Hepatitis Monthly

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Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus

Mojtaba Mortazavi 1 , Mohammad Zarenezhad 2 , 3 , Saeid Gholamzadeh 3 , Seyed Moayed Alavian 4 , Mohammad Ghorbani 5 , Reza Dehghani 6 , Abdorrasoul Malekpour 3 , * , Mohammadhasan Meshkibaf 7 and Ali Fakhrzad 2
Authors Information
1 Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, IR Iran
2 Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
3 Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran
4 Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Middle East Liver Disease Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
5 Department of Pathology, School of Medicine, Fasa University of Medical Sciences, Fasa, IR Iran
6 Pharmacology Department, School of Medicine, Shiraz University of Medical Sciences, Shiraz, IR Iran
7 Department of Biochemistry, School of Medicine, Fasa University of Medical Sciences, Fasa, IR Iran
Article information
  • Hepatitis Monthly: October 01, 2016, 16 (10); e39909
  • Published Online: October 4, 2016
  • Article Type: Research Article
  • Received: June 11, 2016
  • Revised: August 10, 2016
  • Accepted: September 24, 2016
  • DOI: 10.5812/hepatmon.39909

To Cite: Mortazavi M, Zarenezhad M, Gholamzadeh S, Alavian S M, Ghorbani M, et al. Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus, Hepat Mon. 2016 ; 16(10):e39909. doi: 10.5812/hepatmon.39909.

Copyright © 2016, Kowsar Corp. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/) which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.
1. Background
2. Objectives
3. Methods
4. Results
5. Discussion
  • 1. Norder H, Courouce AM, Coursaget P, Echevarria JM, Lee SD, Mushahwar IK, et al. Genetic diversity of hepatitis B virus strains derived worldwide: genotypes, subgenotypes, and HBsAg subtypes. Intervirology. 2004; 47(6): 289-309[DOI][PubMed]
  • 2. Robertson BH, Margolis HS. Primate hepatitis B viruses - genetic diversity, geography and evolution. Rev Med Virol. 2002; 12(3): 133-41[DOI][PubMed]
  • 3. Kramvis A. Genotypes and genetic variability of hepatitis B virus. Intervirology. 2014; 57(3-4): 141-50[DOI][PubMed]
  • 4. Magnius LO, Norder H. Subtypes, genotypes and molecular epidemiology of the hepatitis B virus as reflected by sequence variability of the S-gene. Intervirology. 1995; 38(1-2): 24-34[PubMed]
  • 5. Ocama P, Opio CK, Lee WM. Hepatitis B virus infection: current status. Am J Med. 2005; 118(12): 1413[DOI][PubMed]
  • 6. Locarnini S. Molecular virology of hepatitis B virus. Seminars Liver Dis. 2004; 24: 3-10
  • 7. Summers J, O'Connell A, Millman I. Genome of hepatitis B virus: restriction enzyme cleavage and structure of DNA extracted from Dane particles. Proc Natl Acad Sci U S A. 1975; 72(11): 4597-601[PubMed]
  • 8. Delius H, Gough NM, Cameron CH, Murray K. Structure of the hepatitis B virus genome. J Virol. 1983; 47(2): 337-43[PubMed]
  • 9. Zhang D, Chen J, Deng L, Mao Q, Zheng J, Wu J, et al. Evolutionary selection associated with the multi-function of overlapping genes in the hepatitis B virus. Infect Genet Evol. 2010; 10(1): 84-8[DOI][PubMed]
  • 10. Chen P, Gan Y, Han N, Fang W, Li J, Zhao F, et al. 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. 2013; 8(4)[DOI][PubMed]
  • 11. Alexopoulou A. Mutants in the precore, core promoter, and core regions of Hepatitis B virus, and their clinical relevance. Annals of Gastroenterology. 2009; 22(1): 13-23
