Rates of gene conversions between Escherichia coli ribosomal operons.
Rates of gene conversions between Escherichia coli ribosomal operons.
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DOI：
10.1093/g3journal/jkaa002
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发表时间：
2021-02-09
期刊：
影响因子：
--
通讯作者：
Barrick JE
中科院分区：
文献类型：
--
作者：
Gifford I;Dasgupta A;Barrick JE
由于核糖体RNA（rRNA）序列的普遍存在和高度保守性，其被广泛用于微生物遗传学中推断微生物之间的进化关系，以及用于分析微生物群落组成的宏基因组学。大多数微生物基因组编码rRNA基因的多个拷贝，为细胞提供足够的蛋白质合成能力。这些拷贝通常经历协同进化，保持它们的序列相同，或几乎相同，这是由于基因转换，一种基因组内重组，改变同源序列的一个拷贝以完全匹配另一个。广泛变化的速率rRNA基因转换以前已经估计比较基因组学方法和使用遗传报告基因测定。为了更直接地测量rRNA基因组内重组的速率，我们对15个谱系中的7个大肠杆菌rRNA操纵子进行了测序，这些谱系进化了13，750代，频繁的单细胞瓶颈降低了选择的影响。我们确定了38个基因转换事件，并估计了16S和23S基因内基因组内重组的总体速率，每代每个基因组的rRNA拷贝数为3.6 × 10−4，或每代每个同源供体操纵子的rRNA操纵子为8.6 × 10−6。该速率仅与rRNA基因内不同位点和位于基因组不同位置的rRNA操纵子之间的随机预期略有不同。我们对rRNA基因转化率的准确估计填补了我们对核糖体序列和其他多拷贝元件在微生物基因组进化过程中如何多样化和均质化的定量理解中的空白。
Due to their universal presence and high sequence conservation, ribosomal RNA (rRNA) sequences are used widely in phylogenetics for inferring evolutionary relationships between microbes and in metagenomics for analyzing the composition of microbial communities. Most microbial genomes encode multiple copies of rRNA genes to supply cells with sufficient capacity for protein synthesis. These copies typically undergo concerted evolution that keeps their sequences identical, or nearly so, due to gene conversion, a type of intragenomic recombination that changes one copy of a homologous sequence to exactly match another. Widely varying rates of rRNA gene conversion have previously been estimated by comparative genomics methods and using genetic reporter assays. To more directly measure rates of rRNA intragenomic recombination, we sequenced the seven Escherichia coli rRNA operons in 15 lineages that were evolved for ∼13,750 generations with frequent single-cell bottlenecks that reduce the effects of selection. We identified 38 gene conversion events and estimated an overall rate of intragenomic recombination within the 16S and 23S genes between rRNA copies of 3.6 × 10−4 per genome per generation or 8.6 × 10−6 per rRNA operon per homologous donor operon per generation. This rate varied only slightly from random expectations at different sites within the rRNA genes and between rRNA operons located at different positions in the genome. Our accurate estimate of the rate of rRNA gene conversions fills a gap in our quantitative understanding of how ribosomal sequences and other multicopy elements diversify and homogenize during microbial genome evolution.
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