Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

Nature Biotechnology

Volumn 24, Issue 8, 2006, Pages 997-1004

  Schneiker, Susanne ^a   Dos Santos, Vítor A P Martins ^b   Bartels, Daniela ^a   Bekel, Thomas ^a   Brecht, Martina ^a   Buhrmester, Jens ^a   Chernikova, Tatyana N ^b,c   Denaro, Renata ^d   Ferrer, Manuel ^b,e,f   Gertler, Christoph ^b,c   Goesmann, Alexander ^a   Golyshina, Olga V ^b,c   Kaminski, Filip ^b   Khachane, Amit N ^b   Lang, Siegmund ^c   Linke, Burkhard ^a   McHardy, Alice C ^a,e,g   Meyer, Folker ^a   Nechitaylo, Taras ^b,c   Pühler, Alfred ^a   Regenhardt, Daniela ^b,e   Rupp, Oliver ^a   Sabirova, Julia S ^b,c   Selbitschka, Werner ^a   Yakimov, Michail M ^b,d   Timmis, Kenneth N ^b,c   Vorhölter, Frank Jörg ^a   Weidner, Stefan ^a   Kaiser, Olaf ^a   Golyshin, Peter N ^b   more..

^a BIELEFELD UNIVERSITY   (Germany)

^b HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^c TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^d CNR   (Italy)

^e INSTITUTO DE CATÁLISIS Y PETROLEOQUÍMICA   (Spain)

^f IBM T J WATSON RESEARCH CENTER   (United States)

^g INSTITUTE OF ION BEAM PHYSICS AND MATERIALS RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIOFILMS; CARBON; DNA SEQUENCES; HYDROCARBONS; NITROGEN; OILS AND FATS; SUBSTRATES;

BIOFILM FORMATION; BIOSURFACTANTS; OIL-POLLUTED WATERS; OIL-WATER INTERFACE;

GENES;

HYDROCARBON; NITROGEN; OIL; ORGANIC MATTER; SURFACTANT; WATER;

ALCANIVORAX; ARTICLE; BACTERIOPLANKTON; BIOFILM; ECOLOGY; ENERGY; ENVIRONMENTAL FACTOR; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT; OIL SPILL; PRIORITY JOURNAL; STRESS; WATER POLLUTION;

BASE SEQUENCE; BIODEGRADATION, ENVIRONMENTAL; CHROMOSOME MAPPING; GENOME, BACTERIAL; HALOMONADACEAE; HYDROCARBONS; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ALCANIVORAX BORKUMENSIS; BACTERIA (MICROORGANISMS);

EID: 33747043510     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1232     Document Type: Article

References (51)

