Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

Abstract

Mobile genomic islands (GIs) can be excised from the chromosome, then form a circular intermediate and be reintegrated into the chromosome by the GI internal integrase. Some mobile GIs can also be transferred into a new receptor cell by transformation, conjugation, or transduction. The action sites of the integrase are usually flanked direct repeats (DRs) of the GIs. Accurate localization of the flanking sequences is a precondition for determining the mobility of the GI. Mobile GIs are generally associated with transfer RNAs (tRNAs). Based on the correlation between flanking sequences and tRNA sequences, the flanking sequences of 11 putative mobile GIs in Pseudomonas aeruginosa PAO1, P. aeruginosa PA14, P. fluorescens Pf-5 and P. fluorescens Pf0-1 were identified. Among the 11 GIs, Pf0-1GI-1 is responsible for benzoate degradation. PAO1GI-1, Pf5GI-2, Pf5GI-3, and Pf5GI-4 were confirmed experimentally to be excised from a chromosome to form a circular intermediate. The action sites of the integrases are these GIs direct repeats. Due to distinct DRs, cutting sites for the internal integrase of PAO1GI-1, Pf5GI-2, Pf5GI-3 and Pf5GI-4 were determined outside the T-loop of the tRNA Gly gene, outside the anticodon loop of the tRNA Ser gene and tRNALys gene, and at the asymmetric 3′-end of the tRNA Leu gene, respectively. PAO1GI-1 and other mobile GIs may be transferred into many different strains that belong to different phyla because of the clear flanking sequences. This study describes basic information about the action sites of the integrases, assesses the mobility of GIs, and can help design and transfer mobile GIs to candidate strains. Pseudomonas, genomic islands, accurate localization, excision, integraseCitation: Song L, Zhang X H. Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens.

Structure Analysis of Genomic Islands Flanked by 5’ and 3’ End of the tRNAGly-CCC Gene in Delftia Acidovorans SPH-1

“…So, the cutting site of the integrase is 5'TTCGATT3', and its binding sites are 5'AGGG3' (5'CCCT3'). PAO1GI-1 has been deleted and reintegrated into the corresponding chromosome, but PA14GI-6 can't be deleted and reintegrated [11] . The integrases of PA14GI-6 are different with the integrase of SPHGI Gly -2 and its flanking DRs are shorter than of SPHGI Gly -2, so it is probable that the tRNA Gly-CCC gene has various action sites of the integrases, not only symmetrical anticodon stem-loop, symmetrical TΨC loop, and asymmetrical 3' end of the tRNA gene [12] , but also asymmetrical anticodon stem-loop, asymmetrical T Ψ C loop, symmetrical and asymmetrical DHU stem-loops, asymmetrical 5' end of the tRNA gene.…”