title: Sequence and structure prediction of RNA-dependent RNA polymerase of lily symptomless virus isolated from L. × 'Casablanca'.
abstract: The DNA sequence of the RNA-dependent RNA polymerase (RdRp) gene of lily symptomless virus (LSV), a lily-infecting member of the genus Carlavirus, was determined from nine overlapping cDNA fragments of different sizes. The complete sequence of this RdRp gene (HM070294) consisted of 5,847 nucleotides coding for a protein of 220 kDa. It had 97-98% sequence identity with RdRps of other known isolates at both the DNA and the amino acid level. Phylogenetic analysis indicated that this RdRp (designated as RdRp-DL) was closely related to the RdRp of the Korean isolate (AM516059), as well as to the RdRps from Passiflora latent virus (PLV) and Kalanchoe latent virus (KLV) of the genus Carlavirus. Hydrophobic analysis of RdRp-DL revealed a hydrophobic N-terminus and a hydrophilic C-terminus. Helices and Loops were the major secondary structures of RdRp-DL. In addition, RdRp-DL also had three coil structures. Four conserved domains were identified: typoviral methyltransferase, RNA-dependent RNA polymerase, P-loop-containing nucleoside triphosphate hydrolases and carlavirus endopeptidase. A model of the tertiary structure predicted by I-TASSER was obtained for each of these conserved domains. This is the first report of a detailed phylogenetic analysis of LSV RdRp with those of other members of the genus Carlavirus, and the first to predict the domain structures of LSV RdRp.
authors.affiliation: School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian City, 116024 Liaoning Province, People's Republic of China.
authors.forename: Pinsan
authors.initials: P
authors.lastname: Xu
authors.forename: Huangai
authors.initials: H
authors.lastname: Li
authors.forename: Jiwen
authors.initials: J
authors.lastname: Liu
authors.forename: Yushi
authors.initials: Y
authors.lastname: Luan
authors.forename: Yalei
authors.initials: Y
authors.lastname: Yin
authors.forename: Jianfang
authors.initials: J
authors.lastname: Bai
mesh_terms: D000595:Amino Acid Sequence; D017788:Carlavirus / Q000201:enzymology* / Q000235:genetics; D018076:DNA, Complementary; D016679:Genome, Viral; D057927:Hydrophobic and Hydrophilic Interactions; D027762:Lilium / Q000821:virology*; D008958:Models, Molecular; D010802:Phylogeny; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase