1887

Abstract

Ibu-2 has the unusual ability to cleave the acid side chain from the pharmaceutical ibuprofen and related arylacetic acid derivatives to yield corresponding catechols under aerobic conditions via a previously uncharacterized mechanism. Screening a chromosomal library of Ibu-2 DNA in EPI300 allowed us to identify one fosmid clone (pFOS3G7) that conferred the ability to metabolize ibuprofen to isobutylcatechol. Characterization of pFOS3G7 loss-of-function transposon mutants permitted identification of five ORFs, , whose predicted amino acid sequences bore similarity to the large and small units of an aromatic dioxygenase (), a sterol carrier protein X (SCPx) thiolase (), a domain of unknown function 35 (DUF35) protein () and an aromatic CoA ligase (). Two additional ORFs, and , which encode putative ferredoxin reductase and ferredoxin components of an aromatic dioxygenase system, respectively, were also identified on pFOS3G7. Complementation of a markerless loss-of-function deletion mutant restored catechol production as did complementation of the Tn mutant. Expression of subcloned alone in did not impart full metabolic activity unless coexpressed with . CoA ligation followed by ring oxidation is common to phenylacetic acid pathways. However, the need for a putative SCPx thiolase (IpfD) and DUF35 protein (IpfE) in aerobic arylacetic acid degradation is unprecedented. This work provides preliminary insights into the mechanism behind this novel arylacetic acid-deacylating, catechol-generating activity.

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2013-03-01
2022-01-28
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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[PubMed] [CrossRef]
    [Google Scholar]
  2. Altschul S. F., Madden T. L., Schäffer 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 [View Article][PubMed]
    [Google Scholar]
  3. Aziz R., Saad R., Rizkallah M. ( 2011). PharmacoMicrobiomics or how bugs modulate drugs: an educational initiative to explore the effects of human microbiome on drugs. BMC Bioinformatics 12:Suppl. 7A10 [View Article]
    [Google Scholar]
  4. Bangera M. G., Thomashow L. S. ( 1999). Identification and characterization of a gene cluster for synthesis of the polyketide antibiotic 2,4-diacetylphlorglucinol from Pseudomonas fluorescens Q2-87. J Bacteriol 181:3155–3163[PubMed]
    [Google Scholar]
  5. Black P. N., DiRusso C. C., Metzger A. K., Heimert T. L. ( 1992). Cloning, sequencing, and expression of the fadD gene of Escherichia coli encoding acyl coenzyme A synthetase. J Biol Chem 267:25513–25520[PubMed]
    [Google Scholar]
  6. Buser H. R., Poiger T., Muller M. D. ( 1999). Occurrence and environmental behavior of the chiral pharmaceutical drug ibuprofen in surface waters and in wastewater. Environ Sci Technol 33:2529–2535 [View Article]
    [Google Scholar]
  7. Butler C. S., Mason J. R. ( 1997). Structure–function analysis of the bacterial aromatic ring-hydroxylating dioxygenases. Adv Microb Physiol 38:47–84 [View Article][PubMed]
    [Google Scholar]
  8. Campbell J. W., Cronan J. E. Jr ( 2002). The enigmatic Escherichia coli fadE gene is yafH . J Bacteriol 184:3759–3764 [View Article][PubMed]
    [Google Scholar]
  9. Clayton T. A., Baker D., Lindon J. C., Everett J. R., Nicholson J. K. ( 2009). Pharmacometabonomic identification of a significant host–microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci U S A 106:14728–14733 [View Article][PubMed]
    [Google Scholar]
