Organisms can essentially be classified according to two codon patterns

Amino Acids

Volumn 36, Issue 2, 2009, Pages 261-271

  Okayasu, T ^a   Sorimachi, K ^a  

^a DOKKYO MEDICAL UNIVERSITY   (Japan)

Author keywords

Amino acid compositions; Classification; Cluster analysis; Codon usage; Eukaryotes; GC content; Prokaryotes

Indexed keywords

ALANINE; BACTERIAL PROTEIN; ISOLEUCINE; LYSINE;

AMINO ACID COMPOSITION; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENOME; CLASSIFICATION; CODON USAGE; ESCHERICHIA COLI; EUKARYOTE; GENOME ANALYSIS; NUCLEOTIDE SEQUENCE; ORGANISM; PRIORITY JOURNAL; STAPHYLOCOCCUS AUREUS;

AMINO ACIDS; ANIMALS; BACTERIA; BASE COMPOSITION; CLASSIFICATION; CODON; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; GENOME, BACTERIAL; HUMANS; NUCLEOTIDES; SEQUENCE ANALYSIS, DNA;

ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA; STAPHYLOCOCCUS AUREUS;

EID: 59449107136     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-008-0059-0     Document Type: Article

References (66)

1. IW Althaus JJ Chou AJ Gonzales 1993 Kinetic studies with the nonnucleoside HIV-1 reverse transcriptase inhibitor U-88204E Biochemistry 32 6548 6554
2. IW Althaus JJ Chou AJ Gonzales 1993 Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E J Biol Chem 268 6119 6124
3. IW Althaus AJ Gonzales JJ Chou 1993 The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase J Biol Chem 268 14875 14880
4. F Barloy-Hubler V Lelaure F Galiber 2001 Ribosomal protein gene cluster analysis in eubacterium genomics: homology between Sinorhizobium melioloti strain 1021 and Bacillus subtilis Nucleic Acids Res 29 2747 2756
5. KC Chou 1983 Advances in graphical methods of enzyme kinetics Biophys Chem 17 51 55
6. KC Chou 1989 Graphical rules in steady and non-steady enzyme kinetics J Biol Chem 264 12074 12079
7. KC Chou 1990 Review: applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems Biophys Chem 35 1 24
8. KC Chou DW Elrod 1999 Protein subcellular location prediction Protein Eng 12 107 118
9. KC Chou CT Zhang 1992 Diagrammatization of codon usage in 339 HIV proteins and its biological implication AIDS Res Hum Retrovir 8 1967 1976
10. KC Chou SP Jiang WM Liu 1979 Graph theory of enzyme kinetics: 1. Steady-state reaction system Sci Sin 22 341 358
11. KC Chou FJ Kezdy F Reusser 1994 Review: steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases Anal Biochem 221 217 230
12. KC Chou CT Zhang DW Elrod 1996 Do antisense proteins exist? J Protein Chem 15 59 61
13. Dayhoff MO, Park CM, McLaughlin PJ (1977) Building a phylogenetic trees: cytochrome C. In: Atlas of protein sequence and structure, vol 5. National Biomedical Foundation, Washington, DC, pp 7-16
14. L DePouplana RJ Turner BA Steer 1998 Genetic code origins: tRNAs older than their synthetases? Proc Natl Acad Sci USA 95 11295 11300
15. Y Diao M Li Z Feng 2007 The community structure of human cellular signaling network J Theor Biol 247 608 615
16. Y Diao D Ma Z Wen 2008 Using pseudo amino acid composition to predict transmembrane regions in protein: cellular automata and Lempel-Ziv complexity Amino Acids 34 111 117
17. WF Doolittle 1999 Phylogenetic classification and the universal tree Science 284 2124 2128
18. WF Doolittle JR Brown 1994 Tempo, mode, the progenote, and the universal root Proc Natl Acad Sci USA 91 6721 6728
19. ST Dyhrman 2006 Phosphonate utilization by the globally important marine diazotroph Trichodesmium Nature 439 68 71
20. J Farlow D Postic KL Smith 2002 Strain typing of Borrelia burgdorferi, Borrelia afzelii, and Borrelia garinii by using multiple-locus variable-number tandem repeat analysis J Clin Microbiol 40 4612 4618
21. González-Díaz H, González-Díaz Y, Santana L et al (2008) Proteomics, networks, and connectivity indices. Proteomics. doi: 10.1002/pmic.200700638
22. International Human Genome Sequencing Consortium 2001 Initial sequencing and analysis of the human genome Nature 409 860 921
23. M Kimura 1977 Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution Nature 267 275 276
24. JL King TH Jukes 1989 Non-Darwinian evolution. Most evolutionary change in proteins may be due to neutral mutations and genetic drifts Science 164 788 798
25. P Kuzmic KY Ng TD Heath 1992 Mixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equation Anal Biochem 200 68 73
26. SX Lin KE Neet 1990 Demonstration of a slow conformational change in liver glucokinase by fluorescence spectroscopy J Biol Chem 265 9670 9675
27. JR Lobry 1997 Influence of genomic G + C content on average amino-acid composition of proteins from 59 bacterial species Gene 205 309 316
28. N Maizels AM Weiner 1994 Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation Proc Natl Acad Sci USA 91 6729 6734
29. MJ Martin J Herrero A Mateos 2003 Comparing bacterial genomes through conservation profiles Genome Res 13 991 998
30. Mayer E (1965) Animal species and evolution. Harvard University Press, Cambridge
31. E Mayer 2000 Darwin's influence on modern thought Sci Am 283 79 83
