Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

  • 68 Accesses

Abstract

Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid. The major factors contributing to CUB are evolutionary forces, compositional properties, gene expression, and protein properties. The present analysis was performed to investigate the compositional properties and the extent of CUB across the genomes of members of the family Hepadnaviridae, as previously no work using bioinformatic tools has been reported. The viral genes were found to be AT rich with low CUB. Analysis of relative synonymous codon usage (RSCU) was used to identify overrepresented and underrepresented codons for each amino acid. Correlation analysis of overall nucleotide composition and its composition at the third codon position suggested that mutation pressure might influence the CUB. A highly significant correlation was observed between GC12 and GC3 (r = 0.910, p < 0.01), indicating that directional mutation affected all three codon positions across the genome. Translational selection (P2) and mutational responsive index (MRI) values of genes suggested that mutation plays a more important role than translational selection in members of the family Hepadnaviridae.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

References

  1. 1.

    Bajunaid HA (2013) Genetic variability of Hepatitis B virus, University of Nottingham

  2. 2.

    Beasley RP (1988) Hepatitis B virus. The major etiology of hepatocellular carcinoma. Cancer 61(10):1942–1956

  3. 3.

    Bennetzen JL, Hall BD (1982) Codon selection in yeast. J Biol Chem 257(6):3026–3031

  4. 4.

    Bernardi G, Olofsson B et al (1985) The mosaic genome of warm-blooded vertebrates. Science 228(4702):953–958

  5. 5.

    Bibb M, Findlay P et al (1984) The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene 30(1–3):157–166

  6. 6.

    Blitvich B, Firth A (2015) Insect-specific flaviviruses: a systematic review of their discovery, host range, mode of transmission, superinfection exclusion potential and genomic organization. Viruses 7(4):1927–1959

  7. 7.

    Bouquet J, Cherel P et al (2012) Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution. Infection, Genetics and Evolution 12(8):1842–1853

  8. 8.

    Butt AM, Nasrullah I et al (2016) Evolution of codon usage in Zika virus genomes is host and vector specific. Emerg Microbes Infect 5(1):1–14

  9. 9.

    Butt AM, Nasrullah I et al (2014) “Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. PloS One 9(3):e90905

  10. 10.

    Chakraborty S, Deb B et al (2019) Analysis of codon usage patterns and influencing factors in Nipah virus. Virus Res 263:129–138

  11. 11.

    Choudhury MN, Chakraborty S (2015) Codon usage pattern in human SPANX genes. Bioinformation 11(10):454

  12. 12.

    Cote PJ, Toshkov I et al (2000) Temporal pathogenesis of experimental neonatal woodchuck hepatitis virus infection: increased initial viral load and decreased severity of acute hepatitis during the development of chronic viral infection. Hepatology 32(4):807–817

  13. 13.

    Deb B, Uddin A et al (2018) Analysis of codon usage pattern of mitochondrial protein-coding genes in different hookworms. Mol Biochem Parasitol 219:24–32

  14. 14.

    Deka H, Chakraborty S (2016) Insights into the usage of nucleobase triplets and codon context pattern in five influenza A virus subtypes. J Microbiol Biotechnol 26(11):1972–1982

  15. 15.

    Deka H, Nath D et al (2019) DNA compositional dynamics and codon usage patterns of M1 and M2 matrix protein genes in influenza A virus. Infect Genet Evol 67:7–16

  16. 16.

    Dittmar KA, Goodenbour JM et al (2006) Tissue-specific differences in human transfer RNA expression. PLoS Genet 2(12):e221

  17. 17.

    Eyre-Walker A (1996) Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy? Mol Biol Evol 13(6):864–872

  18. 18.

    Franzo G, Segales J et al (2018) The analysis of genome composition and codon bias reveals distinctive patterns between avian and mammalian circoviruses which suggest a potential recombinant origin for Porcine circovirus 3. PloS One 13(6):e0199950

  19. 19.

    Fu M (2010) Codon usage bias in herpesvirus. Arch Virol 155(3):391–396

  20. 20.

