Genetics of Thermophiles

  • Masatada Tamakoshi
  • Tairo Oshima


Increasing numbers of genomic sequence of thermophiles have been reported so far. In the so-called post-genomic era, much effort has been made for uncovering biological meaning hidden in the genomic context, which is a great challenge in computational biology. In addition to the computer-based analysis, a lot of gene products are analyzed in vitro with the recombinant proteins produced in a mesophile such as Escherichia coli taking advantage of the available nucleotide sequence information. The recombinant proteins from thermophiles can easily be purified by heat treatment to remove the heat-labile mesophilic proteins, followed by column chromatography if necessary. Many of the crystal structures of proteins revealed to date are derived from thermophiles.

Sometimes, however, it is difficult to predict a gene function within a cell by in silico analysis. Genetic manipulation system for the native thermophile host is one of the valuable methods to overcome the problem. In...


Selection Marker Insertional Mutagenesis Cryptic Plasmid lacS Gene Orotate Phosphoribosyl Transferase 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Agari Y, Kashihara A, Yokoyama S, Kuramitsu S, Shinkai A (2008) Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator. Mol Microbiol 70:60–75PubMedCrossRefGoogle Scholar
  2. Akanuma S, Yamagishi A, Tanaka N, Oshima T (1998) Serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution. Protein Sci 7:698–705PubMedCrossRefGoogle Scholar
  3. Alani E, Cao L, Kleckner N (1987) A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics 116:541–545PubMedGoogle Scholar
  4. Albers SV, Driessen AJ (2008) Conditions for gene disruption by homologous recombination of exogenous DNA into the Sulfolobus solfataricus genome. Archaea 2:145–149PubMedCrossRefGoogle Scholar
  5. Albers SV, Jonuscheit M, Dinkelaker S, Urich T, Kletzin A, Tampe R, Driessen AJ, Schleper C (2006) Production of recombinant and tagged proteins in the hyperthermophilic archaeon Sulfolobus solfataricus. Appl Environ Microbiol 72:102–111PubMedCrossRefGoogle Scholar
  6. Aravalli RN, Garrett RA (1997) Shuttle vectors for hyperthermophilic archaea. Extremophiles 1:183–191PubMedCrossRefGoogle Scholar
  7. Arnold HP, She Q, Phan H, Stedman K, Prangishvili D, Holz I, Kristjansson JK, Garrett R, Zillig W (1999) The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Mol Microbiol 34:217–226PubMedCrossRefGoogle Scholar
  8. Ashby MK, Bergquist PL (1990) Cloning and sequence of IS1000, a putative insertion sequence from Thermus thermophilus HB8. Plasmid 24:1–11PubMedCrossRefGoogle Scholar
  9. Atomi H, Fukui T, Kanai T, Morikawa M, Imanaka T (2004) Description of Thermococcus kodakaraensis sp. nov., a well studied hyperthermophilic archaeon previously reported as Pyrococcus sp. KOD1. Archaea 1:263–267PubMedCrossRefGoogle Scholar
  10. Aucelli T, Contursi P, Girfoglio M, Rossi M, Cannio R (2006) A spreadable, non-integrative and high copy number shuttle vector for Sulfolobus solfataricus based on the genetic element pSSVx from Sulfolobus islandicus. Nucleic Acids Res 34:e114PubMedCrossRefGoogle Scholar
  11. Averhoff B (2004) DNA transport and natural transformation in mesophilic and thermophilic bacteria. J Bioenerg Biomembr 36:25–33PubMedCrossRefGoogle Scholar
  12. Averhoff B (2009) Shuffling genes around in hot environments: the unique DNA transporter of Thermus thermophilus. FEMS Microbiol Rev 33:611–626PubMedCrossRefGoogle Scholar
  13. Barthelme D, Scheele U, Dinkelaker S, Janoschka A, Macmillan F, Albers SV, Driessen AJ, Stagni MS, Bill E, Meyer-Klaucke W, Schunemann V, Tampe R (2007) Structural organization of essential iron-sulfur clusters in the evolutionarily highly conserved ATP-binding cassette protein ABCE1. J Biol Chem 282:14598–14607PubMedCrossRefGoogle Scholar
  14. Berkner S, Lipps G (2008) Genetic tools for Sulfolobus spp.: vectors and first applications. Arch Microbiol 190:217–230PubMedCrossRefGoogle Scholar
