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Veronese M, Kallabis S, Kaczmarek AT, Das A, Robers L, Schumacher S, Lofrano A, Brodesser S, Müller S, Hofmann K, Krüger M, Rugarli EI. ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway. Life Sci Alliance 2024; 7:e202402620. [PMID: 38782601 PMCID: PMC11116810 DOI: 10.26508/lsa.202402620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Complexes of ERLIN1 and ERLIN2 (ER lipid raft-associated 1 and 2) form large ring-like cup-shaped structures on the endoplasmic reticulum (ER) membrane and serve as platforms to bind cholesterol and E3 ubiquitin ligases, potentially defining functional nanodomains. Here, we show that ERLIN scaffolds mediate the interaction between the full-length isoform of TMUB1 (transmembrane and ubiquitin-like domain-containing 1) and RNF170 (RING finger protein 170). We identify a luminal N-terminal conserved region in TMUB1 and RNF170, which is required for this interaction. Three-dimensional modelling shows that this conserved motif binds the stomatin/prohibitin/flotillin/HflKC domain of two adjacent ERLIN subunits at different interfaces. Protein variants that preclude these interactions have been previously linked to hereditary spastic paraplegia. Using omics-based approaches in combination with phenotypic characterization of HeLa cells lacking both ERLINs, we demonstrate a role of ERLIN scaffolds in limiting cholesterol esterification, thereby favouring cholesterol transport from the ER to the Golgi apparatus and regulating Golgi morphology and the secretory pathway.
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Affiliation(s)
- Matteo Veronese
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Sebastian Kallabis
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Alexander Tobias Kaczmarek
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Anushka Das
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Lennart Robers
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Simon Schumacher
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Alessia Lofrano
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Stefan Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Kay Hofmann
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
| | - Marcus Krüger
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- https://ror.org/00rcxh774 Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Elena I Rugarli
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- https://ror.org/00rcxh774 Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
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2
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Ha K, Mundt-Machado N, Bisignano P, Pinedo A, Raleigh DR, Loeb G, Reiter JF, Cao E, Delling M. Cilia-enriched oxysterol 7β,27-DHC is required for polycystin ion channel activation. Nat Commun 2024; 15:6468. [PMID: 39085216 PMCID: PMC11291729 DOI: 10.1038/s41467-024-50318-9] [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: 09/13/2023] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
Polycystin-1 (PC-1) and PC-2 form a heteromeric ion channel complex that is abundantly expressed in primary cilia of renal epithelial cells. This complex functions as a non-selective cation channel, and mutations within the polycystin complex cause autosomal dominant polycystic kidney disease (ADPKD). The spatial and temporal regulation of the polycystin complex within the ciliary membrane remains poorly understood. Using both whole-cell and ciliary patch-clamp recordings, we identify a cilia-enriched oxysterol, 7β,27-dihydroxycholesterol (DHC), that serves as a necessary activator of the polycystin complex. We further identify an oxysterol-binding pocket within PC-2 and showed that mutations within this binding pocket disrupt 7β,27-DHC-dependent polycystin activation. Pharmacologic and genetic inhibition of oxysterol synthesis reduces channel activity in primary cilia. In summary, our findings reveal a regulator of the polycystin complex. This oxysterol-binding pocket in PC-2 may provide a specific target for potential ADPKD therapeutics.
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Affiliation(s)
- Kodaji Ha
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Nadine Mundt-Machado
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Paola Bisignano
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Aide Pinedo
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Gabriel Loeb
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Erhu Cao
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Markus Delling
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.
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3
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Borsato G, Carnio F, Lunardon S, Moletta M, Pavan G, Terrin F, Scarso A, Plotegher N, Fabris F. A β-Glucosyl Sterol Probe for in situ Fluorescent Labelling in Neuronal Cells to Investigate Neurodegenerative Diseases. Chemistry 2024; 30:e202400778. [PMID: 38770991 DOI: 10.1002/chem.202400778] [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: 02/26/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 05/22/2024]
Abstract
A β-glucosyl sterol probe bearing a terminal alkyne moiety for fluorescent tagging enables the investigation of the neuronal and intracellular localization of this class of compounds involved in neurodegenerative diseases. The compound showed localization in the neuronal cells, with marked differences in the uptake and metabolism leading to enhanced persistence with respect to the un-glycosylated sterol analogue. In addition, a different impact was observed towards lysosomes, with the simple sterol probe showing the enlargement of the lysosome structures, while the β-glucosyl sterol was less capable to alter the morphology of this specific organelle.
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Affiliation(s)
- Giuseppe Borsato
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
| | - Francesco Carnio
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
| | - Sara Lunardon
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
| | - Mattia Moletta
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
| | - Giulio Pavan
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
| | - Francesca Terrin
- Dipartimento di Biologia, Università degli Studi di Padova, viale G. Colombo 3, 35131, Padova, Italy
| | - Alessandro Scarso
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
| | - Nicoletta Plotegher
- Dipartimento di Biologia, Università degli Studi di Padova, viale G. Colombo 3, 35131, Padova, Italy
| | - Fabrizio Fabris
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172, Mestre Venezia, Italy
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4
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Kundu S, Rohokale R, Lin C, Chen S, Biswas S, Guo Z. Bifunctional glycosphingolipid (GSL) probes to investigate GSL-interacting proteins in cell membranes. J Lipid Res 2024; 65:100570. [PMID: 38795858 PMCID: PMC11261293 DOI: 10.1016/j.jlr.2024.100570] [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: 03/19/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/28/2024] Open
Abstract
Glycosphingolipids (GSLs) are abundant glycolipids on cells and essential for cell recognition, adhesion, signal transduction, and so on. However, their lipid anchors are not long enough to cross the membrane bilayer. To transduce transmembrane signals, GSLs must interact with other membrane components, whereas such interactions are difficult to investigate. To overcome this difficulty, bifunctional derivatives of II3-β-N-acetyl-D-galactosamine-GA2 (GalNAc-GA2) and β-N-acetyl-D-glucosamine-ceramide (GlcNAc-Cer) were synthesized as probes to explore GSL-interacting membrane proteins in live cells. Both probes contain photoreactive diazirine in the lipid moiety, which can crosslink with proximal membrane proteins upon photoactivation, and clickable alkyne in the glycan to facilitate affinity tag addition for crosslinked protein pull-down and characterization. The synthesis is highlighted by the efficient assembly of simple glycolipid precursors followed by on-site lipid remodeling. These probes were employed to profile GSL-interacting membrane proteins in HEK293 cells. The GalNAc-GA2 probe revealed 312 distinct proteins, with GlcNAc-Cer probe-crosslinked proteins as controls, suggesting the potential influence of the glycan on GSL functions. Many of the proteins identified with the GalNAc-GA2 probe are associated with GSLs, and some have been validated as being specific to this probe. The versatile probe design and experimental protocols are anticipated to be widely applicable to GSL research.
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Affiliation(s)
- Sayan Kundu
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Rajendra Rohokale
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Chuwei Lin
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, USA; Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Shayak Biswas
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
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5
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Wozniak JM, Li W, Governa P, Chen LY, Jadhav A, Dongre A, Forli S, Parker CG. Enhanced mapping of small-molecule binding sites in cells. Nat Chem Biol 2024; 20:823-834. [PMID: 38167919 PMCID: PMC11213684 DOI: 10.1038/s41589-023-01514-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Photoaffinity probes are routinely utilized to identify proteins that interact with small molecules. However, despite this common usage, resolving the specific sites of these interactions remains a challenge. Here we developed a chemoproteomic workflow to determine precise protein binding sites of photoaffinity probes in cells. Deconvolution of features unique to probe-modified peptides, such as their tendency to produce chimeric spectra, facilitated the development of predictive models to confidently determine labeled sites. This yielded an expansive map of small-molecule binding sites on endogenous proteins and enabled the integration with multiplexed quantitation, increasing the throughput and dimensionality of experiments. Finally, using structural information, we characterized diverse binding sites across the proteome, providing direct evidence of their tractability to small molecules. Together, our findings reveal new knowledge for the analysis of photoaffinity probes and provide a robust method for high-resolution mapping of reversible small-molecule interactions en masse in native systems.
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Affiliation(s)
- Jacob M Wozniak
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Weichao Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Paolo Governa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Li-Yun Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Appaso Jadhav
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashok Dongre
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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6
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Lihan M, Tajkhorshid E. Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions. J Chem Inf Model 2024; 64:4822-4834. [PMID: 38844760 DOI: 10.1021/acs.jcim.4c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Cholesterol (CHL) plays an integral role in modulating the function and activity of various mammalian membrane proteins. Due to the slow dynamics of lipids, conventional computational studies of protein-CHL interactions rely on either long-time scale atomistic simulations or coarse-grained approximations to sample the process. A highly mobile membrane mimetic (HMMM) has been developed to enhance lipid diffusion and thus used to facilitate the investigation of lipid interactions with peripheral membrane proteins and, with customized in silico solvents to replace phospholipid tails, with integral membrane proteins. Here, we report an updated HMMM model that is able to include CHL, a nonphospholipid component of the membrane, henceforth called HMMM-CHL. To this end, we had to optimize the effect of the customized solvents on CHL behavior in the membrane. Furthermore, the new solvent is compatible with simulations using force-based switching protocols. In the HMMM-CHL, both improved CHL dynamics and accelerated lipid diffusion are integrated. To test the updated model, we have applied it to the characterization of protein-CHL interactions in two membrane protein systems, the human β2-adrenergic receptor (β2AR) and the mitochondrial voltage-dependent anion channel 1 (VDAC-1). Our HMMM-CHL simulations successfully identified CHL binding sites and captured detailed CHL interactions in excellent consistency with experimental data as well as other simulation results, indicating the utility of the improved model in applications where an enhanced sampling of protein-CHL interactions is desired.
