Unless stated otherwise all experiments in this work were performed and analyzed by myself.
Cultivation media were prepared mainly by Antje Wiese. All experiments were developed by and planned by myself and my supervisor Prof. Dr. Bernhard Schink. Unless stated otherwise all manuscripts were written by me and corrected by the coauthors of the respective publications.
In Chapter 4 the genome was sequenced and assembled by Anja Poehlein. She annotated one third of the genome and wrote the sections about Sequencing strategy, Gene prediction and annotation, Sequence analysis and comparative genomics, General genome features and CRISPR defense system. The preprations for electron microcospy as well as the picture were done by Dr.
Joachim Hentschel.
In Chapter 5 the cloning was done by Diliana D. Simeonova and she wrote the section about Cloning and overexpression of the ferredoxin gene.
In Chapter 6 the 2D-Gel, gradient Gels and part of the enzyme assays were done by Patrizia Bonsignore with my supervision. Anja Keller helped me with the HPLC and Gas chromatography measurements.
65
References
1 Lovley, D. R. & Klug, M. J. Intermediary metabolism of organic matter in the sediments of a eutrophic lake. Appl Environ Microbiol 43, 552-560 (1982).
2 Mountfort, D. O. & Asher, R. A. Changes in proportions of acetate and carbon dioxide used as methane precursors during the anaerobic digestion of bovine waste. Appl Environ Microbiol 35, 648-654 (1978).
3 Schink, B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiology and molecular biology reviews : MMBR 61, 262-280 (1997).
4 Barker, H. A. On the biochemistry of the methane fermentation. Archiv. Mikrobiol. 7, 404-419, doi:10.1007/BF00407413 (1936).
5 Hoppe-Seyler, F. Die Methangärung der Essigsäure. Zeitschrift für phsiologische Chemie 11, 7 (1887).
6 Buswell, A. M. Production of Fuel Gas by Anaerobic Fermentations. Industrial & Engineering Chemistry 22, 1168-1172, doi:10.1021/ie50251a016 (1930).
7 Barker, H. A. Studies upon the methane-producing bacteria. Archiv. Mikrobiol. 7, 420-438, doi:10.1007/BF00407414 (1936).
8 Schnellen, C. G. T. P. Onderzoekingen over de methaangisting PhD thesis, University of Delft, (1947).
9 Wieringa, K. T. Over het verdwijnen van waterstof en koolzuur onder anaerobe voorwaarden.
Ant. v. Leeuwenhoek 3, 10 (1936).
10 Hungate, R. E. A roll tube method for cultivation of strict anaerobes. Methods in Microbiology 3B, 15 (1969).
11 Zinder, S. H. & Koch, M. Non-aceticlastic methanogenesis from acetate: acetate oxidation by a thermophilic syntrophic coculture. Arch Microbiol 138, 263-272, doi:10.1007/bf00402133 (1984).
12 Hattori, S., Kamagata, Y., Hanada, S. & Shoun, H. Thermacetogenium phaeum gen. nov., sp.
nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int J Syst Evol Microbiol 50 Pt 4, 1601-1609 (2000).
13 Schnurer, A., Schink, B. & Svensson, B. H. Clostridium ultunense sp. nov., a mesophilic
bacterium oxidizing acetate in syntrophic association with a hydrogenotrophic methanogenic bacterium. International journal of systematic bacteriology 46, 1145-1152 (1996).
14 Karakashev, D., Batstone, D. J., Trably, E. & Angelidaki, I. Acetate oxidation is the dominant methanogenic pathway from acetate in the absence of Methanosaetaceae. Appl Environ Microbiol 72, 5138-5141, doi:10.1128/AEM.00489-06 (2006).
15 Noll, M., Klose, M. & Conrad, R. Effect of temperature change on the composition of the bacterial and archaeal community potentially involved in the turnover of acetate and propionate in methanogenic rice field soil. FEMS Microbiol Ecol 73, 215-225,
doi:10.1111/j.1574-6941.2010.00883.x (2010).
16 Nozhevnikova, A. N. et al. Influence of temperature and high acetate concentrations on methanogenesis in lake sediment slurries. FEMS Microbiol Ecol 62, 336-344,
doi:10.1111/j.1574-6941.2007.00389.x (2007).
17 Shigematsu, T. et al. Effect of dilution rate on metabolic pathway shift between aceticlastic and nonaceticlastic methanogenesis in chemostat cultivation. Appl Environ Microbiol 70, 4048-4052, doi:10.1128/AEM.70.7.4048-4052.2004 (2004).
18 Westerholm, M. et al. Quantification of syntrophic acetate-oxidizing microbial communities in biogas processes. Environ Microbiol Rep 3, 500-505,
doi:10.1111/j.1758-2229.2011.00249.x (2011).
66 19 Conrad, R. & Klose, M. Dynamics of the methanogenic archaeal community in anoxic rice soil
upon addition of straw. European Journal of Soil Science 57, 476-484, doi:10.1111/j.1365-2389.2006.00791.x (2006).
20 Stevenson, B. S. et al. Microbial communities in bulk fluids and biofilms of an oil facility have similar composition but different structure. Environmental microbiology 13, 1078-1090, doi:10.1111/j.1462-2920.2010.02413.x (2011).
21 Nusslein, B., Chin, K. J., Eckert, W. & Conrad, R. Evidence for anaerobic syntrophic acetate oxidation during methane production in the profundal sediment of subtropical Lake Kinneret (Israel). Environmental microbiology 3, 460-470 (2001).
22 Lee, M. J. & Zinder, S. H. Isolation and characterization of a thermophilic bacterium which oxidizes acetate in syntrophic association with a methanogen and which grows
acetogenically on H2-CO2. Applied and environmental microbiology 54, 124-129 (1988).
23 Hattori, S., Galushko, A. S., Kamagata, Y. & Schink, B. Operation of the CO
dehydrogenase/acetyl coenzyme A pathway in both acetate oxidation and acetate formation by the syntrophically acetate-oxidizing bacterium Thermacetogenium phaeum. J Bacteriol 187, 3471-3476, doi:10.1128/JB.187.10.3471-3476.2005 (2005).
24 Drake, H. L., Küsel, K. & Matthies, C. Acetogenic Prokaryotes. 354-420, doi:10.1007/0-387-30742-7_13 (2006).
25 Balk, M., Weijma, J. & Stams, A. J. Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor. Int J Syst Evol Microbiol 52, 1361-1368 (2002).
26 Drake, H. L. Acetogenesis., (Chapman & Hall, 1994).
27 Wofford, N. Q., Beaty, P. S. & McInerney, M. J. Preparation of cell-free extracts and the enzymes involved in fatty acid metabolism in Syntrophomonas wolfei. JOURNAL OF BACTERIOLOGY 167, 6 (1986).
28 Fischer, F., Lieske, R. and K.Winzer. Biologische Gasreaktionen.II:Über die Bildung von
Essigsäure bei der biologischen Umsetzung von Kohlenoxyd und Kohlensäure mit Wasserstoff zu Methan. Biochemie 245, 10 (1932).
29 Fuchs, G. CO2 fixation in acetogenic bacteria: variations on a theme. . FEMS Microbiology Review 39, 32 (1986).
30 Matthies, C., Freiberger, A. & Drake, H. Fumarate dissimilation and differential reductant flow by Clostridium formicoaceticum and Clostridium aceticum. Archives of Microbiology 160, 273-278, doi:10.1007/BF00292076 (1993).
31 Misoph, M. & Drake, H. L. Effect of CO2 on the fermentation capacities of the acetogen Peptostreptococcus productus U-1. J Bacteriol 178, 3140-3145 (1996).
32 Seifritz, C., Daniel, S. L., Gössner, A. & Drake, H. L. Nitrate as a preferred electron sink for the acetogen Clostridium thermoaceticum. Journal of Bacteriology 175, 8008-8013 (1993).
33 Drake, H. L., Gossner, A. S. & Daniel, S. L. Old acetogens, new light. Ann N Y Acad Sci 1125, 100-128, doi:10.1196/annals.1419.016 (2008).
34 Wood, H. G. Life with CO or CO2 and H2 as a source of carbon and energy. The FASEB Journal 5, 156-163 (1991).
35 Deppenmeier, U. & Müller, V. Life Close to the Thermodynamic Limit: How Methanogenic Archaea Conserve Energy. Results Probl Cell Differ 45, 30,
doi:10.1007/400_2006_026/Published (2007).
36 Latimer, W. M. The Oxidation States of the Elements and Their Potentials in Aqueous Solution., Vol. 2 (Englewood Cliffs, 1961).
67 37 Nölling, J., Frijlink, M. & De Vos, W. M. Isolation and characterization of plasmids from
different strains of Methanobacterium thermoformicicum. Journal of General Microbiology 137, 6 (1991).
38 Whitman, W. B., Bowen, T. L. & Boone, D. R. The Methanogenic Bacteria. 165-207, doi:10.1007/0-387-30743-5_9 (2006).
39 Wofford, N. Q., Beaty, P. S. & McInerney, M. J. Preparation of cell-free extracts and the enzymes involved in fatty acid metabolism in Syntrophomonas wolfei. Journal of Bacteriology 167, 179-185 (1986).
40 Lee, M. J. & Zinder, S. H. Hydrogen Partial Pressures in a Thermophilic Acetate-Oxidizing Methanogenic Coculture. Applied and Environmental Microbiology 54, 1457-1461 (1988).
41 Dong, X., Cheng, G. & Stams, A. Butyrate oxidation by Syntrophospora bryantii in co-culture with different methanogens and in pure culture with pentenoate as electron acceptor.
Applied microbiology and biotechnology 42, 647-652 (1994).
42 Dong, X., Plugge, C. M. & Stams, A. J. Anaerobic degradation of propionate by a mesophilic acetogenic bacterium in coculture and triculture with different methanogens. Applied and environmental microbiology 60, 2834-2838 (1994).
43 Wu, W.-M., Jain, M. K. & Zeikus, J. G. Anaerobic degradation of normal-and branched-chain fatty acids with four or more carbons to methane by a syntrophic methanogenic triculture.
Applied and environmental microbiology 60, 2220-2226 (1994).
44 Schink, B. & Stams, A. J. M. Syntrophism among Prokaryotes. 309-335, doi:10.1007/0-387-30742-7_11 (2006).
45 Cord-Ruwisch, R., Lovley, D. R. & Schink, B. Growth of Geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners. Applied and
environmental microbiology 64, 2232-2236 (1998).
46 Ragsdale, S. W., Ljungdahl, L. G. & DerVartanian, D. V. Isolation of carbon monoxide
dehydrogenase from Acetobacterium woodii and comparison of its properties with those of the Clostridium thermoaceticum enzyme. J Bacteriol 155, 1224-1237 (1983).
47 Poehlein, A. et al. An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium ion gradient for ATP synthesis. PloS one 7, e33439,
doi:10.1371/journal.pone.0033439 (2012).
48 Clark, J. E. & Ljungdahl, L. G. Purification and properties of 5,10-methylenetetrahydrofolate reductase, an iron-sulfur flavoprotein from Clostridium formicoaceticum. J Biol Chem 259, 10845-10849 (1984).
49 Hugenholtz, J. & Ljungdahl, L. G. Electron Transport and Electrochemical Proton Gradient in Membrane Vesicles of Clostridium thermoautotrophicum. JOURNAL OF BACTERIOLOGY 171, 6 (1989).
50 Fitch, W. M. & Bruschi, M. The Evolution of Prokaryotic Ferredoxins-with a General Method Correcting for Unobserved Substitutions in Less Branched Lineages. Mol. Biol. Evol. 4, 13 (1987).
51 Capozzi, F., Ciurli, S. & Luchinat, C. in Metal Sites in Proteins and Models Redox Centres Vol.
90 Structure & Bonding (eds H. A. O. Hill, P. J. Sadler, & A. J. Thomson) Ch. 5, 127-160 (Springer Berlin Heidelberg, 1998).
52 Heise, R., Müller, V. & Gottschalk, G. Sodium dependence of acetate formation by the acetogenic bacterium Acetobacterium woodii. JOURNAL OF BACTERIOLOGY 171, 5 (1989).
53 Tschech, A. & Pfennig, N. Growth yield increase linked to caffeate reduction in
Acetobacterium woodii. Archives of Microbiology 137, 163-167, doi:10.1007/BF00414460 (1984).
68 54 Hedderich, R. & Forzi, L. Energy-Converting [NiFe] Hydrogenases: More than Just
H<sub>2</sub> Activation. Journal of Molecular Microbiology and Biotechnology 10, 92-104 (2005).
