Transcribed intergenic regions exhibit a lower frequency of nucleotide polymorphism than the untranscribed intergenic regions in the genomes of Escherichia coli and Salmonella enterica.

The temporary exposure of single-stranded regions in the genome during the process of replication and transcription makes the region vulnerable to cytosine deamination resulting in a higher rate of C→T transition. Intraoperon intergenic regions undergo transcription along with adjacent co-transcribed genes in an operon, whereas interoperon intergenic regions are usually devoid of transcription. Hence these two types of intergenic regions (IGRs) can be compared to find out the contribution of replication-associated mutations (RAM) and transcription-associated mutations (TrAM) towards bringing variation in genomes. In our work, we performed a polymorphism spectra comparison between intraoperon IGRs and interoperon IGRs in genomes of two well-known closely related bacteria such as Escherichia coli and Salmonella enterica. In general, the size of intraoperon IGRs was smaller than that of interoperon IGRs in E. coli and S. enterica. Interestingly, the polymorphism frequency at intraoperon IGRs was 2.5-fold lesser than that in the interoperon IGRs in E. coli genome. Similarly, the polymorphism frequency at intraoperon IGRs was 2.8-fold lesser than that in the inter-operon IGRs in S. enterica genome. Therefore, the intraoperon IGRs were often observed to be more conserved. In the case of interoperon IGRs, the T→C transition frequency was a minimum of two times more frequent than T→A transversion frequency whereas in the case of intraoperon IGRs, T→C transition frequency was similar to that of T→A transversion frequency. The polymorphism was purine-biased and keto-biased more in intraoperon IGRs than the inter-operon IGRs. In E. coli, the transition/transversion ratio was observed as 1.639 and 1.338 in inter-operon and in intraoperon IGRs, respectively. In S. enterica, the transition/transversion ratio was observed as 2.134 and 2.780 in inter-operon and in intraoperon IGRs, respectively. The observation in this study indicates that transcribable IGRs might not always have higher polymorphism frequency than nontranscribable IGRs. The lower polymorphism frequency at intraoperon IGRs might be attributed to different events such as the transcription-coupled DNA repair, sequences facilitating translation initiation and avoidance of Rho-dependent transcription termination.