1
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Hvorecny KL, Hargett K, Quispe JD, Kollman JM. Human PRPS1 filaments stabilize allosteric sites to regulate activity. Nat Struct Mol Biol 2023; 30:391-402. [PMID: 36747094 PMCID: PMC10033377 DOI: 10.1038/s41594-023-00921-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 01/10/2023] [Indexed: 02/08/2023]
Abstract
The universally conserved enzyme phosphoribosyl pyrophosphate synthetase (PRPS) assembles filaments in evolutionarily diverse organisms. PRPS is a key regulator of nucleotide metabolism, and mutations in the human enzyme PRPS1 lead to a spectrum of diseases. Here we determine structures of human PRPS1 filaments in active and inhibited states, with fixed assembly contacts accommodating both conformations. The conserved assembly interface stabilizes the binding site for the essential activator phosphate, increasing activity in the filament. Some disease mutations alter assembly, supporting the link between filament stability and activity. Structures of active PRPS1 filaments turning over substrate also reveal coupling of catalysis in one active site with product release in an adjacent site. PRPS1 filaments therefore provide an additional layer of allosteric control, conserved throughout evolution, with likely impact on metabolic homeostasis. Stabilization of allosteric binding sites by polymerization adds to the growing diversity of assembly-based enzyme regulatory mechanisms.
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Affiliation(s)
- Kelli L Hvorecny
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kenzee Hargett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel D Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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2
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PRPS2 mutations drive acute lymphoblastic leukemia relapse through influencing PRPS1/2 hexamer stability. BLOOD SCIENCE 2022; 5:39-50. [PMID: 36742181 PMCID: PMC9891442 DOI: 10.1097/bs9.0000000000000139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Tumor relapse is the major cause of treatment failure in childhood acute lymphoblastic leukemia (ALL), yet the underlying mechanisms are still elusive. Here, we demonstrate that phosphoribosyl pyrophosphate synthetase 2 (PRPS2) mutations drive ALL relapse through influencing PRPS1/2 hexamer stability. Ultra-deep sequencing was performed to identify PRPS2 mutations in ALL samples. The effects of PRPS2 mutations on cell survival, cell apoptosis, and drug resistance were evaluated. In vitro PRPS2 enzyme activity and ADP/GDP feedback inhibition of PRPS enzyme activity were assessed. Purine metabolites were analyzed by ultra-performance liquid-chromatography tandem mass spectrometry (UPLC-MS/MS). Integrating sequencing data with clinical information, we identified PRPS2 mutations only in relapsed childhood ALL with thiopurine therapy. Functional PRPS2 mutations mediated purine metabolism specifically on thiopurine treatment by influencing PRPS1/2 hexamer stability, leading to reduced nucleotide feedback inhibition of PRPS activity and enhanced thiopurine resistance. The 3-amino acid V103-G104-E105, the key difference between PRPS1 and PRPS2, insertion in PRPS2 caused severe steric clash to the interface of PRPS hexamer, leading to its low enzyme activity. In addition, we demonstrated that PRPS2 P173R increased thiopurine resistance in xenograft models. Our work describes a novel mechanism by which PRPS2 mutants drive childhood ALL relapse and highlights PRPS2 mutations as biomarkers for relapsed childhood ALL.
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3
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Ugbogu EA, Schweizer LM, Schweizer M. Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. Cells 2022; 11:1909. [PMID: 35741038 PMCID: PMC9221600 DOI: 10.3390/cells11121909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphoribosyl pyrophosphate synthetase (PRS EC 2.7.6.1) is a rate-limiting enzyme that irreversibly catalyzes the formation of phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate and adenosine triphosphate (ATP). This key metabolite is required for the synthesis of purine and pyrimidine nucleotides, the two aromatic amino acids histidine and tryptophan, the cofactors nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), all of which are essential for various life processes. Despite its ubiquity and essential nature across the plant and animal kingdoms, PRPP synthetase displays species-specific characteristics regarding the number of gene copies and architecture permitting interaction with other areas of cellular metabolism. The impact of mutated PRS genes in the model eukaryote Saccharomyces cerevisiae on cell signalling and metabolism may be relevant to the human neuropathies associated with PRPS mutations. Human PRPS1 and PRPS2 gene products are implicated in drug resistance associated with recurrent acute lymphoblastic leukaemia and progression of colorectal cancer and hepatocellular carcinoma. The investigation of PRPP metabolism in accepted model organisms, e.g., yeast and zebrafish, has the potential to reveal novel drug targets for treating at least some of the diseases, often characterized by overlapping symptoms, such as Arts syndrome and respiratory infections, and uncover the significance and relevance of human PRPS in disease diagnosis, management, and treatment.
