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Chapter 8 : Metabolic Logic and Pathway Maps

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Abstract:

This chapter makes extensive use of visual images of chemical compounds, in a familiar format, to highlight the underlying patterns of catabolism. Intermediary metabolism is defined as enzyme-catalyzed reactions common to most living things: bacteria, eukaryotic single-celled life, plants, and animals. More specifically, intermediary metabolism deals with (i) common energy metabolism—for example, the catabolism of glucose by the glycolytic, or Embden-Meyerhof, pathway—and (ii) common biosynthetic pathways, such as those that generate necessary amino acids, lipids, and carbohydrates. This is illustrated, in the form of an electronic circuit diagram of the intermediary metabolism of . Catabolic pathways funnel into a limited set of key intermediates, getting the most metabolic bang from the limited genetic buck. Thus, a new pathway is not required for each compound the organism might metabolize if there is redundancy by generating a common intermediate. This is well illustrated in aromatic-ring metabolism, which often proceeds through catecholic intermediates aerobically and benzoylcoenzyme A (CoA) anaerobically. These points are illustrated in the chapter by using a series of metamaps. The metamaps discussed include C metamap, C metamap, cycloalkane metamap, BTEX metamap, PAH metamap, heterocyclic-ring metamap, triazine-ring metamap, organohalogen metamap, and organometallic metamap.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8

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Figures

Image of Figure 8.1
Figure 8.1

Network of intermediary metabolism showing compounds as nodes and interconnecting reactions as lines. Highlighted in boldface is the central linear pathway flowing into the tricarboxylic acid cycle (circle). (From [Rawn, c 1989], by permission of Prentice-Hall, Inc., Upper Saddle River, N.J.)

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.2
Figure 8.2

Network of intermediary metabolism with novel catabolic reactions (shown in green) which funnel into intermediary metabolites.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.3
Figure 8.3

Central methane oxidation pathway of methanotrophs (highlighted in green) showing how single-carbon compounds can potentially funnel into the pathway when specific enzymes are present.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.4
Figure 8.4

Metabolisms of many C compounds funnel into a limited number of intermediary compounds (box) or the C hydrocarbons.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.5
Figure 8.5

Cycloaliphatic compounds are metabolized aerobically via hydroxylation and Baeyer-Villiger-type oxygen insertion reactions.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.6
Figure 8.6

Aerobic metabolism of BTEX compounds, and other aromatic hydrocarbons, typically proceeds through catechol (1,2-dihydroxybenzene) intermediates.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.7
Figure 8.7

Anaerobic metabolism of many substituted aromatic compounds proceeds through the intermediacy of benzoyl-CoA.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.8
Figure 8.8

Aerobic catabolism of fused-ring benzenoid compounds (top) and fused alicyclic and benzenoid ring compounds (bottom).

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.9
Figure 8.9

Prominent metabolic strategy for opening nitrogen, oxygen, or sulfur heterocycles.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.10
Figure 8.10

Metabolic strategy for many triazine-ring compounds proceeds through the intermediacy of cyanuric acid (ring structure at lower right).

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.11
Figure 8.11

Chloroorganic compounds are metabolized via four fundamental mechanisms capable of cleaving the carbon-chlorine bond.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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Image of Figure 8.12
Figure 8.12

The best-studied metabolism of organometallic compounds is that for the catabolism of alkylmercurial compounds. After dealkylation, mercury(II) is reduced to volatile mercury(O), which renders it nontoxic.

Citation: Wackett L, Hershberger C. 2001. Metabolic Logic and Pathway Maps, p 135-155. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch8
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