    Gatherer D, McEwan NR (1997) Small regions of preferential codon usage and their effect on overall codon bias-The case of the plp gene. IUBMB Life 43(1):107–114

  21. 21.

    Goldhirsch A, Wood WC et al (2011) Strategies for subtypes—dealing with the diversity of breast cancer: highlights of the St Gallen international expert consensus on the primary therapy of early breast cancer 2011. Ann Oncol 22(8):1736–1747

  22. 22.

    Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10(22):7055–7074

  23. 23.

    Greco N, Hayes MH et al (2014) Snow goose hepatitis B virus (SGHBV) envelope and capsid proteins independently contribute to the ability of SGHBV to package capsids containing single-stranded DNA in virions. J Virol 88(18):10705–10713

  24. 24.

    Gun L, Haixian P et al (2018) Codon usage characteristics of PB2 gene in influenza A H7N9 virus from different host species. Infect Genet Evol 65:430–435

  25. 25.

    Gupta S, Ghosh T (2001) Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gene 273(1):63–70

  26. 26.

    Gustafsson C, Govindarajan S et al (2004) Codon bias and heterologous protein expression. Trends Biotechnol 22(7):346–353

  27. 27.

    Hargrove JL, Schmidt FH (1989) The role of mRNA and protein stability in gene expression. FASEB J 3(12):2360–2370

  28. 28.

    Hassan H, Mohamed M et al (2010) Effect of using organic acids to substitute antibiotic growth promoters on performance and intestinal microflora of broilers. Asian Austr J Anim Sci 23(10):1348–1353

  29. 29.

    Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 146(1):1–21

  30. 30.

    Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151(3):389–409

  31. 31.

    Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2(1):13–34

  32. 32.

    Jenkins GM, Holmes EC (2003) The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res 92(1):1–7

  33. 33.

    Jiang Y, Deng F et al (2008) An extensive analysis on the global codon usage pattern of baculoviruses. Arch Virol 153(12):2273

  34. 34.

    Karlin S, Blaisdell BE et al (1990) Contrasts in codon usage of latent versus productive genes of Epstein-Barr virus: data and hypotheses. J Virol 64(9):4264–4273

  35. 35.

    Karlin S, Mrázek J (1996) What drives codon choices in human genes? J Mol Biol 262(4):459–472

  36. 36.

    Kaufmann WK, Paules RS (1996) DNA damage and cell cycle checkpoints. FASEB J 10(2):238–247

  37. 37.

    Kober KM, Pogson GH (2013) Genome-wide patterns of codon bias are shaped by natural selection in the purple sea urchin, Strongylocentrotus purpuratus. G3: Genes|Genomes|Genetics 3(7):1069–1083

  38. 38.

    Kumar N, Bera BC et al (2016) Revelation of influencing factors in overall codon usage bias of equine influenza viruses. PloS One 11(4):e0154376

  39. 39.

    Liu Q (2006) Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans. Biosystems 85(2):99–106

  40. 40.

    Liu X-S, Zhang Y-G et al (2012) Patterns and influencing factor of synonymous codon usage in porcine circovirus. Virol J 9(1):68

  41. 41.

    Lobry J (1996) Origin of replication of Mycoplasma genitalium. Science 272:745–746

  42. 42.

    Ma M-R, Ha X-Q et al (2011) The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern. Virol J 8(1):544

  43. 43.

    Marion PL, Knight SS et al (1983) Ground squirrel hepatitis virus infection. Hepatology 3(4):519–527

  44. 44.

    Mazumder GA, Uddin A et al (2018) Codon usage pattern of complex III gene of respiratory chain among platyhelminths. Infect Genet Evol 57:128–137

  45. 45.

    Mazumder GA, Uddin A et al (2018) Preference of A/T ending codons in mitochondrial ATP6 gene under phylum Platyhelminthes: codon usage of ATP6 gene in Platyhelminthes. Mol Biochem Parasitol 225:15–26

  46. 46.