  15. Berkner S, Grogan D, Albers SV, Lipps G (2007) Small multicopy, non-integrative shuttle vectors based on the plasmid pRN1 for Sulfolobus acidocaldarius and Sulfolobus solfataricus, model organisms of the cren-archaea. Nucleic Acids Res 35:e88PubMedCrossRefGoogle Scholar
  16. Blas-Galindo E, Cava F, Lopez-Vinas E, Mendieta J, Berenguer J (2007) Use of a dominant rpsL allele conferring streptomycin dependence for positive and negative selection in Thermus thermophilus. Appl Environ Microbiol 73:5138–5145PubMedCrossRefGoogle Scholar
  17. Blondal T, Thorisdottir A, Unnsteinsdottir U, Hjorleifsdottir S, Aevarsson A, Ernstsson S, Fridjonsson OH, Skirnisdottir S, Wheat JO, Hermannsdottir AG, Sigurdsson ST, Hreggvidsson GO, Smith AV, Kristjansson JK (2005) Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties. Nucleic Acids Res 33:135–142PubMedCrossRefGoogle Scholar
  18. Brock TD, Freeze H (1969) Thermus aquaticus gen. n. and sp. N., a non-sporulating extreme thermophile. J Bacteriol 104:509–517Google Scholar
  19. Brouns SJ, Wu H, Akerboom J, Turnbull AP, de Vos WM, van der Oost J (2005) Engineering a selectable marker for hyperthermophiles. J Biol Chem 280:11422–11431PubMedCrossRefGoogle Scholar
  20. Bruggemann H, Chen C (2006) Comparative genomics of Thermus thermophilus: plasticity of the megaplasmid and its contribution to a thermophilic lifestyle. J Biotechnol 124:654–661PubMedCrossRefGoogle Scholar
  21. Cacciapuoti G, Porcelli M, Moretti MA, Sorrentino F, Concilio L, Zappia V, Liu ZJ, Tempeel W, Schubot F, Rose JP, Wang BC, Brereton PS, Jenney FE, Adams MW (2007) The first agmatine/cadaverin aminopropyl transferase: biochemical and structural characterization of an enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 189:6057–6067PubMedCrossRefGoogle Scholar
  22. Cannio R, Contursi P, Rossi M, Bartolucci S (1998) An autonomously replicating transforming vector for Sulfolobus solfataricus. J Bacteriol 180:3237–3240PubMedGoogle Scholar
  23. Cannio R, Contursi P, Rossi M, Bartolucci S (2001) Thermoadaptation of a mesophilic hygromycin B phosphotransferase by directed evolution in hyperthermophilic archaea: selection of a stable genetic marker for DNA transfer into Sulfolobus solfataricus. Extremophiles 5:153–159PubMedCrossRefGoogle Scholar
  24. Castan P, Zafra O, Moreno R, de Pedro MA, Valles C, Cava F, Caro E, Schwarz H, Berenguer J (2002) The periplasmic space in Thermus thermophilus: evidence from a regulation-defective S-layer mutant overexpressing an alkaline phosphatase. Extremophiles 6:225–232PubMedCrossRefGoogle Scholar
  25. Cava F, de Pedro MA, Blas-Galindo E, Waldo GS, Westblade LF, Berenguer J (2008a) Expression and use of superfolder green fluorescent protein at high temperatures in vivo: a tool to study extreme thermophile biology. Environ Microbiol 10:605–613PubMedCrossRefGoogle Scholar
  26. Cava F, Zafra O, Berenguer J (2008b) A cytochrome c containing nitrate reductase plays a role in electron transport for denitrification in Thermus thermophilus without involvement of the bc respiratory complex. Mol Microbiol 70:507–518PubMedCrossRefGoogle Scholar
  27. Cava F, Hidalgo A, Berenguer J (2009) Thermus thermophilus as biological model. Extremophiles 13:213–231PubMedCrossRefGoogle Scholar
  28. Chautard H, Blas-Galindo E, Menguy T, Grand’Moursel L, Cava F, Berenguer J, Delcourt M (2007) An activity-independent selection system of thermostable protein variants. Nat Meth 4:919–921CrossRefGoogle Scholar
  29. Chen L, Brugger K, Skovgaard M, Redder P, She Q, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA (2005) The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J Bacteriol 187:4992–4999PubMedCrossRefGoogle Scholar
  30. Contursi P, Cannio R, Prato S, Fiorentino G, Rossi M, Bartolucci S (2003) Development of a genetic system for hyperthermophilic archaea: expression of a moderate thermophilic bacterial alcohol dehydrogenase gene in Sulfolobus solfataricus. FEMS Microbiol Lett 218:115–120PubMedCrossRefGoogle Scholar