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Affiliation(s)
- Muyun Lihan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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7
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He N, Depta L, Rossetti C, Caramelle L, Cigler M, Bryce-Rogers HP, Michon M, Rafn Dan O, Hoock J, Barbier J, Gillet D, Forrester A, Winter GE, Laraia L. Inhibition of OSBP blocks retrograde trafficking by inducing partial Golgi degradation. Nat Chem Biol 2024:10.1038/s41589-024-01653-x. [PMID: 38907112 DOI: 10.1038/s41589-024-01653-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/16/2024] [Indexed: 06/23/2024]
Abstract
Sterol-binding proteins are important regulators of lipid homeostasis and membrane integrity; however, the discovery of selective modulators can be challenging due to structural similarities in the sterol-binding domains. We report the discovery of potent and selective inhibitors of oxysterol-binding protein (OSBP), which we term oxybipins. Sterol-containing chemical chimeras aimed at identifying new sterol-binding proteins by targeted degradation, led to a significant reduction in levels of Golgi-associated proteins. The degradation occurred in lysosomes, concomitant with changes in protein glycosylation, indicating that the degradation of Golgi proteins was a downstream effect. By establishing a sterol transport protein biophysical assay panel, we discovered that the oxybipins potently inhibited OSBP, resulting in blockage of retrograde trafficking and attenuating Shiga toxin toxicity. As the oxybipins do not target other sterol transporters and only stabilized OSBP in intact cells, we advocate their use as tools to study OSBP function and therapeutic relevance.
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Affiliation(s)
- Nianzhe He
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Laura Depta
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Cecilia Rossetti
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Lucie Caramelle
- Unit of Research of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), Université de Namur ASBL, Namur, Belgium
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Marine Michon
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Oliver Rafn Dan
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Joseph Hoock
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Julien Barbier
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Daniel Gillet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Alison Forrester
- Unit of Research of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), Université de Namur ASBL, Namur, Belgium
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark.
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8
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Li T, Wang A, Zhang Y, Chen W, Guo Y, Yuan X, Liu Y, Geng Y. Chemoproteomic Profiling of Signaling Metabolite Fructose-1,6-Bisphosphate Interacting Proteins in Living Cells. J Am Chem Soc 2024; 146:15155-15166. [PMID: 38775806 DOI: 10.1021/jacs.4c01335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Fructose-1,6-bisphosphate (FBP), a cellular endogenous sugar metabolite in the glycolytic pathway, has recently been reported to act as a signaling molecule to regulate various cellular events through the engagement of important proteins. Though tremendous progress has been made in identifying specific FBP-protein interactions, the comprehensive identification of FBP-interacting proteins and their regulatory mechanisms remains largely unexplored. Here, we describe a concise synthetic approach for the scalable preparation of a photoaffinity FBP probe that enables the quantitative chemoproteomic profiling of FBP-protein interactions based on photoaffinity labeling (PAL) directly in living cells. Using such a protocol, we captured known FBP targets including PKM2 and MDH2. Furthermore, among unknown FBP-interacting proteins, we identified a mitochondrial metabolic enzyme aldehyde dehydrogenase 2 (ALDH2), against which FBP showed inhibitory activity and resulted in cellular ROS upregulation accompanied by mitochondrial fragmentation. Our findings disclosed a new mode of glucose signaling mediating by the FBP-ALDH2-ROS axis.
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Affiliation(s)
- Tian Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Anhui Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yanling Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wei Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yanshen Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yiqun Geng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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9
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Zung N, Aravindan N, Boshnakovska A, Valenti R, Preminger N, Jonas F, Yaakov G, Willoughby MM, Homberg B, Keller J, Kupervaser M, Dezorella N, Dadosh T, Wolf SG, Itkin M, Malitsky S, Brandis A, Barkai N, Fernández-Busnadiego R, Reddi AR, Rehling P, Rapaport D, Schuldiner M. The molecular mechanism of on-demand sterol biosynthesis at organelle contact sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593285. [PMID: 38766039 PMCID: PMC11100823 DOI: 10.1101/2024.05.09.593285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Contact-sites are specialized zones of proximity between two organelles, essential for organelle communication and coordination. The formation of contacts between the Endoplasmic Reticulum (ER), and other organelles, relies on a unique membrane environment enriched in sterols. However, how these sterol-rich domains are formed and maintained had not been understood. We found that the yeast membrane protein Yet3, the homolog of human BAP31, is localized to multiple ER contact sites. We show that Yet3 interacts with all the enzymes of the post-squalene ergosterol biosynthesis pathway and recruits them to create sterol-rich domains. Increasing sterol levels at ER contacts causes its depletion from the plasma membrane leading to a compensatory reaction and altered cell metabolism. Our data shows that Yet3 provides on-demand sterols at contacts thus shaping organellar structure and function. A molecular understanding of this protein's functions gives new insights into the role of BAP31 in development and pathology.
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Affiliation(s)
- Naama Zung
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Nitya Aravindan
- Interfaculty Institute of Biochemistry, University of Tuebingen, Germany
| | - Angela Boshnakovska
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Germany
- Max Planck Institute for Multidisciplinary Sciences, D-37077, Germany
| | - Rosario Valenti
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Noga Preminger
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Mathilda M Willoughby
- School of Chemistry and Biochemistry, Georgia Institute of Technology, USA
- Biochemistry and Molecular Biology Department, University of Nebraska Medical Center, USA
| | - Bettina Homberg
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Germany
- Max Planck Institute for Multidisciplinary Sciences, D-37077, Germany
| | - Jenny Keller
- University Medical Center Göttingen, Institute for Neuropathology, 37077, Germany
- Collaborative Research Center 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Germany
| | - Meital Kupervaser
- The De Botton Protein Profiling institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Israel
| | - Nili Dezorella
- Electron Microscopy Unit, Chemical Research Support, Weizmann Institute of Science, Israel
| | - Tali Dadosh
- Electron Microscopy Unit, Chemical Research Support, Weizmann Institute of Science, Israel
| | - Sharon G Wolf
- Electron Microscopy Unit, Chemical Research Support, Weizmann Institute of Science, Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Rubén Fernández-Busnadiego
- University Medical Center Göttingen, Institute for Neuropathology, 37077, Germany
- Collaborative Research Center 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077, Germany
- Faculty of Physics, University of Göttingen, 37077, Germany
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, USA
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Germany
- Max Planck Institute for Multidisciplinary Sciences, D-37077, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tuebingen, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
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10
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Chakraborty A, Kamat SS. Lysophosphatidylserine: A Signaling Lipid with Implications in Human Diseases. Chem Rev 2024; 124:5470-5504. [PMID: 38607675 DOI: 10.1021/acs.chemrev.3c00701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Lysophosphatidylserine (lyso-PS) has emerged as yet another important signaling lysophospholipid in mammals, and deregulation in its metabolism has been directly linked to an array of human autoimmune and neurological disorders. It has an indispensable role in several biological processes in humans, and therefore, cellular concentrations of lyso-PS are tightly regulated to ensure optimal signaling and functioning in physiological settings. Given its biological importance, the past two decades have seen an explosion in the available literature toward our understanding of diverse aspects of lyso-PS metabolism and signaling and its association with human diseases. In this Review, we aim to comprehensively summarize different aspects of lyso-PS, such as its structure, biodistribution, chemical synthesis, and SAR studies with some synthetic analogs. From a biochemical perspective, we provide an exhaustive coverage of the diverse biological activities modulated by lyso-PSs, such as its metabolism and the receptors that respond to them in humans. We also briefly discuss the human diseases associated with aberrant lyso-PS metabolism and signaling and posit some future directions that may advance our understanding of lyso-PS-mediated mammalian physiology.
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Affiliation(s)
- Arnab Chakraborty
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
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11
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Zhang L, Cao Z, Hong Y, He H, Chen L, Yu Z, Gao Y. Squalene Epoxidase: Its Regulations and Links with Cancers. Int J Mol Sci 2024; 25:3874. [PMID: 38612682 PMCID: PMC11011400 DOI: 10.3390/ijms25073874] [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: 01/09/2024] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Squalene epoxidase (SQLE) is a key enzyme in the mevalonate-cholesterol pathway that plays a critical role in cellular physiological processes. It converts squalene to 2,3-epoxysqualene and catalyzes the first oxygenation step in the pathway. Recently, intensive efforts have been made to extend the current knowledge of SQLE in cancers through functional and mechanistic studies. However, the underlying mechanisms and the role of SQLE in cancers have not been fully elucidated yet. In this review, we retrospected current knowledge of SQLE as a rate-limiting enzyme in the mevalonate-cholesterol pathway, while shedding light on its potential as a diagnostic and prognostic marker, and revealed its therapeutic values in cancers. We showed that SQLE is regulated at different levels and is involved in the crosstalk with iron-dependent cell death. Particularly, we systemically reviewed the research findings on the role of SQLE in different cancers. Finally, we discussed the therapeutic implications of SQLE inhibitors and summarized their potential clinical values. Overall, this review discussed the multifaceted mechanisms that involve SQLE to present a vivid panorama of SQLE in cancers.
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Affiliation(s)
- Lin Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen 518116, China
| | - Zheng Cao
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yuheng Hong
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Haihua He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Leifeng Chen
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhentao Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen 518116, China
| | - Yibo Gao
- Central Laboratory & Shenzhen Key Laboratory of Epigenetics and Precision Medicine for Cancers, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen 518116, China
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Laboratory of Translational Medicine, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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12
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Farley S, Stein F, Haberkant P, Tafesse FG, Schultz C. Trifunctional Sphinganine: A New Tool to Dissect Sphingolipid Function. ACS Chem Biol 2024; 19:336-347. [PMID: 38284972 PMCID: PMC10878393 DOI: 10.1021/acschembio.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/30/2024]
Abstract
Functions and cell biology of the sphingolipids sphingosine and sphinganine in cells are not well understood. While some signaling roles for sphingosine have been elucidated, the closely related sphinganine has been described only insofar as it does not elicit many of the same signaling responses. Here, we prepared multifunctionalized derivatives of the two lipid species that differ only in a single double bond of the carbon backbone. Using these novel probes, we were able to define their spatiotemporal distributions within cells. Furthermore, we used these tools to systematically map the protein interactomes of both lipids. The lipid-protein conjugates, prepared through photo-crosslinking in live cells and extraction via click chemistry to azide beads, revealed significant differences in the captured proteins, highlighting their distinct roles in various cellular processes. This work elucidates mechanistic differences between these critical lipids and sets the foundation for further studies of the cellular functions of sphingosine and sphinganine.
