The evolution of DNA sequences in
            Escherichia coli

It is proposed that certain families of transposable elements originally evolved in plasmids and functioned in forming replicon fusions to aid in the horizontal transmission of non-conjugational plasmids. This hypothesis is supported by the finding that the transposable elements Tn 3 and γδ are found almost exclusively in plasmids, and also by the distribution of the unrelated insertion sequences IS4 and IS 5 among a reference collection of 67 natural isolates of Escherichia coli. Each insertion sequence was found to be present in only about one-third of the strains. Among the ten strains found to contain both insertion sequences, the number of copies of the elements was negatively correlated. With respect to IS 5 , approximately half of the strains containing a chromosomal copy of the insertion element also contained copies within the plasmid complement of the strain.

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Why do unrelated insertion sequences occur together in the genome of Escherichia coli?

Genetics ◽

10.1093/genetics/118.3.537 ◽

1988 ◽

Vol 118 (3) ◽

pp. 537-541

Author(s):

D L Hartl ◽

S A Sawyer

Keyword(s):

Escherichia Coli ◽

Horizontal Transfer ◽

Process Model ◽

Insertion Sequence ◽

Branching Process ◽

Insertion Sequences ◽

Reference Collection ◽

Natural Isolates ◽

Positive Correlations

Abstract Natural isolates of Escherichia coli are polymorphic for the presence or absence of insertion sequences. Among the ECOR reference collection of 71 natural isolates studied for the number of copies of the insertion sequences IS1, IS2, IS3, IS4, IS5 and IS30, the number of strains containing no copies of the insertion sequences were 11, 28, 23, 43, 46 and 36, respectively. Significant correlations occur in the ECOR strains in the presence or absence of unrelated insertion sequences in the chromosome and plasmid complements. Strains containing any insertion sequence are more likely to contain additional, unrelated insertion sequences than would be expected by chance. We suggest that the positive correlations result from horizontal transfer mediated by plasmids. A branching-process model for the plasmid-mediated transmission of insertion sequences among hosts yields such a correlation, even in the absence of interactions affecting transposition or fitness. The predictions of the model are quantitatively in agreement with the observed correlations among insertion sequences.

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JOINT DISTRIBUTION OF INSERTION ELEMENTS IS4 AND IS5 IN NATURAL ISOLATES OF ESCHERICHIA COLI

Genetics ◽

10.1093/genetics/111.2.219 ◽

1985 ◽

Vol 111 (2) ◽

pp. 219-231

Author(s):

Daniel E Dykhuizen ◽

Stanley A Sawyer ◽

Louis Green ◽

Raymond D Miller ◽

Daniel L Hartl

Keyword(s):

Escherichia Coli ◽

Dna Sequences ◽

Significant Negative Correlation ◽

Single Copy ◽

Common Mechanism ◽

Reference Collection ◽

Insertion Elements ◽

Natural Isolates ◽

Dna Insertion ◽

Flanking Sequences

ABSTRACT A reference collection of natural isolates of Escherichia coli has been studied in order to determine the distribution, abundance and joint occurence of DNA insertion elements IS4 and IS5. Among these isolates, 36% were found to contain IS4 and 30% were found to contain IS5. Among strains containing IS4 the mean number of copies per strain was 4.4 ± 0.8; the comparable figure for IS5 was 3.7 ± 1.0. Although the presence of the elements among the isolates was independent, among those isolates containing both IS4 and IS5, there was a significant negative correlation in the number of copies of the elements.— The reference collection was also studied for the presence of the DNA sequences flanking the single copy of IS4 in the chromosome of E. coli K12. Homologous sequences were found in only 26% of the isolates. The sequences flanking the IS4 invariably occur together, and their presence is significantly correlated with the presence of IS4. In eight of the strains that carry these flanking sequences, an IS4 is located between them, and the sequences are present at the homologous position as in the K12 strain. We suggest that IS4 and its flanking sequences share a common mechanism of dissemination, such as plasmids, and we present evidence that they are included in a much larger transposable element.

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IS103, a new insertion element in Escherichia coli: characterization and distribution in natural populations.

