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5 - Tricarboxylic acid (TCA) cycle, electron transport and oxidative phosphorylation

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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Publisher: Cambridge University Press
Print publication year: 2008

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References

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
Camacho, M., Rodriguez-Arnedo, A. & Bonete, M. J. (2002). NADP-dependent isocitrate dehydrogenase from the halophilic archaeon Haloferax volcanii: cloning, sequence determination and overexpression in Escherichia coli. FEMS Microbiology Letters 209, 155–160.CrossRefGoogle ScholarPubMed
Hu, Y. & Holden, J. F. (2006). Citric acid cycle in the hyperthermophilic archaeon Pyrobaculum islandicum grown autotrophically, heterotrophically, and mixotrophically with acetate. Journal of Bacteriology 188, 4350–4355.CrossRefGoogle ScholarPubMed
Lefebre, M. D., Flannagan, R. S. & Valvano, M. A. (2005). A minor catalase/peroxidase from Burkholderia cenocepacia is required for normal aconitase activity. Microbiology-UK 151, 1975–1985.CrossRefGoogle ScholarPubMed
Makarova, K. S. & Koonin, E. V. (2003). Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis. FEMS Microbiology Letters 227, 17–23.CrossRefGoogle ScholarPubMed
Molenaar, D., Rest, M. E., Drysch, A. & Yucel, R. (2000). Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Corynebacterium glutamicum. Journal of Bacteriology 182, 6884–6891.CrossRefGoogle ScholarPubMed
Muschko, K., Kienzlen, G., Fiedler, H.-P., Wohlleben, W. & Schwartz, D. (2002). Tricarboxylic acid cycle aconitase activity during the life cycle of Streptomyces viridochromogenes Tu494. Archives of Microbiology 178, 499–505.CrossRefGoogle Scholar
Nakano, M. M., Zuber, P. & Sonenshein, A. L. (1998). Anaerobic regulation of Bacillus subtilis Krebs cycle genes. Journal of Bacteriology 180, 3304–3311.Google ScholarPubMed
Serio, A. W., Pechter, K. B. & Sonenshein, A. L. (2006). Bacillus subtilis aconitase is required for efficient late-sporulation gene expression. Journal of Bacteriology 188, 6396–6405.CrossRefGoogle ScholarPubMed
Tang, Y., Guest, J. R., Artymiuk, P. J., Read, R. C. & Green, J. (2004). Post-transcriptional regulation of bacterial motility by aconitase proteins. Molecular Microbiology 51, 1817–1826.CrossRefGoogle ScholarPubMed
Rest, M. E., Frank, C. & Molenaar, D. (2000). Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli. Journal of Bacteriology 182, 6892–6899.CrossRefGoogle ScholarPubMed
Zamboni, N. & Sauer, U. (2003). Knockout of the high-coupling cytochrome aa3 oxidase reduces TCA cycle fluxes in Bacillus subtilis. FEMS Microbiology Letters 226, 121–126.CrossRefGoogle ScholarPubMed
Alber, B. E., Spanheimer, R., Ebenau-Jehle, C. & Fuchs, G. (2006). Study of an alternate glyoxylate cycle for acetate assimilation by Rhodobacter sphaeroides. Molecular Microbiology 61, 297–309.CrossRefGoogle ScholarPubMed
El-Mansi, M., Cozzone, A. J., Shiloach, J. & Eikmanns, B. J. (2006). Control of carbon flux through enzymes of central and intermediary metabolism during growth of Escherichia coli on acetate. Current Opinion in Microbiology 9, 173–179.CrossRefGoogle Scholar
Ensign, S. A. (2006). Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation. Molecular Microbiology 61, 274–276.CrossRefGoogle ScholarPubMed
Fukuda, W., Fukui, T., Atomi, H. & Imanaka, T. (2004). First characterization of an archaeal GTP-dependent phosphoenolpyruvate carboxykinase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Journal of Bacteriology 186, 4620–4627.CrossRefGoogle ScholarPubMed
Gould, T. A., Langemheen, H., Munoz-Elias, E. J., McKinney, J. D. & Sacchettini, J. C. (2006). Dual role of isocitrate lyase 1 in the glyoxylate and methylcitrate cycles in Mycobacterium tuberculosis. Molecular Microbiology 61, 940–947.CrossRefGoogle ScholarPubMed
Kim, H. J., Kim, T. H., Kim, Y. & Lee, H. S. (2004). Identification and characterization of glxR, a gene involved in regulation of glyoxylate bypass in Corynebacterium glutamicum. Journal of Bacteriology 186, 3453–3460.CrossRefGoogle ScholarPubMed
Koebmann, B. J., Westerhoff, H. V., Snoep, J. L., Nilsson, D. & Jensen, P. R. (2002). The glycolytic flux in Escherichia coli is controlled by the demand for ATP. Journal of Bacteriology 184, 3909–3916.CrossRefGoogle ScholarPubMed
Maharjan, R. P., Yu, P. L., Seeto, S. & Ferenci, T. (2005). The role of isocitrate lyase and the glyoxylate cycle in Escherichia coli growing under glucose limitation. Research in Microbiology 156, 178–183.CrossRefGoogle Scholar
Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F. & Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Archives of Microbiology 182, 354–363.CrossRefGoogle ScholarPubMed
Sauer, U. & Eikmanns, B. J. (2005). The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiology Reviews 29, 765–794.CrossRefGoogle ScholarPubMed
Wang, Z. X., Bramer, C. O. & Steinbuchel, A. (2003). The glyoxylate bypass of Ralstonia eutropha. FEMS Microbiology Letters 228, 63–71.CrossRefGoogle ScholarPubMed
Atomi, H. (2002). Microbial enzymes involved in carbon dioxide fixation. Journal of Bioscience and Bioengineering 94, 497–505.CrossRefGoogle ScholarPubMed
Campbell, B. J. & Cary, S. C. (2004). Abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents. Applied and Environmental Microbiology 70, 6282–6289.CrossRefGoogle ScholarPubMed
Yamamoto, M., Arai, H., Ishii, M. & Igarashi, Y. (2006). Role of two 2-oxoglutarate:ferredoxin oxidoreductases in Hydrogenobacter thermophilus under aerobic and anaerobic conditions. FEMS Microbiology Letters 263, 189–193.CrossRefGoogle ScholarPubMed
Amend, J. P. & Shock, E. L. (2001). Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiology Reviews 25, 175–243.CrossRefGoogle ScholarPubMed
Battistuzzi, G., D'Onofrio, M., Borsari, M., Sola, M., Macedo, A. L., Moura, J. J. G. & Rodrigues, P. (2000). Redox thermodynamics of low-potential iron-sulfur proteins. Journal of Biological Inorganic Chemistry 5, 748–760.CrossRefGoogle ScholarPubMed