  10. Datsenko K. A., Wanner B. L. ( 2000). One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640–6645 [View Article][PubMed]
    [Google Scholar]
  11. Eaton R. W. ( 1996). p-Cumate catabolic pathway in Pseudomonas putida Fl: cloning and characterization of DNA carrying the cmt operon. J Bacteriol 178:1351–1362[PubMed]
    [Google Scholar]
  12. El-Said Mohamed M. ( 2000). Biochemical and molecular characterization of phenylacetate-coenzyme A ligase, an enzyme catalyzing the first step in aerobic metabolism of phenylacetic acid in Azoarcus evansii . J Bacteriol 182:286–294 [View Article][PubMed]
    [Google Scholar]
  13. Farré M. L., Ferrer I., Ginebreda A., Figueras M., Olivella L., Tirapu L., Vilanova M., Barceló D. ( 2001). Determination of drugs in surface water and wastewater samples by liquid chromatography-mass spectrometry: methods and preliminary results including toxicity studies with Vibrio fischeri . J Chromatogr A 938:187–197 [View Article][PubMed]
    [Google Scholar]
  14. Fernández C., Ferrández A., Miñambres B., Díaz E., García J. L. ( 2006). Genetic characterization of the phenylacetyl-coenzyme A oxygenase from the aerobic phenylacetic acid degradation pathway of Escherichia coli . Appl Environ Microbiol 72:7422–7426 [View Article][PubMed]
    [Google Scholar]
  15. Fetzner S., Müller R., Lingens F. ( 1992). Purification and some properties of 2-halobenzoate 1,2-dioxygenase, a two-component enzyme system from Pseudomonas cepacia 2CBS. J Bacteriol 174:279–290[PubMed]
    [Google Scholar]
  16. Flippin J. L., Huggett D., Foran C. M. ( 2007). Changes in the timing of reproduction following chronic exposure to ibuprofen in Japanese medaka, Oryzias latipes . Aquat Toxicol 81:73–78 [View Article][PubMed]
    [Google Scholar]
  17. García B., Olivera E. R., Miñambres B., Carnicero D., Muñiz C., Naharro G., Luengo J. M. ( 2000). Phenylacetyl-coenzyme A is the true inducer of the phenylacetic acid catabolism pathway in Pseudomonas putida U. Appl Environ Microbiol 66:4575–4578 [View Article][PubMed]
    [Google Scholar]
  18. Grogan G., Roberts G. A., Bougioukou D., Turner N. J., Flitsch S. L. ( 2001). The desymmetrization of bicyclic β-diketones by an enzymatic retro-Claisen reaction. A new reaction of the crotonase superfamily. J Biol Chem 276:12565–12572 [View Article][PubMed]
    [Google Scholar]
  19. Han S., Choi K., Kim J., Ji K., Kim S., Ahn B., Yun J., Choi K., Khim J. S., Zhang X. ( 2010). Endocrine disruption and consequences of chronic exposure to ibuprofen in Japanese medaka (Oryzias latipes) and freshwater cladocerans Daphnia magna and Moina macrocopa . Aquat Toxicol 98:256–264 [View Article][PubMed]
    [Google Scholar]
  20. Hanlon G. W., Kooloobandi A., Hutt A. J. ( 1994). Microbial metabolism of 2-arylpropionic acids: effect of environment on the metabolism of ibuprofen by Verticillium lecanii . J Appl Microbiol 76:442–447 [View Article]
    [Google Scholar]
  21. Ismail W., El-Said Mohamed M., Wanner B. L., Datsenko K. A., Eisenreich W., Rohdich F., Bacher A., Fuchs G. ( 2003). Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli . Eur J Biochem 270:3047–3054 [View Article][PubMed]
    [Google Scholar]
  22. Jeffrey W. H., Cuskey S. M., Chapman P. J., Resnick S., Olsen R. H. ( 1992). Characterization of Pseudomonas putida mutants unable to catabolize benzoate: cloning and characterization of Pseudomonas genes involved in benzoate catabolism and isolation of a chromosomal DNA fragment able to substitute for xylS in activation of the TOL lower-pathway promoter. J Bacteriol 174:4986–4996[PubMed]
