Identification of a conserved RNA replication element (cre) within the 3Dpol-coding sequence of hepatoviruses

Yan Yang, Min Kyung Yi, David J. Evans, Peter Simmonds, Stanley M. Lemon

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

Internally located, cis-acting RNA replication elements (cre) have been identified within the genomes of viruses representing each of the major picornavirus genera (Enterovirus, Rhinovirus, Aphthovirus, and Cardiovirus) except Hepatovirus. Previous efforts to identify a stem-loop structure with cre function in hepatitis A virus (HAV), the type species of this genus, by phylogenetic analyses or thermodynamic predictions have not succeeded. However, a region of markedly suppressed synonymous codon variability was identified in alignments of HAV sequences near the 5′ end of the 3Dpol-coding sequence of HAV, consistent with noncoding constraints imposed by an underlying RNA secondary structure. Subsequent MFOLD predictions identified a 110-nucleotide (nt) complex stem-loop in this region with a typical AAACA/G cre motif in its top loop. A potentially homologous RNA structure was identified in this region of the avian encephalitis virus genome, despite little nucleotide sequence relatedness between it and HAV. Mutations that disrupted secondary RNA structure or the AAACA/G motif, without altering the amino acid sequence of 3Dpol, ablated replication of a subgenomic HAV replicon in transfected human hepatoma cells. Replication competence could be rescued by reinsertion of the native 110-nt stem-loop structure (but not an abbreviated 45-nt stem-loop) upstream of the HAV coding sequence in the replicon. These results suggest that this stem-loop is functionally similar to cre elements of other picornaviruses and likely involved in templating VPg uridylylation as in other picornaviruses, despite its significantly larger size and lower free folding energy.

Original languageEnglish (US)
Pages (from-to)10118-10128
Number of pages11
JournalJournal of Virology
Volume82
Issue number20
DOIs
StatePublished - Oct 2008

Fingerprint

Hepatovirus
Hepatitis A virus
RNA
Picornaviridae
stems
replicon
Enterovirus
nucleotides
Replicon
Nucleotides
Cardiovirus
Aphthovirus
Encephalitis Viruses
viruses
Genome
genome
prediction
Rhinovirus
hepatoma
encephalitis

ASJC Scopus subject areas

  • Immunology
  • Virology

Cite this

Identification of a conserved RNA replication element (cre) within the 3Dpol-coding sequence of hepatoviruses. / Yang, Yan; Yi, Min Kyung; Evans, David J.; Simmonds, Peter; Lemon, Stanley M.

In: Journal of Virology, Vol. 82, No. 20, 10.2008, p. 10118-10128.

Research output: Contribution to journalArticle

Yang, Yan ; Yi, Min Kyung ; Evans, David J. ; Simmonds, Peter ; Lemon, Stanley M. / Identification of a conserved RNA replication element (cre) within the 3Dpol-coding sequence of hepatoviruses. In: Journal of Virology. 2008 ; Vol. 82, No. 20. pp. 10118-10128.
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