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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

In silico analysis of integrase promoters. (A) Alignment of representative promoter regions of Vibrionaceae intIA homologs. Putative LexA binding sequences are boxed, whereas putative σ70 promoter elements (-35 and -10) are underlined, and the translation start site of intIA is boxed and in bold type. The multiple sequence alignment was performed using CLUSTALW with default parameters [89]. (B) Representative examples of LexA binding sites identified upstream of different integrase genes from mobile integrons, with (1-5) denoting the integrase class. The provided accessors correspond to IntI proteins from: Escherichia coli pSa (AAA92752), Providencia stuartii ABR23a (ABG21674), Serratia marcescens AK9373 (BAA08929), Vibrio cholerae 569B (AAC38424) and Vibrio salmonicida VS224 pRVS1 (CAC35342). (C) Sequence logos [100] of the profile used to search for β/γ-Proteobacteria LexA binding sites (top) and the profile emerging from the 93 distinct binding sites located (bottom). Lan = Listonella anguillarum; Lpe_CIP = L. pelagia CIP 102762T; Val_12G01 = Vibrio alginolyticus 12G01; Vch_N16961 = V. cholerae O1 biovar Eltor str. N16961; Vha_ATCC = Vibrio harveyi ATCC BAA-1116; Vha_HY01 = V. harveyi HY01; Vme = Vibrio metschnikovii; Vmi = Vibrio mimicus; Vna_CIP = Vibrio natriegens strain CIP 10319; Vpa = Vibrio parahaemolyticus; Vpa_RIMD = V. parahaemolyticus RIMD 2210633; Vsh_AK1 = Vibrio shilonii AK1; Vsp_DAT722 = Vibrio sp. DAT722; Vsp_Ex25 = Vibrio sp. Ex25; Vvu_CIP754 = Vibrio vulnificus CIP 75.4; Vvu_YJ016 = V. vulnificus YJ016 (see Additional file 11 for corresponding accession numbers).
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Figure 2: In silico analysis of integrase promoters. (A) Alignment of representative promoter regions of Vibrionaceae intIA homologs. Putative LexA binding sequences are boxed, whereas putative σ70 promoter elements (-35 and -10) are underlined, and the translation start site of intIA is boxed and in bold type. The multiple sequence alignment was performed using CLUSTALW with default parameters [89]. (B) Representative examples of LexA binding sites identified upstream of different integrase genes from mobile integrons, with (1-5) denoting the integrase class. The provided accessors correspond to IntI proteins from: Escherichia coli pSa (AAA92752), Providencia stuartii ABR23a (ABG21674), Serratia marcescens AK9373 (BAA08929), Vibrio cholerae 569B (AAC38424) and Vibrio salmonicida VS224 pRVS1 (CAC35342). (C) Sequence logos [100] of the profile used to search for β/γ-Proteobacteria LexA binding sites (top) and the profile emerging from the 93 distinct binding sites located (bottom). Lan = Listonella anguillarum; Lpe_CIP = L. pelagia CIP 102762T; Val_12G01 = Vibrio alginolyticus 12G01; Vch_N16961 = V. cholerae O1 biovar Eltor str. N16961; Vha_ATCC = Vibrio harveyi ATCC BAA-1116; Vha_HY01 = V. harveyi HY01; Vme = Vibrio metschnikovii; Vmi = Vibrio mimicus; Vna_CIP = Vibrio natriegens strain CIP 10319; Vpa = Vibrio parahaemolyticus; Vpa_RIMD = V. parahaemolyticus RIMD 2210633; Vsh_AK1 = Vibrio shilonii AK1; Vsp_DAT722 = Vibrio sp. DAT722; Vsp_Ex25 = Vibrio sp. Ex25; Vvu_CIP754 = Vibrio vulnificus CIP 75.4; Vvu_YJ016 = V. vulnificus YJ016 (see Additional file 11 for corresponding accession numbers).

