Patterns of Codon Usage in two Ciliates that Reassign the Genetic Code: Tetrahymena thermophila and Paramecium tetraurelia

Protist

Volumn 159, Issue 2, 2008, Pages 283-298

  Salim, Hannah M W ^a   Ring, Karen L ^a   Cavalcanti, Andre R O ^a  

^a POMONA COLLEGE   (United States)

Author keywords

codon bias; codon reassignment; codon usage; genetic code

Indexed keywords

AMINO ACID;

ANIMAL; ARTICLE; CODON; DNA BASE COMPOSITION; GENE; GENE EXPRESSION; GENETICS; NUCLEOTIDE SEQUENCE; PARAMECIUM TETRAURELIA; START CODON; STOP CODON; TETRAHYMENA THERMOPHILA;

AMINO ACIDS; ANIMALS; BASE COMPOSITION; BASE SEQUENCE; CODON; CODON, INITIATOR; CODON, TERMINATOR; GENE EXPRESSION; GENES, PROTOZOAN; PARAMECIUM TETRAURELIA; TETRAHYMENA THERMOPHILA;

CILIOPHORA; PARAMECIUM; PARAMECIUM TETRAURELIA; TETRAHYMENA; TETRAHYMENA THERMOPHILA;

EID: 40949111987     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2007.11.003     Document Type: Article

References (56)

