Natural RNA molecules are heavily decorated by various functional groups to diversify and fine-tune their structures and biological functions. Studying these RNA modifications has great significance in understanding fundamental RNA biology, studying evolution and developing new therapeutics. This project is focused on a recently discovered lipid modification on bacterial tRNAs. tRNA (also known as transfer RNA or soluble RNA) is the RNA molecule that carries amino acids to ribosome for protein synthesis in a cell, therefore is a very critical life molecule. The research will use synthetic biology approaches to address the fundamental question of why nature uses such a hydrophobic lipid group in hydrophilic RNA systems by elucidating the metabolic pathways of this lipid modification, as well as the structural and functional features of the working enzyme called SelU. In addition, based on this special pathway, the research will also develop novel molecular tools to detect, label and monitor specific tRNAs in cells. This project will provide educational and research training opportunities for graduate and undergraduate students, as well as local K12 teachers to use cutting-edge multidisciplinary approaches to solve fundamental biological problems and advance their scientific careers.
The systematic study of post-transcriptional chemical modifications of tRNAs have great significance in understanding RNA biology and its roles in evolution. Furthermore, many enzymes that mediate these processes have been demonstrated as targets for the development of new molecular tools or therapeutics. The main goal of this research is to explore tRNA geranylation, which is a recently discovered hydrophobic tRNA modification in several bacteria such as E. coli, E. aerogenes, P. aeruginosa and S. typhimurium. The geranylated 2-thiouridines are produced in the first anticodon position of tRNAs specific for lysine, glutamine, and glutamic acid by the enzyme SelU using geranyl pyrophosphate as the cofactor. It has been demonstrated that this hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. Specifically, the geranyl group promotes wobble 2-thiouridine pairing with guanosine over adenosine and the long carbon chain of geranyl group is necessary to maintain this base pairing specificity in the context of RNA duplexes. This research will develop new chemical synthesis of RNA strands containing a series of geranyl-uridine analogues and identify the general rules for the in vitro codon specificity and ribosomal binding of these lipid modified tRNAs. In addition, this project will solve crystal structures of geranylated RNAs to elucidate their detailed structural features; and determine the structures of SelU-tRNA complexes for the mechanistic studies of this geranylation step. Furthermore, this research will develop novel molecular tools to detect, label and monitor specific tRNAs in cells.
