A detailed comparative analysis on the overall codon usage pattern in herpesviruses

Virus Research

Volumn 148, Issue 1-2, 2010, Pages 31-43

  RoyChoudhury, Sourav ^a   Mukherjee, Debaprasad ^a,b  

^a INDIAN INSTITUTE OF ENGINEERING SCIENCE AND TECHNOLOGY   (India)

^b DR B C ROY ENGINEERING COLLEGE   (India)

Author keywords

Codon usage bias; Correspondence analysis; GC content; Herpesvirus; Preferred codons

Indexed keywords

ARTICLE; CODON; CODON USAGE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA BASE COMPOSITION; GENE EXPRESSION; GENETIC SELECTION; GENETIC VARIABILITY; HERPES VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRUS GENOME; VIRUS MUTATION; VIRUS TRANSCRIPTION;

BASE COMPOSITION; BASE SEQUENCE; CODON; COMPUTATIONAL BIOLOGY; GENOME, VIRAL; HERPESVIRIDAE; HUMANS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; VIRAL PROTEINS;

HERPESVIRIDAE;

EID: 75149157626     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2009.11.018     Document Type: Article

References (103)

1. Aoki T., Hirono I., Kurokawa K., Fukuda H., Nahary R., Eldar A., Davison A.J., Waltzek T.B., Bercovier H., and Hedrick R.P. Genome sequences of three koi herpesvirus isolates representing the expanding distribution of an emerging disease threatening koi and common carp worldwide. J. Virol. 81 10 (2007) 5058-5065
2. Afonso C.L., Tulman E.R., Lu Z., Zsak L., Rock D.L., and Kutish G.F. The genome of turkey herpesvirus. J. Virol. 75 2 (2001) 971-978
3. Albrecht J.C. Primary structure of the herpesvirus ateles genome. J. Virol. 74 2 (2000) 1033-1037
4. Albrecht J.C., Nicholas J., Biller D., Cameron K.R., Biesinger B., Newman C., Wittmann S., Craxton M.A., Coleman H., Fleckenstein B., et al. Primary structure of the herpesvirus saimiri genome. J. Virol. 66 8 (1992) 5047-5058
5. Bahr U., and Darai G. Analysis and characterization of the complete genome of tupaia (tree shrew) herpesvirus. J. Virol. 75 10 (2001) 4854-4870
6. Benson P.M., Malane S.L., Banks R., Hicks C.B., and Hilliard J. B virus (Herpesvirus simiae) and human infection. Arch. Dermatol. 125 9 (1989) 1247-1248
7. Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics 129 (1991) 897-907
8. Charif D., Thioulouse J., Lobry J.R., and Perriere G. Online synonymous codon usage analyses with the ade4 and seqinR packages. Bioinformatics 21 (2005) 545-547
9. Charif D., and Lobry J.R. SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis in structural approaches to sequence evolution: molecules, networks, populations. In: Bastolla U., Porto M., Roman H.E., and Vendruscolo M. (Eds). Biological and Medical Physics. Biomedical Engineering (2007) 207-232
10. Comeron M.J., and Aguade M. An evaluation of measures of synonymous codon usage bias. J. Mol. Evol. 47 (1998) 268-274
11. Crotzer V.L., Christian R.E., Brooks J.M., Shabanowitz J., Settlage R.E., Marto J.A., White F.M., Rickinson A.B., Hunt D.F., and Engelhard V.H. Immunodominance among EBV-derived epitopes restricted by HLA-B27 does not correlate with epitope abundance in EBV-transformed B-lymphoblastoid cell lines. J. Immunol. 164 (2000) 6120-6129
12. Das S., Paul S., and Dutta C. Synonymous codon usage in adenoviruses: influence of mutation, selection and protein hydropathy. Virus Res. 117 (2006) 227-236
13. Davison A.J. Channel catfish virus: a new type of herpesvirus. Virology 186 1 (1992) 9-14
14. Davison A.J., Cunningham C., Sauerbier W., and McKinnell R.G. Genome sequences of two frog herpesviruses. J. Gen. Virol. 87 Pt 12 (2006) 3509-3514
