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Wood's Way - Ljungdahl

Acetyl-CoA Recovery Path

The Wood – Ljungdahl path , the Acetyl- CoA pathway, the Wood-Ljungdahl pathway [1] is the metabolic pathway, which is a series of biochemical reactions used by some anaerobic chemolithotrophic bacteria ( acetogens during acetogenesis ) and archaea - in the process of methanogenesis ( methanogenesis ) for fixing CO 2 and generating energy. This path allows organisms to use hydrogen as an electron donor and carbon dioxide as an acceptor and building block for the biosynthesis of organic molecules.

This path describes autotrophic production of an acetyl-CoA molecule from two CO 2 molecules using coenzymes and enzymes with metal-containing centers as CO 2 acceptors [2] [3] [4] [5] . The total reaction of the Wood-Lungdal path:2CO2+fourH2+TOaboutBUTSH⟶CH3COKoA+3H2O {\ displaystyle {\ ce {{2CO2} + 4H2 + {KoASH} -> {CH3COKoA} + 3H2O}}} {\ displaystyle {\ ce {{2CO2} + 4H2 + {KoASH} -> {CH3COKoA} + 3H2O}}} comes with the release of energy ΔG 0 ' = -59.2 kJ / mol [6] . This energy is enough to pump a pair of ions through the membrane and create an electrochemical gradient, but not enough for substrate phosphorylation [7] .

Two CO 2 molecules are reduced independently, in different (carbonyl and methyl) branches of the Wood-Ljungdal path. The methyl branch includes a reaction sequence that leads to the reduction of CO 2 to the methyl group —CH 3 . In this case, the methyl group is bound by tetrahydrofolate (FH 4 ) in bacteria and methanofuran (MFR) and tetrahydromethanopterin (H 4 MPT) in archaea, as transfer coenzymes. The carbonyl portion of the pathway involves the reduction of the second CO 2 molecule to a carbonyl group (—CO) linked to the CO dehydrogenase enzyme catalyzing this reaction. Then the methyl group is combined with the carbonyl group and coenzyme A to form an acetyl-CoA molecule. A special enzyme is involved in this: acetyl-CoA synthetase [1] [8] . In microorganisms, they can be represented as two separate enzymes, or as a bifunctional enzyme complex that combines both of these activities. The key enzyme of the pathway (CO-dehydrogenase / acetyl-CoA synthase) can make up a substantial part of the total soluble cellular protein (for example, from 6 to 9% in Moorella thermoacetica ) [9] . CO-dehydrogenase / acetyl-CoA synthase has a common origin in all prokaryotes using this pathway [10] .

A feature of this pathway is the production of large amounts of acetic acid as a by-product that is not used and is removed from the cell. .

Discovery History

This pathway was named after two researchers, Harland G. Wood and Lars G. Ljungdahl, who are responsible for discovering most of the enzymatic properties of the model acetogenic bacterium Moorella thermoacetica . Subsequently, it was reclassified under the name Clostridium thermoaceticum [11] .

Prevalence

The Wood – Ljungdal pathway is found only in prokaryotes, for example, in hydrogenotrophic methanogenic archaea [12] and homoacetogenic bacteria , such as clostridia [13] , ammonium-oxidizing planktomycetes [14] , and some sulfate-reducing bacteria Desulfobacterium sp. , Deltaproteobacteria [15] and autotrophic archaea Archaeoglobales ( Euryarchaeota ) [16] [17] . Thus, this pathway is presented only in strict anaerobes. This is due to the high sensitivity of the enzymes of this pathway and their cofactors to oxygen. This is also due to the high demand for metal ions (Mo, or W, Co, Ni, and Fe), which are dissolved in water mainly in a low oxidation state (i.e., under anaerobic conditions without oxygen). Thus, the restrictions placed on the availability of metals, cofactors and oxygen sensitivity determine the use of this pathway in a limited number of ecological niches, despite its energy efficiency.

The reducing acetyl-CoA pathway functions as well in psychrophiles as in hyperthermophiles . Its functioning is known at temperatures that are maximally possible for cell multiplication ( Methanopyrus kandlery ; 122 ° C) [18] .

Variations

Although the general pathway scheme is conservative, different C1 carriers, cofactors, electron carriers, and enzymes are used in archaea and bacteria [19] Many variants of this pathway are known.

  1. For example, at the initial stage, free formate, or CO, or a formyl group associated with coenzyme can form.
  2. As various C1 transporting coenzymes, tetrahydrofolate, or tetrahydromethanopterin, is used. Both CO2 and various exogenous C1 compounds (CO, formate, formaldehyde, methanol) or containing a methyl group of the compound (methylamine, methyl mercaptan, attached via an O, N, or S atom) can serve as a source of C1 fragments associated with tetrahydrofolic acid. and simple and complex O-aromatic esters). In this case, tetrahydrofolate-dependent demethylation of such methyl esters is carried out in which the R-OH alcohol is released, and the methyl group is transferred to the protein and then to tetrahydrofolic acid. The use of such compounds requires some additional enzymes, for example, specific methyltransferases.
  3. As an electron donor for reduction, NADH, NADPH, ferredoxin, factor F 420 or H 2 can be used.

These differences in the type of cofactor, which differs in different enzymes and types of microorganisms, makes it possible to explain some of the differences observed in productivity and growth rate.

Reverse (oxidative) acetyl-CoA path

All reactions of the reducing acetyl-CoA pathway are reversible. The Wood-Lungdal pathway is used in the opposite direction in metabolism:

  1. sulfate - reducing bacteria. In this case, electrons taken from organic molecules are transferred by means of acetyl-CoA to NADH, acetyl-CoA is oxidized to CO 2 [20] .
  2. Homoacetogens [21] .
  3. With the breakdown of acetate to CO 2 and CH 4 in acetoclastic methanogenic bacteria.
  4. Anaerobic methylotrophs using methyl esters.
  5. Syntrophic bacteria Clostridium ultunenece and Thermoacetogenium phaeum oxidize acetate to CO 2 and H 2 in association with consuming sulfidogens or methanogens. Oxidation of acetate to CO 2 and H 2 is an endergonic reaction (∆G 0 ' = + 107.1 kJ / mol of acetate), and its occurrence is possible at a very low partial pressure of hydrogen. This becomes possible when a partner in a syntrophic pair consumes hydrogen generated during the oxidation of acetate.

Differences from other carbon fixation paths

  1. In contrast to the reverse Krebs cycle and the Calvin cycle , the reducing acetyl-CoA pathway is linear and not cyclic.
  1. Unlike other carbon fixation paths, the Wood-Ljungdahl path can go in the opposite direction, to obtain reducing equivalents from organic compounds during organo-heterotrophic growth [22] [23] [24]
  1. In contrast to other carbon fixation pathways, the Wood-Ljungdahl reduction pathway can be used not only for fixation, but also for energy storage, through the formation of a hydrogen [25] or sodium electrochemical gradient on the membrane [26] [27] [28] [29 ] ] [30] [31] . The created gradient is consumed by ATPase for the synthesis of ATP from ADP and phosphate [32] .

Evolutionary Importance

Currently, hypotheses are actively being discussed that the first living organisms on earth were chemolithic autotrophs capable of synthesizing all or most of their organic compounds from CO 2 using H 2 or another inorganic electron donor as a reducing agent [33] . Methanogens using this pathway (or the ancestors of methanogens) could be the first autotrophic organisms [34] [35] . Since life originated under anoxigenic conditions, the acetyl-CoA pathway or a very similar pathway may be the first process used for autotrophic CO2 fixation [36] [37] . Recent studies of the genomes of a number of bacteria and archaea suggest that the last universal common ancestor (LUCA) used the Wood-Ljungdal path in hydrothermal sources [38] . Phylogenetic reconstructions [39] as well as chemical experiments suggest that this path could be used even when life was born [40] . It is unclear whether the original purpose of using this pathway was to assimilate carbon (carbon reduction and fixation ) or to oxidize acetate. A phylogenetic study of acetyl-CoA synthetase shows that microorganisms (acetogens and methanogens) having this enzyme or enzymes closely related to it have a common ancestor [41] .

See also

  • Carbon binding

Notes

  1. ↑ 1 2 Stephen W. Ragsdale. Metals and Their Scaffolds To Promote Difficult Enzymatic Reactions (Eng.) // Chemical Reviews: Journal. - 2006. - Vol. 106 , no. 8 . - P. 3317–3337 . - DOI : 10.1021 / cr0503153 .
  2. ↑ Ljungdahl, LC The autotrophic pathway of acetate synthesis in acetogenic bacteria (Eng.) // Annu. Rev. Microbiol. : magazine. - 1986. - Vol. 40 . - P. 415-450 .
  3. ↑ Ragsdale, SW Enzymology of the Wood-Ljungdahl pathway of acetogenesis. (Eng.) // Ann. NY Acad. Sci. : magazine. - 2008 .-- Vol. 1125 . - P. 129-136 .
  4. ↑ Ragsdale, SW and Pierce, E. Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. (English) // Biochim. Biophys. Acta: magazine. - 2008 .-- Vol. 1784 . - P. 1873-1898 .
  5. ↑ Wood, HG Life with CO or CO2 and H2 as a source of carbon and energy. (English) // FASEB J.: Journal. - 1991. - Vol. 5 . - P. 156-163 .
  6. ↑ Fuchs, G. Variation of the acetyl-CoA pathway in diversely related microorganisms that are not acetogens (English) // Acetogenesis (Drake, G., Ed.): Book. 1994. P. 506-538 Chapman and Hall, New York .
  7. ↑ Thauer, RK , Jungermann, K. , and Decker, K. Energy-conservation in chemotrophic anaerobic bacteria. (English) // Bacteriol. Rev. : magazine. - 1977. - Vol. 41 . - P. 100-180 .
  8. ↑ Paul A. Lindahl. Nickel-Carbon Bonds in Acetyl-Coenzyme A Synthases / Carbon Monoxide Dehydrogenases (Eng.) // Metal Ions in Life Sciences : collection / comp. Sigel A. , Sigel H. , Sigel RK O. - Royal Society of Chemistry, 2009 .-- February 4 ( vol. 6 ). - P. 133-150 . - ISBN 978-1-84755-915-9 . - DOI : 10.1039 / 9781847559333-00133 . - PMID 20877794 .
  9. ↑ Roberts, JR , W.-P. Lu , and Ragsdale, SW Acetyl-coenzyme A synthesis from methyltetrahydrofolate, CO, and coenzyme A by enzymes purified from Clostridium thermoaceticum : attainment of in vivo rates and identification of rate-limiting steps. (English) // J. Bacteriol. : magazine. - 1992. - Vol. 174 . - P. 4667-4676 .
  10. ↑ Ragsdale, SW , and Kumar, M .,. Nickel-containing carbon monoxide dehydrogenase / acetyl-CoA synthase. (English) // Chem. Rev. : magazine. - 1996. - Vol. 96 . - P. 2515-2539 .
  11. ↑ Collins, MD , Lawson, PA , Cordoba, JJ , Fernandez-Garayzabal, J. , Garsia, P. , Cai, J. , Hippe, H. , Farrow, JAE The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. (Eng.) // Int J Syst Bacteriol: Journal. - 1994. - Vol. 44 . - P. 812-826 .
  12. ↑ Matschiavelli N. , Oelgeschläger E. , Cocchiararo B. , Finke J. , Rother M. Function and Regulation of Isoforms of Carbon Monoxide Dehydrogenase / Acetyl Coenzyme A Synthase in Methanosarcina acetivorans (English) // Journal of Bacteriology: journal. - 2012. - Vol. 194 , no. 19 . - P. 5377-5387 . - DOI : 10.1128 / JB.00881-12 . - PMID 22865842 .
  13. ↑ Jansen, K. , Stupperich, E. , Fuchs, G. Carbohydrate synthesys from acetyl CoA in the autotroph Methanobacterium thermoautotrophicum (Eng.) // Archives of Microbiology: Journal. - 1982. - Vol. 132 , no. 4 . - P. 355-364 .
  14. ↑ Strous, M. , et al. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. (Eng.) // Nature: Journal. - 2006. - Vol. 440 . - P. 790-794 .
  15. ↑ Schauder, R. , Preuß, A. , Jetten, M. , Fuchs, G. Oxidative and reductive acetyl CoA / carbon monoxide dehydrogenase pathway in Desulfobacterium autotrophicum - 2. Demonstration of the enzymes of the pathway and comparision of CO dehydrogenase. (English) // Arch. Microbiol. : magazine. - 1989. - Vol. 151 . - P. 84-89 . - DOI : 10.1007 / BF00444674 .
  16. ↑ Vorholt, JA , Hafenbradl, D. , Stetter, KO , and Thauer, RK Pathways of autotrophic CO2 fixation and of dissimilatory nitrate reduction to N2O in Ferroglobus placidus. (English) // Arch. Microbiol. : magazine. - 1997. - Vol. 167 . - P. 19-23 .
  17. ↑ Vorholt, JA , Kunow, J. , Stetter, KO , and Thauer, RK Enzymes and coenzymes of the carbon monooxide dehydrogenase pathway for autotrophic CO2 fixation in Archaeoglobus lithotrophicus and the lack of carbon monoxide dehydrogenase in the heterotrophic A. profundus. (English) // Arch. Microbiol. : magazine. - 1995. - Vol. 163 . - P. 112-118 .
  18. ↑ Takai, K. , et al. Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. (English) // Proc. Natl. Acad. Sci. USA: magazine. - 2008 .-- Vol. 105 . - P. 10949-10954 .
  19. ↑ Fuchs, G. Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? (Eng.) // Annu. Rev. Microbiol. : magazine. - 2011 .-- Vol. 65 . - P. 631-658 . - DOI : 10.1146 / annurev-micro-090110-102801 .
  20. ↑ Rabus, R. , Hansen, TA , Widdel, F. Dissimilatory Sulfate- and Sulfur-reducing prokaryotes (English) // Prokaryotes: Journal. - 2006. - Vol. 2 . - P. 659-768 .
  21. ↑ Jansen, K. , Stupperich, E. , Fuchs, G. Carbohydrate synthesys from acetyl CoA in the autotroph Methanobacterium thermoautotrophicum (Eng.) // Archives of Microbiology: Journal. - 1982. - Vol. 132 , no. 4 . - P. 355-364 .
  22. ↑ Vorholt, J. , Kunov, J. , Stetter, KO , Thauer, RK Enzymes and coenzymes oh the carbon monoxide dehydrogenase pathway for autotrophic CO2 fixation in Archaeoglobus lithotrophicus and the lack of carbon monoxide dehydrogenase in the heterotrophic A. profundus. (English) // Arch. Microbiol. : magazine. - 1995. - Vol. 163 . - P. 112-118 . - DOI : 10.1007 / BF00381784 .
  23. ↑ Schauder, R. , Preuß, A. , Jetten, M. , Fuchs, G. Oxidative and reductive acetyl CoA / carbon monoxide dehydrogenase pathway in Desulfobacterium autotrophicum - 2. Demonstration of the enzymes of the pathway and comparision of CO dehydrogenase. (English) // Arch. Microbiol. : magazine. - 1989. - Vol. 151 . - P. 84-89 . - DOI : 10.1007 / BF00444674 .
  24. ↑ Hattori, S. , Galushko, AS , Kamagata, Y. , Schink, B. Operation of the CO dehydrogenase / acetyl coenzyme A pathway in both acetate oxidation and acetate formation by the syntrophically acetate-oxidizing bacterium Thermacetogenium phaeum. (English) // J. Bacteriol. : magazine. - 2005. - Vol. 187 . - P. 3471-3476 . - DOI : 10.1128 / JB.187.10.3471-3476.2005 .
  25. ↑ Ljungdahl, LG The acetyl-CoA pathway and the chemiosmotic generation of ATP during acetogenesis. (English) // Drake HL (ed) Acetogenesis. Chapman and Hall, New York. - 1994 .-- P. 63-87 .
  26. ↑ Biegel, E. , and Müller, V. ,. Bacterial Na + -translocating ferredoxin: NAD + oxidoreductase (English) // Proc. Natl. Acad. Sci. USA: magazine. - 2010 .-- Vol. 107 . - P. 18138-18142 .
  27. ↑ Ragsdale, SW and Pierce, E. Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. (English) // Biochim. Biophys. Acta: magazine. - 2008 .-- Vol. 1784 . - P. 1873-1898 .
  28. ↑ Thauer, RK , Kaster, AK , Seedorf, H. , Buckel, W. and Hedderich, R. Methanogenic archaea: ecologically relevant differences in energy conservation. (Eng.) // Nat. Rev. Microbiol. : magazine. - 2008 .-- Vol. 6 . - P. 579-591 .
  29. ↑ Müller, V. , Gottschalk, G. The sodium ion cycle in acetogenic and methanogenic bacteria: generation and utilization of a primary electrochemical sodium ion gradient (Eng.) // Drake HL (ed) Acetogenesis. Chapman and Hall, New York. - 1994 .-- P. 127-156 .
  30. ↑ Müller, V. , Aufurth, S. , Rahlfs, S. The Na + -cycle in Acetobacterium woodii: identification and characterization of a Na + -translocating F1F0-ATPase with a mixed oligomer of 8 and 16-kDa proteolipids. (Eng.) // Biochim Biophys Acta: Journal. - 2001. - No. 1505 . - P. 108-120 .
  31. ↑ Spruth, M. , Reidlinger, J. , Müller, V. Sodium ion dependence of inhibition of the Na + -translocating F1F0-ATPase from Acetobacterium woodii: probing the site (s) involved in ion transport. (Eng.) // Biochim Biophys Acta: Journal. - 1995. - No. 1229 . - P. 96-102 .
  32. ↑ Müller, V. Energy conservation in acetogenic bacteria (English) // Appl. Environ. Microbiol. : magazine. - 2003. - Vol. 69 . - P. 6345-6353 . - DOI : 10.1128 / AEM.69.11.6345-6353.2003 .
  33. ↑ {{article | author = Sousa, FL , Thiergart, T. , Landan, G. , Nelson-Sathi, S. , Pereira, IAC , Allen, JF , et al. | title = Early bioenegetic evolution. | language = en | edition = Philos.Trans. R. Soc. Lond. B Biol. Sci | type = journal | year = 2013 | volume = 368 | number = | pages = 1-30 | doi = 10.1098 / rstb.2013.0088
  34. ↑ {{article | author = Schopf, JW , Hayes, JM , Walter, MR | title = Evolution of the earth's earliest ecosystems: recent progress and unsolved problems. | language = en | edition = Schopf JW (ed) Earth's earliest biosphere. Princeton University Press, Princeton | type = | year = 1983 | volume = | number = | pages = 361-384
  35. ↑ {{article | author = Brock, TD | title = Evolutionary relationships of the autotrophic bacteria. | language = en | edition = Schlegel HG, Bowien B (eds) Autotrophic bacteria. Science Tech, Madison | type = | year = 1989 | volume = | number = | pages = 499-512
  36. ↑ {{article | author = Wood, HG , Ljungdahl, LG | title = Autotrophic character of the acetogenic bacteria. | language = en | edition = Shively JM, Barton LL (eds) Variations in autotrophic life. Academic, San Diego | type = | year = 1991 | volume = | number = | pages = 201-250
  37. ↑ {{article | author = Lindahl, PA , Chang, B. | title = The evolution of acetyl-CoA synthase. | language = en | edition = Orig Life Evol Biosph | type = | year = 2001 | volume = | number = 31 | pages = 403-434
  38. ↑ MC Weiss , et al. The physiology and habitat of the last universal common ancestor (Eng.) // Nature Microbiology: Journal. - 2016. - Vol. 16116 , no. 1 . - DOI : 10.1038 / nmicrobiol.2016.116. . - PMID 27562259 .
  39. ↑ Braakman, Rogier , Smith, Eric. The Emergence and Early Evolution of Biological Carbon-Fixation (Eng.) // PLOS Computational Biology: Journal. - 2012-04-19. - Vol. 8 , no. 4 . - P. e1002455 . - ISSN 1553-7358. . - DOI : doi: 10.1371 / journal.pcbi.1002455 [ Error: Invalid DOI! ] .
  40. ↑ Varma, Sreejith J. , Muchowska, Kamila B. , Chatelain, Paul , Moran, Joseph. Native iron reduces CO2 to intermediates and end-products of the acetyl-CoA pathway (Eng.) // Nature Ecology & Evolution: Journal. - 2018-04-23. - ISSN 2397-334X. . - DOI : 10.1038 / s41559-018-0542-2. .
  41. ↑ Lindahl, PA , Chang, B. The evolution of acetyl-CoA synthase. (Eng.) // Orig Life Evol Biosph: Journal. - 2001. - No. 31 . - P. 403-434 .

Literature

  • Sokolova T.G. Thermophilic hydrogenogenic carboxydotrophic prokaryotes: dissertation for the degree of Doctor of Biological Sciences. - M.: 2008.: 03.00.07. - 283 p.
  • Wood HG. Life with CO or CO2 and H2 as a source of carbon and energy (Eng.) // FASEB Journal: Journal. - 1991 .-- February ( vol. 5 , no. 2 ). - P. 156-163 . - PMID 1900793 .
  • Diekert G., Wohlfarth G. Metabolism of homoacetogens (Eng.) // Antonie Van Leeuwenhoek: Journal. - Kluwer Academic Publishers, 1994 .-- March ( vol. 66 , no. 1-3 ). - P. 209-221 . - DOI : 10.1007 / BF00871640 . - PMID 7747932 .
Source - https://ru.wikipedia.org/w/index.php?title=Wood_path_—_Lyungdal&oldid=94519899


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