Limits...
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

Correlation between inferred LexA regulation and integron integrase functionality. The plot was generated from the frequency values for each trait at each reference panel taxon, as derived from reciprocal BLAST mapping (see Additional file 14). Pearson and Spearman rank correlations and their respective P values were computed in Excel (Microsoft Corp., Redmond, WA, USA). The asterisk rating system is used for correlation P values (***P < 0.001). P values are relative to two-tailed Student t-test on the  hypothesis (no correlation).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3108266&req=5

Figure 4: Correlation between inferred LexA regulation and integron integrase functionality. The plot was generated from the frequency values for each trait at each reference panel taxon, as derived from reciprocal BLAST mapping (see Additional file 14). Pearson and Spearman rank correlations and their respective P values were computed in Excel (Microsoft Corp., Redmond, WA, USA). The asterisk rating system is used for correlation P values (***P < 0.001). P values are relative to two-tailed Student t-test on the hypothesis (no correlation).

Mentions: To explore this hypothesis, we developed an automated system to assess integrase functionality based on the detection of generic (nonsense and indels) and integrase-specific missense mutations known to inactivate the protein (see Methods). This method was applied to 1,135 intIA homologs identified in this work for which sufficient coding sequence was available. Consistent with previous results, we found that a substantial fraction of integrase genes (43%, see Additional file 5) seem to be inactivated [53]. For the 755 intIA homologs with sufficient sequence to apply both analyses, the predicted inactivation status for each integrase sequence (active/inactive) was combined with the predicted presence of a LexA binding site in its promoter (-100, +50) region as computed previously. A correlation analysis was carried out to determine the existence of a link between loss of LexA regulation and integrase inactivation. The results of this analysis showed a significant correlation (Pearson r = 0.58, Spearman ρ = 0.53; P < 0.001) between both traits (Figure 4), and give credence to the idea that loss of LexA regulation is associated with integrase inactivation.


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)

Correlation between inferred LexA regulation and integron integrase functionality. The plot was generated from the frequency values for each trait at each reference panel taxon, as derived from reciprocal BLAST mapping (see Additional file 14). Pearson and Spearman rank correlations and their respective P values were computed in Excel (Microsoft Corp., Redmond, WA, USA). The asterisk rating system is used for correlation P values (***P < 0.001). P values are relative to two-tailed Student t-test on the  hypothesis (no correlation).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Correlation between inferred LexA regulation and integron integrase functionality. The plot was generated from the frequency values for each trait at each reference panel taxon, as derived from reciprocal BLAST mapping (see Additional file 14). Pearson and Spearman rank correlations and their respective P values were computed in Excel (Microsoft Corp., Redmond, WA, USA). The asterisk rating system is used for correlation P values (***P < 0.001). P values are relative to two-tailed Student t-test on the hypothesis (no correlation).
Mentions: To explore this hypothesis, we developed an automated system to assess integrase functionality based on the detection of generic (nonsense and indels) and integrase-specific missense mutations known to inactivate the protein (see Methods). This method was applied to 1,135 intIA homologs identified in this work for which sufficient coding sequence was available. Consistent with previous results, we found that a substantial fraction of integrase genes (43%, see Additional file 5) seem to be inactivated [53]. For the 755 intIA homologs with sufficient sequence to apply both analyses, the predicted inactivation status for each integrase sequence (active/inactive) was combined with the predicted presence of a LexA binding site in its promoter (-100, +50) region as computed previously. A correlation analysis was carried out to determine the existence of a link between loss of LexA regulation and integrase inactivation. The results of this analysis showed a significant correlation (Pearson r = 0.58, Spearman ρ = 0.53; P < 0.001) between both traits (Figure 4), and give credence to the idea that loss of LexA regulation is associated with integrase inactivation.

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