Data from: Environmental and genetic influence on the rate and spectrum of spontaneous mutations in Escherichia coli

Abstract: Spontaneous mutations are the ultimate source of novel genetic variation on which evolution operates. Although mutation rate is often discussed as a single parameter in evolution, it comprises multiple distinct types of changes at the level of DNA. Moreover, the rates of these distinct changes can be independently influenced by genomic background and environmental conditions. Using fluctuation tests, we characterised the spectrum of spontaneous mutations in Escherichia coli grown in low and high glucose environments. These conditions are known to affect the rate of spontaneous mutation in wild-type MG1655, but not in a ΔluxS deletant strain—a gene with roles in both quorum sensing and the recycling of methylation products used in Escherichia coli’s DNA repair process. We find an increase in AT>GC transitions in the low glucose environment, suggesting that processes relating to the production or repair of this mutation could drive the response of overall mutation rate to glucose concentration. Interestingly, this increase in AT>GC transitions is maintained by the glucose non-responsive ΔluxS deletant. Instead, an elevated rate of GC>TA transversions, more common in a high glucose environment, leads to a net non-responsiveness of overall mutation rate for this strain. Our results show how relatively subtle changes, such as the concentration of a carbon substrate or loss of a regulatory gene, can substantially influence the amount and nature of genetic variation available to selection.File S1 contains the mutations found in sequenced rifampicin-resistant strains originating from fluctuation test and used to assess changes in mutational spectrum.File S2 contains the R analysis code used to perform all statistical analyses and generate figures.File S3 contains mutant counts used to estimate mutation rates to rifampicin resistance for MG1655 and ΔluxS strains grown at low and high glucose in the fluctuation test.File S4 contains population density data (Nt) for MG1655 and ΔluxS strains grown at low and high glucose in the fluctuation test.

摘要：自发的突变是进化过程中产生新遗传变异的终极来源，这些变异是进化作用的基石。尽管突变率常被讨论为进化中的一个单一参数，但在DNA层面，它实际上包含了多种不同的变化类型。此外，这些不同变化类型的速率可以独立地受到基因组背景和环境条件的影响。本研究通过波动测试，对在低和高葡萄糖环境下培养的大肠杆菌中的自发突变谱进行了表征。已知这些条件会影响野生型MG1655突变率，但不会影响ΔluxS缺失菌株的突变率——该基因在群体感应和甲基化产物回收过程中具有作用，这些产物用于大肠杆菌的DNA修复过程。我们发现，在低葡萄糖环境中，AT>GC转换的增加，这表明与该突变的生产或修复相关的过程可能驱动整体突变率对葡萄糖浓度的响应。有趣的是，这种AT>GC转换的增加在葡萄糖非响应的ΔluxS缺失菌株中得以维持。相反，GC>TA转换率的升高，这在高葡萄糖环境中更为常见，导致该菌株的整体突变率对葡萄糖浓度表现出非响应性。我们的结果表明，相对细微的变化，如碳底物的浓度或调控基因的丢失，可以显著影响可供选择使用的遗传变异的数量和性质。文件S1包含波动测试中发现的耐药突变菌株的突变，用于评估突变谱的变化。文件S2包含用于执行所有统计分析和生成图形的R分析代码。文件S3包含用于估计MG1655和ΔluxS菌株在波动测试中低和高葡萄糖条件下对利福平耐药性的突变率的突变计数。文件S4包含MG1655和ΔluxS菌株在波动测试中低和高葡萄糖条件下培养的种群密度数据（Nt）。