15. Davison A.J., Dolan A., Akter P., Addison C., Dargan D.J., Alcendor D.J., McGeoch D.J., and Hayward G.S. The human cytomegalovirus genome revisited: comparison with the chimpanzee cytomegalovirus genome. J. Gen. Virol. 84 Pt 1 (2003) 17-28
16. Davison A.J., Trus B.L., Cheng N., Steven A.C., Watson M.S., Cunningham C., Le Deuff R.M., and Renault T. A novel class of herpesvirus with bivalve hosts. J. Gen. Virol. 86 Pt 1 (2005) 41-53
17. Davison A.J., and Scott J.E. The complete DNA sequence of varicella-zoster virus. J. Gen. Virol. 67 Pt 9 (1986) 1759-1816
18. Delhon G., Moraes M.P., Lu Z., Afonso C.L., Flores E.F., Weiblen R., Kutish G.F., and Rock D.L. Genome of bovine herpesvirus 5. J. Virol. 77 19 (2003) 10339-10347
19. Dolan A., Addison C., Gatherer D., Davison A.J., and McGeoch D.J. The genome of Epstein-Barr virus type 2 strain AG876. Virology 350 1 (2006) 164-170
20. Dolan A., Cunningham C., Hector R.D., Hassan-Walker A.F., Lee L., Addison C., Dargan D.J., McGeoch D.J., Gatherer D., Emery V.C., Griffiths P.D., Sinzger C., McSharry B.P., Wilkinson G.W., and Davison A.J. Genetic content of wild-type human cytomegalovirus. J. Gen. Virol. 85 Pt 5 (2004) 1301-1312
21. Dolan A., Jamieson F.E., Cunningham C., Barnett B.C., and McGeoch D.J. The genome sequence of herpes simplex virus type 2. J. Virol. 72 3 (1998) 2010-2021
22. Dominguez G., Dambaugh T.R., Stamey F.R., Dewhurst S., Inoue N., and Pellett P.E. Human herpesvirus 6B genome sequence: coding content and comparison with human herpesvirus 6A. J. Virol. 73 10 (1999) 8040-8052
23. Donofrio G., and Bernardi G. A universal compositional correlation among codon positions. Gene 110 (1992) 81-88
24. Donofrio G., Sartori C., Ravanetti L., Cavirani S., Gillet L., Alain V., Taddei S., and Flammini C.F. Establishment of a bovine herpesvirus 4 based vector expressing a secreted form of the bovine viral diarrhoea virus structural glycoprotein E2 for immunization purposes. BMC Biotechnol. 7 (2007) 68
25. Ensser A., Pflanz R., and Fleckenstein B. Primary structure of the alcelaphine herpesvirus 1 genome. J. Virol. 71 9 (1997) 6517-6525
26. Eyre-Walker A. Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?. Mol. Biol. Evol. 13 (1996) 864-872
27. In: Fauquet C.M., Mayo M.A., Maniloff J., Desselberger U., and Ball L.A. (Eds). Virus Taxonomy: VIIIth Report of the International Committee on Taxonomy of Viruses (2005), Elsevier Academic Press
28. Fickett J.W. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10 (1982) 5303-5318
29. Grantham R., Gautier C., Gouy M., Mercier R., and Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8 (1980) r49-r62
30. Greenacre M.J. Theory and Applications of Correspondence Analysis (1984), Academic Press, London
31. Grocock R.J., and Sharp P.M. Synonymous codon usage in Pseudomonas aeruginosa PA01. Gene 289 1-2 (2002) 131-139
32. Gompels U.A., Nicholas J., Lawrence G., Jones M., Thomson B.J., Martin M.E., Efstathiou S., Craxton M., and Macaulay H.A. The DNA sequence of human herpesvirus-6: structure, coding content, and genome evolution. Virology 209 1 (1995) 29-51
33. Gu W., Zhou T., Ma J., Sun X., and Lu Z. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Res. 101 (2004) 155-161
34. Gupta S.K., Bhattacharyya T.K., and Ghosh T.C. Synonymouscodon usage in Lactococcus lactis: mutational bias versus translational selection. J. Biomol. Struct. Dyn. 21 4 (2004) 527-536
35. Gustafsson C., Govindarajan S., and Minshull J. Codon bias and heterologous protein expression. Trends Biotechnol. 22 (2004) 346-353
36. Han J.H., Choi Y.S., Kim W.J., Jeon Y.H., Lee S.K., Lee B.J., and Ryu K.S. Codon optimization enhances protein expression of human peptide deformylase in E. coli. Protein Expr. Purif. (2009) [Epub]
