A challenge for 21st century molecular biology and biochemistry: What are the causes of obligate autotrophy and methanotrophy?

FEMS Microbiology Reviews

Volumn 28, Issue 3, 2004, Pages 335-352

  Wood, Ann P ^a   Aurikko, Jukka P ^a   Kelly, Donovan P ^b  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Genome probing; Krebs cycle; Methanogens; Methanotrophy; Methylococcus; Nitrosomonas; Obligate autotrophy

Indexed keywords

2 OXOACID DEHYDROGENASE; 2 OXOGLUTARIC ACID; GENE PRODUCT; MESSENGER RNA; OXOGLUTARATE DEHYDROGENASE;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; AUTOTROPHY; BACILLUS SUBTILIS; BACTERIAL GENE; BIOCHEMISTRY; BIOINFORMATICS; CITRIC ACID CYCLE; CYANOBACTERIUM; ENZYME ACTIVITY; ENZYME SUBUNIT; ESCHERICHIA COLI; GENE IDENTIFICATION; GENE PROBE; GENE SEQUENCE; HETEROTROPHY; METHYLOCOCCUS CAPSULATUS; MOLECULAR BIOLOGY; MOLECULAR PROBE; NITROSOMONAS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYSICAL CHEMISTRY; PROTEIN DATABASE; PROTEIN FAMILY; REVIEW; VALIDATION PROCESS;

ARCHAEA; BACTERIA; BIOCHEMISTRY; CITRIC ACID CYCLE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION; GENOME, BACTERIAL; KETOGLUTARATE DEHYDROGENASE COMPLEX; KETOGLUTARIC ACIDS; MODELS, BIOLOGICAL; MOLECULAR BIOLOGY;

AQUIFEX; BACTERIA (MICROORGANISMS); CYANOBACTERIA; METHYLOCOCCUS; METHYLOCOCCUS CAPSULATUS; NITROSOMONAS; NITROSOMONAS EUROPAEA;

EID: 2642562680     PISSN: 01686445     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsre.2003.12.001     Document Type: Review

References (146)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402
2. Amarasingham C.R., Davis B.D. Regulation of α-ketoglutarate dehydrogenase formation in Escherichia coli. J. Biol. Chem. 240:1965;3664-3668
3. Amann R. Who is out there. Microbial aspects of biodiversity. Syst. Appl. Microbiol. 23:2000;1-8
4. Amils R., Irazabel N., Moreira D., Abad J.P., Marin I. Genomic organization of acidophilic chemolithotrophic bacteria using pulsed field gel electrophoretic techniques. Biochimie. 80:1998;911-921
5. Baxter N.J., Scanlan J., De Marco P., Wood A.P., Murrell J.C. Duplicate copies of the genes encoding methanesulfonate monooxygenase in Marinosulfonomonas methylotropha strain TR3 and detection of methanesulfonate utilizers in the environment. Appl. Environ. Microbiol. 68(1):2002;289-296
6. Baxter N.J., Hirt R.P., Bodrossy L., Kovacs K.L., Embley T.M., Prosser J.I., Murrell J.C. The ribulose-1, 5-bisphosphate carboxylase/oxygenase gene cluster of Methylococcus capsulatus (Bath). Arch. Microbiol. 177:2002;279-289
7. Beudeker R.F., Kerver J.W.M., Kuenen J.G. Occurrence, structure and function of intracellular polyglucose in the obligate chemolithotroph Thiobacillus neapolitanus. Arch. Microbiol. 129:1981;221-226
8. Beudeker R.F., de Boer W., Kuenen J.G. Heterolactic fermentation of intracellular polyglucose by the obligate chemolithotroph Thiobacillus neapolitanus under anaerobic conditions. FEMS Microbiol. Lett. 12:1981;337-342
9. Blattner, F.R. and 16 co-authors (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1474
10. Bott M. Anaerobic citrate metabolism and its regulation in enterobacteria. Arch. Microbiol. 167:1997;78-88
11. Buchanan F. Microbial genomes and DNA exchange. Lateral DNA Transfer, Mechanism and Consequences (Cold Spring Harbor Laboratory). 2002;129-169 Cold Spring Harbor Laboratory Press
