Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes

Abstract

Riboswitches are regulatory RNA that control gene expression by undergoing conformational changes on ligand binding. Using phylogenetic analysis and comparative genomics we have been able to identify the class of genes/operons regulated by the purine riboswitch and obtain a high-resolution map of purine riboswitch distribution across all bacterial groups. In the process, we are able to explain the absence of purine riboswitches upstream to specific genes in certain genomes. We also identify the point of origin of various purine riboswitches and argue that not all purine riboswitches are of primordial origin, and that some purine riboswitches must have originated after the divergence of certain Firmicute orders in the course of evolution. Our study also reveals the role of horizontal transfer events in accounting for the presence of purine riboswitches in some gammaproteobacterial species. Our work provides significant insights into the origin, distribution and regulatory role of purine riboswitches in prokaryotes.