Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16

Nature Biotechnology

Volumn 24, Issue 10, 2006, Pages 1257-1262

  Pohlmann, Anne ^a   Fricke, Wolfgang Florian ^b   Reinecke, Frank ^c   Kusian, Bernhard ^b   Liesegang, Heiko ^b   Cramm, Rainer ^a   Eitinger, Thomas ^a   Ewering, Christian ^c   Pötter, Markus ^c   Schwartz, Edward ^a   Strittmatter, Axel ^b   Voß, Ingo ^c   Gottschalk, Gerhard ^b   Steinbüchel, Alexander ^c   Friedrich, Bärbel ^a   Bowien, Botho ^b  

^a HUMBOLDT UNIVERSITY   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGICAL POTENTIAL; GENOME SEQUENCES; VERSATILE ORGANISM;

BIODEGRADATION; CARBON; CHROMOSOMES; GENES; GROWTH KINETICS; METABOLISM;

GENETIC ENGINEERING;

BIOPLAST; CARBON DIOXIDE; HYDROGEN; HYDROXYBUTYRIC ACID; ORGANIC COMPOUND; PLASTIC; POLY(3 HYDROXYBUTYRIC ACID); POLYESTER; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL METABOLISM; BIODEGRADABILITY; BIOTECHNOLOGY; CARBON METABOLISM; CHROMOSOME 1; CHROMOSOME 2; ENERGY METABOLISM; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; PRIORITY JOURNAL; WAUTERSIA EUTROPHA;

AEROBIOSIS; ANAEROBIOSIS; BACTERIAL TOXINS; BIOLOGICAL TRANSPORT; CARBON; CHROMOSOMES, BACTERIAL; CUPRIAVIDUS NECATOR; GENOME, BACTERIAL; HYDROXYBUTYRATES; MOLECULAR SEQUENCE DATA; POLYESTERS;

BACTERIA (MICROORGANISMS); CUPRIAVIDUS NECATOR;

EID: 33749863920     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1244     Document Type: Article

References (48)

