Characteristics of codon usage bias in two regions downstream of the initiation codons of foot-and-mouth disease virus

BioSystems

Volumn 101, Issue 1, 2010, Pages 20-28

  Zhou, Jian hua ^a   Zhang, Jie ^a   Ding, Yao zhong ^a   Chen, Hao tai ^a   Ma, Li na ^a   Liu, Yong sheng ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Codon usage bias; Foot and mouth disease virus; Intertypic recombination; Phylogenetic incongruence

Indexed keywords

CYSTEINE; THREONINE; CODON; START CODON; VIRUS DNA;

AMINO ACID; DISEASE SEVERITY; EFFICIENCY MEASUREMENT; FOOT AND MOUTH DISEASE; GENETIC ANALYSIS; PHYLOGENETICS;

ARTICLE; CODON USAGE; CODON USAGE BIAS; FOOT AND MOUTH DISEASE VIRUS; GENE EXPRESSION REGULATION; GENE MUTATION; NONHUMAN; OPEN READING FRAME; PHYLOGENETIC TREE; RNA SEQUENCE; TRANSCRIPTION INITIATION; CODON; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; START CODON;

FOOT-AND-MOUTH DISEASE VIRUS;

BASE SEQUENCE; CODON; CODON, INITIATOR; CONSERVED SEQUENCE; DNA, VIRAL; FOOT-AND-MOUTH DISEASE VIRUS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 77953621837     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2010.04.001     Document Type: Article

References (62)

