Biodesign and Engineering of Functionalized Spider Silk Variants

蜘蛛丝是一种高性能的生物材料，从个人防护服到医疗植入物的表面涂层，再到神经元再生的引导，都有令人兴奋的应用。从蜘蛛身上采集蛛丝是一件乏味的事情，而且在经济上也不可行。因此，在广泛的宿主生物（从细菌到山羊）中异源产丝一直是合成生物学研究的重点。在这个项目中，我们打算在这些进展的基础上创建用于各种应用的功能化蜘蛛丝衍生物库。该工作将包括四个紧密相连的工作包，它们将在项目生命周期内的几轮迭代设计-构建-测试-学习循环中相互作用。设计：项目的第一部分将利用最近可用的蜘蛛基因组和转录组序列来表征天然蜘蛛丝序列的全谱。目的是确定设计模式的丝绸序列，相关的生物物理性质的结果丝绸。构建：该项目的第二部分将测试推断的设计模式，使用DNA合成和自动化DNA组装管道来创建各种丝蛋白库，用于表达和表征。我们将使用大肠杆菌，以及生物技术上有前途的替代细菌宿主物种，来生产和分离工程丝蛋白。测试：为了促进这些文库的高通量材料测试，该项目的第三部分将侧重于为表达的丝绸开发合适的标签，这将允许快速确定表达水平以及与所得到的纺丝材料的关键生物物理特性的相关性。纺纱将基于一系列干法和湿法纺纱方法，所得到的纤维将使用一系列生物物理和材料科学分析方法进行测试。学习：项目的第四部分使用机器学习方法来预测改进的序列设计，这将在设计周期的几个迭代中进行测试。该项目提供全面的跨学科培训，由管理团队在生物学和工程学的界面上开创了一系列关键学科，对下一代生物技术科学家至关重要。

Spider silk is a high-performance biomaterial with exciting applications ranging from personal protective clothing to surface coatings for medical implants and guides for neuronal regeneration. Harvesting silk from spiders is tedious and economically not viable on a large scale. Consequently, the heterologous production of silk in a wide range of host organisms (from bacteria to goats) has been the focus of intense synthetic biology research. In this project, we intend to build on these advances to create libraries of functionalised spider silk derivatives for various applications.The work will include four closely interlinked work packages, which will interact through an iterative design - build - test - learn cycle in several rounds during the lifetime of the project.Design: The first part of the project will exploit recently available spider genome and transcriptome sequences to characterize the full spectrum of natural spider silk sequences. The aim is to identify design patterns of silk sequences that correlate with biophysical properties of the resulting silk.Build: The second part of the project will test the inferred design patterns, using DNA synthesis and automated DNA assembly pipelines to create diverse libraries of silk proteins, for expression and characterization. We will use Escherichia coli, as well as biotechnologically promising alternative bacterial host species, to produce and isolate the engineered silk proteins.Test: To facilitate the high-throughput materials testing of these libraries, a third part of the project will focus on the development of suitable tags for the expressed silks, which will allow rapid determination of expression levels and correlation with key biophysical properties of the resulting spun material. Spinning will be based on a range of dry- and wet-spinning approaches, and the resulting fibres will be tested using a collection of biophysical and materials science assays.Learn: The fourth part of the project uses machine learning methods to predict improved sequence designs, which will be tested in several iterations of the design cycle.This project provides comprehensive interdisciplinary training in methods pioneered by the supervisory team, across a range of key disciplines at the interface of biology and engineering, essential for the next generation of biotechnology scientists.