1. Akashi H. Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy. Genetics 136 (1994) 927-935
2. Andersson S.G.E., and Kurland C.G. Codon preferences in free-living microorganisms. Microbiol Rev 54 (1990) 198-210
3. Aury J., Jaillon O., Duret L., Noël B., Jubin C., Porcel B., Ségurens B., Daubin V., Anthouard V., Aiach N., et al. Global trends of whole genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444 (2006) 171-178
4. Barrell B.G., Bankier A.T., and Drouin J. A different genetic code in human mitochondria. Nature 282 (1979) 189-194
5. Bernardi G. The compositional evolution of vertebrate genomes. Gene 259 (2000) 31-43
6. Bernardi G., and Bernardi G. Compositional constraints and genome evolution. J Mol Evol 24 (1986) 1-11
7. Bonetti B., Fu L., Moon J., and Bedwell D.M. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J Mol Biol 251 (1995) 334-345
8. Brown C.M., Stockwell P.A., Trotman C.N.A., and Tate W.P. Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes. Nucleic Acids Res 18 (1990) 6339-6345
9. Brunk C.F., and Sadler L.A. Characterization of the promoter region of Tetrahymena genes. Nucleic Acids Res 18 (1990) 323-329
10. Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics 129 (1991) 897-907
11. Cavalcanti A.R.O., Stover N.A., Orecchia L., Doak T.G., and Landweber L.F. Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma 113 (2004) 69-76
12. Coughlan A., and Wolfe K.H. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16 (2000) 1131-1145
13. Crooks G.E., Hon G., Chandonia J.M., and Brenner S.E. WebLogo: A sequence logo generator. Genome Res 14 (2004) 1188-1190
14. Drummond D., Raval A., and Wilke C. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 23 (2006) 327-337
15. Duret L. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet 16 (2000) 287-289
16. Duret L., Mouchiroud D., and Gautier C. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochors. J Mol Evol 40 (1995) 308-317
17. Eisen J.A., Coyne R.S., Wu M., Wu D., Thiagarajan M., Wortman J.R., Badger J.H., Ren Q., Amedeo P., Jones K.M., et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PloS Biol 4 (2006) e286
18. 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
19. Filipski J. Correlation between molecular clock ticking, codon usage, fidelity of DNA repair, chromosome banding and chromatin compactness in germline cells. FEBS Lett 217 (1987) 184-186
20. Fullerton S.M., Carvalho A.B., and Clark A.G. Local rates of recombination are positively correlated with GC content in the human genome. Mol Biol Evol 18 (2001) 1139-1142
21. Gilchrist M.A., and Wagner A. A model of protein translation including codon bias, nonsense errors, and ribosome recycling. J Theor Biol 239 (2006) 417-434
22. Gouy M., and Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10 (1982) 7055-7074
23. Hackett J.D., Scheetz T.E., Yoon H.S., Soares M.B., Bonaldo M.F., Casavant T.L., and Bhattacharya D. Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics 6 (2005) 80
24. Ikemura T. 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 (1981) 389-409
25. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2 (1985) 13-34
26. Invarsson P. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol Biol Evol 24 (2007) 836-844
27. Jabbari K., and Bernardi G. CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families. Gene 224 (1998) 123-127
28. Kent J.W. BLAT - the blast-like alignment tool. Genome Res 12 (2002) 656-664
29. Kotlar D., and Lavner Y. The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids. BMC Genomics 7 (2006) 67
30. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
31. Lekomtsev S., Kolosov P., Bidou L., Frolova L., Rousset J.P., and Kisselev L. Different modes of stop codon restriction by the Stylonychia and Paramecium eRF1 translation termination factors. Proc Natl Acad Sci USA 104 (2007) 10824-10829
32. Liang H., Wong J.Y., Bao Q., Cavalcanti A.R., and Landweber L.F. Decoding the decoding region: analysis of eukaryotic release factor (eRF1) stop codon-binding residues. J Mol Evol 60 (2005) 337-344
33. Lin Z., Yang S., and Mallavia L.P. Codon Usage and nucleotide composition in Coxiella burnetti. Gene 198 (1997) 171-180
34. Lowe T.M., and Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25 (1997) 955-964
35. Lozupone C.A., Knight R.D., and Landweber L.F. The molecular basis of nuclear genetic code change in ciliates. Curr Biol 11 (2001) 65-74
36. Major L.L., Poole E.S., Dalphin M.E., Mannering S.A., and Tate W.P. Is the in-frame termination signal of the Escherichia coli release factor-2 frameshift site weakened by a particularly poor context?. Nucleic Acids Res 24 (1996) 2673-2678
37. Meunier J., and Duret L. Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol 21 (2004) 984-990
38. Moriyama E.N., and Powell J.R. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res 26 (1998) 3188-3193
39. Mouchiroud D., D'Onofrio G., Aïssani B., Macaya G., Gautier C., and Bernardi G. The distribution of genes in the human genome. Gene 100 (1991) 181-187
40. Nekrutenko A., and Li W.H. Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res 10 (2000) 1986-1995
41. Poole E.S., Brown C.M., and Tate W.P. The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. EMBO J 14 (1995) 151-158
42. Powell J.R., and Moriyama E.N. Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA 94 (1997) 7784-7790
43. Qin H., Wu W.B., Comeron J.M., Kreitman M., and Li W.H. Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes. Genetics 168 (2004) 2245-2260
44. Rocha E.P.C. Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res 14 (2004) 2279-2286
45. Salas-Marco J., Fan-Minogue H., Kallmeyer A.K., Klobutcher L.A., Farabaugh P.J., and Bedwell D.M. Distinct paths to stop codon reassignment by the variant-code organisms Tetrahymena and Euplotes. Mol Cell Biol 26 (2006) 438-447
46. 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 (1987) 1281-1295
47. Sharp P.M., Averof M., Lloyd A.T., Matassi G., and Peden J.F. DNA sequence evolution: the sounds of silence. Philos Trans R Soc Lond B Biol Sci 349 (1995) 241-247
48. Soll D., and RajBhandary U.L. The genetic code - thawing the 'frozen accident'. J Biosci 31 (2006) 459-463
49. Stormo G.D., Schneider T.D., and Gold L.M. Characterization of translational initiation sites in E. coli. Nucleic Acids Res 10 (1982) 2971-2996
50. Swire J., Judson O.P., and Burt A. Mitochondrial genetic codes evolve to match amino acid requirements of proteins. J Mol Evol 60 (2005) 128-139
51. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., et al. The sequence of the human genome. Science 291 (2001) 1304-1351
52. Watanabe Y., Fujiyama A., Ichiba Y., Hattori M., Yada T., Sakaki Y., and Ikemura T. Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum Mol Genet 11 (2002) 13-21
53. Wolfe K.H., Sharp P.M., and Li W.H. Mutation rates differ among regions of the mammalian genome. Nature 337 (1989) 283-285
54. Wright F. The 'effective number of codons' used in a gene. Gene 87 (1990) 23-29
55. Wuitschick J.D., and Karrer K.M. Analysis of genomic G+C content, codon usage, initiator codon context and translation termination sites in Tetrahymena thermophila. J Eukaryot Microbiol 46 (1999) 239-247
56. Zhang S., Goldman E., and Zubay G. Clustering of low usage codons and ribosome movement. J Theor Biol 170 (1994) 339-354