    Moritz C, Dowling T et al (1987) Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu Rev Ecol Syst 18(1):269–292

  47. 47.

    Mueller S, Papamichail D et al (2006) “Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity. J Virol 80(19):9687–9696

  48. 48.

    Nakamura Y, Gojobori T et al (1997) Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res 25(1):244–245

  49. 49.

    Palidwor GA, Perkins TJ et al (2010) A general model of codon bias due to GC mutational bias. PloS One 5(10):e13431

  50. 50.

    Pavlov IP, Anrep GV (2003) Conditioned reflexes. Courier Corporation, Mineola

  51. 51.

    Peck KM, Lauring AS (2018) Complexities of viral mutation rates. J Virol 92(14):e01031-01017

  52. 52.

    Plotkin JB, Kudla G (2011) Synonymous but not the same: the causes and consequences of codon bias. Nature Rev Genetics 12(1):32

  53. 53.

    Plotkin JB, Robins H et al (2004) Tissue-specific codon usage and the expression of human genes. Proc Natl Acad Sci 101(34):12588–12591

  54. 54.

    Presnyak V, Alhusaini N et al (2015) Codon optimality is a major determinant of mRNA stability. Cell 160(6):1111–1124

  55. 55.

    Rajewska M, Wegrzyn K et al (2012) AT-rich region and repeated sequences–the essential elements of replication origins of bacterial replicons. FEMS Microbiol Rev 36(2):408–434

  56. 56.

    Reis MD, Savva R et al (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 32(17):5036–5044

  57. 57.

    Ringnér M, Krogh M (2005) Folding free energies of 5′-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS Comput Biol 1(7):e72

  58. 58.

    Samuel A, Knowles N et al (1999) Genetic analysis of type O viruses responsible for epidemics of foot-and-mouth disease in North Africa. Epidemiol Infect 122(3):529–538

  59. 59.

    Sanjuán R, Nebot MR et al (2010) Viral mutation rates. J Virol 84(19):9733–9748

  60. 60.

    Sau K, Gupta S et al (2006) Factors influencing synonymous codon and amino acid usage biases in Mimivirus. Biosystems 85(2):107–113

  61. 61.

    Seeger C, Mason WS (2000) Hepatitis B virus biology. Microbiol Mol Biol Rev 64(1):51–68

  62. 62.

    Shackelton LA, Parrish CR et al (2006) Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol 62(5):551–563

  63. 63.

    Sharp PM, Li W-H (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for ‘rare’ codons. Nucleic Acids Res 14(19):7737–7749

  64. 64.

    Sharp PM, Li W-H (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 24(1–2):28–38

  65. 65.

    Sharp PM, Li W-H (1987) The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15(3):1281–1295

  66. 66.

    Sharp PM, Matassi G (1994) Codon usage and genome evolution. Curr Opin Genet Dev 4(6):851–860

  67. 67.

    Sharp PM, Stenico M et al (1993) Codon usage: mutational bias, translational selection, or both? Biochem Soc Trans 21(4):835

  68. 68.

    Su M-W, Lin H-M et al (2009) Categorizing host-dependent RNA viruses by principal component analysis of their codon usage preferences. J Comput Biol 16(11):1539–1547

  69. 69.

    Sueoka N (1961) Compositional correlation between deoxyribonucleic acid and protein. Cold Spring Harbor symposia on quantitative biology. Cold Spring Harbor Laboratory Press, New York

  70. 70.

    Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci 85(8):2653–2657

  71. 71.

    Sueoka N (1995) Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol 40(3):318–325

  72. 72.

    Sun D, Zhu L et al (2018) Recent progress in potential anti-hepatitis B virus agents: structural and pharmacological perspectives. Eur J Med Chem 147:205–217

  73. 73.

    Sur S, Sen A et al (2007) Mutational drift prevails over translational efficiency in Frankia nif operons. Indian J Biotechnol 6(3):321–328

  74. 74.

    Tamura K, Nei M et al (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci 101(30):11030–11035

  75. 75.

