International Research Fellowship Program: Systems Biology of Glucose Repression in Yeast for Metabolic Engineering

[504168]国际研究奖学金计划使美国科学家和工程师能够到国外进行三到二十四个月的研究。该计划的奖励为联合研究提供了机会，并利用独特或互补的设施、专业知识和国外的实验条件。该奖项将支持Michael C. Jewett博士与Jens Nielsen博士在丹麦林比的丹麦技术大学微生物生物技术中心（CMB）开展为期22个月的研究。基因工程细胞用于生产有价值的蛋白质治疗药物和次生代谢物在制药和化学工业中被广泛利用。然而，考虑到微生物的催化库存、代谢途径、信号回路和调控网络的复杂性，实现理想的表型通常不是“达尔文最优”，这是一个艰巨的挑战。为了合理地设计细胞工厂，我们必须使用系统级的方法来了解重新连接细胞控制元件所必需的生理信息。本项目的目的是利用系统生物学设计葡萄糖去抑制菌株，确定酿酒酵母葡萄糖抑制的关键成分。这些菌株在工业上对改善从糖蜜中生产面包酵母、从糖混合物中生产生物乙醇和异源蛋白质生产具有吸引力。为了实现这一目标，PI和宿主将把基因组尺度的代谢模型与几种葡萄糖抑制突变体的DNA阵列和代谢物分析数据结合起来。通过模型指导的全球细胞功能分析来详细描述这些突变体的特征，将允许绘制所有多养效应，识别共同调节的代谢模式，以及随后对所需菌株的工程设计。除了完成这一主要目标外，他们的研究还有几个预期的成果。首先，将开发用于整合转录组和代谢组数据的新算法。其次，设计基于直接输注质谱的代谢物分析新方法。第三，将阐明参与葡萄糖感知和抑制的调控元件的作用。该研究将在系统生物学和酵母遗传学/生理学领域产生广泛的影响。特别是，新的算法将在代谢工程中得到广泛应用，并直接提高我们设计“定制”生物体的能力。此外，葡萄球菌葡萄糖去抑制菌株的开发将增加其作为工业生产宿主的效用。此外，由于酵母中的葡萄糖抑制可以作为真核细胞中营养感知的模型，因此该系统的有效算法的开发可以应用于包括人类在内的高等真核生物的信号转导途径的绘制。这一研究领域的进展将直接加强和补充科学界的许多技术，同时产生宝贵的国际伙伴关系。CMB在真核微生物的代谢工程、发酵、生理学、功能基因组学和系统生物学方面具有强大的国际地位。

0504168JewettThe International Research Fellowship Program enables U.S. scientists and engineers to conduct three to twenty-four months of research abroad. The program's awards provide opportunities for joint research, and the use of unique or complementary facilities, expertise and experimental conditions abroad.This award will support a twenty-two month research fellowship by Dr. Michael C. Jewett to work with Dr. Jens Nielsen at Technical University of Denmark's Center for Microbial Biotechnology (CMB) in Lyngby, Denmark.Genetically engineering cells for production of valuable protein therapeutics and secondary metabolites is widely exploited in the pharmaceutical and chemical industries. However, achieving desired phenotypes that are, in general, not the "Darwinian optimum," presents a formidable challenge given the complex nature of the catalytic inventory, metabolic pathways, signaling circuits, and regulatory networks of microorganisms. To rationally design cell factories, we must use system-level methods to gain an understanding of the physiological information necessary to rewire cellular control element. The objective of this project is to identify key components of glucose repression in Saccharomyces cerevisiae using systems biology for design of glucose de-repressed strains. Such strains are industrially attractive for improving baker's yeast production from molasses, bioethanol production from sugar mixtures, and heterologous protein production. To achieve this goal, the PI and host will combine genome-scale metabolic models with DNA array and metabolite profiling data of several glucose repression mutants. Detailed characterization of these mutants by model guided analysis of global cellular function will allow mapping of all pleotrophic effects, identification of co-regulated metabolic patterns, and subsequent engineering of desired strains. In addition to accomplishing this main objective, ther study has several expected deliverables. First, novel algorithms for integration of data from both the transcriptome and the metabolome will be developed. Second, new analytical methods for metabolite profiling based on direct infusion mass spectrometry will be designed. Third, the role of regulatory elements involved in glucose sensing and repression will be clarified.This study will have a broad impact on the field of systems biology and yeast genetics/physiology. Particularly, the novel algorithms will find wide use in metabolic engineering and directly enhance our capability to design "made to order" organisms. In addition, the development of glucose de-repressed strains of S. cerevisiae will increase their utility as industrial production hosts. Furthermore, since glucose repression in yeast serves as a model for nutrient sensing in eukaryotic cells, the development of efficient algorithms for this system may be applied to mapping of signal transduction pathways in higher eukaryotes - including humans. Progress in this research area will directly enhance and complement many technologies in the scientific community while generating a valuable international partnership. The CMB has a strong international position in metabolic engineering, fermentation, physiology, functional genomics, and systems biology of eukaryotic microorganisms.