Computational Evolutionary Analysis of the Overlapped Surface (S) and Polymerase (P) Region in Hepatitis B Virus Indicates the Spacer Domain in P Is Crucial for Survival

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Chen, Ping ^a   Gan, Yun ^a   Han, Na ^a   Fang, Wei ^a   Li, Jiafu ^b   Zhao, Fei ^a   Hu, Kanghong ^a,c   Rayner, Simon ^a  

^a WUHAN INSTITUTE OF VIROLOGY   (China)

^b ZHONGNAN HOSPITAL OF WUHAN UNIVERSITY   (China)

^c HUBEI UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; EPITOPE; MEMBRANE PROTEIN;

ALPHA HELIX; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; ENTROPY; GENE MUTATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC SELECTION; GENOTYPE; HEPATITIS B VIRUS; HYDROPHILICITY; IMMUNE RESPONSE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PREDICTION; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; VIRUS GENOME; VIRUS SURVIVAL;

COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, GENETIC; DNA-DIRECTED DNA POLYMERASE; EPITOPES; EVOLUTION, MOLECULAR; GENOME, VIRAL; HEPATITIS B VIRUS; HUMANS; MICROBIAL VIABILITY; MODELS, MOLECULAR; OPEN READING FRAMES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RNA-DIRECTED DNA POLYMERASE; SELECTION, GENETIC; VIRAL PROTEINS;

HEPATITIS B VIRUS;

EID: 84875914676     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060098     Document Type: Article

References (73)