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Affiliation(s)
- Scotland Farley
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
- Department
of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Frank Stein
- European
Molecular Biology Laboratory, Proteomics
Core Facility, Heidelberg 69117, Germany
| | - Per Haberkant
- European
Molecular Biology Laboratory, Proteomics
Core Facility, Heidelberg 69117, Germany
| | - Fikadu G. Tafesse
- Department
of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Carsten Schultz
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
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13
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Skeyni A, Pradignac A, Matz RL, Terrand J, Boucher P. Cholesterol trafficking, lysosomal function, and atherosclerosis. Am J Physiol Cell Physiol 2024; 326:C473-C486. [PMID: 38145298 DOI: 10.1152/ajpcell.00415.2023] [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: 09/05/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
Despite years of study and major research advances over the past 50 years, atherosclerotic diseases continue to rank as the leading global cause of death. Accumulation of cholesterol within the vascular wall remains the main problem and represents one of the early steps in the development of atherosclerotic lesions. There is a complex relationship between vesicular cholesterol transport and atherosclerosis, and abnormalities in cholesterol trafficking can contribute to the development and progression of the lesions. The dysregulation of vesicular cholesterol transport and lysosomal function fosters the buildup of cholesterol within various intracytoplasmic compartments, including lysosomes and lipid droplets. This, in turn, promotes the hallmark formation of foam cells, a defining feature of early atherosclerosis. Multiple cellular processes, encompassing endocytosis, exocytosis, intracellular trafficking, and autophagy, play crucial roles in influencing foam cell formation and atherosclerotic plaque stability. In this review, we highlight recent advances in the understanding of the intricate mechanisms of vesicular cholesterol transport and its relationship with atherosclerosis and discuss the importance of understanding these mechanisms in developing strategies to prevent or treat this prevalent cardiovascular disease.
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Affiliation(s)
- Alaa Skeyni
- UMR-S INSERM 1109, University of Strasbourg, Strasbourg, France
| | - Alain Pradignac
- UMR-S INSERM 1109, University of Strasbourg, Strasbourg, France
| | - Rachel L Matz
- UMR-S INSERM 1109, University of Strasbourg, Strasbourg, France
| | - Jérôme Terrand
- UMR-S INSERM 1109, University of Strasbourg, Strasbourg, France
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14
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Gao Y, Ma M, Li W, Lei X. Chemoproteomics, A Broad Avenue to Target Deconvolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305608. [PMID: 38095542 PMCID: PMC10885659 DOI: 10.1002/advs.202305608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/29/2023] [Indexed: 12/22/2023]
Abstract
As a vital project of forward chemical genetic research, target deconvolution aims to identify the molecular targets of an active hit compound. Chemoproteomics, either with chemical probe-facilitated target enrichment or probe-free, provides a straightforward and effective approach to profile the target landscape and unravel the mechanisms of action. Canonical methods rely on chemical probes to enable target engagement, enrichment, and identification, whereas click chemistry and photoaffinity labeling techniques improve the efficiency, sensitivity, and spatial accuracy of target recognition. In comparison, recently developed probe-free methods detect protein-ligand interactions without the need to modify the ligand molecule. This review provides a comprehensive overview of different approaches and recent advancements for target identification and highlights the significance of chemoproteomics in investigating biological processes and advancing drug discovery processes.
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Affiliation(s)
- Yihui Gao
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Mingzhe Ma
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Wenyang Li
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
- Institute for Cancer ResearchShenzhen Bay LaboratoryShenzhenChina
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15
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Li Y, Lyu J, Wang Y, Ye M, Wang H. Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions. Chem Res Toxicol 2024; 37:1-15. [PMID: 38146056 DOI: 10.1021/acs.chemrestox.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinity-driven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, Beijing, 102206, China
| | - Hailin Wang
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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16
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Vanderroost J, Parpaite T, Avalosse N, Henriet P, Pierreux CE, Lorent JH, Gailly P, Tyteca D. Piezo1 Is Required for Myoblast Migration and Involves Polarized Clustering in Association with Cholesterol and GM1 Ganglioside. Cells 2023; 12:2784. [PMID: 38132106 PMCID: PMC10741634 DOI: 10.3390/cells12242784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
A specific plasma membrane distribution of the mechanosensitive ion channel Piezo1 is required for cell migration, but the mechanism remains elusive. Here, we addressed this question using WT and Piezo1-silenced C2C12 mouse myoblasts and WT and Piezo1-KO human kidney HEK293T cells. We showed that cell migration in a cell-free area and through a porous membrane decreased upon Piezo1 silencing or deletion, but increased upon Piezo1 activation by Yoda1, whereas migration towards a chemoattractant gradient was reduced by Yoda1. Piezo1 organized into clusters, which were preferentially enriched at the front. This polarization was stimulated by Yoda1, accompanied by Ca2+ polarization, and abrogated by partial cholesterol depletion. Piezo1 clusters partially colocalized with cholesterol- and GM1 ganglioside-enriched domains, the proportion of which was increased by Yoda1. Mechanistically, Piezo1 activation induced a differential mobile fraction of GM1 associated with domains and the bulk membrane. Conversely, cholesterol depletion abrogated the differential mobile fraction of Piezo1 associated with clusters and the bulk membrane. In conclusion, we revealed, for the first time, the differential implication of Piezo1 depending on the migration mode and the interplay between GM1/cholesterol-enriched domains at the front during migration in a cell-free area. These domains could provide the optimal biophysical properties for Piezo1 activity and/or spatial dissociation from the PMCA calcium efflux pump.
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Affiliation(s)
- Juliette Vanderroost
- de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (J.V.); (N.A.); (P.H.); (C.E.P.)
| | - Thibaud Parpaite
- Institute of Neuroscience, UCLouvain, 1200 Brussels, Belgium; (T.P.); (P.G.)
| | - Noémie Avalosse
- de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (J.V.); (N.A.); (P.H.); (C.E.P.)
| | - Patrick Henriet
- de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (J.V.); (N.A.); (P.H.); (C.E.P.)
| | | | - Joseph H. Lorent
- Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium;
| | - Philippe Gailly
- Institute of Neuroscience, UCLouvain, 1200 Brussels, Belgium; (T.P.); (P.G.)
| | - Donatienne Tyteca
- de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (J.V.); (N.A.); (P.H.); (C.E.P.)
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17
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Gawden-Bone CM, Lehner PJ, Volkmar N. As a matter of fat: Emerging roles of lipid-sensitive E3 ubiquitin ligases. Bioessays 2023; 45:e2300139. [PMID: 37890275 DOI: 10.1002/bies.202300139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]
Abstract
The dynamic structure and composition of lipid membranes need to be tightly regulated to control the vast array of cellular processes from cell and organelle morphology to protein-protein interactions and signal transduction pathways. To maintain membrane integrity, sense-and-response systems monitor and adjust membrane lipid composition to the ever-changing cellular environment, but only a relatively small number of control systems have been described. Here, we explore the emerging role of the ubiquitin-proteasome system in monitoring and maintaining membrane lipid composition. We focus on the ER-resident RNF145 E3 ubiquitin ligase, its role in regulating adiponectin receptor 2 (ADIPOR2), its lipid hydrolase substrate, and the broader implications for understanding the homeostatic processes that fine-tune cellular membrane composition.
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Affiliation(s)
- Christian M Gawden-Bone
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Norbert Volkmar
- Institute for Molecular Systems Biology (IMSB), ETH Zürich, Zürich, Switzerland
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18
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Uematsu M, Baskin JM. Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level. Cold Spring Harb Perspect Biol 2023; 15:a041407. [PMID: 37604586 PMCID: PMC10691496 DOI: 10.1101/cshperspect.a041407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.
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Affiliation(s)
- Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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19
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Lin Z, Gongora J, Liu X, Xie Y, Zhao C, Lv D, Garcia BA. Automation to Enable High-Throughput Chemical Proteomics. J Proteome Res 2023; 22:3676-3682. [PMID: 37917986 PMCID: PMC11037874 DOI: 10.1021/acs.jproteome.3c00467] [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] [Indexed: 11/04/2023]
Abstract
Chemical proteomics utilizes small-molecule probes to covalently engage with their interacting proteins. Since chemical probes are tagged to the active or binding sites of functional proteins, chemical proteomics can be used to profile protein targets, reveal precise binding sites/mechanisms, and screen inhibitors competing with probes in a biological context. These capabilities of chemical proteomics have great potential to enable discoveries of both drug targets and lead compounds. However, chemical proteomics is limited by the time-consuming bottleneck of sample preparations, which are processed manually. With the advancement of robotics and artificial intelligence, it is now possible to automate workflows to make chemical proteomics sample preparation a high-throughput process. An automated robotic system represents a major technological opportunity to speed up advances in proteomics, open new frontiers in drug target discovery, and broaden the future of chemical biology.
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Affiliation(s)
- Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Joanna Gongora
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Xingyu Liu
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Chenfeng Zhao
- McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63110
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
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20
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Tian Y, Wan N, Zhang H, Shao C, Ding M, Bao Q, Hu H, Sun H, Liu C, Zhou K, Chen S, Wang G, Ye H, Hao H. Chemoproteomic mapping of the glycolytic targetome in cancer cells. Nat Chem Biol 2023; 19:1480-1491. [PMID: 37322158 DOI: 10.1038/s41589-023-01355-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Hyperactivated glycolysis is a metabolic hallmark of most cancer cells. Although sporadic information has revealed that glycolytic metabolites possess nonmetabolic functions as signaling molecules, how these metabolites interact with and functionally regulate their binding targets remains largely elusive. Here, we introduce a target-responsive accessibility profiling (TRAP) approach that measures changes in ligand binding-induced accessibility for target identification by globally labeling reactive proteinaceous lysines. With TRAP, we mapped 913 responsive target candidates and 2,487 interactions for 10 major glycolytic metabolites in a model cancer cell line. The wide targetome depicted by TRAP unveils diverse regulatory modalities of glycolytic metabolites, and these modalities involve direct perturbation of enzymes in carbohydrate metabolism, intervention of an orphan transcriptional protein's activity and modulation of targetome-level acetylation. These results further our knowledge of how glycolysis orchestrates signaling pathways in cancer cells to support their survival, and inspire exploitation of the glycolytic targetome for cancer therapy.
