nolet R, Liao X, Kenney LJ. Amino acids important for DNA recognition by the response regulator OmpR. J Biol Chem 2008; 283:8664-77. [PMID: 18195018 PMCID: PMC2417188 DOI: 10.1074/jbc.m705550200] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 12/27/2007] [Indexed: 11/06/2022] Open
Abstract
Response regulators undergo regulated phosphorylation and dephosphorylation at conserved aspartic acid residues in bacterial signal transduction systems. OmpR is a winged helix-turnhelix DNA-binding protein that functions as a global regulator in bacteria and is also important in pathogenesis. A detailed mechanistic picture of how OmpR binds to DNA and activates transcription is lacking. We used NMR spectroscopy to solve the solution structure of the C-terminal domain of OmpR (OmpR(C)) and to analyze the chemical shift changes that occur upon DNA binding. There is little overlap in the interaction surface with residues of PhoB that were reportedly involved in protein/protein interactions in its head-to-tail dimer. Multiple factors account for the lack of overlap. One is that the spacing between the OmpR half-sites is shorter than observed with PhoB, requiring the arrangement of the two OmpR molecules to be different from that of the PhoB dimer on DNA. A second is the demonstration herein that OmpR can bind to its high affinity site as a monomer. As a result, OmpR(C) appears to be capable of adopting alternative orientations depending on the precise base composition of the binding site, which also contributes to the lack of overlap. In the presence of DNA, chemical shift changes occur in OmpR in the recognition alpha-helix 3, the loop between beta-strand 4 and alpha-helix 1, and the loop between beta-strands 5 and 6. DNA contact residues are Val(203) (T), Arg(207) (G), and Arg(209) (phosphate backbone). Our results suggest that OmpR binds to DNA as a monomer and then forms a symmetric or asymmetric dimer, depending on the binding site. We propose that during activation OmpR binds to DNA and undergoes a conformational change that promotes phosphorylation of the N-terminal receiver domain, the receiver domains dimerize, and then the second monomer binds to DNA. The flexible linker of OmpR enables the second monomer to bind in multiple orientations (head-to-tail and head-to-head), depending on the specific DNA contacts.
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Affiliation(s)
- Jee Eun Rhee
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL 60612, USA
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86
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Pettinari MJ, Nikel PI, Ruiz JA, Méndez BS. ArcA redox mutants as a source of reduced bioproducts. J Mol Microbiol Biotechnol 2008; 15:41-7. [PMID: 18349549 DOI: 10.1159/000111991] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli and other facultative anaerobes can adapt their metabolism according to oxygen availability by means of aerobic and anaerobic respiration and fermentation. ArcAB is a two-component signal transduction system that controls, at the transcriptional level, the choice of energy generation pathway according to the intracellular redox state. High throughput studies on different redox regulator mutants, involving transcriptome analysis, RT-PCR and phenotypic arrays enabled the elucidation of a repertoire of operons coordinated by ArcA which extended beyond respiration control including, among others, those which code for survival, chromosome replication and degradation of fatty acids. Flux analysis by (13)C labeling provided new clues to the understanding of the distribution of metabolites mediated by ArcAB. The genetic manipulation of this regulator proved to be useful for the generation of reduced products of commercial value.
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Affiliation(s)
- M Julia Pettinari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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87
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Wisedchaisri G, Wu M, Sherman DR, Hol WGJ. Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation. J Mol Biol 2008; 378:227-42. [PMID: 18353359 DOI: 10.1016/j.jmb.2008.02.029] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 02/13/2008] [Accepted: 02/18/2008] [Indexed: 10/22/2022]
Abstract
The response regulator DosR is essential for promoting long-term survival of Mycobacterium tuberculosis under low oxygen conditions in a dormant state and may be responsible for latent tuberculosis in one-third of the world's population. Here, we report crystal structures of full-length unphosphorylated DosR at 2.2 A resolution and its C-terminal DNA-binding domain at 1.7 A resolution. The full-length DosR structure reveals several features never seen before in other response regulators. The N-terminal domain of the full-length DosR structure has an unexpected (beta alpha)(4) topology instead of the canonical (beta alpha)(5) fold observed in other response regulators. The linker region adopts a unique conformation that contains two helices forming a four-helix bundle with two helices from another subunit, resulting in dimer formation. The C-terminal domain in the full-length DosR structure displays a novel location of helix alpha 10, which allows Gln199 to interact with the catalytic Asp54 residue of the N-terminal domain. In contrast, the structure of the DosR C-terminal domain alone displays a remarkable unstructured conformation for helix alpha 10 residues, different from the well-defined helical conformations in all other known structures, indicating considerable flexibility within the C-terminal domain. Our structures suggest a mode of DosR activation by phosphorylation via a helix rearrangement mechanism.
