Context-specific action of antibiotics targeting the catalytic center of the bacterial ribosome

  • Mankin, Alexander, (PI)

Research project


Antibiotics that inhibit cell growth by interfering with protein synthesis have been among the mostclinically successful antibacterials. In spite of the importance of these inhibitors, there are significant gaps inour understanding of the most fundamental principles of their action. Many of the protein synthesis inhibitors,from the classic chloramphenicol (CHL) to the newer linezolid (LZD), bind at the catalytic peptidyl transferasecenter (PTC) of the ribosome, where they clash with the placement of aminoacyl-tRNA. Because of thelocation of their binding site, it is commonly assumed that they inhibit translation by interfering with formation ofevery peptide bond, either at the start codon or at any of the internal codons of a gene. However, ourpreliminary data show that this view is principally incorrect. Instead of indiscriminately inhibiting peptide bondformation, CHL and LZD stall elongation of translation only at specific mRNA sites. The nature of the nascentpeptide chain appears to play the major role in specifying the sites of translation arrest, but the general rulesthat define the sites of stalling and the molecular mechanisms that underlie this effect remain unknown. Therefore, the main goal of this project is to gain a detailed understanding of the context specific actionof PTC-targeting antibiotics. The study will primarily focus on LZD and CHL. LZD is the first and most broadlymedically used oxazolidinone. CHL is one of the oldest known ribosomal antibiotics. In spite of its reducedmedical importance, inclusion of CHL in the study is crucial, not only because of the vast amount of informationavailable for this inhibitor, but also to contrast its context specific action with that of LZD and correlate theeffects with individual structural properties of the drugs. In Specific Aim 1, whole-cell ribosome profiling and quantitative biochemical testing will be used toidentify the detailed requirements for the sequence context that defines the preferred sites of inhibition oftranslation by LZD or CHL. In Specific Aim 2, an array of biochemical, structural and genetic approaches willbe employed to understand the molecular mechanisms that account for the context-specific action of the PTC-targeting inhibitors. The use of innovative techniques, such as single molecule FRET or an engineeredtethered ribosome, are expected to provide principally new insights into the most fundamental aspects ofaction of the inhibitors of the ribosomal catalytic center. Specific Aim 3 will address a conceptually importantand medically-relevant question, whether context specificity of drug action results into protein-specific inhibitionof translation by the PTC-targeting antibiotics. The anticipated findings should significantly expand the understanding of the general mode of action ofclinically-important antibacterials that act upon the catalytic center of the ribosome and may open new venuesfor rational development of protein synthesis inhibitors with superior antibiotic properties.
Effective start/end date8/15/167/31/20


Cell growth
Binding sites
Structural properties