Hickey, Donal A. and Singer, Gregory AC
Genomic and proteomic adaptations to growth at high temperature.
Genome Biology, 5
- Published Version
Official URL: http://dx.doi.org/10.1186/gb-2004-5-10-117
Most positively selected mutations cause changes in metabolism, resulting in a better-adapted phenotype. But as well as acting on the information content of genes, natural selection may also act directly on nucleic acid and protein molecules. We review the evidence for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes.
References:1. Russell AP, Holleman DS: The thermal denaturation of DNA: average length and composition of denatured areas. Nucleic Acids Res 1974, 1:959–978.
2. 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.
3. 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 Biol Sci 2001, 268:493-497.
4. Forsdyke DR, Bell SJ: Purine loading, stem-loops and Chargaff’s second parity rule: a discussion of the application of elementary principles to early chemical observations. Appl Bioinformatics 2004, 3:3-8.
5. Muto A, Osawa S: The guanine and cytosine content of genomic DNA and bacterial evolution. Proc Natl Acad Sci USA 1987, 84:166-169.
6. Singer GAC, Hickey DA: Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 2000, 17:1581-1588.
7. Sueoka N: Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine- deamination hypotheses. Gene 2002, 300:141-154.
8. Singer GAC, Hickey DA: Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 2003, 317:39-47.
9. Wang HC, Singer GAC, Hickey DA: Mutational bias affects protein evolution in flowering plants. Mol Biol Evol 2004, 21:90-96.
10. Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH: Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci USA 2004, 101:3480-3485.
11. Forterre P: A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet 2002, 18:236-237.
12. Nakashima H, Fukuchi S, Nishikawa K: Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem (Tokyo) 2003, 133:507-513.
13. Wang HC, Hickey DA: Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Res 2002, 30:2501-2507.
14. Paz A, Mester D, Baca I, Nevo E, Korol A: Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes. Proc Natl Acad Sci USA 2004, 101:2951-2956.
15. Klein RJ, Misulovin Z, Eddy SR: Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc Natl Acad Sci USA 2002, 99:7542-7547.
16. Gutell RR, Cannone JJ, Shang Z, Du Y, Serra MJ: A story: unpaired adenosine bases in ribosomal RNAs. J Mol Biol 2000, 304:335-354.
17. Lao PJ, Forsdyke DR: Thermophilic bacteria strictly obey Szybalski’s transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res 2000, 10:228-236.
18.Lambros RJ, Mortimer JR, Forsdyke DR: Optimum growth temperature and the base composition of open reading frames in prokaryotes. Extremophiles 2003, 7:443-450.
19.Ikemura T: Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 1981, 146:1-21.
20.Sharp PM, Stenico M, Peden JF, Lloyd AT: Codon usage: mutational bias, translational selection, or both? Biochem Soc Trans 1993, 21:835-841.
21.Lobry JR, Chessel D: Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria. J Appl Genet 2003, 44:235-261.
22.Rispe C, Delmotte F, van Ham RC, Moya A: Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res 2004, 14:44-53.
23.Kanaya S, Kinouchi M, Abe T, Kudo Y, Yamada Y, Nishi T, Mori H, Ikemura T: Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene 2001, 276:89-99.
24.Lynn DJ, Singer GAC, Hickey DA: Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 2002, 30:4272-4277.
25.Jaenicke R, Böhm G: The stability of proteins in extreme environments. Curr Opin Struct Biol 1998, 8:738-748.
26.Petsko GA: Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat". Methods Enzymol 2001, 334:469-478.
27.Kreil DP, Ouzounis CA: Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res 2001, 29:1608-1615.
28.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.
29.Farias ST, Bonato MC: Preferred amino acids and thermostability. Genet Mol Res 2003, 2:383-393.
30.Friedman R, Drake JW, Hughes AL: Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles. Genetics 2004, 167:1507-1512.
31.Kawashima T, Amano N, Koike H, Makino S, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto T, et al.: Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium. Proc Natl Acad Sci USA 2000, 97:14257-14262.
