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7 - Heterotrophic metabolism on substrates other than glucose

Published online by Cambridge University Press:  05 September 2012

Byung Hong Kim
Affiliation:
Korea Institute of Science and Technology, Seoul
Geoffrey Michael Gadd
Affiliation:
University of Dundee
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Summary

It has been described previously how glucose and mineral salts can support the growth of certain heterotrophs. In this case, the organisms obtain ATP, NADPH and carbon skeletons for biosynthesis through central metabolism. Almost all natural organic compounds can be utilized through microbial metabolism. In this chapter, the bacterial metabolism of organic compounds other than glucose is discussed. Since central metabolism is reversible in one way or another, it can be assumed that an organism can use a compound if that compound is converted to intermediates of central metabolism. Some bacteria can use an extensive variety of organic compounds as sole carbon and energy sources, while some organisms can only use limited numbers of organic compounds; for example, Bacillus fastidiosus can use only urate.

Hydrolysis of polymers

Plant and animal cells consist mainly of polymers. They include polysaccharides, such as starch and cellulose, as well as proteins, nucleic acids, and many others. Such polymers cannot be easily transported into microbial cells but are first hydrolyzed to monomers or oligomers by extracellular enzymes before being transported into the cell.

Starch hydrolysis

Starch is a glucose polymer consisting of amylose and amylopectin. The former has a straight chain structure with α-1,4-glucoside bonds, while the latter has side chains with α-1,6-glucoside bonds. Starch is the commonest storage material in plants, and many prokaryotes produce amylase to utilize it as their energy and carbon source.

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Publisher: Cambridge University Press
Print publication year: 2008

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References

Bae, H. J., Turcotte, G., Chamberland, H., Karita, S. & Vezina, L. P. (2003). A comparative study between an endoglucanase IV and its fused protein complex Cel5-CBM6. FEMS Microbiology Letters 227, 175–181.CrossRefGoogle ScholarPubMed
Ballschmiter, M., Armbrecht, M., Ivanova, K., Antranikian, G. & Liebl, W. (2005). AmyA, an α-amylase with β-cyclodextrin-forming activity, and AmyB from the thermoalkaliphilic organism Anaerobranca gottschalkii: two α-amylases adapted to their different cellular localizations. Applied and Environmental Microbiology 71, 3709–3715.CrossRefGoogle ScholarPubMed
Bauer, M. W., Driskill, L. E. & Kelly, R. M. (1998). Glycosyl hydrolase from thermophilic microorganisms. Current Opinion in Biotechnology 9, 141–145.CrossRefGoogle Scholar
Bertoldo, C. & Antranikian, G. (2002). Starch-hydrolyzing enzymes from thermophilic archaea and bacteria. Current Opinion in Chemical Biology 6, 151–160.CrossRefGoogle ScholarPubMed
Bertoldo, C., Armbrecht, M., Becker, F., Schafer, T., Antranikian, G. & Liebl, W. (2004). Cloning, sequencing, and characterization of a heat- and alkali-stable type I pullulanase from Anaerobranca gottschalkii. Applied and Environmental Microbiology 70, 3407–3416.CrossRefGoogle ScholarPubMed
Bhat, S. & Owen, E. (2001). Isolation and characterisation of a major cellobiohydrolase (S-8) and a major endoglucanase (S-11) subunit from the cellulosome of Clostridium thermocellum. Anaerobe 7, 171–179.CrossRefGoogle Scholar
Collins, T., Gerday, C. & Feller, G. (2005). Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiology Reviews 29, 3–23.CrossRefGoogle ScholarPubMed
Dahiya, N., Tewari, R. & Hoondal, G. S. (2006). Biotechnological aspects of chitinolytic enzymes: a review. Applied Microbiology and Biotechnology 71, 773–782.CrossRefGoogle ScholarPubMed
Desvaux, M. (2005). The cellulosome of Clostridium cellulolyticum. Enzyme and Microbial Technology 37, 373–385.CrossRefGoogle Scholar
Felse, P. A. & Panda, T. (1999). Regulation and cloning of microbial chitinase genes. Applied and Environmental Microbiology 51, 141–151.Google ScholarPubMed
Folders, J., Algra, J., Roelofs, M. S., Loon, L. C., Tommassen, J. & Bitter, W. (2001). Characterization of Pseudomonas aeruginosa chitinase, a gradually secreted protein. Journal of Bacteriology 183, 7044–7052.CrossRefGoogle ScholarPubMed
Gao, J., Bauer, M. W., Shockley, K. R., Pysz, M. A. & Kelly, R. M. (2003). Growth of hyperthermophilic archaeon Pyrococcus furiosus on chitin involves two family 18 chitinases. Applied and Environmental Microbiology 69, 3119–3128.CrossRefGoogle ScholarPubMed
Jayani, R. S., Saxena, S. & Gupta, R. (2005). Microbial pectinolytic enzymes: a review. Process Biochemistry 40, 2931–2944.CrossRefGoogle Scholar
Kang, S., Vieille, C. & Zeikus, J. G. (2005). Identification of Pyrococcus furiosus amylopullulanase catalytic residues. Applied Microbiology and Biotechnology 66, 408–413.CrossRefGoogle ScholarPubMed
Khalikova, E., Susi, P. & Korpela, T. (2005). Microbial dextran-hydrolyzing enzymes: fundamentals and applications. Microbiology and Molecular Biology Reviews 69, 306–325.CrossRefGoogle ScholarPubMed
Kong, H., Shimosaka, M., Ando, Y., Nishiyama, K., Fujii, T. & Miyashita, K. (2001). Species-specific distribution of a modular family 19 chitinase gene in Burkholderia gladioli. FEMS Microbiology Ecology 37, 135–141.CrossRefGoogle Scholar
Lee, H.-S., Shockley, K. R., Schut, G. J., Conners, S. B., Montero, C. I., Johnson, M. R., Chou, C.-J., Bridger, S. L., Wigner, N., Brehm, S. D., Jenney, F. E., Comfort, D. A. & Kelly, R. M. (2006). Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus. Journal of Bacteriology 188, 2115–2125.CrossRefGoogle ScholarPubMed
Lin, F. P. & Leu, K. L. (2002). Cloning, expression, and characterization of thermostable region of amylopullulanase gene from Thermoanaerobacter ethanolicus 39E. Applied Biochemistry and Biotechnology 97, 33–44.CrossRefGoogle ScholarPubMed
Lynd, L. R., Weimer, P. J., Zyl, W. H. & Pretorius, I. S. (2002). Microbial cellulose utilization: fundamentals and biotechnology. Microbiology and Molecular Biology Reviews 66, 506–577.CrossRefGoogle ScholarPubMed
Murashima, K., Kosugi, A. & Doi, R. H. (2002). Determination of subunit composition of Clostridium cellulovorans cellulosomes that degrade plant cell walls. Applied and Environmental Microbiology 68, 1610–1615.CrossRefGoogle ScholarPubMed
Murashima, K., Kosugi, A. & Doi, R. H. (2002). Synergistic effects on crystalline cellulose degradation between cellulosomal cellulases from Clostridium cellulovorans. Journal of Bacteriology 184, 5088–5095.CrossRefGoogle ScholarPubMed
