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

Genetics ◽  
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.

The evolution of DNA sequences in Escherichia coli

1986 ◽  
Vol 312 (1154) ◽  
pp. 191-204 ◽  
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.

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

Genetics ◽  
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.

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

Genetics ◽  
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.

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

Genetics ◽  
1989 ◽  
Vol 121 (3) ◽  
pp. 423-431 ◽  
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.

scholarly journals Operon formation by insertion sequence IS3 in Escherichia coli

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.

scholarly journals Transposition of IS1397 in the FamilyEnterobacteriaceae and First Characterization of ISKpn1, a New Insertion Sequence Associated withKlebsiella pneumoniae Palindromic Units

2001 ◽  
Vol 183 (15) ◽  
pp. 4395-4404 ◽  
Author(s):  
Caroline Wilde ◽  
Sophie Bachellier ◽  
Maurice Hofnung ◽  
Jean-Marie Clément
Keyword(s):  
Escherichia Coli ◽  
Hot Spots ◽  
Sequence Comparison ◽  
Insertion Sequence ◽  
Klebsiella Oxytoca ◽  
Insertion Sequences ◽  
Serovar Typhimurium ◽  
Intergenic Regions ◽  
First Time

ABSTRACT IS1397 and ISKpn1 are IS3family members which are specifically inserted into the loop of palindromic units (PUs). IS1397 is shown to transpose into PUs with sequences close or identical to the Escherichia coli consensus, even in other enterobacteria (Salmonella enterica serovar Typhimurium, Klebsiella pneumoniae, and Klebsiella oxytoca). Moreover, we show that homologous intergenic regions containing PUs constitute IS1397 transpositional hot spots, despite bacterial interspersed mosaic element structures that differ among the three species. ISKpn1, described here for the first time, is specific for PUs from K. pneumoniae, in which we discovered it. A sequence comparison between the two insertion sequences allowed us to define a motif possibly accounting for their specificity.

scholarly journals Molecular Basis of the Indole-Negative Reaction in Shigella Strains: Extensive Damages to the tna Operon by Insertion Sequences

2004 ◽  
Vol 186 (21) ◽  
pp. 7460-7465 ◽  
Author(s):  
Ferdousi Rezwan ◽  
Ruiting Lan ◽  
Peter R. Reeves
Keyword(s):  
Escherichia Coli ◽  
Molecular Basis ◽  
Insertion Sequence ◽  
Negative Reaction ◽  
Insertion Sequences ◽  
E Coli ◽  
Negative Phenotype

ABSTRACT The molecular basis of the loss of tryptophan utilization (indole-negative phenotype) of Shigella strains, in effect clones of Escherichia coli, was investigated. Analysis of the tna operon of 23 Shigella strains representing each of the indole-negative serotypes revealed that insertion sequence-mediated insertion and/or deletions damaged the tna operon, leading to inability to convert tryptophan to indole. These events differ for cluster 1, cluster 3, and the outlier Shigella strains, confirming our previous observation of independent origins of these lineages from within E. coli. Parallel loss of the trait and prevalence of indole-negative strains suggest that the trait is deleterious in Shigella strains and advantages those without it.

scholarly journals The Probability of Fixation in Populations of Changing Size

Genetics ◽  
1997 ◽  
Vol 146 (2) ◽  
pp. 723-733 ◽  
Author(s):  
Sarah P Otto ◽  
Michael C Whitlock
Keyword(s):  
Diffusion Equation ◽  
Adaptive Evolution ◽  
Process Model ◽  
Branching Process ◽  
Approximate Solutions ◽  
Logistic Growth ◽  
Beneficial Mutations ◽  
Demographic Models ◽  
Deleterious Alleles ◽  
Probability Of Fixation

The rate of adaptive evolution of a population ultimately depends on the rate of incorporation of beneficial mutations. Even beneficial mutations may, however, be lost from a population since mutant individuals may, by chance, fail to reproduce. In this paper, we calculate the probability of fixation of beneficial mutations that occur in populations of changing size. We examine a number of demographic models, including a population whose size changes once, a population experiencing exponential growth or decline, one that is experiencing logistic growth or decline, and a population that fluctuates in size. The results are based on a branching process model but are shown to be approximate solutions to the diffusion equation describing changes in the probability of fixation over time. Using the diffusion equation, the probability of fixation of deleterious alleles can also be determined for populations that are changing in size. The results developed in this paper can be used to estimate the fixation flux, defined as the rate at which beneficial alleles fix within a population. The fixation flux measures the rate of adaptive evolution of a population and, as we shall see, depends strongly on changes that occur in population size.

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