  31. Danno A, Fukuda W, Yoshida M, Aki R, Tanaka T, Kanai T, Imanaka T, Fujiwara S (2008) Expression profiles and physiological roles of two types of prefoldins from the hyperthermophilic archaeon Thermococcus kodakaraensis. J Mol Biol 382:298–311PubMedCrossRefGoogle Scholar
  32. de Grado M, Lasa I, Berenguer J (1998) Characterization of a plasmid replicative origin from an extreme thermophile. FEMS Microbiol Lett 165:51–57PubMedGoogle Scholar
  33. de Grado M, Castan P, Berenguer J (1999) A high-transformation-efficiency cloning vector for Thermus thermophilus. Plasmid 42:241–245PubMedCrossRefGoogle Scholar
  34. Deng L, Zhu H, Chen Z, Liang YX, She Q (2009) Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Extremophiles 13:735–746PubMedCrossRefGoogle Scholar
  35. Fernandez-Herrero LA, Olabarria G, Berenguer J (1997) Surface proteins and a novel transcription factor regulate the expression of the S-layer gene in Thermus thermophilus HB8. Mol Microbiol 24:61–72PubMedCrossRefGoogle Scholar
  36. Fridjonsson O, Watzlawick H, Mattes R (2002) Thermoadaptation of α-galactosidase AgaB1 in Thermus thermophilus. J Bacteriol 184:3385–3391PubMedCrossRefGoogle Scholar
  37. Friedrich A, Hartsch T, Averhoff B (2001) Natural transformation in mesophilic and thermophilic bacteria: identification and characterization of novel, closely related competence genes in Acinetobacter sp. strain BD413 and Thermus thermophilus HB27. Appl Environ Microbiol 67:3140–3148PubMedCrossRefGoogle Scholar
  38. Friedrich A, Prust C, Hartsch T, Henne A, Averhoff B (2002) Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27. Appl Environ Microbiol 68:745–755PubMedCrossRefGoogle Scholar
  39. Friedrich A, Rumszauer J, Henne A, Averhoff B (2003) Pilin-like proteins in the extremely thermophilic bacterium Thermus thermophilus HB27: implication in competence for natural transformation and links to type IV pilus biogenesis. Appl Environ Microbiol 69:3695–3700PubMedCrossRefGoogle Scholar
  40. Frols S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema EJ, Driessen AJ, Schleper C, Albers SV (2008) UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Mol Microbiol 70:938–952PubMedCrossRefGoogle Scholar
  41. Fujiwara K, Tsubouchi T, Kuzuyama T, Nishiyama M (2006) Involvement of the arginine repressor in lysine biosynthesis of Thermus thermophilus. Microbiology 152:3585–3594PubMedCrossRefGoogle Scholar
  42. Fujiwara S, Aki R, Yoshida M, Higashibata H, Imanaka T, Fukuda W (2008) Expression profiles and physiological roles of two types of molecular chaperonins from the hyperthermophilic archaeon Thermococcus kodakarensis. Appl Environ Microbiol 74:7306–7312PubMedCrossRefGoogle Scholar
  43. Fukuda W, Morimoto N, Imanaka T, Fujiwara S (2008) Agmatine is essential for the cell growth of Thermococcus kodakaraensis. FEMS Microbiol Lett 287:113–120PubMedCrossRefGoogle Scholar
  44. Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, Imanaka T (2005) Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res 15:352–363PubMedCrossRefGoogle Scholar
  45. Gerle C, Tani K, Yokoyama K, Tamakoshi M, Yoshida M, Fujiyoshi Y, Mitsuoka K (2006) Two-dimensional crystallization and analysis of projection images of intact Thermus thermophilus V-ATPase. J Struct Biol 153:200–206PubMedCrossRefGoogle Scholar
  46. Hasenohrl D, Lombo T, Kaberdin V, Londei P, Blasi U (2008) Translation initiation factor (a/eIF2-γ) counteracts 5′ to 3′ mRNA decay in the archaeon Sulfolobus solfataricus. Proc Natl Acad Sci USA 105:2146–2150PubMedCrossRefGoogle Scholar
  47. Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, Jacobi C, Starkuviene V, Schlenczeck S, Dencker S, Huber R, Klenk HP, Kramer W, Merkl R, Gottschalk G, Fritz HJ (2004) The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 22:547–553PubMedCrossRefGoogle Scholar