1. Akashi H. Inferring weak selection from patterns of polymorphism and divergence at silent sites in Drosophila DNA. Genetics 1995, 139:1067-1076.
2. Andersson S.G.E., Buckingham H., Kurland C.G. Does codon composition influence ribosome function. EMBO J. 1984, 3:91-94.
3. Arias A., Lázaro E., Escarmís C., Domingo E. Molecular intermediates of fitness gain of an RNA virus: characterization of a mutant spectrum by biological and molecular cloning. J. Gen. Virol. 2001, 82(5):1049-1060.
4. Bastos A.D.S., Haydon D.T., Forsberg R., Knowles N.J., Anderson E.C., Bengis R.G., Nel L.H., Thomson G.R. Genetic heterogeneity of SAT-1 type foot-and-mouth disease viruses in southern Africa. Arch. Virol. 2001, 146(8):1537-1551.
5. Bastos A.D.S., Anderson E.C., Bengis R.G., Keet D.F., Winterbach H.K., Thomson G.R. Molecular epidemiology of SAT 3-type foot-and-mouth disease. Virus Genes 2003, 27(3):283-290.
6. Beck E., Forss S., Strebel K., Cattaneo R., Feil G. Structure of the FMDV translation initiation site and of the structural proteins. Nucleic Acids Res. 1983, 11(22):7873-7885.
7. Belsham J.G. Dual initiation sites of protein synthesis on foot-an-mouth disease virus RNA are selected following internal entry and scanning of ribosomes in vivo. EMBO J. 1992, 11(3):1105-1110.
8. Brown C.C., Piccone M.E., Mason P.W., Mckenna T.S., Grubman M.J. Pathogenesis of wild-type and leaderless foot-and-mouth disease virus in cattle. J. Virol. 1996, 70(8):5638-5641.
9. Cao X., Bergmann I.E., Fullkrug R., Beck E. Functional analysis of the two alternative translation initiation sites of foot-and-mouth disease virus. J. Virol. 1995, 69(1):560-563.
10. Carrillo C., Tulman E.R., Delhon G., Lu Z., Carreno A., Vagnozzi A., Kutish G., Rock F.D.L. Comparative genomics of foot-and-mouth disease virus. J. Virol. 2005, 79(10):6487-6504.
11. Chen G.T., Inouye M. Suppression of the negative effect of minor arginine codon on gene expression; preferential usage of minor codons within the first 25 of the Escherichia coli genes. Nucleic Acids Res. 1990, 18(6):1465-1473.
12. Chen G.T., Inouye M. Role of the AGA/AGG codons, the rarest codons in global gene expression in Escherichia. Genes Dev. 1994, 8(21):2641-2652.
13. Chinsangaram J., Mason P.W., Grubman M.T. Protection of swine by live and inactivated vaccines prepared from a Leader proteinase-deficient serotype A12 foot-and-mouth disease virus. Vaccine 1998, 16(16):1516-1522.
14. Clarke B.E., Sangar D.V., Burroughs J.N., Newton S.E., Carroll A.R., Rowlands D.J. Two initiation sites for foot-and-mouth disease virus polyprotein in vivo. J. Gen. Virol. 1985, 66(12):2615-2626.
15. de los Santos T., de Avila Botten S., Weiblen R., Grubman M.J. The Leader proteinase of foot-and-mouth disease virus inhibits the induction of beta interferon mRNA and blocks the host innate immune response. J. Virol. 2006, 80(4):1906-1914.
16. de los Santos T., Diaz-San Segundo F., Grubman M.J. Degradation of nuclear factor κB during foot-and-mouth disease virus is required cleavage of the p220 component of the cap-binding protein complex. J. Virol. 2007, 81(23):12803-12815.
17. de los Santos T., Diaz-San, Segundo F., Zhou J., Koster M., Dias C.C.A., Grubman M.J. A conserved domain in the Leader proteinase of foot-and-mouth disease virus is required for proper subcellular localization and function. J. Virol. 2009, 83(4):1800-1810.
18. Devaney M.A., Vakharia V.N., Lloyd R.E., Ehrenfeld E., Grubman M.J. Leader protein of foot-and-mouth disease virus is required for cleavage of the p22 component of the cap-binding protein complex. J. Virol. 1988, 62(11):4407-4409.
19. Domingo E., Escarmis C., Baranowski E., Ruiz-Jarabo C.M., Carrilo E., Nunez J.I., Sobrino F. Evolution of foot-and-mouth disease virus. Virus Res. 2003, 91(1):47-63.
20. Duret L., Muchiroud D. Expression pattern and, surpringly, gene length, shap codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 1999, 96(8):4482-4487.
21. Escarmís C., Dávila M., Charpentier N., Bracho A., Moya A., Domingo E. Genetic lesions associated with Muller's ratchet in an RNA virus. J. Mol. Biol. 1996, 264(2):255-267.
22. Escarmís C., Dávila M., Doming E. Multiple molecular pathways for fitness recovery of an RNA virus debilitated by operation of Muller's ratchet. J. Mol. Biol. 1999, 285(2):495-505.
23. Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982, 10(22):7055-7074.
24. Grubaman M.J., Baxt B. Foot-and-mouth disease. Clin. Microbiol. Rev. 2004, 17(2):465-493.
25. Guarne A., Tormo J., Kirchweger R., Pfistermueller D., Fita I., Skern T. Structure of the foot-and-mouth disease virus Leader protease: a papain-like fold adapted for self-processing and eIF4G recognition. EMBO J. 1998, 17(24):7469-7479.
26. Haydo D.T., Bastos A.D., Awadalla P. Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments. J. Gen. Virol. 2004, 85(5):1095-1100.
27. Hinton T.M., Li F., Crabb B.S. Internal ribosomal entry site-mediated translation initiation in equine rhinitis A virus: similarities to and differences from that of foot-and-mouth disease virus. J. Virol. 2000, 74(24):11708-11716.
28. Hooper S.D., Berg O.G. Gradients in nucleotide and codon usage along Escherichia coli genes. Nucleic Acids Res. 2000, 28(18):3517-3523.
29. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the relative occurrence of the respective codons in protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 1981, 151(3):389-419.
30. Ikemura T. Correlation between the abundance of yeast tRNA and the occurrence of the respective codons in protein genes. Differences in synonymous codon choic patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNA. J. Mol. Biol. 1982, 158(4):573-597.
