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Title: CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition

Journal Article · · Proceedings of the National Academy of Sciences of the United States of America
 [1];  [2];  [2];  [3];  [2];  [1]
  1. Rockefeller Univ., New York, NY (United States)
  2. Univ. of Wisconsin, Madison, WI (United States)
  3. New Jersey Medical School, Newark, NJ (United States)
+ Show Author Affiliations

RNA polymerase inhibitors like the CBR class that target the enzyme’s complex catalytic center are attractive leads for new antimicrobials. The catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound NTP and two Mg2+ ions from a preinsertion state to a reactive configuration. CBR inhibitors target a crevice between the N-terminal portion of the bridge helix and a surrounding cap region within which the bridge helix is thought to rearrange during the nucleotide addition cycle. Here, we report crystal structures of CBR inhibitor/Escherichia coli RNA polymerase complexes as well as biochemical tests that establish two distinct effects of the inhibitors on the RNA polymerase catalytic site. One effect involves inhibition of trigger-loop folding via the F loop in the cap, which affects both nucleotide addition and hydrolysis of 3'-terminal dinucleotides in certain backtracked complexes. The second effect is trigger-loop independent, affects only nucleotide addition and pyrophosphorolysis, and may involve inhibition of bridge-helix movements that facilitate reactive triphosphate alignment.

Research Organization:
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
SC00112704
OSTI ID:
1228943
Report Number(s):
BNL-111018-2015-JA
Journal Information:
Proceedings of the National Academy of Sciences of the United States of America, Vol. 112, Issue 31; ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 25 works
Citation information provided by
Web of Science

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Cited By (8)

Discovery, properties, and biosynthesis of pseudouridimycin, an antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase journal November 2018
The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage journal April 2018
Mechanisms of antibiotics inhibiting bacterial RNA polymerase journal January 2019
Oxazinomycin arrests RNA polymerase at the polythymidine sequences journal September 2019
Closing and opening of the RNA polymerase trigger loop posted_content October 2019
Closing and opening of the RNA polymerase trigger loop journal June 2020
Insights into RNA polymerase catalysis and adaptive evolution gained from mutational analysis of a locus conferring rifampicin resistance journal September 2017
Bacterial RNA Polymerase-DNA Interaction—The Driving Force of Gene Expression and the Target for Drug Action journal November 2016

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