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

Anne de Jong123, Hilco Pietersma123, Martijn Cordes123, Oscar P Kuipers123 and Jan Kok12*

Author Affiliations

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

2 Top Institute Food and Nutrition, Wageningen, The Netherlands

3 The Netherlands Kluyver Centre for Genomics of Industrial Fermentations, Delft, The Netherlands/Netherlands Consortium of Systems Biology, Amsterdam, The Netherlands

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BMC Genomics 2012, 13:299  doi:10.1186/1471-2164-13-299

Published: 2 July 2012

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 webcite.