Genetic examination of initial amino acid oxidation and glutamate catabolism in the hyperthermophilic archaeon Thermococcus kodakarensis

Journal of Bacteriology

Volumn 195, Issue 9, 2013, Pages 1940-1948

  Yokooji, Yuusuke ^a   Sato, Takaaki ^a,d   Fujiwar, Shinsuke ^b   Imanak, Tadayuki ^c,d   Atomi, Haruyuki ^a,d  

^a KYOTO UNIVERSITY   (Japan)

^b KWANSEI GAKUIN UNIVERSITY   (Japan)

^c RITSUMEIKAN UNIVERSITY   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

2 OXOGLUTARIC ACID; ALANINE; AMINO ACID; CYSTEINE; FERREDOXIN NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE REDUCTASE; GLUTAMIC ACID; GLUTAMINE; KGDH1 PROTEIN; MEMBRANE PROTEIN; NICOTINAMIDE ADENINE DINUCLEOTIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; OXIDOREDUCTASE; PYRUVIC ACID; SUCCINYL COENZYME A SYNTHETASE; THREONINE; UNCLASSIFIED DRUG; VALINE;

ARTICLE; BACTERIAL GROWTH; ENZYME ACTIVITY; ENZYME DEGRADATION; ENZYME METABOLISM; ENZYME STRUCTURE; GENE DISRUPTION; GENETIC ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; THERMOCOCCUS KODAKARENSIS; THERMOSTABILITY;

AMINO ACIDS; ARCHAEAL PROTEINS; GLUTAMATE DEHYDROGENASE; GLUTAMIC ACID; KETONE OXIDOREDUCTASES; OXIDATION-REDUCTION; THERMOCOCCUS;

ARCHAEA; THERMOCOCCALES; THERMOCOCCUS KODAKARENSIS;

EID: 84876162394     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01979-12     Document Type: Article

References (59)

