Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1

T.J. Todt, M. Wels, R.S. Bongers, R.J. Siezen, S.A.F.T. van Hijum, M. Kleerebezem

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7 Citations (Scopus)

Abstract

Background - In prokaryotes, sigma factors are essential for directing the transcription machinery towards promoters. Various sigma factors have been described that recognize, and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor s70 is commonly involved in transcription of the cell's housekeeping genes, which is mediated by the conserved s70 promoter sequence motifs. In this study the s70-promoter sequences in Lactobacillus plantarum WCFS1 were predicted using a genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with transcription start sites inferred from the 5'-ends of transcripts detected by high-resolution tiling array transcriptome datasets. Results - To identify s70-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focussing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved s70-promoter consensus. Position weight matrices-based models of the recovered s70-promoter sequence motif were employed to identify 3874 motifs with significant similarity (p-value
Original languageEnglish
Article numbere45097
JournalPLoS ONE
Volume7
Issue number9
DOIs
Publication statusPublished - 2012

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Keywords

  • transcription start sites
  • escherichia-coli
  • rna-polymerase
  • sequences
  • identification
  • dna
  • conservation
  • compilation
  • metabolism
  • initiation

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