  48. Hidaka Y, Hasegawa M, Nakahara T, Hoshino T (1994) The entire population of Thermus thermophilus cells is always competent at any growth phase. Biosci Biotechnol Biochem 58:1338–1339PubMedCrossRefGoogle Scholar
  49. Hirata A, Kanai T, Santangelo TJ, Tajiri M, Manabe K, Reeve JN, Imanaka T, Murakami KS (2008) Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature-sensitive. Mol Microbiol 70:623–633PubMedCrossRefGoogle Scholar
  50. Hoseki J, Yano T, Koyama Y, Kuramitsu S, Kagamiyama H (1999) Directed evolution of thermostable kanamycin-resistance gene: a convenient selection marker for Thermus thermophilus. J Biochem 126:951–956PubMedCrossRefGoogle Scholar
  51. Imanaka H, Yamatsu A, Fukui T, Atomi H, Imanaka T (2006) Phosphoenolpyruvate synthase plays an essential role for glycolysis in the modified Embden-Meyerhof pathway in Thermococcus kodakarensis. Mol Microbiol 61:898–909PubMedCrossRefGoogle Scholar
  52. Ishida M, Oshima T (2002) Effective Structure of a leader open reading frame for enhancing the expression of GC-Rich Genes. J Biochem 132:63–70PubMedCrossRefGoogle Scholar
  53. Jonuscheit M, Martusewitsch E, Stedman KM, Schleper C (2003) A reporter gene system for the hyperthermophilic archaeon Sulfolobus solfataricus based on a selectable and integrative shuttle vector. Mol Microbiol 48:1241–1252PubMedCrossRefGoogle Scholar
  54. Kanai T, Akerboom J, Takedomi S, van de Werken HJ, Blombach F, van der Oost J, Murakami T, Atomi H, Imanaka T (2007) A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes. J Biol Chem 282:33659–33670PubMedCrossRefGoogle Scholar
  55. Kayser KJ, Kilbane JJ 2nd (2001) New host-vector system for Thermus spp. based on the malate dehydrogenase gene. J Bacteriol 183:1792–1795PubMedCrossRefGoogle Scholar
  56. Kayser KJ, Kwak JH, Park HS, Kilbane JJ 2nd (2001) Inducible and constitutive expression using new plasmid and integrative expression vectors for Thermus sp. Lett Appl Microbiol 32:412–418PubMedCrossRefGoogle Scholar
  57. Keeling PJ, Klenk HP, Singh RK, Feeley O, Schleper C, Zillig W, Doolittle WF, Sensen CW (1996) Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1. Plasmid 35:141–144PubMedCrossRefGoogle Scholar
  58. Kobashi N, Nishiyama M, Tanokura M (1999) Aspartate kinase-independent lysine synthesis in an extremely thermophilic bacterium, Thermus thermophilus: lysine is synthesized via α-aminoadipic acid not via diaminopimelic acid. J Bacteriol 181:1713–1718PubMedGoogle Scholar
  59. Kobayashi H, Kuwae A, Maseda H, Nakamura A, Hoshino T (2005) Isolation of a low-molecular-weight, multicopy plasmid, pNHK101, from Thermus sp. TK10 and its use as an expression vector for T. thermophilus HB27. Plasmid 54:70–79PubMedCrossRefGoogle Scholar
  60. Kosuge T, Hoshino T (1998) Lysine is synthesized through the α-aminoadipate pathway in Thermus thermophilus. FEMS Microbiol Lett 169:361–367PubMedGoogle Scholar
  61. Kosuge T, Hoshino T (1999) The α-aminoadipate pathway for lysine biosynthesis is widely distributed among Thermus strains. J Biosci Bioeng 88:672–675PubMedCrossRefGoogle Scholar
  62. Kotsuka T, Akanuma S, Tomuro M, Yamagishi A, Oshima T (1996) Further stabilization of 3-isopropylmalate dehydrogenase of an extreme thermophile, Thermus thermophilus, by a suppressor mutation method. J Bacteriol 178:723–727PubMedGoogle Scholar
  63. Koyama Y, Hoshino T, Tomizuka N, Furukawa K (1986) Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp. J Bacteriol 166:338–340PubMedGoogle Scholar
  64. Koyama Y, Arikawa Y, Furukawa K (1990a) A plasmid vector for an extreme thermophile, Thermus thermophilus. FEMS Microbiol Lett 60:97–101PubMedCrossRefGoogle Scholar
  65. Koyama Y, Okamoto S, Furukawa K (1990b) Cloning of α- and β-galactosidase genes from an extreme thermophile, Thermus strain T2, and their expression in Thermus thermophilus HB27. Appl Environ Microbiol 56:2251–2254PubMedGoogle Scholar
  66. Kurosawa N, Grogan DW (2005) Homologous recombination of exogenous DNA with the Sulfolobus acidocaldarius genome: properties and uses. FEMS Microbiol Lett 253:141–149PubMedCrossRefGoogle Scholar
