1
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Arab M, Chen T, Lowe M. Mechanisms governing vesicle traffic at the Golgi apparatus. Curr Opin Cell Biol 2024; 88:102365. [PMID: 38705050 DOI: 10.1016/j.ceb.2024.102365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024]
Abstract
Vesicle transport at the Golgi apparatus is a well-described process, and the major protein components involved have been identified. This includes the coat proteins that function in cargo sorting and vesicle formation, and the proteins that mediate the downstream events of vesicle tethering and membrane fusion. However, despite this knowledge, there remain significant gaps in our mechanistic understanding of these processes which includes how they are coordinated in space and time. In this review we discuss recent advances that have provided new insights into the mechanisms of Golgi trafficking, focussing on vesicle formation and cargo sorting, and vesicle tethering and fusion. These studies point to a high degree of spatial organisation of trafficking components at the Golgi and indicate an inherent plasticity of trafficking. Going forward, further advancements in technology and more sophisticated functional assays are expected to yield greater understanding of the mechanisms that govern Golgi trafficking events.
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Affiliation(s)
- Maryam Arab
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Tong Chen
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Martin Lowe
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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2
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Xing Y, Jian Y, Zhao X, Zhang Y, Zhang Z, Zhang X, Zhang X. Morphological determination of localization and function of Golgi proteins. BIOPHYSICS REPORTS 2024; 10:121-132. [PMID: 38774352 PMCID: PMC11103716 DOI: 10.52601/bpr.2024.240008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 05/24/2024] Open
Abstract
In animal cells, the Golgi apparatus serves as the central hub of the endomembrane secretory pathway. It is responsible for the processing, modification, and sorting of proteins and lipids. The unique stacking and ribbon-like architecture of the Golgi apparatus forms the foundation for its precise functionality. Under cellular stress or pathological conditions, the structure of the Golgi and its important glycosylation modification function may change. It is crucial to employ suitable methodologies to study the structure and function of the Golgi apparatus, particularly when assessing the involvement of a target protein in Golgi regulation. This article provides a comprehensive overview of the diverse microscopy techniques used to determine the specific location of the target protein within the Golgi apparatus. Additionally, it outlines methods for assessing changes in the Golgi structure and its glycosylation modification function following the knockout of the target gene.
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Affiliation(s)
- Yusheng Xing
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yannan Jian
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaodan Zhao
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Zhang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenqian Zhang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xing Zhang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyan Zhang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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3
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Hollingsworth LR, Veeraraghavan P, Paulo JA, Harper JW, Rauch I. Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590338. [PMID: 38659763 PMCID: PMC11042255 DOI: 10.1101/2024.04.19.590338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 3 (NLRP3) is an innate immune sensor that forms an inflammasome in response to various cellular stressors. Gain-of-function mutations in NLRP3 cause autoinflammatory diseases and NLRP3 signalling itself exacerbates the pathogenesis of many other human diseases. Despite considerable therapeutic interest, the primary drivers of NLRP3 activation remain controversial due to the diverse array of signals that are integrated through NLRP3. Here, we mapped subcellular proteome changes to lysosomes, mitochondrion, EEA1-positive endosomes, and Golgi caused by the NLRP3 inflammasome agonists nigericin and CL097. We identified several common disruptions to retrograde trafficking pathways, including COPI and Shiga toxin-related transport, in line with recent studies. We further characterized mouse NLRP3 trafficking throughout its activation using temporal proximity proteomics, which supports a recent model of NLRP3 recruitment to endosomes during inflammasome activation. Collectively, these findings provide additional granularity to our understanding of the molecular events driving NLRP3 activation and serve as a valuable resource for cell biological research. We have made our proteomics data accessible through an open-access Shiny browser to facilitate future research within the community, available at: https://harperlab.connect.hms.harvard.edu/inflame/. We will display anonymous peer review for this manuscript on pubpub.org (https://harperlab.pubpub.org/pub/nlrp3/) rather than a traditional journal. Moreover, we invite community feedback on the pubpub version of this manuscript, and we will address criticisms accordingly.
