Structural studies of rotavirus RNA-dependent RNA polymerase VP1.

摘要

Rotavirus is a major cause of severe, dehydrating childhood diarrhea, leading to approximately 500,000 deaths annually throughout the world. Replication of the segmented double-stranded RNA genome of rotavirus requires the viral RNA-dependent RNA polymerase (RdRP) VP1 to use positive-strand viral RNAs as templates for negative strand synthesis. VP1 can specifically bind the 3' consensus sequence (3'CS) of positive-strand viral RNAs. RNA synthesis in vitro, however, requires the presence of rotavirus inner capsid protein VP2, suggesting the coordination between genome replication and capsid assembly. VP1 can also serve as an in vitro model for studying general mechanisms of RdRPs.; The crystal structures of VP1 apoenzyme and its complexes with five different oligoribonucleotide templates were determined. VP1 apoenzyme has three structural domains: a central polymerase domain, which contains canonical "forgers," "palm," and "thumb" subdomains; an amino-terminal domain, which reinforces the contacts between fingers and thumb on one side of the catalytic cleft; and a carboxyl-terminal "bracelet" domain, which covers the catalytic cleft on the other side. Four channels connect into the hollow catalytic center of VP1: the duplex RNA exit channel, the template entry channel, the nucleotide entry channel, and the putative transcript exit channel.; In the structure of VP1/3'CS template complex, 3'CS sequence is specifically recognized by the template entry channel. The 3'CS template "overshoots" its presumed functional initiation register by one nucleotide, generating an autoinhibited complex. We hypothesize that this autoinhibition would delay synthesis of dsRNA genomic segments until VP1 encounters VP2. Based on the structural similarities between autoinhibited VP1 and catalytically active reovirus RdRPlambda3, we have deduced that the priming loop and the motif A would, upon VP2 binding, undergo conformational changes to activate VP1. We have also identified the carboxyl-terminus of VP1 as a potential switch between transcription and replication, and the motif F as a potential ratchet for promoting polymerase translocation toward downstream of its template. Our work establishes the structural basis for the coupling of rotavirus genome replication and capsid assembly, and provides novel insights into the enzymatic mechanism of RdRPs.