Consideration of a liquid mutation accumulation experiment to measure mutation rates by successive serial dilution.

Abstract

The mutation-accumulation (MA) experiment is a fixture of evolutionary biology, though it is laborious to perform. 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 real 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 4:1 of A:T[->]G:C vs G:C[->]A:T mutations, highlighting the potential role of tautomerization as a DNA mutation mechanism. We also find that using a plate reader to measure OD600 as a proxy for cell growth to be incapable of measuring carrying capacity for MA lines burdened with many mutations.