Molecular screening for alkane hydroxylase genes in Gram-negative and Gram-positive strains

Environmental Microbiology

Volumn 1, Issue 4, 1999, Pages 307-317

  Smits, Theo H M ^a   Röthlisberger, Martina ^a   Witholt, Bernard ^a   Van Beilen, Jan B ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ACINETOBACTER; ACINETOBACTER CALCOACETICUS; ACINETOBACTER SP.; ESCHERICHIA COLI; NEGIBACTERIA; POSIBACTERIA; PSEUDOMONAS; PSEUDOMONAS OLEOVORANS; PSEUDOMONAS PUTIDA;

ALKANE; ALKANE 1 MONOOXYGENASE; BACTERIAL DNA; CYTOCHROME P450; MIXED FUNCTION OXIDASE; PRIMER DNA; RIBOSOME DNA; RNA 16S;

ACINETOBACTER CALCOACETICUS; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; CHEMISTRY; DNA SEQUENCE; ENZYMOLOGY; GENETICS; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PSEUDOMONAS PUTIDA; RNA GENE; SEQUENCE ALIGNMENT; SOUTHERN BLOTTING;

ACINETOBACTER CALCOACETICUS; ALKANE 1-MONOOXYGENASE; ALKANES; AMINO ACID SEQUENCE; BASE SEQUENCE; BLOTTING, SOUTHERN; CLONING, MOLECULAR; CYTOCHROME P-450 ENZYME SYSTEM; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, BACTERIAL; GENES, RRNA; GRAM-NEGATIVE BACTERIA; GRAM-POSITIVE BACTERIA; MIXED FUNCTION OXYGENASES; MOLECULAR SEQUENCE DATA; PSEUDOMONAS PUTIDA; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 0033171433     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.1999.00037.x     Document Type: Article

References (60)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Bagdasarian, M., Lurz, R., Ruckert, B., Franklin, F.C.H., Bagdasarian, M.M., Frey, J., and Timmis, K.N. (1981) Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors for gene cloning in Pseudomonas. Gene 16: 237-247.
3. van Beilen, J.B., Penninga, D., and Witholt, B. (1992) Topology of the membrane-bound alkane hydroxylase of Pseudomonas oleovorans. J Biol Chem 267: 9194-9201.
4. van Beilen, J.B., Wubbolts, M.G., and Witholt, B. (1994a) Genetics of alkane oxidation by Pseudomonas oleovorans. Biodegradation 5: 161-174.
5. van Beilen, J.B., Kingma, J., and Witholt, B. (1994b) Substrate specificity of the Pseudomonas oleovorans alkane hydroxylase. Enzyme Microbiol Techol 16: 161-174.
6. van Beilen, J.B., Veenhoff, L., and Witholt, B. (1998) Alkane hydroxylase systems in Pseudomonas aeruginosa strains able to grow on n-octane. In New Frontiers in Screening for Microbial Biocatalysts. Kieslich, K., van der Beek, C.P., de Bont, J.A.M., and van den Tweel, W.J.J. (eds). Amsterdam: Elsevier Science, pp. 211-215.
7. Birnboim, H.C., and Doly, J. (1979). A rapid alkaline extraction procedure for screening of recombinant plasmid DNA. Nucleic Acids Res 7: 1513-1523.
8. Bolivar, F., Rodriguez, R.L., Greene, P.J., Betlach, H.L., Heynecker, M.C., and Boyer, H.W. (1977) Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene 2: 95-113.
9. Cardini, G., and Jurtshuk, P. (1968) Cytochrome P-450 involvement in the oxidation of n-octane by cell-free extracts of Corynebacterium sp. strain 7E1C. J Biol Chem 243: 6070-6072.
10. Clifford, K.H., Phillips, G.T., and Marx, A.F. (1991) 6 August 1991: United States patent no. US 5037759.
11. Desomer, J., Crespi, M., and Van Montagu, M. (1991) Illegitimate integration of non-replicative vectors in the genome of Rhodococcus fascians upon electrotransformation as an insertional mutagenesis system. Mol Microbiol 5: 2115-2124.
12. Don, R.H., and Pemberton, J.M. (1981) Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutrophus. J Bacteriol 145: 681-686.
13. Dower, W.J., Miller, J.F., and Ragsdale, C.W. (1988) High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res 16: 6127-6145.
14. Eggink, G., van Lelyveld, P.M., Arnberg, A., Arfman, N., Witteveen, C., and Witholt, B. (1987a) Structure of the Pseudomonas putida alkBAC operon. Identification of transcription and translation products. J Biol Chem 262: 6400-6406.
15. Eggink, G., Lageveen, R.G., Altenburg, B., and Witholt, B. (1987b) Controlled and functional expression of Pseudomonas oleovorans alkane utilizing system in Pseudomonas putida and Escherichia coli. J Biol Chem 262: 17712-17718.
16. Fewson, C.A. (1967) The growth and metabolic versatility of the Gram-negative bacterium NCIB 8250 ('Vibrio 01'). J Gen Microbiol 46: 255-266.
17. Fu, H., Newcomb, M., and Wong, C.H. (1991) Pseudomonas oleovorans monooxygenase catalyzed asymmetric epoxidation of allyl alcohol derivatives and hydroxylation of a hypersensitive radical probe with the radical ring opening state exceeding the oxygen rebound state. J Am Chem Soc 113: 5878-5880.
18. Furuhashi, K. (1992) Biological routes to optically active epoxides. In Chirality in Industry. Collins, A.N., Sheldrake, G.N., and Crosby, J. (eds). London: John Wiley & Sons, pp. 167-186.
19. Guerra-Santos, L.H., Käppeli, O., and Fiechter, A. (1986) Dependence of Pseudomonas aeruginosa continuous culture biosurfactant production on nutritional and environmental factors. Appl Microbiol Biotechnol 24: 443-448.
20. Hauben, L., Vauterin, L., Swings, J., and Moore, E.R.B. (1997) Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int J Syst Bacteriol 47: 328-335.
21. Higgins, D.G., and Sharp, P.M. (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73: 237-244.
22. Holloway, B.W. (1969) Genetics of Pseudomonas. Bacteriol Rev 33: 419-443.
23. Hou, C.T., Jackson, M.A., Bagby, M.O., and Becker, L.A. (1994) Microbial oxidation of cumene by octane-grown cells. Appl Microbiol Biotechnol 41: 178-182.
24. Hunger, M.S., Kishan, R.V., and Hillen, W. (1990) Analysis and nucleotide sequence of an origin of DNA replication in Acinetobacter calcoaceticus and its use for Escherichia coli shuttle plasmids. Gene 87: 45-51.
25. Innis, M.A., Gelfand, D.H., Sninsky, J.J., and White, T.J. (1990) PCR Protocols: A Guide to Methods and Applications. San Diego: Academic Press.
26. Juni, E., and Janik, A. (1969). Transformation of Acinetobacter calcoaceticus (Bacterium anitratum). J Bacteriol 98: 281-288.
27. Karlson, U., Dwyer, D.F., Hooper, S.W., Moore, E.R.B., Timmis, K.N., and Eltis, L.D. (1993) Two independently regulated cytochromes P-450 in a Rhodococcus rhodochrous strain that degrades 2-ethoxyphenol and 4-methoxybenzoate. J Bacteriol 175: 1467-1474.
28. Kiener, A. (1992) Enzymatic oxidation of methyl groups on aromatic heterocycles: a versatile method for the preparation of heteroaromatic carboxylic acids. Angew Chem Int Edn England 31: 774-775.
29. Kleber, H.-P., Claus, R., and Asperger, O. (1983) Enzymology der n-alkanoxidation bei Acinetobacter. Acta Biotechnol 3: 251-260.
30. Kok, M. (1988) Alkane utilization by Pseudomonas oleovorans. PhD Thesis: University of Groningen, Groningen.
31. Kok, M., Oldenhuis, R., van der Linden, M.P.G., Meulenberg, C.H.C., Kingma, J., and Witholt, B. (1989a) The Pseudomonas oleovorans alkBAC operon encodes two structurally related rubredoxins and an aldehyde dehydrogenase. J Biol Chem 264: 5442-5451.
