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 Rebooting Synthetic Phage-Inducible Chromosomal Islands: One Method to Forge Them All

2020 ◽  
Vol 2020 ◽  
pp. 1-14 ◽  
Author(s):  
Rodrigo Ibarra-Chávez ◽  
Andreas F. Haag ◽  
Pedro Dorado-Morales ◽  
Iñigo Lasa ◽  
José R. Penadés
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Genetic Manipulation ◽  
Bacterial Species ◽  
Bacterial Pathogenesis ◽  
Proof Of Concept ◽  
Synthetic Genes ◽  
High Frequencies ◽  
Bacterial Diseases ◽  
Synthetic Biology Approach

Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in Saccharomyces cerevisiae based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from Staphylococcus aureus and Escherichia coli and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.

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.

scholarly journals Distribution of the Escherichia coli K12 Insertion Sequences IS1, IS2 and IS3 Among Other Bacterial Species

Microbiology ◽  
1982 ◽  
Vol 128 (10) ◽  
pp. 2229-2234 ◽  
Author(s):  
N. Brahma ◽  
A. Schumacher ◽  
J. Cullum ◽  
H. Saedler
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Insertion Sequences ◽  
Escherichia Coli K12

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 The symmetrical pattern of base-pair substitutions rates across the chromosome in Escherichia coli has multiple causes

2019 ◽  
Author(s):  
Brittany A. Niccum ◽  
Heewook Lee ◽  
Wazim MohammedIsmail ◽  
Haixu Tang ◽  
Patricia L. Foster
Keyword(s):  
Escherichia Coli ◽  
Base Pair ◽  
Bacterial Species ◽  
Replication Timing ◽  
Mutation Rates ◽  
Whole Genome ◽  
Origin Of Replication ◽  
Symmetrical Pattern ◽  
Major Factors ◽  
Eukaryotic Genomes

AbstractMutation accumulation experiments followed by whole-genome sequencing have revealed that for several bacterial species the rate of base-pair substitutions is not constant across the chromosome but varies in a wave-like pattern symmetrical about the origin of replication. The experiments reported here demonstrate that in Escherichia coli several interacting factors determine the wave. Perturbing replication timing, progression, or the structure of the terminus disrupts the pattern. Biases in error-correction by proofreading and mismatch repair are major factors. The activities of the nucleoid binding proteins, HU and Fis, are important, suggesting that mutation rates increase when highly structured DNA is replicated. These factors should apply to most bacterial, and possibly eukaryotic, genomes, and imply that different areas of the genome evolve at different rates.

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 panRGP: a pangenome-based method to predict genomic islands and explore their diversity

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i651-i658 ◽  
Author(s):  
Adelme Bazin ◽  
Guillaume Gautreau ◽  
Claudine Médigue ◽  
David Vallenet ◽  
Alexandra Calteau
Keyword(s):  
Escherichia Coli ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Species Level ◽  
Genomic Islands ◽  
Genome Plasticity ◽  
Reference Dataset ◽  
Prokaryotic Genomes ◽  
Ideal Approach ◽  
Genomic Regions

Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity. Results We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies. Availability and implementation The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.

scholarly journals Adaptive reversion of a frameshift mutation in Escherichia coli.

Genetics ◽  
1991 ◽  
Vol 128 (4) ◽  
pp. 695-701 ◽  
Author(s):  
J Cairns ◽  
P L Foster
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Exponential Growth ◽  
Frameshift Mutation ◽  
Rare Event ◽  
Lacz Fusion ◽  
Mutation Rates ◽  
Classical Studies ◽  
Selective Forces

Abstract Mutation rates are generally thought not to be influenced by selective forces. This doctrine rests on the results of certain classical studies of the mutations that make bacteria resistant to phages and antibiotics. We have studied a strain of Escherichia coli which constitutively expresses a lacI-lacZ fusion containing a frameshift mutation that renders it Lac-. Reversion to Lac+ is a rare event during exponential growth but occurs in stationary cultures when lactose is the only source of energy. No revertants accumulate in the absence of lactose, or in the presence of lactose if there is another, unfulfilled requirement for growth. The mechanism for such mutation in stationary phase is not known, but it requires some function of RecA which is apparently not required for mutation during exponential growth.

Sign in / Sign up

Export Citation Format

Share Document