Schrempf, H. (2001). Recognition and degradation of chitin by streptomycetes. Antonie Van Leeuwenhoek 79, 285–289.CrossRefGoogle ScholarPubMed
Vasella, A., Davies, G. J. & Bohm, M. (2002). Glycosidase mechanisms. Current Opinion in Chemical Biology 6, 619–629.CrossRefGoogle ScholarPubMed
Watanabe, K. (2004). Collagenolytic proteases from bacteria. Applied Microbiology and Biotechnology 63, 520–526.CrossRefGoogle ScholarPubMed
Zhang, Y. H. P. & Lynd, L. R. (2004). Kinetics and relative importance of phosphorolytic and hydrolytic cleavage of cellodextrins and cellobiose in cell extracts of Clostridium thermocellum. Applied and Environmental Microbiology 70, 1563–1569.CrossRefGoogle ScholarPubMed
Zverlov, V. V., Velikodvorskaya, G. A. & Schwarz, W. H. (2002). A newly described cellulosomal cellobiohydrolase, CelO, from Clostridium thermocellum: investigation of the exo-mode of hydrolysis, and binding capacity to crystalline cellulose. Microbiology-UK 148, 247–255.CrossRefGoogle ScholarPubMed
Bausch, C., Ramsey, M. & Conway, T. (2004). Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli. Journal of Bacteriology 186, 1388–1397.CrossRefGoogle Scholar
Abo-Amer, A. E., Munn, J., Jackson, K., Aktas, M., Golby, P., Kelly, D. J. & Andrews, S. C. (2004). DNA interaction and phosphotransfer of the C4-dicarboxylate-responsive DcuS-DcuR two-component regulatory system from Escherichia coli. Journal of Bacteriology 186, 1879–1889.CrossRefGoogle ScholarPubMed
Aoshima, M., Ishii, M. & Igarashi, Y. (2004). A novel enzyme, citryl-CoA lyase, catalysing the second step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6. Molecular Microbiology 52, 763–770.CrossRefGoogle ScholarPubMed
Bramer, C. O. & Steinbuchel, A. (2001). The methylcitric acid pathway in Ralstonia eutropha: new genes identified involved in propionate metabolism. Microbiology-UK 147, 2203–2214.CrossRefGoogle ScholarPubMed
Brasen, C. & Schonheit, P. (2001). Mechanisms of acetate formation and acetate activation in halophilic archaea. Archives of Microbiology 175, 360–368.CrossRefGoogle ScholarPubMed
Brasen, C. & Schonheit, P. (2004). Unusual ADP-forming acetyl-coenzyme A synthetases from the mesophilic halophilic euryarchaeon Haloarcula marismortui and from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Archives of Microbiology 182, 277–287.CrossRefGoogle ScholarPubMed
Braun, V., Mahren, S. & Ogierman, M. (2003). Regulation of the FecI-type ECF sigma factor by transmembrane signalling. Current Opinion in Microbiology 6, 173–180.CrossRefGoogle ScholarPubMed
Claes, W. A., Puhler, A. & Kalinowski, J. (2002). Identification of two prpDBC gene clusters in Corynebacterium glutamicum and their involvement in propionate degradation via the 2-methylcitrate cycle. Journal of Bacteriology 184, 2728–2739.CrossRefGoogle ScholarPubMed
Dimroth, P. & Hilbi, H. (1997). Enzymic and genetic basis for bacterial growth on malonate. Molecular Microbiology 25, 3–10.CrossRefGoogle ScholarPubMed
Ensign, S. A. (2006). Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation. Molecular Microbiology 61, 274–276.CrossRefGoogle ScholarPubMed
Gerstmeir, R., Wendisch, V. F., Schnicke, S., Ruan, H., Farwick, M., Reinscheid, D. & Eikmanns, B. J. (2003). Acetate metabolism and its regulation in Corynebacterium glutamicum. Journal of Biotechnology 104, 99–122.CrossRefGoogle ScholarPubMed
Ingram-Smith, C., Martin, S. R. & Smith, K. S. (2006). Acetate kinase: not just a bacterial enzyme. Trends in Microbiology 14, 249–253.CrossRefGoogle Scholar
Kretzschmar, U., Ruckert, A., Jeoung, J. H. & Gorisch, H. (2002). Malate: quinone oxidoreductase is essential for growth on ethanol or acetate in Pseudomonas aeruginosa. Microbiology-UK 148, 3839–3847.CrossRefGoogle ScholarPubMed
Lau, W. W. Y. & Armbrust, E. V. (2006). Detection of glycolate oxidase gene glcD diversity among cultured and environmental marine bacteria. Environmental Microbiology 8, 1688–1702.CrossRefGoogle ScholarPubMed
Lewis, J. A. & Escalante-Semerena, J. C. (2006). The FAD-dependent tricarballylate dehydrogenase (TcuA) enzyme of Salmonella enterica converts tricarballylate into cis-aconitate. Journal of Bacteriology 188, 5479–5486.CrossRefGoogle ScholarPubMed
Meister, S., Saum, M., Alber, B. E. & Fuchs, G. (2005). L-malyl-coenzyme A/β-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus. Journal of Bacteriology 187, 1415–1425.CrossRefGoogle ScholarPubMed
Munoz-Elias, E. J., Upton, A. M., Cherian, J. & McKinney, J. D. (2006). Role of the methylcitrate cycle in Mycobacterium tuberculosis metabolism, intracellular growth, and virulence. Molecular Microbiology 60, 1109–1122.CrossRefGoogle ScholarPubMed
Palacios, S. & Escalante-Semerena, J. C. (2004). 2-methylcitrate-dependent activation of the propionate catabolic operon (prpBCDE) of Salmonella enterica by the PrpR protein. Microbiology-UK 150, 3877–3887.CrossRefGoogle ScholarPubMed
Palacios, S., Starai, V. J. & Escalante-Semerena, J. C. (2003). Propionyl coenzyme A is a common intermediate in the 1,2-propanediol and propionate catabolic pathways needed for expression of the prpBCDE operon during growth of Salmonella enterica on 1,2-propanediol. Journal of Bacteriology 185, 2802–2810.CrossRefGoogle ScholarPubMed
Sahin, N. (2003). Oxalotrophic bacteria. Research in Microbiology 154, 399–407.CrossRefGoogle ScholarPubMed
Wolfe, A. J. (2005). The acetate switch. Microbiology and Molecular Biology Reviews 69, 12–50.CrossRefGoogle ScholarPubMed
Ali, N. O., Bignon, J., Rapoport, G. & Debarbouille, M. (2001). Regulation of the acetoin catabolic pathway is controlled by sigma L in Bacillus subtilis. Journal of Bacteriology 183, 2497–2504.Google ScholarPubMed
Anthony, C. & Ghosh, M. (1997). The structure and function of PQQ-containing quinoproteins. Current Science 72, 716–727.Google Scholar
Chinnawirotpsan, P., Matsushita, K., Toyama, H., Adachi, O., Limtong, S. & Theeragool, G. (2003). Purification and characterization of two NAD-dependent alcohol dehydrogenases (ADHs) induced in the quinoprotein ADH-deficient mutant of Acetobacter pasteurianus SKU1108. Bioscience, Biotechnology, and Biochemistry 67, 958–965.CrossRefGoogle Scholar
Faveri, D., Torre, P., Molinari, F. & Converti, A. (2003). Carbon material balances and bioenergetics of 2,3-butanediol bio-oxidation by Acetobacter hansenii. Enzyme and Microbial Technology 33, 708–719.CrossRefGoogle Scholar
Havemann, G. D. & Bobik, T. A. (2003). Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar typhimurium LT2. Journal of Bacteriology 185, 5086–5095.CrossRefGoogle ScholarPubMed
Havemann, G. D., Sampson, E. M. & Bobik, T. A. (2002). PduA is a shell protein of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar typhimurium LT2. Journal of Bacteriology 184, 1253–1261.CrossRefGoogle Scholar
Hosaka, T., Ohtsuki, T., Mimura, A. & Ohkuma, M. (2001). Characterization of the NADH-linked acetylacetoin reductase/2,3-butanediol dehydrogenase gene from Bacillus cereus YUF-4. Journal of Bioscience and Bioengineering 91, 539–544.CrossRefGoogle ScholarPubMed
Kotani, T., Yamamoto, T., Yurimoto, H., Sakai, Y. & Kato, N. (2003). Propane monooxygenase and NAD+-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. strain TY-5. Journal of Bacteriology 185, 7120–7128.CrossRefGoogle ScholarPubMed
Matsushita, K., Toyama, H., Yamada, M. & Adachi, O. (2002). Quinoproteins: structure, function, and biotechnological applications. Applied Microbiology and Biotechnology 58, 13–22.CrossRefGoogle ScholarPubMed
Peng, X., Taki, H., Komukai, S., Sekine, M., Kanoh, K., Kasai, H., Choi, S. K., Omata, S., Tanikawa, S., Harayama, S. & Misawa, N. (2006). Characterization of four Rhodococcus alcohol dehydrogenase genes responsible for the oxidation of aromatic alcohols. Applied Microbiology and Biotechnology 71, 824–832.CrossRefGoogle ScholarPubMed
Sher, J., Elevi, R., Mana, L. & Oren, A. (2004). Glycerol metabolism in the extremely halophilic bacterium Salinibacter ruber. FEMS Microbiology Letters 232, 211–215.CrossRefGoogle ScholarPubMed
Tachibana, S., Kuba, N., Kawai, F., Duine, J. A. & Yasuda, M. (2003). Involvement of a quinoprotein (PQQ-containing) alcohol dehydrogenase in the degradation of polypropylene glycols by the bacterium Stenotrophomonas maltophilia. FEMS Microbiology Letters 218, 345–349.CrossRefGoogle ScholarPubMed
Colabroy, K. L. & Begley, T. P. (2005). Tryptophan catabolism: identification and characterization of a new degradative pathway. Journal of Bacteriology 187, 7866–7869.CrossRefGoogle ScholarPubMed
Gruber, K. & Kratky, C. (2002). Coenzyme B12 dependent glutamate mutase. Current Opinion in Chemical Biology 6, 598–603.CrossRefGoogle Scholar
Hoschle, B., Gnau, V. & Jendrossek, D. (2005). Methylcrotonyl-CoA and geranyl-CoA carboxylases are involved in leucine/isovalerate utilization (Liu) and acyclic terpene utilization (Atu), and are encoded by liuB/liuD and atuC/atuF, in Pseudomonas aeruginosa. Microbiology-UK 151, 3649–3656.CrossRefGoogle Scholar
Lan, J. & Newman, E. B. (2003). A requirement for anaerobically induced redox functions during aerobic growth of Escherichia coli with serine, glycine and leucine as carbon source. Research in Microbiology 154, 191–197.CrossRefGoogle ScholarPubMed
Basu, A., Apte, S. K. & Phale, P. S. (2006). Preferential utilization of aromatic compounds over glucose by Pseudomonas putida CSV86. Applied and Environmental Microbiology 72, 2226–2230.CrossRefGoogle ScholarPubMed
Borzenkov, I., Milekhina, E., Gotoeva, M., Rozanova, E. & Belyaev, S. (2006). The properties of hydrocarbon-oxidizing bacteria isolated from the oilfields of Tatarstan, western Siberia, and Vietnam. Microbiology-Moscow 75, 66–72.CrossRefGoogle ScholarPubMed
Corvini, P., Schaeffer, A. & Schlosser, D. (2006). Microbial degradation of nonylphenol and other alkylphenols? Our evolving view. Applied Microbiology and Biotechnology 72, 223–243.CrossRefGoogle ScholarPubMed
Danko, A. S., Saski, C. A., Tomkins, J. P. & Freedman, D. L. (2006). Involvement of coenzyme M during aerobic biodegradation of vinyl chloride and ethene by Pseudomonas putida strain AJ and Ochrobactrum sp. strain TD. Applied and Environmental Microbiology 72, 3756–3758.CrossRefGoogle Scholar
Ensign, S. A., Small, F. J., Allen, J. R. & Sluis, M. K. (1998). New roles for CO2 in the microbial metabolism of aliphatic epoxides and ketones. Archives of Microbiology 169, 179–187.CrossRefGoogle ScholarPubMed
Fetzner, S. (2002). Oxygenases without requirement for cofactors or metal ions. Applied Microbiology and Biotechnology 60, 243–257.Google ScholarPubMed
Fujihara, H., Yoshida, H., Matsunaga, T., Goto, M. & Furukawa, K. (2006). Cross-regulation of biphenyl- and salicylate-catabolic genes by two regulatory systems in Pseudomonas pseudoalcaligenes KF707. Journal of Bacteriology 188, 4690–4697.CrossRefGoogle ScholarPubMed
Funhoff, E. G., Bauer, U., Garcia-Rubio, I., Witholt, B. & Beilen, J. B. (2006). CYP153A6, a soluble P450 oxygenase catalyzing terminal-alkane hydroxylation. Journal of Bacteriology 188, 5220–5227.CrossRefGoogle ScholarPubMed
Gescher, J., Zaar, A., Mohamed, M., Schagger, H. & Fuchs, G. (2002). Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii. Journal of Bacteriology 184, 6301–6315.CrossRefGoogle ScholarPubMed
Harwood, C. S. & Parales, R. E. (1996). The beta-ketoadipate pathway and the biology of self-identity. Annual Review of Microbiology 50, 553–590.CrossRefGoogle ScholarPubMed
Itoh, S. (2006). Mononuclear copper active-oxygen complexes. Current Opinion in Chemical Biology 10, 115–122.CrossRefGoogle ScholarPubMed
Jimenez, J. I., Minambres, B., Garcia, J. L. & Diaz, E. (2002). Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environmental Microbiology 4, 824–841.CrossRefGoogle ScholarPubMed
Johnson, E. L. & Hyman, M. R. (2006). Propane and n-butane oxidation by Pseudomonas putida GPo1. Applied and Environmental Microbiology 72, 950–952.CrossRefGoogle ScholarPubMed
Leahy, J. G., Batchelor, P. J. & Morcomb, S. M. (2003). Evolution of the soluble diiron monooxygenases. FEMS Microbiology Reviews 27, 449–479.CrossRefGoogle ScholarPubMed
Mattevi, A. (2006). To be or not to be an oxidase: challenging the oxygen reactivity of flavoenzymes. Trends in Biochemical Sciences 31, 276–283.CrossRefGoogle ScholarPubMed
Rosenberg, M. (2006). Microbial adhesion to hydrocarbons: twenty-five years of doing MATH. FEMS Microbiology Letters 262, 129–134.CrossRefGoogle ScholarPubMed
Beilen, J. B., Neuenschwander, M., Smits, T. H. M., Roth, C., Balada, S. B. & Witholt, B. (2002). Rubredoxins involved in alkane oxidation. Journal of Bacteriology 184, 1722–1732.CrossRefGoogle ScholarPubMed
Berkel, W. J. H., Kamerbeek, N. M. & Fraaije, M. W. (2006). Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts. Journal of Biotechnology 124, 670–689.CrossRefGoogle ScholarPubMed
Hamme, J. D., Singh, A. & Ward, O. P. (2003). Recent advances in petroleum microbiology. Microbiology and Molecular Biology Reviews 67, 503–549.CrossRefGoogle ScholarPubMed
Vangnai, A. S., Sayavedra-Soto, L. A. & Arp, D. J. (2002). Roles for the two 1-butanol dehydrogenases of Pseudomonas butanovora in butane and 1-butanol metabolism. Journal of Bacteriology 184, 4343–4350.CrossRefGoogle ScholarPubMed
