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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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Rushton MD, Saunderson EA, Patani H, Green MR, Ficz G. An shRNA kinase screen identifies regulators of UHRF1 stability and activity in mouse embryonic stem cells. Epigenetics 2022; 17:1590-1607. [PMID: 35324392 DOI: 10.1080/15592294.2022.2044126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Propagation of DNA methylation through cell division relies on the recognition of methylated cytosines by UHRF1. In reprogramming of mouse embryonic stem cells to naive pluripotency (also known as ground state), despite high levels of Uhrf1 transcript, the protein is targeted for degradation by the proteasome, leading to DNA methylation loss. We have undertaken an shRNA screen to identify the signalling pathways that converge upon UHRF1 and control its degradation, using UHRF1-GFP fluorescence as readout. Many candidates we identified are key enzymes in regulation of glucose metabolism, nucleotide metabolism and Pi3K/AKT/mTOR pathway. Unexpectedly, while downregulation of all candidates we selected for validation rescued UHRF1 protein levels, we found that in some of the cases this was not sufficient to maintain DNA methylation. This has implications for development, ageing and diseased conditions. Our study demonstrates two separate processes that regulate UHRF1 protein abundance and activity.
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Affiliation(s)
- Michael D Rushton
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.,Horizon Discovery, Cambridge Research Park, 8100 Beach Dr, Waterbeach, Cambridge, CB25 9TL
| | - Emily A Saunderson
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Hemalvi Patani
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.,Research And Development, CS Genetics Ltd, Cambridge, UK
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
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Sridharan GV, D'Alessandro M, Bale SS, Bhagat V, Gagnon H, Asara JM, Uygun K, Yarmush ML, Saeidi N. Multi-omic network-based interrogation of rat liver metabolism following gastric bypass surgery featuring SWATH proteomics. TECHNOLOGY 2017; 5:139-184. [PMID: 29780857 PMCID: PMC5956888 DOI: 10.1142/s233954781750008x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Morbidly obese patients often elect for Roux-en-Y gastric bypass (RYGB), a form of bariatric surgery that triggers a remarkable 30% reduction in excess body weight and reversal of insulin resistance for those who are type II diabetic. A more complete understanding of the underlying molecular mechanisms that drive the complex metabolic reprogramming post-RYGB could lead to innovative non-invasive therapeutics that mimic the beneficial effects of the surgery, namely weight loss, achievement of glycemic control, or reversal of non-alcoholic steatohepatitis (NASH). To facilitate these discoveries, we hereby demonstrate the first multi-omic interrogation of a rodent RYGB model to reveal tissue-specific pathway modules implicated in the control of body weight regulation and energy homeostasis. In this study, we focus on and evaluate liver metabolism three months following RYGB in rats using both SWATH proteomics, a burgeoning label free approach using high resolution mass spectrometry to quantify protein levels in biological samples, as well as MRM metabolomics. The SWATH analysis enabled the quantification of 1378 proteins in liver tissue extracts, of which we report the significant down-regulation of Thrsp and Acot13 in RYGB as putative targets of lipid metabolism for weight loss. Furthermore, we develop a computational graph-based metabolic network module detection algorithm for the discovery of non-canonical pathways, or sub-networks, enriched with significantly elevated or depleted metabolites and proteins in RYGB-treated rat livers. The analysis revealed a network connection between the depleted protein Baat and the depleted metabolite taurine, corroborating the clinical observation that taurine-conjugated bile acid levels are perturbed post-RYGB.
