Connecting Environment and Genome Plasticity in the Characterization of Transformation-Induced SOS Regulation and Carbon Catabolite Control of the Vibrio cholerae Integron Integrase

Abstract

bThe human pathogen Vibrio cholerae carries a chromosomal superintegron (SI). The SI contains an array of hundreds of gene cassettes organized in tandem which are stable under conditions when no particular stress is applied to bacteria (such as during laboratory growth). Rearrangements of these cassettes are catalyzed by the activity of the associated integron integrase. Understanding the regulation of integrase expression is pivotal to fully comprehending the role played by this genetic reservoir for bacterial adaptation and its connection with the development of antibiotic resistance. Our previous work established that the integrase is regulated by the bacterial SOS response and that it is induced during bacterial conjugation. Here, we show that transformation, another horizontal gene transfer (HGT) mechanism, also triggers integrase expression through SOS induction, underlining the importance of HGT in genome plasticity. Moreover, we report a new cyclic AMP (cAMP)-cAMP receptor protein (CRP)-dependent regulation mechanism of the integrase, highlighting the influence of the extracellular environment on chromosomal gene content. Altogether, our data suggest an interplay between different stress responses and regulatory pathways for the modulation of the recombinase expression, thus showing how the SI remodeling mechanism is merged into bacterial physiology. Vibrio cholerae is a marine bacterium that in humans is the causative agent of cholera, a condition that can be deadly if not appropriately treated. V. cholerae carries a superintegron (SI) on chromosome 2 that has an array of up to 200 promoterless gene cassettes separated by site-specific recombination sites recognized by the integron integrase IntIA (formerly called IntI4 [49]). IntIA catalyzes cassette excision and integration and generates combinations allowing the expression of some cassettes. Unlike the plasmid multiresistance integrons which carry gene cassettes that code for multiple antibiotic resistance genes, the SI codes mostly for cassettes of unknown functions (12,48). Both types of integrons are extremely stable under laboratory conditions; however, the integron integrases are functional (6), suggesting the existence of conditions in nature where the integrons are rearranged. The V. cholerae life cycle alternates between planktonic growth, biofilm formation on crustacean shells, and colonization of the intestinal tract during infection. In all cases, it cohabits with a variety of other bacteria, thus offering ample opportunities for genetic exchange.The V. cholerae integron integrase expression, like that of most integron integrases, has been found to be regulated by the bacterial SOS response, which is induced when an abnormal amount of single-stranded DNA (ssDNA) is present in the cell (13, 33). Recently, we further showed that ssDNA entry into both Escherichia coli and V. cholerae during conjugation induces the bacterial SOS response and the expression of IntIA, the SI integrase. Moreover, we showed that SOS induction by the incoming DNA d...

The Integron: Adaptation On Demand

“…Conjugative transfer of DNA containing attC sites favors the folding of attC sites of various lengths, and hence their recombination (45). At the same time, conjugation induces the expression of the integrase through the SOS response (58), a phenomenon also observed during transformation (102). Altogether, this allows the integron to recruit incoming cassettes.…”

“…As we will see in depth in this chapter, one of the main sources of ssDNA and therefore drivers of integron activation is the entrance of new DNA during conjugation and natural transformation (58,102), enabling screening of the incoming DNA for new cassettes to capture.…”

Integrons: Past, Present, and Future

“…This regulatory machinery appears to be ancestral, as it is preserved in both chromosomal and mobile integrons (60). Transformation with foreign DNA and bacterial conjugation both induce the SOS response and therefore upregulate integrase activity, as do stress and exposure to antibiotics (61)(62)(63)(64). Integrase-mediated recombination also increases during the stationary phase (65).…”

Characterization of the phd-doc and ccd Toxin-Antitoxin Cassettes from Vibrio Superintegrons

“…Silent cassettes can be called on for expression through recombination to an expression spot, in most cases when brought to the first position(s) in the array (for a review, see reference 21). Cassette recombination is triggered in times of stress, as integron integrase expression is commonly controlled by the SOS response (24,25), but also when horizontal gene exchanges occur (26,27). Thus, between two episodes of stress, the cassette arrays stay steady, and one considers that the selective pressure exerted on distal silent cassettes is low if not absent.…”