Rapid acquisition of entire DNA polymerase gene of a novel herpesvirus from green turtle fibropapilloma by a genomic walking technique

Andy Yu, Ningjie Hu, Yuanan Lu, Vivek R. Nerurkar, Richard Yanagihara

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

A 4837-bp sequence of a newfound green turtle herpesvirus (GTHV), implicated in the etiology of green turtle fibropapilloma, was obtained from tumor tissues of a green turtle with fibropapilloma using a genomic walking method based on restriction enzyme digestion, self-ligation and inverse polymerase chain reaction (IPCR). The 4837-bp sequence was 56.23% G/C rich and contained three nonoverlapping open reading frames (ORF). The largest ORF (3507-bp) encoded the DNA polymerase gene (pol gene), which exhibited a high degree of homology at both amino acid and nucleotide levels with the DNA pol genes of human and animal herpesviruses, with a predicted protein of 1169 amino acids and molecular weight of 132.6 kilodaltons. The ATG at 518 to 520 was the first initiation codon in the ORF and was presumed to be the first methionine codon of the pol gene. Phylogenetic analysis, based on the amino acid sequence of the GTHV DNA pol gene and the corresponding regions of other known human and animal herpesviruses, indicated that GTHV belonged to the Alphaherpesvirinae subfamily. The upstream ORF of the pol gene encoded the N-terminal region of the GTHV homologue of the DNA-binding protein gene, whereas the downstream ORF was the C-terminal region of a gene which was homologous to ORFs conserved in human and animal herpesviruses, i.e., herpes simplex virus 1 (HSV1) gene UL31, Epstein-Barr virus (EBV) gene BFLF2, equine herpesvirus 1 (EHV1) gene 29, and alcelaphine herpesvirus 1 (AHV1) hypothetical protein 69 gene. The arrangement of these three genes in GTHV genome was identical to that seen in other alphaherpesviruses. The sequence and location of the DNA pol gene in the GTHV genome should greatly facilitate future studies of the viral life cycle.

Original languageEnglish (US)
Pages (from-to)183-195
Number of pages13
JournalJournal of Virological Methods
Volume91
Issue number2
DOIs
StatePublished - 2001
Externally publishedYes

Fingerprint

Turtles
Herpesviridae
DNA-Directed DNA Polymerase
Walking
Open Reading Frames
Genes
Alphaherpesvirinae
Equid Herpesvirus 1
Genome
pol Genes
Amino Acids
Gene Order
Initiator Codon
DNA-Binding Proteins
Human Herpesvirus 1
Life Cycle Stages
Human Herpesvirus 4
Codon
Methionine
Ligation

Keywords

  • DNA polymerase gene
  • Fibropapilloma
  • Genomic walking
  • Green turtle herpesvirus
  • Inverse polymerase chain reaction

ASJC Scopus subject areas

  • Virology

Cite this

Rapid acquisition of entire DNA polymerase gene of a novel herpesvirus from green turtle fibropapilloma by a genomic walking technique. / Yu, Andy; Hu, Ningjie; Lu, Yuanan; Nerurkar, Vivek R.; Yanagihara, Richard.

In: Journal of Virological Methods, Vol. 91, No. 2, 2001, p. 183-195.

Research output: Contribution to journalArticle

Yu, Andy ; Hu, Ningjie ; Lu, Yuanan ; Nerurkar, Vivek R. ; Yanagihara, Richard. / Rapid acquisition of entire DNA polymerase gene of a novel herpesvirus from green turtle fibropapilloma by a genomic walking technique. In: Journal of Virological Methods. 2001 ; Vol. 91, No. 2. pp. 183-195.
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