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Affiliation(s)
- Eziuche A. Ugbogu
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Lilian M. Schweizer
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Michael Schweizer
- Institute of Biological Chemistry, Biophysics & Engineering (IB3), School of Engineering &Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK
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4
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Yang Y, Song L, Huang X, Feng Y, Zhang Y, Liu Y, Li S, Zhan Z, Zheng L, Feng H, Li Y. PRPS1-mediated purine biosynthesis is critical for pluripotent stem cell survival and stemness. Aging (Albany NY) 2021; 13:4063-4078. [PMID: 33493137 PMCID: PMC7906169 DOI: 10.18632/aging.202372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 11/10/2020] [Indexed: 01/24/2023]
Abstract
Pluripotent stem cells (PSCs) have a unique energetic and biosynthetic metabolism compared with typically differentiated cells. However, the metabolism profiling of PSCs and its underlying mechanism are still unclear. Here, we report PSCs metabolism profiling and identify the purine synthesis enzymes, phosphoribosyl pyrophosphate synthetase 1/2 (PRPS1/2), are critical for PSCs stemness and survival. Ultra-high performance liquid chromatography/mass spectroscopy (UHPLC-MS) analysis revealed that purine synthesis intermediate metabolite levels in PSCs are higher than that in somatic cells. Ectopic expression of PRPS1/2 did not improve purine biosynthesis, drug resistance, or stemness in PSCs. However, knockout of PRPS1 caused PSCs DNA damage and apoptosis. Depletion of PRPS2 attenuated PSCs stemness and assisted PSCs differentiation. Our finding demonstrates that PRPS1/2-mediated purine biosynthesis is critical for pluripotent stem cell stemness and survival.
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Affiliation(s)
- Yi Yang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lili Song
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xia Huang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yanan Feng
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yingwen Zhang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yanfeng Liu
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, Shandong, China
| | - Shanshan Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhiyan Zhan
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liang Zheng
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Haizhong Feng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yanxin Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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5
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Maldonado R, Talana CA, Song C, Dixon A, Uehara K, Weichhaus M. β-hydroxybutyrate does not alter the effects of glucose deprivation on breast cancer cells. Oncol Lett 2020; 21:65. [PMID: 33281976 PMCID: PMC7709568 DOI: 10.3892/ol.2020.12326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/29/2020] [Indexed: 12/04/2022] Open
Abstract
Ketogenic diets have the potential to lower glucose availability to cancer cells. However, the effect that the resulting increase in ketone bodies has on cancer cells is not fully understood. The present study explored the effect of β-hydroxybutyrate (BHB) on glucose-deprived MCF-7 and T47D breast cancer cells. Cell proliferation was decreased in response to lower glucose conditions, which could not be rescued consistently by 10 or 25 mM BHB supplementation. In addition, gene expression levels were altered when cells were glucose deprived. Reducing glucose availability of cancer cells to 225 mg/l for 4 days significantly decreased the expression of 113 genes and increased the expression of 100 genes in MCF-7 breast cancer cells, and significantly decreased the expression of 425 genes and increased the expression of 447 genes in T47D breast cancer cells. Pathway enrichment analysis demonstrated that glucose deprivation decreased activity of the Hippo-Yap cell signaling pathway in MCF-7 breast cancer cells, whereas it increased the expression of genes in the NRF2-pathaway and genes regulating ferroptosis in T47D breast cancer cells. Treatment of glucose-deprived cells with 10 or 25 mM BHB significantly changed the expression of 14 genes in MCF-7 breast cancer cells and 40 genes in T47D breast cancer cells. No significant pathway enrichment was detected when glucose-deprived cells were treated with BHB. Both cell lines expressed the enzymes (OXCT1/2, BDH1 and ACAT1/2) responsible for metabolizing BHB to acetyl-CoA, yet expression of these enzymes was not altered by either glucose deprivation or BHB treatment. In the publicly available The Cancer Genome Atlas (TCGA), increased expression of ketone body-catabolizing enzymes was observed in various types of cancer based on mRNA expression z-scores. Increased expression of BDH1 and ACAT1 significantly decreased overall survival of patients with breast cancer in TCGA studies, while decreased OXCT1 expression non-significantly decreased overall survival. In conclusion, neither MCF-7 nor T47D breast cancer cells were affected by BHB during glucose deprivation; however, screening of tumors for activation of ketone body-metabolizing enzymes may be able to identify patients that will benefit from ketogenic diet interventions.