  • 12. Spencer PS, Siller E, Anderson JF, Barral JM. Silent substitutions predictably alter translation elongation rates and protein folding efficiencies. J Mol Biol. 2012; 422(3): 328-35[DOI][PubMed]
  • 13. Clarke T, Clark PL. Rare codons cluster. PLoS One. 2008; 3(10)[DOI][PubMed]
  • 14. Varenne S, Buc J, Lloubes R, Lazdunski C. Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J Mol Biol. 1984; 180(3): 549-76[PubMed]
  • 15. Sorensen MA, Kurland CG, Pedersen S. Codon usage determines translation rate in Escherichia coli. J Mol Biol. 1989; 207(2): 365-77[PubMed]
  • 16. Clarke T, Clark PL. Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. BMC Genomics. 2010; 11: 118[DOI][PubMed]
  • 17. Komar AA, Jaenicke R. Kinetics of translation of γB crystallin and its circularly permutated variant in an in vitro cell‐free system: possible relations to codon distribution and protein folding. FEBS letters. 1995; 376(3): 195-8
  • 18. Kypr J. A part of codon bias in genes protects protein spatial structures from destabilization by random single point mutations. Biochem Biophys Res Commun. 1986; 139(3): 1094-7[PubMed]
  • 19. Chartier M, Gaudreault F, Najmanovich R. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. Bioinformatics. 2012; 28(11): 1438-45[DOI][PubMed]
  • 20. Fattahi M, Malekpour A, Mortazavi M, Safarpour A, Naseri N. The characteristics of rare codon clusters in the genome and proteins of hepatitis C virus; a bioinformatics look. Middle East J Dig Dis. 2014; 6(4): 214-27[PubMed]
  • 21. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016; 44-85[DOI][PubMed]
  • 22. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, et al. The Pfam protein families database. Nucleic Acids Res. 2004; 32-41[DOI][PubMed]
  • 23. Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res. 1996; 24(1): 21-5[PubMed]
  • 24. Kay A, Zoulim F. Hepatitis B virus genetic variability and evolution. Virus Res. 2007; 127(2): 164-76[DOI][PubMed]
  • 25. Tong S, Li J, Wands JR, Wen YM. Hepatitis B virus genetic variants: biological properties and clinical implications. Emerg Microbes Infect. 2013; 2(3)[DOI][PubMed]
  • 26. Norder H, Hammas B, Lofdahl S, Courouce AM, Magnius LO. Comparison of the amino acid sequences of nine different serotypes of hepatitis B surface antigen and genomic classification of the corresponding hepatitis B virus strains. J Gen Virol. 1992; 73 ( Pt 5): 1201-8[DOI][PubMed]
  • 27. Rahman MA, Hakim F, Ahmed M, Ahsan CR, Nessa J, Yasmin M. Prevalence of genotypes and subtypes of hepatitis B viruses in Bangladeshi population. Springerplus. 2016; 5: 278[DOI][PubMed]
  • 28. Eddy S. The HMMER User Guide. 2003;
  • 29. Nakamura Y, Gojobori T, Ikemura T. Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 2000; 28(1): 292[PubMed]
  • 30. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The Protein Data Bank. Nucleic Acids Res. 2000; 28(1): 235-42[PubMed]
  • 31. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 2003; 31(13): 3381-5[PubMed]
  • 32. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008; 9: 40[DOI][PubMed]
  • 33. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallograph. 1993; 26(2): 283-91
  • 34. Ramachandran GN, Ramakrishnan C, Sasisekharan V. Stereochemistry of polypeptide chain configurations. J Mol Biol. 1963; 7: 95-9[PubMed]
  • 35. DeLano WL. The PyMOL molecular graphics system. 2002;
  • 36. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, et al. Pfam Protein Fam Database. Nucleic Acids Res. 2009; 1
