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Chapter 24 : Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation
Author:
Rowland H. Davis1
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Affiliations:
1: Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697-3900
Content Type: Monograph
Publication Year:
2010
Category: Microbial Genetics and Molecular Biology; Fungi and Fungal Pathogenesis
Book DOI:
10.1128/9781555816636
Chapter DOI:
10.1128/9781555816636.ch24
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Abstract:
This chapter focuses on three unusual aspects of certain of these pathways: polyfunctional proteins, metabolic cycles, and compartmentation. The study of aromatic amino acid biosynthesis in Neurospora crassa provided some of the earliest insights into unusual genetic relationships among related metabolic enzymes. Most fungi, including yeasts, display a global response to amino acid deprivation. In N. crassa and other filamentous fungi, it is referred to as cross-pathway control, with many of the genes carrying the cpc designation. In S. cerevisiae, the system is called general amino acid control, with gene names starting with GC. It is referred to here as cross-pathway control and is described briefly to fill out the physiological aspects of amino acid synthesis and control. Polyamine metabolism in fungi has been studied mainly in S. cerevisiae and N. crassa. The chapter focuses on features of fungi that organize and optimize metabolic systems. The management of polyamine pools has revealed a complex physiological landscape in which enzyme regulation, metabolic flow, small-molecule binding, and vacuolar activity converge. Very little catabolism of polyamines takes place in N. crassa, even at high external amine concentrations. The ionic binding of spermidine and basic amino acids to polyphosphate in the vacuole explains why the intact organelle becomes so dense upon isolation in sucrose gradients, where they lose water as they sediment. Indeed, it is likely that in fungi, as in plants, they have important roles in fine-tuning and otherwise managing metabolic and ionic traffic, varying widely with the species and the environment.
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
Key Concept Ranking
- Basic Amino Acids
- 0.47994503
- Aromatic Amino Acids
- 0.47977662
- Aliphatic Amino Acids
- 0.45328137
- Aromatic Amino Acid Biosynthesis
- 0.4436144
0.47994503
Figures
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation
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Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24fig01
FIGURE 1
Pathway of chorismate synthesis in N. crassa (top), showing the metabolic positions of aro mutations. The organization of the ARO gene complex on linkage group IIR (bottom) shows the order of the catalytic domains (1 through 5) and of the corresponding component elements of the complex (aro-1, -2, -4, -5, and -9). The complementation groups are represented by lines that group mutants that will not complement; lines that do not overlap signify that complementation will take place between members of the different groups. Note that the translational polarity in this figure is oriented right (N terminal) to left (C terminal). Redrawn from
Rines et al., 1969
, and reprinted from
Davis, 2000
.
10.1128/9781555816636/f0340-01_thmb.gif
10.1128/9781555816636/f0340-01.gif
FIGURE 1
Pathway of chorismate synthesis in N. crassa (top), showing the metabolic positions of aro mutations. The organization of the ARO gene complex on linkage group IIR (bottom) shows the order of the catalytic domains (1 through 5) and of the corresponding component elements of the complex (aro-1, -2, -4, -5, and -9). The complementation groups are represented by lines that group mutants that will not complement; lines that do not overlap signify that complementation will take place between members of the different groups. Note that the translational polarity in this figure is oriented right (N terminal) to left (C terminal). Redrawn from Rines et al., 1969 , and reprinted from Davis, 2000 .
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24fig02
FIGURE 2
Tryptophan, phenylalanine, and tyrosine synthesis in N. crassa, showing the metabolic positions of various genes. Note that the complex of trp-1 and trp-2 gene products catalyzes three nonsequential reactions. Not all substrates are shown; for details of the tryptophan synthase reaction, see
Fig. 3
. Reprinted from
Davis, 2000
.
10.1128/9781555816636/f0341-01_thmb.gif
10.1128/9781555816636/f0341-01.gif
FIGURE 2
Tryptophan, phenylalanine, and tyrosine synthesis in N. crassa, showing the metabolic positions of various genes. Note that the complex of trp-1 and trp-2 gene products catalyzes three nonsequential reactions. Not all substrates are shown; for details of the tryptophan synthase reaction, see Fig. 3 . Reprinted from Davis, 2000 .
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24fig03
FIGURE 3
The tryptophan synthase partial reactions at sites I (reaction 2) and II (reaction 3). The intermediate indole diffuses between sites I and II, largely confined within the protein. Reprinted from
Davis, 2000
.
10.1128/9781555816636/f0342-01_thmb.gif
10.1128/9781555816636/f0342-01.gif
FIGURE 3
The tryptophan synthase partial reactions at sites I (reaction 2) and II (reaction 3). The intermediate indole diffuses between sites I and II, largely confined within the protein. Reprinted from Davis, 2000 .
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24fig04
FIGURE 4
Isoleucine, valine, and leucine biosynthesis in N. crassa, showing the metabolic positions of mutations. Note that the ilv-3 (acetohydroxy acid synthase), ilv-2 (reductoisomerase), and ilv-1 (dehydratase) genes encode single enzymes that carry out reactions in both the isoleucine and valine pathways. Reprinted from
Davis, 2000
.
10.1128/9781555816636/f0343-01_thmb.gif
10.1128/9781555816636/f0343-01.gif
FIGURE 4
Isoleucine, valine, and leucine biosynthesis in N. crassa, showing the metabolic positions of mutations. Note that the ilv-3 (acetohydroxy acid synthase), ilv-2 (reductoisomerase), and ilv-1 (dehydratase) genes encode single enzymes that carry out reactions in both the isoleucine and valine pathways. Reprinted from Davis, 2000 .
