Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria

Journal of Applied Genetics

Volumn 44, Issue 2, 2003, Pages 235-261

  Lobry, Jean R ^a   Chessel, Daniel ^a  

^a LABORATOIRE DE BIOMÉTRIE ET BIOLOGIE EVOLUTIVE   (France)

Author keywords

Amino acid usage; Codon usage; Correspondence analysis; Thermophiles

Indexed keywords

DNA; MESSENGER RNA; PURINE DERIVATIVE;

ARTICLE; CLUSTER ANALYSIS; CODON; CONTROLLED STUDY; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; HIGH TEMPERATURE; NONHUMAN; THERMOPHILIC BACTERIUM; BACTERIAL GENOME; BACTERIUM; BIOLOGICAL MODEL; CHEMISTRY; DATA BASE; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; SPECIES DIFFERENCE; TEMPERATURE;

BACTERIA (MICROORGANISMS);

BACTERIA; BASE SEQUENCE; CODON; DATABASES; DNA; GENOME; GENOME, BACTERIAL; MODELS, GENETIC; PURINES; RNA, MESSENGER; SPECIES SPECIFICITY; TEMPERATURE;

EID: 0038480747     PISSN: 12341983     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (87)

1. AKASHI A. (2001). Gene expression and molecular evolution. Curr. Op. Gene. Dev. 11: 660-666.
2. ASTWOOD A.C., WAIS A.C. (1998). Psychrotrophic bacteria isolated from a constantly warm tropical environment. Curr. Microbiol. 36: 148-151.
3. BARBER M.A. (1908). The rate of multiplication of Bacillus coli at different temperatures. J. Infect. Dis. 5: 379-400.
4. BAROSS J.A., DEMING J.W. (1983). Growth of 'black smoker' bacteria at temperatures of at least 250°C. Nature 303: 423-426.
5. BAENA S., FARDEAU M.L., WOO T.H.S., OLLIVIER B., LABAT M., PATEL B.K.C. (1999). Phylogenetic relationships of three amino-acid-utilizing anaerobes, Selenomonas acidaminovorans, 'Selenomonas acidaminophila' and Eubacterium acidaminophilum, as inferred from partial 16S rDNA nucleotide sequences and proposal of Thermanaerovibrio acidaminovorans gen. nov., comb. nov. and Anaeromusa acidaminophila gen. nov., comb. nov. Int. J. Sys. Bact. 49: 969-974.
6. BELOZERSKY A.N., SPIRIN A.S. (1958). A correlation between the compositions of deoxyribonucleic and ribonucleic acids. Nature 182: 111-112.
7. BENNET A.F., LENSKI R.E., MITTLER J.E. (1992). Evolutionary adaptation to temperature. I. Fitness responses of Escherichia coli to changes in its thermal environment. Evolution 46: 16-30
8. BENSON D.A., KARSCH-MIZRACHI I., LIPMAN D.J., OSTELL J., RAPP B.A., WHEELER D.L. (2002). GenBank. Nucleic Acids Res. 30: 17-20.
9. BERNHARDT G., LÜDEMANN H.-D., JAENICKE R., KÖNIG H., STETTER K.O. (1984). Biomolecules are unstable under "black smoker" conditions. Naturwissenschaften 71: 583-585.
10. BENZÉCRI J.-P. (1973). L'analyse des données tome 2 : l'analyse des correspondances, Bordas Ed., Paris.
11. BENZÉCRI J.-P. (1983). Analyse de l'inertie intra-classe par l'analyse d'un tableau des correspondances. Les Cahiers de l'Analyse des Données 8: 351-358.
12. BIBILLO A., FIGLEROWICZ M., KIERZEK R. (1999). The non-enzymatic hydrolysis of oilogoribonucleotides VI. The role of biogenic polyamines. Nucleic Acids Res. 27: 3931-3937.
13. BINI E., DIKSHIT V., DIRKSEN K., DROZDA M., BLUM P. (2002). Stability of mRNA in the hyperthermophilic archaeon Sulfolobus solfataricus. RNA 8: 1129-1136.
14. BLÖCHL E., RACHEL R., BURGGRAF S., HAFENBRADL D., JANNASCH H.W., STETTER K.O. (1997). Pyrolobus fumarii gen. and sp.nov. represents a group of archaea, extending the upper temperature limit for life to 113°C. Extremophiles 1: 14-21.
15. BUCHANAN R.E. (1918). Life phases in a bacterial culture. J. Infect. Dis. 23: 109-125.
16. CAMBILLAU C., CLAVERIE J.-M. (2000). Structural and genomic correlates of hyperthermostability. J. Biol. Chem. 275: 32383-32386.