    [Google Scholar]
  23. Jones O. A., Lester J. N., Voulvoulis N. ( 2005). Pharmaceuticals: a threat to drinking water?. Trends Biotechnol 23:163–167 [View Article][PubMed]
    [Google Scholar]
  24. Kinney C. A., Furlong E. T., Werner S. L., Cahill J. D. ( 2006). Presence and distribution of wastewater-derived pharmaceuticals in soil irrigated with reclaimed water. Environ Toxicol Chem 25:317–326 [View Article][PubMed]
    [Google Scholar]
  25. Kolpin D. W., Furlong E. T., Meyer M. T., Thurman E. M., Zaugg S. D., Barber L. B., Buxton H. T. ( 2002). Pharmaceuticals, hormones, and other organic wastewater contaminants in U.S. streams, 1999–2000: a national reconnaissance. Environ Sci Technol 36:1202–1211 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  27. Krishna S. S., Aravind L., Bakolitsa C., Caruthers J., Carlton D., Miller M. D., Abdubek P., Astakhova T., Axelrod H. L. & other authors ( 2010). The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role. Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1160–1166 [View Article][PubMed]
    [Google Scholar]
  28. Kube M., Heider J., Amann J., Hufnagel P., Kahner S., Beck A., Reinhardt R., Rabus R. ( 2004). Genes involved in the anaerobic degradation of toluene in a denitrifying bacterium, strain EbN1. Arch Microbiol 181182–194 [View Article]
    [Google Scholar]
  29. Kühner S., Wöhlbrand L., Fritz I., Wruck W., Hultschig C., Hufnagel P., Kube M., Reinhardt R., Rabus R. ( 2005). Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol 187:1493–1503[PubMed] [CrossRef]
    [Google Scholar]
  30. Kunau W. H., Dommes V., Schulz H. ( 1995). β-Oxidation of fatty acids in mitochondria, peroxisomes, and bacteria: a century of continued progress. Prog Lipid Res 34:267–342[PubMed] [CrossRef]
    [Google Scholar]
  31. Lawrence J. R., Swerhone G. D. W., Wassenaar L. I., Neu T. R. ( 2005). Effects of selected pharmaceuticals on riverine biofilm communities. Can J Microbiol 51:655–669 [View Article][PubMed]
    [Google Scholar]
  32. Leuthner B., Heider J. ( 2000). Anaerobic toluene catabolism of Thauera aromatica: the bbs operon codes for enzymes of βoxidation of the intermediate benzylsuccinate. J Bacteriol 182:272–277 [View Article][PubMed]
    [Google Scholar]
  33. Liu Y., Moënne-Loccoz P., Hildebrand D. P., Wilks A., Loehr T. M., Mauk A. G., Ortiz de Montellano P. R. ( 1999). Replacement of the proximal histidine iron ligand by a cysteine or tyrosine converts heme oxygenase to an oxidase. Biochemistry 38:3733–3743 [View Article][PubMed]
    [Google Scholar]
  34. Marchler-Bauer A., Bryant S. H. ( 2004). CD-Search: protein domain annotations on the fly. Nucleic Acids Res 32:Web Server issueW327–W331 [View Article][PubMed]
    [Google Scholar]
  35. Marchler-Bauer A., Anderson J. B., DeWeese-Scott C., Fedorova N. D., Geer L. Y., He S., Hurwitz D. I., Jackson J. D., Jacobs A. R. & other authors ( 2003). CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res 31:383–387 [View Article][PubMed]
    [Google Scholar]
  36. Marco-Urrea E., Pérez-Trujillo M., Vicent T., Caminal G. ( 2009). Ability of white-rot fungi to remove selected pharmaceuticals and identification of degradation products of ibuprofen by Trametes versicolor . Chemosphere 74:765–772 [View Article][PubMed]
    [Google Scholar]
  37. Martínez-Blanco H., Reglero A., Rodriguez-Aparicio L. B., Luengo J. M. ( 1990). Purification and biochemical characterization of phenylacetyl-CoA ligase from Pseudomonas putida. A specific enzyme for the catabolism of phenylacetic acid. J Biol Chem 265:7084–7090[PubMed]
