Global features of the Alcanivorax borkumensis SK2 genome

Environmental Microbiology

Volumn 10, Issue 3, 2008, Pages 614-625

  Reva, Oleg N ^a,c   Hallin, Peter F ^b   Willenbrock, Hanni ^b   Sicheritz Ponten, Thomas ^b   Tümmler, Burkhard ^a   Ussery, David W ^b  

^a HANNOVER MEDICAL SCHOOL   (Germany)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; OLIGONUCLEOTIDE;

ALCANIVORAXACEAE; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; PHYSIOLOGY;

ALCANIVORACEAE; CHROMOSOMES, BACTERIAL; DNA, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; OLIGONUCLEOTIDES; SEQUENCE ANALYSIS, DNA;

ACINETOBACTER; ALCANIVORAX; ALCANIVORAX BORKUMENSIS; GAMMAPROTEOBACTERIA; PSEUDOMONADALES; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS PUTIDA; YERSINIA;

EID: 38549083567     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2007.01483.x     Document Type: Article

References (47)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 : 3389 3402.
2. Baldi, P. Baisnee, P.F. (2000) Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics 16 : 865 889.
3. van Beilen, J.B., Panke, S., Lucchini, S., Franchini, A.G., Rothlisberger, M. Witholt, B. (2001) Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology 147 : 1621 1630.
4. van Beilen, J.B., Marin, M.M., Smits, T.H.M., Röthlisberger, M., Franchini, A.G., Witholt, B. Rojo, F. (2004) Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Environ Microbiol 6 : 264 273.
5. Brukner, I., Sanchez, R., Suck, D. Pongor, S. (1995) Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J 14 : 1812 1818.
6. Chen, X.-H., Koumoutsi, A., Scholz, R., Eisenreich, A., Schneider, K., Schneider, I., et al. (2007) Comparative analysis of the complete genome sequence of the plant growth promoting Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25 : 1007 1014.
7. Dlakic, M., Ussery, D. Brunak, S. (2004) DNA bendability and nucleosome positioning in transcriptional regulation. In DNA Conformation and Transcription. Ohyama, T. (ed.). Austin, TX : Landes Bioscience, pp. 198 211.
8. Dobrindt, U., Hochhut, B., Hentschel, U. Hacker, J. (2004) Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2 : 414 424.
9. Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309 : 1242 1245.
10. Golyshin, P.N., Martins Dos Santos, V.A., Kaiser, O., Ferrer, M., Sabirova, Y.S., Lunsdorf, H., et al. (2003) 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.
11. Hara, A., Syutsubo, K. Harayama, S. (2003) Alcanivorax which prevails in oil-contaminated seawater exhibits broad substrate specificity for alkane degradation. Environ Microbiol 5 : 746 753.
12. Hara, A., Baik, S.H., Syutsubo, K., Misawa, N., Smits, T.H., van Beilen, J.B. Harayama, S. (2004) Cloning and functional analysis of alkB genes in Alcanivorax borkumensis SK2. Environ Microbiol 6 : 191 197.
13. Harayama, S., Kishira, H., Kasai, Y. Shutsubo, K. (1999) Petroteum biodegradation in marine environments. J Mol Microbiol Biotechnol 1 : 63 70.
14. Jensen, L.J., Friis, C. Ussery, D.W. (1999) Three views of microbial genomes. Res Microbiol 150 : 773 777.
15. Kasai, Y., Kishira, H., Sasaki, I., Syutsubo, K., Watanabe, K. Harama, S. (2002) Prodominant growth of Alcanivorax strains in oil-contaminated and nutrient-supplemented sea water. Environ Microbiol 4 : 141 147.
16. Kasai, Y., Kishira, H., Syutsubo, K. Harayama, S. (2001) Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-accident. Environ Microbiol 3 : 246 255.
17. Klockgether, J., Würdemann, D., Reva, O., Wiehlmann, L. Tümmler, B. (2007) Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa. J Bacteriol 189 : 2443 2459.
18. Luiten, R.G., Putterman, D.G., Schoenmakers, J.G., Konings, R.N. Day, L.A. (1985) Nucleotide sequence of the genome of Pf3, an IncP-1 plasmid-specific filamentous bacteriophage of Pseudomonas aeruginosa. J Virol 56 : 268 276.
19. McKew, B.A., Coulon, F., Osborn, A.M., Timmis, K.N. McGenity, T.J. (2007a) Determining the identity and roles of oil-metabolizing marine bacteria from the Thames estuary, UK. Environ Microbiol 9 : 165 176.
20. McKew, B.A., Coulon, F., Yakimov, M.M., Denaro, R., Genovese, M., Smith, C.J., et al. (2007b) Efficacy of intervention strategies for bioremediation of crude oil in marine systems and effects on indigenous hydrocarbonoclastic bacteria. Environ Microbiol 9 : 1562 1571.
21. Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Martins dos Santos, V.A., et al. (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4 : 799 808.
22. Ornstein, R., Rein, R., Breen, D. MacElroy, R. (1978) An optimized potential function for the calculation of nucleic acid interaction energies. Biopolymers 17 : 2341 2360.
23. Pedersen, A.G., Jensen, L.J., Brunak, S., Staerfeldt, H.H. Ussery, D.W. (2000) A DNA structural atlas for Escherichia coli. J Mol Biol 299 : 907 930.
24. Pride, D.T., Meinersmann, R.J., Wassenaar, T.M. Blaser, M.J. (2003) Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 13 : 145 158.
25. Reva, O.N. Tümmler, B. (2004) Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. BMC Bioinformatics 5 : 90.
26. Reva, O.N. Tümmler, B. (2005) Differentiation of regions with atypical oligonucleotide composition in bacterial genomes. BMC Bioinformatics 6 : 251.
27. Röling, W.F., Milner, M.G., Jones, D.M., Lee, K., Daniel, F., Swannell, R.J., et al. (2002) Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient - enhanced oil spill bioremediation. Appl Environ Microbiol 68 : 5537 5548.
28. Sabirova, J.S., Ferrer, M., Regenhardt, D., Timmis, K.N. Golyshin, P.N. (2006) Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization. J Bacteriol 188 : 3763 3773.
29. Saitou, N. Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 : 406 425.
30. Satchwell, S.C., Drew, H.R. Travers, A.A. (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191 : 659 675.
31. Schneiker, S., Martins dos Santos, V.A., Bartels, D., Bekel, T., Brecht, M., Buhrmester, J., et al. (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24 : 997 1004.
32. Sharp, P.M. Li, W.H. (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res 14 : 7737 7749.
33. Shpigelman, E.S., Trifonov, E.N. Bolshoy, A. (1993) CURVATURE: software for the analysis of curved DNA. Comput Appl Biosci 9 : 435 440.
34. Sicheritz-Ponten, T. Andersson, S.G. (2001) A phylogenomic approach to microbial evolution. Nucleic Acids Res 29 : 545 552.
35. Skovgaard, M., Jensen, L.J., Friis, C., Stærfeldt, H.H., Worning, P., Brunak, S. Ussery, D.W. (2002) The atlas visualisation of genome-wide information. In Methods in Microbiology. Wren, B. Dorrell, N. (eds). London, UK : Academic Press, pp. 49 63.
36. Smits, T.H., Balada, S.B., Witholt, B. van Beilen, J.B. (2002) Functional analysis of alkane hydroxylases from gram-negative and gram-positive bacteria. J Bacteriol 184 : 1733 1742.
37. Spangenberg, C., Fislage, R., Römling, U. Tümmler, B. (1997) Disrespectful type IV pilins. Mol Microbiol 25 : 203 204.
38. Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406 : 959 964.
39. Syutsubo, K., Kishira, H. Harayama, S. (2001) Development of specific oliogonucleotide probes for the identification and in situ defection of hydrocarbon - degrading Alcanivorax strains. Environ Microbiol 3 : 371 379.
40. Teeling, H., Meyerdierks, A., Bauer, M., Amann, R. Glockner, F.O. (2004) Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 6 : 938 947.
41. Ussery, D., Soumpasis, D.M., Brunak, S., Staerfeldt, H.H., Worning, P. Krogh, A. (2002) Bias of purine stretches in sequenced chromosomes. Comput Chem 26 : 531 541.
42. Wang, H., Noordewier, M. Benham, C.J. (2004) Stress-Induced DNA Duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters. Genome Res 14 : 1575 1584.
43. Weinel, C., Nelson, K.E. Tümmler, B. (2002) Global features of the Pseudomonas putida KT2440 genome sequence. Environ Microbiol 4 : 809 818.
44. Willenbrock, H. Ussery, D.W. (2007) Prediction of highly expressed genes in microbes based on chromatin accessibility. BMC Mol Biol 8 : 11.
45. Willenbrock, H., Friis, C., Juncker, A.S. Ussery, D.W. (2006) An environmental signature for 323 microbial genomes based on codon adaptation indices. Genome Biol 7 : R114.
46. Worning, P., Jensen, L.J., Hallin, P.F., Staerfeldt, H.H. Ussery, D.W. (2006) Origin of replication in circular prokaryotic chromosomes. Environ Microbiol 8 : 353 361.
47. Yakimov, M.M., Golyshin, P.N., Lang, S., Moore, E.R., Abraham, W.R., Lunsdorf, H. Timmis, K.N. (1998) Alcanivorax borkumensis General nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int J Syst Bacteriol 48 : 339 348.