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Background  The genome of  Protochlamydia amoebophila  UWE25, a  Parachlamydia -related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs).    Results  On the residual cumulative G+C content curve, a G+C-rich 19-kb region was observed. This sequence is part of a 100-kb chromosome region, containing 100 highly co-oriented ORFs, flanked by two 17-bp direct repeats. Two identical  gly-tRNA  genes in tandem are present at the proximal end of this genetic element. Several mobility genes encoding transposases and bacteriophage-related proteins are located within this chromosome region. Thus, this region largely fulfills the criteria of GIs. The G+C content analysis shows that several modules compose this GI. Surprisingly, one of them encodes all genes essential for F-like conjugative DNA transfer ( traF ,  traG ,  traH ,  traN ,  traU ,  traW , and  trbC ), involved in sex pilus retraction and mating pair stabilization, strongly suggesting that, similarly to the other F-like operons, the parachlamydial  tra  unit is devoted to DNA transfer. A close relatedness of this  tra  unit to F-like  tra  operons involved in conjugative transfer is confirmed by phylogenetic analyses performed on concatenated genes and gene order conservation. These analyses and that of  gly-tRNA  distribution in 140 GIs suggest a proteobacterial origin of the parachlamydial  tra  unit.    Conclusions  A GI of the UWE25 chromosome encodes a potentially functional F-like DNA conjugative system. This is the first hint of a putative conjugative system in chlamydiae. Conjugation most probably occurs within free-living amoebae, that may contain hundreds of  Parachlamydia  bacteria tightly packed in vacuoles. Such a conjugative system might be involved in DNA transfer between internalized bacteria. Since this system is absent from the sequenced genomes of  Chlamydiaceae , we hypothesize that it was acquired after the divergence between  Parachlamydiaceae  and  Chlamydiaceae , when the  Parachlamydia -related symbiont was an intracellular bacteria. It suggests that this heterologous DNA was acquired from a phylogenetically-distant bacteria sharing an amoebal vacuole. Since  Parachlamydiaceae  are emerging agents of pneumonia, this GI might be involved in pathogenicity. In future, conjugative systems might be developed as genetic tools for  Chlamydiales .

bmc microbiology

A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system.