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The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria.

Rhodes G, Bosma H, Studholme D, Arnold DL, Jackson RW, Pickup RW - Environ. Microbiol. (2014)

Bottom Line: Here, for the first time, we show that rulB on plasmid pWW0 is a hotspot for the active site-specific integration of related integron-like elements (ILEs) found in six environmental pseudomonads (strains FH1-FH6).Integration into rulB on pWW0 occurred at position 6488 generating a 3 bp direct repeat.Collectively, these ILEs share features with the previously described type III protein secretion system effector ILEs and are considered important to host survival and transfer of fitness enhancing and (a)virulence genes between bacteria.

View Article: PubMed Central - PubMed

Affiliation: Centre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK.

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The structure of ILEs from FH1/FH5 and FH4 aligned with regions of closest similarity. (A) The general structure of ILEs inserted into rulB on pWW0 with ORFs flanking the insertion point on pWW0 is illustrated. (B) The detailed structure of chromosomally located ILEFH1–FH5 alongside predicted ILEs in P. putida DOT-1E plasmid pGRT1 and P. aeruginosa genomic islands PAGI-5 and RGP63. ILEs are shown inside black rectangles with interrupted flanking rulB-like regions (light blue). Related regions are linked by adjoining black lines. When not specifically indicated, other colours indicate the following: Blue: rulB-like regions; purple: rulA-like gene; red: site-specific recombinase/phage integrase; pink: transposase, dark green, fitness-related; pale green: helicase; orange: mercury resistance genes; grey: hypothetical proteins (HP); yellow: hypothetical proteins with domains of unknown function. Predicted ORFs for ILEFH1/5 and ILEFH4 are numbered inside arrows, whereas those of relatives are shown above the sequence and are numbered in accordance with deposited sequences. ORFs 87a and b and ORF 88a in RGP63 are predicted in the present study and not in the original genome sequence. The sequences of pGRT1, PA7 (RGP63) and PAGI-5 are HM626202, CP000744 and EF611301 respectively.
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fig03: The structure of ILEs from FH1/FH5 and FH4 aligned with regions of closest similarity. (A) The general structure of ILEs inserted into rulB on pWW0 with ORFs flanking the insertion point on pWW0 is illustrated. (B) The detailed structure of chromosomally located ILEFH1–FH5 alongside predicted ILEs in P. putida DOT-1E plasmid pGRT1 and P. aeruginosa genomic islands PAGI-5 and RGP63. ILEs are shown inside black rectangles with interrupted flanking rulB-like regions (light blue). Related regions are linked by adjoining black lines. When not specifically indicated, other colours indicate the following: Blue: rulB-like regions; purple: rulA-like gene; red: site-specific recombinase/phage integrase; pink: transposase, dark green, fitness-related; pale green: helicase; orange: mercury resistance genes; grey: hypothetical proteins (HP); yellow: hypothetical proteins with domains of unknown function. Predicted ORFs for ILEFH1/5 and ILEFH4 are numbered inside arrows, whereas those of relatives are shown above the sequence and are numbered in accordance with deposited sequences. ORFs 87a and b and ORF 88a in RGP63 are predicted in the present study and not in the original genome sequence. The sequences of pGRT1, PA7 (RGP63) and PAGI-5 are HM626202, CP000744 and EF611301 respectively.

Mentions: The sequence of the ILE on pWW0::ILEFH1 ascertained from pFBA1001 elucidated the structure and location on pWW0 but did not confirm its location or structure in the genome of strain FH1. To better understand this, we obtained the draft genome sequences of strains FH1, FH4 and FH5, which based on RFLP profile, data represented three different ILEs. The ILEs within strains FH1, FH4 and FH5 were located in the draft sequences by alignment using the ILE sequences inserted into rulB on pWW0 in each strain. Interestingly, in the case of all three strains, ILEs were located inside a chromosomal rulB gene within a disrupted rulAB-like operon that differed to rulAB on pWW0 (see Fig. 3).


The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria.