55 Li, F. et al. Coupled ferredoxin and crotonyl coenzyme A (CoA) reduction with NADH catalyzed by the butyryl-CoA dehydrogenase/Etf complex from Clostridium kluyveri. J Bacteriol 190, 843-850, doi:10.1128/JB.01417-07 (2008).
56 Herrmann, G., Jayamani, E., Mai, G. & Buckel, W. Energy conservation via electron-transferring flavoprotein in anaerobic bacteria. J Bacteriol 190, 784-791,
doi:10.1128/JB.01422-07 (2008).
57 Müller, V. Energy conservation in acetogenic bacteria. Appl Environ Microbiol 69, 6345-6353 (2003).
58 Dangel, W., Schulz, H., Diekert, G., Konig, H. & Fuchs, G. Occurrence of Corrinoid-Containing Membrane-Proteins in Anaerobic-Bacteria. Arch Microbiol 148, 52-56 (1987).
59 Fontaine, F., Peterson, W., McCoy, E., Johnson, M. J. & Ritter, G. J. A new type of glucose fermentation by Clostridium thermoaceticum. Journal of bacteriology 43, 701 (1942).
60 Kerby, R. & Zeikus, J. G. Growth ofClostridium thermoaceticum on H2/CO2 or CO as energy source. Current Microbiology 8, 27-30, doi:10.1007/BF01567310 (1983).
61 Das, A., Silaghi-Dumitrescu, R., Ljungdahl, L. G. & Kurtz, D. M. Cytochrome bd Oxidase, Oxidative Stress, and Dioxygen Tolerance of the Strictly Anaerobic Bacterium Moorella thermoacetica. Journal of Bacteriology 187, 2020-2029, doi:10.1128/jb.187.6.2020-2029.2005 (2005).
62 Huang, H., Wang, S., Moll, J. & Thauer, R. K. Electron bifurcation involved in the energy metabolism of the acetogenic bacterium Moorella thermoacetica growing on glucose or H2 plus CO2. Journal of bacteriology 194, 3689-3699 (2012).
63 Hattori, S., Luo, H., Shoun, H. & Kamagata, Y. Involvement of formate as an interspecies electron carrier in a syntrophic acetate-oxidizing anaerobic microorganism in coculture with methanogens. Journal of bioscience and bioengineering 91, 294-298 (2001).
64 Röder, J. C. Syntrophe Oxidation der Fettsäure Acetat und des biogenen Amins Cadaverin (1,5-Diaminopentan) durch definierte methanogene Kokulturen Ph.D. thesis, Universität Konstanz, (2010).
65 Rothfuss, F. & Conrad, R. Thermodynamics of methanogenic intermediary metabolism in littoral sediment of Lake Constance. FEMS Microbiol Ecol 12, 265-276, doi:10.1111/j.1574-6941.1993.tb00039.x (1993).
66 Conrad, R. Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS Microbiol Ecol 28, 193-202, doi:10.1016/s0168-6496(98)00086-5 (1999).
67 Conrad, R. Quantification of methanogenic pathways using stable carbon isotopic signatures:
a review and a proposal. Org Geochem 36, 739-752, doi:10.1016/j.orggeochem.2004.09.006 (2005).
68 Zehnder, A. J. B., Ingvorsen, K. & Marti, T. Microbiology of methane bacteria. Elsevier Biomedical press B.V., 22 (1982).
69 Jetten, M. S. M., Stams, A. J. M. & Zehnder, A. J. B. Methanogenesis from acetate: a
comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp.
FEMS Microbiol Lett 88, 181-197, doi:10.1016/0378-1097(92)90802-u (1992).
70 Rui, J., Qiu, Q. & Lu, Y. Syntrophic acetate oxidation under thermophilic methanogenic condition in Chinese paddy field soil. FEMS Microbiol Ecol 77, 264-273, doi:10.1111/j.1574-6941.2011.01104.x (2011).
69 71 Westerholm, M., Roos, S. & Schnurer, A. Syntrophaceticus schinkii gen. nov., sp. nov., an
anaerobic, syntrophic acetate-oxidizing bacterium isolated from a mesophilic anaerobic filter. FEMS Microbiol Lett 309, 100-104, doi:10.1111/j.1574-6968.2010.02023.x (2010).