1. Rehermann B, Nascimbeni M, (2005) Immunology of hepatitis B virus and hepatitis C virus infection. Nat Rev Immunol 5: 215-229.
2. Guidotti LG, Chisari FV, (2006) Immunobiology and pathogenesis of viral hepatitis. Annu Rev Pathol 1: 23-61.
3. Hoofnagle JH, (2002) Course and outcome of hepatitis C. Hepatology. 36: S21-29.
4. Ganem D, Prince AM, (2004) Hepatitis B virus infection-natural history and clinical consequences. N Engl J Med 350: 1118-1129.
5. Reed KE, Rice CM, (2000) Overview of hepatitis C virus genome structure, polyprotein processing, and protein properties. Curr Top Microbiol Immunol 242: 55-84.
6. Hughes AL, Westover K, da Silva J, O'Connor DH, Watkins DI, (2001) Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus. J Virol 75: 7966-7972.
7. Guyader S, Ducray DG, (2002) Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J Gen Virol 83: 1799-1807.
8. Narechania A, Terai M, Burk RD, (2005) Overlapping reading frames in closely related human papillomaviruses result in modular rates of selection within E2. J Gen Virol 86: 1307-1313.
9. Pybus OG, Barnes E, Taggart R, Lemey P, Markov PV, et al. (2009) Genetic history of hepatitis C virus in East Asia. J Virol 83: 1071-1082.
10. Salemi M, Vandamme AM, (2002) Hepatitis C virus evolutionary patterns studied through analysis of full-genome sequences. J Mol Evol 54: 62-70.
11. Tanaka Y, Hanada K, Mizokami M, Yeo AE, Shih JW, et al. (2002) A comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United States will increase over the next two decades. Proc Natl Acad Sci U S A 99: 15584-15589.
12. Radziwill G, Tucker W, Schaller H, (1990) Mutational analysis of the hepatitis B virus P gene product: domain structure and RNase H activity. J Virol 64: 613-620.
13. Nassal M, (2008) Hepatitis B viruses: reverse transcription a different way. Virus Res 134: 235-249.
14. Feng H, Hu K, (2009) Structural Characteristics and Molecular Mechanism of Hepatitis B Virus Reverse Transcriptase. Virol Sin 24: 509-517.
15. Ni Y, Sonnabend J, Seitz S, Urban S, (2010) The pre-s2 domain of the hepatitis B virus is dispensable for infectivity but serves a spacer function for L-protein-connected virus assembly. J Virol 84: 3879-3888.
16. Stirk HJ, Thornton JM, Howard CR, (1992) A topological model for hepatitis B surface antigen. Intervirology 33: 148-158.
17. Carman WF, (1997) The clinical significance of surface antigen variants of hepatitis B virus. J Viral Hepat 4Suppl 1: 11-20.
18. Wu C, Deng W, Deng L, Cao L, Qin B, et al. (2012) Amino acid substitutions at positions 122 and 145 of hepatitis B virus surface antigen (HBsAg) determine the antigenicity and immunogenicity of HBsAg and influence in vivo HBsAg clearance. J Virol 86: 4658-4669.
19. Chisari FV, Ferrari C, (1995) Hepatitis B virus immunopathogenesis. Annu Rev Immunol 13: 29-60.
20. Huang CF, Lin SS, Ho YC, Chen FL, Yang CC, (2006) The immune response induced by hepatitis B virus principal antigens. Cell Mol Immunol 3: 97-106.
21. Ogura Y, Kurosaki M, Asahina Y, Enomoto N, Marumo F, et al. (1999) Prevalence and significance of naturally occurring mutations in the surface and polymerase genes of hepatitis B virus. J Infect Dis 180: 1444-1451.
22. Kakimi K, Isogawa M, Chung J, Sette A, Chisari FV, (2002) Immunogenicity and tolerogenicity of hepatitis B virus structural and nonstructural proteins: implications for immunotherapy of persistent viral infections. J Virol 76: 8609-8620.
23. Rehermann B, Fowler P, Sidney J, Person J, Redeker A, et al. (1995) The cytotoxic T lymphocyte response to multiple hepatitis B virus polymerase epitopes during and after acute viral hepatitis. J Exp Med 181: 1047-1058.
24. Mizukoshi E, Sidney J, Livingston B, Ghany M, Hoofnagle JH, et al. (2004) Cellular immune responses to the hepatitis B virus polymerase. J Immunol 173: 5863-5871.
25. Depla E, Van der Aa A, Livingston BD, Crimi C, Allosery K, et al. (2008) Rational design of a multiepitope vaccine encoding T-lymphocyte epitopes for treatment of chronic hepatitis B virus infections. J Virol 82: 435-450.
26. Sobao Y, Sugi K, Tomiyama H, Saito S, Fujiyama S, et al. (2001) Identification of hepatitis B virus-specific CTL epitopes presented by HLA-A*2402, the most common HLA class I allele in East Asia. J Hepatol 34: 922-929.
27. van der Burg SH, Visseren MJ, Brandt RM, Kast WM, Melief CJ, (1996) Immunogenicity of peptides bound to MHC class I molecules depends on the MHC-peptide complex stability. J Immunol 156: 3308-3314.
28. Mizokami M, Orito E, Ohba K, Ikeo K, Lau JY, et al. (1997) Constrained evolution with respect to gene overlap of hepatitis B virus. J Mol Evol 44Suppl 1: S83-90.
29. Zaaijer HL, van Hemert FJ, Koppelman MH, Lukashov VV, (2007) Independent evolution of overlapping polymerase and surface protein genes of hepatitis B virus. J Gen Virol 88: 2137-2143.
30. van de Klundert MA, Cremer J, Kootstra NA, Boot HJ, Zaaijer HL, (2012) Comparison of the hepatitis B virus core, surface and polymerase gene substitution rates in chronically infected patients. J Viral Hepat 19: e34-40.
31. Myers R, Clark C, Khan A, Kellam P, Tedder R, (2006) Genotyping Hepatitis B virus from whole- and sub-genomic fragments using position-specific scoring matrices in HBV STAR. J Gen Virol 87: 1459-1464.
32. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
33. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
34. Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
35. Yang Z, Wong WS, Nielsen R, (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol 22: 1107-1118.
36. Pond SL, Frost SD, Muse SV, (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
