Carbon capture and utilisation to replace sugar-based fermentations in the biotechnology industry

工业生物技术依靠农业以糖的形式为细菌发酵提供输入能量。糖是这些传统结构中的碳源和能源。然而，某些细菌物种能够利用二氧化碳作为它们的碳源，同时依赖氢气作为它们的能源；这些物种是氢氧化细菌(HOB)。在HOB中进行的生化途径是包括光合藻在内的最有效的生物固碳形式。几家公司正试图将HOB用于制造单细胞蛋白(SCP)的用途商业化，单细胞蛋白作为蛋白质类饲料成分出售。作为一种饲料成分，SCP与传统饲料蛋白相比具有重大的环境优势：除了显著减少土地和水资源的使用外，它还具有更低的总体碳足迹。然而，为了在商业上充分采用该技术，产品必须具有足够高的价值，以补偿商业工厂的投入成本和相对较高的资本成本。这项技术的采用得益于人们对氢气经济兴趣的提高和规模的扩大。提高SCP价值的一个特别有吸引力的方法是联合生产其他具有商业价值的生物化合物，如染料、香料、香料或抗氧化剂。如果这些都能由细菌产生并在下游加工过程中提取，那么SCP作为饲料成分的经济性可能会变得明显更有利。从长远来看，滚刀的设计将在技术上与目前生产更高价值化合物的现有品种竞争，但滚刀的优势是使用氢和二氧化碳输入流，而不是基于糖的输入。工业生物技术中的现有菌株经过高度适应或改造，以最大限度地提高生产率。从历史上看，HOB并不是这些操纵的目标，因为作为生产有机体，HOB缺乏内在的易感性。然而，能够在二氧化碳和氢气的混合物上生长是一个非常可取的特征，因为与依赖农产品作为输入流的过程相比，这种过程对环境的好处很大。此外，这种能力不是一种可以轻易转移到现有生产菌株上的能力。一种简单得多的方法是将相关特性从已建立的生产菌株转移到滚刀上。深支部有一个能够利用二氧化碳生长的滚刀图书馆。在该文库中，有几个菌株已经开发了基因工具包，可以进行复杂的基因工程。大肠杆菌是最广泛用于表达高价值蛋白的物种，这在很大程度上是因为为其开发的遗传工具箱。该项目的目的首先是通过设计强大的蛋白质表达系统，包括启动子、核糖体结合位点和强大的专用RNA聚合酶，来模仿使大肠杆菌成为工业生物技术中优势物种的许多发展。某些细菌物种自然进化得很好，能够产生特定类别的生物化合物，例如抗生素。其他物种将以这种方式进化，使它们成为生产化学上不同的化合物，如染料或香料的理想候选者。为了评估所选滚刀是否适合生产不同类别的化合物，将选择一系列化合物进行表达。这将有助于为商业环境中的优化和部署提供最合适的目标。另一个目标是通过蛋白质工程提高碳捕获的效率。这将包括确定碳固定的生物化学途径中的瓶颈，并建立瓶颈蛋白的不同版本的文库。

Industrial biotechnology relies on agriculture to provide the input energy in the form of sugars for bacterial fermentations. Sugars are the carbon source and the energy source in these traditional setups. However, certain bacterial species are able to utilise carbon dioxide as their carbon source while relying on hydrogen gas as their energy source; these species are Hydrogen Oxidising Bacteria (HOB). The biochemical route exercised in HOB is the most efficient form of biological carbon fixation including photosynthetic algae. Several companies are attempting to commercialise the use of HOB to make Single Cell Protein (SCP), which is sold as a proteinaceous feed ingredient. As a feed ingredient SCP has major environmental advantages over traditional feed proteins: it has a lower overall carbon footprint in addition to a dramatically lower land and water use. However, for full uptake of the technology commercially the product must have sufficiently high value to compensate for the input costs and relatively high capital costs of a commercial plant. Adoption of this technology benefits from the ramp up in interest and scaling of the hydrogen economy. One particularly attractive route for improving the value of SCP is to co-produce other biological compounds of commercial interest such as dyes, flavourings, fragrances, or antioxidants. If these can be produced by the bacteria and extracted during downstream processing then the economics of SCP as a feed ingredient may become significantly more favourable. In the long-term the HOB will be engineered to compete technically with established species which currently make higher value compounds, but the HOB will have the advantage of using a hydrogen and carbon dioxide input stream rather than a sugar-based input. Established strains in industrial biotechnology are highly adapted or engineered to maximise productivity. HOB have not been the target of these manipulations historically because of a lack of inherent predisposition as a production organism. However, the ability to grow on a mixture of carbon dioxide and hydrogen is a highly desirable trait because of the environmental benefits of this process compared to one dependent on agricultural products as an input stream. In addition, this ability is not one that can be easily transferred to the established production strains. A far simpler approach would be to transfer the relevant properties from the established production strains to the HOB. Deep Branch has a library of HOB capable of growing on carbon dioxide. Within that library there are several strains for which a genetic toolkit has been developed which allows sophisticated genetic engineering to be performed. Escherichia coli is the most widely used species for expressing high value proteins largely because of the genetic toolkit which has been developed for it. This project aims firstly to emulate many of the developments which have made E. coli the dominant species in industrial biotechnology primarily by engineering strong protein expression systems comprising promoters, ribosome binding sites, and powerful dedicated RNA polymerases. Certain bacterial species are naturally well evolved to produce a given class of biological compound for instance an antibiotic. Other species would have evolved in such a way as to make them ideal candidates for the production of chemically dissimilar compounds such as dyes or flavours. To assess the suitability of the chosen HOB for the production of different classes of compounds a range of compounds will be chosen for expression. This will help to inform the most appropriate target for optimisation and deployment in a commercial setting. Another goal will be to increase the efficiency of carbon capture via protein engineering. This will involve identifying the bottleneck in the biochemical pathway of carbon fixation and making a library of different versions of the bottleneck protein.