title: Structural properties of prokaryotic promoter regions correlate with functional features.
abstract: 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.
authors: Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium ; Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium.
authors: Pieter
authors: P
authors: Meysman
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors: Julio
authors: J
authors: Collado-Vides
authors: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico ; Instituto Nacional de Medicina Genómica, Mexico City, Mexico.
authors: Enrique
authors: E
authors: Morett
authors: Department of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
authors: Roberto
authors: R
authors: Viola
authors: Department of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
authors: Kristof
authors: K
authors: Engelen
authors: Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium ; Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium.
authors: Kris
authors: K
authors: Laukens
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D011387:Prokaryotic Cells / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic