Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism

Archaea

Volumn 1, Issue 3, 2003, Pages 199-221

  Ronimus, Ron S ^a   Morgan, Hugh W ^a  

^a UNIVERSITY OF WAIKATO   (New Zealand)

Author keywords

Enolase; Evolution; Gluconeogenesis; Glyceraldehyde 3 phosphate dehydrogenase; Glycolysis; Origins of life; Phosphoglycerate kinase; Triosephosphate isomerase

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 0142197447     PISSN: 14723646     EISSN: None     Source Type: Journal    
DOI: 10.1155/2003/162593     Document Type: Article

References (156)

1. Altekar, W. and V. Rangaswamy. 1990. Indication of a modified EMP pathway for fructose breakdown in a halophilic archaebacterium. FEMS Microbiol. Lett. 69:139-144.
2. Altekar, W. and V. Rangaswamy. 1992. Degradation of endogenous fructose during catabolism of sucrose and mannitol in halophilic archaebacteria. Arch. Microbiol. 158:356-363.
3. Altschul, S.F., W. Gish, W. Miller, W. Myers and D.L. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
4. Altschul, S.F., T.L Madden, A.A. Schäffer, Z. Zhang, W. Miller and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
5. Amend, J.P. and E.L. Shock. 2001. Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiol. Rev. 25:175-243.
6. Babbit, P.C., M.S. Hasson, J.E. Wedekind, D.R.J. Palmer, W.C. Barrett, G.H. Reed, I. Rayment, D. Ringe, G.L. Kenyon and J.A. Gerlt. 1996. The enolase super family: a general strategy for enzyme-catalyzed abstraction of the α-protons of carboxylic acids. Biochemistry 35:16,489-16,501.
7. Baross, J.A. 1998. Do the geological and geochemical records of the early Earth support the prediction from global phylogenetic models of a thermophilic cenancestor? In Thermophiles: the Keys to Molecular Evolution and the Origin of Life? Eds. J. Wiegel and M.W.W. Adams. Taylor and Francis, Philadelphia, pp 3-18.
8. Beaucamp, N., A. Hofmann, B. Kellerer and R. Jaenicke. 1997. Dissection of the gene of the bifunctional pgk-tim fusion protein from the hyperthermophilic bacterium Thermotoga maritima - design and characterization of the separate triosephosphate isomerase. Protein Sci. 6:2159-2165.
9. Beh, M., G. Strauss, R. Huber, K.-O. Stetter and G. Fuchs. 1993. Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus. Arch. Microbiol. 160:306-311.
10. Brinkmann, H. and W. Martin. 1996. Higher-plant chloroplast and cytosolic 3-phosphoglycerate kinases: a case of endosymbiotic gene replacement. Plant Mol. Biol. 30:65-75.
11. Brown, J.R. and W.F. Doolittle. 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. 92:2441-2445.
12. Brown, J.R. and W.F. Doolittle. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61:456-502.
13. Brunner, N.A. and R. Hensel. 2001. Nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. Methods Enzymol. 331:117-131.
14. +-dependent glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. J. Biol. Chem. 273:6149-6156.
15. Brunner, N.A., B. Siebers and R. Hensel. 2001. Role of two different glyceraldehyde-3-phosphate dehydrogenases in controlling the reversible Embden-Meyerhof-Parnas pathway in Thermoproteus tenax: regulation on protein and transcript level. Extremophiles 5:101-109.
16. Budgen, N. and M.J. Danson. 1986. Metabolism of glucose via a modified Entner-Doudoroff pathway in the thermoacidophilic archaebacterium Thermoplasma acidophilum. FEBS Lett. 196:207-210.
17. Canback, B., S.G.E. Andersson and C.G. Kurland. 2002. The global phylogeny of glycolytic enzymes. Proc. Natl. Acad. Sci. 99:6097-6102.
18. Cárdenas, M.L., A. Cornish-Bowden and T. Ureta. 1998. Evolution and regulatory role of the hexokinases. Biochim. Biophys. Acta. 1401:242-264.
19. Cicicopol, C., J. Peters, A. Lupas, Z. Cejka, S.A. Muller, R. Golbik, G. Pfeifer, H. Lilie, A. Engel and W. Baumeister. 1999. Novel molecular architecture of the multimeric archaeal PEP-synthase homologue (MAPS) from Staphylothermus marinus. J. Mol. Biol. 290:347-361.
20. Cooper, S.J., G.A. Leonard, S.M. McSweeney, A.W. Thompson, J.H. Naismith, S. Qamar, A. Plater, A. Berry and W.N. Hunter. 1996. The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold. Structure 4:1303-1315.
21. 8 barrels: implications for the evolution of metabolic pathways. J. Mol. Biol. 303:627-640.
22. Cordwell, S.J. 1999. Microbial genomes and "missing enzymes": redefining biochemical pathways. Arch. Microbiol. 172:269-279.
23. Crowhurst, G., J. McHarg and J.A. Littlechild. 2001. Phosphoglycerate kinases from bacteria and Archaea. Methods Enzymol. 331:90-104.
24. Dandekar, T., S. Schuster, B. Snel, M. Huynen and P. Bork. 1999. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J. 343:115-124.
25. Danson, M.J. and D.W. Hough. 1991. The enzymology of archaebacterial pathways of central metabolism. Biochem. Soc. Symp. 58:7-21.
26. Danson, M.J., R.J.M. Russell, D.W. Hough and G.L. Taylor. 1998. Comparative enzymology as an aid to understanding evolution. In Thermophiles: the Keys to Molecular Evolution and the Origin of Life? Eds. J. Wiegel and M.W.W. Adams. Taylor and Francis, Philadelphia, pp 255-266.
27. Dayhoff, M.O. 1978. Atlas of protein sequence and structure. Vol. 5, Suppl. 3. National Biomedical Research Foundation, Silver Spring, MD.
28. De Rosa, M., A. Gambacorta, B. Nicolaus, P. Giardina, E. Poerio and V. Bounocore. 1984. Glucose metabolism in the extreme thermoacidophilic archaebacterium Sulfolobus solfataricus. Biochem. J. 224:407-414.
29. Dhar, N.M. and W. Altekar. 1986. Distribution of class I and II fructose biphosphate aldolases in halophilic archaebacteria. FEMS Microbiol. Lett. 35:177-181.
30. Ding, Y.-H.R. 2000. Phosphofructokinases from extremely thermophilic microorganisms. Ph.D. Thesis, Univ. Waikato, Hamilton, New Zealand, 403 p.
31. Ding, Y.-H.R., R.S. Ronimus and H.W. Morgan. 2001. The phosphofructokinases from Thermotoga: expression and characterisation of two unique enzymes. J. Bacteriol. 183:791-794.
32. Donahue, J.L., J.L. Bownas, W.G. Niehaus and T.J. Larson. 2000. Purification and characterization of glpX-encoded fructose 1,6-bisphosphatase, a new enzyme of the glycerol 3-phosphate regulon of Escherichia coli. J. Bacteriol. 182:5624-5627.
33. D'Souza, S.E. and W. Altekar. 1983. Demonstration of some glycolytic activities in Halobacterium halobium and their significance. Indian J. Biochem. Biophys. 20:29-32.
34. D'Souza, S.E. and W. Altekar. 1998. A class II fructose-6-phosphate aldolase from a halophilic archaebacterium Haloferax mediterranei. J. Gen. Appl. Microbiol. 44:235-241.
35. Ezyaguirre, J., K. Jansen and G. Fuchs. 1982. Phosphoenolpyruvate synthetase in Methanobacterium thermoautotrophicum. Arch. Microbiol. 132:67-74.
36. Fabry, S. and R. Hensel. 1987. Purification and characterisation of D-glyceraldehyde-3-phosphate dehydrogenase from the thermophilic archaebacterium Methanothermus fervidus. Eur. J. Biochem. 165:147-155.
37. Fabry, S., A. Lehmacher, W. Bode and R. Hensel. 1988. Expression of the glyceraldehyde-3-phosphate dehydrogenase gene from the extremely thermophilic archaebacterium Methanothermus fervidus in E. coli. FEBS Lett. 213-217.
38. Fabry, S., J. Lang, T. Niermann, M. Vingron and R. Hensel. 1989. Nucleotide sequence of the glyceraldehyde-3-phosphate dehydrogenase gene from the mesophilic methanogenic archaebacteria Methanobacterium bryantii and Methanbacterium formicicum. Eur. J. Biochem. 179:405-413.
39. Fabry, S., W. Heppner, W. Dietmaier and R. Hensel. 1990. Cloning and sequencing the gene encoding 3-phosphoglycerate kinase from mesophilic Methanobacterium bryantii and thermophilic Methanothermus fervidus. Gene 91:19-25.
