Galperin Michael Y, Wolf Yuri I, Garushyants Sofya K, Vera Alvarez Roberto, Koonin Eugene V
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
J Bacteriol. 2021 Jun 1;203(11). doi: 10.1128/JB.00058-21. Epub 2021 Mar 22.
Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.In many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 16 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in and These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.
核糖体蛋白（RPs）在细菌域和古菌域中高度保守。尽管许多核糖体蛋白对生存至关重要，但基因组分析表明，许多细菌和古菌基因组中缺少一些核糖体蛋白基因。此外，全基因组转座子诱变和/或靶向缺失表明，去除一些核糖体蛋白基因对细菌生长速率只有中等影响。在这里，我们通过汇编直系同源基因簇（COG）数据库最新版本中一个或多个基因组缺失的核糖体基因列表，系统地分析了原核生物中核糖体蛋白的进化保守性。其中一些缺失是因为相应基因发生了移码突变，推测是测序错误导致的，而其他一些则在基因组注释过程中被忽略且未被翻译。除了这些注释错误，我们还在多种细菌和古菌中发现了多个核糖体蛋白基因的真正缺失。其中一些缺失是特定分支特有的，而其他一些则发生在基因组大幅减少的共生菌和寄生菌中。通过计算和实验确定的非必需核糖体基因列表显示出大量重叠，揭示了原核生物核糖体进化中的一个共同趋势，这可能与核糖体的结构和组装有关。因此，位于核糖体表面和/或在核糖体组装后期整合的核糖体蛋白更有可能是非必需的，并且在微生物进化过程中，特别是在基因组压缩过程中更容易丢失。
在许多原核生物基因组中，一个或多个核糖体蛋白（RP）基因缺失。对COG数据库中包含的1309个原核生物基因组的分析表明，只有约一半的核糖体蛋白在细菌和古菌中普遍保守。相比之下，在一些基因组中，多达16种其他核糖体蛋白缺失，主要是宿主相关细菌和古菌的微小（<1 Mb）基因组。十种普遍存在的和九种古菌特有的核糖体蛋白显示出明显的谱系特异性基因丢失模式。大多数经常从细菌基因组中丢失的核糖体蛋白位于核糖体外围，并且在[此处原文可能缺失相关信息]中是非必需的。这些结果揭示了原核生物核糖体结构和进化的一般趋势和共同限制。
