Synonymous codon usage bias in 16 Staphylococcus aureus phages: Implication in phage therapy

Virus Research

Volumn 113, Issue 2, 2005, Pages 123-131

  Sau, K ^a   Gupta, S K ^a   Sau, S ^a   Ghosh, T C ^a  

^a BOSE INSTITUTE   (India)

Author keywords

Mutational bias; Phage therapy; Staphylococcal phages; Synonymous codon usage; Translational selection

Indexed keywords

ANTIBIOTIC THERAPY; ARTICLE; AT RICH SEQUENCE; BACTERIAL GENOME; BACTERIAL MUTATION; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIOPHAGE; CODON USAGE; DRUG TARGETING; GENETIC ANALYSIS; GENETIC CODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA TRANSLATION; STAPHYLOCOCCUS AUREUS; STOP CODON;

ANIMALS; CODON; GENOME, VIRAL; HUMANS; MUTATION; PROTEIN BIOSYNTHESIS; STAPHYLOCOCCAL INFECTIONS; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS PHAGES; VARIATION (GENETICS); VIRUS REPLICATION;

STAPHYLOCOCCAL PHAGES; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS PHAGE 44AHJD;

EID: 24944467406     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2005.05.001     Document Type: Article

References (44)

1. H.W. Ackermann Frequency of morphological phage descriptions in the year 2000 Arch. Virol. 146 2001 843 857
2. S.K. Basak, Banerjee, S.K. Gupta, and T.C. Ghosh Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis J. Biomol. Struct. Dynam. 22 2004 205 214
3. H. Brüssow, C. Canchaya, and W.D. Hardt Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion Microbiol. Mol. Biol. Rev. 68 2004 560 602
4. S. Chibani-Chennoufi, J. Sidoti, A. Bruttin, E. Kutter, S. Sarker, and H. Brüssow In vitro and in vivo bacteriolytic activities of Escherichia coli phages: implications for phage therapy Antimicrob. Agents Chemother. 48 2004 2558 2569
5. M.L. Chiusano, F. Alvarez-Valin, M. Di Giulio, G. D'Onofrio, G. Ammirato, G. Colonna, and G. Bernardi Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code Gene 261 2000 63 69
6. G. D'Onofrio, and G. Bernardi A universal compositional correlation among codon positions Gene 110 1992 81 88
7. T.C. Ghosh, S.K. Gupta, and S. Majumdar Studies on codon usage in Entamoeba histolytica Int. J. Parasitol. 30 2000 715 722
8. M. Gouy Codon contexts in enterobacterial and coliphage genes Mol. Biol. Evol. 4 1987 426 444
9. R. Grantham, C. Gautier, M. Gouy, M. Jacobzone, and R. Mercier Codon catalog usage is a genome strategy modulated for gene expressivity Nucl. Acids Res. 9 1981 r43 r74
10. M.J. Greenacre Theory and Applications of Correspondence Analysis 1984 Academic Press London
11. W. Gu, T. Zhou, J. Ma, X. Sun, and Z. Lu Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales Virus Res. 101 2004 155 161
12. S.K. Gupta, S. Majumdar, T.K. Bhattacharya, and T.C. Ghosh Studies on the relationships between the synonymous codon usage and protein secondary structural units Biochem. Biophys. Res. Commun. 269 2000 692 696
13. S.K. Gupta, and T.C. Ghosh Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa Gene 273 2001 63 70
14. J.J. Iandolo, V. Worrell, K.H. Groicher, Y. Qian, R. Tian, S. Kenton, A. Dorman, H. Ji, S. Lin, P. Loh, S. Qi, H. Zhu, and B.A. Roe Comparative analysis of the genomes of the temperate bacteriophages φ11, φ12 and φ13 of Staphylococcus aureus 8325 Gene 289 2002 109 118
15. T. Ikemura Codon usage and tRNA content in unicellular and multicellular organisms Mol. Biol. Evol. 2 1985 13 34
16. T. Ikemura Transfer RNA in Protein Synthesis 1992 CRC Press Ann Arbor, Tokyo, London
17. G.M. Jenkins, and E.C. Holmes The extent of codon usage bias in human RNA viruses and its evolutionary origin Virus Res. 92 2003 1 7
18. D. Jikia, N. Chkhaidze, E. Imedashvili, I. Mgaloblishvili, G. Tsitlanadze, R. Katsarava, J.G. Morris Jr., and A. Sulakvelidze The use of a novel biodegradable preparation capable of the sustained release of bacteriophages and ciprofloxacin, in the complex treatment of multidrug-resistant Staphylococcus aureus-infected local radiation injuries caused by exposure to Sr90 Clin. Exp. Dermatol. 30 2005 23 26
19. S. Kanaya, Y. Yamada, Y. Kudo, and T. Ikemura Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis Gene 238 1999 143 155
