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Chapter 12 : Central Metabolism

Authors: Michael J. Danson1, Henry J. Lamble2, David W. Hough3
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Affiliations: 1: Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom; 2: Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom; 3: Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
Content Type: Monograph
Publication Year: 2007

Category: Microbial Genetics and Molecular Biology; Environmental Microbiology

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Abstract:

The pathways of central metabolism are at the heart of an organism’s total metabolic capacity, and their wide conservation suggests they were an early evolutionary invention. Consistent with this view are common themes that are found spanning the , , and , although variations are observed that reflect not only phylogeny but also particular lifestyles and requirements. The principal aim of this chapter is to describe the central metabolic pathways of the and to identify the unique or unusual features of archaeal metabolism. This chapter talks about the conversion of sugars to pyruvate, and the metabolic fate of pyruvate, either to organic end products or to CO by complete oxidation via the citric acid cycle. Growth on acetate is discussed as this may involve an additional cyclic pathway, the glyoxylate cycle. The catabolism of amino acids is included; while these do feed into the citric acid cycle, catabolism of branched-chain amino acids in particular deserves a special mention as it is in these reactions that the presence of a family of multienzyme complexes was discovered, which were until recently thought to be absent from all archaea. species exhibit considerable metabolic diversity and versatility and are commonly considered to be opportunistic heterotrophs, capable of utilizing a wide range of carbohydrate energy sources. Central metabolism represents one of the most fundamental aspects of the biochemistry of the cell and is commonly perceived as invariant and sacrosanct.

Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
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Central Metabolism
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Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
/content/10.1128/9781555815516.ch12.ch12fig01
Figure 1.
Labeling of pyruvate during glucose catabolism. The characteristic labeling pattern of pyruvate resulting from glucose catabo-lism by the Embden-Meyerhof and Entner-Doudoroff pathways.
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Image of Figure 1.
Figure 1.

Labeling of pyruvate during glucose catabolism. The characteristic labeling pattern of pyruvate resulting from glucose catabo-lism by the Embden-Meyerhof and Entner-Doudoroff pathways.

Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
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Figure 2.
Pathways of glucose metabolism. The classical Embden-Meyerhof and Entner-Doudoroff pathways of bacteria and eucarya are shown in bold with each step shown connected by large full arrows, while the alternative pathways of selected archaeal genera are displayed with various small arrows (see key). Unless specified, the cofactor usage is as shown for the classical pathways. Enzymes are denoted by numbers: 1 = glucokinase, 2 = phosphoglucose isomerase, 3 = phosphofructokinase, 4 = fructose-1,6-bisphosphate aldolase, 5 = triose-phosphate isomerase, 6 = glyceraldehyde-3-phosphate dehydrogenase, 7 = phosphoglycerate kinase, 8 = phosphoglycerate mutase, 9 = enolase, 10 = pyruvate kinase, 11 = glyceraldehyde-3-phosphate ferredoxin oxidoreductase, 12 = nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase, 13 = glucose-6-phosphate dehydrogenase, 14 = 6-phosphogluconate dehydratase, 15 = KDPG aldolase, 16 = glucose dehydrogenase, 17 = gluconate dehydratase, 18 = KDG kinase, 19 = KDG aldolase, 20 = glyceraldehyde dehydrogenase, 21 = glycerate kinase. In species it is not yet clear whether the conversion of glyceraldehyde to glycerate is catalyzed by glyceraldehyde dehydrogenase ( ) or glyceraldehyde oxidoreductase; see text for details. The reactions involved in the conversion of glucose, or other C6 sugars, to C3 intermediates make up the upper pathway, whereas the lower pathway refers to the conversion of C3 intermediates to pyruvate.
10.1128/9781555815516/f0262-01_thmb.gif
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Image of Figure 2.
Figure 2.