    [Google Scholar]
  38. Mason J. R., Cammack R. ( 1992). The electron-transport proteins of hydroxylating bacterial dioxygenases. Annu Rev Microbiol 46:277–305 [View Article][PubMed]
    [Google Scholar]
  39. McCullar M. V., Brenner V., Adams R. H., Focht D. D. ( 1994). Construction of a novel polychlorinated biphenyl-degrading bacterium; utilization of 3,4′-dichlorobiphenyl by Pseudomonas acidovorans M3GY. Appl Environ Microbiol 60:3833–3839[PubMed]
    [Google Scholar]
  40. Murdoch R. W., Hay A. G. ( 2005). Formation of catechols via removal of acid side chains from ibuprofen and related aromatic acids. Appl Environ Microbiol 71:6121–6125 [View Article][PubMed]
    [Google Scholar]
  41. Pagani F., Zagato L., Merati G., Paone G., Gridelli B., Maier J. A. ( 1994). A histidine to tyrosine replacement in lysosomal acid lipase causes cholesteryl ester storage disease. Hum Mol Genet 3:1605–1609 [View Article][PubMed]
    [Google Scholar]
  42. Pedersen J. A., Yeager M. A., Suffet I. H. ( 2003). Xenobiotic organic compounds in runoff from fields irrigated with treated wastewater. J Agric Food Chem 51:1360–1372 [View Article][PubMed]
    [Google Scholar]
  43. Pedersen J. A., Soliman M., Suffet I. H. ( 2005). Human pharmaceuticals, hormones, and personal care product ingredients in runoff from agricultural fields irrigated with treated wastewater. J Agric Food Chem 53:1625–1632 [View Article][PubMed]
    [Google Scholar]
  44. Pomati F., Netting A. G., Calamari D., Neilan B. A. ( 2004). Effects of erythromycin, tetracycline and ibuprofen on the growth of Synechocystis sp. and Lemna minor . Aquat Toxicol 67:387–396 [View Article][PubMed]
    [Google Scholar]
  45. Quintana J. B., Weiss S., Reemtsma T. ( 2005). Pathways and metabolites of microbial degradation of selected acidic pharmaceutical and their occurrence in municipal wastewater treated by a membrane bioreactor. Water Res 39:2654–2664 [View Article][PubMed]
    [Google Scholar]
  46. Reiner A. M. ( 1971). Metabolism of benzoic acid by bacteria: 3,5-cyclohexadiene-1,2-diol-1-carboxylic acid is an intermediate in the formation of catechol. J Bacteriol 108:89–94[PubMed]
    [Google Scholar]
  47. Richards S. M., Wilson C. J., Johnson D. J., Castle D. M., Lam M., Mabury S. A., Sibley P. K., Solomon K. R. ( 2004). Effects of pharmaceutical mixtures in aquatic microcosms. Environ Toxicol Chem 23:1035–1042 [View Article][PubMed]
    [Google Scholar]
  48. Roberts G. A., Grogan G., Turner N. J., Flitsch S. L. ( 2004). Nucleotide sequence of a portion of the camphor-degrading gene cluster from Rhodococcus sp. NCIMB 9784. DNA Seq 15:96–103 [View Article][PubMed]
    [Google Scholar]
  49. Rost R., Haas S., Hammer E., Herrmann H., Burchhardt G. ( 2002; Molecular analysis of aerobic phenylacetate degradation in Azoarcus evansii. Mol Genet Genomics 267656–663 [CrossRef]
    [Google Scholar]
  50. 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]
  51. Santos L. H. M. L. M., Araújo A. N., Fachini A., Pena A., Delerue-Matos C., Montenegro M. C. B. S. M. ( 2010). Ecotoxicological aspects related to the presence of pharmaceuticals in the aquatic environment. J Hazard Mater 175:45–95[PubMed] [CrossRef]
    [Google Scholar]
  52. Siemens J., Huschek G., Siebe C., Kaupenjohann M. ( 2008). Concentrations and mobility of human pharmaceuticals in the world’s largest wastewater irrigation system, Mexico City–Mezquital Valley. Water Res 42:2124–2134 [View Article][PubMed]
