Genomics of Cellulose Fermentation for Process Optimization

利用生物技术和微生物生产增值生物制品对工业具有重要意义。化学和过程工程方法被用来优化微生物的生长和产品产量。然而，工程方法本身并没有考虑微生物新陈代谢和生理学的基因组基础。通过了解基因组含量、基因和基因产物表达、代谢途径利用和最终产物合成模式之间的关系，可以更深入地了解不同的生长条件如何影响微生物的代谢和生理。目前的NSERC发现拨款旨在了解工艺参数的变化如何在基因组水平上影响微生物新陈代谢和生理学，以便为发酵工艺优化建立合理的、基于证据的策略。我的研究是多学科的，应用基因组学(生物信息学、基因组学、转录组学和蛋白质组学)的工具来阐明两种可以直接利用纤维素作为碳源的模式生物的基因和基因产物表达水平的变化：中温细菌白蚁梭菌和嗜热细菌热梭菌。这些细菌将在不同类型的反应容器(没有pH控制的封闭式管式或瓶式反应器，与具有pH控制的开放式生物反应器系统)以及不同的发酵过程(分批与补料分批与半连续补料系统)中生长在纤维素基质上。这项研究的短期目标是：1)研究高温假单胞菌和白蚁假单胞菌在分批、补料分批和半连续发酵反应中对细胞团和发酵最终产物的转化效率；2)利用转录组和蛋白质组学确定与高效发酵系统相关的生物合成机制；以及3)利用基于质谱学的在线监测系统开发一个模型来预测发酵最终产物的合成模式。这项研究将通过i)提供一种在基因组水平上了解发酵过程的机制的方法；ii)将过程工程和最终产品合成结果与基因组事件联系起来；以及iii)提供在线监测复杂发酵反应的工具，从而使通过合并生物处理直接将纤维素转化为生物燃料的放大过程得以发展。通过我的多学科研究计划，3名博士、2名硕士和5名本科生将获得一系列技能，这些技能对于加拿大经济中不断增长的工业生物技术部门至关重要。

The use of biotechniology and microorganisms for production of value-added bioproducts is of great importance to industry. Chemical and process engineering methods are used to optimize growth of microorganisms and product yields. However, engineering approaches alone do not take into consideration the genomic basis of microbial metabolism and physiology. Deeper insight into how different growth conditions influence microbial metabolism and physiology may be obtained by understanding the relationships between genome content, gene and gene product expression, metabolic pathway utilization, and end-product synthesis patterns. The current NSERC Discovery grant seeks to understand how changes in process parameters influence microbial metabolism and physiology at the genomic level so that rational, evidence-based strategies for fermentation process optimization may be established. My research is multidisciplinary and applies the tools of genome science (bioinformatics, genomics, transcriptomics, and proteomics) to elucidate changes in gene and gene product expression levels in two model organisms that can utilize cellulose directly as a carbon source: the mesophilic bacterium Clostridium termiditis, and the thermophilic bacterium Clostridium thermocellum. These bacteria will be grown on cellulosic substrates in different types of reactions vessels (sealed tube or bottle reactors without pH control, versus open bioreactor systems with pH control), and with different fermentation processes (batch versus fed-batch versus semi-continuous-feed systems). The short-term objectives of the research are to: 1) investigate the efficiency of cellulose conversion by C. thermocellum and C. termiditis to cell mass and fermentation end-products in batch, fed-batch, and semi-continuous fermentation reactions; 2) identify the biosynthetic mechanisms associated with efficient fermentation systems using transcriptomics and proteomics; and 3) develop a model to predict fermentation end-product synthesis patterns using a mass-spectrometry-based, on-line monitoring system. This research will enable the development of scaled-up processes for direct conversion of cellulose to biofuels via consolidated bioprocessing by i) providing an approach to understanding the mechanisms of fermentation processes at the genomic level; ii) linking process engineering and end-product synthesis outcomes to genomic events; and iii) providing tools for online monitoring of complex fermentation reactions. Through my multidisciplinary research program, 3 PhD, 2 MSc, and 5 undergraduate students will acquire a range of skills that are essential to the growing industrial biotechnology sector of the Canadian economy.