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

<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 common...

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Autores principales:	Tilman J Todt, Michiel Wels, Roger S Bongers, Roland S Siezen, Sacha A F T van Hijum, Michiel Kleerebezem
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/651bc55e9db94bbabc01a13aa95f41d8
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spelling	oai:doaj.org-article:651bc55e9db94bbabc01a13aa95f41d82021-11-18T07:04:48ZGenome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.1932-620310.1371/journal.pone.0045097https://doaj.org/article/651bc55e9db94bbabc01a13aa95f41d82012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23028780/?tool=EBIhttps://doaj.org/toc/1932-6203<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 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.<h4>Results</h4>To identify σ(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 σ(70)-promoter consensus. Position weight matrices-based models of the recovered σ(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)).<h4>Conclusions</h4>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.Tilman J TodtMichiel WelsRoger S BongersRoland S SiezenSacha A F T van HijumMichiel KleerebezemPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e45097 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tilman J Todt Michiel Wels Roger S Bongers Roland S Siezen Sacha A F T van Hijum Michiel Kleerebezem Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.
description	<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 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.<h4>Results</h4>To identify σ(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 σ(70)-promoter consensus. Position weight matrices-based models of the recovered σ(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)).<h4>Conclusions</h4>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.
format	article
author	Tilman J Todt Michiel Wels Roger S Bongers Roland S Siezen Sacha A F T van Hijum Michiel Kleerebezem
author_facet	Tilman J Todt Michiel Wels Roger S Bongers Roland S Siezen Sacha A F T van Hijum Michiel Kleerebezem
author_sort	Tilman J Todt
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.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/651bc55e9db94bbabc01a13aa95f41d8
work_keys_str_mv	AT tilmanjtodt genomewidepredictionandvalidationofsigma70promotersinlactobacillusplantarumwcfs1 AT michielwels genomewidepredictionandvalidationofsigma70promotersinlactobacillusplantarumwcfs1 AT rogersbongers genomewidepredictionandvalidationofsigma70promotersinlactobacillusplantarumwcfs1 AT rolandssiezen genomewidepredictionandvalidationofsigma70promotersinlactobacillusplantarumwcfs1 AT sachaaftvanhijum genomewidepredictionandvalidationofsigma70promotersinlactobacillusplantarumwcfs1 AT michielkleerebezem genomewidepredictionandvalidationofsigma70promotersinlactobacillusplantarumwcfs1
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Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.

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