Ekemezie, C. L. | bioRxiv Science

bioRxiv2024

Natural variation of the drug-binding residues in eukaryotic ribosomes

Drugs that target eukaryotic ribosomes are becoming increasingly important as research tools and potential therapies against cancer and pathogenic eukaryotes. However, in the absence of comparative studies, we currently do not know how many eukaryotes possess ribosomal drug-binding sites identical to those in humans, and how many significantly differ from humans. To address this, we traced the evolutionary history of individual ribosomal drug-binding residues from the emergence of eukaryotes to the present day. We found that ribosomal drug-binding sites are divergent across eukaryotic clades, with some of the clades exhibiting more substitutions in their ribosomal drug-binding sites compared to humans than humans do compared to bacteria. Overall, our work provides a resource for understanding the evolutionary divergence of drug-binding sites in eukaryotic ribosomes, which may inform the use of ribosome inhibitors as research tools and lineage-specific drugs against eukaryotic parasites.

microbiology↗

bioRxiv2024

Evolutionary divergence of drug-binding sites in bacterial ribosomes

Ribosomes from certain bacteria possess divergent drug-binding sites compared to those of Escherichia coli, leading to natural evasion or hypersensitivity to antibiotics. However, in the absence of systematic studies, it is unknown whether this observed divergence is a rare exception or a common occurrence among bacterial species. Here, we address this question by reconstructing the evolutionary history of drug-binding residues of the ribosome from the origin of bacteria to the present day. This analysis reveals the extent of natural diversity of ribosomal drug-binding sites between bacterial species, which may inform the development of species-specific antimicrobials and a more accurate and personalized choice of ribosome-targeting drugs for a given pathogen.

microbiology↗

bioRxiv2022

Structure of dormant bacterial ribosomes reveals an elusive translation factor with evolutionary connections to eukaryotic protein synthesis factors

During starvation and stress, virtually all organisms arrest protein synthesis to conserve energy. Inactive ribosomes are converted into a dormant state, in which they are protected from damage by hibernation factor proteins. In bacteria, two major families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats, and environmental stressors has confounded their discovery. In this study, using proteomics and cryo-EM, we identify a new dormancy factor from the psychrophilic bacterium Psychrobacter urativorans. By isolating ribosomes under cold-shock conditions, we observe a previously unknown protein bound to the ribosomal A site, protecting critical elements of both the decoding and peptidyl transferase centers. We show that this new factor, which we term Balon, is a homolog of the archaeo-eukaryotic translation factor aeRF1, providing a long-predicted evolutionary "missing link" between the eukaryotic and bacterial translation machinery. Our structures reveal that Balon is delivered to both vacant and actively translating ribosomes by EF-Tu, highlighting an unexpected and previously unknown role for this elongation factor in the bacterial stress response. We describe several unique structural motifs that allow Balon to bind ribosomes in an mRNA-independent manner, initiating a new mode of ribosome dormancy that can commence while ribosomes are still engaged in protein synthesis. Our bioinformatic analysis shows that putative Balon-encoding genes can be found within stress-response operons in nearly 20 % of all known bacterial species, including many human pathogens. Taken together, our work suggests that Balon/EF-Tu regulated ribosome dormancy is likely to be a ubiquitous stress-response mechanism throughout the bacterial kingdom. These findings call for a revision of our model of bacterial translation inferred from common model organisms and hold numerous implications for how we understand and study ribosome dormancy.

molecular biology↗