32. JP Qi SH Shao DD Li GP Zhou 2007 A dynamic model for the p53 stress response networks under ion radiation Amino Acids 33 75 83
33. XQ Qi J Wen ZH Qi 2007 New 3D graphical representation of DNA sequence based on dual nucleotides J Theor Biol 249 681 690
34. G.W Rowe VL Szabo LHE Trainor 1984 Cluster analysis of genes in codon space J Mol Evol 20 167 174
35. M Sakagami T Nakayama T Hashimoto 2006 Phylogeny of the centrohelida inferred from SSU rRNA, tubulin, and actin genes J Mol Evol 61 765 775
36. N Shikata Y Maki Y Noguchi 2007 Multi-layered network structure of amino acid (AA) metabolism characterized by each essential AA-deficient condition Amino Acids 33 113 121
37. ML Sogin HJ Elwood JH Gunderson 1986 Evolutionary diversity of eukaryotic small subunit rRNA genes Proc Natl Acad Sci USA 83 1383 1387
38. K Sorimachi 1999 Evolutionary changes reflected by the cellular amino acid composition Amino Acids 17 207 226
39. K Sorimachi T Okayasu 2003 Gene assembly consisting of small units with similar amino acid composition in the Saccharomyces cerevisiae genome Mycosicence 44 415 417
40. K Sorimachi T Okayasu 2004 An evaluation of evolutionary theories based on genomic structures in Saccharomyces cerevisiae and Encephalitozoon cuniculi Mycoscience 45 345 350
41. K Sorimachi T Okayasu 2004 Classification of eubacteria based on their complete genome: where does Mycoplasmataceae belong? Proc R B Suppl Biol Lett 271 S127 S130
42. Sorimachi K, Okayasu T (2005a) Simulation analysis of genomic amino acid composition homogeneity based on putative small units. In Proceedings of the 9th world multi-conference on systemics, cybernetics and informatics, Orlando, Florida, USA, vol VI, pp 190-196
43. K Sorimachi T Okayasu 2005 Genomic structure consisting of putative units coding similar amino acid composition: synchronous mutations in biological evolution Dokkyo J Med Sci 32 101 106
44. Sorimachi K, Okayasu T (2008a) Codon evolution is governed by linear formulas. Amino Acids. doi: 10.1007/s00726-007-0024-3
45. Sorimachi K, Okayasu T (2008b) Mathematical proof of the chronological precedence of protein formation over codon formation. Curr Top Pept Protein Res (in press)
46. Sorimachi K, Okayasu T (2008c) Genome structure is homogeneous based on codon usages. Curr Top Pept Protein Res (in press)
47. K Sorimachi T Okayasu K Akimoto 2000 Conservation of the basic pattern of cellular amino acid composition during biological evolution in plants Amino Acids 18 193 196
48. K Sorimachi T Itoh Y Kawarabayasi 2001 Conservation of the basic pattern of cellular amino acid composition during biological evolution and the putative amino acid composition of primitive life forms Amino Acids 21 393 399
49. N Sueoka 1961 Correlation between base composition of deoxyribonucleic acid and amino acid composition of proteins Proc Natl Acad Sci USA 47 1141 1149
50. N Sueoka 1988 Directional mutation pressure and neutral molecular evolution Proc Natl Acad Sci USA 85 2653 2657
51. LM Stuart J Boulais GM Charriere 2007 A systems biology analysis of the Drosophila phagosome Nature 445 95 101
52. F Takeuchi Y Futamura H Yoshikura K Yamamoto 2003 Statistics of trinucleotides in coding sequences and evolution J Theor Biol 222 139 149
53. JC Venter 2001 The sequence of the human genome Science 291 1304 1351
54. CR Woese 1998 The universal ancestor Proc Natl Acad Sci USA 95 6854 6859
55. CR Woese O Kandler MI Wheelis 1990 Towards a natural system of programs: proposal for the domains archaea, bacteria, and eucarya Proc Natl Acad Sci USA 87 4576 4579
56. S Wolfram 1984 Cellular automation as models of complexity Nature 311 419 424
57. Wolfram S (2002) A new kind of science. Wolfram Media Inc., Champaign
58. X Xiao S Shao Y Ding 2005 An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation J Theor Biol 235 555 565
59. X Xiao S Shao Y Ding 2005 Using cellular automata to generate image representation for biological sequences Amino Acids 28 29 35
60. X Xiao SH Shao KC Chou 2006 A probability cellular automaton model for hepatitis B viral infections Biochem Biophys Res Commun 342 605 610
61. X Xiao SH Shao YS Ding 2006 Using cellular automata images and pseudo amino acid composition to predict protein subcellular location Amino Acids 30 49 54
62. C-T Zhang K-C Chou 1993 Graphic analysis of codon usage strategy in1490 human proteins J Protein Chem 12 329 335
63. CT Zhang KC Chou 1994 Analysis of codon usage in 1562 E. coli protein coding sequences J Mol Biol 238 1 8
64. C-T Zhang K-C Chou 1994 A graphic approach to analyzing codon usage in 1562 Echerichia coli protein coding sequences J Mol Biol 238 1 8
65. C-T Zhang K-C Chou 1996 An analysis of base frequencies in the anti-sense strands corresponding to the 180 human protein coding sequences Amino Acids 10 253 262
66. GP Zhou MH Deng 1984 An extension of Chou's graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways Biochem J 222 169 176