Promiscuous anaerobes: New and unconventional metabolism in methanogenic archaea

Annals of the New York Academy of Sciences

Volumn 1125, Issue , 2008, Pages 190-214

  Grochowski, Laura L ^a   White, Robert H ^a  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

Amino acid biosynthesis; Archaea; Archaeal lipids; Carbohydrate metabolism; Central metabolism; Isoprenoid biosynthesis; Purine biosynthesis; Pyrimidine biosynthesis

Indexed keywords

4 AMINOBENZOIC ACID; AMINO ACID DERIVATIVE; AROMATIC AMINO ACID; CYSTEINE; GLUTAMIC ACID DERIVATIVE; ISOPRENE; METHIONINE; NUCLEOSIDE; NUCLEOTIDE; OXYGEN; POLYAMINE DERIVATIVE; PROLINE; RIBOSE; RIBULOSE PHOSPHATE; SUGAR;

AMINO ACID SYNTHESIS; ATMOSPHERE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL METABOLISM; CONFERENCE PAPER; GLUCONEOGENESIS; LAST COMMON ANCESTOR; METHANOCALDOCOCCUS JANNASCHII; METHANOGENIC ARCHAEON; NONHUMAN; NUCLEOTIDE METABOLISM; PURINE SYNTHESIS; PYRIMIDINE SYNTHESIS;

ARCHAEA; METHANOCALDOCOCCUS JANNASCHII; PROKARYOTA;

EID: 41349108509     PISSN: 00778923     EISSN: 17496632     Source Type: Book Series    
DOI: 10.1196/annals.1419.001     Document Type: Conference Paper

References (150)

1. IMLAY, J.A. 2006. Iron-sulphur clusters and the problem with oxygen. Mol. Microbiol. 59: 1073-1082.
2. BUCKEL, W. & B.T. GOLDING. 2006. Radical enzymes in anaerobes. Annu. Rev. Microbiol. 60: 27-49.
3. JOHNSON, D.C. et al. 2005. Structure, function, and formation of biological iron-sulfur clusters. Annu. Rev. Biochem. 74: 247-281.
4. CAMBA, R. & F.A. ARMSTRONG. 2000. Investigations of the oxidative disassembly of Fe-S clusters in Clostridium pasteurianum 8Fe ferredoxin using pulsed-protein-film voltammetry. Biochemistry 39: 10587-10598.
5. ROGERS, P.A. et al. 2003. Reversible inactivation of E. coli endonuclease III via modification of its [4Fe-4S] cluster by nitric oxide. DNA Repair (Amst). 2: 809-817.
6. DJAMAN, O., F.W. OUTTEN & J.A. IMLAY. 2004. Repair of oxidized iron-sulfur clusters in Escherichia coli. J. Biol. Chem. 279: 44590-44599.
7. OUTTEN, F.W., O. DJAMAN & G. STORZ. 2004. A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli. Mol. Microbiol. 52: 861-872.
8. RUBIO, L.M. & P.W. LUDDEN. 2005. Maturation of nitrogenase: a biochemical puzzle. J. Bacteriol. 187: 405-414.
9. POSTGATE, J.R. 1998. Nitrogn Fixation. Cambridge: Cambridge University Press.
10. DOWNIE, J.A. 2005. Legume haemoglobins: symbiotic nitrogen fixation needs bloody nodules. Curr. Biol. 15: R196-R198.
11. GOLDEN, J.W. & H.S. YOON. 2003. Heterocyst development in Anabaena. Curr. Opin. Microbiol. 6: 557-563.
12. REES, D.C. & J.B. HOWARD. 2003. The interface between the biological and inorganic worlds: iron-sulfur metalloclusters. Science 300: 929-931.
13. DRENNAN, C.L. & J.W. PETERS. 2003. Surprising cofactors in metalloenzymes. Curr. Opin. Struct. Biol. 13: 220-226.
14. BRODA, E. & G.A. PESCHEK. 1983. Nitrogen fixation as evidence for the reducing nature of the early biosphere. Biosystems 16: 1-8.
15. KILEY, P.J. & H. BEINERT. 1999. Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster. FEMS Microbiol. Rev. 22: 341-352.
16. CRACK, J.C. et al. 2006. Detection of sulfide release from the oxygen-sensing [4Fe-4S] cluster of FNR. J. Biol. Chem. 281: 18909-18913.
