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Chapter 9 : Predicting Microbial Biocatalysis and Biodegradation

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Predicting Microbial Biocatalysis and Biodegradation, Page 1 of 2

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Abstract:

The ability to accurately predict biodegradation has enormous implications. Industries will continue to synthesize new materials faster than they, or regulatory agencies and academic researchers, can study their environmental fates. This chapter focuses largely on the prediction of biodegradation pathways. It is recognized that the use of the term "metabolic pathway" is coming under criticism, as pathways do not exist in isolation and occur as many variations on a theme. One approach to prediction is the quantitative structure activity relationships (QSAR) method, in which certain structural features of a molecule are correlated with some outcome, in this case biodegradability. Another set of systems have had the goal of predicting metabolic pathways for biodegradation. The basic principles needed for prediction are defining (i) the metabolic trunk pathways that initial biodegradation reactions funnel into and (ii) the enzymatic mechanisms by which different organic functional groups are metabolized. It is readily apparent that many compounds in anaerobic benzenoid ring metabolism feed into the common intermediate benzoyl-coenzyme A (CoA). Benzoyl-CoA is further metabolized reductively, and the ring is cleaved to produce 3-hydroxypimelyl-CoA.

Citation: Wackett L, Hershberger C. 2001. Predicting Microbial Biocatalysis and Biodegradation, p 157-170. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch9

Key Concept Ranking

Organic Chemicals
0.6070361
Benzoyl-Coenzyme A
0.5222222
Carbon Dioxide
0.48659244
Vinyl Chloride
0.46250376
Terephthalic acid
0.45286822
0.6070361
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Figures

Image of Figure 9.1
Figure 9.1

Knowledge cycle for developing an expert system to predict microbial catabolism.

Citation: Wackett L, Hershberger C. 2001. Predicting Microbial Biocatalysis and Biodegradation, p 157-170. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch9
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Image of Figure 9.2
Figure 9.2

Organic functional groups known in intermediary and specialized metabolism.

Citation: Wackett L, Hershberger C. 2001. Predicting Microbial Biocatalysis and Biodegradation, p 157-170. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch9
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Image of Figure 9.3
Figure 9.3

Prediction of metabolism when two functional groups (left) or three functional groups (right) are fused, showing the increase in complexity.

Citation: Wackett L, Hershberger C. 2001. Predicting Microbial Biocatalysis and Biodegradation, p 157-170. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch9
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References

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*1. Alexander, M. 1994. Effect of chemical structure on biodegradation, p. 159176. In Biodegradation and Bioremediation. Academic Press, San Diego, Calif..
2. Cowan, C. E.,, T. W. Federle,, R. J. Larson,, and T. C. Feijtel. 1996. Impact of biodegradation test methods on the development and applicability of biodegradation QSARs. SAR QSAR Environ. Res. 5:3749.
*3. Dagley, S., 1979. Summary of the conference, p. 534542. In A. W. Bourquin, and P. H. Pritchard (ed.), Proceedings of the Workshop on Microbial Degradation of Pollutants in Marine Environments. U.S. Environmental Protection Agency, Washington, D.C..
4. Howard, P. H.,, R. S. Boethling,, W. Stiteler,, W. Meylan,, and J. Beauman. 1991. Development of a predictive model for biodegradability based on BIODEG, the evaluated biodegradation data base. Sci. Total Environ. 109-110:635641.
5. Kanehisa, M.,, and S. Goto. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:2730.
6. Klopman, G.,, and M. Tu. 1997. Structure-biodegradability study and computer-automated prediction of aerobic biodegradation of chemicals. Environ. Toxicol. Chem. 16:18291835.
7. Klopman, G.,, Z. Zhang,, D. M. Balthasar,, and H. S. Rosencranz. 1996. Computer-automated predictions of metabolic transformations of chemicals. Environ. Toxicol. Chem. 14:395403.
*8. Parke, D.,, D. A. D'Argenio,, and L. N. Ornston. 2000. Bacteria are not what they eat: that is why they are so diverse. J. Bacteriol. 182:257263.
9. Punch, B.,, A. Patton,, K. Wight,, B. Larson,, P. Masscheleyn,, and L. Forney,. 1996. A biodegradability and simulation system (BESS) based on knowledge of biodegradability pathways, p. 6573. In W. J. G. M. Peijnenburg, and J. Damborsky (ed.), Biodegradability Prediction. Kluwer Academic Publishers, Dordrecht, The Netherlands.
10. Storck, W. J.,, P. L. Layman,, M. S. Reisch,, A. M. Thayer,, E. M. Kirschner,, G. Peaff,, and J. F. Tremblay. 1996. Facts and figures for the chemical industry. Chem. Eng. News 74(26):42.
*11. Wackett, L. P.,, L. B. M. Ellis,, S. M. Speedie,, C. D. Hershberger,, H.-J. Knackmuss,, A. M. Spormann,, C. T. Walsh,, L. J. Forney,, W. F. Punch,, T. Kazic,, M. Kanehisa,, and D. J. Berndt. 1999. Predicting microbial biodegradation pathways. ASM News 65:8793.

Tables

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Table 9.1

Top 30 organic chemicals in U.S. commerce (1995)

Citation: Wackett L, Hershberger C. 2001. Predicting Microbial Biocatalysis and Biodegradation, p 157-170. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch9
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Table 9.2

Heuristics used with enzyme reaction rules for predicting biodegradation pathways: highly general rules

Citation: Wackett L, Hershberger C. 2001. Predicting Microbial Biocatalysis and Biodegradation, p 157-170. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch9
Generic image for table
Table 9.3

Heuristics used with enzyme reaction rules for predicting biodegradation pathways: general rules

Citation: Wackett L, Hershberger C. 2001. Predicting Microbial Biocatalysis and Biodegradation, p 157-170. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch9
Generic image for table
Table 9.4

Heuristics used with enzyme reaction rules for predicting biodegradation pathways: specific rules for halogenated compounds

Citation: Wackett L, Hershberger C. 2001. Predicting Microbial Biocatalysis and Biodegradation, p 157-170. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch9

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