Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, NY 10016.
Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201.
Proc Natl Acad Sci U S A. 2023 Jun 27;120(26):e2304082120. doi: 10.1073/pnas.2304082120. Epub 2023 Jun 20.
A synthetic biology approach toward constructing an RNA-based genome expands our understanding of living things and opens avenues for technological advancement. For the precise design of an artificial RNA replicon either from scratch or based on a natural RNA replicon, understanding structure-function relationships of RNA sequences is critical. However, our knowledge remains limited to a few particular structural elements intensively studied so far. Here, we conducted a series of site-directed mutagenesis studies of yeast narnaviruses ScNV20S and ScNV23S, perhaps the simplest natural autonomous RNA replicons, to identify RNA elements required for maintenance and replication. RNA structure disruption corresponding to various portions of the entire narnavirus genome suggests that pervasive RNA folding, in addition to the precise secondary structure of genome termini, is essential for maintenance of the RNA replicon in vivo. Computational RNA structure analyses suggest that this scenario likely applies to other "narna-like" viruses. This finding implies selective pressure on these simplest autonomous natural RNA replicons to fold into a unique structure that acquires both thermodynamic and biological stability. We propose the importance of pervasive RNA folding for the design of RNA replicons that could serve as a platform for in vivo continuous evolution as well as an interesting model to study the origin of life.
一种基于 RNA 的合成生物学方法构建基因组，拓展了我们对生物的认识，并为技术进步开辟了道路。为了精确设计人工 RNA 复制子，无论是从头开始还是基于天然 RNA 复制子，理解 RNA 序列的结构-功能关系至关重要。然而，我们的知识仍然局限于迄今为止深入研究的少数特定结构元件。在这里，我们对酵母 narnavirus ScNV20S 和 ScNV23S 进行了一系列定点诱变研究，这两种病毒可能是最简单的天然自主 RNA 复制子，以鉴定维持和复制所需的 RNA 元件。与整个 narnavirus 基因组的各个部分相对应的 RNA 结构破坏表明，除了基因组末端的精确二级结构之外，普遍的 RNA 折叠对于 RNA 复制子在体内的维持是必不可少的。计算 RNA 结构分析表明，这种情况可能适用于其他“narna-like”病毒。这一发现意味着对这些最简单的自主天然 RNA 复制子施加了选择性压力，要求它们折叠成一种独特的结构，从而获得热力学和生物学稳定性。我们提出了普遍的 RNA 折叠对于 RNA 复制子设计的重要性，这可以作为体内连续进化的平台，以及研究生命起源的有趣模型。