Adachi, O., Moonmangmee, D., Toyama, H., Yamada, M., Shinagawa, E. & Matsushita, K. (2003). New developments in oxidative fermentation. Applied Microbiology and Biotechnology 60, 643–653.CrossRefGoogle ScholarPubMed
Holscher, T. & Gorisch, H. (2006). Knockout and overexpression of pyrroloquinoline quinone biosynthetic genes in Gluconobacter oxydans 621H. Journal of Bacteriology 188, 7668–7676.CrossRefGoogle ScholarPubMed
Keliang, G. & Dongzhi, W. (2006). Asymmetric oxidation by Gluconobacter oxydans. Applied Microbiology and Biotechnology 70, 135–139.CrossRefGoogle ScholarPubMed
Chistoserdova, L., Chen, S. W., Lapidus, A. & Lidstrom, M. E. (2003). Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. Journal of Bacteriology 185, 2980–2987.CrossRefGoogle ScholarPubMed
Chistoserdova, L., Rasche, M. E. & Lidstrom, M. E. (2005). Novel dephosphotetrahydromethanopterin biosynthesis genes discovered via mutagenesis in Methylobacterium extorquens AM1. Journal of Bacteriology 187, 2508–2512.CrossRefGoogle ScholarPubMed
Choi, D. W., Kunz, R. C., Boyd, E. S., Semrau, J. D., Antholine, W. E., Han, J.-I., Zahn, J. A., Boyd, J. M., dela Mora, A. M. & Dispirito, A. A. (2003). The membrane-associated methane monooxygenase (pMMO) and pMMO-NADH:quinone oxidoreductase complex from Methylococcus capsulatus Bath. Journal of Bacteriology 185, 5755–5764.CrossRefGoogle ScholarPubMed
Dedysh, S. N., Smirnova, K. V., Khmelenina, V. N., Suzina, N. E., Liesack, W. & Trotsenko, Y. A. (2005). Methylotrophic autotrophy in Beijerinckia mobilis. Journal of Bacteriology 187, 3884–3888.CrossRefGoogle ScholarPubMed
Kelly, D. P. & Murrell, J. C. (1999). Microbial metabolism of methanesulfonic acid. Archives of Microbiology 172, 341–348.CrossRefGoogle ScholarPubMed
Kelly, D. P., Anthony, C. & Murrell, J. C. (2005). Insights into the obligate methanotroph Methylococcus capsulatus. Trends in Microbiology 13, 195–198.CrossRefGoogle ScholarPubMed
McDonald, I. R., Miguez, C. B., Rogge, G., Bourque, D., Wendlandt, K. D., Groleau, D. & Murrell, J. C. (2006). Diversity of soluble methane monooxygenase-containing methanotrophs isolated from polluted environments. FEMS Microbiology Letters 255, 225–232.CrossRefGoogle ScholarPubMed
Murrell, J. C. (1992). Genetics and molecular biology of methanotrophs. FEMS Microbiology Reviews 88, 233–248.CrossRefGoogle Scholar
Orita, I., Yurimoto, H., Hirai, R., Kawarabayasi, Y., Sakai, Y. & Kato, N. (2005). The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. Journal of Bacteriology 187, 3636–3642.CrossRefGoogle ScholarPubMed
Orita, I., Sato, T., Yurimoto, H., Kato, N., Atomi, H., Imanaka, T. & Sakai, Y. (2006). The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. Journal of Bacteriology 188, 4698–4704.CrossRefGoogle ScholarPubMed
Schubert, C. J., Coolen, M. J. L., Neretin, L. N., Schippers, A., Abbas, B., Durisch-Kaiser, E., Wehrli, B., Hopmans, E. C., Damste, J. S. S., Wakeham, S. & Kuypers, M. M. M. (2006). Aerobic and anaerobic methanotrophs in the Black Sea water column. Environmental Microbiology 8, 1844–1856.CrossRefGoogle ScholarPubMed
Theisen, A. R., Ali, M. H., Radajewski, S., Dumont, M. G., Dunfield, P. F., McDonald, I. R., Dedysh, S. N., Miguez, C. B. & Murrell, J. C. (2005). Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2. Molecular Microbiology 58, 682–692.CrossRefGoogle ScholarPubMed
Vorholt, J. A. (2002). Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Archives of Microbiology 178, 239–249.CrossRefGoogle ScholarPubMed
Wood, A. P., Aurikko, J. P. & Kelly, D. P. (2004). A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy?FEMS Microbiology Reviews 28, 335–352.CrossRefGoogle ScholarPubMed
Carterson, A. J., Morici, L. A., Jackson, D. W., Frisk, A., Lizewski, S. E., Jupiter, R., Simpson, K., Kunz, D. A., Davis, S. H., Schurr, J. R., Hassett, D. J. & Schurr, M. J. (2004). The transcriptional regulator AlgR controls cyanide production in Pseudomonas aeruginosa. Journal of Bacteriology 186, 6837–6844.CrossRefGoogle ScholarPubMed
Charoenpanich, J., Tani, A., Moriwaki, N., Kimbara, K. & Kawai, F. (2006). Dual regulation of a polyethylene glycol degradative operon by AraC-type and GalR-type regulators in Sphingopyxis macrogoltabida strain 103. Microbiology-UK 152, 3025–3034.CrossRefGoogle ScholarPubMed
Ciferri, O. (1999). Microbial degradation of paintings. Applied and Environmental Microbiology 65, 879–885.Google ScholarPubMed
Coleman, N. V. & Spain, J. C. (2003). Epoxyalkane:coenzyme M transferase in the ethene and vinyl chloride biodegradation pathways of Mycobacterium strain JS60. Journal of Bacteriology 185, 5536–5545.CrossRefGoogle ScholarPubMed
Ebbs, S. (2004). Biological degradation of cyanide compounds. Current Opinion in Biotechnology 15, 231–236.CrossRefGoogle ScholarPubMed
Hawari, J., Beaudet, S., Halasz, A., Thiboutot, S. & Ampleman, G. (2000). Microbial degradation of explosives: biotransformation versus mineralization. Applied Microbiology and Biotechnology 54, 605–618.CrossRefGoogle ScholarPubMed
Hirota-Mamoto, R., Nagai, R., Tachibana, S., Yasuda, M., Tani, A., Kimbara, K. & Kawai, F. (2006). Cloning and expression of the gene for periplasmic poly(vinyl alcohol) dehydrogenase from Sphingomonas sp. strain 113P3, a novel-type quinohaemoprotein alcohol dehydrogenase. Microbiology-UK 152, 1941–1949.CrossRefGoogle ScholarPubMed
Jendrossek, D. & Handrick, R. (2002). Microbial degradation of polyhydroxyalkanoates. Annual Review of Microbiology 56, 403–432.CrossRefGoogle ScholarPubMed
Karpouzas, D. G. & Singh, B. K. (2006). Microbial degradation of organophosphorus xenobiotics: metabolic pathways and molecular basis. Advances in Microbial Physiology 51, 119–225.CrossRefGoogle ScholarPubMed
Kutsu-Shigeno, Y., Adachi, Y., Yamada, C., Toyoshima, K., Nomura, N., Uchiyama, H. & Nakajima-Kambe, T. (2006). Isolation of a bacterium that degrades urethane compounds and characterization of its urethane hydrolase. Applied Microbiology and Biotechnology 70, 422–429.CrossRefGoogle Scholar
Mooney, A., Ward, P. G. & O'Connor, K. E. (2006). Microbial degradation of styrene: biochemistry, molecular genetics, and perspectives for biotechnological applications. Applied Microbiology and Biotechnology 72, 1–10.CrossRefGoogle ScholarPubMed
Ohta, T., Tani, A., Kimbara, K. & Kawai, F. (2005). A novel nicotinoprotein aldehyde dehydrogenase involved in polyethylene glycol degradation. Applied Microbiology and Biotechnology 68, 639–646.CrossRefGoogle ScholarPubMed
