Genomic and biochemical studies demonstrating the absence of an alkane-producing phenotype in Vibrio furnissii M1

Applied and Environmental Microbiology

Volumn 73, Issue 22, 2007, Pages 7192-7198

  Wackett, Lawrence P ^a   Frias, Janice A ^a   Seffernick, Jennifer L ^a   Sukovich, David J ^a   Cameron, Stephan M ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL ENGINEERING; BIOPOLYMERS; BIOSYNTHESIS; DNA; ELECTROPHORESIS; GENES; RNA;

CELL EXTRACTS; PHENOTYPES; PULSED FLELD GEL ELECTROPHORESIS; VIBRIO STRAINS;

MICROORGANISMS;

ALKANE; CARBON 14; CELL EXTRACT; GENOMIC DNA; HEXADECANOL; RNA 16S; SOLVENT;

ALKANE; BACTERIUM; BIOCHEMISTRY; CHROMOSOME; DNA; GENOMICS; MASS SPECTROMETRY; PHENOTYPE; POLYMERASE CHAIN REACTION; RELATEDNESS; RNA; SOLVENT;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM CULTURE; CULTURE MEDIUM; DEGRADATION; DNA SEQUENCE; GAS CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; POLYMERASE CHAIN REACTION; PULSED FIELD GEL ELECTROPHORESIS; RNA GENE; SEQUENCE ANALYSIS; SYNTHESIS; VIBRIO FURNISSII;

ALKANES; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; GENE ORDER; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHENOTYPE; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; VIBRIO;

VIBRIO; VIBRIO FURNISSII;

EID: 36649006253     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01785-07     Document Type: Article

