Rate limits and isotopologue fractionations for microbial methanogenesis examined with combined pathway protein cost and isotopologue flow network models
Rate limits and isotopologue fractionations for microbial methanogenesis examined with combined pathway protein cost and isotopologue flow network models
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DOI：
10.1016/j.gca.2022.03.017
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发表时间：
2022-03
影响因子：
5
通讯作者：
S. Ono;Jeemin H. Rhim;Eric C. Ryberg
中科院分区：
文献类型：
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作者：
S. Ono;Jeemin H. Rhim;Eric C. Ryberg
微生物产甲烷产生一系列同位素（13 C/12 C和D/H）和同位素体（13 CH 3D和12 CH 2D 2）分馏。酶促反应的微分可逆性定性地解释了在实验室培养物和环境样品中观察到的同位素和同位素体分馏。应用通道热力学和同位素流网络模型对氢营养型甲烷生成过程中的13 C/12 C、D/H、13 CH 3D和12 CH 2D 2分馏进行了定量描述。该模型由甲烷生成途径的10个酶促反应组成，并通过考虑单氘和双氘同位素的反应对称性来跟踪同位素的质量平衡。根据热力学和酶动力学数据，该模型从预测的17种代谢物和辅因子的体内浓度估计了8个反应的可逆性。同位素流网络模型计算了产物甲烷以及所有中间产物的同位素组成，作为可逆性和指定分馏因子的函数，该模型解释了实验室培养实验中的一些观察结果，包括CH 4和CO2之间的13 C/12 C分馏范围高达80‰，随着pH值的降低，分馏幅度增加。甲烷和水之间相对恒定的300 ± 40‰的D/H分馏可以解释为当甲烷由甲基辅酶M中的三个近平衡H产生时，在甲烷生成的最后一步中加入一个动力学贫D的H。双取代同位素13 CH 3D和12 CH 2D 2的丰度反映了动力学和平衡端员的非线性混合和/或组合效应，我们的模型可以预测在能量有限的深层沉积环境中，在缓慢的甲烷生成速率下，产生大量甲烷的同位素分馏。近平衡同位素比值常在海洋沉积环境中观察到，当pH 2小于10 Pa时产生。我们的模型结果表明，甲烷不会发生或只进行在极低的速度在此低pH值2，因为低浓度的甲基-四氢甲烷蝶呤限制的速率和热力学可行性的甲烷。因此，有人提出，近平衡甲烷同位素信号在深海沉积物中产生的甲基辅酶M还原酶的催化可逆性，可能从厌氧甲烷古菌进行厌氧甲烷氧化或净产甲烷。本文提出的途径热力学和同位素流网络模型方案可以应用和扩展以预测甲烷生成以外的代谢范围的同位素分馏。
Microbial methanogenesis produces a range of isotope (13C/12C and D/H) and isotopologue (13CH3D and12CH2D2) fractionations. Differential reversibility of enzymatic reactions qualitatively explains the isotope and isotopologue fractionations observed in both laboratory cultures and environmental samples. We applied pathway thermodynamics and isotopologue flow network models to quantitatively describe13C/12C, D/H,13CH3D, and12CH2D2fractionations during hydrogenotrophic methanogenesis. The model consists of the 10 enzymatic reactions of the methanogenesis pathway and tracks mass balance of isotopologues by taking into account the reaction symmetries of singly- and doubly-deuterated isotopologues. Based on the thermodynamics and enzyme kinetic data, the model estimates the reversibilities of 8 reactions from predictedin vivoconcentrations of 17 metabolites and cofactors. The isotopologue flow network model calculates the isotopologue composition of product methane as well as all intermediates as a function of reversibilities and prescribed fractionation factors.The model explains a number of observations for laboratory culture experiments, including the range of13C/12C fractionation up to 80‰ between CH4and CO2, with increasing magnitudes while decreasing pH2. Relatively constant D/H fractionations of 300 ± 40‰ between methane and water can be explained when methane is produced from three near-equilibrium H in methyl-coenzyme M with the addition of one kinetic D-depleted H during the last step of methanogenesis. Abundances of the doubly substituted isotopologues,13CH3D and12CH2D2, reflect kinetic and equilibrium end-members with additional complications due to non-linear mixing and/or combinatorial effect.Our model can make predictions for isotopologue fractionations under slow rates of methanogenesis in energy-limiting deep sedimentary environments, where a large quantity of methane is produced. Near-equilibrium isotopologue ratios, often observed in marine sedimentary environments, are produced when pH2is less than 10 Pa. Our model results indicate that methanogenesis does not occur or only proceeds at extremely slow rates at this low pH2because low concentration of methyl-tetrahydromethanopterin limits the rate and thermodynamic feasibility of methanogenesis. Accordingly, it is proposed that near-equilibrium methane isotopologue signals in deep marine sediments are produced by the catalytic reversibility of methyl-coenzyme M reductase, likely from anaerobic methanotrophic archaea performing either anaerobic methane oxidation or net methanogenesis. The pathway thermodynamics and isotopologue flow network model scheme presented herein can be applied and expanded to predict isotopologue fractionations for a range of metabolisms beyond methanogenesis.