40. Fitz-Gibbon, S., A.J. Choi, J.H. Miller, K.O. Stetter, M.I. Simon, R. Swanson and U.-J. Kim. 1997. A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum. Extremophiles 1:36-51.
41. Fitz-Gibbon, S.T., H. Ladner, U.J. Kim, K.O. Stetter, M.I. Simon and J.H. Miller. 2002. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc. Natl. Acad. Sci. 99:984-989.
42. Fleming, T. and J. Littlechild. 1997. Sequence and structural comparison of thermophilic phosphoglycerate kinases with a mesophilic equivalent. Comp. Biochem. Physiol. 118A:439-451.
43. Forterre, P. 1996. A hot topic: the origin of hyperthermophiles. Cell 85:789-792.
44. Fothergill-Gilmore, L.A. 1986. The evolution of the glycolytic pathway. Trends Biochem. Sci. 11:47-51.
45. Fothergill-Gilmore, L.A. and P.A.M. Michels. 1993. Evolution of glycolysis. Prog. Biophys. Mol. Biol. 59:105-235.
46. Fraser, H.I., M. Kvaraskhelia and M.F. White. 1999. The two analogous phosphoglycerate mutases of Escherichia coli. FEBS Lett. 455:344-348.
47. 2 fixation pathway in Methanobacterium thermoautotrophicum. Zentbl. Bakteriol. Mikrobiol. Hyg. 1 Abt Orig. C 3:277-288.
48. Fuchs, G., H. Winter, I. Steiner and E. Stupperich. 1983. Enzymes of gluconeogenesis in the autotroph Methanobacterium thermoautotrophicum. Arch. Microbiol. 136:160-162.
49. Fujita, Y., K.-I. Yoshida, Y. Miwa, N. Yanai, E. Nagkawa and Y. Kasahara. 1998. Identification and expression of the Bacillus subtilis fructose-1,6-bisphosphate gene (fbp). J. Bacteriol. 180:4309-4313.
50. Galperin, M.Y. and E.V. Koonin. 1999. Functional genomics and enzyme evolution. Genetica 106:159-170.
51. Galperin, M.Y., D.R. Walker and E.V. Koonin. 1998a. Analogous enzymes: independent inventions in enzyme evolution. Genome Res. 8:779-790.
52. Galperin, M.Y., A. Bairoch and E.V. Koonin. 1998b. A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutases with alkaline phosphatases and sulfatases. Protein Sci. 7:1829-1835.
53. Galperin, M.Y., L. Aravind and E.V. Koonin. 2000. Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea. FEMS Microbiol. Lett. 183:259-264.
54. Ghalambor, M.A. and E.C. Heath. 1966. L-fuculose-1-phosphate aldolase. Methods Enzymol. 9:538-542.
55. Graham, D.E., H.M. Xu and R.H. White. 2002. A divergent archaeal member of the alkaline phosphatase binuclear metalloenzyme superfamily has phosphoglycerate mutase activity. FEBS Lett. 517:190-194.
56. Graña, X., P. Pérez de la Ossa, C. Broceño, M. Stöcker, J. Garriga, P. Puigdomènech and F. Climent. 1995. 2,3-bisphosphoglycerate-independent phosphoglycerate mutase is conserved among different phylogenetic kingdoms. Comp. Biochem. Physiol. 112B:287-293.
57. Grattinger, M., A. Dankesreiter, H. Schurig and R. Jaenicke. 1998. Recombinant phosphoglycerate kinase from the hyperthermophilic bacterium Thermotoga maritima - catalytic, spectral and thermodynamic properties. J. Mol. Biol. 280:525-533.
58. Gupta, R.S. 1998. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiol. Mol. Biol. Rev. 62:1435-1491.
59. Hannaert, V., H. Brinkmann, U. Nowitzki, J.A. Lee, M.-A. Albert, C.W. Sensen, T. Gaasterland, M. Müller, P. Michels and W. Martin. 2000. Enolase from Trypanosoma brucei, from the amitochondriate protist Mastigamoeba balamuthi, and from the chloroplast and cytosol of Euglena gracilis: pieces in the evolutionary puzzle of the eukaryotic glycolytic pathway. Mol. Biol. Evol. 17:989-1000.
60. Hansen, T. and P. Schönheit. 2000. Purification and properties of the first identified, archaeal, ATP-dependent 6-phosphofructokinase, an extremely thermophilic non-allosteric enzyme, from the hyperthermophile Desulfurococcus amylolyticus. Arch. Microbiol. 173:103-109.
