Encoding microbial metabolic logic: predicting biodegradation

  • Bo Kyeng Hou
  • Lynda B. M. Ellis
  • Lawrence P. Wackett
Original Paper

Abstract

Prediction of microbial metabolism is important for annotating genome sequences and for understanding the fate of chemicals in the environment. A metabolic pathway prediction system (PPS) has been developed that is freely available on the world wide web (http://umbbd.ahc.umn.edu/predict/), recognizes the organic functional groups found in a compound, and predicts transformations based on metabolic rules. These rules are designed largely by examining reactions catalogued in the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) and are generalized based on metabolic logic. The predictive accuracy of the PPS was tested: (1) using a 113-member set of compounds found in the database, (2) against a set of compounds whose metabolism was predicted by human experts, and (3) for consistency with experimental microbial growth studies. First, the system correctly predicted known metabolism for 111 of the 113 compounds containing C and H, O, N, S, P and/or halides that initiate existing pathways in the database, and also correctly predicted 410 of the 569 known pathway branches for these compounds. Second, computer predictions were compared to predictions by human experts for biodegradation of six compounds whose metabolism was not described in the literature. Third, the system predicted reactions liberating ammonia from three organonitrogen compounds, consistent with laboratory experiments showing that each compound served as the sole nitrogen source supporting microbial growth. The rule-based nature of the PPS makes it transparent, expandable, and adaptable.

