Dr. Adrian R. Ferre-D'Amare

Despite its chemical simplicity (compared to proteins) RNA can fold into intricate three-dimensional structures that can recognize other RNAs, proteins and small molecules with high affinity and specificity and carry out biological catalysis. We employ structural, biophysical, biochemical, and in vitro genetic techniques to study ribozymes, riboswitches, and ribonucleoprotein complexes.

We study ribozymes (catalytic RNAs), both cellular and in vitro selected, because they starkly demonstrate the chemical versatility of this nucleic acid. We study riboswitches. These are RNA elements of 5' and 3' untranslated regions of messenger RNAs that can switch between two conformations, depending on whether they are bound to a metabolite. Riboswitches are used by bacteria and eukaryotes to regulate gene expression at both the transcriptional and translational levels. We study protein enzymes responsible for post-transcriptional modification of RNAs. These modifications expand the chemical repertoire of the nucleic acid; the enzymes responsible may also serve as chaperones, facilitating RNA folding in vivo. We study a family of protein enzymes called pseudouridine synthases. These are responsible for the most abundant and phylogenetically conserved modification of cellular RNAs.

We are particularly interested in the human pseudouridine synthase Dyskerin, and its close homologs from other eukaryotes, archaea, and bacteria. Dyskerin assembles into a versatile RNA-protein (RNP) complex capable of catalyzing pseudouridylation at hundreds of different, specific sites in ribosomal and spliceosomal RNAs. The RNA component of the RNP is provided by one of hundreds of box H/ACA RNAs encoded by the human genome. Box H/ACA RNAs have a conserved architecture that presumably nucleates complex formation, and also have segments of variable sequence that are complementary to the substrate RNAs, and thus guide the pseudouridylation activity to its target. Box H/ACA RNPs are essential for the biogenesis of ribosomes and spliceosomes. Remarkably, Dyskerin is also essential for the biogenesis and stability of telomerase, the RNP responsible for maintenance of chromosome ends. In order to understand the multiple cellular roles of the box H/ACA RNP at the molecular level, we have reconstituted the particle from recombinant proteins. We are analyzing the structures of the isolated components, of specific subcomplexes that lie in the assembly pathway of the RNP, and of the complete particle.