Complementary tendencies in the use of regulatory elements (Transcription factors, sigma factors, and riboswitches) in bacteria and archaea

In prokaryotes, the key players in transcription initiation are sigma factors and transcription factors that bind to DNA to modulate the process, while premature transcription termination at the 5′ end of the genes is regulated by attenuation and, in particular, by attenuation associated with riboswitches. In this study, we describe the distribution of these regulators across phylogenetic groups of bacteria and archaea and find that their abundance not only depends on the genome size, as previously described, but also varies according to the phylogeny of the organism. Furthermore, we observed a tendency for organisms to compensate for the low frequencies of a particular type of regulatory element (i.e., transcription factors) with a high frequency of other types of regulatory elements (i.e., sigma factors). This study provides a comprehensive description of the more abundant COG, KEGG, and Rfam families of transcriptional regulators present in prokaryotic genomes.We acknowledge the Programa de Maestría y Doctorado en Ciencias Bioquímicas at the Instituto de Biotecnología-UNAM and the Consejo Nacional de Ciencia y Tecnología (CONACyT) for the Ph.D. scholarship, number 565669, awarded to J.C