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Affiliation(s)
- Rylee Maldonado
- Laboratory of Molecular Cancer Research, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA
| | - Chloe Adrienna Talana
- Laboratory of Molecular Cancer Research, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA
| | - Cassaundra Song
- Laboratory of Molecular Cancer Research, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA.,Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marchall University, Huntington, WV 25755, USA
| | - Alyssa Dixon
- Laboratory of Molecular Cancer Research, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA
| | - Kahealani Uehara
- Laboratory of Molecular Cancer Research, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA.,Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael Weichhaus
- Laboratory of Molecular Cancer Research, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA
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6
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Sauvaget M, Hutton F, Coull R, Vavassori S, Wang K, Reznik A, Chyker T, Newfield CG, Euston E, Benary G, Schweizer LM, Schweizer M. The NHR1-1 of Prs1 and the pentameric motif 284KKCPK288 of Prs3 permit multi-functionality of the PRPP synthetase in Saccharomyces cerevisiae. FEMS Yeast Res 2019; 19:5288342. [PMID: 30649305 DOI: 10.1093/femsyr/foz006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/10/2019] [Indexed: 12/23/2022] Open
Abstract
The five-membered PRS gene family of Saccharomyces cerevisiae is an example of gene duplication allowing the acquisition of novel functions. Each of the five Prs polypeptides is theoretically capable of synthesising PRPP but at least one of the following heterodimers is required for survival: Prs1/Prs3, Prs2/Prs5 and Prs4/Prs5. Prs3 contains a pentameric motif 284KKCPK288 found only in nuclear proteins. Deletion of 284KKCPK288 destabilises the Prs1/Prs3 complex resulting in a cascade of events, including reduction in PRPP synthetase activity and altered cell wall integrity (CWI) as measured by caffeine sensitivity and Rlm1 expression. Prs3 also interacts with the kinetochore-associated protein, Nuf2. Following the possibility of 284KKCPK288-mediated transport of the Prs1/Prs3 complex to the nucleus, it may interact with Nuf2 and phosphorylated Slt2 permitting activation of Rlm1. This scenario explains the breakdown of CWI encountered in mutants lacking PRS3 or deleted for 284KKCPK288. However, removal of NHR1-1 from Prs1 does not disrupt the Prs1/Prs3 interaction as shown by increased PRPP synthetase activity. This is evidence for the separation of the two metabolic functions of the PRPP-synthesising machinery: provision of PRPP and maintenance of CWI and is an example of evolutionary development when multiple copies of a gene were present in the ancestral organism.
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Affiliation(s)
- Maëlle Sauvaget
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Fraser Hutton
- Institute of Life & Earth Sciences, School of Energy, Geoscience, Infrastructure & Society, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Robert Coull
- Institute of Life & Earth Sciences, School of Energy, Geoscience, Infrastructure & Society, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Stefano Vavassori
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Ke Wang
- School of Life Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Aleksandra Reznik
- School of Life Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Tatsiana Chyker
- School of Life Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Chelsea G Newfield
- Institute of Life & Earth Sciences, School of Energy, Geoscience, Infrastructure & Society, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Eloise Euston
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Gerrit Benary
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Lilian M Schweizer
- School of Life Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Michael Schweizer
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
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7
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Chen P, Liu Z, Wang X, Peng J, Sun Q, Li J, Wang M, Niu L, Zhang Z, Cai G, Teng M, Li X. Crystal and EM structures of human phosphoribosyl pyrophosphate synthase I (PRS1) provide novel insights into the disease-associated mutations. PLoS One 2015; 10:e0120304. [PMID: 25781187 PMCID: PMC4363470 DOI: 10.1371/journal.pone.0120304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 02/05/2015] [Indexed: 11/30/2022] Open
Abstract
Human PRS1, which is indispensable for the biosynthesis of nucleotides, deoxynucleotides and their derivatives, is associated directly with multiple human diseases because of single base mutation. However, a molecular understanding of the effect of these mutations is hampered by the lack of understanding of its catalytic mechanism. Here, we reconstruct the 3D EM structure of the PRS1 apo state. Together with the native stain EM structures of AMPNPP, AMPNPP and R5P, ADP and the apo states with distinct conformations, we suggest the hexamer is the enzymatically active form. Based on crystal structures, sequence analysis, mutagenesis, enzyme kinetics assays, and MD simulations, we reveal the conserved substrates binding motifs and make further analysis of all pathogenic mutants.