12. Buchanan F. DNA transfer among the domains of life. Lateral DNA Transfer, Mechanism and Consequences (Cold Spring Harbor Laboratory). 2002;365-385 Cold Spring Harbor Laboratory Press
13. Bult, G.J. and 23 co-authors (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1057-1073
14. Carlsson P., Hedersted T.L. Genetic characterization of Bacillus subtilis odhA and odhB, encoding 2-oxoglutarate dehydrogenase and dihydrolipoamide transsuccinylase, respectively. J. Bacteriol. 171:1989;3667-3672
15. Cavalier-Smith T. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int. J. Syst. Evol. Microbiol. 52:2002;7-76
16. Chain, P. and 14 co-authors (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 185, 2759-2773
17. Chi T.T., Chang H.Y., Wang N.N., Chang D.S., Dumphy N., Brown P.O. Genomewide view of gene silencing by small interfering RNAs. Proc. Nat. Acad. Sci. USA. 100:2003;6343-6346
18. ′ -phosphate-dependent enzymes Chem. Record. 1:2001;436-447
19. Christoserdova L., Chen S.-W., Lapidus A., Lidstrom M.L. Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J. Bacteriol. 185:2003;2980-2987
20. Connaris H., West S.M., Hough D.W., Danson M.J. Cloning and overexpression in Escherichia coli of the gene encoding citrate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus. Extremophiles. 2:1998;61-66
21. Danson M.J., Black S.C., Woodland D.L., Wood P.A. Citric acid cycle enzymes of the Archaebacteria - citrate synthase and succinate thiokinase. FEBS Lett. 179:1985;120-124
22. Darlison M.G., Spencer M.E., Guest J.R. Nucleotide sequence of the sucA gene encoding the 2-oxoglutarate dehydrogenase of Escherichia coli K-12. Eur. J. Biochem. 141:1984;351-359
23. Dastoor F.P., Forrest M.E., Beatty J.T. Cloning, sequencing and oxygen regulation of the Rhodobacter capsulatus α-ketoglutarate dehydrogenase operon. J. Bacteriol. 179:1997;4559-4566
24. Davey J.F., Whittenbury R., Wilkinson J.F. The distribution in the methylobacteria of some key enzymes concerned with intermediary metabolism. Arch. Mikrobiol. 87:1972;359-371
25. Deckert, G. and 14 co-authors (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392, 353-358
26. Dufresne, A. and 20 co-authors (2003) Genome sequence of the cyanobactertium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Nature 100, 10021-10025
27. Eccleston M., Kelly D.P. Assimilation and toxicity of exogenous amino acids in the methane-oxidizing bacterium Methylococcus capsulatus. J. Gen. Microbiol. 71:1972;541-554
28. Eccleston M., Kelly D.P. Assimilation and toxicity of some exogenous C-1 compounds, alcohols, sugars and acetate in the methane-oxidizing bacterium Methylococcus capsulatus. J. Gen. Microbiol. 75:1973;211-221
29. Eccleston M., Kelly D.P. Inhibition by L-threonine of aspartokinase as a cause of threonine-toxicity to Methylococcus capsulatus. J. Gen. Microbiol. 75:1973;223-226
30. Ferry J.G. Carbon monoxide dehydrogenase. Ann. Rev. Microbiol. 49:1995;305-333
31. Ferry J.G. Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiol. Rev. 23:1999;13-38
32. Ferry J.G. One-carbon metabolism in methanogenic anaerobes. Ljungdahl L.G., Adams M.W., Barton L.L., Ferry J.G., Johnson M.K. Biochemistry and Physiology of Anaerobic Bacteria. 2003;143-156 Springer-Verlag, New York
33. Finster K., Tanimoto Y., Bak F. Fermentation of methanethiol and dimethylsulfide by a newly isolated methanogenic bacterium. Arch. Microbiol. 157:1992;425-430
34. 2 fixation. Schlegel H.G., Bowien B. Autotrophic Bacteria. 1989;365-382 Science Tech Publishers and Springer-Verlag, New York
