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Chapter 16 : An Interplay between Metabolic and Physicochemical Constraints: Lessons from the Psychrophilic Prokaryote Genomes

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An Interplay between Metabolic and Physicochemical Constraints: Lessons from the Psychrophilic Prokaryote Genomes, Page 1 of 2

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Abstract:

This chapter summarizes the knowledge about the genomes of psychrophilic bacteria, a subclass of the cold-adapted bacteria, with emphasis on the specific selective features relevant to cold adaptation. A detailed analysis of the general features of genomes and proteomes from psychrophilic bacteria is presented. All investigators involved in sequencing the genomes of psychrophilic looked for common features which would account for cold-adaptation. The genomes of psychrophilic bacteria also have the counterpart of major chaperonins such as the essential GroES GroEL complex. A remarkable observation poses interesting questions about the role of this complex. In the presence of molecular oxygen (dioxygen), this has the consequence that reactive oxygen species (ROS) are more frequent and stable for a longer time. Membrane fluidity can be increased in two ways: either by incorporating unsaturated fatty acids or by including branched-chain fatty acids in the diglycerides. SS9 was found to exhibit enhanced proportions of both monounsaturated and polyunsaturated fatty acids when grown at a decreased temperature or elevated pressure. Three main features can be observed in the genomes and proteomes of these organisms: a variety of means to cope with ROS, a multiplicity of nucleic acid folding and unfolding devices, and, finally, a bias in the amino acid composition of their proteome.

Citation: Danchin A. 2007. An Interplay between Metabolic and Physicochemical Constraints: Lessons from the Psychrophilic Prokaryote Genomes, p 208-220. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch16

Key Concept Ranking

Gene Expression and Regulation
0.6654938
Acidic Amino Acids
0.6313867
Chemicals
0.47735727
Gram-Negative Coccobacilli
0.41823256
Unsaturated Fatty Acids
0.41644654
Reactive Oxygen Species
0.41336942
Amino Acids
0.4119359
16s rRNA Sequencing
0.40635237
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References