  67. Lasa I, Caston JR, Fernandez-Herrero LA, de Pedro MA, Berenguer J (1992) Insertional mutagenesis in the extreme thermophilic eubacteria Thermus thermophilus HB8. Mol Microbiol 6:1555–1564PubMedCrossRefGoogle Scholar
  68. Liao H, McKenzie T, Hageman R (1986) Isolation of a thermostable enzyme variant by cloning and selection in a thermophile. Proc Natl Acad Sci USA 83:576–580PubMedCrossRefGoogle Scholar
  69. Louvel H, Kanai T, Atomi H, Reeve JN (2009) The Fur iron regulator-like protein is cryptic in the hyperthermophilic archaeon Thermococcus kodakaraensis. FEMS Microbiol Lett 295:117–128PubMedCrossRefGoogle Scholar
  70. Lubelska JM, Jonuscheit M, Schleper C, Albers SV, Driessen AJ (2006) Regulation of expression of the arabinose and glucose transporter genes in the thermophilic archaeon Sulfolobus solfataricus. Extremophiles 10:383–391PubMedCrossRefGoogle Scholar
  71. Lucas S, Toffin L, Zivanovic Y, Charlier D, Moussard H, Forterre P, Prieur D, Erauso G (2002) Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi. Appl Environ Microbiol 68:5528–5536PubMedCrossRefGoogle Scholar
  72. Maehara T, Hoshino T, Nakamura A (2008) Characterization of three putative Lon proteases of Thermus thermophilus HB27 and use of their defective mutants as hosts for production of heterologous proteins. Extremophiles 12:285–296PubMedCrossRefGoogle Scholar
  73. Maseda H, Hoshino T (1995) Screening and analysis of DNA fragments that show promoter activities in Thermus thermophilus. FEMS Microbiol Lett 128:127–134PubMedCrossRefGoogle Scholar
  74. Matsumi R, Manabe K, Fukui T, Atomi H, 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 189:2683–2691PubMedCrossRefGoogle Scholar
  75. Matsumura M, Aiba S (1985) Screening for thermostable mutant of kanamycin nucleotidyltransferase by the use of a transformation system for a thermophile, Bacillus stearothermophilus. J Biol Chem 260:15298–15303PubMedGoogle Scholar
  76. Matsushita I, Yanase H (2008) A novel thermophilic lysozyme from bacteriophage ϕIN93. Biochem Biophys Res Commun 377:89–92PubMedCrossRefGoogle Scholar
  77. Matsushita I, Yanase H (2009) A novel insertion sequence transposed to thermophilic bacteriophage ϕIN93. J Biochem 146:797–803PubMedCrossRefGoogle Scholar
  78. Miyazaki J, Kobashi N, Nishiyama M, Yamane H (2001) Functional and evolutionary relationship between arginine biosynthesis and prokaryotic lysine biosynthesis through α-aminoadipate. J Bacteriol 183:5067–5073PubMedCrossRefGoogle Scholar
  79. Miyazaki J, Kobashi N, Fujii T, Nishiyama M, Yamane H (2002) Characterization of a lysK gene as an argE homolog in Thermus thermophilus HB27. FEBS Lett 512:269–274PubMedCrossRefGoogle Scholar
  80. Miyazaki J, Kobashi N, Nishiyama M, Yamane H (2003) Characterization of homoisocitrate dehydrogenase involved in lysine biosynthesis of an extremely thermophilic bacterium, Thermus thermophilus HB27, and evolutionary implication of β-decarboxylating dehydrogenase. J Biol Chem 278:1864–1871PubMedCrossRefGoogle Scholar
  81. Moreno R, Zafra O, Cava F, Berenguer J (2003) Development of a gene expression vector for Thermus thermophilus based on the promoter of the respiratory nitrate reductase. Plasmid 49:2–8PubMedCrossRefGoogle Scholar
  82. Moreno R, Hidalgo A, Cava F, Fernandez-Lafuente R, Guisan JM, Berenguer J (2004) Use of an antisense RNA strategy to investigate the functional significance of Mn-catalase in the extreme thermophile Thermus thermophilus. J Bacteriol 186:7804–7806PubMedCrossRefGoogle Scholar
  83. Moreno R, Haro A, Castellanos A, Berenguer J (2005) High-level overproduction of His-tagged Tth DNA polymerase in Thermus thermophilus. Appl Environ Microbiol 71:591–593PubMedCrossRefGoogle Scholar
  84. Nanako Morimoto N, Fukuda W, Nakajima N, Masuda T, Terui Y, Kanai T, Oshima T, Imanaka T, Fujiwara S (2010) Dual biosynthesis pathway for longer-chain polyamines in the hyperthermophilic archaeon Thermococcus kodakarensis. J Bacteriol 192:4991–5001PubMedCrossRefGoogle Scholar
