IDENTIFICATION OF FACTORS THAT PREVENT RIBOSOME STALLING IN BACILLUS SUBTILIS AND BACILLUS ANTHRACIS
The quality control of ribosomes is required for the rapid growth of bacteria and adaptation to their environment. During translation elongation, the ribosome is arrested when it encounters poly-proline tracts because the geometry of poly-proline blocks the exit tunnel of the ribosome. Elongation Factor P (EF-P) rescues ribosomes stalled at poly-proline tracts. EF-P recognizes a stalled P-site tRNA and empty E-site, binding to the E-site and interacting with the proline anti-codon of the P-site tRNA. This interaction promotes rapid peptide bond formation and stabilizes the peptidyl-tRNA in the catalytic center of the ribosome. EF-P is highly conserved across all three domains of life, and phenotypes associated with efp deletion range from modest in Escherichia coli to lethal in clinically important pathogens like Mycobacterium tuberculosis and Acinetobacter baumannii. In this study, Bacillus anthracis shows severe sporulation and growth defects when EF-P is deleted, whereas the mutant Bacillus subtilis grows at almost the same rate as the wild-type strain, and sporulation is somewhat delayed. This variability in phenotypes suggests that B. subtilis may have an alternative pathway for preventing stalls at poly-prolines. To identify proteins that may have redundant function with EF-P, we used Tn-seq to identify genes that are essential in the absence of efp. This screen identified a new translation factor, YfmR, and a factor that is associated with translation, YeeI. Here, I present the discovery and characterization of two new factors, YfmR and YeeI, as functional substitutes of EF-P in two gram-positive Bacilli, B. anthracis, and B. subtilis. In chapter 2 and 3, we found that both YfmR and YeeI associate with ribosomes and contribute to polyproline-induced stalling in translation elongation. This work expands the understanding of the mechanism of translation factors in relation to the previously known factor EF-P in ribosome stalling and provides information for ongoing investigations into the complexity of translation.