Nucleotide degradation and ribose salvage in yeast
Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated wi...
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| Published in | Molecular systems biology Vol. 9; no. 1; pp. 665 - n/a |
|---|---|
| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
2013
John Wiley & Sons, Ltd EMBO Press Wiley European Molecular Biology Organization Springer Nature |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1744-4292 1744-4292 |
| DOI | 10.1038/msb.2013.21 |
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| Abstract | Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose‐derived carbon accumulates as sedoheptulose‐7‐phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde‐3‐phosphate. Oxidative stress increases glyceraldehyde‐3‐phosphate, resulting in rapid consumption of sedoheptulose‐7‐phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress.
Metabolomics, genetics and biochemistry were combined to obtain the first complete map of the nucleotide degradation and ribose salvage pathway in yeast. This pathway promotes yeast survival in starvation and oxidative stress.
Synopsis
Metabolomics, genetics and biochemistry were combined to obtain the first complete map of the nucleotide degradation and ribose salvage pathway in yeast. This pathway promotes yeast survival in starvation and oxidative stress.
During carbon starvation, ribose salvage from nucleotides promotes yeast survival.
The salvage pathway requires the previously misannotated nucleotidase Phm8.
Ribose‐derived carbon accumulates as sedoheptulose‐7‐phosphate.
This carbon reserve enables rapid NADPH production in oxidative stress. |
|---|---|
| AbstractList | Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose-derived carbon accumulates as sedoheptulose-7-phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde-3-phosphate. Oxidative stress increases glyceraldehyde-3-phosphate, resulting in rapid consumption of sedoheptulose-7-phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress. Metabolomics, genetics and biochemistry were combined to obtain the first complete map of the nucleotide degradation and ribose salvage pathway in yeast. This pathway promotes yeast survival in starvation and oxidative stress. During carbon starvation, ribose salvage from nucleotides promotes yeast survival. The salvage pathway requires the previously misannotated nucleotidase Phm8. Ribose-derived carbon accumulates as sedoheptulose-7-phosphate. This carbon reserve enables rapid NADPH production in oxidative stress. Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose-derived carbon accumulates as sedoheptulose-7-phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde-3-phosphate. Oxidative stress increases glyceraldehyde-3-phosphate, resulting in rapid consumption of sedoheptulose-7-phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress. Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose‐derived carbon accumulates as sedoheptulose‐7‐phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde‐3‐phosphate. Oxidative stress increases glyceraldehyde‐3‐phosphate, resulting in rapid consumption of sedoheptulose‐7‐phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress. Metabolomics, genetics and biochemistry were combined to obtain the first complete map of the nucleotide degradation and ribose salvage pathway in yeast. This pathway promotes yeast survival in starvation and oxidative stress. Metabolomics, genetics and biochemistry were combined to obtain the first complete map of the nucleotide degradation and ribose salvage pathway in yeast. This pathway promotes yeast survival in starvation and oxidative stress. image During carbon starvation, ribose salvage from nucleotides promotes yeast survival. The salvage pathway requires the previously misannotated nucleotidase Phm8. Ribose‐derived carbon accumulates as sedoheptulose‐7‐phosphate. This carbon reserve enables rapid NADPH production in oxidative stress. Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose-derived carbon accumulates as sedoheptulose-7-phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde-3-phosphate. Oxidative stress increases glyceraldehyde-3-phosphate, resulting in rapid consumption of sedoheptulose-7-phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress. Metabolomics, genetics and biochemistry were combined to obtain the first complete map of the nucleotide degradation and ribose salvage pathway in yeast. This pathway promotes yeast survival in starvation and oxidative stress. Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose-derived carbon accumulates as sedoheptulose-7-phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde-3-phosphate. Oxidative stress increases glyceraldehyde-3-phosphate, resulting in rapid consumption of sedoheptulose-7-phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress.Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose-derived carbon accumulates as sedoheptulose-7-phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde-3-phosphate. Oxidative stress increases glyceraldehyde-3-phosphate, resulting in rapid consumption of sedoheptulose-7-phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress. Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose‐derived carbon accumulates as sedoheptulose‐7‐phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde‐3‐phosphate. Oxidative stress increases glyceraldehyde‐3‐phosphate, resulting in rapid consumption of sedoheptulose‐7‐phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress. Metabolomics, genetics and biochemistry were combined to obtain the first complete map of the nucleotide degradation and ribose salvage pathway in yeast. This pathway promotes yeast survival in starvation and oxidative stress. Synopsis Metabolomics, genetics and biochemistry were combined to obtain the first complete map of the nucleotide degradation and ribose salvage pathway in yeast. This pathway promotes yeast survival in starvation and oxidative stress. During carbon starvation, ribose salvage from nucleotides promotes yeast survival. The salvage pathway requires the previously misannotated nucleotidase Phm8. Ribose‐derived carbon accumulates as sedoheptulose‐7‐phosphate. This carbon reserve enables rapid NADPH production in oxidative stress. Abstract Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose‐derived carbon accumulates as sedoheptulose‐7‐phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde‐3‐phosphate. Oxidative stress increases glyceraldehyde‐3‐phosphate, resulting in rapid consumption of sedoheptulose‐7‐phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress. |
| Author | Absalan, Farnaz Lu, Wenyun Caudy, Amy A Yakunin, Alexander F Létisse, Fabien Kuznetsova, Ekaterina Broach, James R Brown, Greg Xu, Yi‐Fan Rabinowitz, Joshua D |
| Author_xml | – sequence: 1 givenname: Yi‐Fan surname: Xu fullname: Xu, Yi‐Fan organization: Lewis Sigler Institute for Integrative Genomics, Princeton University, Department of Chemistry, Princeton University – sequence: 2 givenname: Fabien surname: Létisse fullname: Létisse, Fabien organization: Université de Toulouse, INSA, UPS, INP; LISBP – sequence: 3 givenname: Farnaz surname: Absalan fullname: Absalan, Farnaz organization: Department of Molecular Biology, Princeton University – sequence: 4 givenname: Wenyun surname: Lu fullname: Lu, Wenyun organization: Lewis Sigler Institute for Integrative Genomics, Princeton University – sequence: 5 givenname: Ekaterina surname: Kuznetsova fullname: Kuznetsova, Ekaterina organization: Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto – sequence: 6 givenname: Greg surname: Brown fullname: Brown, Greg organization: Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto – sequence: 7 givenname: Amy A surname: Caudy fullname: Caudy, Amy A organization: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto – sequence: 8 givenname: Alexander F surname: Yakunin fullname: Yakunin, Alexander F organization: Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto – sequence: 9 givenname: James R surname: Broach fullname: Broach, James R organization: Department of Molecular Biology, Princeton University – sequence: 10 givenname: Joshua D surname: Rabinowitz fullname: Rabinowitz, Joshua D email: joshr@princeton.edu organization: Lewis Sigler Institute for Integrative Genomics, Princeton University, Department of Chemistry, Princeton University, Chemistry and Genomics, Princeton University |
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| Keywords | nutrient starvation mass spectrometry metabolism autophagy Subject Categories: RNA cellular metabolism Keywords: autophagy Saccharomyces cerevisiae |
| Language | English |
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| Snippet | Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient... Metabolomics, genetics and biochemistry were combined to obtain the first complete map of the nucleotide degradation and ribose salvage pathway in yeast. This... Abstract Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway.... |
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| SubjectTerms | Ablation AMP-Activated Protein Kinases - genetics AMP-Activated Protein Kinases - metabolism Antioxidants autophagy BASIC BIOLOGICAL SCIENCES Biochemistry Biochemistry & Molecular Biology Biodegradation Carbon Chromatography Consumption Cyclic AMP-Dependent Protein Kinases - genetics Cyclic AMP-Dependent Protein Kinases - metabolism Degradation Depletion E coli EMBO21 EMBO36 Enzymes Experiments Gene deletion Gene Expression Regulation, Fungal Genetics Genomes Glyceraldehyde Glyceraldehyde 3-Phosphate - metabolism Grants Hydrolase INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY Kinases Life Sciences mass spectrometry Metabolism Metabolites Metabolomics N-Glycosyl Hydrolases - deficiency N-Glycosyl Hydrolases - genetics NADP NADP - metabolism Nitrogen Nucleosides Nucleotides Nucleotides - metabolism nutrient starvation Nutrients Oxidative stress Pentose Pentose phosphate pathway Pentose Phosphate Pathway - genetics Phosphatase Phosphorylase Phosphorylases Physiology Protein Serine-Threonine Kinases - genetics Protein Serine-Threonine Kinases - metabolism Proteins Purine-Nucleoside Phosphorylase - deficiency Purine-Nucleoside Phosphorylase - genetics Ribose Ribose - metabolism Ribosomes Saccharomyces cerevisiae Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - metabolism Saccharomyces cerevisiae Proteins - genetics Saccharomyces cerevisiae Proteins - metabolism Signal Transduction Software Starvation Stress, Physiological - genetics Substrates Sugar Phosphates Transaldolase Transaldolase - genetics Transaldolase - metabolism Yeast |
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| Title | Nucleotide degradation and ribose salvage in yeast |
| URI | https://link.springer.com/article/10.1038/msb.2013.21 https://onlinelibrary.wiley.com/doi/abs/10.1038%2Fmsb.2013.21 https://www.ncbi.nlm.nih.gov/pubmed/23670538 https://www.proquest.com/docview/2299128941 https://www.proquest.com/docview/1351611801 https://www.proquest.com/docview/1566835059 https://insa-toulouse.hal.science/hal-02170940 https://www.osti.gov/servlets/purl/1623808 https://pubmed.ncbi.nlm.nih.gov/PMC4039369 https://doaj.org/article/3604c67e8fc44eb89cba3406fe3e0b45 |
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