61. Hansen, T. and P. Schönheit. 2001a. Sequence, expression, and characterization of the first archaeal ATP-dependent 6-phosphofructokinase, a non-allosteric enzyme related to the phosphofructokinase-B sugar kinase family, from the hyperthermophilic crenarchaeote Aeropyrum pernix. Arch. Microbiol. 177:62-69.
62. Hansen, T. and P. Schönheit. 2001b. Novel type of glucose-6-phosphate isomerase in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183:3428-3435.
63. Hansen, T., M. Musfeldt and P. Schönheit. 2002. ATP-dependent 6-phosphofructokinase from the hyperthermophilic bacterium Thermotoga maritima: characterisation of an extremely thermophilic, allosterically regulated enzyme. Arch. Microbiol. 177:401-409.
64. Hensel, R., A. Schramm, D. Hess and R.J.M. Russell. 2001. 3-phosphoglycerate kinase and triosephosphate isomerase from hyperthermophilic archaea: features of biochemical thermoadaptation. Methods Enzymol. 331:311-323.
65. Henze, K., A. Badr, M. Wettern, R. Cerff and W. Martin. 1995. A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution. Proc. Natl. Acad. Sci. 92:9122-9126.
66. Hess, D., K. Kruger, A. Knappik, P. Palm and R. Hensel. 1995. Dimeric 3-phosphoglycerate kinases from hyperthermophilic Archaea. Cloning, sequencing and expression of the 3-phosphoglycerate kinase gene of Pyrococcus woesei in Escherichia coli and characterization of the protein. Structural and functional comparison with the 3-phosphoglycerate kinase of Methanothermus fervidus. Eur. J. Biochem. 233:227-237.
67. Hutchins, A.M., J.F. Holden and M.W.W. Adams. 2001. Phosphoenolpyruvate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183:709-715.
68. Ito, S., S. Fushinobu, I. Yoshioka, S. Koga, H. Matsuzawa and T. Wakagi. 2001. Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon. Structure 9:205-214.
69. Iwabe, N., K.-I. Kuma, M. Hasegawa, S. Osawa and T. Miyata. 1989. Evolutionary relationships of archaebacteria, eubacteria and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. 86:9355-9359.
70. Iwabe, N., K.-I. Kuma, H. Kishino and M. Hasegawa. 1991. Evolution of RNA polymerases and branching points of the three major groups of archaebacteria. J. Mol. Evol. 32:70-78.
71. Jansen, K., E. Stupperich and G. Fuchs. 1982. Carbohydrate synthesis from acetyl-CoA in the autotroph Methanobacterium thermoautotrophicum. Arch. Microbiol. 132:355-364.
72. Jonnsen, U., M. Selig, K.B. Xavier, H. Santos and P. Schönheit. 2001. Different glycolytic pathways for glucose and fructose in the halophilic archaeon Halococcus saccharolyticus. Arch. Microbiol. 175:52-61.
73. Johnson, K.A., L. Chen, H. Yang, M.F. Roberts and B. Stec. 2001. Crystal structure and catalytic mechanism of the MJ0109 gene product: a bifunctional enzyme with inositol monophosphatase and fructose-1,6-bisphosphatase activities. Biochemistry 40:618-630.
74. Jones, C.E., T.M. Fleming, D.A. Cowan, J.A. Littlechild and P.W. Piper. 1995. The phosphoglycerate kinase and glyceraldehyde-3-phosphate dehydrogenase genes from the thermophilic archaeon Sulfolobus solfataricus overlap by 8-bp-isolation, sequencing of the genes and expression in Escherichia coli. Eur. J. Biochem. 233:800-808.
75. Keeling, P.J. and W.F. Doolittle. 1997. Evidence for the eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin. Proc. Natl. Acad. Sci. 94:1270-1275.
76. Kengen, S.W.M., F.A.M. de Bok, N.-D. van Loo, C. Dijkema, A.J.M. Stams and W.M. de Vos. 1994. Evidence for the operation of a novel Embden-Meyerhof pathway that involves ADP-dependent kinases during sugar fermentation by Pyrococcus furiosus. J. Biol. Chem. 269:17,537-17,541.
77. Kengen, S.W.M., J.E. Tuininga, F.A.M. de Bok, A.J.M. Stams and W.M. de Vos. 1995. Purification and characterization of a novel ADP-dependent glucokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. Chem. 270:30,453-30,457.