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Affiliation(s)
- L. Robert Hollingsworth
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University
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4
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Haney MS, Pálovics R, Munson CN, Long C, Johansson PK, Yip O, Dong W, Rawat E, West E, Schlachetzki JCM, Tsai A, Guldner IH, Lamichhane BS, Smith A, Schaum N, Calcuttawala K, Shin A, Wang YH, Wang C, Koutsodendris N, Serrano GE, Beach TG, Reiman EM, Glass CK, Abu-Remaileh M, Enejder A, Huang Y, Wyss-Coray T. APOE4/4 is linked to damaging lipid droplets in Alzheimer's disease microglia. Nature 2024; 628:154-161. [PMID: 38480892 PMCID: PMC10990924 DOI: 10.1038/s41586-024-07185-7] [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: 01/02/2022] [Accepted: 02/09/2024] [Indexed: 03/26/2024]
Abstract
Several genetic risk factors for Alzheimer's disease implicate genes involved in lipid metabolism and many of these lipid genes are highly expressed in glial cells1. However, the relationship between lipid metabolism in glia and Alzheimer's disease pathology remains poorly understood. Through single-nucleus RNA sequencing of brain tissue in Alzheimer's disease, we have identified a microglial state defined by the expression of the lipid droplet-associated enzyme ACSL1 with ACSL1-positive microglia being most abundant in patients with Alzheimer's disease having the APOE4/4 genotype. In human induced pluripotent stem cell-derived microglia, fibrillar Aβ induces ACSL1 expression, triglyceride synthesis and lipid droplet accumulation in an APOE-dependent manner. Additionally, conditioned media from lipid droplet-containing microglia lead to Tau phosphorylation and neurotoxicity in an APOE-dependent manner. Our findings suggest a link between genetic risk factors for Alzheimer's disease with microglial lipid droplet accumulation and neurotoxic microglia-derived factors, potentially providing therapeutic strategies for Alzheimer's disease.
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Affiliation(s)
- Michael S Haney
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Róbert Pálovics
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Christy Nicole Munson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Chris Long
- Department of Materials Science & Engineering Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrik K Johansson
- Department of Materials Science & Engineering Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Oscar Yip
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Wentao Dong
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Eshaan Rawat
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Elizabeth West
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
| | - Andy Tsai
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Ian Hunter Guldner
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Bhawika S Lamichhane
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Amanda Smith
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Kruti Calcuttawala
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Andrew Shin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Yung-Hua Wang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Chengzhong Wang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Nicole Koutsodendris
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Development and Stem Cell Biology Graduate Program, University of California, San Francisco, CA, USA
| | - Geidy E Serrano
- Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G Beach
- Banner Alzheimer's Institute and Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute and Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Christopher K Glass
- Development and Stem Cell Biology Graduate Program, University of California, San Francisco, CA, USA
| | - Monther Abu-Remaileh
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Annika Enejder
- Department of Materials Science & Engineering Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Yadong Huang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Development and Stem Cell Biology Graduate Program, University of California, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
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5
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Reinhard J, Starke L, Klose C, Haberkant P, Hammarén H, Stein F, Klein O, Berhorst C, Stumpf H, Sáenz JP, Hub J, Schuldiner M, Ernst R. MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress. EMBO J 2024; 43:1653-1685. [PMID: 38491296 PMCID: PMC11021466 DOI: 10.1038/s44318-024-00063-y] [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: 09/14/2022] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
Biological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work has provided insights into the subcellular distribution of lipids in the yeast Saccharomyces cerevisiae, but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remains insufficiently characterized. Here, we describe a method for purifying organelle membranes from yeast, MemPrep. We demonstrate the purity of our ER membrane preparations by proteomics, and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings provide a baseline for studying membrane protein biogenesis and have important implications for understanding the role of lipids in regulating the unfolded protein response (UPR). The combined preparative and analytical MemPrep approach uncovers dynamic remodeling of ER membranes in stressed cells and establishes distinct molecular fingerprints of lipid bilayer stress.
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Affiliation(s)
- John Reinhard
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Leonhard Starke
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | | | - Per Haberkant
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | | | - Frank Stein
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | - Ofir Klein
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Charlotte Berhorst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Heike Stumpf
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - James P Sáenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Jochen Hub
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | - Maya Schuldiner
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Robert Ernst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany.
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany.
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6
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Ugur B, Schueder F, Shin J, Hanna MG, Wu Y, Leonzino M, Su M, McAdow AR, Wilson C, Postlethwait J, Solnica-Krezel L, Bewersdorf J, De Camilli P. VPS13B is localized at the cis-trans Golgi complex interface and is a functional partner of FAM177A1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572081. [PMID: 38187698 PMCID: PMC10769246 DOI: 10.1101/2023.12.18.572081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mutations in VPS13B, a member of a protein family implicated in bulk lipid transport between adjacent membranes, cause Cohen syndrome. VPS13B is known to be concentrated in the Golgi complex, but its precise location within this organelle and thus the site(s) where it achieves lipid transport remains unclear. Here we show that VPS13B is localized at the interface between cis and trans Golgi sub-compartments and that Golgi complex re-formation after Brefeldin A (BFA) induced disruption is delayed in VPS13B KO cells. This delay is phenocopied by loss of FAM177A1, a Golgi complex protein of unknown function reported to be a VPS13B interactor and whose mutations also result in a developmental disorder. In zebrafish, the vps13b orthologue, not previously annotated in this organism, genetically interacts with fam177a1. Collectively, these findings raise the possibility that bulk lipid transport by VPS13B may play a role in expanding Golgi membranes and that VPS13B may be assisted in this function by FAM177A1.
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Affiliation(s)
- Berrak Ugur
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Florian Schueder
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael G. Hanna
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Yumei Wu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Marianna Leonzino
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Maohan Su
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony R. McAdow
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Catherine Wilson
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
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7
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Pal P, Taylor M, Lam PY, Tonelli F, Hecht CA, Lis P, Nirujogi RS, Phung TK, Yeshaw WM, Jaimon E, Fasimoye R, Dickie EA, Wightman M, Macartney T, Pfeffer SR, Alessi DR. Parkinson's VPS35[D620N] mutation induces LRRK2-mediated lysosomal association of RILPL1 and TMEM55B. SCIENCE ADVANCES 2023; 9:eadj1205. [PMID: 38091401 PMCID: PMC10848721 DOI: 10.1126/sciadv.adj1205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
We demonstrate that the Parkinson's VPS35[D620N] mutation alters the expression of ~220 lysosomal proteins and stimulates recruitment and phosphorylation of Rab proteins at the lysosome. This recruits the phospho-Rab effector protein RILPL1 to the lysosome where it binds to the lysosomal integral membrane protein TMEM55B. We identify highly conserved regions of RILPL1 and TMEM55B that interact and design mutations that block binding. In mouse fibroblasts, brain, and lung, we demonstrate that the VPS35[D620N] mutation reduces RILPL1 levels, in a manner reversed by LRRK2 inhibition and proteasome inhibitors. Knockout of RILPL1 enhances phosphorylation of Rab substrates, and knockout of TMEM55B increases RILPL1 levels. The lysosomotropic agent LLOMe also induced LRRK2 kinase-mediated association of RILPL1 to the lysosome, but to a lower extent than the D620N mutation. Our study uncovers a pathway through which dysfunctional lysosomes resulting from the VPS35[D620N] mutation recruit and activate LRRK2 on the lysosomal surface, driving assembly of the RILPL1-TMEM55B complex.
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Affiliation(s)
- Prosenjit Pal
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Matthew Taylor
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Pui Yiu Lam
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Chloe A. Hecht
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Pawel Lis
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Raja S. Nirujogi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Toan K. Phung
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Wondwossen M. Yeshaw
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Ebsy Jaimon
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Rotimi Fasimoye
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Emily A. Dickie
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Melanie Wightman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Suzanne R. Pfeffer
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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8
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Sathe G, Sapkota GP. Proteomic approaches advancing targeted protein degradation. Trends Pharmacol Sci 2023; 44:786-801. [PMID: 37778939 DOI: 10.1016/j.tips.2023.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023]
Abstract
Targeted protein degradation (TPD) is an emerging modality for research and therapeutics. Most TPD approaches harness cellular ubiquitin-dependent proteolytic pathways. Proteolysis-targeting chimeras (PROTACs) and molecular glue (MG) degraders (MGDs) represent the most advanced TPD approaches, with some already used in clinical settings. Despite these advances, TPD still faces many challenges, pertaining to both the development of effective, selective, and tissue-penetrant degraders and understanding their mode of action. In this review, we focus on progress made in addressing these challenges. In particular, we discuss the utility and application of recent proteomic approaches as indispensable tools to enable insights into degrader development, including target engagement, degradation selectivity, efficacy, safety, and mode of action.
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Affiliation(s)
- Gajanan Sathe
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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9
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Yeshaw WM, Adhikari A, Chiang CY, Dhekne HS, Wawro PS, Pfeffer SR. Localization of PPM1H phosphatase tunes Parkinson's disease-linked LRRK2 kinase-mediated Rab GTPase phosphorylation and ciliogenesis. Proc Natl Acad Sci U S A 2023; 120:e2315171120. [PMID: 37889931 PMCID: PMC10622911 DOI: 10.1073/pnas.2315171120] [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: 08/31/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
PPM1H phosphatase reverses Parkinson's disease-associated, Leucine Rich Repeat Kinase 2-mediated Rab GTPase phosphorylation. We show here that PPM1H relies on an N-terminal amphipathic helix for Golgi localization. The amphipathic helix enables PPM1H to bind to liposomes in vitro, and small, highly curved liposomes stimulate PPM1H activity. We artificially anchored PPM1H to the Golgi, mitochondria, or mother centriole. Our data show that regulation of Rab10 GTPase phosphorylation requires PPM1H access to Rab10 at or near the mother centriole. Moreover, poor colocalization of Rab12 explains in part why it is a poor substrate for PPM1H in cells but not in vitro. These data support a model in which localization drives PPM1H substrate selection and centriolar PPM1H is critical for regulation of Rab GTPase-regulated ciliogenesis. Moreover, Golgi localized PPM1H may maintain active Rab GTPases on the Golgi to carry out their nonciliogenesis-related functions in membrane trafficking.
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Affiliation(s)
- Wondwossen M. Yeshaw
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Ayan Adhikari
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Claire Y. Chiang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Herschel S. Dhekne
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Paulina S. Wawro
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
| | - Suzanne R. Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
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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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11
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Melero A, Jiménez-Rojo N. Cracking the membrane lipid code. Curr Opin Cell Biol 2023; 83:102203. [PMID: 37437490 DOI: 10.1016/j.ceb.2023.102203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 07/14/2023]
Abstract
Why has nature acquired such a huge lipid repertoire? Although it would be theoretically possible to make a lipid bilayer fulfilling barrier functions with only one glycerophospholipid, there are diverse and numerous different lipid species. Lipids are heterogeneously distributed across the evolutionary tree with lipidomes evolving in parallel to organismal complexity. Moreover, lipids are different between organs and tissues and even within the same cell, different organelles have characteristic lipid signatures. At the molecular level, membranes are asymmetric and laterally heterogeneous. This lipid asymmetry at different scales indicates that these molecules may play very specific molecular functions in biology. Some of these roles have been recently uncovered: lipids have been shown to be essential in processes such as hypoxia and ferroptosis or in protein sorting and trafficking but many of them remain still unknown. In this review we will discuss the importance of understanding lipid diversity in biology across scales and we will share a toolbox with some of the emerging technologies that are helping us to uncover new lipid molecular functions in cell biology and, step by step, crack the membrane lipid code.
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Affiliation(s)
- Alejandro Melero
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Noemi Jiménez-Rojo
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain; Instituto Biofisika (UPV/EHU, CSIC), 48940, Leioa, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
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