RNA interference (RNAi) is a major antiviral defense mechanism in nematodes. In Caenorhabditis elegans (C. elegans), Dicer-related helicase 1 (DRH-1) acts to enhance the production of primary virus-derived small interfering RNA (siRNA) in antiviral RNAi pathway. However, Dicer-related helicase 3 (DRH-3), is involved in the biogenesis of secondary siRNA in both endogenous and exogenous RNAi pathways. DRH-1 and DRH-3 are orthologs to RIG-I like receptors (RLRs), based on their structural and sequential conservation of the helicase domain (HEL) and the C-terminal RNA binding domain (CTD). The structure and function of worm-specific N-terminal domains (NTDs) of DRH-1 and DRH-3 are currently unknown.
This thesis describes biochemical, biophysical and structural studies of DRH-1 and DRH-3 (DRHs) to provide new insights into the RNAi mechanism at the molecular level. We first established the methods for expressing and purifying the full-length and various domains of DRHs. The purified recombinant proteins were then fully characterized to understand their functions in RNA recognition. For DRH-3, we applied X-ray crystallography and solved the crystal structure of DRH-3 NTD, as well as two crystal structures of DRH-3 CTD in complex with 5′-triphosphate (5′-ppp) RNAs. The NTD of DRH-3 adopts a novel fold of tandem CARDs that is different from the CARDs of RIG-I. This suggests DRH-3 may recruit an unknown protein partner in the endogenous RNAi pathway. Crystal structures and RNA binding assay confirmed that CTD preferentially recognizes RNAs with 5′-ppp, which is the typical feature of secondary siRNA transcript. Furthermore, the full-length DRH-3 displays unique structural dynamics and RNA differentiation patterns that are different from RIG-I and MDA5, as revealed by the hydrogen/deuterium exchange coupled to mass spectrometry experiment (HDX-MS). For DRH-1, we provided the first evidence that the Hel-CTD of DRH-1 has a dsRNA-dependent ATPase function. Moreover, we demonstrated that DRH-1 preferred short dsRNAs, especially those with 5'-ppp and 3' overhang for its ATPase hydrolysis activity and the protein stability. Collectively, our findings reveal unique molecular features of DRHs in RNAi and provide new perspectives for advancing our understanding of small RNA processing and antiviral defense mechanism in worms.Doctor of Philosoph
