Consideration of a Liquid Mutation-accumulation Experiment to Measure Mutation Rates by Successive Serial Dilution.

IF 3.2 2区 生物学 Q2 EVOLUTIONARY BIOLOGY
Stephan Baehr, Wei-Chin Ho, Sam Perez, Alyssa Cenzano, Katelyn Hancock, Lea Patrick, Adalyn Brown, Sam Miller, Michael Lynch
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Abstract

The mutation-accumulation (MA) experiment is a fixture of evolutionary biology, though its execution is laborious. MA experiments typically take between months and years to acquire sufficient mutations to measure DNA mutation rates and mutation spectra. MA experiments for many organisms rely on colony formation on agar plates and repetitive streaking, an environment which at first glance appears somewhat contrived, a poor imitation of actual environmental living conditions. We propose that a fully liquid-phase mutation-accumulation experiment may at times more accurately reflect the environment of an organism. We note also that whereas automation of streaking plates is a daunting prospect, automation of liquid handling and serial dilution is already commonplace. In principle, this type of MA experiment can be automated so as to reduce the human capital requirements of measuring mutation rates. We demonstrate that a liquid MA recapitulates the mutation rate estimated for MMR- E. coli in liquid LB culture vs. plate LB culture. We detect a modified mutation spectrum with a transition skew of 4.7:1 of A:T→G:C vs G:C→A:T mutations, highlighting the potential role of tautomerization as a mechanism of DNA mutation.

突变-积累(MA)实验是进化生物学的一个固定实验,但其执行过程十分费力。突变积累实验通常需要数月到数年的时间才能获得足够的突变,以测量 DNA 突变率和突变谱。许多生物的 MA 实验都依赖于在琼脂平板上形成菌落和重复条纹,这种环境乍一看有些做作,是对实际环境生活条件的拙劣模仿。我们认为,完全液相的突变-积累实验有时能更准确地反映生物的生存环境。我们还注意到,虽然条纹板的自动化前景令人生畏,但液体处理和连续稀释的自动化已经很普遍。原则上,这种类型的 MA 实验可以实现自动化,从而减少测量突变率所需的人力资本。我们证明,液体 MA 重现了 MMR 大肠杆菌在液体 LB 培养液与平板 LB 培养液中的突变率。我们检测到了一种变异谱,A:T→G:C 与 G:C→A:T 变异的转换偏度为 4.7:1,突出了同分异构作为 DNA 变异机制的潜在作用。
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来源期刊
Genome Biology and Evolution
Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY
CiteScore
5.80
自引率
6.10%
发文量
169
审稿时长
1 months
期刊介绍: About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.
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