Molecular bases of thermophily in hyperthermophiles

Proceedings of the Japan Academy Series B: Physical and Biological Sciences

Volumn 87, Issue 9, 2011, Pages 587-602

  Imanaka, Tadayuki ^a  

^a RITSUMEIKAN UNIVERSITY   (Japan)

Author keywords

Cytoplasmic membrane; DNA; Hyperthermophile; Protein; RNA; Thermostability

Indexed keywords

ARCHAEAL PROTEIN; DNA; RNA;

ARCHAEON; CHEMISTRY; CYTOLOGY; ENZYME STABILITY; ENZYMOLOGY; GENETICS; HEAT; METABOLISM; REVIEW;

ARCHAEA; ARCHAEAL PROTEINS; DNA; ENZYME STABILITY; HOT TEMPERATURE; RNA;

ARCHAEA; THERMOCOCCUS KODAKARENSIS;

EID: 81055147626     PISSN: 03862208     EISSN: 13492896     Source Type: Journal    
DOI: 10.2183/pjab.87.587     Document Type: Review

References (57)

1. Fujii, M., Takagi, M., Imanaka, T. and Aiba, S. (1983) Molecular cloning of a thermostable neutral protease gene from Bacillus stearothermophilus in a vector plasmid and its expression in Bacillus stearothermophilus and Bacillus subtilis. J. Bacteriol. 154, 831-837.
2. Fischer, F., Zillig, W., Stetter, K.O. and Schreiber, G. (1983) Chemolithoautotrophic metabolism of anaerobic extremely thermophilic archaebacteria. Nature 301, 511-513.
3. Stetter, K.O. (1999) Extremophiles and their adaptation to hot environments. FEBS Lett. 452, 22-25.
4. Adams, M.W. and Kelly, R.M. (1998) Finding and using hyperthermophilic enzymes. Trends Biotechnol. 16, 329-332.
5. Woese, C.R., Kandler, O. and Wheelis, M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. U.S.A. 87, 4576-4579.
6. Barns, S.M., Delwiche, C.F., Palmer, J.D. and Pace, N.R. (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. U.S.A. 93, 9188-9193.
7. Morikawa, M., Izawa, Y., Rashid, N., Hoaki, T. and Imanaka, T. (1994) Purification and characterization of a thermostable thiol protease from a newly isolated hyperthermophilic Pyrococcus sp. Appl. Environ. Microbiol. 60, 4559-4566.
8. Atomi, H., Fukui, T., Kanai, T., Morikawa, M. and Imanaka, T. (2004) Description of Thermococcus kodakaraensis sp. nov., a well studied hyperthermophilic archaeon previously reported as Pyrococcus sp. KOD1. Archaea 1, 263-267.
9. Fukui, T., Atomi, H., Kanai, T., Matsumi, R., Fujiwara, S. and Imanaka, T. (2005) Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 15, 352-363.
10. Sato, T., Fukui, T., Atomi, H. and Imanaka, T. (2003) Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 185, 210-220.
11. Sato, T., Fukui, T., Atomi, H. and Imanaka, T. (2005) An improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis. Appl. Environ. Microbiol. 71, 3889-3899.
12. Matsumi, R., Manabe, K., Fukui, T., Atomi, H. and Imanaka, T. (2007) Disruption of a sugar transporter gene cluster in a hyperthermophilic archaeon using a host/marker system based on antibiotic resistance. J. Bacteriol. 189, 2683-2691.
13. Imanaka, T. and Atomi, H. (2002) Innzyme Catalysis in Organic Synthesis (eds. Drauz, K. and Waldmann, E.). Wiley-VCH Verlag, Weinheim, pp. 67-93.
14. Takagi, M., Imanaka, T. and Aiba, S. (1985) Nucleotide sequence and promoter region for the neutral protease gene from Bacillus stearothermophilus. J. Bacteriol. 163, 824-831.
15. Imanaka, T., Shibazaki, M. and Takagi, M. (1986) A new way of enhancing the thermostability of proteases. Nature 324, 695-697.
16. Rahman, R.N.Z.A., Fujiwara, S., Nakamura, H., Takagi, M. and Imanaka, T. (1998) Ion pairs involved for maintaining a thermastable structure of glutamate dehydrogenase (GDH) from a hyperthermophilic archaeon. Biochem. Biophys. Res. Commun. 248, 920-926.
17. Hashimoto, H., Matsumoto, T., Nishioka, M., Yuasa, T., Takeuchi, S., Inoue, T., Fujiwara, S., Takagi, M., Imanaka, T. and Kai, Y. (1999) Crystallographic studies on family B DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1. J. Biochem. 125, 983-986.
