A Specialized Polythioamide‐Binding Protein Confers Antibiotic Self‐Resistance in Anaerobic Bacteria

Abstract

Understanding antibiotic resistance mechanisms is central to the development of anti‐infective therapies and genomics‐based drug discovery. Yet, many knowledge gaps remain regarding the resistance strategies employed against novel types of antibiotics from less‐explored producers such as anaerobic bacteria, among them the Clostridia. Through the use of genome editing and functional assays, we found that CtaZ confers self‐resistance against the copper chelator and gyrase inhibitor closthioamide (CTA) in Ruminiclostridium cellulolyticum. Bioinformatics, biochemical analyses, and X‐ray crystallography revealed CtaZ as a founding member of a new group of GyrI‐like proteins. CtaZ is unique in binding a polythioamide scaffold in a ligand‐optimized hydrophobic pocket, thereby confining CTA. By genome mining using CtaZ as a handle, we discovered previously overlooked homologs encoded by diverse members of the phylum Firmicutes, including many pathogens. In addition to characterizing both a new role for a GyrI‐like domain in self‐resistance and unprecedented thioamide binding, this work aids in uncovering related drug‐resistance mechanisms.

Naturally Occurring and Widespread Resistance to Bioactive Natural Products

“…[14] Recently, a GyrI-like protein encoding gene ctaZ from the biosynthetic gene cluster of CTA was identified as the self-resistance gene of R. cellulolyticum to CTA. [15] CtaZ confers self-resistance to CTA producer by binding CTA, preventing its interaction with the gyrase of CTA producer. Surprisingly, only 2 % of the CtaZ homologs found in loci similar to the CTA BGC.…”

“…Most CtaZ homologs are found to be in loci that don't resemble typical BGCs, which means CtaZ homologs are prevalent in CTA nonproducers including many pathogenic Firmicutes. [15] The naturally wide spread of CtaZ homologs in environmental microbes indicates a co-evolutionary relationship between CTA producers and non-producers, that is, the CTA non-producers evolved the corresponding resistance gene for the fitness of the interacting CTA producers. Resistance in antibiotic producers provides map for the evolution of resistance in antibiotic non-producers.…”

“…CTA is considered as a promising drug candidate since bacteria that are resistant to other DNA gyrase inhibitors are susceptible to CTA [14] . Recently, a GyrI‐like protein encoding gene ctaZ from the biosynthetic gene cluster of CTA was identified as the self‐resistance gene of R. cellulolyticum to CTA [15] . CtaZ confers self‐resistance to CTA producer by binding CTA, preventing its interaction with the gyrase of CTA producer.…”