17. MANSOURI, A. & A.A. LURIE. 1993. Concise review: methemoglobinemia. Am. J. Hematol. 42: 7-12.
18. IRETON, G.C. et al. 2002. The structure of Escherichia coli cytosine deaminase. J. Mol. Biol. 315: 687-697.
19. PORTER, D.J. & E.A. AUSTIN. 1993. Cytosine deaminase. The roles of divalentmetal ions in catalysis. J. Biol. Chem. 268: 24005-24011.
20. RAJAGOPALAN, P.T., X.C. YU & D. PEI. 1997. Peptide deformylase: a new type of mononuclear iron protein. J. Am. Chem. Soc. 119: 12418.
21. ZHU, J. et al. 2003. S-Ribosylhomocysteinase (LuxS) is a mononuclear iron protein. Biochemistry. 42: 4717-4726.
22. D'SOUZA V.M. & R.C. HOLZ. 1999. The methionyl aminopeptidase from Escherichia coli can function as an iron(II) enzyme. Biochemistry 38: 11079-11085.
23. SEFFERNICK, J.L. et al. 2002. Atrazine chlorohydrolase from Pseudomonas sp. strain ADP is a metalloenzyme. Biochemistry 41: 14430-14437.
24. 2+-dependent archaeal specific GTP cyclohydrolase, MptA, from Methanocaldococcus jannaschii. Biochemistry 46: 6658-6667.
25. FONTECAVE, M., E. MULLIEZ & D.T. LOGAN. 2002. Deoxyribonucleotide synthesis in anaerobic microorganisms: the class III ribonucleotide reductase. Prog. Nucleic Acid Res. Mol. Biol. 72: 95-127.
26. NORDLUND, P. & P. REICHARD. 2006. Ribonucleotide reductases. Annu. Rev. Biochem. 75: 681-706.
27. ALEXANDER, K. & I.G. YOUNG. 1978. Three hydroxylations incorporating molecular oxygen in the aerobic biosynthesis of ubiquinone in Escherichia coli. Biochemistry 17: 4745-4750.
28. ALEXANDER, K. & I.G. YOUNG. 1978. Alternative hydroxylases for the aerobic and anaerobic biosynthesis of ubiquinone in Escherichia coli. Biochemistry 17: 4750-4755.
29. DEPPENMEIER, U. 2002. The unique biochemistry of methanogenesis. Prog. Nucleic Acid Res. Mol. Biol. 71: 223-283.
30. CHATTERJEE, A. et al. 2007. Biosynthesis of thiamin thiazole in eukaryotes: conversion of NAD to an advanced intermediate. J. Am. Chem. Soc. 129: 2914-2922.
31. 12. Nature 446: 449-453.
32. KELLOGG, R. et al. 1992. Structural analysis of a stereochemical modification of flavin adenine dinucleotide in alcohol oxidase frommethylotrophic yeasts. Tetrahedron 48: 4147-4162.
33. WALSH, C. 2006. Posttranslational Modification of Proteins Expanding Nature's Inventory. Englewood, CO: Roberts and Company Publishers.
34. LAWHORN, B.G., R.A. MEHL & T.P. BEGLEY. 2004. Biosynthesis of the thiamin pyrimidine: the reconstitution of a remarkable rearrangement reaction. Org. Biomol. Chem. 2: 2538-2546.
35. BUCHANAN, J.M. & S.C. HARTMAN. 1959. Enzymatic reactions in the synthesis of purines. Adv. Enzymol. 21: 199-261.
36. ZALKIN, H. & J.E. DIXON. 1992. De novo purine nucleotide biosynthesis. Prog. Nucleic Acid Res. Mol. Biol. 42: 259-287.
37. RAYL, E.A., B.A. MOROSON & G.P. BEARDSLEY. 1996. The human purH gene product, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase. Cloning, sequencing, expression, purification, kinetic analysis, and domain mapping. J. Biol. Chem. 271: 2225-2233.
38. GREASLEY, S.E. et al. 2001. Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis. Nat. Struct. Biol. 8: 402-406.
39. WHITE, R.H. 1997. Purine biosynthesis in the domain Archaea without folates or modified folates. J. Bacteriol. 179: 3374-3377.
