Insertion Sequence (IS)-Excision Enhancer (IEE)-Mediated IS Excision from the
            <i>lacZ</i>
            Gene Restores the Lactose Utilization Defect of Shiga Toxin-Producing Escherichia coli O121:H19 Strains and Is Responsible for Their Delayed Lactose Utilization Phenotype

Nakamura, Keiji; Seto, Kazuko; Isobe, Junko; Taniguchi, Itsuki; Gotoh, Yasuhiro; Hayashi, Tetsuya

doi:10.1128/aem.00760-22

Cited by 7 publications

(6 citation statements)

References 36 publications

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“…In conclusion, although initially described as common in E. coli O157:H7, our results show that IEE protein is highly conserved and shows a patchy distribution among EHEC, EPEC and ETEC/STEC genomes, suggesting not only promiscuous horizontal transfer across diverse E. coli serovars and phylogroups, but also a significant biological role in enhancing adaptability, as was recently proposed ( 11 , 13 ). Thus, IEE could be part of a generalized mechanism that supports adaptability to changing environmental conditions.…”

Section: Resultssupporting

confidence: 70%

“…Among them, the IS 3 family member IS 629 is the most abundant (23 copies) and is responsible for many polymorphisms associated with gene inactivation and/or genomic deletions ( 9 ). Detailed analysis of the transposition mechanism of IS 629 enabled the identification of a new protein, termed IS-excision enhancer (IEE), which promotes excision of IS 629 and other members of the IS 3 , IS 1 and IS 30 families in a transposase-dependent manner ( 10 , 11 ). The simultaneous presence of both IEE and IS 629 elements in almost all E. coli STEC strains from seropathotypes A and B, responsible for high pathogenicity and human disease, and the absence of at least one of them in the less pathogenic seropathotypes C and D, has led to the suggestion that their combined presence drives evolution towards increased virulence ( 12 ), which makes the study of this transposition system clinically important.…”

Section: Introductionmentioning

confidence: 99%

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The enterohemorrhagicEscherichia coliinsertion sequence-excision enhancer protein is a DNA polymerase with microhomology-mediated end-joining activity

Calvo

Mateo-Cáceres

Díaz-Arco

et al. 2023

Nucleic Acids Research

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Bacterial genomes contain an abundance of transposable insertion sequence (IS) elements that are essential for genome evolution and fitness. Among them, IS629 is present in most strains of enterohemorrhagic Escherichia coli O157 and accounts for many polymorphisms associated with gene inactivation and/or genomic deletions. The excision of IS629 from the genome is promoted by IS-excision enhancer (IEE) protein. Despite IEE has been identified in the most pathogenic serotypes of E. coli, its biochemical features that could explain its role in IS excision are not yet understood. We show that IEE is present in >30% of all available E. coli genome assemblies, and is highly conserved and very abundant within enterohemorrhagic, enteropathogenic and enterotoxigenic genomes. In vitro analysis of the recombinant protein from E. coli O157:H7 revealed the presence of a Mn2+-dependent error-prone DNA polymerase activity in its N-terminal archaeo-eukaryotic primase (AEP) domain able to promote dislocations of the primer and template strands. Importantly, IEE could efficiently perform in vitro an end-joining reaction of 3’-single-strand DNA overhangs with ≥4 bp of homology requiring both the N-terminal AEP and C-terminal helicase domains. The proposed role for IEE in the novel IS excision mechanism is discussed.

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Section: Resultssupporting

confidence: 70%

Section: Introductionmentioning

confidence: 99%

The enterohemorrhagicEscherichia coliinsertion sequence-excision enhancer protein is a DNA polymerase with microhomology-mediated end-joining activity

Calvo

Mateo-Cáceres

Díaz-Arco

et al. 2023

Nucleic Acids Research

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“…Although ISs are considered selfish genes, they can be utilized by different pathogens for the regulation of capsule production ( Acinetobacter baumannii (Whiteway et al , 2022)), for the regulation of metabolic pathways (Shiga toxin-producing Escherichia coli (Nakamura et al , 2022)) and the variation of O1 antigen ( Vibrio cholerae (Nesper et al , 2000)); however, how environmental factors regulate the excision of ISs is not well understood. For ixotrophy, our data suggest that the levels of available nutrients may regulate IS activity.…”

