Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium.
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.
Karpathy
Sandor E
SE
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America; Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America.
Qin
Xiang
X
Gioia
Jason
J
Jiang
Huaiyang
H
Liu
Yamei
Y
Petrosino
Joseph F
JF
Yerrapragada
Shailaja
S
Fox
George E
GE
Haake
Susan Kinder
SK
Weinstock
George M
GM
Highlander
Sarah K
SK
D000596:Amino Acids / Q000378:metabolism; D001483:Base Sequence; D003013:Clostridium / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D016967:Fusobacterium nucleatum / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D018014:Gene Transfer Techniques; D016680:Genome, Bacterial; D006801:Humans; D007239:Infections / Q000382:microbiology; D007438:Introns; D005810:Multigene Family; D016366:Open Reading Frames; D010455:Peptides / Q000737:chemistry / Q000235:genetics; D010957:Plasmids / Q000235:genetics; D011110:Polymorphism, Genetic; D012091:Repetitive Sequences, Nucleic Acid
D000596:Amino Acids; D004269:DNA, Bacterial; D010455:Peptides