35. Fuchs G. Variations of the acetyl-CoA pathway in diversely related microorganisms that are not acetogens. Drake H.L. Acetogenesis. 1994;506-538 Chapman & Hall, New York
36. 1 Compounds. 1984;199-202 American Society for Microbiology, Washington, DC
37. Fukuda E., Wakagi T. Substrate recognition by 2-oxoacid:ferredoxin oxidoreductase from Sulfolobus sp. strain S7. Biochim. Biophys. Acta. 1597:2002;74-80
38. Fukuda E., Kino H., Matsuzawa H., Wakagi T. Role of highly conserved YTITP motif in 2-oxoacid:ferredoxin oxidoreductase. Eur. J. Biochem. 268:2001;5639-5646
39. Galperin M.Y., Koonin E.V. Functional genomics and enzyme evolution - homologous and analagous enzymes encoded in microbial genomes. Genetica. 106:1999;159-170
40. Galperin M.Y., Walker D.R., Koonin E.V. Analagous enzymes: independent inventions in enzyme evolution. Genome Res. 8:1998;779-790
41. Gest H. Evolutionary roots of the citric acid cycle in prokaryotes. Biochem. Soc. Symp. 54:1981;3-16
42. Gest, H. (2003) Anaerobes in the recycling of elements in the biosphere. In: Biochemistry and Physiology of Anaerobic Bacteria (Ljungdahl, L. and 4 co-Eds.), pp. 1-10. Springer, New York
43. Gil R., Sabater-Muñoz B., Latorre A., Silva F.J., Moya A. Extreme genome reduction in Buchnera spp.: towards the minimal genome needed for symbiotic life. Proc. Natl. Acad. Sci. USA. 99:2002;4454-4458
44. Gogarten J.P., Hilario E., Olendzenski L. Gene duplication and horizontal gene transfer during early evolution. Roberts D.McL., Sharp P., Alderson G., Collins M.A. Evolution of Microbial Life. 1996;268-292 Cambridge University Press
45. Gottschal J.C., de Vries S., Kuenen J.G. Competition between the facultatively chemolithotrophic Thiobacillus A2, an obligately chemolithotrophic Thiobacillus, and a heterotrophic Spirillum for inorganic and organic substrates. Arch. Microbiol. 121:1979;241-249
46. Gottschal J.C., Nanninga H., Kuenen J.G. Growth of Thiobacillus A2 under alternating conditions in the chemostat. J. Gen. Microbiol. 126:1981;85-96
47. Green L.S., Emerich D.W., Bergerson F.J., Day D.A. Catabolism of alpha-ketoglutarate by a sucA mutant of Bradyrhizobium japonicum: evidence for an alternative tricarboxylic acid cycle. J. Bacteriol. 182:2000;2838-2844
48. Gribskov M., Devereux J. Sequence Analysis Primer. 1991;Stockton Press, New York. pp. 140-141
49. Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 89:1992;10915-10919
50. Hipp W.M., Pott A.S., ThumSchmitz N., Faath I., Dahl C., Trüper H.G. Towards the phylogeny of APS reductase and sirohaem sulfite reductases in sulfate-reducung and sulfur-oxidizing prokaryotes. Microbiology UK. 143:1997;2891-2902
51. Hoare D.S., Hoare S.L., Moore R.B. The photoassimilation of organic compounds by autotrophic blue-green algae. J. Gen. Microbiol. 49:1967;351-370
52. 2 fixation of Chloroflexus aurantiacus. Arch. Microbiol. 145:1986;173-180
53. Holmes A.J., Owens N.J.P., Murrell J.C. Detection of novel marine methanotrophs using phylogenetic and functional gene probes after methane enrichment. Microbiology UK. 141:1995;1947-1955
54. Hooper A.B. Biochemical basis of obligate autotrophy in Nitrosomonas europaea. J. Bacteriol. 97:1969;776-779
55. 2 fixation pathways in archaea (Crenarchaeota). Arch. Microbiol. 179:2003;160-173
56. Hugenholz P., Pace N.R. Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol. 14:1996;190-197
