Role of the 5'-proximal stem-loop structure of the 5' untranslated region in replication and translation of hepatitis C virus RNA

J Virol. 2003 Mar;77(5):3312-8. doi: 10.1128/jvi.77.5.3312-3318.2003.


Sequences of the untranslated regions at the 5' and 3' ends (5'UTR and 3'UTR) of the hepatitis C virus (HCV) RNA genome are highly conserved and contain cis-acting RNA elements for HCV RNA replication. The HCV 5'UTR consists of two distinct RNA elements, a short 5'-proximal stem-loop RNA element (nucleotides 1 to 43) and a longer element of internal ribosome entry site. To determine the sequence and structural requirements of the 5'-proximal stem-loop RNA element in HCV RNA replication and translation, a mutagenesis analysis was preformed by nucleotide deletions and substitutions. Effects of mutations in the 5'-proximal stem-loop RNA element on HCV RNA replication were determined by using a cell-based HCV replicon replication system. Deletion of the first 20 nucleotides from the 5' end resulted in elimination of cell colony formation. Likewise, disruption of the 5'-proximal stem-loop by nucleotide substitutions abolished the ability of HCV RNA to induce cell colony formation. However, restoration of the 5'-proximal stem-loop by compensatory mutations with different nucleotides rescued the ability of the subgenomic HCV RNA to replicate in Huh7 cells. In addition, deletion and nucleotide substitutions of the 5'-proximal stem-loop structure, including the restored stem-loop by compensatory mutations, all resulted in reduction of translation by two- to fivefold, suggesting that the 5'-proximal stem-loop RNA element also modulates HCV RNA translation. These findings demonstrate that the 5'-proximal stem-loop of the HCV RNA is a cis-acting RNA element that regulates HCV RNA replication and translation.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • 5' Untranslated Regions / chemistry*
  • 5' Untranslated Regions / genetics
  • 5' Untranslated Regions / metabolism*
  • Base Sequence
  • Gene Expression Regulation, Viral*
  • Hepacivirus / genetics
  • Hepacivirus / metabolism
  • Hepacivirus / physiology*
  • Humans
  • Molecular Sequence Data
  • Mutagenesis
  • Protein Biosynthesis*
  • RNA, Viral / biosynthesis*
  • Replicon
  • Sequence Deletion
  • Tumor Cells, Cultured
  • Virus Replication


  • 5' Untranslated Regions
  • RNA, Viral

Associated data

  • GENBANK/AJ242652
  • GENBANK/AJ242654