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和少量大RNA分子组成。这两种成分对于核糖体在翻译过程中的功能都是必需的。根据广泛接受的观点，细菌核糖体总是含有相同的核糖体蛋白补体。比较细菌基因组学数据表明，多个核糖体蛋白由多个旁系同源基因编码，表明核糖体在结构上具有异质性。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蛋白质旁系同源物bL31A和bL31B，以及rpmJ和ykgO分别编码bL36蛋白旁系同源物bL36A和bL36B。通过使用定量质谱和X射线晶体学，我们发现了指数生长期的核糖体和静止生长期的核糖体之间的一些相似之处和不同之处。首先，随着细胞从指数生长期过渡到静止生长期，核糖体相关蛋白的组成发生了深刻的变化。核糖体核心蛋白bL31A和bL36A分别替换为bL31B和bL36B。其次，我们的70S核糖体的X射线结构表明bL31B和bL36B蛋白具有与其A对应物相似的核糖体结合位点。第三，同时存在含有A或B旁系同源物的核糖体亚群，表明大肠杆菌 核糖体的旁源核糖体蛋白质组成通过蛋白质交换而改变，因此是异质的。