57. Irazabal N., Marin I., Amils R. Genomic organization of the acidophilic chemolithoautotrophic bacterium Thiobacillus ferrooxidans ATCC 21834. J. Bacteriol. 179:1997;1946-1950
58. Iwasaki T., Wakagi T., Oshima T. Ferredoxin-dependent redox system of a novel reduced ferredoxin-reoxidizing iron-sulfur flavoprotein. J. Biol. Chem. 270:1995;17878-17883
59. Jeanthon C. Molecular ecology of hydrothermal vent microbial communities. Antonie van Leeuwenhoek. 77:2000;117-133
60. Jensen S., Holmes A.J., Olsen R.A., Murrell J.C. Detection of methane oxidizing bacteria in forest soil by monooxygenase PCR amplification. Microbial Ecol. 39:2000;282-289
61. Jolley K.A., Maddocks D.G., Gyles S.L., Mullan Z., Tang S.L., Dyall-Smith M.L., Hough D.W., Danson M.J. 2-Oxoacid dehydrogenase multienzyme complexes in the halophilic Archaea. Gene sequences and protein structural predictions. Microbiology UK. 146:2000;1061-1069
62. Jordan I.K., Rogozin I.B., Wolf Y.I., Koomin E.V. Microevolutionary genomics of bacteria. Theoret. Pop. Biol. 61:2002;435-447
63. Kanagawa T., Kelly D.P. Breakdown of dimethyl sulphide by mixed cultures and by Thiobacillus thioparus. FEMS Microbiol. Lett. 34:1986;13-19
64. Kaneko, T. and 23 co-authors (1996) Sequence analysis of the entire genome of the unicellular Cyanobacterium synechocystis sp. strain PCC6803. DNA Res. 3, 109-136
65. Kelly, D.P. (1967a) Problems of the autotrophic microorganisms. Sci. Progr. 55, 35-51
66. Kelly D.P. The incorporation of acetate by the chemoautotroph Thiobacillus neapolitanus strain C. Arch. Mikrobiol. 58:1967;99-116
67. Kelly D.P. Regulation of chemoautotrophic metabolism III. DAHP synthetase in Thiobacillus neapolitanus. Arch. Microbiol. 69:1969;360-369
68. Kelly D.P. Continued debate on autotrophy. Nature. 221:1969;1198
69. Kelly D.P. Autotrophy: concepts of lithotrophic bacteria and their organic metabolism. Annu. Rev. Microbiol. 25:1971;177-210
70. Kelly D.P. Growth and metabolism of the obligate photolithotroph Chlorobium thiosulfatophilum in the presence of added organic nutrients. Arch. Microbiol. 100:1974;163-178
71. Kelly D.P., Wood A.P. The chemolithotrophic prokaryotes. Dworkin M., Falkow S., Rosenberg E., Schleiffer K.-H., Stackebrandt E. The Prokaryotes, An Evolving Electronic Resource for the Microbiological Community (PKIIIE). 2000;Springer-Verlag, New York. (http://www.prokaryotes.com)
72. Kerscher L., Oesterhalt D. Purification and properties of two 2-oxoacid:ferredoxin oxidoreductases from Halobacterium halobium. Eur. J. Biochem. 116:1981;587-594
73. Klenk, H.-P. and 50 co-authors (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364-370
74. Kuenen J.G., Veldkamp H. Effect of organic compounds on growth of chemostat cultures of Thiomicrospira pelophila, Thiobacillus thioparus and Thiobacillus neapolitanus. Arch. Mikrobiol. 94:1973;173-190
75. Kuenen J.G., Beudeker R.F. Microbiology of thiobacilli and other sulphur-oxidizing autotrophs, mixotrophs and heterotrophs. Phil. Trans. Roy. Soc. London. B298:1982;473-497
76. Kunst, F. and 150 co-authors (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390, 249-256
77. Lopez P., Casane D., Philippe H. Bio-informatics (5) - molecular phylogeny and evolution. Méd. Sci. 18:2002;1146-1154
78. Madigan, M.T., Martinko, J.M. and Parker, J. (2003) Brock - Biology of Microorganisms, 10th ed. Prentice-Hall, Pearson Education International, London