1. Itoh T. 2003. Taxonomy of nonmethanogenic hyperthermophilic and related thermophilic archaea. J. Biosci. Bioeng. 96:203-212.
2. Schut GJ, Boyd ES, Peters JW, Adams MW. 2013. The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol. Rev. 37:182-203.
3. Sato T, Atomi H. 2011. Novel metabolic pathways in Archaea. Curr. Opin. Microbiol. 14:307-314.
4. Siebers B, Schönheit P. 2005. Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Curr. Opin. Microbiol. 8:695-705.
5. Verhees CH, Kengen SW, Tuininga JE, Schut GJ, Adams MW, De Vos WM, van der Oost J. 2003. The unique features of glycolytic pathways in Archaea. Biochem. J. 375:231-246.
6. Schut GJ, Menon AL, Adams MW. 2001. 2-Keto acid oxidoreductases from Pyrococcus furiosus and Thermococcus litoralis. Methods Enzymol. 331:144-158.
7. Consalvi V, Chiaraluce R, Politi L, Vaccaro R, De Rosa M, Scandurra R. 1991. Extremely thermostable glutamate dehydrogenase from the hyperthermophilic archaebacterium Pyrococcus furiosus. Eur. J. Biochem. 202:1189-1196.
8. Rahman R, Fujiwara S, Takagi M, Imanaka T. 1998. Sequence analysis of glutamate dehydrogenase (GDH) from the hyperthermophilic archaeon Pyrococcus sp. KOD1 and comparison of the enzymatic characteristics of native and recombinant GDHs. Mol. Gen. Genet. 257:338-347.
9. DiRuggiero J, Robb FT, Jagus R, Klump HH, Borges KM, Kessel M, Mai X, Adams MW. 1993. Characterization, cloning, and in vitro expression of the extremely thermostable glutamate dehydrogenase from the hyperthermophilic archaeon, ES4. J. Biol. Chem. 268:17767-17774.
10. Klump H, Di Ruggiero J, Kessel M, Park JB, Adams MW, Robb FT. 1992. Glutamate dehydrogenase from the hyperthermophile Pyrococcus furiosus. Thermal denaturation and activation. J. Biol. Chem. 267:22681- 22685.
11. Kobayashi T, Higuchi S, Kimura K, Kudo T, Horikoshi K. 1995. Properties of glutamate dehydrogenase and its involvement in alanine production in a hyperthermophilic archaeon, Thermococcus profundus. J. Biochem. 118:587-592.
12. Lee MK, Gonzalez JM, Robb FT. 2002. Extremely thermostable glutamate dehydrogenase (GDH) from the freshwater archaeon Thermococcus waiotapuensis: cloning and comparison with two marine hyperthermophilic GDHs. Extremophiles 6:151-159.
13. Ma K, Loessner H, Heider J, Johnson MK, Adams MW. 1995. Effects of elemental sulfur on the metabolism of the deep-sea hyperthermophilic archaeon Thermococcus strain ES-1: characterization of a sulfur-regulated, non-heme iron alcohol dehydrogenase. J. Bacteriol. 177:4748-4756.
14. Ma K, Robb FT, Adams MW. 1994. Purification and characterization of NADP-specific alcohol dehydrogenase and glutamate dehydrogenase from the hyperthermophilic archaeon Thermococcus litoralis. Appl. Environ. Microbiol. 60:562-568.
15. Ohshima T, Nishida N. 1993. Purification and properties of extremely thermostable glutamate dehydrogenases from two hyperthermophilic archaebacteria, Pyrococcus woesei and Pyrococcus furiosus. Biosci. Biotechnol. Biochem. 57:945-951.
16. Rahman R, Fujiwara S, Nakamura H, Takagi M, Imanaka T. 1998. Ion pairs involved in maintaining a thermostable structure of glutamate dehydrogenase from a hyperthermophilic archaeon. Biochem. Biophys. Res. Commun. 248:920-926.
17. Yip KS, Stillman TJ, Britton KL, Artymiuk PJ, Baker PJ, Sedelnikova SE, Engel PC, Pasquo A, Chiaraluce R, Consalvi V. 1995. The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ionpair networks in maintaining enzyme stability at extreme temperatures. Structure 3:1147-1158.
18. Ward DE, Kengen SW, van der Oost J, de Vos WM. 2000. Purification and characterization of the alanine aminotransferase from the hyperthermophilic archaeon Pyrococcus furiosus and its role in alanine production. J. Bacteriol. 182:2559-2566.
19. Ward DE, de Vos WM, van der Oost J. 2002. Molecular analysis of the role of two aromatic aminotransferases and a broad-specificity aspartate aminotransferase in the aromatic amino acid metabolism of Pyrococcus furiosus. Archaea 1:133-141.
