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Computer analysis of rrn regulatory signals on both DNA sequence and structural levels in proteobacteria

Alexey Vitreschak 1 Sergey Hosid Alexander Bolshoy Gregory Kucherov 1
1 ADAGE - Applying discrete algorithms to genomics
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : DNA curvature has been shown to play an important role in a number of biological processes: transcription initiation, DNA replication, etc. We used a combination of two techniques - prediction of protein binding sites as well as of DNA curvature - to study FIS/H-NS mediated regulation of rrn operons in proteobacteria. Significant conserved DNA curvature signals have been found in rrn promoter regions around -100, -120 positions mostly in three phylogenetic groups: Enterobacteriales, Vibrionales and Pasteurellales. Moreover, FIS binding sites have also been detected only in these three phylogenetic groups. In other proteobacteria, only few significant curved regions have been detected and grouped FIS sites have not been found in rrn promoter regions. This implies a strong correlation between grouped FIS DNA-binding motifs and significant conserved DNA curvature in rrn promoter regions in proteobacteria. As a conclusion, H-NS/FIS mediated antagonistic regulation of rrn operons is possibly evolutionarily conserved only in these three gamma-proteobacterial groups. From a more general perspective, we demonstrated that DNA curvature signals are conserved among various bacteria and a simultaneous prediction of conserved curved DNA sites as well as protein binding sites is important for the evolutionary analysis of gene regulation. To our knowledge, this paper is the first attempt of massive comparative analysis of regulatory sites in bacteria at both DNA sequence and structural levels.
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Submitted on : Tuesday, September 26, 2006 - 10:15:46 AM
Last modification on : Friday, February 4, 2022 - 3:30:09 AM


  • HAL Id : inria-00100228, version 1



Alexey Vitreschak, Sergey Hosid, Alexander Bolshoy, Gregory Kucherov. Computer analysis of rrn regulatory signals on both DNA sequence and structural levels in proteobacteria. [Intern report] A04-R-331 || vitreschak04a, 2004, 19 p. ⟨inria-00100228⟩



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