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Affiliation(s)
- Goragot Wisedchaisri
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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88
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Donaldson LW. The NMR structure of the Staphylococcus aureus response regulator VraR DNA binding domain reveals a dynamic relationship between it and its associated receiver domain. Biochemistry 2008; 47:3379-88. [PMID: 18293926 DOI: 10.1021/bi701844q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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.
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Affiliation(s)
- Logan W Donaldson
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.
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89
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Barbieri CM, Stock AM. Universally applicable methods for monitoring response regulator aspartate phosphorylation both in vitro and in vivo using Phos-tag-based reagents. Anal Biochem 2008; 376:73-82. [PMID: 18328252 DOI: 10.1016/j.ab.2008.02.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 01/30/2008] [Accepted: 02/07/2008] [Indexed: 11/26/2022]
Abstract
Recent development of the phosphate chelator, Phos-tag, together with Phos-tag pendant reagents, has provided new methods for detection of phosphorylated serine, threonine, tyrosine, and histidine residues in phosphoproteins. We have investigated the use of Phos-tag for detection and quantification of phospho-aspartate in response regulator proteins that function within two-component signaling systems. Alternative methods are especially important, because the labile nature of the acylphosphate bond in response regulator proteins has restricted the application of many traditional methods of phosphoprotein analysis. We demonstrate that Phos-tag gel stain can be used to detect phospho-Asp in response regulators and that Phos-tag acrylamide gel electrophoresis can be used to separate phosphorylated and unphosphorylated forms of response regulator proteins. The latter method, coupled to Western blot analysis, enables detection of specific phosphorylated proteins in complex mixtures such as cell lysates. Standards of phosphorylated proteins can be used to correct for hydrolysis of the labile phospho-Asp bond that invariably occurs during analysis. We have employed Phos-tag methods to characterize the phosphorylation state of the Escherichia coli response regulator PhoB both in vitro, using purified protein, and in vivo, by analyzing lysates of cells grown under different conditions of induction of the PhoR/PhoB phosphate assimilation pathway.
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Affiliation(s)
- Christopher M Barbieri
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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90
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Wang S, Engohang-Ndong J, Smith I. Structure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis. Biochemistry 2007; 46:14751-61. [PMID: 18052041 DOI: 10.1021/bi700970a] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The PhoP-PhoR two-component signaling system from Mycobacterium tuberculosis is essential for the virulence of the tubercle bacillus. The response regulator, PhoP, regulates expression of over 110 genes. In order to elucidate the regulatory mechanism of PhoP, we determined the crystal structure of its DNA-binding domain (PhoPC). PhoPC exhibits a typical fold of the winged helix-turn-helix subfamily of response regulators. The structure starts with a four-stranded antiparallel beta-sheet, followed by a three-helical bundle of alpha-helices, and then a C-terminal beta-hairpin, which together with a short beta-strand between the first and second helices forms a three-stranded antiparallel beta-sheet. Structural elements are packed through a hydrophobic core, with the first helix providing a scaffold for the rest of the domain to pack. The second and third helices and the long, flexible loop between them form the helix-turn-helix motif, with the third helix being the recognition helix. The C-terminal beta-hairpin turn forms the wing motif. The molecular surfaces around the recognition helix and the wing residues show strong positive electrostatic potential, consistent with their roles in DNA binding and nucleotide sequence recognition. The crystal packing of PhoPC gives a hexamer ring, with neighboring molecules interacting in a head-to-tail fashion. This packing interface suggests that PhoPC could bind DNA in a tandem association. However, this mode of DNA binding is likely to be nonspecific because the recognition helix is partially blocked and would be prevented from inserting into the major groove of DNA. Detailed structural analysis and implications with respect to DNA binding are discussed.
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Affiliation(s)
- Shuishu Wang
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA.
