Permutation of the Active Site of Putative RNA-dependent RNA Polymerase in a Newly Identified Species of Plant Alpha-like Virus

Sabanadzovic, S., Abou Ghanem-Sabanadzovic, N., & Gorbalenya, A. E. (2009). Permutation of the Active Site of Putative RNA-dependent RNA Polymerase in a Newly Identified Species of Plant Alpha-like Virus. Virology. 394(1), 1-7.

To direct the genome synthesis, RNA viruses without a DNA stage in the replication cycle use RNA-dependent RNA polymerase (RdRp). All RdRps have conserved right hand-like shape that includes characteristic A-->B-->C sequence motifs forming the active site. Recently, the structural permutation of the RdRp active site (C-->A-->B) has been described in few double-stranded RNA birnaviruses and a subset of positive-stranded RNA tetraviruses distantly related to Picorna-like viruses. Here we describe a permuted RdRp in the newly identified plant alpha-like virus with 6.5 kb-long polyadenylated genome, dubbed Grapevine virus Q (GVQ). The multi-domain layout and sequence similarities place GVQ into the genus Marafivirus of the family Tymoviridae. In contrast to other tymovirids, GVQ has 21 amino acid residues corresponding to the motif C relocated upstream of the motif A in the putative RdRp. This unique sequence characteristic was extensively verified and identified in several GVQ isolates infecting wild and cultivated Vitis and Rubus spp.