A large-scale computational analysis for significance assessment of frequencies relative to potentially strong sigma 70 promoters - comparison between 32 bacterial genomes -

Christine Sinoquet (1) , Sylvain Demey (1) , Frédérique Braun (2)

1 LINA - Laboratoire d'Informatique de Nantes Atlantique
2 Recherches en cancérologie

The platform BacTrans2 has been designed to help select putative strong sigma 70-like promoter candidates in prokaryotic genomes. It was run to investigate the importance of sigma 70-like potentially high transcription in bacteria other than Escherichia coli. We performed a genome-comparative analysis of high ORF expression potentialities over 32 prokaryotic genomes. Besides, we put an emphasis on transcription strength reinforcement through the UP element presence and on translation potentiality enhancement through an optimal Shine-Dalgarno sequence. We compared frequencies of putative strong promoters between various genomes. We show that in the AT-rich Firmicutes' genomes, frequencies of potentially strong sigma 70-like promoters are exceptionally high. Besides, though they contain a low number of strong promoters, some genomes may show a high proportion of promoters harbouring an UP element. Putative strong promoters 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 frequencies in bacterial genomes with frequencies in 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 but originates in the abundance of optimal Shine-Dalgarno sequences, a typical and significant feature of Firmicutes more thoroughly analysed in our study.

Mots clés: Computational Biology; comparative genomics; structured motif; prokaryote; ORF expression; sigma 70 promoter

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Christine Sinoquet, Sylvain Demey, Frédérique Braun. A large-scale computational analysis for significance assessment of frequencies relative to potentially strong sigma 70 promoters - comparison between 32 bacterial genomes -. 2007. ⟨hal-00153303v3⟩