31. Ikemura T. Codon usage and tRNA is unicellular and multicellular organisms. Mol. Biol. Evol. 1985, 2(1):13-34.
32. Jackson A.L., O'Neill H., Maree F., Blignaut B., Carrillo C., Rodriguez L., Haydon D.T. Mosaic structure of foot-and-mouth disease virus genomes. J. Gen. Virol. 2007, 88(2):487-492.
33. Kaminski A., Belsham G.J., Jackson R.J. Translation of encephalomyocarditis virus RNA: paramenters influencing the selection of the internal initiation site. EMBO J. 1994, 13(7):1673-1681.
34. Kirchweger R., Ziegler E., Lamphear B.J., Water D., Liebig H.D., Sommergruber W., Sobrino F., Hohendl C., Blaas D., Rhoads R.E., Skern T. Foot-and-mouth disease virus Leader proteinase: purification of the Lb form and determination of its cleavage site on eIF-4 gamma. J. Virol. 1994, 68(9):5677-5684.
35. Klein J. Understanding the molecular epidemiology of foot-and-mouth disease virus. Infect. Genet. Evol. 2009, 9(2):153-161.
36. Klein J., Hussain M., Ahmad M., Normann P., Afzal M., Alexandersen S. Genetic characterization of the recent foot-and-mouth disease virus subtype A/IRN/2005. Virol. J. 2007, 4(1):122-133.
37. Kleina L.G., Grubman M.J. Antiviral effects of a thiol protease inhibitor on foot-and-mouth disease virus. J. Virol. 1992, 66(12):7168-7175.
38. Knowles N.J., Samuel A.R. Molcular epidemiology of foot-and-mouth disease virus. Virus Res. 2003, 91:65-80.
39. Kozak M. Selection on initiation sites by eukaryotic ribosome: effect of inserting AUG triplets upstream from the coding sequence for preproinsulin. Nucleic Acids Res. 1984, 12(9):3873-3893.
40. Kozak M. The scanning model for translation: an update. J. Cell Biol. 1989, 108(2):229-241.
41. Kudla G., Murray A.W., Tollervey D., Plotkin J.B. Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324(10):255-258.
42. Kurland C.G. Strategies for efficiency and accuracy in gene expression. Trends Biochem. Sci. 1987, 12:126-128.
43. Lee K.N., Oem J.K., Park J.H., Kim S.M., Lee S.Y., Tserendorj S., Sodnomdarjaa R., Joo Y.S., Kiw H. Evidence of recombination in a new isolate of foot-and-mouth disease virus serotype Asia 1. Virus Res. 2009, 139(1):117-121.
44. Liljenstrom H., von Heijne G. Translation rate modification by preferential codon usage: intragenic position effects. J. Theor. Biol. 1987, 124(1):43-55.
45. Lopez de Quinto S., Martinez-Salas E. Involvement of the aphthovirus RNA region located between the two functional AUGs in start codon selection. Virology 1999, 255(2):324-336.
46. Medina M., Domingo E., Brangwyn J.K., Belsham G.J. The two species of the foot-and-mouth disease virus Leader protein, expressed individually, exhibit the same activities. Virology 1993, 194(1):355-359.
47. Miyasaka H. The positive relationship between codon usage bias and translation initiation AUG context in Saccharomyces cerevisiae. Yeast 1999, 15(8):633-637.
48. Ohno H., Sakai H., Washio T., Tomita M. Preferential usage of some minor codons in bacteria. Gene 2001, 276(1-2):107-115.
49. Piccone M.E., Rieder E., Mason P.W., Grubman M.J. The foot-and-mouth disease virus Leader proteinase gene is not required for viral replication. J. Virol. 1995, 69(9):5376-5382.
50. Roberts P.J., Belsham G.J. Identification of critical amino acids within the foot-and-mouth disease virus Leader protein, a cysteine protease. Virology 1995, 213(1):140-146.
51. Robertson B.H., Grubman M.J., Weddell G.N., Moore D.M., Welsh J.D., Fischer T., Dowbenko D.J., Yansura D.G., Kleid D.G. Nucleotide and amino acid sequence coding for polypeptides of foot-and-mouth disease virus type A12. J. Virol. 1985, 54(3):651-660.
52. Sangar D.V., Black D.N., Rowlands D.J., Harris T.J., Brown F. Location of the initiation site for protein synthesis on foot-and-mouth disease virus RNA by in vitro translation of defined fragments of the RNA. J. Virol. 1980, 33(1):59-68.
53. Sangar D.V., Newton S.E., Rowlands D.J., Clarke B.E. All foot and mouth disease virus serotypes initiate protein synthesis at two separate AUGs. Nucleic Acids Res. 1987, 15(8):3305-3315.
54. Sharp P.M., Tuohy T.M.F., Mosurski K.R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986, 14(13):5125-5143.
55. Simmonds P. Recombination and selection in the evolution of Picornaviruses and other mammalian positive-stranded RNA viruses. J. Virol. 2006, 80(22):11124-11140.
56. Skern T., Fita I., Guarne A. A structural model of picornavirus Leader proteinases based on papain and bleomycin hydrolase. J. Gen. Virol. 1998, 79(2):301-307.
57. Sørensen M.A., Kurland C.G., Pedersen S. Codon usage determines translation rate in Escherichia coli. J. Mol. Biol. 1989, 207(2):367-377.
58. Strebel K., Beck E. A second protease of foot-and-mouth disease virus. J. Virol. 1986, 58(3):893-899.
59. Tosh C., Hemadri D., Sanyal A. Evidence of recombination in the caspsid coding region of type A foot-and-mouth disease virus. J. Gen. Virol. 2002, 83(10):2455-2460.
60. Van Rensburg H., Haydon D., Joubert F., Bastos A., Heath L., Nel L. Genetic heterogeneity in the foot-and-mouth disease virus Leader and 3C proteinases. Gene 2002, 289(1-2):19-29.
61. Vervoot E.B., van Ravestein A., van Peij N.N., Heikoop J.C., van Haastert P.J., Verheijden G.F., Linskens M.H. Optimizing heterologous expression in Dictyostelium: importance of 5' codon adaptation. Nucleic Acids Res. 2000, 28(10):2069-2074.
62. Zhong J.C., Li Y., Zhao S., Liu S., Zhang Z.D. Mutation pressure sharps codon usage in the GC-rich genome of foot-and-mouth disease virus. Virus Genes 2007, 35(3):767-776.