Neijssel, O. M. & Demattos, M. J. T. (1994). The energetics of bacterial growth: a reassessment. Molecular Microbiology 13, 179–182.CrossRefGoogle ScholarPubMed
Schaefer, G., Engelhard, M. & Mueller, V. (1999). Bioenergetics of the Archaea. Microbiology and Molecular Biology Reviews 63, 570–620.Google Scholar
Stockar, U., Maskow, T., Liu, J., Marison, I. W. & Patino, R. (2006). Thermodynamics of microbial growth and metabolism: an analysis of the current situation. Journal of Bacteriology 121, 517–533.Google Scholar
Yumoto, I. (2002). Bioenergetics of alkaliphilic Bacillus spp. Journal of Bioenergetics and Biomembranes 93, 342–353.Google ScholarPubMed
Au, K. M., Barabote, R. D., Hu, K. Y. & Saier, M. H. J. (2006). Evolutionary appearance of H+-translocating pyrophosphatases. Microbiology-UK 152, 1243–1247.CrossRefGoogle ScholarPubMed
Barriuso-Iglesias, M., Barreiro, C., Flechoso, F. & Martin, J. F. (2006). Transcriptional analysis of the F0F1 ATPase operon of Corynebacterium glutamicum ATCC 13032 reveals strong induction by alkaline pH. Microbiology-UK 152, 11–21.CrossRefGoogle ScholarPubMed
Brusilow, W. S. A. (1993). Assembly of the Escherichia coli F1Fo ATPase, a large multimeric membrane-bound enzyme. Molecular Microbiology 9, 419–424.CrossRefGoogle Scholar
Capaldi, R. & Aggeler, R. (2002). Mechanism of the F1Fo-type ATP synthase, a biological rotary motor. Trends in Biochemical Sciences 27, 154–160.CrossRefGoogle Scholar
Deckershebestreit, G. & Altendorf, K. (1996). The F1Fo-type ATP synthases of bacteria: structure and function of the Fo complex. Annual Review of Microbiology 50, 791–824.CrossRefGoogle Scholar
Dimroth, P. & Cook, G. M. (2004). Bacterial Na+- or H+-coupled ATP synthases operating at low electrochemical potential. Advances in Microbial Physiology 49, 175–218.CrossRefGoogle ScholarPubMed
Ferguson, S. A., Keis, S. & Cook, G. M. (2006). Biochemical and molecular characterization of a Na+-translocating F1Fo-ATPase from the thermoalkaliphilic bacterium Clostridium paradoxum. Journal of Bacteriology 188, 5045–5054.CrossRefGoogle ScholarPubMed
Iida, T., Inatomi, K., Kamagata, Y. & Maruyama, T. (2002). F- and V-type ATPases in the hyperthermophilic bacterium Thermotoga neapolitana. Extremophiles 6, 369–375.CrossRefGoogle ScholarPubMed
Kinosita, K. Jr., Adachi, K., & Itoh, H. (2004). Rotation of F1-ATPase: how an ATP-driven molecular machine may work. Annual Review of Biophysics and Biomolecular Structure 33, 245–268.CrossRefGoogle ScholarPubMed
Lapierre, P., Shial, R. & Gogarten, J. P. (2006). Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species. Systematic and Applied Microbiology 29, 15–23.CrossRefGoogle Scholar
Muller, V., Lemker, T., Lingl, A., Weidner, C., Coskun, U. & Gruber, G. (2005). Bioenergetics of archaea: ATP synthesis under harsh environmental conditions. Journal of Molecular Microbiology and Biotechnology 10, 167–180.CrossRefGoogle ScholarPubMed
Noda, S., Takezawa, Y., Mizutani, T., Asakura, T., Nishiumi, E., Onoe, K., Wada, M., Tomita, F., Matsushita, K. & Yokota, A. (2006). Alterations of cellular physiology in Escherichia coli in response to oxidative phosphorylation impaired by defective F1-ATPase. Journal of Bacteriology 188, 6869–6876.CrossRefGoogle ScholarPubMed
Pitryuk, A. V. & Pusheva, M. A. (2001). Different ionic specificities of ATP synthesis in extremely alkaliphilic sulfate-reducing and acetogenic bacteria. Microbiology-Moscow 70, 398–402.CrossRefGoogle Scholar
Schafer, I. B., Bailer, S. M., Duser, M. G., Borsch, M., Bernal, R. A., Stock, D. & Gruber, G. (2006). Crystal structure of the archaeal A1Ao ATP synthase subunit B from Methanosarcina mazei Go1: implications of nucleotide-binding differences in the major A1Ao subunits A and B. Journal of Molecular Biology 358, 725–740.CrossRefGoogle ScholarPubMed
Arnold, C. N., McElhanon, J., Lee, A., Leonhart, R. & Siegele, D. A. (2001). Global analysis of Escherichia coli gene expression during the acetate-induced acid tolerance response. Journal of Bacteriology 183, 2178–2186.CrossRefGoogle ScholarPubMed
Azcarate-Peril, M. A., Altermann, E., Hoover-Fitzula, R. L., Cano, R. J. & Klaenhammer, T. R. (2004). Identification and inactivation of genetic loci involved with Lactobacillus acidophilus acid tolerance. Applied and Environmental Microbiology 70, 5315–5322.CrossRefGoogle ScholarPubMed
Cotter, P. D. & Hill, C. (2003). Surviving the acid test: responses of Gram-positive bacteria to low pH. Microbiology and Molecular Biology Reviews 67, 429–453.CrossRefGoogle ScholarPubMed
Dover, N. & Padan, E. (2001). Transcription of nhaA, the main Na+/H+ antiporter of Escherichia coli, is regulated by Na+ and growth phase. Journal of Bacteriology 183, 644–653.CrossRefGoogle ScholarPubMed
Flythe, M. D. & Russell, J. B. (2005). The ability of acidic pH, growth inhibitors, and glucose to increase the proton motive force and energy spilling of amino acid-fermenting Clostridium sporogenes MD1 cultures. Archives of Microbiology 183, 236–242.CrossRefGoogle ScholarPubMed
Foster, J. W. (1999). When protons attack: microbial strategies of acid adaptation. Current Opinion in Microbiology 2, 170–174.CrossRefGoogle ScholarPubMed
Fozoa, E. M., Kajfasza, J. K. & Quivey, R. G. Jr. (2004). Low pH-induced membrane fatty acid alterations in oral bacteria. FEMS Microbiology Letters 238, 291–295.CrossRefGoogle Scholar
Herz, K., Vimont, S., Padan, E. & Berche, P. (2003). Roles of NhaA, NhaB, and NhaD Na+/H+ antiporters in survival of Vibrio cholerae in a saline environment. Journal of Bacteriology 185, 1236–1244.CrossRefGoogle Scholar
Hunte, C., Screpanti, E., Venturi, M., Rimon, A., Padan, E. & Michel, H. (2005). Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH. Nature 435, 1197–1202.CrossRefGoogle ScholarPubMed
Kieboom, J. & Abee, T. (2006). Arginine-dependent acid resistance in Salmonella enterica serovar typhimurium. Journal of Bacteriology 188, 5650–5653.CrossRefGoogle ScholarPubMed
Kim, J. S., Sung, M. H., Kho, D. H. & Lee, J. K. (2005). Induction of manganese-containing superoxide dismutase is required for acid tolerance in Vibrio vulnificus. Journal of Bacteriology 187, 5984–5995.CrossRefGoogle ScholarPubMed
