3' RNA elements in hepatitis C virus replication: kissing partners and long poly(U). Academic Article uri icon

Overview

abstract

  • The hepatitis C virus (HCV) genomic RNA possesses conserved structural elements that are essential for its replication. The 3' nontranslated region (NTR) contains several of these elements: a variable region, the poly(U/UC) tract, and a highly conserved 3' X tail, consisting of stem-loop 1 (SL1), SL2, and SL3. Studies of drug-selected, cell culture-adapted subgenomic replicons have indicated that an RNA element within the NS5B coding region, 5BSL3.2, forms a functional kissing-loop tertiary structure with part of the 3' NTR, 3' SL2. Recent advances now allow the efficient propagation of unadapted HCV genomes in the context of a complete infectious life cycle (HCV cell culture [HCVcc]). Using this system, we determine that the kissing-loop interaction between 5BSL3.2 and 3' SL2 is required for replication in the genotype 2a HCVcc context. Remarkably, the overall integrity of the 5BSL3 cruciform is not an absolute requirement for the kissing-loop interaction, suggesting a model in which trans-acting factor(s) that stabilize this interaction may interact initially with the 3' X tail rather than 5BSL3. The length and composition of the poly(U/UC) tract were also critical determinants of HCVcc replication, with a length of 33 consecutive U residues required for maximal RNA amplification. Interrupting the U homopolymer with C residues was deleterious, implicating a trans-acting factor with a preference for U over mixed pyrimidine nucleotides. Finally, we show that both the poly(U) and kissing-loop RNA elements can function outside of their normal genome contexts. This suggests that the poly(U/UC) tract does not function simply as an unstructured spacer to position the kissing-loop elements.

publication date

  • October 17, 2007

Research

keywords

  • 3' Untranslated Regions
  • Hepacivirus
  • Nucleic Acid Conformation
  • Poly U
  • RNA, Viral
  • Viral Nonstructural Proteins
  • Virus Replication

Identity

PubMed Central ID

  • PMC2224383

Scopus Document Identifier

  • 37349012884

Digital Object Identifier (DOI)

  • 10.1128/JVI.01796-07

PubMed ID

  • 17942554

Additional Document Info

volume

  • 82

issue

  • 1