Evolutionary divergence of drug-binding residues in bacterial ribosomes

Drugs that target bacterial ribosomes are widely used in modern medicine and veterinary practice to treat bacterial infections and prevent the spread of antimicrobial resistance. However, most studies on targeting ribosomes with drugs are limited to just a few model organisms. Consequently, we do not know whether the ribosomal drug-binding sites observed in model bacteria are as highly conserved across bacteria as is currently implied. In this study, we address this question using a simple but powerful computational pipeline that filters out rare variants and sequencing errors to identify conserved changes at ribosomal drug-binding sites across the bacterial tree of life. This allows us to assess the conservation of 82 individual drug-binding residues of bacterial ribosomes from 8,809 bacterial species. For each of these residues, we trace its evolution throughout >4 billion years of bacterial history. Contrary to the common belief in the high conservation of ribosomal drug-binding residues, we find extensive variation among bacterial phyla at drug-binding sites. Furthermore, we show that approximately 10% of bacterial species bear ribosomal RNA (rRNA) substitutions that were previously observed only in clinical isolates of drug-resistant bacteria. Overall, our work illustrates that our traditional division of ribosomes into bacterial and eukaryotic types is oversimplistic and misleading, as it overlooks widespread lineage-specific variations that make the drug-binding sites of some bacteria more dissimilar to Escherichia coli than E. coli is to humans. These findings will have numerous implications for the lineage-specific use of ribosome-targeting antibiotics that are currently viewed as universal inhibitors of bacterial protein synthesis.