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Journal of Bacteriology, March 2007, p. 2443-2459, Vol. 189, No. 6
0021-9193/07/$08.00+0     doi:10.1128/JB.01688-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Diversity of the Abundant pKLC102/PAGI-2 Family of Genomic Islands in Pseudomonas aeruginosa{triangledown} ,{dagger}

Jens Klockgether, Dieco Würdemann, Oleg Reva,{ddagger} Lutz Wiehlmann, and Burkhard Tümmler*

Klinische Forschergruppe, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany

Received 1 November 2006/ Accepted 8 January 2007

The known genomic islands of Pseudomonas aeruginosa clone C strains are integrated into tRNALys (pKLC102) or tRNAGly (PAGI-2 and PAGI-3) genes and differ from their core genomes by distinctive tetranucleotide usage patterns. pKLC102 and the related island PAPI-1 from P. aeruginosa PA14 were spontaneously mobilized from their host chromosomes at frequencies of 10% and 0.3%, making pKLC102 the most mobile genomic island known with a copy number of 30 episomal circular pKLC102 molecules per cell. The incidence of islands of the pKLC102/PAGI-2 type was investigated in 71 unrelated P. aeruginosa strains from diverse habitats and geographic origins. pKLC102- and PAGI-2-like islands were identified in 50 and 31 strains, respectively, and 15 and 10 subtypes were differentiated by hybridization on pKLC102 and PAGI-2 macroarrays. The diversity of PAGI-2-type islands was mainly caused by one large block of strain-specific genes, whereas the diversity of pKLC102-type islands was primarily generated by subtype-specific combination of gene cassettes. Chromosomal loss of PAGI-2 could be documented in sequential P. aeruginosa isolates from individuals with cystic fibrosis. PAGI-2 was present in most tested Cupriavidus metallidurans and Cupriavidus campinensis isolates from polluted environments, demonstrating the spread of PAGI-2 across habitats and species barriers. The pKLC102/PAGI-2 family is prevalent in numerous beta- and gammaproteobacteria and is characterized by high asymmetry of the cDNA strands. This evolutionarily ancient family of genomic islands retained its oligonucleotide signature during horizontal spread within and among taxa.

* Corresponding author. Mailing address: Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany. Phone: 49-511-5322920. Fax: 49-511-5326723. E-mail: tuemmler.burkhard{at}mh-hannover.de.

{triangledown} Published ahead of print on 28 December 2006.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

{ddagger} Present address: Bioinformatics and Computational Biology Unit, University of Pretoria, Pretoria 0002, South Africa.

Journal of Bacteriology, March 2007, p. 2443-2459, Vol. 189, No. 6
0021-9193/07/$08.00+0     doi:10.1128/JB.01688-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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