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Affiliation(s)
- Gautham Vivek Sridharan
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Matthew D'Alessandro
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Shyam Sundhar Bale
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Vicky Bhagat
- Warren Alpert Medical School of Brown University, 222 Richmond St., Providence, RI 02903, USA
| | - Hugo Gagnon
- Phenoswitch Bioscience, 3001 12e Avenue N, Sherbrooke, QC J1H 5N4, Canada
| | - John M Asara
- Beth Israel Deaconness Medical Center, 3 Blackfan Circle Rm 425, Boston, MA 02115, USA
| | - Korkut Uygun
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Martin L Yarmush
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Nima Saeidi
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
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Bassett JHD, Gogakos A, White JK, Evans H, Jacques RM, van der Spek AH, Ramirez-Solis R, Ryder E, Sunter D, Boyde A, Campbell MJ, Croucher PI, Williams GR. Rapid-throughput skeletal phenotyping of 100 knockout mice identifies 9 new genes that determine bone strength. PLoS Genet 2012; 8:e1002858. [PMID: 22876197 PMCID: PMC3410859 DOI: 10.1371/journal.pgen.1002858] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/11/2012] [Indexed: 01/08/2023] Open
Abstract
Osteoporosis is a common polygenic disease and global healthcare priority but its genetic basis remains largely unknown. We report a high-throughput multi-parameter phenotype screen to identify functionally significant skeletal phenotypes in mice generated by the Wellcome Trust Sanger Institute Mouse Genetics Project and discover novel genes that may be involved in the pathogenesis of osteoporosis. The integrated use of primary phenotype data with quantitative x-ray microradiography, micro-computed tomography, statistical approaches and biomechanical testing in 100 unselected knockout mouse strains identified nine new genetic determinants of bone mass and strength. These nine new genes include five whose deletion results in low bone mass and four whose deletion results in high bone mass. None of the nine genes have been implicated previously in skeletal disorders and detailed analysis of the biomechanical consequences of their deletion revealed a novel functional classification of bone structure and strength. The organ-specific and disease-focused strategy described in this study can be applied to any biological system or tractable polygenic disease, thus providing a general basis to define gene function in a system-specific manner. Application of the approach to diseases affecting other physiological systems will help to realize the full potential of the International Mouse Phenotyping Consortium. Chronic disease represents a global healthcare burden but its genetic basis is largely unknown. To address this, a massive international investment is generating a resource of mutant mice to investigate the function of every gene. Although current characterization of mutants is broadbased, it lacks specificity. Here, we describe a new and rapid functional screening approach to identify genes involved in disease susceptibility. Using bone and osteoporosis as a paradigm, we identify nine new genes that determine bone structure and strength from a screen of 100 knockout mice. Deletion of five of the genes leads to low bone mass, whereas deletion of four results in high bone mass. We also report a novel functional classification that relates bone structure to bone strength and opens the field to collaborative research between material scientists, bioengineers and biologists. Our rapid throughput phenotyping approach can be applied to complex diseases in other physiological systems, thus realizing the full potential of the International Mouse Phenotyping Consortium.
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Affiliation(s)
- J. H. Duncan Bassett
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London, United Kingdom
| | - Apostolos Gogakos
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London, United Kingdom
| | - Jacqueline K. White
- Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Holly Evans
- The Mellanby Centre for Bone Research, Department of Human Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Richard M. Jacques
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
| | - Anne H. van der Spek
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London, United Kingdom
| | | | - Ramiro Ramirez-Solis
- Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Edward Ryder
- Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - David Sunter
- Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alan Boyde
- Queen Mary University of London, Oral Growth and Development, Institute of Dentistry, Bart's and The London School of Medicine, London, United Kingdom
| | - Michael J. Campbell
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
| | - Peter I. Croucher
- The Mellanby Centre for Bone Research, Department of Human Metabolism, University of Sheffield, Sheffield, United Kingdom
- Garvan Institute of Medical Research, Sydney, Australia
- * E-mail: (GRW), (PIC)
| | - Graham R. Williams
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London, United Kingdom
- * E-mail: (GRW), (PIC)
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Hyperuricemia cosegregating with osteogenesis imperfecta is associated with a mutation in GPATCH8. Hum Genet 2011; 130:671-83. [DOI: 10.1007/s00439-011-1006-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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