  85. Nakamura A, Takakura Y, Kobayashi H, Hoshino T (2005) In vivo directed evolution for thermostabilization of Escherichia coli hygromycin B phosphotransferase and the use of the gene as a selection marker in the host-vector system of Thermus thermophilus. J Biosci Bioeng 100:158–163PubMedCrossRefGoogle Scholar
  86. Nakano M, Imamura H, Toei M, Tamakoshi M, Yoshida M, Yokoyama K (2008) ATP hydrolysis and synthesis of a rotary motor V-ATPase from Thermus thermophilus. J Biol Chem 283:20789–20796PubMedCrossRefGoogle Scholar
  87. Naryshkina T, Liu J, Florens L, Swanson SK, Pavlov AR, Pavlova NV, Inman R, Minakhin L, Kozyavkin SA, Washburn M, Mushegian A, Severinov K (2006) Thermus thermophilus bacteriophage φYS40 genome and proteomic characterization of virions. J Mol Biol 364:667–677PubMedCrossRefGoogle Scholar
  88. Ohnuma M, Terui Y, Tamakoshi M, Mitome H, Niitsu M, Samejima K, Kawashima E, Oshima T (2005) N1-aminopropylagmatine, a new polyamine produced as a key intermediate in polyamine biosynthesis of an extreme thermophile, Thermus thermophilus. J Biol Chem 280:30073–30082PubMedCrossRefGoogle Scholar
  89. Ohta T, Tokishita S, Imazuka R, Mori I, Okamura J, Yamagata H (2006) β-Glucosidase as a reporter for the gene expression studies in Thermus thermophilus and constitutive expression of DNA repair genes. Mutagenesis 21:255–260PubMedCrossRefGoogle Scholar
  90. Orita I, Sato T, Yurimoto H, Kato N, Atomi H, Imanaka T, Sakai Y (2006) The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. J Bacteriol 188:4698–4704PubMedCrossRefGoogle Scholar
  91. Oshima T (1983) Novel polyamines in Thermus thermophilus: isolation, identification and chemical synthesis. Meth Enzymol 94:401–411CrossRefGoogle Scholar
  92. Oshima T (2007) Unique polyamines produced by an extreme thermophile, Thermus thermophilus. Amino Acids 33:367–372PubMedCrossRefGoogle Scholar
  93. Oshima T, Imahori K (1974) Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a nonsporulating thermophilic bacterium from a Japanese thermal spa. Int J Syst Bacteriol 24:102–112CrossRefGoogle Scholar
  94. Park HS, Kilbane JJ 2nd (2004) Gene expression studies of Thermus thermophilus promoters PdnaK, Parg and Pscs-mdh. Lett Appl Microbiol 38:415–422PubMedCrossRefGoogle Scholar
  95. Pederson DM, Welsh LC, Marvin DA, Sampson M, Perham RN, Yu M, Slater MR (2001) The protein capsid of filamentous bacteriophage PH75 from Thermus thermophilus. J Mol Biol 309:401–421PubMedCrossRefGoogle Scholar
  96. Peeters E, Albers SV, Vassart A, Driessen AJ, Charlier D (2009) Ss-LrpB, a transcriptional regulator from Sulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes. Mol Microbiol 71:972–988PubMedCrossRefGoogle Scholar
  97. Ramirez-Arcos S, Fernandez-Herrero LA, Marin I, Berenguer J (1998) Anaerobic growth, a property horizontally transferred by an Hfr-like mechanism among extreme thermophiles. J Bacteriol 180:3137–3143PubMedGoogle Scholar
  98. Reilly MS, Grogan DW (2001) Characterization of intragenic recombination in a hyperthermophilic archaeon via conjugational DNA exchange. J Bacteriol 183:2943–2946PubMedCrossRefGoogle Scholar
  99. Rumszauer J, Schwarzenlander C, Averhoff B (2006) Identification, subcellular localization and functional interactions of PilMNOWQ and PilA4 involved in transformation competency and pilus biogenesis in the thermophilic bacterium Thermus thermophilus HB27. FEBS J 273:3261–3272PubMedCrossRefGoogle Scholar
  100. Sakai T, Tokishita S, Mochizuki K, Motomiya A, Yamagata H, Ohta T (2008) Mutagenesis of uracil-DNA glycosylase deficient mutants of the extremely thermophilic eubacterium Thermus thermophilus. DNA Repair (Amst) 7:663–669CrossRefGoogle Scholar
  101. Sakaki Y, Oshima T (1975) Isolation and characterization of a bacteriophage infectious to an extreme thermophile, Thermus thermophilus HB8. J Virol 15:1449–1453PubMedGoogle Scholar
