The Structural Dynamics of Translation Initiation

Columbia Univ New York Morningside, New York NY

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Abstract

DESCRIPTION (provided by applicant): The emergence of bacterial superbugs with resistance to even the most powerful antibiotics currently available poses a serious threat to human health and demands the development of new antibiotics. Approximately half of all clinically used antibiotics target the process of protein synthesis in bacteria. Protein synthesis s an essential cellular process whereby messenger RNA (mRNA) copies of the genes encoded by an organism's DNA genome are translated into their corresponding protein products by the cellular translational machinery (TM). Antibiotics that specifically target bacterial protein synthesis do so by exploiting subtle differences between the bacterial and eukaryotic TMs. The ultimate goal of this proposal is to inform antibiotic development efforts through the identificatin of new antibiotic targets within the bacterial TM. Herein, we focus on the initiation phase of translation, the step of the protein synthesis pathway where bacteria and eukaryotes differ the most. Translation initiation is a dynamic, multi-step process that, in bacteria, begins with the formation of a 30S initiation complex (30S IC) comprised of the small 30S ribosomal subunit, the mRNA to be translated, an initiator formylmethionyl-transfer RNA (tRNA), and three initiation factors (IFs). Subsequently, the large 50S ribosomal subunit joins to the 30S IC to form a functional 70S initiation complex. Subunit joining is an essential feature of this process and bacterial-specific aspects of subunit joining consequently represent viable antibiotic targets. In this proposal, we will use a combination of molecular biological, single-molecule biophysical, biochemical, and structural strategies to investigate three poorly understood aspects of the subunit joining reaction: In Aim 1, we will investigate how the conformational dynamics of the 30S IC-bound IFs drive and regulate subunit joining; In Aim 2, we will examine how structural rearrangements of the 30S subunit and associated changes in the positions of IF- and tRNA ligands within the 30S IC regulate subunit joining; In Aim 3, we will study the roles that the individual components of the factor-binding site of the 50S subunit play in directing the subunit joining reaction. Our guiding hypothesis, based on extensive ensemble studies of translation initiation and accumulating single-molecule studies of the elongation phase of translation, is that the IFs, tRNA, 30S subunit, and 50S subunit stochastically fluctuate between various conformational states, some of which are conducive to subunit joining, and others that are inhibitory. In this model, shifts towards subunit joining-competent states would up-regulate protein synthesis, while shifts towards subunit joining-inhibitory states would down-regulate protein synthesis; development of small-molecule drugs designed to destabilize the competent states or stabilize the inhibitory states in a bacteria-specific manner could therefore provide a means of generating new antibiotics. The proposed studies will provide a comprehensive mechanistic understanding of the subunit joining reaction and, in doing so, will aid in the identification of novel bacteria- specific aspects of the reaction that can serve as targets for th development of next-generation antibiotics.