1887

Abstract

The Gram-positive actinobacterium 1CP is able to utilize several (chloro)aromatic compounds as sole carbon sources, and gene clusters for various catabolic enzymes and pathways have previously been identified. Pulsed-field gel electrophoresis indicates the occurrence of a 740 kb megaplasmid, designated p1CP. Linear topology and the presence of covalently bound proteins were shown by the unchanged electrophoretic mobility after S1 nuclease treatment and by the immobility of the native plasmid during non-denaturing agarose gel electrophoresis, respectively. Sequence comparisons of both termini revealed a perfect 13 bp terminal inverted repeat (TIR) as part of an imperfect 583/587 bp TIR, as well as two copies of the highly conserved centre (GCTXCGC) of a palindromic motif. An initial restriction analysis of p1CP was performed. By means of PCR and hybridization techniques, p1CP was screened for several genes encoding enzymes of (chloro)aromatic degradation. A single maleylacetate reductase gene , the gene cluster for 4-chloro-/3,5-dichlorocatechol degradation, and the gene cluster for 3-chlorocatechol degradation were found on p1CP whereas the and gene clusters for the catechol and the protocatechuate pathways, respectively, were not. Prolonged cultivation of the wild-type strain 1CP under non-selective conditions led to the isolation of the - and -deficient mutants 1CP.01 and 1CP.02 harbouring the shortened plasmid variants p1CP.01 (500 kb) and p1CP.02 (400 kb).

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.27217-0
2004-09-01
2019-11-22
Loading full text...

Full text loading...

/deliver/fulltext/micro/150/9/mic1503075.html?itemId=/content/journal/micro/10.1099/mic.0.27217-0&mimeType=html&fmt=ahah

