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

Supplementary Material for 'Environmental and genetic influence on the rate and spectrum of spontaneous mutations in <em>Escherichia coli </em>', as described in <em>Microbiology.</em>
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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 <em>Escherichia coli</em> 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 Δ<em>luxS</em> deletant strain—a gene with roles in both quorum sensing and the recycling of methylation products used in <em>Escherichia coli</em>’s DNA repair process. We find an increase in AT&gt;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&gt;GC transitions is maintained by the glucose non-responsive Δ<em>luxS</em> deletant. Instead, an elevated rate of GC&gt;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.
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Strains are available upon request.
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File S1, available in the online version of this article, contains the mutations found in sequenced rifampicin-resistant strains originating from the fluctuation test and used to assess changes in mutational spectrum.
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File S2 contains the R analysis code used to perform all statistical analyses and generate figures.
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File S3 contains mutant counts used to estimate mutation rates to rifampicin resistance for MG1655 and Δ<em>luxS</em> strains grown at low and high glucose in the fluctuation test.
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File S4 contains population density data (<em>Nt</em>) for MG1655 and Δ<em>luxS</em> strains grown at low and high glucose in the fluctuation test.
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Supplemental Methods

发表于《Microbiology》的《大肠杆菌（*Escherichia coli*）自发突变率与突变谱的环境及遗传影响》补充材料

自发突变是进化所依赖的新型遗传变异的终极来源。尽管在进化研究中突变率常被视为单一参数，但在DNA层面上，突变实则包含多种不同类型的改变。此外，这些不同类型突变的发生速率可分别受基因组背景与环境条件的调控。

本研究通过波动试验（fluctuation test），对在低葡萄糖与高葡萄糖环境中培养的大肠杆菌（*Escherichia coli*）的自发突变谱进行了表征。已有研究表明，此类环境条件会影响野生型MG1655菌株的自发突变率，但不会对ΔluxS缺失菌株产生此效应——luxS基因同时参与群体感应与大肠杆菌DNA修复过程中所用甲基化产物的回收循环。

我们发现，低葡萄糖环境下AT→GC转换的发生频率有所上升，这提示与该类突变的产生或修复相关的过程，可能是整体突变率随葡萄糖浓度变化的驱动因素。值得注意的是，葡萄糖不响应型ΔluxS缺失菌株仍保留了这一AT→GC转换频率上升的特征。与之相反，该菌株在高葡萄糖环境下GC→TA颠换的发生速率升高，这最终导致其整体突变率对葡萄糖浓度无响应。本研究结果揭示了诸如碳底物浓度变化或调控基因缺失这类相对细微的改变，可如何显著影响选择可利用的遗传变异的数量与性质。

菌株可应请求提供。

本文在线版本提供的补充文件S1，收录了通过波动试验获得并经测序的利福平抗性菌株中的突变信息，用于评估突变谱的变化。

补充文件S2包含用于完成所有统计分析并生成图表的R分析代码。

补充文件S3收录了波动试验中，在低葡萄糖与高葡萄糖环境下培养的MG1655与ΔluxS菌株的突变计数数据，用于估算利福平抗性突变率。

补充文件S4包含波动试验中，在低葡萄糖与高葡萄糖环境下培养的MG1655与ΔluxS菌株的种群密度数据（*Nt*）。

补充方法