Genetics ◽

10.1093/genetics/121.3.423 ◽

1989 ◽

Vol 121 (3) ◽

pp. 423-431 ◽

Cited By ~ 2

Author(s):

B G Hall ◽

L L Parker ◽

P W Betts ◽

R F DuBose ◽

S A Sawyer ◽

...

Keyword(s):

Escherichia Coli ◽

Copy Number ◽

Insertion Sequence ◽

Natural Populations ◽

Single Copy ◽

Target Sequence ◽

Wild Type ◽

Insertion Element ◽

E Coli ◽

Natural Isolates

Abstract IS103 is a previously unknown insertion sequence found in Escherichia coli K12. We have sequenced IS103 and find that it is a 1441-bp element that consists of a 1395-bp core flanked by imperfect 23-bp inverted repeats. IS103 causes a 6-bp duplication of the target sequence into which it inserts. There is a single copy of IS103 present in wild-type E. coli K12 strain HfrC. In strain X342 and its descendents there are two additional copies, one of which is located within the bglF gene. IS103 is capable of excising from within bglF and restoring function of that gene. IS103 exhibits 44% sequence identity with IS3, suggesting that the two insertion sequences are probably derived from a common ancestor. We have examined the distribution of IS103 in the chromosomes and plasmids of the ECOR collection of natural isolates of E. coli. IS103 is found in 36 of the 71 strains examined, and it strongly tends to inhabit plasmids rather than chromosomes. Comparison of the observed distribution of IS103 with distributions predicted by nine different models for the regulation of transposition according to copy number and of the effects of copy number on fitness suggest that transposition of IS103 is strongly regulated and that it has only minor effects on fitness. The strong clustering of IS103 within one phylogenetic subgroup of the E. coli population despite its presence on plasmids suggests that plasmids tend to remain within closely related strains and that transfer to distantly related strains is inhibited.

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

Genetics ◽

10.1093/genetics/115.1.51 ◽

1987 ◽

Vol 115 (1) ◽

pp. 51-63

Author(s):

Stanley A Sawyer ◽

Daniel E Dykhuizen ◽

Robert F DuBose ◽

Louis Green ◽

T Mutangadura-Mhlanga ◽

...

Keyword(s):

Escherichia Coli ◽

Copy Number ◽

Positive Association ◽

Process Models ◽

Insertion Sequences ◽

Significant Positive Association ◽

Reference Collection ◽

Insertion Elements ◽

Dna Restriction Fragments ◽

Natural Isolates

ABSTRACT A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been studied with respect to the distribution and abundance of transposable insertion sequences using DNA hybridization. The data include 1173 occurrences of six unrelated insertion sequences (IS 1, IS2, IS3, IS4, IS5 and IS 30). The number of insertion elements per strain, and the sizes of DNA restriction fragments containing them, is highly variable and can be used to discriminate even among closely related strains. The occurrence and abundance of pairs of unrelated insertion sequences are apparently statistically independent, but significant correlations result from stratifications in the reference collection. However, there is a highly significant positive association among the insertion sequences considered in the aggregate. Nine branching process models, which differ in assumptions regarding the regulation of transposition and the effect of copy number on fitness, have been evaluated with regard to their fit of the observed distributions. No single model fits all copy number distributions. The best models incorporate no regulation of transposition and a moderate to strong decrease in fitness with increasing copy number for IS1 and IS5, strong regulation of transposition and a negligible to weak decrease in fitness with increasing copy number for IS3, and less than strong regulation of transposition for IS2, IS 4 and IS30.

