Structural relationships in the OmpR family of winged-helix transcription factors 1 1Edited by M. Gottesman

Martı́nez-Hackert, Erik; Stock, Ann

doi:10.1006/jmbi.1997.1065

Cited by 252 publications

(251 citation statements)

References 65 publications

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“…Rotter et al (2006) have shown through sequence alignment that Rem is a member of the OmpR family of transcriptional regulators. This family of regulators is characterized by a regulatory domain at the N terminus and a DNA-binding domain with a 'winged helix-turn-helix' pattern at the C terminus (Martínez-Hackert & Stock, 1997;Rotter et al, 2006). The possible dual roles of Rem as an activator and a repressor of flagellin genes in R. leguminosarum have a precedent in E. coli, where it has been reported that OmpR can act as an activator and a repressor of a gene encoding a major outermembrane protein (OmpF) (Rampersaud et al, 1994).…”

Section: Tambalo and Others Unpublished Results)mentioning

confidence: 99%

Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade

et al. 2010

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In this paper, we describe the regulatory roles of VisN, VisR and Rem in the expression of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum biovar viciae strains VF39SM and 3841. Individual mutations in the genes encoding these proteins resulted in a loss of motility and an absence of flagella, indicating that these regulatory genes are essential for flagellar synthesis and function. Transcriptional experiments involving gusA-gene fusions in wild-type and mutant backgrounds were performed to identify the genes under VisN/R and Rem regulation. Results showed that the chemotaxis and motility genes of R. leguminosarum could be separated into two groups: one group under VisN/R-Rem regulation and another group that is independent of this regulation. VisN and VisR regulate the expression of rem, while Rem positively regulates the expression of flaA, flaB, flaC, flaD, motA, motB, che1 and mcpD. All of these genes except mcpD are located within the main motility and chemotaxis gene cluster of R. leguminosarum. Other chemotaxis and motility genes, which are found outside of the main motility gene cluster (che2 operon, flaH for VF39SM, and flaG) or are plasmid-borne (flaE and mcpC), are not part of the VisN/R-Rem regulatory cascade. In addition, all genes exhibited the same regulation pattern in 3841 and in VF39SM, except flaE and flaH. flaE is not regulated by VisN/R-Rem in 3841 but it is repressed by Rem in VF39SM. flaH is under VisN/R-Rem regulation in 3841, but not in VF39SM. A kinetics experiment demonstrated that a subset of the flagellar genes is continuously expressed in all growth phases, indicating the importance of continuous motility for R. leguminosarum under free-living conditions. On the other hand, motility is repressed under symbiotic conditions. Nodulation experiments showed that the transcriptional activators VisN and Rem are dramatically downregulated in the nodules, suggesting that the symbiotic downregulation of motility-related genes could be mediated by repressing the expression of VisN/R and Rem.

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Section: Tambalo and Others Unpublished Results)mentioning

confidence: 99%

Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade

et al. 2010

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“…The Effector Domain-The crystal structures of isolated effector domains of OmpR (50,51) and PhoB complexed with DNA (47) as well as the uncomplexed full-length response regulators DrrB (15) and DrrD (14) have been described in the literature. A structure-based sequence alignment is shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…For OmpR, which interacts with the ␣-subunit of the RNA polymerase II (54,55), phosphorylation of the regulatory domain enhances its DNA binding activity, whereas unphosphorylated OmpR, and the effector domain alone, do bind DNA but with substantially lower affinity (50). In contrast with PhoB, which interacts with 70, the isolated effector domain is constitutively active for transcription (56) and has a higher FIGURE 5.…”

Section: Resultsmentioning

confidence: 99%

The Structural Basis of Signal Transduction for the Response Regulator PrrA from Mycobacterium tuberculosis

Nowak

Panjikar

Konarev

et al. 2006

Journal of Biological Chemistry

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The structure of the two-domain response regulator PrrA from Mycobacterium tuberculosis shows a compact structure in the crystal with a well defined interdomain interface. The interface, which does not include the interdomain linker, makes the recognition helix and the trans-activation loop of the effector domain inaccessible for interaction with DNA. Part of the interface involves hydrogen-bonding interactions of a tyrosine residue in the receiver domain that is believed to be involved in signal transduction, which, if disrupted, would destabilize the interdomain interface, allowing a more extended conformation of the molecule, which would in turn allow access to the recognition helix. In solution, there is evidence for an equilibrium between compact and extended forms of the protein that is far toward the compact form when the protein is inactivated but moves toward a more extended form when activated by the cognate sensor kinase PrrB.The use of regulatory systems to sense and respond to changing environmental conditions is an intrinsic feature that enables bacteria to survive and adapt to a variety of external challenges. Two-component signaling (TCS) 2 systems are the principle mechanism used by bacteria to perform this task (1). A typical TCS consists of a sensor histidine kinase and a response regulator (RR). Histidine kinases are usually membrane-anchored proteins with a characteristic core consisting of a histidine-containing dimerization domain and a catalytic domain. In response to extracellular, and in a few cases, intracellular, conditions, the histidine kinase autophosphorylates at a histidine residue, usually in the dimerization domain, by phosphotransfer from the catalytic (ATPase) domain of the adjacent protomer. It then acts as a phosphodonor to a universally conserved aspartic acid residue in the response regulator. RRs typically consist of two domains with the N-terminal (receiver) domain being the phosphoacceptor domain and the C-terminal domain being the effector. The effector domain is, in most cases, DNA binding and is involved in transcriptional regulation of the genes necessary to respond to the sensed environment. Phosphorylation of the aspartic acid residue located in the receiver domain activates the effector domain in a manner that is still incompletely understood, not least because there is little structural information on full-length response regulators and no structural information on activated full-length (i.e. multidomain) response regulators.TCSs have been identified as potential antibacterial targets because they play a key role in controlling cellular processes (2). The lack of these systems in higher eukaryotes makes them potentially selective and unique antibacterial drug targets, There is, however, little biochemical information available on the TCSs of pathogenic bacteria such as Mycobacterium tuberculosis (MtB). The H37Rv strain of MtB has 12 putative TCSs including the recently discovered Rv3220-Rv1626 pair (3) as well as five putative orphan response regulator and se...

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“…Paradoxically, no overall correlation exists between ΔG SC and Leu phenotype in the four strains. Instead, a Leu + phenotype correlates with the absence of DNA topoisomerase I (TopA − ) other proteins that bind to A + T-rich DNA, including proteins that bind using a winged helix-turn-helix motif (Brennan 1993;Dolan et al 2011;Kenney 2002;Martínez-Hackert and Stock 1997). Here, the protein is interacting with both the major groove (where the DNA base sequence is accessible) and the minor groove (where a specific DNA sequence is not being sought).…”

Section: Protein Binding As a Function Of Dna Topologymentioning

confidence: 99%

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

Dorman

2016

Biophys Rev

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Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.

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Structural relationships in the OmpR family of winged-helix transcription factors 1 1Edited by M. Gottesman

Cited by 252 publications

References 65 publications

Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade

Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade

The Structural Basis of Signal Transduction for the Response Regulator PrrA from Mycobacterium tuberculosis

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

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