Researchers get two genetic codes to work at the same time
Researchers get two genetic codes to work at the same time
研究人员实现两种遗传密码同时运作
The genetic code is what life everywhere uses to convert the information contained in DNA into specific protein sequences. With minor variations, the same genetic code is used by every living thing on Earth, suggesting it was already present in the last common ancestor of all of them. It’s not an easy thing to change, because so many things in every cell depend on it. 遗传密码是地球上所有生命用来将 DNA 中包含的信息转化为特定蛋白质序列的工具。除了细微的差异外，地球上所有的生物都使用相同的遗传密码，这表明它在所有生物的最后共同祖先中就已经存在了。改变遗传密码并非易事，因为细胞内的许多功能都依赖于它。
Nevertheless, some preliminary steps have been taken. Researchers have managed to add some new amino acids to a bacterial cell and were able to make proteins that were one amino acid less than usual. But it’s a slog; for some of this work, people have had to re-engineer every single gene in a bacterial genome. Now, researchers have found a way to operate two separate genetic codes simultaneously, avoiding the need to do any work to compensate for altering the code that every protein in a cell relies on. They didn’t test it in an actual cell, and it might cause some problems there. But it’s a creative solution that should accelerate some synthetic biology work. 尽管如此，研究人员已经迈出了一些初步步伐。他们成功地向细菌细胞中添加了一些新的氨基酸，并能够制造出比平时少一个氨基酸的蛋白质。但这过程非常艰巨；为了完成部分工作，人们不得不重新设计细菌基因组中的每一个基因。现在，研究人员找到了一种同时运行两种独立遗传密码的方法，从而避免了因改变细胞内所有蛋白质所依赖的密码而必须进行的补偿工作。虽然他们尚未在实际细胞中进行测试，且该方法在实际应用中可能会引发一些问题，但这仍是一个创造性的解决方案，有望加速合成生物学的研究进程。
Biology 101
生物学基础
To understand how this works, we need to go back to that high school biology class you might not have paid much attention to. In the genome, part of most genes is dedicated to encoding a protein. The linear arrangement of bases in the DNA gets directly translated into the linear sequence of amino acids that make up a protein. Each set of three bases in the DNA corresponds to a specific amino acid (with three exceptions, each of which signals the end of the protein). 要理解其工作原理，我们需要回顾一下你可能没怎么留意的中学生物课。在基因组中，大多数基因的一部分专门用于编码蛋白质。DNA 中碱基的线性排列被直接翻译成构成蛋白质的氨基酸线性序列。DNA 中每三个碱基对应一个特定的氨基酸（有三个例外，它们分别代表蛋白质合成的终止信号）。
That translation isn’t direct. DNA is first copied into a messenger RNA. Then, a complex of proteins and RNA called a ribosome latches onto the messenger RNA and starts translating it, one amino acid at a time. That translation relies on yet another type of RNA, the transfer RNA (tRNA). While transfer RNAs fold up into a complex structure, they all have two key parts. On one side is a set of three bases that can pair with the messenger RNA, matching the three bases of the genetic code. At the other end, the tRNA is chemically linked to the corresponding amino acid. The ribosome ensures that the right transfer RNA is base paired, and then transfers the amino acid it carries to the growing protein chain. 这种翻译并非直接进行。DNA 首先被复制成信使 RNA (mRNA)。随后，一种由蛋白质和 RNA 组成的复合体——核糖体，会附着在信使 RNA 上，并开始逐个氨基酸地进行翻译。这种翻译依赖于另一种 RNA，即转运 RNA (tRNA)。虽然 tRNA 折叠成复杂的结构，但它们都有两个关键部分：一端是一组可以与信使 RNA 配对的三个碱基，与遗传密码的三个碱基相匹配；另一端则通过化学键连接到相应的氨基酸上。核糖体确保正确的 tRNA 完成碱基配对，然后将其携带的氨基酸转移到正在生长的蛋白质链上。
A key part of this system is not directly involved in the process: the enzymes that chemically link the transfer RNAs to the correct amino acid. These enzymes need to recognize both the three-base code on the transfer RNA, and the appropriate amino acid to add to it. (This process is often referred to as “charging” a tRNA.) To make comprehensive changes to the genetic code, you have to modify some combination of these factors: the sequence of genes, the sequence of transfer RNAs, and/or the enzymes that charge the transfer RNAs. (The only thing that doesn’t need to be changed is the ribosome itself.) And you have to do it in a way that either doesn’t impact every gene in an organism’s genome, or edit all the genes to compensate. All of which is, not surprisingly, rather difficult. 该系统中有一个关键部分并不直接参与翻译过程：即负责将 tRNA 与正确氨基酸进行化学连接的酶。这些酶需要识别 tRNA 上的三碱基密码，以及需要添加的相应氨基酸。（这个过程通常被称为 tRNA 的“充电”。）要对遗传密码进行全面修改，必须结合修改以下因素：基因序列、tRNA 序列和/或负责 tRNA 充电的酶。（唯一不需要改变的是核糖体本身。）而且，你必须以一种不影响生物体基因组中所有基因的方式进行，或者通过编辑所有基因来进行补偿。不出所料，这一切都相当困难。
Why not both?