Pathways of glucose metabolism. The classical Embden-Meyerhof and Entner-Doudoroff pathways of bacteria and eucarya are shown in bold with each step shown connected by large full arrows, while the alternative pathways of selected archaeal genera are displayed with various small arrows (see key). Unless specified, the cofactor usage is as shown for the classical pathways. Enzymes are denoted by numbers: 1 = glucokinase, 2 = phosphoglucose isomerase, 3 = phosphofructokinase, 4 = fructose-1,6-bisphosphate aldolase, 5 = triose-phosphate isomerase, 6 = glyceraldehyde-3-phosphate dehydrogenase, 7 = phosphoglycerate kinase, 8 = phosphoglycerate mutase, 9 = enolase, 10 = pyruvate kinase, 11 = glyceraldehyde-3-phosphate ferredoxin oxidoreductase, 12 = nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase, 13 = glucose-6-phosphate dehydrogenase, 14 = 6-phosphogluconate dehydratase, 15 = KDPG aldolase, 16 = glucose dehydrogenase, 17 = gluconate dehydratase, 18 = KDG kinase, 19 = KDG aldolase, 20 = glyceraldehyde dehydrogenase, 21 = glycerate kinase. In species it is not yet clear whether the conversion of glyceraldehyde to glycerate is catalyzed by glyceraldehyde dehydrogenase ( ) or glyceraldehyde oxidoreductase; see text for details. The reactions involved in the conversion of glucose, or other C6 sugars, to C3 intermediates make up the upper pathway, whereas the lower pathway refers to the conversion of C3 intermediates to pyruvate.

Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
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Figure 3.
Gluconeogenesis. The reactions of the gluconeogenic pathway. Enzymes are denoted by numbers: 1 = phospho-enolpyruvate synthase, 2 = enolase, 3 = phosphoglycerate mutase, 4 = phosphoglycerate kinase, 5 = glyceraldehyde-3-phosphate dehydrogenase, 6 = triose-phosphate isomerase, 7 = fructose-1,6-bisphosphate aldolase, 8 = fructose-1,6-bisphosphatase, 9 = phos-phoglucose isomerase.
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Image of Figure 3.
Figure 3.

Gluconeogenesis. The reactions of the gluconeogenic pathway. Enzymes are denoted by numbers: 1 = phospho-enolpyruvate synthase, 2 = enolase, 3 = phosphoglycerate mutase, 4 = phosphoglycerate kinase, 5 = glyceraldehyde-3-phosphate dehydrogenase, 6 = triose-phosphate isomerase, 7 = fructose-1,6-bisphosphate aldolase, 8 = fructose-1,6-bisphosphatase, 9 = phos-phoglucose isomerase.

Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
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Figure 4.
Pyruvate ferredoxin oxidoreductase. Schematic representation of the four-subunit (αβγδ) pyruvate ferredoxin oxidoreductase and the proposed pathway of electron flow (adapted from reference ). Ferredoxin (Fd) is the electron acceptor. CoA, coenzyme A; TPP, thiamine pyrophosphate; [4Fe-4S], iron sulfur cluster.
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Image of Figure 4.
Figure 4.

Pyruvate ferredoxin oxidoreductase. Schematic representation of the four-subunit (αβγδ) pyruvate ferredoxin oxidoreductase and the proposed pathway of electron flow (adapted from reference ). Ferredoxin (Fd) is the electron acceptor. CoA, coenzyme A; TPP, thiamine pyrophosphate; [4Fe-4S], iron sulfur cluster.

Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
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Figure 5.
The oxidative citric acid cycle and the glyoxylate cycle. The reactions of the citric acid cycle are denoted by solid arrows, and the reactions unique to the glyoxylate cycle are shown with dotted lines. Enzymes are denoted by numbers: 1 = citrate synthase, 2 = aconitase, 3 = isocitrate dehydrogenase, 4 = 2-oxoglutarate dehydrogenase complex (aerobic bacteria and eucarya), 5 = 2-oxoglutarate ferredoxin oxidoreductase (archaea), 6 = succinate thiokinase, 7 = succinate dehydrogenase, 8 = fumarase, 9 = malate dehydrogenase, 10 = isocitrate lyase, 11 = malate synthase.
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Image of Figure 5.
Figure 5.