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1. Baross, J.,, and J. Deming. 1983. Growth of “black smoker” bacteria at temperatures of at least 250°C. Nature 303:423426.
2. Bartlett, D. H. 1999. Microbial adaptations to the psychrosphere/ piezosphere. J. Mol. Microbiol. Biotechnol. 1:93100.
3. Basu, M. K.,, and E. V. Koonin. 2005. Evolution of eukaryotic cysteine sulfinic acid reductase, sulfiredoxin (Srx), from bacterial chromosome partitioning protein ParB. Cell Cycle 4:947952.
4. Bera, A. K.,, and R. Bernhardt. 1999. GroEL-assisted and -unassisted refolding of mature and precursor adrenodoxin: the role of the precursor sequence. Arch. Biochem. Biophys. 367:8994.
5. Bernardet, J. F.,, and B. Kerouault. 1989. Phenotypic and genomic studies of “Cytophaga psychrophila” isolated from diseased rainbow trout (Oncorhynchus mykiss) in France. Appl. Environ. Microbiol. 55:17961800.
6. Bowman, J. P.,, S. A. McCammon,, M. V. Brown,, D. S. Nichols, and, T. A. McMeekin. 1997. Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl. Environ. Microbiol. 63:30683078.
7. Cavicchioli, R. 2006. Cold-adapted archaea. Nat. Rev. Microbiol. 4:331343.
8. Cilia, V.,, B. Lafay, and, R. Christen. 1996. Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol. Biol. Evol. 13:451461.
9. Cordin, O.,, J. Banroques,, N. K. Tanner, and, P. Linder. 2005. The DEAD-box protein family of RNA helicases. Gene. (in press)
10. Cottrell, M. T.,, L. Yu, and, D. L. Kirchman. 2005. Sequence and expression analyses of cytophaga-like hydrolases in a Western arctic metagenomic library and the Sargasso Sea. Appl. Environ. Microbiol. 71:85068513.
11. Cox, E. C.,, and C. Yanofsky. 1967. Altered base ratios in the DNA of an Escherichia coli mutator strain. Proc. Natl. Acad. Sci. USA 58:18951902.
12. Cybulski, L. E.,, D. Albanesi,, M. C. Mansilla,, S. Altabe,, P. S. Aguilar, and, D. de Mendoza. 2002. Mechanism of membrane fluidity optimization: isothermal control of the Bacillus subtilis acyl-lipid desaturase. Mol. Microbiol. 45:13791388.
13. Danchin, A. 1989. Homeotopic transformation and the origin of translation. Prog Biophys Mol Biol 54:8186.
14. DeLong, E. F.,, K. Y. Wu,, B. B. Prezelin, and, R. V. Jovine. 1994. High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695697.
15. Deming, J.,, L. Somers,, W. Straube,, D. Swartz, and, M. MacDonell. 1988. Isolation of an obligately barophilic bacterium and description of a new genus, Colwellia gen. nov. Syst. Appl. Microbiol. 10:152160.
16. Deming, J. W. 2002. Psychrophiles and polar regions. Curr Opin Microbiol 5:301309.
17. Deppenmeier, U.,, A. Johann,, T. Hartsch,, R. Merkl,, R. A. Schmitz,, R. Martinez-Arias,, A. Henne,, A. Wiezer,, S. Baumer,, C. Jacobi,, H. Bruggemann,, T. Lienard,, A. Christmann,, M. Bomeke,, S. Steckel,, A. Bhattacharyya,, A. Lykidis,, R. Overbeek,, H. P. Klenk,, R. P. Gunsalus,, H. J. Fritz, and, G. Gottschalk. 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between Bacteria and Archaea. J. Mol. Microbiol. Biotechnol. 4:453461.
18. Di Giulio, M. 2005. The origin of the genetic code: theories and their relationships, a review. Biosystems 80:175184.
19. Ezraty, B.,, L. Aussel, and, F. Barras. 2005. Methionine sulfoxide reductases in prokaryotes. Biochim Biophys Acta 1703:221229.
20. Fang, G.,, E. Rocha, and, A. Danchin. 2005. How essential are nonessential genes? Mol. Biol. Evol. 22:21472156.
21. Ferrer, M.,, H. Lunsdorf,, T. N. Chernikova,, M. Yakimov,, K. N. Timmis, and, P. N. Golyshin. 2004. Functional consequences of single:double ring transitions in chaperonins: life in the cold. Mol. Microbiol. 53:167182.