72 Shigematsu, T. et al. Effect of dilution rate on metabolic pathway shift between aceticlastic and nonaceticlastic methanogenesis in chemostat cultivation. Appl Environ Microbiol 70, 4 (2004).
73 Fukuzaki, S., Nishio, N. & Nagai, S. Kinetics of the methanogenic fermentation of acetate.
Appl Environ Microbiol 56, 3158-3163 (1990).
74 Schnürer, A., Zellner, G. & Svensson, B. H. Mesophilic syntrophic acetate oxidation during methane formation in biogas reactors. FEMS Microbiol Ecol 29, 249-261, doi:10.1111/j.1574-6941.1999.tb00616.x (1999).
75 Hao, L. P., Lu, F., He, P. J., Li, L. & Shao, L. M. Predominant contribution of syntrophic acetate oxidation to thermophilic methane formation at high acetate concentrations. Environmental science & technology 45, 508-513, doi:10.1021/es102228v (2011).
76 Westerholm, M., Roos, S. & Schnurer, A. Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes. Systematic and applied microbiology 34, 260-266, doi:10.1016/j.syapm.2010.11.018 (2011).
77 Hattori, S., Galushko, A. S., Kamagata, Y. & Schink, B. Operation of the CO
dehydrogenase/acetyl coenzyme A pathway in both acetate oxidation and acetate formation by the syntrophically acetate-oxidizing bacterium Thermacetogenium phaeum. Journal of Bacteriology 187, 3471-3476, doi:Doi 10.1128/Jb.187.10.3471-3476.2005 (2005).
78 Schnürer, A., Houwen, F. P. & Svensson, B. H. Mesophilic syntrophic acetate oxidation during methane formation by a triculture at high ammonium concentration. Arch Microbiol 162, 70-74, doi:10.1007/bf00264375 (1994).
79 Gottwald, M., Andreesen, J. R., LeGall, J. & Ljungdahl, L. G. Presence of cytochrome and menaquinone in Clostridium formicoaceticum and Clostridium thermoaceticum. J Bacteriol 122, 325-328 (1975).
80 Hugenholtz, J. & Ljungdahl, L. G. Electron transport and electrochemical proton gradient in membrane vesicles of Clostridium thermoautotrophicum. J Bacteriol 171, 2873-2875 (1989).
81 Pierce, E. et al. The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environmental microbiology 10, 2550-2573,
doi:10.1111/j.1462-2920.2008.01679.x (2008).
82 Biegel, E., Schmidt, S. & Muller, V. Genetic, immunological and biochemical evidence for a Rnf complex in the acetogen Acetobacterium woodii. Environmental microbiology 11, 1438-1443, doi:10.1111/j.1462-2920.2009.01871.x (2009).
83 Kopke, M. et al. Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc Natl Acad Sci U S A 107, 13087-13092, doi:10.1073/pnas.1004716107 (2010).
84 Kosaka, T. et al. The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota. Genome research 18, 442-448, doi:10.1101/gr.7136508 (2008).
85 McInerney, M. J. et al. The genome of Syntrophus aciditrophicus: life at the thermodynamic limit of microbial growth. Proc Natl Acad Sci U S A 104, 7600-7605,
doi:10.1073/pnas.0610456104 (2007).
86 Müller, N., Worm, P., Schink, B., Stams, A. J. M. & Plugge, C. M. Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanisms. Environ Microbiol Rep 2, 489-499, doi:10.1111/j.1758-2229.2010.00147.x (2010).
70 87 Sieber, J. R. et al. The genome of Syntrophomonas wolfei: new insights into syntrophic
metabolism and biohydrogen production. Environmental microbiology 12, 2289-2301, doi:10.1111/j.1462-2920.2010.02237.x (2010).
88 Tech, M. & Merkl, R. YACOP: Enhanced Gene Prediction Obtained by a Combination of Existing Methods. In Silico Biology 3, 441-451 (2003).
89 Carver, T. J. et al. ACT: the Artemis Comparison Tool. Bioinformatics 21, 3422-3423, doi:10.1093/bioinformatics/bti553 (2005).
90 Overbeek, R. et al. The ERGO genome analysis and discovery system. Nucleic Acids Res 31, 164-171 (2003).
91 Markowitz, V. M. et al. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25, 2271-2278, doi:10.1093/bioinformatics/btp393 (2009).
