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. 2018 Aug 27;8(3):35. doi: 10.3390/life8030035

Table 1.

Steps toward ligand-accelerated autocatalytic denitrifying methanotrophic acetogenesis: demonstrated, analogous, probable, possible, and predicted, with comparisons to enzymes.

Biosyntonically ‘Engineered’ Steps, Mineral Barriers, Engines, Catalysts Abiotic Reaction Coupling and/or Gradient References
cf. Prebiotic Enzyme Analogues
0. {5OH− + HS−} + 2Fe2+ + Fe3+ + Ni2+ → {FeS + Fe2(OH)5} + ē Green rust and [FeNi]S set in SiO2? Spontaneous barrier precipitation [6,22,24,30,31,35,45,59,65,67]
membrane
1. H2 → 2H• → 2H+ + 2e− GR>FeS>NiS>MoS2/Chimneys Redox gradient [68,69,70,71,72,73,74,75,76,77,78,79]
NiFe[Mo]-Hydrogenasase
1a. proton-coupled electron transfer processes GR, mackinawite, greigite Proton gradient [79]
Ferredoxin
1b. electron bifurcation, conformation plasticity, electron and proton transfer, gating MMO, Nir GR, mackinawite, greigite, MoSx Redox gradient [4,7,8,18,19,20,61,67,72,73,74,75,76,77,78,79,80]
2. H+ + 2ē + CO2 → HCOO− + H2O FHL Ni3Fe, or [FeNi]S or MoS Serpentinization, or redox, pH gradient [24,60]
2a. CO2 + 2ē + H+ → CO + OH− CODH Violarite Electron conduction [34,81,82,83]
3. CH4 + NO3− + H2 + H+ → •CH3 + 2H2O + NO GR & Mo-dosed greigite (redox/pH gradients) Undemonstrated (Redox and pH gradient) [54,55,61,80,84,85]
MMO
4. NO3− + 4H2 + 2H+ → NH4+ + 3H2O GR (redox/pH gradients) Redox (~180 min) [86,87,88,89,90,91]
Nar/Nir/NOR
5. •CH3 + OH−/SH−?) → CH3OH/ CH3SH) + ē GR? high T Low yield [43,44]
MMO?
6. CH3OH + [2FeIII] → HCHO + [2FeII] + 2H+ MDH GR [FeNi]S? Fe2(MoO4)3 Undemonstrated [54]
7. HCHO+HP2O73− + [OH−] → [HCOPO4]2− +HPO42− ? Undemonstrated (exergonic) [92]
FK
8. HCOPO42− + HS− + 2H+ + 2ē → CH3S− + HPO42− ? Undemonstrated (exergonic) [92,93]
9. CH3S− + HCOO− + H+ → CH3COOH + HS− Fe4NiS9(HN)2 cf. Reppe chemistry [29,42,92,93,94,95,96]
ACS
9a. CH3S− + CO → CH3COS− Fe4NiS9(HN)2 High yield (20 h) [42]
9b. (CH3COS− + HPO42− → CH3COPO42− + HS−) ? Low yield [94]
10. HCOO− + CH3CO~SCH3 + ē → CH3COCOO− + HSCH3− Fe2(RS)2(CO)6 Undemonstrated [97,98]
PFL
10a. CH3COCOO− + (HP2O7)3− + CO2 → CH2C=C(OPO3)2−COO− + HPO42− +H+ GR/mackinawite? Predicted [16]
PPase
10b. CH2=C(OPO3)2−COO− + CO2 + H2O → −OOCCH2COCOO− + HPO42− + H+ ACC GR/mackinawite? Predicted [16]
11. CH3COCOO− + NH4+ + 2ē + 2H+ → CH3CH(NH2)COO− + H2O ALT GR/mackinawite? 24 h [39]
12. (CH3CH(NH2)COOH)4 + CH3CH(NH2)COOH → CH3CH(NH2)CO-CH3CH(NH)CO-CH3CH(NH)CO-CH3CH(NH)CO-CH3CH(NH)COOH + 4H2O Dolomite (ab initio simulations mackinawite and double layer hydroxide) Spontaneous (Dolomite) [99,100,101,102,103,104,105,106,107,108]
DLH [cf. “DNA pol”]
13. Pi + Pi → PPi by GR H+-PPase FeS, GR Only at ~equilibrium [109]
ligand-assisted recapitulation?
{13} poly-alanine peptide-strengthened membrane? mineral-organic framework Spontaneous [65,110,111,112]
{14} SGAGKT peptide + Pi    → P-loop 6mer peptide Spontaneous [113]
{15} CH3CH(NH2)CO-CH3CH(NH)CO-CH3CH(NH2)CO-CH3CH(NH)COOH + Ni2+ → Ni-CH3CH(NH2)CO-CH3CH(NH)CO-CH3CH(NH)CO-CH3CH(NH)COOH ATCUN motif 4mer peptide Spontaneous [94,95,96,97,98,99,100,101,102,103,104,105,106,107]
[114,115,116]
{16} (Fe4NiS) + CH3CH(NH2)CO-CH3CH(NH)CO-CH3CH(NH)CO-CH3CH(NH)CO-CH3CH(NH)COOH → [Fe4NiS]-CH3CH(NH2)CO-CH3CH(NH)CO-CH3CH(NH)CO-CH3CH(NH)CO-CH3CH(NH)COOH Proto-fd, ACS, CODH 6mer peptide Partial demonstration [117,118]
→ {16}{1}{2}{3}{4}{5}{6}{7}{8}{9}{10}{11}{12}{13} → repeat GR breakout metabolism? Figure 1

ACC = Acetyl-CoA carboxylase; ACS = Acetyl-CoA synthase; ALT = Alanine transaminase; ATCUN motif = Amino terminal Cu(II) and Ni(II) binding motif; CODH = Carbon monoxide dehydrogenase; (DLH = Double Layer Hydroxide; DNA pol = DNA polymerase); Fd = Ferredoxin; FHL = Formate hydrogen lyase; FK = Formate kinase; H+-PPase = proton pyrophosphatase; MMO = methane monooxygenase; MDH = methanol dehydrogenase; Nar = nitrate reductase; Nir = nitrite reductase; NOR = nitric oxide reductase; NiFe[Mo]-H2ase = NiFe[Mo]-hydrogenase; PFL = Pyruvate formate lyase; ? = uncertain.