Rhodes G, Bosma H, Studholme D, Arnold DL, Jackson RW, Pickup RW - Environ. Microbiol. (2014)

The structure of ILEs from FH1/FH5 and FH4 aligned with regions of closest similarity. (A) The general structure of ILEs inserted into rulB on pWW0 with ORFs flanking the insertion point on pWW0 is illustrated. (B) The detailed structure of chromosomally located ILEFH1–FH5 alongside predicted ILEs in P. putida DOT-1E plasmid pGRT1 and P. aeruginosa genomic islands PAGI-5 and RGP63. ILEs are shown inside black rectangles with interrupted flanking rulB-like regions (light blue). Related regions are linked by adjoining black lines. When not specifically indicated, other colours indicate the following: Blue: rulB-like regions; purple: rulA-like gene; red: site-specific recombinase/phage integrase; pink: transposase, dark green, fitness-related; pale green: helicase; orange: mercury resistance genes; grey: hypothetical proteins (HP); yellow: hypothetical proteins with domains of unknown function. Predicted ORFs for ILEFH1/5 and ILEFH4 are numbered inside arrows, whereas those of relatives are shown above the sequence and are numbered in accordance with deposited sequences. ORFs 87a and b and ORF 88a in RGP63 are predicted in the present study and not in the original genome sequence. The sequences of pGRT1, PA7 (RGP63) and PAGI-5 are HM626202, CP000744 and EF611301 respectively.
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Related In: Results  -  Collection

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fig03: The structure of ILEs from FH1/FH5 and FH4 aligned with regions of closest similarity. (A) The general structure of ILEs inserted into rulB on pWW0 with ORFs flanking the insertion point on pWW0 is illustrated. (B) The detailed structure of chromosomally located ILEFH1–FH5 alongside predicted ILEs in P. putida DOT-1E plasmid pGRT1 and P. aeruginosa genomic islands PAGI-5 and RGP63. ILEs are shown inside black rectangles with interrupted flanking rulB-like regions (light blue). Related regions are linked by adjoining black lines. When not specifically indicated, other colours indicate the following: Blue: rulB-like regions; purple: rulA-like gene; red: site-specific recombinase/phage integrase; pink: transposase, dark green, fitness-related; pale green: helicase; orange: mercury resistance genes; grey: hypothetical proteins (HP); yellow: hypothetical proteins with domains of unknown function. Predicted ORFs for ILEFH1/5 and ILEFH4 are numbered inside arrows, whereas those of relatives are shown above the sequence and are numbered in accordance with deposited sequences. ORFs 87a and b and ORF 88a in RGP63 are predicted in the present study and not in the original genome sequence. The sequences of pGRT1, PA7 (RGP63) and PAGI-5 are HM626202, CP000744 and EF611301 respectively.
Mentions: The sequence of the ILE on pWW0::ILEFH1 ascertained from pFBA1001 elucidated the structure and location on pWW0 but did not confirm its location or structure in the genome of strain FH1. To better understand this, we obtained the draft genome sequences of strains FH1, FH4 and FH5, which based on RFLP profile, data represented three different ILEs. The ILEs within strains FH1, FH4 and FH5 were located in the draft sequences by alignment using the ILE sequences inserted into rulB on pWW0 in each strain. Interestingly, in the case of all three strains, ILEs were located inside a chromosomal rulB gene within a disrupted rulAB-like operon that differed to rulAB on pWW0 (see Fig. 3).

Bottom Line: Here, for the first time, we show that rulB on plasmid pWW0 is a hotspot for the active site-specific integration of related integron-like elements (ILEs) found in six environmental pseudomonads (strains FH1-FH6).Integration into rulB on pWW0 occurred at position 6488 generating a 3 bp direct repeat.Collectively, these ILEs share features with the previously described type III protein secretion system effector ILEs and are considered important to host survival and transfer of fitness enhancing and (a)virulence genes between bacteria.

View Article: PubMed Central - PubMed

Affiliation: Centre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK.

Show MeSH
Related in: MedlinePlus