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Metabolic Labeling of Inositol Phosphates and Phosphatidylinositols in Yeast and Mammalian Cells. Methods Mol Biol 2020; 2091:83-92. [PMID: 31773572 DOI: 10.1007/978-1-0716-0167-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Inositol phosphate (IP) and phosphatidylinositol (PI) signaling are critical signal transduction pathways responsible for generating numerous receptor-mediated cellular responses. Biochemical and genetic studies have revealed diverse roles of IP and PI signaling in eukaryotic signaling, but detailed characterization of unique IP and PI signaling profiles in response to different agonists and among cell types remains largely unexplored. Here, we outline steady-state inositol metabolic-labeling techniques that can be leveraged to assess the IP and PI signaling state in eukaryotic cells. This flexible technique can be amended and optimized to your cell line of interest, perturbed with biochemical, genetic, or pharmacological alteration, and used to provide comprehensive inositol profiling in various cellular systems.
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Clarke BP, Logeman BL, Hale AT, Luka Z, York JD. A synthetic biological approach to reconstitution of inositide signaling pathways in bacteria. Adv Biol Regul 2019; 73:100637. [PMID: 31378699 DOI: 10.1016/j.jbior.2019.100637] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 11/19/2022]
Abstract
Inositide lipid (PIP) and soluble (IP) signaling pathways produce essential cellular codes conserved in eukaryotes. In many cases, deconvoluting metabolic and functional aspects of individual pathways are confounded by promiscuity and multiplicity of PIP and IP kinases and phosphatases. We report a molecular genetic approach that reconstitutes eukaryotic inositide lipid and soluble pathways in a prokaryotic cell which inherently lack inositide kinases and phosphatases in their genome. By expressing synthetic cassettes of eukaryotic genes, we have reconstructed the heterologous formation of a range of inositide lipids, including PI(3)P, PI(4,5)P2 and PIP3. In addition, we report the reconstruction of lipid-dependent production of inositol hexakisphosphate (IP6). Our synthetic system is scalable, reduces confounding metabolic issues, for example it is devoid of inositide phosphatases and orthologous kinases, and enables accurate characterization gene product enzymatic activity and substrate selectivity. This genetically engineered tool is designed to help interpret metabolic pathways and may facilitate in vivo testing of regulators and small molecule inhibitors. In summary, heterologous expression of inositide pathways in bacteria provide a malleable experimental platform for aiding signaling biologists and offers new insights into metabolism of these essential pathways.
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Affiliation(s)
- Bradley P Clarke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Brandon L Logeman
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Andrew T Hale
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Zigmund Luka
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - John D York
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
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McNamara DE, Dovey CM, Hale AT, Quarato G, Grace CR, Guibao CD, Diep J, Nourse A, Cai CR, Wu H, Kalathur RC, Green DR, York JD, Carette JE, Moldoveanu T. Direct Activation of Human MLKL by a Select Repertoire of Inositol Phosphate Metabolites. Cell Chem Biol 2019; 26:863-877.e7. [PMID: 31031142 DOI: 10.1016/j.chembiol.2019.03.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/08/2019] [Accepted: 03/15/2019] [Indexed: 12/29/2022]
Abstract
Necroptosis is an inflammatory form of programmed cell death executed through plasma membrane rupture by the pseudokinase mixed lineage kinase domain-like (MLKL). We previously showed that MLKL activation requires metabolites of the inositol phosphate (IP) pathway. Here we reveal that I(1,3,4,6)P4, I(1,3,4,5,6)P5, and IP6 promote membrane permeabilization by MLKL through directly binding the N-terminal executioner domain (NED) and dissociating its auto-inhibitory region. We show that IP6 and inositol pentakisphosphate 2-kinase (IPPK) are required for necroptosis as IPPK deletion ablated IP6 production and inhibited necroptosis. The NED auto-inhibitory region is more extensive than originally described and single amino acid substitutions along this region induce spontaneous necroptosis by MLKL. Activating IPs bind three sites with affinity of 100-600 μM to destabilize contacts between the auto-inhibitory region and NED, thereby promoting MLKL activation. We therefore uncover MLKL's activating switch in NED triggered by a select repertoire of IP metabolites.
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Affiliation(s)
- Dan E McNamara
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cole M Dovey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew T Hale
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Giovanni Quarato
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christy R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cristina D Guibao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jonathan Diep
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amanda Nourse
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Casey R Cai
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hong Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ravi C Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John D York
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Tudor Moldoveanu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Fujii M, Kita S, Hirata M, Iwamoto T. [Quantitative analysis of phosphoinositides and inositol polyphosphates using an HPLC system]. Nihon Yakurigaku Zasshi 2013; 142:236-40. [PMID: 24212593 DOI: 10.1254/fpj.142.236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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