Low temperature adaptation is not the opposite process of high temperature adaptation in terms of changes in amino acid composition

Genome Biology and Evolution

Volumn 7, Issue 12, 2015, Pages 3426-3433

  Yang, Ling Ling ^a   Tang, Shu Kun ^a   Huang, Ying ^b   Zhi, Xiao Yang ^a,b  

^a YUNNAN UNIVERSITY   (China)

^b INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

Amino acid composition; Asymmetric substitution; Homologous protein; Low temperature adaptation

Indexed keywords

PROTEOME;

ADAPTATION; AMINO ACID SUBSTITUTION; ARCHAEON; BACTERIUM; COLD; GENETICS; HEAT; MOLECULAR EVOLUTION;

ADAPTATION, PHYSIOLOGICAL; AMINO ACID SUBSTITUTION; ARCHAEA; BACTERIA; COLD TEMPERATURE; EVOLUTION, MOLECULAR; HOT TEMPERATURE; PROTEOME;

EID: 84982118643     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv232     Document Type: Article

References (54)

1. Ayala-del-Rio HL, et al. 2010. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl Environ Microbiol. 76:2304-2312.
2. Berezovsky IN, Zeldovich KB, Shakhnovich EI. 2007. Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput Biol. 3:498-507.
3. Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M. 2008. Parallel adaptations to high temperatures in the Archaean eon. Nature 456:942-945.
4. Brochier-Armanet C, Forterre P. 2007.Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2:83-93.
5. Casanueva A, Tuffin M, Cary C, Cowan DA. 2010. Molecular adaptations to psychrophily: the impact of 'omic' technologies. Trends Microbiol. 18:374-381.
6. De Maayer P, Anderson D, Cary C, Cowan DA. 2014. Some like it cold: understanding the survival strategies of psychrophiles. EMBO Rep 15:508-517.
7. De Vendittis E, et al. 2008. Adaptation of model proteins from cold to hot environments involves continuous and small adjustments of average parameters related to amino acid composition. J Theor Biol. 250:156-171.
8. Feller G. 2010. Protein stability and enzyme activity at extreme biological temperatures. J Phys Condens Matter 22:323101.
9. Feller G, Gerday C. 2003. Psychrophilic enzymes: hot topics in cold adaptation. Nat Rev Microbiol. 1:200-208.
10. Fields PA, Dong Y, Meng X, Somero GN. 2015. Adaptations of protein structure and function to temperature: there is more than one way to 'skin a cat'. J Exp Biol. 218:1801-1811.
11. Forterre P. 2002. A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet. 18:236-237.
12. Fukuchi S, Nishikawa K. 2001. Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria. J Mol Biol. 309:835-843.
13. Galtier N, Tourasse N, Gouy M. 1999. A nonhyperthermophilic common ancestor to extant life forms. Science 283:220-221.
14. Gaucher EA, Govindara Jan S, Ganesh OK. 2008. Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature 451:704-707.
15. Glyakina AV, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV. 2007. Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms. Bioinformatics 23:2231-2238.
16. Goihberg E, et al. 2007. A single proline substitution is critical for the thermostabilization of Clostridium beijerinckii alcohol dehydrogenase. Proteins 66:196-204.
17. Gribaldo S, Brochier-Armanet C. 2006. The origin and evolution of archaea: a state of the art. Philos Trans R Soc Lond B Biol Sci. 361:1007-1022.
18. Haney PJ, et al. 1999. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc Natl Acad Sci U S A. 96:3578-3583.
19. Hobbs JK, et al. 2012. On the origin and evolution of thermophily: reconstruction of functional precambrian enzymes from ancestors of Bacillus. Mol Biol Evol. 29:825-835.
20. Jones DT. 1999. Protein secondary structure prediction based on positionspecific scoring matrices. J Mol Biol. 292:195-202.
21. Koga Y. 2012. Thermal adaptation of the archaeal and bacterial lipid membranes. Archaea 2012:789652.
22. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. 2001. Predicting transmembrane protein topology with a Hidden Markov Model: application to complete genomes. J Mol Biol. 305:567-580.
23. Larkin MA, et al. 2007. ClustalWand Clustal X version 2.0. Bioinformatics 23:2947-2948.
24. Li L, Stoeckert CJ, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189.
25. López-García P, Zivanovic Y, Deschamps P, Moreira D. 2015. Bacterial gene import and mesophilic adaptation in archaea. Nat Rev Microbiol. 13:447-456.
