The ribosome plays the key role in protein synthesis and is one of the main targets for antibiotics that inhibit the growth of bacterial cells. Several key aspects of the functions of the ribosome are not fully understood and antibiotics could play a critical role in gaining insights into unknown facets of translation. Our laboratory has been on the forefront of antibiotics research and studies of the functional role of ribosomal RNA (rRNA). We have elucidated the binding modes and mechanisms of action of a number of major classes of antibiotics. On the basis of our findings we have proposed the new concept of context- and protein-specific action of several types of protein synthesis inhibitors. We have also unveiled the operations of several resistance mechanisms and revealed the principles of regulation of expression of inducible antibiotic resistance genes. In parallel with our studies of antibiotics, we have advanced the field of ribosome engineering having constructed the first ribosome with inseparable subunits based on a hybrid of 16S-23S rRNA, opening new experimental venues for basic research and bioengineering. Building upon our expertise in antibiotics, gene regulation and ribosome engineering, we will now advance these areas to principally new frontiers. Our future research will proceed in three main directions: 1) We will dedicate our effort to advancing the concept of context-specificity of bacterial ribosomal inhibitors to become applicable to the eukaryotic ribosome. By using ribosome engineering, structural analysis and genome-wide tests, we will identify compounds capable of binding in the nascent peptide exit tunnel of the eukaryotic ribosome and interfering with production of a subset of proteins. 2) Our antibiotic-enforced ribosome profiling experiments led to an unexpected and exciting finding of internal translation initiation inside a number of bacterial genes. We will analyze the physiological significance of internal initiation, test the production of the `alternative' gene products, study the regulation of expression of the genes from two different start codons and explore the evolutionary penetrance of this phenomenon. 3) The ribosome is believed to have originated in the pre-protein RNA World. However, all the previous attempts to demonstrate the ability of protein-free rRNA to catalyze peptide bond formation have been unsuccessful. We will use the synergy between ribosome engineering and antibiotic studies to generate catalytically active rRNA core. Altogether, the proposed directions of research should significantly advance the use of antibiotics as medicines and as tools for exploring ribosome functions in protein synthesis and translation regulation. We will use the knowledge of antibiotic action to expand our understanding of genome plasticity and gene coding and illuminate the critical questions of the ribosome origin and evolution.

Public Health Relevance

Antibiotics that inhibit protein synthesis are important medicines and, in addition, useful tools for our better understanding of how proteins are made in the cell. In the proposed project, the application of antibiotics to study translation will be significantly expanded. By repurposing the antibacterial drugs to target protein synthesis in eukaryotic organisms, new clinically useful compounds could be conceived and the knowledge of the mechanisms of protein synthesis in host cells will be broadened. Genome-wide effects of antibiotics will be used to uncover and examine unknown traits of protein coding and regulation of gene expression. Advanced bioengineering paired up with the use of antibiotics will be used to explore key questions about the evolutionary origin of the protein synthesis apparatus.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Unknown (R35)
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Special Emphasis Panel (ZRG1)
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Fabian, Miles
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University of Illinois at Chicago
Schools of Pharmacy
United States
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Vázquez-Laslop, Nora; Mankin, Alexander S (2018) How Macrolide Antibiotics Work. Trends Biochem Sci 43:668-684