Structural basis of Rifampin resistance in bacterial RNA polymerase (939.1)

Abstract

For over four decades, Rifampin (Rif), a semi‐synthetic derivative of Rifamycin, has been used as a first line antibiotic treatment of tuberculosis and is the cornerstone of current short‐term tuberculosis treatment. The mode of action involves tight Rif binding to a beta subunit of bacterial RNA polymerase (RNAP) to inhibit RNA transcription. Although many Rif resistant (RifR) strains with mutations in the Rif‐binding pocket can be isolated in bacterial culture, only three specific RifR mutations account for over 80 % of Mycobacterium tuberculosis (MTB) RifR strains in clinical isolates due to RifR associated fitness costs.In this study, we have determined the X‐ray crystal structures of the E. coli RNAP RifR mutants each having one of three major RifR mutations found in clinical isolates. Each RifR RNAP structure shows a unique conformation of the Rif binding pocket and their structural deviations from the wild‐type Rif binding pocket are consistent with their Rif resistances suggesting that the RifR results from alternating the shape complementary between the Rif binding pocket and Rif rather than disrupting their hydrophilic and hydrophobic interactions. This study provides an important step for understanding the structure−activity relationship of Rif against RifR RNAP inhibition and toward developing superior Rif analogues against RifR MTB.Grant Funding Source: Supported by NIH