Roberts Seth B, Gowen Christopher M, Brooks J Paul, Fong Stephen S
Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA.
BMC Syst Biol. 2010 Mar 22;4:31. doi: 10.1186/1752-0509-4-31.
Microorganisms possess diverse metabolic capabilities that can potentially be leveraged for efficient production of biofuels. Clostridium thermocellum (ATCC 27405) is a thermophilic anaerobe that is both cellulolytic and ethanologenic, meaning that it can directly use the plant sugar, cellulose, and biochemically convert it to ethanol. A major challenge in using microorganisms for chemical production is the need to modify the organism to increase production efficiency. The process of properly engineering an organism is typically arduous.
Here we present a genome-scale model of C. thermocellum metabolism, iSR432, for the purpose of establishing a computational tool to study the metabolic network of C. thermocellum and facilitate efforts to engineer C. thermocellum for biofuel production. The model consists of 577 reactions involving 525 intracellular metabolites, 432 genes, and a proteomic-based representation of a cellulosome. The process of constructing this metabolic model led to suggested annotation refinements for 27 genes and identification of areas of metabolism requiring further study. The accuracy of the iSR432 model was tested using experimental growth and by-product secretion data for growth on cellobiose and fructose. Analysis using this model captures the relationship between the reduction-oxidation state of the cell and ethanol secretion and allowed for prediction of gene deletions and environmental conditions that would increase ethanol production.
By incorporating genomic sequence data, network topology, and experimental measurements of enzyme activities and metabolite fluxes, we have generated a model that is reasonably accurate at predicting the cellular phenotype of C. thermocellum and establish a strong foundation for rational strain design. In addition, we are able to draw some important conclusions regarding the underlying metabolic mechanisms for observed behaviors of C. thermocellum and highlight remaining gaps in the existing genome annotations.
微生物具有多样的代谢能力，这有可能被用于高效生产生物燃料。嗜热栖热菌（ATCC 27405）是一种嗜热厌氧菌，具有纤维素分解和产乙醇的能力，也就是说它可以直接利用植物糖——纤维素，并将其生化转化为乙醇。利用微生物进行化学品生产的一个主要挑战是需要对生物体进行改造以提高生产效率。对生物体进行合理工程改造的过程通常很艰巨。
在此，我们提出了嗜热栖热菌代谢的基因组规模模型iSR432，目的是建立一个计算工具来研究嗜热栖热菌的代谢网络，并促进对嗜热栖热菌进行生物燃料生产的工程改造。该模型由577个反应组成，涉及525种细胞内代谢物、432个基因以及基于蛋白质组学的纤维小体表示。构建这个代谢模型的过程导致对27个基因的注释建议得到改进，并确定了需要进一步研究的代谢领域。使用纤维二糖和果糖生长的实验生长和副产物分泌数据对iSR432模型的准确性进行了测试。使用该模型进行分析捕捉了细胞的还原 - 氧化状态与乙醇分泌之间的关系，并能够预测会增加乙醇产量的基因缺失和环境条件。
通过整合基因组序列数据、网络拓扑结构以及酶活性和代谢物通量的实验测量，我们生成了一个在预测嗜热栖热菌细胞表型方面相当准确的模型，并为合理的菌株设计奠定了坚实基础。此外，我们能够就嗜热栖热菌观察到的行为的潜在代谢机制得出一些重要结论，并突出现有基因组注释中仍然存在的差距。
