Connections between distinct catalytic RNA motifs through networks of mutations that retain catalytic function (neutral networks) were likely central to the evolution of biocatalysis. Despite suggestions that functional RNAs collectively form an interconnected web of neutral networks, little evidence has emerged to demonstrate the existence of such intersecting networks in naturally occurring RNAs. Here we show that neutral networks of two naturally occurring, seemingly unrelated endonucleolytic ribozymes, the hammerhead (HH) and hairpin (HP), intersect. Sequences at the intersection of these networks exhibit catalytic functions corresponding to both ribozymes by potentially populating both catalytic folds and enable a smooth crossover between the two. Small and structurally simple endonucleolytic motifs like the HH ribozyme could, through mutational walks along their neutral networks, encounter novel catalytic phenotypes, and structurally flexible, bifunctional sequences at the intersection of these networks could have acted as nodes for evolutionary diversification in an RNA world. Considering the simplicity and small size of the HH ribozyme, we propose that this self-cleaving motif could have been a precursor to other more complex endonucleolytic ribozymes. More generally, our results suggest that RNAs that possess distinct sequences, structures, and catalytic functions, can potentially share evolutionary history through mutational connections in sequence space.

中文翻译：

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作为复杂核酸内切核酶前体的锤头自切割基序

通过保留催化功能的突变网络（中性网络），不同催化 RNA 基序之间的联系可能是生物催化进化的核心。尽管建议功能性 RNA 共同形成一个相互连接的中性网络网络，但几乎没有证据表明在天然存在的 RNA 中存在这种相交网络。在这里，我们展示了两种天然存在的、看似无关的内切核酶、锤头状 (HH) 和发夹 (HP) 的中性网络相交。这些网络交叉处的序列通过潜在地填充两个催化折叠并实现两者之间的平滑交叉，表现出与两种核酶相对应的催化功能。像 HH 核酶这样的小而结构简单的核酸内切基序可以，通过沿着它们的中性网络进行突变行走，遇到新的催化表型，并且在这些网络的交叉点处结构灵活的双功能序列可以作为 RNA 世界中进化多样化的节点。考虑到 HH 核酶的简单性和小尺寸，我们提出这种自切割基序可能是其他更复杂的内切核酶的前体。更一般地说，我们的研究结果表明，具有不同序列、结构和催化功能的 RNA，可以通过序列空间中的突变连接潜在地共享进化历史。这些网络交汇处的双功能序列可以作为 RNA 世界中进化多样化的节点。考虑到 HH 核酶的简单性和小尺寸，我们提出这种自切割基序可能是其他更复杂的内切核酶的前体。更一般地说，我们的研究结果表明，具有不同序列、结构和催化功能的 RNA，可以通过序列空间中的突变连接潜在地共享进化历史。这些网络交汇处的双功能序列可以作为 RNA 世界中进化多样化的节点。考虑到 HH 核酶的简单性和小尺寸，我们提出这种自切割基序可能是其他更复杂的内切核酶的前体。更一般地说，我们的研究结果表明，具有不同序列、结构和催化功能的 RNA，可以通过序列空间中的突变连接潜在地共享进化历史。