Distribution and Abundance of Insertion Sequences Among Natural Isolates of <i>Escherichia coli</i>

Sawyer, Stanley; Dykhuizen, Daniel E.; DuBose, Robert; Green, Louis; Mutangadura-Mhlanga, T.; Wolczyk, David F.; Hartl, Daniel L.

doi:10.1093/genetics/115.1.51

Cited by 137 publications

(20 citation statements)

References 19 publications

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“…In contrast to REPINs, IS 5 is present in less than half of all E. coli genomes (133 out of 300, Figure 3D ). The patchy presence of insertion sequences has been previously reported and indicates, together with the lack of genetic variation within genomes, that insertion sequences are frequently purged from genomes, with constant reinfection of new hosts being necessary for persistence [10].…”

Section: Resultsmentioning

confidence: 99%

Ancient Darwinian replicators nested within eubacterial genomes

Bertels

Rainey

2021

Preprint

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Relationships among organisms, in which one lives inside of another, with benefits accruing to both partners, are referred to as endosymbiotic. Such relationships are common in the biological world, yet descriptions are confined to organismal life. Here we argue that short sequence repeats known as REPINs – whose replication is dependent on a non-jumping RAYT transposase – form a similar facultative symbiotic relationship with the bacterial chromosome. Evidence stems from distribution patterns across the eubacteria: persistence times of many millions of years, exceedingly rare duplication rates, vertical transmission, and population biology typical of living organisms, including population size fluctuations that correlate with available genome space. Additional analysis of patterns of REPIN evolution conform with theoretical predictions of conflict (and resolution) arising from the effects of selection operating simultaneously on REPINs and host cells. A search for similar kinds of genomic symbionts suggests that the REPIN-RAYT system is not unique.

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Section: Resultsmentioning

confidence: 99%

Ancient Darwinian replicators nested within eubacterial genomes

Bertels

Rainey

2021

Preprint

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“…Bacteria and archaea exhibit extensive natural variation in IS element number; most bacterial genomes contain no or few (<10) elements, whereas others have hundreds ( Sawyer et al 1987 ; Touchon and Rocha 2007 ; Bobay and Ochman 2017 ). There is also great variation within and between bacterial species in transposition activity and IS-mediated ectopic recombination rates ( Nzabarushimana and Tang 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Bacterial adaptation by a transposition burst of an invading IS element

Miller

Abresch

Ulrich

et al. 2021

Genome Biology and Evolution

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The general importance of transposable elements (TEs) for adaptive evolution remains unclear. This in part reflects a poor understanding of the role of TEs for adaptation in non-model systems. Here, we investigated whether insertion sequence (IS) elements are a major source of beneficial mutations during 400 generations of laboratory evolution of the cyanobacterium Acaryochloris marina strain CCMEE 5410, which has experienced a recent or on-going IS element expansion and has among the highest transposase gene contents for a bacterial genome. Most mutations detected in the eight independent experimental populations were IS transposition events. Surprisingly, however, the majority of these involved the copy-and-paste activity of only a single copy of an unclassified element (ISAm1) that has recently invaded the strain CCMEE 5410 genome. ISAm1 transposition was largely responsible for the highly repeatable evolutionary dynamics observed among populations. Notably, this included mutations in multiple targets involved in the acquisition of inorganic carbon for photosynthesis that were exclusively due to ISAm1 activity. These mutations were associated with an increase in linear growth rate under conditions of reduced carbon availability but did not appear to impact fitness when carbon was readily available. Our study reveals that the activity of a single transposase can fuel adaptation for at least several hundred generations but may also potentially limit the rate of adaptation through clonal interference.

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“…Consistent with the selfish DNA hypothesis, TEs can nevertheless be maintained because of their high transposition rate despite the deleterious effects they may cause. 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]. Knowledge about transposition and excision rates is therefore crucial for understanding TE abundance in natural populations [8].…”

Section: Introductionmentioning

confidence: 99%

Rates of transposition in Escherichia coli

et al. 2013

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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.

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Distribution and Abundance of Insertion Sequences Among Natural Isolates of Escherichia coli

Cited by 137 publications

References 19 publications

Ancient Darwinian replicators nested within eubacterial genomes

Ancient Darwinian replicators nested within eubacterial genomes

Bacterial adaptation by a transposition burst of an invading IS element

Rates of transposition in Escherichia coli

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