20. Andreotti G, Cubellis MV, Nitti G, Sannia G, Mai X, Adams MW, Marino G. 1995. An extremely thermostable aromatic aminotransferase from the hyperthermophilic archaeon Pyrococcus furiosus. Biochim. Biophys. Acta 1247:90-96.
21. Andreotti G, Cubellis MV, Nitti G, Sannia G, Mai X, Marino G, Adams MW. 1994. Characterization of aromatic aminotransferases from the hyperthermophilic archaeon Thermococcus litoralis. Eur. J. Biochem. 220: 543-549.
22. Matsui I, Matsui E, Sakai Y, Kikuchi H, Kawarabayasi Y, Ura H, Kawaguchi S, Kuramitsu S, Harata K. 2000. The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii. J. Biol. Chem. 275:4871- 4879.
23. Sakuraba H, Kawakami R, Takahashi H, Ohshima T. 2004. Novel archaeal alanine:glyoxylate aminotransferase from Thermococcus litoralis. J. Bacteriol. 186:5513-5518.
24. Blamey JM, Adams MW. 1993. Purification and characterization of pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. Biochim. Biophys. Acta 1161:19-27.
25. Kletzin A, Adams MW. 1996. Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima. J. Bacteriol. 178:248-257.
26. Ma K, Hutchins A, Sung SJ, Adams MW. 1997. Pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon, Pyrococcus furiosus, functions as a CoA-dependent pyruvate decarboxylase. Proc. Natl. Acad. Sci. U. S. A. 94:9608-9613.
27. Menon AL, Hendrix H, Hutchins A, Verhagen MF, Adams MW. 1998. The δ-subunit of pyruvate ferredoxin oxidoreductase from Pyrococcus furiosus is a redox-active, iron-sulfur protein: evidence for an ancestral relationship with 8Fe-type ferredoxins. Biochemistry 37:12838-12846.
28. Smith ET, Blamey JM, Adams MW. 1994. Pyruvate ferredoxin oxidoreductases of the hyperthermophilic archaeon, Pyrococcus furiosus, and the hyperthermophilic bacterium, Thermotoga maritima, have different catalytic mechanisms. Biochemistry 33:1008-1016.
29. Heider J, Mai X, Adams MW. 1996. Characterization of 2-ketoisovalerate ferredoxin oxidoreductase, a new and reversible coenzyme A-dependent enzyme involved in peptide fermentation by hyperthermophilic archaea. J. Bacteriol. 178:780-787.
30. Ozawa Y, Nakamura T, Kamata N, Yasujima D, Urushiyama A, Yamakura F, Ohmori D, Imai T. 2005. Thermococcus profundus 2-ketoisovalerate ferredoxin oxidoreductase, a key enzyme in the archaeal energy- producing amino acid metabolic pathway. J. Biochem. 137:101-107.
31. Mai X, Adams MW. 1994. Indolepyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. A new enzyme involved in peptide fermentation. J. Biol. Chem. 269:16726-16732.
32. Ozawa Y, Siddiqui MA, Takahashi Y, Urushiyama A, Ohmori D, Yamakura F, Arisaka F, Imai T. 2012. Indolepyruvate ferredoxin oxidoreductase: an oxygen-sensitive iron-sulfur enzyme from the hyperthermophilic archaeon Thermococcus profundus. J. Biosci. Bioeng. 114:23-27.
33. Siddiqui MA, Fujiwara S, Imanaka T. 1997. Indolepyruvate ferredoxin oxidoreductase from Pyrococcus sp. KOD1 possesses a mosaic structure showing features of various oxidoreductases. Mol. Gen. Genet. 254:433- 439.
34. Mai X, Adams MW. 1996. Characterization of a fourth type of 2-keto acid-oxidizing enzyme from a hyperthermophilic archaeon: 2-ketoglutarate ferredoxin oxidoreductase from Thermococcus litoralis. J. Bacteriol. 178:5890-5896.
35. Glasemacher J, Bock AK, Schmid R, Schönheit P. 1997. Purification and properties of acetyl-CoA synthetase (ADP-forming), an archaeal enzyme of acetate formation and ATP synthesis, from the hyperthermophile Pyrococcus furiosus. Eur. J. Biochem. 244:561-567.
36. Hutchins AM, Mai X, Adams MW. 2001. Acetyl-CoA synthetases I and II from Pyrococcus furiosus. Methods Enzymol. 331:158-167.
37. Mai X, Adams MW. 1996. Purification and characterization of two reversible and ADP-dependent acetyl coenzyme A synthetases from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 178:5897- 5903.
38. Schäfer T, Schönheit P. 1991. Pyruvate metabolism of the hyperthermophilic archaebacterium Pyrococcus furiosus. Arch. Microbiol. 155:366- 377.