Section: Discussionmentioning

confidence: 99%

Mechanism of bacterial predation via ixotrophy

Lien,

Amendola,

Lee

et al. 2024

Preprint

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Predation allows bacteria to access alternative substrates in low-nutrient conditions. Ixotrophy has been proposed as a predatory lifestyle of multicellular filamentous bacteria in aquatic environments; however, the molecular mechanism remains unknown.Here we uncover by a multidisciplinary approach that ixotrophy requires the interplay of multiple cellular machineries and a regulatory mechanism. Attacker-prey contacts are established by gliding motility and extracellular grappling hook-like structures that bind prey flagella. Cryo-electron microscopy identifies the grappling hooks as a heptameric assembly of a Type 9 Secretion System substrate. Cryo-electron tomography and functional assays show that killing is mediated by puncturing of the prey cell using a Type 6 Secretion System, possibly triggered by extracellular antennae. Single-cell analyses with stable isotope-labeled prey demonstrate that prey components are taken up by the attacker. Depending on nutrient availability, ixotrophy is switched off by endogenous Insertion Sequence Elements and re-activated through their excision. A marine metagenomic time series provides evidence for coupled dynamics of ixotrophic bacteria and their prey.Our study reveals the complex mechanism of a conserved microbial predatory lifestyle and indicates the need for its regulation in conditions where the expression of costly pathways is dispensable.

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“…The co‐existence of IS 629 and the iee gene, which encodes IEE, may promote genomic diversity in enterotoxigenic E. coli (Kusumoto et al, 2014) and enhance the adaptability to environmental fluctuations in EHEC (Toro et al, 2015). IS excision can modify the phenotype of EHEC cultured under laboratory conditions (Kusumoto et al, 2001; Nakamura et al, 2022). It has also been reported that the combined activity of IS 3 and IEE enables the rapid formation of operons (Kanai et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Insertion sequence excision is enhanced by a protein that catalyzes branch migration and promotes microhomology‐mediated end joining

Kishino,

Saito,

Muto

et al. 2023

Genes to Cells

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Insertion sequence (IS)‐excision enhancer (IEE) promotes the excision of ISs in the genome of enterohemorrhagic Escherichia coli O157. Because IEE‐dependent IS excision occurs in the presence of transposase, the process of IS transposition may be involved in IS excision; however, little is understood about the molecular mechanisms of IS excision. Our in vitro analysis revealed that IEE exhibits DNA‐dependent ATPase activity, which is activated by branched DNA. IEE also catalyzes the branch migration of fork‐structured DNA. These results suggest that IEE remodels branched structures of the IS transposition intermediate. Sequence analysis of recombination sites in IS‐excision products suggested that microhomologous sequences near the ends of the IS are involved in IS excision. IEE promoted microhomology‐mediated end joining (MMEJ), in which base pairing between 6‐nucleotides complementary ends of two 3′‐protruding DNAs and subsequent elongation of the paired DNA strand occurred. IS‐excision frequencies were significantly decreased in cells producing IEE mutants that had lost either branch migration or MMEJ activity, which suggests that these activities of IEE are required for IS excision. Based on our results, we propose a model for IS excision triggered by IEE and transposase.

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Insertion Sequence (IS)-Excision Enhancer (IEE)-Mediated IS Excision from the lacZ Gene Restores the Lactose Utilization Defect of Shiga Toxin-Producing Escherichia coli O121:H19 Strains and Is Responsible for Their Delayed Lactose Utilization Phenotype

Abstract: Insertion sequences (ISs) can modulate gene expression by gene inactivation or activation. While phenotypic changes due to IS insertion/transposition are frequently observed, gene reactivation by precise or simple IS excision rarely occurs.

Cited by 7 publications

References 36 publications

The enterohemorrhagicEscherichia coliinsertion sequence-excision enhancer protein is a DNA polymerase with microhomology-mediated end-joining activity

The enterohemorrhagicEscherichia coliinsertion sequence-excision enhancer protein is a DNA polymerase with microhomology-mediated end-joining activity

Mechanism of bacterial predation via ixotrophy

Insertion sequence excision is enhanced by a protein that catalyzes branch migration and promotes microhomology‐mediated end joining

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