RESUMEN
It is known that DNA curvature plays a certain role in gene regulation. The distribution of curved DNA in promoter regions is evolutionarily preserved, and it is mainly determined by temperature of habitat. However, very little is known on the distribution of DNA curvature in termination sites. Our main objective was to comprehensively analyze distribution of curved sequences upstream and downstream to the coding genes in prokaryotic genomes. We applied CURVATURE software to 170 complete prokaryotic genomes in a search for possible typical distribution of DNA curvature around starts and ends of genes. Performing cluster analyses and other statistical tests, we obtained novel results regarding various factors influencing curvature distribution in intergenic regions, such as growth temperature, A+T composition and genome size. We also analyzed intergenic regions between converging genes in 15 selected genomes. The results show that six genomes presented peaks of curvature excess larger than 3 SDs. Insufficient statistics did not allow us to draw further conclusion. Our hypothesis is that DNA curvature could affect transcription termination in many prokaryotes either directly, through contacts with RNA polymerase, or indirectly, via contacts with some regulatory proteins.
Asunto(s)
ADN de Archaea/química , ADN Bacteriano/química , Regiones Promotoras Genéticas , Regiones Terminadoras Genéticas , Análisis por Conglomerados , Genoma Arqueal , Genoma Bacteriano , Genómica , Conformación de Ácido NucleicoRESUMEN
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.