Homoacetogenesis

Edge evidence

• Homoacetogenesis occurs in anaerobic condition biolink:occurs_in

  Homoacetogenesis is an anaerobic acetogenic metabolism.

  • DOI:10.1023/A:1020514617738 obligately anaerobic bacteria Supports anaerobic context for acetogens.
• Homoacetogenesis has mechanistic pathway Wood-Ljungdahl pathway

  Homoacetogenesis proceeds through the Wood-Ljungdahl pathway.

  • DOI:10.1016/j.tibtech.2019.05.008 Wood-Ljungdahl pathway Supports pathway assignment for acetogens.
• carbon dioxide participates in Wood-Ljungdahl pathway biolink:participates_in

  CO2 is reduced through the Wood-Ljungdahl pathway.

  • DOI:10.1016/j.tibtech.2019.05.008 carbon dioxide are reduced Supports CO2 as substrate.
• molecular hydrogen provides electrons for Wood-Ljungdahl pathway METPO:2007402

  Hydrogen can provide reducing equivalents for CO2 reduction.

  • DOI:10.1016/j.bbapap.2008.08.012 acetyl-CoA from CO or CO2 + H2 Supports H2 as an electron donor with CO2.
• carbon monoxide participates in Wood-Ljungdahl pathway biolink:participates_in

  CO can serve as a C1 input or intermediate for acetyl-CoA synthesis.

  • DOI:10.1016/j.bbapap.2008.08.012 acetyl-CoA from CO or CO2 + H2 Supports CO as substrate or intermediate.
• Wood-Ljungdahl pathway has output acetyl-CoA RO:0002234

  Wood-Ljungdahl carbon fixation produces acetyl-CoA.

  • DOI:10.1016/j.tibtech.2019.05.008 reduced to one mol of acetyl-CoA Supports acetyl-CoA synthesis from CO2.
• acetyl-CoA converted to acetate

  Acetyl-CoA is converted to acetate as the reduced product.

  • DOI:10.1016/j.tibtech.2019.05.008 further to acetate Supports acetate formation downstream of acetyl-CoA.
• Homoacetogenesis produces acetate METPO:2007800

  Homoacetogenesis produces acetate as the sole reduced end product.

  • DOI:10.1023/A:1020514617738 reduce CO2 to acetate Supports acetate as the defining acetogenic product.
• acetyl-CoA supports formation of ATP

  Conversion to acetate can conserve energy as ATP.

  • DOI:10.1016/j.tibtech.2019.05.008 further to acetate Review discusses acetate formation as the energy-conserving product branch.
• carbon dioxide reduced by enzyme to formate

  CO2 is reduced to formate by formate dehydrogenase in the methyl branch.

  • DOI:10.1039/d4cb00099d CO2 to formate catalyzed by formate dehydrogenase (Fdh); core WLP methyl-branch step.
• formate dehydrogenase catalyzes formate biolink:catalyzes

  Formate dehydrogenase produces formate from CO2.

  • DOI:10.1039/d4cb00099d CO2 -> formate catalyzed by formate dehydrogenase (Fdh).
• formate converted by enzyme to formyl-tetrahydrofolate

  Formate is converted to formyl-THF by formyl-THF synthetase.

  • DOI:10.1039/d4cb00099d formate -> formyl-THF by formyl-THF synthetase (Fhs); methyl-branch step.
• formyl-THF synthetase (Fhs) catalyzes formyl-tetrahydrofolate biolink:catalyzes

  Formyl-THF synthetase (Fhs) forms formyl-THF from formate.

  • DOI:10.1039/d4cb00099d formate -> formyl-THF by formyl-THF synthetase (Fhs).
• methyl branch of WLP converges with carbonyl branch of WLP

  The methyl and carbonyl branches of the WLP converge at the ACS/CODH complex.

  • DOI:10.1186/s13068-024-02554-w eastern/methyl branch and carbonyl/western branch meet at the acetyl-CoA synthase/carbon monoxide dehydrogenase complex (ACS/CODH); canonical WLP architecture.
• ACS/CODH complex produces acetyl-CoA METPO:2007800

  The ACS/CODH complex condenses the methyl and carbonyl groups into acetyl-CoA.

  • DOI:10.1186/s13068-024-02554-w the two WLP branches meet at the ACS/CODH complex to form acetyl-CoA.
• acetate kinase generates ATP biolink:produces

  Acetate kinase generates ATP by substrate-level phosphorylation during acetate formation, the only WLP ATP-yielding step.

  • DOI:10.1039/d4cb00099d acetyl-CoA -> acetate via acetyl-phosphate with ATP from substrate-level phosphorylation (acetate kinase); WLP is otherwise net-zero ATP.
• acetate kinase participates in substrate-level phosphorylation biolink:participates_in

  Acetate kinase mediates substrate-level phosphorylation in the acetate branch.

  • DOI:10.1039/d4cb00099d ATP from substrate-level phosphorylation at acetate kinase.
• membrane energy-conservation module (Rnf/Ech) generates transmembrane ion gradient biolink:produces

  The membrane Rnf or Ech module translocates Na+/H+ to generate the transmembrane ion gradient.

  • DOI:10.1039/d4cb00099d Rnf transfers electrons from Fdred to NAD+ while translocating Na+/H+; Ech acts as Fd:H+ oxidoreductase.
  • DOI:10.3389/fmicb.2023.1185739 membrane-associated energy-conservation module involving Rnf or Ech plus ATP synthase.
• transmembrane ion gradient drives ATP synthase

  The transmembrane ion gradient drives ATP synthase to conserve energy during acetogenesis.

  • DOI:10.3389/fmicb.2023.1185739 membrane-associated energy-conservation module ... plus ATP synthase.
• ATP synthase produces ATP METPO:2007800

  ATP synthase produces ATP from the ion gradient, conserving energy in the near-thermodynamic-limit acetogenic metabolism.

  • DOI:10.3389/fmicb.2023.1185739 ATP synthase couples the ion gradient to ATP synthesis in acetogens.
• methyl branch of WLP part of Wood-Ljungdahl pathway biolink:part_of

  The methyl branch is one of the two converging branches of the Wood-Ljungdahl pathway.

  • DOI:10.1186/s13068-024-02554-w The WLP, which was elucidated over decades, proceeds through two branches Verified against the public PMC full text; the existing edge between methyl and carbonyl branches keeps both branches connected.