Cryo-EM studies of antibiotic resistance and RNA modification in bacterial ribosomes
The ribosome is the large RNA-protein complex (the E. coli ribosome is 2.7 MDa) that polymerizes amino acids based on the genetic information in mRNAs. Bacterial ribosomes are structurally distinct from the human ribosome and are therefore good drug targets for antibiotics. We study the assembly and maturation processes of the bacterial ribosome and how antibiotics inhibit critical steps in the elongation cycle using biochemical and structural methods. One project aims to clarify molecular mechanisms of resistance to the antibiotic fusidic acid (FA) in Staphylococcus aureus. FA binds to elongation factor G (EF-G) on the ribosome and blocks its release, causing ribosome stalling. By expressing a resistance protein that can release EF-G, the ribosome can be rescued from this locked state. In another project, we study how ribosomal RNA is modified by methyltransferase enzymes involved in ribosome biogenesis and antibiotic resistance. These specifically recognize their target nucleotides and catalyze the transfer of a methyl group. We are interested in how these enzymes recognize short-lived pre-ribosomal particles during ribosome biogenesis and how the resulting methylations influences the structure, stability and function of the local RNA region as well as the mature ribosome. Both ribosome projects require extensive sorting of particles to obtain structures of rare states that help us understand detailed molecular mechanisms. In this proposal, we wish to use Berzelius for processing large cryo-EM data sets of ribosomal complexes using advanced AI and statistical methods.