Keywords

Bacteria Metabolism Biodegradation Prediction Metabolic logic 

References

  1. 1.
    Alexander M (1994) Effect of chemical structure on biodegradation. In: Biodegradation and bioremediation. Academic Press, San Diego, pp 159–176Google Scholar
  2. 2.
    Beller HR (2002) Anaerobic biotransformation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) by aquifer bacteria using hydrogen as the sole electron donor. Water Res 36:2533–2540CrossRefPubMedGoogle Scholar
  3. 3.
    Bestetti G, Galli E (1987) Characterization of a novel TOL-like plasmid from Pseudomonas putida involved in 1,2,4-trimethylbenzene degradation. J Bacteriol 169:1780–1783PubMedGoogle Scholar
  4. 4.
    Chen X, Christopher A, Jones JP, Bell SG, Guo Q, Xu F, Rao Z, Wong LL (2002) Crystal structure of the F87 W/Y96F/V247L mutant of cytochrome P-450CAM with 1,3,5-trichlorobenzene bound and further protein engineering for the oxidation of pentachlorobenzene and hexachlorobenzene. J Biol Chem 277:37519–37526CrossRefPubMedGoogle Scholar
  5. 5.
    Dangmann E, Stolz A, Kuhm AE, Hammer A, Feigel B, Noisommit-Rizzi N, Rizzi M, Reuss MM, Knackmuss HJ (1996) Degradation of 4-aminobenzene-sulfonate by a two-species bacterial coculture. Physiological interactions between Hydrogenophaga palleronii S1 and Agrobacterium radiobacter S2. Biodegradation 7:223–229PubMedGoogle Scholar
  6. 6.
    Darvas F (1988) Predicting metabolic pathways by logic programming. J Mol Graph 6:80–85CrossRefGoogle Scholar
  7. 7.
    DeSouza ML, Newcombe D, Alvey S, Crowley DE, Hay A, Sadowsky MJ, Wackett LP (1998) Molecular basis of a bacterial consortium: interspecies catabolism of atrazine. Appl Environ Microbiol 64:178–184Google Scholar
  8. 8.
    Ellis LBM, Hou BK, Wenjun K, Wackett LP (2003) The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining. Nucleic Acids Res 31:262–265CrossRefPubMedGoogle Scholar
  9. 9.
    Fathepure BZ, Tiedje JM, Boyd SA (1988) Reductive dechlorination of hexachlorobenzene to tri- and dichlorobenzenes in anaerobic sewage sludge. Appl Environ Microbiol 54:327–330PubMedGoogle Scholar
  10. 10.
    Greene N (1999) Knowledge based expert systems for toxicity and metabolism prediction. In: Erhardt PW (ed) Drug metabolism. Blackwell, London, pp 289–292Google Scholar
  11. 11.
    Hou BK, Wackett LP, Ellis LBM (2003) Microbial pathway prediction: A functional group approach. J Chem Inf Comput Sci 43:1051–1057CrossRefPubMedGoogle Scholar
  12. 12.
    Kanehisa M, Goto S, Kawashima S, Nakaya A (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30:42–46CrossRefPubMedGoogle Scholar
  13. 13.
    Klopman G, Tu M (1997) Structure-biodegradability study and computer-automated prediction of aerobic biodegradation of chemicals. Environ Toxicol Chem 16:1829–1835Google Scholar
  14. 14.
    Klopman G, Wang S, Balthasar DM (1992) Estimation of aqueous solubility of organic molecules by the group contribution approach. Application to the study of biodegradation. J Chem Inf Comp Sci 32:474–482Google Scholar
  15. 15.
    Klopman G, Zhang Z, Balthasar DM, Rosenkranz HS (1995) Computer automated predictions of aerobic biodegradation transforms in the environment. Environ Toxicol Chem 14:395–403Google Scholar
  16. 16.
    Langowski JJ, Long, A (2002) Computer systems for the prediction of xenobiotic metabolism. Adv Drug Deliv Rev 54:407–415CrossRefPubMedGoogle Scholar
  17. 17.
    Long A (2002) Rule based prioritisation of metabolites. Some recent developments in METEOR. Drug Metab Rev 34(Suppl 1):71Google Scholar
  18. 18.
    Maymo-Gatell X, Anguish T, Zinder SH (1999) Reductive dechlorination of chlorinated ethenes and 1,2-dichloroethane by “Dehalococcoides ethenogenes” 195. Appl Environ Microbiol 65:3108–3113PubMedGoogle Scholar
  19. 19.
    Meylan WM, Howard PH (1995) Atom/fragment contribution method for estimating octanol-water partition coefficients. J Pharm Sci 84:83–92PubMedGoogle Scholar
  20. 20.
    Nojiri H, Habe H, Ornori T (2001) Bacterial degradation of aromatic compounds via angular dioxygenation. J Gen Appl Microbiol 47:279–305PubMedGoogle Scholar
  21. 21.
    Rorije E, Germa F, Philipp B, Schink B, Beimborn DB (2002) Prediction of biodegradability from structure: Imidazoles. SAR QSAR Environ Res 13:199–204CrossRefPubMedGoogle Scholar
  22. 22.
    Schenzle A, Lenke H, Spain JC, Knackmuss HJ (1999) 3-Hydroxylaminophenol mutase from Ralstonia eutropha JMP134 catalyzes a Bamberger rearrangement. J Bacteriol 181:1444–1450PubMedGoogle Scholar
  23. 23.
    Scholten JD, Chang KH, Babbitt PC, Charest H, Sylvestre M, Dunaway-Mariano D (1991) Novel enzymic hydrolytic dehalogenation of a chlorinated aromatic. Science 253:182–185PubMedGoogle Scholar
  24. 24.
    Stanier RY, Palleroni NJ, Duodoroff M (1966) The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43:159–271PubMedGoogle Scholar
  25. 25.
    Wackett LP, Ellis LBM, Speedie SM, Hershberger CD, Knackmuss H-J, Spormann AM, Walsh CT, Forney LJ, Punch WF, Kazic T, Kanehisa M, Berndt DJ (1999) Predicting microbial biodegradation pathways. ASM News 65:87–93Google Scholar
  26. 26.
    Wackett LP, Hershberger CD (2001) Predicting microbial biocatalysis and biodegradation. In: Biocatalysis and biodegradation. ASM Press, Washington DC, pp 157–170Google Scholar
  27. 27.
    Wackett LP, Sadowsky MJ, Martinez B, Shapir N (2002) Biodegradation of atrazine and related triazine compounds: from enzymes to field studies. Appl Microbiol Biotechnol 58:39–45CrossRefPubMedGoogle Scholar
  28. 28.
    Walker JD, Carlsen L (2002) QSARs for identifying and prioritizing substances with persistence and bioconcentration potential. SAR QSAR Environ Res 13:713–725CrossRefPubMedGoogle Scholar
  29. 29.
    Webb EC (1992) Enzyme nomenclature: recommendations of the nomenclature committee of the international union of biochemistry and molecular biology on the nomenclature and classification of enzymes. Academic, San DiegoGoogle Scholar
  30. 30.
    Wu Q, Milliken CE, Meier GP, Watts JE, Sowers KR, May HD (2002) Dechlorination of chlorobenzenes by a culture containing bacterium DF-1, a PCB dechlorinating microorganism. Environ Sci Technol 36:3290–3294CrossRefPubMedGoogle Scholar
  31. 31.
    Wyndham RC, Cashore AE, Nakatsu CH, Peel MC (1994) Catabolic transposons. Biodegradation 5:323–342PubMedGoogle Scholar

Copyright information

© Society for Industrial Microbiology 2004

Authors and Affiliations

  • Bo Kyeng Hou
    • 3
  • Lynda B. M. Ellis
    • 2
  • Lawrence P. Wackett
    • 1
  1. 1.Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology InstituteUniversity of MinnesotaSt PaulUSA
  2. 2.Department of Laboratory Medicine and PathologyUniversity of MinnesotaMinneapolisUSA
  3. 3.Department of Laboratory Medicine and PathologyUniversity of MinnesotaSt PaulUSA

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