Abstract
The tricarboxylic acid (TCA) cycle is an energy-producing pathway for aerobic organisms. However, it is widely accepted that the phylogenetic origin of the TCA cycle is the reductive TCA cycle, which is a non-Calvin-type carbon-dioxide-fixing pathway. Most of the enzymes responsible for the oxidative and reductive TCA cycles are common to the two pathways, the difference being the direction in which the reactions operate. Because the reductive TCA cycle operates in an energetically unfavorable direction, some specific mechanisms are required for the reductive TCA-cycle-utilizing organisms. Recently, the molecular mechanism for the “citrate cleavage reaction” and the “reductive carboxylating reaction from 2-oxoglutarate to isocitrate” in Hydrogenobacter thermophilus have been demonstrated. Both of these reactions comprise two distinct consecutive reactions, each catalyzed by two novel enzymes. Sequence analyses of the newly discovered enzymes revealed phylogenetic and functional relationships between other TCA-cycle-related enzymes. The occurrence of novel enzymes involved in the citrate-cleaving reaction seems to be limited to the family Aquificaceae. In contrast, the key enzyme in the reductive carboxylation of 2-oxoglutarate appears to be more widely distributed in extant organisms. The four newly discovered enzymes have a number of potential biotechnological applications.
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Acca M, Bocchetta M, Ceccarelli E, Creti R, Stetter KO, Cammarano P (1994) Updating mass and composition of archaeal and bacterial ribosomes: archaeal-like features of ribosomes from the deep-branching bacterium Aquifex pyrophilus. Syst Appl Microbiol 16:629–637
Adams IP, Dack S, Dickinson M, Ratledge C (2002) The distinctiveness of ATP:citrate lyase from Aspergillus nidulans. Biochim Biophys Acta 1597:36–41
Antranikian G, Herzberg C, Gottschalk G (1982) Characterization of ATP citrate lyase from Chlorobium limicola. J Bacteriol 152:1284–1287
Aoshima M, Igarashi Y (2006) A novel oxalosuccinate-forming enzyme involved in the reductive carboxylation of 2-oxoglutarate in Hydrogenobacter thermophilus TK-6. Mol Microbiol 62:748–759
Aoshima M, Ishii M, Igarashi Y (2004a) A novel enzyme, citryl-CoA synthetase, catalysing the first step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6. Mol Microbiol 52:751–761
Aoshima M, Ishii M, Igarashi Y (2004b) A novel enzyme, citryl-CoA lyase, catalysing the second step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6. Mol Microbiol 52:763–770
Aoshima M, Ishii M, Igarashi Y (2004c) A novel biotin protein required for reductive carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6. Mol Microbiol 51:791–798
Beh M, Strauss G, Huber R, Stetter KO, Fuchs G (1993) Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus. Arch Microbiol 160:306–311
Buckel W, Lenz H, Wunderwald P, Buschmeier V, Eggerer H, Gottschalk G (1971) Stereochemistry of the citrate-lyase reaction. Eur J Biochem 24:201–206
Buckel W, Ziegert K, Eggerer H (1973) Acetyl-CoA-dependent cleavage of citrate on inactivated citrate lyase. Eur J Biochem 37:295–304
Canfield DE, Teske A (1996) Late Proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies. Nature 382:127–132
Elshourbagy NA, Near JC, Kmetz PJ, Sathe GM, Southan C, Strickler JE, Gross M, Young JF, Wells TNC, Groot PHE (1990) Rat ATP citrate-lyase. Molecular cloning and sequence analysis of a full-length cDNA and mRNA abundance as a function of diet, organ, and age. J Biol Chem 265:1430–1435
Evans MCW, Buchanan BB, Arnon DI (1966) A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Proc Natl Acad Sci USA 55:928–934
Fatland BL, Ke J, Anderson MD, Mentzen WI, Cui LW, Allred CC, Johnston JL, Nikolau BJ, Wurtele ES (2002) Molecular characterization of a heteromeric ATP-citrate lyase that generates cytosolic acetyl-coenzyme A in Arabiodopsis. Plant Physiol 130:740–756
Hatzivassiliou G, Zhao F, Bauer DE, Andreadis C, Shaw AN, Dhanak D, Hingorani SR, Tuveson DA, Thompson CB (2005) ATP citrate lyase inhibition can suppress tumor cell growth. Cancer Cell 8:311–321
House CH, Fitz-Gibbon ST (2002) Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol 54:539–547
Hügler M, Huber H, Stetter KO, Fuchs G (2003) Autotrophic CO2 fixation pathways in archaea (Crenarchaeota). Arch Microbiol 179:160–173
Hügler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM (2005) Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the ɛ subdivision of proteobacteria. J Bacteriol 187:3020–3027
Hügler M, Huber H, Molyneaux SJ, Vetriani C, Sievert SM (2007) Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage. Environ Microbiol 9:81–92
Ivanovsky RN, Sintsov NV, Kondratieva EN (1980) ATP-linked citrate lyase activity in the green sulfur bacterium Chlorobium limicola forma thiosulfatophilum. Arch Microbiol 128:239–241
Kanao T, Fukui T, Atomi H, Imanaka T (2001) ATP-citrate lyase from the green sulfur bacterium Chlorobium limicola is a heteromeric enzyme composed of two distinct gene products. Eur J Biochem 268:1670–1678
Kanao T, Kawamura M, Fukui T, Atomi H, Imanaka T (2002) Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola. Eur J Biochem 269:1926–1931
Keech DB, Mattoo AK, Carabott MJJ, Wallace JC (1976) The ATP-dependent reductive carboxylation of 2-oxoglutarate using cytosol from rat liver. Biochem Biophys Res Commun 71:712–718
Koh HJ, Lee SM, Son BG, Lee SH, Ryoo ZY, Chang KT, Park JW, Park DC, Song BJ, Veech RL, Song H, Huh TL (2004) Cytosolic NADP+-dependent isocitrate dehydrogenase plays a key role in lipid metabolism. J Biol Chem 279:39968–39974
Kurz LC, Shah S, Frieden C, Nakra T, Stein RE, Drysdale GR, Evans CT, Srere PA (1995) Catalytic strategy of citrate synthase: subunit interactions revealed as a consequence of a single amino-acid change in the oxaloacetate binding site. Biochemistry 34:13278–13288
Lenz H, Buckel W, Wunderwald P, Biedermann G, Buschmeier V, Eggerer H, Cornforth JW, Redmond JW, Mallaby R (1971) Stereochemistry of si-citrate synthase and ATP-citrate-lyase reactions. Eur J Biochem 24:207–215
Löhlein G, Eggerer H (1982) Nicotinic acid metabolism: stereochemical course of the (2R, 3S)-2,3-dimethylmalate lyase reaction. Hoppe-Seylers Z Physiol Chem 363:1103–1109
Mattoo AK, Carabott MJJ, Keech DB, Wallace JC (1976) Properties of the isocitrate synthase system from rat liver. Biochem Soc Trans 4:1058–1060
Ochoa S (1948) Biosynthesis of tricarboxylic acids by carbon dioxide fixation, III. Enzymatic mechanisms. J Biol Chem 174:133–157
Pace NR (1991) Origin of life—facing up to the physical settings. Cell 65:531–533
Pearce NJ, Yates JW, Berkhout TA, Jackson B, Tew D, Boyd H, Camilleri P, Sweeney P, Gribble AD, Shaw A, Groot PH (1998) The role of ATP citrate-lyase in the metabolic regulation of plasma lipids. Hypolipidaemic effects of SB-204990, a lactone prodrug of the potent ATP citrate-lyase inhibitor SB-201076. Biochem J 334:113–119
Ross DS (2007) The viability of a nonenzymatic reductive citric acid cycle—kinetics and thermochemistry. Orig Life Evol Biosph 37:61–65
Schauder R, Widdel F, Fuchs G (1987) Carbon assimilation pathways in sulfate-reducing bacteria, II. Enzymes of a reductive citric acid cycle in the autotrophic Desulfobacter hydrogenophilus. Arch Microbiol 148:218–225
Shara M, Ohia SE, Yasmin T, Zardetto-Smith A, Kincaid A, Bagchi M, Chatterjee A, Bagchi D, Stohs SJ (2003) Dose-and time-dependent effects of a novel (−)-hydroxycitric acid extract on body weight, hepatic and testicular lipid peroxidation, DNA fragmentation and histopathological data over a period of 90 days. Mol Cell Biochem 254:339–346
Shashi K, Bachhawat AK, Joseph R (1990) ATP:citrate lyase of Rhodotorula gracilis: purification and properties. Biochim Biophys Acta 1033:23–30
Shiba H, Kawasumi T, Igarashi Y, Kodama T, Minoda Y (1985) The CO2 assimilation via the reductive tricarboxylic acid cycle in an obligately autotrophic, aerobic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus. Arch Microbiol 141:198–203
Siebert G, Carsiotis M, Plaut GWE (1957) The enzymatic properties of isocitric dehydrogenase. J Biol Chem 226:977–991
Singh M, Richards EG, Mukherjee A, Srere PA (1976) Structure of ATP citrate lyase from rat liver. J Biol Chem 251:5242–5250
Speyer JF, Dickman SR (1956) On the mechanism of action of aconitase. J Biol Chem 220:193–208
Srere PA (1961) The citrate cleavage enzyme, II. Stoichiometry substrate specificity and its use for coenzyme A assay. J Biol Chem 236:50–53
Sullivan AC, Singh M, Srere PA, Glusker JP (1977) Reactivity and inhibitor potential of hydroxycitrate isomers with citrate synthase, citrate lyase, and ATP citrate lyase. J Biol Chem 252:7583–7590
Wächtershäuser G (1990) Evolution of the first metabolic cycles. Proc Natl Acad Sci USA 87:200–204
Williams TJ, Zhang CL, Scott JH, Bazylinski DA (2006) Evidence for autotrophy via the reverse tricarboxylic acid cycle in the marine magnetotactic coccus strain MC-1. Appl Environ Microbiol 72:1322–1329
Wunderwald P, Buckel W, Lenz H, Buschmeier V, Eggerer H, Gottschalk G, Cornforth JW, Redmond JW, Mallaby R (1971) Stereochemistry of the re-citrate-synthase reaction. Eur J Biochem 24:216–221
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Aoshima, M. Novel enzyme reactions related to the tricarboxylic acid cycle: phylogenetic/functional implications and biotechnological applications. Appl Microbiol Biotechnol 75, 249–255 (2007). https://doi.org/10.1007/s00253-007-0893-0
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DOI: https://doi.org/10.1007/s00253-007-0893-0