1887

Abstract

The carbazole-degradative plasmid pCAR1 carries the class II transposon Tn, which contains the and genes, essential for conversion of carbazole into anthranilate, and anthranilate into catechol, respectively. In our previous study, DNA rearrangements in pCAR1 were frequently detected in the host Pf0-1 in the presence of carbazole, resulting in the improvement of host survivability. Several Pf0-1 mutants harbouring pCAR1 were isolated, and deletion of DNA in the plasmid gene was found. Here, we compared genome sequences of the parent strain Pf0-1L(pCAR1 : : ) and one of its mutants, 5EP83, to assess whether other DNA rearrangements occurred in either the plasmid or the host chromosome. We found transposition of Tn into the 5EP83 chromosome. In addition, IS had transposed into the gene intergenic region on the pCAR1-derivative plasmid of 5EP83, which inhibited transcription. As a result of these transpositions, 5EP83 was able to metabolize carbazole due to the Tn on its chromosome, although the genes on its plasmid were non-functional. We also found that one copy of duplicate genes had been deleted, and that IS had transposed into both the host chromosome and the plasmid. Our findings suggest that Pf0-1 harbouring pCAR1 is subjected to DNA rearrangements not only on the plasmid but also on its chromosome in the presence of carbazole.

Funding
This study was supported by the:
  • Ministry of Education, Culture, Sports, Science and Technology (Award S0801025)
  • RIKEN
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.053280-0
2011-12-01
2024-10-03
Loading full text...

Full text loading...

/deliver/fulltext/micro/157/12/3405.html?itemId=/content/journal/micro/10.1099/mic.0.053280-0&mimeType=html&fmt=ahah

References

  1. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. (editors) ( 1990). Current Protocols in Molecular Biology New York: Wiley;
    [Google Scholar]
  2. Bagdasarian M., Lurz R., Rückert B., Franklin F. C., Bagdasarian M. M., Frey J., Timmis K. N. ( 1981). Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. Gene 16:237–247 [View Article][PubMed]
    [Google Scholar]
  3. Barrick J. E., Yu D. S., Yoon S. H., Jeong H., Oh T. K., Schneider D., Lenski R. E., Kim J. F. ( 2009). Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461:1243–1247 [View Article][PubMed]
    [Google Scholar]
  4. Chen K., Wallis J. W., McLellan M. D., Larson D. E., Kalicki J. M., Pohl C. S., McGrath S. D., Wendl M. C., Zhang Q. et al. ( 2009). BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6:677–681 [View Article][PubMed]
    [Google Scholar]
  5. Compeau G., Al-Achi B. J., Platsouka E., Levy S. B. ( 1988). Survival of rifampin-resistant mutants of Pseudomonas fluorescens and Pseudomonas putida in soil systems. Appl Environ Microbiol 54:2432–2438[PubMed]
    [Google Scholar]
  6. Grindley N. D. F. ( 2002). The movement of Tn3-like elements: transposition and cointegrate resolution. Mobile DNA II272–302 Craig L. N. et al. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  7. Harwood C. S., Parales R. E. ( 1996). The β-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50:553–590 [View Article][PubMed]
    [Google Scholar]
  8. Kivistik P. A., Kivisaar M., Hõrak R. ( 2007). Target site selection of Pseudomonas putida transposon Tn4652. J Bacteriol 189:3918–3921 [View Article][PubMed]
    [Google Scholar]
  9. Klockgether J., Munder A., Neugebauer J., Davenport C. F., Stanke F., Larbig K. D., Heeb S., Schöck U., Pohl T. M. et al. ( 2010). Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains. J Bacteriol 192:1113–1121 [View Article][PubMed]
    [Google Scholar]
  10. Kouzuma A., Endoh T., Omori T., Nojiri H., Yamane H., Habe H. ( 2008). Transcription factors CysB and SfnR constitute the hierarchical regulatory system for the sulfate starvation response in Pseudomonas putida. J Bacteriol 190:4521–4531 [View Article][PubMed]
    [Google Scholar]
  11. Kovach M. E., Elzer P. H., Hill D. S., Robertson G. T., Farris M. A., Roop R. M. II, Peterson K. M. ( 1995). Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175–176 [View Article][PubMed]
    [Google Scholar]
  12. Li H., Durbin R. ( 2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760 [View Article][PubMed]
    [Google Scholar]
  13. Maeda K., Nojiri H., Shintani M., Yoshida T., Habe H., Omori T. ( 2003). Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676. J Mol Biol 326:21–33 [View Article][PubMed]
    [Google Scholar]
  14. Mahillon J., Chandler M. ( 1998). Insertion sequences. Microbiol Mol Biol Rev 62:725–774[PubMed]
    [Google Scholar]
  15. Miller J. R., Koren S., Sutton G. ( 2010). Assembly algorithms for next-generation sequencing data. Genomics 95:315–327 [View Article][PubMed]
    [Google Scholar]
  16. Nelson K. E., Weinel C., Paulsen I. T., Dodson R. J., Hilbert H., Martins dos Santos V. A., Fouts D. E., Gill S. R., Pop M. et al. ( 2002). Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4:799–808 [View Article][PubMed]
    [Google Scholar]
  17. Nojiri H., Sekiguchi H., Maeda K., Urata M., Nakai S., Yoshida T., Habe H., Omori T. ( 2001). Genetic characterization and evolutionary implications of a car gene cluster in the carbazole degrader Pseudomonas sp. strain CA10. J Bacteriol 183:3663–3679 [View Article][PubMed]
    [Google Scholar]
  18. Rist M., Kertesz M. A. ( 1998). Construction of improved plasmid vectors for promoter characterization in Pseudomonas aeruginosa and other Gram-negative bacteria. FEMS Microbiol Lett 169:179–183 [View Article][PubMed]
    [Google Scholar]
  19. Robinson J. T., Thorvaldsdóttir H., Winckler W., Guttman M., Lander E. S., Getz G., Mesirov J. P. ( 2011). Integrative genomics viewer. Nat Biotechnol 29:24–26 [View Article][PubMed]
    [Google Scholar]
  20. Sambrook J., Russell D. W. ( 2001). Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  21. Sato S. I., Nam J. W., Kasuga K., Nojiri H., Yamane H., Omori T. ( 1997). Identification and characterization of genes encoding carbazole 1,9a-dioxygenase in Pseudomonas sp. strain CA10. J Bacteriol 179:4850–4858[PubMed]
    [Google Scholar]
  22. Shintani M., Habe H., Tsuda M., Omori T., Yamane H., Nojiri H. ( 2005a). Recipient range of IncP-7 conjugative plasmid pCAR2 from Pseudomonas putida HS01 is broader than from other Pseudomonas strains. Biotechnol Lett 27:1847–1853 [View Article][PubMed]
