title: Analysis of a novel 8.9kb cryptic plasmid from Bacteroides uniformis, its long-term stability and spread within human microbiota.
abstract: The analysis of plasmid content in dominant Bacteroidales order intestinal strains isolated from the same child at a 5 year interval identified a 8.9 kb plasmid in Bacteroides uniformis BUN24 strain isolated at age 6 and indistinguishably sized plasmids in the isolates of B. uniformis, B. vulgatus, B. intesinalis, and Parabacteroides distasonis at age 11. We sequenced a B. uniformis BUN24 plasmid, designated pBUN24, and using molecular surveys of diverse species we established that this 8944bp molecule (G+C content 43.5%) represents a novel family of small cryptic Bacteroidales plasmids. The replication region of pBUN24 was experimentally localized to a 1707-bp fragment that includes a putative repA gene, coding for a protein of Rep_3 superfamily of replication proteins of theta-type plasmids preceded by a putative iteron-containing origin of replication. The other open reading frames (ORFs) identified in pBUN24 sequence include a putative tad-ata-type toxin-antitoxin and mobA-mobB mobilization modules, as well as seven additional cryptic ORFs. The interaction of Tad and Ada components demonstrated by a pull-down assay and the toxicity of Tad in Escherichia coli host suggests the functionality of the plasmid addiction module. Re-sequencing of plasmids in two Bacteroides strains isolated at the age of 11 showed 100% nucleotide identity to pBUN24. This data supports the notion that this plasmid is transmissible to other Bacteroidales strains in the natural ecosystem. The possible roles of toxin-antitoxin system and other proteins encoded by pBUN24 in providing an apparent ecological advantage to the plasmid-harbouring strains of a bacterial symbiont in the human gut deserve further investigation.
authors.affiliation: Department of Microbiology and Virology, The Russian National Research Medical University, 1, Ostrovitjanova St., Moscow 117997, Russia. a.shkoporov@gmail.com
authors.forename: Andrei N
authors.initials: AN
authors.lastname: Shkoporov
authors.forename: Ekaterina V
authors.initials: EV
authors.lastname: Khokhlova
authors.forename: Elena V
authors.initials: EV
authors.lastname: Kulagina
authors.forename: Vladimir V
authors.initials: VV
authors.lastname: Smeianov
authors.forename: Anna A
authors.initials: AA
authors.lastname: Kuchmiy
authors.forename: Lyudmila I
authors.initials: LI
authors.lastname: Kafarskaya
authors.forename: Boris A
authors.initials: BA
authors.lastname: Efimov
mesh_terms: D000595:Amino Acid Sequence; D000992:Antitoxins / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001427:Bacterial Toxins / Q000378:metabolism; D001439:Bacteroides / Q000235:genetics*; D020029:Base Pairing / Q000235:genetics*; D001483:Base Sequence; D002648:Child; D006801:Humans; D007422:Intestines / Q000382:microbiology; D064307:Microbiota / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010957:Plasmids / Q000235:genetics*; D018741:Replication Origin / Q000235:genetics
chemical_list: D000992:Antitoxins; D001426:Bacterial Proteins; D001427:Bacterial Toxins