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Chapter 12 : The Extent of Microbial Catalysis and Biodegradation: Are Microbes Infallible?

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Abstract:

It is often speculated that every non-polymeric compound conceived of by humans and occurring in nature will be metabolized by some microorganism somewhere in the soil or water of the Earth. Is this true? Can it be studied systematically? This chapter provides answers to these questions. The beginnings of an answer are first addressed with existing knowledge. Then, ideas are presented as to how the far reaches of microbial metabolism can be further identified. This effort is also linked to the widespread enterprise of microbial functional genomics. The total extent of genomic diversity is unknown, but comparative genomic analysis to date suggests that genetic diversity in prokaryotes is greater than previously anticipated. This, along with other evidence presented in the chapter, suggests that there is much catalytic diversity yet to be discovered. In the wealth of catalytic diversity possessed by microbial enzymes, two issues are relevant. First, it is unlikely that we have uncovered all of the catalytic potential of these known cofactors. Moreover, it is unclear how many new cofactors, metals, and modified amino acids remain to be discovered in microbial systems. To determine the potential for microbes to transform the exotic compounds for which metabolism is unknown, several compounds containing such functional groups were put into standard enrichment cultures in which the compounds were used as sole carbon or nitrogen sources to support growth. Most of these yielded actively growing cultures of microorganisms, and the target compound was transformed in the cultures, as demonstrated by high-pressure liquid chromatography.

Citation: Wackett L, Hershberger C. 2001. The Extent of Microbial Catalysis and Biodegradation: Are Microbes Infallible?, p 205-212. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch12

Key Concept Ranking

Catechol 2,3-Dioxygenase
0.46161917
Benzylsuccinate Synthase
0.45533332
Escherichia coli
0.4551175
Liquid Chromatography
0.44302705
0.46161917
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Figures

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Figure 12.1

General rate of discovery of new biochemical reactions versus the rate of discovery of new genes over the last century.

Citation: Wackett L, Hershberger C. 2001. The Extent of Microbial Catalysis and Biodegradation: Are Microbes Infallible?, p 205-212. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch12
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Image of Figure 12.2
Figure 12.2

Screening program for identifying new biocatalytic reactions in microbes. The order is (I) enrichment culture, (II) bacterial isolation, (III) chromatographic separation of the enzyme(s), (IV) identification of protein sequence information by mass spectrometry, and (V) use of the sequence to identify possible homologs and to clone the gene(s) responsible for the activity.

Citation: Wackett L, Hershberger C. 2001. The Extent of Microbial Catalysis and Biodegradation: Are Microbes Infallible?, p 205-212. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch12
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Image of Figure 12.3
Figure 12.3

Evolutionarily and mechanistically related proteins catalyzing overall very different reactions. The enzymes share sequence identity, a common coordination environment for a metal atom, and a bidentate coordination of substrate oxygen atoms during the reaction (left). However, the enzymes are (right, from top to bottom) a transferase, a dioxygenase, and an isomerase.

Citation: Wackett L, Hershberger C. 2001. The Extent of Microbial Catalysis and Biodegradation: Are Microbes Infallible?, p 205-212. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch12
Permissions and Reprints Request Permissions
Download as Powerpoint

References

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1. Babbitt, R. C.,, and J. A. Gerlt. 1997. Understanding enzyme superfamilies: chemistry as the fundamental determinant in the evolution of new catalytic activities. J. Biol. Chem. 272: 30591 30594.
2. Genthner, B. R.,, G. T. Townsend,, and R. J. Chapman. 1989. Anaerobic transformation of phenol to benzoate via para-carboxylation: use of fluorinated analogues to elucidate the mechanism of transformation. Biochem. Biophys. Res. Commun. 162: 945 951.
3. Gouverneur, V. E.,, K. N. Houk,, B. de Pascual-Teresa,, B. Beno,, K. D. Janda,, and R. A. Lerner. 1993. Control of the exo and endo pathways of the Diels-Alder reaction by antibody catalysis. Science 262: 204 208.
4. Leuthner, B.,, C. Leutwein,, H. Schulz,, P. Horth,, W. Haehnel,, E. Schiltz,, H. Schagger,, and J. Heider. 1998. Biochemical and genetic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. Mol. Microbiol. 28: 615 628.
5. Mangold, J. B.,, B. L. Mangold,, and A. Spina. 1986. Rat liver aryl sulfotransferasecatalyzed sulfation and rearrangement of 9-fluorenone oxime. Biochim. Biophys. Acta 87: 37 43.
6. Shirota, O.,, K. Takizawa,, S. Sekita,, M. Satake,, Y. Hirayama,, Y. Hakamata,, T. Hayashi,, and T. Yanagawa. 1997. Antiandrogenic natural Diels-Alder-type adducts from Brosimum rubescens. J. Nat. Prod. 10: 997 1002.
7. Spiess, T.,, F. Desiere,, P. Fischer,, J. C. Spain,, H. J. Knackmuss,, and H. Lenke. 1998. A new 4-nitrotoluene degradation pathway in a Mycobacterium strain. Appl. Environ. Microbiol. 64: 446 452.
8. Wackett, L. P.,, J. F. Honek,, T. P. Begley,, S. L. Shames,, E. C. Niederhoffer,, R. P. Hausinger,, W. H. Orme-Johnson,, and C. T. Walsh,. 1988. Methyl-S-coenzyme M reductase: a nickel-dependent enzyme catalyzing the terminal redox step in methane biogenesis, p. 249–w . In J. Lancaster (ed.), Bioinorganic Chemistry of Nickel. VCH, New York, N.Y..

Tables

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Table 12.1

Enzymes in the UM-BBD encoded by genes with no discernible homology to other known genes or with homology to genes encoding different functions

Citation: Wackett L, Hershberger C. 2001. The Extent of Microbial Catalysis and Biodegradation: Are Microbes Infallible?, p 205-212. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch12
Generic image for table
Table 12.2

Evidence for undiscovered unique organic-functional-group metabolism

Citation: Wackett L, Hershberger C. 2001. The Extent of Microbial Catalysis and Biodegradation: Are Microbes Infallible?, p 205-212. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch12

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