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Affiliation(s)
- Peng Chen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Zheng Liu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Xuejuan Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Junhui Peng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Qianqian Sun
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Jianzhong Li
- Department of Otolaryngology Head and Neck Surgery, Fuzhou general hospital of Nanjing Command, PLA, Fuzhou 350025, China
| | - Mingxing Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Gang Cai
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
- * E-mail: (XL); (MT); (GC)
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
- * E-mail: (XL); (MT); (GC)
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
- * E-mail: (XL); (MT); (GC)
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8
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Goo JS, Kim YN, Choi KM, Hwang IS, Kim JE, Lee YJ, Kwak MH, Shim SB, Jee SW, Lim CJ, Seong JK, Hwang DY. Proteomic analysis of kidneys from selenoprotein M transgenic rats in response to increased bioability of selenium. Clin Proteomics 2013; 10:10. [PMID: 23937859 PMCID: PMC3751301 DOI: 10.1186/1559-0275-10-10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 07/31/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To characterize changes in global protein expression in kidneys of transgenic rats overexpressing human selenoprotein M (SelM) in response to increased bioabivility of selenium (Sel), total proteins extracted from kidneys of 10-week-old CMV/hSelM Tg and wild-type rats were separated by 2-dimensional gel electrophoresis and measured for changes in expression. RESULTS Ten and three proteins showing high antioxidant enzymatic activity were up- and down-regulated, respectively, in SelM-overexpressing CMV/hSelM Tg rats compared to controls based on an arbitrary 2-fold difference. Up-regulated proteins included LAP3, BAIAP2L1, CRP2, CD73 antigen, PDGF D, KIAA143 homolog, PRPPS-AP2, ZFP313, HSP-60, and N-WASP, whereas down-regulated proteins included ALKDH3, rMCP-3, and STC-1. After Sel treatment, five of the up-regulated proteins were significantly increased in expression in wild-type rats, whereas there were no changes in CMV/hSelM Tg rats. Only two of the down-regulated proteins showed reduced expression in wild-type and Tg rats after Sel treatment. CONCLUSIONS These results show the primary novel biological evidences that new functional protein groups and individual proteins in kidneys of Tg rats relate to Sel biology including the response to Sel treatment and SelM expression.
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Affiliation(s)
- Jun Seo Goo
- Department of Biomaterials Science, College of Natural Resources & Life Science, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea
| | - Yo Na Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, BK21 Program for Veterinary Science, Seoul National University, Seoul 151-742, South Korea
| | - Kyung Mi Choi
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, BK21 Program for Veterinary Science, Seoul National University, Seoul 151-742, South Korea
| | - In Sik Hwang
- Department of Biomaterials Science, College of Natural Resources & Life Science, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea
| | - Ji Eun Kim
- Department of Biomaterials Science, College of Natural Resources & Life Science, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea
| | - Young Ju Lee
- Department of Biomaterials Science, College of Natural Resources & Life Science, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea
| | - Moon Hwa Kwak
- Department of Biomaterials Science, College of Natural Resources & Life Science, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea
| | - Sun Bo Shim
- Department of Laboratory Animal Resources, National Institute of Food and Drug Safety, Korea FDA, Osong 363-700, Korea
| | - Seung Wan Jee
- Department of Laboratory Animal Resources, National Institute of Food and Drug Safety, Korea FDA, Osong 363-700, Korea
| | - Chul Joo Lim
- Department of Laboratory Animal Resources, National Institute of Food and Drug Safety, Korea FDA, Osong 363-700, Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, BK21 Program for Veterinary Science, Seoul National University, Seoul 151-742, South Korea.,Interdisciplinary Program for Bioinformatics, Program or Cancer Biology and BIO-MAX Institute, Seoul National University, Seoul 151-742, South Korea
| | - Dae Youn Hwang
- Department of Biomaterials Science, College of Natural Resources & Life Science, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea
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9
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Oka T, Tagawa K, Ito H, Okazawa H. Dynamic changes of the phosphoproteome in postmortem mouse brains. PLoS One 2011; 6:e21405. [PMID: 21731734 PMCID: PMC3120861 DOI: 10.1371/journal.pone.0021405] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 05/27/2011] [Indexed: 12/13/2022] Open
Abstract
Protein phosphorylation is deeply involved in the pathological mechanism of various neurodegenerative disorders. However, in human pathological samples, phosphorylation can be modified during preservation by postmortem factors such as time and temperature. Postmortem changes may also differ among proteins. Unfortunately, there is no comprehensive database that could support the analysis of protein phosphorylation in human brain samples from the standpoint of postmortem changes. As a first step toward addressing the issue, we performed phosphoproteome analysis with brain tissue dissected from mouse bodies preserved under different conditions. Quantitative whole proteome mass analysis showed surprisingly diverse postmortem changes in phosphoproteins that were dependent on temperature, time and protein species. Twelve hrs postmortem was a critical time point for preservation at room temperature. At 4°C, after the body was cooled down, most phosphoproteins were stable for 72 hrs. At either temperature, increase greater than 2-fold was exceptional during this interval. We found several standard proteins by which we can calculate the postmortem time at room temperature. The information obtained in this study will be indispensable for evaluating experimental data with human as well as mouse brain samples.