78. Kengen, S.W.M., J.E. Tuininga, C.H. Verhees, J. van der Oost, A.J.M. Stams and W.M. de Vos. 2001. ADP-dependent glucokinase and phosphofructokinase from Pyrococcus furiosus. Methods Enzymol. 331:41-53.
79. Klenk, H.-P., P. Palm and W. Zillig. 1994. DNA-dependent RNA polymerases as phylogenetic marker molecules. Syst. Appl. Microbiol. 16:638-647.
80. Koga, S., I. Yoshioka, H. Sakuraba, M. Takahashi, S. Sakasegawa, S. Shimizu and T. Ohshima. 2000. Biochemical characterization, cloning, and sequencing of ADP-dependent (AMP-forming) glucokinase from two hyperthermophilic archaea, Pyrococcus furiosus and Thermococcus litoralis. J. Biochem. 128:1079-1085.
81. Koike, H., T. Kawashima and M. Suzuki. 1999. Comparison of archaebacterial central metabolic pathways using the genomic DNA sequences. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 5:101-106.
82. Koonin, E.V., A.R. Mushegian, M.Y. Galperin and D.R. Walker. 1997. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25:619-637.
83. Krishnan, G. and W. Altekar. 1991. An unusual class I (Schiff base) fructose-1,6-bisphosphate aldolase from the halophilic archaebacterium Haloarcula vallismortis. Eur. J. Biochem. 195:343-350.
84. 2 via a modified Embden-Meyerhof pathway and acetyl-CoA synthetase. Arch. Microbiol. 176:329-338.
85. Labesse, G., D. Douget, L. Assairi and A.-M. Gilles. 2002. Diacylglyceride kinases, sphingosine kinases and NAD kinases: distant relatives of 6-phosphofructokinases. Trends Biochem. Sci. 27:273-275.
86. Liaud, M.-F., C. Lichtlé, K. Apt, W. Martin and R. Cerff. 2000. Compartment-specific isoforms of TPI and GAPDH are imported into diatom mitochondria as a fusion protein: evidence in favor of a mitochondrial origin of a eukaryotic glycolytic pathway. Mol. Biol. Evol. 17:213-223.
87. Lim, A. and L. Zhang. 1999. WebPhylip: a web interface to Phylip. Bioinformatics 15:1068-1069.
88. Littlechild, J.A. and M. Isupov. 2001. Glyceraldehyde-3-phosphate dehydrogenase from Sulfolobus solfataricus. Methods Enzymol. 331:105-117.
89. Ludwig, W., O. Strunk, S. Klugbauer, M. Weizenegger, J. Neumaier, M. Bachleitner and K.H. Schleifer. 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554-568.
90. Maden, B.E.H. 1995. No soup for starters? Autotrophy and the origins of metabolism. Trends Biochem. Sci. 20:337-341.
91. Makarova, K.S., L. Aravind, M.Y. Galperin, N.V. Grishin, R.L. Tatusov, Y.I. Wolf and E.V. Koonin. 1999. Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res. 9:608-628.
92. Morgan, H.W. and R.S. Ronimus. 1998. Pyrophosphate-dependent phosphofructokinases in thermophilic and nonthermophilic microorganisms. In Thermophiles: the Keys to Molecular Evolution and the Origin of Life. Eds. J. Wiegel and M. Adams. Taylor and Francis, Philadelphia, pp 269-277.
93. Orgel, L.E. 1998. The origin of life - a review of the facts and the speculations. Trends Biochem. Sci. 23:491-495.
94. Peak, M.J., J.G. Peak, F.J. Stevens, J. Blamey, X. Mai, Z.H. Zhou and M.W.W. Adams. 1994. The hyperthermophilic glycolytic enzyme enolase in the archaeon, Pyrococcus furiosus: comparison with mesophilic enolases. Arch. Biochem. Biophys. 313:280-286.
95. Pellerin, P., B. Gruson, G. Prensier, G. Albagnac and P. Debiere. 1987. Glycogen in Methanothrix. Arch. Microbiol. 146:377-381.
96. Poole, A.M., D.C. Jeffares and D. Penny. 1999. The path from the RNA world. J. Mol. Evol. 46:1-17.
97. Potter, S. and L.A. Fothergill-Gilmore. 1992. Purification and properties of pyruvate kinase from Thermoplasma acidophilum. FEMS Microbiol. Lett. 94:235-240.