Pessi, G. & Haas, D. (2000). Transcriptional control of the hydrogen cyanide biosynthetic genes hcnABC by the anaerobic regulator ANR and the quorum-sensing regulators LasR and RhlR in Pseudomonas aeruginosa. Journal of Bacteriology 182, 6940–6949.CrossRefGoogle ScholarPubMed
Shimao, M. (2001). Biodegradation of plastics. Current Opinion in Biotechnology 12, 242–247.CrossRefGoogle ScholarPubMed
Urgun-Demirtas, M., Stark, B. & Pagilla, K. (2006). Use of genetically engineered microorganisms (GEMs) for the bioremediation of contaminants. Critical Reviews in Biotechnology 26, 145–164.CrossRefGoogle ScholarPubMed
Vaillancourt, F. H., Haro, M. A., Drouin, N. M., Karim, Z., Maaroufi, H. & Eltis, L. D. (2003). Characterization of extradiol dioxygenases from a polychlorinated biphenyl-degrading strain that possesses higher specificities for chlorinated metabolites. Journal of Bacteriology 185, 1253–1260.CrossRefGoogle Scholar
Vimr, E. R., Kalivoda, K. A., Deszo, E. L. & Steenbergen, S. M. (2004). Diversity of microbial sialic acid metabolism. Microbiology and Molecular Biology Reviews 68, 132–153.CrossRefGoogle ScholarPubMed
Bae, H. J., Turcotte, G., Chamberland, H., Karita, S. & Vezina, L. P. (2003). A comparative study between an endoglucanase IV and its fused protein complex Cel5-CBM6. FEMS Microbiology Letters 227, 175–181.CrossRefGoogle ScholarPubMed
Ballschmiter, M., Armbrecht, M., Ivanova, K., Antranikian, G. & Liebl, W. (2005). AmyA, an α-amylase with β-cyclodextrin-forming activity, and AmyB from the thermoalkaliphilic organism Anaerobranca gottschalkii: two α-amylases adapted to their different cellular localizations. Applied and Environmental Microbiology 71, 3709–3715.CrossRefGoogle ScholarPubMed
Bauer, M. W., Driskill, L. E. & Kelly, R. M. (1998). Glycosyl hydrolase from thermophilic microorganisms. Current Opinion in Biotechnology 9, 141–145.CrossRefGoogle Scholar
Bertoldo, C. & Antranikian, G. (2002). Starch-hydrolyzing enzymes from thermophilic archaea and bacteria. Current Opinion in Chemical Biology 6, 151–160.CrossRefGoogle ScholarPubMed
Bertoldo, C., Armbrecht, M., Becker, F., Schafer, T., Antranikian, G. & Liebl, W. (2004). Cloning, sequencing, and characterization of a heat- and alkali-stable type I pullulanase from Anaerobranca gottschalkii. Applied and Environmental Microbiology 70, 3407–3416.CrossRefGoogle ScholarPubMed
Bhat, S. & Owen, E. (2001). Isolation and characterisation of a major cellobiohydrolase (S-8) and a major endoglucanase (S-11) subunit from the cellulosome of Clostridium thermocellum. Anaerobe 7, 171–179.CrossRefGoogle Scholar
Collins, T., Gerday, C. & Feller, G. (2005). Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiology Reviews 29, 3–23.CrossRefGoogle ScholarPubMed
Dahiya, N., Tewari, R. & Hoondal, G. S. (2006). Biotechnological aspects of chitinolytic enzymes: a review. Applied Microbiology and Biotechnology 71, 773–782.CrossRefGoogle ScholarPubMed
Desvaux, M. (2005). The cellulosome of Clostridium cellulolyticum. Enzyme and Microbial Technology 37, 373–385.CrossRefGoogle Scholar
Felse, P. A. & Panda, T. (1999). Regulation and cloning of microbial chitinase genes. Applied and Environmental Microbiology 51, 141–151.Google ScholarPubMed
Folders, J., Algra, J., Roelofs, M. S., Loon, L. C., Tommassen, J. & Bitter, W. (2001). Characterization of Pseudomonas aeruginosa chitinase, a gradually secreted protein. Journal of Bacteriology 183, 7044–7052.CrossRefGoogle ScholarPubMed
Gao, J., Bauer, M. W., Shockley, K. R., Pysz, M. A. & Kelly, R. M. (2003). Growth of hyperthermophilic archaeon Pyrococcus furiosus on chitin involves two family 18 chitinases. Applied and Environmental Microbiology 69, 3119–3128.CrossRefGoogle ScholarPubMed
Jayani, R. S., Saxena, S. & Gupta, R. (2005). Microbial pectinolytic enzymes: a review. Process Biochemistry 40, 2931–2944.CrossRefGoogle Scholar
Kang, S., Vieille, C. & Zeikus, J. G. (2005). Identification of Pyrococcus furiosus amylopullulanase catalytic residues. Applied Microbiology and Biotechnology 66, 408–413.CrossRefGoogle ScholarPubMed
Khalikova, E., Susi, P. & Korpela, T. (2005). Microbial dextran-hydrolyzing enzymes: fundamentals and applications. Microbiology and Molecular Biology Reviews 69, 306–325.CrossRefGoogle ScholarPubMed
Kong, H., Shimosaka, M., Ando, Y., Nishiyama, K., Fujii, T. & Miyashita, K. (2001). Species-specific distribution of a modular family 19 chitinase gene in Burkholderia gladioli. FEMS Microbiology Ecology 37, 135–141.CrossRefGoogle Scholar
Lee, H.-S., Shockley, K. R., Schut, G. J., Conners, S. B., Montero, C. I., Johnson, M. R., Chou, C.-J., Bridger, S. L., Wigner, N., Brehm, S. D., Jenney, F. E., Comfort, D. A. & Kelly, R. M. (2006). Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus. Journal of Bacteriology 188, 2115–2125.CrossRefGoogle ScholarPubMed
Lin, F. P. & Leu, K. L. (2002). Cloning, expression, and characterization of thermostable region of amylopullulanase gene from Thermoanaerobacter ethanolicus 39E. Applied Biochemistry and Biotechnology 97, 33–44.CrossRefGoogle ScholarPubMed
Lynd, L. R., Weimer, P. J., Zyl, W. H. & Pretorius, I. S. (2002). Microbial cellulose utilization: fundamentals and biotechnology. Microbiology and Molecular Biology Reviews 66, 506–577.CrossRefGoogle ScholarPubMed
Murashima, K., Kosugi, A. & Doi, R. H. (2002). Determination of subunit composition of Clostridium cellulovorans cellulosomes that degrade plant cell walls. Applied and Environmental Microbiology 68, 1610–1615.CrossRefGoogle ScholarPubMed
Murashima, K., Kosugi, A. & Doi, R. H. (2002). Synergistic effects on crystalline cellulose degradation between cellulosomal cellulases from Clostridium cellulovorans. Journal of Bacteriology 184, 5088–5095.CrossRefGoogle ScholarPubMed
Schrempf, H. (2001). Recognition and degradation of chitin by streptomycetes. Antonie Van Leeuwenhoek 79, 285–289.CrossRefGoogle ScholarPubMed
Vasella, A., Davies, G. J. & Bohm, M. (2002). Glycosidase mechanisms. Current Opinion in Chemical Biology 6, 619–629.CrossRefGoogle ScholarPubMed
Watanabe, K. (2004). Collagenolytic proteases from bacteria. Applied Microbiology and Biotechnology 63, 520–526.CrossRefGoogle ScholarPubMed
Zhang, Y. H. P. & Lynd, L. R. (2004). Kinetics and relative importance of phosphorolytic and hydrolytic cleavage of cellodextrins and cellobiose in cell extracts of Clostridium thermocellum. Applied and Environmental Microbiology 70, 1563–1569.CrossRefGoogle ScholarPubMed
Zverlov, V. V., Velikodvorskaya, G. A. & Schwarz, W. H. (2002). A newly described cellulosomal cellobiohydrolase, CelO, from Clostridium thermocellum: investigation of the exo-mode of hydrolysis, and binding capacity to crystalline cellulose. Microbiology-UK 148, 247–255.CrossRefGoogle ScholarPubMed