32. Kok, M., Oldenhuis, R., van der Linden, M.P.G., Raatjes, P., Kingma, J., van Lelyveld, P.M., and Witholt, B. (1989b) The Pseudomonas oleovorans alkane hydroxylase gene. Sequence and expression. J Biol Chem 264: 5435-5441.
33. Lageveen, R.G., Huisman, G.W., Preusting, H., Ketelaar, P.E.F., Eggink, G., and Witholt, B. (1988) Formation of polyester by Pseudomonas oleovorans: the effect of substrate on the formation and composition of poly-(R)-3-hydroxyalkanoates and poly-(R)-3-hydroxyalkenoates. Appl Environ Microbiol 54: 2924-2932.
34. Lee, M., and Chandler, A.C. (1941) A study of the nature, growth and control of bacteria in cutting compounds. J Bacteriol 41: 373-386.
35. Lee, N.R., Hwang, M.O., Jung, G.H., Kim, Y.S., and Min, K.H. (1996) Physical structure and expression of alkBA encoding alkane hydroxylase and rubredoxin reductase from Pseudomonas maltophilia. Biochem Biophys Res Common 218: 17-21.
36. Maeng, J.H., Sakai, Y., Ishige, T., Tani, Y., and Kato, N. (1996) Diversity of dioxygenases that catalyze the first step of oxidation of long-chain n-alkanes in Acinetobacter sp M-1. FEMS Microbiol Lett 141: 177-182.
37. Maniatis, T., Fritsch, E.H., and Sambrook, J. (1982) Molecular Cloning, a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
38. McKenna, E.J., and Coon, M.J. (1970) Enzymatic ω-oxidation. IV. Purification and properties of the ω-hydroxylase of Pseudomonas oleovorans. J Biol Chem 245: 3882-3889.
39. Müller, R., Asperger, O., and Kleber, H.-P. (1989) Purification of cytochrome P-450 from n-hexadecane-grown Acinetobacter calcoaceticus. Biomed Biochim Acta 48: 243-254.
40. Palleroni, N.J., Kunisawa, R., Contopoulou, R., and Douderoff, M. (1973) Nucleic acid homologies in the genus Pseudomonas. Int J Syst Bacteriol 23: 333-339.
41. Palmen, R., Vosman, B., Buijsman, P., Breek, C.K., and Hellingwerf, K.J. (1993) Physiological characterization of natural transformation in Acinetobacter calcoaceticus. J Gen Microbiol 139: 295-305.
42. Parche, S., Geiβdörfer, W., and Hillen, W. (1997) Identification and characterization of xcpR encoding a subunit of the general secretory pathway necessary for dodecane degradation in Acinetobacter calcoaceticus ADP1. J Bacteriol 179: 4631-4634.
43. Peterson, J.A., and Coon, M.J. (1968) Enzymatic ω-oxidation. III. Purification and properties of rubredoxin, a component of the ω-hydroxylation system of Pseudomonas oleovorans. J Biol Chem 243: 329-334.
44. Philipp, W.J., Poulet, S., Eiglmeier, K., Pascopella, L., Balasubramanian, V., Heym, B., et al. (1996) An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae. Proc Natl Acad Sci USA 93: 3132-3137.
45. Phillips, G.T., Robertson, B.W., Bertola, M.A., Koger, H.S., Marx, A.F., and Watts, P.O. (1990) 11 September, 1990: United States patent no. US 4956284.
46. Ratajczak, A., Geiβdörfer, W., and Hillen, W. (1998a) Alkane hydroxylase from Acinetobacter sp. strain ADP1 is encoded by alkM and belongs to a new family of bacterial integral-membrane hydrocarbon hydroxylases. Appl Environ Microbiol 64: 1175-1179.
47. Ratajczak, A., Geiβdörfer, W., and Hillen, W. (1998b) Expression of alkane hydroxylase from Acinetobacter sp. strain ADP1 is induced by a broad range of n-alkanes and requires the transcriptional activator AlkR. J Bacteriol 180: 5822-5827.
48. Rheinwald, J.G., Chakrabarty, A.M., and Gunsalus, I.C. (1973) A transmissible plasmid controlling camphor oxidation in Pseudomonas putida. Proc Natl Acad Sci USA 70: 885-889.
49. Schorcht, S. (1998) Mikrobiologische und molekularbiologische Charakterisierung alkanabbauender Bakteriengemeinschaften. PhD Thesis: Universität Bremen, Bremen.
50. Schwartz, R.D., and McCoy, C.J. (1973) Pseudomonas oleovorans hydroxylation-epoxidation system: additional strain improvements. Appl Microbiol 26: 217-218.
51. Shanklin, J., Whittle, E., and Fox, B.G. (1994) Eight histidine residues are catalytically essential in a membrane-associated iron enzyme, stearoyl-CoA desaturase, and are conserved in alkane hydroxylase and xylene monooxygenase. Biochemistry 33: 12787-12794.
52. Sotsky, J.B., Greer, C.W., and Atlas, R.M. (1994) Frequency of genes in aromatic and aliphatic hydrocarbon biodegradation pathways within bacterial populations from Alaskan sediments. Can J Microbiol 40: 981-985.
53. Stanier, R.Y., Palleroni, N.J., and Doudoroff, M. (1966) The aerobic Pseudomonads: a taxonomic study. J Gen Microbiol 43: 159-271.
54. Stutz, E.W., Défago, G., and Kern, H. (1986) Naturally occurring fluorescent Pseudomonads involved in suppression of black root rot of Tobacco. Phytopathology 76:181-185.
55. Suzuki, M., Hayakawa, T., Shaw, J.P., Rekik, M., and Harayama, S. (1991) Primary structure of xylene monooxygenase: similarities to and differences from the alkane hydroxylation system. J Bacteriol 173: 1690-1695.
56. Thysse, G.J.E., and van der Linden, A.C. (1958) N-alkane oxidation by a Pseudomonas. Studies on the intermediate metabolism. Anton Leeuwenhoek 24: 298-308.
57. Ueda, T., and Coon, M.J. (1972a). Enzymatic ω-oxidation. VII. Reduced diphosphopyridine nucleotide-rubredoxin reductase: properties and function as an electron carrier in ω-hydroxylation. J Biol Chem 247: 5010-5016.
58. Ueda, T., Lode, E.T., and Coon, M.J. (1972b) Enzymatic ω-oxidation. VI. Isolation of homogeneous reduced diphosphopyridine nucleotide-rubredoxin reductase. J Biol Chem 247: 2109-2116.
59. Wilbur, W.J., and Lipman, D.J. (1983) Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci USA 80: 726-730.
60. Yanish-Perron, C., Vieira, J., and Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33: 103-119.