22. Galagan, J. E.,, C. Nusbaum,, A. Roy,, M. G. Endrizzi,, P. Macdonald,, W. FitzHugh,, S. Calvo,, R. Engels,, S. Smirnov,, D. Atnoor,, A. Brown,, N. Allen,, J. Naylor,, N. Stange-Thomann,, K. DeArellano,, R. Johnson,, L. Linton,, P. McEwan,, K. McKernan,, J. Talamas,, A. Tirrell,, W. Ye,, A. Zimmer,, R. D. Barber,, I. Cann,, D. E. Graham,, D. A. Grahame,, A. M. Guss,, R. Hedderich,, C. Ingram-Smith,, H. C. Kuettner,, J. A. Krzycki,, J. A. Leigh,, W. Li,, J. Liu,, B. Mukhopadhyay,, J. N. Reeve,, K. Smith,, T. A. Springer,, L. A. Umayam,, O. White,, R. H. White,, E. Conway de Macario,, J. G. Ferry,, K. F. Jarrell,, H. Jing,, A. J. Macario,, I. Paulsen,, M. Pritchett,, K. R. Sowers,, R. V. Swanson,, S. H. Zinder,, E. Lander,, W. W. Metcalf,, and B. Birren. 2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532542.
23. Galat, A. 2003. Peptidylprolyl cis/trans isomerases (immunophilins): biological diversity—targets—functions. Curr. Top. Med. Chem. 3:13151347.
24. Galtier, N.,, and J. R. Lobry. 1997. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44:632636.
25. Giovannoni, S. J.,, H. J. Tripp,, S. Givan,, M. Podar,, K. L. Vergin,, D. Baptista,, L. Bibbs,, J. Eads,, T. H. Richardson,, M. Noordewier,, M. S. Rappe,, J. M. Short,, J. C. Carrington, and, E. J. Mathur. 2005. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:12421245.
26. Glansdorff, N.,, and Y. Xu. 2002. Microbial life at low temperatures: mechanisms of adaptation and extreme biotopes. Implications for exobiology and the origin of life. Recent Res. Devel. Microbiol. 6:121.
27. Glaser, P.,, L. Frangeul,, C. Buchrieser,, C. Rusniok,, A. Amend,, F. Baquero,, P. Berche,, H. Bloecker,, P. Brandt,, T. Chakraborty,, A. Charbit,, F. Chetouani,, E. Couve,, A. de Daruvar,, P. Dehoux,, E. Domann,, G. Dominguez-Bernal,, E. Duchaud,, L. Durant,, O. Dussurget,, K. D. Entian,, H. Fsihi,, F. Garcia-del Portillo,, P. Garrido,, L. Gautier,, W. Goebel,, N. Gomez-Lopez,, T. Hain,, J. Hauf,, D. Jackson,, L. M. Jones,, U. Kaerst,, J. Kreft,, M. Kuhn,, F. Kunst,, G. Kurapkat,, E. Madueno,, A. Maitournam,, J. M. Vicente,, E. Ng,, H. Nedjari,, G. Nordsiek,, S. Novella,, B. de Pablos,, J. C. Perez-Diaz,, R. Purcell,, B. Remmel,, M. Rose,, T. Schlueter,, N. Simoes,, A. Tierrez,, J. A. Vazquez-Boland,, H. Voss,, J. Wehland, and, P. Cossart. 2001. Comparative genomics of Listeria species. Science 294:849852.
28. Golbik, R.,, C. Yu,, E. Weyher-Stingl,, R. Huber,, L. Moroder,, N. Budisa, and, C. Schiene-Fischer. 2005. Peptidyl Prolyl cis/ trans-Isomerases: comparative reactivities of Cyclophilins, FK506-Binding Proteins, and Parvulins with Fluorinated Oligo-peptide and Protein Substrates. Biochemistry 44:1602616034.
29. Gottesman, S. 2005. Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet. 21:399404.
30. Hendrickson, E. L.,, R. Kaul,, Y. Zhou,, D. Bovee,, P. Chapman,, J. Chung,, E. Conway de Macario,, J. A. Dodsworth,, W. Gillett,, D. E. Graham,, M. Hackett,, A. K. Haydock,, A. Kang,, M. L. Land,, R. Levy,, T. J. Lie,, T. A. Major,, B. C. Moore,, I. Porat,, A. Palmeiri,, G. Rouse,, C. Saenphimmachak,, D. Soll,, S. Van Dien,, T. Wang,, W. B. Whitman,, Q. Xia,, Y. Zhang,, F. W. Larimer,, M. V. Olson,, and J. A. Leigh. 2004. Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J. Bacteriol. 186:69566969.
31. Huang, C. C.,, L. T. Li,, M. C. Shen,, J. Y. Chen, and, S. W. Lin. 2001. Domain specific monoclonal anti-factor VIII antibodies generated by inclusion body-renatured factor VIII peptides. Thromb. Res. 101:405415.
32. Ivanova, E. P.,, S. Flavier, and, R. Christen. 2004. Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int. J. Syst. Evol. Microbiol. 54:17731788.
