Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity.
Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity.
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DOI：
10.3389/fmicb.2021.739000
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发表时间：
2021
影响因子：
5.2
通讯作者：
Ebersberger I
中科院分区：
文献类型：
--
作者：
Birikmen M;Bohnsack KE;Tran V;Somayaji S;Bohnsack MT;Ebersberger I
核糖体组装是一个重要且精心设计的细胞过程。在真核生物中，分布在核仁、细胞核和细胞质中的 100 种蛋白质协调四种核糖体 RNA (rRNA) 和大约 80 种核糖体蛋白质 (RP) 逐步组装成成熟核糖体亚基。由于组装过程固有的复杂性，识别核糖体生物发生因素的功能研究，更重要的是，它们的精确功能和相互作用仅限于少数且非常完善的模型生物体。尽管在酵母（酿酒酵母）中得到了最好的表征，但与疾病的新联系以及额外调控层的发现最近鼓励了对人类细胞中的途径进行更深入的分析。在古细菌中，核糖体的生物发生尚不清楚。然而，它们更简单的亚细胞结构应该允许不太复杂的组装程序，有可能提供对核糖体生物发生的功能要素的深入了解，这种生物发生早在古细菌和真核生物多样化之前就已经进化了。在这里，我们使用全面的系统发育分析设置，将目标直系同源搜索与蛋白质结构域相似性的自动评分相结合，并评估搜索敏感性何时受到限制，以追踪跨生命树的 982 个分类群（包括 727 个古细菌）中的 301 个精心策划的真核核糖体生物发生因子。我们表明因子丢失和因子功能的谱系特异性修饰都会调节核糖体生物发生，并且我们强调直系同源搜索的有限敏感性可能会混淆进化结论。投射到古菌领域，我们发现在分析的分类群中只有少数因素一致存在，并且谱系特异性损失很常见。虽然 Asgard 组的成员在核糖体生物发生因子 (RBF) 的库存方面并不特殊，但他们在一个分类群中将最多数量的真核 RBF 直系同源物结合在一起。以大核糖体亚基成熟为例，我们证明古细菌追求真核生物中相应步骤的简化版本。这一过程的大部分复杂性是在真核谱系上通过核糖体蛋白的复制及其随后功能多样化而进化成核糖体生物发生因子的。这凸显了研究古细菌核糖体生物发生也为理解真核生物的过程提供了基础信息。
Ribosome assembly is an essential and carefully choreographed cellular process. In eukaryotes, several 100 proteins, distributed across the nucleolus, nucleus, and cytoplasm, co-ordinate the step-wise assembly of four ribosomal RNAs (rRNAs) and approximately 80 ribosomal proteins (RPs) into the mature ribosomal subunits. Due to the inherent complexity of the assembly process, functional studies identifying ribosome biogenesis factors and, more importantly, their precise functions and interplay are confined to a few and very well-established model organisms. Although best characterized in yeast (Saccharomyces cerevisiae), emerging links to disease and the discovery of additional layers of regulation have recently encouraged deeper analysis of the pathway in human cells. In archaea, ribosome biogenesis is less well-understood. However, their simpler sub-cellular structure should allow a less elaborated assembly procedure, potentially providing insights into the functional essentials of ribosome biogenesis that evolved long before the diversification of archaea and eukaryotes. Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. Projecting into the archaeal domain, we find that only few factors are consistently present across the analyzed taxa, and lineage-specific loss is common. While members of the Asgard group are not special with respect to their inventory of ribosome biogenesis factors (RBFs), they unite the highest number of orthologs to eukaryotic RBFs in one taxon. Using large ribosomal subunit maturation as an example, we demonstrate that archaea pursue a simplified version of the corresponding steps in eukaryotes. Much of the complexity of this process evolved on the eukaryotic lineage by the duplication of ribosomal proteins and their subsequent functional diversification into ribosome biogenesis factors. This highlights that studying ribosome biogenesis in archaea provides fundamental information also for understanding the process in eukaryotes.
影响因子：
3
作者：
Koestler T;von Haeseler A;Ebersberger I
通讯作者：
Ebersberger I
影响因子：
14.9
作者：
Benelli D;Marzi S;Mancone C;Alonzi T;la Teana A;Londei P
通讯作者：
Londei P