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Shaw AL, Suresh S, Parson MAH, Harris NJ, Jenkins ML, Yip CK, Burke JE. Structure of calcineurin bound to PI4KA reveals dual interface in both PI4KA and FAM126A. Structure 2024:S0969-2126(24)00324-1. [PMID: 39216471 DOI: 10.1016/j.str.2024.08.007] [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: 04/16/2024] [Revised: 07/02/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Phosphatidylinositol 4-kinase alpha (PI4KA) maintains the phosphatidylinositol 4-phosphate (PI4P) and phosphatidylserine pools of the plasma membrane. A key regulator of PI4KA is its association into a complex with TTC7 and FAM126 proteins. This complex can be regulated by the CNAβ1 isoform of the phosphatase calcineurin. We previously identified that CNAβ1 directly binds to FAM126A. Here, we report a cryoelectron microscopic (cryo-EM) structure of a truncated PI4KA complex bound to calcineurin, revealing a unique direct interaction between PI4KA and calcineurin. Hydrogen deuterium exchange mass spectrometry (HDX-MS) and computational analysis show that calcineurin forms a complex with an evolutionarily conserved IKISVT sequence in PI4KA's horn domain. We also characterized conserved LTLT and PSISIT calcineurin binding sequences in the C terminus of FAM126A. These dual sites in PI4KA and FAM126A are both in close proximity to phosphorylation sites in the PI4KA complex, suggesting key roles of calcineurin-regulated phosphosites in PI4KA regulation. This work reveals novel insight into how calcineurin can regulate PI4KA activity.
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Affiliation(s)
- Alexandria L Shaw
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Sushant Suresh
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada.
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2
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Sang Y, Niu C, Xu J, Zhu T, You S, Wang J, Zhang L, Du X, Zhang H. PI4KIIIβ-Mediated Phosphoinositides Metabolism Regulates Function of the VTA Dopaminergic Neurons and Depression-Like Behavior. J Neurosci 2024; 44:e0555232024. [PMID: 38267258 PMCID: PMC10941068 DOI: 10.1523/jneurosci.0555-23.2024] [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: 03/27/2023] [Revised: 12/18/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
Phosphoinositides, including phosphatidylinositol-4,5-bisphosphate (PIP2), play a crucial role in controlling key cellular functions such as membrane and vesicle trafficking, ion channel, and transporter activity. Phosphatidylinositol 4-kinases (PI4K) are essential enzymes in regulating the turnover of phosphoinositides. However, the functional role of PI4Ks and mediated phosphoinositide metabolism in the central nervous system has not been fully revealed. In this study, we demonstrated that PI4KIIIβ, one of the four members of PI4Ks, is an important regulator of VTA dopaminergic neuronal activity and related depression-like behavior of mice by controlling phosphoinositide turnover. Our findings provide new insights into possible mechanisms and potential drug targets for neuropsychiatric diseases, including depression. Both sexes were studied in basic behavior tests, but only male mice could be used in the social defeat depression model.
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Affiliation(s)
- Yuqi Sang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of New Drug Pharmacology and Toxicology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Collaborative Innovation Center of Hebei Province for Mechanism, Diagnosis and Treatment of Neuropsychiatric Diseases, Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Chenxu Niu
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of New Drug Pharmacology and Toxicology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Collaborative Innovation Center of Hebei Province for Mechanism, Diagnosis and Treatment of Neuropsychiatric Diseases, Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Jiaxi Xu
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Department of Physiology and Pathophysiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shanxi 710061, China
| | - Tiantian Zhu
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of New Drug Pharmacology and Toxicology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Collaborative Innovation Center of Hebei Province for Mechanism, Diagnosis and Treatment of Neuropsychiatric Diseases, Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Shuangzhu You
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of New Drug Pharmacology and Toxicology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Collaborative Innovation Center of Hebei Province for Mechanism, Diagnosis and Treatment of Neuropsychiatric Diseases, Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Jing Wang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of New Drug Pharmacology and Toxicology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Collaborative Innovation Center of Hebei Province for Mechanism, Diagnosis and Treatment of Neuropsychiatric Diseases, Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Ludi Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of New Drug Pharmacology and Toxicology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Collaborative Innovation Center of Hebei Province for Mechanism, Diagnosis and Treatment of Neuropsychiatric Diseases, Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Xiaona Du
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of New Drug Pharmacology and Toxicology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Collaborative Innovation Center of Hebei Province for Mechanism, Diagnosis and Treatment of Neuropsychiatric Diseases, Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Hailin Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- The Key Laboratory of New Drug Pharmacology and Toxicology, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Collaborative Innovation Center of Hebei Province for Mechanism, Diagnosis and Treatment of Neuropsychiatric Diseases, Hebei Medical University, Shijiazhuang, Hebei 050011, China
- Department of Psychiatry, The First Hospital of Hebei Medical University, Mental Health Institute of Hebei Medical University, Shijiazhuang, Hebei 050000, China
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3
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Li G, Wu Y, Zhang Y, Wang H, Li M, He D, Guan W, Yao H. Research progress on phosphatidylinositol 4-kinase inhibitors. Biochem Pharmacol 2024; 220:115993. [PMID: 38151075 DOI: 10.1016/j.bcp.2023.115993] [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: 10/23/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023]
Abstract
Phosphatidylinositol 4-kinases (PI4Ks) could phosphorylate phosphatidylinositol (PI) to produce phosphatidylinositol 4-phosphate (PI4P) and maintain its metabolic balance and location. PI4P, the most abundant monophosphate inositol in eukaryotic cells, is a precursor of higher phosphoinositols and an essential substrate for the PLC/PKC and PI3K/Akt signaling pathways. PI4Ks regulate vesicle transport, signal transduction, cytokinesis, and cell unity, and are involved in various physiological and pathological processes, including infection and growth of parasites such as Plasmodium and Cryptosporidium, replication and survival of RNA viruses, and the development of tumors and nervous system diseases. The development of novel drugs targeting PI4Ks and PI4P has been the focus of the research and clinical application of drugs, especially in recent years. In particular, PI4K inhibitors have made great progress in the treatment of malaria and cryptosporidiosis. We describe the biological characteristics of PI4Ks; summarize the physiological functions and effector proteins of PI4P; and analyze the structural basis of selective PI4K inhibitors for the treatment of human diseases in this review. Herein, this review mainly summarizes the developments in the structure and enzyme activity of PI4K inhibitors.
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Affiliation(s)
- Gang Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Yanting Wu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China; Department of Chemistry, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, 999077, China
| | - Yali Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Huamin Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Mengjie Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Dengqin He
- School of Biotechnology and Health Science, Wuyi University, 22 Dongchengcun, Jiangmen, Guangdong, 529020, China
| | - Wen Guan
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Hongliang Yao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China.