1. Aragno, M. & Schlegel, H.G. The mesophilic hydrogen-oxidizing (knallgas) bacteria. in The Prokaryotes (eds. Balows, A., Trüper, H.G., Dworkin, M., Harder, W. & Schleifer, K.-H.) 344-384, (Springer-Verlag, New York, NY, 1992).
2. 2-metabolizing prokaryotes. in The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community release 3.13, Edn. 3 (eds. Dworkin, M., Schleifer, K.H. & Stackebrandt, E.) (Springer-Verlag, New York, NY, 2003).
3. 2 assimilation in the chemoautotroph Ralstonia eutropha. Arch. Microbiol. 178, 85-93 (2002).
4. Steinbüchel, A. & Füchtenbusch, B. Bacterial and other biological systems for polyester production. Trends Biotechnol. 16, 419-427 (1998).
5. Steinbüchel, A. Biodegradable plastics. Curr. Opin. Biotechnol. 3, 291 (1992).
6. Lee, S.Y. & Park, S.J. Fermentative production of short-chain-length PHAs. in Biotechnology of Biopolymers-From Synthesis to Patents Vol. 1 (eds. Steinbüchel, A. & Doi, Y.) 207-234, (Wiley-VCH, Weinheim, 2005).
7. Asrar, J. & Gruys, K.J. Biodegradable polymer (Biopol®). in Biopolymers Vol. 4 (eds. Doi, Y. & Steinbüchel, A.) 53-90, (Wiley-VCH, Weinheim, 2002).
8. Heumann, H. Method for labeling biopolymers using isotopes. International patent PCT Int. Appl. Publ. WO0012140 (2000).
9. Schlegel, H.G. & Lafferty, R. Growth of Knallgas bacteria (Hydrogenomonas) using direct electrolysis of culture medium. Nature 205, 308-309 (1965).
10. Armstrong, F.A., Vincent, K.A., Friedrich, B. & Lenz, O. Biochemical fuel cell comprising oxygen-tolerant hydrogenases adsorbed on anode surfaces. Int. patent PCT Int. Appl. Publ. WO2006030196 (2006).
11. Vincent, K.A. et al. Electrocatalytic hydrogen oxidation by an enzyme at high carbon monoxide or oxygen levels. Proc. Natl. Acad. Sci. USA 102, 16951-16954 (2005).
12. Ihara, M. et al. Light-driven hydrogen production by a hybrid complex of a [NiFe]-hydrogenase and the cyanobacterial photosystem I. Photochem. Photobiol. 82, 676-682 (2006).
13. Lutz, B.J., Fan, Z.H., Burgdorf, T. & Friedrich, B. Hydrogen sensing by enzyme-catalyzed electrochemical detection. Anal. Chem. 77, 4969-4975 (2005).
14. 2-based lithoautotrophy and anaerobiosis. J. Mol. Biol. 332, 369-383 (2003).
15. Schwartz, E. & Friedrich, B. A physical map of the megaplasmid pHG1, one of three genomic replicons in Ralstonia eutropha H16. FEMS Microbiol. Lett. 201, 213-219 (2001).
16. Kung, S.S., Chen, J. & Chow, W.Y. Molecular and genetic characterization of an Alcaligenes eutrophus insertion element. J. Bacteriol. 174, 8023-8029 (1992).
17. 2 fixation in Alcaligenes eutrophus. Mol. Microbiol. 5, 2695-2705 (1991).
18. Friedrich, C.G., Bowien, B. & Friedrich, B. Formate and oxalate metabolism in Alcaligenes eutrophus. J. Gen. Microbiol. 115, 185-192 (1979).
19. Oh, J.I. & Bowien, B. Structural analysis of the fds operon encoding the NAD+-linked formate dehydrogenase of Ralstonia eutropha. J. Biol. Chem. 273, 26349-26360 (1998).
20. Burgdorf, T., Bömmer, D. & Bowien, B. Involvement of an unusual mol operon in molybdopterin cofactor biosynthesis in Ralstonia eutropha. J. Mol. Microbiol. Biotechnol. 3, 619-629 (2001).
21. Kersters, K. & De Ley, J. Genus Alcaligenes Castellani and Chalmers 1919. in Bergey's Manual of Systematic Bacteriology Vol. 1 (eds. Krieg, N.R. & Holt, J.G.) 381-373, (Williams & Wilkins, Baltimore, 1984).
22. Gottschalk, G., Eberhardt, U. & Schlegel, H.G. Utilization of fructose by Hydrogenomonas H16 (I). Arch. Mikrobiol. 48, 95-108 (1964).
23. Salanoubat, M. et al. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415, 497-502 (2002).
24. Nierman, W.C. et al. Structural flexibility in the Burkholderia mallei genome. Proc. Natl. Acad. Sci. USA 101, 14246-14251 (2004).
25. Holden, M.T. et al. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc. Natl. Acad. Sci. USA 101, 14240-14245 (2004).
26. Cramm, R., Pohlmann, A. & Friedrich, B. Purification and characterization of the single-component nitric oxide reductase from Ralstonia eutropha H16. FEBS Lett. 460, 6-10 (1999).
27. Pohlmann, A., Cramm, R., Schmelz, K. & Friedrich, B. A novel NO-responding regulator controls the reduction of nitric oxide in Ralstonia eutropha. Mol. Microbiol. 38, 626-638 (2000).
28. Siedow, A., Cramm, R., Siddiqui, R.A. & Friedrich, B. A megaplasmid-borne anaerobic ribonucleotide reductase in Alcaligenes eutrophus H16. J. Bacteriol. 181, 4919-4928 (1999).
29. Brämer, C.O. & Steinbüchel, A. The methylcitric acid pathway in Ralstonia eutropha: new genes identified involved in propionate metabolism. Microbiology 147, 2203-2214 (2001).
30. Antoine, R. et al. Overrepresentation of a gene family encoding extracytoplasmic solute receptors in Bordetella. J. Bacteriol. 185, 1470-1474 (2003).
31. Antoine, R. et al. The periplasmic binding protein of a tripartite tricarboxylate transporter is involved in signal transduction. J. Mol. Biol. 351, 799-809 (2005).
32. Schlegel, H.G., Gottschalk, G. & Von Bartha, R. Formation and utilization of poly-β-hydroxybutyric acid by Knallgas bacteria (Hydrogenomonas). Nature 191, 463-465 (1961).
33. Slater, S. et al. Multiple β-ketothiolases mediate poly(β-hydroxyalkanoate) copolymer synthesis in Ralstonia eutropha. J. Bacteriol. 180, 1979-1987 (1998).
34. Pötter, M. et al. The complex structure of polyhydroxybutyrate (PHB) granules: four orthologous and paralogous phasins occur in Ralstonia eutropha. Microbiology 150, 2301-2311 (2004).
35. York, G.M. et al. Ralstonia eutropha H16 encodes two and possibly three intracellular Poly[D-(-)-3-hydroxybutyrate] depolymerase genes. J. Bacteriol. 185, 3788-3794 (2003).
36. Saegusa, H., Shiraki, M. & Saito, T. Cloning of an intracellular D(-)-3-hydroxybutyrate-oligomer hydrolase gene from Ralstonia eutropha H16 and identification of the active site serine residue by site-directed mutagenesis. J. Biosci. Bioeng. 94, 106-112 (2002).
37. Johnson, B.F. & Stanier, R.Y. Dissimilation of aromatic compounds by Alcaligenes eutrophus. J. Bacteriol. 107, 468-475 (1971).
38. Bowen, D. et al. Insecticidal toxins from the bacterium Photorhabdus luminescens. Science 280, 2129-2132 (1998).
39. Pemberton, J.M., Corney, B. & Don, R.H. Evolution and spread of pesticide-degrading ability among soil microorganisms. in Plasmids of Medical, Environmental and Commercial Importance (eds. Timmis, K.N. & Pühler, A.) 287-299 (Elsevier/North-Holland Biomedical Press, 1979).
40. Ren, Q. & Paulsen, I.T. Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput. Biol., Published online 19 August 2005 (doi:1T0.1371/journal.pcbi. 0010027).
41. Lütke-Eversloh, T. et al. Biosynthesis of polythioesters by engineered Escherichia coli as novel thermoplastic materials. Nat. Mater. 1, 236-240 (2002).
42. Kim do, Y., Lütke-Eversloh, T., Elbanna, K., Thakor, N. & Steinbüchel, A. Poly (3-mercaptopropionate): a nonbiodegradable biopolymer? Biomacromolecules 6, 897-901 (2005).
43. Staden, R. The Staden sequence analysis package. Mol. Biotechnol. 5, 233-241 (1996).
44. Tech, M. & Merkl, R. YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biol. 3, 441-451 (2003).
45. Schiex, T., Gouzy, J., Moisan, A. & de Oliveira, Y. FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Res. 31, 3738-3741 (2003).
46. Overbeek, R. et al. The ERGO genome analysis and discovery system. Nucleic Acids Res. 31, 164-171 (2003).
47. Overbeek, R. et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691-5702 (2005).
48. Ghai, R., Hain, T. & Chakraborty, T. GenomeViz: visualizing microbial genomes. BMC Bioinformatics 5, 198 (2004).