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

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 of insertion element IS1 in natural isolates of Escherichia coli

MGG Molecular & General Genetics ◽

10.1007/bf00325920 ◽

1983 ◽

Vol 189 (3) ◽

pp. 516-518 ◽

Cited By ~ 16

Author(s):

Kate Nyman ◽

Hisako Ohtsubo ◽

Daniel Davison ◽

Eiichi Ohtsubo

Keyword(s):

Escherichia Coli ◽

Insertion Element ◽

Natural Isolates

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The evolution of DNA sequences in Escherichia coli

Philosophical Transactions of the Royal Society of London Series B Biological Sciences ◽

10.1098/rstb.1986.0001 ◽

1986 ◽

Vol 312 (1154) ◽

pp. 191-204 ◽

Cited By ~ 18

Keyword(s):

Escherichia Coli ◽

Transposable Elements ◽

Dna Sequences ◽

Insertion Sequence ◽

Horizontal Transmission ◽

Insertion Sequences ◽

Insertion Element ◽

Reference Collection ◽

Natural Isolates ◽

Chromosomal Copy

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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Cloning of the nupC gene of Escherichia coli encoding a nucleoside transport system, and identification of an adjacent Insertion element, IS 186

Molecular Microbiology ◽

10.1111/j.1365-2958.1994.tb00392.x ◽

1994 ◽

Vol 11 (6) ◽

pp. 1159-1168 ◽

Cited By ~ 64

Author(s):

Jane E. Craig ◽

Yianbiao Zhang ◽

Maurice P. Gallagher

Keyword(s):

Escherichia Coli ◽

Transport System ◽

Nucleoside Transport ◽

Insertion Element

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Functional genes for cellobiose utilization in natural isolates of Escherichia coli.

Journal of Bacteriology ◽

10.1128/jb.169.6.2713-2717.1987 ◽

1987 ◽

Vol 169 (6) ◽

pp. 2713-2717 ◽

Cited By ~ 4

Author(s):

B G Hall ◽

W Faunce

Keyword(s):

Escherichia Coli ◽

Functional Genes ◽

Natural Isolates

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Chromosomal Integration of Heterologous DNA in Escherichia coli with Precise Removal of Markers and Replicons Used during Construction

Journal of Bacteriology ◽

10.1128/jb.181.22.7143-7148.1999 ◽

1999 ◽

Vol 181 (22) ◽

pp. 7143-7148 ◽

Cited By ~ 60

Author(s):

F. Martinez-Morales ◽

A. C. Borges ◽

A. Martinez ◽

K. T. Shanmugam ◽

L. O. Ingram

Keyword(s):

Escherichia Coli ◽

Helper Plasmid ◽

Flp Recombinase ◽

E Coli ◽

Homologous Fragment ◽

Genes Encoding ◽

Dna Insertion ◽

K 12 ◽

Multiple Cloning Sites

ABSTRACT A set of vectors which facilitates the sequential integration of new functions into the Escherichia coli chromosome by homologous recombination has been developed. These vectors are based on plasmids described by Posfai et al. (J. Bacteriol. 179:4426–4428, 1997) which contain conditional replicons (pSC101 or R6K), a choice of three selectable markers (ampicillin, chloramphenicol, or kanamycin), and a single FRT site. The modified vectors contain twoFRT sites which bracket a modified multiple cloning region for DNA insertion. After integration, a helper plasmid expressing the flippase (FLP) recombinase allows precise in vivo excision of the replicon and the marker used for selection. Sites are also available for temporary insertion of additional functions which can be subsequently deleted with the replicon. Only the DNA inserted into the multiple cloning sites (passenger genes and homologous fragment for targeting) and a single FRT site (68 bp) remain in the chromosome after excision. The utility of these vectors was demonstrated by integrating Zymomonas mobilis genes encoding the ethanol pathway behind the native chromosomaladhE gene in strains of E. coli K-12 andE. coli B. With these vectors, a single antibiotic selection system can be used repeatedly for the successive improvement of E. coli strains with precise deletion of extraneous genes used during construction.

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Response to Comment on “RNA-guided DNA insertion with CRISPR-associated transposases”

Science ◽

10.1126/science.abb2920 ◽

2020 ◽

Vol 368 (6495) ◽

pp. eabb2920 ◽

Cited By ~ 4

Author(s):

Jonathan Strecker ◽

Alim Ladha ◽

Kira S. Makarova ◽

Eugene V. Koonin ◽

Feng Zhang

Keyword(s):

Escherichia Coli ◽

Donor Plasmid ◽

Dna Insertion ◽

Simple Integration

Rice et al. suggest that the CRISPR-associated transposase ShCAST system could lead to additional insertion products beyond simple integration of the donor. We clarify the outcomes of ShCAST-mediated insertions in Escherichia coli, which consist of both simple insertions and integration of the donor plasmid. This latter outcome can be avoided by use of a 5′ nicked DNA donor.

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