39. Schäfer T, Selig M, Schönheit P. 1993. Acetyl-CoA synthetase (ADP forming) in archaea, a novel enzyme involved in acetate formation and ATP synthesis. Arch. Microbiol. 159:72- 83.
40. Shikata K, Fukui T, Atomi H, Imanaka T. 2007. A novel ADP-forming succinyl-CoA synthetase in Thermococcus kodakaraensis structurally related to the archaeal nucleoside diphosphate-forming acetyl-CoA synthetases. J. Biol. Chem. 282:26963-26970.
41. Bräsen C, Schmidt M, Grötzinger J, Schönheit P. 2008. Reaction mechanism and structural model of ADP-forming acetyl-CoA synthetase from the hyperthermophilic archaeon Pyrococcus furiosus: evidence for a second active site histidine residue. J. Biol. Chem. 283:15409-15418.
42. Musfeldt M, Selig M, Schönheit P. 1999. Acetyl coenzyme A synthetase (ADP forming) from the hyperthermophilic archaeon Pyrococcus furiosus: identification, cloning, separate expression of the encoding genes, acdAI and acdBI, in Escherichia coli, and in vitro reconstitution of the active heterotetrameric enzyme from its recombinant subunits. J. Bacteriol. 181: 5885-5888.
43. 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 1:263-267.
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. 15:352-363.
45. Morikawa M, Izawa Y, Rashid N, Hoaki T, Imanaka T. 1994. Purification and characterization of a thermostable thiol protease from a newly isolated hyperthermophilic Pyrococcus sp. Appl. Environ. Microbiol. 60: 4559-4566.
46. Robb FT, Place AR. 1995. Media for thermophiles, p 167-168. In Robb FT, Place AR (ed), Archaea: a laboratory manual-thermophiles. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
47. Sato T, Fukui T, Atomi H, Imanaka T. 2003. Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 185:210-220.
48. Yokooji Y, Tomita H, Atomi H, Imanaka T. 2009. Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. J. Biol. Chem. 284:28137-28145.
49. 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. 71:3889-3899.
50. Santangelo TJ,Čuboňová L, Reeve JN. 2008. Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl. Environ. Microbiol. 74: 3099-3104.
51. Takeda Y, Suzuki F, Inoue H. 1969. ATP citrate lyase (citrate-cleavage enzyme). Methods Enzymol. 13:153-160.
52. Bashir Q, Rashid N, Jamil F, Imanaka T, Akhtar M. 2009. Highly thermostable L-threonine dehydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis. J. Biochem. 146:95-102.
53. Bowyer A, Mikolajek H, Stuart JW, Wood SP, Jamil F, Rashid N, Akhtar M, Cooper JB. 2009. Structure and function of the L-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis. J. Struct. Biol. 168:294-304.
54. Kanai T, Ito S, Imanaka T. 2003. Characterization of a cytosolic NiFehydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 185:1705-1711.
55. Kanai T, Matsuoka R, Beppu H, Nakajima A, Okada Y, Atomi H, Imanaka T. 2011. Distinct physiological roles of the three [NiFe]- hydrogenase orthologs in the hyperthermophilic archaeon Thermococcus kodakarensis. J. Bacteriol. 193:3109-3116.
56. Adul Rahman RN, Jongsareejit B, Fujiwara S, Imanaka T. 1997. Characterization of recombinant glutamine synthetase from the hyperthermophilic archaeon Pyrococcus sp. strain KOD1. Appl. Environ. Microbiol. 63:2472-2476.
57. Jongsareejit B, Rahman R, Fujiwara S, Imanaka T. 1997. Gene cloning, sequencing and enzymatic properties of glutamate synthase from the hyperthermophilic archaeon Pyrococcus sp. KOD1. Mol. Gen. Genet. 254: 635-642.
58. Hagen WR, Silva PJ, Amorim MA, Hagedoorn PL, Wassink H, Haaker H, Robb FT. 2000. Novel structure and redox chemistry of the prosthetic groups of the iron-sulfur flavoprotein sulfide dehydrogenase from Pyrococcus furiosus; evidence for a [2Fe-2S] cluster with Asp(Cys)3 ligands. J. Biol. Inorg. Chem. 5:527-534.
59. Dincturk HB, Cunin R, Akce H. 2011. Expression and functional analysis of glutamate synthase small subunit-like proteins from archaeon Pyrococcus horikoshii. Microbiol. Res. 166:294-303.