1887

Abstract

DTP0602 utilizes 2,4,6-trichlorophenol (2,4,6-TCP) as its sole source of carbon. The expression of catabolic pathway genes (, and ) for 2,4,6-TCP has been reported to be regulated by the LysR-type transcriptional regulator (LTTR) HadR. Generally, coinducers are recognized as being important for the function of LTTRs, and alteration of the LTTR-protection sequence and the degree of DNA bending are characteristic of LTTRs with or without a recognized coinducer. In this study, we describe the mechanism by which HadR regulates the expression of 2,4,6-TCP catabolic genes. The 2,4,6-TCP catabolic pathway genes in DTP0602 consist of two transcriptional units: and monocistronic . Purified HadR binds to the promoter and HadR–DNA complex formation was induced in the presence of 16 types of substituted phenols, including chloro- and nitro-phenols and tribromo-phenol. In contrast with observations of other well-characterized LTTRs, the tested phenols showed no diversity of the bending angle of the HadR binding fragment. The expression of 2,4,6-TCP catabolic pathway genes, which are regulated by HadR, was not influenced by the DNA bending angle of HadR. Moreover, the transcription of , and was induced in the presence of seven types of substituted phenols, whereas the other substituted phenols, which induced formation of the HadR–DNA complex, did not induce the transcription of , or .

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.063396-0
2013-04-01
2021-10-17
Loading full text...

Full text loading...

/deliver/fulltext/micro/159/4/665.html?itemId=/content/journal/micro/10.1099/mic.0.063396-0&mimeType=html&fmt=ahah

