Linked Life Data

12180709

Source:http://linkedlifedata.com/resource/pubmed/id/12180709

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2002-8-15
pubmed:databankReference
pubmed:abstractText
We report the sequence of an 8503 nucleotide (nt) region of the genome of yellow head virus (YHV) encompassing the open reading frame (ORF) 1b gene. Comparison with the sequence of Australian gill-associated virus (GAV) indicated that the region, comprising approximately 30% of the YHV genome, commences 268 nt upstream of the putative ORF1a termination codon and continues through ORF1b to a site 30 nt downstream of the ORF2 initiation codon. YHV ORF1a and ORF1b overlap by 37 nt. MFOLD analysis of the overlap and downstream region predicted a 131 nt folding structure (deltaG = -47.3 kcal mol(-1)) with potential to form an RNA pseudoknot. The structure resides 3 nt downstream of a ribosomal frame-shift 'slippery' sequence (AAAUUUU) and a -1 frame-shift at this site would extend the ORF1 polyprotein by 2616 amino acids (299322 Da). In ORF1b, YHV shares 88.9% amino acid sequence identity with GAV and includes conserved polymerase, metal ion binding, helicase and other domains (Motifs 1 and 3) characteristic of nidoviruses. Compared to GAV, the YHV non-coding region linking the ORF 1b and ORF2 genes contains a 263 nt insertion. However, the region contains a conserved core sequence of 46 nucleotides (84.8% identity) that includes a stretch of 20 identical nucleotides surrounding a sub-genomic RNA transcription termination site. The data confirms the taxonomic placement of YHV in the Nidovirales and supports biological and topographical evidence that YHV and GAV may be classified as distinct species.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jul
pubmed:issn
0177-5103
pubmed:author
pubmed:issnType
Print
pubmed:day
8
pubmed:volume
50
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
87-93
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed:year
2002
pubmed:articleTitle
Complete ORF1b-gene sequence indicates yellow head virus is an invertebrate nidovirus.
pubmed:affiliation
Department of Biochemistry and CENTEX Shrimp, Faculty of Science, Mahidol University, Bangkok, Thailand.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't