Evolution of a designed protein assembly encapsulating its own RNA genome.
Evolution of a designed protein assembly encapsulating its own RNA genome.
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DOI：
10.1038/nature25157
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发表时间：
2017-12-21
期刊：
影响因子：
64.8
通讯作者：
Baker D
中科院分区：
文献类型：
--
作者：
Butterfield GL;Lajoie MJ;Gustafson HH;Sellers DL;Nattermann U;Ellis D;Bale JB;Ke S;Lenz GH;Yehdego A;Ravichandran R;Pun SH;King NP;Baker D
在复杂的生物化学环境中，基因型与表型的耦合以及遗传物质的保护在生物系统中通过核酸封装巧妙地解决了进化的挑战。在最简单的例子中，病毒使用衣壳包裹它们的基因组。虽然这些自然发生的系统已经被修改以改变其趋向性并显示蛋白质或肽，但数十亿年的进化以牺牲模块性为代价来支持效率，使得病毒衣壳难以设计。由非病毒蛋白质组成的合成系统可以为药物输送和其他生物医学应用提供“空白石板”，同时避免与病毒相关的安全风险和工程挑战。在这里，我们创造了人工合成的核衣壳——通过计算设计的二十面体蛋白组件，其内表面带正电，能够包装它们自己的全长mRNA基因组——并通过使用大肠杆菌作为表达宿主产生多样化的群体，探索它们进化出病毒样特性的能力。几代人的进化导致基因组包装（>133倍），全鼠血液稳定性（处理6小时后保护的包装RNA从不足3.7%增加到71%）和体内循环时间（从不到5分钟到4.5小时）的显著改善。合成的核衣壳每11个二十面体组装一个全长RNA基因组，类似于最好的重组腺相关病毒（AAV）载体。我们的研究结果表明，通过简单的进化途径，蛋白质组装可以获得病毒样的基因组包装和保护。在对病毒进行“自上而下”的修改，使其在药物输送和疫苗应用方面安全有效方面作出了相当大的努力；通过计算设计合成纳米材料并通过进化优化它们的能力，现在使一种互补的“自下而上”方法在可编程性和控制方面具有相当大的优势。
The challenges of evolution in a complex biochemical environment—coupling genotype to phenotype and protecting the genetic material—are solved elegantly in biological systems by nucleic acid encapsulation. In the simplest examples, viruses use capsids to surround their genomes. While these naturally occurring systems have been modified to change their tropism and to display proteins or peptides, billions of years of evolution have favored efficiency at the expense of modularity, making viral capsids difficult to engineer. Synthetic systems composed of non-viral proteins could provide a “blank slate” to evolve desired properties for drug delivery and other biomedical applications, while avoiding the safety risks and engineering challenges associated with viruses. Here we create synthetic nucleocapsids—computationally designed icosahedral protein assemblies with positively charged inner surfaces capable of packaging their own full-length mRNA genomes—and explore their ability to evolve virus-like properties by generating diversified populations using Escherichia coli as an expression host. Several generations of evolution resulted in drastically improved genome packaging (>133-fold), stability in whole murine blood (from less than 3.7% to 71% of packaged RNA protected after 6 hours of treatment), and in vivo circulation time (from less than 5 minutes to 4.5 hours). The resulting synthetic nucleocapsids package one full-length RNA genome for every 11 icosahedral assemblies, similar to the best recombinant adeno-associated virus (AAV) vectors. Our results show that there are simple evolutionary paths through which protein assemblies can acquire virus-like genome packaging and protection. Considerable effort has been directed at “top-down” modification of viruses to be safe and effective for drug delivery and vaccine applications; the ability to computationally design synthetic nanomaterials and to optimize them through evolution now enables a complementary “bottom-up” approach with considerable advantages in programmability and control.
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