Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Pasamontes, Alberto ^a   Garcia Vallve, Santiago ^a  

^a UNIVERSITAT ROVIRA I VIRGILI   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID COMPOSITIONS; BIOCHEMICAL CHARACTERISTICS; ESSENTIAL PROTEINS; NUCLEOTIDE COMPOSITION; ORTHOLOGOUS PROTEINS; RIBOSOMAL PROTEINS; SUBCELLULAR LOCALIZATIONS; TRANSLATIONAL INITIATION;

AMINO ACIDS; MICROORGANISMS;

PROTEINS;

AMINO ACID; ARGININE; BACTERIAL PROTEIN; ELONGATION FACTOR; INITIATION FACTOR; LYSINE; RIBOSOME PROTEIN; TRANSFER RNA; AMINO ACID TRANSFER RNA LIGASE;

AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; ANALYTIC METHOD; ARTICLE; FUNCTIONAL PROTEOMICS; NONHUMAN; ORTHOLOGY; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN CONTENT; PROTEIN DATABASE; PROTEIN FUNCTION; SPECIES DIFFERENCE; TEMPERATURE SENSITIVITY; TRANSLATION INITIATION; ARCHAEBACTERIUM; BIOLOGY; CHEMISTRY; CODON; COMPARATIVE STUDY; DNA BASE COMPOSITION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HELICOBACTER; METHANOCOCCUS; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; TEMPERATURE;

PROKARYOTA;

AMINO ACIDS; AMINO ACYL-TRNA SYNTHETASES; ARCHAEA; BACTERIAL PROTEINS; BASE COMPOSITION; CODON; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; HELICOBACTER; METHANOCOCCUS; PEPTIDE ELONGATION FACTORS; RIBOSOMAL PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SPECIES SPECIFICITY; TEMPERATURE;

EID: 33745819577     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-257     Document Type: Article

References (44)

