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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

Phylogenetic tree of IntI protein sequences. The tree is the majority-rule consensus tree generated by MrBayes. The tree was rooted using the Escherichia coli and Thiobacillus denitrificans XerCD protein sequences as outgroup. Bayesian posterior probabilities for each branch are displayed at each branching point. Inferred states for phenotypic traits derived from parsimony ancestral-state reconstruction analysis are displayed as follows. Integrase functionality: solid lines on tree branches represent inferred integrase functionality in that branch, and dotted lines indicate non-functionality. LexA regulation: at each taxon and branching point, small filled circles represent inferred presence of LexA regulation, and open circles indicate loss of LexA regulation. For clarity, the results of maximum likelihood reconstruction are not shown (see Additional file 6 and see Additional file 7 for these). The number of sequences mapping to each taxon in the reciprocal BLAST mapping analysis is shown between brackets after the taxon name. Stacked pie charts next to this number indicate the observed percentage of integrase functionality (upper pie) and LexA regulation (lower pie) in all the analyzed integrase sequences mapping to that specific taxon. The M letter followed by a subscript number (MX) legend indicates mobile integron classes (1 to 5). Background colors delineate the main division into marine and soil/freshwater radiations and the XerCD outgroup.
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Figure 5: Phylogenetic tree of IntI protein sequences. The tree is the majority-rule consensus tree generated by MrBayes. The tree was rooted using the Escherichia coli and Thiobacillus denitrificans XerCD protein sequences as outgroup. Bayesian posterior probabilities for each branch are displayed at each branching point. Inferred states for phenotypic traits derived from parsimony ancestral-state reconstruction analysis are displayed as follows. Integrase functionality: solid lines on tree branches represent inferred integrase functionality in that branch, and dotted lines indicate non-functionality. LexA regulation: at each taxon and branching point, small filled circles represent inferred presence of LexA regulation, and open circles indicate loss of LexA regulation. For clarity, the results of maximum likelihood reconstruction are not shown (see Additional file 6 and see Additional file 7 for these). The number of sequences mapping to each taxon in the reciprocal BLAST mapping analysis is shown between brackets after the taxon name. Stacked pie charts next to this number indicate the observed percentage of integrase functionality (upper pie) and LexA regulation (lower pie) in all the analyzed integrase sequences mapping to that specific taxon. The M letter followed by a subscript number (MX) legend indicates mobile integron classes (1 to 5). Background colors delineate the main division into marine and soil/freshwater radiations and the XerCD outgroup.

Mentions: To gain insight into the evolutionary history of this correlation, we generated a phylogenetic tree of 44 representative IntI sequences, and applied ancestral-state reconstruction methods for both phenotypic characters (predicted integrase functionality and LexA regulation). The tree (Figure 5) is in overall agreement with previously published IntI phylogenies [9,53,56]. As in previous phylogenies, two major ecological groups can be outlined on the tree: marine and freshwater/soil bacteria. Chromosomal superintegrons and class 5 mobile integrons borne by marine species form a monophyletic clade that sits at the root of the tree. From this early branch, a second radiation of integrons encompassing both chromosomal integrons and all other mobile integron classes splits neatly into integrons borne by, respectively, marine and soil/freshwater bacteria. In the marine species, class 2 and 4 mobile integrons form a monophyletic cluster with Shewanella chromosomal integrons that is also in agreement with previous analyses [57,58]. In the soil/freshwater clade, class 1 and 3 mobile integrases form a distinct group, suggesting an early split from their chromosomal counterparts in the Proteobacteria [59].


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)

Phylogenetic tree of IntI protein sequences. The tree is the majority-rule consensus tree generated by MrBayes. The tree was rooted using the Escherichia coli and Thiobacillus denitrificans XerCD protein sequences as outgroup. Bayesian posterior probabilities for each branch are displayed at each branching point. Inferred states for phenotypic traits derived from parsimony ancestral-state reconstruction analysis are displayed as follows. Integrase functionality: solid lines on tree branches represent inferred integrase functionality in that branch, and dotted lines indicate non-functionality. LexA regulation: at each taxon and branching point, small filled circles represent inferred presence of LexA regulation, and open circles indicate loss of LexA regulation. For clarity, the results of maximum likelihood reconstruction are not shown (see Additional file 6 and see Additional file 7 for these). The number of sequences mapping to each taxon in the reciprocal BLAST mapping analysis is shown between brackets after the taxon name. Stacked pie charts next to this number indicate the observed percentage of integrase functionality (upper pie) and LexA regulation (lower pie) in all the analyzed integrase sequences mapping to that specific taxon. The M letter followed by a subscript number (MX) legend indicates mobile integron classes (1 to 5). Background colors delineate the main division into marine and soil/freshwater radiations and the XerCD outgroup.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Phylogenetic tree of IntI protein sequences. The tree is the majority-rule consensus tree generated by MrBayes. The tree was rooted using the Escherichia coli and Thiobacillus denitrificans XerCD protein sequences as outgroup. Bayesian posterior probabilities for each branch are displayed at each branching point. Inferred states for phenotypic traits derived from parsimony ancestral-state reconstruction analysis are displayed as follows. Integrase functionality: solid lines on tree branches represent inferred integrase functionality in that branch, and dotted lines indicate non-functionality. LexA regulation: at each taxon and branching point, small filled circles represent inferred presence of LexA regulation, and open circles indicate loss of LexA regulation. For clarity, the results of maximum likelihood reconstruction are not shown (see Additional file 6 and see Additional file 7 for these). The number of sequences mapping to each taxon in the reciprocal BLAST mapping analysis is shown between brackets after the taxon name. Stacked pie charts next to this number indicate the observed percentage of integrase functionality (upper pie) and LexA regulation (lower pie) in all the analyzed integrase sequences mapping to that specific taxon. The M letter followed by a subscript number (MX) legend indicates mobile integron classes (1 to 5). Background colors delineate the main division into marine and soil/freshwater radiations and the XerCD outgroup.
Mentions: To gain insight into the evolutionary history of this correlation, we generated a phylogenetic tree of 44 representative IntI sequences, and applied ancestral-state reconstruction methods for both phenotypic characters (predicted integrase functionality and LexA regulation). The tree (Figure 5) is in overall agreement with previously published IntI phylogenies [9,53,56]. As in previous phylogenies, two major ecological groups can be outlined on the tree: marine and freshwater/soil bacteria. Chromosomal superintegrons and class 5 mobile integrons borne by marine species form a monophyletic clade that sits at the root of the tree. From this early branch, a second radiation of integrons encompassing both chromosomal integrons and all other mobile integron classes splits neatly into integrons borne by, respectively, marine and soil/freshwater bacteria. In the marine species, class 2 and 4 mobile integrons form a monophyletic cluster with Shewanella chromosomal integrons that is also in agreement with previous analyses [57,58]. In the soil/freshwater clade, class 1 and 3 mobile integrases form a distinct group, suggesting an early split from their chromosomal counterparts in the Proteobacteria [59].

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