14TSB_SynBio P2P: Pentoses to products

合成生物学提供了非凡的空间，将工程学和生物学方法结合在一起，制造新的设备和产品。最早的工业影响预计将发生在高价值化学品制造领域，前提是能够为生物催化剂开发开发出可靠的工具和服务。将合成生物学应用于化学品的早期成功将对英国经济产生重大影响。英国化学工业是英国的一个主要部门，占世界市场的8%。2009年，英国有3000多家公司创造了约550亿GB的年营业额，该行业一直以每年约5%的速度增长。然而，化学品制造业依赖日益昂贵的石油和天然气作为起始原料，需要可持续的替代品。幸运的是，合成生物学提供了新的机会，可以利用农业、林业和食品加工的废物来制造生物化学品和临时生物燃料。这些废物含有丰富的糖类聚合物(纤维素和半纤维素)，可以被水解制得C5和C6糖。虽然C6糖已经被广泛用作发酵原料，但C5糖在经济上几乎没有可行的用途。C5糖的利用将从几乎零成本的废物中形成高价值的产品，从而改变以生物为基础的制造的经济性。该项目旨在开发创新的生物催化模块，用于将C5糖转化为化学品。到目前为止，工程微生物利用C5的问题采用了一种完整的系统方法，基于自然发生途径的代谢工程。由于这些途径效率低，产品范围有限，我们将利用模块化、特征化和标准化的工程概念，开发新的、人工的C5糖转化为化学品的途径。我们将应用模块化，将代谢过程分解为组成代谢单元，以设计灵活、可互换的代谢模块。然后，这些将被组装成完整的生物催化系统，以在制造中获得最佳性能。这些模块将包括编码酶的基因，这些酶需要(A)将C5糖转化为关键的代谢中间体(异柠檬酸或2-羟基戊二酸)，以及(B)将中间体转化为有用的化学产品。我们将使用生物信息学的方法来设计最有效和最兼容的一组酶来组装模块。我们还将检查大肠杆菌的代谢图谱，以确定将与我们的代谢模块竞争的酶，以便我们可以删除相应的基因。然后，我们将克隆、表达和表征这些酶(缺少文献信息)，这样我们就可以定义和了解它们在组合到模块中时的行为和功能，并微调设计。然后，我们将继续构建定义的、标准化的核心模块，并对其性能进行表征。接下来，这些模块将与辅助代谢模块对接，形成有用的化学产品，为化学品制造提供定制的微生物系统。我们将演示一种定制的偏孔酸生产系统，该系统是Lucite生产甲基丙烯酸所需的。这将确定与上下文依赖性和可预测性相关的任何问题，使设计能够针对稳健的工业生物催化进行微调。新的代谢模块将为化学品制造行业提供标准化组件，使新的生物催化剂能够快速、可预测地组装起来，以制造化学产品。模块化将大大缩短新的生物催化工艺的开发时间，并加快上市进程。总体而言，该项目将降低与生物催化制造相关的商业和技术风险。

Synthetic biology provides extraordinary scope to bring engineering and biological approaches together to manufacture new devices and products. The earliest industrial impacts are expected to be in high value chemicals manufacturing, provided that reliable tools and services can be developed for biocatalyst development. Early success in synthetic biology applied to chemicals will have significant impact on the UK economy. The UK chemical industry comprises a major sector in the UK, with > 8% of the world market. In 2009, the UK had over 3,000 companies generating an annual turnover of around £55bn, and the sector has been growing at about 5% a year. However, the chemicals manufacturing industry is dependent on increasingly expensive oil and gas as the starting materials, and sustainable alternatives are needed. Fortunately, synthetic biology provides new opportunities to use wastes from agriculture, forestry and food processing to manufacture bio-based chemicals and drop-in biofuels. These wastes are rich in sugar polymers (cellulose and hemicellulose) that can be hydrolyzed to produce C5 and C6 sugars. Although the C6 sugars are already used widely as fermentation feedstocks, there are few economically viable uses for C5 sugars. Utilization of C5 sugars would transform the economics of bio-based manufacturing, by forming high value products from almost zero cost wastes. This project aims to develop innovative biocatalytic modules for conversion of C5 sugars to chemicals. Until now, the problem of engineering microorganisms for C5 utilization has employed a whole systems approach, based on metabolic engineering of naturally occurring pathways. Since these pathways are inefficient and the product range is restricted, we will use the engineering concepts of modularization, characterization and standardization to develop new, artificial pathways for C5 sugar conversion to chemicals. We will apply modularization by breaking the metabolic process down intocomponent metabolic units, to design flexible, interchangeable metabolic modules. These will then be assembled into complete biocatalytic systems to obtain optimum performance in manufacturing. The modules will comprise genes coding for enzymes needed to (a) convert C5 sugars to key metabolic intermediates (isocitrate or 2-oxoglutarate) and (b) convert the intermediates to useful chemical products. We will use a bioinformatics approach to design the most efficient and compatible sets of enzymes to assemble the modules. We will also check the metabolic map of E. coli to identify enzymes that would compete with our metabolic modules, so that we can delete the corresponding genes. We will then clone, express and characterize the enzymes (where literature information is missing), so that we can define and understand their behaviour and function when combined into the modules, and fine-tune the designs. We shall then proceed to construct defined, standardized core modules, and characterize their performance. Next, the modules will be interfaced with accessory metabolic modules to form useful chemical products, providing bespoke microbial systems for chemicals manufacturing. We will demonstrate a bespoke system for production of mesaconic acid, needed by Lucite for methacrylic acid production. This will identify any issues relating to context dependency and predictability, enabling the designs to be fine-tuned for robust, industrial biocatalysis. The new metabolic modules will provide standardized components for the chemicals manufacturing industry, enabling rapid, predictable assembly of new biocatalysts to manufacture chemical products. Modularity will greatly reduce development time for new biocatalytic processes and accelerate the journey to market. Overall, the project will reduce the commercial and technical risk associated with biocatalytic manufacturing.