40. SELKOV, E. et al. 1997. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene 197: GC11-26.
41. KOONIN, E.V., R.L. TATUSOV & M.Y. GALPERIN. 1998. Beyond complete genomes: from sequence to structure and function. Curr. Opin. Struct. Biol. 8: 355-363.
42. KOIKE, H., T. KAWASHIMA & M. SUZUKI. 1999. Enzymes identified using genomic DNA sequences suggests some atypical characteristics of de novo biosynthesis of purines in archaea. Proc. Jpn. Acad. 75, Ser.B: 263-268.
43. GRAUPNER, M., H. XU & R.H. WHITE. 2002. New Class of IMP Cyclohydrolases in Methanococcus jannaschii. J. Bacteriol. 184: 1471-1473.
44. OWNBY, K., H. XU & R. WHITE. 2005. A Methanocaldococcus jannaschii archeal signature gene encodes for a 5-formaminoimidazole-4-carboxamide-1-β-D-ribofuranosyl 5′- monophosphate synthetase: a new enzyme in purine biosynthesis. J. Biol. Chem. 280: 10881-10887.
45. KANGA, Y.-N. et al. 2007. A novel function for the NTN hydrolase fold demonstrated by the structure of an archeal inosine monophosphate cyclohydrolase. Biochemistry 46: 5050-5062.
46. LI, H. et al. 2003. The Methanococcus jannaschii dCTP deaminase is a bifunctional deaminase and diphosphatase. J. Biol. Chem. 278: 11100-11106.
47. HUFFMAN, J.L. et al. 2003. Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii. J. Mol. Biol. 331: 885-896.
48. AURORA, R. & G.D. ROSE. 1998. Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons. Proc. Natl. Acad. Sci. USA 95: 2818-2823.
49. XU, H. et al. 1999. Identifying two ancient enzymes in Archaea using predicted secondary structure alignment. Nat. Struct. Biol. 6: 750-754.
50. LEDUC, D. et al. 2004. Two distinct pathways for thymidylate (dTMP) synthesis in (hyper)thermophilic bacteria and Archaea. Biochem. Soc. Trans. 32: 231-235.
51. HIGUCHI, S., T. KAWASHIMA & M. SUZUKI. 1999. Comparison of pathways for amino acid biosynthesis in archaebacteria using their genomic DNA sequences. Proc. Jpn. Acad. 75, Ser. B: 241-245.
52. BORUP, B. & J.G. FERRY. 2000.O-Acetylserine sulfhydrylase from Methanosarcina thermophila. J. Bacteriol. 182: 45-50.
53. BORUP, B. & J.G. FERRY. 2000. Cysteine biosynthesis in the Archaea: Methanosarcina thermophila utilizes O-acetylserine sulfhydrylase. FEMS Microbiol. Lett. 189: 205-210.
54. KITABATAKE, M. et al. 2000. Cysteine biosynthesis pathway in the archaeon Methanosarcina barkeri encoded by acquired bacterial genes? J. Bacteriol. 182: 143-145.
55. MINO, K. & K. ISHIKAWA. 2003. Characterization of a novel thermostable O-acetylserine sulfhydrylase from Aeropyrum pernix K1. J. Bacteriol. 185: 2277-2284.
56. MINO, K. et al. 2003. Crystallization and preliminary X-ray diffraction analysis of O-acetylserine sulfhydrylase from Aeropyrum pernix K1. Acta Crystallogr. D Biol. Crystallogr. 59: 338-340.
57. WHITE, R.H. 2003. The biosynthesis of cysteine and homocysteine in Methanococcus jannaschii. Biochim. Biophys. Acta 1624: 46-53.
58. SAUERWALD, A. et al. 2005. RNA-dependent cysteine biosynthesis in archaea. Science 307: 1969-1972.
59. HELGADOTTIR, S. et al. 2007. Biosynthesis of phosphoserine in the Methanococcales. J. Bacteriol. 189: 575-582.
60. TCHONG, S.-I., H. XU & R. WHITE. 2004. Cysteine desulfidase: an [4Fe-4S] enzyme isolated from Methanocaldococcus jannaschii that catalyzes the breakdown of cysteine into pyruvate, ammonia and sulfide. Biochemistry 44: 1659-1670.
61. BURNS, K.E. et al. 2005. Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. J. Am. Chem. Soc. 127: 11602-11603.
62. WANG, C. et al. 2001. Solution structure of ThiS and implications for the evolutionary roots of ubiquitin. Nat. Struct. Biol. 8: 47-51.