98. Pruss, B., H.E. Meyer and A.W. Holldorf. 1993. Characterisation of the glyceraldehyde-3-phosphate dehydrogenase from the extremely halophilic archaebacterium Haloarcula vallismortis. Arch. Microbiol. 160:5-11.
99. Rangaswamy, V. and W. Altekar. 1994. Characterisation of 1-phosphofructokinase from halophilic archaebacterium Haloarcula vallismortis. Biochim. Biophys. Acta 1201:106-112.
100. Rashid, N., H. Imanaka, T. Kanai, T. Fukui, H. Atomi and T. Imanaka. 2002. A novel candidate for the true fructose-1,6-bisphosphatase in archaea. J. Biol. Chem. 277:30,649-30,655.
101. Reeves, R.E. 1968. A new enzyme with the glycolytic function of pyruvate kinase. J. Biol. Chem. 243:3202-3204.
102. Reysenbach, A.L. and E. Shock. 2002. Merging genomes with geochemistry in hydrothermal ecosystems. Science 296:1077-1082.
103. Rivera, M.C., R. Jain, J.E. Moore and J.A. Lake. 1998. Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. 95:6239-6244.
104. Roberson, R.S., R.S. Ronimus, S. Gephard and H.W. Morgan. 2001. Biochemical characterization of an active pyrophosphate-dependent phosphofructokinase from Treponema pallidum. FEMS Microbiol. Lett. 194:257-260.
105. Romano, A.H. and T. Conway. 1996. Evolution of carbohydrate metabolic pathways. Res. Microbiol. 147:448-455.
106. Ronimus, R.S. and H.W. Morgan. 2001. The biochemical properties and phylogenies of phosphofructokinases from extremophiles. Extremophiles 5:357-373.
107. Ronimus, R.S., J. Koning and H.W. Morgan. 1999. Purification and characterisation of an ADP-dependent phosphofructokinase from Thermococcus zilligii. Extremophiles 3:121-129.
108. Ronimus, R.S., E. de Heus and H.W. Morgan. 2001a. Sequencing, expression, characterisation and phylogeny of the ADP-dependent phosphofructokinase from the hyperthermophilic, euryarchaeal Thermococcus zilligii. Biochim. Biophys. Acta 1517:384-391.
109. Ronimus, R.S., Y. Kawarabayasi, H. Kikuchi and H.W. Morgan. 2001b. Cloning, expression and characterisation of a Family B ATP-dependent phosphofructokinase activity from the hyperthermophilic crenarachaeon Aeropyrum pernix. FEMS Microbiol. Lett. 202:85-90.
110. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
111. Sakuraba, H. and T. Ohshima. 2002. Novel energy metabolism in anaerobic hyperthermophilic archaea: a modified Embden-Meyerhof pathway. J. Biosci. Bioeng. 93:441-448.
112. Sakuraba, H., E. Utsumi, C. Kujo and T. Ohshima. 1999. An AMP-dependent (ATP-forming) kinase in the hyperthermophilic archaeon Pyrococcus furiosus: characterization and novel physiological role. Arch. Biochem. Biophys. 364:125-128.
113. Sakuraba, H., E. Utsumi, H.J. Schreier and T. Ohshima. 2001. Transcriptional regulation of phosphoenolpyruvate synthase by maltose in the hyperthermophilic archaeon, Pyrococcus furiosus. J. Biosci. Bioeng. 92:108-113.
114. Sakuraba, H., I. Yoshioka, S. Koga, M. Takahashi, Y. Kitahama, T. Satomura, R. Kawakimi and T. Ohshima. 2002. ADP-dependent glucokinase/ phosphofructokinase, a novel bifunctional enzyme from the hyperthermophilic archaeon Methanococcus jannaschii. J. Biol. Chem. 277:12,495-12,498.
115. 2 in the anaerobic hyperthermophilic archaeon Pyrococcus furiosus: evidence for the operation of a novel sugar fermentation pathway. Arch. Microbiol. 158:188-202.
116. Schäfer, T. and P. Schönheit. 1993. Gluconeogenesis from pyruvate in the hyperthermophilic archaeon Pyrococcus furiosus: involvement of reactions of the Embden-Meyerhof pathway. Arch. Microbiol. 159:354-363.
