Institute for Cell Biology and Neuroscience, Goethe University, Frankfurt 60438, Germany, Center for Integrative Bioinformatics, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna 1030, Austria, Institute for Molecular Biosciences, Goethe University, Frankfurt 60438, Germany, Faculty of Computer Science, University of Vienna, Vienna 1030, Austria, Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt 60438, Germany, Department of Biochemistry I, Universitätsmedizin Göttingen, Göttingen 37073, Germany and Center of Membrane Proteomics, Goethe University, Frankfurt 60438, Germany.
Nucleic Acids Res. 2014 Feb;42(3):1509-23. doi: 10.1093/nar/gkt1137. Epub 2013 Nov 14.
Ribosome biogenesis is fundamental for cellular life, but surprisingly little is known about the underlying pathway. In eukaryotes a comprehensive collection of experimentally verified ribosome biogenesis factors (RBFs) exists only for Saccharomyces cerevisiae. Far less is known for other fungi, animals or plants, and insights are even more limited for archaea. Starting from 255 yeast RBFs, we integrated ortholog searches, domain architecture comparisons and, in part, manual curation to investigate the inventories of RBF candidates in 261 eukaryotes, 26 archaea and 57 bacteria. The resulting phylogenetic profiles reveal the evolutionary ancestry of the yeast pathway. The oldest core comprising 20 RBF lineages dates back to the last universal common ancestor, while the youngest 20 factors are confined to the Saccharomycotina. On this basis, we outline similarities and differences of ribosome biogenesis across contemporary species. Archaea, so far a rather uncharted domain, possess 38 well-supported RBF candidates of which some are known to form functional sub-complexes in yeast. This provides initial evidence that ribosome biogenesis in eukaryotes and archaea follows similar principles. Within eukaryotes, RBF repertoires vary considerably. A comparison of yeast and human reveals that lineage-specific adaptation via RBF exclusion and addition characterizes the evolution of this ancient pathway.
核糖体生物发生对于细胞生命至关重要，但令人惊讶的是，我们对其潜在途径知之甚少。在真核生物中，仅有酿酒酵母拥有全面的经实验验证的核糖体生物发生因子 (RBF) 集合。对于其他真菌、动物或植物，我们的了解要少得多，对于古菌，我们的见解甚至更为有限。我们从 255 个酵母 RBF 开始，通过同源搜索、结构域架构比较，以及部分手动整理，研究了 261 种真核生物、26 种古菌和 57 种细菌中 RBF 候选物的库存。由此产生的系统发育谱揭示了酵母途径的进化起源。最古老的核心由 20 个 RBF 谱系组成，可以追溯到最后普遍共同祖先，而最年轻的 20 个因子仅限于 Saccharomycotina。在此基础上，我们概述了当代物种之间核糖体生物发生的异同。迄今为止，古菌是一个相当未知的领域，拥有 38 个有充分依据的 RBF 候选物，其中一些在酵母中已知形成功能性亚复合物。这为真核生物和古菌的核糖体生物发生遵循相似的原则提供了初步证据。在真核生物中，RBF 种类差异很大。将酵母和人类进行比较表明，通过 RBF 排除和添加进行谱系特异性适应是这一古老途径进化的特征。
