Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, Tartu, 51010, Estonia.
Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA.
Biochimie. 2019 Jan;156:169-180. doi: 10.1016/j.biochi.2018.10.013. Epub 2018 Oct 23.
Ribosomes consist of many small proteins and few large RNA molecules. Both components are necessary for ribosome functioning during translation. According to widely accepted view, bacterial ribosomes contain always the same complement of ribosomal proteins. Comparative bacterial genomics data indicates that several ribosomal proteins are encoded by multiple paralogous genes suggesting structural heterogeneity of ribosomes. In E. coli, two r-proteins bL31 and bL36 are encoded by two genes: rpmE and ykgM encode bL31 protein paralogs bL31A and bL31B, and rpmJ and ykgO encode bL36 protein paralogs bL36A and bL36B respectively. We have found several similarities and differences between ribosomes of exponential and stationary growth phases by using quantitative mass spectrometry and X-ray crystallography. First, composition of ribosome associating proteins changes profoundly as cells transition from exponential to stationary growth phase. Ribosomal core proteins bL31A and bL36A are replaced by bL31B and bL36B, respectively. Second, our X-ray structure of the 70S ribosome demonstrates that bL31B and bL36B proteins have similar ribosome binding sites to their A counterparts. Third, ribosome subpopulations containing A or B paralogs existed simultaneously demonstrating that E. coli ribosomes are heterogeneous with respect to their paralogous ribosomal protein composition that changes via protein exchange.
核糖体由许多小蛋白质和少数几个大的 RNA 分子组成。这两个组成部分都是核糖体在翻译过程中发挥功能所必需的。根据广泛接受的观点，细菌核糖体总是包含相同的核糖体蛋白组成。比较细菌基因组学数据表明，几个核糖体蛋白由多个基因的同源基因编码，这表明核糖体的结构具有异质性。在大肠杆菌中，两个 r 蛋白 bL31 和 bL36 由两个基因编码：rpmE 和 ykgM 编码 bL31 蛋白的同源基因 bL31A 和 bL31B，而 rpmJ 和 ykgO 分别编码 bL36 蛋白的同源基因 bL36A 和 bL36B。我们通过使用定量质谱和 X 射线晶体学发现，在指数生长和静止生长阶段的核糖体之间存在几个相似性和差异。首先，当细胞从指数生长向静止生长过渡时，核糖体结合蛋白的组成发生了深刻的变化。核糖体核心蛋白 bL31A 和 bL36A 分别被 bL31B 和 bL36B 取代。其次，我们的 70S 核糖体的 X 射线结构表明，bL31B 和 bL36B 蛋白与它们的 A 对应物具有相似的核糖体结合位点。第三，同时存在含有 A 或 B 同源基因的核糖体亚群，这表明大肠杆菌核糖体在其核糖体蛋白组成上具有异质性，这种变化是通过蛋白质交换实现的。