17. CAZES P., CHESSEL D., DOLÉDEC S. (1988). L'analyse des correspondances internes d'un tableau partitionné: son usage en hydrobiologie. Rev. Stat. Appl. 36: 39-54.
18. Gln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc. Natl. Acad. Sci. USA 94: 11819-11826.
19. D'ONOFRIO G., JABBARI K., MUSTO H., BERNARDI G. (1999). The correlation of protein hydropathy with the base composition of coding sequences. Gene 238: 3-14.
20. EISENBERG H. (1995). Life in unusual environments: Progress in understanding the structure and function of enzymes from extreme halophilic bacteria. Arch. Biochem. Biophys. 318: 1-5.
21. FENDRICH C., HIPPE H., GOTTSCHALK G. (1990). Clostridium halophilium sp. nov. and C. litorale sp. nov., an obligate halophilic and a marine species degrading betaine in the Stickland reaction. Arch. Microbiol. 154: 127-132.
22. FITZ-GIBBON S.T., LADNER H., KIM U.-J., STETTER K.O., SIMON M.I., MILLER J.H. (2002). Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc. Natl. Acad. Sci. USA 99: 984-989.
23. GALTIER N., LOBRY J.R. (1997). Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44: 632-636.
24. GALTIER N., TOURASSE N., GOUY M. (1999). A nonhyperthermophile common ancestor to extant life forms. Science 283: 220-221.
25. GAUTIER C. (2000). Compositional bias in DNA. Curr. Opinion Genet. Dev. 10: 656-661.
26. GOUY M., GAUTIER C. (1982). Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10: 7055-7073.
27. GOUY M., MILLERET F., MUGNIER C., JACOBZONE M., GAUTIER C. (1984). ACNUC: a nucleic acid sequence data base and analysis system. Nucleic Acids Res. 12: 121-127.
28. GRANTHAM R., GAUTIER C., GOUY M. (1980). Codon frequencies in 119 individual genes confirm consistent choices of degenerate base according to genome type. Nucleic Acids Res. 8: 1892-1912.
29. GU X., HEWETT-EMMET D., LI W.-H. (1998). Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica 103: 383-391.
30. HANEY P.J., BADGER J.H., BULDAK G.L., TEICH C.I., WOESE C.R., OLSEN G.J. (1999). Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl. Acad. Sci. USA 96: 3578-3583.
31. HUBER R., HUBER H., STETTER K.O. (2000). Towards the ecology of hyperthermophiles: biotopes, new isolation strategies and novel metabolic properties. FEMS Microbiol. Rev. 24: 615-623.
32. IHAKA R., GENTLEMAN R. (1996). R: A language for data analysis and graphics. J. Comp. Graph. Stat. 5: 299-314.
33. IKEMURA T. (1981). Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J. Mol. Biol. 146: 1-21.
34. KANAYA S., YAMADA Y., KUDO Y., IKEMURA T. (1999). 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: 143-155.
35. KAUKINEN U., LYYTIKÄINEN S., MIKKOLA S., LÖNNBERG H. (2002). The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence. Nucleic Acids Res. 30: 468-474.
36. KAWASHIMA T., AMANO N., KOIKE H., MAKINO S.-I., HIGUCHI S., KAWASHIMA-OHYA Y., WATANABE K., YAMAZAKI M., KANEHORI K., KAWAMOTO T., NUNOSHIBA T., YAMAMOTO Y., ARAMAKI H., MAKINO K., SUZUKI M. (2000). Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium. Proc. Natl. Acad. Sci. USA 97: 14257-14262.
37. KENNEDY S.P., NG W.V., SALZBERG S.L., HOOD L., DASARMA S. (2001). Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Gen. Res. 11: 1641-1650.
38. KNIGHT R.D., FREELAND S.J., LANDWEBER L.F. (2001a). Rewiring the keyboard: evolvability of the genetic code. Nat. Rev. Genet. 2: 49-58.
39. KNIGHT R.D., FREELAND S.J., LANDWEBER L.F. (2001b). A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Gen. Biol. 2: research0010.1-research0010.13.