79. Martin W., Russell M.J. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Phil. Trans. Roy. Soc. B. 358:2003;59-83
80. Matin A. Organic nutrition of chemolithotrophic bacteria. Annu. Rev. Microbiol. 32:1978;433-469
81. Matuda S., Nakano K., Ohta S., Saheki T., Kawanishi Y., Miyata T. The α-ketoacid dehydrogenase complexes. Sequence similarity of rat pyruvate dehydrogenase with Escherichia coli and Azotobacter vinelandii α-ketoglutarate dehydrogenase. Biochim. Biophys. Acta. 1089:1991;1-7
82. Meléndez-Hevia E., Waddell T.G., Cascante M. The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution. J. Mol. Evol. 43:1996;293-303
83. Mendzhul M.I., Lysenko T.G., Shainskaia O.A., Busakina I.V. Activity of tricarboxylic acid cycle enzymes in the cyanobacterium Spirulina platensis. Mikrobiol. Z. 62:2000;3-10
84. Miles, J.S. and Guest, J.R. (1987) Molecular genetics aspects of the citric acid cycle of Escherichia coli. In: Krebs' Citric Acid Cycle - Half a Century and Still Turning. Biochem. Soc. Symp. 54, 45-65
85. Mira A., Ochman H., Moran N.A. Deletional bias and the evolution of bacterial genomes. Trends Gen. 17:2001;589-596
86. Mittenthal J.E., Clarke B., Waddell T.G., Fawcett G. A new method for assembling metabolic networks, with application to the Krebs citric acid cycle. J. Theor. Biol. 208:2001;361-382
87. Morohashi M., Winn E.E., Borisuk M.T., Balouri H., Doyle E.J., Kitano H. Robustness as a measure of plausibility in models of biochemical networks. J. Theor. Biol. 216:2002;19-30
88. Murrell J.C., Radejewski S. Cultivation-independent techniques for studying methanotroph ecology. Res. Microbiol. 151:2000;807-814
89. Neilson A.H., Holm-Hansen O., Lewin R.A. An obligately autotrophic mutant of Chlamydomonas dysosmos; a biochemical elucidation. J. Gen. Microbiol. 71:1972;141-148
90. Pace N.R. New perspectives on the natural microbial world: molecular microbial ecology. ASM News. 62:1996;463-470
91. Pacheco-Oliver M., McDonald I.R., Groleau D., Murrell J.C., Miguez C.B. Detection of methanotrophs with highly divergent pmoA genes from arctic soils. FEMS Microbiol. Lett. 209:2002;313-319
92. Palleroni N.J. Prokaryotic diversity and the importance of culturing. Antonie van Leeuwenhoek. 72:1997;3-19
93. Park S.-J., Chao C., Gunsalus R.P. Aerobic regulation of the sucABCD genes of Escherichia coli, which encode α-ketoglutarate dehydrogenase and succinyl coenzyme A synthase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter. J. Bacteriol. 179:1997;4138-4142
94. Pearce J., Carr N.G. The metabolism of acetate by the blue-green algae, Anabaena variabilis and Anacystis nidulans. J. Gen. Microbiol. 49:1967;301-313
95. Pearce J., Carr N.G. An incomplete tricarboxylic acid cycle in the blue-green alga Anabaena variabilis. Biochem. J. 105:1967;45
96. Pearce J., Leach C.K., Carr N.G. The incomplete tricarboxylic acid cycle in the blue-green alga Anabaena variabilis. J. Gen. Microbiol. 55:1969;371-378
97. Peeters T.L., Liu M.S., Aleem M.I.H. The tricarboxylic acid cycle in Thiobacillus denitrificans and Thiobacillus-A2. J. Gen. Microbiol. 64:1970;29-35
98. Perna, N.T. and 27 co-authors (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529-533
99. Pfeffer, W. (1897) Pflanzenphysiologie, 2nd edn., Vol. 1. W. Engelmann, Leipzig
100. Prescott, L.M., Harley, J.P. and Klein, D.A. (1996) Microbiology. William C. Brown, Dubuque
101. Reed I.J. Multienzyme complexes. Acc. Chem. Res. 7:1974;40-46