26. Ma BG, Goncearenco A, Berezovsky IN. 2010. Thermophilic adaptation of protein complexes inferred from proteomic homology modeling. Structure 18:819-828.
27. Maugini E, Tronelli D, Bossa F, Pascarella S. 2009. Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes. Comput Biol Chem. 33:137-148.
28. McDonald JH. 2001. Patterns of temperature adaptation in proteins from the bacteria Deinococcus radiodurans and Thermus thermophilus. Mol Biol Evol. 18:741-749.
29. McDonald JH. 2010. Temperature adaptation at homologous sites in proteins from nine thermophile-mesophile species pairs. Genome Biol Evol. 2:267-276.
30. MethéBA, et al. 2005. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc Natl Acad Sci U S A. 102:10913-10918.
31. Metpally RP, Reddy BV. 2009. Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: insights into the molecular basis of cold adaptation of proteins. BMC Genomics 10:11.
32. Nakashima H, Fukuchi S, Nishikawa K. 2003. Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem. 133:507-513.
33. Paredes DI, Watters K, Pitman DJ, Bystroff C, Dordick JS. 2011. Comparative void-volume analysis of psychrophilic and mesophilic enzymes: structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility. BMC Struct Biol. 11:42.
34. Parvizpour S, Razmara J, Jomah AF, Shamsir MS, Illias RM. 2015. Structural prediction of a novel laminarinase from the psychrophilic Glaciozyma antarctica PI12 and its temperature adaptation analysis. J Mol Model 21:63.
35. Pasi M, Riccardi L, Fantucci P, De Gioia L, Papaleo E. 2009. Dynamic properties of a psychrophilic alpha-amylase in comparison with a mesophilic homologue. J Phys Chem B. 113:13585-13595.
36. Puigbò P, Pasamontes A, Garcia-Vallve S. 2008. Gaining and losing the thermophilic adaptation in prokaryotes. Trends Genet. 24:10-14.
37. Pulido MA, Koga Y, Takano K, Kanaya S. 2007. Directed evolution of Tksubtilisin from a hyperthermophilic archaeon: identification of a single amino acid substitution responsible for low-temperature adaptation. Protein Eng Des Sel 20:143-153.
38. R Core Team. 2014. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing. Available from: http://www.R-project.org/.
39. Reed CJ, Lewis H, Trejo E,Winston V, Evilia C. 2013. Protein adaptations in archaeal extremophiles. Archaea 2013:373275.
40. Sadeghi M, Naderi-Manesh H, Zarrabi M, Ranjbar B. 2006. Effective factors in thermostability of thermophilic proteins. Biophys Chem. 119:256-270.
41. Saunders NF, et al. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13:1580-1588.
42. Sharp CE, et al. 2014. Humboldt's spa: microbial diversity is controlled by temperature in geothermal environments. Isme J. 8:1166-1174.
43. Siglioccolo A, Bossa F, Pascarella S. 2010. Structural adaptation of serine hydroxymethyltransferase to low temperatures. Int J Biol Macromol 46:37-46.
44. Singer GAC, Hickey DA. 2003. Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 317:39-47.
45. Sterner R, Liebl W. 2001. Thermophilic adaptation of proteins. Crit Rev Biochem Mol Biol. 36:39-106.
46. Struvay C, Feller G. 2012. Optimization to low temperature activity in psychrophilic enzymes. Int J Mol Sci. 13:11643-11665.
47. Suhre H, Claverie JM. 2003. Genomic correlates of hyperthermostability, an update. J Biol Chem. 278:17198-17202.
48. Takano K, Yutani K. 2001. A new scale for side-chain contribution to protein stability based on the empirical stability analysis of mutant protines. Protein Eng 14:535-538.
49. Trivedi S, Gehlot HS, Rao SR. 2006. Protein thermostability in archaea and eubacteria. Genet Mol Res. 5:816-827.
50. Wang J, Ma BG, Zhang HY, Chen LL, Zhang SC. 2008. How does gene expression level contribute to thermophilic adaptation of prokaryotes? An exploration based on predictors. Gene 421:32-36.
51. Wijma HJ, Floor RJ, Janssen DB. 2013. Structure-and sequence-analysis inspired engineering of proteins for enhanced thermostability. Curr Opin Struct Biol. 23:588-594.
52. Xie BB, et al. 2009. Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: new insights into relationship between conformational flexibility and hydrogen bonding. J Biol Chem. 284:9257-9269.
53. Zeldovich KB, Berezovsky IN, Shakhnovich EI. 2007. Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol. 3:e5.
54. Zhao JS, Deng Y, Manno D, Hawari J. 2010. Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation. PLoS One 5:e9109.