  • 37. Tu X, Das K, Han Q, Bauman JD, Clark AJ, Hou X, et al. Structural basis of HIV-1 resistance to AZT by excision. Nat Struct Mol Biol. 2010; 17(10): 1202-9[DOI][PubMed]
  • 38. Pasek M, Goto T, Gilbert W, Zink B, Schaller H, MacKay P, et al. Hepatitis B virus genes and their expression in E. coli. Nature. 1979; 282(5739): 575-9[PubMed]
  • 39. Kidd-Ljunggren K, Oberg M, Kidd AH. The hepatitis B virus X gene: analysis of functional domain variation and gene phylogeny using multiple sequences. J Gen Virol. 1995; 76: 2119-30[DOI][PubMed]
  • 40. Renner M, Haniel A, Burgelt E, Hofschneider PH, Koch W. Transactivating function and expression of the x gene of hepatitis B virus. J Hepatol. 1995; 23(1): 53-65[PubMed]
  • 41. Cao F, Jones S, Li W, Cheng X, Hu Y, Hu J, et al. Sequences in the terminal protein and reverse transcriptase domains of the hepatitis B virus polymerase contribute to RNA binding and encapsidation. J Viral Hepat. 2014; 21(12): 882-93[DOI][PubMed]
  • 42. Thanaraj TA, Argos P. Protein secondary structural types are differentially coded on messenger RNA. Protein Sci. 1996; 5(10): 1973-83[DOI][PubMed]
  • 43. da Silveira NJ, Arcuri HA, Bonalumi CE, de Souza FP, Mello IM, Rahal P, et al. Molecular models of NS3 protease variants of the Hepatitis C virus. BMC Struct Biol. 2005; 5: 1[DOI][PubMed]
  • 44. Lovell SC, Davis IW, Arendall W3, de Bakker PI, Word JM, Prisant MG, et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003; 50(3): 437-50[DOI][PubMed]
  • 45. Roberts L, Holcik M. RNA structure: new messages in translation, replication and disease. Workshop on the role of RNA structures in the translation of viral and cellular RNAs. EMBO Rep. 2009; 10(5): 449-53[DOI][PubMed]
  • 46. Daga PR, Duan J, Doerksen RJ. Computational model of hepatitis B virus DNA polymerase: molecular dynamics and docking to understand resistant mutations. Protein Sci. 2010; 19(4): 796-807[DOI][PubMed]
  • 47. Mortazavi M, Nezafat N, Negahdaripour M, Gholami A, Torkzadeh-Mahani M, Lotfi S, et al. In silico evaluation of rare codons and their positions in the structure of cytosine deaminase and substrate docking studies. Trends Pharm Sci. 2016; 2(2)
  • 48. Bina S, Shenavar F, Khodadad M, Haghshenas MR, Mortazavi M, Fattahi MR, et al. Impact of RGD Peptide Tethering to IL24/mda-7 (Melanoma Differentiation Associated Gene-7) on Apoptosis Induction in Hepatocellular Carcinoma Cells. Asian Pac J Cancer Prev. 2015; 16(14): 6073-80[PubMed]
  • 49. Mortazavi M, Hosseinkhani S. Design of thermostable luciferases through arginine saturation in solvent-exposed loops. Protein Eng Des Sel. 2011; 24(12): 893-903[DOI][PubMed]
  • 50. Junker M, Galle P, Schaller H. Expression and replication of the hepatitis B virus genome under foreign promoter control. Nucleic Acids Res. 1987; 15(24): 10117-32[PubMed]
  • 51. Garcia PD, Ou JH, Rutter WJ, Walter P. Targeting of the hepatitis B virus precore protein to the endoplasmic reticulum membrane: after signal peptide cleavage translocation can be aborted and the product released into the cytoplasm. J Cell Biol. 1988; 106(4): 1093-104[PubMed]
  • 52. Wang J, Lee AS, Ou JH. Proteolytic conversion of hepatitis B virus e antigen precursor to end product occurs in a postendoplasmic reticulum compartment. J Virol. 1991; 65(9): 5080-3[PubMed]
  • 53. Laine S, Salhi S, Rossignol JM. Overexpression and purification of the hepatitis B e antigen precursor. J Virol Methods. 2002; 103(1): 67-74[PubMed]
  • 54. Ganem D, Schneider RJ. Hepadnaviridae: the viruses and their replication. Fields Virol. 2001; 2: 2923-69