40. KREIL D.P., OUZOUNIS C.A. (2001). Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res. 29: 1608-1615.
41. KUMAR S., NUSSINOV R. (2001). How do thermophilic proteins deal with heat? Cell. Mol. Life Sci. 58: 1216-1233.
42. LAFAY B., LLOYD A.T., MCLEAN M.J., DEVINE K.M., SHARP P.M., WOLFE K.H. (1999). Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res. 27: 1642-1649.
43. LANYI J.K. (1978). Light energy conversion in Halobacterium halobium. Microbiol. Rev. 42: 682-706.
44. LAO P.J., FORSDYKE D.R. (2000). Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Gen. Res. 10: 228-236.
45. LEE K.Y., WAHL R., BARBU E. (1956). Contenu en bases puriques et pyrimidiques des acides désoxyribonucléiques des bactéries. Ann. Inst. Pasteur 91: 212-224.
46. LI Y., BREAKER R.R. (1999). Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group. J. Am. Chem. Soc. 121: 5364-5372.
47. LOBRY J.R. (1996). Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13: 660-665.
48. LOBRY J.R. (1997). Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species. Gene 205: 309-316.
49. LOBRY J.R., GAUTIER C. (1994). Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res. 22: 3174-3180.
50. LOBRY J.R., SUEOKA N. (2002). Asymmetric directional mutation pressures in bacteria. Gen. Biol. 3: research0058.1-0058.14.
51. LYNN D.J., SINGER G.A.C., HICKEY D.A. (2002). Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 19: 1-6.
52. MACKIEWICZ P., GIERLIK A., KOWALCZUK M., DUDEK M.R., CEBRAT S. (1999). How does replication-associated mutational pressure influence amino acid composition of proteins? Gen. Res. 9: 409-416.
53. MARGUET E., FORTERRE P. (1994). DNA stability at temperature typical for hyperthermophiles. Nucleic Acids Res. 11: 1681-1686.
54. MCCLOSKEY J.A., GRAHAM D.E., ZHOU S., CRAIN P.F., IBBA M., KONISKY J., SÖLL D., OLSEN G.J. (2001). Post-transcriptional modification in archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales. Nucleic Acids Res. 29: 4699-4706.
55. MCDONALD J.H., GRASSO A.M., REJTO L.K. (1999). Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. Mol. Biol. Evol. 16: 1785-1790.
56. MCDONALD J.H. (2001). Patterns of Temperature Adaptation in Proteins from the Bacteria Deinococcus radiodurans and Thermus thermophilus. Mol. Biol. Evol. 18: 741-749.
57. NAYA H., ROMERO H., ZAVALA A., ALVAREZ B., MUSTO H. (2002). Aerobiosis increases genomic GC% in prokaryotes. J. Mol. Evol. 55: 260-264.
58. OCHMAN H. (2002). Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. Trends Genet. 18: 335-337.
59. PERRIÈRE G., LOBRY J.R., THIOULOUSE J. (1996). Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acids sequences. Comp. Appl. Biosci. 12: 519-524.
60. PERRIÈRE G., THIOULOUSE J. (2002). Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res. 30: 4548-4555.
61. PERUTZ M.F. (1978). Electrostatic effects in proteins. Science 201: 1187-1191.
62. RADOMSKI J.P., SLONIMSKI P.P. (2001). Genomic style of proteins: concepts, methods and analyses of ribosomal proteins from 16 microbial species. FEMS Microbiol. Rev. 25: 425-435.
63. RATKOWSKY D.A., LOWRY R.K., MCMEEKIN T.A., STOKES A.N., CHANDLER R.E. (1983). Model for bacterial culture growth rate throughout the entire biokinetic temperature rage. J. Bact. 154: 1222-1226.
64. ROCHA E.P.C., DANCHIN A., VIARI A. (1999). Universal replication biases in bacteria. Mol. Microbiol. 32: 11-16.
65. ROLFE R., MESELSON M. (1959). The relative homogeneity of microbial DNA. Proc. Natl. Acad. Sci. USA 45: 1039-1043.
66. ROSSO L., LOBRY J.R., FLANDROIS J.P. (1993). An unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model. J. Theor. Biol. 162: 447-463.