92 ExPASy. ExPASy: SIB Bioinformatics Resource Portal. http://expasy.org/.
93 Zdobnov, E. M. & Apweiler, R. InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847-848 (2001).
94 Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families.
Science 278, 631-637 (1997).
95 Schmeisser, C. et al. Rhizobium sp. strain NGR234 possesses a remarkable number ofsecretion systems. Appl Environ Microbiol 75, 10 (2009).
96 Needleman, S. B. & Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48, 443-453 (1970).
97 Carver, T., Thomson, N., Bleasby, A., Berriman, M. & Parkhill, J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25, 119-120,
doi:10.1093/bioinformatics/btn578 (2009).
98 BioCyc Database Collection. http://biocyc.org/.
99 Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948, doi:10.1093/bioinformatics/btm404 (2007).
100 Bagos, P. G., Nikolaou, E. P., Liakopoulos, T. D. & Tsirigos, K. D. Combined prediction of Tat and Sec signal peptides with hidden Markov models. Bioinformatics 26, 2811-2817, doi:DOI 10.1093/bioinformatics/btq530 (2010).
101 Müller, V. & Bowien, S. Differential effects of sodium ions on motility in the homoacetogenic bacteria Acetobacterium woodii and Sporomusa sphaeroides. Arch Microbiol 164, 363-369 (1995).
102 Horvath, P. & Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167-170, doi:10.1126/science.1179555 (2010).
103 Haft, D. H., Selengut, J., Mongodin, E. F. & Nelson, K. E. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS computational biology 1, e60, doi:10.1371/journal.pcbi.0010060 (2005).
104 Westra, E. R. & Brouns, S. J. The rise and fall of CRISPRs - dynamics of spacer acquisition and loss. Mol Microbiol 85, 1021-1025, doi:10.1111/j.1365-2958.2012.08170.x (2012).
105 Makarova, K. S. et al. Evolution and classification of the CRISPR-Cas systems. Nature reviews.
Microbiology 9, 467-477, doi:10.1038/nrmicro2577 (2011).
106 Frazzon, J. & Dean, D. R. Formation of iron-sulfur clusters in bacteria: an emerging field in bioinorganic chemistry. Current opinion in chemical biology 7, 166-173 (2003).
107 Gerber, J. & Lill, R. Biogenesis of iron-sulfur proteins in eukaryotes: components, mechanism and pathology. Mitochondrion 2, 71-86 (2002).
108 Wilquet, V., Van de Casteele, M., Gigot, D., Legrain, C. & Glansdorff, N. Dihydropteridine reductase as an alternative to dihydrofolate reductase for synthesis of tetrahydrofolate in
71 Thermus thermophilus. J Bacteriol 186, 351-355, doi:Doi 10.1128/Jb.186.2.351-355.2004 (2004).
109 Zhao, G., Xia, T., Song, J. & Jensen, R. A. Pseudomonas aeruginosa possesses homologues of mammalian phenylalanine hydroxylase and 4 alpha-carbinolamine dehydratase/DCoH as part of a three-component gene cluster. Proc Natl Acad Sci U S A 91, 1366-1370 (1994).
110 Martens, J. H., Barg, H., Warren, M. J. & Jahn, D. Microbial production of vitamin B12. Appl Microbiol Biotechnol 58, 275-285, doi:10.1007/s00253-001-0902-7 (2002).
111 Rodionov, D. A., Vitreschak, A. G., Mironov, A. A. & Gelfand, M. S. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem 278, 41148-41159, doi:10.1074/jbc.M305837200 (2003).
112 Raux, E., Schubert, H. L. & Warren *, M. J. Biosynthesis of cobalamin: a bacterial conundrum.
Cell Mol Life Sci 57, 1880-1893, doi:10.1007/pl00000670 (2000).
113 Goldman, B. S. & Roth, J. R. Genetic-Structure and Regulation of the cysG gene in Salmonella typhimurium. J Bacteriol 175, 1457-1466 (1993).
114 Fazzio, T. G. & Roth, J. R. Evidence that the CysG protein catalyzes the first reaction specific to B-12 synthesis in Salmonella typhimurium, insertion of cobalt. J Bacteriol 178, 6952-6959 (1996).
115 Biegel, E. & Müller, V. Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase. Proc Natl Acad Sci U S A 107, 18138-18142, doi:10.1073/pnas.1010318107 (2010).
