Infectious Salmon Anemia Virus (ISAV), an RNA virus of negative polarity in the family orthomyxoviridae, has emerged as a virus of great concern to the aquaculture industry, as it can lead to highly contagious and lethal infections in farm-raised salmon populations. While little is known about the transcription and replication of ISAV, initial evidence suggests that it follows molecular mechanisms similar to those found in other orthomyxoviruses, which includes the highly pathogenic influenza A (inf A) virus. During the inf A viral life cycle, a panhandle structure is formed by the pairing of the highly conserved 5 and 3 ends of each genomic segment and serves as both a promoter of the viral RNA-dependent RNA polymerase and one of the regulatory elements in the transcription/replication cycle. As a first step towards characterizing the structure of the ISAV panhandle and gaining insight into structural features that may govern recognition by the viral RNA polymerase, here we establish the secondary structure of the viral RNA (vRNA) and the complementary RNA (cRNA) panhandles based on solution NMR and thermal melting data. The vRNA is characterized by three U:G wobble pairs, one U:U mismatch, and lower and upper stem helices that are structurally coupled by a highly stacked internal loop. For the cRNA, the panhandle contains a C:A wobble pair near the terminus, stabilized by the protonation of the adenosine, and tandem downstream U:U wobble pairs. The observed non-canonical base pairs and base stacking patterns of the ISAV RNA panhandle motif provide the first insight into structural features that may govern recognition of this RNA motif by the viral RNA polymerase.
Citation: Journal of Virology
Pub Type: Journals
Infectious Salmon Anemia Virus, NMR, orthomyxovirus, panhandle, RNA