title: RNA transcription analysis and completion of the genome sequence of yellow head nidovirus.
abstract: Yellow head virus (YHV) is a pathogen of the black tiger shrimp (Penaeus monodon) and, with gill-associated virus (GAV), is one of two known invertebrate nidoviruses. We describe sequences of the large replicase gene (ORF1a) and 5'- and 3'-terminal UTRs, completing the 26,662 nt sequence of the YHV genome. ORF1a (12,219 nt) encodes a approximately 462,662 Da polypeptide containing a putative 3C-like protease and a putative papain-like protease with the canonical C/H catalytic dyad and alpha+beta fold. The read-through pp1ab polyprotein contains putative uridylate-specific endoribonuclease and ribose-2'-O-methyl transferase domains, and an exonuclease domain incorporating unusual dual Zn2+-binding fingers. Upstream of ORF1a, the 71 nt 5'-UTR shares 82.4% identity with the 68 nt 5'-UTR of GAV. The 677 nt 3'-terminal region contains a single 60 nt ORF, commencing 298 nt downstream of ORF3, that is identical to N-terminal coding region of the 249 nt GAV ORF4. Northern blots using RNA from YHV-infected shrimp and probes directed at ORF1a, ORF1b, ORF2 and ORF3 identified a nested set of 3'-coterminal RNAs comprising the full-length genomic RNA and two sub-genomic (sg) mRNAs. Intergenic sequences upstream of ORF2 and ORF3 share high identity with GAV, particularly in the conserved domains predicted to mediate sgmRNA transcription.
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Phathumthani 12120, Thailand.
authors.forename: Nusra
authors.initials: N
authors.lastname: Sittidilokratna
authors.forename: Sirintip
authors.initials: S
authors.lastname: Dangtip
authors.forename: Jeff A
authors.initials: JA
authors.lastname: Cowley
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Walker
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D020869:Gene Expression Profiling; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D033561:Penaeidae / Q000821:virology; D017434:Protein Structure, Tertiary; D012367:RNA, Viral / Q000096:biosynthesis* / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D046828:Roniviridae / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D012367:RNA, Viral; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase