Nucleic Acids Research Advance Access originally published online on April 25, 2008
Nucleic Acids Research 2008 36(10):3332-3340; doi:10.1093/nar/gkn135
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, No. 10 3332-3340
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes
1Computer 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 and 2Inserm U601, Cancerology Research Department, University of Nantes, 9 quai Moncousu, 44093 Nantes Cedex 01, France
*To whom correspondence should be addressed. Tel: +33(0)25112 5805; Fax: +33(0)25112 5815; Email: christine.sinoquet{at}univ-nantes.fr
Received December 22, 2007. Revised February 20, 2008. Accepted March 10, 2008.
This article compares 32 bacterial genomes with respect to their high transcription potentialities. The 
70 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 70 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 70-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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Collado-Vides, H. Salgado, E. Morett, S. Gama-Castro, V. Jimenez-Jacinto, I. Martinez-Flores, A. Medina-Rivera, L. Muniz-Rascado, M. Peralta-Gil, and A. Santos-Zavaleta Bioinformatics Resources for the Study of Gene Regulation in Bacteria J. Bacteriol., January 1, 2009; 191(1): 23 - 31. [Full Text] [PDF]
|
|