Sequence and structural analysis of the 5' noncoding region of hepatitis C virus in patients with chronic infection.
Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well conserved 5' noncoding region (5' NCR) among all genotypes. In this study, the structural features and translational efficiency of the HCV 5' NCR sequences were analyzed using the programs RNAfold, RNAshapes and RNApdist and with a bicistronic dual luciferase expression system, respectively. RNA structure prediction software indicated that base substitutions will alter potentially the 5' NCR structure. The heterogeneous sequence observed on 5' NCR led to important changes in their translation efficiency in different cell culture lines. Interactions of the viral RNA with cellular transacting factors may vary according to the cell type and viral genome polymorphisms that may result in the translational efficiency observed.
Araújo
Flávio Marcos Gomes
FM
Instituto René Rachou/FIOCRUZ. Av. Augusto de Lima, Minas Gerais, Brazil. araujo@cpqrr.fiocruz.br
Machado-Lima
Ariane
A
Durham
Alan Mitchell
AM
Teixeira
Rosangela
R
Oliveira
Guilherme
G
D020121:5' Untranslated Regions; D000368:Aged; D001483:Base Sequence; D002460:Cell Line; D005260:Female; D017930:Genes, Reporter; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D019698:Hepatitis C, Chronic / Q000821:virology*; D006801:Humans; D008156:Luciferases / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA
D020121:5' Untranslated Regions; D012367:RNA, Viral; D008156:Luciferases