The oxidative citric acid cycle and the glyoxylate cycle. The reactions of the citric acid cycle are denoted by solid arrows, and the reactions unique to the glyoxylate cycle are shown with dotted lines. Enzymes are denoted by numbers: 1 = citrate synthase, 2 = aconitase, 3 = isocitrate dehydrogenase, 4 = 2-oxoglutarate dehydrogenase complex (aerobic bacteria and eucarya), 5 = 2-oxoglutarate ferredoxin oxidoreductase (archaea), 6 = succinate thiokinase, 7 = succinate dehydrogenase, 8 = fumarase, 9 = malate dehydrogenase, 10 = isocitrate lyase, 11 = malate synthase.

Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
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Figure 6.
The reductive citric acid cycle. Enzymes are denoted by numbers: 1 = malate dehydrogenase, 2 = fumarase, 3 = fumarate reductase, 4 = succinate thiokinase, 5 = 2-oxoglutarate ferredoxin oxidoreductase, 6 = isocitrate dehydrogenase, 7 = aconitase, 8 = ATP citrate lyase.
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Image of Figure 6.
Figure 6.

The reductive citric acid cycle. Enzymes are denoted by numbers: 1 = malate dehydrogenase, 2 = fumarase, 3 = fumarate reductase, 4 = succinate thiokinase, 5 = 2-oxoglutarate ferredoxin oxidoreductase, 6 = isocitrate dehydrogenase, 7 = aconitase, 8 = ATP citrate lyase.

Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
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Figure 7.
General mechanism of the 2-oxoacid dehydrogenase multienzyme complexes. The 2-oxoacid dehydrogenase complexes of bacteria and eucarya comprise enzymes E1 (2-oxoacid decarboxylase), E2 (dihydrolipoyl acyltransferase), and E3 (dihydrolipoamide dehydrogenase). B, histidine base; Lip, enzyme-bound lipoic acid, showing the structure of the dithiolane ring; SUS, protein disulfide bond; TPPH, thiamine pyrophosphate.
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10.1128/9781555815516/f0278-01.gif
Image of Figure 7.
Figure 7.

General mechanism of the 2-oxoacid dehydrogenase multienzyme complexes. The 2-oxoacid dehydrogenase complexes of bacteria and eucarya comprise enzymes E1 (2-oxoacid decarboxylase), E2 (dihydrolipoyl acyltransferase), and E3 (dihydrolipoamide dehydrogenase). B, histidine base; Lip, enzyme-bound lipoic acid, showing the structure of the dithiolane ring; SUS, protein disulfide bond; TPPH, thiamine pyrophosphate.

Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
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Figure 8.
Gene clusters encoding the components of a putative archaeal 2-oxoacid dehydrogenase complex. The arrangement and intergene distances (bp) of the ORFs constituting the E1α, E1β, E2, and E3 genes of the proposed archaeal 2-oxoacid dehydrogenase are shown. The proposed direction of transcription (left to right, as drawn) is the same for all the genes. See text for details of the (— 1) frameshift in the E2 gene of
10.1128/9781555815516/f0279-01_thmb.gif
10.1128/9781555815516/f0279-01.gif
Image of Figure 8.
Figure 8.

Gene clusters encoding the components of a putative archaeal 2-oxoacid dehydrogenase complex. The arrangement and intergene distances (bp) of the ORFs constituting the E1α, E1β, E2, and E3 genes of the proposed archaeal 2-oxoacid dehydrogenase are shown. The proposed direction of transcription (left to right, as drawn) is the same for all the genes. See text for details of the (— 1) frameshift in the E2 gene of

Citation: Danson M, Lamble H, Hough D. 2007. Central Metabolism, p 260-287. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch12
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