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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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Related in: MedlinePlus

Presence of regulon in query organisms by protein Blast. WalRK regulon genes of B. subtilis (a) and S. pneumoniae (b) were used to perform a protein Blast in order to examine whether a WalRK regulon might be present in Lactococci and Streptococci. Colors from light to dark blue are indicative of increasing protein similarity; for more details see the PePPER webserver.
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Figure 2: Presence of regulon in query organisms by protein Blast. WalRK regulon genes of B. subtilis (a) and S. pneumoniae (b) were used to perform a protein Blast in order to examine whether a WalRK regulon might be present in Lactococci and Streptococci. Colors from light to dark blue are indicative of increasing protein similarity; for more details see the PePPER webserver.

Mentions: Streptococci are phylogenetically closely related to Lactococci and therefore we performed an analysis of the WalRK regulons in both groups using the PePPER toolbox. The result (Figure 2) shows the similarity of the known WalRK regulons (B. subtilis, S. pneumoniae, Staphylococcus aureus) with the predicted regulons of Lactococci and Streptococci. The B. subtilis regulon (Figure 2a) showed the high conservation between the two groups where 6 genes were not found and 9 genes out of 23 were found in all species (protein blast e-value cutoff of 10−20). The difference between the two groups is shown in Figure 2b where 11 out of 24 genes of the S. pneumoniae R6 WalRK regulon were not found in Lactococci.


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)

Presence of regulon in query organisms by protein Blast. WalRK regulon genes of B. subtilis (a) and S. pneumoniae (b) were used to perform a protein Blast in order to examine whether a WalRK regulon might be present in Lactococci and Streptococci. Colors from light to dark blue are indicative of increasing protein similarity; for more details see the PePPER webserver.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Presence of regulon in query organisms by protein Blast. WalRK regulon genes of B. subtilis (a) and S. pneumoniae (b) were used to perform a protein Blast in order to examine whether a WalRK regulon might be present in Lactococci and Streptococci. Colors from light to dark blue are indicative of increasing protein similarity; for more details see the PePPER webserver.
Mentions: Streptococci are phylogenetically closely related to Lactococci and therefore we performed an analysis of the WalRK regulons in both groups using the PePPER toolbox. The result (Figure 2) shows the similarity of the known WalRK regulons (B. subtilis, S. pneumoniae, Staphylococcus aureus) with the predicted regulons of Lactococci and Streptococci. The B. subtilis regulon (Figure 2a) showed the high conservation between the two groups where 6 genes were not found and 9 genes out of 23 were found in all species (protein blast e-value cutoff of 10−20). The difference between the two groups is shown in Figure 2b where 11 out of 24 genes of the S. pneumoniae R6 WalRK regulon were not found in Lactococci.

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
Related in: MedlinePlus