The Bacterial Transcription Apparatus
L. Aravind and Lakshminarayan M. Iyer
from: Bacterial Gene Regulation and Transcriptional Networks (Edited by: M. Madan Babu). Caister Academic Press, U.K. (2013)
We provide a portrait of the bacterial transcription apparatus in light of recent structural studies, sequence analysis and comparative genomics to bring out several key underappreciated features. Comparisons of cellular RNA polymerase subunits with the RNA-dependent RNA polymerase involved in RNAi in eukaryotes and their homologs from newly identified bacterial selfish elements have helped in the identification of novel domains and the possible evolutionary stages leading to the RNA polymerases of extant life forms. We present the case for the ancient orthology of the basal transcription factors, the sigma factor and TFIIB, in the bacterial and the archaeo-eukaryotic lineages. Further, we furnish a synopsis of the structural and architectural taxonomy of specific transcription factors and their genome-scale demography. Although the proteome-wide trends in transcription factor distribution are generally invariant, there are certain notable deviations in firmicutes like Paenibacillus and Geobacillus due to unusual lineage-specifically expanded two-component signaling systems that might have a special biological significance. We then discuss the intersection between functional properties of transcription factors and the organization of transcriptional networks. Finally, we bring attention to some puzzling questions raised by our new understanding of the bacterial transcription apparatus and potential areas for future explorations read more ...