Structure of the largest, most complex ribosome Ribosomes are two-subunit ribonucleoprotein assemblies that catalyze the translation of messenger RNA into protein. Ribosomal RNAs (rRNAs) play key structural and functional roles. Ramrath et al. report the high-resolution structure of mitochondrial ribosomes from the unicellular parasite Trypanosoma brucei that contain the smallest known rRNAs. The trypanosomal mitoribosome is the most complex ribosomal assembly characterized, with two rRNAs and 126 proteins. The increased protein subunits have substituted for rRNA as an architectural scaffold. The structure also reveals the minimal core needed for ribosome function. Science, this issue p. eaau7735 The structure of the trypanosomal mitochondrial ribosome reveals how ribosomal proteins have substituted for the highly reduced ribosomal RNA. The structure of the trypanosomal mitochondrial ribosome reveals how ribosomal proteins have taken over architectural roles from the highly reduced ribosomal RNA. INTRODUCTION Ribosomes are universally conserved assemblies composed of ribosomal RNA (rRNA) and proteins, where rRNA plays key structural and functional roles. Despite their high degree of conservation, considerable variability is observed in mitochondrial ribosomes (mitoribosomes), with an extreme example found in Trypanosoma brucei, the parasite that causes sleeping sickness. In these mitoribosomes featuring the smallest known rRNAs, the severe rRNA reduction is accompanied by the recruitment of many additional proteins. RATIONALE The extreme differences in rRNA size and the substitution of many proteins present in all other ribosomes render trypanosomal mitoribosomes an excellent system to reveal the minimal set of rRNA and protein elements essential for ribosomal function and to investigate how ribosomal proteins compensated for the missing rRNA. To address these questions, we determined the atomic structure of the mitoribosome from T. brucei using cryo–electron microscopy. RESULTS The trypanosomal mitoribosome, composed of 127 ribosomal proteins and two rRNAs, is larger and architecturally more complex than any other ribosome described so far with a molecular weight of 4.5 MDa and a RNA/protein ratio of 1:6. The structural changes are most prominent in the small subunit that exceeds the size of the “large” subunit. Notably, the reduced rRNA is found at the core of the assembly and is encased in a large shell of mitoribosomal proteins. The universally conserved regions are reduced to a minimum and include only a few rRNA and protein elements in the vicinity of key functional regions of the ribosome, namely, the decoding center, the active site, and the binding region for translation factors. In contrast to other ribosomes, where the rRNA fold is dominated by a base-paired structure, the proteins take over the architectural role by providing a scaffold for binding of predominantly single-stranded rRNA. The switch to the protein-based architecture is accompanied by a marked increase in the size of conserved ribosomal proteins and the recruitment of novel proteins, including proteins with multiple domains or proteins with homology to various enzymes. Because many proteins contain helical repeat motifs, the assembly contains a disproportionately large fraction of α-helical elements that structurally substitute the reduced rRNA. Our results show that, because of the extensive remodeling, the trypanosomal translational machinery adopted unusual solutions to accomplish some basic protein synthesis mechanisms. Their nascent polypeptide exit tunnel branches into two exits providing for an interesting possibility that nascent proteins with different characteristics may take different paths. Furthermore, in a subpopulation of isolated small-subunit particles, we observed mitochondrial initiation factor 3 interacting with the decoding center via its unique C-terminal extension, which might compensate for the essential function of initiation factor 1 that is absent in all mitochondria. CONCLUSION The unusual architecture and composition of the trypanosomal mitoribosome that we have revealed shows how proteins have taken over a key architectural role from rRNA by forming an autonomous outer shell that serves as a mold for binding flexible single-stranded rRNAs. Moreover, our results show the universally conserved features of ribosomes that are responsible for the most basic functions. Last, structural information on these ribosomes may be helpful for developing new drugs to treat sleeping sickness and other diseases caused by trypanosomes and its relatives. The universally conserved core of the ribosome. In the highly remodeled trypanosomal mitoribosome, where the “small” subunit is larger than the large subunit, proteins took over the key architectural role from the rRNA. The massive protein shell interacts with the extremely reduced rRNA to position functionally critical rRNA elements. The structure helps us define the “minimal” set of conserved rRNA regions and protein components shared by all ribosomes. Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of Trypanosoma brucei, a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the “minimal” set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.