37. Hansen S.G., Strelow L.I., Franchi D.C., Anders D.G., and Wong S.W. Complete sequence and genomic analysis of rhesus cytomegalovirus. J. Virol. 77 12 (2003) 6620-6636
38. Hatfull G., Bankier A.T., Barrell B.G., and Farrell P.J. Sequence analysis of Raji Epstein-Barr virus DNA. Virology 164 2 (1988) 334-340
39. Heitzer M., Eckert A., Fuhrmann M., and Griesbeck C. Influence of codon bias on the expression of foreign genes in microalgae. Adv. Exp. Med. Biol. 616 (2007) 46-53
40. Hinkley S., Ambagala A.P., Jones C.J., and Srikumaran S. A vhs-like activity of bovine herpesvirus-1. Arch. Virol. 145 (2000) 2027-2046
41. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2 (1985) 13-34
42. Izumiya Y., Jang H.K., Ono M., and Mikami T. A complete genomic DNA sequence of Marek's disease virus type 2, strain HPRS24. Curr. Top. Microbiol. Immunol. 255 (2001) 191-221
43. Jazayeri M., Soleimanjahi H., Fotouhi F., and Pakravan N. Comparison of intramuscular and footpad subcutaneous immunization with DNA vaccine encoding HSV-gD2 in mice. Comp. Immun. Microbiol. Infect. Dis. 32 (2009) 453-461
44. Jenkins G.M., and Holmes E.C. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 92 (2003) 1-7
45. Klupp B.G., Hengartner C.J., Mettenleiter T.C., and Enquist L.W. Complete, annotated sequence of the pseudorabies virus genome. J. Virol. 78 1 (2004) 424-440
46. Levin D.B., and Whittome B. Codon usage in nucleopolyhedroviruses. J. Gen. Virol. 81 (2000) 2313-2325
47. Lloyd A.T., and Sharp P.M. Evolution of codon usage patterns: the extent and nature of divergence between Candida albicansand Saccharomyces cerevisiae. Nucleic Acids Res. 20 (1992) 5289-5295
48. Liu H., He R., Zhang H., Huang Y., Tian M., and Zhang J. Analysis of synonymous codon usage in Zea mays. Mol. Biol. Rep. (2009) [Epub]
49. Liu Q. Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans. Biosystems 85 2. (2006) 99-106 [Epub]
50. Lynn D.J., Singer G.A., and Hickey D.A. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30 (2002) 4272-4277
51. Mark D.S., Tammy A.T., Taryn A.D., Martin D.M.B., Annabel G.W., Roger K.M., and Matti K. New hosts for equine herpesvirus 9. Emerg. Infect. Dis. 14 10 (2008) 1616-1619
52. Matis J., and Kúdelová M. Early shutoff of host protein synthesis in cells infected with herpes simplex viruses. Acta Virol. 45 5-6 (2001) 269-277
53. McGeoch D.J., Dalrymple M.A., Davison A.J., Dolan A., Frame M.C., McNab D., Perry L.J., Scott J.E., and Taylor P. The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J. Gen. Virol. 69 Pt 7 (1988) 1531-1574
54. McInerney J.O. GCUA: general codon usage analysis. Bioinformatics 14 4 (1998) 372-373. http://bioinf.may.ie/downloads.html http://bioinf.may.ie/downloads.html
55. Megaw A.G., Rapaport D., Avidor B., Frenkel N., and Davison A.J. The DNA sequence of the RK strain of human herpesvirus 7. Virology 244 1 (1998) 119-132
56. Meier-Trummer C.S., Tobler K., Hilbe M., Stewart J.P., Hart J., Campbell I., Haig D.M., Glauser D.L., Ehrensperger F., and Ackermann M. Ovine herpesvirus 2 structural proteins in epithelial cells and M-cells of the appendix in rabbits with malignant catarrhal fever. Vet. Microbiol. 137 3-4 (2009) 235-242
57. Moriyama E.N., and Powell J.R. Codon usage bias and tRNA abundance in Drosophila. J. Mol. Evol. 45 (1997) 514-523
58. Naya H., Romero H., Carels N., Zavala A., and Musto H. Translational selection shapes codon usage in the GC-rich genomes of Chlamydomonas reinhardtii. FEBS Lett. 501 2-3 (2001) 127-130