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Suresh S, Burke JE. Structural basis for the conserved roles of PI4KA and its regulatory partners and their misregulation in disease. Adv Biol Regul 2023; 90:100996. [PMID: 37979461 DOI: 10.1016/j.jbior.2023.100996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/17/2023] [Indexed: 11/20/2023]
Abstract
The type III Phosphatidylinositol 4-kinase alpha (PI4KA) is an essential lipid kinase that is a master regulator of phosphoinositide signalling at the plasma membrane (PM). It produces the predominant pool of phosphatidylinositol 4-phosphate (PI4P) at the PM, with this being essential in lipid transport and in regulating the PLC and PI3K signalling pathways. PI4KA is essential and is highly conserved in all eukaryotes. In yeast, the PI4KA ortholog stt4 predominantly exists as a heterodimer with its regulatory partner ypp1. In higher eukaryotes, PI4KA instead primarily forms a heterotrimer with a TTC7 subunit (ortholog of ypp1) and a FAM126 subunit. In all eukaryotes PI4KA is recruited to the plasma membrane by the protein EFR3, which does not directly bind PI4KA, but instead binds to the TTC7/ypp1 regulatory partner. Misregulation in PI4KA or its regulatory partners is involved in myriad human diseases, including loss of function mutations in neurodevelopmental and inflammatory intestinal disorders and gain of function in human cancers. This review describes an in-depth analysis of the structure function of PI4KA and its regulatory partners, with a major focus on comparing and contrasting the differences in regulation of PI4KA throughout evolution.
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Affiliation(s)
- Sushant Suresh
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
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5
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Bura A, Čabrijan S, Đurić I, Bruketa T, Jurak Begonja A. A Plethora of Functions Condensed into Tiny Phospholipids: The Story of PI4P and PI(4,5)P 2. Cells 2023; 12:1411. [PMID: 37408244 DOI: 10.3390/cells12101411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Phosphoinositides (PIs) are small, phosphorylated lipids that serve many functions in the cell. They regulate endo- and exocytosis, vesicular trafficking, actin reorganization, and cell mobility, and they act as signaling molecules. The most abundant PIs in the cell are phosphatidylinositol-4-monophosphate (PI4P) and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. PI4P is mostly localized at the Golgi apparatus where it regulates the anterograde trafficking from the Golgi apparatus to the plasma membrane (PM), but it also localizes at the PM. On the other hand, the main localization site of PI(4,5)P2 is the PM where it regulates the formation of endocytic vesicles. The levels of PIs are regulated by many kinases and phosphatases. Four main kinases phosphorylate the precursor molecule phosphatidylinositol into PI4P, divided into two classes (PI4KIIα, PI4KIIβ, PI4KIIIα, and PI4KIIIβ), and three main kinases phosphorylate PI4P to form PI(4,5)P2 (PI4P5KIα, PI4P5KIβ, and PI4P5KIγ). In this review, we discuss the localization and function of the kinases that produce PI4P and PI(4,5)P2, as well as the localization and function of their product molecules with an overview of tools for the detection of these PIs.
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Affiliation(s)
- Ana Bura
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Sara Čabrijan
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Iris Đurić
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Tea Bruketa
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Antonija Jurak Begonja
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
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Burke JE, Triscott J, Emerling BM, Hammond GRV. Beyond PI3Ks: targeting phosphoinositide kinases in disease. Nat Rev Drug Discov 2023; 22:357-386. [PMID: 36376561 PMCID: PMC9663198 DOI: 10.1038/s41573-022-00582-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2022] [Indexed: 11/16/2022]
Abstract
Lipid phosphoinositides are master regulators of almost all aspects of a cell's life and death and are generated by the tightly regulated activity of phosphoinositide kinases. Although extensive efforts have focused on drugging class I phosphoinositide 3-kinases (PI3Ks), recent years have revealed opportunities for targeting almost all phosphoinositide kinases in human diseases, including cancer, immunodeficiencies, viral infection and neurodegenerative disease. This has led to widespread efforts in the clinical development of potent and selective inhibitors of phosphoinositide kinases. This Review summarizes our current understanding of the molecular basis for the involvement of phosphoinositide kinases in disease and assesses the preclinical and clinical development of phosphoinositide kinase inhibitors.
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Affiliation(s)
- John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - Joanna Triscott
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Gerald R V Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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McPhail JA, Burke JE. Molecular mechanisms of PI4K regulation and their involvement in viral replication. Traffic 2023; 24:131-145. [PMID: 35579216 DOI: 10.1111/tra.12841] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/07/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Lipid phosphoinositides are master signaling molecules in eukaryotic cells and key markers of organelle identity. Because of these important roles, the kinases and phosphatases that generate phosphoinositides must be tightly regulated. Viruses can manipulate this regulation, with the Type III phosphatidylinositol 4-kinases (PI4KA and PI4KB) being hijacked by many RNA viruses to mediate their intracellular replication through the formation of phosphatidylinositol 4-phosphate (PI4P)-enriched replication organelles (ROs). Different viruses have evolved unique approaches toward activating PI4K enzymes to form ROs, through both direct binding of PI4Ks and modulation of PI4K accessory proteins. This review will focus on PI4KA and PI4KB and discuss their roles in signaling, functions in membrane trafficking and manipulation by viruses. Our focus will be the molecular basis for how PI4KA and PI4KB are activated by both protein-binding partners and post-translational modifications, with an emphasis on understanding the different molecular mechanisms viruses have evolved to usurp PI4Ks. We will also discuss the chemical tools available to study the role of PI4Ks in viral infection.
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Affiliation(s)
- Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
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He R, Liu F, Wang H, Huang S, Xu K, Zhang C, Liu Y, Yu H. ORP9 and ORP10 form a heterocomplex to transfer phosphatidylinositol 4-phosphate at ER-TGN contact sites. Cell Mol Life Sci 2023; 80:77. [PMID: 36853333 PMCID: PMC11072704 DOI: 10.1007/s00018-023-04728-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023]
Abstract
Oxysterol-binding protein (OSBP) and its related proteins (ORPs) are a family of lipid transfer proteins (LTPs) that mediate non-vesicular lipid transport. ORP9 and ORP10, members of the OSBP/ORPs family, are located at the endoplasmic reticulum (ER)-trans-Golgi network (TGN) membrane contact sites (MCSs). It remained unclear how they mediate lipid transport. In this work, we discovered that ORP9 and ORP10 form a binary complex through intermolecular coiled-coil (CC) domain-CC domain interaction. The PH domains of ORP9 and ORP10 specially interact with phosphatidylinositol 4-phosphate (PI4P), mediating the TGN targeting. The ORP9-ORP10 complex plays a critical role in regulating PI4P levels at the TGN. Using in vitro reconstitution assays, we observed that while full-length ORP9 efficiently transferred PI4P between two apposed membranes, the lipid transfer kinetics was further accelerated by ORP10. Interestingly, our data showed that the PH domains of ORP9 and ORP10 participate in membrane tethering simultaneously, whereas ORDs of both ORP9 and ORP10 are required for lipid transport. Furthermore, our data showed that the depletion of ORP9 and ORP10 led to increased vesicle transport to the plasma membrane (PM). These findings demonstrate that ORP9 and ORP10 form a binary complex through the CC domains, maintaining PI4P homeostasis at ER-TGN MCSs and regulating vesicle trafficking.
