Dataset Information

Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.

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 ?(70) is commonly involved in transcription of the cell's housekeeping genes, which is mediated by the conserved ?(70) promoter sequence motifs. In this study the ?(70)-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 ?(70)-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 ?(70)-promoter consensus. Position weight matrices-based models of the recovered ?(70)-promoter sequence motif were employed to identify 3874 motifs with significant similarity (p-value<10(-4)) to the model-motif in the L. plantarum genome. Genome-wide transcript information deduced from whole genome tiling-array transcriptome datasets, was used to infer transcription start sites (TSSs) from the 5'-end of transcripts. By this procedure, 1167 putative TSSs were identified that were used to corroborate the transcriptionally active fraction of these predicted promoters. In total, 568 predicted promoters were found in proximity (? 40 nucleotides) of the putative TSSs, showing a highly significant co-occurrence of predicted promoter and TSS (p-value<10(-263)). CONCLUSIONS: High-resolution tiling arrays provide a suitable source to infer TSSs at a genome-wide level, and allow experimental verification of in silico predicted promoter sequence motifs.

SUBMITTER: Todt TJ

PROVIDER: S-EPMC3447810 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.

Todt Tilman J TJ Wels Michiel M Bongers Roger S RS Siezen Roland S RS van Hijum Sacha A F T SA Kleerebezem Michiel M

PloS one 20120920 9

<h4>Background</h4>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 σ(70) is commonly involved in transcription of the cell's housekeeping genes, which is mediated by the conserved σ(70) promoter sequence motifs. In this study the σ(70)-promoter sequences in Lactobacillus plantarum WCFS1 were p ...[more]

PMID: 23028780

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Project description:Background: In prokaryotes, sigma factors are essential for the targeting of the transcription machinery to promoters. Various sigma factors have been described that recognize and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor σ70 is commonly involved in transcription of the cell's general housekeeping genes, which is mediated by the conserved σ70 promoter sequence motifs. This study detects and predicts the general σ70-promoter sequences in Lactobacillus plantarum WCFS1 using genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with experimentally detected transcription starts sites (TSSs) using high-resolution tiling array transcriptome datasets. Results: To identify σ70-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focusing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved σ70-promoter consensus. Position weight matrices-based models of the recovered σ70-promoter sequence motif were employed to identify 4746 motifs with significant similarity (p-value < 10-4) to the model-motif in the L. plantarum genome. Genome-wide transcription start site information deduced from whole genome tiling-array transcriptome datasets revealed 936 TSSs that were employed to validate the transcriptionally active fraction of these predicted promoters. In total, 578 predicted promoters were found in proximity (≤ 100 nucleotides) of the identified TSSs, showing a highly significant co-occurrence of predicted promoter and measured TSS (p-value < 10-23). An additional 224 predicted promoters was validated when the significant similarity to the model-motif was applied less strictly (10-4 ≤ p-value < 10-3). Conclusions: High-resolution tiling arrays provide a suitable source for TSS detection at a genome-wide level, and allow experimental verification of in silico-predicted promoter sequence motifs.

Project description:Background: In prokaryotes, sigma factors are essential for the targeting of the transcription machinery to promoters. Various sigma factors have been described that recognize and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor M-OM-^C70 is commonly involved in transcription of the cell's general housekeeping genes, which is mediated by the conserved M-OM-^C70 promoter sequence motifs. This study detects and predicts the general M-OM-^C70-promoter sequences in Lactobacillus plantarum WCFS1 using genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with experimentally detected transcription starts sites (TSSs) using high-resolution tiling array transcriptome datasets. Results: To identify M-OM-^C70-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focusing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved M-OM-^C70-promoter consensus. Position weight matrices-based models of the recovered M-OM-^C70-promoter sequence motif were employed to identify 4746 motifs with significant similarity (p-value < 10-4) to the model-motif in the L. plantarum genome. Genome-wide transcription start site information deduced from whole genome tiling-array transcriptome datasets revealed 936 TSSs that were employed to validate the transcriptionally active fraction of these predicted promoters. In total, 578 predicted promoters were found in proximity (M-bM-^IM-$ 100 nucleotides) of the identified TSSs, showing a highly significant co-occurrence of predicted promoter and measured TSS (p-value < 10-23). An additional 224 predicted promoters was validated when the significant similarity to the model-motif was applied less strictly (10-4 M-bM-^IM-$ p-value < 10-3). Conclusions: High-resolution tiling arrays provide a suitable source for TSS detection at a genome-wide level, and allow experimental verification of in silico-predicted promoter sequence motifs. Triplicate hybridizations (technical replicates) of two L. plantarum WCFS1 samples (biological replicates) gathered from a fermentation run at OD600 of 1. Dye swap applied to one of the three technical replicates.

Dataset Information

Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.

Publications

Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.

Similar Datasets

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