Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium.

TitleGenome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium.
Publication TypeJournal Article
Year of Publication2007
AuthorsKarpathy, SE, Qin, X, Gioia, J, Jiang, H, Liu, Y, Petrosino, JF, Yerrapragada, S, Fox, GE, Haake, SKinder, Weinstock, GM, Highlander, SK
JournalPLoS One
Volume2
Issue7
Paginatione659
Date Published2007 Aug 01
ISSN1932-6203
KeywordsAmino Acids, Base Sequence, Clostridium, DNA, Bacterial, Evolution, Molecular, Fusobacterium nucleatum, Gene Transfer Techniques, Genome, Bacterial, Humans, Infection, Introns, Multigene Family, Open Reading Frames, Peptides, Plasmids, Polymorphism, Genetic, Repetitive Sequences, Nucleic Acid
Abstract

Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and animalis. F. nucleatum subsp. polymorphum ATCC 10953 has been well characterized phenotypically and, in contrast to previously sequenced strains, is amenable to gene transfer. We sequenced and annotated the 2,429,698 bp genome of F. nucleatum subsp. polymorphum ATCC 10953. Plasmid pFN3 from the strain was also sequenced and analyzed. When compared to the other two available fusobacterial genomes (F. nucleatum subsp. nucleatum, and F. nucleatum subsp. vincentii) 627 open reading frames unique to F. nucleatum subsp. polymorphum ATCC 10953 were identified. A large percentage of these mapped within one of 28 regions or islands containing five or more genes. Seventeen percent of the clustered proteins that demonstrated similarity were most similar to proteins from the clostridia, with others being most similar to proteins from other gram-positive organisms such as Bacillus and Streptococcus. A ten kilobase region homologous to the Salmonella typhimurium propanediol utilization locus was identified, as was a prophage and integrated conjugal plasmid. The genome contains five composite ribozyme/transposons, similar to the CdISt IStrons described in Clostridium difficile. IStrons are not present in the other fusobacterial genomes. These findings indicate that F. nucleatum subsp. polymorphum is proficient at horizontal gene transfer and that exchange with the Firmicutes, particularly the Clostridia, is common.

DOI10.1371/journal.pone.0000659
Alternate JournalPLoS ONE
PubMed ID17668047
PubMed Central IDPMC1924603
Grant ListR01 DA013759 / DA / NIDA NIH HHS / United States
R01 DE015348 / DE / NIDCR NIH HHS / United States
R01 EY013759 / EY / NEI NIH HHS / United States
R01 DE013759 / DE / NIDCR NIH HHS / United States