Rates of transposition in
            <i>Escherichia coli</i>

Sousa, Ana; Bourgard, Catarina; Wahl, Lindi M.; Gordo, Isabel

doi:10.1098/rsbl.2013.0838

Cited by 63 publications

(64 citation statements)

References 20 publications

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“…Although PMPs are much shorter sequences than ISs, if we take 10 26 as a conservative estimate of a possible HGT rate for PMPs, this would imply that the duplication and loss rates for PMPs would be of order 10 25 . These values would be consistent with recent direct estimates of IS replicative transposition rates of 10 25 for six transposable elements in Escherichea coli (Sousa et al 2013). Sousa et al also found that for at least two of these ISs (IS2 and IS5), the excision rate was almost as large as the duplication rate.…”

Section: Discussionsupporting

confidence: 80%

Birth, Death, and Diversification of Mobile Promoters in Prokaryotes

2014

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A previous study of prokaryotic genomes identified large reservoirs of putative mobile promoters (PMPs), that is, homologous promoter sequences associated with nonhomologous coding sequences. Here we extend this data set to identify the full complement of mobile promoters in sequenced prokaryotic genomes. The expanded search identifies nearly 40,000 PMP sequences, 90% of which occur in noncoding regions of the genome. To gain further insight from this data set, we develop a birth-deathdiversification model for mobile genetic elements subject to sequence diversification; applying the model to PMPs we are able to quantify the relative importance of duplication, loss, horizontal gene transfer (HGT), and diversification to the maintenance of the PMP reservoir. The model predicts low rates of HGT relative to the duplication and loss of PMP copies, rapid dynamics of PMP families, and a pool of PMPs that exist as a single copy in a genome at any given time, despite their mobility. We report evidence of these "singletons" at high frequencies in prokaryotic genomes. We also demonstrate that including selection, either for or against PMPs, was not necessary to describe the observed data.

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Section: Discussionsupporting

confidence: 80%

Birth, Death, and Diversification of Mobile Promoters in Prokaryotes

2014

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“…coli [17]. In fact, IS insertions occurred in 6 out of the 7 targets of adaptation identified through parallelism.…”

Section: Resultsmentioning

confidence: 99%

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

et al. 2016

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The relative role of drift versus selection underlying the evolution of bacterial species within the gut microbiota remains poorly understood. The large sizes of bacterial populations in this environment suggest that even adaptive mutations with weak effects, thought to be the most frequently occurring, could substantially contribute to a rapid pace of evolutionary change in the gut. We followed the emergence of intra-species diversity in a commensal Escherichia coli strain that previously acquired an adaptive mutation with strong effect during one week of colonization of the mouse gut. Following this first step, which consisted of inactivating a metabolic operon, one third of the subsequent adaptive mutations were found to have a selective effect as high as the first. Nevertheless, the order of the adaptive steps was strongly affected by a mutational hotspot with an exceptionally high mutation rate of 10−5. The pattern of polymorphism emerging in the populations evolving within different hosts was characterized by periodic selection, which reduced diversity, but also frequency-dependent selection, actively maintaining genetic diversity. Furthermore, the continuous emergence of similar phenotypes due to distinct mutations, known as clonal interference, was pervasive. Evolutionary change within the gut is therefore highly repeatable within and across hosts, with adaptive mutations of selection coefficients as strong as 12% accumulating without strong constraints on genetic background. In vivo competitive assays showed that one of the second steps (focA) exhibited positive epistasis with the first, while another (dcuB) exhibited negative epistasis. The data shows that strong effect adaptive mutations continuously recur in gut commensal bacterial species.

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“…Previous reports indicated that transposition frequency can be perturbed by growth temperatures (McClintock, 1984; Ohtsubo et al, 2005; Sousa et al, 2013). To tune the transposition rate, experiments were carried out with cells cultured at a lower 34 °C temperature, which was shown to slow down crosstalk triggered mutation of this circuit (Figure S4B).…”

Section: Resultsmentioning

confidence: 99%

Quorum-Sensing Crosstalk-Driven Synthetic Circuits: From Unimodality to Trimodality

Menn

Wang

2014

Chemistry & Biology

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SUMMARY Widespread quorum-sensing (QS) enables bacteria to communicate and plays a critical role in controlling bacterial virulence. However, effects of promiscuous QS crosstalk and its implications for gene regulation and cell decision-making remain largely unknown. Here we systematically studied the crosstalk between LuxR/I and LasR/I systems and found that QS crosstalk can be dissected into signal crosstalk and promoter crosstalk. Further investigations using synthetic positive feedback circuits revealed that signal crosstalk significantly decreases circuit’s bistable potential while maintaining unimodality. Promoter crosstalk, however, reproducibly generates complex trimodal responses resulting from noise-induced state transitions and host-circuit interactions. A mathematical model that integrates the circuit’s nonlinearity, stochasticity, and host-circuit interactions was developed, and its predictions of conditions for trimodality were verified experimentally. Combining synthetic biology and mathematical modeling, this work sheds light on the complex behaviors emerging from QS crosstalk, which could be exploited for therapeutics and biotechnology.

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Rates of transposition in Escherichia coli

Cited by 63 publications

References 20 publications

Birth, Death, and Diversification of Mobile Promoters in Prokaryotes

Birth, Death, and Diversification of Mobile Promoters in Prokaryotes

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

Quorum-Sensing Crosstalk-Driven Synthetic Circuits: From Unimodality to Trimodality

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