References (30)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Alvarez, H. M., and A. Steinbuchel. 2002. Triacylglycerols in prokaryotic microorganisms. Appl. Microbiol. Biotechnol. 60:367-376.
3. Bassler, B. L., C. Yu, Y. C. Lee, and S. Roseman. 1991. Chitin utilization by marine bacteria. Degradation and catabolism of chitin oligosaccharides by Vibrio furnissii. J. Biol. Chem. 266:24276- 24286.
4. Bligh, E. G., and W. J. Dyer. 1959. A rapid method for total lipid extraction and purification. Can. J. Biochem. Physiol. 37:911-917.
5. Bobik, T. A. 2006. Polyhedral organelles compartmenting bacterial metabolic processes. Appl. Microbiol. Biotechnol. 70:517-525.
6. Brenner, D. J., F. W. Hickman-Brenner, J. V. Lee, A. G. Steigerwalt, G. R. Fanning, D. G. Hollis, J. J. Farmer, R. E. Weaver, S. W. Joseph, and R. J. Seidler. 1983. Vibrio furnissii (formerly aerogenic biogroup of Vibrio fluvialis), a new species isolated from human feces and the environment. J. Clin. Microbiol. 18:816-824.
7. Chen, C. Y., K. M. Wu, Y. C. Chang, C. H. Chang, H. C. Tsai, T. L. Liao, Y. M. Liu, H. J. Chen, A. B. Shen, J. C. Li, T. L. Su, C. P. Shao, C. T. Lee, L. I. Hor, and S. F. Tsai. 2003. Comparative genome analysis of Vibrio vulnificus, a marine pathogen. Genome Res. 13:2577-2587.
8. Colwell, R. R. 2004. Infectious disease and environment: cholera as a paradigm for waterborne disease. Int. Microbiol. 7:285-289.
9. Dombek, P. E., L. K. Johnson, S. T. Zimmerley, and M. J. Sadowsky. 2000. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl. Environ. Microbiol. 66:2572-2577.
10. Eddy, S. R. 1998. Profile hidden Markov models. Bioinformatics 14:755-763.
11. Fakhr, M. K., L. K. Nolan, and C. M. Logue. 2005. Multilocus sequence typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium. J. Clin. Microbiol. 43:2215-2219.
12. Heidelberg, J. F., J. A. Eisen, W. C. Nelson, R. A. Clayton, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, L. Umayam, S. R. Gill, K. E. Nelson, T. D. Read, H. Tettelin, D. Richardson, M. D. Ermolaeva, J. Vamathevan, S. Bass, H. Qin, I. Dragoi, P. Sellers, L. McDonald, T. Utterback, R. D. Fleishmann, W. C. Nierman, O. White, S. L. Salzberg, H. O. Smith, R. R. Colwell, J. J. Mekalanos, J. C. Venter, and C. M. Fraser. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477-483.
13. Ishii, S., T. Yan, D. A. Shively, M. N. Byappanahalli, R. L. Whitman, and M. J. Sadowsky. 2006. Cladophora (Chlorophyta) spp. harbor human bacterial pathogens in nearshore water of Lake Michigan. App. Environ. Microbiol. 72:4545-4553.
14. Johnson, L. K., M. B. Brown, E. A. Carruthers, J. A. Ferguson, P. E. Dombek, and M. J. Sadowsky. 2004. Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Appl. Environ. Microbiol. 70:4478-4485.
15. Kerfeld, C. A., M. R. Sawaya, S. Tanaka, C. V. Nguyen, M. Phillips, M. Beeby, and T. O. Yeates. 2005. Protein structures forming the shell of primitive bacterial organelles. Science 309:936-938.
16. Kessler, D., I. Leibrecht, and J. Knappe. 1991. Pyruvate-formate-lyase-deactivase and acetyl-CoA reductase activities of Escherichia coli reside on a polymeric protein particle encoded by adhE. FEBS Lett. 281:59-63.
17. Keyhani, N. O., and S. Roseman. 1996. The chitin catabolic cascade in the marine bacterium Vibrio furnissii. Molecular cloning, isolation, and characterization of a periplasmic chitodextrinase. J. Biol. Chem. 271:33414-33424.
18. Li, X., and S. Roseman. 2004. The chitinolytic cascade in vibrios is regulated by chitin oligosaccharides and a two-component chitin catabolic sensor/kinase. Proc. Natl. Acad. Sci. USA 101:627-631.
19. Meyer, F., A. Goesmann, A. C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, and A. Pühler. 2003. GenDB - an open source genome annotation system for prokaryotic genomes. Nucleic Acids Res. 31:2187-2195.
20. Miyamato, K. 2001. Microorganisms and process for producing petroleum substitute oil by using these microorganisms. Japanese patent P2001-190323.
21. Okada, K., T. Iida, K. Kita-Tsukamoto, and T. Honda. 2005. Vibrios commonly possess two chromosomes. J. Bacteriol. 187:752-757.
22. Park, M. O. 2005. New pathway for long-chain n-alkane synthesis via 1-alcohol in Vibrio furnissii M1. J. Bacteriol. 187:1426-1429.
23. Park, M. O., K. Heguri, K. Hirata, and K. Miyamoto. 2005. Production of alternatives to fuel oil from organic waste by the alkane-producing bacterium, Vibrio furnissii M1. J. Appl. Microbiol. 98:324-331.
24. Park, M. O., M. Tanabe, K. Hirata, and K. Miyamoto. 2001. Isolation and characterization of a bacterium that produces hydrocarbons extracellularly which are equivalent to light oil. Appl. Microbiol. Biotechnol. 56:448-452.
25. Ruby, E. G., M. Urbanowski, J. Campbell, A. Dunn, M. Faini, R. Gunsalus, P. Lostroh, C. Lupp, J. McCann, D. Millikan, A. Schaefer, E. Stabb, A. Stevens, K. Visick, C. Whistler, and E. P. Greenberg. 2005. Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners. Proc. Natl. Acad. Sci. USA 102:3004-3009.
26. Sadowsky, M. J., R. E. Tully, P. B. Cregan, and H. H. Keyser. 1987. Genetic diversity in Bradyrhizobium japonicum serogroup 123 and its relation to genotype-specific nodulation of soybeans. Appl. Environ. Microbiol. 53:2624-2630.
27. Sonnhammer, E. L. L., S. R. Eddy, and R. Durbin. 1997. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405-420.
28. Steinbuchel, A., and S. Hein. 2001. Biochemical and molecular basis of microbial synthesis of polyhydroxyalkanoates in microorganisms. Adv. Biochem. Eng. Biotechnol. 71:81-123.
29. Tettelin, H., V. Masignani, M. J. Cieslewicz, C. Donati, D. Medini, N. L. Ward, S. V. Angiuoli, J. Crabtree, A. L. Jones, A. S. Durkin, R. T. DeBoy, T. M. Davidsen, M. Mora, M. Scarselli, I. M. Ros, J. D. Peterson, C. R. Hauser, J. P. Sundaram, W. C. Nelson, R. Madupu, L. M. Brinkac, R. J. Dodson, M. J. Rosovitz, S. A. Sullivan, S. C. Daugherty, D. H. Haft, J. Selengut, M. L. Gwinn, L. Zhou, N. Zafar, H. Khouri, D. Radune, G. Dimitrov, K. Watkins, K. J. B. O'Connor, S. Smith, T. R. Utterback, O. White, C. E. Rubens, G. Grandi, L. C. Madoff, D. L. Kasper, J. L. Telford, M. R. Wessels, R. Rappuoli, and C. M. Fraser. 2005. Genomic analysis of multiple pathogenic islands of Streptococcus agalactiae: Implications for the microbial "pan-genome." Proc. Natl. Acad. Sci. USA 102:13950-13955.
30. Yeung, P. S., and K. J. Boor. 2004. Epidemiology, pathogenesis, and prevention of foodborne Vibrio parahaemolyticus infections. Foodborne Pathog. Dis. 1:74-88.