Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
PLoS One. 2011;6(11):e27316. doi: 10.1371/journal.pone.0027316. Epub 2011 Nov 4.
Biofuels derived from lignocellulosic biomass offer promising alternative renewable energy sources for transportation fuels. Significant effort has been made to engineer Saccharomyces cerevisiae to efficiently ferment pentose sugars such as D-xylose and L-arabinose into biofuels such as ethanol through heterologous expression of the fungal D-xylose and L-arabinose pathways. However, one of the major bottlenecks in these fungal pathways is that the cofactors are not balanced, which contributes to inefficient utilization of pentose sugars. We utilized a genome-scale model of S. cerevisiae to predict the maximal achievable growth rate for cofactor balanced and imbalanced D-xylose and L-arabinose utilization pathways. Dynamic flux balance analysis (DFBA) was used to simulate batch fermentation of glucose, D-xylose, and L-arabinose. The dynamic models and experimental results are in good agreement for the wild type and for the engineered D-xylose utilization pathway. Cofactor balancing the engineered D-xylose and L-arabinose utilization pathways simulated an increase in ethanol batch production of 24.7% while simultaneously reducing the predicted substrate utilization time by 70%. Furthermore, the effects of cofactor balancing the engineered pentose utilization pathways were evaluated throughout the genome-scale metabolic network. This work not only provides new insights to the global network effects of cofactor balancing but also provides useful guidelines for engineering a recombinant yeast strain with cofactor balanced engineered pathways that efficiently co-utilizes pentose and hexose sugars for biofuels production. Experimental switching of cofactor usage in enzymes has been demonstrated, but is a time-consuming effort. Therefore, systems biology models that can predict the likely outcome of such strain engineering efforts are highly useful for motivating which efforts are likely to be worth the significant time investment.
木质纤维素生物质衍生的生物燃料为运输燃料提供了有前途的可再生能源替代品。人们已经做出了巨大的努力，通过异源表达真菌的 D-木糖和 L-阿拉伯糖途径，来工程化酿酒酵母，以有效地将戊糖（如 D-木糖和 L-阿拉伯糖）发酵成生物燃料，如乙醇。然而，这些真菌途径中的一个主要瓶颈是辅因子不平衡，这导致戊糖的利用效率低下。我们利用酿酒酵母的基因组规模模型来预测平衡和不平衡 D-木糖和 L-阿拉伯糖利用途径的最大可实现生长速率。动态通量平衡分析（DFBA）用于模拟葡萄糖、D-木糖和 L-阿拉伯糖的分批发酵。动态模型和实验结果对于野生型和工程化的 D-木糖利用途径都非常吻合。平衡工程化的 D-木糖和 L-阿拉伯糖利用途径的辅因子模拟了乙醇分批生产的增加 24.7%，同时预测的底物利用时间减少了 70%。此外，还评估了平衡工程化戊糖利用途径的辅因子对整个基因组规模代谢网络的影响。这项工作不仅为辅因子平衡的全局网络效应提供了新的见解，而且为工程化具有平衡的工程化途径的重组酵母菌株提供了有用的指导，这些途径可以有效地共同利用戊糖和己糖生产生物燃料。已经证明了酶中辅因子使用的实验切换，但这是一项耗时的工作。因此，能够预测这种菌株工程努力可能结果的系统生物学模型对于激发哪些努力值得投入大量时间非常有用。
