Structural and functional characterization of nuclease-resistant viral RNAs

• Applicant: Dr. Anna-Lena Steckelberg
• Subject Area: General Genetics and Functional Genome Biology ; Biochemistry
• Term: from 2017 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 363751433

RNA turnover is a central feature of eukaryotic gene expression, involved in maintaining steady RNA levels and degrading non-functional, old or defective transcripts. Most cytoplasmic RNAs are degraded by one of two exonucleolytic decay pathways: 5’-3’ degradation by the exonuclease XRN1 or 3’-5’ degradation by the exosome complex. Despite the nonselective nature of eukaryotic exonucleases, distinct RNA species display vastly different turnover rates, suggesting that RNA decay is a highly regulated process. To date we know surprisingly little about the specific features that dictate decay rates of eukaryotic RNA. The proposed project will explore a particularly fascinating mechanism of exonuclease regulation employed by viruses that use highly structured RNA elements to provide protection from RNA degradation. Exonuclease-resistant viral RNA structures were first identified in arthropod-borne flaviviruses (e.g. Dengue and Zika virus) where a highly structured RNA element protects the viral 3’UTR from 5’-3’ degradation by XRN1, a process that leads to the generation of viral non-coding RNAs. The central role of XRN1 during eukaryotic RNA decay suggests that other viral (or cellular) RNAs might have evolved similar mechanisms. Accordingly, I identified a short RNA sequence from plant-infecting Dianthoviruses as another structure that can protect RNAs from degradation by XRN1. Interestingly, there is absolutely no sequence similarity between the XRN1-resistant RNAs found in Flaviviruses and the newly discovered Dianthovirus nuclease-resistant RNA, suggesting completely independent mechanisms for nuclease resistance. The proposed project aims to functionally and structurally characterize the newly identified nuclease-resistant Dianthovirus RNA using a combination of biochemical, cell biological and structural methods. It is my ultimate goal to establish a detailed molecular model for RNA-based exonuclease inhibition. Furthermore, I will use the new information on viral XRN1-resistancy to search for other nuclease-resistant RNAs in viral and eukaryotic genomes, which could potentially reveal that RNA-based nuclease inhibition is more prevalent in nature than hitherto appreciated. Together, my work will highlight how different RNA structures can function to selectively protect RNA from exonucleolytic degradation and thus provide valuable new information about the molecular mechanisms that regulate the cellular RNA decay machinery.

• DFG Programme: Research Fellowships
• International Connection: USA
• Host: Professor Jeffrey Kieft, Ph.D.