21ENGBIO BBEB: Boosting the Bandwidth of Engineered Biology

21ENGBIO BBEB：提高工程生物学的带宽

• 批准号: BB/W012642/1
• 负责人: Ciarán Kelly
• 金额: $ 10.23万
• 依托单位: Northumbria University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FW012642%2F1
• 关键词: 21ENGBIO; BBEB; Boosting; Bandwidth; Engineered

In natural biological systems many regulatory processes and functions operate with incredibly short timescales (within milliseconds). This enables organisms such as bacteria to rapidly change their behaviour in response to external triggers. In contrast, most engineered biological systems to date (e.g. bacterial cells containing synthetic networks of genes and proteins as circuits), operate with much longer timescales (tens of minutes). This is because they typically rely on the expression of genes, the production of proteins and the accumulation of sufficient concentrations of the fully folded active protein in the cell. We are defining this slow rate of sensing and production of a measurable response in engineered biological systems, as having "low bandwidth". To address this shortcoming of typical engineered biotechnologies, we aim to boost the bandwidth by combining cells containing completely novel, fast-acting, non-native biological circuits, with robotic measurement and actuation hardware, allowing rapid measurement and control of individual cells in an array. To realise this exciting and ambitious aim, we will divide the work into three components.The biological component of this work will focus on the construction of electron-conducting protein wires from the surface of a bacterial cell to specific protein targets inside the cell. Light-harvesting proteins will be introduced to harvest the energy of light at the cell membrane and drive electrons along these wires. Combinations of proteins that are able to receive and transfer electrons will be tested to propagate the signal along the wires. Finally, the electrons will be used to switch on and off important enzymes inside the cell, using a variety of processes that are highly-responsive to electron transfer. Once identified, we will fuse promising wire protein candidates to each other, using flexible amino-acid linkers, to optimise the switchability and specificity of the system. We believe this approach will allow us to realise engineered biological systems with the sub-second timescales that are crucial for complex biotechnologies.Supporting the biological engineering work, the team will develop an automated and massively parallelised experimental hardware platform that can interface with an off-the-shelf microscope. This platform will use a modified data projector to dynamically regulate the wavelength and intensity of light delivered to single-cells. This will be integrated with high-speed image processing and control algorithms to rapidly measure and regulate the behaviour of many cells simultaneously. Combining the above technologies, we will demonstrate an integrated platform for high-bandwidth engineered biology. This will be applied to realise rapid control of microbial pattern formation across hundreds of single-cells. Additionally, as a public engagement demonstrator, we will use the "bio-hybrid" platform to transmit real-time audio data, thereby acting as a "microbial telephone repeater". These demonstrations will form the basis of the longer-term vision of our project: to create the biological and robotic technologies required to dramatically increase the speed of action of engineered biotechnologies in disparate applications.

在自然生物系统中，许多调节过程和功能的运行时间非常短（毫秒内）。这使得细菌等生物能够迅速改变其行为以响应外部触发。相比之下，迄今为止大多数工程生物系统（例如含有基因和蛋白质合成网络作为电路的细菌细胞）的运行时间要长得多（数十分钟）。这是因为它们通常依赖于基因的表达、蛋白质的产生和细胞中足够浓度的完全折叠的活性蛋白的积累。我们将这种缓慢的感知速度和工程生物系统中可测量反应的产生定义为“低带宽”。为了解决典型的工程生物技术的这一缺点，我们的目标是通过将包含完全新颖的，快速作用的，非原生生物电路的细胞与机器人测量和驱动硬件相结合来提高带宽，从而允许快速测量和控制阵列中的单个细胞。为了实现这个令人兴奋和雄心勃勃的目标，我们将把工作分为三个部分：生物学部分的工作将集中在构建从细菌细胞表面到细胞内特定蛋白质目标的电子传导蛋白质导线。将引入捕光蛋白以在细胞膜上收集光能并驱动电子沿着这些导线。能够接收和传递电子的蛋白质组合将被测试沿着电线沿着传播信号。最后，电子将被用来打开和关闭细胞内的重要酶，使用各种对电子转移高度敏感的过程。一旦确定，我们将使用灵活的氨基酸接头将有希望的金属丝蛋白候选物相互融合，以优化系统的可切换性和特异性。我们相信这种方法将使我们能够实现亚秒级的工程生物系统，这对复杂的生物技术至关重要。为了支持生物工程工作，该团队将开发一个自动化和大规模并行化的实验硬件平台，该平台可以与现成的显微镜连接。该平台将使用改进的数据投影仪来动态调节传递到单细胞的光的波长和强度。这将与高速图像处理和控制算法相结合，以快速测量和同时调节许多细胞的行为。结合上述技术，我们将展示一个高带宽工程生物学的集成平台。这将被应用于实现快速控制数百个单细胞的微生物模式形成。此外，作为公众参与的示范者，我们将使用“生物混合”平台传输实时音频数据，从而充当“微生物电话中继器”。这些演示将构成我们项目长期愿景的基础：创造所需的生物和机器人技术，以大幅提高工程生物技术在不同应用中的行动速度。