32.Kumar S, Nussinov R: How do thermophilic proteins deal with heat? Cell Mol Life Sci 2001, 58:1216-1233.
33.Suhre K, Claverie JM: Genomic correlates of hyperthermostability, an update. J Biol Chem 2003, 278:17198-17202.
34.Thompson MJ, Eisenberg D: Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. J Mol Biol 1999, 290:595-604.
35.Zhang J: Protein-length distributions for the three domains of life. Trends Genet 2000, 16:107-109.
36.Das R, Gerstein M: The stability of thermophilic proteins: a study based on comprehensive genome comparison. Funct Integr Genomics 2000, 1:76-88.
37.Chakravarty S, Varadarajan R: Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 2002, 41:8152-8161.
38.Alsop E, Silver M, Livesay DR: Optimized electrostatic surfaces parallel increased thermostability : a structural bioinformatic analysis. Protein Eng 2003, 16:871-874.
39.Pack SP, Yoo YJ: Protein thermostability: structure-based difference of amino acid between thermophilic and mesophilic proteins. J Biotechnol 2004, 111:269-277.
40.Kumar S, Nussinov R: Fluctuations in ion pairs and their stabilities in proteins. Proteins 2001, 43:433-454.
41.Shockley KR, Ward DE, Chhabra SR, Conners SB, Montero CI, Kelly RM: Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus. Appl Environ Microbiol 2003, 69:2365-2371.
42.Makarova KS, Wolf YI, Koonin EV: Potential genomic determinants of hyperthermophily. Trends Genet 2003, 19:172-176.
43.Foster PG, Jermiin LS, Hickey DA: Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 1997, 44:282-288.
44.Knight RD, Freeland SJ, Landweber LF: A simple model based on mutation and selection explains trends in codon and aminoacid usage and GC composition within and across genomes. Genome Biol 2001, 2:research0010.1-0010.13.
45.Lobry JR: Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 1996, 13:660-665.
46.Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH: Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res 1999, 27:1642-1649.
47.Foster PG, Hickey DA: Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol 1999, 48:284-290.
48.Phillips MJ, Delsuc F, Penny D: Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 2004, 21:1455-1458.
49.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.
50.Roberts D: Eukaryotic cells under extreme conditions. In Enigmatic Microorganisms and Life in Extreme Environments. Edited by Seckbach J. Dordrecht: Kluwer; 1999:163-173.
51.Tansey MR, Brock TD: The upper temperature limit for eukaryotic organisms. Proc Natl Acad Sci USA 1972, 69:2426-2428.
52.Forterre P: Thermoreduction, a hypothesis for the origin of prokaryotes. C R Acad Sci III 1995, 318:415-422.
53.Sprott GD: Structures of archaebacterial membrane lipids. J Bioenerg Biomembr 1992, 24:555-566.
54.Portner HO: Climate variations and the physiological basis of temperature dependent biogeography: systemic to molecular hierarchy of thermal tolerance in animals. Comp Biochem Physiol A Mol Integr Physiol 2002, 132:739-761.
55.Bernardi G: Isochores and the evolutionary genomics of vertebrates. Gene 2000, 241:3-17.
56.Montoya-Burgos JI, Boursot P, Galtier N: Recombination explains isochores in mammalian genomes. Trends Genet 2003, 19:128-130.
57.Meunier J, Duret L: Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol 2004, 21:984-990.
58.Vieille C, Zeikus GJ: Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 2001, 65:1-43.
59.Haki GD, Rakshit SK: Developments in industrially important thermostable enzymes: a review. Bioresour Technol 2003, 89:17-34.
60.Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, et al.: The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 2004, 22:547-553.
61.Huang SL, Wu LC, Liang HK, Pan KT, Horng JT, Ko MT: PGTdb: a database providing growth temperatures of prokaryotes. Bioinformatics 2004, 20:276-278.
62.Korbel JO, Snel B, Huynen MA, Bork P: SHOT: a web server for the construction of genome phylogenies. Trends Genet 2002, 18:158-162.
All items in Spectrum are protected by copyright, with all rights reserved. The use of items is governed by Spectrum's terms of access
Repository Staff Only: item control page