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Affiliation(s)
- Yang Tian
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ning Wan
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hanqing Zhang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chang Shao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ming Ding
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Qiuyu Bao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Haiyang Hu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Huiyong Sun
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chenguang Liu
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Kun Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Shuai Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Guangji Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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21
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Goellner S, Enkavi G, Prasad V, Denolly S, Eu S, Mizzon G, Witte L, Kulig W, Uckeley ZM, Lavacca TM, Haselmann U, Lozach PY, Brügger B, Vattulainen I, Bartenschlager R. Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly. Nat Commun 2023; 14:7344. [PMID: 37957166 PMCID: PMC10643666 DOI: 10.1038/s41467-023-42985-x] [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: 03/02/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
For successful infection of host cells and virion production, enveloped viruses, including Zika virus (ZIKV), extensively rely on cellular lipids. However, how virus protein-lipid interactions contribute to the viral life cycle remains unclear. Here, we employ a chemo-proteomics approach with a bifunctional cholesterol probe and show that cholesterol is closely associated with the ZIKV structural protein prM. Bioinformatic analyses, reverse genetics alongside with photoaffinity labeling assays, and atomistic molecular dynamics simulations identified two functional cholesterol binding motifs within the prM transmembrane domain. Loss of prM-cholesterol association has a bipartite effect reducing ZIKV entry and leading to assembly defects. We propose a model in which membrane-resident M facilitates cholesterol-supported lipid exchange during endosomal entry and, together with cholesterol, creates a platform promoting virion assembly. In summary, we identify a bifunctional role of prM in the ZIKV life cycle by mediating viral entry and virus assembly in a cholesterol-dependent manner.
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Affiliation(s)
- Sarah Goellner
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Giray Enkavi
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vibhu Prasad
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Solène Denolly
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Sungmin Eu
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
- d-fine GmbH, Frankfurt, Germany
| | - Giulia Mizzon
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - Leander Witte
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Zina M Uckeley
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
- Department of Molecular Genetics & Microbiology, University of Florida, Florida, USA
| | - Teresa M Lavacca
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Uta Haselmann
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Pierre-Yves Lozach
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
- INRAE, EPHE, IVPC, University of Lyon, Lyon, France
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ralf Bartenschlager
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany.
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany.
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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22
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Abstract
The sorting and trafficking of lipids between organelles gives rise to a dichotomy of bulk membrane properties between organelles of the secretory and endolysosome networks, giving rise to two "membrane territories" based on differences in lipid-packing density, net membrane charge, and bilayer leaflet asymmetries. The cellular organelle membrane dichotomy emerges from ER-to-PM anterograde membrane trafficking and the synthesis of sphingolipids and cholesterol flux at the trans-Golgi network, which constitutes the interface between the two membrane territories. Organelle homeostasis is maintained by vesicle-mediated retrieval of bulk membrane from the distal organelles of each territory to the endoplasmic reticulum or plasma membrane and by soluble lipid transfer proteins that traffic particular lipids. The concept of cellular membrane territories emphasizes the contrasting features of organelle membranes of the secretory and endolysosome networks and the essential roles of lipid-sorting pathways that maintain organelle function.
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Affiliation(s)
- Yeongho Kim
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Christopher G Burd
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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23
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Yang RJ, Zou J, Liu JY, Dai JK, Wan JB. Click chemistry-based enrichment strategy for tracing cellular fatty acid metabolism by LC-MS/MS. J Pharm Anal 2023; 13:1221-1231. [PMID: 38024853 PMCID: PMC10657974 DOI: 10.1016/j.jpha.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 12/01/2023] Open
Abstract
Fatty acids (FAs), which were initially recognized as energy sources and essential building blocks of biomembranes, serve as the precursors of important signaling molecules. Tracing FA metabolism is essential to understanding the biochemical activity and role of FAs in physiological and pathological events. Inspired by the advances in click chemistry for protein enrichment, we herein established a click chemistry-based enrichment (CCBE) strategy for tracing the cellular metabolism of eicosapentaenoic acid (EPA, 20:5 n-3) in neural cells. Terminal alkyne-labeled EPA (EPAA) used as a surrogate was incubated with N2a, mouse neuroblastoma cells, and alkyne-labeled metabolites (ALMs) were selectively captured by an azide-modified resin via a Cu(I)-catalyzed azide-alkyne cycloaddition reaction for enrichment. After removing unlabeled metabolites, ALMs containing a triazole moiety were cleaved from solid-phase resins and subjected to liquid chromatography mass spectrometry (LC-MS) analysis. The proposed CCBE strategy is highly selective for capturing and enriching alkyne-labeled metabolites from the complicated matrices. In addition, this method can overcome current detection limits by enhancing MS sensitivity of targets, improving the chromatographic separation of sn-position glycerophospholipid regioisomers, facilitating structural characterization of ALMs by a specific MS/MS fragmentation signature, and providing versatile fluorescence detection of ALMs for cellular distribution. This CCBE strategy might be expanded to trace the metabolism of other FAs, small molecules, or drugs.
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Affiliation(s)
- Ru-Jie Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Jian Zou
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Jia-Yue Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Jiang-Kun Dai
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Jian-Bo Wan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
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24
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Li Z, Peng B, Chen S, Li J, Hu K, Liao L, Xie Q, Yao M, Liang L, Tomlinson S, Yuan G, He S. Transcriptome sequencing and metabolome analysis reveal the metabolic reprogramming of partial hepatectomy and extended hepatectomy. BMC Genomics 2023; 24:532. [PMID: 37679685 PMCID: PMC10486020 DOI: 10.1186/s12864-023-09647-0] [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: 04/06/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023] Open
Abstract
Surgical resection remains a critical treatment option for many patients with primary and secondary hepatic neoplasms. Extended hepatectomy (eHx) may be required for some patients with large tumors, which may cause liver failure and death. Partial hepatectomy (pHx) and eHx mouse models were constructed, liver tissues were sampled at 18, 36, and 72 h posthepatectomy. Transcriptome and metabolome analyses were employed to explore the different potential mechanisms in regeneration and injury between pHx and eHx. The results showed that eHx was associated with more severe liver injury and lower survival rates than pHx. Transcriptomics data showed there were 1842, 2129, and 1277 differentially expressed genes (DEGs) in eHx and 962, 1305, and 732 DEGs in pHx at 18, 36, and 72 h posthepatectomy, respectively, compared with the those in the sham groups. Compared with pHx, the number of DEGs in the eHx group reached a maximum of 230 at 18 h after surgery and decreased sequentially to 87 and 43 at 36 and 72 h. Metabolomics analysis identified a total of 1399 metabolites, and 48 significant differentially produced metabolites (DPMs) were screened between eHx and pHx. Combined analysis of DEGs and DPMs indicated that cholesterol metabolism and insulin resistance may be two important pathways for liver regeneration and mouse survival postextended hepatectomy. Our results showed the global influence of pHx and eHx on the transcriptome and metabolome in mouse liver, and revealed cholesterol metabolism and insulin resistance pathways might be involved in regeneration post-pHx and -eHx.
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Affiliation(s)
- Zeyuan Li
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, NO 6 Shuangyong Road, Nanning, Guangxi, 530021, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, 530021, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Bo Peng
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, NO 6 Shuangyong Road, Nanning, Guangxi, 530021, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, 530021, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Shilian Chen
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, NO 6 Shuangyong Road, Nanning, Guangxi, 530021, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, 530021, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jiaping Li
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Kai Hu
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Lijuan Liao
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, NO 6 Shuangyong Road, Nanning, Guangxi, 530021, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, 530021, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Qiuli Xie
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, NO 6 Shuangyong Road, Nanning, Guangxi, 530021, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, 530021, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Mei Yao
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, NO 6 Shuangyong Road, Nanning, Guangxi, 530021, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, 530021, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Lixing Liang
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Stephen Tomlinson
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Guandou Yuan
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, NO 6 Shuangyong Road, Nanning, Guangxi, 530021, China.
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, 530021, China.
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Songqing He
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, NO 6 Shuangyong Road, Nanning, Guangxi, 530021, China.
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, 530021, China.
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China.
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25
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Risinger M, Kim PS, Rodriguez RX, Rivas MN, Setchell KDR, Zhang W, Kalfa TA. Hemolytic anemia and macrothrombocytopenia: A lipid problem? Am J Hematol 2023; 98:1335-1340. [PMID: 36974979 PMCID: PMC10523966 DOI: 10.1002/ajh.26916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Affiliation(s)
- Mary Risinger
- Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Phyllis S. Kim
- Hematology and Medical Oncology Department, Kaiser Permanente Los Angeles Medical Center, Los Angeles, CA
| | - Roberto X. Rodriguez
- Hematology and Medical Oncology Department, Kaiser Permanente Los Angeles Medical Center, Los Angeles, CA
| | - Monica Narvaez Rivas
- Division of Pathology & Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Kenneth D. R. Setchell
- Division of Pathology & Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Wenying Zhang
- Genetics and Genomics Diagnostic Laboratory, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Theodosia A. Kalfa
- Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
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26
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Zhang WB, Huang Y, Guo XR, Zhang MQ, Yuan XS, Zu HB. DHCR24 reverses Alzheimer's disease-related pathology and cognitive impairment via increasing hippocampal cholesterol levels in 5xFAD mice. Acta Neuropathol Commun 2023; 11:102. [PMID: 37344916 DOI: 10.1186/s40478-023-01593-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023] Open
Abstract
Accumulating evidences reveal that cellular cholesterol deficiency could trigger the onset of Alzheimer's disease (AD). As a key regulator, 24-dehydrocholesterol reductase (DHCR24) controls cellular cholesterol homeostasis, which was found to be downregulated in AD vulnerable regions and involved in AD-related pathological activities. However, DHCR24 as a potential therapeutic target for AD remains to be identified. In present study, we demonstrated the role of DHCR24 in AD by employing delivery of adeno-associated virus carrying DHCR24 gene into the hippocampus of 5xFAD mice. Here, we found that 5xFAD mice had lower levels of cholesterol and DHCR24 expression, and the cholesterol loss was alleviated by DHCR24 overexpression. Surprisingly, the cognitive impairment of 5xFAD mice was significantly reversed after DHCR24-based gene therapy. Moreover, we revealed that DHCR24 knock-in successfully prevented or reversed AD-related pathology in 5xFAD mice, including amyloid-β deposition, synaptic injuries, autophagy, reactive astrocytosis, microglial phagocytosis and apoptosis. In conclusion, our results firstly demonstrated that the potential value of DHCR24-mediated regulation of cellular cholesterol level as a promising treatment for AD.