59. Pan A., Dutta C., and Das J. Codon usage in highly expressed genes of Haemophilus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias. Gene 215 (1998) 405-413
60. Peden, J., 1997. Analysis of codon usage. In PhD Thesis, University of Nottingham, Department of Genetics (http://codonw.sourceforge.net).
61. Perelygina L., Zhu L., Zurkuhlen H., Mills R., Borodovsky M., and Hilliard J.K. Complete sequence and comparative analysis of the genome of herpes B virus (Cercopithecine herpesvirus 1) from a rhesus monkey. J. Virol. 77 11 (2003) 6167-6177
62. Perrie're G., and Thioulouse J. Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res. 30 (2002) 4548-4555
63. Powell J.R., and Moriyama E.N. Evolution of codon usage bias in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 7784-7790
64. R Development Core Team. R: A Language and Environment for Statistical Computing (2008), R Foundation for Statistical Computing, Vienna, Austria ISBN: 3-900051r-r07-0
65. Rawlinson W.D., Farrell H.E., and Barrell B.G. Analysis of the complete DNA sequence of murine cytomegalovirus. J. Virol. 70 12 (1996) 8833-8849
66. Rezaee S.A., Cunningham C., Davison A.J., and Blackbourn D.J. Kaposi's sarcoma-associated herpesvirus immune modulation: an overview. J. Gen. Virol. 87 Pt 7 (2006) 1781-1804
67. Rivailler P., Cho Y.G., and Wang F. Complete genomic sequence of an Epstein-Barr virus-related herpesvirus naturally infecting a new world primate: a defining point in the evolution of oncogenic lymphocryptoviruses. J. Virol. 76 23 (2002) 12055-12068
68. Rivailler P., Jiang H., Cho Y.G., Quink C., and Wang F. Complete nucleotide sequence of the rhesus lymphocryptovirus: genetic validation for an Epstein-Barr virus animal model. J. Virol. 76 1 (2002) 421-426
69. Roizman B., and Pellet P.E. The family Herpesviridae: a brief introduction. In: Knipe D.M., Howley P.M., Griffi{ligature}n D.E., Lamb R.A., Martin M.A., Roizman B., and Strauss S.E. (Eds). Fields Virology. 4th ed. (2001), Lippincott Williams & Wilkins, Philadelphia, PA 2381-2397
70. Russo J.J., Bohenzky R.A., Chien M.C., Chen J., Yan M., Maddalena D., Parry J.P., Peruzzi D., Edelman I.S., Chang Y., and Moore P.S. Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8). Proc. Natl. Acad. Sci. U.S.A. 93 25 (1996) 14862-14867
71. Schwyzer M., and Ackermann M. Molecular virology of ruminant herpesviruses. Vet. Microbiol. 53 1-2 (1996) 17-29
72. Searles R.P., Bergquam E.P., Axthelm M.K., and Wong S.W. Sequence and genomic analysis of a Rhesus macaque rhadinovirus with similarity to Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8. J. Virol. 73 4 (1999) 3040-3053
73. Sewatanon J., Srichatrapimuk S., and Auewarakul P. Compositional bias and size of genomes of human DNA viruses. Intervirology 50 (2007) 123-132
74. Shackelton L.A., Parrish C.R., and Holmes E.C. Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J. Mol. Evol. 62 (2006) 551-563
75. Sharp P.M., and Li W.H. An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol. 24 (1986) 28-38
76. Sharp P.M., and Li W.H. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 14 (1986) 7737-7749
77. Sharp P.M., and Li W.H. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol. Biol. Evol. 4 (1987) 222-230
78. Sharp P.M., and Li W.H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15 3 (1987) 1281-1295
79. Sharp P.M., and Lloyd A.T. Codon usage. In: Maroni G. (Ed). An Atlas of Drosophila genes (1993), Oxford University Press, New York
80. Smiley R.J. Herpes simplex virus virion host shutoff protein: immune evasion mediated by a viral RNase?. J. Virol. (2004) 1063-1068