Kitada, M., Kosono, S. & Kudo, T. (2000). The Na+/H+ antiporter of alkaliphilic Bacillus sp. Extremophiles 4, 253–258.CrossRefGoogle ScholarPubMed
Leaphart, A. B., Thompson, D. K., Huang, K., Alm, E., Wan, X. F., Arkin, A., Brown, S. D., Wu, L., Yan, T., Liu, X., Wickham, G. S. & Zhou, J. (2006). Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH. Journal of Bacteriology 188, 1633–1642.CrossRefGoogle ScholarPubMed
Liu, J., Xue, Y., Wang, Q., Wei, Y., Swartz, T. H., Hicks, D. B., Ito, M., Ma, Y. & Krulwich, T. A. (2005). The activity profile of the NhaD-type Na+(Li+)/H+ antiporter from the soda lake haloalkaliphile Alkalimonas amylolytica is adaptive for the extreme environment. Journal of Bacteriology 187, 7589–7595.CrossRefGoogle ScholarPubMed
Ma, Z., Richard, H., Tucker, D. L., Conway, T. & Foster, J. W. (2002). Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW). Journal of Bacteriology 184, 7001–7012.CrossRefGoogle Scholar
Ma, Z., Gong, S., Richard, H., Tucker, D. L., Conway, T. & Foster, J. W. (2003). GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12. Molecular Microbiology 49, 1309–1320.CrossRefGoogle ScholarPubMed
Ma, Z., Richard, H. & Foster, J. W. (2003). pH-dependent modulation of cyclic AMP levels and GadW-dependent repression of RpoS affect synthesis of the GadX regulator and Escherichia coli acid resistance. Journal of Bacteriology 185, 6852–6859.CrossRefGoogle ScholarPubMed
Martin-Galiano, A. J., Overweg, K., Ferrandiz, M. J., Reuter, M., Wells, J. M. & Campa, A. G. (2005). Transcriptional analysis of the acid tolerance response in Streptococcus pneumoniae. Microbiology-UK 151, 3935–3946.CrossRefGoogle ScholarPubMed
Miwa, T., Abe, T., Fukuda, S., Ohkawara, S. & Hino, T. (2001). Regulation of H+-ATPase synthesis in response to reduced pH in ruminal bacteria. Current Microbiology 42, 106–110.CrossRefGoogle ScholarPubMed
Padan, E., Tzubery, T., Herz, K., Kozachkov, L., Rimon, A. & Galili, L. (2004). NhaA of Escherichia coli, as a model of a pH-regulated Na+/H+antiporter. Biochimica et Biophysica Acta – Bioenergetics 1658, 2–13.CrossRefGoogle ScholarPubMed
Padan, E., Bibi, E., Ito, M. & Krulwich, T. A. (2005). Alkaline pH homeostasis in bacteria: new insights. Biochimica et Biophysica Acta – Biomembranes 1717, 67–88.CrossRefGoogle ScholarPubMed
Palmer, G. & Reedijk, J. (1992). Nomenclature of electron-transfer proteins. Recommendations 1989. Journal of Biological Chemistry 267, 665–677.Google Scholar
Rhee, J. E., Kim, K. S. & Choi, S. H. (2005). CadC activates pH-dependent expression of the Vibrio vulnificus cadBA operon at a distance through direct binding to an upstream region. Journal of Bacteriology 187, 7870–7875.CrossRefGoogle Scholar
Rhee, J. E., Jeong, H. G., Lee, J. H. & Choi, S. H. (2006). AphB influences acid tolerance of Vibrio vulnificus by activating expression of the positive regulator CadC. Journal of Bacteriology 188, 6490–6497.CrossRefGoogle ScholarPubMed
Small, P. L. & Waterman, S. R. (1998). Acid stress, anaerobiosis and gadCB: lessons from Lactococcus lactis and Escherichia coli. Trends in Microbiology 6, 214–216.CrossRefGoogle ScholarPubMed
Bott, M. & Niebisch, A. (2003). The respiratory chain of Corynebacterium glutamicum. Journal of Biotechnology 104, 129–153.CrossRefGoogle ScholarPubMed
Branden, G., Gennis, R. B. & Brzezinski, P. (2006). Transmembrane proton translocation by cytochrome c oxidase. Biochimica et Biophysica Acta – Bioenergetics 1757, 1052–1063.CrossRefGoogle ScholarPubMed
Brandt, U. (2006). Energy converting NADH:quinone oxidoreductase (complex I). Annual Review of Biochemistry 75, 69–92.CrossRefGoogle Scholar
Brandt, U. & Trumpower, B. (1994). The protonmotive Q cycle in mitochondria and bacteria. Critical Reviews in Biochemistry and Molecular Biology 29, 165–197.CrossRefGoogle ScholarPubMed
Brzezinski, P. & Adelroth, P. (2006). Design principles of proton-pumping haem-copper oxidases. Current Opinion in Structural Biology 16, 465–472.CrossRefGoogle ScholarPubMed
Brzezinski, P. & Larsson, G. (2003). Redox-driven proton pumping by heme-copper oxidases. Biochimica et Biophysica Acta – Bioenergetics 1605, 1–13.CrossRefGoogle ScholarPubMed
Cosseau, C. & Batut, J. (2004). Genomics of the ccoNOQP-encoded cbb 3 oxidase complex in bacteria. Archives of Microbiology 181, 89–96.CrossRefGoogle Scholar
Crofts, A. R. (2004). The cytochrome bc1 complex: function in the context of structure. Annual Review of Physiology 66, 689–733.CrossRefGoogle ScholarPubMed
Crofts, A. R., Lhee, S., Crofts, S. B., Cheng, J. & Rose, S. (2006). Proton pumping in the bc1 complex: a new gating mechanism that prevents short circuits. Biochimica et Biophysica Acta – Bioenergetics 1757, 1019–1034.CrossRefGoogle ScholarPubMed
Degier, J. W. L., Lubben, M., Reijnders, W. N. M., Tipker, C. A., Slotboom, D. J., Vanspanning, R. J. M., Stouthamer, A. H. & Vanderoost, J. (1994). The terminal oxidases of Paracoccus denitrificans. Molecular Microbiology 13, 183–196.CrossRefGoogle Scholar
Faxen, K., Gilderson, G., Adelroth, P. & Brzezinski, P. (2005). A mechanistic principle for proton pumping by cytochrome c oxidase. Nature 437, 286–289.CrossRefGoogle ScholarPubMed
Friedrich, T. & Bottcher, B. (2004). The gross structure of the respiratory complex I: a Lego System. Biochimica et Biophysica Acta – Bioenergetics 1608, 1–9.CrossRefGoogle ScholarPubMed
Hickman, J. W., Barber, R. D., Skaar, E. P. & Donohue, T. J. (2002). Link between the membrane-bound pyridine nucleotide transhydrogenase and glutathione-dependent processes in Rhodobacter sphaeroides. Journal of Bacteriology 184, 400–409.CrossRefGoogle ScholarPubMed
Hinsley, A. P. & Berks, B. C. (2002). Specificity of respiratory pathways involved in the reduction of sulfur compounds by Salmonella enterica. Microbiology-UK 148, 3631–3638.CrossRefGoogle ScholarPubMed
Hosler, J. P., Ferguson-Miller, S. & Mills, D. A. (2006). Energy transduction: proton transfer through the respiratory complexes. Annual Review of Biochemistry 75, 165–187.CrossRefGoogle ScholarPubMed
Hunte, C., Palsdottir, H. & Trumpower, B. L. (2003). Protonmotive pathways and mechanisms in the cytochrome bc1 complex. FEBS Letters 545, 39–46.CrossRefGoogle ScholarPubMed