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. 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.[CrossRef]
    [Google Scholar]
  3. Barton, B. M., Harding, G. P. & Zuccarelli, A. J. ( 1995; ). A general method for detecting and sizing large plasmids. Anal Biochem 226, 235–240.[CrossRef]
    [Google Scholar]
  4. Bauer, J. ( 2002; ). Klonierung und Sequenzierung der peripheren Benzoat-Abbaugene aus Rhodococcus opacus 1CP und Untersuchungen zu ihrer Substratspezifität. Senior project thesis, Technische Universität Bergakademie Freiberg.
  5. Bey, S. J., Tsou, M. F., Huang, C. H., Yang, C. C. & Chen, C. W. ( 2000; ). The homologous terminal sequence of the Streptomyces lividans chromosome and SLP2 plasmid. Microbiology 146, 911–922.
    [Google Scholar]
  6. Cain, R. B. ( 1981; ). Regulation of aromatic and hydroaromatic catabolic pathways in nocardioform actinomycetes. Zentbl Bakteriol Mikrobiol Hyg Abt 1 Suppl 11, 335–354.
    [Google Scholar]
  7. Chen, C. W. ( 1996; ). Complications and implications of linear bacterial chromosomes. Trends Genet 12, 192–196.[CrossRef]
    [Google Scholar]
  8. Chen, C. W., Yu, T. W., Lin, Y. S., Kieser, H. M. & Hopwood, D. A. ( 1993; ). The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule. Mol Microbiol 7, 925–932.[CrossRef]
    [Google Scholar]
  9. Chu, G., Vollrath, D. & Davis, R. W. ( 1986; ). Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science 234, 1582–1585.[CrossRef]
    [Google Scholar]
  10. Dabrock, B., Kesseler, M., Averhoff, B. & Gottschalk, G. ( 1994; ). Identification and characterization of a transmissible linear plasmid from Rhodococcus erythropolis BD2 that encodes isopropylbenzene and trichloroethene catabolism. Appl Environ Microbiol 60, 853–860.
    [Google Scholar]
  11. Don, R. H. & Pemberton, J. M. ( 1985; ). Genetic and physical map of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pJP4. J Bacteriol 161, 466–468.
    [Google Scholar]
  12. Dorn, E., Hellwig, M., Reineke, W. & Knackmuss, H. J. ( 1974; ). Isolation and characterization of a 3-chlorobenzoate degrading pseudomonad. Arch Microbiol 99, 61–70.[CrossRef]
    [Google Scholar]
  13. Doten, R. C., Ngai, K. L., Mitchell, D. J. & Ornston, L. N. ( 1987; ). Cloning and genetic organization of the pca gene cluster from Acinetobacter calcoaceticus. J Bacteriol 169, 3168–3174.
    [Google Scholar]
  14. Dugan, I. N. & Golovlev, E. L. ( 1983; ). Induction of dioxygenases for aromatic substrates in rhodococci under nutrient limitation. Microbiology (English translation of Mikrobiologiya) 52, 751–755.
    [Google Scholar]
  15. Eulberg, D. ( 1997; ). Genetik von Wegen des Aromatenabbaus durch Rhodococcus opacus 1CP – Konvergente Evolution des Chlorbrenzkatechin-Katabolismus. PhD thesis, Universität Stuttgart.
  16. Eulberg, D., Golovleva, L. A. & Schlömann, M. ( 1997; ). Characterization of catechol catabolic genes from Rhodococcus erythropolis 1CP. J Bacteriol 179, 370–381.
    [Google Scholar]
  17. Eulberg, D., Kourbatova, E. M., Golovleva, L. A. & Schlömann, M. ( 1998a; ). Evolutionary relationship between chlorocatechol catabolic enzymes from Rhodococcus opacus 1CP and their counterparts in Proteobacteria: sequence divergence and functional convergence. J Bacteriol 180, 1082–1094.
    [Google Scholar]
  18. Eulberg, D., Lakner, S., Golovleva, L. A. & Schlömann, M. ( 1998b; ). Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus 1CP: evidence for a merged enzyme with 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity. J Bacteriol 180, 1072–1081.
    [Google Scholar]
  19. Eulberg, D., Seibert, V. & Schlömann, M. ( 1998c; ). A linear megaplasmid, p1CP, carrying the chlorocatechol catabolic genes from Rhodococcus opacus 1CP. Biospektrum special edn, p. 125, poster PF214.
  20. Finnerty, W. R. ( 1992; ). The biology and genetics of the genus Rhodococcus. Annu Rev Microbiol 46, 193–218.[CrossRef]
    [Google Scholar]
  21. Frantz, B. & Chakrabarty, A. M. ( 1987; ). Organization and nucleotide sequence determination of a gene cluster involved in 3-chlorocatechol degradation. Proc Natl Acad Sci U S A 84, 4460–4464.[CrossRef]
    [Google Scholar]
  22. Ghosal, D., You, I. S., Chatterjee, D. K. & Chakrabarty, A. M. ( 1985; ). Genes specifying degradation of 3-chlorobenzoic acid in plasmids pAC27 and pJP4. Proc Natl Acad Sci U S A 82, 1638–1642.[CrossRef]
    [Google Scholar]
  23. Golovlev, E. L. ( 1995; ). Ecological physiology of rhodococci. In Abstract Book of European Environmental Research Organization Workshop: Enzymatic and Genetic Aspects of Environmental Biotechnology, p. 18. Pushchino, Russia: European Environmental Research Organization.
  24. Gorlatov, S. N., Maltseva, O. V., Shevchenko, V. I. & Golovleva, L. A. ( 1989; ). Degradation of chlorophenols by Rhodococcus erythropolis. Microbiology (English translation of Mikrobiologiya) 58, 647–651.