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Affiliation(s)
- Ruyue He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Furong Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Hui Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shuai Huang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Conggang Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yinghui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Haijia Yu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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Abstract
Birnaviruses are members of the Birnaviridae family, responsible for major economic losses to poultry and aquaculture. The family is composed of non-enveloped viruses with a segmented double-stranded RNA (dsRNA) genome. Infectious bursal disease virus (IBDV), the prototypic family member, is the etiological agent of Gumboro disease, a highly contagious immunosuppressive disease in the poultry industry worldwide. We previously demonstrated that IBDV hijacks the endocytic pathway for establishing the viral replication complexes on endosomes associated with the Golgi complex (GC). In this work, we report that IBDV reorganizes the GC to localize the endosome-associated replication complexes without affecting its secretory functionality. Analyzing crucial proteins involved in the secretory pathway, we showed the essential requirement of Rab1b for viral replication. Rab1b comprises a key regulator of GC transport and we demonstrate that transfecting the negative mutant Rab1b N121I or knocking down Rab1b expression by RNA interference significantly reduces the yield of infectious viral progeny. Furthermore, we showed that the Rab1b downstream effector Golgi-specific BFA resistance factor 1 (GBF1), which activates the small GTPase ADP-ribosylation factor 1 (ARF1), is required for IBDV replication since inhibiting its activity by treatment with brefeldin A (BFA) or Golgicide A (GCA) significantly reduces the yield of infectious viral progeny. Finally, we show that ARF1 dominant negative-mutant T31N over-expression hampered the IBDV infection. Taken together, these results demonstrate that IBDV requires the function of the Rab1b-GBF1-ARF1 axis to promote its replication, making a substantial contribution to the field of birnaviruses-host cell interactions. IMPORTANCE Birnaviruses are unconventional members of the dsRNA viruses, being the lack of a transcriptionally active core the main differential feature. This structural trait, among others that resemble the plus single-stranded (+ssRNA) viruses features, suggests that birnaviruses might follow a different replication program from that conducted by prototypical dsRNA members and have argued the hypothesis that birnaviruses could be evolutionary links between +ssRNA and dsRNA viruses. Here, we present original data showing the IBDV-induced GC reorganization and the crosstalk between IBDV and the Rab1b-GBF1-ARF1 mediated intracellular trafficking pathway. The replication of several +ssRNA viruses depends on the cellular protein GBF1, but its role in the replication process is not clear. Thus, our findings make a substantial contribution to the field of birnaviruses-host cells and provide further evidence supporting the proposed evolutionary connection role of birnaviruses, an aspect which we consider especially relevant for researchers working in the virology field.
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Yuan T, Wang J, Shi C, Wang Y, Xia B, Xu W, Yang H, Yang Y, Ye MT, Khalid S, Liang Y, Tian C, You MJ, Wang Y. Downregulation of FAPP2 gene induces cell autophagy and inhibits PI3K/AKT/mTOR pathway in T-cell acute lymphoblastic leukemia. Hematol Oncol 2021; 40:249-257. [PMID: 34796518 DOI: 10.1002/hon.2948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/16/2021] [Accepted: 11/08/2021] [Indexed: 11/09/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy. Most patients with T-ALL are treated with high-dose multi-agent chemotherapy due to limited targeted therapeutic options. To further investigate its pathogenesis and establish new therapeutic targets, we studied the role of FAPP2, a Golgi protein, that is, highly expressed in T-ALL, in the growth and function of T-ALL. We found that T-ALL cells underwent reduced cell proliferation and sub-G1 accumulation after knocking down of FAPP2 gene using shRNA systems. Instead, FAPP2 downregulation promoted cell autophagy. The level of autophagy markers, LC3Ⅱ/Ⅰ, Beclin1, and ATG5, was markedly increased, whereas that of P62 decreased after FAPP2 knocking down in T-ALL cells. FAPP2 knocking down led to the accumulation of LC3 in the cytoplasm of T-ALL cells as shown by fluorescence microscopy. In addition, the level of PI(4)P and PI(3,4,5)P decreased and phosphorylation of P-AKT and P-mTOR were downregulated in FAPP2 knock-down cells. In summary, our results show that decreased expression of FAPP2 inhibited cell proliferation, resulted in the sub-G1 phase accumulation of T-ALL cells, and enhanced autophagy of T-ALL cells, likely mediated by PI(4)P, PI(3,4,5)P, and PI3K/AKT/mTOR pathway. Our results provide a new insight into the pathogenesis and development of potential targeted therapy of T-ALL.
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Affiliation(s)
- Tian Yuan
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jinhuan Wang
- Department of Oncology, Second Hospital of Tianjin Medical University, Institute of Urology, Tianjin, China
| | - Ce Shi
- NHC Key Laboratory of Cell Transplantation, First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yi Wang
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Bing Xia
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Wen Xu
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Hongliang Yang
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yaling Yang
- NHC Key Laboratory of Cell Transplantation, First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Matthew T Ye
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samah Khalid
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yong Liang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Clinical Medicine, Taizhou University School of Medicine, Taizhou, Zhejiang Province, China
| | - Chen Tian
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - M James You
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yafei Wang
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
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11
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Li YP, Mikrani R, Hu YF, Faran Ashraf Baig MM, Abbas M, Akhtar F, Xu M. Research progress of phosphatidylinositol 4-kinase and its inhibitors in inflammatory diseases. Eur J Pharmacol 2021; 907:174300. [PMID: 34217706 DOI: 10.1016/j.ejphar.2021.174300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 01/08/2023]
Abstract
Phosphatidylinositol 4-kinase (PI4K) is a lipid kinase that can catalyze the transfer of phosphate group from ATP to the inositol ring of phosphatidylinositol (PtdIns) resulting in the phosphorylation of PtdIns at 4-OH sites, to generate phosphatidylinositol 4-phosphate (PI4P). Studies on biological functions reveal that PI4K is closely related to the occurrence and development of various inflammatory diseases such as obesity, cancer, viral infections, malaria, Alzheimer's disease, etc. PI4K-related inhibitors have been found to have the effects of inhibiting virus replication, anti-cancer, treating malaria and reducing rejection in organ transplants, among which MMV390048, an anti-malaria drug, has entered phase II clinical trial. This review discusses the classification, structure, distribution and related inhibitors of PI4K and their role in the progression of cancer, viral replication, and other inflammation induced diseases to explore their potential as therapeutic targets.
