title: CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium.
abstract: Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,285 bp megaplasmid. For the first time within the Chlamydiales order, we describe the presence of a clustered regularly interspaced short palindromic repeats (CRISPR) system, the immune system of bacteria, located on the chromosome. It is composed of a small CRISPR locus comprising eight repeats and associated cas-cse genes of the subtype I-E. A CRISPR locus is also present within Chlamydia sp. Diamant, another Pr. naegleriophila strain, suggesting that the CRISPR system was acquired by a common ancestor of Pr. naegleriophila, after its divergence from Pr. amoebophila. Both nucleotide bias and comparative genomics approaches identified probable horizontal gene acquisitions within two and four genomic islands in Pr. naegleriophila KNic and Diamant genomes, respectively. The plasmid encodes an F-type conjugative system highly similar to 1) that found in the Pam100G genomic island of Pr. amoebophila UWE25 chromosome, as well as on the plasmid of Rubidus massiliensis and 2) to the three genes remaining in the chromosome of Parachlamydia acanthamoebae strains. Therefore, this conjugative system was likely acquired on an ancestral plasmid before the divergence of Parachlamydiaceae Overall, this new complete Pr. naegleriophila genome sequence enables further investigation of the dynamic processes shaping the genomes of the family Parachlamydiaceae and the genus Protochlamydia.
authors: Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors: Claire
authors: C
authors: Bertelli
authors: Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland.
authors: Ousmane H
authors: OH
authors: Cissé
authors: Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland.
authors: Brigida
authors: B
authors: Rusconi
authors: Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland.
authors: Carole
authors: C
authors: Kebbi-Beghdadi
authors: Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland.
authors: Antony
authors: A
authors: Croxatto
authors: Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Germany.
authors: Alexander
authors: A
authors: Goesmann
authors: Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland.
authors: François
authors: F
authors: Collyn
authors: Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland gilbert.greub@chuv.ch.
authors: Gilbert
authors: G
authors: Greub
mesh_terms: D064113:CRISPR-Cas Systems / Q000235:genetics*; D002689:Chlamydia / Q000235:genetics*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands / Q000235:genetics; D058977:Molecular Sequence Annotation; D009253:Naegleria / Q000235:genetics / Q000382:microbiology; D010957:Plasmids / Q000235:genetics
keywords: CRISPR; Chlamydiales; T4SS; comparative genomics; genomic island; plasmid