1887

Microbiology Society logo

Volume 147, Issue 8

Molecular characterization of a deletion/duplication rearrangement in genes from JMP134(pJP4) that improves growth on 3-chlorobenzoic acid but abolishes growth on 2,4-dichlorophenoxyacetic acid

The GenBank accession numbers for the 3115 nt HI-F and 2833 nt RI-F fragments of pJP4 and the 4037 nt RI-E′ fragment of pJP4-F3 are AF225972, AF225973 and AF225974, respectively.

Free

Abstract

JMP134(pJP4) is able to grow on minimal media containing the pollutants 3-chlorobenzoate (3-CB) or 2,4-dichlorophenoxyacetate (2,4-D). genes from the 88 kb plasmid pJP4 encode enzymes involved in the degradation of these compounds. During growth of strain JMP134 in liquid medium containing 3-CB, a derivative strain harbouring a ∼∼95 kb plasmid was isolated. This derivative, designated JMP134(pJP4-F3), had an improved ability to grow on 3-CB, but had lost the ability to grow on 2,4-D. Sequence analysis of pJP4-F3 indicated that the plasmid had undergone a deletion of ∼∼16 kb, which included the intergenic region, spanning the gene to a previously unreported IS element. The loss of the gene explains the failure of the derivative to grow on 2,4-D. A ∼∼23 kb duplication of the region spanning - - --ISJP4-- - , giving rise to a 51-kb-long inverted repeat, was also observed. The increase in gene copy number for the () gene cluster may provide an explanation for the derivative strain’s improved growth on 3-CB. These observations are additional examples of the metabolic plasticity of JMP134, one of the more versatile pollutant-degrading bacteria.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): 2,4-D, 2,4-dichlorophenoxyacetate , 3-CB, 3-chlorobenzoate , catabolic plasmid , chloroaromatics , chlorocatechol pathway and IS1071 insertion sequence
© Microbiology Society
Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-147-8-2141
2001-08-01
2024-04-30
Loading full text...

Full text loading...