102. Ritchie D.A., Edwards C., McDonald I.R., Murrell J.C. Detection of methanogens and methanotrophs in natural environments. Global Change Biol. 3:1997;339-350
103. Rittenberg S.C. The roles of exogenous organic matter in the physiology of chemolithotrophic bacteria. Adv. Microb. Physiol. 3:1969;159-196
104. Rittenberg S.C. The obligate autotroph - the demise of a concept. Antonie van Leeuwenhoek. 38:1972;457-478
105. Rocap, G. and 23 co-authors (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042-1047
106. Roche, T.E. and Patel, M.S. (Eds.) (1989) Alpha-keto acid dehydrogenase complexes: organization, regulation, and biochemical ramifications: a tribute to Lester J. Reed. Ann. N. Y. Acad. Sci. 573
107. Schlegel H.G. Mechanisms of chemoautotrophy. Kinne O. Marine Ecology. Vol. 2:1975;9-60 Wiley, London. part 1
108. Schlegel H.G. General Microbiology. seventh edition:1992;The University Press, Cambridge
109. Scholten J.C.M., Kelly D.P., Murrell J.C. Growth of sulfate-reducing bacteria and methanogenic archaea with methylated sulfur compounds: a commentary on the thermodynamic aspects. Arch. Microbiol. 179:2003;135-144
110. Schroder W., Burger M., Edwards C., Douglas M., Innes D., Beacham I.R., Burns D.M. The Escherichia coli orthologue of the Salmonella ushB (ushB(c)) gene produces neither UDP-sugar hydrolase activity nor detectable protein but has an identical sequence to that of Escherichia coli cdh. FEMS Microbiol. Lett. 203:2001;63-68
111. Shishkina V.N., Yurchenko V.V., Romanovskaia V.A., Malashenko Y.R., Trotsenko Y.A. Alternativity of methane assimilation pathways in obligate methylotrophs. Mikrobiologiya (Moscow). 45:1976;417-419
112. Smith A.J., Hoare D.S. Specialist phototrophs, lithotrophs, and methylotrophs: unity among a diversity of prokaryotes. Bacteriol. Rev. 41:1977;419-448
113. Smith A.J., London J., Stanier R.Y. Biochemical basis of obligate autotrophy in blue-green algae and thiobacilli. J. Bacteriol. 94:1967;972-983
114. Smith A.L., Kelly D.P. Competition in the chemostat between an obligately and a facultatively chemolithotrophic Thiobacillus. J. Gen. Microbiol. 115:1979;377-384
115. Smith N.A., Kelly D.P. Mechanism of oxidation of dimethyl disulphide by Thiobacillus thioparus strain E6. J. Gen. Microbiol. 134:1988;3031-3039
116. Smith, D.R. and 36 co-authors (1997) Complete genome sequence of Methanobacterium thermoautotrophicum DeltaH: functional analysis and comparative genomics. J. Bacteriol. 179, 7135-7155
117. Spencer M.E., Darlison M.G., Stephens P.E., Duckemfield I.K., Guest J.R. Nucleotide sequence of the sucB gene encoding the dihydrolipoamide succinyltransferase of Escherichia coli K-12 and homology with the corresponding acetyl transferase. Eur. J. Biochem. 141:1984;361-374
118. Steiert P.S., Stauffer L.T., Stauffer G.V. The lpd gene product functions as the L protein in the Escherichia coli glycine cleavage enzyme system. J. Bacteriol. 172:1990;6142-6144
119. Stephens P.E., Stauffer L.T., Stauffer G.V. Nucleotide sequence of the lipoamide dehydrogenase gene of Escherichia coli K-12. Eur. J. Biochem. 135:1983;519-527
120. Still, G.G. (1965) The role of some of the Krebs cycle reactions in the biosynthetic functions of Thiobacillus thioparus. Ph.D. Dissertation, Oregon State University
121. 2 fixation pathway in the photosynthetic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle. Eur. J. Biochem. 215:1993;633-643