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Distribution of DNA insertion element IS5 in natural isolates of Escherichia coli.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.81.14.4500 ◽

1984 ◽

Vol 81 (14) ◽

pp. 4500-4504 ◽

Cited By ~ 14

Author(s):

L. Green ◽

R. D. Miller ◽

D. E. Dykhuizen ◽

D. L. Hartl

Keyword(s):

Escherichia Coli ◽

Insertion Element ◽

Natural Isolates ◽

Dna Insertion

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Genetic Rearrangements of the Regions Adjacent to Genes Encoding Heat-Labile Enterotoxins (eltAB) of EnterotoxigenicEscherichia coli Strains

Applied and Environmental Microbiology ◽

10.1128/aem.66.1.352-358.2000 ◽

2000 ◽

Vol 66 (1) ◽

pp. 352-358 ◽

Cited By ~ 19

Author(s):

Stefan Schlör ◽

Sabine Riedl ◽

Julia Blaß ◽

Joachim Reidl

Keyword(s):

Escherichia Coli ◽

Dna Sequences ◽

Insertion Sequence ◽

Is Element ◽

Heat Stable ◽

Heat Labile ◽

Genes Encoding ◽

Encoding Genes ◽

Genetic Rearrangements ◽

Dependent Mechanism

ABSTRACT One of the most common bacterially mediated diarrheal infections is caused by enterotoxigenic Escherichia coli (ETEC) strains. ETEC-derived plasmids are responsible for the distribution of the genes encoding the main toxins, namely, the heat-labile and heat-stable enterotoxins. The origins and transfer modes (intra- or interplasmid) of the toxin-encoding genes have not been characterized in detail. In this study, we investigated the DNA regions located near the heat-labile enterotoxin-encoding genes (eltAB) of several clinical isolates. It was found that the eltAB region is flanked by conserved 236- and 280-bp regions, followed by highly variable DNA sequences which consist mainly of partial insertion sequence (IS) elements. Furthermore, we demonstrated that rearrangements of the eltAB region of one particular isolate, which harbors an IS91R sequence next toeltAB, could be produced by a recA-independent but IS91 sequence-dependent mechanism. Possible mechanisms of dissemination of IS element-associated enterotoxin-encoding genes are discussed.

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Mosaic Structure of Plasmids From Natural Populations of Escherichia coli

Genetics ◽

10.1093/genetics/143.3.1091 ◽

1996 ◽

Vol 143 (3) ◽

pp. 1091-1100 ◽

Cited By ~ 9

Author(s):

E Fidelma Boyd ◽

Charles W Hill ◽

Stephen M Rich ◽

Daniel L Hartl

Keyword(s):

Escherichia Coli ◽

Dna Sequences ◽

Dna Hybridization ◽

Natural Populations ◽

High Rate ◽

Naturally Occurring ◽

Chromosomal Genes ◽

Reference Collection ◽

Plasmid Genes ◽

Different Sources

Abstract The distribution of plasmids related to the fertility factor F was examined in the ECOR reference collection of Escherichia coli. Probes specific for four F-related genes were isolated and used to survey the collection by DNA hybridization. To estimate the genetic diversity of genes in F-like plasmids, DNA sequences were obtained for four plasmid genes. The phylogenetic relationships among the plasmids in the ECOR strains is very different from that of the strains themselves. This finding supports the view that plasmid transfer has been frequent within and between the major groups of ECOR. Furthermore, the sequences indicate that recombination between genes in plasmids takes place at a considerably higher frequency than that observed for chromosomal genes. The plasmid genes, and by inference the plasmids themselves, are mosaic in structure with different regions acquired from different sources. Comparison of gene sequences from a variety of naturally occurring plasmids suggested a plausible donor of some of the recombinant regions as well as implicating a chi site in the mechanism of genetic exchange. The relatively high rate of recombination in F-plasmid genes suggests that conjugational gene transfer may play a greater role in bacterial population structure than previously appreciated.