18. Hashimoto, H., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Inoue, T. and Kai, Y. (2001) Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. J. Mol. Biol. 306, 469-477.
19. Leclere, M.M., Nishioka, M., Yuasa, T., Fujiwara, S., Takagi, M. and Imanaka, T. (1998) The O6-methylguanine-DNA methyltransferase from a hyperthermophilic archaeon Pyrococcus sp. KOD1: A thermostable repair enzyme. Mol. Gen. Genet. 258, 69-77.
20. 6-methyl-guanine-DNA methyltransferase. Acta Crystallogr. D, Biol. Crystallogr. 54, 1395-1396.
21. 6-methylguanine-DNA methyltransferase. J. Mol. Biol. 292, 707-716.
22. Shiraki, K., Nishikori, S., Fujiwara, S., Hashimoto, H., Kai, Y., Takagi, M. and Imanaka, T. (2001) Comparative analyses of the conformational stability of a hyperthermophilic protein and its mesophilic counterpart. Eur. J. Biochem. 268, 4144-4150.
23. Imanaka, T., Lee, S., Takagi, M. and Fujiwara, S. (1995) Aspartyl-tRNA synthetase of the hyperthermophilic archaeon Pyrococcus sp. KOD1 has a chimerical structure of eukaryotic and bacterial enzymes. Gene 164, 153-156.
24. Fujiwara, S., Lee, S., Haruki, M., Kanaya, S., Takagi, M. and Imanaka, T. (1996) Unusual enzyme characteristics of aspartyl-tRNA synthetase from hyperthermophilic archaeon Pyrococcus sp. KOD1. FEBS Lett. 394, 66-70.
25. Schmitt, E., Moulinier, L., Fujiwara, S., Imanaka, T., Thierry, J.C. and Moras, D. (1998) Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD1; archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 17, 5227-5237.
26. Maeda, N., Kitano, K., Fukui, T., Ezaki, S., Atomi, H., Miki, K. and Imanaka, T. (1999) Ribulose bisphosphate carboxylase/oxygenase from the hyperthermopholic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal strucuture. J. Mol. Biol. 293, 57-66.
27. Kitano, K., Maeda, N., Fukui, T., Atomi, H., Imanaka, T. and Miki, K. (2001) Crystal structure of a novel-type archaeal Rubisco with pentagonal symmetry. Structure 9, 473-481.
28. Takagi, M., Kai, Y. and Imanaka, T. (2001) Methylguanine methyltransferase from Thermococcus kodakaraensis KOD1. Methods Enzymol. 334, 239-248.
29. 6-methylguanine-DNA methyltransferase from E. coli. EMBO J. 13, 1495-1501.
30. Shively, J.M., van Keulen, G. and Meijer, W.G. (1998) Something from almost nothing: carbon dioxide fixation in chemoautotrophs. Annu. Rev. Microbiol. 52, 191-230.
31. Watson, G.M. and Tabita, F.R. (1997) Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. FEMS Microbiol. Lett. 146, 13-22.
32. Hartman, F.C. and Harpel, M.R. (1994) Structure, function, regulation, and assembly of D-ribulose-1,5-bisphosphate carboxylase/oxygenase. Annu. Rev. Biochem. 63, 197-234.
33. Ezaki, S., Maeda, N., Kishimoto, T., Atomi, H. and Imanaka, T. (1999) Presence of a structurally novel type Rubisco in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. J. Biol. Chem. 274, 5078-5082.
34. Atomi, H., Ezaki, S. and Imanaka, T. (2001) Ribulose 1,5-bisphosphate carboxylase/oxygenase from Thermococcus kodakaraensis KOD1. Methods Enzymol. 331, 353-365.
35. Maeda, N., Kanai, T., Atomi, H. and Imanaka, T. (2002) The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability. J. Biol. Chem. 277, 31656-31662.
36. Sato, T., Atomi, H. and Imanaka, T. (2007) Archaeal Type III Rubiscos function in a pathway for AMP metabolism. Science 315, 1003-1006.
37. Takagi, M., Nishioka, M., Kakihara, H., Kitabayashi, M., Inoue, H., Kawakami, B., Oka, M. and Imanaka, T. (1997) Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR. Appl. Environ. Microbiol. 63, 4504-4510.
38. Yan, Z., Fujiwara, S., Kohda, K., Takagi, M. and Imanaka, T. (1997) In vitro stabilization and in vivo solubilization of foreign proteins by the Osubunit of a chaperonin from the hyperthermophilic archaeon Pyrococcus sp. strain KOD1. Appl. Environ. Microbiol. 63, 785-789.
