The Superintegron Integrase and the Cassette Promoters Are Co-Regulated in Vibrio cholerae

Krin, Evelyne; Cambray, Guillaume; Mazel, Didier

doi:10.1371/journal.pone.0091194

Cited by 15 publications

(21 citation statements)

References 48 publications

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“…It is noteworthy that CRP is also directly and indirectly linked to the uptake of ssDNA, via TfoX and HapR (regulators of natural competence), respectively (102). Finally, low-level induction of the expression of intIA has also been observed at high temperature (42°C) (103).…”

Section: Expression Of the Integron Elements The Integrasementioning

confidence: 89%

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The Integron: Adaptation On Demand

Loot²,

et al. 2015

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The integron is a powerful system which, by capturing, stockpiling, and rearranging new functions carried by gene encoding cassettes, confers upon bacteria a rapid adaptation capability in changing environments. Chromosomally located integrons (CI) have been identified in a large number of environmental Gram-negative bacteria. Integron evolutionary history suggests that these sedentary CIs acquired mobility among bacterial species through their association with transposable elements and conjugative plasmids. As a result of massive antibiotic use, these so-called mobile integrons are now widespread in clinically relevant bacteria and are considered to be the principal agent in the emergence and rise of antibiotic multiresistance in Gram-negative bacteria. Cassette rearrangements are catalyzed by the integron integrase, a site-specific tyrosine recombinase. Central to these reactions is the single-stranded DNA nature of one of the recombination partners, the attC site. This makes the integron a unique recombination system. This review describes the current knowledge on this atypical recombination mechanism, its implications in the reactions involving the different types of sites, attC and attI, and focuses on the tight regulation exerted by the host on integron activity through the control of attC site folding. Furthermore, cassette and integrase expression are also highly controlled by host regulatory networks and the bacterial stress (SOS) response. These intimate connections to the host make the integron a genetically stable and efficient system, granting the bacteria a low cost, highly adaptive evolution potential "on demand".

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Section: Expression Of the Integron Elements The Integrasementioning

confidence: 89%

“…The analysis of the P C in the V. cholerae SI has recently been carried out in our group (103). As stated before, a CRP binding box is present between P int and P C , from where the cAMP-CRP complex activates not only the integrase, but also the expression of the cassette array.…”

Section: The Cassettesmentioning

confidence: 94%

The Integron: Adaptation On Demand

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et al. 2015

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“…The newly inserted cassette would thus be immediately tested for adaptive value, and only systems having integrated the antibiotic resistance cassette in correct orientation would be selected. In SCIs, the function of most cassettes is unknown but is also likely to be involved in adaptation to stressful conditions and be selected for, especially as cassette expression can also be dependent on the SOS response ( 43 ).…”

Section: Discussionmentioning

confidence: 99%

Efficiency of integron cassette insertion in correct orientation is ensured by the interplay of the three unpaired features ofattCrecombination sites

et al. 2016

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The integron is a bacterial recombination system that allows acquisition, stockpiling and expression of cassettes carrying protein-coding sequences, and is responsible for the emergence and rise of multiresistance in Gram-negative bacteria. The functionality of this system depends on the insertion of promoterless cassettes in correct orientation, allowing their expression from the promoter located upstream of the cassette array. Correct orientation is ensured by strand selectivity of integron integrases for the bottom strand of cassette recombination sites (attC), recombined in form of folded single-stranded hairpins. Here, we investigated the basis of such strand selectivity by comparing recombination of wild-type and mutated attC sites with different lengths, sequences and structures. We show that all three unpaired structural features that distinguish the bottom and top strands contribute to strand selectivity. The localization of Extra-Helical Bases (EHBs) directly favors integrase binding to the bottom strand. The Unpaired Central Spacer (UCS) and the Variable Terminal Structure (VTS) influence strand selectivity indirectly, probably through the stabilization of the bottom strand and the resulting synapse due to the nucleotide skew between the two strands. These results underscore the importance of the single-stranded nature of the attC site that allows such tight control over integron cassette orientation.

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“…This rare property guarantees that they are transcribed independently of their location inside the cassette array. Indeed, integron cassettes seldom carry a promoter, and their expression occurs when they are recombined at, or close to, the attI site, which carries a strong promoter, Pc (44,47). This dynamic expression model, which allows the expression of adaptive genes only when needed, is considered to be central for integron evolutionary success (31).…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Functional Analysis of the 18 Vibrio cholerae N16961 Toxin-Antitoxin Systems Substantiates Their Role in Stabilizing the Superintegron

et al. 2015

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The role of chromosomal toxin-antitoxin (TA) systems, which are ubiquitous within the genomes of free-living bacteria, is still debated. We have scanned the Vibrio cholerae N16961 genome for class 2 TA genes and identified 18 gene pair candidates. Interestingly, all but one are located in the chromosome 2 superintegron (SI). The single TA found outside the SI is located on chromosome 1 and is related to the well-characterized HipAB family, which is known to play a role in antibiotic persistence. We investigated this clustering within the SI and its possible biological consequences by performing a comprehensive functional analysis on all of the putative TA systems. We demonstrate that the 18 TAs identified encode functional toxins and that their cognate antitoxins are able to neutralize their deleterious effects when expressed in Escherichia coli. In addition, we reveal that the 17 predicted TA systems of the SI are transcribed and expressed in their native context from their own promoters, a situation rarely found in integron cassettes. We tested the possibility of interactions between noncognate pairs of all toxins and antitoxins and found no cross-interaction between any of the different TAs. Although these observations do not exclude other roles, they clearly strengthen the role of TA systems in stabilizing the massive SI cassette array of V. cholerae. IMPORTANCEThe chromosomal toxin-antitoxin systems have been shown to play various, sometimes contradictory roles, ranging from genomic stabilization to bacterial survival via persistence. Determining the interactions between TA systems hosted within the same bacteria is essential to understand the hierarchy between these different roles. We identify here the full set of class 2 TAs carried in the Vibrio cholerae N16961 genome and found they are all, with a single exception, located in the chromosome 2 superintegron. Their characterization, in terms of functionality, expression, and possible cross-interactions, supports their main role as being the stabilization of the 176-cassette-long array of the superintegron but does not exclude dual roles, such as stress response elements, persistence, and bacteriophage defense through abortive infection mechanisms.T oxin-antitoxin (TA) systems were discovered in 1983 on plasmid F of Escherichia coli (1) and were shown to be involved in stable plasmid maintenance by postsegregational killing, a mechanism distinct from replication and partition. These systems typically consist of an operon of two genes, which encode a toxin that targets an essential cellular function and an antitoxin that binds to and inhibits the toxin. Toxin activity is regulated through differential stability of the stable toxin and the labile antitoxin; loss of a TA system by the progeny during cell division results in cell death by the action of the stable toxin (for reviews, see references 2 and 3). The antitoxin, in most cases, also acts as a transcriptional autorepressor of the operon, and the degradation of the antitoxin results in the tran...

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The Superintegron Integrase and the Cassette Promoters Are Co-Regulated in Vibrio cholerae

Cited by 15 publications

References 48 publications

The Integron: Adaptation On Demand

The Integron: Adaptation On Demand

Efficiency of integron cassette insertion in correct orientation is ensured by the interplay of the three unpaired features ofattCrecombination sites

Comprehensive Functional Analysis of the 18 Vibrio cholerae N16961 Toxin-Antitoxin Systems Substantiates Their Role in Stabilizing the Superintegron

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