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91
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Wassmann P, Chan C, Paul R, Beck A, Heerklotz H, Jenal U, Schirmer T. Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition. Structure 2007; 15:915-27. [PMID: 17697997 DOI: 10.1016/j.str.2007.06.016] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2007] [Revised: 06/25/2007] [Accepted: 06/25/2007] [Indexed: 11/24/2022]
Abstract
Cyclic di-guanosine monophosphate (c-di-GMP) is a ubiquitous bacterial second messenger involved in the regulation of cell surface-associated traits and persistence. We have determined the crystal structure of PleD from Caulobacter crescentus, a response regulator with a diguanylate cyclase (DGC) domain, in its activated form. The BeF(3)(-) modification of its receiver domain causes rearrangement with respect to an adaptor domain, which, in turn, promotes dimer formation, allowing for the efficient encounter of two symmetric catalytic domains. The substrate analog GTPalphaS and two putative cations are bound to the active sites in a manner similar to adenylate cyclases, suggesting an analogous two-metal catalytic mechanism. An allosteric c-di-GMP-binding mode that crosslinks DGC and an adaptor domain had been identified before. Here, a second mode is observed that crosslinks the DGC domains within a PleD dimer. Both modes cause noncompetitive product inhibition by domain immobilization.
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Affiliation(s)
- Paul Wassmann
- Core Program of Structural Biology and Biophysics, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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92
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Zhao X, Copeland DM, Soares AS, West AH. Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog. J Mol Biol 2007; 375:1141-51. [PMID: 18076904 DOI: 10.1016/j.jmb.2007.11.045] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 11/09/2007] [Accepted: 11/14/2007] [Indexed: 11/17/2022]
Abstract
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.
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Affiliation(s)
- Xiaodong Zhao
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA
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93
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Paul R, Abel S, Wassmann P, Beck A, Heerklotz H, Jenal U. Activation of the Diguanylate Cyclase PleD by Phosphorylation-mediated Dimerization. J Biol Chem 2007; 282:29170-7. [PMID: 17640875 DOI: 10.1074/jbc.m704702200] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Diguanylate cyclases (DGCs) are key enzymes of second messenger signaling in bacteria. Their activity is responsible for the condensation of two GTP molecules into the signaling compound cyclic di-GMP. Despite their importance and abundance in bacteria, catalytic and regulatory mechanisms of this class of enzymes are poorly understood. In particular, it is not clear if oligomerization is required for catalysis and if it represents a level for activity control. To address this question we perform in vitro and in vivo analysis of the Caulobacter crescentus diguanylate cyclase PleD. PleD is a member of the response regulator family with two N-terminal receiver domains and a C-terminal diguanylate cyclase output domain. PleD is activated by phosphorylation but the structural changes inflicted upon activation of PleD are unknown. We show that PleD can be specifically activated by beryllium fluoride in vitro, resulting in dimerization and c-di-GMP synthesis. Cross-linking and fractionation experiments demonstrated that the DGC activity of PleD is contained entirely within the dimer fraction, confirming that the dimer represents the enzymatically active state of PleD. In contrast to the catalytic activity, allosteric feedback regulation of PleD is not affected by the activation status of the protein, indicating that activation by dimerization and product inhibition represent independent layers of DGC control. Finally, we present evidence that dimerization also serves to sequester activated PleD to the differentiating Caulobacter cell pole, implicating protein oligomerization in spatial control and providing a molecular explanation for the coupling of PleD activation and subcellular localization.
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Affiliation(s)
- Ralf Paul
- Biozentrum, University of Basel, Klingelbergstrasse 70, Basel CH-4056, Switzerland
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94
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Bachhawat P, Stock AM. Crystal structures of the receiver domain of the response regulator PhoP from Escherichia coli in the absence and presence of the phosphoryl analog beryllofluoride. J Bacteriol 2007; 189:5987-95. [PMID: 17545283 PMCID: PMC1952025 DOI: 10.1128/jb.00049-07] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The response regulator PhoP is part of the PhoQ/PhoP two-component system involved in responses to depletion of extracellular Mg(2+). Here, we report the crystal structures of the receiver domain of Escherichia coli PhoP determined in the absence and presence of the phosphoryl analog beryllofluoride. In the presence of beryllofluoride, the active receiver domain forms a twofold symmetric dimer similar to that seen in structures of other regulatory domains from the OmpR/PhoB family, providing further evidence that members of this family utilize a common mode of dimerization in the active state. In the absence of activating agents, the PhoP receiver domain crystallizes with a similar structure, consistent with the previous observation that high concentrations can promote an active state of PhoP independent of phosphorylation.
