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26 October 2012

Draft Genome Sequence of Fusobacterium nucleatum ChDC F128, Isolated from a Periodontitis Lesion

ABSTRACT

Fusobacterium nucleatum is classified into five subspecies. F. nucleatum ChDC F128 was isolated from a periodontitis lesion and proposed as a new subspecies based on the comparison of the nucleotide sequences of the RNA polymerase beta subunit and zinc protease genes. Here, we report the draft genome sequence of the strain.

GENOME ANNOUNCEMENT

Fusobacterium nucleatum is a Gram-negative, nonmotile, obligately anaerobic rod bacterium which is frequently isolated from the oral cavity (3, 4). Fusobacterium nucleatum is classified into 5 subspecies (nucleatum, polymorphum, vincentii, animalis, and fusiforme) based on the polyacrylamide gel electrophoretic pattern of the whole-cell proteins and DNA homology (2) or electrophoretic patterns of glutamate dehydrogenase and 2-oxoglutarate reductase and DNA-DNA hybridization patterns (4). Recently, 4 strains (ChDC F128, ChDC F145, ChDC F174, and ChDC F206) of F. nucleatum were isolated from periodontitis or gingivitis lesions and a 5th strain (ChDC F300) from a healthy site, and a new subspecies was proposed based on the comparison of the nucleotide sequences of the RNA polymerase beta subunit gene (rpoB) and the zinc protease gene (7). We propose ChDC F128 (= KCOM 1249 = KCTC 5108) as the type strain for the new subspecies of F. nucleatum.
In this report, we present the draft genome sequence of F. nucleatum ChDC F128. Draft sequencing was performed by SolGent, Co., Ltd. (Daejeon, Republic of Korea), using the 454 GS-FLX Titanium system (Roche Diagnostics, Basel, Switzerland). Following an initial round of shotgun pyrosequencing, 30 contigs with a size range between 255 and 463,726 bp were assembled using the Newbler Assembler software-gsAssembler version 2.5.3 (454 Life Sciences, Branford, CT), and the percentage of GC content was 26%. Open reading frames were predicted and annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The predicted protein sequences were annotated in Gene Ontology using the basic local alignment search tool (BLAST) (1). Then, the GO classes were grouped into a total of 124 GO-Slim terms using the web tool CateGOrizer (5).
A total of 67.2% (1, 479) of ORFs were annotatable with known proteins. The genome contained 2,200 protein-coding genes, 3 copies of 23S rRNA, 1 copy of 5S rRNA, and 43 tRNA genes.
The draft genome sequence contains several key pathways for amino acids, carbohydrates, lipids, and organic acids. Biosynthetic pathways exist for at least 7 amino acids: aspartate, asparagine, threonine, methionine, glutamate, glutamine, and cysteine (from serine). The amino acid biosynthesis activity is different from the known activity in F. nucleatum strains. For example, F. nucleatum subsp. nucleatum ATCC 25586T and F. nucleatum subsp. nucleatum ATCC 51190T can synthesize just 3 amino acids (glutamate, aspartate, and asparagine) and at least 4 amino acids (aspartate, asparagine, glutamate, and glutamine), respectively (6, 8). The draft genome sequence also contains virulence factors, such as hemolysin, zinc metalloprotease, collagenase, serine protease, butyrate fermentation-related genes, 5-nitroimidazole antibiotic resistance proteins, beta-lactamase, macrolide-efflux protein, toxin YoeB, zeta toxin, virulence factor MviN, and TonB and TolC proteins. The genome also contains oxidative stress-response genes, such as glutathione peroxidase and NADH oxidase, but not superoxide dismutase.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number ALVD00000000. The version described in this paper is the first version, ALVD01000000. The Bioproject designation for this project is PRJNA171181.

ACKNOWLEDGMENTS

This research was supported by the Basic Science Research Program (grant 2012-003324) through the National Research Foundation of Korea (NRF), funded by the Ministry of Education, Science and Technology.

REFERENCES

1.
Altschul S et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402.
2.
Dzink JL, Sheenan MT, and Socransky SS. 1990. Proposal of three subspecies of Fusobacterium nucleatum Knorr 1922: Fusobacterium nucleatum subsp. nucleatum subsp. nov., comb. nov.; Fusobacterium nucleatum subsp. polymorphum subsp. nov., nom. rev., comb. nov.; and Fusobacterium nucleatum subsp. vincentii subsp. nov., nom. rev., comb. nov. Int. J. Syst. Bacteriol. 40:74–78.
3.
Gharbia SE and Shah HN. 1990. Heterogeneity within Fusobacterium nucleatum, proposal of four subspecies. Lett. Appl. Microbiol. 10:105–108.
4.
Gharbia SE and Shah HN. 1992. Fusobacterium nucleatum subsp. fusiforme subsp. nov. and Fusobacterium nucleatum subsp. animalis subsp. nov. as additional subspecies within Fusobacterium nucleatum. Int. J. Syst. Bacteriol. 42:296–298.
5.
Hu ZL, Bao J, and Reecy JM. 2008. CateGOrizer: a web-based program to batch analyze Gene Ontology classification categories. Online J. Bioinform. 9:108–112.
6.
Kapatral V et al. 2002. Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J. Bacteriol. 184:2005–2018.
7.
Kim HS et al. 2010. Application of rpoB and zinc protease gene for use in molecular discrimination of Fusobacterium nucleatum subspecies. J. Clin. Microbiol. 48:545–553.
8.
Park SN et al. 2012. Draft genome sequence of Fusobacterium nucleatum subsp. fusiforme ATCC 51190T. J. Bacteriol. 194:5445–5446.

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Published In

cover image Journal of Bacteriology
Journal of Bacteriology
Volume 194Number 2215 November 2012
Pages: 6322 - 6323
PubMed: 23105064

History

Received: 27 August 2012
Accepted: 31 August 2012
Published online: 26 October 2012

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Contributors

Authors

Soon-Nang Park
Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
Si-Won Kong
SolGent Co., Ltd., Yuseong-Gu, Daejeon, Republic of Korea
Hwa-Sook Kim
Department of Dental Hygiene, Chunnam Techno University, Chunnam, Republic of Korea
Mo-Se Park
SolGent Co., Ltd., Yuseong-Gu, Daejeon, Republic of Korea
Jee-Won Lee
SolGent Co., Ltd., Yuseong-Gu, Daejeon, Republic of Korea
Eugene Cho
Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
Yun Kyong Lim
Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
Mi-Hwa Choi
Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
Young-Hyo Chang
Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Daejeon, Republic of Korea
Jeong Hwan Shin
Department of Laboratory Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
Hong-Seog Park
Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
University of Science and Technology (UST), Daejeon, Republic of Korea
Sang-Haeng Choi
Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
Joong-Ki Kook
Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea

Notes

Address correspondence to Joong-Ki Kook, [email protected].
S.-N.P. and S.-W.K. contributed equally to this article.

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