Features of smaller ribosomes in Candidate Phyla Radiation (CPR) bacteria revealed with a molecular evolutionary analysis
Features of smaller ribosomes in Candidate Phyla Radiation (CPR) bacteria revealed with a molecular evolutionary analysis
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通过分子进化分析揭示候选门辐射（CPR）细菌中较小核糖体的特征
DOI：
10.1101/2022.01.07.475337
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Akio Kanai
中科院分区：
文献类型：
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作者：
Megumi Tsurumaki;Motofumi Saito;Masaru Tomita;Akio Kanai
候选辐射门（CPR）是一个主要由未培养谱系组成的大细菌群。它们细胞小，基因组小，通常缺乏核糖体蛋白uL1、bL9和/或uL30，而这些蛋白在非cpr细菌中基本普遍存在。在这里，我们综合分析了CPR细菌的基因组信息，并确定了它们的独特性质。CPR细菌的蛋白质长度分布在100-150个氨基酸左右，而自由生活的非CPR细菌的蛋白质长度分布在100-300个氨基酸范围内，而大多数共生的非CPR细菌的蛋白质长度分布在100-200个氨基酸左右。这些结果表明，CPR细菌的蛋白质平均比自由生活的非CPR细菌小，如共生的非CPR细菌。我们发现核糖体蛋白bL28、uL29、bL32和bL33在CPR细菌中以分类谱系特异性的方式丢失。此外，CPR细菌大约一半的核糖体蛋白序列与非CPR细菌部分不同，缺失区域或专门添加区域。我们还发现，CPR细菌的16S、23S和5S rnas中有几个区域缺失，这可能是导致CPR细菌的三个rnas总预测长度小于非CPR细菌的原因。在CPR核糖体蛋白和rrna中缺失的区域位于核糖体表面附近，有些区域彼此靠近。这些观察结果表明，CPR细菌中的核糖体比自由生活的非CPR细菌中的核糖体更小，表面结构更简单。
The candidate phyla radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and they often lack ribosomal proteins uL1, bL9, and/or uL30, which are basically ubiquitous in non-CPR bacteria. Here, we comprehensively analyzed the genomic information on CPR bacteria and identified their unique properties. The distribution of protein lengths in CPR bacteria peaks at around 100–150 amino acids, whereas the position of the peak varies in the range of 100–300 amino acids in free-living non-CPR bacteria, and at around 100–200 amino acids in most symbiotic non-CPR bacteria. These results show that the proteins of CPR bacteria are smaller, on average, than those of free-living non-CPR bacteria, like those of symbiotic non-CPR bacteria. We found that ribosomal proteins bL28, uL29, bL32, and bL33 have been lost in CPR bacteria in a taxonomic lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins of CPR differ, in part, from those of non-CPR bacteria, with missing regions or specifically added regions. We also found that several regions in the 16S, 23S, and 5S rRNAs of CPR bacteria are lacking, which presumably caused the total predicted lengths of the three rRNAs of CPR bacteria to be smaller than those of non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than those in free-living non-CPR bacteria, with simplified surface structures.