63. PARK, J.H. et al. 2003. Biosynthesis of the thiazole moiety of thiamin pyrophosphate (vitamin B1). Biochemistry 42: 12430-12438.
64. RUDOLPH, M.J. et al. 2001. Crystal structure of molybdopterin synthase and its evolutionary relationship to ubiquitin activation. Nat. Struct. Biol. 8: 42-46.
65. DAUGHERTY, M. et al. 2001. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J. Bacteriol. 183: 292-300.
66. WHITE, R.H. 2004. L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii. Biochemistry 43: 7618-7627.
67. PORAT, I. et al. 2006. Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis. Mol. Microbiol. 62: 1117-1131.
68. WHITE, R.H. & H. XU. 2006. Methylglyoxal is an intermediate in the biosynthesis of 6-deoxy-5-ketofructose-1-phosphate: a precursor for aromatic amino acid biosynthesis in Methanocaldococcus jannaschii. Biochemistry 45: 12366-12379.
69. 420 biosynthesis. J. Bacteriol. 188: 2836-2844.
70. ROBERTSON, D.E. et al. 1990. Occurrence of β-glutamate, a novel osmolyte, in marine methanogenic bacteria. Appl. Environ. Microbiol. 56: 1504-1508.
71. BURDIGE, D. & C. MARTENS. 1984. Amino acid cycling in an organic-rich marine sediment. EOS Trans. Am. Geophys. Union. 65: 960.
72. HENRICHS, S. & R. CHEL. 1985. Occurrence of β-aminoglutaric acid in marine bacteria. Appl. Environ. Microbiol. 50: 543-545.
73. HENRICHS, S. & J. FARRINGTON. 1987. Early diagenesis of amino acids and organic matter in two coastal marine sediments. Geochim. Cosmochim. Acta 51: 1-15.
74. ROBERTSON, D.E. & M.F. ROBERTS. 1991. Organic osmolytes in methanogenic archaebacteria. Biofactors 3: 1-9.
75. ROBERTS, M.F. 2000. Osmoadaptation and osmoregulation in archaea. Front. Biosci. 5: D796-812.
76. MARTIN, D.D., R.A. CIULLA & M.F. ROBERTS. 1999. Osmoadaptation in archaea. Appl. Environ. Microbiol. 65: 1815-1825.
77. ROBERTS, M.F. 2004. Osmoadaptation and osmoregulation in archaea: update 2004. Front. Biosci. 9: 1999-2019.
78. ROBERTSON, D.E., S. LESAGE & M.F. ROBERTS. 1989. β-Aminoglutaric acid is a major soluble component of Methanococcus thermolithotrophicus. Biochim. Biophys. Acta 992: 320-326.
79. ε-acetyl- β-lysine, β-glutamine, and betaine in Methanohalophilus strain FDF1 suggested by nuclearmagnetic resonance analyses. J. Bacteriol. 174: 6688-6693.
80. ROBERTSON, D.E., D. NOLL & M.F. ROBERTS. 1992. Free amino acid dynamics in marine methanogens. β-Amino acids as compatible solutes. J. Biol. Chem. 267: 14893-14901.
81. FUCHS, G. & E. STUPPERICH. 1978. Evidence for an incomplete reductive carboxylic acid cycle in Methanobacterium thermoautotrophicum. Arch. Microbiol. 118: 121-125.
82. WHITE, R.H. 1987. Biosynthesis of the 1,3,4,6- hexanetetracarboxylic acid subunit of methanofuran. Biochemistry 26: 3163-3167.
83. WHITE, R.H. 1989. A novel biosynthesis of medium chain length α-ketodicarboxylic acids in methanogenic archaebacteria. Arch. Biochem. Biophys. 270: 691-697.
84. DANSON, M.J. 1993. Central metabolism of the archaea. In The Biochemistry of the Archaea (Archaebacteria). M. Kates, D.J. Kushner & A.T. Matheson, Eds.: 1-24. Amsterdam, The Netherlands: Elsevier.
85. LEIGH, J.A., K.L. RINEHART, JR. & R.S. WOLFE. 1985. Methanofuran (carbon dioxide reduction factor), a formyl carrier in methane production from carbon dioxide in Methanobacterium. Biochemistry 24: 995-999.
