title: 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.
abstract: 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.
authors.affiliation: Center for Research on Intracellular Bacteria, Institute of Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland. gilbert.greub@hospvd.ch
authors.forename: Gilbert
authors.initials: G
authors.lastname: Greub
authors.forename: François
authors.initials: F
authors.lastname: Collyn
authors.forename: Lionel
authors.initials: L
authors.lastname: Guy
authors.forename: Claude-Alain
authors.initials: CA
authors.lastname: Roten
mesh_terms: D000048:Acanthamoeba / Q000382:microbiology; D000818:Animals; D001482:Base Composition / Q000235:genetics; D002695:Chlamydiales / Q000145:classification / Q000235:genetics*; D002876:Chromosomes, Bacterial / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D003227:Conjugation, Genetic / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D023061:Gene Order / Q000235:genetics; D044404:Genomic Islands / Q000235:genetics*; D009876:Operon / Q000235:genetics*; D010802:Phylogeny; D013559:Symbiosis
chemical_list: D004269:DNA, Bacterial