Bausch, C., Ramsey, M. & Conway, T. (2004). Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli. Journal of Bacteriology 186, 1388–1397.CrossRefGoogle Scholar
Abo-Amer, A. E., Munn, J., Jackson, K., Aktas, M., Golby, P., Kelly, D. J. & Andrews, S. C. (2004). DNA interaction and phosphotransfer of the C4-dicarboxylate-responsive DcuS-DcuR two-component regulatory system from Escherichia coli. Journal of Bacteriology 186, 1879–1889.CrossRefGoogle ScholarPubMed
Aoshima, M., Ishii, M. & Igarashi, Y. (2004). A novel enzyme, citryl-CoA lyase, catalysing the second step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6. Molecular Microbiology 52, 763–770.CrossRefGoogle ScholarPubMed
Bramer, C. O. & Steinbuchel, A. (2001). The methylcitric acid pathway in Ralstonia eutropha: new genes identified involved in propionate metabolism. Microbiology-UK 147, 2203–2214.CrossRefGoogle ScholarPubMed
Brasen, C. & Schonheit, P. (2001). Mechanisms of acetate formation and acetate activation in halophilic archaea. Archives of Microbiology 175, 360–368.CrossRefGoogle ScholarPubMed
Brasen, C. & Schonheit, P. (2004). Unusual ADP-forming acetyl-coenzyme A synthetases from the mesophilic halophilic euryarchaeon Haloarcula marismortui and from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Archives of Microbiology 182, 277–287.CrossRefGoogle ScholarPubMed
Braun, V., Mahren, S. & Ogierman, M. (2003). Regulation of the FecI-type ECF sigma factor by transmembrane signalling. Current Opinion in Microbiology 6, 173–180.CrossRefGoogle ScholarPubMed
Claes, W. A., Puhler, A. & Kalinowski, J. (2002). Identification of two prpDBC gene clusters in Corynebacterium glutamicum and their involvement in propionate degradation via the 2-methylcitrate cycle. Journal of Bacteriology 184, 2728–2739.CrossRefGoogle ScholarPubMed
Dimroth, P. & Hilbi, H. (1997). Enzymic and genetic basis for bacterial growth on malonate. Molecular Microbiology 25, 3–10.CrossRefGoogle ScholarPubMed
Ensign, S. A. (2006). Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation. Molecular Microbiology 61, 274–276.CrossRefGoogle ScholarPubMed
Gerstmeir, R., Wendisch, V. F., Schnicke, S., Ruan, H., Farwick, M., Reinscheid, D. & Eikmanns, B. J. (2003). Acetate metabolism and its regulation in Corynebacterium glutamicum. Journal of Biotechnology 104, 99–122.CrossRefGoogle ScholarPubMed
Ingram-Smith, C., Martin, S. R. & Smith, K. S. (2006). Acetate kinase: not just a bacterial enzyme. Trends in Microbiology 14, 249–253.CrossRefGoogle Scholar
Kretzschmar, U., Ruckert, A., Jeoung, J. H. & Gorisch, H. (2002). Malate: quinone oxidoreductase is essential for growth on ethanol or acetate in Pseudomonas aeruginosa. Microbiology-UK 148, 3839–3847.CrossRefGoogle ScholarPubMed
Lau, W. W. Y. & Armbrust, E. V. (2006). Detection of glycolate oxidase gene glcD diversity among cultured and environmental marine bacteria. Environmental Microbiology 8, 1688–1702.CrossRefGoogle ScholarPubMed
Lewis, J. A. & Escalante-Semerena, J. C. (2006). The FAD-dependent tricarballylate dehydrogenase (TcuA) enzyme of Salmonella enterica converts tricarballylate into cis-aconitate. Journal of Bacteriology 188, 5479–5486.CrossRefGoogle ScholarPubMed
Meister, S., Saum, M., Alber, B. E. & Fuchs, G. (2005). L-malyl-coenzyme A/β-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus. Journal of Bacteriology 187, 1415–1425.CrossRefGoogle ScholarPubMed
Munoz-Elias, E. J., Upton, A. M., Cherian, J. & McKinney, J. D. (2006). Role of the methylcitrate cycle in Mycobacterium tuberculosis metabolism, intracellular growth, and virulence. Molecular Microbiology 60, 1109–1122.CrossRefGoogle ScholarPubMed
Palacios, S. & Escalante-Semerena, J. C. (2004). 2-methylcitrate-dependent activation of the propionate catabolic operon (prpBCDE) of Salmonella enterica by the PrpR protein. Microbiology-UK 150, 3877–3887.CrossRefGoogle ScholarPubMed
Palacios, S., Starai, V. J. & Escalante-Semerena, J. C. (2003). Propionyl coenzyme A is a common intermediate in the 1,2-propanediol and propionate catabolic pathways needed for expression of the prpBCDE operon during growth of Salmonella enterica on 1,2-propanediol. Journal of Bacteriology 185, 2802–2810.CrossRefGoogle ScholarPubMed
Sahin, N. (2003). Oxalotrophic bacteria. Research in Microbiology 154, 399–407.CrossRefGoogle ScholarPubMed
Wolfe, A. J. (2005). The acetate switch. Microbiology and Molecular Biology Reviews 69, 12–50.CrossRefGoogle ScholarPubMed
Ali, N. O., Bignon, J., Rapoport, G. & Debarbouille, M. (2001). Regulation of the acetoin catabolic pathway is controlled by sigma L in Bacillus subtilis. Journal of Bacteriology 183, 2497–2504.Google ScholarPubMed
Anthony, C. & Ghosh, M. (1997). The structure and function of PQQ-containing quinoproteins. Current Science 72, 716–727.Google Scholar
Chinnawirotpsan, P., Matsushita, K., Toyama, H., Adachi, O., Limtong, S. & Theeragool, G. (2003). Purification and characterization of two NAD-dependent alcohol dehydrogenases (ADHs) induced in the quinoprotein ADH-deficient mutant of Acetobacter pasteurianus SKU1108. Bioscience, Biotechnology, and Biochemistry 67, 958–965.CrossRefGoogle Scholar
Faveri, D., Torre, P., Molinari, F. & Converti, A. (2003). Carbon material balances and bioenergetics of 2,3-butanediol bio-oxidation by Acetobacter hansenii. Enzyme and Microbial Technology 33, 708–719.CrossRefGoogle Scholar
Havemann, G. D. & Bobik, T. A. (2003). Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar typhimurium LT2. Journal of Bacteriology 185, 5086–5095.CrossRefGoogle ScholarPubMed
Havemann, G. D., Sampson, E. M. & Bobik, T. A. (2002). PduA is a shell protein of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar typhimurium LT2. Journal of Bacteriology 184, 1253–1261.CrossRefGoogle Scholar
Hosaka, T., Ohtsuki, T., Mimura, A. & Ohkuma, M. (2001). Characterization of the NADH-linked acetylacetoin reductase/2,3-butanediol dehydrogenase gene from Bacillus cereus YUF-4. Journal of Bioscience and Bioengineering 91, 539–544.CrossRefGoogle ScholarPubMed
Kotani, T., Yamamoto, T., Yurimoto, H., Sakai, Y. & Kato, N. (2003). Propane monooxygenase and NAD+-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. strain TY-5. Journal of Bacteriology 185, 7120–7128.CrossRefGoogle ScholarPubMed
Matsushita, K., Toyama, H., Yamada, M. & Adachi, O. (2002). Quinoproteins: structure, function, and biotechnological applications. Applied Microbiology and Biotechnology 58, 13–22.CrossRefGoogle ScholarPubMed