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Affiliation(s)
- Yan-Ping Li
- Department of Clinical Pharmacy, School of Preclinical Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Reyaj Mikrani
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria 3052, Australia
| | - Yi-Fan Hu
- Department of Clinical Pharmacy, School of Preclinical Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Mirza Muhammad Faran Ashraf Baig
- Laboratory of Biomedical Engineering for Novel Bio-functional and Pharmaceutical Nano-materials, Prince Philip Dental Hospital, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, 999077, China
| | - Muhammad Abbas
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, PR China
| | - Fahad Akhtar
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China; School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Xu
- Department of Clinical Pharmacy, School of Preclinical Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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12
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Plasma Membrane Phosphatidylinositol-4-Phosphate Is Not Necessary for Candida albicans Viability yet Is Key for Cell Wall Integrity and Systemic Infection. mBio 2021; 13:e0387321. [PMID: 35164565 PMCID: PMC8942462 DOI: 10.1128/mbio.03873-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Phosphatidylinositol phosphates are key phospholipids with a range of regulatory roles, including membrane trafficking and cell polarity. Phosphatidylinositol-4-phosphate [PI(4)P] at the Golgi apparatus is required for the budding-to-filamentous-growth transition in the human-pathogenic fungus Candida albicans; however, the role of plasma membrane PI(4)P is unclear. We have investigated the importance of this phospholipid in C. albicans growth, stress response, and virulence by generating mutant strains with decreased levels of plasma membrane PI(4)P, via deletion of components of the PI-4-kinase complex, i.e., Efr3, Ypp1, and Stt4. The amounts of plasma membrane PI(4)P in the efr3Δ/Δ and ypp1Δ/Δ mutants were ∼60% and ∼40%, respectively, of that in the wild-type strain, whereas it was nearly undetectable in the stt4Δ/Δ mutant. All three mutants had reduced plas7ma membrane phosphatidylserine (PS). Although these mutants had normal yeast-phase growth, they were defective in filamentous growth, exhibited defects in cell wall integrity, and had an increased exposure of cell wall β(1,3)-glucan, yet they induced a range of hyphal-specific genes. In a mouse model of hematogenously disseminated candidiasis, fungal plasma membrane PI(4)P levels directly correlated with virulence; the efr3Δ/Δ mutant had wild-type virulence, the ypp1Δ/Δ mutant had attenuated virulence, and the stt4Δ/Δ mutant caused no lethality. In the mouse model of oropharyngeal candidiasis, only the ypp1Δ/Δ mutant had reduced virulence, indicating that plasma membrane PI(4)P is less important for proliferation in the oropharynx. Collectively, these results demonstrate that plasma membrane PI(4)P levels play a central role in filamentation, cell wall integrity, and virulence in C. albicans. IMPORTANCE While the PI-4-kinases Pik1 and Stt4 both produce PI(4)P, the former generates PI(4)P at the Golgi apparatus and the latter at the plasma membrane, and these two pools are functionally distinct. To address the importance of plasma membrane PI(4)P in Candida albicans, we generated deletion mutants of the three putative plasma membrane PI-4-kinase complex components and quantified the levels of plasma membrane PI(4)P in each of these strains. Our work reveals that this phosphatidylinositol phosphate is specifically critical for the yeast-to-hyphal transition, cell wall integrity, and virulence in a mouse systemic infection model. The significance of this work is in identifying a plasma membrane phospholipid that has an infection-specific role, which is attributed to the loss of plasma membrane PI(4)P resulting in β(1,3)-glucan unmasking.
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13
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Koch PA, Dornan GL, Hessenberger M, Haucke V. The molecular mechanisms mediating class II PI 3-kinase function in cell physiology. FEBS J 2021; 288:7025-7042. [PMID: 33387369 DOI: 10.1111/febs.15692] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/14/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
The phosphoinositide 3-kinase (PI3K) family of lipid-modifying enzymes plays vital roles in cell signaling and membrane trafficking through the production of 3-phosphorylated phosphoinositides. Numerous studies have analyzed the structure and function of class I and class III PI3Ks. In contrast, we know comparably little about the structure and physiological functions of the class II enzymes. Only recent studies have begun to unravel their roles in development, endocytic and endolysosomal membrane dynamics, signal transduction, and cell migration, while the mechanisms that control their localization and enzymatic activity remain largely unknown. Here, we summarize our current knowledge of the class II PI3Ks and outline open questions related to their structure, enzymatic activity, and their physiological and pathophysiological functions.
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Affiliation(s)
- Philipp Alexander Koch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,Faculty of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Germany
| | | | - Manuel Hessenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,Faculty of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Germany
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14
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Li X, Wang M, Cheng A, Wen X, Ou X, Mao S, Gao Q, Sun D, Jia R, Yang Q, Wu Y, Zhu D, Zhao X, Chen S, Liu M, Zhang S, Liu Y, Yu Y, Zhang L, Tian B, Pan L, Chen X. Enterovirus Replication Organelles and Inhibitors of Their Formation. Front Microbiol 2020; 11:1817. [PMID: 32973693 PMCID: PMC7468505 DOI: 10.3389/fmicb.2020.01817] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/10/2020] [Indexed: 12/23/2022] Open
Abstract
Enteroviral replication reorganizes the cellular membrane. Upon infection, viral proteins and hijacked host factors generate unique structures called replication organelles (ROs) to replicate their viral genomes. ROs promote efficient viral genome replication, coordinate the steps of the viral replication cycle, and protect viral RNA from host immune responses. More recent researches have focused on the ultrastructure structures, formation mechanism, and functions in the virus life cycle of ROs. Dynamic model of enterovirus ROs structure is proposed, and the secretory pathway, the autophagy pathway, and lipid metabolism are found to be associated in the formation of ROs. With deeper understanding of ROs, some compounds have been found to show inhibitory effects on viral replication by targeting key proteins in the process of ROs formation. Here, we review the recent findings concerning the role, morphology, biogenesis, formation mechanism, and inhibitors of enterovirus ROs.