39. Izumi, M., Fujiwara, S., Takagi, M., Kanaya, S. and Imanaka, T. (1999) Isolation and characterization of a second subunit of molecular chaperonin from Pyrococcus kodakaraensis KOD1: Analysis of ATPase deficient mutant. Appl. Environ. Microbiol. 65, 1801-1805.
40. Izumi, M., Fujiwara, S., Takagi, M., Fukui, K. and Imanaka, T. (2001) Two kinds of archaeal chaperonin with different temperature dependency from a hyperthermophile. Biochem. Biophys. Res. Commun. 280, 581-587.
41. Rahman, R.N.Z.A., Fujiwara, S., Takagi, M., Kanaya, S. and Imanaka, T. (1997) Effect of heat treatment on proper oligomeric structure forma-tion of thermostable glutamate dehydrogenase from a hyperthermophilic archaeon. Biochem. Biophys. Res. Commun. 241, 646-652.
42. Rahman, R.N.Z.A., Fujiwara, S., Takagi, M. and Imanaka, T. (1998) Sequence analysis of glutamate dehydrogenase (GDH) from the hyperthermophilic archaeon Pyrococcus sp. KOD1 and comparison of enzyme characteristics of native and recombinant GDHs. Mol. Gen. Genet. 257, 338-347.
43. Higashibata, H., Fujiwara, S., Takagi, M. and Imanaka, T. (1999) Analysis of DNA compaction profile and intracellular contents of archaeal histones from Pyrococcus kodakaraensis KOD1. Biochem. Biophys. Res. Commun. 258, 416-424.
44. Higashibata, H., Fujiwara, S., Ezaki, S., Takagi, M., Fukui, K. and Imanaka, T. (2000) Effect of polyamines on histone-induced DNA compaction of hyperthermophilic archaea. J. Biosci. Bioeng. 89, 103-106.
45. Atomi, H., Matsumi, R. and Imanaka, T. (2004) Reverse gyrase is not a prerequisite for hyperthermophilic life. J. Bacteriol. 186, 4829-4833.
46. McCloskey, J.A., Graham, D.E., Zhou, S., Crain, P.F., Ibba, M., Konisky, J., Soll, D. and 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.
47. Kowalak, J.A., Dalluge, J.J., McCloskey, J.A. and Stetter, K.O. (1994) The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochemistry 33, 7869-7876.
48. Oshima, T., Moriya, T. and Terui, Y. (2011) Identification, chemical synthesis, and biological functions of unusual polyamines produced by extreme thermophiles. Methods Mol. Biol. 720, 81-111.
49. Morimoto, N., Fukuda, W., Nakajima, N., Masuda, T., Terui, Y., Kanai, T., Oshima, T., Imanaka, T. and Fujiwara, S. (2010) Dual biosynthesis pathway for longer-chain polyamines in the hyperthermophilic archaeon Thermococcus kodakarensis. J. Bacteriol. 192, 4991-5001.
50. Albers, S.V., van de Vossenberg, J.L., Driessen, A.J. and Konings, W.N. (2000) Adaptations of the archaeal cell membrane to heat stress. Front. Biosci. 5, D813-D820.
51. Hanford, M.J. and Peeples, T.L. (2002) Archaeal tetraether lipids: unique structures and applications. Appl. Biochem. Biotechnol. 97, 45-62.
52. Carballeira, N.M., Reyes, M., Sostre, A., Huang, H., Verhagen, M.F. and Adams, M.W. (1997) Unusual fatty acid compositions of the hyperthermophilic archaeon Pyrococcus furiosus and the bacterium Thermotoga maritime. J. Bacteriol. 179, 2766-2768.
53. Matsuno, Y., Sugai, A., Higashibata, H., Fukuda, W., Ueda, K., Uda, I., Sato, I., Itoh, T., Imanaka, T. and Fujiwara, S. (2009) Effect of growth temperature and growth phase on the lipid composition of the archaeal membrane from Thermococcus kodakaraensis. Biosci. Biotechnol. Biochem. 73, 104-108.
54. Borges, N., Matsumi, R., Imanaka, T., Atomi, H. and Santos, H. (2010) Thermococcus kodakaraensis mutants deficient in di-myo-inositol phosphate use aspartate to cope with heat stress. J. Bacteriol. 192, 191-197.
55. Tang, X.-F., Ezaki, S., Atomi, H. and Imanaka, T. (2000) Biochemical analysis of a thermostable tryptophan synthase from a hyperthermophilic archaeon. Eur. J. Biochem. 267, 6369-6377.
56. Say, R.F. and Fuchs, G. (2010) Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. Nature 464, 1077-1081.
57. Kudou, M., Shiraki, K., Fujiwara, S., Imanaka, T. and Takagi, M. (2003) Prevention of thermal inactivation and aggregation of lysozyme by polyamines. Eur. J. Biochem. 270, 4547-4554.