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Four genes essential for recombination define GInts, a new type of mobile genomic island widespread in bacteria

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ABSTRACT

Integrases are a family of tyrosine recombinases that are highly abundant in bacterial genomes, actively disseminating adaptive characters such as pathogenicity determinants and antibiotics resistance. Using comparative genomics and functional assays, we identified a novel type of mobile genetic element, the GInt, in many diverse bacterial groups but not in archaea. Integrated as genomic islands, GInts show a tripartite structure consisting of the ginABCD operon, a cargo DNA region from 2.5 to at least 70 kb, and a short AT-rich 3′ end. The gin operon is characteristic of GInts and codes for three putative integrases and a small putative helix-loop-helix protein, all of which are essential for integration and excision of the element. Genes in the cargo DNA are acquired mostly from phylogenetically related bacteria and often code for traits that might increase fitness, such as resistance to antimicrobials or virulence. GInts also tend to capture clusters of genes involved in complex processes, such as the biosynthesis of phaseolotoxin by Pseudomonas syringae. GInts integrate site-specifically, generating two flanking direct imperfect repeats, and excise forming circular molecules. The excision process generates sequence variants at the element attachment site, which can increase frequency of integration and drive target specificity.

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General structure of GInts.The GInt element (orange, with bacterial sequences in grey) has a tripartite structure: The highly conserved ginABCD operon, the cargo DNA (broken line), and a 0.2–0.4 kb poorly conserved 3′ end. GInts integrate site-specifically; the GInt carrying the Pht-PAI from P. syringae pv. phaseolicola 1448A, and related elements, integrate within a putative ABC transporter gene (PSPPH_4293 in strain 1448A; indicated as ABC). Small grey and orange arrows represent primers for testing excision and circularization. The site-specific integration of GInts generates two direct imperfect repeats (attL and attR) of 10 and 11 nucleotides, which are chimeras of the attI sequence from the GInt (orange letters) and the attB sequence from the bacterial chromosome (grey lettering). The sequence logo was generated from alignments of the att repeats from GInts related to the Pht-PAI (Table S1).
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f1: General structure of GInts.The GInt element (orange, with bacterial sequences in grey) has a tripartite structure: The highly conserved ginABCD operon, the cargo DNA (broken line), and a 0.2–0.4 kb poorly conserved 3′ end. GInts integrate site-specifically; the GInt carrying the Pht-PAI from P. syringae pv. phaseolicola 1448A, and related elements, integrate within a putative ABC transporter gene (PSPPH_4293 in strain 1448A; indicated as ABC). Small grey and orange arrows represent primers for testing excision and circularization. The site-specific integration of GInts generates two direct imperfect repeats (attL and attR) of 10 and 11 nucleotides, which are chimeras of the attI sequence from the GInt (orange letters) and the attB sequence from the bacterial chromosome (grey lettering). The sequence logo was generated from alignments of the att repeats from GInts related to the Pht-PAI (Table S1).

Mentions: Using blastn, we found many examples among pseudomonads of genomic islands showing the same organization than the Pht-PAI, namely, a tripartite structure consisting of 1) the highly conserved ginABCD operon in the 5′ end; 2) a variable amount of cargo DNA, starting immediately before or after the stop codon of ginD; and 3) a short and poorly conserved 3′ end containing some well-conserved AT-rich sequence stretches (Fig. 1 and Table S1). All these islands inserted into the same chromosomal location, the 5′ end of an ABC transporter gene (PSPPH_4293 in strain 1448A) and are flanked by 10–11 nt direct imperfect repeats, the attL and attR (Fig. 1 and Table S2). Since they show characteristics of novel MGEs (see below), we have collectively designated these elements GInts (Genomic Island with three Integrases),


Four genes essential for recombination define GInts, a new type of mobile genomic island widespread in bacteria
General structure of GInts.The GInt element (orange, with bacterial sequences in grey) has a tripartite structure: The highly conserved ginABCD operon, the cargo DNA (broken line), and a 0.2–0.4 kb poorly conserved 3′ end. GInts integrate site-specifically; the GInt carrying the Pht-PAI from P. syringae pv. phaseolicola 1448A, and related elements, integrate within a putative ABC transporter gene (PSPPH_4293 in strain 1448A; indicated as ABC). Small grey and orange arrows represent primers for testing excision and circularization. The site-specific integration of GInts generates two direct imperfect repeats (attL and attR) of 10 and 11 nucleotides, which are chimeras of the attI sequence from the GInt (orange letters) and the attB sequence from the bacterial chromosome (grey lettering). The sequence logo was generated from alignments of the att repeats from GInts related to the Pht-PAI (Table S1).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5385486&req=5

f1: General structure of GInts.The GInt element (orange, with bacterial sequences in grey) has a tripartite structure: The highly conserved ginABCD operon, the cargo DNA (broken line), and a 0.2–0.4 kb poorly conserved 3′ end. GInts integrate site-specifically; the GInt carrying the Pht-PAI from P. syringae pv. phaseolicola 1448A, and related elements, integrate within a putative ABC transporter gene (PSPPH_4293 in strain 1448A; indicated as ABC). Small grey and orange arrows represent primers for testing excision and circularization. The site-specific integration of GInts generates two direct imperfect repeats (attL and attR) of 10 and 11 nucleotides, which are chimeras of the attI sequence from the GInt (orange letters) and the attB sequence from the bacterial chromosome (grey lettering). The sequence logo was generated from alignments of the att repeats from GInts related to the Pht-PAI (Table S1).
Mentions: Using blastn, we found many examples among pseudomonads of genomic islands showing the same organization than the Pht-PAI, namely, a tripartite structure consisting of 1) the highly conserved ginABCD operon in the 5′ end; 2) a variable amount of cargo DNA, starting immediately before or after the stop codon of ginD; and 3) a short and poorly conserved 3′ end containing some well-conserved AT-rich sequence stretches (Fig. 1 and Table S1). All these islands inserted into the same chromosomal location, the 5′ end of an ABC transporter gene (PSPPH_4293 in strain 1448A) and are flanked by 10–11 nt direct imperfect repeats, the attL and attR (Fig. 1 and Table S2). Since they show characteristics of novel MGEs (see below), we have collectively designated these elements GInts (Genomic Island with three Integrases),

View Article: PubMed Central - PubMed

ABSTRACT

Integrases are a family of tyrosine recombinases that are highly abundant in bacterial genomes, actively disseminating adaptive characters such as pathogenicity determinants and antibiotics resistance. Using comparative genomics and functional assays, we identified a novel type of mobile genetic element, the GInt, in many diverse bacterial groups but not in archaea. Integrated as genomic islands, GInts show a tripartite structure consisting of the ginABCD operon, a cargo DNA region from 2.5 to at least 70 kb, and a short AT-rich 3′ end. The gin operon is characteristic of GInts and codes for three putative integrases and a small putative helix-loop-helix protein, all of which are essential for integration and excision of the element. Genes in the cargo DNA are acquired mostly from phylogenetically related bacteria and often code for traits that might increase fitness, such as resistance to antimicrobials or virulence. GInts also tend to capture clusters of genes involved in complex processes, such as the biosynthesis of phaseolotoxin by Pseudomonas syringae. GInts integrate site-specifically, generating two flanking direct imperfect repeats, and excise forming circular molecules. The excision process generates sequence variants at the element attachment site, which can increase frequency of integration and drive target specificity.

No MeSH data available.


Related in: MedlinePlus