Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme

Vanja Stojković, Lianet Noda-Garcia, Dan S. Tawfik, Danica Galonić Fujimori, Vanja Stojkovic, Danica Galonic Fujimori

Research output: Contribution to journalArticlepeer-review

Abstract

Modifications of the bacterial ribosome regulate the function of the ribosome and modulate its susceptibility to antibiotics. By modifying a highly conserved adenosine A2503 in 23S rRNA, methylating enzyme Cfr confers resistance to a range of ribosome-targeting antibiotics. The same adenosine is also methylated by RlmN, an enzyme widely distributed among bacteria. While RlmN modifies C2, Cfr modifies the C8 position of A2503. Shared nucleotide substrate and phylogenetic relationship between RlmN and Cfr prompted us to investigate evolutionary origin of antibiotic resistance in this enzyme family. Using directed evolution of RlmN under antibiotic selection, we obtained RlmN variants that mediate low-level resistance. Surprisingly, these variants confer resistance not through the Cfr-like C8 methylation, but via inhibition of the endogenous RlmN C2 methylation of A2503. Detection of RlmN inactivating mutations in clinical resistance isolates suggests that the mechanism used by the in vitro evolved variants is also relevant in a clinical setting. Additionally, as indicated by a phylogenetic analysis, it appears that Cfr did not diverge from the RlmN family but from another distinct family of predicted radical SAM methylating enzymes whose function remains unknown.

Original languageEnglish
Pages (from-to)8897-8907
Number of pages11
JournalNucleic acids research
Volume44
Issue number18
Early online date5 Aug 2016
DOIs
StatePublished - 14 Oct 2016

All Science Journal Classification (ASJC) codes

  • Genetics

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