Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation

Lynda Bm Ellis,Lawrence P Wackett

doi:10.1186/2042-5783-2-1

Abstract

Microorganisms are ubiquitous on earth and have diverse metabolic transformative capabilities important for environmental biodegradation of chemicals that helps maintain ecosystem and human health. Microbial biodegradative metabolism is the main focus of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD). UM-BBD data has also been used to develop a computational metabolic pathway prediction system that can be applied to chemicals for which biodegradation data is currently lacking. The UM-Pathway Prediction System (UM-PPS) relies on metabolic rules that are based on organic functional groups and predicts plausible biodegradative metabolism. The predictions are useful to environmental chemists that look for metabolic intermediates, for regulators looking for potential toxic products, for microbiologists seeking to understand microbial biodegradation, and others with a wide-range of interests.

Highlights

Microbial degradation here refers to the microbial conversion of organic compounds, often those of that negatively impact human health, to less toxic or more useful forms, in the environment or the laboratory
Until recently [5], there was no information about the enzymes that biosynthesize the azoxy group, and information is still lacking on the catabolism of azoxy groups
Since the structures have been rigorously identified, and the compounds derive from biological sources, novel biosynthetic enzymes must exist. Since these natural product compounds are not observed to accumulate in the biosphere, it is likely that enzymes participate in their biodegradation

Summary

Introduction

Microbial degradation here refers to the microbial conversion of organic compounds, often those of that negatively impact human health, to less toxic or more useful forms, in the environment or the laboratory. It is anticipated that there will be new discoveries of novel metabolic transformations with as yet uninvestigated chemical functional groups This can be predicted with confidence because the natural product chemistry literature contains references to more than one hundred organic functional groups present in molecules biosynthesized by living things [1]. This latter focus best reflects environmental biodegradation where it is thought that many bacteria often team up to biodegrade anthropogenic chemicals In this context, the UM-PPS brings a constellation of known microbial catabolic reactions to bear on a compound entered by the user to transform it into metabolic intermediates. A few rules, for example the hydrolysis of acyl chlorides to a carboxylic acid, rule bt0026, occur rapidly and spontaneously in water This reaction has been shown to occur non-enzymatically in biological systems and contribute to the overall biodegradation of certain chlorinated compounds. The PathPred system will improve as more compounds are entered into KEGG and there is more metabolism for the system to map to

Conclusions

Findings

38. Copley SD