    Tao P, Dai L et al (2009) Analysis of synonymous codon usage in classical swine fever virus. Virus Genes 38(1):104–112

  76. 76.

    Uddin A, Chakraborty S (2016) Codon usage trend in mitochondrial CYB gene. Gene 586(1):105–114

  77. 77.

    Uddin A, Chakraborty S (2018) Codon usage pattern of genes involved in central nervous system. Mol Neurobiol 2018:1–12

  78. 78.

    van Hemert FJ, Berkhout B et al (2007) Host-related nucleotide composition and codon usage as driving forces in the recent evolution of the Astroviridae. Virology 361(2):447–454

  79. 79.

    Wan X-F, Xu D et al (2004) Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol Biol 4(1):19

  80. 80.

    Wei L, He J et al (2014) Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution. BMC Evol Biol 14(1):262

  81. 81.

    Wong EH, Smith DK et al (2010) Codon usage bias and the evolution of influenza A viruses. Codon usage biases of influenza virus. BMC Evol Biol 10(1):253

  82. 82.

    Woo PC, Wong BH et al (2007) Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Virology 369(2):431–442

  83. 83.

    World Health Organization (2017) Hepatitis B factsheet. World Health Organization, Geneva

  84. 84.

    Wright F (1990) The ‘effective number of codons’ used in a gene. Gene 87(1):23–29

  85. 85.

    Xu C, Guo H et al (2010) “Interferons accelerate decay of replication-competent nucleocapsids of hepatitis B virus. J Virol 84(18):9332–9340

  86. 86.

    Zanetti AR, Van Damme P et al (2008) The global impact of vaccination against hepatitis B: a historical overview. Vaccine 26(49):6266–6273

  87. 87.

    Zhang J, Wang M et al (2011) Analysis of codon usage and nucleotide composition bias in polioviruses. Virol J 8(1):146

  88. 88.

    Zhang Z, Dai W et al (2013) Synonymous codon usage in TTSuV2: analysis and comparison with TTSuV1. PloS One 8(11):e81469

  89. 89.

    Zhang Z, Dai W, Wang Y, Lu C, Fan H (2013) Analysis of synonymous codon usage patterns in torque teno sus virus 1 (TTSuV1). Arch Virol 158:145–154

  90. 90.

    Zhao S, Zhang Q et al (2007) The factors shaping synonymous codon usage in the genome of Burkholderia mallei. J Genet Genom 34(4):362–372

  91. 91.

    Zhao S, Zhang Q et al (2008) Analysis of synonymous codon usage in 11 Human Bocavirus isolates. Biosystems 92(3):207–214

  92. 92.

    Zhong J, Li Y et al (2007) Mutation pressure shapes codon usage in the GC-Rich genome of foot-and-mouth disease virus. Virus Genes 35(3):767–776

  93. 93.

    Zhou H, Wang H et al (2005) “Heterogeneity in codon usages of sobemovirus genes. Arch Virol 150(8):1591–1605

  94. 94.

    Zhou J-H, Gao Z-L et al (2013) The analysis of codon bias of foot-and-mouth disease virus and the adaptation of this virus to the hosts. Infect Genet Evol 14:105–110

  95. 95.

    Zhou J, Liu WJ et al (1999) Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability. J Virol 73(6):4972–4982

  96. 96.

    Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. Evol Genes Proteins 97:97–166

Download references

Acknowledgements

The authors are grateful to Assam University, Silchar, Assam India, for providing necessary facilities to carry out the research work.

Author information

Correspondence to Supriyo Chakraborty.

Ethics declarations

The study is based on DNA sequence analysis accessed from publicly available database. Ethical clearance is therefore not required.

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Handling Editor: Carolina Scagnolari.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 28 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Deb, B., Uddin, A. & Chakraborty, S. Codon usage pattern and its influencing factors in different genomes of hepadnaviruses. Arch Virol 165, 557–570 (2020). https://doi.org/10.1007/s00705-020-04533-6

Download citation