EVO-ENGINE: A directed evolution engine for engineering proteins and logic gates

自然选择是生物学中最强大的力量，它通过不断丰富那些存活和复制的生物来推动复杂有机体的进化，比如我们自己。这在以人工方式复制自然选择以获得有用蛋白质的“定向进化”领域已经被长期利用。定向进化使我们能够制造出具有复杂性质的蛋白质，这是单靠设计是不可能实现的。也许最著名的例子是现在广泛使用的抗癌药物赫赛汀，它最初是在实验室中使用一种名为“噬菌体展示”的技术进化而来的。这种方法使用被称为噬菌体的微小病毒--它只感染细菌--来进化新的蛋白质。随机蛋白质是由噬菌体制造的，只有粘在所需靶点上的蛋白质才会被保留并存活--因此它们被认为是在进化。在每次实验结束时，蛋白质都会被回收，并可以大量生产和纯化。通过人工选择(噬菌体展示)制造的大约20种药物已经被批准在人类身上使用，或者正在进行后期临床试验。因此，这项技术非常强大，已经极大地造福了人类。利用噬菌体和定向进化技术不仅可以制造具有新的“粘性”特性的蛋白质，而且还可以设计复杂的功能。此外，还有一个名为合成生物学的新科学领域，旨在重新设计生物网络和系统，以制造有用的酶、分子甚至小型机器--如生物计算机和选择性癌细胞调节器。合成生物学的一个分支旨在产生遗传电路--类似于标准电子学和计算机中使用的逻辑门--目前这些电路的制作非常费力，一个接一个，需要大量的反复试验。我们相信，通过应用定向进化，我们可以通过简单地进化噬菌体和细菌中的逻辑门来节省大量的时间和精力，以获得新一代有用的生物工具。我们已经建造了一个机器人原型(EVO引擎)，它可以在一系列选择压力下生长噬菌体和细菌。这样，只有包含功能逻辑门的逻辑门才能存活。随着时间的推移，随着随机突变和不断增加的选择压力，越来越好的逻辑门会进化。由此产生的组件具有广泛的生物技术应用，例如制造生物传感器(例如，检测环境中的污染物)或控制细菌中的合成电路以制造有用的产品(塑料、燃料和药品)。我们才刚刚开始利用定向进化的力量--大自然已经利用了数百万年--这个由BBSRC资助的项目有可能提供重大进展。

Natural selection is the most powerful force in biology and drives the evolution of complex organisms, such as ourselves, simply by continually enriching for those that survive and replicate. This has been long exploited in the field of "directed evolution" which copies natural selection in an artificial manner, to obtain useful proteins. Directed evolution allows us to make proteins with complex properties that would be impossible to achieve by design alone. Perhaps the best-known example is the now widely-used cancer drug, Herceptin, which was originally evolved in the laboratory using a technique called "phage display". This method uses tiny viruses called phage - which only infect bacteria - to evolve new proteins. Randomised proteins are made by the phage and only ones which stick to a desired target are retained and survive - and so they are said to be evolving. At the end of each experiment, the proteins are recovered and can be made in large quantities and purified. Around 20 drugs made by artificial selection (phage display) are already approved for use in humans or are in in late stage clinical trials. This technology is therefore very powerful and has already benefited humanity greatly. It is possible to use phage and directed evolution not just for making proteins with new "sticky" properties but for engineering complex functions. Moreover, there is a new scientific field called synthetic biology which aims to re-engineer biological networks and systems to make useful enzymes, molecules and even small machines - such as biological computers and selective cancer cell modulators. One branch of synthetic biology aims to generate genetic circuits - similar to the logic gates that are used in standard electronics and computers - and these are currently made very laboriously, one-by-one, with a huge amount of trial-and-error. By applying directed evolution we believe that we can save a lot of time and effort by simply evolving logic gates in phage and bacteria, in order to obtain a new generation of useful biological tools. We have already built a prototype robot (The EVO-ENGINE) that grows phage and bacteria under a series of selective pressures. In this way, only the ones containing a functional logic gate survive. Over time, with random mutations, and increasing selection pressures, better and better logic gates evolve. The resulting components have a vast range of biotechnology applications, such as making biological sensors (for example, to detect pollutants in the environment) or for controlling synthesis circuits in bacteria to make useful products (plastics, fuels and medicines). We are only beginning to harness the power of directed evolution - which nature has exploited for millions of years - and this BBSRC-funded project has the potential to provide a major advance.