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Affiliation(s)
- Priti Bachhawat
- Department of Biochemistry, Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854-5627, USA
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95
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Friedland N, Mack TR, Yu M, Hung LW, Terwilliger TC, Waldo GS, Stock AM. Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation. Biochemistry 2007; 46:6733-43. [PMID: 17511470 PMCID: PMC2528954 DOI: 10.1021/bi602546q] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The structure of MtrA, an essential gene product for the human pathogen Mycobacterium tuberculosis, has been solved to a resolution of 2.1 A. MtrA is a member of the OmpR/PhoB family of response regulators and represents the fourth family member for which a structure of the protein in its inactive state has been determined. As is true for all OmpR/PhoB family members, MtrA possesses an N-terminal regulatory domain and a C-terminal winged helix-turn-helix DNA-binding domain, with phosphorylation of the regulatory domain modulating the activity of the protein. In the inactive form of MtrA, these two domains form an extensive interface that is composed of the alpha4-beta5-alpha5 face of the regulatory domain and the C-terminal end of the positioning helix, the trans-activation loop, and the recognition helix of the DNA-binding domain. This domain orientation suggests a mechanism of mutual inhibition by the two domains. Activation of MtrA would require a disruption of this interface to allow the alpha4-beta5-alpha5 face of the regulatory domain to form the intermolecule interactions that are associated with the active state and to allow the recognition helix to interact with DNA. Furthermore, the interface appears to stabilize the inactive conformation of MtrA, potentially reducing the rate of phosphorylation of the N-terminal domain. This combination of effects may form a switch, regulating the activity of MtrA. The domain orientation exhibited by MtrA also provides a rationale for the variation in linker length that is observed within the OmpR/PhoB family of response regulators.
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Affiliation(s)
| | | | | | | | | | | | - Ann M. Stock
- To whom correspondence should be addressed at Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854. Telephone: (732) 235−4844. Fax (732) 235−5289. E-mail:
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96
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Hong E, Lee HM, Ko H, Kim DU, Jeon BY, Jung J, Shin J, Lee SA, Kim Y, Jeon YH, Cheong C, Cho HS, Lee W. Structure of an atypical orphan response regulator protein supports a new phosphorylation-independent regulatory mechanism. J Biol Chem 2007; 282:20667-75. [PMID: 17491010 DOI: 10.1074/jbc.m609104200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two-component signal transduction systems, commonly found in prokaryotes, typically regulate cellular functions in response to environmental conditions through a phosphorylation-dependent process. A new type of response regulator, hp1043 (HP-RR) from Helicobacter pylori, has been recently identified. HP-RR is essential for cell growth and does not require the well known phosphorelay scheme. Unphosphorylated HP-RR binds specifically to its own promoter (P(1043)) and autoregulates the promoter of the tlpB gene (P(tlpB)). We have determined the structure of HP-RR by NMR and x-ray crystallography, revealing a symmetrical dimer with two functional domains. The molecular topology resembles that of the OmpR/PhoB subfamily, however, the symmetrical dimer is stable even in the unphosphorylated state. The dimer interface, formed by three secondary structure elements (alpha4-beta5-alpha5), resembles that of the active, phosphorylated forms of ArcA and PhoB. Several conserved residues of the HP-RR dimeric interface deviate from the OmpR/PhoB subfamily, although there are similar salt bridges and hydrophobic patches within the interface. Our findings reveal how a new type of response regulator protein could function as a cell growth-associated regulator in the absence of post-translational modification.
