Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes

The EMBL accession numbers for the sequences reported in this paper are AJ245436 [P. putida (oleovorans) GPo1 alk gene clusters and flanking DNA], AJ233397 (P. putida P1 alk gene clusters and flanking DNA), AJ249793 (P. putida P1 nahKJ genes), AJ249825 [P. putida (oleovorans) GPo1 16S RNA gene] and AJ271219 (P. putida P1 16S RNA gene).

References

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410 [CrossRef]
   [Google Scholar]
2. Bachmann B. others 1987; Derivations and genotypes of some mutant derivatives of Escherichia coli K-12. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology pp 1190–1219 Edited by Neidhardt F. C. Washington, DC: American Society for Microbiology;
   [Google Scholar]
3. Baptist J. N., Gholson R. K., Coon M. J. 1963; Hydrocarbon oxidation by a bacterial enzyme system: I. Products of octane oxidation. Biochim Biophys Acta 69:40–47 [CrossRef]
   [Google Scholar]
4. van Beilen J. B. 1994 Alkane oxidation by Pseudomonas oleovorans: genes and proteins. PhD thesis, University of Groningen;
   [Google Scholar]
5. van Beilen J. B., Eggink G., Enequist H., Bos R., Witholt B. 1992a; DNA sequence determination and functional characterization of the OCT-plasmid-encoded alkJKL genes of Pseudomonas oleovorans . Mol Microbiol 6:3121–3136 [CrossRef]
   [Google Scholar]
6. van Beilen J. B., Penninga D., Witholt B. 1992b; Topology of the membrane-bound alkane hydroxylase of Pseudomonas oleovorans. . J Biol Chem 267:9194–9201
   [Google Scholar]
7. van Beilen J. B., Wubbolts M. G., Witholt B. 1994; Genetics of alkane oxidation by Pseudomonas oleovorans. . Biodegradation 5:161–174 [CrossRef]
   [Google Scholar]
8. Benson S., Fennewald M., Shapiro J., Huettner C. 1977; Fractionation of inducible alkane hydroxylase activity in Pseudomonas putida and characterization of hydroxylase-negative plasmid mutations. J Bacteriol 132:614–621
   [Google Scholar]
9. Bustamante C., Gurrieri S., Smith S. B. 1993; Towards a molecular description of pulsed-field gel electrophoresis. Trends Biotechnol 11:23–30 [CrossRef]
   [Google Scholar]
10. Canosa I., Yuste L., Rojo F. 1999; Role of the alternative sigma factor σ^s in the expression of the AlkS regulator of the Pseudomonas oleovorans alkane degradation pathway. J Bacteriol 181:1748–1754
    [Google Scholar]
11. Canosa I., Sanchez-Romero J. M., Yuste L., Rojo F. 2000; A positive feedback mechanism controls expression of AlkS, the transcriptional regulator of the Pseudomonas oleovorans alkane degradation pathway. Mol Microbiol 35:791–799 [CrossRef]
    [Google Scholar]
12. Chakrabarty A. M., Chou G., Gunsalus I. C. 1973; Genetic regulation of octane dissimulation plasmid in Pseudomonas. . Proc Natl Acad Sci USA 70:1137–1140 [CrossRef]
    [Google Scholar]
13. Collado-Vides J., Magasanik B., Gralla J. D. 1991; Control site location and transcriptional regulation in Escherichia coli. . Microbiol Rev 55:371–394
    [Google Scholar]
14. Dower W. J., Miller J. F., Ragsdale C. W. 1988; High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res 16:6127 [CrossRef]
    [Google Scholar]
15. Eggink G., Lageveen R. G., Altenburg B., Witholt B. 1987a; Controlled and functional expression of Pseudomonas oleovorans alkane utilizing system in Pseudomonas putida and Escherichia coli. . J Biol Chem 262:17712–17718
    [Google Scholar]
16. Eggink G., Arnberg A., Arfman N., Witteveen C., Witholt B., van Lelyveld P. H. 1987b; Structure of the Pseudomonas putida alkBAC operon. Identification of transcription and translation products. J Biol Chem 262:6400–6406
    [Google Scholar]
17. Eggink G., Engel H., Vriend G., Terpstra P., Witholt B. 1990; Rubredoxin reductase of Pseudomonas oleovorans . Structural relationship to other flavoprotein oxidoreductases based on one NAD and two FAD fingerprints. J Mol Biol 212:135–142 [CrossRef]
    [Google Scholar]
18. Fennewald M., Shapiro J. 1977; Regulatory mutations of the Pseudomonas plasmid alk regulon. J Bacteriol 132:622–627
    [Google Scholar]
19. Fennewald M., Prevatt W., Meyer R., Shapiro J. 1978; Isolation of Inc P-2 plasmid DNA from Pseudomonas aeruginosa. . Plasmid 1:164–173 [CrossRef]
    [Google Scholar]
20. Fennewald M., Benson S., Oppici M., Shapiro J. 1979; Insertion element analysis and mapping of the Pseudomonas plasmid alk regulon. J Bacteriol 139:940–952
    [Google Scholar]
21. Fournier P., Paulus F., Otten L. 1993; IS 870 requires a 5′-CTAG-3′ target sequence to generate the stop-codon for its large ORF1. J Bacteriol 175:3151–3160
    [Google Scholar]
22. Grimm A. C., Harwood C. S. 1999; NahY, a catabolic plasmid-encoded receptor required for chemotaxis of Pseudomonas putida to the aromatic hydrocarbon naphthalene. J Bacteriol 181:3310–3316
    [Google Scholar]