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Affiliation(s)
- Wen-Bin Zhang
- Department of Neurology, Jinshan Hospital Affiliated to Fudan University, No.1508 Long-Hang Road, Jinshan District, Shanghai, 201508, China
| | - Yue Huang
- Department of Neurology, Jinshan Hospital Affiliated to Fudan University, No.1508 Long-Hang Road, Jinshan District, Shanghai, 201508, China
| | - Xiao-Rou Guo
- Department of Neurology, Jinshan Hospital Affiliated to Fudan University, No.1508 Long-Hang Road, Jinshan District, Shanghai, 201508, China
| | - Meng-Qi Zhang
- Department of Neurology, Jinshan Hospital Affiliated to Fudan University, No.1508 Long-Hang Road, Jinshan District, Shanghai, 201508, China
| | - Xiang-Shan Yuan
- Department of Neurology, Jinshan Hospital Affiliated to Fudan University, No.1508 Long-Hang Road, Jinshan District, Shanghai, 201508, China.
- Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
- State Key Laboratory of Medical Neurobiology and Ministry of Education Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China.
| | - Heng-Bing Zu
- Department of Neurology, Jinshan Hospital Affiliated to Fudan University, No.1508 Long-Hang Road, Jinshan District, Shanghai, 201508, China.
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27
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Wu Y, Bertran MT, Joshi D, Maslen SL, Hurd C, Walport LJ. Identification of photocrosslinking peptide ligands by mRNA display. Commun Chem 2023; 6:103. [PMID: 37258712 PMCID: PMC10232439 DOI: 10.1038/s42004-023-00898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023] Open
Abstract
Photoaffinity labelling is a promising method for studying protein-ligand interactions. However, obtaining a specific, efficient crosslinker can require significant optimisation. We report a modified mRNA display strategy, photocrosslinking-RaPID (XL-RaPID), and exploit its ability to accelerate the discovery of cyclic peptides that photocrosslink to a target of interest. As a proof of concept, we generated a benzophenone-containing library and applied XL-RaPID screening against a model target, the second bromodomain of BRD3. This crosslinking screening gave two optimal candidates that selectively labelled the target protein in cell lysate. Overall, this work introduces direct photocrosslinking screening as a versatile technique for identifying covalent peptide ligands from mRNA display libraries incorporating reactive warheads.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK
| | - M Teresa Bertran
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Dhira Joshi
- Chemical Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics, The Francis Crick Institute, London, NW1 1AT, UK
| | - Catherine Hurd
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK.
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28
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Planas-Serra L, Launay N, Goicoechea L, Heron B, Jou C, Juliá-Palacios N, Ruiz M, Fourcade S, Casasnovas C, De La Torre C, Gelot A, Marsal M, Loza-Alvarez P, García-Cazorla À, Fatemi A, Ferrer I, Portero-Otin M, Area-Gómez E, Pujol A. Sphingolipid desaturase DEGS1 is essential for mitochondria-associated membrane integrity. J Clin Invest 2023; 133:e162957. [PMID: 36951944 PMCID: PMC10178845 DOI: 10.1172/jci162957] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/22/2023] [Indexed: 03/24/2023] Open
Abstract
Sphingolipids function as membrane constituents and signaling molecules, with crucial roles in human diseases, from neurodevelopmental disorders to cancer, best exemplified in the inborn errors of sphingolipid metabolism in lysosomes. The dihydroceramide desaturase Δ4-dihydroceramide desaturase 1 (DEGS1) acts in the last step of a sector of the sphingolipid pathway, de novo ceramide biosynthesis. Defects in DEGS1 cause the recently described hypomyelinating leukodystrophy-18 (HLD18) (OMIM #618404). Here, we reveal that DEGS1 is a mitochondria-associated endoplasmic reticulum membrane-resident (MAM-resident) enzyme, refining previous reports locating DEGS1 at the endoplasmic reticulum only. Using patient fibroblasts, multiomics, and enzymatic assays, we show that DEGS1 deficiency disrupts the main core functions of the MAM: (a) mitochondrial dynamics, with a hyperfused mitochondrial network associated with decreased activation of dynamin-related protein 1; (b) cholesterol metabolism, with impaired sterol O-acyltransferase activity and decreased cholesteryl esters; (c) phospholipid metabolism, with increased phosphatidic acid and phosphatidylserine and decreased phosphatidylethanolamine; and (d) biogenesis of lipid droplets, with increased size and numbers. Moreover, we detected increased mitochondrial superoxide species production in fibroblasts and mitochondrial respiration impairment in patient muscle biopsy tissues. Our findings shed light on the pathophysiology of HLD18 and broaden our understanding of the role of sphingolipid metabolism in MAM function.
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Affiliation(s)
- Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Nathalie Launay
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Leire Goicoechea
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Bénédicte Heron
- Department of Paediatric Neurology, Reference Centre for Neurogenetic Diseases, Armand Trousseau–La Roche Guyon University Hospital, and I2-D2 Federation, Sorbonne-Université, Paris, France
| | - Cristina Jou
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Neurometabolic Unit and Synaptic Metabolism Lab, Neurology and Pathology Department, Institut Pediàtric de Recerca, Hospital Sant Joan de Déu, and MetabERN, Barcelona, Catalonia, Spain
| | - Natalia Juliá-Palacios
- Neurometabolic Unit and Synaptic Metabolism Lab, Neurology and Pathology Department, Institut Pediàtric de Recerca, Hospital Sant Joan de Déu, and MetabERN, Barcelona, Catalonia, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Neuromuscular Unit, Neurology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona, L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | | | - Antoinette Gelot
- Armand Trousseau–La Roche Guyon University Hospital, Sorbonne-Université, Paris, France
| | - Maria Marsal
- ICFO–Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Catalonia, Spain
| | - Pablo Loza-Alvarez
- ICFO–Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Catalonia, Spain
| | - Àngels García-Cazorla
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Neurometabolic Unit and Synaptic Metabolism Lab, Neurology and Pathology Department, Institut Pediàtric de Recerca, Hospital Sant Joan de Déu, and MetabERN, Barcelona, Catalonia, Spain
| | - Ali Fatemi
- Departments of Neurology and Pediatrics, The Kennedy Krieger Institute, and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Isidre Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Network Centre of Biomedical Research of Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Manel Portero-Otin
- Departament de Medicina Experimental, Universitat de Lleida–Institut de Recerca Biomedica de Lleida, Lleida, Catalonia, Spain
| | - Estela Area-Gómez
- Department of Neurology, Columbia University Medical Center, New York, New York, USA
- Centro de Investigaciones Biológicas “Margarita Salas,” Madrid, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
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29
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Fairlamb AH, Wyllie S. The critical role of mode of action studies in kinetoplastid drug discovery. FRONTIERS IN DRUG DISCOVERY 2023; 3:fddsv.2023.1185679. [PMID: 37600222 PMCID: PMC7614965 DOI: 10.3389/fddsv.2023.1185679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Understanding the target and mode of action of compounds identified by phenotypic screening can greatly facilitate the process of drug discovery and development. Here, we outline the tools currently available for target identification against the neglected tropical diseases, human African trypanosomiasis, visceral leishmaniasis and Chagas' disease. We provide examples how these tools can be used to identify and triage undesirable mechanisms, to identify potential toxic liabilities in patients and to manage a balanced portfolio of target-based campaigns. We review the primary targets of drugs that are currently in clinical development that were initially identified via phenotypic screening, and whose modes of action affect protein turnover, RNA trans-splicing or signalling in these protozoan parasites.
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Affiliation(s)
- Alan H. Fairlamb
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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30
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Qian L, Scott NA, Capell-Hattam IM, Draper EA, Fenton NM, Luu W, Sharpe LJ, Brown AJ. Cholesterol synthesis enzyme SC4MOL is fine-tuned by sterols and targeted for degradation by the E3 ligase MARCHF6. J Lipid Res 2023; 64:100362. [PMID: 36958722 PMCID: PMC10176258 DOI: 10.1016/j.jlr.2023.100362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/09/2023] [Accepted: 02/25/2023] [Indexed: 03/25/2023] Open
Abstract
Cholesterol biosynthesis is a highly regulated pathway, with over 20 enzymes controlled at the transcriptional and post-translational level. Whilst some enzymes remain stable, increased sterol levels can trigger degradation of several synthesis enzymes via the ubiquitin-proteasome system. Of note, we previously identified four cholesterol synthesis enzymes as substrates for one E3 ubiquitin ligase, membrane-associated RING-CH-type finger 6 (MARCHF6). Whether MARCHF6 targets the cholesterol synthesis pathway at other points is unknown. In addition, the post-translational regulation of many cholesterol synthesis enzymes, including the C4-demethylation complex (sterol-C4-methyl oxidase-like, SC4MOL; NAD(P) dependent steroid dehydrogenase-like, NSDHL; hydroxysteroid 17-beta dehydrogenase, HSD17B7) is largely uncharacterized. Using cultured mammalian cell-lines (human-derived and Chinese Hamster Ovary cells), we show SC4MOL, the first acting enzyme of C4-demethylation, is a MARCHF6 substrate, and is rapidly turned over and sensitive to sterols. Sterol depletion stabilizes SC4MOL protein levels, whilst sterol excess downregulates both transcript and protein levels. Furthermore, we found SC4MOL depletion by siRNA results in a significant decrease in total cell cholesterol. Thus, our work indicates SC4MOL is the most regulated enzyme in the C4-demethylation complex. Our results further implicate MARCHF6 as a crucial post-translational regulator of cholesterol synthesis, with this E3 ubiquitin ligase controlling levels of at least five enzymes of the pathway.
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Affiliation(s)
- Lydia Qian
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Nicola A Scott
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Isabelle M Capell-Hattam
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Eliza A Draper
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Nicole M Fenton
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Winnie Luu
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Laura J Sharpe
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Andrew J Brown
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia.
