Rates of transposition in Escherichia coli

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.

Keywords: Escherichia coli; insertion sequences; mutation accumulation; rate of transposition; transposable elements.

Figure 1.

Number of transposition events as a function of initial copy number (for a given IS element). The regression equation is y = 0.83x – 0.67, r² = 0.30, p = 0.04.

Figure 2.

Estimates of transposition rates per element, per generation. Standard deviations are given between brackets. These estimates are based on data reported in table 1. See §2 for details of the analysis. Black and grey dots represent u and w, respectively. Open circles represent rates of excision. n.d. means non determined. Please note that the minimum estimate of u for IS186 and e for IS30 cover zero, therefore these cannot be represented in a logarithmic scale.