86. GORKOVENKO, A., M.F. ROBERTS & R.H. WHITE. 1994. Identification, biosynthesis, and function of 1,3,4,6- hexanetetracarboxylic acid in Methanobacterium thermoautotrophicum strain ΔH. Appl. Environ. Microbiol. 60: 1249-1253.
87. BUCKEL, W. & H.A. BARKER. 1974. Two pathways of glutamate fermentation by anaerobic bacteria. J. Bacteriol. 117: 1248-1260.
88. HANS, M. et al. 1999. 2-Hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum. Eur. J. Biochem. 265: 404-414.
89. KIM, J. et al. 2004. Dehydration of (R)-2- hydroxyacyl-CoA to enoyl-CoA in the fermentation of α-amino acids by anaerobic bacteria. FEMS Microbiol. Rev. 28: 455-468.
90. WHITE, R.H. 2001. Biosynthesis of the methanogenic cofactors. In Vitamins and Hormones, Vol. 61. T. Begley, Ed.: 299-337. New York: Academic Press.
91. GRAHAM, D.E. & R.H. WHITE. 2002. Elucidation of methanogenic coenzyme biosynthesis: from spectroscopy to genomics. Nat. Prod. Rep. 19: 133-147.
92. +-dependent (R)-2-hydroxyglutarate dehydrogenase catalysis in from Acidaminococcus fermentans. FEBS J. 272: 269-281.
93. GRANT, G.A. 1989. A new family of 2-hydroxyacid dehydrogenases. Biochem. Biophys. Res. Commun. 165: 1371-1374.
94. BUNCH, P.K. et al. 1997. The ldhA gene encoding the fermentative lactate dehydrogenase of Escherichia coli. Microbiology 143(Pt 1): 187-195.
95. LOCHER, K.P. et al. 2001. Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A. J. Mol. Biol. 307: 297-308.
96. RUZICKA, F.J. & P.A. FREY. 2007. Glutamate 2,3-aminomutase: a new member of the radical SAM superfamily of enzymes. Biochim. Biophys. Acta 1774: 286-296.
97. SANCHEZ, L.B., M.Y. GALPERIN & M. MULLER. 2000. Acetyl-CoA synthetase from the amitochondriate eukaryote Giardia lamblia belongs to the newly recognized superfamily of acyl-CoA synthetases (nucleoside diphosphate-forming). J. Biol. Chem. 275: 5794-5803.
98. LATIMER, M.T. & J.G. FERRY. 1993. Cloning, sequence analysis, and hyperexpression of the genes encoding phosphotransacetylase and acetate kinase from Methanosarcina thermophila. J. Bacteriol. 175: 6822-6829.
99. GLASEMACHER, J. et al. 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.
100. JACOB, U. et al. 1997. Glutaconate CoA-transferase from Acidaminococcus fermentans: the crystal structure reveals homology with other CoA-transferases. Structure 5: 415-426.
101. EGGEN, R.I. et al. 1991. Cloning, sequence analysis, and functional expression of the acetyl coenzyme A synthetase gene from Methanothrix soehngenii in Escherichia coli. J. Bacteriol. 173: 6383-6389.
102. JETTEN, M. et al. 1989. Isolation and characterization of acetyl-coenzyme A synthetase from Methanothrix soehngenii. J. Bacteriol. 171: 5430-5435.
103. HEIDER, J. 2001. A new family of CoA-transferases. FEBS Lett. 509: 345-349.
104. GRAUPNER, M., H. XU & R.H. WHITE. 2000. Identification of an archaeal 2-hydroxy acid dehydrogenase catalyzing reactions involved in coenzyme biosynthesis in methanoarchaea. J. Bacteriol. 182: 3688-3692.
105. WHITE, R.H. 1990. Biosynthesis of methanopterin. Biochemistry 29: 5397-5404.
106. WHITE, R.H. 1996. Biosynthesis of methanopterin. Biochemistry 35: 3447-3456.
107. GRAHAM, D.E., H. XU & R.H. WHITE. 2002. Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis. J. Biol. Chem. 277: 23500-23507.
108. TOLBERT, W.D. et al. 2003. Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii. Crystal structures of the self-cleaved and S53A proenzyme forms. Structure (Camb.). 11: 285-294.
109. LU, Z.J. & G.D. MARKHAM. 2002. Enzymatic properties of S-adenosylmethionine synthetase from the archaeon Methanococcus jannaschii. J. Biol. Chem. 277: 16624-16631.