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31
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Altuzar J, Notbohm J, Stein F, Haberkant P, Hempelmann P, Heybrock S, Worsch J, Saftig P, Höglinger D. Lysosome-targeted multifunctional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor. Proc Natl Acad Sci U S A 2023; 120:e2213886120. [PMID: 36893262 PMCID: PMC10089177 DOI: 10.1073/pnas.2213886120] [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: 08/12/2022] [Accepted: 01/31/2023] [Indexed: 03/11/2023] Open
Abstract
Lysosomes are catabolic organelles involved in macromolecular digestion, and their dysfunction is associated with pathologies ranging from lysosomal storage disorders to common neurodegenerative diseases, many of which have lipid accumulation phenotypes. The mechanism of lipid efflux from lysosomes is well understood for cholesterol, while the export of other lipids, particularly sphingosine, is less well studied. To overcome this knowledge gap, we have developed functionalized sphingosine and cholesterol probes that allow us to follow their metabolism, protein interactions, and their subcellular localization. These probes feature a modified cage group for lysosomal targeting and controlled release of the active lipids with high temporal precision. An additional photocrosslinkable group allowed for the discovery of lysosomal interactors for both sphingosine and cholesterol. In this way, we found that two lysosomal cholesterol transporters, NPC1 and to a lesser extent LIMP-2/SCARB2, bind to sphingosine and showed that their absence leads to lysosomal sphingosine accumulation which hints at a sphingosine transport role of both proteins. Furthermore, artificial elevation of lysosomal sphingosine levels impaired cholesterol efflux, consistent with sphingosine and cholesterol sharing a common export mechanism.
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Affiliation(s)
- Janathan Altuzar
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
| | - Judith Notbohm
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, 69117Heidelberg, Germany
| | - Per Haberkant
- European Molecular Biology Laboratory, 69117Heidelberg, Germany
| | - Pia Hempelmann
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
| | - Saskia Heybrock
- Institute of Biochemistry, Christian-Albrechts-Universität Kiel, 24118Kiel, Germany
| | - Jutta Worsch
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
| | - Paul Saftig
- Institute of Biochemistry, Christian-Albrechts-Universität Kiel, 24118Kiel, Germany
| | - Doris Höglinger
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
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32
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Forrest I, Parker CG. Proteome-Wide Fragment-Based Ligand and Target Discovery. Isr J Chem 2023; 63:e202200098. [PMID: 38213795 PMCID: PMC10783656 DOI: 10.1002/ijch.202200098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/10/2023]
Abstract
Chemical probes are invaluable tools to investigate biological processes and can serve as lead molecules for the development of new therapies. However, despite their utility, only a fraction of human proteins have selective chemical probes, and more generally, our knowledge of the "chemically-tractable" proteome is limited, leaving many potential therapeutic targets unexploited. To help address these challenges, powerful chemical proteomic approaches have recently been developed to globally survey the ability of proteins to bind small molecules (i. e., ligandability) directly in native systems. In this review, we discuss the utility of such approaches, with a focus on the integration of chemoproteomic methods with fragment-based ligand discovery (FBLD), to facilitate the broad mapping of the ligandable proteome while also providing starting points for progression into lead chemical probes.
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Affiliation(s)
- Ines Forrest
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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33
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Lipidomics analysis in drug discovery and development. Curr Opin Chem Biol 2023; 72:102256. [PMID: 36586190 DOI: 10.1016/j.cbpa.2022.102256] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/08/2022] [Accepted: 11/28/2022] [Indexed: 12/30/2022]
Abstract
Despite being a relatively new addition to the Omics' landscape, lipidomics is increasingly being recognized as an important tool for the identification of druggable targets and biochemical markers. In this review we present recent advances of lipid analysis in drug discovery and development. We cover current state of the art technologies which are constantly evolving to meet demands in terms of sensitivity and selectivity. A careful selection of important examples is then provided, illustrating the versatility of lipidomics analysis in the drug discovery and development process. Integration of lipidomics with other omics', stem-cell technologies, and metabolic flux analysis will open new avenues for deciphering pathophysiological mechanisms and the discovery of novel targets and biomarkers.
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34
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Shanbhag K, Sharma K, Kamat SS. Photoreactive bioorthogonal lipid probes and their applications in mammalian biology. RSC Chem Biol 2023; 4:37-46. [PMID: 36685253 PMCID: PMC9811504 DOI: 10.1039/d2cb00174h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
Lipids are an important class of biological molecules that possess many critical physiological functions, which enable the optimal survival of all organisms, including humans. While the role of lipids in the formation of biological cellular membranes and as a source of energy is fairly well understood, the cellular signalling pathways that lipids modulate in mammals are, in comparison, poorly characterized mechanistically and/or largely unknown. In an effort to dissect these mammalian cellular pathways regulated by signalling lipids and map hitherto unknown protein-lipid interactions, the last two decades have seen tremendous progress in the development of multifunctional lipid probes that, in conjunction with well-established bioorthogonal chemistries and chemoproteomics platforms, has almost exponentially expanded our knowledge in this field. In this review, we focus on the various photoreactive bioorthogonal lipid probes described in the literature, and briefly summarize the different photo-crosslinking groups and bioorthogonal chemistries used by them. Furthermore, we report specific case examples of such photoreactive bioorthogonal lipid probes, and discuss the new biological pathways and insights that have emerged from their use through chemoproteomics in mammalian cells. Finally, we highlight the challenges associated with the use of lipid probes in biological systems, and highlight their importance in the discovery and mechanistic understanding of lipid signalling pathways in the years to come.
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Affiliation(s)
- Karthik Shanbhag
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, PashanPune411008MaharashtraIndia
| | - Kavita Sharma
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, PashanPune411008MaharashtraIndia
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, PashanPune411008MaharashtraIndia
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35
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Xia W, Wang H, Zhou X, Wang Y, Xue L, Cao B, Song J. The role of cholesterol metabolism in tumor therapy, from bench to bed. Front Pharmacol 2023; 14:928821. [PMID: 37089950 PMCID: PMC10117684 DOI: 10.3389/fphar.2023.928821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 03/28/2023] [Indexed: 04/25/2023] Open
Abstract
Cholesterol and its metabolites have important biological functions. Cholesterol is able to maintain the physical properties of cell membrane, play an important role in cellular signaling, and cellular cholesterol levels reflect the dynamic balance between biosynthesis, uptake, efflux and esterification. Cholesterol metabolism participates in bile acid production and steroid hormone biosynthesis. Increasing evidence suggests a strict link between cholesterol homeostasis and tumors. Cholesterol metabolism in tumor cells is reprogrammed to differ significantly from normal cells, and disturbances of cholesterol balance also induce tumorigenesis and progression. Preclinical and clinical studies have shown that controlling cholesterol metabolism suppresses tumor growth, suggesting that targeting cholesterol metabolism may provide new possibilities for tumor therapy. In this review, we summarized the metabolic pathways of cholesterol in normal and tumor cells and reviewed the pre-clinical and clinical progression of novel tumor therapeutic strategy with the drugs targeting different stages of cholesterol metabolism from bench to bedside.
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Affiliation(s)
- Wenhao Xia
- Cancer Center of Peking University Third Hospital, Beijing, China
- School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hao Wang
- Cancer Center of Peking University Third Hospital, Beijing, China
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China
| | - Xiaozhu Zhou
- Department of Clinical Pharmacy, School of Pharmacy, Capital Medical University, Beijing, China
| | - Yan Wang
- Cancer Center of Peking University Third Hospital, Beijing, China
- Third Hospital Institute of Medical Innovation and Research, Beijing, China
| | - Lixiang Xue
- Cancer Center of Peking University Third Hospital, Beijing, China
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China
- Third Hospital Institute of Medical Innovation and Research, Beijing, China
- *Correspondence: Lixiang Xue, ; Baoshan Cao, ; Jiagui Song,
| | - Baoshan Cao
- Cancer Center of Peking University Third Hospital, Beijing, China
- Department of Medical Oncology and Radiation Sickness, Peking University Third Hospital, Beijing, China
- *Correspondence: Lixiang Xue, ; Baoshan Cao, ; Jiagui Song,
| | - Jiagui Song
- Cancer Center of Peking University Third Hospital, Beijing, China
- Third Hospital Institute of Medical Innovation and Research, Beijing, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University as the Third Responsibility Unit of Song Jiagui, Beijing, China
- *Correspondence: Lixiang Xue, ; Baoshan Cao, ; Jiagui Song,
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36
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Enrich C, Lu A, Tebar F, Rentero C, Grewal T. Ca 2+ and Annexins - Emerging Players for Sensing and Transferring Cholesterol and Phosphoinositides via Membrane Contact Sites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:393-438. [PMID: 36988890 DOI: 10.1007/978-3-031-21547-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Maintaining lipid composition diversity in membranes from different organelles is critical for numerous cellular processes. However, many lipids are synthesized in the endoplasmic reticulum (ER) and require delivery to other organelles. In this scenario, formation of membrane contact sites (MCS) between neighbouring organelles has emerged as a novel non-vesicular lipid transport mechanism. Dissecting the molecular composition of MCS identified phosphoinositides (PIs), cholesterol, scaffolding/tethering proteins as well as Ca2+ and Ca2+-binding proteins contributing to MCS functioning. Compelling evidence now exists for the shuttling of PIs and cholesterol across MCS, affecting their concentrations in distinct membrane domains and diverse roles in membrane trafficking. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) at the plasma membrane (PM) not only controls endo-/exocytic membrane dynamics but is also critical in autophagy. Cholesterol is highly concentrated at the PM and enriched in recycling endosomes and Golgi membranes. MCS-mediated cholesterol transfer is intensely researched, identifying MCS dysfunction or altered MCS partnerships to correlate with de-regulated cellular cholesterol homeostasis and pathologies. Annexins, a conserved family of Ca2+-dependent phospholipid binding proteins, contribute to tethering and untethering events at MCS. In this chapter, we will discuss how Ca2+ homeostasis and annexins in the endocytic compartment affect the sensing and transfer of cholesterol and PIs across MCS.
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Affiliation(s)
- Carlos Enrich
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain.
| | - Albert Lu
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Tebar
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Carles Rentero
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Thomas Grewal
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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37
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Rister AB, Gudermann T, Schredelseker J. E as in Enigma: The Mysterious Role of the Voltage-Dependent Anion Channel Glutamate E73. Int J Mol Sci 2022; 24:ijms24010269. [PMID: 36613710 PMCID: PMC9820230 DOI: 10.3390/ijms24010269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) is the main passageway for ions and metabolites over the outer mitochondrial membrane. It was associated with many physiological processes, including apoptosis and modulation of intracellular Ca2+ signaling. The protein is formed by a barrel of 19 beta-sheets with an N-terminal helix lining the inner pore. Despite its large diameter, the channel can change its selectivity for ions and metabolites based on its open state to regulate transport into and out of mitochondria. VDAC was shown to be regulated by a variety of cellular factors and molecular partners including proteins, lipids and ions. Although the physiological importance of many of these modulatory effects are well described, the binding sites for molecular partners are still largely unknown. The highly symmetrical and sleek structure of the channel makes predictions of functional moieties difficult. However, one residue repeatedly sticks out when reviewing VDAC literature. A glutamate at position 73 (E73) located on the outside of the channel facing the hydrophobic membrane environment was repeatedly proposed to be involved in channel regulation on multiple levels. Here, we review the distinct hypothesized roles of E73 and summarize the open questions around this mysterious residue.
