Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1
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
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Format: | Article/Letter to editor biblioteca |
Language: | English |
Subjects: | compilation, conservation, dna, escherichia-coli, identification, initiation, metabolism, rna-polymerase, sequences, transcription start sites, |
Online Access: | https://research.wur.nl/en/publications/genome-wide-prediction-and-validation-of-sigma70-promoters-in-lac |
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dig-wur-nl-wurpubs-4382622024-09-30 Todt, T.J. Wels, M. Bongers, R.S. Siezen, R.J. van Hijum, S.A.F.T. Kleerebezem, M. Article/Letter to editor PLoS ONE 7 (2012) 9 ISSN: 1932-6203 Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1 2012 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 en application/pdf https://research.wur.nl/en/publications/genome-wide-prediction-and-validation-of-sigma70-promoters-in-lac 10.1371/journal.pone.0045097 https://edepot.wur.nl/253974 compilation conservation dna escherichia-coli identification initiation metabolism rna-polymerase sequences transcription start sites Wageningen University & Research |
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compilation conservation dna escherichia-coli identification initiation metabolism rna-polymerase sequences transcription start sites compilation conservation dna escherichia-coli identification initiation metabolism rna-polymerase sequences transcription start sites |
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compilation conservation dna escherichia-coli identification initiation metabolism rna-polymerase sequences transcription start sites compilation conservation dna escherichia-coli identification initiation metabolism rna-polymerase sequences transcription start sites Todt, T.J. Wels, M. Bongers, R.S. Siezen, R.J. van Hijum, S.A.F.T. Kleerebezem, M. Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1 |
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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 |
format |
Article/Letter to editor |
topic_facet |
compilation conservation dna escherichia-coli identification initiation metabolism rna-polymerase sequences transcription start sites |
author |
Todt, T.J. Wels, M. Bongers, R.S. Siezen, R.J. van Hijum, S.A.F.T. Kleerebezem, M. |
author_facet |
Todt, T.J. Wels, M. Bongers, R.S. Siezen, R.J. van Hijum, S.A.F.T. Kleerebezem, M. |
author_sort |
Todt, T.J. |
title |
Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1 |
title_short |
Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1 |
title_full |
Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1 |
title_fullStr |
Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1 |
title_full_unstemmed |
Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1 |
title_sort |
genome-wide prediction and validation of sigma70 promoters in lactobacillus plantarum wcfs1 |
url |
https://research.wur.nl/en/publications/genome-wide-prediction-and-validation-of-sigma70-promoters-in-lac |
work_keys_str_mv |
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1813025554988793856 |