1. Medina-Bellver, J.I. et al. Evidence for in situ crude oil biodegradation after the Prestige oil spill. Environ. Microbiol. 7, 773-779 (2005).
2. Yakimov, M.M. et al. Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int. J. Syst. Bacteriol. 48, 339-348 (1998).
3. Harayama, S., Kishira, H., Kasai, Y. & Shutsubo, K. Petroleum biodegradation in marine environments. J. Mol. Microbiol. Biotechnol. 1, 63-70 (1999).
4. Kasai, Y., Kishira, H., Syutsubo, K. & Harayama, S. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident. Environ. Microbiol. 3, 246-255 (2001).
5. Hara, A., Syutsubo, K. & Harayama, S. Alcanivorax which prevails in oil-contaminated seawater exhibits broad substrate specificity for alkane degradation. Environ. Microbiol. 5, 746-753 (2003).
6. Yakimov, M.M. et al. Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. Environ. Microbiol. 7, 1426-1441 (2005).
7. Röling, W.F.M. et al. Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil. Appl. Environ. Microbiol. 70, 2603-2613 (2004).
8. Golyshin, P.N. et al. Genome sequence completed of Alcanivorax borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems. J. Biotechnol. 106, 215-220 (2003).
9. Syutsubo, K., Kishira, H. & Harayama, S. Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains. Environ. Microbiol. 3, 371-379 (2001).
10. van Beilen, J.B. et al. Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Environ. Microbiol. 6, 264-273 (2004).
11. Abraham, W.R., Meyer, H. & Yakimov, M. Novel glycine containing glucolipids from the alkane using bacterium Alcanivorax borkumensis. Biochim. Biophys. Acta 1393, 57-62 (1998).
12. Hara, A. et al. Cloning and functional analysis of alkB genes in Alcanivorax borkumensis SK2. Environ. Microbiol. 6, 191-197 (2004).
13. Kok, M. et al. The Pseudomonas oleovorans alkane hydroxylase gene - sequence and expression. J. Biol. Chem. 264, 5435-5441 (1989).
14. van Beilen, J.B. et al. Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology 147, 1621-1630 (2001).
15. van Beilen, J.B., Li, Z., Duetz, W.A., Smits, T.H.M. & Witholt, B. Diversity of alkane hydroxylase systems in the environment. Oil Gas Sci. Technol. 58, 427-440 (2003).
16. Danot, O. A complex signalling module governs the activity of MalT, the prototype of an emerging transactivator family. Proc. Natl. Acad. Sci. USA 98, 435-440 (2001).
17. Smits, T.H.M., Balada, S.B., Withold, B. & van Beilen, J.B. Functional analysis of alkane hydroxylases from Gram-negative and Gram-positive bacteria. J. Bacteriol. 184, 1733-1742 (2002).
18. van Beilen, J.B. et al. Identification of an amino acid position that determines the substrate range of integral membrane alkane hydroxylases. J. Bacteriol. 187, 85-91 (2005).
19. Venter, J.C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74 (2004).
20. Dutta, T.K. & Harayama, S. Biodegradation of n-alkylcycloalkanes and n-alkylbenzenes via new pathways in Alcanivorax sp. strain MBIC 4326. Appl. Environ. Microbiol. 67, 1970-1974 (2001).
21. Sabirova, J.S., Ferrer, M., Regenhardt, D., Timmis, K.N. & Golyshin, P.N. Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization. J. Bacteriol. 188, 3763-3773 (2006).
22. Maier, T., Förster, H.H., Asperger, O. & Hahn, U. Molecular characterization of the 56-kDa CYP153 from Acinetobacter sp. EB104. Biochem. Biophys. Res. Commun. 286, 652-658 (2001).
23. Passeri, A. et al. Marine biosurfactants. 4. Production, characterization and biosynthesis of an anionic glucose lipid from the marine bacterial strain MM1. Appl. Microbiol. Biotechnol. 37, 281-286 (1992).
24. Ochsner, U.A., Fiechter, A. & Reiser, J. Isolation, characterization, and expression in Escherichia coli of the Pseudomonas aeruginosa rhlAB genes encoding a rhamnosyl-transferase involved in rhamnolipid biosurfactant synthesis. J. Biol. Chem. 269, 19787-19795 (1994).
25. Toren, A., Orr, E., Paitan, Y., Ron, E.Z. & Rosenberg, E. The active component of the bioemulsifier alasan from Acinetobacter radioresistens KA53 is an OmpA-like protein. J. Bacteriol. 184, 165-170 (2002).
26. Ron, E.Z. & Rosenberg, E. Natural roles of biosurfactants. Environ. Microbiol. 3, 229-236 (2001).
27. Averhoff, B. & Friedrich, A. Type IV pili-related natural transformation systems: DNA transport in mesophilic and thermophilic bacteria. Arch. Microbiol. 180, 385-393 (2003).
28. Berman, T. & Bronk, D.A. Dissolved organic nitrogen: a dynamic participant in aquatic ecosystems. Aquat. Microb. Ecol. 31, 279-305 (2003).
29. Hou, S. et al. Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc. Natl. Acad. Sci. USA 101, 18036-18041 (2004).
30. Head, I.M., Jones, D.M. & Röling, F.M. Marine microorganisms make a meal of oil. Nat. Rev. Microbiol. 4, 173-182 (2006).
31. Dyksterhouse, S.E., Gray, J.P., Herwig, R.P., Lara, J.C. & Staley, J.T. Cycloclastis pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int. J. Syst. Bacteriol. 45, 116-123 (1995).
32. Yanisch-Perron, C., Vieira, J. & Messing, J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33, 103-119 (1985).
33. Ewing, B., Hillier, L., Wendl, M. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175-185 (1998).
34. Ewing, B. & Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194 (1998).
35. Kaiser, O. et al. Whole genome shotgun sequencing guided by bioinformatics pipelines - an optimized approach for an established technique. J. Biotechnol. 106, 121-133 (2003).
36. Gordon, D., Abajian, C. & Green, P. Consed: A graphical tool for sequence finishing. Genome Res. 8, 195-202 (1998).
37. Gordon, D., Desmarais, C. & Green, P. Automated finishing with Autofinish. Genome Res. 11, 614-625 (2001).
38. Bartels, D. et al. BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics 21, 853-859 (2005).
39. Tauch, A. et al. Strategy to sequence the genome of Corynebacterium glutamicum ATCC 13032: use of a cosmid and a bacterial artificial chromosome library. J. Biotechnol. 95, 25-38 (2002).
40. Meyer, F. et al. GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31, 2187-2195 (2003).
41. McHardy, A.C., Goesmann, A., Pühler, A. & Meyer, F. Development of joint application strategies for two microbial gene finders. Bioinformatics 20, 1622-1631 (2004).
42. Suzek, B.E., Ermolaeva, M.D., Schreiber, M. & Salzberg, S.L. A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics 17, 1123-1130 (2001).
43. 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).
44. Tatusov, R.L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
45. Harris, M.A. et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-D261 (2004).
46. Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
47. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882 (1997).
48. Perrière, G. & Gouy, M. WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364-369 (1996).
49. Kumar, S., Tamura, K., Jakobsen, I.B. & Nei, M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244-1245 (2001).
50. Stover, C.K. et al. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406, 959-964 (2000).
51. Nelson, K.E. et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 4, 799-808 (2002).