中文翻译：

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锥虫线粒体核糖体向基于蛋白质的结构的进化转变

最大、最复杂的核糖体的结构 核糖体是两个亚基的核糖核蛋白组装体，可催化信使 RNA 翻译成蛋白质。核糖体 RNA (rRNA) 起着关键的结构和功能作用。拉姆拉斯等人。报告了来自单细胞寄生虫布氏锥虫的线粒体核糖体的高分辨率结构，其中包含最小的已知 rRNA。锥虫核糖体是最复杂的核糖体组装，具有两个 rRNA 和 126 个蛋白质。增加的蛋白质亚基已取代 rRNA 作为建筑支架。该结构还揭示了核糖体功能所需的最小核心。科学，这个问题 p。eaau7735 锥虫线粒体核糖体的结构揭示了核糖体蛋白如何取代高度减少的核糖体 RNA。锥虫线粒体核糖体的结构揭示了核糖体蛋白如何从高度减少的核糖体 RNA 中接管结构作用。引言 核糖体是普遍保守的装配体，由核糖体 RNA (rRNA) 和蛋白质组成，其中 rRNA 在结构和功能上起着关键作用。尽管它们高度保守，但在线粒体核糖体（mitoribosomes）中观察到相当大的变异性，在导致昏睡病的寄生虫布氏锥虫中发现了一个极端的例子。在这些具有最小已知 rRNA 的线粒体糖体中，严重的 rRNA 减少伴随着许多额外蛋白质的募集。基本原理 rRNA 大小的极端差异和所有其他核糖体中存在的许多蛋白质的替代使锥虫线粒体糖体成为揭示核糖体功能必需的最小 rRNA 和蛋白质元素集并研究核糖体蛋白质如何补偿缺失的 rRNA 的绝佳系统。为了解决这些问题，我们使用低温电子显微镜确定了布氏木霉线粒体糖体的原子结构。结果 锥虫核糖体由 127 个核糖体蛋白和两个 rRNA 组成，比迄今为止描述的任何其他核糖体更大，结构更复杂，分子量为 4.5 MDa，RNA/蛋白质比为 1:6。结构变化在超过“大”亚基大小的小亚基中最为突出。尤其，减少的 rRNA 位于组装的核心，并被包裹在一个大的线粒体蛋白壳中。普遍保守的区域被减少到最少，只包括核糖体关键功能区域附近的少数 rRNA 和蛋白质元件，即解码中心、活性位点和翻译因子的结合区域。与其他核糖体相比，rRNA 折叠由碱基配对结构主导，蛋白质通过提供用于结合主要单链 rRNA 的支架来接管结构作用。向基于蛋白质的结构的转变伴随着保守核糖体蛋白质大小的显着增加和新蛋白质的募集，包括具有多个结构域的蛋白质或与各种酶具有同源性的蛋白质。由于许多蛋白质包含螺旋重复基序，因此组装包含不成比例的大部分 α-螺旋元件，这些元件在结构上替代了还原的 rRNA。我们的结果表明，由于广泛的重塑，锥虫的翻译机制采用了不寻常的解决方案来完成一些基本的蛋白质合成机制。它们的新生多肽出口隧道分支成两个出口，提供了一个有趣的可能性，即具有不同特征的新生蛋白质可能采取不同的路径。此外，在分离的小亚基粒子的亚群中，我们观察到线粒体起始因子 3 通过其独特的 C 端延伸与解码中心相互作用，这可能补偿所有线粒体中不存在的起始因子 1 的基本功能。结论 我们所揭示的锥虫核糖体的不同寻常的结构和组成表明，蛋白质如何通过形成一个自主外壳，作为结合柔性单链 rRNA 的模具，从 rRNA 中接管了关键的结构作用。此外，我们的结果显示了负责最基本功能的核糖体的普遍保守特征。最后，这些核糖体的结构信息可能有助于开发治疗昏睡病和其他由锥虫及其亲属引起的疾病的新药。核糖体普遍保守的核心。在高度改造的锥虫核糖体中，“小”亚基大于大亚基，蛋白质从 rRNA 接管了关键的结构作用。巨大的蛋白质外壳与极度减少的 rRNA 相互作用，以定位功能关键的 rRNA 元件。该结构帮助我们定义了所有核糖体共享的保守 rRNA 区域和蛋白质成分的“最小”集。核糖体 RNA (rRNA) 在核糖体中起着关键的功能和结构作用。使用电子显微镜，我们确定了在布氏锥虫线粒体中发现的高度发散的核糖体的原子结构，这是一种导致人类昏睡病的单细胞寄生虫。锥虫核糖体具有最小的 rRNA，并且比所有已知的核糖体含有更多的蛋白质。该结构显示了蛋白质如何从 rRNA 接管建筑支架的作用：它们形成一个自主外壳，包围整个颗粒并稳定和定位 rRNA 的重要功能区域。我们的结果还揭示了所有核糖体共享的“最小”保守 rRNA 和蛋白质组分集，这些组分帮助我们定义了最重要的功能元件。