References

  1. Akakura R., Winans S. C. ( 2002a). Constitutive mutations of the OccR regulatory protein affect DNA bending in response to metabolites released from plant tumors. J Biol Chem 277:5866–5874 [View Article][PubMed]
    [Google Scholar]
  2. Akakura R., Winans S. C. ( 2002b). Mutations in the occQ operator that decrease OccR-induced DNA bending do not cause constitutive promoter activity. J Biol Chem 277:15773–15780[PubMed] [CrossRef]
    [Google Scholar]
  3. Ashworth R. B., Cormier M. J. ( 1967). Isolation of 2,6-dibromophenol from the marine hemichordate, Balanoglossus biminiensis . Science 155:1558–1559 [View Article][PubMed]
    [Google Scholar]
  4. Blatny J. M., Brautaset T., Winther-Larsen H. C., Karunakaran P., Valla S. ( 1997). Improved broad-host-range RK2 vectors useful for high and low regulated gene expression levels in gram-negative bacteria. Plasmid 38:35–51 [View Article][PubMed]
    [Google Scholar]
  5. 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 [View Article][PubMed]
    [Google Scholar]
  6. Bundy B. M., Collier L. S., Hoover T. R., Neidle E. L. ( 2002). Synergistic transcriptional activation by one regulatory protein in response to two metabolites. Proc Natl Acad Sci U S A 99:7693–7698 [View Article][PubMed]
    [Google Scholar]
  7. Cai M., Xun L. ( 2002). Organization and regulation of pentachlorophenol-degrading genes in Sphingobium chlorophenolicum ATCC 39723. J Bacteriol 184:4672–4680 [View Article][PubMed]
    [Google Scholar]
  8. Cebolla A., Sousa C., de Lorenzo V. ( 1997). Effector specificity mutants of the transcriptional activator NahR of naphthalene degrading Pseudomonas define protein sites involved in binding of aromatic inducers. J Biol Chem 272:3986–3992[PubMed] [CrossRef]
    [Google Scholar]
  9. Chang M., Crawford I. P. ( 1991). In vitro determination of the effect of indoleglycerol phosphate on the interaction of purified TrpI protein with its DNA-binding sites. J Bacteriol 173:1590–1597[PubMed]
    [Google Scholar]
  10. Czaplicka M. ( 2004). Sources and transformations of chlorophenols in the natural environment. Sci Total Environ 322:21–39 [View Article][PubMed]
    [Google Scholar]
  11. Dennis J. J., Sokol P. A. ( 1995). Electrotransformation of Pseudomonas . Methods Mol Biol 47:125–133[PubMed]
    [Google Scholar]
  12. Field J. A., Sierra-Alvarez R. ( 2008). Microbial degradation of chlorinated phenols. Rev Environ Sci Biotechnol 7:211–241 [View Article]
    [Google Scholar]
  13. Fielman K. T., Woodin S. A., Walla M. D., Lincoln D. E. ( 1999). Widespread occurrence of natural halogenated organics among temperate marine infauna. Mar Ecol Prog 181:1–12 [View Article]
    [Google Scholar]
  14. Gao J., Gussin G. N. ( 1991). Mutations in TrpI binding site II that differentially affect activation of the trpBA promoter of Pseudomonas aeruginosa . EMBO J 10:4137–4144[PubMed]
    [Google Scholar]
  15. Hatta T., Nakano O., Imai N., Takizawa N., Kiyohara H. ( 1999). Cloning and sequence analysis of hydroxyquinol 1,2-dioxygenase gene in 2,4,6-trichlorophenol-degrading Ralstonia pickettii DTP0602 and characterization of its product. J Biosci Bioeng 87:267–272 [View Article][PubMed]
    [Google Scholar]
  16. Hatta T., Fujii E., Takizawa N. ( 2012). Analysis of two gene clusters involved in 2,4,6-trichlorophenol degradation by Ralstonia pickettii DTP0602. Biosci Biotechnol Biochem 76:892–899 [View Article][PubMed]
    [Google Scholar]
  17. Ju K. S., Parales J. V., Parales R. E. ( 2009). Reconstructing the evolutionary history of nitrotoluene detection in the transcriptional regulator NtdR. Mol Microbiol 74:826–843 [View Article][PubMed]
    [Google Scholar]
  18. Kalogeraki V. S., Winans S. C. ( 1997). Suicide plasmids containing promoterless reporter genes can simultaneously disrupt and create fusions to target genes of diverse bacteria. Gene 188:69–75 [View Article][PubMed]
    [Google Scholar]
  19. King G. M. ( 1986). Inhibition of microbial activity in marine sediments by a bromophenol from a hemichordate. Nature 323:257–259 [View Article]
    [Google Scholar]
  20. Kiyohara H., Takizawa N., Uchiyama T., Ikarugi H., Nagao K. ( 1989). Degradability of polychlorinated phenols by bacterial populations in soil. J Ferment Bioeng 67:339–344 [View Article]
    [Google Scholar]
  21. Kiyohara H., Hatta T., Ogawa Y., Kakuda T., Yokoyama H., Takizawa N. ( 1992). Isolation of Pseudomonas pickettii strains that degrade 2,4,6-trichlorophenol and their dechlorination of chlorophenols. Appl Environ Microbiol 58:1276–1283[PubMed]
    [Google Scholar]
  22. Kullik I., Toledano M. B., Tartaglia L. A., Storz G. ( 1995). Mutational analysis of the redox-sensitive transcriptional regulator OxyR: regions important for oxidation and transcriptional activation. J Bacteriol 177:1275–1284[PubMed]
    [Google Scholar]
  23. Latus M., Seitz H., Eberspacher J., Lingens F. ( 1995). Purification and characterization of hydroxyquinol 1,2-dioxygenase from Azotobacter sp. strain GP1. Appl Environ Microbiol 61:2453–2460[PubMed]
    [Google Scholar]
  24. Lessner D. J., Parales R. E., Narayan S., Gibson D. T. ( 2003). Expression of the nitroarene dioxygenase genes in Comamonas sp. strain JS765 and Acidovorax sp. strain JS42 is induced by multiple aromatic compounds. J Bacteriol 185:3895–3904 [View Article][PubMed]
    [Google Scholar]
  25. Lönneborg R., Smirnova I., Dian C., Leonard G. A., Brzezinski P. ( 2007). In vivo and in vitro investigation of transcriptional regulation by DntR. J Mol Biol 372:571–582 [View Article][PubMed]
    [Google Scholar]