122. Stryer L. Biochemistry. third ed:1988;Freeman, New York
123. Takami, H. and 11 co-authors (2000) Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genome sequence comparison with Bacillus subtilis. Nucleic Acids Res. 28, 4317-4331
124. Taylor B.F., Hoare D.S. Thiobacillus denitrificans as an obligate chemolithotroph. Arch. Mikrobiol. 80:1971;262-276
125. Taylor I.J., Anthony C. A biochemical basis for obligate methylotrophy: properties of a mutant of Pseudomonas AM1 lacking 2-oxoglutarate dehydrogenase. J. Gen. Microbiol. 93:1976;259-265
126. Taylor S.C., Dalton H., Dow C.S. Ribulose-1, 5-bisphosphate carboxylase/oxygenase and carbon assimilation in Methylococcus capsulatus (Bath). J. Gen. Microbiol. 122:1981;89-94
127. Tian K.L, Lin J.Q., Liu X.M., Liu Y., Zhang C.K., Yan W.M. Conversion of an obligate autotrophic bacteria to heterotrophic growth: expression of a heterologous phosphofructokinase gene in the chemolithotroph Acidithiobacillus thiooxidans. Biotechnol. Lett. 25:2003;749-754
128. TIGR (2003a) NCBI Entrez genomes: Acidithiobacillus ferrooxidans, unfinished sequence. Accession: NC_002923
129. TIGR (2003b) NCBI Entrez genomes: Methylococcus capsulatus, unfinished sequence. Accession: NC_002977
130. Trudinger P.A., Kelly D.P. Reduced nicotinamide adenine dinucleotide oxidation by Thiobacillus neapolitanus and Thiobacillus strain C. J. Bacteriol. 95:1968;1962-1963
131. Turner M., Schuch W. Post-transcriptional gene-silencing and RNA interference: genetic immunity, mechanisms and applications. J. Chem. Technol. Biotechnol. 75:2000;869-882
132. Umbreit W.W. Problems of autotrophy. Bacteriol. Rev. 11:1947;157-182
133. 4 metabolism in Methylobacterium extorquens AM1 using transposon mutagenesis. Microbiology UK. 149:2003;601-609
134. Wächtershäuser G. Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. USA. 87:1990;200-204
135. Wächtershäuser, G. (1990) The case for the chemo-autotrophic origin of life in an iron-sulfur world. Origins Life 21
136. Wallace W., Knowles S.E., Nicholas D.J.D. Intermediary metabolism of carbon compounds by nitrifying bacteria. Arch. Mikrobiol. 70:1970;26-42
137. Whittenbury R., Kelly D.P. Autotrophy: a conceptual phoenix. Symp. Soc. Gen. Microbiol. 27:1977;121-149
138. Wilkins M.R., Sanchez J.-C., Gooley A.A., Appel R.D., Humphery-Smith I., Hochstrasser D.F., Williams K.L. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genetic Eng. Rev. 13:1995;19-50
139. Wilkins M.R., Williams K.L. Cross-species protein identification using amino acid composition, peptide mass fingerprinting, isoelectric point and molecular mass: a theoretical evaluation. J. Theor. Biol. 186:1997;7-15
140. Winogradsky, S. (1887) Über Schwefelbakterien. Bot. Ztg. 45, 489-600, 604-616
141. Woese C.R. Bacterial evolution. Microbiol. Rev. 51:1987;221-271
142. Woese C.R. Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. USA. 97:2000;8392-8396
143. Wolska K.I. Horizontal DNA transfer between bacteria in the environment. Acta Microbiol. Polon. 52:2003;233-243
144. Wood A.P., Kelly D.P. Growth and sugar metabolism of a thermophilic iron-oxidizing mixotrophic bacterium. J. Gen. Microbiol. 130:1984;1337-1349
145. Zaigler A., Schuster S.C., Soppa J. Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii. Mol. Microbiol. 48:2003;1089-1105
146. Zhang C.C., Jeanjean R., Joset F. Obligate autotrophy in cyanobacteria: more than a lack of sugar transport. FEMS Microbiol. Lett. 161:1998;285-292