Research

The Gregory lab studies the structure, function, and assembly of the ribosome, the macromolecular machine responsible for protein synthesis. The ribosome serves as the link between genetic information encoded in DNA and biological function governed by proteins. The means by which the ribosome carries out the highly intricate process of protein synthesis is a fundamental question in biology. How the ribosome assembles from its constituent parts is an even more complex process that is only partly understood. Using a combination of molecular genetics, structural biochemistry, and structural biology, we are working to understand the molecular mechanisms of protein synthesis and ribosome biogenesis.

Ribosome Structure and Function. The ribosome is composed of ribosomal RNA (rRNA) and ribosomal proteins. It is the rRNA that forms substrate binding and catalytic sites, revealing the ribosome’s prebiotic origin as an RNA-only mechanism. Ribosomal proteins evolved to aid assembly, establish an active rRNA conformation, and facilitate rRNA conformational changes that are intrinsic to the ribosome’s mechanism. One of our major goals is to understand the role of specific protein-RNA and rRNA-rRNA interactions in establishing the active ribosome conformation and their role in modulating ribosome conformational dynamics. Further, we seek to understand how antibiotics impair ribosome conformational transitions and how such inhibition can be overcome by mutations in the ribosome.

Ribosome Assembly. All ribosomes are composed of two subunits, each of which is assembled from rRNA and ribosomal proteins. In bacteria, the small or 30S subunit is composed of 16S rRNA and around 21 proteins, while the large or 50S subunit is composed of 23S rRNA, 5S rRNA, and around 33 proteins. During subunit assembly, ribosomal proteins facilitate the folding of rRNA into its correct three-dimensional structure and prevent its misfolding into aberrant, kinetically trapped folding intermediates. Mutations disrupting protein-rRNA or rRNA-rRNA interactions can severely compromise the folding process; such mutations provide a valuable experimental tool. We are using a combination of mutagenesis and RNA structure probing by chemical modification to dissect the rRNA folding pathway during ribosomal subunit assembly.

Our experimental system. Our laboratory uses as a model system the extremely thermophilic bacterium Thermus thermophilus. This species is commonly found in high-temperature environments across the globe. In many ways an ideal model organism, it is amenable to genetic manipulation due to its natural competence for transformation and efficient homologous recombination. It is thus possible to engineer the T. thermophilus genome using a variety of genetic tools such as CRISPR. Importantly, there exists a wealth of high-resolution structural data describing the T. thermophilus ribosome in various functional states, allowing a structural interpretation of genetic and chemical probing data. Through our collaborative efforts we are determining the structures of mutant ribosomes using X-ray crystallography and cryo-electron microscopy.