Echinomycin is a natural product DNA bisintercalator antibiotic. The echinomycin biosynthetic gene cluster in Streptomyces lasalocidi includes a gene encoding the self-resistance protein Ecm16. Here, we present the 2.0 Å resolution crystal structure of Ecm16 bound to adenosine diphosphate. The structure of Ecm16 closely resembles that of UvrA, the DNA damage sensor component of the prokaryotic nucleotide excision repair system, but Ecm16 lacks the UvrB-binding domain and its associated zinc-binding module found in UvrA. Mutagenesis study revealed that the insertion domain of Ecm16 is required for DNA binding. Furthermore, the specific amino acid sequence of the insertion domain allows Ecm16 to distinguish echinomycin-bound DNA from normal DNA and link substrate binding to ATP hydrolysis activity. Expression of ecm16 in the heterologous host Brevibacillus choshinensis conferred resistance against echinomycin and other quinomycin antibiotics, including thiocoraline, quinaldopeptin, and sandramycin. Our study provides new insight into how the producers of DNA bisintercalator antibiotics fend off the toxic compounds that they produce.

Echinomycin is a nonribosomal peptide antibiotic that acts by intercalating double‐stranded DNA. The echinomycin biosynthetic gene cluster of Streptomyces lasaliensis contains a gene of unverified function, ecm16. We show that expression of Ecm16 in the echinomycin‐sensitive E. coli K12 renders cells resistant to echinomycin. Additionally, we have determined the X‐ray crystal structure of Ecm16 at 2.0 Å resolution. Interestingly, the three‐dimensional structure of Ecm16 resembles that of UvrA, the DNA damage sensor protein from the prokaryotic nucleotide excision repair pathway. Ecm16, like UvrA, contains two nucleotide binding domains on a single polypeptide chain, and it can bind double‐stranded DNA. However, our results show that neither UvrA nor Ecm16 can complement each other's function in vivo.

Bacteria 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.

Echinomycin is a nonribosomal peptide antibiotic that acts by intercalating double‐stranded DNA. The echinomycin biosynthetic gene cluster of Streptomyces lasaliensis contains a gene of unverified function, ecm16. We show that expression of Ecm16 in the echinomycin‐sensitive E. coli K12 renders cells resistant to echinomycin. Additionally, we have determined the X‐ray crystal structure of Ecm16 at 2.0 Å resolution. Interestingly, the three‐dimensional structure of Ecm16 resembles that of UvrA, the DNA damage sensor protein from the prokaryotic nucleotide excision repair pathway. Ecm16, like UvrA, contains two nucleotide binding domains on a single polypeptide chain, and it can bind double‐stranded DNA. However, our results show that neither UvrA nor Ecm16 can complement each other’s function in vivo. Support or Funding Information The University of Texas System STARs Award