PREDetector: A new tool to identify regulatory elements in bacterial genomes

Hiard, Samuel; Marée, Raphaël; Colson, Séverine; Hoskisson, Paul A.; Titgemeyer, Fritz; Wezel, Gilles P. van; Joris, Bernard; Wehenkel, Louis; Rigali, Sébastien

doi:10.1016/j.bbrc.2007.03.180

Cited by 97 publications

(83 citation statements)

References 11 publications

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“…At the same time, using the list of cre targets in B. subtilis reported by Fujita (22), we used the PREDetector software program (33) to identify an additional 14-bp sequence, cre chiB (ATAAAGC GTTTACA), which is similar to the cis-acting element cre, in the promoter of chiB in the genomic sequence of B. thuringiensis HD-789 (see Data Set S1 in the supplemental material). The cre chiB element overlaps the Ϫ35 box of the chiB promoter (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, we found that nagA and nagP of Bti75 contain a 16-bp dre-like sequence within their upstream regions that is also directly repressed by YvoA Bt (data not shown). To identify further possible YvoA Bt binding sites in the genome of B. thuringiensis HD-789, we used the PREDetector software program (33) to identify corresponding16-bp dre-like sequence of nagA, nagP, and chiB. The data are listed in Data Set S2 in the supplemental material.…”

Section: Discussionmentioning

confidence: 99%

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YvoA and CcpA Repress the Expression of chiB in Bacillus thuringiensis

Jiang

Pan

et al. 2015

Appl Environ Microbiol

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c Bacillus thuringiensis produces chitinases, which are involved in its antifungal activity and facilitate its insecticidal activity. In our recent work, we found that a 16-bp sequence, dre chiB (AGACTTCGTGATGTCT), downstream of the minimal promoter region of the chitinase B gene (chiB) was a critical site for the inducible expression of chiB in B. thuringiensis Bti75. In this work, we show that a GntR family transcriptional regulator (named YvoA Bt ), which is homologous to YvoA of Bacillus subtilis, can specifically bind to the dre chiB oligonucleotide sequences in vitro by using electrophoretic mobility shift assays (EMSAs) and isothermal titration calorimetry (ITC) assays. The results of quantitative real-time reverse transcription-PCR (qRT-PCR) and Western blotting indicated that deletion of yvoA caused an ϳ7.5-fold increase in the expression level of chiB. Furthermore, binding of purified YvoA Bt to its target DNA could be abolished by glucosamine-6-phosphate (GlcN-6-P). We also confirmed, in the presence of the phosphoprotein Hpr-Ser 45 -P, that purified CcpA Bt bound specifically to the promoter of chiB, which contains the "cre chiB " sequence (ATAAAGCGTTTACA). According to the results of qRT-PCR and Western blotting, deletion of ccpA resulted in a 39-fold increase in the chiB expression level, and glucose no longer influenced the expression of chiB. We confirm that chiB is negatively controlled by both CcpA Bt and YvoA Bt in Bti75.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

YvoA and CcpA Repress the Expression of chiB in Bacillus thuringiensis

Jiang

Pan

et al. 2015

Appl Environ Microbiol

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“…YvoA-binding sites upstream of nagP (dre nagP ; ATTGGTATAGATCACT) and upstream of the nagAB-yvoA locus (dre nagA ; GCTGGTCTAGATCACT) of B. subtilis were used to search similar sequences upstream of nagP and nagA orthologues in Bacillus species using the PREDetector software program (24). This list of 18 dre sites (see Table S1 in the supplemental material) was used to generate a position weight matrix (named NagR 2011) for NagR (YvoA) regulon prediction in Bacillus species.…”

Section: Methodsmentioning

confidence: 99%

Regulon of the N -Acetylglucosamine Utilization Regulator NagR in Bacillus subtilis

et al. 2011

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N-Acetylglucosamine (GlcNAc) is the most abundant carbon-nitrogen biocompound on earth and has been shown to be an important source of nutrients for both catabolic and anabolic purposes in Bacillus species. In this work we show that the GntR family regulator YvoA of Bacillus subtilis serves as a negative transcriptional regulator of GlcNAc catabolism gene expression. YvoA represses transcription by binding a 16-bp sequence upstream of nagP encoding the GlcNAc-specific EIIBC component of the sugar phosphotransferase system involved in GlcNAc transport and phosphorylation, as well as another very similar 16-bp sequence upstream of the nagAB-yvoA locus, wherein nagA codes for N-acetylglucosamine-6-phosphate deacetylase and nagB codes for the glucosamine-6-phosphate (GlcN-6-P) deaminase. In vitro experiments demonstrated that GlcN-6-P acts as an inhibitor of YvoA DNA-binding activity, as occurs for its Streptomyces ortholog, DasR. Interestingly, we observed that the expression of nag genes was still activated upon addition of GlcNAc in a ⌬yvoA mutant background, suggesting the existence of an auxiliary transcriptional control instance. Initial computational prediction of the YvoA regulon showed a distribution of YvoA binding sites limited to nag genes and therefore suggests renaming YvoA to NagR, for N-acetylglucosamine utilization regulator. Whole-transcriptome studies showed significant repercussions of nagR deletion for several major B. subtilis regulators, probably indirectly due to an excess of the crucial molecules acetate, ammonia, and fructose-6-phosphate, resulting from complete hydrolysis of GlcNAc. We discuss a model deduced from NagR-mediated gene expression, which highlights clear connections with pathways for GlcNAc-containing polymer biosynthesis and adaptation to growth under oxygen limitation.

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“…In order to determine the putative sequence of the SigK binding site, promoter sequences have been aligned using the AlignX program from VectorNTI (Invitrogen). Subsequently, this short alignment of similar sequences was used as a matrix to detect other putative binding sites in sequenced mycobacterial genomes using the programs PredictRegulon (34) and PREDetector (16).…”

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confidence: 99%

Evolution of the Mycobacterial SigK Regulon

2008

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Previous studies have established that members of the Mycobacterium tuberculosis complex exhibit variable production of the antigenic proteins MPT70 and MPT83 due to mutations in their positive regulator, SigK (sigma factor K), and their negative regulator, RskA (regulator of sigma K). To further understand this highly specific SigK-controlled regulon, we have undertaken evolutionary studies to determine the presence of homologues of SigK-regulated genes in other organisms and to predict its transcriptional network. Evolutionary analysis indicates that the positive and negative regulators are conserved across many organisms, but that the genes under their control are variable. Moreover, the addition, loss, and movement of various genes in the mpt70/83 locus suggest that these genes are unlikely to be cotranscribed. To test predictions from sequence analysis, we have used promoter luciferase fusions and Northern blots to show that the majority of genes in this locus have their own promoters, of which a subset are SigK regulated (mpt83, dipZ, mpt70, and Rv0449c). Next, we have shown that the intracellular inducibility of mpt70 and mpt83 is a conserved property, shared between M. tuberculosis and Mycobacterium marinum. In addition, we have shown that SigK and RskA from an environmental mycobacterium isolate (M. gilvum PYR-GCK) complemented the regulatory activity of M. tuberculosis ⌬sigK rskA. Together, our data indicate that the regulatory system SigK/RskA is conserved across the Mycobacterium genus, whereas the regulon under its control varies considerably across species.Mycobacterium tuberculosis is an extremely successful pathogen of humans, infecting an estimated one-third of the world's population. This capacity to persist in the host, despite the dynamic alterations effected by the host immune response, testifies to an evolved capacity of the organism to regulate its genetic expression to the conditions encountered during infection. Indeed, a number of studies have demonstrated that disruption of M. tuberculosis regulatory elements, such as sigma factors, results in reduced virulence in experimental models (21,28,30).The determination of genomic sequences for a number of nonpathogenic mycobacteria has revealed that homologues of many genes, including regulatory elements, are often present in organisms that are not virulent to humans. For instance, comparative analysis has demonstrated conservation of biochemical pathways and a secretory system important for full virulence of M. tuberculosis (7,10). This indicates that genetic elements and the proteins they encode that exist in other mycobacteria either serve an important function in M. tuberculosis pathogenicity or have evolved a specific role in M. tuberculosis complex organisms. As a number of predicted regulatory elements are also conserved between environmental mycobacteria and M. tuberculosis, it follows that an evolutionary analysis may guide predictions about the origins of such elements, the transcriptional networks they control, and the stimuli that...

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PREDetector: A new tool to identify regulatory elements in bacterial genomes

Cited by 97 publications

References 11 publications

YvoA and CcpA Repress the Expression of chiB in Bacillus thuringiensis

YvoA and CcpA Repress the Expression of chiB in Bacillus thuringiensis

Regulon of the N -Acetylglucosamine Utilization Regulator NagR in Bacillus subtilis

Evolution of the Mycobacterial SigK Regulon

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