Comparative Analysis of Superintegrons: Engineering Extensive Genetic Diversity in the Vibrionaceae

Rowe‐Magnus, Dean A.; Guérout, Anne-Marie; Biskri, Latéfa; Bouige, Philippe; Mazel, Didier

doi:10.1101/gr.617103

Cited by 199 publications

(233 citation statements)

References 55 publications

Supporting

Mentioning

215

Contrasting

Unclassified

Order By: Relevance

“…The V. cholerae N16961 chromosomal integron has been annotated and reported to contain 179 MGCs (Rowe-Magnus et al, 2003); however, our annotation gave 178 MGCs. The gene cassettes of this array are referred to as MGC1-MGC178, with the numbering representing their position in the array beginning with the first cassette located at attI (a fully annotated text file is available as Supplementary Table S1).…”

Section: Methodsmentioning

confidence: 66%

“…A similar promoter probably exists in V. cholerae integrons, but this has not been demonstrated experimentally. The genome of V. cholerae N16961 has been completely sequenced and contains a 126 kb integron that carries 179 MGCs (Rowe-Magnus et al, 2003). Many of these are present in multiple paralogous copies and encode unique products (Rowe-Magnus et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

“…The integron is a 'hotspot' for LGT in the genomes of V. cholerae strains (Rowe-Magnus et al, 2003). Integrons possess a gene, intI, which encodes a site-specific recombinase (IntI) and an attachment site recognized by this protein, attI, into which individual mobile gene cassettes (MGCs) are inserted (Hall et al, 1999).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains

et al. 2007

View full text Add to dashboard Cite

Approximately 200 serogroups of Vibrio cholerae exist, with only two, O1 and O139, responsible for epidemic and pandemic cholera. Strains from these serogroups have evolved from a common progenitor, with lateral gene transfer largely driving their emergence. These strains are so closely related that separation using single-or multi-locus phylogeny has proven difficult. V. cholerae strains contain a genetic system called the integron that is located in the chromosome and that can integrate and excise DNA elements called mobile gene cassettes (MGCs) by site-specific recombination. Large arrays of MGCs are found in V. cholerae strains. For instance, the O1 El Tor strain N16961 contains 179 MGCs. Since integron arrays are dynamic through recombination and excision of MGCs, it was hypothesized that the MGC composition in a given V. cholerae pandemic strain would be useful as a phylogenetic typing system. To address this, a PCR-based method was used to rapidly characterize the MGC composition of V. cholerae arrays. The results showed that the MGC composition of pandemic V. cholerae cassette arrays is relatively conserved, providing further evidence that these strains have evolved from a common progenitor. Comparison of MGC composition between the V. cholerae pandemic strains was also able to resolve the evolution of O139 from a subgroup of O1 El Tor. This level of differentiation of closely related V. cholerae isolates was more sensitive than conventional single-gene phylogeny or multi-locus sequence analysis. Using this method, novel MGCs from an O1 classical strain and an Argentinian O139 isolate were also identified, and a major deletion in the MGC array in all pandemic O139 strains and a subset of O1 El Tor strains was identified. Analysis of sequenced V. cholerae integron arrays showed that their evolution can proceed by rearrangements and deletions/insertions of large portions of MGCs in addition to the insertion or excision of single MGCs.

show abstract

Section: Methodsmentioning

confidence: 66%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains

et al. 2007

View full text Add to dashboard Cite

show abstract

“…Generally, identification of chromosomal integrons is based on conservation of structure and comparative sequence analysis rather than demonstration of function. However, the presence of an intI homolog, a plausible attI recombination site, and a gene cassette array bounded by 59-be sites (17), argues that they have properties similar to those of the extensively characterized class 1 and 3 integrons (6,18,19).…”