37. Strait BJ, Dewey TG, (1996) The Shannon information entropy of protein sequences. Biophys J 71: 148-155.
38. Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M, (1995) Evaluation of comparative protein modeling by MODELLER. Proteins 23: 318-326.
39. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.
40. Zhang Y, (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9: 40.
41. Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
42. Wang Z, Zhao F, Peng J, Xu J, (2011) Protein 8-class secondary structure prediction using conditional neural fields. Proteomics 11: 3786-3792.
43. Daga PR, Duan J, Doerksen RJ, (2010) Computational model of hepatitis B virus DNA polymerase: molecular dynamics and docking to understand resistant mutations. Protein Sci 19: 796-807.
44. Pirovano W, Heringa J, (2010) Protein secondary structure prediction. Methods Mol Biol 609: 327-348.
45. Bettella F, Rasinski D, Knapp EW, (2012) Protein secondary structure prediction with SPARROW. J Chem Inf Model 52: 545-556.
46. Cheng J, Tegge AN, Baldi P, (2008) Machine learning methods for protein structure prediction. IEEE Rev Biomed Eng 1: 41-49.
47. Mikulska M, Taramasso L, Giacobbe DR, Caligiuri P, Bruzzone B, et al. (2012) Case report: Management and HBV sequencing in a patient co-infected with HBV and HIV failing tenofovir. J Med Virol 84: 1340-1343.
48. Schewe K, Noah C, Sirma H, Schmiedel S, van Lunzen J, et al. (2010) Is there Emergence of Clinical HBV Resistance Under Long-Term HBV Combination Therapy? A Challenging Case Report. Viruses 2: 1564-1570.
49. Durantel D, (2010) Fitness and infectivity of drug-resistant and cross-resistant hepatitis B virus mutants: why and how is it studied? Antivir Ther 15: 521-527.
50. Snoeck J, Fellay J, Bartha I, Douek DC, Telenti A, (2011) Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints. Retrovirology 8: 87.
51. Coleman PF, (2006) Detecting hepatitis B surface antigen mutants. Emerg Infect Dis 12: 198-203.
52. Lai MW, Yeh CS, Yeh CT, (2010) Infection with hepatitis B virus carrying novel pre-S/S gene mutations in female siblings vaccinated at birth: two case reports. J Med Case Rep 4: 190.
53. Jung MC, Diepolder HM, Pape GR, (1994) T cell recognition of hepatitis B and C viral antigens. Eur J Clin Invest 24: 641-650.
54. Chang JJ, Lewin SR, (2007) Immunopathogenesis of hepatitis B virus infection. Immunol Cell Biol 85: 16-23.
55. Bertoletti A, Maini MK, Ferrari C, (2010) The host-pathogen interaction during HBV infection: immunological controversies. Antivir Ther 15Suppl 3: 15-24.
56. Chen MT, Billaud JN, Sallberg M, Guidotti LG, Chisari FV, et al. (2004) A function of the hepatitis B virus precore protein is to regulate the immune response to the core antigen. Proc Natl Acad Sci U S A 101: 14913-14918.
57. Milich DR, Jones JE, Hughes JL, Price J, Raney AK, et al. (1990) Is a function of the secreted hepatitis B e antigen to induce immunologic tolerance in utero? Proc Natl Acad Sci U S A 87: 6599-6603.
58. Hu Z, Zhang Z, Doo E, Coux O, Goldberg AL, et al. (1999) Hepatitis B virus X protein is both a substrate and a potential inhibitor of the proteasome complex. J Virol 73: 7231-7240.
59. Yewdell JW, Bennink JR, (1999) Mechanisms of viral interference with MHC class I antigen processing and presentation. Annu Rev Cell Dev Biol 15: 579-606.
60. Nikolich-Zugich J, Slifka MK, Messaoudi I, (2004) The many important facets of T-cell repertoire diversity. Nat Rev Immunol 4: 123-132.
61. Doherty PC, (1993) Immune exhaustion: driving virus-specific CD8+ T cells to death. Trends Microbiol 1: 207-209.
62. Stoop JN, van der Molen RG, Baan CC, van der Laan LJ, Kuipers EJ, et al. (2005) Regulatory T cells contribute to the impaired immune response in patients with chronic hepatitis B virus infection. Hepatology 41: 771-778.
63. Donlin MJ, Szeto B, Gohara DW, Aurora R, Tavis JE, (2012) Genome-wide networks of amino acid covariances are common among viruses. J Virol 86: 3050-3063.
64. Hu J, Boyer M, (2006) Hepatitis B virus reverse transcriptase and epsilon RNA sequences required for specific interaction in vitro. J Virol 80: 2141-2150.
65. Badtke MP, Khan I, Cao F, Hu J, Tavis JE, (2009) An interdomain RNA binding site on the hepadnaviral polymerase that is essential for reverse transcription. Virology 390: 130-138.
66. Hu J, Flores D, Toft D, Wang X, Nguyen D, (2004) Requirement of heat shock protein 90 for human hepatitis B virus reverse transcriptase function. J Virol 78: 13122-13131.
67. Hu J, Toft D, Anselmo D, Wang X, (2002) In vitro reconstitution of functional hepadnavirus reverse transcriptase with cellular chaperone proteins. J Virol 76: 269-279.
68. Stahl M, Retzlaff M, Nassal M, Beck J, (2007) Chaperone activation of the hepadnaviral reverse transcriptase for template RNA binding is established by the Hsp70 and stimulated by the Hsp90 system. Nucleic Acids Res 35: 6124-6136.
69. Wang X, Grammatikakis N, Hu J, (2002) Role of p50/CDC37 in hepadnavirus assembly and replication. J Biol Chem 277: 24361-24367.
70. Blanchet M, Sureau C, (2007) Infectivity determinants of the hepatitis B virus pre-S domain are confined to the N-terminal 75 amino acid residues. J Virol 81: 5841-5849.
71. Le Seyec J, Chouteau P, Cannie I, Guguen-Guillouzo C, Gripon P, (1999) Infection process of the hepatitis B virus depends on the presence of a defined sequence in the pre-S1 domain. J Virol 73: 2052-2057.
72. Prange R, Streeck RE, (1995) Novel transmembrane topology of the hepatitis B virus envelope proteins. EMBO J 14: 247-256.
73. Bruss V, (1997) A short linear sequence in the pre-S domain of the large hepatitis B virus envelope protein required for virion formation. J Virol 71: 9350-9357.