Investigators Figure Out How Methylating Protein Makes S. aureus Antibiotic Resistant

Methylation carried out by evolved cfr protein was found to block binding of antibiotics to bacterial ribosome.

Researchers may have identified how a bacterial ribosome methylating protein present in certain strains of Staphylococcus aureus renders the pathogen resistant to seven classes of antibiotics. The work, by scientists from Northwestern University in Evanston, IL, and Pennsylvania State University, is published in the early online edition of Science. The paper is titled “Structural Basis for Methyl Transfer by a Radical SAM Enzyme.”

The work by Penn State associate professor Squire Booker, Ph.D., and colleagues, is founded on the discovery a number of years ago that a nonhuman Staphylococcus pathogen, S. sciuri, had evolved a new nucleic acid methylating gene, cfr, which effectively rendered the bacterium resistant to antibiotics. This same cfr gene was subsequently found to have crossed over into pathogenic human strains of S. aureus, and these bacteria were also resistant to a number of antibiotics that target the large subunit of the bacterial ribosome.

The researchers have now looked more closely at how the cfr protein catalyzes methylation of a bacterial 23S rRNA nucleotide in comparison with organism’s native methylating protein, rlmN. Both rlmN and cfr belong to the radical SAM (RS) superfamily of enzymes.

What they have found through this work and previous research published in Science earlier this month, is that while the two proteins catalyze methylation of adenosine A2503 on the ribosomal RNA, rlmN methylates the C2 position of A2503, whereas cfr, which is evolutionarily related to rlmN, catalyzes a similar modification at C8 of A2503. It is this modification that confers drug resistance, because it prevents the antibiotic from binding to the ribosome.

“What had perplexed scientist is that the locations to which RlmN and Cfr add molecular tags are chemically different from all others to which tags routinely are appended and should be resistant to modification by standard chemical methods,” Dr. Booker explains. “What we’ve discovered here is so exciting because it represents a truly new chemical mechanism for methylation. We now have a very clear chemical picture of a very clever mechanism for antibiotic resistance that some bacteria have evolved.”