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PePPER: a webserver for prediction of prokaryote promoter elements and regulons.

de Jong A, Pietersma H, Cordes M, Kuipers OP, Kok J - BMC Genomics (2012)

Bottom Line: Improved prediction and comparison algorithms are currently available for identifying transcription factor binding sites (TFBSs) and their accompanying TFs and regulon members.Identification of putative regulons and full annotation of intergenic regions in any bacterial genome on the basis of existing knowledge on a related organism can now be performed by biologists and it can be done for a wide range of regulons.On the basis of the PePPER output, biologist can design experiments to further verify the existence and extent of the proposed regulons.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, 9747 AG Groningen, The Netherlands.

ABSTRACT

Background: Accurate prediction of DNA motifs that are targets of RNA polymerases, sigma factors and transcription factors (TFs) in prokaryotes is a difficult mission mainly due to as yet undiscovered features in DNA sequences or structures in promoter regions. Improved prediction and comparison algorithms are currently available for identifying transcription factor binding sites (TFBSs) and their accompanying TFs and regulon members.

Results: We here extend the current databases of TFs, TFBSs and regulons with our knowledge on Lactococcus lactis and developed a webserver for prediction, mining and visualization of prokaryote promoter elements and regulons via a novel concept. This new approach includes an all-in-one method of data mining for TFs, TFBSs, promoters, and regulons for any bacterial genome via a user-friendly webserver. We demonstrate the power of this method by mining WalRK regulons in Lactococci and Streptococci and, vice versa, use L. lactis regulon data (CodY) to mine closely related species.

Conclusions: The PePPER webserver offers, besides the all-in-one analysis method, a toolbox for mining for regulons, promoters and TFBSs and accommodates a new L. lactis regulon database in addition to already existing regulon data. Identification of putative regulons and full annotation of intergenic regions in any bacterial genome on the basis of existing knowledge on a related organism can now be performed by biologists and it can be done for a wide range of regulons. On the basis of the PePPER output, biologist can design experiments to further verify the existence and extent of the proposed regulons. The PePPER webserver is freely accessible at http://pepper.molgenrug.nl.

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CodY regulon prediction by PePPER all-in-one. The inserted table shows the CodY-TFBS[MG1363] found in L. lactis IL1403 (p-value < 10-5); the drawings show the intergenic regions upstream of CodY regulon members. At the bottom of this figure the WebLogo is shown of the TFBS derived from the MEME search. Predicted promoters with a correct spacing between −35 and −10 are colored dark green. Green arrows indicate predicted TSSs, light green boxes represent individual conserved −10 and −35 DNA motifs.
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Figure 4: CodY regulon prediction by PePPER all-in-one. The inserted table shows the CodY-TFBS[MG1363] found in L. lactis IL1403 (p-value < 10-5); the drawings show the intergenic regions upstream of CodY regulon members. At the bottom of this figure the WebLogo is shown of the TFBS derived from the MEME search. Predicted promoters with a correct spacing between −35 and −10 are colored dark green. Green arrows indicate predicted TSSs, light green boxes represent individual conserved −10 and −35 DNA motifs.

Mentions: The well-studied global transcriptional regulator CodY of L. lactis MG1363 [67,68] binds to the CodY-box (AATTTTCWGAAAATT) and influences the expression of genes involved in (branched-chain) amino acid uptake and biosynthesis as well as several other genes involved in N-metabolism (proteolysis and peptide uptake). The CodY regulon of L. lactis MG1363 was used in the PePPER all-in-one system to mine the L. lactis IL1403 genome for the presence of homologs of the CodY[MG1363] regulon and the CodY-TFBS[MG1363]. Subsequently, a MEME search was performed. The results showed that a CodY-TFBS is present in the upstream intergenic regions of 5 genes/operons in L. lactis IL1403, namely codY, serCAB, gltA-citB-icd, dppA and dppPBCDF. In L. lactis IL1403, Dpp, erroneously annotated as Opt [69], functions as a di/tripeptide transporter, with DppA as the substrate binding protein, and as an oligopeptide transporter employing DppP. The dppP gene in the dppA-dppPBCDF gene cluster of L. lactis MG1363 is mutated; in this strain CodY binds upstream of dppA but not upstream of dppP. Oligopeptide uptake in L. lactis MG1363 is encoded by the oppDFBCA operon, which is under CodY control [68]. The Opp system in L. lactis IL1403 is present but non-functional [69] and no CodY-TFBS[MG1363] was found in the DNA region upstream of opp. Despite the differences in the activities of these transport systems, our analysis indicates that in both lactococcal strains CodY regulates di/tri- and oligopeptide transport. The graphical overview of intergenic regions (Figure 4) shows that CodY represses gene expression by binding in or closely downstream of the promoter regions. The DNA binding motif that was identified in L. lactis IL1403 resembles CodY-TFBS[MG1363][68] and the CodY-TFBS[IL1403] reported by Guedon et al. [67].