117. Schönheit, P. and T. Schäfer. 1995. Metabolism of hyperthermophiles. World J. Microbiol. Biotechnol. 11:26-57.
118. Schramm, A., B. Siebers, B. Tjaden, H. Brinkmann and R. Hensel. 2000. Pyruvate kinase of the hyperthermophilic crenarchaeote Thermoproteus tenax: physiological role and phylogenetic aspects. J. Bacteriol. 182:2001-2009.
119. Schramm, A., M. Kohlhoff and R. Hensel. 2001. Triose-phosphate isomerase from Pyrococcus woesei and Methanothermus fervidus. Methods Enzymol. 331:62-77.
120. 2 in the anaerobic hyperthermophilic eubacterium Thermotoga maritima: involvement of the Embden-Meyerhof pathway. Arch. Microbiol. 161:460-470.
121. Schurig, H., K. Rutkat, R. Rachel and R. Jaenicke. 1995a. Octameric enolase from the hyperthermophilic bacterium Thermotoga maritima - purification, characterization, and image processing. Protein Sci. 4:228-236.
122. Schurig, H., N. Beaucamp, R. Ostendorp, R. Jaenicke, E. Adler and J.R. Knowles. 1995b. Phosphoglycerate kinase and triosephosphate isomerase from the hyperthermophilic bacterium Thermotoga maritima form a covalent bifunctional enzyme complex. EMBO J. 14:442-451.
123. 2 with sulfur and thiosulfate as electron acceptor in the anaerobic hyperthermophilic archaea Thermoproteus tenax and Pyrobaculum islandicum proceeds via the citric acid cycle. Arch. Microbiol. 162:286-294.
124. Selig, M., K.B. Xavier, H. Santos and P. Schönheit. 1997. Comparative analysis of Embden-Meyerhof and Entner-Doudoroff glycolytic pathways in hyperthermophilic archaea and the bacterium Thermotoga. Arch. Microbiol. 167:217-232.
125. Shieh, J. and W.B. Whitman. 1987. Pathway of acetate assimilation in autotrophic and heterotrophic methanococci. J. Bacteriol. 169:5327-5329.
126. Siebers, B. and R. Hensel. 1993. Glucose catabolism of the hyperthermophilc archaeum Thermoproteus tenax. FEMS Microbiol. Lett. 111:1-8.
127. Siebers, B. and R. Hensel. 2001. Pyrophosphate-dependent phosphofructokinase from Thermoproteus tenax. Methods Enzymol. 331:54-62.
128. i-dependent phosphofructokinase from Thermoproteus tenax, an archaeal descendant of an ancient line in phosphofructokinase evolution. J. Bacteriol. 180:2137-2143.
129. Siebers, B., H. Brinkmann, C. Dorr, B. Tjaden, H. Lilie, J. van der Oost and C.H. Verhees. 2001. Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal class I aldolase. J. Biol. Chem. 276:28,710-28,718.
130. Sigrell, J.A., A.D. Cameron, T.A. Jones and S.L. Mowbray. 1998. Structure of the Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 angstrom resolution: insights into a new family of kinase structures. Structure 6:183-193.
131. Simpson, P.G. and W.B. Whitman. 1993. Anabolic pathways in methanogens. In Methanogenesis: Ecology, Physiology, Biochemistry and Genetics. Ed. J.G. Ferry. Chapman and Hall, New York, pp 445-472.
132. Sonnhammer, E.L.L., S.R. Eddy and R. Durbin. 1997. Pfam: a comprehensive database of protein families based on seed alignments. Proteins 28:405-420.
133. Stieglitz, K.A., K.A. Johnson, H.Y. Yang, M.E. Roberts, B.A. Seaton, J.F. Head and B. Stec. 2002. Crystal structure of a dual activity IMPase/FBPase (AF2372) from Archaeoglobus fulgidus - the story of a mobile loop. J. Biol. Chem. 277:22,863-22,874.
134. Swofford, D.L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MA.
135. Swofford, D., G. Olsen, P. Waddell and D.M. Hillis. 1996. Phylogenetic inference. In Molecular Systematics. 2nd Edn. Eds. D.M. Hillis, C. Moritz and B.K. Mable. Sinauer Associates, Sunderland, MA, 655 p.
136. Tatusov, R.L., D.A. Natale, I.V. Garkavtsev, T.A. Tatusova, U.T. Shankavaram, B.S. Rao, B. Kiryutin, M.Y. Galperin, N.D. Fedorova and E.V. Koonin. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:22-28.
137. Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalites and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
138. Tomlinson, G.A, T.K. Koch and L.I. Hochstein. 1974. The metabolism of carbohydrates by extremely halophilic bacteria: glucose metabolism via a modified Entner-Doudoroff pathway. Can. J. Microbiol. 20:1085-1091.
139. Tomschy, A., R. Glockshuber and R. Jaenicke. 1993. Functional expression of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima in Escherichia coli - authenticity and kinetic properties of the recombinant enzyme. Eur. J. Biochem. 214:43-50.
140. Tuininga, J.E., C.H. Verhees, J. van der Oost, S.W.M. Kengen, A.J.M. Stams and W.M. de Vos. 1999. Molecular and biochemical characterisation of the ADP-dependent phosphofructokinase from the hyperthermophilic Pyrococcus furiosus. J. Biol. Chem. 274:21,023-21,028.
141. van der Oost, J., G. Schut, S.W.M. Kengen, W.R. Hagen, M. Thomm and W.M. de Vos. 1998. The ferredoxin-dependent conversion of glyceraldehyde-3-phosphate in the hyperthermophilic archaeon Pyrococcus furiosus represents a novel site of glycolytic regulation. J. Biol. Chem. 273:28,149-28,154.
142. van der Oost, J., M.A. Huynen and C.H. Verhees. 2002. Molecular characterization of phosphoglycerate mutase in archaea. FEMS Microbiol. Lett. 212:111-120.
143. Verhees, C.H., J.E. Tuininga, S.W.M. Kengen, A.J.M. Stams, J. van der Oost and W.M. de Vos. 2001a. ADP-dependent phosphofructokinases in mesophilic and thermophilic methanogenic archaea. J. Bacteriol. 183:7145-7153.
144. Verhees, C.H., M.A. Huynen, D.E. Ward, E. Schiltz, W.M. de Vos and J. van der Oost. 2001b. The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus is a unique glycolytic enzyme that belongs to the Cupin superfamily. J. Biol. Chem. 276:40,926-40,932.
145. Verhees, C.H., J. Akerboom, E. Schiltz, W.M. de Vos and J. van der Oost. 2002a. Molecular and biochemical characterisation of a distinct type of fructose-1-6-bisphosphatase from Pyrococcus furiosus. J. Bacteriol. 184:3401-3405.
146. Verhees, C.H., D.G.M. Koot, T.J.G. Ettema, C. Dijkema, W.M. de Vos and J. van der Oost. 2002b. Biochemical adaptations of two sugar kinases from the hyperthermophilic archaeon Pyrococcus furiosus. Biochem. J. 366:121-127.
147. von Korff, R.W. 1969. Purity and stability of pyruvate and α-ketoglutarate. Methods Enzymol. 13:519-523.
148. Wächtershäuser, G. 1988a. Pyrite formation, the first energy source for life: a hypothesis. Syst. Appl. Microbiol. 10:207-210.
149. Wächtershäuser, G. 1988b. Before enzymes and templates: theory of metabolism. Microbiol. Rev. 52:452-484.
150. Wächtershäuser, G. 1994. Life in a ligand sphere. Proc. Natl. Acad. Sci. 91:4283-4287.
151. Woese, C.R., O. Kandler and M.L. Wheelis. 1990. Towards a natural system of organisms: a proposal for the domains Archaea, Bacteria and Eucarya. Proc. Natl. Acad. Sci. 87:4576-4579.
152. 13C-labeling experiments and nuclear magnetic resonance analysis. J. Bacteriol. 182:4632-4636.
153. Yu, J.-S. and K.M. Noll. 2001. Phosphoglycerate kinase-triosephosphate isomerase complex from Thermotoga neapolitana. Methods Enzymol. 331:78-89.
154. Yu, J.-P., J. Lapado and W.B. Whitman. 1994. Pathway of glycogen metabolism in Methanococcus maripaludis. J. Bacteriol. 176:325-332.
155. Zeikus, J.G., G. Fuchs, W. Kenealy and R.K. Thauer. 1977. Oxidoreductases involved in cell carbon synthesis of Methanobacterium thermoautotrophicum. J. Bacteriol. 132:604-613.
156. Zwickl, P., S. Fabry, C. Bogedain, A. Haas and R. Hensel. 1990. Glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaebacterium Pyrococcus woesei: characterisation of the enzyme, cloning and sequencing of the gene, and expression in Escherichia coli. J. Bacteriol. 172:4329-4338.