1. Rispe C, Delmotte F, van Ham RCHJ, Moya A: Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res 2004, 14:44-53.
2. Mackiewicz P, Gierlik A, Kowalczuk M, Dudek MR, Cebrat S: How does replication-associated mutational pressure influence amino acid composition of proteins? Genome Res 1999, 9:409-416.
3. Rocha EPC, Danchin A, Viari A: Universal replication biases in bacteria. Mol Microbiol 1999, 32:11-16.
4. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL: Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 2001, 305:567-580.
5. Fujiwara Y, Asogawa M: Prediction of subcellular localizations using amino acid composition and order. Genome Informatics 2001, 12:103-112.
6. Lin K, Kuang Y, Joseph JS, Kolatkar PR: Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics. Nucleic Acids Res 2002, 30:2599-2607.
7. Singer GAC, Hickey DA: Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 2000, 17:1581-1588.
8. Kreil DP, Ouzounis CA: Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res 2001, 29:1608-1615.
9. Tekaia F, Yeramian E, Dujon B: Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene 2002, 297:51-60.
10. Lobry JR, Chessel D: Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria. J Appl Genet 2003, 44:235-261.
11. Pe'er I, Felder CE, Man O, Silman I, Sussman JL, Beckmann JS: Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla. Proteins 2004, 54:20-40.
12. Lynn D, Singer GAC, Hickey DA: Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 2002, 30:4272-4277.
13. Gu X, Hewett-Emmett D, Li W-H: Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica 1998, 102/103:383-391.
14. Jordan IK, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV, Kondrashov AS, Sunyaev S: A universal trend of amino acid gain and loss in protein evolution. Nature 2005, 433:633-638.
15. Trifonov EN: The triplet code from first principles. J Biomol Struct Dyn 2004, 22:1-11.
16. Brodersen DE, Clemons WM, Carter AP, Wimberly BT, Ramakrishnan V: Crystal structure of the 30 S Ribosomal subunit from Thermus thermophilus: Structure of the proteins and their interactions with 16 S RNA. J Mol Biol 2002, 316:725-768.
17. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA: The complete atomic structure of the large ribosomal subunit at 2.4 A Resolution. Science 2000, 289:905-920.
18. Vieille C, Zeikus GY: Hyperthermophilic enzymes: sources, uses and molecular mechanisms for thermostability. Microbiol. Mol Biol Rev 2001, 65:1-43.
19. Bohm G, Jaenicke R: Relevance of sequence statistics for the properties of extremophilic proteins. Int J Pept Protein Res 1994, 43:97-106.
20. Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aulay M, Huber R, Feldman RA, Short JM, Olsen GJ, Swanson RV: The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 1998, 392:353-358.
21. Cambillau C, Claverie J-M: Structural and genomic correlates of hyperthermostability. J Biol Chem 2000, 275:32383-32386.
22. Farias ST, Bonato MCM: Preferred amino acids and thermostability. Genetics Mol Res 2003, 2:383-393.
23. Nakashima H, Fukuchi S, Nishikawa K: Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem 2003, 133:507-513.
24. Saunders NFW, Thomas T, Curmi PM, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M, Cavicchioli R: Mechanisms of thermal adaptation revealed from the genomes of the Antarctic archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res 2003, 13:1580-1588.
25. Singer GAC, Hickey DA: Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 2003, 317:39-47.
26. Rossi M, Ciaramella M, Cannio R, Pisani FM, Moracci M, Bartolucci S: Extremophiles 2002. J Bacteriol 2003, 185:3683-3689.
27. Forterre P: A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet 2003, 18:236-237.
28. Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV: A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res 2002, 30:482-496.
29. Guy CP, Majernik AI, Chong JPJ, Bolt EL: A novel nuclease-ATPase (Nar71) from archaea is part of a proposed thermophilic DNA repair system. Nucleic Acids Res 2004, 32:6176-6186.
30. Klinger C, Robbach M, Howe R, Kaufmann M: Thermophile-specific proteins: the gene product of aq_1292 from Aquifex aeolicus is an NTPase. BMC Biochemistry 2003, 4:12.
31. White MF: Archaeal DNA repair: paradigms and puzzles. Biochemical Society Transactions 2003, 31:690-693.
32. Jelinska C, Conroy MJ, Craven CJ, Hounslow AM, Bullough PA, Waltho JP, Taylor GL, White MF: Obligate heterodimerization of the archaeal Alba2 protein with Alba1 provides a mechanism for control of DNA packaging. Structure 2005, 13:963-971.
33. Xue H, Guo R, Wen Y, Liu D, Huang L: An abundant DNA binding protein from the hyperthermophilic archaeon Sulfolobus shibatae affects DNA supercoiling in a temperature-dependent fashion. J Bacteriol 2000, 182:3929-3933.
34. Wang H-C, Susko E, Roger AJ: On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: Data quality and confounding factors. Biochem Biophys Res Commun 2006, 342:681-684.
35. Galtier N, Lobry JR: Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol 1997, 44:632-636.
36. Hurst LD, Merchant AR: High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes. Proc R Soc Lond B 2001, 268:493-497.
37. Musto H, Naya H, Zavala A, Romero H, Alvarez-Valin F, Bernardi G: Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett 2004, 573:73-77.
38. Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science 1997, 278:631-637.
39. Garcia-Vallve S, Romeu A, Palau J: Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 2000, 10:1719-1725.
40. Garcia-Vallve S, Guzman E, Montero MA, Romeu A: HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res 2003, 31:187-189.
41. Kroonenberg PM, de Leeuw J: Principal component analysis of three-mode data by means of alternating leats squares algorithms. Psychometrika 1980, 45:69-97.
42. Tucker L: Some mathematical notes on three-mode factor analysis. Psychometrika 1966, 31:279-311.
43. Henrion R: N-way principal component analysis. Theory, algorithms and applications. Chemom Intell Lab Syst 1994, 25:1-23.
44. Andersson CA, Munck L, Henrion R, Henrion G: Analysis of N-dimensional data arrays from fluorescence spectroscopy of an intermediary sugar product. Fresenius J Anal Chem 1997, 359:138-142.