CRP Binding and Transcription Activation at CRP-S Sites

Cameron, Andrew D. S.; Redfield, Rosemary J.

doi:10.1016/j.jmb.2008.08.027

Cited by 30 publications

(41 citation statements)

References 49 publications

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“…The inability of H. influenzae Sxy to induce most of the genes regulated by E. coli Sxy may be due to differences in CRP-S site structure. The E. coli CRP-S motif identified by the arrays described above strongly resembles the previously characterized H. influenzae CRP-S motif in overrepresentation of the CRP binding bases G5, G7, A8, T15, and C18, the AT-rich sequence at positions 1 to 3 and 20 to 22, and the noncanonical bases at positions 6 and 17 (11). However, the E. coli motif favors T rather than C at position 16 while retaining the strong G at position 7.…”

supporting

confidence: 63%

“…The differences in CRP-S motifs and the absence of full cross-complementation provide additional insights into the action of Sxy and CRP at CRP-S sites and suggest that both CRP and Sxy have evolved species-specific features. The CRP-N sites (canonical CRP binding sites) of H. influenzae and E. coli are very similar, and their CRPs are identical at the residues known to interact with DNA (11). In contrast, their CRP-S motifs differ at two core positions and in flanking sequences (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Each promoter in the H. influenzae Sxy-CRP regulon contains a CRP-S site (termed "S" for Sxy-dependent), variant CRP-binding sites that match the canonical CRP consensus sequence except for two positions where nonconsensus bases hinder stable CRP-DNA interactions in the absence of Sxy (11). Sxy is thus thought to enable CRP to activate transcription at these unusual binding sites, although its toxicity when it is overexpressed for purification has hindered attempts to characterize its exact mode of action (11,35,45,56).…”

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confidence: 99%

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Sxy Induces a CRP-S Regulon in Escherichia coli

2009

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Escherichia coli is not considered naturally competent, yet it has homologues of the genes that most competent bacteria use for DNA uptake and processing. In Haemophilus influenzae and Vibrio cholerae, these genes are regulated by the Sxy and cyclic AMP receptor (CRP) proteins. We used microarrays to find out whether similar regulation occurs in E. coli. Expression of sxy strongly induced 63 transcriptional units, 34 of which required CRP for transcriptional activation and had promoter sites resembling the Sxy-and CRPdependent CRP-S motif previously characterized in H. influenzae. As previously reported, sxy expression also induced the sigma-H regulon. Flagellar operons were downregulated by sxy expression, although motility remained unaffected. The CRP-S regulon included all of E. coli's known competence gene homologues, so we investigated Sxy's effect on competence-associated phenotypes. A sxy knockout reduced both "natural" plasmid transformation and competitive fitness in long-term culture. In addition, expression of plasmid-borne sxy led to production of type IV pilin, the main subunit of the DNA uptake machinery of most bacteria. Although H. influenzae Sxy only weakly activated the E. coli Sxy regulon, induction was dramatically improved when it was coexpressed with its cognate CRP, suggesting that intimate interactions between Sxy and CRP are required for transcriptional activation at CRP-S sites.

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supporting

confidence: 63%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Sxy Induces a CRP-S Regulon in Escherichia coli

2009

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“…This resembles the situation of the NtcA homolog CRP that, at certain promoters dependent on the Sxy factor, binds to low-affinity, degenerated CRP-binding sites, the so-called CRP-S sites, and activates transcription aided by the Sxy protein (9). In some of these promoters, AϩT-rich sequences upstream from or in the upstream end of CRP-S sites, resembling UP elements, have been implicated in promoter activation (10). Notably, several AϩT runs can be found upstream of the putative suboptimal NtcA-binding regions in the devB proximal promoter (Fig.…”

Section: Discussionmentioning

confidence: 81%

Transcription Activation by NtcA in the Absence of Consensus NtcA-Binding Sites in an Anabaena Heterocyst Differentiation Gene Promoter

et al. 2012

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Heterocyst differentiation is orchestrated by the N control transcriptional regulator NtcA and the differentiation-specific factor HetR. In Anabaena sp. strain PCC 7120, the devBCA operon is expressed from two different promoters activated upon N stepdown. The distal devB promoter (transcription start point [TSP] located at position −704) represents a canonical class II NtcA-activated promoter, including a consensus NtcA-binding site centered 39.5 nucleotides upstream from the TSP. Transcription activation from a second TSP (−454) requires NtcA and is impaired in hetR mutants. In a wild-type background, three different DNA fragments, including both or each individual promoter, directed gfp expression localized mainly to proheterocysts and heterocysts. Expression was undetectable in an ntcA background and, for the fragment including the proximal promoter alone, also in a hetR background. In spite of the absence of consensus NtcA-binding sequences between the two TSPs, NtcA was shown to interact with this DNA region, and NtcA and its effector, 2-oxoglutarate, were necessary and sufficient for in vitro transcription from the −454 TSP. No HetR binding to the DNA or in vitro transcription from the proximal devB TSP promoted by HetR alone were detected. However, a moderate positive effect of HetR on NtcA binding to the DNA between the two devB TSPs was observed. The proximal devB promoter appears to represent a suboptimal NtcA-activated promoter for which HetR may act as a coactivator, with the physiological effect of restricting gene activation to conditions of prevalence of high NtcA and HetR levels, such as those taking place during heterocyst differentiation.

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“…H. influenzae competence genes are induced by nutrient starvation, when a set of 13 operons (26 genes) is strongly upregulated (44,61,62,67). These operons are united by a common promoter motif (Sxydependent cyclic AMP receptor protein [CRP-S] site) induced by two transcriptional regulators, CRP and the competence-specific activator Sxy (16,17,85). For some of these genes, transposon insertions were previously characterized, demonstrating roles in natural competence (10,20,32,42,48,100,101,107,112).…”

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confidence: 99%

Seventeen Sxy-Dependent Cyclic AMP Receptor Protein Site-Regulated Genes Are Needed for Natural Transformation in Haemophilus influenzae

2012

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Natural competence is the ability of bacteria to actively take up extracellular DNA. This DNA can recombine with the host chromosome, transforming the host cell and altering its genotype. In Haemophilus influenzae , natural competence is induced by energy starvation and the depletion of nucleotide pools. This induces a 26-gene competence regulon (Sxy-dependent cyclic AMP receptor protein [CRP-S] regulon) whose expression is controlled by two regulators, CRP and Sxy. The role of most of the CRP-S genes in DNA uptake and transformation is not known. We have therefore created in-frame deletions of each CRP-S gene and studied their competence phenotypes. All but one gene ( ssb ) could be deleted. Although none of the remaining CRP-S genes were required for growth in rich medium or survival under starvation conditions, DNA uptake and transformation were abolished or reduced in most of the mutants. Seventeen genes were absolutely required for transformation, with 14 of these genes being specifically required for the assembly and function of the type IV pilus DNA uptake machinery. Only five genes were dispensable for both competence and transformation. This is the first competence regulon for which all genes have been mutationally characterized.

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CRP Binding and Transcription Activation at CRP-S Sites

Cited by 30 publications

References 49 publications

Sxy Induces a CRP-S Regulon in Escherichia coli

Sxy Induces a CRP-S Regulon in Escherichia coli

Transcription Activation by NtcA in the Absence of Consensus NtcA-Binding Sites in an Anabaena Heterocyst Differentiation Gene Promoter

Seventeen Sxy-Dependent Cyclic AMP Receptor Protein Site-Regulated Genes Are Needed for Natural Transformation in Haemophilus influenzae

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