Collaborative Research: A Systems Biology Approach for Metabolically Engineering Escherichia coli for Producing Hydrogen via Fermentation

无害细菌可用于生产供人类使用的化学品，包括燃料。分子氢是一种环保燃料；因此，如果细菌能够有效地合成氢气，那么我们就可以减少空气污染，减少对外国石油的依赖，并避免温室气体(我们过程中形成的二氧化碳将被回收到植物质量中，并再次用于形成氢气，因此没有净排放)。这项研究将使氢气能够作为一种清洁的能源从细菌中通过发酵单糖来生产。在发酵生产氢的过程中，葡萄糖转化为丙酮酸，丙酮酸转化为甲酸盐，甲酸盐再转化为氢气。因此，必须通过防止竞争的葡萄糖反应和将丙酮酸转化为醋酸盐、乳酸和乙醇或去除甲酸盐的反应来引导细菌细胞中的碳流形成氢气。为了实现这一目标，将使用系统生物学方法来生产更多的氢，其中包括(I)通过消除不需要的途径来改变细菌的新陈代谢，(Ii)使用蛋白质工程进化必要的酶，以及(Iii)对细菌细胞的所有代谢途径进行建模，以便产生更好的细菌。我们选择大肠杆菌作为我们的模型系统，是因为(I)大肠杆菌BW25113菌株的所有3985个非致命性单一突变都是可用的；(Ii)我们可以使用我们新颖的、连续的、基于病毒的方法快速组合突变；(Iii)大肠杆菌是研究最深入的细菌，因此人们很好地了解了它的代谢；(Iv)它的基因组被测序，所以DNA微阵列可用，代谢通量分析可以在基因组水平上进行。除了研究结果，参与这项研究的三位教授将培训本科生和研究生，通过万维网提供该项目的具体成果，并将通过播客向不同的受众传播一些研究成果。

CBET-0753702WoodNon-harmful bacteria may be used to produce chemicals for humans and this includes fuels. Molecular hydrogen is an environmentally-clean fuel; hence, if hydrogen can be synthesized efficiently by bacteria, then we may reduce air pollution, reduce our dependence on foreign oil, and avoid greenhouse gases (the carbon dioxide formed by our process will be recycled to plant mass and used again to form hydrogen so there are no net emissions). This research will enable hydrogen to be produced as a clean form of energy from bacteria using fermentation of simple sugars. In fermentative production of hydrogen, glucose is converted into pyruvate which is converted to formate which is then converted to hydrogen. Hence, it is imperative to direct the carbon flux in the bacterial cell to hydrogen formation by preventing competing glucose reactions and those that convert pyruvate to acetate, lactate, and ethanol or that remove formate. To achieve this aim, a systems biology approach will be used to produce more hydrogen that includes (i) altering the metabolism of the bacteria by removing unwanted pathways, (ii) evolving the necessary enzymes using protein engineering, and (iii) modeling all the metabolic pathways of the bacterial cell so that even better bacteria may be generated. We have chosen Escherichia coli as our model system since (i) all 3985 non-lethal single mutations of strain E. coli BW25113 are available; (ii) we may combine mutations rapidly using our novel, successive, virus-based method; (iii) E. coli is the best-studied bacterium so its metabolism is well understood; and (iv) its genome is sequenced so DNA microarrays are available and metabolic flux analysis may be carried out at the genome-scale. Along with the research results, the three professors involved in this research will train undergraduate and graduate students, will make accessible, via the World-Wide Web, specific outcomes of the project, and will disseminate some of the research results to a diverse audience using podcasting.