Peng, X., Taki, H., Komukai, S., Sekine, M., Kanoh, K., Kasai, H., Choi, S. K., Omata, S., Tanikawa, S., Harayama, S. & Misawa, N. (2006). Characterization of four Rhodococcus alcohol dehydrogenase genes responsible for the oxidation of aromatic alcohols. Applied Microbiology and Biotechnology 71, 824–832.CrossRefGoogle ScholarPubMed
Sher, J., Elevi, R., Mana, L. & Oren, A. (2004). Glycerol metabolism in the extremely halophilic bacterium Salinibacter ruber. FEMS Microbiology Letters 232, 211–215.CrossRefGoogle ScholarPubMed
Tachibana, S., Kuba, N., Kawai, F., Duine, J. A. & Yasuda, M. (2003). Involvement of a quinoprotein (PQQ-containing) alcohol dehydrogenase in the degradation of polypropylene glycols by the bacterium Stenotrophomonas maltophilia. FEMS Microbiology Letters 218, 345–349.CrossRefGoogle ScholarPubMed
Colabroy, K. L. & Begley, T. P. (2005). Tryptophan catabolism: identification and characterization of a new degradative pathway. Journal of Bacteriology 187, 7866–7869.CrossRefGoogle ScholarPubMed
Gruber, K. & Kratky, C. (2002). Coenzyme B12 dependent glutamate mutase. Current Opinion in Chemical Biology 6, 598–603.CrossRefGoogle Scholar
Hoschle, B., Gnau, V. & Jendrossek, D. (2005). Methylcrotonyl-CoA and geranyl-CoA carboxylases are involved in leucine/isovalerate utilization (Liu) and acyclic terpene utilization (Atu), and are encoded by liuB/liuD and atuC/atuF, in Pseudomonas aeruginosa. Microbiology-UK 151, 3649–3656.CrossRefGoogle Scholar
Lan, J. & Newman, E. B. (2003). A requirement for anaerobically induced redox functions during aerobic growth of Escherichia coli with serine, glycine and leucine as carbon source. Research in Microbiology 154, 191–197.CrossRefGoogle ScholarPubMed
Basu, A., Apte, S. K. & Phale, P. S. (2006). Preferential utilization of aromatic compounds over glucose by Pseudomonas putida CSV86. Applied and Environmental Microbiology 72, 2226–2230.CrossRefGoogle ScholarPubMed
Borzenkov, I., Milekhina, E., Gotoeva, M., Rozanova, E. & Belyaev, S. (2006). The properties of hydrocarbon-oxidizing bacteria isolated from the oilfields of Tatarstan, western Siberia, and Vietnam. Microbiology-Moscow 75, 66–72.CrossRefGoogle ScholarPubMed
Corvini, P., Schaeffer, A. & Schlosser, D. (2006). Microbial degradation of nonylphenol and other alkylphenols? Our evolving view. Applied Microbiology and Biotechnology 72, 223–243.CrossRefGoogle ScholarPubMed
Danko, A. S., Saski, C. A., Tomkins, J. P. & Freedman, D. L. (2006). Involvement of coenzyme M during aerobic biodegradation of vinyl chloride and ethene by Pseudomonas putida strain AJ and Ochrobactrum sp. strain TD. Applied and Environmental Microbiology 72, 3756–3758.CrossRefGoogle Scholar
Ensign, S. A., Small, F. J., Allen, J. R. & Sluis, M. K. (1998). New roles for CO2 in the microbial metabolism of aliphatic epoxides and ketones. Archives of Microbiology 169, 179–187.CrossRefGoogle ScholarPubMed
Fetzner, S. (2002). Oxygenases without requirement for cofactors or metal ions. Applied Microbiology and Biotechnology 60, 243–257.Google ScholarPubMed
Fujihara, H., Yoshida, H., Matsunaga, T., Goto, M. & Furukawa, K. (2006). Cross-regulation of biphenyl- and salicylate-catabolic genes by two regulatory systems in Pseudomonas pseudoalcaligenes KF707. Journal of Bacteriology 188, 4690–4697.CrossRefGoogle ScholarPubMed
Funhoff, E. G., Bauer, U., Garcia-Rubio, I., Witholt, B. & Beilen, J. B. (2006). CYP153A6, a soluble P450 oxygenase catalyzing terminal-alkane hydroxylation. Journal of Bacteriology 188, 5220–5227.CrossRefGoogle ScholarPubMed
Gescher, J., Zaar, A., Mohamed, M., Schagger, H. & Fuchs, G. (2002). Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii. Journal of Bacteriology 184, 6301–6315.CrossRefGoogle ScholarPubMed
Harwood, C. S. & Parales, R. E. (1996). The beta-ketoadipate pathway and the biology of self-identity. Annual Review of Microbiology 50, 553–590.CrossRefGoogle ScholarPubMed
Itoh, S. (2006). Mononuclear copper active-oxygen complexes. Current Opinion in Chemical Biology 10, 115–122.CrossRefGoogle ScholarPubMed
Jimenez, J. I., Minambres, B., Garcia, J. L. & Diaz, E. (2002). Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environmental Microbiology 4, 824–841.CrossRefGoogle ScholarPubMed
Johnson, E. L. & Hyman, M. R. (2006). Propane and n-butane oxidation by Pseudomonas putida GPo1. Applied and Environmental Microbiology 72, 950–952.CrossRefGoogle ScholarPubMed
Leahy, J. G., Batchelor, P. J. & Morcomb, S. M. (2003). Evolution of the soluble diiron monooxygenases. FEMS Microbiology Reviews 27, 449–479.CrossRefGoogle ScholarPubMed
Mattevi, A. (2006). To be or not to be an oxidase: challenging the oxygen reactivity of flavoenzymes. Trends in Biochemical Sciences 31, 276–283.CrossRefGoogle ScholarPubMed
Rosenberg, M. (2006). Microbial adhesion to hydrocarbons: twenty-five years of doing MATH. FEMS Microbiology Letters 262, 129–134.CrossRefGoogle ScholarPubMed
Beilen, J. B., Neuenschwander, M., Smits, T. H. M., Roth, C., Balada, S. B. & Witholt, B. (2002). Rubredoxins involved in alkane oxidation. Journal of Bacteriology 184, 1722–1732.CrossRefGoogle ScholarPubMed
Berkel, W. J. H., Kamerbeek, N. M. & Fraaije, M. W. (2006). Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts. Journal of Biotechnology 124, 670–689.CrossRefGoogle ScholarPubMed
Hamme, J. D., Singh, A. & Ward, O. P. (2003). Recent advances in petroleum microbiology. Microbiology and Molecular Biology Reviews 67, 503–549.CrossRefGoogle ScholarPubMed
Vangnai, A. S., Sayavedra-Soto, L. A. & Arp, D. J. (2002). Roles for the two 1-butanol dehydrogenases of Pseudomonas butanovora in butane and 1-butanol metabolism. Journal of Bacteriology 184, 4343–4350.CrossRefGoogle ScholarPubMed
Adachi, O., Moonmangmee, D., Toyama, H., Yamada, M., Shinagawa, E. & Matsushita, K. (2003). New developments in oxidative fermentation. Applied Microbiology and Biotechnology 60, 643–653.CrossRefGoogle ScholarPubMed
Holscher, T. & Gorisch, H. (2006). Knockout and overexpression of pyrroloquinoline quinone biosynthetic genes in Gluconobacter oxydans 621H. Journal of Bacteriology 188, 7668–7676.CrossRefGoogle ScholarPubMed
Keliang, G. & Dongzhi, W. (2006). Asymmetric oxidation by Gluconobacter oxydans. Applied Microbiology and Biotechnology 70, 135–139.CrossRefGoogle ScholarPubMed
Chistoserdova, L., Chen, S. W., Lapidus, A. & Lidstrom, M. E. (2003). Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. Journal of Bacteriology 185, 2980–2987.CrossRefGoogle ScholarPubMed
Chistoserdova, L., Rasche, M. E. & Lidstrom, M. E. (2005). Novel dephosphotetrahydromethanopterin biosynthesis genes discovered via mutagenesis in Methylobacterium extorquens AM1. Journal of Bacteriology 187, 2508–2512.CrossRefGoogle ScholarPubMed