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MESH Headings
- Crystallography, X-Ray
- DNA, Bacterial/chemistry
- DNA, Bacterial/metabolism
- Dimerization
- Gene Expression Regulation, Bacterial/physiology
- Helicobacter pylori/chemistry
- Helicobacter pylori/metabolism
- Models, Molecular
- Nuclear Magnetic Resonance, Biomolecular
- Phosphorylation
- Promoter Regions, Genetic/physiology
- Protein Binding/physiology
- Protein Processing, Post-Translational
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Transcription Factors/chemistry
- Transcription Factors/metabolism
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Affiliation(s)
- Eunmi Hong
- Department of Biochemistry and HTSD-NMR & Application NRL, College of Science, Yonsei University, 134 Shinchon-Dong, Seodaemoon-Gu, Seoul 120-749, Korea
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97
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Gao R, Mack TR, Stock AM. Bacterial response regulators: versatile regulatory strategies from common domains. Trends Biochem Sci 2007; 32:225-34. [PMID: 17433693 PMCID: PMC3655528 DOI: 10.1016/j.tibs.2007.03.002] [Citation(s) in RCA: 243] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 02/07/2007] [Accepted: 03/15/2007] [Indexed: 01/29/2023]
Abstract
Response regulators (RRs) comprise a major family of signaling proteins in prokaryotes. A modular architecture that consists of a conserved receiver domain and a variable effector domain enables RRs to function as phosphorylation-regulated switches that couple a wide variety of cellular behaviors to environmental cues. Recently, advances have been made in understanding RR functions both at genome-wide and molecular levels. Global techniques have been developed to analyze RR input and output, expanding the scope of characterization of these versatile components. Meanwhile, structural studies have revealed that, despite common structures and mechanisms of function within individual domains, a range of interactions between receiver and effector domains confer great diversity in regulatory strategies, optimizing individual RRs for the specific regulatory needs of different signaling systems.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Howard Hughes Medical Institute, Piscataway, NJ 08854, USA
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98
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Gao T, Zhang X, Ivleva NB, Golden SS, LiWang A. NMR structure of the pseudo-receiver domain of CikA. Protein Sci 2007; 16:465-75. [PMID: 17322531 PMCID: PMC2203319 DOI: 10.1110/ps.062532007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The circadian input kinase (CikA) is a major element of the pathway that provides environmental information to the circadian clock of the cyanobacterium Synechococcus elongatus. CikA is a polypeptide of 754 residues and has three recognizable domains: GAF, histidine protein kinase, and receiver-like. This latter domain of CikA lacks the conserved phospho-accepting aspartyl residue of bona fide receiver domains and is thus a pseudo-receiver (PsR). Recently, it was shown that the PsR domain (1) attenuates the autokinase activity of CikA, (2) is necessary to localize CikA to the cell pole, and (3) is necessary for the destabilization of CikA in the presence of the quinone analog 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB). The solution structure of the PsR domain of CikA, CikAPsR, is presented here. A model of the interaction between the PsR domain and HPK portion of CikA provides a potential explanation for how the PsR domain attenuates the autokinase activity of CikA. Finally, a likely quinone-binding surface on CikAPsR is shown here.
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Affiliation(s)
- Tiyu Gao
- Center for Research on Biological Clocks, Texas A&M University College Station, Texas 77843, USA
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99
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Ravcheev DA, Gerasimova AV, Mironov AA, Gelfand MS. Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae). BMC Genomics 2007; 8:54. [PMID: 17313674 PMCID: PMC1805755 DOI: 10.1186/1471-2164-8-54] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 02/21/2007] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Gamma-proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems controlled by multiple transcription regulators. Thus, in E. coli, global control of respiration is mediated by four transcription factors, Fnr, ArcA, NarL and NarP. However, in other Gamma-proteobacteria the composition of global respiration regulators may be different. RESULTS In this study we applied a comparative genomic approach to the analysis of three global regulatory systems, Fnr, ArcA and NarP. These systems were studied in available genomes containing these three regulators, but lacking NarL. So, we considered several representatives of Pasteurellaceae, Vibrionaceae and Yersinia spp. As a result, we identified new regulon members, functioning in respiration, central metabolism (glycolysis, gluconeogenesis, pentose phosphate pathway, citrate cicle, metabolism of pyruvate and lactate), metabolism of carbohydrates and fatty acids, transcriptional regulation and transport, in particular: the ATP synthase operon atpIBEFHAGCD, Na+-exporting NADH dehydrogenase operon nqrABCDEF, the D-amino acids dehydrogenase operon dadAX. Using an extension of the comparative technique, we demonstrated taxon-specific changes in regulatory interactions and predicted taxon-specific regulatory cascades. CONCLUSION A comparative genomic technique was applied to the analysis of global regulation of respiration in ten gamma-proteobacterial genomes. Three structurally different but functionally related regulatory systems were described. A correlation between the regulon size and the position of a transcription factor in regulatory cascades was observed: regulators with larger regulons tend to occupy top positions in the cascades. On the other hand, there is no obvious link to differences in the species' lifestyles and metabolic capabilities.
