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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #220469
Title: MOLECULAR CHARACTERIZATION AND DETECTION OF PLUM BARK NECROSIS STEM PITTING-ASSOCIATED VIRUS

Author
item AL RWAHNIH, M. - DEPT PLANT PATH, UC DAVIS
item UYEMOTO, J. - USDA, ARS, CPGRU
item FALK, B. - DEPT PLANT PATH, UC DAVIS
item ROWHANI, A. - DEPT PLANT PATH, UC DAVIS

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/1/2007
Publication Date: 9/21/2007
Citation: Al Rwahnih, M., Uyemoto, J.K., Falk, B.W., Rowhani, A. 2007. Molecular characterization and detection of plum bark necrosis stem pitting-associated virus. Archives of Virology.

Interpretive Summary:

Technical Abstract: The complete RNA genome of plum bark necrosis stem pitting-associated virus (PBNSPaV) was cloned and sequenced and was determined to be 14, 214 nts long. The genome structure revealed seven major open reading frames (ORFs), and nontranslated regions at the 5' abd 3' ends. PBNSPaV represents the simplest genome organization in the genus Ampelovirus, family Closteroviridae. The ORFs 1a and 1b encode, respectively, a large polyprotein with a molecular mass (Mr) of 259.6kDa containing conserved domains characteristic of a papa-in-like protease, methyltranferase and helicase (ORF1a) and a 64.1-kDa protein of eight conserved motifs characteristic of viral RNA-dependent RNA polymerase (RdRp) (ORF1b). ORF1b is presumably expressed via a +1 ribosomal frameshift mechanism. ORF2 encodes a small 6.3-kDa hydrophobic protein of unknown function. ORF3 encodes a 57.4-kDa protein, a homologue of the HSP70 family of heat shock proteins. ORF4 encodes a 61.6-kDa protein with unknown function. ORF5 encodes a 35.9-kDa capsid protein (CP). Lastly, ORF6 encodes a 25.2-kDa minor capsid protein (CPm). Phylogenetic analyses performed on sequences of the HSP70h RdRp and CP support classification of the virus in the genus Ampelovirus. A real-time TaqMan RT-PCR assay and a one-step RT-PCR were developed for PBNSPaV detection and compared using three different sample preparation methods.