/deliver/fulltext/micro/147/8/1472141a.html?itemId=/content/journal/micro/10.1099/00221287-147-8-2141&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 1992 Short Protocols in Molecular Biology , 2nd edn. New York: Greene Publishing Associates;
     [Google Scholar]
  2. Bradford M. M. 1976; A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein–dye binding. Anal Biochem 72:248–254 [CrossRef]
     [Google Scholar]
  3. Brown N. L., Ford S. J., Pridmore R. D., Fritzinger D. C. 1983; Nucleotide sequence of a gene from the Pseudomonas transposon Tn 501 encoding mercuric reductase. Biochemistry 22:4089–4095 [CrossRef]
     [Google Scholar]
  4. Bullock W. O., Fernandez J. M., Short J. M. 1987; XL1-Blue: a high efficiency plasmid transforming rec A Escherichia coli strain with beta-galactosidase selection. BioTechniques 5:376–379
     [Google Scholar]
  5. Burlage R. S., Bemis L. A., Layton A. C., Sayler G. S., Larimer F. 1990; Comparative genetic organization of incompatibility group P degradative plasmids. J Bacteriol 172:6818–6825
     [Google Scholar]
  6. Clément P., Matus V., Cárdenas L., González B. 1995; Degradation of trichlorophenols by Alcaligenes eutrophus JMP134. FEMS Microbiol Lett 127:51–55 [CrossRef]
     [Google Scholar]
  7. Clément P., Springael D., González B. 2000; Deletions of mob and tra pJP4 transfer functions after mating of Ralstonia eutropha JMP134 (pJP4) with Escherichia coli harboring F′:: Tn 10 . Can J Microbiol 46:485–489 [CrossRef]
     [Google Scholar]
  8. Don R. H., Pemberton J. 1981; Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and A. eutrophus. J Bacteriol 145:681–686
     [Google Scholar]
  9. Don R. H., Pemberton J. 1985; Genetic and physical map of the 2,4-dichlorophenoxyacetic acid degradative plasmid pJP4. J Bacteriol 161:466–468
     [Google Scholar]
  10. Fukumuri F., Hausinger R. P. 1993; Alcaligenes eutrophus JMP134 ‘‘2,4-dichlorophenoxyacetate monooxygenase’’ is an α-ketoglutarate-dependent dioxygenase. J Bacteriol 175:2083–2086
     [Google Scholar]
  11. Ghosal D., You I.-S. 1988; Gene duplication in haloaromatic degradative plasmids pJP4 and pJP2. Can J Microbiol 34:709–715 [CrossRef]
     [Google Scholar]
  12. 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 USA 82:1638–1642 [CrossRef]
     [Google Scholar]
  13. Holben W. E., Schroeter B. M., Calabrese V. G. M., Olsen R. H., Kukor J. K., Biederbeck V. O., Smith A. E., Tiedje J. M. 1992; Gene probe analysis of soil microbial populations selected by amendment with 2,4-dichlorophenoxyacetic acid. Appl Environ Microbiol 58:3941–3948
     [Google Scholar]
  14. 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]
  15. Klemba M., Jakobs B., Wittich R.-M., Pieper D. H. 2000; Chromosomal integration of tcb chlorocatechol degradation pathway genes as a means of expanding the growth substrate range of bacteria to include haloaromatics. Appl Environ Microbiol 66:3255–3261 [CrossRef]
     [Google Scholar]
  16. Kröckel L., Focht D. 1987; Construction of chlorobenzene-utilizing recombinants by progenitive manifestation of a rare event. Appl Environ Microbiol 53:2470–2475
     [Google Scholar]
  17. Laemmli C. M., Leveau J. H., Zehnder A. J. B., van der Meer J. R. 2000; Characterization of a second tfd gene cluster for chlorophenol and chlorocatechol metabolism on plasmid pJP4 in Ralstonia eutropha JMP134 (pJP4). J Bacteriol 182:4165–4172 [CrossRef]
     [Google Scholar]
  18. Leveau J. H. J., van der Meer J. R. 1996; The tfd R gene product can successfully take over the role of the insertion element-inactivated TfdT protein as a transcriptional activator of the tfd CDEF gene cluster, which encodes chlorocatechol degradation in Ralstonia eutropha JMP134. J Bacteriol 178:6824–6832
     [Google Scholar]
  19. Leveau J. H. J., Konig F., Fuchslin H., Werlen C., van der Meer J. R. 1999; Dynamics of multigene expression during catabolic adaptation of Ralstonia eutropha JMP134 (pJP4) to the herbicide 2,4-dichlorophenoxyacetate. Mol Microbiol 33:396–406 [CrossRef]
     [Google Scholar]
  20. Matrubutham U., Harker A. R. 1994; Analysis of duplicated gene sequences associated with tfd R and tfd S in Alcaligenes eutrophus JMP134. J Bacteriol 176:2348–2353
     [Google Scholar]
  21. Nakatsu C., Ng J., Singh R., Straus N., Wyndham R. C. 1991; Chlorobenzoate catabolic transposon Tn 5271 is a composite class I element with flanking class II insertion sequences. Proc Natl Acad Sci USA 88:8312–8316 [CrossRef]
     [Google Scholar]
  22. Peel M. C., Wyndham R. C. 1999; Selection of clc, cba , and fcb chlorobenzoate-catabolic genotypes from groundwater and surface waters adjacent to the Hyde park, Niagara Falls, chemical landfill. Appl Environ Microbiol 65:1627–1635
     [Google Scholar]
  23. Pérez-Pantoja D., Guzmán L., Manzano M., Pieper D. H., González B. 2000; Role of tfd CIDIEIFI and tfd DIICIIEIIFII gene modules in catabolism of 3-chlorobenzoate by Ralstonia eutropha JMP134 (pJP4). Appl Environ Microbiol 66:1602–1608 [CrossRef]
     [Google Scholar]
  24. Perkins E. J., Gordon M. P., Cáceres O., Lurquin P. F. 1990; Organization and sequence analysis of the 2,4-dichlorophenol hydroxylase and dichlorocatechol oxidative operons of plasmid pJP4. J Bacteriol 172:2352–2359
     [Google Scholar]
  25. Pieper D. H., Reineke W., Engesser K. H., Knackmuss H.-J. 1988; Metabolism of 2,4-dichlorophenoxyacetic acid, 4-chloro-2-methylphenoxyacetic acid and 2-methylphenoxyacetic acid by Alcaligenes eutrophus JMP134. Arch Microbiol 150:95–102 [CrossRef]
     [Google Scholar]
  26. Pieper D. H., Knackmuss H.-J., Timmis K. N. 1993; Accumulation of 2-chloromuconate during metabolism of 3-chlorobenzoate by Alcaligenes eutrophus JMP134. Appl Microbiol Biotechnol 39:563–567 [CrossRef]
     [Google Scholar]
  27. Ravatn R., Studer S., Springael D., Zehnder A. J. B., van der Meer J. R. 1998; Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp.B13. . J Bacteriol 180:5505–5514
     [Google Scholar]
  28. Reniero D., Mozzon E., Galli E., Barbieri P. 1998; Two aberrant mercury resistance transposons in the Pseudomonas stutzeri plasmid pPB. Gene 208:37–42 [CrossRef]
     [Google Scholar]
  29. Smith C. A., Thomas C. M. 1987; Comparison of the organization of the genomes of phenotypically diverse plasmids of incompatibility group P: members of the IncPβ sub-group are closely related. Mol Gen Genet 206:419–427 [CrossRef]
     [Google Scholar]
  30. Tan H. M. 1999; Bacterial catabolic transposons. Appl Microbiol Biotechnol 51:1–12 [CrossRef]
     [Google Scholar]
  31. Vedler E., Koiv V., Heinaru A. 2000; Analysis of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pEST4011 of Achromobacter xylosooxidans subsp. denitrificans strain EST4002. Gene 255:281–288 [CrossRef]
     [Google Scholar]
  32. Wyndham R. C., Singh R. K., Straus N. A. 1988; Catabolic instability, plasmid gene deletion and recombination in Alcaligenes sp . BR60. Arch Microbiol 150:237–243 [CrossRef]
     [Google Scholar]
  33. Xia X.-S., Aathithan S., Oswiecimska K., Smith A. R., Bruce J. 1998; A novel plasmid pIJB1 possessing a putative 2,4-dichlorophenoxyacetate degradative transposon Tn 5530 in Burkholderia cepacia strain 2a. Plasmid 39:154–159 [CrossRef]
     [Google Scholar]
  34. You I.-S., Ghosal D. 1995; Genetic and molecular analysis of a regulatory region of the herbicide 2,4-dichlorophenoxyacetate catabolic plasmid pJP4. Mol Microbiol 16:321–331 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-147-8-2141
Loading
Molecular characterization of a deletion/duplication rearrangement in tfd genes from Ralstonia eutropha JMP134(pJP4) that improves growth on 3-chlorobenzoic acid but abolishes growth on 2,4-dichlorophenoxyacetic acidThe GenBank accession numbers for the 3115 nt BamHI-F and 2833 nt EcoRI-F fragments of pJP4 and the 4037 nt EcoRI-E′ fragment of pJP4-F3 are AF225972, AF225973 and AF225974, respectively.
Microbiology 147, 2141 (2001); https://doi.org/10.1099/00221287-147-8-2141
/content/journal/micro/10.1099/00221287-147-8-2141
/content/journal/micro/10.1099/00221287-147-8-2141
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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