Predicted secondary structure of the hepatitis G virus and GB virus-A 5′ untranslated regions consistent with an internal ribosome entry site

Journal of Viral Hepatitis

Volumn 4, Issue 3, 1997, Pages 175-184

  Pickering, J M ^a   Thomas, H C ^a   Karayiannis, P ^a  

^a IMPERIAL COLLEGE SCHOOL OF MEDICINE   (United Kingdom)

Author keywords

Hepatitis G virus; Internal ribosome entry site; RNA folding

Indexed keywords

CORE PROTEIN; VIRUS RNA;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMISTRY; COMPARATIVE STUDY; CONFORMATION; FLAVIVIRUS; GENETIC VARIABILITY; GENETICS; HUMAN; INTRON; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN SYNTHESIS; RIBOSOME; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; FLAVIVIRIDAE; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, VIRAL; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, AMINO ACID; VARIATION (GENETICS); VIRAL CORE PROTEINS;

EID: 0031136447     PISSN: 13520504     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2893.1997.00143.x     Document Type: Article

References (41)

1. Simons JN, Leary TP, Dawson GJ et al. Isolation of novel virus-like sequences associated with human hepatitis. Nature Medicine 1995; 1: 564-569.
2. Leary TP, Muerhoff AS, Simons JN et al. Sequence and genomic organisation of GBV-C: a novel member of the flaviviridae associated with human non-A-E hepatitis. J Med Virol 1996; 48: 60-67.
3. Linnen J, Wages J, Zhang-Keck ZY et al. Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent. Science 1996; 271: 505-508.
4. Muerhoff AS, Leary TP, Simons JN et al. Genomic organisation of GB viruses A and B: two new members of the flaviviridae associated with GB agent hepatitis. J Virol 1995; 69: 5621-5630.
5. Schlauder GG, Dawson GJ, Simons JN et al. Molecular and serological analysis in the transmission of the GB hepatitis agent. J Med Virol 1995; 46: 81-90.
6. Simons JN, Pilot-Matias TJ, Leary TP et al. Identification of two flavivirus-like genomes in the GB hepatitis agent. Proc Natl Acad Sci USA 1995; 92: 3401-3405.
7. Deinhardt F, Holmes A, Capps R, Popper H. Studies on the transmission of human viral hepatitis to marmoset monkeys. Transmission of disease, serial passage and description of liver lesions. J Exp Med 1967; 125: 673-687.
8. Pickering JM, Thomas H, Karayiannis P. Genetic diversity between HGV isolates: analysis of nucleotide variation in the NS-3 and putative core peptide. J Gen Virol 1997; 78: 53-60.
9. Matzura O, RNADRAW (RNA secondary structure prediction package): distributed by the author. Department of Medical Physics, Karolinska Institute, Sweden: 1996.
10. Jackson RL, Howel MT, Kaminski A. The novel mechanism of initiation of picornavirus RNA translation. Trends Biochem Sci 1990; 15: 477-483.
11. Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxilliary information. Nucl Acids Res 1981; 9: 133-148.
12. McCaskill JS. The equilibrium position function and base pair binding-probability for RNA secondary structure. Biopolymers 1990; 29: 1105-1119.
13. Freier SM, Kierzek R, Jaeger JA et al. Improved free energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA 1986; 83: 9373-9377.
14. Jaeger JA, Turner DH, Zuker M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci USA 1989; 86: 7706-7710.
15. Turner DH, Sugimoto N, Freier SM. RNA structure prediction. Annu Rev Biophys Chem 1988; 17: 167-192.
16. Brown EA, Zhang H, Ping LH, Lemon SM. Secondary structure of the 5′ nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. Nucl Acids Res 1992; 20: 5041-5045.
17. James BD, Olsen GJ, Pace NR. Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol 1989; 180: 227-239.
18. Jaeger JA, Turner DH, Zuker M. Predicting optimal and sub-optimal secondary structure of RNA. Methods Enzymol 1990; 183: 281-306.
19. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science 1989; 244: 48-52.
20. Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the vax. Nucl Acids Res 1984; 12: 387-395.
21. Turner DH, Sugimoto N, Jaeger JA, Longfellow CE, Freier SM, Kierzek R. Improved parameters for prediction of RNA structure. Cold Spring Harbor Symp Quant Biol 1987; 52: 123-133.
22. Kozak M. An analysis of 5′-noncoding sequences from 699 vertebrate messenger-RNAs. Nucl Acids Res 1987; 15: 8125-8148.
23. Simmonds P, Holmes EC, Cha TA et al. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J Gen Virol 1993; 74: 2391-2399.
24. Simmonds P, Smith DB, McOmish F et al. Identification of genotypes of hepatitis C virus by sequence comparison in the core, E1 and NS-5 regions. J Gen Virol 1994; 75: 1053-1061.
25. Bukh J, Purcell RH, Miller RH. At least 12 genotypes of hepatitis C predicted by sequence analysis of the putative E1 gene of isolates collected worldwide. Proc Natl Acad Sci USA 1993; 90: 8234-8238.
26. Tsukiyama-Kohara K, Iizua N, Kohara M, Nomoto A. Internal ribosome entry site within hepatitis C virus RNA. J Virol 1992; 66: 1476-1483.
27. Meerovitch K, Sonenberg N. Internal initiation of picornavirus RNA translation. Semin Virol 1993; 4: 217-227.
28. Kozak M. The scanning model for translation: an update. J Cell Biol 1989; 108: 229-241.
29. Kozak M. A consideration of alternative models for the initiation of translation in eukaryotes. Crit Rev Biochem Mol Biol 1992; 27: 385-102.
30. Wang C, Sarnow P, Siddiqui A. Translation of human hepatitis C virus RNA in cultured cells is mediated by an internal ribosome-binding mechanism. J Virol 1993; 67: 3338-3344.
31. Jang SK, Wimmer E. Cap-independent translation of encephalomyocarditis virus RNA: structural elements of the internal ribosome site and involvement of a cellular 57-KD RNA-binding protein. Genes Dev 1990; 4: 1560-1572.
32. Kuhn R, Liz N, Beck E. Functional analysis of the internal translation initiation site of foot and mouth disease virus. J Virol 1990; 64: 4625-4631.
33. Nicholson R, Pelletier J, Le S-Y, Sonenberg N. Structural and functional analysis of the ribosome landing pad of poliovirus type 2: in vivo translational studies. J Virol 1991; 5886-5894.
34. Pilipenko EV, Gmyl AP, Maslova SV, Svitkin AN, Sinyakov AN, Agol VI. Prokaryotic-like cis elements in the cap independent internal initiation of translation on picornavirus RNA. Cell 1992; 68: 119-131.
35. Pilipenko EV, Gmyl AP, Maslova SV et al. Starting window, a distinct element in the cap-independent internal initiation of translation on picornaviral RNA. J Mol Biol 1994; 241: 398-414.
36. Bailly JL, Borman AM, Peigue-Lafeuille H, Kean KM. Natural isolates of ECHO virus type 25 with extensive variations in IRES sequences and different translational efficiencies. Virology 1996; 215: 83-96.
37. Kaminski A, Belsham GJ, Jackson RJ. Translation of encephalomyocarditis virus RNA: parameters influencing the selection of the internal initiation site. EMBO J 1994; 13: 1673-1681.
38. Wang C, Sarnow P, Siddiqui A. A conserved helical element is essential for internal initiation of translation of hepatitis C virus RNA. J Virol 1994; 68: 7301-7307.
39. Le S-Y, Chen J-H, Sonenburg N, Maizel JV. Conserved tertiary structural elements in the 5′ nontranslated region of human enteroviruses and rhinoviruses. Virology 1992; 191: 858-866.
40. Le S-Y, Chen J-H, Sonenburg N, Maizel JV. Conserved tertiary structural elements in the 5′ nontranslated region of cardiovirus, aphthovirus and hepatitis A virus RNAs. Nucl Acids Res 1993; 21: 2445-2451.
41. Simons JN, Desai SM, Schultz DE, Lemon SM, Mushawar IK. Translation initiation in GB viruses A and C: evidence for internal ribosome entry and implications for genome organisation. J Virol 1996: 6126-6135.