  • 55. Jaoude GA, Sureau C. Role of the antigenic loop of the hepatitis B virus envelope proteins in infectivity of hepatitis delta virus. J Virol. 2005; 79(16): 10460-6[DOI][PubMed]
  • 56. Echevarria JM, Avellon A. Hepatitis B virus genetic diversity. J Med Virol. 2006; 78 Suppl 1-42[DOI][PubMed]
  • 57. Funk A, Mhamdi M, Will H, Sirma H. Avian hepatitis B viruses: molecular and cellular biology, phylogenesis, and host tropism. World J Gastroenterol. 2007; 13(1): 91-103[PubMed]
  • 58. Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 1997; 28(3): 405-20[PubMed]
  • 59. Widmann M, Clairo M, Dippon J, Pleiss J. Analysis of the distribution of functionally relevant rare codons. BMC Genomics. 2008; 9: 207[DOI][PubMed]
  • 60. Churin Y, Roderfeld M, Roeb E. Hepatitis B virus large surface protein: function and fame. Hepatobiliary Surg Nutr. 2015; 4(1): 1-10[DOI][PubMed]
  • 61. Mizokami M, Orito E, Ohba K, Ikeo K, Lau JY, Gojobori T. Constrained evolution with respect to gene overlap of hepatitis B virus. J Mol Evol. 1997; 44 Suppl 1-90[PubMed]
  • 62. van Hemert FJ, Zaaijer HL, Berkhout B, Lukashov VV. Mosaic amino acid conservation in 3D-structures of surface protein and polymerase of hepatitis B virus. Virology. 2008; 370(2): 362-72[DOI][PubMed]
  • 63. Bartholomeusz A, Locarnini S. Hepatitis B virus mutations associated with antiviral therapy. J Med Virol. 2006; 78 Suppl 1-5[DOI][PubMed]
  • 64. Kamer G, Argos P. Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res. 1984; 12(18): 7269-82[PubMed]
  • 65. Wainberg MA, Drosopoulos WC, Salomon H, Hsu M, Borkow G, Parniak M, et al. Enhanced fidelity of 3TC-selected mutant HIV-1 reverse transcriptase. Science. 1996; 271(5253): 1282-5[PubMed]
  • 66. Tantillo C, Ding J, Jacobo-Molina A, Nanni RG, Boyer PL, Hughes SH, et al. Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase. Implications for mechanisms of drug inhibition and resistance. J Mol Biol. 1994; 243(3): 369-87[DOI][PubMed]
  • 67. Poch O, Sauvaget I, Delarue M, Tordo N. Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J. 1989; 8(12): 3867-74[PubMed]
  • 68. Lingner J, Hughes TR, Shevchenko A, Mann M, Lundblad V, Cech TR. Reverse transcriptase motifs in the catalytic subunit of telomerase. Science. 1997; 276(5312): 561-7[PubMed]
  • 69. Ono-Nita SK, Kato N, Shiratori Y, Masaki T, Lan KH, Carrilho FJ, et al. YMDD motif in hepatitis B virus DNA polymerase influences on replication and lamivudine resistance: A study by in vitro full-length viral DNA transfection. Hepatology. 1999; 29(3): 939-45[DOI][PubMed]
  • 70. Rosano GM, Vitale C, Fini M. Cardiovascular aspects of menopausal hormone replacement therapy. Climacteric. 2009; 12 Suppl 1: 41-6[PubMed]
  • 71. Mauro VP, Chappell SA. A critical analysis of codon optimization in human therapeutics. Trends Mol Med. 2014; 20(11): 604-13[DOI][PubMed]
  • 72. Glebe D. Hepatitis B virus morphogenesis. World J Gastroenterol. 2007; 13(1): 65-73
  • 73. Glebe D, Urban S, Knoop EV, Cag N, Krass P, Grun S, et al. Mapping of the hepatitis B virus attachment site by use of infection-inhibiting preS1 lipopeptides and tupaia hepatocytes. Gastroenterology. 2005; 129(1): 234-45[PubMed]
  • 74. Meier A, Mehrle S, Weiss TS, Mier W, Urban S. Myristoylated PreS1-domain of the hepatitis B virus L-protein mediates specific binding to differentiated hepatocytes. Hepatology. 2013; 58(1): 31-42[DOI][PubMed]
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