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Affiliation(s)
- Xinhong Li
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xingjian Wen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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15
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Banerjee S, Kane PM. Regulation of V-ATPase Activity and Organelle pH by Phosphatidylinositol Phosphate Lipids. Front Cell Dev Biol 2020; 8:510. [PMID: 32656214 PMCID: PMC7324685 DOI: 10.3389/fcell.2020.00510] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Luminal pH and the distinctive distribution of phosphatidylinositol phosphate (PIP) lipids are central identifying features of organelles in all eukaryotic cells that are also critical for organelle function. V-ATPases are conserved proton pumps that populate and acidify multiple organelles of the secretory and the endocytic pathway. Complete loss of V-ATPase activity causes embryonic lethality in higher animals and conditional lethality in yeast, while partial loss of V-ATPase function is associated with multiple disease states. On the other hand, many cancer cells increase their virulence by upregulating V-ATPase expression and activity. The pH of individual organelles is tightly controlled and essential for function, but the mechanisms for compartment-specific pH regulation are not completely understood. There is substantial evidence indicating that the PIP content of membranes influences organelle pH. We present recent evidence that PIPs interact directly with subunit isoforms of the V-ATPase to dictate localization of V-ATPase subpopulations and participate in their regulation. In yeast cells, which have only one set of organelle-specific V-ATPase subunit isoforms, the Golgi-enriched lipid PI(4)P binds to the cytosolic domain of the Golgi-enriched a-subunit isoform Stv1, and loss of PI(4)P binding results in mislocalization of Stv1-containing V-ATPases from the Golgi to the vacuole/lysosome. In contrast, levels of the vacuole/lysosome-enriched signaling lipid PI(3,5)P2 affect assembly and activity of V-ATPases containing the Vph1 a-subunit isoform. Mutations in the Vph1 isoform that disrupt the lipid interaction increase sensitivity to stress. These studies have decoded “zip codes” for PIP lipids in the cytosolic N-terminal domain of the a-subunit isoforms of the yeast V-ATPase, and similar interactions between PIP lipids and the V-ATPase subunit isoforms are emerging in higher eukaryotes. In addition to direct effects on the V-ATPase, PIP lipids are also likely to affect organelle pH indirectly, through interactions with other membrane transporters. We discuss direct and indirect effects of PIP lipids on organelle pH, and the functional consequences of the interplay between PIP lipid content and organelle pH.
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Affiliation(s)
- Subhrajit Banerjee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
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16
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McPhail JA, Lyoo H, Pemberton JG, Hoffmann RM, van Elst W, Strating JRPM, Jenkins ML, Stariha JTB, Powell CJ, Boulanger MJ, Balla T, van Kuppeveld FJM, Burke JE. Characterization of the c10orf76-PI4KB complex and its necessity for Golgi PI4P levels and enterovirus replication. EMBO Rep 2020; 21:e48441. [PMID: 31829496 PMCID: PMC7001497 DOI: 10.15252/embr.201948441] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/25/2019] [Accepted: 11/11/2019] [Indexed: 11/09/2022] Open
Abstract
The lipid kinase PI4KB, which generates phosphatidylinositol 4-phosphate (PI4P), is a key enzyme in regulating membrane transport and is also hijacked by multiple picornaviruses to mediate viral replication. PI4KB can interact with multiple protein binding partners, which are differentially manipulated by picornaviruses to facilitate replication. The protein c10orf76 is a PI4KB-associated protein that increases PI4P levels at the Golgi and is essential for the viral replication of specific enteroviruses. We used hydrogen-deuterium exchange mass spectrometry to characterize the c10orf76-PI4KB complex and reveal that binding is mediated by the kinase linker of PI4KB, with formation of the heterodimeric complex modulated by PKA-dependent phosphorylation. Complex-disrupting mutations demonstrate that PI4KB is required for membrane recruitment of c10orf76 to the Golgi, and that an intact c10orf76-PI4KB complex is required for the replication of c10orf76-dependent enteroviruses. Intriguingly, c10orf76 also contributed to proper Arf1 activation at the Golgi, providing a putative mechanism for the c10orf76-dependent increase in PI4P levels at the Golgi.
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Affiliation(s)
- Jacob A McPhail
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Heyrhyoung Lyoo
- Department of Infectious Diseases & ImmunologyVirology DivisionFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Joshua G Pemberton
- Section on Molecular Signal TransductionEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMDUSA
| | - Reece M Hoffmann
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Wendy van Elst
- Department of Infectious Diseases & ImmunologyVirology DivisionFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Jeroen RPM Strating
- Department of Infectious Diseases & ImmunologyVirology DivisionFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Meredith L Jenkins
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Jordan TB Stariha
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Cameron J Powell
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Martin J Boulanger
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Tamas Balla
- Section on Molecular Signal TransductionEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMDUSA
| | - Frank JM van Kuppeveld
- Department of Infectious Diseases & ImmunologyVirology DivisionFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - John E Burke
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
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17
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McPhail JA, Burke JE. Drugging the Phosphoinositide 3-Kinase (PI3K) and Phosphatidylinositol 4-Kinase (PI4K) Family of Enzymes for Treatment of Cancer, Immune Disorders, and Viral/Parasitic Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1274:203-222. [DOI: 10.1007/978-3-030-50621-6_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Abstract
Since I started doing scientific research, I've been fascinated by the interplay of protein structure and dynamics and how they together mediate protein function. A particular area of interest has been in understanding the mechanistic basis of how lipid-signaling enzymes function on membrane surfaces. In this award lecture article, I will describe my laboratory's studies on the structure and dynamics of lipid-signaling enzymes on membrane surfaces. This is important, as many lipid-signaling enzymes are regulated through dynamic regulatory mechanisms that control their enzymatic activity. This article will discuss my continued enthusiasm in using a synergistic application of hydrogen-deuterium exchange MS (HDX-MS) with other structural biology techniques to probe the mechanistic basis for how membrane-localized signaling enzymes are regulated and how these approaches can be used to understand how they are misregulated in disease. I will discuss specific examples of how we have used HDX-MS to study phosphoinositide kinases and the protein kinase Akt. An important focus will be on a description of how HDX-MS can be used as a powerful tool to optimize the design of constructs for X-ray crystallography and EM. The use of a diverse toolbox of biophysical methods has revealed novel insight into the complex and varied regulatory networks that control the function of lipid-signaling enzymes and enabled unique insight into the mechanics of membrane recruitment.
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Affiliation(s)
- John E Burke
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
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19
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Chalupska D, Różycki B, Humpolickova J, Faltova L, Klima M, Boura E. Phosphatidylinositol 4-kinase IIIβ (PI4KB) forms highly flexible heterocomplexes that include ACBD3, 14-3-3, and Rab11 proteins. Sci Rep 2019; 9:567. [PMID: 30679637 PMCID: PMC6345845 DOI: 10.1038/s41598-018-37158-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
Phosphatidylinositol 4-kinase IIIβ (PI4KB) is a key enzyme of the Golgi system because it produces its lipid hallmark - the phosphatidylinositol 4-phosphate (PI4P). It is recruited to Golgi by the Golgi resident ACBD3 protein, regulated by 14-3-3 proteins and it also serves as an adaptor because it recruits the small GTPase Rab11. Here, we analyzed the protein complexes formed by PI4KB in vitro using small angle x-ray scattering (SAXS) and we discovered that these protein complexes are highly flexible. The 14-3-3:PI4KB:Rab11 protein complex has 2:1:1 stoichiometry and its different conformations are rather compact, however, the ACBD3:PI4KB protein complex has both, very compact and very extended conformations. Furthermore, in vitro reconstitution revealed that the membrane is necessary for the formation of ACBD3:PI4KB:Rab11 protein complex at physiological (nanomolar) concentrations.
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Affiliation(s)
- Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic
| | - Lenka Faltova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen, PSI, Switzerland
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic.