81. Smiley J.R., Elgadi M.M., and Saffran H.A. Herpes simplex virus vhs protein. Methods Enzymol. 342 (2001) 440-451
82. Sorensen H.P., and Mortensen K.K. Advanced genetic strategies for recombinant protein expression in Escherichia coli. J. Biotechnol. 115 (2005) 113-128
83. Stephanie S.S., Vanheyningen T.K., and Leib D.A. The virion host shutoff protein of herpes simplex virus type 1 has RNA degradation activity in primary neurons. J. Virol. (2004) 8400-8403
84. Stoletzki N., and Eyre-Walker A. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol. Biol. Evol. 24 2 (2007) 374-378
85. Suzuki H., Brown C.J., Forney L.J., and Top E.M. Comparison of correspondence analysis methods for synonymous codon usage in bacteria. DNA Res. 15 (2008) 357-365
86. Telford E.A., Watson M.S., Aird H.C., Perry J., and Davison A.J. The DNA sequence of equine herpesvirus 2. J. Mol. Biol. 249 3 (1995) 520-528
87. Telford E.A., Watson M.S., McBride K., and Davison A.J. The DNA sequence of equine herpesvirus-1. Virology 189 1 (1992) 304-316
88. Telford E.A., Watson M.S., Perry J., Cullinane A.A., and Davison A.J. The DNA sequence of equine herpesvirus-4. J. Gen. Virol. 79 Pt 5 (1998) 1197-1203
89. Thioulouse J., Chessel D., Dolédec S., and Olivier J.M. ADE-4: a multivariate analysis and graphical display software. Stat. Comput. 7 (1997) 75-83
90. Thureen D.R., and Keeler Jr. C.L. Psittacid herpesvirus 1 and infectious laryngotracheitis virus: comparative genome sequence analysis of two avian alphaherpesviruses. J. Virol. 80 16 (2006) 7863-7872
91. Trapp A., Einem J.V., Hofmann H., Kostler J., Wild J., Wagner R., Beer M., and Osterrieder N. Potential of equine herpesvirus 1 as a vector for immunization. J. Virol. (2005) 5445-5454
92. Tulman E.R., Afonso C.L., Lu Z., Zsak L., Rock D.L., and Kutish G.F. The genome of a very virulent Marek's disease virus. J. Virol. 74 17 (2000) 7980-7988
93. Tyler S.D., Peters G.A., and Severini A. Complete genome sequence of cercopithecine herpesvirus 2 (SA8) and comparison with other simplexviruses. Virology 331 2 (2005) 429-440
94. Tyler S.D., and Severini A. The complete genome sequence of herpesvirus papio 2 (Cercopithecine herpesvirus 16) shows evidence of recombination events among various progenitor herpesviruses. J. Virol. 80 3 (2006) 1214-1221
95. Vicario S., Moriyama E.N., and Powell J.R. Codon usage in twelve species of Drosophila. BMC Evol. Biol. 7 (2007) 226
96. Vink C., Beuken E., and Bruggeman C.A. Complete DNA sequence of the rat cytomegalovirus genome. J. Virol. 74 16 (2000) 7656-7665
97. Virgin IV H.W., Latreille P., Wamsley P., Hallsworth K., Weck K.E., Dal Canto A.J., and Speck S.H. Complete sequence and genomic analysis of murine gammaherpesvirus 68. J. Virol. 71 8 (1997) 5894-5904
98. Wang H.C., and Hickey D.A. Rapid divergence of codon usage patterns within the rice genome. BMC Evol. Biol. 7 Suppl. 1 (2006) S6
99. Whitley R.J. Herpesviruses. In: Baron S., et al. (Ed). Baron's Medical Microbiology. 4th ed. (1996), Univ. of Texas Medical Branch
100. Wright F. The effective number of codons' used in a gene. Gene 87 (1990) 23-29
101. Zhou T., Gu W., Ma J., Sun X., and Lu Z. Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. BioSystems 81 (2005) 77-86
102. Zhao S., Zhang Q., Chen Z., Zhao Y., and Zhong J. The factors shaping synonymous codon usage in the genome of Burkholderia mallei. J. Genet. Genomics 34 4. (2007) 362-372
103. Zimmermann W., Broll H., Ehlers B., Buhk H.J., Rosenthal A., and Goltz M. Genome sequence of bovine herpesvirus 4, a bovine Rhadinovirus, and identification of an origin of DNA replication. J. Virol. 75 3 (2001) 1186-1194