Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes

Abstract

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.

Figure 1.

Frequencies of genes harbouring a putative strong promoter (SP), under four constraint sets, in 32 prokaryotic genomes. See text, Subsection “Genome analysis upon request” for the definition of CI and CII constraints. (A) and (B): UP element optional; (C) and (D): UP element required. Along the x-axis, the following phyla and groups are encountered: Actinobacteria, Chlamydia, Firmicutes (among which Mollicutes), “Others” group, Proteobacteria, Spirochaetales. (A) y-axis: number of genes harbouring a SP (sp); (B) y-axis: ratio p1 of genes harbouring a SP (sp) to the total number of genes encoding proteins in the genome (g), p1 = 100 × sp / g; (C) y-axis: number of genes identified with an UP element harboured in the SP (upsp); (D) y-axis: ratio p2 of the number of genes with an UP element in the SP (upsp) to the number of genes with a SP (sp), p2 = 100 × upsp / sp.

Figure 2.

Observed bacterial genome values versus minimal, average and maximal values observed over 100 similarly AT-rich genomes generated at random, for sp and upsp, respectively, under four constraint sets. See Figure 1 for definition of sp and upsp, and for genome abbreviations. See text, Subsection “Genome analysis upon request” for the definition of CI and CII constraints. (A): CI, UP element optional; (B): CII, UP element optional; (C): CI, UP element required; (D): CII, UP element required.