PePPER: a webserver for prediction of prokaryote promoter elements and regulons.

de Jong A, Pietersma H, Cordes M, Kuipers OP, Kok J - BMC Genomics (2012)

CodY regulon prediction by PePPER all-in-one. The inserted table shows the CodY-TFBS[MG1363] found in L. lactis IL1403 (p-value < 10-5); the drawings show the intergenic regions upstream of CodY regulon members. At the bottom of this figure the WebLogo is shown of the TFBS derived from the MEME search. Predicted promoters with a correct spacing between −35 and −10 are colored dark green. Green arrows indicate predicted TSSs, light green boxes represent individual conserved −10 and −35 DNA motifs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472324&req=5

Figure 4: CodY regulon prediction by PePPER all-in-one. The inserted table shows the CodY-TFBS[MG1363] found in L. lactis IL1403 (p-value < 10-5); the drawings show the intergenic regions upstream of CodY regulon members. At the bottom of this figure the WebLogo is shown of the TFBS derived from the MEME search. Predicted promoters with a correct spacing between −35 and −10 are colored dark green. Green arrows indicate predicted TSSs, light green boxes represent individual conserved −10 and −35 DNA motifs.
Mentions: The well-studied global transcriptional regulator CodY of L. lactis MG1363 [67,68] binds to the CodY-box (AATTTTCWGAAAATT) and influences the expression of genes involved in (branched-chain) amino acid uptake and biosynthesis as well as several other genes involved in N-metabolism (proteolysis and peptide uptake). The CodY regulon of L. lactis MG1363 was used in the PePPER all-in-one system to mine the L. lactis IL1403 genome for the presence of homologs of the CodY[MG1363] regulon and the CodY-TFBS[MG1363]. Subsequently, a MEME search was performed. The results showed that a CodY-TFBS is present in the upstream intergenic regions of 5 genes/operons in L. lactis IL1403, namely codY, serCAB, gltA-citB-icd, dppA and dppPBCDF. In L. lactis IL1403, Dpp, erroneously annotated as Opt [69], functions as a di/tripeptide transporter, with DppA as the substrate binding protein, and as an oligopeptide transporter employing DppP. The dppP gene in the dppA-dppPBCDF gene cluster of L. lactis MG1363 is mutated; in this strain CodY binds upstream of dppA but not upstream of dppP. Oligopeptide uptake in L. lactis MG1363 is encoded by the oppDFBCA operon, which is under CodY control [68]. The Opp system in L. lactis IL1403 is present but non-functional [69] and no CodY-TFBS[MG1363] was found in the DNA region upstream of opp. Despite the differences in the activities of these transport systems, our analysis indicates that in both lactococcal strains CodY regulates di/tri- and oligopeptide transport. The graphical overview of intergenic regions (Figure 4) shows that CodY represses gene expression by binding in or closely downstream of the promoter regions. The DNA binding motif that was identified in L. lactis IL1403 resembles CodY-TFBS[MG1363][68] and the CodY-TFBS[IL1403] reported by Guedon et al. [67].

Bottom Line: Improved prediction and comparison algorithms are currently available for identifying transcription factor binding sites (TFBSs) and their accompanying TFs and regulon members.Identification of putative regulons and full annotation of intergenic regions in any bacterial genome on the basis of existing knowledge on a related organism can now be performed by biologists and it can be done for a wide range of regulons.On the basis of the PePPER output, biologist can design experiments to further verify the existence and extent of the proposed regulons.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, 9747 AG Groningen, The Netherlands.

ABSTRACT

Background: Accurate prediction of DNA motifs that are targets of RNA polymerases, sigma factors and transcription factors (TFs) in prokaryotes is a difficult mission mainly due to as yet undiscovered features in DNA sequences or structures in promoter regions. Improved prediction and comparison algorithms are currently available for identifying transcription factor binding sites (TFBSs) and their accompanying TFs and regulon members.

Results: We here extend the current databases of TFs, TFBSs and regulons with our knowledge on Lactococcus lactis and developed a webserver for prediction, mining and visualization of prokaryote promoter elements and regulons via a novel concept. This new approach includes an all-in-one method of data mining for TFs, TFBSs, promoters, and regulons for any bacterial genome via a user-friendly webserver. We demonstrate the power of this method by mining WalRK regulons in Lactococci and Streptococci and, vice versa, use L. lactis regulon data (CodY) to mine closely related species.

Conclusions: The PePPER webserver offers, besides the all-in-one analysis method, a toolbox for mining for regulons, promoters and TFBSs and accommodates a new L. lactis regulon database in addition to already existing regulon data. Identification of putative regulons and full annotation of intergenic regions in any bacterial genome on the basis of existing knowledge on a related organism can now be performed by biologists and it can be done for a wide range of regulons. On the basis of the PePPER output, biologist can design experiments to further verify the existence and extent of the proposed regulons. The PePPER webserver is freely accessible at http://pepper.molgenrug.nl.

Show MeSH