33. Klosch, B.,, W. Furst,, R. Kneidinger,, M. Schuller,, B. Rupp,, A. Banerjee, and, H. Redl. 2005. Expression and purification of biologically active rat bone morphogenetic protein-4 produced as inclusion bodies in recombinant Escherichia coli. Biotechnol. Lett. 27:15591564.
34. Kreil, D. P.,, and C. A. Ouzounis. 2001. Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res 29:16081615.
35. Larralde, R.,, M. P. Robertson, and, S. L. Miller. 1995. Rates of decomposition of ribose and other sugars: implications for chemical evolution. Proc. Natl. Acad. Sci. USA 92:81588160.
36. Lobry, J. R.,, A. Necsulae 2006. Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes. Gene 385:128136.
37. Mandal, M.,, M. Lee,, J. E. Barrick,, Z. Weinberg,, G. M. Emilsson,, W. L. Ruzzo, and, R. R. Breaker. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306:275279.
38. Maruyama, T.,, R. Suzuki, and, M. Furutani. 2004. Archaeal peptidyl prolyl cistrans isomerases (PPIases) update 2004. Front. Biosci. 9:16801720.
39. Medigue, C.,, E. Krin,, G. Pascal,, V. Barbe,, A. Bernsel,, P. N. Bertin,, F. Cheung,, S. Cruveiller,, S. D’Amico,, A. Duilio,, G. Fang,, G. Feller,, C. Ho,, S. Mangenot,, G. Marino,, J. Nilsson,, E. Parrilli,, E. P. Rocha,, Z. Rouy,, A. Sekowska,, M. L. Tutino,, D. Vallenet,, G. von Heijne, and, A. Danchin. 2005. Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res. 15:13251335.
40. Methe, B. A.,, K. E. Nelson,, J. W. Deming,, B. Momen,, E. Melamud,, X. Zhang,, J. Moult,, R. Madupu,, W. C. Nelson,, R. J. Dodson,, L. M. Brinkac,, S. C. Daugherty,, A. S. Durkin,, R. T. DeBoy,, J. F. Kolonay,, S. A. Sullivan,, L. Zhou,, T. M. Davidsen,, M. Wu,, A. L. Huston,, M. Lewis,, B. Weaver,, J. F. Weidman,, H. Khouri,, T. R. Utterback,, T. V. Feldblyum,, and C. M. Fraser. 2005. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc. Natl. Acad. Sci. USA 102:1091310918.
41. Miller, J. H.,, P. Funchain,, W. Clendenin,, T. Huang,, A. Nguyen,, E. Wolff,, A. Yeung,, J. H. Chiang,, L. Garibyan,, M. M. Slupska,, and H. Yang. 2002. Escherichia coli strains (ndk) lacking nucleoside diphosphate kinase are powerful mutators for base substitutions and frameshifts in mismatch-repair-deficient strains. Genetics 162:513.
42. Miteva, V. I.,, and J. E. Brenchley. 2005. Detection and isolation of ultrasmall microorganisms from a 120,000-year-old greenland glacier ice core. Appl. Environ. Microbiol. 71:78067818.
43. Murray, A. E.,, C. M. Preston,, R. Massana,, L. T. Taylor,, A. Blakis,, K. Wu, and, E. F. DeLong. 1998. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 64:25852595.
44. Nakashima, H.,, S. Fukuchi, and, K. Nishikawa. 2003. Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J. Biochem. (Tokyo) 133:507513.
45. Nozhevnikova, A. N.,, M. V. Simankova,, S. N. Parshina, and, O. R. Kotsyurbenko. 2001. Temperature characteristics of methanogenic archaea and acetogenic bacteria isolated from cold environments. Water Sci. Technol. 44:4148.
46. Oikawa, T.,, N. Yamamoto,, K. Shimoke,, S. Uesato,, T. Ikeuchi,, and T. Fujioka. 2005. Purification, characterization, and overexpression of psychrophilic and thermolabile malate dehydrogenase of a novel Antarctic psychrotolerant, Flavobacterium frigidimaris KUC-1. Biosci. Biotechnol. Biochem. 69:21462154.
47. Oikawa, T.,, K. Yamanaka,, T. Kazuoka,, N. Kanzawa, and, K. Soda. 2001. Psychrophilic valine dehydrogenase of the Antarctic psychrophile, Cytophaga sp. KUC-1: purification, molecular characterization and expression. Eur. J. Biochem. 268:43754383.
48. Okada, K.,, T. Iida,, K. Kita-Tsukamoto, and, T. Honda. 2005. Vibrios commonly possess two chromosomes. J. Bacteriol. 187:752757.
