(Georgia Institute of Technology, 2020-08)
Meade, Caeden Daniel
RiboVision is a collection of applications housed on servers at the Georgia Institute of Technology which serves to facilitate the development of publication-quality diagrams of ribosomal RNA (rRNA) and ribosomal protein (rProtein) structures (Petrov et. al, 2014). In particular, RiboVision seeks to promote analysis of key properties of rRNA and rProteins in primary, secondary, and tertiary structures.
As key semantides (ubiquitous macromolecules which carry genetic equivalent to the information intrinsic to DNA molecules and may be used by comparison to inform phylogenetic relationships), comparison of the primary and secondary structures of 16S and 18S RNA allows for the phylogenetic comparison of prokaryotic species and eukaryotic species, respectively (Fuerst, 2001). Sequence alignments are housed on the RiboVision server and stored in a MySQL database. Over the next two semesters, major improvements will be made to the server resulting in the newest edition, RiboVision3, which will feature improvements over the preceding RiboVision2 including the integration of XRNA, a program responsible for the generation of rRNA secondary structures and their exportation of their data into common computer-file formats (CSV, SVG, PDF, etc.) and the PDB Topology Viewer, a program responsible for production of protein secondary structures and their exportation into SVG image files.
The core functionality of XRNA - demonstration and editing tools of rRNA secondary structures needs to be iterated upon to allow for a more diverse set of purposes, including processing of high-quality hand-edited images into formats which are compatible with on-server management and conversion into formats native to web browsers.
(Georgia Institute of Technology, 2020-07-14)
Mestre Fos, Santiago
The ribosome is a macromolecular ribonucleoprotein machine that is responsible for the synthesis of all proteins in cells. Mammalian ribosomal RNAs (rRNAs) are nearly twice as large as those of prokaryotes. Differences in rRNA size are due to expansion segments (ESs), which are double-stranded RNA ramifications that protrude from the ribosomal surface. Here we show that numerous human rRNA ESs are capable of forming stable G-quadruplexes (G4s) in vitro and in vivo. G4s are non-canonical nucleic acid secondary structures that are thought to play key regulatory roles in cells. In addition, by taking a chemical biology approach that integrates results from immunofluorescence, G4 ligands, heme affinity reagents, and a genetically encoded fluorescent heme sensor, we report that human ribosomal G4s appropriate heme and regulate its cytosolic bioavailability. Immunofluorescence experiments indicate that the vast majority of extra-nuclear G4s are associated with rRNA. Overall, these results indicate that the RNA G-quadruplexome is ribosome-centric and suggest ribosomes are hubs of heme metabolism.