Mentions: We recently identified E. coli-like LexA binding sites in the promoter region of intI1 integrase genes from mobile integrons and of the intIA integrase from the V. cholerae superintegron (Figure 2AB). In V. cholerae and some of these mobile integrons, the identified LexA boxes partially overlap the -10 element of the intI promoter in a classic operator organization. We have shown that expression of V. cholerae and E. coli pAT674 integrase genes is indeed controlled by the SOS response, leading to heightened rates of integrase-mediated recombination upon SOS induction [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)

In silico analysis of integrase promoters. (A) Alignment of representative promoter regions of Vibrionaceae intIA homologs. Putative LexA binding sequences are boxed, whereas putative σ70 promoter elements (-35 and -10) are underlined, and the translation start site of intIA is boxed and in bold type. The multiple sequence alignment was performed using CLUSTALW with default parameters [89]. (B) Representative examples of LexA binding sites identified upstream of different integrase genes from mobile integrons, with (1-5) denoting the integrase class. The provided accessors correspond to IntI proteins from: Escherichia coli pSa (AAA92752), Providencia stuartii ABR23a (ABG21674), Serratia marcescens AK9373 (BAA08929), Vibrio cholerae 569B (AAC38424) and Vibrio salmonicida VS224 pRVS1 (CAC35342). (C) Sequence logos [100] of the profile used to search for β/γ-Proteobacteria LexA binding sites (top) and the profile emerging from the 93 distinct binding sites located (bottom). Lan = Listonella anguillarum; Lpe_CIP = L. pelagia CIP 102762T; Val_12G01 = Vibrio alginolyticus 12G01; Vch_N16961 = V. cholerae O1 biovar Eltor str. N16961; Vha_ATCC = Vibrio harveyi ATCC BAA-1116; Vha_HY01 = V. harveyi HY01; Vme = Vibrio metschnikovii; Vmi = Vibrio mimicus; Vna_CIP = Vibrio natriegens strain CIP 10319; Vpa = Vibrio parahaemolyticus; Vpa_RIMD = V. parahaemolyticus RIMD 2210633; Vsh_AK1 = Vibrio shilonii AK1; Vsp_DAT722 = Vibrio sp. DAT722; Vsp_Ex25 = Vibrio sp. Ex25; Vvu_CIP754 = Vibrio vulnificus CIP 75.4; Vvu_YJ016 = V. vulnificus YJ016 (see Additional file 11 for corresponding accession numbers).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: In silico analysis of integrase promoters. (A) Alignment of representative promoter regions of Vibrionaceae intIA homologs. Putative LexA binding sequences are boxed, whereas putative σ70 promoter elements (-35 and -10) are underlined, and the translation start site of intIA is boxed and in bold type. The multiple sequence alignment was performed using CLUSTALW with default parameters [89]. (B) Representative examples of LexA binding sites identified upstream of different integrase genes from mobile integrons, with (1-5) denoting the integrase class. The provided accessors correspond to IntI proteins from: Escherichia coli pSa (AAA92752), Providencia stuartii ABR23a (ABG21674), Serratia marcescens AK9373 (BAA08929), Vibrio cholerae 569B (AAC38424) and Vibrio salmonicida VS224 pRVS1 (CAC35342). (C) Sequence logos [100] of the profile used to search for β/γ-Proteobacteria LexA binding sites (top) and the profile emerging from the 93 distinct binding sites located (bottom). Lan = Listonella anguillarum; Lpe_CIP = L. pelagia CIP 102762T; Val_12G01 = Vibrio alginolyticus 12G01; Vch_N16961 = V. cholerae O1 biovar Eltor str. N16961; Vha_ATCC = Vibrio harveyi ATCC BAA-1116; Vha_HY01 = V. harveyi HY01; Vme = Vibrio metschnikovii; Vmi = Vibrio mimicus; Vna_CIP = Vibrio natriegens strain CIP 10319; Vpa = Vibrio parahaemolyticus; Vpa_RIMD = V. parahaemolyticus RIMD 2210633; Vsh_AK1 = Vibrio shilonii AK1; Vsp_DAT722 = Vibrio sp. DAT722; Vsp_Ex25 = Vibrio sp. Ex25; Vvu_CIP754 = Vibrio vulnificus CIP 75.4; Vvu_YJ016 = V. vulnificus YJ016 (see Additional file 11 for corresponding accession numbers).
Mentions: We recently identified E. coli-like LexA binding sites in the promoter region of intI1 integrase genes from mobile integrons and of the intIA integrase from the V. cholerae superintegron (Figure 2AB). In V. cholerae and some of these mobile integrons, the identified LexA boxes partially overlap the -10 element of the intI promoter in a classic operator organization. We have shown that expression of V. cholerae and E. coli pAT674 integrase genes is indeed controlled by the SOS response, leading to heightened rates of integrase-mediated recombination upon SOS induction [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