  26. Lorenz E., Stauffer G. V. ( 1995). Characterization of the MetR binding sites for the glyA gene of Escherichia coli . J Bacteriol 177:4113–4120[PubMed]
    [Google Scholar]
  27. Maddocks S. E., Oyston P. C. ( 2008). Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154:3609–3623 [View Article][PubMed]
    [Google Scholar]
  28. McAllister K. A., Lee H., Trevors J. T. ( 1996). Microbial degradation of pentachlorophenol. Biodegradation 7:1–40 [View Article]
    [Google Scholar]
  29. Miller J. H. ( 1972). Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  30. Miller B. E., Kredich N. M. ( 1987). Purification of the cysB protein from Salmonella typhimurium . J Biol Chem 262:6006–6009[PubMed]
    [Google Scholar]
  31. Miller V. L., Mekalanos J. J. ( 1988). A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR . J Bacteriol 170:2575–2583[PubMed]
    [Google Scholar]
  32. Miyauchi K., Lee H. S., Fukuda M., Takagi M., Nagata Y. ( 2002). Cloning and characterization of linR, involved in regulation of the downstream pathway for γ-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. Appl Environ Microbiol 68:1803–1807 [View Article][PubMed]
    [Google Scholar]
  33. Muraoka S., Okumura R., Ogawa N., Nonaka T., Miyashita K., Senda T. ( 2003). Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: unusual combination of two subunit forms and molecular bases for causing and changing DNA bend. J Mol Biol 328:555–566 [View Article][PubMed]
    [Google Scholar]
  34. Nishihara K., Kanemori M., Kitagawa M., Yanagi H., Yura T. ( 1998). Chaperone coexpression plasmids: differential and synergistic roles of DnaK-DnaJ-GrpE and GroEL-GroES in assisting folding of an allergen of Japanese cedar pollen, Cryj2, in Escherichia coli . Appl Environ Microbiol 64:1694–1699[PubMed]
    [Google Scholar]
  35. Nishihara K., Kanemori M., Yanagi H., Yura T. ( 2000). Overexpression of trigger factor prevents aggregation of recombinant proteins in Escherichia coli . Appl Environ Microbiol 66:884–889 [View Article][PubMed]
    [Google Scholar]
  36. Ogawa N., McFall S. M., Klem T. J., Miyashita K., Chakrabarty A. M. ( 1999). Transcriptional activation of the chlorocatechol degradative genes of Ralstonia eutropha NH9. J Bacteriol 181:6697–6705[PubMed]
    [Google Scholar]
  37. Park W., Jeon C. O., Madsen E. L. ( 2002). Interaction of NahR, a LysR-type transcriptional regulator, with the alpha subunit of RNA polymerase in the naphthalene degrading bacterium, Pseudomonas putida NCIB 9816-4. FEMS Microbiol Lett 213:159–165[PubMed]
    [Google Scholar]
  38. Pedersén M., Saenger P., Fries L. ( 1974). Simple brominated phenols in red algae. Phytochemistry 13:2273–2279 [View Article]
    [Google Scholar]
  39. Piñeiro S., Olekhnovich I., Gussin G. N. ( 1997). DNA bending by the TrpI protein of Pseudomonas aeruginosa . J Bacteriol 179:5407–5413[PubMed]
    [Google Scholar]
  40. Porrúa O., García-Jaramillo M., Santero E., Govantes F. ( 2007). The LysR-type regulator AtzR binding site: DNA sequences involved in activation, repression and cyanuric acid-dependent repositioning. Mol Microbiol 66:410–427[PubMed] [CrossRef]
    [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. Sánchez M. A., González B. ( 2007). Genetic characterization of 2,4,6-trichlorophenol degradation in Cupriavidus necator JMP134. Appl Environ Microbiol 73:2769–2776 [View Article][PubMed]
    [Google Scholar]
  43. Schäfer A., Tauch A., Jäger W., Kalinowski J., Thierbach G., Pühler A. ( 1994). Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum . Gene 145:69–73[PubMed] [CrossRef]
    [Google Scholar]
  44. Schell M. A. ( 1993). Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47:597–626 [View Article][PubMed]
    [Google Scholar]
  45. Schell M. A., Brown P. H., Raju S. ( 1990). Use of saturation mutagenesis to localize probable functional domains in the NahR protein, a LysR-type transcription activator. J Biol Chem 265:3844–3850[PubMed]
    [Google Scholar]
  46. 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 [CrossRef]
    [Google Scholar]
  47. Smith A. W., Iglewski B. H. ( 1989). Transformation of Pseudomonas aeruginosa by electroporation. Nucleic Acids Res 17:10509 [View Article][PubMed]
    [Google Scholar]
  48. Takizawa N., Yokoyama H., Yanagihara K., Hatta T., Kiyohara H. ( 1995). A locus of Pseudomonas pickettii DTP0602, had, that encodes 2,4,6-trichlorophenol-4-dechlorinase with hydroxylase activity, and hydroxylation of various chlorophenols by the enzyme. J Ferment Bioeng 80:318–326 [View Article]
    [Google Scholar]
  49. Thompson J. F., Landy A. ( 1988). Empirical estimation of protein-induced DNA bending angles: applications to λ site-specific recombination complexes. Nucleic Acids Res 16:9687–9705 [View Article][PubMed]
    [Google Scholar]
  50. Tropel D., van der Meer J. R. ( 2004). Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 68:474–500 [View Article][PubMed]
    [Google Scholar]
  51. Whelan J. A., Russell N. B., Whelan M. A. ( 2003). A method for the absolute quantification of cDNA using real-time PCR. J Immunol Methods 278:261–269 [View Article][PubMed]
    [Google Scholar]
  52. Yamada T., Takahama Y., Yamada Y. ( 2008). Biodegradation of 2,4,6-tribromophenol by Ochrobactrum sp. strain TB01. Biosci Biotechnol Biochem 72:1264–1271 [View Article][PubMed]
    [Google Scholar]
  53. Yanisch-Perron C., Vieira J., Messing J. ( 1985). Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–119 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.063396-0
Loading
/content/journal/micro/10.1099/mic.0.063396-0
Loading

Data & Media loading...

Most cited this month 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