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Xavier JC, Hordijk W, Kauffman S, Steel M, Martin WF. Autocatalytic chemical networks at the origin of metabolism. Proc Biol Sci 2020; 287:20192377. [PMID: 32156207 PMCID: PMC7126077 DOI: 10.1098/rspb.2019.2377] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022] Open
Abstract
Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is lacking. Here, we identify reflexively autocatalytic food-generated networks (RAFs)-self-sustaining networks that collectively catalyse all their reactions-embedded within microbial metabolism. RAFs in the metabolism of ancient anaerobic autotrophs that live from H2 and CO2 provided with small-molecule catalysts generate acetyl-CoA as well as amino acids and bases, the monomeric components of protein and RNA, but amino acids and bases without organic catalysts do not generate metabolic RAFs. This suggests that RAFs identify attributes of biochemical origins conserved in metabolic networks. RAFs are consistent with an autotrophic origin of metabolism and furthermore indicate that autocatalytic chemical networks preceded proteins and RNA in evolution. RAFs uncover intermediate stages in the emergence of metabolic networks, narrowing the gaps between early Earth chemistry and life.
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Affiliation(s)
- Joana C. Xavier
- Institut für Molekulare Evolution, Heinrich Heine Universität, 40225 Düsseldorf, Germany
| | - Wim Hordijk
- Konrad Lorenz Institute for Evolution and Cognition Research, 3400 Klosterneuburg, Austria
| | | | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch 8041, New Zealand
| | - William F. Martin
- Institut für Molekulare Evolution, Heinrich Heine Universität, 40225 Düsseldorf, Germany
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
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Abstract
Growth of Methanobacterium thermoautotrophicum, an anaerobic archaebacterium using methanogenesis as the catabolic pathway, is characterized by large heat production rates, up to 13 W g-1, and low biomass yields, in the order of 0.02 C-mol mol-1 H2 consumed. These values, indicating a possibly "inefficient" growth mechanism, warrant a thermodynamic analysis to obtain a better understanding of the growth process. The growth-associated heat production (DeltarHX0, min) and the growth-associated Gibbs energy dissipation per mol biomass formed (DeltarGXmin) were -3730 kJ C-mol-1 and -802 kJ C-mol-1, respectively. The Gibbs energy change found in this study is indeed unusually high as compared to aerobic methylotrophes, but not untypical for methanogens grown on CO2. It explains the low biomass yield. Based on the information available on the energetic metabolism and on an ATP balance, the biomass yield can be predicted to be approximately in the range of the experimentally determined value. The fact that the exothermicity exceeds vastly even the Gibbs energy change can be explained by a dramatic entropy decrease of the catabolic reaction. Microbial growth characterized by entropy reduction and correspondingly by unusually large heat production may be called entropy-retarded growth. Copyright 1999 John Wiley & Sons, Inc.
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Affiliation(s)
- NA Schill
- Institute of Chemical Engineering, Swiss Federal Institute of Technology Lausanne (EPFL),CH-1015 Lausanne, Switzerland
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3
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Strevett KA, Vieth RF, Grasso D. Chemo-autotrophic biogas purification for methane enrichment: mechanism and kinetics. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0923-0467(95)06095-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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4
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Choquet CG, Richards JC, Patel GB, Sprott GD. Ribose biosynthesis in methanogenic bacteria. Arch Microbiol 1994. [DOI: 10.1007/bf00307768] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Eisenreich W, Schwarzkopf B, Bacher A. Biosynthesis of nucleotides, flavins, and deazaflavins in Methanobacterium thermoautotrophicum. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)92866-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
Methanosarcina barkeri
MS and 227 and
Methanosarcina mazei
S-6 produced acetate when grown on H
2
-CO
2
, methanol, or trimethylamine. Marked differences in acetate production by the two bacterial species were found, even though methane and cell yields were nearly the same.
M. barkeri
produced 30 to 75 μmol of acetate per mmol of CH
4
formed, but
M. mazei
produced only 8 to 9 μmol of acetate per mmol of CH
4
.
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Affiliation(s)
- P Westermann
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of California at Los Angeles, Los Angeles, California 90024
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8
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Abstract
To detect autotrophic CO2 assimilation in cell extracts of Methanococcus maripaludis, lactate dehydrogenase and NADH were added to convert pyruvate formed from autotrophically synthesized acetyl coenzyme A to lactate. The lactate produced was determined spectrophotometrically. When CO2 fixation was pulled in the direction of lactate synthesis, CO2 reduction to methane was inhibited. Bromoethanesulfonate (BES), a potent inhibitor of methanogenesis, enhanced lactate synthesis, and methyl coenzyme M inhibited it in the absence of BES. Lactate synthesis was dependent on CO2 and H2, but H2 + CO2-independent synthesis was also observed. In cell extracts, the rate of lactate synthesis was about 1.2 nmol min-1 mg of protein-1. When BES was added, the rate of lactate synthesis increased to 2.3 nmol min-1 mg of protein-1. Because acetyl coenzyme A did not stimulate lactate synthesis, pyruvate synthase may have been the limiting activity in these assays. Radiolabel from 14CO2 was incorporated into lactate. The percentages of radiolabel in the C-1, C-2, and C-3 positions of lactate were 73, 33, and 11%, respectively. Both carbon monoxide and formaldehyde stimulated lactate synthesis. 14CH2O was specifically incorporated into the C-3 of lactate, and 14CO was incorporated into the C-1 and C-2 positions. Low concentrations of cyanide also inhibited autotrophic growth, CO dehydrogenase activity, and autotrophic lactate synthesis. These observations are in agreement with the acetogenic pathway of autotrophic CO2 assimilation.
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Affiliation(s)
- J Shieh
- Department of Microbiology, University of Georgia, Athens 30602
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9
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ROBERTS MARYF, EVANS JEREMYNS, TOLMAN CYNTHIAJ, RALEIGH DANIELP. NMR Studies of Methanogens: What Good Is a Cyclic Pyrophosphate? Ann N Y Acad Sci 1987. [DOI: 10.1111/j.1749-6632.1987.tb32891.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Schauder R, Widdel F, Fuchs G. Carbon assimilation pathways in sulfate-reducing bacteria II. Enzymes of a reductive citric acid cycle in the autotrophic Desulfobacter hydrogenophilus. Arch Microbiol 1987. [DOI: 10.1007/bf00414815] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Bonam D, Ludden P. Purification and characterization of carbon monoxide dehydrogenase, a nickel, zinc, iron-sulfur protein, from Rhodospirillum rubrum. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61456-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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12
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Länge S, Fuchs G. Autotrophic synthesis of activated acetic acid from CO2 in Methanobacterium thermoautotrophicum. Synthesis from tetrahydromethanopterin-bound C1 units and carbon monoxide. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 163:147-54. [PMID: 3102234 DOI: 10.1111/j.1432-1033.1987.tb10748.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The synthesis of acetyl-CoA from CO2, H2, and various C1 compounds was studied in vitro with extracts and with protein fractions of Methanobacterium thermoautotrophicum. Acetyl-CoA synthesis from CO2 and H2 by extracts required CO2 reduction to CH4 to proceed. Both processes were highly stimulated by formaldehyde which served as the carbon precursor of both CH4 and the CH3 group of acetate. Carbon monoxide in combination with formaldehyde dramatically stimulated the acetyl-CoA synthesis up to 150-fold. In this system, which did not require CO2 reduction to the formaldehyde and CO level, acetyl-CoA synthesis was no longer dependent on CH4 formation. The soluble (100,000 X g supernatant) cell protein was resolved into a protein fraction [45-60% (NH4)2SO4-fraction] which catalyzed acetyl-CoA synthesis at a specific rate of 15 nmol X min-1 X (equivalent of mg cell protein)-1 (60 degrees C). This oxygen-sensitive enzyme reaction required dithioerythritol for activity and was strictly dependent on coenzyme A, CO, and N5,N10-methylene tetrahydromethanopterin, N5-methyl tetrahydromethanopterin or formaldehyde plus tetrahydromethanopterin. The incorporation of formaldehyde is explained by the spontaneous formation of methylene tetrahydromethanopterin. The product of the reaction, acetyl-CoA, was quantitatively derived from CO (carboxyl of acetate) and a C1 derivative of tetrahydromethanopterin (methyl of acetate). The C1 derivative of tetrahydromethanopterin could not be replaced by a C1 derivative of tetrahydrofolate or by methyl-coenzyme M; ATP was not required. The active protein fraction contained CO dehydrogenase and at least on corrinoid protein. These results provide strong biochemical arguments for the proposed mechanism of autotrophic acetyl-CoA synthesis in Methanobacterium.
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14
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Schauder R, Eikmanns B, Thauer RK, Widdel F, Fuchs G. Acetate oxidation to CO2 in anaerobic bacteria via a novel pathway not involving reactions of the citric acid cycle. Arch Microbiol 1986. [DOI: 10.1007/bf00446775] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Evans JN, Tolman CJ, Roberts MF. Indirect observation by 13C NMR spectroscopy of a novel CO2 fixation pathway in methanogens. Science 1986; 231:488-91. [PMID: 3079919 DOI: 10.1126/science.3079919] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
High-field carbon-13 nuclear magnetic resonance (NMR) spectroscopy has been used to monitor the isotopic dilution of doubly carbon-13-labeled precursors for 2,3-cyclopyrophosphoglycerate, a novel primary metabolite that occurs in certain methanogens. A unique carbon dioxide fixation pathway that gives rise to asymmetric labeling of acetyl coenzyme A has been demonstrated in Methanobacterium thermoautotrophicum. The effect of selected metabolic inhibitors on the labeled species in the pathway has been examined by NMR. These techniques establish a general, sensitive method for the delineation of convergent biosynthetic pathways.
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19
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Wood HG, Ragsdale SW, Pezacka E. The acetyl-CoA pathway: a newly discovered pathway of autotrophic growth. Trends Biochem Sci 1986. [DOI: 10.1016/0968-0004(86)90223-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Bott MH, Eikmanns B, Thauer RK. Defective formation and/or utilization of carbon monoxide in H2/CO2 fermenting methanogens dependent on acetate as carbon source. Arch Microbiol 1985. [DOI: 10.1007/bf00411248] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Jansen K, Fuchs G, Thauer RK. Autotrophic CO2fixation byDesulfovibrio baarsii: Demonstration of enzyme activities characteristic for the acetyl-CoA pathway. FEMS Microbiol Lett 1985. [DOI: 10.1111/j.1574-6968.1985.tb00812.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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22
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R�hlemann M, Ziegler K, Stupperich E, Fuchs G. Detection of acetyl coenzyme A as an early CO2 assimilation intermediate in Methanobacterium. Arch Microbiol 1985. [DOI: 10.1007/bf00428856] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Autotrophic synthesis of activated acetic acid from two CO2 in Methanobacterium thermoautotrophicum. Arch Microbiol 1985. [DOI: 10.1007/bf00408064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Smith MR, Lequerica JL, Hart MR. Inhibition of methanogenesis and carbon metabolism in Methanosarcina sp. by cyanide. J Bacteriol 1985; 162:67-71. [PMID: 3980448 PMCID: PMC218954 DOI: 10.1128/jb.162.1.67-71.1985] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
NaCN was tested for its inhibitory effects on growth of and metabolism by Methanosarcina barkeri 227. NaCN (10 microM) inhibited catabolism of acetate methyl groups to CH4 and CO2 but did not inhibit methanogenesis from methanol, CO2, methylamine, or trimethylamine. NaCN also inhibited the assimilation of methanol or CO2 (as the sole carbon source) into cell carbon and stimulated the assimilation of acetate. These results suggest that inhibition by NaCN was a result of its action as an inhibitor of in vivo CO dehydrogenase. The results also implicate CO dehydrogenase in the oxidation of acetate but not methanol methyl groups to CO2.
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25
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Länge S, Fuchs G. Tetrahydromethanopterin, a coenzyme involved in autotrophic acetyl coenzyme A synthesis from 2 CO 2in Methanobacterium. FEBS Lett 1985. [DOI: 10.1016/0014-5793(85)80281-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Eikmanns B, Fuchs G, Thauer RK. Formation of carbon monoxide from CO2 and H2 by Methanobacterium thermoautotrophicum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 146:149-54. [PMID: 3917916 DOI: 10.1111/j.1432-1033.1985.tb08631.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cell suspensions of Methanobacterium thermoautotrophicum were found to reduce CO2 with H2 to CO at a maximal rate of 100 nmol X min-1 X mg protein-1. Half-maximal rates were obtained at a H2 and a CO2 concentration in the gas phase of 10% and 30%, respectively. The CO concentration in the gas phase surpassed the equilibrium concentration by a factor of more than 15 which indicates that CO2 reduction with H2 to CO was energy-driven. This was substantiated by the observation that the cells only formed CO when they also generated methane and that CO formation was completely inhibited by uncouplers. CO formation by cell suspensions and by growing cells was inhibited by cyanide. Neither methane formation nor the electrochemical proton potential were affected by this inhibitor. Cyanide was shown to inactivate specifically the carbon monoxide dehydrogenase present in M. thermoautotrophicum. It is therefore concluded that reduction of CO2 to CO is catalyzed by this enzyme. CO production by growing cells was 5-10-times slower than by resting cells. This is explained by effective CO assimilation in growing cells; when CO assimilation was inhibited by propyl iodide the rate of CO production immediately increased more than tenfold.
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27
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Stupperich E, Fuchs G. Autotrophic synthesis of activated acetic acid from two CO2 inMethanobacterium thermoautotrophicum. Arch Microbiol 1984. [DOI: 10.1007/bf00692705] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Jansen K, Thauer RK, Widdel F, Fuchs G. Carbon assimilation pathways in sulfate reducing bacteria. Formate, carbon dioxide, carbon monoxide, and acetate assimilation by Desulfovibrio baarsii. Arch Microbiol 1984. [DOI: 10.1007/bf00402132] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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