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Affiliation(s)
- Alexander Bernhard Rister
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, 80336 Munich, Germany
| | - Thomas Gudermann
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, 80336 Munich, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung, Partner Site Munich Heart Alliance, Munich, Germany
| | - Johann Schredelseker
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, 80336 Munich, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung, Partner Site Munich Heart Alliance, Munich, Germany
- Correspondence: ; Tel.: +49-(0)89-2180-73831
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38
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Ge J, Du S, Yao SQ. Bifunctional Lipid-Derived Affinity-Based Probes (A fBPs) for Analysis of Lipid-Protein Interactome. Acc Chem Res 2022; 55:3663-3674. [PMID: 36484537 DOI: 10.1021/acs.accounts.2c00593] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although lipids are not genetically encoded, they are fundamental building blocks of cell membranes and essential components of cell metabolites. Lipids regulate various biological processes, including energy storage, membrane trafficking, signal transduction, and protein secretion; therefore, their metabolic imbalances cause many diseases. Approximately 47 000 lipid species with diverse structures have been identified, but little is known about their crucial roles in cellular systems. Particularly the structural, metabolic, and signaling functions of lipids often arise from interactions with proteins. Lipids attach to proteins not only by covalent bonds but also through noncovalent interactions, which also influence protein functions and localization. Therefore, it is important to explore this lipid-protein "interactome" to understand its roles in health and disease, which may further provide insight for medicinal development. However, lipid structures are generally quite complicated, rendering the systematic characterization of lipid-protein interactions much more challenging.Chemoproteomics is a well-known chemical biology platform in which small-molecule chemical probes are utilized in combination with high-resolution, quantitative mass spectrometry to study protein-ligand interactions in living cells or organisms, and it has recently been applied to the study of protein-lipid interactions as well. The study of these complicated interactions has been advanced by the development of bifunctional lipid probes, which not only enable probes to form covalent cross-links with lipid-interacting proteins under UV irradiation, but are also capable of enriching these proteins through bioorthogonal reactions.In this Account, we will discuss recent developments in bifunctional lipid-derived, affinity-based probes (AfBP)s that have been developed to investigate lipid-protein interactions in live cell systems. First, we will give a brief introduction of fundamental techniques based on AfBPs which are related to lipid research. Then, we will focus on three aspects, including probes developed on the basis of lipidation, lipid-derived probes with different modification positions (e.g., hydrophobic or hydrophilic parts of a lipid), and, finally, in situ biosynthesis of probes through intrinsic metabolic pathways by using chemically modified building blocks. We will present some case studies to describe these probes' design principles and cellular applications. At the end, we will also highlight key limitations of current approaches so as to provide inspirations for future improvement. The lipid probes that have been constructed are only the tip of the iceberg, and there are still plenty of lipid species that have yet to be explored. We anticipate that AfBP-based chemoproteomics and its further advancement will pave the way for a deep understanding of lipid-protein interactions in the future.
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Affiliation(s)
- Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore
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39
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Yu W, Lin Z, Woo CM, Baskin JM. A Chemoproteomics Approach to Profile Phospholipase D-Derived Phosphatidyl Alcohol Interactions. ACS Chem Biol 2022; 17:3276-3283. [PMID: 34908404 DOI: 10.1021/acschembio.1c00584] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Alcohol consumption leads to formation of phosphatidylethanol (PEth) via the transphosphatidylation activity of phospholipase D (PLD) enzymes. Though this non-natural phospholipid routinely serves as a biomarker of chronic alcoholism, its pathophysiological roles remain unknown. We use a minimalist diazirine alkyne alcohol as an ethanol surrogate to generate clickable, photoaffinity lipid reporters of PEth localization and lipid-protein interactions via PLD-mediated transphosphatidylation. We use these tools to visualize phosphatidyl alcohols in a manner compatible with standard permeabilization and immunofluorescence methods. We also use click chemistry tagging, enrichment, and proteomics analysis to define the phosphatidyl alcohol interactome. Our analysis reveals an enrichment of putative interactors at various membrane locations, and we validate one such interaction with the single-pass transmembrane protein basigin/CD147. This study provides a comprehensive view of the molecular interactions of phosphatidyl alcohols with the cellular proteome and points to future work to connect such interactions to potential pathophysiological roles of PEth.
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Affiliation(s)
- Weizhi Yu
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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40
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West AV, Woo CM. Photoaffinity Labeling Chemistries Used to Map Biomolecular Interactions. Isr J Chem 2022. [DOI: 10.1002/ijch.202200081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Alexander V. West
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford St Cambridge MA USA
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford St Cambridge MA USA
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41
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Gagestein B, von Hegedus JH, Kwekkeboom JC, Heijink M, Blomberg N, van der Wel T, Florea BI, van den Elst H, Wals K, Overkleeft HS, Giera M, Toes REM, Ioan-Facsinay A, van der Stelt M. Comparative Photoaffinity Profiling of Omega-3 Signaling Lipid Probes Reveals Prostaglandin Reductase 1 as a Metabolic Hub in Human Macrophages. J Am Chem Soc 2022; 144:18938-18947. [PMID: 36197299 PMCID: PMC9585591 DOI: 10.1021/jacs.2c06827] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The fish oil constituent
docosahexaenoic acid (DHA, 22:6
n-3) is
a signaling lipid with anti-inflammatory properties. The molecular
mechanisms underlying the biological effect of DHA are poorly understood.
Here, we report the design, synthesis, and application of a complementary
pair of bio-orthogonal, photoreactive probes based on the polyunsaturated
scaffold DHA and its oxidative metabolite 17-hydroxydocosahexaenoic
acid (17-HDHA). In these probes, an alkyne serves as a handle to introduce
a fluorescent reporter group or a biotin-affinity tag via copper(I)-catalyzed
azide-alkyne cycloaddition. This pair of chemical probes was used
to map specific targets of the omega-3 signaling lipids in primary
human macrophages. Prostaglandin reductase 1 (PTGR1) was identified
as an interaction partner that metabolizes 17-oxo-DHA, an oxidative
metabolite of 17-HDHA. 17-oxo-DHA reduced the formation of pro-inflammatory
lipids 5-HETE and LTB4 in human macrophages and neutrophils. Our results
demonstrate the potential of comparative photoaffinity protein profiling
for the discovery of metabolic enzymes of bioactive lipids and highlight
the power of chemical proteomics to uncover new biological insights.
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Affiliation(s)
- Berend Gagestein
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Johannes H von Hegedus
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Joanneke C Kwekkeboom
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Marieke Heijink
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Niek Blomberg
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Tom van der Wel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Bogdan I Florea
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Hans van den Elst
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Kim Wals
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Herman S Overkleeft
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Andreea Ioan-Facsinay
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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42
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Liu B, Zhuang S, Tian R, Liu Y, Wang Y, Lei X, Wang C. Chemoproteomic Profiling Reveals the Mechanism of Bile Acid Tolerance in Bacteria. ACS Chem Biol 2022; 17:2461-2470. [PMID: 36049085 DOI: 10.1021/acschembio.2c00286] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Bile acids (BAs) are a class of endogenous metabolites with important functions. As amphipathic molecules, BAs have strong antibacterial effects, preventing overgrowth of the gut microbiota and defending the invasion of pathogens. However, some disease-causing pathogens can survive the BA stress and knowledge is limited about how they develop BA tolerance. In this work, we applied a quantitative chemoproteomic strategy to profile BA-interacting proteins in bacteria, aiming to discover the sensing pathway of BAs. Using a clickable and photo-affinity BA probe with quantitative mass spectrometry, we identified a list of histidine kinases (HKs) of the two-component systems (TCS) in bacteria as the novel binding targets of BA. Genetic screening revealed that knocking out one specific HK, EnvZ, renders bacteria with significant sensitivity to BA. Further biochemical and genetic experiments demonstrated that BA binds to a specific pocket in EnvZ and activates a downstream signaling pathway to help efflux of BA from bacteria, resulting in BA tolerance. Collectively, our data revealed that EnvZ is a novel sensor of BA in bacteria and its associated TCS signaling pathway plays a critical role in mediating bacterial BA tolerance, which opens new opportunities to combat BA-tolerating pathogens.
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Affiliation(s)
- Biwei Liu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shentian Zhuang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Runze Tian
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yanqi Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaoguang Lei
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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43
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Nourse JL, Leung VM, Abuwarda H, Evans EL, Izquierdo-Ortiz E, Ly AT, Truong N, Smith S, Bhavsar H, Bertaccini G, Monuki ES, Panicker MM, Pathak MM. Piezo1 regulates cholesterol biosynthesis to influence neural stem cell fate during brain development. J Gen Physiol 2022; 154:213449. [PMID: 36069933 PMCID: PMC9458470 DOI: 10.1085/jgp.202213084] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/28/2022] [Indexed: 02/02/2023] Open
Abstract
Mechanical forces and tissue mechanics influence the morphology of the developing brain, but the underlying molecular mechanisms have been elusive. Here, we examine the role of mechanotransduction in brain development by focusing on Piezo1, a mechanically activated ion channel. We find that Piezo1 deletion results in a thinner neuroepithelial layer, disrupts pseudostratification, and reduces neurogenesis in E10.5 mouse embryos. Proliferation and differentiation of Piezo1 knockout (KO) mouse neural stem cells (NSCs) isolated from E10.5 embryos are reduced in vitro compared to littermate WT NSCs. Transcriptome analysis of E10.5 Piezo1 KO brains reveals downregulation of the cholesterol biosynthesis superpathway, in which 16 genes, including Hmgcr, the gene encoding the rate-limiting enzyme of the cholesterol biosynthesis pathway, are downregulated by 1.5-fold or more. Consistent with this finding, membrane lipid composition is altered, and the cholesterol levels are reduced in Piezo1 KO NSCs. Cholesterol supplementation of Piezo1 KO NSCs partially rescues the phenotype in vitro. These findings demonstrate a role for Piezo1 in the neurodevelopmental process that modulates the quantity, quality, and organization of cells by influencing cellular cholesterol metabolism. Our study establishes a direct link in NSCs between PIEZO1, intracellular cholesterol levels, and neural development.