110. KIM, A.D. et al. 2000. S-Adenosylmethionine decarboxylase from the archaeon Methanococcus jannaschii: identification of a novel family of pyruvoyl enzymes. J. Bacteriol. 182: 6667-6672.
111. GRAUPNER, M. & R.H. WHITE. 2001. Methanococcus jannaschii generates L-proline by cyclization of L-ornithine. J. Bacteriol. 183: 5203-5205.
112. MUTH, W.L. & R.N. COSTILOW. 1974. Ornithine cyclase (deaminating). III. Mechanism of the conversion of ornithine to proline. J. Biol. Chem. 249: 7463-7467.
113. SIEBERS, B. & P. SCHONHEIT. 2005. Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Curr. Opin. Microbiol. 8: 695-705.
114. VERHEES, C.H. et al. 2003. The unique features of glycolytic pathways in Archaea. Biochem. J. 375: 231-246.
115. GRAHAM, D.E., H. XU & R.H. WHITE. 2002. A divergent archaeal member of the alkaline phosphatase binuclear metalloenzyme superfamily has phosphoglycerate mutase activity. FEBS Lett. 517: 190-194.
116. SIEBERS, B. et al. 2001. Archaeal fructose-1,6- bisphosphate aldolases constitute a new family of archaeal type class I aldolase. J. Biol. Chem. 276: 28710-28728.
117. SODERBERG, T. & R.C. ALVER. 2004. Transaldolase of Methanocaldococcus jannaschii. Archaea 1: 255-262.
118. GROCHOWSKI, L.L., H. XU&R.H. WHITE. 2005. Ribose-5-phosphate biosynthesis in Methanocaldococcus jannaschii occurs in the absence of a pentose-phosphate pathway. J. Bacteriol. 187: 7382-7389.
119. ORITA, I. et al. 2006. The ribulosemonophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. J. Bacteriol. 188: 4698-4704.
120. VORHOLT, J.A. et al. 2000. Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. J. Bacteriol. 182: 6645-6650.
121. ORITA, I. et al. 2005. The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. J. Bacteriol. 187: 3636-3642.
122. DECKER, P., H. SCHWEER & R. POLHMANN. 1982. Identification of formose sugars, presumable prebiotic metabolites, using capillary gas chromatography/gas chromatography-mass spectrometry of n-butoximine trifluoroacetates on OV-225. J. Chromatogr. 244: 281-291.
123. DE ROSA, M. et al. 1980. Structure of calditol, a new branched-chain nonitol, and of the derived tetraether lipids in thermoacidopile archaebacteria of the Caldariella group. Phytochemistry 19: 249-254.
124. DE ROSA, M. et al. 1977. Chemical structure of the ether lipids of thermophilic acidophilic bacteria of the Caldariella goup. Phytochemistry 16: 1961-1965.
125. KOGA, Y. & H. MORII. 2007. Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations. Microbiol. Mol. Biol. Rev. 71: 97-120.
126. BISCHOFF, K.M. & V.W. RODWELL. 1996. 3-Hydroxy-3-methylglutaryl-coenzyme A reductase from Haloferax volcanii: purification, characterization, and expression in Escherichia coli. J. Bacteriol. 178: 19-23.
127. HUANG, K.X., A.I. SCOTT & G.N. BENNETT. 1999. Overexpression, purification, and characterization of the thermostable mevalonate kinase from Methanococcus jannaschii. Protein Exp. Purif. 17: 33-40.
128. BOCHAR, D.A. et al. 1997. 3-Hydroxy-3-methylglutaryl coenzyme A reductase of Sulfolobus solfataricus: DNA sequence, phylogeny, expression in Escherichia coli of the hmgA gene, and purification and kinetic characterization of the gene product. J. Bacteriol. 179: 3632-3638.
129. SMIT, A. & A. MUSHEGIAN. 2000. Biosynthesis of isoprenoids via mevalonate in archaea: the lost pathway. Genome Res. 10: 1468-1484.
130. GROCHOWSKI, L.L., H. XU & R. WHITE. 2006. Methanocaldococcus jannaschii uses amodified mevalonate pathway for the biosynthesis of isopentenyl diphosphate. J. Bacteriol. 188: 3192-3198.
131. KANEDA, K. et al. 2001. An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. strain CL190. Proc. Natl. Acad. Sci. USA 98: 932-937.
