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Virology. 2009 Nov 10;394(1):1-7. doi: 10.1016/j.virol.2009.08.006. Epub 2009 Sep 29.

Permutation of the active site of putative RNA-dependent RNA polymerase in a newly identified species of plant alpha-like virus.

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  • 1Department of Entomology, Mississippi State University, Mississippi State, MS 39762, USA. ss501@msstate.edu


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.

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