116 Schuchmann, K. & Muller, V. A bacterial electron-bifurcating hydrogenase. J Biol Chem 287, 31165-31171, doi:10.1074/jbc.M112.395038 (2012).
117 Das, A., Hugenholtz, J., Van Halbeek, H. & Ljungdahl, L. G. Structure and function of a menaquinone involved in electron transport in membranes of Clostridium
thermoautotrophicum and Clostridium thermoaceticum. J Bacteriol 171, 5823-5829 (1989).
118 Wohlfarth, G. & Diekert, G. Thermodynamics of methylenetetrahydrofolate reduction to methyltetrahydrofolate and its implications for the energy metabolism of homoacetogenic bacteria. Arch Microbiol 155, 378-381, doi:10.1007/bf00243458 (1991).
119 Huang, H., Wang, S., Moll, J. & Thauer, R. K. Electron Bifurcation Involved in the Energy Metabolism of the Acetogenic Bacterium Moorella thermoacetica Growing on Glucose or H2 plus CO2. J Bacteriol 194, 10, doi:10.1128/JB.00385-12 (2012).
120 Verhagen, M. F., O'Rourke, T. & Adams, M. W. The hyperthermophilic bacterium, Thermotoga maritima, contains an unusually complex iron-hydrogenase: amino acid
sequence analyses versus biochemical characterization. Biochim Biophys Acta 1412, 212-229 (1999).
121 Schut, G. J. & Adams, M. W. The iron-hydrogenase of Thermotoga maritima utilizes
ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production. J Bacteriol 191, 4451-4457, doi:10.1128/JB.01582-08 (2009).
122 Welte, C. et al. Function of Ech hydrogenase in ferredoxin-dependent, membrane-bound electron transport in Methanosarcina mazei. J Bacteriol 192, 674-678, doi:10.1128/JB.01307-09 (2010).
123 Bagramyan, K. & Trchounian, A. Structural and functional features of formate hydrogen lyase, an enzyme of mixed-acid fermentation from Escherichia coli. Biochemistry 68, 1159-1170 (2003).
124 Dobbek, H., Gremer, L., Meyer, O. & Huber, R. Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S-selanylcysteine. Proc Natl Acad Sci U S A 96, 8884-8889 (1999).
72 125 Ragsdale, S. W., Clark, J. E., Ljungdahl, L. G., Lundie, L. L. & Drake, H. L. Properties of purified
carbon monoxide dehydrogenase from Clostridium thermoaceticum, a nickel, iron-sulfur protein. J Biol Chem 258, 2364-2369 (1983).
126 Bott, M. & Thauer, R. K. Proton translocation coupled to the oxidation of carbon monoxide to CO2 and H2 in Methanosarcina barkeri. Eur J Biochem 179, 469-472 (1989).
127 Ragsdale, S. W. & Pierce, E. Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation.
Biochim Biophys Acta 1784, 1873-1898, doi:10.1016/j.bbapap.2008.08.012 (2008).
128 Walsby, A. E. Gas vesicles. Microbiological reviews 58, 94-144 (1994).
129 Duine, J. A. & Frank, J. The role of PQQ and quinoproteins in methylotrophic bacteria. FEMS Microbiol Lett 87, 221-226, doi:10.1111/j.1574-6968.1990.tb04916.x (1990).
130 Diekert, G. & Wohlfarth, G. Metabolism of homoacetogens. A VAN LEEUW J MICROB 66, 12 (1994).
131 Meijden, P., Drift, C. & Vogels, G. D. Methanol conversion in Eubacterium limosum. Arch Microbiol 138, 360-364, doi:10.1007/bf00410904 (1984).
132 Thauer, R. K., Jungermann, K. & Decker, K. Energy conservation in chemotrophic anaerobic bacteria. Bacteriological reviews 41, 100-180 (1977).
133 Mortenson, L. E., Valentine, R. C. & Carnahan, J. E. An electron transport factor from Clostridium pasteurianum. Biochemical and Biophysical Research Communications 7, 448-452, doi:http://dx.doi.org/10.1016/0006-291X(62)90333-9 (1962).
134 Bruschi, M. & Guerlesquin, F. Structure, function and evolution of bacterial ferredoxins.
FEMS Microbiology Reviews 54, 19 (1988).
