Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes.
This article compares 32 bacterial genomes with respect to their high transcription potentialities. The sigma70 promoter has been widely studied for Escherichia coli model and a consensus is known. Since transcriptional regulations are known to compensate for promoter weakness (i.e. when the promoter similarity with regard to the consensus is rather low), predicting functional promoters is a hard task. Instead, the research work presented here comes within the scope of investigating potentially high ORF expression, in relation with three criteria: (i) high similarity to the sigma70 consensus (namely, the consensus variant appropriate for each genome), (ii) transcription strength reinforcement through a supplementary binding site--the upstream promoter (UP) element--and (iii) enhancement through an optimal Shine-Dalgarno (SD) sequence. We show that in the AT-rich Firmicutes' genomes, frequencies of potentially strong sigma70-like promoters are exceptionally high. Besides, though they contain a low number of strong promoters (SPs), some genomes may show a high proportion of promoters harbouring an UP element. Putative SPs of lesser quality are more frequently associated with an UP element than putative strong promoters of better quality. A meaningful difference is statistically ascertained when comparing bacterial genomes with similarly AT-rich genomes generated at random; the difference is the highest for Firmicutes. Comparing some Firmicutes genomes with similarly AT-rich Proteobacteria genomes, we confirm the Firmicutes specificity. We show that this specificity is neither explained by AT-bias nor genome size bias; neither does it originate in the abundance of optimal SD sequences, a typical and significant feature of Firmicutes more thoroughly analysed in our study.
Sinoquet
Christine
C
Computer Science Institute of Nantes-Atlantic (Lina), U.M.R. C.N.R.S. 6241, University of Nantes, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex, France. christine.sinoquet@univ-nantes.fr
Demey
Sylvain
S
Braun
Frédérique
F
D020856:AT Rich Sequence; D001483:Base Sequence; D019295:Computational Biology; D016384:Consensus Sequence; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D003627:Data Interpretation, Statistical; D004742:Enhancer Elements, Genetic; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D023281:Genomics; D016366:Open Reading Frames; D011401:Promoter Regions, Genetic; D012808:Sigma Factor / Q000378:metabolism*; D020124:Thermotoga maritima / Q000235:genetics; D014158:Transcription, Genetic
D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases