Helicobacter pylori RNA polymerase α‐subunit C‐terminal domain shows features unique to ɛ‐proteobacteria and binds NikR/DNA complexes

Abstract

Bacterial RNA polymerase is a large, multi-subunit enzyme responsible for transcription of genomic information. The C-terminal domain of the a subunit of RNA polymerase (aCTD) functions as a DNA and protein recognition element localizing the polymerase on certain promoter sequences and is essential in all bacteria. Although aCTD is part of RNA polymerase, it is thought to have once been a separate transcription factor, and its primary role is the recruitment of RNA polymerase to various promoters. Despite the conservation of the subunits of RNA polymerase among bacteria, the mechanisms of regulation of transcription vary significantly. We have determined the tertiary structure of Helicobacter pylori aCTD. It is larger than other structurally determined aCTDs due to an extra, highly amphipathic helix near the C-terminal end. Residues within this helix are highly conserved among E-proteobacteria. The surface of the domain that binds A/T rich DNA sequences is conserved and showed binding to DNA similar to aCTDs of other bacteria. Using several NikR dependent promoter sequences, we observed cooperative binding of H. pylori aCTD to NikR:DNA complexes. We also produced aCTD lacking the 19 C-terminal residues, which showed greatly decreased stability, but maintained the core domain structure and binding affinity to NikR:DNA at low temperatures. The modeling of H. pylori aCTD into the context of transcriptional complexes suggests that the additional amphipathic helix mediates interactions with transcriptional regulators.

Comprehensive mapping of the Helicobacter pylori NikR regulon provides new insights in bacterial nickel responses

“…In fact, the evidence that the unique NikR binding site upstream of the urease promoter is clearly associated with nickel-responsive repression of the divergent Nrr2 transcript, poses the question whether NikR binding to this operator also directly activates the ure promoter. A recent study suggested that NikR has acquired a RNA polymerase (RNAP) interacting domain50 and could therefore act as transcriptional activator. In this scenario, it is surprising to notice that upon the acquisition of a RNAP interacting domain a key transcription factor like NikR is engaged in the control of only one (urease) operon.…”

Plumbagin Inhibits Expression of Virulence Factors and Growth of Helicobacter pylori

“…RNA polymerase is an indispensible protein responsible for transcription of DNA into RNA. Bacterial RNA polymerase consists of α, β and ω subunits (α2ββ'ω) [1]. β and β' are the largest subunits of bacterial RNA polymerase possessing catalytic site, and β and β' subunits in H. pylori exist as a single fused protein [1,5].…”

“…Bacterial RNA polymerase consists of α, β and ω subunits (α2ββ'ω) [1]. β and β' are the largest subunits of bacterial RNA polymerase possessing catalytic site, and β and β' subunits in H. pylori exist as a single fused protein [1,5]. α subunit binds to β and β' subunits and stabilizes the complex, and ω subunit has both structural and functional role [1,20].…”

“…β and β' are the largest subunits of bacterial RNA polymerase possessing catalytic site, and β and β' subunits in H. pylori exist as a single fused protein [1,5]. α subunit binds to β and β' subunits and stabilizes the complex, and ω subunit has both structural and functional role [1,20]. In addition, there are σ factors which binds to core complex and facilitate promoter specific initiation of transcription [1,28].…”

“…α subunit binds to β and β' subunits and stabilizes the complex, and ω subunit has both structural and functional role [1,20]. In addition, there are σ factors which binds to core complex and facilitate promoter specific initiation of transcription [1,28].…”