20. S. Kanaya, Y. Yamada, M. Kinouchi, Y. Kudo, and T. Ikemura Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis J. Mol. Evol. 53 2001 290 298
21. T. Kunisawa, S. Kanaya, and E. Kutter Comparison of synonymous codon distribution patterns of bacteriophage and host genomes DNA Res. 5 1998 319 326
22. M. Kuroda, T. Ohta, I. Uchiyama, and T. Baba Whole genome sequencing of meticillin-resistant Staphylococcus aureus Lancet 357 2001 1225 1240
23. T. Lesnik, J. Solomovici, A. Deana, R. Ehrlich, and C. Reiss Ribosome traffic in E. coli and regulation of gene expression J. Theor. Biol. 202 2000 175 185
24. D.B. Levine, and B. Whitemore Codon usage in nucleopolyhedroviruses J. Gen. Virol. 81 2000 2313 2325
25. J. Liu, M. Dehbi, G. Moeck, F. Arhin, P. Bauda, D. Bergeron, M. Callejo, V. Ferretti, N. Ha, T. Kwan, J. McCarty, R. Srikumar, D. Williams, J.J. Wu, P. Gros, J. Pelletier, and M. DuBow Antimicrobial drug discovery through bacteriophage genomics Nat. Biotechnol. 22 2004 185 191
26. D.J. Lynn, G.A. Singer, and D.A. Hickey Synonymous codon usage is subject to selection in thermophilic bacteria Nucl. Acids Res. 30 2002 4272 4277
27. S. Majumdar, S.K. Gupta, V.S. Sundararajan, and T.C. Ghosh Compositional correlation studies among the three different codon positions in 12 bacterial genomes Biochem. Biophys. Res. Commun. 266 1999 66 71
28. K.V. Mardia, J.T. Kent, and J.M. Bibby Multivariate Analysis 1979 Academic Press New York pp. 305-378
29. K. Markoishvili, G. Tsitlanadze, R. Katsarava, J.G. Morris Jr., and A. Sulakvelidze A novel sustained-release matrix based on biodegradable poly(ester amide)s and impregnated with bacteriophages and an antibiotic shows promise in management of infected venous stasis ulcers and other poorly healing wounds Int. J. Dermatol. 41 2002 453 458
30. J.O. McInerney Replicational and transcriptional selection on codon usage in Borrelia burgdorferi Proc. Natl. Acad. Sci. U.S.A. 95 1998 10698 10703
31. E.N. Moriyama, and J.R. Powell Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli Nucl. Acids Res. 26 1998 3188 3193
32. S. O'Flaherty, A. Coffey, R. Edwards, W. Meaney, G.F. Fitzgerald, and R.P. Ross Genome of staphylococcal phage K: a new lineage of Myoviridae infecting gram-positive bacteria with a low G + C content J. Bacteriol. 186 2004 2862 2871
33. M. Oresisc, and D. Shalloway Specific correlations between relative synonymous codon usage and protein secondary structure J. Mol. Biol. 281 1998 31 48
34. R. Pantůček, J. Doškař, V. Růžičková, P. Kašparek, E. Oráčova, V. Kvardová, and S. Rosypal Identification of bacteriophage types and their carriage in Staphylococcus aureus Arch. Virol. 149 2004 1689 1703
35. H. Romero, A. Zavala, and H. Musto Compositional pressure and translational selection determine codon usage in the extremely GC-poor unicellular eukaryote Entamoeba histolytica Gene 242 2000 307 311
36. P.M. Sharp, M.S. Rogers, and D.J. McConnell Selection pressures on codon usage in the complete genome of bacteriophage T7 J. Mol. Evol. 21 1984-1985 150 160
37. P.M. Sharp, and W.-H. Li The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications Nucl. Acids Res. 15 1987 1281 1295
38. P.M. Sharp, and E. Cowe Synonymous codon usage in Saccharomyces cerevisiae Yeast 7 1991 657 678
39. R.R. Sokal, and P.H.A. Sneath Principles of Numerical Taxonomy 1973 W.H. Freeman San Francisco
40. A. Sulakvelidze, Z. Alavidze, and J.G. Morris Jr. Bacteriophage therapy Antimicrob. Ag. Chem. 45 2001 649 659
41. D. Vybiral, M. Takac, M. Loessner, A. Witte, U. Von Ahsen, and U. Bläsi Complete nucleotide sequence and molecular characterization of two lytic Staphylococcus aureus phages: 44AHJD and P68 FEMS Microbiol. Lett. 219 2003 275 283
42. F. Wright The effective number of codons used in a gene Gene 87 1990 23 29
43. T. Xie, and D.F. Ding The relationship between synonymous codon usage and protein structure FEBS Lett. 434 1998 93 96
44. J. Zhou, W.J. Liu, S.W. Peng, X.Y. Sun, and I. Frazer Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability J. Virol. 73 1999 4972 4982