为什么不能两者兼得？
The new work comes from a research group led by synthetic biologist and serial entrepreneur George Church. He’s definitely interested in exploring alternate genetic codes and found the slog needed to do so frustrating. A lot of the paper describing this work focuses on developing automated systems that could streamline some of the testing and screening. If those sorts of things interest you, the paper will be great. But for here, we’re going to focus on the biology. 这项新研究来自合成生物学家兼连续创业者乔治·丘奇 (George Church) 领导的研究小组。他一直热衷于探索替代遗传密码，并发现实现这一目标的过程极其繁琐。描述这项工作的论文中，很大一部分重点在于开发能够简化测试和筛选流程的自动化系统。如果你对这些感兴趣，这篇论文会非常棒。但在这里，我们将重点关注其生物学原理。
The key insight behind the work is that the ribosome matters, but in a way that doesn’t really matter. Some parts of the ribosome’s RNA base pair with a group of bases near one of the ends of the transfer RNA, ensuring that it’s working with the correct type of RNA. While this is critical biochemically, it doesn’t matter practically because every single transfer RNA has the same sequence in that location. But what, the new paper asks, if it didn’t? 这项研究背后的关键洞察在于：核糖体虽然重要，但在某种程度上又“没那么重要”。核糖体 RNA 的某些部分会与 tRNA 末端附近的碱基组进行配对，以确保其处理的是正确类型的 RNA。虽然这在生物化学上至关重要，但在实际操作中却无关紧要，因为每一个 tRNA 在该位置都有相同的序列。但新论文提出了一个问题：如果它们不相同会怎样？
Since we know the precise locations that base pair on the ribosome and transfer RNA, we can potentially change the sequence of one of those—that breaks the normal base pairing, but we can then make a change in the other that restores it. In theory, we can use this to create two populations of transfer RNAs that only differ at this small sequence. One of them would only be able to interact with the normal ribosomes, while the other could only interact with a separate population of ribosomes engineered to use a modified RNA. The paper converts this theory into practice. 既然我们已经知道了核糖体和 tRNA 上进行碱基配对的精确位置，我们就有可能改变其中一个的序列——这会破坏正常的碱基配对，但我们可以通过改变另一个序列来恢复它。理论上，我们可以利用这一点创建两组仅在这一小段序列上存在差异的 tRNA。其中一组只能与正常核糖体相互作用，而另一组只能与经过改造、使用修饰后 RNA 的核糖体相互作用。该论文将这一理论转化为了实践。
Two codes
两种密码
One of the big questions was whether you could charge a transfer RNA after modifying this sequence. This seems like a simple question, but it’s much less so, since it’s not something anybody has asked before. So the team here had to invent its own method for answering it, one involving a subtle difference in the chemical reactions that charged and uncharged amino acids can participate in. Detecting that required “cell-free translation, robotics, next-generation sequencing, and analytical chemistry.” 一个重大问题是：在修改了这段序列后，是否还能对 tRNA 进行充电？这看起来是个简单的问题，但实际上复杂得多，因为此前从未有人提出过。因此，研究团队不得不发明自己的方法来回答这个问题，该方法涉及已充电和未充电氨基酸在化学反应中参与度的细微差异。检测这一点需要用到“无细胞翻译、机器人技术、下一代测序和分析化学”。
But it did provide an answer: Depending on the specific changes made to the transfer RNAs, most of them could be charged, albeit typically at a lower efficiency than a normal transfer RNA. Some sequence changes were tolerated better than others. With these charged alternative transfer RNAs in hand, the researchers confirmed that they were ignored by normal ribosomes. But if you used a ribosome with the corresponding changes that restored base pairing, it would happily make a protein using them. So, the researchers had two different populations of tRNA. 但它确实给出了答案：根据对 tRNA 所做的具体修改，大多数 tRNA 都可以被充电，尽管效率通常低于正常的 tRNA。某些序列变化比其他变化更容易被接受。在获得这些已充电的替代 tRNA 后，研究人员证实它们会被正常核糖体忽略。但如果你使用经过相应修改以恢复碱基配对的核糖体，它就能顺利地利用这些 tRNA 合成蛋白质。至此，研究人员成功获得了两组不同的 tRNA。