    [Google Scholar]
  53. Stolowich N. J., Petrescu A. D., Huang H., Martin G. G., Scott A. I., Schroeder F. ( 2002). Sterol carrier protein-2: structure reveals function. Cell Mol Life Sci 59:193–212 [View Article][PubMed]
    [Google Scholar]
  54. Stumpf M., Ternes T. A., Wilken R.-D., Rodrigues S. V., Baumann W. ( 1999). Polar drug residues in sewage and natural waters in the state of Rio de Janeiro, Brazil. Sci Total Environ 225:135–141 [View Article][PubMed]
    [Google Scholar]
  55. Takeuchi H., Chen J. H., Jenkins J. R., Bun-Ya M., Turner P. C., Rees H. H. ( 2004). Characterization of a sterol carrier protein 2/3-oxoacyl-CoA thiolase from the cotton leafworm (Spodoptera littoralis): a lepidopteran mechanism closer to that in mammals than that in dipterans. Biochem J 382:93–100 [View Article][PubMed]
    [Google Scholar]
  56. Teufel R., Mascaraque V., Ismail W., Voss M., Perera J., Eisenreich W., Haehnel W., Fuchs G. ( 2010). Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc Natl Acad Sci U S A 107:14390–14395 [View Article][PubMed]
    [Google Scholar]
  57. Teufel R., Friedrich T., Fuchs G. ( 2012). An oxygenase that forms and deoxygenates toxic epoxide. Nature 483:359–362 [View Article][PubMed]
    [Google Scholar]
  58. Trotter P. J. ( 2001). The genetics of fatty acid metabolism in Saccharomyces cerevisiae . Annu Rev Nutr 21:97–119 [View Article][PubMed]
    [Google Scholar]
  59. Verhoeven N. M., Jakobs C. ( 2001). Human metabolism of phytanic acid and pristanic acid. Prog Lipid Res 40:453–466 [View Article][PubMed]
    [Google Scholar]
  60. Vessey D. A., Hu J., Kelley M. ( 1996). Interaction of salicylate and ibuprofen with the carboxylic acid: CoA ligases from bovine liver mitochondria. J Biochem Toxicol 11:73–78 [View Article][PubMed]
    [Google Scholar]
  61. Wanders R. J. A., Denis S., Wouters F., Wirtz K. W. A., Seedorf U. ( 1997). Sterol carrier protein X (SCPx) is a peroxisomal branched-chain β-ketothiolase specifically reacting with 3-oxo-pristanoyl-CoA: a new, unique role for SCPx in branched-chain fatty acid metabolism in peroxisomes. Biochem Biophys Res Commun 236:565–569[PubMed] [CrossRef]
    [Google Scholar]
  62. Westin M. A. K., Hunt M. C., Alexson S. E. H. ( 2007). Peroxisomes contain a specific phytanoyl-CoA/pristanoyl-CoA thioesterase acting as a novel auxiliary enzyme in α- and β-oxidation of methyl-branched fatty acids in mouse. J Biol Chem 282:26707–26716 [View Article][PubMed]
    [Google Scholar]
  63. Wilson I. D. ( 2009). Drugs, bugs, and personalized medicine: pharmacometabonomics enters the ring. Proc Natl Acad Sci U S A 106:14187–14188[PubMed] [CrossRef]
    [Google Scholar]
  64. Winkler M., Lawrence J. R., Neu T. R. ( 2001). Selective degradation of ibuprofen and clofibric acid in two model river biofilm systems. Water Res 35:3197–3205 [View Article][PubMed]
    [Google Scholar]
  65. Xu J., Wu L., Chen W., Jiang P., Chang A. C.-S. ( 2009). Pharmaceuticals and personal care products (PPCPs), and endocrine disrupting compounds (EDCs) in runoff from a potato field irrigated with treated wastewater in southern California. J Health Sci 55:306–310 [View Article]
    [Google Scholar]
  66. Zwiener C., Seeger S., Glauner T., Frimmel F. H. ( 2002). Metabolites from the biodegradation of pharmaceutical residues of ibuprofen in biofilm reactors and batch experiments. Anal Bioanal Chem 372:569–575 [View Article][PubMed]
    [Google Scholar]
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