Ishikawa, R., Ishido, Y., Tachikawa, A., Kawasaki, H., Matsuzawa, H. & Wakagi, T. (2002). Aeropyrum pernix K1, a strictly aerobic and hyperthermophilic archaeon, has two terminal oxidases, cytochrome ba3 and cytochrome aa3. Archives of Microbiology 179, 42–49.CrossRefGoogle ScholarPubMed
Johnson, D. C., Dean, D. R., Smith, A. D. & Johnson, M. K. (2005). Structure, function and formation of iron-sulfur clusters. Annual Review of Biochemistry 74, 247–281.CrossRefGoogle ScholarPubMed
Lalucque, H. & Silar, P. (2003). NADPH oxidase: an enzyme for multicellularity? Trends in Microbiology 11, 9–12.CrossRefGoogle ScholarPubMed
Lanyi, J. K. & Pohorille, A. (2001). Proton pumps: mechanism of action and applications. Trends in Biotechnology 19, 140–144.CrossRefGoogle ScholarPubMed
Link, T. A. (1997). The role of the ‘Rieske’ iron sulfur protein in the hydroquinone oxidation (QP) site of the cytochrome bc1 complex. The ‘proton-gated affinity change’ mechanism. FEBS Letters 412, 257–264.CrossRefGoogle Scholar
Ludwig, R. A. (2004). Microaerophilic bacteria transduce energy via oxidative metabolic gearing. Research in Microbiology 155, 61–70.CrossRefGoogle ScholarPubMed
Melo, A., Bandeiras, T. & Teixeira, M. (2004). New insights into Type II NAD(P)H:quinone oxidoreductases. Microbiology and Molecular Biology Reviews 68, 603–616.CrossRefGoogle ScholarPubMed
Mendz, G. L., Smith, M. A., Finel, M. & Korolik, V. (2000). Characteristics of the aerobic respiratory chains of the microaerophiles Campylobacter jejuni and Helicobacter pylori. Archives of Microbiology 174, 1–10.Google Scholar
Minohara, S., Sakamoto, J. & Sone, N. (2002). Improved H+/O ratio and cell yield of Escherichia coli with genetically altered terminal quinol oxidases. Journal of Bioscience and Bioengineering 93, 464–469.CrossRefGoogle ScholarPubMed
Morales, G., Ugidos, A. & Rojo, F. (2006). Inactivation of the Pseudomonas putida cytochrome o ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases. Environmental Microbiology 8, 1764–1774.CrossRefGoogle ScholarPubMed
Mulkidjanian, A. Y. (2005). Ubiquinol oxidation in the cytochrome bc1 complex: reaction mechanism and prevention of short-circuiting. Biochimica et Biophysica Acta – Bioenergetics 1709, 5–34.CrossRefGoogle ScholarPubMed
Osyczka, A., Moser, C. C. & Dutton, P. L. (2005). Fixing the Q cycle. Trends in Biochemical Sciences 30, 176–182.CrossRefGoogle ScholarPubMed
Otten, M. F., Stork, D. R., Reijnders, W. N. M., Westerhoff, H. V. & Spanning, R. J. M. (2001). Regulation of expression of terminal oxidases in Paracoccus denitrificans. European Journal of Biochemistry 268, 2486–2497.CrossRefGoogle ScholarPubMed
Rich, P. R. (1986). A perspective on Q-cycles. Journal of Bioenergetics and Biomembranes 18, 145–156.CrossRefGoogle ScholarPubMed
Rich, P. R. (2004). The quinone chemistry of bc complexes. Biochimica et Biophysica Acta – Bioenergetics 1658, 165–171.CrossRefGoogle ScholarPubMed
Richardson, D. J. (2000). Bacterial respiration: a flexible process for a changing environment. Microbiology-UK 146, 551–571.CrossRefGoogle ScholarPubMed
Schneider, D. & Schmidt, C. L. (2005). Multiple Rieske proteins in prokaryotes: where and why? Biochimica et Biophysica Acta – Bioenergetics 1710, 1–12.CrossRefGoogle Scholar
Shimada, H., Shida, Y., Nemoto, N., Oshima, T. & Yamagishi, A. (2001). Quinone profiles of Thermoplasma acidophilum HO-62. Journal of Bacteriology 183, 1462–1465.CrossRefGoogle ScholarPubMed
Snyder, C. H., Merbitz-Zahradnik, T., Link, T. A. & Trumpower, B. L. (1999). Role of the Rieske iron-sulfur protein midpoint potential in the protonmotive Q-cycle mechanism of the cytochrome bc1 complex. Journal of Bioenergetics and Biomembranes 31, 235–242.CrossRefGoogle ScholarPubMed
Trumpower, B. L. & Gennis, R. B. (1994). Energy transduction by cytochrome complexes in mitochondrial and bacterial respiration: the enzymology of coupling electron transfer reactions to transmembrane proton translocation. Annual Review of Biochemistry 63, 675–716.CrossRefGoogle ScholarPubMed
Wikstrom, M. & Verkhovsky, M. I. (2006). Towards the mechanism of proton pumping by the haem-copper oxidases. Biochimica et Biophysica Acta – Bioenergetics 1757, 1047–1051.CrossRefGoogle ScholarPubMed
Williams, H. D., Zlosnik, J. E. A. & Ryall, B. (2006). Oxygen, cyanide and energy generation in the cystic fibrosis pathogen Pseudomonas aeruginosa. Advances in Microbial Physiology 52, 1–71.CrossRefGoogle Scholar
Zlosnik, J. E. A., Tavankar, G. R., Bundy, J. G., Mossialos, D., O'Toole, R. & Williams, H. D. (2006). Investigation of the physiological relationship between the cyanide-insensitive oxidase and cyanide production in Pseudomonas aeruginosa. Microbiology-UK 152, 1407–1415.CrossRefGoogle ScholarPubMed
Abe, K., Ohnishi, F., Yagi, K., Nakajima, T., Higuchi, T., Sano, M., Machida, M., Sarker, R. I. & Maloney, P. C. (2002). Plasmid-encoded asp operon confers a proton motive metabolic cycle catalyzed by an aspartate-alanine exchange reaction. Journal of Bacteriology 184, 2906–2913.CrossRefGoogle ScholarPubMed
Dimroth, P. & Schink, B. (1998). Energy conservation in the decarboxylation of dicarboxylic acids in fermenting bacteria. Archives of Microbiology 170, 69–77.CrossRefGoogle ScholarPubMed
Gregory, K. B., Bond, D. R. & Lovley, D. R. (2004). Graphite electrodes as electron donors for anaerobic respiration. Environmental Microbiology 6, 596–604.CrossRefGoogle ScholarPubMed
Iyer, R., Williams, C. & Miller, C. (2003). Arginine-agmatine antiporter in extreme acid resistance in Escherichia coli. Journal of Bacteriology 185, 6556–6561.CrossRefGoogle ScholarPubMed
Kroger, A., Geisler, V., Lemma, E., Theis, F. & Lenger, R. (1992). Bacterial fumarate respiration. Archives of Microbiology 158, 311–314.CrossRefGoogle Scholar
Okane, D. J. & Prasher, D. C. (1992). Evolutionary origins of bacterial bioluminescence. Molecular Microbiology 6, 443–449.CrossRefGoogle Scholar
Poolman, B. (1993). Energy transduction in lactic acid bacteria. FEMS Microbiology Reviews 12, 125–147.CrossRefGoogle ScholarPubMed