    [Google Scholar]
  25. Hirochika, H., Nakamura, K. & Sakaguchi, K. ( 1984; ). A linear DNA plasmid from Streptomyces rochei with an inverted terminal repetition of 614 base pairs. EMBO J 3, 761–766.
    [Google Scholar]
  26. Holloway, B. W., Römling, U. & Tümmler, B. ( 1994; ). Genomic mapping of Pseudomonas aeruginosa PAO. Microbiology 140, 2907–2929.[CrossRef]
    [Google Scholar]
  27. Huang, C.-H., Lin, Y.-S., Yang, Y.-L., Huang, S.-W. & Chen, C. W. ( 1998; ). The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol Microbiol 28, 905–916.[CrossRef]
    [Google Scholar]
  28. Kalkus, J., Reh, M. & Schlegel, H. G. ( 1990; ). Hydrogen autotrophy of Nocardia opaca strains is encoded by linear megaplasmids. J Gen Microbiol 136, 1145–1151.[CrossRef]
    [Google Scholar]
  29. Kalkus, J., Dörrie, C., Fischer, D., Reh, M. & Schlegel, H. G. ( 1993; ). The giant linear plasmid pHG207 from Rhodococcus sp. encoding hydrogen autotrophy: characterization of the plasmid and its termini. J Gen Microbiol 139, 2055–2065.[CrossRef]
    [Google Scholar]
  30. Kalkus, J., Menne, R., Reh, M. & Schlegel, H. G. ( 1998; ). The terminal structures of linear plasmids from Rhodococcus opacus. Microbiology 144, 1271–1279.[CrossRef]
    [Google Scholar]
  31. Kesseler, M., Dabbs, E. R., Averhoff, B. & Gottschalk, G. ( 1996; ). Studies on the isopropylbenzene 2,3-dioxygenase and the 3-isopropylcatechol 2,3-dioxygenase genes encoded by the linear plasmid of Rhodococcus erythropolis BD2. Microbiology 142, 3241–3251.[CrossRef]
    [Google Scholar]
  32. Köiv, V., Marits, R. & Heinaru, A. ( 1996; ). Sequence analysis of the 2,4-dichlorophenol hydroxylase gene tfdB and 3,5-dichlorocatechol 1,2-dioxygenase gene tfdC of 2,4-dichlorophenoxyacetic acid degrading plasmid pEST4011. Gene 174, 293–297.[CrossRef]
    [Google Scholar]
  33. Koronelli, T. V., Dermicheva, S. G. & Korotaeva, E. V. ( 1988; ). Survival of hydrocarbon-oxidizing bacteria under complete starvation conditions. Mikrobiologiya 57, 298–304.
    [Google Scholar]
  34. Kosono, S., Maeda, M., Fuji, F., Arai, H. & Kudo, T. ( 1997; ). Three of the seven bphC genes of Rhodococcus erythropolis TA421, isolated from a termite ecosystem, are located on an indigenous plasmid associated with biphenyl degradation. Appl Environ Microbiol 63, 3282–3285.
    [Google Scholar]
  35. Krauß, U. ( 2002; ). Überexpression der 5-Chlormuconolacton-Dehalogenase. Ein Enzym eines neuen modifizierten ortho-Abbauweges von 2-Chlorphenol des Stammes Rhodococcus opacus 1CP. Senior project thesis, Technische Universität Bergakademie Freiberg.
  36. Lin, Y. S., Kieser, H. M., Hopwood, D. A. & Chen, C. W. ( 1993; ). The chromosomal DNA of Streptomyces lividans 66 is linear. Mol Microbiol 10, 923–933.[CrossRef]
    [Google Scholar]
  37. Mae, A. A., Marits, R. O., Ausmees, N. R., Koiv, V. M. & Heinaru, A. L. ( 1993; ). Characterization of a new 2,4-dichlorophenoxyacetic acid degrading plasmid pEST4011: physical map and localization of catabolic genes. J Gen Microbiol 139, 3165–3170.[CrossRef]
    [Google Scholar]
  38. Maes, T., Vereecke, D., Ritsema, T., Cornelis, K., Thu, H. N., Van Montagu, M., Holsters, M. & Goethals, K. ( 2001; ). The att locus of Rhodococcus fascians strain D188 is essential for full virulence on tobacco through the production of an autoregulatory compound. Mol Microbiol 42, 13–28.
    [Google Scholar]
  39. Masai, E., Sugiyama, K., Iwashita, N., Shimizu, S., Hauschild, J. E., Hatta, T., Kimbara, K., Yano, K. & Fukuda, M. ( 1997; ). The bphDEF meta-cleavage pathway genes involved in biphenyl/polychlorinated biphenyl degradation are located on a linear plasmid and separated from the initial bphACB genes in Rhodococcus sp. strain RHA1. Gene 187, 141–149.[CrossRef]
    [Google Scholar]
  40. Moiseeva, O. V., Lin'ko, E. V., Baskunov, B. P. & Golovleva, L. A. ( 1999; ). Degradation of 2-chlorophenol and 3-chlorobenzoate by Rhodococcus opacus 1CP. Microbiology (English translation of Mikrobiologiya) 68, 400–405.
    [Google Scholar]
  41. Moiseeva, O. V., Belova, O. V., Solyanikova, I. P., Schlömann, M. & Golovleva, L. A. ( 2001; ). Enzymes of a new modified ortho-pathway utilizing 2-chlorophenol in Rhodococcus opacus 1CP. Biochemistry (English translation of Biokhimiya) 66, 548–555.
    [Google Scholar]
  42. Moiseeva, O. V., Solyanikova, I. P., Kaschabek, S. R., Gröning, J., Thiel, M., Golovleva, L. A. & Schlömann, M. ( 2002; ). A new modified ortho-cleavage pathway of 3-chlorocatechol degradation by Rhodococcus opacus 1CP: genetic and biochemical evidence. J Bacteriol 184, 5282–5292.[CrossRef]
    [Google Scholar]
  43. Pandza, S., Biukovic, G., Paravic, A., Dadbin, A., Cullum, J. & Hranueli, D. ( 1998; ). Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exchange of ends. Mol Microbiol 28, 1165–1176.[CrossRef]