mentioning

confidence: 99%

Integrons inXanthomonas: A source of species genome diversity

Gillings

Holley

Stokes

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

130

View full text Add to dashboard Cite

Integrons are best known for assembling antibiotic resistance genes in clinical bacteria. They capture genes by using integrasemediated site-specific recombination of mobile gene cassettes. Integrons also occur in the chromosomes of many bacteria, notably ␤-and ␥-Proteobacteria. In a survey of Xanthomonas, integrons were found in all 32 strains representing 12 pathovars of two species. Their chromosomal location was downstream from the acid dehydratase gene, ilvD, suggesting that an integron was present at this site in the ancestral xanthomonad. There was considerable sequence and structural diversity among the extant integrons. The majority of integrase genes were predicted to be inactivated by frameshifts, stop codons, or large deletions, suggesting that the associated gene cassettes can no longer be mobilized. In support, groups of strains with the same deletions or stop codons͞frameshifts in their integrase gene usually contained identical arrays of gene cassettes. In general, strains within individual pathovars had identical cassettes, and these exhibited no similarity to cassettes detected in other pathovars. The variety and characteristics of contemporary gene cassettes suggests that the ancestral integron had access to a diverse pool of these mobile elements, and that their genes originated outside the Xanthomonas genome. Subsequent inactivation of the integrase gene in particular lineages has largely fixed the gene cassette arrays in particular pathovars during their differentiation and specialization into ecological niches. The acquisition of diverse gene cassettes by different lineages within Xanthomonas has contributed to the species-genome diversity of the genus. The role of gene cassettes in survival on plant surfaces is currently unknown. genome evolution ͉ lateral gene transfer ͉ mobile DNA ͉ pathovar

show abstract

“…This latest definition actually applies to only 3 of the integrons for which an analysis is available. The integrons so far found in the chromosomes of Vibrionaceae have more than 20 cassettes associated with them, but only in the case of V. cholerae is there a single sequence type for the 59-be (attC) associated with the vast majority of these cassettes 5,6 . Among the remaining chromosomally located integrons for which an analysis of the cassette array has been published 7-12 , only 3 have over 20 cassettes (TABLE 1).…”

mentioning

confidence: 99%

What are superintegrons?

et al. 2007

View full text Add to dashboard Cite

Although integrons have been found in transposons, in plasmids and in bacterial chromosomes, all integrons have the same basic properties, namely an intI gene and an attI site that allow them to capture gene cassettes 1 . When an integron is part of a transposon, as is the case for integron classes 1, 2 and probably 3 (REF.2), it is obvious that this would vastly increase the capacity of the integron to capture cassettes from a wide range of bacterial sources. However, their location does not make them either structurally or functionally different from the more sedentary integrons found in bacterial genomes.Mazel and co-workers initially noted that the integron in Vibrio cholerae N16961 was different to the integrons that had been described previously because it is found in the chromosome and had a large number (178) of cassettes associated with it, and they referred to it as a 'superintegron' (REF. 3). Subsequently, confusion arose because the term superintegron was applied to other integrons that were chromosomally located, even though most of these do not have a large cassette array. Defining a distinct type of integron based on arbitrary features of the cassette array is dangerous because the size and composition of the cassette array associated with an integron can easily change. This variability is necessarily intrinsic to a system that captures and harbours mobile elements, such as gene cassettes. These discrepancies were pointed out by Hall and Stokes 1 who recommended that, as all integrons have the same basic properties, they should all be called integrons.Despite this recommendation, a recent review 4 continues to use, and re-defines, the term 'superintegron'. The three features that are now claimed to make superintegrons a 'distinct type' of integron are: first, that there are at least 20 cassettes in the associated array; second, that a single type (over 80% identical) of attC site (59-be) is predominantly found in these cassettes; andthird, that the integron is not associated with mobile elements 4 . However, in subsequent sections of the review, integrons that do not comply with this definition are also described as superintegrons.So, what are superintegrons? This latest definition actually applies to only 3 of the integrons for which an analysis is available. The integrons so far found in the chromosomes of Vibrionaceae have more than 20 cassettes associated with them, but only in the case of V. cholerae is there a single sequence type for the 59-be (attC) associated with the vast majority of these cassettes 5,6 . Among the remaining chromosomally located integrons for which an analysis of the cassette array has been published 7-12 , only 3 have over 20 cassettes (TABLE 1). Our analysis of these cassette arrays to determine if there is a single predominant 59-be type at the 80% identity level revealed that only the integrons in Xanthomonas campestris and Treponema denticola meet this criterion (TABLE 1). Therefore, based on currently available information, integrons with the features of a 'superi...

show abstract

Comparative Analysis of Superintegrons: Engineering Extensive Genetic Diversity in the Vibrionaceae

Cited by 199 publications

References 55 publications

Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains

Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains

Integrons inXanthomonas: A source of species genome diversity

What are superintegrons?

Contact Info

Product

Resources

About