Genome prediction of putative genome-linked viral protein (VPg) of astroviruses

• Published in: Virus genes 2005-08, Vol.31 (1), p.21-30
• Main Authors: Al-Mutairy, Badr, Walter, Jolan E, Pothen, Alex, Mitchell, Douglas K
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Animals; Astroviridae; Astrovirus; Caliciviridae; Calicivirus; Genome, Viral; Humans; Mamastrovirus - chemistry; Mamastrovirus - enzymology; Mamastrovirus - genetics; Molecular Sequence Data; Pestivirus; Potyviridae; Potyvirus; RNA Helicases - chemistry; RNA Helicases - genetics; RNA Replicase - chemistry; RNA Replicase - genetics; Sequence Alignment; Viral Proteins - chemistry; Viral Proteins - genetics
• ISSN: 0920-8569; 1572-994X
• DOI: 10.1007/s11262-004-2196-1

Positive-sense single-stranded RNA (+ssRNA) viruses replicate by uncoating the RNA genome for translation to provide viral proteins essential for genome replication and the production of new viral particles. The viral proteins are synthesized from a polyprotein precursor, which is cleaved nascently. The synthesized proteins include viral RNA-dependent RNA polymerase (RdRP), viral genome-linked protein (VPg), and a helicase. VPg is covalently attached to the genomic form of +ssRNA viruses. Helicases and NTPase unwind the RNA before replication. VPg and helicases have been identified in +ssRNA families, however, the presence of VPg and helicase in the Astroviridae, another +ssRNA family, has not been fully elucidated. Computational tools were utilized to provide sequence analysis evidence for the presence and genomic location of astrovirus VPg and helicase. HMMER program v2.1.1 was used to build Hidden Markov Model (HMM) profile for calicivirus VPg to search for conserved motifs in the astrovirus genome. We performed phylogenetic analysis of two genomic regions of astroviruses and caliciviruses (encoding the RdRP and VPg). We identified a putative VPg coding region in astrovirus. This region was located in open reading frame 1a (ORF1 a) and included sites with high sequence similarity to the VPg coding regions of Caliciviridae, Piconaviridae, and Potyviridae. A region encoding a putative astrovirus helicase identified conserved motifs only with pestivirus helicase sequences. Sequence analysis and comparison to other +ssRNA viruses supports the presence of VPg in the Astroviridae. Further laboratory analysis will be necessary to confirm these findings.