Structural Perspective on Mutations Affecting the Function of Multisubunit RNA Polymerases

Abstract

SUMMARY High-resolution crystallographic structures of multisubunit RNA polymerases (RNAPs) have increased our understanding of transcriptional mechanisms. Based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit RNA polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and eukaryotic enzymes. The observations support many previous hypotheses on the transcriptional process, including the implication of the bridge helix and the trigger loop in the processivity of RNAP, the importance of contacts between the RNAP jaw-lobe module and the downstream DNA in the establishment of a transcription bubble and selection of the transcription start site, the destabilizing effects of ppGpp on the open promoter complex, and the link between RNAP processivity and termination. This study also revealed novel, remarkable features of the RNA polymerase catalytic mechanisms that will require additional investigation, including the putative roles of fork loop 2 in the establishment of a transcription bubble, the trigger loop in start site selection, and the uncharacterized funnel domain in RNAP processivity.

Search for Proteins Required for Accurate Gene Expression under Oxidative Stress

“…The molecular sizes and the gross structures of the enzymes from prokaryotes and eukaryotes are essentially similar, and the critical amino acid substitution site found in the E. coli enzyme in the present study is also located near the active site of the mammalian enzyme (41,42). For the RNA polymerase, mammalian cells possess three distinct classes of enzymes, RNA polymerase I, II, and III (25,43). Among them, RNA polymerase II, which is responsible for the synthesis of most of messenger RNAs, is structurally similar to the E. coli RNA polymerase.…”

Mutational neighbourhood and mutation supply rate constrain adaptation inPseudomonas aeruginosa

“…Rifampicin works by binding to a conserved domain of the b-subunit of RNA polymerase (RNAP), thereby blocking elongation of the RNA transcript (Severinov et al 1993;Campbell et al 2001). Resistance can result from any of several possible mutations on the rpoB gene that change the structure of RNAP and prevent binding (Telenti et al 1993;Pozzi et al 1999;Campbell et al 2001;Trinh et al 2006). Rif R mutations often incur a fitness cost in terms of reduced growth rate and the magnitude of the cost varies among different mutations for P. aeruginosa (MacLean & Buckling 2009).…”

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

“…Mismatched NTPs are proposed to be destabilizing, so that the trigger loop does not achieve the closed conformation that allows it to trigger catalysis. Mutation of the trigger loop in both eukaryotic pol II and the closely related bacterial enzyme RNAP alters the elongation behavior of the enzyme (11)(12)(13)(14)(15). However, mutation does not always render the enzyme inactive, even upon deletion of the entire trigger loop (12,16).…”