Next Generation Strain Engineering via OptKnock

通过 OptKnock 进行下一代应变工程

• 批准号: 6991078
• 负责人: ANTHONY P BURGARD
• 金额: $ 15.13万
• 依托单位: GENOMATICA, INC.
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-08-01 至 2006-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6991078
• 关键词: biochemistry; biotechnology; computer simulation; gene deletion mutation; gene targeting; genetic manipulation; genetic strain; succinates; technology /technique development

DESCRIPTION (provided by applicant): Metabolic engineering has gained significance in both industrial and medical biotechnology for the synthesis of a wide variety of products including small metabolites and other antibiotics. However, due to the lack of rational and systematic approaches to metabolic engineering the timelines and cost for strain development can be large and at times prohibitive for many products. This proposal addresses this need for more rational approaches through the implementation of modeling and simulation technologies to design cellular metabolic networks for practical objectives. The bilevel programming framework OptKnock, in particular, focuses on identifying multiple gene deletion strategies for forcing growth-coupled biochemical production following laboratory adaptive evolution. Specifically, knockouts are selected in such a way that the drain towards necessary growth resources (i.e., biomass components, redox potential and energy) must be accompanied, due to stoichiometry, by the production of the desired chemical product. The overall goal of this Phase I SBIR is the completion of an integrated computational and experimental study aimed at demonstrating the technical feasibility of utilizing the OptKnock approach to drive strain engineering efforts. The production of succinate in Escherichia coli will serve as an exemplary case study towards this end. The initial aims of this application are to enumerate sets of multiple gene deletions leading to growth-coupled succinate production and incorporate the three most promising into E. coli. The three unique designed strains will then be subjected to adaptive evolution to enhance their rates of growth, and thus the coupled objective of succinate production will be indirectly optimized. Finally, we will reconcile the experimental findings with the original predictions to gauge the overall success of the combined modeling/experimental platform. In subsequent phases of the project, we will target several compounds of biotechnological and biomedical importance with the goal of generating at least one industrially competitive production strain. This program will lead to the development of a systematic approach to metabolic engineering that leverages genomic information and a host of experimental data for the rational design of production hosts. The developed technology will significantly expedite and lesson the cost of strain development for the production of a plethora of compounds with therapeutic value.

描述（由申请人提供）： 代谢工程在工业和医学生物技术中具有重要意义，用于合成各种各样的产品，包括小代谢物和其他抗生素。然而，由于缺乏合理和系统的代谢工程方法，菌株开发的时间表和成本可能很大，有时对许多产品来说是禁止的。该提案通过实施建模和仿真技术来设计用于实际目标的细胞代谢网络，从而满足了对更合理方法的需求。双层编程框架OptKnock，特别是，专注于确定多个基因删除策略，迫使生长耦合生化生产实验室适应性进化。具体地，以这样的方式选择敲除，使得向必要的生长资源（即，生物质组分、氧化还原电位和能量）必须由于化学计量而伴随着所需化学产物的产生。第一阶段SBIR的总体目标是完成一项综合计算和实验研究，旨在证明利用OptKnock方法推动应变工程工作的技术可行性。在大肠杆菌中琥珀酸的生产将作为一个典型的案例研究实现这一目标。本申请的最初目的是列举导致生长偶联琥珀酸生产的多个基因缺失的集合，并将三个最有希望的基因并入E.杆菌这三种独特设计的菌株将进行适应性进化，以提高它们的生长速率，从而间接优化琥珀酸生产的耦合目标。最后，我们将协调实验结果与原始预测，以衡量综合建模/实验平台的整体成功。在该项目的后续阶段，我们将针对几种具有生物技术和生物医学重要性的化合物，目标是产生至少一种具有工业竞争力的生产菌株。该计划将导致代谢工程的系统方法的发展，该方法利用基因组信息和大量实验数据来合理设计生产宿主。所开发的技术将显著加快和减少菌株开发的成本，以生产大量具有治疗价值的化合物。