The genomes of the non-clearing-zone-forming and natural-rubber-degrading species Gordonia polyisoprenivorans and Gordonia westfalica harbor genes expressing Lcp activity in Streptomyces strains

Applied and Environmental Microbiology

Volumn 74, Issue 8, 2008, Pages 2288-2297

  Bröker, Daniel ^a   Dietz, David ^a   Arenskötter, Matthias ^a   Steinbüchel, Alexander ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GORDONIA POLYISOPRENIVORANS; GORDONIA WESTFALICA HARBOR; STREPTOMYCES STRAINS;

BACTERIA; KETONES; PROTEINS; RUBBER;

GENE EXPRESSION;

ACETIC ACID; ALDEHYDE; BACTERIAL PROTEIN; ISOPRENE; ISOPRENOID; KETONE; OLIGONUCLEOTIDE; POLY(1,4 ISOPRENE); POLYMER; PROTEIN LCP; RUBBER; UNCLASSIFIED DRUG;

BACTERIUM; BIODEGRADATION; GENE EXPRESSION; GENOME; RECOMBINATION; RUBBER;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CARBON SOURCE; CONCENTRATION (PARAMETERS); GEL PERMEATION CHROMATOGRAPHY; GENETIC TRANSCRIPTION; GORDONIA; GORDONIA ALKANIVORANS; GORDONIA POLYISOPRENIVORANS; GORDONIA WESTFALICA; LCP GENE; MICROBIAL DEGRADATION; MOLECULAR WEIGHT; NOCARDIA FARCINICA; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; STREPTOMYCES; STREPTOMYCES COELICOLOR; STREPTOMYCES LIVIDANS;

ACTINOMYCETALES; ANTIBODIES, BACTERIAL; BACTERIAL PROTEINS; CLONING, MOLECULAR; GENE DELETION; GENE EXPRESSION PROFILING; HEMITERPENES; LATEX; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; MUTAGENESIS, INSERTIONAL; RNA, BACTERIAL; RNA, MESSENGER; RUBBER; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; TERPENES;

BACTERIA (MICROORGANISMS); GORDONIA ALKANIVORANS; GORDONIA POLYISOPRENIVORANS; GORDONIA WESTFALICA; NOCARDIA FARCINICA; STREPTOMYCES; STREPTOMYCES COELICOLOR; STREPTOMYCES LIVIDANS; STREPTOMYCES SP.;

EID: 42349083652     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02145-07     Document Type: Article

References (42)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Arenskötter, M., D. Baumeister, M. M. Berekaa, G. Pötter, R. M. Kroppenstedt, A. Linos, and A. Steinbüchel. 2001. Taxonomic characterization of two rubber-degrading bacteria belonging to the species Gordonia polyisoprenivorans and analysis of hypervariable regions of 16S rDNA sequences. FEMS Microbiol. Lett. 205:277-282.
3. Arenskötter, M., D. Baumeister, R. Kalscheuer, and A. Steinbüchel. 2003. Identification and application of plasmids suitable for transfer of foreign DNA to members of the genus Gordonia. Appl. Environ. Microbiol. 69:4971-4974.
4. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1987. Current protocols in molecular biology, vol. 1, 1st ed. John Wiley & Sons, Inc., New York, NY.
5. Banh, Q., M. Arenskötter, and A. Steinbüchel. 2005. Establishment of Tn5096-based transposon mutagenesis in Gordonia polyisoprenivorans. Appl. Environ. Microbiol. 71:5077-5084.
6. Bender, E., K. P. Koller, and J. W. Engels. 1990. Secretory synthesis of human interleukin-2 by Streptomyces lividans. Gene 86:227-232.
7. Bentley, S. D., K. F. Chater, A. M. Cerdeño-Tárraga, G. L. Challis, N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C. H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M. A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill, and D. A. Hopwood. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141-147.
8. Birnboim, H. C., and J. Doly. 1979. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7:1513-1523.
9. Braaz, R., P. Fischer, and D. Jendrossek. 2004. Novel type of heme-dependent oxygenase catalyses oxidative cleavage of rubber poly(cis-1,4-isoprene). Appl. Environ. Microbiol. 70:7388-7395.
10. Braaz, R., W. Armbruster, and D. Jendrossek. 2005. Heme-dependent rubber oxygenase RoxA of Xanthomonas sp. cleaves the carbon backbone of poly(cis-1,4-isoprene) by a dioxygenase mechanism. Appl. Environ. Microbiol. 71:2473-2478.
11. Bradford, M. M. 1976. A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
12. Bröker, D., M. Arenskötter, A. Legatzki, D. H. Nies, and A. Steinbüchel. 2004. Characterization of the 101-kilobase-pair megaplasmid pKB1 isolated from the rubber-degrading bacterium Gordonia westfalica Kb1. J. Bacteriol. 186:212-225.
13. Bullock, W. O., J. M. Fernandez, and J. M. Stuart. 1987. XL1-Blue: a high efficiency plasmid transforming recA Escherichia coli strain with β-galactosidase selection. BioTechniques 5:376-379.
14. Eckhardt, T., J. Strickler, L. Gorniak, W. V. Burnett, and L. R. Fare. 1987. Characterization of the promoter, signal sequence, and amino terminus of a secreted β-galactosidase from "Streptomyces lividans." J. Bacteriol. 169:4249-4256.
15. Emanuelsson, O., S. Brunak, G. von Heijne, and H. Nielsen. 2007. Locating proteins in the cell using TargetP, SignalP, and related tools. Nat. Protoc. 2:953-971.
16. Hjelm, H., K. Hjelm, and J. Sjöquist. 1972. Protein A from Staphylococcus aureus. Its isolation by affinity chromatography and its use as an immunosorbent for isolation of immunoglobulins. FEBS Lett. 28:73-76.
17. Hohn, B. 1979. In vitro packaging of lambda and cosmid DNA. Methods Enzymol. 68:299-309.
18. Hohn, B., and J. Collins. 1980. A small cosmid for efficient cloning of large DNA fragments. Gene 11:291-298.
19. Hopwood, D. A., M. J. Bibb, K. F. Chater, T. Kieser, C. J. Bruton, H. M. Kieser, D. J. Lydiate, C. P. Smith, J. M. Ward, and H. Schrempf. 1985. Genetic manipulation of Streptomyces. A laboratory manual. John Innes Foundation, Norwich, United Kingdom.
20. Ibrahim, E. M. A., M. Arenskötter, H. Luftmann, and A. Steinbüchel. 2006. Identification of poly(cis-1,4-isoprene) degradation intermediates during growth of moderately thermophilic actinomycetes on rubber and cloning of a functional lcp homologue from Nocardia farcinica strain E1. Appl. Environ. Microbiol. 72:3375-3382.
21. Ishikawa, J., A. Yamashita, Y. Mikami, Y. Hoshino, H. Kurita, K. Hotta, T. Shiba, and M. Hattori. 2004. The complete genomic sequence of Nocardia farcinica IFM 10152. Proc. Natl. Acad. Sci. USA 101:14925-14930.
22. Jendrossek, D., G. Tomasi, and R. M. Kroppenstedt. 1997. Bacterial degradation of natural rubber: a privilege of actinomycetes? FEMS Microbiol. Lett. 150:179-188.
23. Jendrossek, D., G. Tomasi, and H. G. Schlegel. 1997. Mikrobiologischer Abbau von Kautschuk. Nachrichten der Akademie der Wissenschaften in Göttingen. II mathematisch-physikalische Klasse. Nr 1. Vandenhoeck and Ruprecht, Göttingen, Germany.
24. Jendrossek, D., and S. Reinhardt. 2003. Sequence analysis of a gene product synthesized by Xanthomonas sp. during growth on natural rubber latex. FEMS Microbiol. Lett. 224:61-65.
25. Kieser, T., M. J. Bipp, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical streptomyces genetics. John Innes Foundation. Norwich, United Kingdom.
26. Kummer, C., P. Schumann, and E. Stackebrandt. 1999. Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil. Int. J. Syst. Bacteriol. 49:1513-1522.
27. Laemmli, U. K. 1970. Cleavage of structural proteins during assembly of the head of bacteriophage T4. Nature 227:680-685.
28. Linos, A., and A. Steinbüchel. 1998. Microbial degradation of natural and synthetic rubbers by novel bacteria belonging to the genus Gordona. Kautsch. Gummi. Kunstst. 51:496-499.
29. Linos, A., A. Steinbüchel, C. Spröer, and R. M. Kroppenstedt. 1999. Gordonia polyisoprenivorans sp. nov., a rubber-degrading actinomycete isolated from automobile tire. Int. J. Syst. Bacteriol. 49:1785-1791.
30. Linos, A., M. M. Berekaa, A. Steinbüchel, K. K. Kim, C. Spröer, and R. M. Kroppenstedt. 2002. Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete. Int. J. Syst. Evol. Microbiol. 52:1133-1139.
31. Mattow, J., U. E. Schaible, F. Schmidt, K. Hagens, F. Siejak, G. Brestrich, G. Haeselbarth, E.-C. Müller, P. R. Jungblut, and S. H. E. Kaufmann. 2003. Comparative proteome analysis of culture supernatant proteins from virulent Mycobacterium tuberculosis H37Rv and attenuated M. bovis BCG Copenhagen. Electrophoresis 24:3405-3420.
32. Mishra, R. N., S. L. Singla-Pareek, S. Nair, S. K. Sopory, and M. K. Reddy. 2002. Directional genome walking using PCR. BioTechniques 33:830-832.
33. Rose, K., K. B. Tenberge, and A. Steinbüchel. 2005. Identification and characterization of genes from Streptomyces sp. strain K30 responsible for clear zone formation on natural rubber latex and poly(cis-1,4-isoprene) rubber degradation. Biomacromolecules 6:180-188.
34. Rose, K., and A. Steinbüchel. 2005. Biodegradation of natural rubber and related compounds: recent insights into a hardly understood catabolic capability of microorganisms. Appl. Environ. Microbiol. 71:2803-2812.
35. Rowland, S. S., J. J. Zulty, M. Sathyamoorthy, B. M. Pogell, and M. K. Speedie. 1992. The effect of signal sequences on the efficiency of secretion of a heterologous phosphotriesterase by Streptomyces lividans. Appl. Microbiol. Biotechnol. 38:94-100.
36. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
37. Sathyamoorthy, M., D. Stemke, and M. K. Speedie. 1996. Native and heterologous protein secretion by Streptomyces lividans. Appl. Microbiol. Biotechnol. 46:347-352.
38. Schlegel, H. G., H. Kaltwasser, and G. Gottschalk. 1961. Ein Submersverfahren zur Kultur wasserstoffoxidierender Bakterien: Wachstumsphysiologische Untersuchungen. Arch. Mikrobiol. 38:209-222.
39. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882.
40. Towbin, H., T. Staehelin, and J. Gordon. 1979. Electrophoretic transfer of proteins from Polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc. Natl. Acad. Sci. USA 76:4350-1354.
41. Tsuchii, A., K. Takeda, and Y. Tokiwa. 1996. Colonization and degradation of rubber pieces by Nocardia sp. Biodegradation 7:41-48.
42. Weber, K., and M. Osborn. 1969. The reliability of molecular weight determinations by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. J. Biol. Chem. 244:4406-4412.