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Affiliation(s)
- Tsutomu Oka
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuhiko Tagawa
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hikaru Ito
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hitoshi Okazawa
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- * E-mail:
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10
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Huang EP, Fridlyand J, Lewin-Koh N, Yue P, Shi X, Dornan D, Burington B. Statistical techniques to construct assays for identifying likely responders to a treatment under evaluation from cell line genomic data. BMC Cancer 2010; 10:586. [PMID: 20979617 PMCID: PMC2984428 DOI: 10.1186/1471-2407-10-586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 10/27/2010] [Indexed: 11/17/2022] Open
Abstract
Background Developing the right drugs for the right patients has become a mantra of drug development. In practice, it is very difficult to identify subsets of patients who will respond to a drug under evaluation. Most of the time, no single diagnostic will be available, and more complex decision rules will be required to define a sensitive population, using, for instance, mRNA expression, protein expression or DNA copy number. Moreover, diagnostic development will often begin with in-vitro cell-line data and a high-dimensional exploratory platform, only later to be transferred to a diagnostic assay for use with patient samples. In this manuscript, we present a novel approach to developing robust genomic predictors that are not only capable of generalizing from in-vitro to patient, but are also amenable to clinically validated assays such as qRT-PCR. Methods Using our approach, we constructed a predictor of sensitivity to dacetuzumab, an investigational drug for CD40-expressing malignancies such as lymphoma using genomic measurements of cell lines treated with dacetuzumab. Additionally, we evaluated several state-of-the-art prediction methods by independently pairing the feature selection and classification components of the predictor. In this way, we constructed several predictors that we validated on an independent DLBCL patient dataset. Similar analyses were performed on genomic measurements of breast cancer cell lines and patients to construct a predictor of estrogen receptor (ER) status. Results The best dacetuzumab sensitivity predictors involved ten or fewer genes and accurately classified lymphoma patients by their survival and known prognostic subtypes. The best ER status classifiers involved one or two genes and led to accurate ER status predictions more than 85% of the time. The novel method we proposed performed as well or better than other methods evaluated. Conclusions We demonstrated the feasibility of combining feature selection techniques with classification methods to develop assays using cell line genomic measurements that performed well in patient data. In both case studies, we constructed parsimonious models that generalized well from cell lines to patients.
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Affiliation(s)
- Erich P Huang
- Biometric Research Branch - Department of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health. Rockville, MD 20852, USA
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Valproic acid- and lithium-sensitivity in prs mutants of Saccharomyces cerevisiae. Biochem Soc Trans 2009; 37:1115-20. [PMID: 19754463 DOI: 10.1042/bst0371115] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Prs [PRPP (phosphoribosyl pyrophosphate) synthetase] catalyses the transfer of pyrophosphate from ATP to ribose 5-phosphate, thereby activating the pentose sugar for incorporation into purine and pyrimidine nucleotides. The Saccharomyces cerevisiae genome contains five genes, PRS1-PRS5, whose products display characteristic PRPP and bivalent-cation-binding sites of Prs polypeptides. Deletion of one or more of the five PRS genes has far-reaching and unexpected consequences, e.g. impaired cell integrity, temperature-sensitivity and sensitivity to VPA (valproic acid) and LiCl. CTP pools in prs1Delta and prs3Delta are reduced to 12 and 31% of the wild-type respectively, resulting in an imbalance in phospholipid metabolism which may have an impact on the intracellular inositol pool which is affected by the administration of either VPA or LiCl. Overexpression of CTP synthetase in prs1Delta prs3Delta strains partially reverses the VPA-sensitive phenotype. Yeast two-hybrid screening revealed that Prs3 and the yeast orthologue of GSK3 (glycogen synthase kinase 3), Rim11, a serine/threonine kinase involved in several signalling pathways, interact with each other. Furthermore, Prs5, an essential partner of Prs3, which also interacts with GSK3 contains three neighbouring phosphorylation sites, typical of GSK3 activation. These studies on yeast PRPP synthetases bring together and expand the current theories for the mood-stabilizing effects of VPA and LiCl in bipolar disorder.
