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Niphadkar S, Karinje L, Laxman S. The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and enables adaptation to glucose depletion. PLoS Genet 2024; 20:e1011202. [PMID: 38452140 PMCID: PMC10950219 DOI: 10.1371/journal.pgen.1011202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/19/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
To sustain growth in changing nutrient conditions, cells reorganize outputs of metabolic networks and appropriately reallocate resources. Signaling by reversible protein phosphorylation can control such metabolic adaptations. In contrast to kinases, the functions of phosphatases that enable metabolic adaptation as glucose depletes are poorly studied. Using a Saccharomyces cerevisiae deletion screen, we identified the PP2A-like phosphatase Ppg1 as required for appropriate carbon allocations towards gluconeogenic outputs-trehalose, glycogen, UDP-glucose, UDP-GlcNAc-after glucose depletion. This Ppg1 function is mediated via regulation of the assembly of the Far complex-a multi-subunit complex that tethers to the ER and mitochondrial outer membranes forming localized signaling hubs. The Far complex assembly is Ppg1 catalytic activity-dependent. Ppg1 regulates the phosphorylation status of multiple ser/thr residues on Far11 to enable the proper assembly of the Far complex. The assembled Far complex is required to maintain gluconeogenic outputs after glucose depletion. Glucose in turn regulates Far complex amounts. This Ppg1-mediated Far complex assembly, and Ppg1-Far complex dependent control of gluconeogenic outputs enables adaptive growth under glucose depletion. Our study illustrates how protein dephosphorylation is required for the assembly of a multi-protein scaffold present in localized cytosolic pools, to thereby alter gluconeogenic flux and enable cells to metabolically adapt to nutrient fluctuations.
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Affiliation(s)
- Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lavanya Karinje
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
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Wang Y, Engel T, Teng X. Post-translational regulation of the mTORC1 pathway: A switch that regulates metabolism-related gene expression. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195005. [PMID: 38242428 DOI: 10.1016/j.bbagrm.2024.195005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is a kinase complex that plays a crucial role in coordinating cell growth in response to various signals, including amino acids, growth factors, oxygen, and ATP. Activation of mTORC1 promotes cell growth and anabolism, while its suppression leads to catabolism and inhibition of cell growth, enabling cells to withstand nutrient scarcity and stress. Dysregulation of mTORC1 activity is associated with numerous diseases, such as cancer, metabolic disorders, and neurodegenerative conditions. This review focuses on how post-translational modifications, particularly phosphorylation and ubiquitination, modulate mTORC1 signaling pathway and their consequential implications for pathogenesis. Understanding the impact of phosphorylation and ubiquitination on the mTORC1 signaling pathway provides valuable insights into the regulation of cellular growth and potential therapeutic targets for related diseases.
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Affiliation(s)
- Yitao Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China; Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Tobias Engel
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Xinchen Teng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.
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Broder BA, Bhuiyan M, Freifelder R, Rotsch DA, Chitneni SK, Makinen MW, Chen CT. Efficient Synthesis and HPLC-Based Characterization for Developing Vanadium-48-Labeled Vanadyl Acetylacetonate as a Novel Cancer Radiotracer for PET Imaging. Molecules 2024; 29:799. [PMID: 38398551 PMCID: PMC10892645 DOI: 10.3390/molecules29040799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/21/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Bis(acetylacetonato)oxidovanadium(IV) [(VO(acac)2], generally known as vanadyl acetylacetonate, has been shown to be preferentially sequestered in malignant tissue. Vanadium-48 (48V) generated with a compact medical cyclotron has been used to label VO(acac)2 as a potential radiotracer in positron emission tomography (PET) imaging for the detection of cancer, but requires lengthy synthesis. Current literature protocols for the characterization of VO(acac)2 require macroscale quantities of reactants and solvents to identify products by color and to enable crystallization that are not readily adaptable to the needs of radiotracer synthesis. We present an improved method to produce vanadium-48-labeled VO(acac)2, [48V]VO(acac)2, and characterize it using high-performance liquid chromatography (HPLC) with radiation detection in combination with UV detection. The approach is suitable for radiotracer-level quantities of material. These methods are readily applicable for production of [48V]VO(acac)2. Preliminary results of preclinical, small-animal PET studies are presented.
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Affiliation(s)
- Brittany A. Broder
- Department of Radiology, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637, USA; (M.B.); (M.W.M.)