Wolken, W. A. M., Lucas, P. M., Lonvaud-Funel, A. & Lolkema, J. S. (2006). The mechanism of the tyrosine transporter TyrP supports a proton motive tyrosine decarboxylation pathway in Lactobacillus brevis. Journal of Bacteriology 188, 2198–2206.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
Camacho, M., Rodriguez-Arnedo, A. & Bonete, M. J. (2002). NADP-dependent isocitrate dehydrogenase from the halophilic archaeon Haloferax volcanii: cloning, sequence determination and overexpression in Escherichia coli. FEMS Microbiology Letters 209, 155–160.CrossRefGoogle ScholarPubMed
Hu, Y. & Holden, J. F. (2006). Citric acid cycle in the hyperthermophilic archaeon Pyrobaculum islandicum grown autotrophically, heterotrophically, and mixotrophically with acetate. Journal of Bacteriology 188, 4350–4355.CrossRefGoogle ScholarPubMed
Lefebre, M. D., Flannagan, R. S. & Valvano, M. A. (2005). A minor catalase/peroxidase from Burkholderia cenocepacia is required for normal aconitase activity. Microbiology-UK 151, 1975–1985.CrossRefGoogle ScholarPubMed
Makarova, K. S. & Koonin, E. V. (2003). Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis. FEMS Microbiology Letters 227, 17–23.CrossRefGoogle ScholarPubMed
Molenaar, D., Rest, M. E., Drysch, A. & Yucel, R. (2000). Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Corynebacterium glutamicum. Journal of Bacteriology 182, 6884–6891.CrossRefGoogle ScholarPubMed
Muschko, K., Kienzlen, G., Fiedler, H.-P., Wohlleben, W. & Schwartz, D. (2002). Tricarboxylic acid cycle aconitase activity during the life cycle of Streptomyces viridochromogenes Tu494. Archives of Microbiology 178, 499–505.CrossRefGoogle Scholar
Nakano, M. M., Zuber, P. & Sonenshein, A. L. (1998). Anaerobic regulation of Bacillus subtilis Krebs cycle genes. Journal of Bacteriology 180, 3304–3311.Google ScholarPubMed
Serio, A. W., Pechter, K. B. & Sonenshein, A. L. (2006). Bacillus subtilis aconitase is required for efficient late-sporulation gene expression. Journal of Bacteriology 188, 6396–6405.CrossRefGoogle ScholarPubMed
Tang, Y., Guest, J. R., Artymiuk, P. J., Read, R. C. & Green, J. (2004). Post-transcriptional regulation of bacterial motility by aconitase proteins. Molecular Microbiology 51, 1817–1826.CrossRefGoogle ScholarPubMed
Rest, M. E., Frank, C. & Molenaar, D. (2000). Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli. Journal of Bacteriology 182, 6892–6899.CrossRefGoogle ScholarPubMed
Zamboni, N. & Sauer, U. (2003). Knockout of the high-coupling cytochrome aa3 oxidase reduces TCA cycle fluxes in Bacillus subtilis. FEMS Microbiology Letters 226, 121–126.CrossRefGoogle ScholarPubMed
Alber, B. E., Spanheimer, R., Ebenau-Jehle, C. & Fuchs, G. (2006). Study of an alternate glyoxylate cycle for acetate assimilation by Rhodobacter sphaeroides. Molecular Microbiology 61, 297–309.CrossRefGoogle ScholarPubMed
El-Mansi, M., Cozzone, A. J., Shiloach, J. & Eikmanns, B. J. (2006). Control of carbon flux through enzymes of central and intermediary metabolism during growth of Escherichia coli on acetate. Current Opinion in Microbiology 9, 173–179.CrossRefGoogle Scholar
Ensign, S. A. (2006). Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation. Molecular Microbiology 61, 274–276.CrossRefGoogle ScholarPubMed
Fukuda, W., Fukui, T., Atomi, H. & Imanaka, T. (2004). First characterization of an archaeal GTP-dependent phosphoenolpyruvate carboxykinase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Journal of Bacteriology 186, 4620–4627.CrossRefGoogle ScholarPubMed
Gould, T. A., Langemheen, H., Munoz-Elias, E. J., McKinney, J. D. & Sacchettini, J. C. (2006). Dual role of isocitrate lyase 1 in the glyoxylate and methylcitrate cycles in Mycobacterium tuberculosis. Molecular Microbiology 61, 940–947.CrossRefGoogle ScholarPubMed
Kim, H. J., Kim, T. H., Kim, Y. & Lee, H. S. (2004). Identification and characterization of glxR, a gene involved in regulation of glyoxylate bypass in Corynebacterium glutamicum. Journal of Bacteriology 186, 3453–3460.CrossRefGoogle ScholarPubMed
Koebmann, B. J., Westerhoff, H. V., Snoep, J. L., Nilsson, D. & Jensen, P. R. (2002). The glycolytic flux in Escherichia coli is controlled by the demand for ATP. Journal of Bacteriology 184, 3909–3916.CrossRefGoogle ScholarPubMed
Maharjan, R. P., Yu, P. L., Seeto, S. & Ferenci, T. (2005). The role of isocitrate lyase and the glyoxylate cycle in Escherichia coli growing under glucose limitation. Research in Microbiology 156, 178–183.CrossRefGoogle Scholar
Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F. & Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Archives of Microbiology 182, 354–363.CrossRefGoogle ScholarPubMed
Sauer, U. & Eikmanns, B. J. (2005). The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiology Reviews 29, 765–794.CrossRefGoogle ScholarPubMed
Wang, Z. X., Bramer, C. O. & Steinbuchel, A. (2003). The glyoxylate bypass of Ralstonia eutropha. FEMS Microbiology Letters 228, 63–71.CrossRefGoogle ScholarPubMed
Atomi, H. (2002). Microbial enzymes involved in carbon dioxide fixation. Journal of Bioscience and Bioengineering 94, 497–505.CrossRefGoogle ScholarPubMed
Campbell, B. J. & Cary, S. C. (2004). Abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents. Applied and Environmental Microbiology 70, 6282–6289.CrossRefGoogle ScholarPubMed
Yamamoto, M., Arai, H., Ishii, M. & Igarashi, Y. (2006). Role of two 2-oxoglutarate:ferredoxin oxidoreductases in Hydrogenobacter thermophilus under aerobic and anaerobic conditions. FEMS Microbiology Letters 263, 189–193.CrossRefGoogle ScholarPubMed
Amend, J. P. & Shock, E. L. (2001). Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiology Reviews 25, 175–243.CrossRefGoogle ScholarPubMed
Battistuzzi, G., D'Onofrio, M., Borsari, M., Sola, M., Macedo, A. L., Moura, J. J. G. & Rodrigues, P. (2000). Redox thermodynamics of low-potential iron-sulfur proteins. Journal of Biological Inorganic Chemistry 5, 748–760.CrossRefGoogle ScholarPubMed
Neijssel, O. M. & Demattos, M. J. T. (1994). The energetics of bacterial growth: a reassessment. Molecular Microbiology 13, 179–182.CrossRefGoogle ScholarPubMed
Schaefer, G., Engelhard, M. & Mueller, V. (1999). Bioenergetics of the Archaea. Microbiology and Molecular Biology Reviews 63, 570–620.Google Scholar
Stockar, U., Maskow, T., Liu, J., Marison, I. W. & Patino, R. (2006). Thermodynamics of microbial growth and metabolism: an analysis of the current situation. Journal of Bacteriology 121, 517–533.Google Scholar
Yumoto, I. (2002). Bioenergetics of alkaliphilic Bacillus spp. Journal of Bioenergetics and Biomembranes 93, 342–353.Google ScholarPubMed
Au, K. M., Barabote, R. D., Hu, K. Y. & Saier, M. H. J. (2006). Evolutionary appearance of H+-translocating pyrophosphatases. Microbiology-UK 152, 1243–1247.CrossRefGoogle ScholarPubMed
Barriuso-Iglesias, M., Barreiro, C., Flechoso, F. & Martin, J. F. (2006). Transcriptional analysis of the F0F1 ATPase operon of Corynebacterium glutamicum ATCC 13032 reveals strong induction by alkaline pH. Microbiology-UK 152, 11–21.CrossRefGoogle ScholarPubMed
Brusilow, W. S. A. (1993). Assembly of the Escherichia coli F1Fo ATPase, a large multimeric membrane-bound enzyme. Molecular Microbiology 9, 419–424.CrossRefGoogle Scholar
Capaldi, R. & Aggeler, R. (2002). Mechanism of the F1Fo-type ATP synthase, a biological rotary motor. Trends in Biochemical Sciences 27, 154–160.CrossRefGoogle Scholar
Deckershebestreit, G. & Altendorf, K. (1996). The F1Fo-type ATP synthases of bacteria: structure and function of the Fo complex. Annual Review of Microbiology 50, 791–824.CrossRefGoogle Scholar
Dimroth, P. & Cook, G. M. (2004). Bacterial Na+- or H+-coupled ATP synthases operating at low electrochemical potential. Advances in Microbial Physiology 49, 175–218.CrossRefGoogle ScholarPubMed
Ferguson, S. A., Keis, S. & Cook, G. M. (2006). Biochemical and molecular characterization of a Na+-translocating F1Fo-ATPase from the thermoalkaliphilic bacterium Clostridium paradoxum. Journal of Bacteriology 188, 5045–5054.CrossRefGoogle ScholarPubMed
Iida, T., Inatomi, K., Kamagata, Y. & Maruyama, T. (2002). F- and V-type ATPases in the hyperthermophilic bacterium Thermotoga neapolitana. Extremophiles 6, 369–375.CrossRefGoogle ScholarPubMed
Kinosita, K. Jr., Adachi, K., & Itoh, H. (2004). Rotation of F1-ATPase: how an ATP-driven molecular machine may work. Annual Review of Biophysics and Biomolecular Structure 33, 245–268.CrossRefGoogle ScholarPubMed
Lapierre, P., Shial, R. & Gogarten, J. P. (2006). Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species. Systematic and Applied Microbiology 29, 15–23.CrossRefGoogle Scholar
Muller, V., Lemker, T., Lingl, A., Weidner, C., Coskun, U. & Gruber, G. (2005). Bioenergetics of archaea: ATP synthesis under harsh environmental conditions. Journal of Molecular Microbiology and Biotechnology 10, 167–180.CrossRefGoogle ScholarPubMed
Noda, S., Takezawa, Y., Mizutani, T., Asakura, T., Nishiumi, E., Onoe, K., Wada, M., Tomita, F., Matsushita, K. & Yokota, A. (2006). Alterations of cellular physiology in Escherichia coli in response to oxidative phosphorylation impaired by defective F1-ATPase. Journal of Bacteriology 188, 6869–6876.CrossRefGoogle ScholarPubMed
Pitryuk, A. V. & Pusheva, M. A. (2001). Different ionic specificities of ATP synthesis in extremely alkaliphilic sulfate-reducing and acetogenic bacteria. Microbiology-Moscow 70, 398–402.CrossRefGoogle Scholar
Schafer, I. B., Bailer, S. M., Duser, M. G., Borsch, M., Bernal, R. A., Stock, D. & Gruber, G. (2006). Crystal structure of the archaeal A1Ao ATP synthase subunit B from Methanosarcina mazei Go1: implications of nucleotide-binding differences in the major A1Ao subunits A and B. Journal of Molecular Biology 358, 725–740.CrossRefGoogle ScholarPubMed
Arnold, C. N., McElhanon, J., Lee, A., Leonhart, R. & Siegele, D. A. (2001). Global analysis of Escherichia coli gene expression during the acetate-induced acid tolerance response. Journal of Bacteriology 183, 2178–2186.CrossRefGoogle ScholarPubMed
Azcarate-Peril, M. A., Altermann, E., Hoover-Fitzula, R. L., Cano, R. J. & Klaenhammer, T. R. (2004). Identification and inactivation of genetic loci involved with Lactobacillus acidophilus acid tolerance. Applied and Environmental Microbiology 70, 5315–5322.CrossRefGoogle ScholarPubMed
Cotter, P. D. & Hill, C. (2003). Surviving the acid test: responses of Gram-positive bacteria to low pH. Microbiology and Molecular Biology Reviews 67, 429–453.CrossRefGoogle ScholarPubMed
Dover, N. & Padan, E. (2001). Transcription of nhaA, the main Na+/H+ antiporter of Escherichia coli, is regulated by Na+ and growth phase. Journal of Bacteriology 183, 644–653.CrossRefGoogle ScholarPubMed
Flythe, M. D. & Russell, J. B. (2005). The ability of acidic pH, growth inhibitors, and glucose to increase the proton motive force and energy spilling of amino acid-fermenting Clostridium sporogenes MD1 cultures. Archives of Microbiology 183, 236–242.CrossRefGoogle ScholarPubMed
Foster, J. W. (1999). When protons attack: microbial strategies of acid adaptation. Current Opinion in Microbiology 2, 170–174.CrossRefGoogle ScholarPubMed
Fozoa, E. M., Kajfasza, J. K. & Quivey, R. G. Jr. (2004). Low pH-induced membrane fatty acid alterations in oral bacteria. FEMS Microbiology Letters 238, 291–295.CrossRefGoogle Scholar
Herz, K., Vimont, S., Padan, E. & Berche, P. (2003). Roles of NhaA, NhaB, and NhaD Na+/H+ antiporters in survival of Vibrio cholerae in a saline environment. Journal of Bacteriology 185, 1236–1244.CrossRefGoogle Scholar
Hunte, C., Screpanti, E., Venturi, M., Rimon, A., Padan, E. & Michel, H. (2005). Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH. Nature 435, 1197–1202.CrossRefGoogle ScholarPubMed
Kieboom, J. & Abee, T. (2006). Arginine-dependent acid resistance in Salmonella enterica serovar typhimurium. Journal of Bacteriology 188, 5650–5653.CrossRefGoogle ScholarPubMed
Kim, J. S., Sung, M. H., Kho, D. H. & Lee, J. K. (2005). Induction of manganese-containing superoxide dismutase is required for acid tolerance in Vibrio vulnificus. Journal of Bacteriology 187, 5984–5995.CrossRefGoogle ScholarPubMed
Kitada, M., Kosono, S. & Kudo, T. (2000). The Na+/H+ antiporter of alkaliphilic Bacillus sp. Extremophiles 4, 253–258.CrossRefGoogle ScholarPubMed
Leaphart, A. B., Thompson, D. K., Huang, K., Alm, E., Wan, X. F., Arkin, A., Brown, S. D., Wu, L., Yan, T., Liu, X., Wickham, G. S. & Zhou, J. (2006). Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH. Journal of Bacteriology 188, 1633–1642.CrossRefGoogle ScholarPubMed
Liu, J., Xue, Y., Wang, Q., Wei, Y., Swartz, T. H., Hicks, D. B., Ito, M., Ma, Y. & Krulwich, T. A. (2005). The activity profile of the NhaD-type Na+(Li+)/H+ antiporter from the soda lake haloalkaliphile Alkalimonas amylolytica is adaptive for the extreme environment. Journal of Bacteriology 187, 7589–7595.CrossRefGoogle ScholarPubMed
Ma, Z., Richard, H., Tucker, D. L., Conway, T. & Foster, J. W. (2002). Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW). Journal of Bacteriology 184, 7001–7012.CrossRefGoogle Scholar
Ma, Z., Gong, S., Richard, H., Tucker, D. L., Conway, T. & Foster, J. W. (2003). GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12. Molecular Microbiology 49, 1309–1320.CrossRefGoogle ScholarPubMed
Ma, Z., Richard, H. & Foster, J. W. (2003). pH-dependent modulation of cyclic AMP levels and GadW-dependent repression of RpoS affect synthesis of the GadX regulator and Escherichia coli acid resistance. Journal of Bacteriology 185, 6852–6859.CrossRefGoogle ScholarPubMed
Martin-Galiano, A. J., Overweg, K., Ferrandiz, M. J., Reuter, M., Wells, J. M. & Campa, A. G. (2005). Transcriptional analysis of the acid tolerance response in Streptococcus pneumoniae. Microbiology-UK 151, 3935–3946.CrossRefGoogle ScholarPubMed
Miwa, T., Abe, T., Fukuda, S., Ohkawara, S. & Hino, T. (2001). Regulation of H+-ATPase synthesis in response to reduced pH in ruminal bacteria. Current Microbiology 42, 106–110.CrossRefGoogle ScholarPubMed
Padan, E., Tzubery, T., Herz, K., Kozachkov, L., Rimon, A. & Galili, L. (2004). NhaA of Escherichia coli, as a model of a pH-regulated Na+/H+antiporter. Biochimica et Biophysica Acta – Bioenergetics 1658, 2–13.CrossRefGoogle ScholarPubMed
Padan, E., Bibi, E., Ito, M. & Krulwich, T. A. (2005). Alkaline pH homeostasis in bacteria: new insights. Biochimica et Biophysica Acta – Biomembranes 1717, 67–88.CrossRefGoogle ScholarPubMed
Palmer, G. & Reedijk, J. (1992). Nomenclature of electron-transfer proteins. Recommendations 1989. Journal of Biological Chemistry 267, 665–677.Google Scholar
Rhee, J. E., Kim, K. S. & Choi, S. H. (2005). CadC activates pH-dependent expression of the Vibrio vulnificus cadBA operon at a distance through direct binding to an upstream region. Journal of Bacteriology 187, 7870–7875.CrossRefGoogle Scholar
Rhee, J. E., Jeong, H. G., Lee, J. H. & Choi, S. H. (2006). AphB influences acid tolerance of Vibrio vulnificus by activating expression of the positive regulator CadC. Journal of Bacteriology 188, 6490–6497.CrossRefGoogle ScholarPubMed
Small, P. L. & Waterman, S. R. (1998). Acid stress, anaerobiosis and gadCB: lessons from Lactococcus lactis and Escherichia coli. Trends in Microbiology 6, 214–216.CrossRefGoogle ScholarPubMed
Bott, M. & Niebisch, A. (2003). The respiratory chain of Corynebacterium glutamicum. Journal of Biotechnology 104, 129–153.CrossRefGoogle ScholarPubMed
Branden, G., Gennis, R. B. & Brzezinski, P. (2006). Transmembrane proton translocation by cytochrome c oxidase. Biochimica et Biophysica Acta – Bioenergetics 1757, 1052–1063.CrossRefGoogle ScholarPubMed
Brandt, U. (2006). Energy converting NADH:quinone oxidoreductase (complex I). Annual Review of Biochemistry 75, 69–92.CrossRefGoogle Scholar
Brandt, U. & Trumpower, B. (1994). The protonmotive Q cycle in mitochondria and bacteria. Critical Reviews in Biochemistry and Molecular Biology 29, 165–197.CrossRefGoogle ScholarPubMed
Brzezinski, P. & Adelroth, P. (2006). Design principles of proton-pumping haem-copper oxidases. Current Opinion in Structural Biology 16, 465–472.CrossRefGoogle ScholarPubMed
Brzezinski, P. & Larsson, G. (2003). Redox-driven proton pumping by heme-copper oxidases. Biochimica et Biophysica Acta – Bioenergetics 1605, 1–13.CrossRefGoogle ScholarPubMed
Cosseau, C. & Batut, J. (2004). Genomics of the ccoNOQP-encoded cbb 3 oxidase complex in bacteria. Archives of Microbiology 181, 89–96.CrossRefGoogle Scholar
Crofts, A. R. (2004). The cytochrome bc1 complex: function in the context of structure. Annual Review of Physiology 66, 689–733.CrossRefGoogle ScholarPubMed
Crofts, A. R., Lhee, S., Crofts, S. B., Cheng, J. & Rose, S. (2006). Proton pumping in the bc1 complex: a new gating mechanism that prevents short circuits. Biochimica et Biophysica Acta – Bioenergetics 1757, 1019–1034.CrossRefGoogle ScholarPubMed
Degier, J. W. L., Lubben, M., Reijnders, W. N. M., Tipker, C. A., Slotboom, D. J., Vanspanning, R. J. M., Stouthamer, A. H. & Vanderoost, J. (1994). The terminal oxidases of Paracoccus denitrificans. Molecular Microbiology 13, 183–196.CrossRefGoogle Scholar
Faxen, K., Gilderson, G., Adelroth, P. & Brzezinski, P. (2005). A mechanistic principle for proton pumping by cytochrome c oxidase. Nature 437, 286–289.CrossRefGoogle ScholarPubMed
Friedrich, T. & Bottcher, B. (2004). The gross structure of the respiratory complex I: a Lego System. Biochimica et Biophysica Acta – Bioenergetics 1608, 1–9.CrossRefGoogle ScholarPubMed
Hickman, J. W., Barber, R. D., Skaar, E. P. & Donohue, T. J. (2002). Link between the membrane-bound pyridine nucleotide transhydrogenase and glutathione-dependent processes in Rhodobacter sphaeroides. Journal of Bacteriology 184, 400–409.CrossRefGoogle ScholarPubMed
Hinsley, A. P. & Berks, B. C. (2002). Specificity of respiratory pathways involved in the reduction of sulfur compounds by Salmonella enterica. Microbiology-UK 148, 3631–3638.CrossRefGoogle ScholarPubMed
Hosler, J. P., Ferguson-Miller, S. & Mills, D. A. (2006). Energy transduction: proton transfer through the respiratory complexes. Annual Review of Biochemistry 75, 165–187.CrossRefGoogle ScholarPubMed
Hunte, C., Palsdottir, H. & Trumpower, B. L. (2003). Protonmotive pathways and mechanisms in the cytochrome bc1 complex. FEBS Letters 545, 39–46.CrossRefGoogle ScholarPubMed
Ishikawa, R., Ishido, Y., Tachikawa, A., Kawasaki, H., Matsuzawa, H. & Wakagi, T. (2002). Aeropyrum pernix K1, a strictly aerobic and hyperthermophilic archaeon, has two terminal oxidases, cytochrome ba3 and cytochrome aa3. Archives of Microbiology 179, 42–49.CrossRefGoogle ScholarPubMed
Johnson, D. C., Dean, D. R., Smith, A. D. & Johnson, M. K. (2005). Structure, function and formation of iron-sulfur clusters. Annual Review of Biochemistry 74, 247–281.CrossRefGoogle ScholarPubMed
Lalucque, H. & Silar, P. (2003). NADPH oxidase: an enzyme for multicellularity? Trends in Microbiology 11, 9–12.CrossRefGoogle ScholarPubMed
Lanyi, J. K. & Pohorille, A. (2001). Proton pumps: mechanism of action and applications. Trends in Biotechnology 19, 140–144.CrossRefGoogle ScholarPubMed
Link, T. A. (1997). The role of the ‘Rieske’ iron sulfur protein in the hydroquinone oxidation (QP) site of the cytochrome bc1 complex. The ‘proton-gated affinity change’ mechanism. FEBS Letters 412, 257–264.CrossRefGoogle Scholar
Ludwig, R. A. (2004). Microaerophilic bacteria transduce energy via oxidative metabolic gearing. Research in Microbiology 155, 61–70.CrossRefGoogle ScholarPubMed
Melo, A., Bandeiras, T. & Teixeira, M. (2004). New insights into Type II NAD(P)H:quinone oxidoreductases. Microbiology and Molecular Biology Reviews 68, 603–616.CrossRefGoogle ScholarPubMed
Mendz, G. L., Smith, M. A., Finel, M. & Korolik, V. (2000). Characteristics of the aerobic respiratory chains of the microaerophiles Campylobacter jejuni and Helicobacter pylori. Archives of Microbiology 174, 1–10.Google Scholar
Minohara, S., Sakamoto, J. & Sone, N. (2002). Improved H+/O ratio and cell yield of Escherichia coli with genetically altered terminal quinol oxidases. Journal of Bioscience and Bioengineering 93, 464–469.CrossRefGoogle ScholarPubMed
Morales, G., Ugidos, A. & Rojo, F. (2006). Inactivation of the Pseudomonas putida cytochrome o ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases. Environmental Microbiology 8, 1764–1774.CrossRefGoogle ScholarPubMed
Mulkidjanian, A. Y. (2005). Ubiquinol oxidation in the cytochrome bc1 complex: reaction mechanism and prevention of short-circuiting. Biochimica et Biophysica Acta – Bioenergetics 1709, 5–34.CrossRefGoogle ScholarPubMed
Osyczka, A., Moser, C. C. & Dutton, P. L. (2005). Fixing the Q cycle. Trends in Biochemical Sciences 30, 176–182.CrossRefGoogle ScholarPubMed
Otten, M. F., Stork, D. R., Reijnders, W. N. M., Westerhoff, H. V. & Spanning, R. J. M. (2001). Regulation of expression of terminal oxidases in Paracoccus denitrificans. European Journal of Biochemistry 268, 2486–2497.CrossRefGoogle ScholarPubMed
Rich, P. R. (1986). A perspective on Q-cycles. Journal of Bioenergetics and Biomembranes 18, 145–156.CrossRefGoogle ScholarPubMed
Rich, P. R. (2004). The quinone chemistry of bc complexes. Biochimica et Biophysica Acta – Bioenergetics 1658, 165–171.CrossRefGoogle ScholarPubMed
Richardson, D. J. (2000). Bacterial respiration: a flexible process for a changing environment. Microbiology-UK 146, 551–571.CrossRefGoogle ScholarPubMed
Schneider, D. & Schmidt, C. L. (2005). Multiple Rieske proteins in prokaryotes: where and why? Biochimica et Biophysica Acta – Bioenergetics 1710, 1–12.CrossRefGoogle Scholar
Shimada, H., Shida, Y., Nemoto, N., Oshima, T. & Yamagishi, A. (2001). Quinone profiles of Thermoplasma acidophilum HO-62. Journal of Bacteriology 183, 1462–1465.CrossRefGoogle ScholarPubMed
Snyder, C. H., Merbitz-Zahradnik, T., Link, T. A. & Trumpower, B. L. (1999). Role of the Rieske iron-sulfur protein midpoint potential in the protonmotive Q-cycle mechanism of the cytochrome bc1 complex. Journal of Bioenergetics and Biomembranes 31, 235–242.CrossRefGoogle ScholarPubMed
Trumpower, B. L. & Gennis, R. B. (1994). Energy transduction by cytochrome complexes in mitochondrial and bacterial respiration: the enzymology of coupling electron transfer reactions to transmembrane proton translocation. Annual Review of Biochemistry 63, 675–716.CrossRefGoogle ScholarPubMed
Wikstrom, M. & Verkhovsky, M. I. (2006). Towards the mechanism of proton pumping by the haem-copper oxidases. Biochimica et Biophysica Acta – Bioenergetics 1757, 1047–1051.CrossRefGoogle ScholarPubMed
Williams, H. D., Zlosnik, J. E. A. & Ryall, B. (2006). Oxygen, cyanide and energy generation in the cystic fibrosis pathogen Pseudomonas aeruginosa. Advances in Microbial Physiology 52, 1–71.CrossRefGoogle Scholar
Zlosnik, J. E. A., Tavankar, G. R., Bundy, J. G., Mossialos, D., O'Toole, R. & Williams, H. D. (2006). Investigation of the physiological relationship between the cyanide-insensitive oxidase and cyanide production in Pseudomonas aeruginosa. Microbiology-UK 152, 1407–1415.CrossRefGoogle ScholarPubMed
Abe, K., Ohnishi, F., Yagi, K., Nakajima, T., Higuchi, T., Sano, M., Machida, M., Sarker, R. I. & Maloney, P. C. (2002). Plasmid-encoded asp operon confers a proton motive metabolic cycle catalyzed by an aspartate-alanine exchange reaction. Journal of Bacteriology 184, 2906–2913.CrossRefGoogle ScholarPubMed
Dimroth, P. & Schink, B. (1998). Energy conservation in the decarboxylation of dicarboxylic acids in fermenting bacteria. Archives of Microbiology 170, 69–77.CrossRefGoogle ScholarPubMed
Gregory, K. B., Bond, D. R. & Lovley, D. R. (2004). Graphite electrodes as electron donors for anaerobic respiration. Environmental Microbiology 6, 596–604.CrossRefGoogle ScholarPubMed
Iyer, R., Williams, C. & Miller, C. (2003). Arginine-agmatine antiporter in extreme acid resistance in Escherichia coli. Journal of Bacteriology 185, 6556–6561.CrossRefGoogle ScholarPubMed
Kroger, A., Geisler, V., Lemma, E., Theis, F. & Lenger, R. (1992). Bacterial fumarate respiration. Archives of Microbiology 158, 311–314.CrossRefGoogle Scholar
Okane, D. J. & Prasher, D. C. (1992). Evolutionary origins of bacterial bioluminescence. Molecular Microbiology 6, 443–449.CrossRefGoogle Scholar
Poolman, B. (1993). Energy transduction in lactic acid bacteria. FEMS Microbiology Reviews 12, 125–147.CrossRefGoogle ScholarPubMed
Wolken, W. A. M., Lucas, P. M., Lonvaud-Funel, A. & Lolkema, J. S. (2006). The mechanism of the tyrosine transporter TyrP supports a proton motive tyrosine decarboxylation pathway in Lactobacillus brevis. Journal of Bacteriology 188, 2198–2206.CrossRefGoogle ScholarPubMed

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