Towards designing synthetic molecular motors: in situ visualization of the progressive evolution of molecular gearing by bacteria

我们正在进入一个新时代，我们将制造自己的微型“纳米级”机械。我们希望这种机器能够生产食物、燃料和清洁水，帮助对抗疾病，准确地读取和写入DNA信息，并执行零排放的机械任务。最近的成功来自于使用在微生物内部进化的机器，这些机器使用活细胞制造化学品并将信息存储在DNA中，但我们还没有做太多的工作来制造我们自己的“分子马达”，在细胞内执行物理任务。这主要是因为我们受到了技术的限制：我们无法看到在billenia上细胞内自然进化的机器，所以我们很难理解它们是如何工作或进化的-以及如何自己做（相反，我们不得不打破细胞并净化机器来研究它们，这个过程通常会严重影响我们试图研究的机器）。值得庆幸的是，最近我们已经开发出了一种方法，通过冷冻细菌并将其放入电子显微镜中，来对细胞内的机器进行三维成像。我最近接受了使用这项新技术的培训。我用它来研究可能是分子发动机最迷人的例子，一个旋转螺旋形推进器（“鞭毛”）的发动机，把细菌推向好的方向。但是鞭毛马达不仅仅是地球生命奇迹的一个迷人的例子，研究它对我们有很多有用的东西。其中一个用途是研究如何利用它的低排放能源。一个电动机从E。大肠杆菌（一种研究得很好的细菌），如果它是人的大小，将像飞机的涡轮螺旋桨发动机一样强大！一段时间以来，人们已经知道，不同的发动机比E。但是我们不知道为什么因为我们还没能看到它们。当我们使用新技术对整个细胞进行成像时，这一切都发生了变化，以观察各种细菌来观察它们的马达。一种名为空肠弯曲杆菌（Campylobacter jejuni）的细菌，或简称为“Campy”，让我们感到有趣：它不仅比其他细菌更好地在非常粘稠的液体中游泳，而且产生旋转的部分比其他细菌更大，我们认为这使得一个更强大的马达帮助Campy游泳。特别有趣的是，Campy已经进化出了这种适应。如果我们能理解它是如何做到这一点的，我们可能会尝试复制它来修改我们自己的规格的电机。然后，我们可以控制细菌运送货物，选择性地寻找和破坏癌细胞，推动微型转子，或将液体混合在一起。我的目标是收集数据，以充分了解Campy电机是如何进化的。为了做到这一点，我将图像坎比，并同时改变DNA改变外观的电机。这样我们就能知道发动机的零件在哪里了。同时，我会想象一种细菌，它看起来像是在Campy和E之间。大肠杆菌中，看看这个“中途”表亲是否告诉我们关于Campy必须遵循的进化途径的任何信息。最后，我们将从所有这些细菌中取出马达的每一部分，并使用它们的DNA序列来确定它们的祖先。这将帮助我们看到Campy电机在哪里招募了额外的部件，使其更强大。除了这些目标，我还计划开发方法来确定电机的哪些部件可以用于何处。为了做到这一点，我将开发计算机程序来设计更好的方法，用额外的比特来“标记”马达的组件。这些额外的比特将很容易在我们收集的3D结构中看到，使我们能够直接可视化标记的组件在哪里。事实上，如果这一研究成功，它将开启下一个篇章：我们将不再使用这些标签来理解马达，而是将它们作为修改，通过指导进化来改进。也许有一天我们会有一个马达，我们可以齿轮，因为我们希望。

We are entering a new era in which we will make our own tiny 'nanoscale' machinery. We hope that this machinery will produce food, fuel, and clean water, help fight disease, accurately read and write information to DNA, and perform emission-free mechanical tasks. Recent successes have come from using machines that have evolved inside microbes in making chemicals using living cells and storing information in DNA, but we haven't done much work to make our own "molecular motors" that perform physical tasks inside cells. This is mainly because we've been limited by our techniques: we haven't been able to see the machines that have naturally evolved inside cells over the billenia, so we've found it difficult to understand how they work or evolved - and how to do it ourselves (instead we've had to break open cells and purify the machines to study them, a process that often badly affects the machinery that we're trying to study). Thankfully recently we've developed ways to to image machines in 3-D inside cells by freezing the bacteria and putting them in an electron microscope. I recently trained to use this new technology. I've used it to study probably the most captivating example of molecular motors, a motor that spins a spiral-shaped propellor (the "flagellum") to push bacteria in good directions. But the flagellar motor is more than just a fascinating example of the wonders of life on earth, and studying it promises many useful things to us. One use would be to work out how to harness its emission-less power. A single motor from E. coli (a very well studied bacterium), if it were the man-sized, would be as powerful as an airplane turboprop engine! It has been known for some time that different motors are stronger or weaker than the E. coli motor, but we don't know why because we haven't been able to see them. This all changed when we used the new technique for imaging whole cells to look at a wide range of bacteria to see their motors. A bacterium called Campylobacter jejuni, or just "Campy", struck us as interesting: not only was it known to swim through very sticky fluids better than other bacteria, but the part that generates rotation is bigger than other bacteria, which we think makes a stronger motor that helps Campy swim. What makes this particularly interesting is that Campy has evolved this adaptation. If we could understand how it did this, we might try to copy it to modify motors to our own specifications. Then we might control bacteria to ferry cargoes around, selectively seek and destroy cancers cells, push miniature rotors, or mix fluids together.I aim to collect data to fully understand how the Campy motor evolved. To do this I'll image Campy, and simultaneously alter the DNA to change the appearance of the motor. In this way we'll be able to work out where parts of the motor are. At the same time I'll image a bacterium that looks like it's halfway between Campy and E. coli to see if this "half-way" cousin tells us anything about the evolutionary pathway that Campy had to follow. Finally we'll take each part of the motors from all of these bacteria and use their DNA sequences to work out their ancestry. This will help us to see where the Campy motor recruited the additional parts that it uses to be more powerful.As well as these aims I'm planning on developing methods to work out which parts of the motor go where. To do this I'm going to develop computer programs to design better ways to 'tag' components of the motor with extra bits. These extra bits will be easily visible in the 3-D structures that we collect, enabling us to directly visualize where the tagged components are. Indeed, if this works out it will open the next chapter: instead of using these tags to understand the motor, we'll use them as modifications that we can improve by directing evolution. Maybe someday we'll have a motor that we can gear as we wish.