The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens

Nature Biotechnology

Volumn 22, Issue 10, 2004, Pages 1275-1281

  Hong, Soon Ho ^a   Kim, Jin Sik ^a   Lee, Sang Yup ^a   In, Yong Ho ^b,e   Choi, Sun Shim ^b   Rih, Jeong Keun ^c   Kim, Chang Hoon ^c   Jeong, Haeyoung ^c,d   Hur, Cheol Goo ^c   Kim, Jae Jong ^d  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b Bioinfomatix Inc   (South Korea)

^c Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^d GenoTech Corporation   (South Korea)

^e IDRTech Inc   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CARBOXYLATION; GENETIC ENGINEERING; INDUSTRIAL CHEMICALS; METABOLISM; METABOLITES; ORGANIC ACIDS;

ELECTRON ACCEPTOR; GENOME SEQUENCE; MENAQUINONE SYSTEMS; RUMEN;

GENES;

CARBON DIOXIDE; INDUSTRIAL CHEMICAL; OXALOACETIC ACID; PHOSPHOENOLPYRUVATE;

ADAPTATION; ARTICLE; BACTERIAL GENOME; BACTERIAL METABOLISM; BASE PAIRING; CARBOXYLATION; CITRIC ACID CYCLE; ELECTRON TRANSPORT; GENE ISOLATION; GENE SEQUENCE; MANNHEIMIA; MANNHEIMIA SUCCINICIPRODUCENS; MBEL55E GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REDUCTION; RUMINATION;

AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; BASE SEQUENCE; CARBON DIOXIDE; CHROMOSOME MAPPING; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; MANNHEIMIA; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PROTEOME; RUMEN; SUCCINIC ACID;

ANIMALIA; BACTERIA (MICROORGANISMS); BOVINAE; MANNHEIMIA; MANNHEIMIA SUCCINICIPRODUCENS; NEGIBACTERIA; PROKARYOTA;

EID: 5044220423     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt1010     Document Type: Article

References (32)

1. Sniffen, C.J. & Herdt, H.H. The Veterinary Clinics of North America: Food Animal Practice (W.B. Saunders Company, Pennsylvania, USA, 1991).
2. Lee, P.C., Lee, S.Y., Hong, S.H. & Chang, H.N. Isolation and characterization of a new succinic acid-producing bacterium, Mannheimia succiniciproducens MBEL55E, from bovine rumen. Appl. Microbiol. Biotechnol. 58, 663-668 (2002).
3. Lee, S.Y., Hong, S.H., Lee, S.H. & Park, S.J. Fermentative production of chemicals that can be used for polymer synthesis. Macromol. Biosci. 4, 157-164 (2004).
4. Salzberg, S.L., Salzberg, A.J., Kerlavage, A.R. & Tomb, J.F. Skewed oligomers and origins of replication. Gene 217, 57-67 (1998).
5. Blattner, F.R. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1462 (1997).
6. Kunst, F. et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390, 249-256 (1997).
7. May, B.J. et al. Complete genomic sequence of Pasteurella multocida, Pm70. Proc. Natl. Acad. Sci. USA 98, 3460-3465 (2001).
8. Kanehisa, M., Goto, S., Kawashima, S. & Nakaya, A. The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002).
9. Karp, P.D. Pathway databases: a case study in computational symbolic theories. Science 293, 2040-2044 (2001).
10. Fleischmann, R.D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512 (1995).
11. Angen, Ø., Mutters, R., Caugant, D.A., Olsen, J.E. & Bisgaard, M. Taxonomic relationships of the [Pasteurella] haemolytica complex as evaluated by DNA-DNA hybridizations and 16S rRNA sequencing with proposal of Mannheimia haemolytica gen. nov., comb. nov., Mannheimia granulomatis comb. nov., Mannheimia glucosida sp. nov., Mannheimia ruminalis sp. nov. and Mannheimia varigena sp. nov. Int. J. Syst. Bacteriol. 49, 67-86 (1999).
12. Osawa, R. et al. Lonepinella koalarum gen. nov., sp. nov., a new tannin-protein complex degrading bacterium. Syst. Appl. Microbiol. 18, 368-373 (1995).
13. Guettler, M.V., Rumler, D. & Jain, M.K. Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing strain from the bovine rumen. Int. J. Syst. Bacteriol. 49, 207-216 (1999).
14. Church, D.C. The Ruminant Animal: Digestive Physiology and Nutrition (Prentice Hall, New Jersey, USA, 1988).
15. Ibarra, R.U., Edwards, J.S. & Palsson, B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silco predicted optimal growth. Nature 420, 186-189 (2002).
16. Edwards, J.S., Ibarra, R.U. & Palsso, B.O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19, 125-130 (2001).
17. Price, N.D., Papin, J.A., Schilling, C.H. & Palsson, B.O. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 21, 162-169 (2003).
18. Favello, A., Hillier, L. & Wilson, R.K. Genomic DNA sequencing methods. Methods Cell Biol. 48, 551-569 (1995).
19. Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989).
20. Gordon, D., Abajian, C. & Green, P. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195-202 (1998).
21. Delcher, A.L., Harmon, D., Kasif, S., White, O. & Salzberg, S.L. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27, 4636-4641 (1999).
22. Rutherford, K. et al. Artemis: sequence visualization and annotation. Bioinformatics 16, 944-945 (2000).
23. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
24. Eddy, S.R. Profile hidden Markov models. Bioinformatics 14, 755-763 (1998).
25. Tatusov, R.L. et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22-28 (2001).
26. Lowe, T.M. & Eddy, S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997).
27. Varma, A. & Palsson, B.O. Metabolic flux balancing - basic concepts, scientific and practical use. Bio/Technology 12, 994-998 (1994).
28. Neidhardt, F.C. & Umbarger, H.E. in Escherichia coli and Salmonella: Cellular and Molecular Biology, edn. 2 (ed. Neidhardt, F.C.) 13-16 (ASM Press, Washington, DC, 1996).
29. Lee, D.Y., Yun, H., Park, S. & Lee, S.Y. MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics 19, 2144-2146 (2003).
30. Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863-14868 (1998).
31. Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254 (1976).
32. Burton, K. A study of the conditions and mechanism of the diphenylamine reaction for the colorimetric estimation of deoxyribonucleic acid. Biochem. J. 62, 314-323 (1956).