BIOSCIENCE FOR RENEWABLE RESOURCES AND CLEAN GROWTH - Expanding Synthetic Biology using Biocompatible Reactions

生物相容化学这一新兴领域的目标是“改变”传统有机化学中使用的化学反应的用途，使之在活体微生物内和工程代谢途径旁运行。[1]这使得生物生产具有工业价值的非天然小分子成为可能，这些小分子无法通过合成生物学获得，否则将继续依赖于石化产品。然而，尽管近年来取得了重大进展，但对定义成功的生物相容性反应的分子描述符缺乏详细的了解。从学术角度来看，这一点特别耐人寻味，因为许多生物相容催化剂已经被设计成在没有电池的非水环境(例如有机溶剂)中工作。其中一个原因可能是微生物膜的存在。这些两亲性结构对所有微生物都是普遍存在的，并利用表面多糖和至少一个磷脂双层来保护细胞内部免受外部因素的影响。然而，细胞膜的有机环境也可以积累疏水代谢物(如苯乙烯)，并被假设通过将反应成分共同定位在细胞膜中而对生物相容反应产生积极影响，但尚未得到证实。这得到了我们实验室最近的一项观察的支持，即膜相关胶束可以共同定位生物相容反应的成分，并在工程大肠杆菌中加速产物的形成。[2]然而，这些理论仍然存在，细胞膜对生物相容反应的影响仍然完全没有被探索。本博士项目将在体外和体内研究微生物膜对生物相容性反应的影响(S)。我们还将使用现代合成生物学技术来操纵细胞膜，创建细胞内的‘纳米反应器’来定位活细菌内的生物相容反应，目的是创造新的途径，从二氧化碳、木质素和PET塑料废料等可持续原料中获得工业化合物和产品。[3，4]在四个全球工业合作伙伴的支持下，该项目结合了现代合成生物学、微生物学和化学生物学，利用工程微生物来推动目前工业生物技术的发展。该项目的多学科性质将使博士生能够熟练掌握一系列生物和化学实验室技术，包括一维/二维核磁共振、质谱学、高效液相色谱、气相色谱、DNA测序和组装方法、聚合酶链式反应、透射电子显微镜和大规模发酵生物反应器的使用。

The emerging field of biocompatible chemistry aims to "repurpose" chemical reactions traditionally used in organic chemistry to operate within living microorganisms and alongside engineered metabolic pathways.[1] This enables the bio-production of non-natural small molecules of industrial value that cannot be accessed via synthetic biology and would otherwise remain reliant on petrochemicals. However, despite significant progress in recent years, a detailed understanding of the molecular descriptors that define a successful biocompatible reaction are lacking. This is particularly intriguing from an academic perspective, as many biocompatible catalysts have been designed to operate in a non-aqueous environment (e.g. organic solvent) in the absence of cells. One reason for this could be the presence of microbial membranes. These amphiphilic structures are ubiquitous to all microorganisms and serve to protect the cell interior from external factors using surface glycans and at least one phospholipid bilayer. However, the organic environment of the cell membrane can also accumulate hydrophobic metabolites (e.g. styrene) and has been hypothesised, yet not proven, to impart a positive influence on biocompatible reactions by co-localising reaction components in the cell envelope. This is supported by a recent observation from our lab that membrane-associated micelles can both co-localise the components of a biocompatible reaction and accelerate product formation in engineered E. coli.[2] However, these theories remain just that and the influence of the cell membrane on biocompatible reactions remains completely unexplored. This PhD project will investigate the effect(s) of microbial membranes on biocompatible reactions in vitro and in vivo. We will also use modern synthetic biology techniques to manipulate the cell membrane, creating intracellular 'nano-reactors' to localise biocompatible reactions inside living bacteria with the aim of creating new pathways to industrial compounds and products from sustainable feedstocks such as CO2, lignin and PET plastic waste.[3,4] Supported by four global industrial partners, this project combines modern synthetic biology, microbiology and chemical biology to push the boundaries of what is currently possible in industrial biotechnology using engineered microorganisms.The multidisciplinary nature of this project will enable the PhD student to develop a strong proficiency in a range of biological and chemical laboratory techniques, including 1D/2D-NMR, mass spectrometry, HPLC, GC, DNA sequencing and assembly methods, PCR, transmission electron microscopy and the use of bioreactors for large-scale fermentations.