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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DOI：
10.1261/rna.079103.122
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发表时间：
2022-08
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影响因子：
--
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辐射门（CPR）是一个主要由未培养的谱系组成的大型细菌群。它们具有小细胞和小基因组，并且它们通常缺乏核糖体蛋白uL 1，bL 9和/或uL 30，这些蛋白在非CPR细菌中基本上普遍存在。在这里，我们全面分析了CPR细菌的基因组信息，并确定了它们的独特特性。CPR细菌中蛋白质长度的分布在约100-150个氨基酸处达到峰值，而在自由生活的非CPR细菌中峰值的位置在100-300个氨基酸的范围内变化，并且在大多数共生的非CPR细菌中在约100-200个氨基酸处变化。这些结果表明，CPR细菌的蛋白质平均比自由生活的非CPR细菌的蛋白质小，就像共生的非CPR细菌的蛋白质一样。我们发现，核糖体蛋白bL 28，uL 29，bL 32，和bL 33已经失去了CPR细菌在分类谱系特异性的方式。此外，CPR的所有核糖体蛋白质中约有一半的序列部分不同于非CPR细菌的核糖体蛋白质，具有缺失区域或特别添加的区域。我们还发现，CPR细菌的16 S、23 S和5S rRNA中的几个区域缺失，这可能导致CPR细菌的三种rRNA的总预测长度小于非CPR细菌。CPR核糖体蛋白和rRNA中缺失的区域位于核糖体表面附近，并且一些区域彼此靠近。这些观察结果表明，CPR细菌中的核糖体比自由生活的非CPR细菌中的核糖体小，具有简化的表面结构。
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.
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影响因子：
15.5
作者：
Danczak RE;Johnston MD;Kenah C;Slattery M;Wrighton KC;Wilkins MJ
通讯作者：
Wilkins MJ
影响因子：
4.5
作者：
Grosjean H;Breton M;Sirand-Pugnet P;Tardy F;Thiaucourt F;Citti C;Barré A;Yoshizawa S;Fourmy D;de Crécy-Lagard V;Blanchard A
通讯作者：
Blanchard A
影响因子：
14.9
作者：
Kalvari I;Argasinska J;Quinones-Olvera N;Nawrocki EP;Rivas E;Eddy SR;Bateman A;Finn RD;Petrov AI
通讯作者：
Petrov AI
影响因子：
10.7
作者：
Bernier, Chad R.;Petrov, Anton S.;Williams, Loren Dean
通讯作者：
Williams, Loren Dean
影响因子：
3.4
作者：
Gong, Jun;Qing, Yao;Warren, Alan
通讯作者：
Warren, Alan