67. RUSSEL R.J.M., TAYLOR G.L. (1995). Engineering thermostability: lessons from thermophilic proteins. Curr. Opinion Biotechnology 6: 370-374.
68. SHARP P.M., TUOHY T.M.F., MOSURSKI K.R. (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14: 5125-5143.
69. SINGER G.A.C., HICKEY D.A. (2000). Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol. 17: 1581-1588.
70. SLESAREV A.I., MEZHEVAYA K.V., MAKAROVA K.S., POLUSHIN N.N., SHCHERBININA O.V., SHAKHOVA V.V., BELOVA G.I., ARAVIND L., NATALE D.A., ROGOZIN I.B., TATUSOV R.L., WOLF Y.I., STETTER K.O., MALYKH A.G., KOONIN E.V., KOZYAVKIN S.A. (2002). The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. USA 99: 4644-4649.
71. SOUKUP G.A., BREAKER R.R. (1999). Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5: 1308-1325.
72. STROM P.E. (1985a). Effect of temperature on bacterial species diversity in thermophilic solid-waste composting. Appl. Environ. Microbiol. 50: 899-905.
73. STROM P.E. (1985b). Identification of thermophilic bacteria in solid-waste composting. Appl. Environ. Microbiol. 50: 906-913.
74. SUEOKA N., MARMUR J., DOTY P. (1959). Heterogeneity in deoxyribonucleic acids. II. Dependence of the density of deoxyribonucleic acids on guanine-cytosine. Nature 183: 1427-1431.
75. SUEOKA N. (1961). Correlation between base composition of deoxyribonucleic acid and amino acid composition of protein. Proc. Natl. Acad. Sci. USA 47: 1141-1149.
76. SUEOKA N. (1962). On the genetic basis of variation and heterogeneity of DNA base composition. Proc. Natl. Acad. Sci. USA 48: 582-592.
77. SUEOKA N. (1988). Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85: 2653-2657.
78. SUNG M.-H., KIM H., BAE J.-W., RHEE S.-K., JEON C.O., KIM K., KIM J.-J., HONG S.-P., LEE S.-G., YOON J.-H., PARK Y.-H., BAEK D.-H. (2002). Geobacillus toebii sp. nov., a new thermophilic bacterium isolated from hay compost. Int. J. Syst. Evol. Microbiol. 52: 2251-2255.
79. SZYBALSKI W., KUBINSKI H., SHELDRICK O. (1966). Pyrimidine clusters on the transcribing strand of DNA and their possible role in the initiation of RNA synthesis. Cold Spring Harbor. Symp. Quant. Biol. 31: 123-127.
80. TAKAHE Y., YANAI H., MAYEKAWA S. (1991). Relationships among several methods of linearly constrained correspondence analysis. Psychometrika 56: 667-684.
81. THAO M.L., MORAN N.A., ABBOT P., BRENNAN E.B., BURCKHARDT D.H., BAUMANN P. (2000) Cospeciation of psyllids and their primary prokaryotic endosymbionts. Appl. Environ. Microbiol. 66: 2898-2905.
82. THIOULOUSE J., CHESSEL D., DOLÉDEC S., OLIVIER J.M. (1997). ADE-4: a multivariate analysis and graphical display software. Stat. Comp. 7: 75-83.
83. TRENT D.T., CHASTAIN R.A., YAYANOS A.A. (1984). Possible artefactual basis for apparent bacterial growth at 250°C. Nature 307: 737-740.
84. WALD A., WOLFOWITZ J. (1940). On a test whether two samples are from the same population. Ann. Math. Stat. 11: 147-162.
85. WHITE R.H. (1984). Hydrolytic stability of biomolecules at high temperatures and its implication for life at 250°C. Nature 310: 430-432.
86. WILQUET V., VAN DE CASTEELE M. (1999). The role of the codon first letter in the relationship between genomic GC content and protein amino acid composition. Res. Microbiol. 150: 21-32.
87. ZINDEL U., FREUDENBERG W., RIETH M., ANDREESEN J. R., SCHNELL J., WIDDEL F. (1988). Eubacterium acidaminophilum sp. nov., a versatile amino acid-degrading anaerobe producing or utilizing H2 or formate. Description and enzymatic studies. Arch. Microbiol. 150: 254-266.