  102. Sakamoto K, Agari Y, Yokoyama S, Kuramitsu S, Shinkai A (2008) Functional identification of an anti-σE factor from Thermus thermophilus HB8. Gene 423:153–159PubMedCrossRefGoogle Scholar
  103. Santangelo TJ, Cubonova L, Matsumi R, Atomi H, Imanaka T, Reeve JN (2008a) Polarity in archaeal operon transcription in Thermococcus kodakaraensis. J Bacteriol 190:2244–2248PubMedCrossRefGoogle Scholar
  104. Santangelo TJ, Cubonova L, Reeve JN (2008b) Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl Environ Microbiol 74:3099–3104PubMedCrossRefGoogle Scholar
  105. Sato T, Fukui T, Atomi H, Imanaka T (2003) Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 185:210–220PubMedCrossRefGoogle Scholar
  106. Sato T, Imanaka H, Rashid N, Fukui T, Atomi H, Imanaka T (2004) Genetic evidence identifying the true gluconeogenic fructose-1, 6-bisphosphatase in Thermococcus kodakaraensis and other hyperthermophiles. J Bacteriol 186:5799–5807PubMedCrossRefGoogle Scholar
  107. Sato T, Fukui T, Atomi H, Imanaka T (2005) Improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis. Appl Environ Microbiol 71:3889–3899PubMedCrossRefGoogle Scholar
  108. Sato T, Atomi H, Imanaka T (2007) Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 315:1003–1006PubMedCrossRefGoogle Scholar
  109. Schelert J, Dixit V, Hoang V, Simbahan J, Drozda M, Blum P (2004) Occurrence and characterization of mercury resistance in the hyperthermophilic archaeon Sulfolobus solfataricus by use of gene disruption. J Bacteriol 186:427–437PubMedCrossRefGoogle Scholar
  110. Schelert J, Drozda M, Dixit V, Dillman A, Blum P (2006) Regulation of mercury resistance in the crenarchaeote Sulfolobus solfataricus. J Bacteriol 188:7141–7150PubMedCrossRefGoogle Scholar
  111. Schleper C, Kubo K, Zillig W (1992) The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA. Proc Natl Acad Sci USA 89:7645–7649PubMedCrossRefGoogle Scholar
  112. Schwarzenlander C, Averhoff B (2006) Characterization of DNA transport in the thermophilic bacterium Thermus thermophilus HB27. FEBS J 273:4210–4218PubMedCrossRefGoogle Scholar
  113. Schwarzenlander C, Haase W, Averhoff B (2009) The role of single subunits of the DNA transport machinery of Thermus thermophilus HB27 in DNA binding and transport. Environ Microbiol 11:801–808PubMedCrossRefGoogle Scholar
  114. Sevostyanova A, Djordjevic M, Kuznedelov K, Naryshkina T, Gelfand MS, Severinov K, Minakhin L (2007) Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage φYS40. J Mol Biol 366:420–435PubMedCrossRefGoogle Scholar
  115. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PM, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoc HP, Redder P, Schenk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, Van der Oost J (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci USA 98:7835–7840PubMedCrossRefGoogle Scholar
  116. Shigi N, Suzuki T, Tamakoshi M, Oshima T, Watanabe K (2002) Conserved bases in the Tψ C loop of tRNA are determinants for thermophile-specific 2-thiouridylation at position 54. J Biol Chem 277:39128–39135PubMedCrossRefGoogle Scholar
  117. Shigi N, Sakaguchi Y, Suzuki T, Watanabe K (2006a) Identification of two tRNA thiolation genes required for cell growth at extremely high temperatures. J Biol Chem 281:14296–14306PubMedCrossRefGoogle Scholar
  118. Shigi N, Suzuki T, Terada T, Shirouzu M, Yokoyama S, Watanabe K (2006b) Temperature-dependent biosynthesis of 2-thioribothymidine of Thermus thermophilus tRNA. J Biol Chem 281:2104–2113PubMedCrossRefGoogle Scholar
  119. Shigi N, Sakaguchi Y, Asai S, Suzuki T, Watanabe K (2008) Common thiolation mechanism in the biosynthesis of tRNA thiouridine and sulphur-containing cofactors. EMBO J 27:3267–3278PubMedCrossRefGoogle Scholar
  120. Shinkai A, Kira S, Nakagawa N, Kashihara A, Kuramitsu S, Yokoyama S (2007a) Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8. J Bacteriol 189:3891–3901PubMedCrossRefGoogle Scholar
