Nikolaeva Daria D, Gelfand Mikhail S, Garushyants Sofya K
Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia.
Mol Biol Evol. 2021 Jan 4;38(1):58-66. doi: 10.1093/molbev/msaa184.
The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine-Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.
核糖体是进行蛋白质生物合成的重要细胞机器。其结构和组成在所有物种中高度保守。然而，据报道一些细菌的核糖体蛋白不完整。我们分析了214个小细菌基因组（<1 Mb）中的核糖体蛋白组成，发现尽管核糖体组成相当稳定，但某些核糖体蛋白可能缺失，尤其是在基因组大幅缩减的细菌中。大亚基的蛋白质组成比小亚基的保守性更低。我们确定了一组经常缺失的核糖体蛋白，并证明它们往往位于核糖体表面，与其他核糖体组分的接触较少。此外，一些蛋白质以进化相关的方式缺失。核糖体RNA的减少也很常见，缺失大多发生在自由环中。最后，抗Shine-Dalgarno序列的缺失与更多核糖体蛋白的缺失相关。
