Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
Institute of Molecular Biology, University of Oregon, Eugene, OR 97403.
Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):E2816-E2825. doi: 10.1073/pnas.1617777114. Epub 2017 Mar 20.
Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of transcription factors and their cognate sites. The evolution of RNA-protein regulatory networks is far less understood. The PUF (Pumilio and FBF) family of RNA regulatory proteins controls the translation, stability, and movements of hundreds of mRNAs in a single species. We probe the evolution of PUF-RNA networks by direct identification of the mRNAs bound to PUF proteins in budding and filamentous fungi and by computational analyses of orthologous RNAs from 62 fungal species. Our findings reveal that PUF proteins gain and lose mRNAs with related and emergent biological functions during evolution. We demonstrate at least two independent rewiring events for PUF3 orthologs, independent but convergent evolution of PUF4/5 binding specificity and the rewiring of the PUF4/5 regulons in different fungal lineages. These findings demonstrate plasticity in RNA regulatory networks and suggest ways in which their rewiring occurs.
调控网络的改变有助于进化的改变。转录因子及其同源结合位点的结合特异性的改变会导致转录网络的重新配置。RNA 蛋白调控网络的进化还远未被了解。PUF（Pumilio 和 FBF）家族的 RNA 调控蛋白控制着一个物种中数百个 mRNA 的翻译、稳定性和运动。我们通过直接鉴定出在芽殖和丝状真菌中与 PUF 蛋白结合的 mRNA，以及对来自 62 种真菌的同源 RNA 的计算分析，来探测 PUF-RNA 网络的进化。我们的研究结果表明，PUF 蛋白在进化过程中获得和失去了具有相关和新兴生物学功能的 mRNAs。我们至少证明了 PUF3 同源物的两个独立重布线事件，PUF4/5 结合特异性的独立但趋同进化，以及不同真菌谱系中 PUF4/5 调控网络的重布线。这些发现证明了 RNA 调控网络的灵活性，并提出了其重布线的方式。
