Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets.
Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets.
复制标题
PUF RNA结合蛋白及其mRNA靶标的进化保守和多样化。
DOI：
10.1371/journal.pbio.1002307
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发表时间：
2015
期刊：
影响因子：
9.8
通讯作者：
Herschlag D
中科院分区：
文献类型：
--
作者：
Hogan GJ;Brown PO;Herschlag D
通过获得和丢失由特异性调节RNA结合蛋白识别的序列来重编程基因的表达模式可能是生物调节程序进化中的主要机制。我们发现Puf 3直系同源物的RNA靶标在五个真核谱系中经过1亿至5亿年的进化而保守。针对80种真菌中的Puf蛋白及其靶点，我们构建了一个简约的进化历史模型。该模型需要Puf靶标的广泛和协调变化以及Puf基因数量的变化和RNA结合特异性的改变，包括：1）Puf 3与超过200种RNA的结合，这些RNA的蛋白质产物主要参与线粒体复合物的产生和组织，这种结合早于芽殖酵母和丝状真菌的起源，并保持了5亿年，在芽殖酵母的进化过程中。2)在丝状真菌中，值得注意的是，超过150个祖先Puf 3靶标通过Puf 4获得，其中一个谱系保持Puf 3和Puf 4作为调节剂，而姐妹谱系失去Puf 3作为这些RNA的调节剂。在丝状真菌中缺失Puf 4后这些mRNA的基因表达降低（N. crassa），而在芽殖酵母（S.酿酒酵母）表明，RNA调控网络的输出与丝状真菌中的Puf 4不同，而与芽殖酵母中的Puf 3不同。3)丝状真菌中的共调节Puf 4靶点集扩展到包括参与三羧酸（TCA）循环的线粒体基因以及芽殖酵母中不受Puf 3结合的其他具有线粒体功能的核编码RNA，这些观察结果为实质性重新布线提供了额外的证据转录后调节。4)Puf 3还在丝状真菌中扩大和多样化了其靶点，与编码线粒体电子传递链（ETC）复合物I的mRNA以及数百种具有非线粒体功能的其他mRNA相互作用。Puf蛋白的RNA靶点中的许多协调一致和保守的变化强烈支持RNA结合蛋白在协调基因表达中的广泛作用，正如Keene最初提出的那样。Puf协调的mRNA靶点和相同基因的转录控制的重新布线发生在进化的不同点，这表明通过RNA结合蛋白和转录因子进行了不同的适应。Puf目标和Puf蛋白的变化表明RNA结合蛋白及其RNA目标在基因表达的适应、重编程和功能中的不可或缺的参与。Puf蛋白及其RNA靶标的进化历史图显示，通过影响蛋白质-RNA相互作用的适应性突变对全球基因表达程序进行重编程是生物多样性的重要来源。我们开始追踪RNA结合蛋白的进化历史，以及它与靶标的相互作用如何随着进化而变化。识别这种自然历史是理解生物体之间的关键差异以及基因表达程序在进化过程中如何重新连接的一步。利用生物信息学和实验方法，我们广泛调查了一个特定的家庭的RNA结合蛋白的Puf蛋白，其蛋白质序列和靶RNA序列的相对良好的特点，在99个真核生物物种的结合目标的演变。我们发现了五组目标已经保守了至少1亿年的物种，然后利用大量真菌物种的基因组序列深入研究了Puf蛋白及其RNA靶标的保守性和变化。我们的分析确定了真菌自然史中的多种广泛的重新配置，并表明RNA结合蛋白及其RNA靶点深刻参与了基因表达的进化重编程，并有助于定义每个生物体独特的程序。继续揭示RNA结合蛋白及其相互作用的自然历史将为当今物种的基因表达程序提供一个独特的窗口，并指出设计基因表达程序的新方法。
Reprogramming of a gene’s expression pattern by acquisition and loss of sequences recognized by specific regulatory RNA binding proteins may be a major mechanism in the evolution of biological regulatory programs. We identified that RNA targets of Puf3 orthologs have been conserved over 100–500 million years of evolution in five eukaryotic lineages. Focusing on Puf proteins and their targets across 80 fungi, we constructed a parsimonious model for their evolutionary history. This model entails extensive and coordinated changes in the Puf targets as well as changes in the number of Puf genes and alterations of RNA binding specificity including that: 1) Binding of Puf3 to more than 200 RNAs whose protein products are predominantly involved in the production and organization of mitochondrial complexes predates the origin of budding yeasts and filamentous fungi and was maintained for 500 million years, throughout the evolution of budding yeast. 2) In filamentous fungi, remarkably, more than 150 of the ancestral Puf3 targets were gained by Puf4, with one lineage maintaining both Puf3 and Puf4 as regulators and a sister lineage losing Puf3 as a regulator of these RNAs. The decrease in gene expression of these mRNAs upon deletion of Puf4 in filamentous fungi (N. crassa) in contrast to the increase upon Puf3 deletion in budding yeast (S. cerevisiae) suggests that the output of the RNA regulatory network is different with Puf4 in filamentous fungi than with Puf3 in budding yeast. 3) The coregulated Puf4 target set in filamentous fungi expanded to include mitochondrial genes involved in the tricarboxylic acid (TCA) cycle and other nuclear-encoded RNAs with mitochondrial function not bound by Puf3 in budding yeast, observations that provide additional evidence for substantial rewiring of post-transcriptional regulation. 4) Puf3 also expanded and diversified its targets in filamentous fungi, gaining interactions with the mRNAs encoding the mitochondrial electron transport chain (ETC) complex I as well as hundreds of other mRNAs with nonmitochondrial functions. The many concerted and conserved changes in the RNA targets of Puf proteins strongly support an extensive role of RNA binding proteins in coordinating gene expression, as originally proposed by Keene. Rewiring of Puf-coordinated mRNA targets and transcriptional control of the same genes occurred at different points in evolution, suggesting that there have been distinct adaptations via RNA binding proteins and transcription factors. The changes in Puf targets and in the Puf proteins indicate an integral involvement of RNA binding proteins and their RNA targets in the adaptation, reprogramming, and function of gene expression. A map of the evolutionary history of Puf proteins and their RNA targets shows that reprogramming of global gene expression programs via adaptive mutations that affect protein-RNA interactions is an important source of biological diversity. We set out to trace the evolutionary history of an RNA binding protein and how its interactions with targets change over evolution. Identifying this natural history is a step toward understanding the critical differences between organisms and how gene expression programs are rewired during evolution. Using bioinformatics and experimental approaches, we broadly surveyed the evolution of binding targets of a particular family of RNA binding proteins—the Puf proteins, whose protein sequences and target RNA sequences are relatively well-characterized—across 99 eukaryotic species. We found five groups of species in which targets have been conserved for at least 100 million years and then took advantage of genome sequences from a large number of fungal species to deeply investigate the conservation and changes in Puf proteins and their RNA targets. Our analyses identified multiple and extensive reconfigurations during the natural history of fungi and suggest that RNA binding proteins and their RNA targets are profoundly involved in evolutionary reprogramming of gene expression and help define distinct programs unique to each organism. Continuing to uncover the natural history of RNA binding proteins and their interactions will provide a unique window into the gene expression programs of present day species and point to new ways to engineer gene expression programs.