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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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Annotation of the intergenic region upstream of acmA. The genes acmA and the first upstream gene, llmg_0281, are indicated with gray arrows and are not drawn to scale. The WebLogo is based on the MEME weight matrix; light grey box is the predicted RBS. No transcription terminator was found in this area.
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Figure 3: Annotation of the intergenic region upstream of acmA. The genes acmA and the first upstream gene, llmg_0281, are indicated with gray arrows and are not drawn to scale. The WebLogo is based on the MEME weight matrix; light grey box is the predicted RBS. No transcription terminator was found in this area.

Mentions: The WalR binding site (TGTAA-n6-TGTAA) was mapped using DNAseI footprinting and EMSAs in 4 organisms; B. subtilis, Staph. aureus, S. pneumoniae and S. mutans[61]. We added the WalR TFBSs derived from these 4 organisms separately, as well as an averaged (combined) WalR motif (WalR[combined]) to the PePPER database and subsequently screened the genomes of the L. lactis strains for the presence of these DNA motifs. The upstream DNA regions of two genes of L. lactis MG1363 that are orthologous to WalRK regulon members carry the WalR[combined] TFBS, namely xynD (TGTAT-n6-TGTTA) and htrA (TGAAA-n6-TGAAG). In the upstream DNA region of the other 4 WalRK operon orthologs no WalR[combined] was found. Interestingly, WalR[combined] (Figure 3) was present upstream of the cell wall hydrolase genes acmA and acmB[65,66], which could indicate that these genes might be regulated by WalRK and that the WalRK stress response system of L. lactis also influences their expression.


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)

Annotation of the intergenic region upstream of acmA. The genes acmA and the first upstream gene, llmg_0281, are indicated with gray arrows and are not drawn to scale. The WebLogo is based on the MEME weight matrix; light grey box is the predicted RBS. No transcription terminator was found in this area.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Annotation of the intergenic region upstream of acmA. The genes acmA and the first upstream gene, llmg_0281, are indicated with gray arrows and are not drawn to scale. The WebLogo is based on the MEME weight matrix; light grey box is the predicted RBS. No transcription terminator was found in this area.
Mentions: The WalR binding site (TGTAA-n6-TGTAA) was mapped using DNAseI footprinting and EMSAs in 4 organisms; B. subtilis, Staph. aureus, S. pneumoniae and S. mutans[61]. We added the WalR TFBSs derived from these 4 organisms separately, as well as an averaged (combined) WalR motif (WalR[combined]) to the PePPER database and subsequently screened the genomes of the L. lactis strains for the presence of these DNA motifs. The upstream DNA regions of two genes of L. lactis MG1363 that are orthologous to WalRK regulon members carry the WalR[combined] TFBS, namely xynD (TGTAT-n6-TGTTA) and htrA (TGAAA-n6-TGAAG). In the upstream DNA region of the other 4 WalRK operon orthologs no WalR[combined] was found. Interestingly, WalR[combined] (Figure 3) was present upstream of the cell wall hydrolase genes acmA and acmB[65,66], which could indicate that these genes might be regulated by WalRK and that the WalRK stress response system of L. lactis also influences their expression.

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