Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA.
The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA.
RNA. 2019 May;25(5):521-538. doi: 10.1261/rna.069823.118. Epub 2019 Feb 7.
It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal protein (RP) content and posttranslational modifications (PTMs), as well as bound nonribosomal proteins. In some cases, the existence of these diverse ribosome populations has been verified by biochemical or structural methods. Furthermore, knockout or knockdown of RPs can diversify ribosome populations, while also affecting the translation of some mRNAs (but not others) with biological consequences. However, the effects on translation arising from depletion of diverse proteins can be highly similar, suggesting that there may be a more general defect in ribosome function or stability, perhaps arising from reduced ribosome numbers. Consistently, overall reduced ribosome numbers can differentially affect subclasses of mRNAs, necessitating controls for specificity. Moreover, in order to study the functional consequences of ribosome diversity, perturbations including affinity tags and knockouts are introduced, which can also affect the outcome of the experiment. Here we review the available literature to carefully evaluate whether the published data support functional diversification, defined as diverse ribosome populations differentially affecting translation of distinct mRNA (classes). Based on these observations and the commonly observed cellular responses to perturbations in the system, we suggest a set of important controls to validate functional diversity, which should include gain-of-function assays and the demonstration of inducibility under physiological conditions.
最近人们清楚地认识到，核糖体远比人们之前认为的更为多样化，这种多样性源于 rRNA 序列和修饰、核糖体蛋白（RP）含量和翻译后修饰（PTMs），以及结合的非核糖体蛋白。在某些情况下，这些不同核糖体群体的存在已经通过生化或结构方法得到了验证。此外，RP 的敲除或敲低可以使核糖体群体多样化，同时也会影响一些 mRNA 的翻译（但不是其他），从而产生生物学后果。然而，由于多样性蛋白的消耗而产生的对翻译的影响可能非常相似，这表明可能存在核糖体功能或稳定性的更普遍缺陷，也许是由于核糖体数量减少引起的。一致地，核糖体数量的整体减少会对不同的 mRNA 亚类产生不同的影响，因此需要进行特异性控制。此外，为了研究核糖体多样性的功能后果，引入了亲和标签和敲除等扰动，这也会影响实验的结果。在这里，我们回顾了现有的文献，以仔细评估已发表的数据是否支持功能多样化，即不同的核糖体群体对不同的 mRNA（类）的翻译产生不同的影响。基于这些观察结果以及系统中扰动的常见细胞反应，我们提出了一组重要的控制措施来验证功能多样性，其中应包括功能获得性测定和在生理条件下诱导的证明。
