Structural properties of prokaryotic promoter regions correlate with functional features.

The structural properties of the DNA molecule are known to play a critical role in transcription. In this paper, the structural profiles of promoter regions were studied within the context of their diversity and their function for eleven prokaryotic species; Escherichia coli, Klebsiella pneumoniae,...

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Autores principales:	Pieter Meysman, Julio Collado-Vides, Enrique Morett, Roberto Viola, Kristof Engelen, Kris Laukens
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/90efc0eee16644e186240b945c86d518
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spelling	oai:doaj.org-article:90efc0eee16644e186240b945c86d5182021-11-18T08:33:15ZStructural properties of prokaryotic promoter regions correlate with functional features.1932-620310.1371/journal.pone.0088717https://doaj.org/article/90efc0eee16644e186240b945c86d5182014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24516674/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The structural properties of the DNA molecule are known to play a critical role in transcription. In this paper, the structural profiles of promoter regions were studied within the context of their diversity and their function for eleven prokaryotic species; Escherichia coli, Klebsiella pneumoniae, Salmonella Typhimurium, Pseudomonas auroginosa, Geobacter sulfurreducens Helicobacter pylori, Chlamydophila pneumoniae, Synechocystis sp., Synechoccocus elongates, Bacillus anthracis, and the archaea Sulfolobus solfataricus. The main anchor point for these promoter regions were transcription start sites identified through high-throughput experiments or collected within large curated databases. Prokaryotic promoter regions were found to be less stable and less flexible than the genomic mean across all studied species. However, direct comparison between species revealed differences in their structural profiles that can not solely be explained by the difference in genomic GC content. In addition, comparison with functional data revealed that there are patterns in the promoter structural profiles that can be linked to specific functional loci, such as sigma factor regulation or transcription factor binding. Interestingly, a novel structural element clearly visible near the transcription start site was found in genes associated with essential cellular functions and growth in several species. Our analyses reveals the great diversity in promoter structural profiles both between and within prokaryotic species. We observed relationships between structural diversity and functional features that are interesting prospects for further research to yet uncharacterized functional loci defined by DNA structural properties.Pieter MeysmanJulio Collado-VidesEnrique MorettRoberto ViolaKristof EngelenKris LaukensPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e88717 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pieter Meysman Julio Collado-Vides Enrique Morett Roberto Viola Kristof Engelen Kris Laukens Structural properties of prokaryotic promoter regions correlate with functional features.
description	The structural properties of the DNA molecule are known to play a critical role in transcription. In this paper, the structural profiles of promoter regions were studied within the context of their diversity and their function for eleven prokaryotic species; Escherichia coli, Klebsiella pneumoniae, Salmonella Typhimurium, Pseudomonas auroginosa, Geobacter sulfurreducens Helicobacter pylori, Chlamydophila pneumoniae, Synechocystis sp., Synechoccocus elongates, Bacillus anthracis, and the archaea Sulfolobus solfataricus. The main anchor point for these promoter regions were transcription start sites identified through high-throughput experiments or collected within large curated databases. Prokaryotic promoter regions were found to be less stable and less flexible than the genomic mean across all studied species. However, direct comparison between species revealed differences in their structural profiles that can not solely be explained by the difference in genomic GC content. In addition, comparison with functional data revealed that there are patterns in the promoter structural profiles that can be linked to specific functional loci, such as sigma factor regulation or transcription factor binding. Interestingly, a novel structural element clearly visible near the transcription start site was found in genes associated with essential cellular functions and growth in several species. Our analyses reveals the great diversity in promoter structural profiles both between and within prokaryotic species. We observed relationships between structural diversity and functional features that are interesting prospects for further research to yet uncharacterized functional loci defined by DNA structural properties.
format	article
author	Pieter Meysman Julio Collado-Vides Enrique Morett Roberto Viola Kristof Engelen Kris Laukens
author_facet	Pieter Meysman Julio Collado-Vides Enrique Morett Roberto Viola Kristof Engelen Kris Laukens
author_sort	Pieter Meysman
title	Structural properties of prokaryotic promoter regions correlate with functional features.
title_short	Structural properties of prokaryotic promoter regions correlate with functional features.
title_full	Structural properties of prokaryotic promoter regions correlate with functional features.
title_fullStr	Structural properties of prokaryotic promoter regions correlate with functional features.
title_full_unstemmed	Structural properties of prokaryotic promoter regions correlate with functional features.
title_sort	structural properties of prokaryotic promoter regions correlate with functional features.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/90efc0eee16644e186240b945c86d518
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Structural properties of prokaryotic promoter regions correlate with functional features.

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