Class II UvrA protein Ecm16 requires ATPase activity to render resistance against echinomycin

Abstract

II.SummaryBacteria use various strategies to become antibiotic resistant. The molecular details of these strategies are not fully understood. We can increase our understanding by investigating the same strategies found in antibiotic-producing bacteria. In this work, we characterize the self-resistance protein Ecm16 encoded by echinomycin-producing bacteria. Ecm16 is a structural homolog of the Nucleotide Excision Repair (NER) protein UvrA. Expression of ecm16 in the heterologous system Escherichia coli was sufficient to render resistance against echinomycin. Ecm16 preferentially binds double-stranded DNA over single-stranded DNA and is likely to primarily interact with the backbone of DNA using a nucleotide-independent binding mode. Ecm16’s binding affinity for DNA increased significantly when the DNA is intercalated with echinomycin. Ecm16 can repair echinomycin-induced DNA damage independently of NER. Like UvrA, Ecm16 has ATPase activity and this activity is essential for Ecm16’s ability to render echinomycin resistance. Notably, UvrA and Ecm16 were unable to complement each other’s function. Increasing the cellular levels of UvrA in E. coli was insufficient to render echinomycin resistance. Similarly, Ecm16 was unable to repair DNA damage that is specific to UvrA. Together, our findings identify new mechanistic details of how a refurbished DNA repair protein Ecm16 can specifically render resistance to the DNA intercalator echinomycin. Our results, together with past observations, suggest a model where Ecm16 recognizes double helix distortions caused by echinomycin and repairs the problem independently of NER.