Positive activation of gene expression

Rhodius, Virgil A.; Busby, Stephen J. W.

doi:10.1016/s1369-5274(98)80005-2

Cited by 122 publications

(118 citation statements)

References 45 publications

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“…Finally, to obtain full-length transcripts, the RNA polymerase must escape from the promoter region (13,14,30). Activators can exert an effect at each of these steps (13,14), but most response regulators appear to be involved in the recruitment of RNA polymerase to the promoter.…”

Section: Discussionmentioning

confidence: 99%

“…Activators can exert an effect at each of these steps (13,14), but most response regulators appear to be involved in the recruitment of RNA polymerase to the promoter. It has been postulated that protein-protein interactions between the activator and RNA polymerase stabilize the binding of the enzyme to the promoter (14,30). For example, in the BvgA (8) and PhoB (21) systems, RNA polymerase is not able to bind to promoter DNA in the absence of the response regulator.…”

Section: Discussionmentioning

confidence: 99%

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The Spatial Organization of the VirR Boxes Is Critical for VirR-Mediated Expression of the Perfringolysin O Gene, pfoA , from Clostridium perfringens

et al. 2004

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The transcriptional regulation of toxin production in the gram-positive anaerobe Clostridium perfringens involves a two-component signal transduction system that comprises the VirS sensor histidine kinase and its cognate response regulator, VirR. Previous studies showed that VirR binds independently to a pair of imperfect direct repeats, now designated VirR box 1 and VirR box 2, located immediately upstream of the promoter of the pfoA gene, which encodes the cholesterol-dependent cytolysin, perfringolysin O. For this study, we introduced mutated VirR boxes into a C. perfringens pfoA mutant and found that both VirR boxes are essential for transcriptional activation. Furthermore, the spacing between the VirR boxes and the distance between the VirR boxes and the ؊35 region are shown to be critical for perfringolysin O production. Other VirR boxes that were previously identified from the strain 13 genome sequence were also analyzed, with perfringolysin O production used as a reporter system. The results showed that placement of the different VirR boxes at the same position upstream of the pfoA promoter yields different levels of perfringolysin O activity. In all of these constructs, VirR was still capable of binding to the target DNA, indicating that DNA binding alone is not sufficient for transcriptional activation. Finally, we show that the C. perfringens RNA polymerase binds more efficiently to the pfoA promoter in the presence of VirR, indicating that interactions must occur between these proteins. We propose that these interactions are required for VirR-mediated transcriptional activation.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The Spatial Organization of the VirR Boxes Is Critical for VirR-Mediated Expression of the Perfringolysin O Gene, pfoA , from Clostridium perfringens

et al. 2004

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“…Various combinations of these two mechanisms can be found in promoters with multiple CRP binding sites. They show synergistic activation by two CRPs that both function through a class I mechanism or a combination of class I and class II mechanisms (reviewed by Rhodius and Busby, 1998). At some promoters, however, CRP functions not through direct contact with RNAP, but via direct protein-protein interaction with a second activator, which then interacts directly with RNAP.…”

Section: Direct Interactions Of Crp With Rnap At the Ompt Promotermentioning

confidence: 99%

“…At some promoters, however, CRP functions not through direct contact with RNAP, but via direct protein-protein interaction with a second activator, which then interacts directly with RNAP. At such promoters, the AR1 and AR2 interactions play little or no role in transcriptional activation (Rhodius and Busby, 1998).…”

Section: Direct Interactions Of Crp With Rnap At the Ompt Promotermentioning

confidence: 99%

ToxR interferes with CRP‐dependent transcriptional activation of ompT in Vibrio cholerae

Merrell

Camilli

et al. 2002

Molecular Microbiology

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SummaryIn pathogenic Vibrio cholerae, the transmembrane DNA-binding protein ToxR co-ordinates the expression of over 20 genes, including those encoding important virulence factors such as cholera toxin and the toxin-co-regulated pilus. The outer membrane protein OmpT is the only member of the ToxR regulon known to be repressed by ToxR. In this study, we examined the environmental conditions that regulate OmpT expression and demonstrated that ompT transcription is upregulated 14-fold when the bacteria enter late log phase from early log phase. Deletion of the crp gene completely abolishes OmpT expression. Comparison of ompT transcription levels in the isogenic crp -, toxR -and crp -toxR -mutants revealed that (i) in the absence of ToxR, constitutive high-level ompT transcription is dependent on cAMP receptor protein (CRP); (ii) ToxR not only interferes with CRPdependent ompT activation, but also abolishes the CRP-independent, basal level ompT transcription; thus, the mechanism by which ToxR represses ompT transcription involves both antiactivation and direct repression; (iii) both CRP and ToxR are required for the regulation of OmpT expression by growth phase. To provide further insights into the molecular mechanism of CRP-dependent activation of ompT transcription, we demonstrated that CRP-dependent activation requires a CRP binding site centred at -310 of the ompT promoter, without which the interaction of CRP with other CRP binding site(s) more proximal to the promoter results in repression. Mutations in two regions on CRP (AR1 and AR2) that directly

