title: Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586.
abstract: We present a complete DNA sequence and metabolic analysis of the dominant oral bacterium Fusobacterium nucleatum. Although not considered a major dental pathogen on its own, this anaerobe facilitates the aggregation and establishment of several other species including the dental pathogens Porphyromonas gingivalis and Bacteroides forsythus. The F. nucleatum strain ATCC 25586 genome was assembled from shotgun sequences and analyzed using the ERGO bioinformatics suite (http://www.integratedgenomics.com). The genome contains 2.17 Mb encoding 2,067 open reading frames, organized on a single circular chromosome with 27% GC content. Despite its taxonomic position among the gram-negative bacteria, several features of its core metabolism are similar to that of gram-positive Clostridium spp., Enterococcus spp., and Lactococcus spp. The genome analysis has revealed several key aspects of the pathways of organic acid, amino acid, carbohydrate, and lipid metabolism. Nine very-high-molecular-weight outer membrane proteins are predicted from the sequence, none of which has been reported in the literature. More than 137 transporters for the uptake of a variety of substrates such as peptides, sugars, metal ions, and cofactors have been identified. Biosynthetic pathways exist for only three amino acids: glutamate, aspartate, and asparagine. The remaining amino acids are imported as such or as di- or oligopeptides that are subsequently degraded in the cytoplasm. A principal source of energy appears to be the fermentation of glutamate to butyrate. Additionally, desulfuration of cysteine and methionine yields ammonia, H(2)S, methyl mercaptan, and butyrate, which are capable of arresting fibroblast growth, thus preventing wound healing and aiding penetration of the gingival epithelium. The metabolic capabilities of F. nucleatum revealed by its genome are therefore consistent with its specialized niche in the mouth.
authors.affiliation: Integrated Genomics, Chicago, Illinois 60612, USA. vinayak@integratedgenomics.com
authors.forename: Vinayak
authors.initials: V
authors.lastname: Kapatral
authors.forename: Iain
authors.initials: I
authors.lastname: Anderson
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Gary
authors.initials: G
authors.lastname: Reznik
authors.forename: Tamara
authors.initials: T
authors.lastname: Los
authors.forename: Athanasios
authors.initials: A
authors.lastname: Lykidis
authors.forename: Anamitra
authors.initials: A
authors.lastname: Bhattacharyya
authors.forename: Allen
authors.initials: A
authors.lastname: Bartman
authors.forename: Warren
authors.initials: W
authors.lastname: Gardner
authors.forename: Galina
authors.initials: G
authors.lastname: Grechkin
authors.forename: Lihua
authors.initials: L
authors.lastname: Zhu
authors.forename: Olga
authors.initials: O
authors.lastname: Vasieva
authors.forename: Lien
authors.initials: L
authors.lastname: Chu
authors.forename: Yakov
authors.initials: Y
authors.lastname: Kogan
authors.forename: Oleg
authors.initials: O
authors.lastname: Chaga
authors.forename: Eugene
authors.initials: E
authors.lastname: Goltsman
authors.forename: Axel
authors.initials: A
authors.lastname: Bernal
authors.forename: Niels
authors.initials: N
authors.lastname: Larsen
authors.forename: Mark
authors.initials: M
authors.lastname: D'Souza
authors.forename: Theresa
authors.initials: T
authors.lastname: Walunas
authors.forename: Gordon
authors.initials: G
authors.lastname: Pusch
authors.forename: Robert
authors.initials: R
authors.lastname: Haselkorn
authors.forename: Michael
authors.initials: M
authors.lastname: Fonstein
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.forename: Ross
authors.initials: R
authors.lastname: Overbeek
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D001425:Bacterial Outer Membrane Proteins / Q000378:metabolism; D001692:Biological Transport; D002455:Cell Division; D003067:Coenzymes / Q000378:metabolism; D004260:DNA Repair; D004261:DNA Replication; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000032:analysis; D024881:Drug Resistance, Bacterial; D016967:Fusobacterium nucleatum / Q000235:genetics* / Q000378:metabolism; D016680:Genome, Bacterial; D050356:Lipid Metabolism; D008070:Lipopolysaccharides / Q000378:metabolism; D016254:Mutagenesis, Insertional; D009711:Nucleotides / Q000378:metabolism; D014176:Protein Biosynthesis; D011522:Protons; D015398:Signal Transduction / Q000502:physiology; D014158:Transcription, Genetic; D014774:Virulence
chemical_list: D000596:Amino Acids; D001425:Bacterial Outer Membrane Proteins; D003067:Coenzymes; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D008070:Lipopolysaccharides; D009711:Nucleotides; D011522:Protons