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20
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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21
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Reuberson J, Horsley H, Franklin RJ, Ford D, Neuss J, Brookings D, Huang Q, Vanderhoydonck B, Gao LJ, Jang MY, Herdewijn P, Ghawalkar A, Fallah-Arani F, Khan AR, Henshall J, Jairaj M, Malcolm S, Ward E, Shuttleworth L, Lin Y, Li S, Louat T, Waer M, Herman J, Payne A, Ceska T, Doyle C, Pitt W, Calmiano M, Augustin M, Steinbacher S, Lammens A, Allen R. Discovery of a Potent, Orally Bioavailable PI4KIIIβ Inhibitor (UCB9608) Able To Significantly Prolong Allogeneic Organ Engraftment in Vivo. J Med Chem 2018; 61:6705-6723. [PMID: 29952567 DOI: 10.1021/acs.jmedchem.8b00521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The primary target of a novel series of immunosuppressive 7-piperazin-1-ylthiazolo[5,4- d]pyrimidin-5-amines was identified as the lipid kinase, PI4KIIIβ. Evaluation of the series highlighted their poor solubility and unwanted off-target activities. A medicinal chemistry strategy was put in place to optimize physicochemical properties within the series, while maintaining potency and improving selectivity over other lipid kinases. Compound 22 was initially identified and profiled in vivo, before further modifications led to the discovery of 44 (UCB9608), a vastly more soluble, selective compound with improved metabolic stability and excellent pharmacokinetic profile. A co-crystal structure of 44 with PI4KIIIβ was solved, confirming the binding mode of this class of inhibitor. The much-improved in vivo profile of 44 positions it as an ideal tool compound to further establish the link between PI4KIIIβ inhibition and prolonged allogeneic organ engraftment, and suppression of immune responses in vivo.
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Affiliation(s)
- James Reuberson
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Helen Horsley
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Richard J Franklin
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Daniel Ford
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Judi Neuss
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Daniel Brookings
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Qiuya Huang
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Bart Vanderhoydonck
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Ling-Jie Gao
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Mi-Yeon Jang
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Piet Herdewijn
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Anant Ghawalkar
- SAI Life Sciences Ltd , International Biotech Park , Hinjewadi, Pune 411 057 , India
| | | | - Adnan R Khan
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Jamie Henshall
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Mark Jairaj
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Sarah Malcolm
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Eleanor Ward
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | | | - Yuan Lin
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Shengqiao Li
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Thierry Louat
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Mark Waer
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Jean Herman
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Andrew Payne
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Tom Ceska
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Carl Doyle
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Will Pitt
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Mark Calmiano
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Martin Augustin
- Proteros Biostructures GmbH , Bunsenstrasse 7a , 82152 Martinsried , Germany
| | - Stefan Steinbacher
- Proteros Biostructures GmbH , Bunsenstrasse 7a , 82152 Martinsried , Germany
| | - Alfred Lammens
- Proteros Biostructures GmbH , Bunsenstrasse 7a , 82152 Martinsried , Germany
| | - Rodger Allen
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
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22
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Banerjee S, Aponte-Diaz D, Yeager C, Sharma SD, Ning G, Oh HS, Han Q, Umeda M, Hara Y, Wang RYL, Cameron CE. Hijacking of multiple phospholipid biosynthetic pathways and induction of membrane biogenesis by a picornaviral 3CD protein. PLoS Pathog 2018; 14:e1007086. [PMID: 29782554 PMCID: PMC5983871 DOI: 10.1371/journal.ppat.1007086] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 06/01/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022] Open
Abstract
RNA viruses induce specialized membranous structures for use in genome replication. These structures are often referred to as replication organelles (ROs). ROs exhibit distinct lipid composition relative to other cellular membranes. In many picornaviruses, phosphatidylinositol-4-phosphate (PI4P) is a marker of the RO. Studies to date indicate that the viral 3A protein hijacks a PI4 kinase to induce PI4P by a mechanism unrelated to the cellular pathway, which requires Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1, GBF1, and ADP ribosylation factor 1, Arf1. Here we show that a picornaviral 3CD protein is sufficient to induce synthesis of not only PI4P but also phosphatidylinositol-4,5-bisphosphate (PIP2) and phosphatidylcholine (PC). Synthesis of PI4P requires GBF1 and Arf1. We identified 3CD derivatives: 3CDm and 3CmD, that we used to show that distinct domains of 3CD function upstream of GBF1 and downstream of Arf1 activation. These same 3CD derivatives still supported induction of PIP2 and PC, suggesting that pathways and corresponding mechanisms used to induce these phospholipids are distinct. Phospholipid induction by 3CD is localized to the perinuclear region of the cell, the outcome of which is the proliferation of membranes in this area of the cell. We conclude that a single viral protein can serve as a master regulator of cellular phospholipid and membrane biogenesis, likely by commandeering normal cellular pathways. Picornaviruses replicate their genomes in association with host membranes. Early during infection, existing membranes are used but remodeled to contain a repertoire of lipids best suited for virus multiplication. Later, new membrane synthesis occurs, which requires biosynthesis of phosphatidylcholine in addition to the other more specialized lipids. We have learned that a single picornaviral protein is able to induce membrane biogenesis and decorate these membranes with some of the specialized lipids induced by the virus. A detailed mechanism of induction has been elucidated for one of these lipids. The ability of a single viral protein to commandeer host pathways that lead to membrane biogenesis was unexpected. This discovery reveals a new target for antiviral therapy with the potential to completely derail all aspects of the viral lifecycle requiring membrane biogenesis.
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Affiliation(s)
- Sravani Banerjee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - David Aponte-Diaz
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Calvin Yeager
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Suresh D. Sharma
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Gang Ning
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Hyung S. Oh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Qingxia Han
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Masato Umeda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuji Hara
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Robert Y. L. Wang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial and Children’s Hospital, Linkou, Taiwan
| | - Craig E. Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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23
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Del Bel LM, Brill JA. Sac1, a lipid phosphatase at the interface of vesicular and nonvesicular transport. Traffic 2018; 19:301-318. [PMID: 29411923 DOI: 10.1111/tra.12554] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/02/2018] [Accepted: 02/02/2018] [Indexed: 12/14/2022]
Abstract
The lipid phosphatase Sac1 dephosphorylates phosphatidylinositol 4-phosphate (PI4P), thereby holding levels of this crucial membrane signaling molecule in check. Sac1 regulates multiple cellular processes, including cytoskeletal organization, membrane trafficking and cell signaling. Here, we review the structure and regulation of Sac1, its roles in cell signaling and development and its links to health and disease. Remarkably, many of the diverse roles attributed to Sac1 can be explained by the recent discovery of its requirement at membrane contact sites, where its consumption of PI4P is proposed to drive interorganelle transfer of other cellular lipids, thereby promoting normal lipid homeostasis within cells.