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“…Promoter activity is likely to be affected by the composition and relative positions of elements within promoter regions, and other factors such as gene-specific activators and repressors (Lloyd et al, 2001;Rhodius & Busby, 1998;Rojo, 2001), ppGpp (Barker et al, 2001;Chatterji & Ojha, 2001), termination and antitermination factors (Henkin, 1996;Henkin & Yanofsky, 2002), anti-sigma factors (Helmann, 1999), NTP concentration (Schneider et al, 2002), transcript cleavage factors (Hsu et al, 1995) and factor-dependent DNA curvature or torsional state (Dai & Rothman-Denes, 1999;Xu & Hoover, 2001). Indeed computational analysis (data not shown) suggests that promoter 46 may be regulated by NarL/NarP (Dong et al, 1992;Householder et al, 1999;Li & Stewart, 1992) and promoter 10 contained five repetitive elements that may act as binding motifs for regulatory proteins.…”

Section: T D Schoep and K Greggmentioning

confidence: 99%

Isolation and characterization of putative Pseudobutyrivibrio ruminis promoters

Schoep

Gregg

2007

Microbiology

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Novel plasmids were constructed for the analysis of DNA fragments from the rumen bacterium Pseudobutyrivibrio ruminis. Five previously unidentified promoters were characterized using a novel primer extension method to identify transcription start sites. The genes downstream of these promoters were not identified, and their activity in expression of genomic traits in wild-type P. ruminis remains putative. Comparison with promoters from this and closely related species revealed a consensus sequence resembling the binding motif for the RNA polymerase s 70 -like factor complex. Consensus "35 and "10 sequences within these elements were TTGACA and ATAATATA respectively, interspaced by 15-16 bp. The consensus for the "10 element was extended by one nucleotide upstream and downstream of the standard hexamer (indicated in bold). Promoter strengths were measured by reverse transcription quantitative PCR and bglucuronidase assays. No correlation was found between the composition and context of elements within P. ruminis promoters, and promoter strength. However, a mutation within the "35 element of one promoter revealed that transcriptional strength and choice of transcription start site were sensitive to this single nucleotide change. INTRODUCTIONDNA binding specificity of bacterial RNA polymerase and the rate of transcription are largely dictated by the sequence of the upstream (UP) element (Estrem et al., 1998), and 210 and 235 motifs, which are common to most bacteria. However, atypical aspects of transcription initiation are still being identified in prokaryotes (Bayley et al., 2000;Gaal et al., 2001;Weiner et al., 2000). Novel structural properties of DNA are also being reported, but their effects on gene expression remain unknown (Petersen et al., 2003;Vanet et al., 2000;Vogel et al., 2003).Pseudobutyrivibrio ruminis (previously classified as Butyrivibrio fibrisolvens) is present in the rumen (Kopecny et al., 2003) and gastrointestinal tract of some animals. Butyrivibrio-like organisms may account for as much as 24-30 % of culturable bacteria from the rumen (Forster et al., 1996), although individual species may constitute much lower proportions of total bacterial numbers (Kobayashi et al., 2000). These bacteria are important for projects that aim to alter rumen function using genetically modified bacteria (Brooker et al., 1989;Gregg et al., 1987 Gregg et al., , 1994Gregg et al., , 1998Gregg & Sharpe, 1991;Mackie & White, 1990;Rogers, 1990;Smith & Hespell, 1983;Teather, 1985;Teather & Forster, 1998). Understanding their transcriptional regulation is essential for controlling the expression of foreign genes within the rumen. Molecular mechanisms governing transcription initiation in P. ruminis and closely related species remain poorly understood. To date, only four promoters have been studied using transcriptional analysis in their species of origin: the flaA and flaB promoters in P. ruminis OR77 (Beard et al., 2000), the Pseudobutyrivibrio sp. OB156 thl promoter (Asanuma et al., 2003), and the rep promoter in B. ...

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Positive activation of gene expression

Cited by 122 publications

References 45 publications

The Spatial Organization of the VirR Boxes Is Critical for VirR-Mediated Expression of the Perfringolysin O Gene, pfoA , from Clostridium perfringens

The Spatial Organization of the VirR Boxes Is Critical for VirR-Mediated Expression of the Perfringolysin O Gene, pfoA , from Clostridium perfringens

ToxR interferes with CRP‐dependent transcriptional activation of ompT in Vibrio cholerae

Isolation and characterization of putative Pseudobutyrivibrio ruminis promoters

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