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Rates of gene conversions between Escherichia coli ribosomal operons
bioRxiv - Genetics Pub Date : 2020-08-03 , DOI: 10.1101/2020.08.03.235192
Isaac Gifford , Aurko Dasgupta , Jeffrey E. Barrick

Due to their universal presence and high sequence conservation, 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 ribosomal RNA (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 of cells that were evolved for ~13,750 generations with frequent single-cell bottlenecks that reduce the effects of selection. We identified 34 gene conversion events and estimate an overall rate of intragenomic recombination events between rRNA copies of 3.2 x 10−4 per generation or 5.3 x 10−5 per potential donor sequence. This rate varied only slightly from random expectations between different portions of the rRNA genes and between rRNA operons located at different locations in the genome. This 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.

中文翻译:

大肠杆菌核糖体操纵子之间的基因转化率

由于它们的普遍存在和高度的序列保守性,rRNA序列被广泛用于系统发育学中以推断微生物之间的进化关系,并被用于宏基因组学中以分析微生物群落的组成。大多数微生物基因组编码核糖体RNA(rRNA)基因的多个副本,以为细胞提供足够的蛋白质合成能力。这些拷贝通常经历协调的进化,由于基因转化,这种进化使它们的序列保持相同或接近,这是一种基因组内重组,其改变同源序列的一个拷贝以完全匹配另一个拷贝。先前已经通过比较基因组学方法和使用遗传报告基因分析方法估计了rRNA基因转化率的差异。为了更直接地测量rRNA基因组重组的速率,我们对七个大肠埃希菌rRNA操纵子在15个细胞谱系中进化了约13,750代,并具有频繁的单细胞瓶颈,降低了选择的效果。我们确定了34个基因转化事件,并估计了每代3.2 x 10 -4或每个潜在供体序列5.3 x 10 -5的rRNA拷贝之间的基因组内重组事件的总体发生率。该速率与rRNA基因的不同部分之间以及位于基因组不同位置的rRNA操纵子之间的随机预期仅略有不同。对rRNA基因转化率的这种准确估计填补了我们对微生物基因组进化过程中核糖体序列和其他多拷贝元件如何多样化和同质化的定量理解的空白。
更新日期:2020-08-04
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