23. Grund A., Shapiro J., Fennewald M., Bacha P., Leahy J., Markbreiter K., Nieder M., Toepfer M. 1975; Regulation of alkane oxidation in Pseudomonas putida. . J Bacteriol 123:546–556
    [Google Scholar]
24. Hanekamp T., Kobayashi D., Hayes S., Stayton M. M. 1997; Avirulence gene D of Pseudomonas syringae pv. tomato may have undergone horizontal gene transfer. FEBS Lett 415:40–44 [CrossRef]
    [Google Scholar]
25. Hauben L., Vauterin L., Swings J., Moore E. R. B. 1997; Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int J Syst Bacteriol 47:328–335 [CrossRef]
    [Google Scholar]
26. Henikoff S. 1984; Unidirectional digestion with exonuclease-III creates targeted breakpoints for DNA sequencing. Gene 28:351–359 [CrossRef]
    [Google Scholar]
27. Innis M. A., Gelfand D. H., Sninsky J. J., White T. J. 1990 PCR Protocols. A Guide to Methods and Applications San Diego: Academic Press;
    [Google Scholar]
28. Kado C. I., Liu S.-T. 1981; Rapid procedure for detection and isolation of large and small plasmids. J Bacteriol 145:1365–1373
    [Google Scholar]
29. Kleckner N. 1981; Transposable elements in prokaryotes. Annu Rev Genet 15:341–404 [CrossRef]
    [Google Scholar]
30. Kok M., Oldenhuis R., Meulenberg C. H. C., Kingma J., Witholt B., van der Linden M. P. G. 1989a; The Pseudomonas oleovorans alkBAC operon encodes two structurally related rubredoxins and an aldehyde dehydrogenase. J Biol Chem 264:5442–5451
    [Google Scholar]
31. Kok M., Oldenhuis R., Raatjes P., Kingma J., van Lelyveld P. H., Witholt B., van der Linden M. P. G. 1989b; The Pseudomonas oleovorans alkane hydroxylase gene. Sequence and expression. J Biol Chem 264:5435–5441
    [Google Scholar]
32. Lageveen R. G., Huisman G. W., Preusting H., Ketelaar P. E. F., Eggink G., 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
    [Google Scholar]
33. Lee M., Chandler A. C. 1941; A study of the nature, growth and control of bacteria in cutting compounds. J Bacteriol 41:373–386
    [Google Scholar]
34. Luria S. E., Adam J. N., Teng R. C. 1960; Transduction of lactose utilizing ability among strains of Escherichia coli and Shigella dysenteriae and the properties of the transducing phage particle. Virology 12:348–390 [CrossRef]
    [Google Scholar]
35. Mahillon J., Chandler M. 1998; Insertion sequences. Microbiol Mol Biol Rev 62:725–774
    [Google Scholar]
36. Nozaki M. 1970; Metapyrocatechase. Methods Enzymol 17:522–525
    [Google Scholar]
37. Owen D. J. 1986; Molecular cloning and characterization of sequences from the regulatory cluster of the Pseudomonas plasmid alk system. Mol Gen Genet 203:64–72 [CrossRef]
    [Google Scholar]
38. Panke S., Kaiser A., Witholt B., Wubbolts M. G., de Lorenzo V. 1999a; Engineering of a stable whole-cell biocatalyst capable of ( S )-styrene oxide formation for continuous two-liquid phase applications. Appl Environ Microbiol 65:5619–5623
    [Google Scholar]
39. Panke S., Meyer A., Huber C. M., Witholt B., Wubbolts M. G. 1999b; An alkane-responsive expression system for the production of fine chemicals. Appl Environ Microbiol 65:2324–2332
    [Google Scholar]
40. Rakin A., Heesemann J. 1995; Virulence-associated fyuA / irp2 gene cluster of Yersinia enterocolitica biotype 1B carries a novel insertion sequence IS 1328. . FEMS Microbiol Lett 129:287–292
    [Google Scholar]
41. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual , 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
42. Schwartz R. D. 1973; Octene epoxidation by a cold-stable alkane-oxidizing isolate of Pseudomonas oleovorans. . Appl Microbiol 25:574–577
    [Google Scholar]
43. Schwartz R. D., McCoy C. J. 1973; Pseudomonas oleovorans hydroxylation-epoxidation system: additional strain improvements. Appl Microbiol 26:217–218
    [Google Scholar]
44. Smits T. H. M., Witholt B., Röthlisberger M., van Beilen J. B. 1999; Molecular screening for alkane hydroxylase genes in Gram-negative and Gram-positive strains. Environ Microbiol 1:307–318 [CrossRef]
    [Google Scholar]
45. Stanier R. Y., Palleroni N. J., Doudoroff M. 1966; The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43:159–271 [CrossRef]
    [Google Scholar]
46. Taguchi K., Fukutomi H., Kuroda A., Kato J., Ohtake H. 1997; Genetic identification of chemotactic transducers for amino acids in Pseudomonas aeruginosa. . Microbiology 143:3223–3229 [CrossRef]
    [Google Scholar]
47. Tan H.-M. 1999; Bacterial catabolic transposons. Appl Microbiol Biotechnol 51:1–12 [CrossRef]
    [Google Scholar]
48. Witholt B., Kingma J., Kok M., Lageveen R. G., Eggink G., de Smet M. J., van Beilen J. B. 1990; Bioconversions of aliphatic compounds by Pseudomonas oleovorans in multiphase bioreactors: background and economic potential. Trends Biotechnol 8:46–52 [CrossRef]
    [Google Scholar]