    [Google Scholar]
  44. Perkins, E. J., Gordon, M. P., Caceres, O. & Lurquin, P. F. ( 1990; ). Organization and sequence analysis of the 2,4-dichlorophenol hydroxylase and dichlorocatechol oxidative operons of plasmid pJP4. J Bacteriol 172, 2351–2359.
    [Google Scholar]
  45. Picardeau, M. & Vincent, V. ( 1998; ). Mycobacterial linear plasmids have an invertron-like structure related to other linear replicons in actinomycetes. Microbiology 144, 1981–1988.[CrossRef]
    [Google Scholar]
  46. Qin, Z. & Cohen, S. N. ( 1998; ). Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol Microbiol 28, 893–903.[CrossRef]
    [Google Scholar]
  47. Redenbach, M. & Altenbuchner, J. ( 2002; ). Why do some bacteria have linear chromosomes and plasmids? Biospektrum 8, 158–163.
    [Google Scholar]
  48. Robertson, J. G. & Batt, R. D. ( 1973; ). Survival of Nocardia corallina and degradation of constituents during starvation. J Gen Microbiol 78, 109–117.[CrossRef]
    [Google Scholar]
  49. Saeki, H., Akira, M., Furuhashi, K., Averhoff, B. & Gottschalk, G. ( 1999; ). Degradation of trichloroethene by a linear-plasmid-encoded alkene monooxygenase in Rhodococcus corallinus (Nocardia corallina) B-276. Microbiology 145, 1721–1730.[CrossRef]
    [Google Scholar]
  50. Sakaguchi, K. ( 1990; ). Invertrons, a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and genomes of adeno-type viruses. Microbiol Rev 54, 66–74.
    [Google Scholar]
  51. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 2001; ). Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  52. Sauret-Ignazi, G., Gagnon, J., Beguin, C., Barrelle, M., Markowicz, Y., Pelmont, J. & Toussaint, A. ( 1996; ). Characterisation of a chromosomally encoded catechol 1,2-dioxygenase (E.C. 1.13.11.1) from Alcaligenes eutrophus CH34. Arch Microbiol 166, 42–50.[CrossRef]
    [Google Scholar]
  53. Seibert, V., Kourbatova, E. M., Golovleva, L. A. & Schlömann, M. ( 1998; ). Characterization of the maleylacetate reductase MacA of Rhodococcus opacus 1CP and evidence for the presence of an isofunctional enzyme. J Bacteriol 180, 3503–3508.
    [Google Scholar]
  54. Shimizu, S., Kobayashi, H., Masai, E. & Fukuda, M. ( 2001; ). Characterization of the 450-kb linear plasmid in a polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl Environ Microbiol 67, 2021–2028.[CrossRef]
    [Google Scholar]
  55. Solyanikova, I. P., Maltseva, O. V., Vollmer, M. D., Golovleva, L. A. & Schlömann, M. ( 1995; ). Characterization of muconate and chloromuconate cycloisomerase from Rhodococcus erythropolis 1CP: indications for functionally convergent evolution among bacterial cycloisomerases. J Bacteriol 177, 2821–2826.
    [Google Scholar]
  56. Stecker, C., Johann, A., Herzberg, C., Averhoff, B. & Gottschalk, G. ( 2003; ). Complete nucleotide sequence and genetic organization of the 210-kilobase linear plasmid of Rhodococcus erythropolis BD2. J Bacteriol 185, 5269–5274.[CrossRef]
    [Google Scholar]
  57. van der Meer, J. R., Eggen, R. I., Zehnder, A. J. & de Vos, W. M. ( 1991a; ). Sequence analysis of the Pseudomonas sp. strain P51 tcb gene cluster, which encodes metabolism of chlorinated catechols: evidence for specialization of catechol 1,2-dioxygenases for chlorinated substrates. J Bacteriol 173, 2425–2434.
    [Google Scholar]
  58. van der Meer, J. R., van Neerven, A. R. W., De Vries, E. J., De Vos, W. M. & Zehnder, A. J. B. ( 1991b; ). Cloning and characterization of plasmid-encoded genes for the degradation of 1,2-dichloro-, 1,4-dichloro-, and 1,2,4-trichlorobenzene of Pseudomonas sp. strain P51. J Bacteriol 173, 6–15.
    [Google Scholar]
  59. van der Meer, J. R., Ravatn, R. & Sentchilo, V. ( 2001; ). The clc element of Pseudomonas sp. strain B13 and other mobile degradative elements employing phage-like integrases. Arch Microbiol 175, 79–85.[CrossRef]
    [Google Scholar]
  60. Warhurst, A. M. & Fewson, C. A. ( 1994; ). Biotransformations catalyzed by the genus Rhodococcus. Crit Rev Biotechnol 14, 29–73.[CrossRef]
    [Google Scholar]
  61. Wu, X. & Roy, K. L. ( 1993; ). Complete nucleotide sequence of a linear plasmid from Streptomyces clavuligerus and characterization of its RNA transcripts. J Bacteriol 175, 37–52.
    [Google Scholar]
  62. Zylstra, G. J., Olsen, R. H. & Ballou, D. P. ( 1989; ). Genetic organization and sequence of the Pseudomonas cepacia genes for the alpha and beta subunits of protocatechuate 3,4-dioxygenase. J Bacteriol 171, 5915–5921.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.27217-0
Loading
/content/journal/micro/10.1099/mic.0.27217-0
Loading

Data & Media loading...

Supplements

vol. , part 9, pp. 3075 - 3087

Sequence alignment(PDF file) of p1CP-J and p1CP-S.



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