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Chapter 7 : Evolution of Catabolic Enzymes and Pathways

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Abstract:

This chapter focuses on prokaryotic evolution in the context of biodegradation and microbial biocatalysis. It discusses the major evolutionary families of microbial catabolic enzymes, current ideas as to how genes are recruited and acquire new functions, and how new metabolic pathways arise and are disseminated among different prokaryotes. The discussion starts with a brief history of molecular-evolution studies. Then, it will be developed using primarily one example: how soil bacteria have evolved to use the herbicide atrazine as their sole source of nitrogen. Some microbial protein superfamilies important in biodegradation and biocatalysis are provided in a tabular form in which the major headings generally follow the major Enzyme Commission (EC) headings: (i) oxidoreductases, (ii) transferases, (iii) hydrolases, (iv) lyases, (v) isomerases, and (vi) ligases; except that lyases and isomerases are clustered together. The scientific literature suggests that in some cases, industrial chemicals initially evade microbial catabolism, as evidenced by their persistence in the environment, but are later found to be readily biodegraded. Evolution is especially instructive to study microbial catabolic enzymes to learn how new enzymes evolve and are transferred globally. In this context, the study of evolution is expanding from its historical role of providing fundamental explanations to become a biological tool that offers great promise for using microbes in our efforts to develop a sustainable human society.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7

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Figures

Image of Figure 7.1
Figure 7.1

Rate of change of amino acid sequence as a function of time differs with different proteins. Adapted from reference 16.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.2
Figure 7.2

Comparison of enzymes in the bacterial mandelate pathway (left) with other evolutionarily related enzymes which catalyze reactions with structurally distinct substrates.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.3
Figure 7.3

Oxygenative route of microbial atrazine catabolism, which generally results in the accumulation of aminotriazine metabolites.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.4
Figure 7.4

Pathway of atrazine catabolism catalyzed by sp. strain ADP and other atrazine-catabolizing bacteria. (A) First three steps in atrazine catabolism. (B) Sequence identity in a short stretch of AtzABC. (C) Hypothetical divalent metal coordination by AtzABC.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.5
Figure 7.5

Global distribution of bacteria isolated for their abilities to catabolize atrazine and known to process atrazine via an initial dechlorination reaction.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.6
Figure 7.6

In-well lysis gel showing plasmids from atrazine-degrading bacteria containing atrazine catabolism genes (shown in green). From left to right, the DNAs in the wells are derived from the following bacterial strains: sp. strain ADP; sp. strain M91-3, sp. strain PATR 2, and sp. strain SGI.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Tables

Generic image for table
Table 7.1

Microbial biodegradative-enzyme families based on signature sequences

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
Generic image for table
Table 7.2

Catabolic transposons in bacteria

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7

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