Christopher D. Lima: RNA Processing and Repair

Eukaryotic messenger RNA requires the addition of a nucleotide cap for proper function in the cell. We are interested in understanding the molecular basis for cap maturation and how those enzymes are regulated in the cell, especially through their recruitment to the transcription apparatus. In addition to studies addressing cap formation, we have also focused our attention to those enzymes involved in cap degradation.

Our interest in RNA processing also extends to RNA repair. In collaboration with the Shuman laboratory, we have addressed the structural basis for RNA repair through the structure determination of RNA ligase intermediates.

RNA capping

We have described the structural and genetic basis for the 3 essential steps in cap formation.

i.) The triphosphatase enzyme catalyzes the gamma phosphate hydrolysis from the nascent 5' triphosphate mRNA end;

ii.) the guanylyltransferase capped the 5' diphosphate terminated mRNA in the next step; and

iii.) the final essential step involved methylation at the N7 guanine position.

We are actively engaged in understanding the structural basis for catalysis in this system as well as the structural basis for association of the capping apparatus on RNA polymerase II.

RNA decapping

Eukaryotic messenger RNA degradation plays a critical role in regulating the turnover of RNA in the cell. In eukaryotic cells, 2 major pathways are utilized to degrade mRNA and both are initiated with deadenylation of the polyadenylated (poly[A]) tail. In the 5' to 3' decay pathway, the mRNA cap is hydrolyzed following deadenylation, exposing the 5' end to 5' to 3' exoriboribonuclease activities. In the 3' to 5' decay pathway, degradation of the mRNA body continues from the 3' end following deadenylation to generate a cap structure, which is subsequently hydrolyzed. We have determined the structural and biochemical basis for RNA decapping in the 3' to 5' pathway, and continue to work on aspects of the 5' to 3' pathway and exosome mediated RNA degradation.

RNA repair

T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation, AMP transfer to the nick 5'PO(4), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester. We have determined crystal structures for Rnl2 at discrete steps along this pathway, illuminating the stereochemistry of nucleotidyl transfer and revealing how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. By comparing structures of Rnl2 and human DNA ligase I, we were able to highlight common and divergent themes of substrate recognition that explain their specialization for RNA versus DNA repair.