Sequence-motif analysis of 5'-untranslated region of GB virus-C in Japanese patients.
BACKGROUND
GB Virus C (GBV-C) is considered to belong to the Flaviviridae; however, the structures of the N-terminal end of its putative polyprotein are not well known. The internal ribosomal entry site (IRES) at the 5'-untranslated region of GBV-C and an initiating codon at nucleotides (nt) 552-554 have been proposed. We investigated the validity of this proposal.


METHODS
The 5'-untranslated region of GBV-C was amplified from serum samples of 17 Japanese patients. Polymerase chain reaction-amplified products were directly sequenced and the obtained sequences were analysed by comparing them with the IRES structure of other viruses.


RESULTS
Fifteen of the 17 (88%) GBV-C strains in our patients were classified as being Asian type. The box-A-like sequence (UUUC) and box-B-like sequence (AUCAUGG) observed in the IRES of picornaviruses were highly conserved in all the strains. Based on pair-wise comparisons with the multiple alignment data, overall sequence divergence for the 5'-terminus was 2.9-12%. When compared with the proposed secondary structure of the IRES model, the sequence divergences of the Asian-type GBV-C were higher at the regions of loop structures and lower at the regions of double-stranded RNA. The AUG codons, except for the one located at nt 552-554, produced truncated polyproteins or were not in-frame with the putative protein.


CONCLUSIONS
Our examination of the sequence motif of GBV-C supports the proposal that the GBV-C has common structural motifs for IRES at its 5'-untranslated region and the AUG codon at nt 552-554 may be an initiating codon.
Kanda
T
T
First Department of Medicine, Chiba University School of Medicine, Japan. kandat@ho.chiba-u.ac.jp
Yokosuka
O
O
Kawal
S
S
Imazeki
F
F
Saisho
H
H
D020121:5' Untranslated Regions / Q000032:analysis*; D000328:Adult; D000368:Aged; D000595:Amino Acid Sequence; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D005260:Female; D018067:Flaviviridae / Q000145:classification / Q000235:genetics*; D006525:Hepatitis, Viral, Human / Q000235:genetics*; D006801:Humans; D007564:Japan; D008103:Liver Cirrhosis / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000235:genetics*; D012270:Ribosomes; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
D020121:5' Untranslated Regions; D003062:Codon; D012367:RNA, Viral