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Affiliation(s)
- Jamison L. Nourse
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Vivian M. Leung
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Hamid Abuwarda
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Elizabeth L. Evans
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Esmeralda Izquierdo-Ortiz
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Alan T. Ly
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Nguyen Truong
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Samantha Smith
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Harsh Bhavsar
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Gabriella Bertaccini
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Edwin S. Monuki
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA,Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA
| | - Mitradas M. Panicker
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | - Medha M. Pathak
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA,Center for Complex Biological Systems, University of California, Irvine, Irvine, CA,Department of Biomedical Engineering, University of California, Irvine, Irvine, CA,Correspondence to Medha M. Pathak:
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44
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Das T, Yang X, Lee H, Garst EH, Valencia E, Chandran K, Im W, Hang HC. S-Palmitoylation and Sterol Interactions Mediate Antiviral Specificity of IFITMs. ACS Chem Biol 2022; 17:2109-2120. [PMID: 35861660 PMCID: PMC10597057 DOI: 10.1021/acschembio.2c00176] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Interferon-induced transmembrane proteins (IFITM1, 2, and 3) are important antiviral proteins that are active against many viruses, including influenza A virus (IAV), dengue virus (DENV), Ebola virus (EBOV), Zika virus (ZIKV), and severe acute respiratory syndrome coronavirus (SARS-CoV). IFITM proteins exhibit specificity in activity, but their distinct mechanisms of action and regulation are unclear. Since S-palmitoylation and cholesterol homeostasis are crucial for viral infections, we investigated IFITM interactions with cholesterol by photoaffinity cross-linking in mammalian cells along with molecular dynamic simulations and nuclear magnetic resonance analysis in vitro. These studies suggest that cholesterol can directly interact with S-palmitoylated IFITMs in cells and alter the conformation of IFITMs in membrane bilayers. Notably, we discovered that the S-palmitoylation levels regulate differential IFITM protein interactions with cholesterol in mammalian cells and specificity of antiviral activity toward IAV, SARS-CoV-2, and EBOV. Our studies suggest that modulation of IFITM S-palmitoylation levels and cholesterol interaction influence host susceptibility to different viruses.
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Affiliation(s)
- Tandrila Das
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, United States
- Tri-Institutional Ph.D. Program in Chemical Biology, New York, NY 10065, United States
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, United States
| | - Xinglin Yang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, United States
| | - Hwayoung Lee
- Department of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA 18015, United States
| | - Emma H. Garst
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, United States
- Tri-Institutional Ph.D. Program in Chemical Biology, New York, NY 10065, United States
| | - Estefania Valencia
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA 18015, United States
| | - Howard C. Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, United States
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, United States
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45
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Buyan A, Allender DW, Corry B, Schick M. Lipid redistribution in the highly curved footprint of Piezo1. Biophys J 2022:S0006-3495(22)00595-1. [PMID: 35927961 DOI: 10.1016/j.bpj.2022.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/06/2022] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
We investigate the effects on the distribution of lipids in the plasma membrane that are caused by the insertion of a protein, Piezo1, that significantly distorts the membrane toward the cytosol. From coarse-grained molecular dynamics simulations, we find that the major effects occur in the outer, extracellular, leaflet. The mol fraction of cholesterol increases significantly in the curved region of the membrane close to Piezo1, while those of phosphatidylcholine and of sphingomyelin decrease. In the inner leaflet, mol fractions of cholesterol and of phosphatidylethanolamine decrease slightly as the protein is approached, while that of phosphatidylserine increases slightly. The mol fraction of phosphatidylcholine decreases markedly as the protein is approached. Most of these results are understood in the context of a theoretical model that utilizes two elements; (i) a coupling between the leaflets' actual curvatures and their compositionally-dependent spontaneous curvatures and, (ii) the dependence of the spontaneous curvatures not only on the mol fractions of the phospholipids, but also on the effect that cholesterol has on the spontaneous curvatures of the phospholipids.
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Affiliation(s)
- Amanda Buyan
- Research School of Biology, The Australian National University, Acton, Australia
| | - D W Allender
- Department of Physics, University of Washington, Seattle WA; Department of Physics, Kent State University, Kent OH
| | - Ben Corry
- Research School of Biology, The Australian National University, Acton, Australia
| | - M Schick
- Department of Physics, University of Washington, Seattle WA
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46
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Schultz C, Farley SE, Tafesse FG. "Flash & Click": Multifunctionalized Lipid Derivatives as Tools To Study Viral Infections. J Am Chem Soc 2022; 144:13987-13995. [PMID: 35900117 PMCID: PMC9377334 DOI: 10.1021/jacs.2c02705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this perspective article, we describe the current status of lipid tools for studying host lipid-virus interactions at the cellular level. We discuss the potential lipidomic changes that viral infections impose on host cells and then outline the tools available and the resulting options to investigate the host cell lipid interactome. The future outcome will reveal new targets for treating virus infections.
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Affiliation(s)
- Carsten Schultz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | - Scotland E Farley
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States.,Department of Molecular Microbiology and Immunology, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
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47
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Lin Y, Buyan A, Corry B. Characterizing the lipid fingerprint of the mechanosensitive channel Piezo2. J Gen Physiol 2022; 154:213361. [PMID: 35861699 PMCID: PMC9532583 DOI: 10.1085/jgp.202113064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/22/2022] [Accepted: 07/01/2022] [Indexed: 01/23/2023] Open
Abstract
Piezo2 is a mechanosensitive ion channel that plays critical roles in sensing touch and pain, proprioception, and regulation of heart rate. Global knockout of Piezo2 leads to perinatal lethality in mice, and Piezo2 gain-of-function mutations are associated with distal arthrogryposis, a disease characterized by congenital joint contractures. Emerging evidence suggests that Piezo channels (Piezo1 and Piezo2) can be regulated by their local membrane environment and particularly by cholesterol and phosphoinositides. To characterize the local Piezo2 lipid environment and investigate key lipid-protein interactions, we carried out coarse-grained molecular dynamics simulations of Piezo2 embedded in a complex mammalian membrane containing >60 distinct lipid species. We show that Piezo2 alters its local membrane composition such that it becomes enriched with specific lipids, such as phosphoinositides, and forms specific, long-term interactions with a variety of lipids at functionally relevant sites.
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Affiliation(s)
| | | | - Ben Corry
- Research School of Biology, Canberra, Australia,Correspondence to Ben Corry:
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48
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Linking Late Endosomal Cholesterol with Cancer Progression and Anticancer Drug Resistance. Int J Mol Sci 2022; 23:ijms23137206. [PMID: 35806209 PMCID: PMC9267071 DOI: 10.3390/ijms23137206] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer cells undergo drastic metabolic adaptions to cover increased bioenergetic needs, contributing to resistance to therapies. This includes a higher demand for cholesterol, which often coincides with elevated cholesterol uptake from low-density lipoproteins (LDL) and overexpression of the LDL receptor in many cancers. This implies the need for cancer cells to accommodate an increased delivery of LDL along the endocytic pathway to late endosomes/lysosomes (LE/Lys), providing a rapid and effective distribution of LDL-derived cholesterol from LE/Lys to other organelles for cholesterol to foster cancer growth and spread. LDL-cholesterol exported from LE/Lys is facilitated by Niemann–Pick Type C1/2 (NPC1/2) proteins, members of the steroidogenic acute regulatory-related lipid transfer domain (StARD) and oxysterol-binding protein (OSBP) families. In addition, lysosomal membrane proteins, small Rab GTPases as well as scaffolding proteins, including annexin A6 (AnxA6), contribute to regulating cholesterol egress from LE/Lys. Here, we summarize current knowledge that links upregulated activity and expression of cholesterol transporters and related proteins in LE/Lys with cancer growth, progression and treatment outcomes. Several mechanisms on how cellular distribution of LDL-derived cholesterol from LE/Lys influences cancer cell behavior are reviewed, some of those providing opportunities for treatment strategies to reduce cancer progression and anticancer drug resistance.
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49
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Rossetti C, Laraia L. Thermal Proteome Profiling Reveals Distinct Target Selectivity for Differentially Oxidized Oxysterols. ACS Chem Biol 2022; 17:1677-1684. [PMID: 35763711 DOI: 10.1021/acschembio.2c00383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxysterols are produced physiologically by many species; however, their distinct roles in regulating human physiology have not been studied systematically. The role of differing oxidation states and sites in mediating their biological functions is also unclear. As oxysterols have been associated with atherosclerosis, neurodegeneration, and cancer, a better understanding of their protein targets is desirable. To address this, we mapped the oxysterol interactome with three A- and B-ring oxidized sterols as well as 25-hydroxy cholesterol using thermal proteome profiling, validating selected targets with the cellular thermal shift assay and isothermal dose response fingerprinting. This revealed that the site of oxidation has a profound impact on target selectivity, with each oxysterol possessing an almost unique set of target proteins. Overall, targets clustered in pathways relating to vesicular transport and phosphoinositide metabolism, suggesting that while individual oxysterols bind to a unique set of proteins, the processes they modulate are highly interconnected.
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Affiliation(s)
- Cecilia Rossetti
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
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50
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Yu W, Baskin JM. Photoaffinity labeling approaches to elucidate lipid-protein interactions. Curr Opin Chem Biol 2022; 69:102173. [PMID: 35724595 DOI: 10.1016/j.cbpa.2022.102173] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022]
Abstract
Lipid-protein interactions serve as the basis for many of the diverse roles of lipids. However, these noncovalent binding events are often weak, transient, or dependent upon environmental cues. Photoaffinity labeling can preserve these interactions under native conditions, enabling their biochemical profiling. Typically, photoaffinity labeling probes contain a diazirine photocrosslinker and a click chemistry handle for enrichment and downstream analysis. In this review, we summarize recent advances in the understanding the mechanisms of diazirine photocrosslinking, and we provide an overview of recent applications of photoaffinity labeling to reveal the interactions of diverse types of lipids with specific members of the proteome.
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Affiliation(s)
- Weizhi Yu
- Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, 14853, NY, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, 14853, NY, USA.
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