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A functional analysis of the pyrimidine catabolic pathway in Arabidopsis.

Zrenner R, Riegler H, Marquard CR, Lange PR, Geserick C, Bartosz CE, Chen CT, Slocum RD - New Phytol. (2009)

Bottom Line: * Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to beta-alanine, CO(2) and NH(3) through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and beta-ureidopropionase (EC 3.5.1.6, PYD3). * A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism.PYD expression and catabolism of [2-(14)C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source. * PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-(14)C]-uracil or to grow on uracil as the sole nitrogen source.By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute of Molecular Plant Physiology, Golm, Germany. zrenner@igzev.de

ABSTRACT
* Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to beta-alanine, CO(2) and NH(3) through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and beta-ureidopropionase (EC 3.5.1.6, PYD3). * A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism. PYD expression and catabolism of [2-(14)C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source. * PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-(14)C]-uracil or to grow on uracil as the sole nitrogen source. By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source. These results confirm PYD1 function and suggest the possible existence of another, as yet unknown, activity for uracil degradation to dihydrouracil in this plant. * The localization of PYD-green fluorescent protein fusions in the plastid (PYD1), secretory system (PYD2) and cytosol (PYD3) suggests potentially complex metabolic regulation.

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The reductive pathway for the degradation of pyrimidine nucleotides in Arabidopsis. Names of enzymes catalysing each reaction are given with the AGI locus and gene name. The asterisk indicates C-2 of the pyrimidine ring, which is released as CO2 in the PYD3 reaction. The N-3 pyrimidine nitrogen (light highlighting) is also released as ammonia at this step. The fourth step, in which the putative β-alanine aminotransferase (BAT) transfers pyrimidine N-1 (darker highlighting) to pyruvate or 2-oxoglutarate to form l-alanine or l-glutamate, respectively, is not considered to be part of the reductive pathway. It is included here to illustrate the route by which both pyrimidine nitrogen atoms are assimilated into general nitrogen metabolism.
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fig01: The reductive pathway for the degradation of pyrimidine nucleotides in Arabidopsis. Names of enzymes catalysing each reaction are given with the AGI locus and gene name. The asterisk indicates C-2 of the pyrimidine ring, which is released as CO2 in the PYD3 reaction. The N-3 pyrimidine nitrogen (light highlighting) is also released as ammonia at this step. The fourth step, in which the putative β-alanine aminotransferase (BAT) transfers pyrimidine N-1 (darker highlighting) to pyruvate or 2-oxoglutarate to form l-alanine or l-glutamate, respectively, is not considered to be part of the reductive pathway. It is included here to illustrate the route by which both pyrimidine nitrogen atoms are assimilated into general nitrogen metabolism.

Mentions: In many bacteria, animals and plants (Wasternack, 1978; Rawls, 2006; Piskur et al., 2007), pyrimidine catabolism occurs via the ‘reductive’ pathway shown in Fig. 1. In this pathway, uracil (Ura) or thymine (Thy) degradation is initiated by dihydropyrimidine dehydrogenase (DHPDH, EC 1.3.1.2, PYD1) through NAD(P)H-dependent reduction of the C-5, C-6 double bond. The dihydrouracil (DHU) product of Ura reduction is hydrolytically degraded by dihydropyrimidinase (DHPase, EC 3.5.2.2, PYD2) to β-ureidopropionate (N-carbamyl-β-alanine), which is further metabolized to β-alanine, CO2 and NH3 by β-ureidopropionase (β-UPase, EC 3.5.1.6, PYD3). Thy catabolism to β-aminoisobutyrate (β-ΑΙΒ) in this pathway, with dihydrothymine and N-carbamyl-β-AIB intermediates, is also shown in Fig. 1. In Arabidopsis, each of the enzymes catalysing this three-step pathway is encoded by a single gene (Zrenner et al., 2006).


A functional analysis of the pyrimidine catabolic pathway in Arabidopsis.

Zrenner R, Riegler H, Marquard CR, Lange PR, Geserick C, Bartosz CE, Chen CT, Slocum RD - New Phytol. (2009)

The reductive pathway for the degradation of pyrimidine nucleotides in Arabidopsis. Names of enzymes catalysing each reaction are given with the AGI locus and gene name. The asterisk indicates C-2 of the pyrimidine ring, which is released as CO2 in the PYD3 reaction. The N-3 pyrimidine nitrogen (light highlighting) is also released as ammonia at this step. The fourth step, in which the putative β-alanine aminotransferase (BAT) transfers pyrimidine N-1 (darker highlighting) to pyruvate or 2-oxoglutarate to form l-alanine or l-glutamate, respectively, is not considered to be part of the reductive pathway. It is included here to illustrate the route by which both pyrimidine nitrogen atoms are assimilated into general nitrogen metabolism.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2713857&req=5

fig01: The reductive pathway for the degradation of pyrimidine nucleotides in Arabidopsis. Names of enzymes catalysing each reaction are given with the AGI locus and gene name. The asterisk indicates C-2 of the pyrimidine ring, which is released as CO2 in the PYD3 reaction. The N-3 pyrimidine nitrogen (light highlighting) is also released as ammonia at this step. The fourth step, in which the putative β-alanine aminotransferase (BAT) transfers pyrimidine N-1 (darker highlighting) to pyruvate or 2-oxoglutarate to form l-alanine or l-glutamate, respectively, is not considered to be part of the reductive pathway. It is included here to illustrate the route by which both pyrimidine nitrogen atoms are assimilated into general nitrogen metabolism.
Mentions: In many bacteria, animals and plants (Wasternack, 1978; Rawls, 2006; Piskur et al., 2007), pyrimidine catabolism occurs via the ‘reductive’ pathway shown in Fig. 1. In this pathway, uracil (Ura) or thymine (Thy) degradation is initiated by dihydropyrimidine dehydrogenase (DHPDH, EC 1.3.1.2, PYD1) through NAD(P)H-dependent reduction of the C-5, C-6 double bond. The dihydrouracil (DHU) product of Ura reduction is hydrolytically degraded by dihydropyrimidinase (DHPase, EC 3.5.2.2, PYD2) to β-ureidopropionate (N-carbamyl-β-alanine), which is further metabolized to β-alanine, CO2 and NH3 by β-ureidopropionase (β-UPase, EC 3.5.1.6, PYD3). Thy catabolism to β-aminoisobutyrate (β-ΑΙΒ) in this pathway, with dihydrothymine and N-carbamyl-β-AIB intermediates, is also shown in Fig. 1. In Arabidopsis, each of the enzymes catalysing this three-step pathway is encoded by a single gene (Zrenner et al., 2006).

Bottom Line: * Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to beta-alanine, CO(2) and NH(3) through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and beta-ureidopropionase (EC 3.5.1.6, PYD3). * A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism.PYD expression and catabolism of [2-(14)C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source. * PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-(14)C]-uracil or to grow on uracil as the sole nitrogen source.By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute of Molecular Plant Physiology, Golm, Germany. zrenner@igzev.de

ABSTRACT
* Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to beta-alanine, CO(2) and NH(3) through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and beta-ureidopropionase (EC 3.5.1.6, PYD3). * A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism. PYD expression and catabolism of [2-(14)C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source. * PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-(14)C]-uracil or to grow on uracil as the sole nitrogen source. By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source. These results confirm PYD1 function and suggest the possible existence of another, as yet unknown, activity for uracil degradation to dihydrouracil in this plant. * The localization of PYD-green fluorescent protein fusions in the plastid (PYD1), secretory system (PYD2) and cytosol (PYD3) suggests potentially complex metabolic regulation.

Show MeSH
Related in: MedlinePlus