Synonymous codon usage bias dependent on local nucleotide context in the class deinococci

Journal of Molecular Evolution

Volumn 67, Issue 3, 2008, Pages 301-314

  Cutler, Robert W ^a   Chantawannakul, Panuwan ^b  

^a BARD COLLEGE   (United States)

^b CHIANG MAI UNIVERSITY   (Thailand)

Author keywords

Computational biology; Deinococcus; Genomics; Nucleotide co occurrence; Nucleotide context; Synonymous codon usage; Thermus

Indexed keywords

NUCLEOTIDE; PURINE; PYRIMIDINE;

ARTICLE; CODON USAGE; CONTROLLED STUDY; DEINOCOCCUS RADIODURANS; GENE MUTATION; GENETIC CONSERVATION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; THERMUS THERMOPHILUS;

AMINO ACIDS; CODON; CPG ISLANDS; DEINOCOCCUS; DNA METHYLATION; MUTATION; NUCLEOTIDES; THERMUS THERMOPHILUS;

DEINOCOCCI; DEINOCOCCUS; DEINOCOCCUS GEOTHERMALIS; DEINOCOCCUS RADIODURANS; THERMUS; THERMUS THERMOPHILUS;

EID: 51749119885     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9152-y     Document Type: Article

References (37)

1. AW Anderson HC Nordon RF Cain G Parish D Duggan 1956 Studies on a radio-resistant Micrococcus. I. Isolation, morphology, cultural characteristics, and resistance to gamma radiation Food Technol 10 575 578
2. JR Battista 1997 Against all odds: the survival strategies of Deinococcus radiodurans Annu Rev Microbiol 51 203 224
3. OG Berg M Martelius 1995 Synonymous substitution-rate constants in Escherichia coli and Salmonella typhimurium and their relationship to gene expression and selection pressure J Mol Evol 41 4 449 456
4. OG Berg PJN Silva 1997 Codon bias in Escherichia coli: the influence of codon context on mutation and selection Nucleic Acids Res 25 1397 1404
5. MJ Bessman DN Frick SF O'Handley 1996 The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "house cleaning" enzyme J Biol Chem 271 25059 25062
6. H Brim SC McFarlan JK Fredrickson KW Minton M Zhai LP Wackett MJ Daly 2000 Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments Nature Biotech 18 85 90
7. LC Cleston LP Wackett KW Minton MJ Daly 1998 Engineering a recombinant Deinococcus radiodurans for organopollutant degradation in radioactive mixed waste environments Nature Biotech 16 929 933
8. C Coulondre JH Miller PJ Farabaugh W Gilbert 1978 Molecular basis of base substitution hotspots in Escherichia coli Nature 274 775 780
9. TJ Counsell RGE Murray 1986 Polar lipid profiles of the genus Deinococcus Int J Syst Bacteriol 36 202 206
10. RW Cutler P Chantawannakul 2007 The effect of local nucleotides on synonymous codon usage in the honeybee (Apis mellifera L.) genome J Mol Evol 64 637 645
11. L Duret 2000 tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes Trends Genet 16 287 289
12. AC Ferreira MF Nobre FA Rainey MT Silva R Wait J Burghardt AP Chung MS da Costa 1997 Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs Int J Syst Bacteriol 47 939 947
13. R Grantham C Gautier M Gouy R Mercier A Pave 1980 Codon catalog usage and the genome hypothesis Nucleic Acids Res 8 49 62
14. H Grosjean W Fiers 1982 Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed gene Gene 18 199 209
15. W Gu T Zhong J Ma X Sun Z Lu 2004 The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens Biosystem 73 89 97
16. T Ikemura 1981 Correlation between the abundances 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 translation system J Mol Biol 151 573 597
17. T Ikemura 1982 Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Difference in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs J Mol Biol 158 573 597
18. S Karlin J Mrázek AM Cambell 1997 Compositional biases of bacterial genomes and evolutionary implications J Bacteriol 179 12 3899 3913
19. S Karlin AM Campbell J Mrázek 1998 Comparative DNA analysis across diverse genomes Annu Rev Genet 32 185 225
20. C Lange LP Wackett KW Minton MJ Daly 1998 Engineering a recombinant Deinococcus radiodurans for organopollutant degradation in radioactive mixed waste environment Nature Biotech 16 929 933
21. Q Lui 2006 Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans Biosystems 85 99 106
22. KS Makarova YI Wolf O White K Minton MJ Daly 1999 Short repeats and IS elements in the extremely radiation-resistant bacterium Deinococcus radiodurans and comparison to other bacterial species Res Microbiol 150 711 724
23. CI Masters RG Murray BE Moseley KW Minton 1991 DNA polymorphisms in new isolates of Deinococcus radiopugnans J Gen Microbiol 137 1459 1469
24. M Matsuzaki O Misumi T Shin-i S Maruyama M Takahara S Miyagishima T Mori K Nishida F Yagisawa K Nishida Y Yoshida Y Nishimura S Nakao T Kobayashi Y Momoyama T Higashiyama A Minoda M Sano H Nomoto K Oishi H Hayashi F Ohta S Nishizaka S Haga S Miura T Morishita Y Kabeya K Terasawa Y Suzuki Y Ishii S Asakawa H Takano N Ohta H Kuroiwa K Tanaka N Shimizu S Sugano N Sato H Nozaki N Ogasawara Y Kohara T Kuroiwa 2004 Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10 D Nature 428 653 657
25. GAT McVean GDD Hurst 2000 Evolutionary liability of context dependent codon bias in bacteria J Mol Evol 50 264 275
26. R Merkl 2003 A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency J Mol Evol 57 453 466
27. KW Minton 1994 DNA repair in the extremely radioresistant bacterium Deinococcus radiodurans Mol Microbiol 13 9 15
28. KS Mita MZ Ichimura TC James 1988 Specific codon usage pattern and its implications on the secondary structure of silk fibroin mRNA J Mol Biol 203 917 925
29. BR Morton 1998 Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineage J Mol Evol 46 449 459
30. I Narumi 2003 Unlocking radiation resistance mechanisms: still a long way to go Trends Microbiol 11 9 422 425
31. MV Omelchenko YI Wolf EK Gaidamakova VY Matrosova A Vasilenko M Zhai MJ Daly EV Koonin KS Makarova 1995 Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance BMC Evol Biol 5 57 1 22
32. PM Sharp M Stenico JF Peden AT Lloyd 1993 Codon usage:mutational bias, translational selection, or both? Biochem Soc Trans 21 835 841
33. N Sueka Y Kawanishi 2000 DNA G + C content of the third codon position and codon usage biases of human gene Gene 261 53 62
34. The Honey Bee Sequencing Consortium 2006 Insights into social insects from the genome of the honeybee Apis mellifera Nature 443 931 949
35. O White JA Eisen JF Heidelberg EK Hickey JD Peterson RJ Dodson DH Haft ML Gwinn WC Nelson DL Richardson KS Moffat H Qin L Jiang W Pamphile M Crosby M Shen JJ Vamathevan P Lam L McDonald T Utterback C Zalewski KS Makarova L Aravind MJ Daly KW Minton RD Fleischmann KA Ketchum KE Nelson S Salzberg HO Smith JC Venter CM Fraser 1999 Genome sequence of the radioresistant bacterium Deinococcus radiodurans R14 Science 286 1571 1577
36. CR Woese 1987 Bacterial evolution Microbiol Rev 51 2 221 271
37. KH Wolfe PM Sharp W-H Li 1989 Mutation rates differ among regions of the mammalian genome Nature 337 283 285