132. SIDDIQUI, M.A. et al. 2005. Enzymatic and structural characterization of type II isopentenyl diphosphate isomerase from hyperthermophilic archaeon Thermococcus kodakaraensis. Biochem. Biophys. Res. Commun. 331: 1127-1136.
133. LAUPITZ, R. et al. 2004. Biochemical characterization of Bacillus subtilis type II isopentenyl diphosphate isomerase, and phylogenetic distribution of isoprenoid biosynthesis pathways. Eur. J. Biochem. 271: 2658-2669.
134. BARKLEY, S.J., R.M. CORNISH & C.D. POULTER. 2004. Identification of an archaeal type II isopentenyl diphosphate isomerase in Methanothermobacter thermautotrophicus. J. Bacteriol. 186: 1811-1817.
135. YAMASHITA, S. et al. 2004. Type 2 isopentenyl diphosphate isomerase from a thermoacidophilic archaeon Sulfolobus shibatae. Eur. J. Biochem. 271: 1087-1093.
136. HOSHINO, T. et al. 2006. Inhibition of type 2 isopentenyl diphosphate isomerase from Methanocaldococcus jannaschii by a mechanism-based inhibitor of type 1 isopentenyl diphosphate isomerase. Bioorg. Med. Chem. 14: 6555-6559.
137. HEMMI, H. et al. 2004. Catalytic mechanism of type 2 isopentenyl diphosphate:dimethylallyl diphosphate isomerase: verification of a redox role of the flavin cofactor in a reaction with no net redox change. Biochem. Biophys. Res. Commun. 322: 905-910.
138. ROTHMAN, S.C., T.R. HELM & C.D. POULTER. 2007. Kinetic and spectroscopic characterization of type II isopentenyl diphosphate isomerase from Thermus thermophilus: evidence for formation of substrate-induced flavin species. Biochemistry 46: 5437-5445.
139. MURAKAMI, M. et al. 2007. Geranylgeranyl reductase involved in the biosynthesis of archaeal membrane lipids in the hyperthermophilic archaeon Archaeoglobus fulgidus. FEBS J. 274: 805-814.
140. SPROTT, G.D., M. MELOCHE & J.C. RICHARDS. 1991. Proportions of diether, macrocyclic diether, and tetraether lipids in Methanococcus jannaschii grown at different temperatures. J. Bacteriol. 173: 3907-3910.
141. MACALADY, J.L. et al. 2004. Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid. Extremophiles 8: 411-419.
142. SHINODA, K. et al. 2004. Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers. J. Chem. Phys. 121: 9648-9654.
143. BARTUCCI, R. et al. 2005. Bipolar tetraether lipids: chain flexibility and membrane polarity gradients from spinlabel electron spin resonance. Biochemistry 44: 15017-15023.
144. VAN DE VOSSENBERG, J.L., A.J. DRIESSEN & W.N. KONINGS. 1998. The essence of being extremophilic: the role of the unique archaeal membrane lipids. Extremophiles 2: 163-170.
145. WEIJERS, J.W. et al. 2006. Membrane lipids of mesophilic anaerobic bacteria thriving in peats have typical archaeal traits. Environ. Microbiol. 8: 648-657.
146. SINNINGHE DAMSTE, J.S. et al. 2004. A mixed ladderane/nalkyl glycerol diether membrane lipid in an anaerobic ammonium-oxidizing bacterium. Chem. Commun. 22: 2590-2591.
147. SINNINGHE DAMSTE, J.S. et al. 2002. Linearly concatenated cyclobutane lipids form a dense bacterial membrane. Nature 419: 708-712.
148. VAN NIFTRIK, L.A. et al. 2004. The anammoxosome: an intracytoplasmic compartment in anammox bacteria. FEMS Microbiol. Lett. 233: 7-13.
149. DE ROSA, M. et al. 1988. A new 15,16-dimethyl-30-glyceryloxytriacontanoic acid from lipids of Termotoga maritima. J. Chem. Soc., Chem. Commun. 1300-1301.
150. JUNG, S., J.G. ZEIKUS & R.I. HOLLINGSWORTH. 1994. A new family of very long chain α, ω-dicarboxylic acids is a major structural fatty acyl component of the membrane lipids of Thermoanaerobacter ethanolicus 39E. J. Lipid Res. 35: 1057-1065.