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Becker MA. Phosphoribosylpyrophosphate synthetase and the regulation of phosphoribosylpyrophosphate production in human cells. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2001; 69:115-48. [PMID: 11550793 DOI: 10.1016/s0079-6603(01)69046-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
between purine nucleoside diphosphate inhibition and inorganic phosphate (Pi) activation; and intracellular concentration of the PRS1 isoform. The operation of additional determinants of rates of PRPP synthesis in human cells is suggested by: (1) multiple PRS isoforms with distinctive physical and kinetic properties; (2) nearly immediate activation of intracellular PRPP synthesis in response to mitogens, growth-promoters, and increased intracellular Mg2+ concentrations; (3) tissue-specific differences in PRS1 and PRS2 transcript and isoform expression; and (4) reversible association of PRS subunits with one another and/or with PRS-associated proteins (PAPs), as a result of which the catalytic and perhaps regulatory properties of PRS isoforms are modified.
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Affiliation(s)
- M A Becker
- The Unversity of Chicago, University of Chicago Medical Center, Illinois 60637, USA
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Hernando Y, Carter AT, Parr A, Hove-Jensen B, Schweizer M. Genetic analysis and enzyme activity suggest the existence of more than one minimal functional unit capable of synthesizing phosphoribosyl pyrophosphate in Saccharomyces cerevisiae. J Biol Chem 1999; 274:12480-7. [PMID: 10212224 DOI: 10.1074/jbc.274.18.12480] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PRS gene family in Saccharomyces cerevisiae consists of five genes each capable of encoding a 5-phosphoribosyl-1(alpha)-pyrophosphate synthetase polypeptide. To gain insight into the functional organization of this gene family we have constructed a collection of strains containing all possible combinations of disruptions in the five PRS genes. Phenotypically these deletant strains can be classified into three groups: (i) a lethal phenotype that corresponds to strains containing a double disruption in PRS2 and PRS4 in combination with a disruption in either PRS1 or PRS3; simultaneous deletion of PRS1 and PRS5 or PRS3 and PRS5 are also lethal combinations; (ii) a second phenotype that is encountered in strains containing disruptions in PRS1 and PRS3 together or in combination with any of the other PRS genes manifests itself as a reduction in growth rate, enzyme activity, and nucleotide content; (iii) a third phenotype that corresponds to strains that, although affected in their phosphoribosyl pyrophosphate-synthesizing ability, are unimpaired for growth and have nucleotide profiles virtually the same as the wild type. Deletions of PRS2, PRS4, and PRS5 or combinations thereof cause this phenotype. These results suggest that the polypeptides encoded by the members of the PRS gene family may be organized into two functional entities. Evidence that these polypeptides interact with each other in vivo was obtained using the yeast two-hybrid system. Specifically PRS1 and PRS3 polypeptides interact strongly with each other, and there are significant interactions between the PRS5 polypeptide and either the PRS2 or PRS4 polypeptides. These data suggest that yeast phosphoribosyl pyrophosphate synthetase exists in vivo as multimeric complex(es).
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Affiliation(s)
- Y Hernando
- Genetics and Microbiology Department, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, United Kingdom
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Katashima R, Iwahana H, Fujimura M, Yamaoka T, Itakura M. Assignment of the human phosphoribosylpyrophosphate synthetase-associated protein 41 gene (PRPSAP2) to 17p11.2-p12. Genomics 1998; 54:180-1. [PMID: 9806849 DOI: 10.1006/geno.1998.5432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- R Katashima
- School of Medicine, Institute for Genome Research, Tokushima, 770-8503, Japan
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