Abstract
The evolutionary role of transposable elements (TEs) is still highly controversial. Two key parameters, the transposition rate (u and w, for replicative and non-replicative transposition) and the excision rate (e) are fundamental to understanding their evolution and maintenance in populations. We have estimated u, w and e for six families of TEs (including eight members: IS1, IS2, IS3, IS4, IS5, IS30, IS150 and IS186) in Escherichia coli, using a mutation accumulation (MA) experiment. In this experiment, mutations accumulate essentially at the rate at which they appear, during a period of 80 500 (1610 generations × 50 lines) generations, and spontaneous transposition events can be detected. This differs from other experiments in which insertions accumulated under strong selective pressure or over a limited genomic target. We therefore provide new estimates for the spontaneous rates of transposition and excision in E. coli. We observed 25 transposition and three excision events in 50 MA lines, leading to overall rate estimates of u ∼ 1.15 × 10–5, w ∼ 4 × 10−8 and e ∼ 1.08 × 10−6 (per element, per generation). Furthermore, extensive variation between elements was found, consistent with previous knowledge of the mechanisms and regulation of transposition for the different elements.
Highlights
Transposable elements (TEs) are thought to be major players in genome organization and evolution
Theory [6] suggests that, in prokaryotes, TEs can be maintained if there is horizontal transfer and the rate of transposition and excision decreases with copy number [7]
Half of the non-confirmed events were due to another insertion sequences (ISs) element (IS10), which was present in the ancestor, but was not targeted in this study
Summary
Transposable elements (TEs) are thought to be major players in genome organization and evolution. Theory [6] suggests that, in prokaryotes, TEs can be maintained if there is horizontal transfer and the rate of transposition and excision decreases with copy number [7]. We estimate the spontaneous rates of copy-and-paste (u), cut-and-paste (w) and excision (e) per element, per generation for eight different IS elements, using mutation accumulation (MA) in a mutator strain of Escherichia coli. Number of transposition events, even if deleterious, accumulate This approach aims at an unbiased estimation of the transposition rate, excluding lethal events. Half of the non-confirmed events were due to another IS element (IS10), which was present in the ancestor, but was not targeted in this study We used nonlinear minimization (Nelder– Mead) to find values of u, w and e that minimize the sum of squared error between observed and predicted frequencies of each type
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