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

Abstract

BackgroundAccurate 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.ResultsWe 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.ConclusionsThe 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.

Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum

“…56) from Softberry. Promoter regions were predicted using PePPER software (University of Groningen) 57 . To confirm the identity of the gene as discovered by Tn5 mutagenesis, each mutant was complemented with the corresponding predicted wild-type coding sequence, which was synthesized (VectorBuilder, Cyagen Biosciences) using a pPR322 vector backbone (Novagen) under the control of the T7 promoter.…”

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

“…Transcriptional regulator-binding motifs in well-studied model bacteria can be predicted with some certainty based on degenerate sequence motifs (40,41). Such an identification of transcriptional regulators can start with a search for sigma factor-binding motifs, since some sigma factors are linked to specific processes, as is the case in B. subtilis, which employs a large number of alternative sigma factors for different processes (42).…”

Molecular mechanism of PdxR – a transcriptional activator involved in the regulation of vitamin B6 biosynthesis in the probiotic bacterium Bacillus clausii

“…Intergenic regions between pdxR gene and pdxST genes were analyzed using the PEPPER tool [38] and the MEME suite webserver [30,31] to detect the canonical À35 and À10 promoter elements and to identify directed and inverted repeats, respectively. Alignment of promoter sequences was obtained by the PRO-COFFEE method [32].…”