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Affiliation(s)
- Dmitry A Ravcheev
- Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, 119992, Russia
- Institute for Information Transmission Problems, Moscow, 127994, Russia
| | | | - Andrey A Mironov
- Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, 119992, Russia
- Institute for Information Transmission Problems, Moscow, 127994, Russia
- State Scientific Center GosNIIGenetika, Moscow, 113545, Russia
| | - Mikhail S Gelfand
- Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, 119992, Russia
- Institute for Information Transmission Problems, Moscow, 127994, Russia
- State Scientific Center GosNIIGenetika, Moscow, 113545, Russia
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Arribas-Bosacoma R, Kim SK, Ferrer-Orta C, Blanco AG, Pereira PJ, Gomis-Rüth FX, Wanner BL, Coll M, Solà M. The X-ray crystal structures of two constitutively active mutants of the Escherichia coli PhoB receiver domain give insights into activation. J Mol Biol 2007; 366:626-41. [PMID: 17182055 PMCID: PMC1855202 DOI: 10.1016/j.jmb.2006.11.038] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 11/07/2006] [Accepted: 11/09/2006] [Indexed: 11/22/2022]
Abstract
The PhoR/PhoB two-component system is a key regulatory protein network enabling Escherichia coli to respond to inorganic phosphate (Pi) starvation conditions by turning on Pho regulon genes for more efficient Pi uptake and use of alternative phosphorus sources. Under environmental Pi depletion, the response regulator (RR) component, PhoB, is phosphorylated at the receiver domain (RD), a process that requires Mg(2+) bound at the active site. Phosphorylation of the RD relieves the inhibition of the PhoB effector domain (ED), a DNA-binding region that binds to Pho regulon promoters to activate transcription. The molecular details of the activation are proposed to involve dimerization of the RD and a conformational change in the RD detected by the ED. The structure of the PhoB RD shows a symmetrical interaction involving alpha1, loop beta5alpha5 and N terminus of alpha5 elements, also seen in the complex of PhoB RD with Mg(2+), in which helix alpha4 highly increases its flexibility. PhoB RD in complex with Mg(2+) and BeF(3) (an emulator of the phosphate moiety) undergoes a dramatic conformational change on helix alpha4 and shows another interaction involving alpha4, beta5 and alpha5 segments. We have selected a series of constitutively active PhoB mutants (PhoB(CA)) that are able to turn on the Pho regulon promoters in the absence phosphorylation and, as they cannot be inactivated, should therefore mimic the active RD state of PhoB and its functional oligomerisation. We have analysed the PhoB(CA) RD crystal structures of two such mutants, Asp53Ala/Tyr102Cys and Asp10Ala/Asp53Glu. Interestingly, both mutants reproduce the homodimeric arrangement through the symmetric interface encountered in the unbound and magnesium-bound wild-type PhoB RD structures. Besides, the mutant RD structures show a modified active site organization as well as changes at helix alpha4 that correlate with repositioning of surrounding residues, like the active-site events indicator Trp54, putatively redifining the interaction with the ED in the full-length protein.
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Affiliation(s)
- Raquel Arribas-Bosacoma
- Institut de Biologia Molecular de Barcelona (CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain, and IRB - Parc Científic de Barcelona, c/Josep Samitier 1-5, 08028 Barcelona, Spain
| | - Soo-Ki Kim
- Department of Biological Sciences; Purdue University; West Lafayette; Indiana 47907 USA
| | - Cristina Ferrer-Orta
- Institut de Biologia Molecular de Barcelona (CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain, and IRB - Parc Científic de Barcelona, c/Josep Samitier 1-5, 08028 Barcelona, Spain
| | - Alexandre G. Blanco
- Institut de Biologia Molecular de Barcelona (CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain, and IRB - Parc Científic de Barcelona, c/Josep Samitier 1-5, 08028 Barcelona, Spain
| | - Pedro J.B. Pereira
- Institut de Biologia Molecular de Barcelona (CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain, and IRB - Parc Científic de Barcelona, c/Josep Samitier 1-5, 08028 Barcelona, Spain
| | - F. Xavier Gomis-Rüth
- Institut de Biologia Molecular de Barcelona (CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain, and IRB - Parc Científic de Barcelona, c/Josep Samitier 1-5, 08028 Barcelona, Spain
| | - Barry L. Wanner
- Department of Biological Sciences; Purdue University; West Lafayette; Indiana 47907 USA
| | - Miquel Coll
- Institut de Biologia Molecular de Barcelona (CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain, and IRB - Parc Científic de Barcelona, c/Josep Samitier 1-5, 08028 Barcelona, Spain
| | - Maria Solà
- Institut de Biologia Molecular de Barcelona (CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain, and IRB - Parc Científic de Barcelona, c/Josep Samitier 1-5, 08028 Barcelona, Spain
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