Genome-comparative computational approach for investigating prokaryotic ORF expression potentialities, in relation with potentially high transcription

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

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

To synthesize a protein of interest, biotechnological techniques associate a strong promoter and a synthetical 5' UnTranslated Region (UTR) optimized to enhance gene expression. Besides, in prokaryotic genomes, transcription and translation are temporally and spatially related events. Therefore, it is worth investigating whether potentially high transcription is associated or not with high translation potentiality. Secondly, since bacteria share common characteristics related to transcription (binding sites); a cross-genome comparison of 5' UTRs' features is of importance for insights into genome organization. We implemented BacTrans2, a software platform dedicated to the identification of genes harbouring putative strong promoters in prokaryotic genomes. Through a complementary software suite, we analysed such genes identified in 32 bacterial genomes, with respect to various characteristics related to translation: nature of start codon, location of Shine-Dalgarno sequence upstream of the start codon, AT-richness in the regions flanking translation signals, interference of secondary structure with translation signals, possible influence of mRNA 5' terminal secondary structure on mRNA stability. In particular, regarding AT-richness and interference with secondary structure, we show that putative strong promoters are characterized by a typical bias common to the known functional promoters of Escherichia coli genome. Generally speaking, all five criteria related to translation indicate that putative strong promoters are not favoured over known functional promoters. On the other hand, the large-scale genome-comparison implemented highlights the similarity of the 5' UTR characteristics for genes harbouring putative strong promoters.

Mots clés: computational biology; comparative genomics; structured motif; data-mining; prokaryote; ORF expression; transcription; translation; sigma 70 promoter

Domaines: Bio-informatique [q-bio.QM]; Biotechnologies

Christine Sinoquet, Sylvain Demey, Frédérique Braun. Genome-comparative computational approach for investigating prokaryotic ORF expression potentialities, in relation with potentially high transcription. 2007. ⟨hal-00163675⟩