Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586.
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.
Kapatral
Vinayak
V
Integrated Genomics, Chicago, Illinois 60612, USA. vinayak@integratedgenomics.com
Anderson
Iain
I
Ivanova
Natalia
N
Reznik
Gary
G
Los
Tamara
T
Lykidis
Athanasios
A
Bhattacharyya
Anamitra
A
Bartman
Allen
A
Gardner
Warren
W
Grechkin
Galina
G
Zhu
Lihua
L
Vasieva
Olga
O
Chu
Lien
L
Kogan
Yakov
Y
Chaga
Oleg
O
Goltsman
Eugene
E
Bernal
Axel
A
Larsen
Niels
N
D'Souza
Mark
M
Walunas
Theresa
T
Pusch
Gordon
G
Haselkorn
Robert
R
Fonstein
Michael
M
Kyrpides
Nikos
N
Overbeek
Ross
R
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
D000596:Amino Acids; D001425:Bacterial Outer Membrane Proteins; D003067:Coenzymes; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D008070:Lipopolysaccharides; D009711:Nucleotides; D011522:Protons