    [Google Scholar]
  23. Shintani M., Yoshida T., Habe H., Omori T., Nojiri H. ( 2005b). Large plasmid pCAR2 and class II transposon Tn4676 are functional mobile genetic elements to distribute the carbazole/dioxin-degradative car gene cluster in different bacteria. Appl Microbiol Biotechnol 67:370–382 [View Article][PubMed]
    [Google Scholar]
  24. Shintani M., Yano H., Habe H., Omori T., Yamane H., Tsuda M., Nojiri H. ( 2006). Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin degradation. Appl Environ Microbiol 72:3206–3216 [View Article][PubMed]
    [Google Scholar]
  25. Shintani M., Fukushima N., Tezuka M., Yamane H., Nojiri H. ( 2008a). Conjugative transfer of the IncP-7 carbazole degradative plasmid, pCAR1, in river water samples. Biotechnol Lett 30:117–122 [View Article][PubMed]
    [Google Scholar]
  26. Shintani M., Matsui K., Takemura T., Yamane H., Nojiri H. ( 2008b). Behavior of the IncP-7 carbazole-degradative plasmid pCAR1 in artificial environmental samples. Appl Microbiol Biotechnol 80:485–497 [View Article][PubMed]
    [Google Scholar]
  27. Shintani M., Takahashi Y., Yamane H., Nojiri H. ( 2010a). The behavior and significance of degradative plasmids belonging to Inc groups in Pseudomonas within natural environments and microcosms. Microbes Environ 25:253–265 [View Article][PubMed]
    [Google Scholar]
  28. Shintani M., Yamane H., Nojiri H. ( 2010b). Behavior of various hosts of the IncP-7 carbazole-degradative plasmid pCAR1 in artificial microcosms. Biosci Biotechnol Biochem 74:343–349 [View Article][PubMed]
    [Google Scholar]
  29. Shintani M., Horisaki T., Yamane H., Ohkuma M., Nojiri H. ( 2011). Evolution of the IncP-7 carbazole-degradative plasmid pCAR1 improves survival of its host Pseudomonas fluorescens Pf0-1 in artificial water microcosms. Microbiology 157:2276–2286 [View Article][PubMed]
    [Google Scholar]
  30. Silby M. W., Cerdeño-Tárraga A. M., Vernikos G. S., Giddens S. R., Jackson R. W., Preston G. M., Zhang X. X., Moon C. D., Gehrig S. M. et al. ( 2009). Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol 10:R51 [View Article][PubMed]
    [Google Scholar]
  31. Simon R., Priefer U., Pühler A. ( 1983). A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram-negative bacteria. Biotechnology 1:784–791 [View Article]
    [Google Scholar]
  32. Sukchawalit R., Vattanaviboon P., Sallabhan R., Mongkolsuk S. ( 1999). Construction and characterization of regulated l-arabinose-inducible broad host range expression vectors in Xanthomonas. FEMS Microbiol Lett 181:217–223[PubMed]
    [Google Scholar]
  33. Takahashi Y., Shintani M., Li L., Yamane H., Nojiri H. ( 2009a). Carbazole-degradative IncP-7 plasmid pCAR1.2 is structurally unstable in Pseudomonas fluorescens Pf0-1, which accumulates catechol, the intermediate of the carbazole degradation pathway. Appl Environ Microbiol 75:3920–3929 [View Article][PubMed]
    [Google Scholar]
  34. Takahashi Y., Shintani M., Yamane H., Nojiri H. ( 2009b). The complete nucleotide sequence of pCAR2: pCAR2 and pCAR1 were structurally identical IncP-7 carbazole degradative plasmids. Biosci Biotechnol Biochem 73:744–746 [View Article][PubMed]
    [Google Scholar]
  35. Urata M., Miyakoshi M., Kai S., Maeda K., Habe H., Omori T., Yamane H., Nojiri H. ( 2004). Transcriptional regulation of the ant operon, encoding two-component anthranilate 1,2-dioxygenase, on the carbazole-degradative plasmid pCAR1 of Pseudomonas resinovorans strain CA10. J Bacteriol 186:6815–6823 [View Article][PubMed]
    [Google Scholar]
  36. Yano H., Garruto C. E., Sota M., Ohtsubo Y., Nagata Y., Zylstra G. J., Williams P. A., Tsuda M. ( 2007). Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elements. J Mol Biol 369:11–26 [View Article][PubMed]
    [Google Scholar]
  37. Yano H., Miyakoshi M., Ohshima K., Tabata M., Nagata Y., Hattori M., Tsuda M. ( 2010). Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids. J Bacteriol 192:4337–4347 [View Article][PubMed]
    [Google Scholar]
  38. Yun C. S., Suzuki C., Naito K., Takeda T., Takahashi Y., Sai F., Terabayashi T., Miyakoshi M., Shintani M. et al. ( 2010). Pmr, a histone-like protein H1 (H-NS) family protein encoded by the IncP-7 plasmid pCAR1, is a key global regulator that alters host function. J Bacteriol 192:4720–4731 [View Article][PubMed]
    [Google Scholar]
/content/journal/micro/10.1099/mic.0.053280-0
Loading
/content/journal/micro/10.1099/mic.0.053280-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF

Supplementary material 3

PDF

Supplementary material 4

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error