135 Imlay, J. A. Iron-sulphur clusters and the problem with oxygen. Molecular Microbiology 59, 11, doi:10.1111/j.1365-2958.2005.05028.x (2006).
136 Lauble, H., Kennedy, M. C., Beinert, H. & Stout, C. D. Crystal structures of aconitase with isocitrate and nitroisocitrate bound. Biochemistry 31, 2735-2748, doi:10.1021/bi00125a014 (1992).
137 Chabrière, E. et al. Crystal structures of the key anaerobic enzyme pyruvate: ferredoxin oxidoreductase, free and in complex with pyruvate. Nature structural & molecular biology 6, 182-190 (1999).
138 Berkovitch, F., Nicolet, Y., Wan, J. T., Jarrett, J. T. & Drennan, C. L. Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science 303, 76-79 (2004).
139 Bertini, I. et al. Solution structure of the oxidized 2[4Fe-4S] ferredoxin from Clostridium pasteurianum. Eur. J. Biochem. 232, 13 (1995).
140 Tanaka, M., Nakashima, T., Mower, H. F. & Yasunobu, K. T. The C- and N- terminal sequence of Clostridium pasteurianum ferredoxin. Archives of biochemistry and biophysics 105, 5 (1964).
141 Graves, M. C., Mullenbach, G. T. & Rabinowitz, J. C. Cloning and nucleotide sequence determination of the Clostridium pasteurianum ferredoxin gene. Proc. Nati. Acad. Sci. 82, 4 (1985).
142 Moulis, J. M., Meyer, J. & Lutz, M. Characterization of [4Fe-4S]2+, [4Fe-4Se]2+ and hybrid (S, Se) clusters in Clostridium pasteurianum ferredoxin. Biochem. J. 219, 3 (1984).
143 Prince, R. C. & Adams, M. W. W. Oxidation-Reduction Properties of the two 4Fe-4S clusters in Clostridium pasteurianum Ferredoxin. THE JOURNAL OF BIOLOGICAL CHEMISTRY 262, 3 (1987).
144 Wang, S., Huang, H., Kahnt, J. & Thauer, R. K. A reversible electron-bifurcating ferredoxin- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Moorella thermoacetica. J Bacteriol 195, 1267-1275, doi:10.1128/JB.02158-12 (2013).
73 145 Tagawa, K. & Arnon, D. I. Ferredoxins as electron carriers in photosynthesis and in the
biological production and consumption of hydrogen gas. Nature 195, 6 (1962).
146 Schönheit, P., Wäscher, C. & Thauer, R. K. A rapid procedure for the purification of ferredoxin from clostridia using polyethylenemine. FEBS Lett 89, 3 (1978).
147 Mortenson, L. E. Purification and analysis of ferredoxin from Clostridium pasteurianum.
BIOCHIMICA ET BIOPHYSICA ACTA 81, 7 (1964).
148 Baur, J. R., Graves, M. C., Feinberg, B. A. & Ragsdale, S. W. Characterization of the
recombinant C. pasteurianum ferredoxin and comparison of its properties with those of the native protein. BioFactors 2, 7 (1990).
149 Jouanneau, Y., Duport, C., Meyer, C. & Gailllard, J. Expression in Escherichia coli and characterization of a recombinant 7Fe ferredoxin of Rhodobacter capsulatus. Biochem. J.
286, 4 (1992).
150 Ta, D. T. & Vickery, L. E. Cloning, Sequencing, and Overexpression oaf [2Fe-2S]
Ferredoxin.pdf. THE JOURNAL OF BIOLOGICAL CHEMISTRY 267, 5 (1992).
151 Sterner, R. Ferredoxin from Thermotoga maritima Methods in Enzymology 334, 7 (2001).
152 Böhme , H. & Haselkorn, R. Expression of Anabaena ferredoxin genes in Escherichia coli. Plant Molecular Biology 12, 5 (1989).
153 Busch, J. L. H. et al. Expression in Escherichia coli and characterization of a reconstituted recombinant 7Fe ferredoxin from Desulfovibrio africanus. Biochem. J. 314, 8 (1996).
154 Xia, B., Cheng, H., Bandarian, V., Reed, G. H. & Markley, J. L. Human Ferredoxin:
154 Xia, B., Cheng, H., Bandarian, V., Reed, G. H. & Markley, J. L. Human Ferredoxin: