Archaea

Research Article

Towards a Computational Model of a Methane Producing Archaeum

Table 1

Kinetic model of methanogenesis. Reactions are from iMB745 [22]. Rate constants used in the kinetic model are taken from the literature where indicated or were fit to experiments of growth on methanol. Water molecules and the intracellular protons (H⁺), which are shown for completeness, are assumed to be constant and are not explicitly modeled. The “Type” column specifies the reaction mechanism: B: irreversible bimolecular Michaelis-Menten, B/C: irreversible bimolecular Michaelis-Menten for the two underlined reactants with a constant flux term for the others, which is set to the flux calculated for bimolecular reaction, M: irreversible unimolecular Michaelis-Menten, F: first order reaction.


Enzyme	Reaction	(s⁻¹)	(mM)	Type	Citation

Acetoclastic pathway
Ack	ATP + Ac → AcP + ADP	1055	0.0713	B	[32]
Ack	ADP + AcP → Ac + ATP	1260	0.098	B	[33]
Pta	CoA + AcP → AcCoA + P_i	1500	0.186	B	[34]
Pta	AcCoA + P_i → CoA + AcP	65.8	0.18	B	[35]
Cdh	A cCoA + 2Fd_ox + H4SPT + H₂O → CO + CoA + 2Fd_red + MeH4SPT + 2H⁺	358.5	7.1	B/C	[36]
Cdh	CO + CoA + 2Fd_red + MeH4SPT + 2H⁺ → AcCoA + 2Fd_ox + H4SPT + H₂O	1130	0.9	B/C	[37]

Methylotrophic pathway
MtaCBA1	MeOH + CoM + H⁺ → MeCoM + H₂O	17	50	M	[38, 39]
MtaCBA2	MeOH + CoM + H⁺ → MeCoM + H₂O	15	50	M	[38, 39]
MtaCBA3	MeOH + CoM + H⁺ → MeCoM + H₂O	5	50	M	[38, 39]
Mer	MeH4SPT + F₄₂₀ + H⁺ → MethyleneH4SPT + F₄₂₀H₂	119.7	0.25	B	[40]
Mer	MethyleneH4SPT + F₄₂₀H₂ → MeH4SPT + F₄₂₀ + H⁺	815	0.3	B	[41]
Mtd	MethyleneH4SPT + F₄₂₀ + 2H⁺ → MethenylH4SPT + F₄₂₀H₂	2650	0.065	B	[42]
Mtd	MethenylH4SPT + F₄₂₀H₂ → MethyleneH4SPT + F₄₂₀ + 2H⁺	408	0.065	B	—
Mch	MethenylH4SPT + H₂O → FormylH4SPT + H⁺	701	0.57	M	[43]
Mch	FormylH4SPT + H⁺ → MethenylH4SPT + H₂O	100	0.57	M	—
Ftr	FormylH4SPT + Mfr → H4SPT + H⁺ + FormylMfr	1787	0.1	B	[42]
Ftr	H4SPT + H⁺ + FormylMfr → FormylH4SPT + Mfr	262	0.1	B	—
Fmd/Fwd	FormylMfr + 2Fd_ox + H₂O → CO₂ + 2Fd_red + H⁺ + Mfr	1225	0.02	B/C	[44]
Fmd/Fwd	CO₂ + 2Fd_red + H⁺ + Mfr → FormylMfr + 2Fd_ox + H₂O	175	0.02	B/C	—

Shared pathway
Mtr	H⁺ + MeH4SPT + 2Na_c⁺ + CoM → H4SPT + 2Na_e⁺ + MeCoM	50	3.7	B	—
Mtr	H4SPT + 2Na_e⁺+ MeCoM → H⁺ + MeH4SPT + 2Na_c⁺ + CoM	50	3.7	B	—
Mcr	MeCoM + CoB → CoBCoM + CH₄	5.0	2	B	[45]

Electron transport pathway
HdrDE	CobCoM + MphenH₂ + 2H⁺ → Cob + CoM + Mphen + 2H_e⁺	74	0.092	B	[46]
Rnf	2Fd_red + 3Na_c⁺ + Mphen + 2H⁺ → 2Fd_ox + 3Na_e⁺ + MphenH₂	80	0.1	B/C	—
Fpo	F₄₂₀H₂ + Mphen + H⁺ → F₄₂₀ + MphenH₂ + 2H_e⁺	80	0.1	B	—

Cell growth
ATP synthase	ADP + P_i + 4 → ATP + H₂O + 3H⁺	16	0.1	B/C	[47]
Cell Mass^a	ATP → ADP + P_i + Cell mass	0.125^b	—	F	[22, 31]

The reaction that converts ATP into ADP and cell mass, generating proteins via the stoichiometry in Table 2. ^bThis rate is in units of hr⁻¹ which is equivalent to an 8 hr doubling time for M. acetivorans.