Insights from the architecture of the bacterial transcription apparatus

Abstract

We provide a portrait of the bacterial transcription apparatus in light of the data emerging from structural studies, sequence analysis and comparative genomics to bring out important but underappreciated features. We first describe the key structural highlights and evolutionary implications emerging from comparison of the cellular RNA polymerase subunits with the RNA-dependent RNA polymerase involved in RNAi in eukaryotes and their homologs from newly identified bacterial selfish elements. We describe some previously unnoticed domains and the possible evolutionary stages leading to the RNA polymerases of extant life forms. We then 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. We also present a synopsis of the structural and architectural taxonomy of specific transcription factors and their genome-scale demography. In this context, we present certain notable deviations from the otherwise invariant prote-ome-wide trends in transcription factor distribution and use it to predict the presence of an unusual lineage-specifically expanded signaling system in certain firmicutes like Paenibacillus. We then discuss the intersection between functional properties of transcription factors and the organization of transcriptional networks. Finally, we present some of the interesting evolutionary conundrums posed by our newly gained understanding of the bacterial transcription apparatus and potential areas for future explorations.

TheCryptosporidium parvumApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems

“…Evidence of retrotransposable elements has been reported in another early branch of the Apicomplexa, the gregarines (28), and there is evidence that apicomplexan genomes which lack mobile elements used to contain them (29,30), or contain inactive elements as is the case in the apicomplexan coccidian parasite Eimeria tenella (31). More recently, non-integrase-associated bacterial AP2 proteins with architectures similar to AP2 proteins found in plants and alveolates have been reported (32). These AP2 proteins are also predicted to function as novel, specific transcription factors.…”

Computational analysis of 1,3-propanediol operon transcriptional regulators: Insights into Clostridium sp. glycerol metabolism regulation

“…The presence of the G-hydrophobic residue in the smallresidue triad could be observed in the HTH DNAbinding domain , located in the α4/α5 loop (G-349, F-350, S-351); comparable, to the canonical hydrophobic residues in α3 (L-334) and α5 (F-356) (Figure 1-c). DNA binding motifs, from the HTH domain, were organized to facilitate DNAprotein interface binding to α3 residues (recognition helix) and the presence of hydrophobic residues in α1 and α3, stabilizing the domain (Iyer & Aravind 2012). It was also confirmed that these domains presented a tetra-helicoidal conformation, characterized by an additional C-terminal helix .…”

The Old and New Testaments of gene regulation

“…For DDRPs, the β subunit type DPBB was invaded by a SBHM that became the interaction surface for initiation and elongation factors (Fig. 3) required for use of a DNA template 4 , 6 . In this way, DDRPs evolved from RDRPs, prior to LUCA.…”

“…Eubacteria, by contrast, because their gene regulatory networks are focused on the DNA interactome (Fig. 8B) 6 and mostly lack additional dimensions, have much simpler signal transduction mechanisms. The surprising similarities comparing the eukaryotic RNAP II transcription cycle and the eukaryotic cell cycle indicate that these processes are co-evolved 32 .…”