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Affiliation(s)
- Lauren M Del Bel
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julie A Brill
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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24
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Olivença DV, Uliyakina I, Fonseca LL, Amaral MD, Voit EO, Pinto FR. A Mathematical Model of the Phosphoinositide Pathway. Sci Rep 2018; 8:3904. [PMID: 29500467 PMCID: PMC5834545 DOI: 10.1038/s41598-018-22226-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/19/2018] [Indexed: 01/10/2023] Open
Abstract
Phosphoinositides are signalling lipids that constitute a complex network regulating many cellular processes. We propose a computational model that accounts for all species of phosphoinositides in the plasma membrane of mammalian cells. The model replicates the steady-state of the pathway and most known dynamic phenomena. Sensitivity analysis demonstrates model robustness to alterations in the parameters. Model analysis suggest that the greatest contributor to phosphatidylinositol 4,5-biphosphate (PI(4,5)P2) production is a flux representing the direct transformation of PI into PI(4,5)P2, also responsible for the maintenance of this pool when phosphatidylinositol 4-phosphate (PI(4)P) is decreased. PI(5)P is also shown to be a significant source for PI(4,5)P2 production. The model was validated with siRNA screens that knocked down the expression of enzymes in the pathway. The screen monitored the activity of the epithelium sodium channel (ENaC), which is activated by PI(4,5)P2. While the model may deepen our understanding of other physiological processes involving phosphoinositides, we highlight therapeutic effects of ENaC modulation in Cystic Fibrosis (CF). The model suggests control strategies where the activities of the enzyme phosphoinositide 4-phosphate 5-kinase I (PIP5KI) or the PI4K + PIP5KI + DVL protein complex are decreased and cause an efficacious reduction in PI(4,5)P2 levels while avoiding undesirable alterations in other phosphoinositide pools.
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Affiliation(s)
- Daniel V Olivença
- University of Lisbon, Faculty of Sciences, BIOISI: Biosystems and Integrative Sciences Institute. Campo Grande, 1749-016, Lisbon, Portugal.
| | - Inna Uliyakina
- University of Lisbon, Faculty of Sciences, BIOISI: Biosystems and Integrative Sciences Institute. Campo Grande, 1749-016, Lisbon, Portugal
| | - Luis L Fonseca
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, Georgia, 30332-2000, USA
| | - Margarida D Amaral
- University of Lisbon, Faculty of Sciences, BIOISI: Biosystems and Integrative Sciences Institute. Campo Grande, 1749-016, Lisbon, Portugal
| | - Eberhard O Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, Georgia, 30332-2000, USA
| | - Francisco R Pinto
- University of Lisbon, Faculty of Sciences, BIOISI: Biosystems and Integrative Sciences Institute. Campo Grande, 1749-016, Lisbon, Portugal
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25
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Dubankova A, Humpolickova J, Klima M, Boura E. Negative charge and membrane-tethered viral 3B cooperate to recruit viral RNA dependent RNA polymerase 3D pol. Sci Rep 2017; 7:17309. [PMID: 29230036 PMCID: PMC5725453 DOI: 10.1038/s41598-017-17621-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 11/29/2017] [Indexed: 12/28/2022] Open
Abstract
Most single stranded plus RNA viruses hijack phosphatidylinositol 4-kinases (PI4Ks) to generate membranes highly enriched in phosphatidylinositol 4-phosphate (PI4P). These membranous compartments known as webs, replication factories or replication organelles are essential for viral replication because they provide protection from the innate intracellular immune response while serving as platforms for viral replication. Using purified recombinant proteins and biomimetic model membranes we show that the nonstructural viral 3A protein is sufficient to promote membrane hyper-phosphorylation given the proper intracellular cofactors (PI4KB and ACBD3). However, our bio-mimetic in vitro reconstitution assay revealed that rather than the presence of PI4P specifically, negative charge alone is sufficient for the recruitment of 3Dpol enzymes to the surface of the lipid bilayer. Additionally, we show that membrane tethered viral 3B protein (also known as Vpg) works in combination with the negative charge to increase the efficiency of membrane recruitment of 3Dpol.
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Affiliation(s)
- Anna Dubankova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
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26
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Chalupska D, Eisenreichova A, Różycki B, Rezabkova L, Humpolickova J, Klima M, Boura E. Structural analysis of phosphatidylinositol 4-kinase IIIβ (PI4KB) - 14-3-3 protein complex reveals internal flexibility and explains 14-3-3 mediated protection from degradation in vitro. J Struct Biol 2017; 200:36-44. [PMID: 28864297 DOI: 10.1016/j.jsb.2017.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/26/2017] [Accepted: 08/28/2017] [Indexed: 12/31/2022]
Abstract
Phosphatidylinositol 4-kinase IIIβ (PI4KB) is responsible for the synthesis of the Golgi and trans-Golgi network (TGN) pool of phosphatidylinositol 4-phospahte (PI4P). PI4P is the defining lipid hallmark of Golgi and TGN and also serves as a signaling lipid and as a precursor for higher phosphoinositides. In addition, PI4KB is hijacked by many single stranded plus RNA (+RNA) viruses to generate PI4P-rich membranes that serve as viral replication organelles. Given the importance of this enzyme in cells, it has to be regulated. 14-3-3 proteins bind PI4KB upon its phosphorylation by protein kinase D, however, the structural basis of PI4KB recognition by 14-3-3 proteins is unknown. Here, we characterized the PI4KB:14-3-3 protein complex biophysically and structurally. We discovered that the PI4KB:14-3-3 protein complex is tight and is formed with 2:2 stoichiometry. Surprisingly, the enzymatic activity of PI4KB is not directly modulated by 14-3-3 proteins. However, 14-3-3 proteins protect PI4KB from proteolytic degradation in vitro. Our structural analysis revealed that the PI4KB:14-3-3 protein complex is flexible but mostly within the disordered regions connecting the 14-3-3 binding site of the PI4KB with the rest of the PI4KB enzyme. It also predicted no direct modulation of PI4KB enzymatic activity by 14-3-3 proteins and that 14-3-3 binding will not interfere with PI4KB recruitment to the membrane by the ACBD3 protein. In addition, the structural analysis explains the observed protection from degradation; it revealed that several disordered regions of PI4KB become protected from proteolytical degradation upon 14-3-3 binding. All the structural predictions were subsequently biochemically validated.
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Affiliation(s)
- Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Andrea Eisenreichova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic.
