Curvature Distribution in Prokaryotic Genomes

Article type: Research Article

Authors: Kozobay-Avraham, Limor | Hosid, Sergey | Bolshoy, Alexander

Affiliations: Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel. E-mail: [email protected]

Note: [] Corresponding author

Abstract: DNA curvature is known to play a biological role in gene regulation, in particular, initiation of transcription. We applied the software CURVATURE based on the wedge model to predict whether promoter regions of certain prokaryotes may be characterized by higher intrinsic DNA curvature located within or upstream to these regions. The main purpose was to verify our earlier hypothesis that the DNA curvature plays a biological role in gene regulation in mesophilic as compared to hyperthermophilic prokaryotes, i.e., DNA curvature presumably has a functional adaptive significance determined by temperature selection. Therefore, we analyzed all available complete prokaryotic genomes. The analysis showed that there is a group of genomes with a relatively high average DNA curvature upstream of start of genes. Remarkably, all organisms of this group appeared to be mesophilic, which is a full confirmation of the former hypothesis. The conservative patterns of genomic curvature distribution across different mesophilic bacterial and archaeal genomes presented in this study provide a new, convincing indication that curved DNA is evolutionarily preserved and determined by temperature selection. Moreover, we found a rather peculiar property of hyperthermophilic prokaryotes: the coding regions are predicted to be significantly more curved than it would be expected from their dinucleotide composition.

Keywords: promoter, A+T composition, comparative genomics, sequence periodicity, wedge model

Journal: In Silico Biology, vol. 4, no. 3, pp. 361-375, 2004