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Bacterial Interspersed Mosaic Elements (BIMEs) Are a Major Source of Sequence Polymorphism in Escherichia coli Intergenic Regions Including Specific Associations With a New Insertion Sequence

Genetics ◽

10.1093/genetics/145.3.551 ◽

1997 ◽

Vol 145 (3) ◽

pp. 551-562 ◽

Cited By ~ 5

Author(s):

Sophie Bachellier ◽

Jean-Marie Clément ◽

Maurice Hofnung ◽

Eric Gilson

Keyword(s):

Escherichia Coli ◽

Dna Sequences ◽

Multiple Sequence ◽

E Coli ◽

Sequence Organization ◽

Is Element ◽

Integration Sites ◽

Intergenic Regions ◽

Natural Isolates ◽

K 12

A significant fraction of Escherichia coli intergenic DNA sequences is composed of two families of repeated bacterial interspersed mosaic elements (BIME-1 and BIME-2). In this study, we determined the sequence organization of six intergenic regions in 51 E. coli and Shigella natural isolates. Each region contains a BIME in E. coli K-12. We found that multiple sequence variations are located within or near these BIMEs in the different bacteria. Events included excisions of a whole BIME-1, expansion/deletion within a BIME-2 and insertions of non-BIME sequences like the boxC repeat or a new IS element, named IS 1397. Remarkably, 14 out of 14 IS 1397 integration sites correspond to a BIME sequence, strongly suggesting that this IS element is specifically associated with BIMEs, and thus inserts only in extragenic regions. Unlike BIMEs, IS 1397 is not detected in all E. coli isolates. Possible relationships between the presence of this IS element and the evolution of BIMEs are discussed.

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Association of Composite IS26-sul3Elements with Highly Transmissible IncI1 Plasmids in Extended-Spectrum-β-Lactamase-Producing Escherichia coli Clones from Humans

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01448-10 ◽

2011 ◽

Vol 55 (5) ◽

pp. 2451-2457 ◽

Cited By ~ 33

Author(s):

Tânia Curiao ◽

Rafael Cantón ◽

M. Pilar Garcillán-Barcia ◽

Fernando de la Cruz ◽

Fernando Baquero ◽

...

Keyword(s):

Escherichia Coli ◽

Comparative Analysis ◽

Transposable Elements ◽

In Silico ◽

Insertion Element ◽

Content Type ◽

Class 1 Integrons ◽

Extended Spectrum ◽

Class 1 ◽

M 14

ABSTRACTThe association of an IS440-sul3platform with Tn21class 1 integrons carried by IncI1 plasmids encoding extended-spectrum β-lactamases (ESBLs; mainly SHV-12 and CTX-M-14) among worldwideEscherichia coliclones of phylogroups A (ST10, ST23, and ST46), B1 (ST155, ST351, and ST359), and D/B2 (ST131) is reported. Anin silicocomparative analysis ofsul3elements available in the GenBank database shows the evolution ofsul3platforms by hosting different transposable elements facilitating the potential genesis of IS26composite transposons and further insertion element-mediated promoted arrangements.

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Operon formation by insertion sequence IS3 in Escherichia coli

10.1101/2021.11.02.466885 ◽

2021 ◽

Author(s):

Yuki Kanai ◽

Saburo Tsuru ◽

Chikara Furusawa

Keyword(s):

Escherichia Coli ◽

Insertion Sequence ◽

Bacterial Species ◽

Mutation Rates ◽

Insertion Sequences ◽

Proof Of Concept ◽

Regulatory Architecture ◽

Expression Of Genes ◽

Prokaryotic Genomes ◽

Rapid Formation

Operons are a hallmark of the genomic and regulatory architecture of prokaryotes. However, the mechanism by which two genes placed far apart gradually come close and form operons remains to be elucidated. Here, we propose a new model of the origin of operons: Mobile genetic elements called insertion sequences can facilitate the formation of operons by consecutive insertion-deletion-excision reactions. This mechanism barely leaves traces of insertion sequences and is difficult to detect in evolution in nature. We performed, to the best of our knowledge, the first experimental demonstration of operon formation, as a proof of concept. The insertion sequence IS3 and the insertion sequence excision enhancer are genes found in a broad range of bacterial species. We introduced these genes into insertion sequence-less Escherichia coli and found that, supporting our hypothesis, the activity of the two genes altered the expression of genes surrounding IS3, closed a 2.7 kilobase pair gap between a pair of genes, and formed new operons. This study shows how insertion sequences can facilitate the rapid formation of operons through locally increasing the structural mutation rates and highlights how coevolution with mobile elements may shape the organization of prokaryotic genomes and gene regulation.

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