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Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons.

Cambray G, Sanchez-Alberola N, Campoy S, Guerin E, Da Re S, González-Zorn B, Ploy MC, Barbé J, Mazel D, Erill I - Mob DNA (2011)

Bottom Line: Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens.In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons.Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France. mazel@pasteur.fr.

ABSTRACT

Background: Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens. The SOS response is a regulatory network under control of the repressor protein LexA targeted at addressing DNA damage, thus promoting genetic variation in times of stress. We recently reported a direct link between the SOS response and the expression of integron integrases in Vibrio cholerae and a plasmid-borne class 1 mobile integron. SOS regulation enhances cassette swapping and capture in stressful conditions, while freezing the integron in steady environments. We conducted a systematic study of available integron integrase promoter sequences to analyze the extent of this relationship across the Bacteria domain.

Results: Our results showed that LexA controls the expression of a large fraction of integron integrases by binding to Escherichia coli-like LexA binding sites. In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons. There was a significant correlation between lack of LexA control and predicted inactivation of integrase genes, even though experimental evidence also indicates that LexA regulation may be lost to enhance expression of integron cassettes.

Conclusions: Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA. The data also indicated that SOS regulation has been actively preserved in mobile integrons and large chromosomal integrons, suggesting that unregulated integrase activity is selected against. Nonetheless, additional adaptations have probably arisen to cope with unregulated integrase activity. Identifying them may be fundamental in deciphering the uneven distribution of integrons in the Bacteria domain.

No MeSH data available.


Related in: MedlinePlus

Schematic organization of integrons. The functional platform of integrons is constituted by an intI gene encoding an integrase, its own promoter Pint, a cassette promoter PC, and a primary recombination site attI. The system maintains an array that can consist of more than 200 cassettes. Only the few first cassettes are strongly expressed by the PC promoter, as indicated by the fading fill color. Cassettes generally contain a promoterless open reading frame (ORF) flanked by two recombination sites termed attC. Cassettes can be excised from any position in the array through attC × attC recombination mediated by the integrase. The resulting circular intermediate can then be integrated by the integrase, preferentially at attI. Exogenous circular intermediates can also be integrated, owing to the low specificity of the integrase activity, rendering the system prone to horizontal transfer. The SOS response directly controls the expression of many integron integrases by binding of its repressor protein, LexA, to a target site in the Pint promoter.
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Figure 1: Schematic organization of integrons. The functional platform of integrons is constituted by an intI gene encoding an integrase, its own promoter Pint, a cassette promoter PC, and a primary recombination site attI. The system maintains an array that can consist of more than 200 cassettes. Only the few first cassettes are strongly expressed by the PC promoter, as indicated by the fading fill color. Cassettes generally contain a promoterless open reading frame (ORF) flanked by two recombination sites termed attC. Cassettes can be excised from any position in the array through attC × attC recombination mediated by the integrase. The resulting circular intermediate can then be integrated by the integrase, preferentially at attI. Exogenous circular intermediates can also be integrated, owing to the low specificity of the integrase activity, rendering the system prone to horizontal transfer. The SOS response directly controls the expression of many integron integrases by binding of its repressor protein, LexA, to a target site in the Pint promoter.

Mentions: Integrons are bacterial genetic elements capable of incorporating exogenous and promoterless open reading frames (ORF), referred to as gene cassettes, by site-specific recombination (Figure 1). First described in the late 1980s in connection with the emergence of antibiotic resistance [1], integrons always contain three functional components: an integrase gene (intI), which mediates recombination; a primary recombination site (attI); and an outward-orientated promoter (PC) [2]. Cassette integrations occur mainly at the attI site, ensuring the correct expression of newly captured cassettes by placing them under the control of the PC promoter [3,4]. To date, two main subsets of integrons have been described. On the one hand, mobile integrons, also referred to as multiresistance integrons, contain relatively few (two to eight) cassettes, and collectively encode resistance to a broad spectrum of antibiotics [5-7]. They have been conventionally divided into five different classes according to their intI gene sequence: class 1 for intI1, class 2 for intI2, class 3 for intI3, class 4 for intISXT (formerly intI9) and class 5 for intIHS [8,9]. Mobile integrons are typically associated with transposons and conjugative plasmids, ensuring their dissemination across bacterial species. They are present mostly in the Proteobacteria, but have also been reported in other bacterial phyla, such as Gram-positive bacteria [9]. By contrast, chromosomal integrons have been identified in the genomes of many bacterial species [10]. Because their phylogeny reflects a predominant pattern of vertical inheritance, these integrons are not catalogued based on the class nomenclature described above, but according to their host species [8,9]. A subfamily of these, termed superintegrons (SIs), has been specifically identified in the Vibrionaceae and, to some extent, in the Xanthomonadaceae and Pseudomonadaceae [11-16]. Superintegrons typically encompass between 20 and 200 cassettes with species-specific sequence signatures [9], and seem to be ancient residents of the host genome [13]. Most of the genes in the superintegron cassettes are of unknown function [10], but some of them are related to existing resistance cassettes [17-20]. Although stable under laboratory conditions, superintegrons have been reported to be the most variable loci of V. cholerae natural isolates [12,21], suggesting that integron reorganization might be occasionally upregulated in natural environments. Integron integrases mediate recombination by interacting with single-stranded (ss) attC sites present in all reported cassettes, employing a unique, site-specific recombination process [22-24]. Despite the importance of integrons in the acquisition and spread of antibiotic-resistance determinants and, from a broader perspective, in bacterial adaptation, little was known about the regulatory control and dynamics of cassette recombination until recently, when we reported that the expression of the integron integrases in the V. cholerae superintegron and in a class 1 mobile integron was controlled by the SOS response [25].


Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons.

Cambray G, Sanchez-Alberola N, Campoy S, Guerin E, Da Re S, González-Zorn B, Ploy MC, Barbé J, Mazel D, Erill I - Mob DNA (2011)

Schematic organization of integrons. The functional platform of integrons is constituted by an intI gene encoding an integrase, its own promoter Pint, a cassette promoter PC, and a primary recombination site attI. The system maintains an array that can consist of more than 200 cassettes. Only the few first cassettes are strongly expressed by the PC promoter, as indicated by the fading fill color. Cassettes generally contain a promoterless open reading frame (ORF) flanked by two recombination sites termed attC. Cassettes can be excised from any position in the array through attC × attC recombination mediated by the integrase. The resulting circular intermediate can then be integrated by the integrase, preferentially at attI. Exogenous circular intermediates can also be integrated, owing to the low specificity of the integrase activity, rendering the system prone to horizontal transfer. The SOS response directly controls the expression of many integron integrases by binding of its repressor protein, LexA, to a target site in the Pint promoter.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3108266&req=5

Figure 1: Schematic organization of integrons. The functional platform of integrons is constituted by an intI gene encoding an integrase, its own promoter Pint, a cassette promoter PC, and a primary recombination site attI. The system maintains an array that can consist of more than 200 cassettes. Only the few first cassettes are strongly expressed by the PC promoter, as indicated by the fading fill color. Cassettes generally contain a promoterless open reading frame (ORF) flanked by two recombination sites termed attC. Cassettes can be excised from any position in the array through attC × attC recombination mediated by the integrase. The resulting circular intermediate can then be integrated by the integrase, preferentially at attI. Exogenous circular intermediates can also be integrated, owing to the low specificity of the integrase activity, rendering the system prone to horizontal transfer. The SOS response directly controls the expression of many integron integrases by binding of its repressor protein, LexA, to a target site in the Pint promoter.
Mentions: Integrons are bacterial genetic elements capable of incorporating exogenous and promoterless open reading frames (ORF), referred to as gene cassettes, by site-specific recombination (Figure 1). First described in the late 1980s in connection with the emergence of antibiotic resistance [1], integrons always contain three functional components: an integrase gene (intI), which mediates recombination; a primary recombination site (attI); and an outward-orientated promoter (PC) [2]. Cassette integrations occur mainly at the attI site, ensuring the correct expression of newly captured cassettes by placing them under the control of the PC promoter [3,4]. To date, two main subsets of integrons have been described. On the one hand, mobile integrons, also referred to as multiresistance integrons, contain relatively few (two to eight) cassettes, and collectively encode resistance to a broad spectrum of antibiotics [5-7]. They have been conventionally divided into five different classes according to their intI gene sequence: class 1 for intI1, class 2 for intI2, class 3 for intI3, class 4 for intISXT (formerly intI9) and class 5 for intIHS [8,9]. Mobile integrons are typically associated with transposons and conjugative plasmids, ensuring their dissemination across bacterial species. They are present mostly in the Proteobacteria, but have also been reported in other bacterial phyla, such as Gram-positive bacteria [9]. By contrast, chromosomal integrons have been identified in the genomes of many bacterial species [10]. Because their phylogeny reflects a predominant pattern of vertical inheritance, these integrons are not catalogued based on the class nomenclature described above, but according to their host species [8,9]. A subfamily of these, termed superintegrons (SIs), has been specifically identified in the Vibrionaceae and, to some extent, in the Xanthomonadaceae and Pseudomonadaceae [11-16]. Superintegrons typically encompass between 20 and 200 cassettes with species-specific sequence signatures [9], and seem to be ancient residents of the host genome [13]. Most of the genes in the superintegron cassettes are of unknown function [10], but some of them are related to existing resistance cassettes [17-20]. Although stable under laboratory conditions, superintegrons have been reported to be the most variable loci of V. cholerae natural isolates [12,21], suggesting that integron reorganization might be occasionally upregulated in natural environments. Integron integrases mediate recombination by interacting with single-stranded (ss) attC sites present in all reported cassettes, employing a unique, site-specific recombination process [22-24]. Despite the importance of integrons in the acquisition and spread of antibiotic-resistance determinants and, from a broader perspective, in bacterial adaptation, little was known about the regulatory control and dynamics of cassette recombination until recently, when we reported that the expression of the integron integrases in the V. cholerae superintegron and in a class 1 mobile integron was controlled by the SOS response [25].

Bottom Line: Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens.In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons.Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France. mazel@pasteur.fr.

ABSTRACT

Background: Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens. The SOS response is a regulatory network under control of the repressor protein LexA targeted at addressing DNA damage, thus promoting genetic variation in times of stress. We recently reported a direct link between the SOS response and the expression of integron integrases in Vibrio cholerae and a plasmid-borne class 1 mobile integron. SOS regulation enhances cassette swapping and capture in stressful conditions, while freezing the integron in steady environments. We conducted a systematic study of available integron integrase promoter sequences to analyze the extent of this relationship across the Bacteria domain.

Results: Our results showed that LexA controls the expression of a large fraction of integron integrases by binding to Escherichia coli-like LexA binding sites. In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons. There was a significant correlation between lack of LexA control and predicted inactivation of integrase genes, even though experimental evidence also indicates that LexA regulation may be lost to enhance expression of integron cassettes.

Conclusions: Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA. The data also indicated that SOS regulation has been actively preserved in mobile integrons and large chromosomal integrons, suggesting that unregulated integrase activity is selected against. Nonetheless, additional adaptations have probably arisen to cope with unregulated integrase activity. Identifying them may be fundamental in deciphering the uneven distribution of integrons in the Bacteria domain.

No MeSH data available.


Related in: MedlinePlus