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Mohammed Bhuiyan
- Department of Radiology, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637, USA; (M.B.); (M.W.M.)
| | - Richard Freifelder
- Department of Radiology, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637, USA; (M.B.); (M.W.M.)
| | - David A. Rotsch
- Argonne National Laboratory, 9700 S Cass Avenue, Lemont, IL 60439, USA;
- Oak Ridge National Laboratory, 5200, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA
| | - Satish K. Chitneni
- Department of Radiology, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637, USA; (M.B.); (M.W.M.)
| | - Marvin W. Makinen
- Department of Radiology, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637, USA; (M.B.); (M.W.M.)
| | - Chin-Tu Chen
- Department of Radiology, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637, USA; (M.B.); (M.W.M.)
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Guo J, Guo S, Lu S, Gong J, Wang L, Ding L, Chen Q, Liu W. The development of proximity labeling technology and its applications in mammals, plants, and microorganisms. Cell Commun Signal 2023; 21:269. [PMID: 37777761 PMCID: PMC10544124 DOI: 10.1186/s12964-023-01310-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023] Open
Abstract
Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.
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Affiliation(s)
- Jieyu Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Shuang Guo
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Siao Lu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Jun Gong
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Long Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Liqiong Ding
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Qingjie Chen
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
| | - Wu Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
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Kumar A, Schwab M, Laborit Labrada B, Silveira MAD, Goudreault M, Fournier É, Bellmann K, Beauchemin N, Gingras AC, Bilodeau S, Laplante M, Marette A. SHP-1 phosphatase acts as a coactivator of PCK1 transcription to control gluconeogenesis. J Biol Chem 2023; 299:105164. [PMID: 37595871 PMCID: PMC10504565 DOI: 10.1016/j.jbc.2023.105164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/20/2023] Open
Abstract
We previously reported that the protein-tyrosine phosphatase SHP-1 (PTPN6) negatively regulates insulin signaling, but its impact on hepatic glucose metabolism and systemic glucose control remains poorly understood. Here, we use co-immunoprecipitation assays, chromatin immunoprecipitation sequencing, in silico methods, and gluconeogenesis assay, and found a new mechanism whereby SHP-1 acts as a coactivator for transcription of the phosphoenolpyruvate carboxykinase 1 (PCK1) gene to increase liver gluconeogenesis. SHP-1 is recruited to the regulatory regions of the PCK1 gene and interacts with RNA polymerase II. The recruitment of SHP-1 to chromatin is dependent on its association with the transcription factor signal transducer and activator of transcription 5 (STAT5). Loss of SHP-1 as well as STAT5 decrease RNA polymerase II recruitment to the PCK1 promoter and consequently PCK1 mRNA levels leading to blunted gluconeogenesis. This work highlights a novel nuclear role of SHP-1 as a key transcriptional regulator of hepatic gluconeogenesis adding a new mechanism to the repertoire of SHP-1 functions in metabolic control.
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Affiliation(s)
- Amit Kumar
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Michael Schwab
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Beisy Laborit Labrada
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Maruhen Amir Datsch Silveira
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada; Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada
| | - Marilyn Goudreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Éric Fournier
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada; Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Quebec, Canada
| | - Kerstin Bellmann
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Nicole Beauchemin
- Department of Oncology, Medicine and Biochemistry, Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Steve Bilodeau
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada; Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Quebec, Canada
| | - Mathieu Laplante
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada
| | - André Marette
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada; Institute of Nutrition and Functional Foods, Laval University, Québec, Quebec, Canada.
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6
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Bennett AM. Teaching an old dog new tricks: A new tool for protein tyrosine phosphatase substrate discovery. J Biol Chem 2023; 299:104731. [PMID: 37080392 PMCID: PMC10193000 DOI: 10.1016/j.jbc.2023.104731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2023] [Indexed: 04/22/2023] Open
Abstract
The identification of substrates for protein tyrosine phosphatases (PTPs) is critical for a complete understanding of how these enzymes function. In a recent study in the JBC, Bonham et al. developed a modified method combining substrate-trapping mutations with proximity-labeling MS to identify the protein substrates and interactors of PTP1B. This method revealed interaction networks in breast cancer cell models and discovered novel targets of PTP1B that regulate HER2 signaling pathways. This strategy represents a versatile new tool for identifying the functional interactions between PTPs and their substrates.
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Affiliation(s)
- Anton M Bennett
- Yale University School of Medicine, Department of Pharmacology, New Haven, Connecticut, USA; Yale University School of Medicine, Yale Center for Molecular and Systems Metabolism, New Haven, Connecticut, USA.
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DeMarco AG, Hall MC. Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates. Molecules 2023; 28:3675. [PMID: 37175085 PMCID: PMC10180314 DOI: 10.3390/molecules28093675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes.
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Affiliation(s)
- Andrew G. DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C. Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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