49. Pascal, G.,, C. Medigue, and, A. Danchin. 2005. Universal biases in protein composition of model prokaryotes. Proteins 60:2735.
50. Pe’er, I.,, C. E. Felder,, O. Man,, I. Silman,, J. L. Sussman, and, J. S. Beckmann. 2004. Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla. Proteins 54:2040.
51. Phadtare, S. 2004. Recent developments in bacterial cold-shock response. Curr. Issues Mol. Biol. 6:125136.
52. Phadtare, S.,, J. Alsina, and, M. Inouye. 1999. Cold-shock response and cold-shock proteins. Curr. Opin. Microbiol. 2:175180.
53. Ponder, M. A.,, S. J. Gilmour,, P. W. Bergholz,, C. A. Mindock,, R. Hollingsworth,, M. F. Thomashow, and, J. M. Tiedje. 2005. Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria. FEMS Microbiol. Ecol. 53:103115.
54. Rabus, R.,, A. Ruepp,, T. Frickey,, T. Rattei,, B. Fartmann,, M. Stark,, M. Bauer,, A. Zibat,, T. Lombardot,, I. Becker,, J. Amann,, K. Gellner,, H. Teeling,, W. D. Leuschner,, F. O. Glockner,, A. N. Lupas,, R. Amann, and, H. P. Klenk. 2004. The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ. Microbiol. 6:887902.
55. Rocha, E. P.,, and A. Danchin. 2002. Base composition bias might result from competition for metabolic resources. Trends Genet. 18:291294.
56. Ron, E. Z. 1975. Growth rate of Enterobacteriaceae at elevated temperatures: limitation by methionine. J. Bacteriol. 124:243246.
57. Russell, N. J. 1990. Cold adaptation of microorganisms. Philos. Trans. R. Soc. Lond. B Biol. Sci. 326:595608, discussion 608511.
58. Sakamoto, T.,, and D. A. Bryant. 2002. Synergistic effect of highlight and low temperature on cell growth of the Delta12 fatty acid desaturase mutant in Synechococcus sp. PCC 7002. Photo-synth. Res. 72:231242.
59. Sakamoto, T.,, and N. Murata. 2002. Regulation of the desaturation of fatty acids and its role in tolerance to cold and salt stress. Curr. Opin. Microbiol. 5:208210.
60. Sauerwald, A.,, W. Zhu,, T. A. Major,, H. Roy,, S. Palioura,, D. Jahn,, W. B. Whitman,, J. R. Yates, III,, M. Ibba, and, D. Soll. 2005. RNA-dependent cysteine biosynthesis in archaea. Science 307:19691972.
61. Saunders, N. F.,, T. Thomas,, P. M. Curmi,, J. S. Mattick,, E. Kuczek,, R. Slade,, J. Davis,, P. D. Franzmann,, D. Boone,, K. Rusterholtz,, R. Feldman,, C. Gates,, S. Bench,, K. Sowers,, K. Kadner,, A. Aerts,, P. Dehal,, C. Detter,, T. Glavina,, S. Lucas,, P. Richardson,, F. Larimer,, L. Hauser,, M. Land, and, R. Cavicchioli. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13:15801588.
62. Schleper, C.,, E. F. DeLong,, C. M. Preston,, R. A. Feldman,, K. Y. Wu, and, R. V. Swanson. 1998. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180:50035009.
63. Schleper, C.,, W. Holben, and, H. P. Klenk. 1997a. Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments. Appl. Environ. Microbiol. 63:321323.
64. Schleper, C.,, R. V. Swanson,, E. J. Mathur, and, E. F. DeLong. 1997b. Characterization of a DNA polymerase from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 179:78037811.
65. Sheridan, P. P.,, V. I. Miteva, and, J. E. Brenchley. 2003. Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a Greenland glacier ice core. Appl. Environ. Microbiol. 69:21532160.
66. Simankova, M. V.,, O. R. Kotsyurbenko,, T. Lueders,, A. N. Nozhevnikova,, B. Wagner,, R. Conrad, and, M. W. Friedrich. 2003. Isolation and characterization of new strains of methanogens from cold terrestrial habitats. Syst. Appl. Microbiol. 26:312318.
67. Slesarev, A. I.,, K. V. Mezhevaya,, K. S. Makarova,, N. N. Polushin,, O. V. Shcherbinina,, V. V. Shakhova,, G. I. Belova,, L. Aravind,, D. A. Natale,, I. B. Rogozin,, R. L. Tatusov,, Y. I. Wolf,, K. O. Stetter,, A. G. Malykh,, E. V. Koonin, and, S. A. Kozyavkin. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. USA 99:46444649.