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27
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Rajkhowa S, Borah SM, Jha AN, Deka RC. Design of Plasmodium falciparum PI(4)KIIIβ Inhibitor using Molecular Dynamics and Molecular Docking Methods. ChemistrySelect 2017. [DOI: 10.1002/slct.201601052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sanchaita Rajkhowa
- Department of Chemical Sciences; Tezpur University, Napaam; Tezpur - 784028, Assam India
| | - Sapna Mayuri Borah
- Department of Molecular Biology & Biotechnology; Tezpur University, Napaam; Tezpur - 784028, Assam India
| | - Anupam Nath Jha
- Department of Molecular Biology & Biotechnology; Tezpur University, Napaam; Tezpur - 784028, Assam India
| | - Ramesh Chandra Deka
- Department of Chemical Sciences; Tezpur University, Napaam; Tezpur - 784028, Assam India
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28
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Humpolickova J, Mejdrová I, Matousova M, Nencka R, Boura E. Fluorescent Inhibitors as Tools To Characterize Enzymes: Case Study of the Lipid Kinase Phosphatidylinositol 4-Kinase IIIβ (PI4KB). J Med Chem 2016; 60:119-127. [PMID: 28004946 DOI: 10.1021/acs.jmedchem.6b01466] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The lipid kinase phosphatidylinositol 4-kinase IIIβ (PI4KB) is an essential host factor for many positive-sense single-stranded RNA (+RNA) viruses including human pathogens hepatitis C virus (HCV), Severe acute respiratory syndrome (SARS), coxsackie viruses, and rhinoviruses. Inhibitors of PI4KB are considered to be potential broad-spectrum virostatics, and it is therefore critical to develop a biochemical understanding of the kinase. Here, we present highly potent and selective fluorescent inhibitors that we show to be useful chemical biology tools especially in determination of dissociation constants. Moreover, we show that the coumarin-labeled inhibitor can be used to image PI4KB in cells using fluorescence-lifetime imaging microscopy (FLIM) microscopy.
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Affiliation(s)
- Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Ivana Mejdrová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.,Department of Chemistry of Natural Compounds, Institute of Chemical Technology Prague , Technicka 5, Prague 166 28, Czech Republic
| | - Marika Matousova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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29
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McPhail JA, Ottosen EH, Jenkins ML, Burke JE. The Molecular Basis of Aichi Virus 3A Protein Activation of Phosphatidylinositol 4 Kinase IIIβ, PI4KB, through ACBD3. Structure 2016; 25:121-131. [PMID: 27989622 DOI: 10.1016/j.str.2016.11.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/19/2016] [Accepted: 11/18/2016] [Indexed: 01/12/2023]
Abstract
Phosphatidylinositol 4-kinase III beta (PI4KIIIβ) is an essential enzyme in mediating membrane transport, and plays key roles in facilitating viral infection. Many pathogenic positive-sense single-stranded RNA viruses activate PI4KIIIβ to generate phosphatidylinositol 4-phosphate (PI4P)-enriched organelles for viral replication. The molecular basis for PI4KIIIβ activation during viral infection has remained largely unclear. We describe the biochemical reconstitution and characterization of the complex of PI4KIIIβ with the Golgi protein Acyl-coenzyme A binding domain containing protein 3 (ACBD3) and Aichi virus 3A protein on membranes. We find that 3A directly activates PI4KIIIβ, and this activation is sensitized by ACBD3. The interfaces between PI4KIIIβ-ACBD3 and ACBD3-3A were mapped with hydrogen-deuterium exchange mass spectrometry (HDX-MS). Determination of the crystal structure of the ACBD3 GOLD domain revealed a unique N terminus that mediates the interaction with 3A. Rationally designed complex-disrupting mutations in both ACBD3 and PI4KIIIβ completely abrogated the sensitization of 3A activation by ACBD3.
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Affiliation(s)
- Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Erik H Ottosen
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada.
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30
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Baumlova A, Gregor J, Boura E. The structural basis for calcium inhibition of lipid kinase PI4K IIalpha and comparison with the apo state. Physiol Res 2016; 65:987-993. [PMID: 27539108 DOI: 10.33549/physiolres.933344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PI4K IIalpha is a critical enzyme for the maintenance of Golgi and is also known to function in the synaptic vesicles. The product of its catalytical function, phosphatidylinositol 4-phosphate (PI4P), is an important lipid molecule because it is a hallmark of the Golgi and TGN, is directly recognized by many proteins and also serves as a precursor molecule for synthesis of higher phosphoinositides. Here, we report crystal structures of PI4K IIalpha enzyme in the apo-state and inhibited by calcium. The apo-structure reveals a surprising rigidity of the active site residues important for catalytic activity. The structure of calcium inhibited kinase reveals how calcium locks ATP in the active site.
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Affiliation(s)
- A Baumlova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.
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31
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Rutaganira FU, Fowler ML, McPhail JA, Gelman MA, Nguyen K, Xiong A, Dornan GL, Tavshanjian B, Glenn JS, Shokat KM, Burke JE. Design and Structural Characterization of Potent and Selective Inhibitors of Phosphatidylinositol 4 Kinase IIIβ. J Med Chem 2016; 59:1830-9. [PMID: 26885694 DOI: 10.1021/acs.jmedchem.5b01311] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Type III phosphatidylinositol 4-kinase (PI4KIIIβ) is an essential enzyme in mediating membrane trafficking and is implicated in a variety of pathogenic processes. It is a key host factor mediating replication of RNA viruses. The design of potent and specific inhibitors of this enzyme will be essential to define its cellular roles and may lead to novel antiviral therapeutics. We previously reported the PI4K inhibitor PIK93, and this compound has defined key functions of PI4KIIIβ. However, this compound showed high cross reactivity with class I and III PI3Ks. Using structure-based drug design, we have designed novel potent and selective (>1000-fold over class I and class III PI3Ks) PI4KIIIβ inhibitors. These compounds showed antiviral activity against hepatitis C virus. The co-crystal structure of PI4KIIIβ bound to one of the most potent compounds reveals the molecular basis of specificity. This work will be vital in the design of novel PI4KIIIβ inhibitors, which may play significant roles as antiviral therapeutics.
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Affiliation(s)
- Florentine U Rutaganira
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF) , San Francisco, California 94143, United States
| | - Melissa L Fowler
- Department of Biochemistry and Microbiology, University of Victoria , Victoria, BC V8W 2Y2, Canada
| | - Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria , Victoria, BC V8W 2Y2, Canada
| | - Michael A Gelman
- Department of Medicine and Department of Microbiology & Immunology, Stanford University , Palo Alto, California 94305, United States
| | - Khanh Nguyen
- Department of Medicine and Department of Microbiology & Immunology, Stanford University , Palo Alto, California 94305, United States
| | - Anming Xiong
- Department of Medicine and Department of Microbiology & Immunology, Stanford University , Palo Alto, California 94305, United States
| | - Gillian L Dornan
- Department of Biochemistry and Microbiology, University of Victoria , Victoria, BC V8W 2Y2, Canada
| | - Brandon Tavshanjian
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF) , San Francisco, California 94143, United States
| | - Jeffrey S Glenn
- Department of Medicine and Department of Microbiology & Immunology, Stanford University , Palo Alto, California 94305, United States.,Veterans Administration Medical Center , Palo Alto, California 94304, United States
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF) , San Francisco, California 94143, United States
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria , Victoria, BC V8W 2Y2, Canada
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