  121. Shinkai A, Ohbayashi N, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S (2007b) Identification of promoters recognized by RNA polymerase-σE holoenzyme from Thermus thermophilus HB8. J Bacteriol 189:8758–8764PubMedCrossRefGoogle Scholar
  122. Soler N, Justome A, Quevillon-Cheruel S, Lorieux F, Le Cam E, Marguet E, Forterre P (2007) The rolling-circle plasmid pTN1 from the hyperthermophilic archaeon Thermococcus nautilus. Mol Microbiol 66:357–370PubMedCrossRefGoogle Scholar
  123. Szabo Z, Sani M, Groeneveld M, Zolghadr B, Schelert J, Albers SV, Blum P, Boekema EJ, Driessen AJ (2007) Flagellar motility and structure in the hyperthermoacidophilic archaeon Sulfolobus solfataricus. J Bacteriol 189:4305–4309PubMedCrossRefGoogle Scholar
  124. Tamakoshi M, Yamagishi A, Oshima T (1995) Screening of stable proteins in an extreme thermophile, Thermus thermophilus. Mol Microbiol 16:1031–1036PubMedCrossRefGoogle Scholar
  125. Tamakoshi M, Uchida M, Tanabe K, Fukuyama S, Yamagishi A, Oshima T (1997) A new Thermus-Escherichia coli shuttle integration vector system. J Bacteriol 179:4811–4814PubMedGoogle Scholar
  126. Tamakoshi M, Yaoi T, Oshima T, Yamagishi A (1999) An efficient gene replacement and deletion system for an extreme thermophile, Thermus thermophilus. FEMS Microbiol Lett 173:431–437PubMedCrossRefGoogle Scholar
  127. Tamakoshi M, Nakano Y, Kakizawa S, Yamagishi A, Oshima T (2001) Selection of stabilized 3-isopropylmalate dehydrogenase of Saccharomyces cerevisiae using the host-vector system of an extreme thermophile, Thermus thermophilus. Extremophiles 5:17–22PubMedCrossRefGoogle Scholar
  128. Tsubouchi T, Mineki R, Taka H, Kaga N, Murayama K, Nishiyama C, Yamane H, Kuzuyama T, Nishiyama M (2005) Leader peptide-mediated transcriptional attenuation of lysine biosynthetic gene cluster in Thermus thermophilus. J Biol Chem 280:18511–18516PubMedCrossRefGoogle Scholar
  129. Utsumi R, Ikeda M, Horie T, Yamamoto M, Ichihara A, Taniguchi Y, Hashimoto R, Tanabe H, Obata K, Noda M (1995) Isolation and characterization of the IS3-like element from Thermus aquaticus. Biosci Biotechnol Biochem 59:1707–1711PubMedCrossRefGoogle Scholar
  130. Wagner M, Berkner S, Ajon M, Driessen AJ, Lipps G, Albers SV (2009) Expanding and understanding the genetic toolbox of the hyperthermophilic genus Sulfolobus. Biochem Soc Trans 37:97–101PubMedCrossRefGoogle Scholar
  131. Wang Y, Duan Z, Zhu H, Guo X, Wang Z, Zhou J, She Q, Huang L (2007) A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus. Virology 363:124–133PubMedCrossRefGoogle Scholar
  132. Worthington P, Hoang V, Perez-Pomares F, Blum P (2003) Targeted disruption of the α-amylase gene in the hyperthermophilic archaeon Sulfolobus solfataricus. J Bacteriol 185:482–488PubMedCrossRefGoogle Scholar
  133. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S (2000) Structural genomics projects in Japan. Nat Struct Biol 7(Suppl):943–945PubMedCrossRefGoogle Scholar
  134. Yokoyama K, Nagata K, Imamura H, Ohkuma S, Yoshida M, Tamakoshi M (2003a) Subunit arrangement in V-ATPase from Thermus thermophilus. J Biol Chem 278:42686–42691PubMedCrossRefGoogle Scholar
  135. Yokoyama K, Nakano M, Imamura H, Yoshida M, Tamakoshi M (2003b) Rotation of the proteolipid ring in the V-ATPase. J Biol Chem 278:24255–24258PubMedCrossRefGoogle Scholar
  136. Yu MX, Slater MR, Ackermann HW (2006) Isolation and characterization of Thermus bacteriophages. Arch Virol 151:663–679PubMedCrossRefGoogle Scholar
  137. Zolghadr B, Weber S, Szabo Z, Driessen AJ, Albers SV (2007) Identification of a system required for the functional surface localization of sugar binding proteins with class III signal peptides in Sulfolobus solfataricus. Mol Microbiol 64:795–806PubMedCrossRefGoogle Scholar

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© Springer 2011

Authors and Affiliations

  1. 1.Department of Molecular BiologyTokyo University of Pharmacy and Life SciencesHachiojiJapan
  2. 2.Institute of Environmental MicrobiologyKyowa-kako Co.MachidaJapan

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