68. Srinivasan, G.,, C. M. James, and, J. A. Krzycki. 2002. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296:14591462.
69. Stein, J. L.,, T. L. Marsh,, K. Y. Wu,, H. Shizuya, and, E. F. DeLong. 1996. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178:591599.
70. Strocchi, M.,, M. Ferrer,, K. N. Timmis, and, P. N. Golyshin. 2006. Low temperature-induced systems failure in Escherichia coli: insights from rescue by cold-adapted chaperones. Proteomics 6:193206.
71. Sundby, C.,, U. Harndahl,, N. Gustavsson,, E. Ahrman, and, D. J. Murphy. 2005. Conserved methionines in chloroplasts. Biochim. Biophys. Acta 1703:191202.
72. Tekaia, F.,, E. Yeramian, and, B. Dujon. 2002. Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene 297:5160.
73. Trent, J. D.,, R. A. Chastain, and, A. A. Yayanos. 1984. Possible artefactual basis for apparent bacterial growth at 250 degrees C. Nature 307:737740.
74. Trotsenko, Y. A.,, and V. N. Khmelenina. 2005. Aerobic methanotrophic bacteria of cold ecosystems. FEMS Microbiol. Ecol. 53:1526.
75. Tsai, C. J.,, J. V. Maizel, Jr., and, R. Nussinov. 2002. The hydrophobic effect: a new insight from cold denaturation and a two-state water structure. Crit. Rev. Biochem. Mol. Biol. 37:5569.
76. Tucker, B. J.,, and R. R. Breaker. 2005. Riboswitches as versatile gene control elements. Curr Opin Struct Biol 15:342348.
77. Tutino, M. L.,, A. Duilio,, R. Parrilli,, E. Remaut,, G. Sannia, and, G. Marino. 2001. A novel replication element from an Antarctic plasmid as a tool for the expression of proteins at low temperature. Extremophiles 5:257264.
78. Tutino, M. L.,, E. Parrilli,, L. Giaquinto,, A. Duilio,, G. Sannia,, G. Feller, and, G. Marino. 2002. Secretion of alpha-amylase from Pseudoalteromonas haloplanktis TAB23: two different pathways in different hosts. J. Bacteriol. 184:58145817.
79. Vetriani, C.,, H. W. Jannasch,, B. J. MacGregor,, D. A. Stahl, and, A. L. Reysenbach. 1999. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl. Environ. Microbiol. 65:43754384.
80. Vezzi, A.,, S. Campanaro,, M. D’Angelo,, F. Simonato,, N. Vitulo,, F. M. Lauro,, A. Cestaro,, G. Malacrida,, B. Simionati,, N. Cannata,, C. Romualdi,, D. H. Bartlett,, and G. Valle. 2005. Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307:14591461.
81. Wernet, P.,, D. Nordlund,, U. Bergmann,, M. Cavalleri,, M. Odelius,, H. Ogasawara,, L. A. Naslund,, T. K. Hirsch,, L. Ojamae,, P. Glatzel,, L. G. Pettersson, and, A. Nilsson. 2004. The structure of the first coordination shell in liquid water. Science 304:995999.
82. White, R. H. 1984. Hydrolytic stability of biomolecules at high temperatures and its implication for life at 250°C. Nature 310:430432.
83. Woese, C. R.,, and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74:50885090.
84. Xu, Y.,, Y. Zhang,, Z. Liang,, M. Van de Casteele,, C. Legrain,, and N. Glansdorff. 1998. Aspartate carbamoyltransferase from a psychrophilic deep-sea bacterium, Vibrio strain 2693: properties of the enzyme, genetic organization and synthesis in Escherichia coli. Microbiology 144:14351441.

Tables

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Table 1.

List of cold-growing bacteria for which complete genomes are available

Citation: Danchin A. 2007. An Interplay between Metabolic and Physicochemical Constraints: Lessons from the Psychrophilic Prokaryote Genomes, p 208-220. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch16

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