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24fig05
FIGURE 5
The pathways of pyrimidine, arginine, proline, and polyamine synthesis in N. crassa, showing the localization of enzymes and the metabolic positions of mutations. See
Table 1
for gene-enzyme assignments. Reprinted from
Davis, 2000
.
10.1128/9781555816636/f0344-01_thmb.gif
10.1128/9781555816636/f0344-01.gif
FIGURE 5
The pathways of pyrimidine, arginine, proline, and polyamine synthesis in N. crassa, showing the localization of enzymes and the metabolic positions of mutations. See Table 1 for gene-enzyme assignments. Reprinted from Davis, 2000 .
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24fig06
FIGURE 6
Carbamyl phosphate (CAP) overflow between pathways in two types of double mutants of Neurospora. Mutations pyr-3d (top) and arg-12
s
(bottom) block CAP utilization in one pathway and thereby relieve nutritional requirements imposed by CPS mutants in the other. Parenthesized compounds are not synthesized. CAP is arginine or pyrimidine specific. Reprinted from
Davis, 1972
.
10.1128/9781555816636/f0345-01_thmb.gif
10.1128/9781555816636/f0345-01.gif
FIGURE 6
Carbamyl phosphate (CAP) overflow between pathways in two types of double mutants of Neurospora. Mutations pyr-3d (top) and arg-12 s (bottom) block CAP utilization in one pathway and thereby relieve nutritional requirements imposed by CPS mutants in the other. Parenthesized compounds are not synthesized. CAP is arginine or pyrimidine specific. Reprinted from Davis, 1972 .
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24fig07
FIGURE 7
Steady-state flux of arginine and ornithine in exponential cultures of N. crassa grown in minimal medium. Values are in nanomoles per minute per milligram, dry weight, of mycelium. Boxed numbers identify ornithine decarboxylase (1), ornithine transaminase (2), and ornithine carbamoyltransferase (3). Based on
Karlin et al., 1976
, and reprinted from
Davis, 2000
.
10.1128/9781555816636/f0350-01_thmb.gif
10.1128/9781555816636/f0350-01.gif
FIGURE 7
Steady-state flux of arginine and ornithine in exponential cultures of N. crassa grown in minimal medium. Values are in nanomoles per minute per milligram, dry weight, of mycelium. Boxed numbers identify ornithine decarboxylase (1), ornithine transaminase (2), and ornithine carbamoyltransferase (3). Based on Karlin et al., 1976 , and reprinted from Davis, 2000 .
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24fig08
FIGURE 8
Polyamine synthesis in N. crassa, with the structures of relevant intermediates and the metabolic positions of mutations. The dotted line signifies allosteric feedback inhibition of argi-nine synthesis by arginine. MTA, methylthioadenosine. Reprinted from
Davis, 2000
.
10.1128/9781555816636/f0352-01_thmb.gif
10.1128/9781555816636/f0352-01.gif
FIGURE 8
Polyamine synthesis in N. crassa, with the structures of relevant intermediates and the metabolic positions of mutations. The dotted line signifies allosteric feedback inhibition of argi-nine synthesis by arginine. MTA, methylthioadenosine. Reprinted from Davis, 2000 .
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24fig09
FIGURE 9
Relationship between spermidine concentrations within and outside mycelial cells growing in the presence of different concentrations of spermidine. The strain used carries an ODC-deficient spe-1 mutation; therefore, all spermidine in the cells originates in the medium. Cellular spermidine is expressed as nanomoles of spermidine per milligram, dry weight (left ordinate) or as millimolar in cell water (2.5 ml per g, dry weight) (right ordinate). The dotted line shows the 1:1 relationship expected of a diffusional equilibrium. Over the range from 0.5 to 5 mM spermidine in the medium, cellular spermi-dine rises from 9 to ~14 mM (solid line). The arrow on the left ordinate shows the normal concentration of spermidine in wild-type cells grown in minimal medium. Reprinted from
Davis, 2000
.
10.1128/9781555816636/f0354-01_thmb.gif
10.1128/9781555816636/f0354-01.gif
FIGURE 9
Relationship between spermidine concentrations within and outside mycelial cells growing in the presence of different concentrations of spermidine. The strain used carries an ODC-deficient spe-1 mutation; therefore, all spermidine in the cells originates in the medium. Cellular spermidine is expressed as nanomoles of spermidine per milligram, dry weight (left ordinate) or as millimolar in cell water (2.5 ml per g, dry weight) (right ordinate). The dotted line shows the 1:1 relationship expected of a diffusional equilibrium. Over the range from 0.5 to 5 mM spermidine in the medium, cellular spermi-dine rises from 9 to ~14 mM (solid line). The arrow on the left ordinate shows the normal concentration of spermidine in wild-type cells grown in minimal medium. Reprinted from Davis, 2000 .
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
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Tables
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation
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Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24
/content/10.1128/9781555816636.ch24.ch24tab01
TABLE 1
Gene-enzyme assignments in the arginine, proline, pyrimidine, and polyamine pathways
TABLE 1
Gene-enzyme assignments in the arginine, proline, pyrimidine, and polyamine pathways
Citation:
Davis R.
2010.
Amino Acids and Polyamines: Polyfunctional Proteins, Metabolic Cycles, and Compartmentation,
p 339-358.
In
Borkovich K, Ebbole D (ed),
Cellular and Molecular Biology of Filamentous Fungi.
ASM Press, Washington, DC.
doi: 10.1128/9781555816636.ch24