Choi, D. W., Kunz, R. C., Boyd, E. S., Semrau, J. D., Antholine, W. E., Han, J.-I., Zahn, J. A., Boyd, J. M., dela Mora, A. M. & Dispirito, A. A. (2003). The membrane-associated methane monooxygenase (pMMO) and pMMO-NADH:quinone oxidoreductase complex from Methylococcus capsulatus Bath. Journal of Bacteriology 185, 5755–5764.CrossRefGoogle ScholarPubMed
Dedysh, S. N., Smirnova, K. V., Khmelenina, V. N., Suzina, N. E., Liesack, W. & Trotsenko, Y. A. (2005). Methylotrophic autotrophy in Beijerinckia mobilis. Journal of Bacteriology 187, 3884–3888.CrossRefGoogle ScholarPubMed
Kelly, D. P. & Murrell, J. C. (1999). Microbial metabolism of methanesulfonic acid. Archives of Microbiology 172, 341–348.CrossRefGoogle ScholarPubMed
Kelly, D. P., Anthony, C. & Murrell, J. C. (2005). Insights into the obligate methanotroph Methylococcus capsulatus. Trends in Microbiology 13, 195–198.CrossRefGoogle ScholarPubMed
McDonald, I. R., Miguez, C. B., Rogge, G., Bourque, D., Wendlandt, K. D., Groleau, D. & Murrell, J. C. (2006). Diversity of soluble methane monooxygenase-containing methanotrophs isolated from polluted environments. FEMS Microbiology Letters 255, 225–232.CrossRefGoogle ScholarPubMed
Murrell, J. C. (1992). Genetics and molecular biology of methanotrophs. FEMS Microbiology Reviews 88, 233–248.CrossRefGoogle Scholar
Orita, I., Yurimoto, H., Hirai, R., Kawarabayasi, Y., Sakai, Y. & Kato, N. (2005). The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. Journal of Bacteriology 187, 3636–3642.CrossRefGoogle ScholarPubMed
Orita, I., Sato, T., Yurimoto, H., Kato, N., Atomi, H., Imanaka, T. & Sakai, Y. (2006). The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. Journal of Bacteriology 188, 4698–4704.CrossRefGoogle ScholarPubMed
Schubert, C. J., Coolen, M. J. L., Neretin, L. N., Schippers, A., Abbas, B., Durisch-Kaiser, E., Wehrli, B., Hopmans, E. C., Damste, J. S. S., Wakeham, S. & Kuypers, M. M. M. (2006). Aerobic and anaerobic methanotrophs in the Black Sea water column. Environmental Microbiology 8, 1844–1856.CrossRefGoogle ScholarPubMed
Theisen, A. R., Ali, M. H., Radajewski, S., Dumont, M. G., Dunfield, P. F., McDonald, I. R., Dedysh, S. N., Miguez, C. B. & Murrell, J. C. (2005). Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2. Molecular Microbiology 58, 682–692.CrossRefGoogle ScholarPubMed
Vorholt, J. A. (2002). Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Archives of Microbiology 178, 239–249.CrossRefGoogle ScholarPubMed
Wood, A. P., Aurikko, J. P. & Kelly, D. P. (2004). A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy?FEMS Microbiology Reviews 28, 335–352.CrossRefGoogle ScholarPubMed
Carterson, A. J., Morici, L. A., Jackson, D. W., Frisk, A., Lizewski, S. E., Jupiter, R., Simpson, K., Kunz, D. A., Davis, S. H., Schurr, J. R., Hassett, D. J. & Schurr, M. J. (2004). The transcriptional regulator AlgR controls cyanide production in Pseudomonas aeruginosa. Journal of Bacteriology 186, 6837–6844.CrossRefGoogle ScholarPubMed
Charoenpanich, J., Tani, A., Moriwaki, N., Kimbara, K. & Kawai, F. (2006). Dual regulation of a polyethylene glycol degradative operon by AraC-type and GalR-type regulators in Sphingopyxis macrogoltabida strain 103. Microbiology-UK 152, 3025–3034.CrossRefGoogle ScholarPubMed
Ciferri, O. (1999). Microbial degradation of paintings. Applied and Environmental Microbiology 65, 879–885.Google ScholarPubMed
Coleman, N. V. & Spain, J. C. (2003). Epoxyalkane:coenzyme M transferase in the ethene and vinyl chloride biodegradation pathways of Mycobacterium strain JS60. Journal of Bacteriology 185, 5536–5545.CrossRefGoogle ScholarPubMed
Ebbs, S. (2004). Biological degradation of cyanide compounds. Current Opinion in Biotechnology 15, 231–236.CrossRefGoogle ScholarPubMed
Hawari, J., Beaudet, S., Halasz, A., Thiboutot, S. & Ampleman, G. (2000). Microbial degradation of explosives: biotransformation versus mineralization. Applied Microbiology and Biotechnology 54, 605–618.CrossRefGoogle ScholarPubMed
Hirota-Mamoto, R., Nagai, R., Tachibana, S., Yasuda, M., Tani, A., Kimbara, K. & Kawai, F. (2006). Cloning and expression of the gene for periplasmic poly(vinyl alcohol) dehydrogenase from Sphingomonas sp. strain 113P3, a novel-type quinohaemoprotein alcohol dehydrogenase. Microbiology-UK 152, 1941–1949.CrossRefGoogle ScholarPubMed
Jendrossek, D. & Handrick, R. (2002). Microbial degradation of polyhydroxyalkanoates. Annual Review of Microbiology 56, 403–432.CrossRefGoogle ScholarPubMed
Karpouzas, D. G. & Singh, B. K. (2006). Microbial degradation of organophosphorus xenobiotics: metabolic pathways and molecular basis. Advances in Microbial Physiology 51, 119–225.CrossRefGoogle ScholarPubMed
Kutsu-Shigeno, Y., Adachi, Y., Yamada, C., Toyoshima, K., Nomura, N., Uchiyama, H. & Nakajima-Kambe, T. (2006). Isolation of a bacterium that degrades urethane compounds and characterization of its urethane hydrolase. Applied Microbiology and Biotechnology 70, 422–429.CrossRefGoogle Scholar
Mooney, A., Ward, P. G. & O'Connor, K. E. (2006). Microbial degradation of styrene: biochemistry, molecular genetics, and perspectives for biotechnological applications. Applied Microbiology and Biotechnology 72, 1–10.CrossRefGoogle ScholarPubMed
Ohta, T., Tani, A., Kimbara, K. & Kawai, F. (2005). A novel nicotinoprotein aldehyde dehydrogenase involved in polyethylene glycol degradation. Applied Microbiology and Biotechnology 68, 639–646.CrossRefGoogle ScholarPubMed
Pessi, G. & Haas, D. (2000). Transcriptional control of the hydrogen cyanide biosynthetic genes hcnABC by the anaerobic regulator ANR and the quorum-sensing regulators LasR and RhlR in Pseudomonas aeruginosa. Journal of Bacteriology 182, 6940–6949.CrossRefGoogle ScholarPubMed
Shimao, M. (2001). Biodegradation of plastics. Current Opinion in Biotechnology 12, 242–247.CrossRefGoogle ScholarPubMed
Urgun-Demirtas, M., Stark, B. & Pagilla, K. (2006). Use of genetically engineered microorganisms (GEMs) for the bioremediation of contaminants. Critical Reviews in Biotechnology 26, 145–164.CrossRefGoogle ScholarPubMed
Vaillancourt, F. H., Haro, M. A., Drouin, N. M., Karim, Z., Maaroufi, H. & Eltis, L. D. (2003). Characterization of extradiol dioxygenases from a polychlorinated biphenyl-degrading strain that possesses higher specificities for chlorinated metabolites. Journal of Bacteriology 185, 1253–1260.CrossRefGoogle Scholar
Vimr, E. R., Kalivoda, K. A., Deszo, E. L. & Steenbergen, S. M. (2004). Diversity of microbial sialic acid metabolism. Microbiology and Molecular Biology Reviews 68, 132–153.CrossRefGoogle ScholarPubMed

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