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引用次数: 0
摘要
如何获得新的蛋白质功能是分子生物学的一个核心问题。获得新功能的主要途径包括基因复制、重组或水平获取。可转座元件(Transposable elements,TE)越来越被认为是新型结构域编码序列的主要来源。然而,人们对可转座元件编码序列对蛋白质组进化的影响仍然缺乏研究。在这里,我们分析了横跨真菌王国系统发育广度的 1237 个基因组。我们扫描了蛋白质组,以寻找TE衍生结构域与其他常规蛋白质功能域共存的证据。我们检测到了 13,000 多种含有潜在 TE 衍生结构域的预测蛋白质,其中 825 种蛋白质在 5 个以上的基因组中被鉴定出来,这表明许多宿主与 TE 的融合可能在漫长的进化过程中持续存在。我们利用系统发育背景来确定单个 TE 衍生结构域的起源和保留情况。最常见的 TE 衍生结构域是源自 Academ、Kolobok 或 Helitron 的螺旋酶。我们在酵母科动物的基因组中发现了更高比例的假定 TE 共用,为这些普遍缺乏 TE 的基因组提供了意想不到的蛋白质新来源。我们详细研究了一个候选的宿主-TE融合基因,它具有异色转录沉默功能,可能在子囊菌的TE和基因调控中发挥作用。受影响的基因在该门中经历了多次完全或部分缺失。总之,我们的工作为推定的宿主-TE融合建立了一个全王国的视角,并促进了对候选融合蛋白的系统研究。
A systematic screen for co-option of transposable elements across the fungal kingdom
How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1237 genomes spanning the phylogenetic breadth of the fungal kingdom. We scanned proteomes for evidence of co-occurrence of TE-derived domains along with other conventional protein functional domains. We detected more than 13,000 predicted proteins containing potentially TE-derived domain, of which 825 were identified in more than five genomes, indicating that many host-TE fusions may have persisted over long evolutionary time scales. We used the phylogenetic context to identify the origin and retention of individual TE-derived domains. The most common TE-derived domains are helicases derived from Academ, Kolobok or Helitron. We found putative TE co-options at a higher rate in genomes of the Saccharomycotina, providing an unexpected source of protein novelty in these generally TE depleted genomes. We investigated in detail a candidate host-TE fusion with a heterochromatic transcriptional silencing function that may play a role in TE and gene regulation in ascomycetes. The affected gene underwent multiple full or partial losses within the phylum. Overall, our work establishes a kingdom-wide view of putative host-TE fusions and facilitates systematic investigations of candidate fusion proteins.
期刊介绍:
Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.