Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, 630090 Novosibirsk, Russia.
Int J Mol Sci. 2021 Dec 15;22(24):13485. doi: 10.3390/ijms222413485.
Protein uL5 (formerly called L11) is an integral component of the large (60S) subunit of the human ribosome, and its deficiency in cells leads to the impaired biogenesis of 60S subunits. Using RNA interference, we reduced the level of uL5 in HEK293T cells by three times, which caused an almost proportional decrease in the content of the fraction corresponding to 80S ribosomes, without a noticeable diminution in the level of polysomes. By RNA sequencing of uL5-deficient and control cell samples, which were those of total mRNA and mRNA from the polysome fraction, we identified hundreds of differentially expressed genes (DEGs) at the transcriptome and translatome levels and revealed dozens of genes with altered translational efficiency (GATEs). Transcriptionally up-regulated DEGs were mainly associated with rRNA processing, pre-mRNA splicing, translation and DNA repair, while down-regulated DEGs were genes of membrane proteins; the type of regulation depended on the GC content in the 3' untranslated regions of DEG mRNAs. The belonging of GATEs to up-regulated and down-regulated ones was determined by the coding sequence length of their mRNAs. Our findings suggest that the effects observed in uL5-deficient cells result from an insufficiency of translationally active ribosomes caused by a deficiency of 60S subunits.
蛋白质 uL5（以前称为 L11）是人类核糖体大亚基（60S）的一个组成部分，其在细胞中的缺乏会导致 60S 亚基生物发生受损。使用 RNA 干扰，我们将 HEK293T 细胞中的 uL5 水平降低了三倍，这导致与 80S 核糖体相对应的分数含量几乎成比例下降，而多核糖体的水平没有明显减少。通过对 uL5 缺陷和对照细胞（即总 mRNA 和多核糖体部分的 mRNA）进行 RNA 测序，我们在转录组和翻译组水平上鉴定了数百个差异表达基因（DEGs），并揭示了数十个翻译效率改变的基因（GATEs）。转录上调的 DEGs 主要与 rRNA 加工、前体 mRNA 剪接、翻译和 DNA 修复有关，而下调的 DEGs 是膜蛋白的基因；调节的类型取决于 DEG mRNA 3'非翻译区的 GC 含量。GATEs 属于上调和下调的基因取决于它们的 mRNA 的编码序列长度。我们的发现表明，uL5 缺陷细胞中观察到的效应是由 60S 亚基缺乏导致翻译活性核糖体不足引起的。
