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Coukos R, Krainc D. Key genes and convergent pathogenic mechanisms in Parkinson disease. Nat Rev Neurosci 2024; 25:393-413. [PMID: 38600347 DOI: 10.1038/s41583-024-00812-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Parkinson disease (PD) is a neurodegenerative disorder marked by the preferential dysfunction and death of dopaminergic neurons in the substantia nigra. The onset and progression of PD is influenced by a diversity of genetic variants, many of which lack functional characterization. To identify the most high-yield targets for therapeutic intervention, it is important to consider the core cellular compartments and functional pathways upon which the varied forms of pathogenic dysfunction may converge. Here, we review several key PD-linked proteins and pathways, focusing on the mechanisms of their potential convergence in disease pathogenesis. These dysfunctions primarily localize to a subset of subcellular compartments, including mitochondria, lysosomes and synapses. We discuss how these pathogenic mechanisms that originate in different cellular compartments may coordinately lead to cellular dysfunction and neurodegeneration in PD.
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Affiliation(s)
- Robert Coukos
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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2
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Kumar S, Davis RM, Ruiz N. YdbH and YnbE form an intermembrane bridge to maintain lipid homeostasis in the outer membrane of Escherichia coli. Proc Natl Acad Sci U S A 2024; 121:e2321512121. [PMID: 38748582 PMCID: PMC11126948 DOI: 10.1073/pnas.2321512121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/09/2024] [Indexed: 05/27/2024] Open
Abstract
The outer membrane (OM) of didermic gram-negative bacteria is essential for growth, maintenance of cellular integrity, and innate resistance to many antimicrobials. Its asymmetric lipid distribution, with phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet, is required for these functions. Lpt proteins form a transenvelope bridge that transports newly synthesized LPS from the inner membrane (IM) to OM, but how the bulk of phospholipids are transported between these membranes is poorly understood. Recently, three members of the AsmA-like protein family, TamB, YhdP, and YdbH, were shown to be functionally redundant and were proposed to transport phospholipids between IM and OM in Escherichia coli. These proteins belong to the repeating β-groove superfamily, which includes eukaryotic lipid-transfer proteins that mediate phospholipid transport between organelles at contact sites. Here, we show that the IM-anchored YdbH protein interacts with the OM lipoprotein YnbE to form a functional protein bridge between the IM and OM in E. coli. Based on AlphaFold-Multimer predictions, genetic data, and in vivo site-directed cross-linking, we propose that YnbE interacts with YdbH through β-strand augmentation to extend the continuous hydrophobic β-groove of YdbH that is thought to shield acyl chains of phospholipids as they travel through the aqueous intermembrane periplasmic compartment. Our data also suggest that the periplasmic protein YdbL prevents extensive amyloid-like multimerization of YnbE in cells. We, therefore, propose that YdbL has a chaperone-like function that prevents uncontrolled runaway multimerization of YnbE to ensure the proper formation of the YdbH-YnbE intermembrane bridge.
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Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, OH43210
| | - Rebecca M. Davis
- Department of Microbiology, The Ohio State University, Columbus, OH43210
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, OH43210
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3
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Wang Y, Yang J. ER-organelle contacts: A signaling hub for neurological diseases. Pharmacol Res 2024; 203:107149. [PMID: 38518830 DOI: 10.1016/j.phrs.2024.107149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Neuronal health is closely linked to the homeostasis of intracellular organelles, and organelle dysfunction affects the pathological progression of neurological diseases. In contrast to isolated cellular compartments, a growing number of studies have found that organelles are largely interdependent structures capable of communicating through membrane contact sites (MCSs). MCSs have been identified as key pathways mediating inter-organelle communication crosstalk in neurons, and their alterations have been linked to neurological disease pathology. The endoplasmic reticulum (ER) is a membrane-bound organelle capable of forming an extensive network of pools and tubules with important physiological functions within neurons. There are multiple MCSs between the ER and other organelles and the plasma membrane (PM), which regulate a variety of cellular processes. In this review, we focus on ER-organelle MCSs and their role in a variety of neurological diseases. We compared the biological effects between different tethering proteins and the effects of their respective disease counterparts. We also discuss how altered ER-organelle contacts may affect disease pathogenesis. Therefore, understanding the molecular mechanisms of ER-organelle MCSs in neuronal homeostasis will lay the foundation for the development of new therapies targeting ER-organelle contacts.
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Affiliation(s)
- Yunli Wang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, PR China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, PR China
| | - Jinghua Yang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, PR China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, PR China.
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4
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Alkahtani S, Alkahtane AA, Alarifi S. Physiological and Pathogenesis Significance of Chorein in Health and Disease. Physiol Res 2024; 73:189-203. [PMID: 38710051 PMCID: PMC11081191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/30/2023] [Indexed: 05/08/2024] Open
Abstract
This comprehensive review explores the physiological and pathophysiological significance of VPS13A, a protein encoded by the VPS13A gene. The VPS13A gene is associated with Chorea-acanthocytosis (ChAc), a rare hereditary neurodegenerative disorder. The review covers essential aspects, beginning with the genetics of VPS13A, highlighting its role in the pathogenesis of ChAc, and addressing the spectrum of genetic variants involved. It delves into the structure and function of the VPS13A protein, emphasizing its presence in various tissues and its potential involvement in protein trafficking and lipid homeostasis. Molecular functions of VPS13A in the brain tissue and other cell types or tissues with respect to their role in cytoskeletal regulation and autophagy are explored. Finally, it explores the intriguing link between VPS13A mutations, lipid imbalances, and neurodegeneration, shedding light on future research directions. Overall, this review serves as a comprehensive resource for understanding the pivotal role of VPS13A in health and disease, particularly in the context of ChAc. Key words: Chorein , Tumor, Actin, Microfilament, Gene expression, Chorea-acanthocytosis.
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Affiliation(s)
- S Alkahtani
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.
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5
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Suzuki SW, West M, Zhang Y, Fan JS, Roberts RT, Odorizzi G, Emr SD. A role for Vps13-mediated lipid transfer at the ER-endosome contact site in ESCRT-mediated sorting. J Cell Biol 2024; 223:e202307094. [PMID: 38319250 PMCID: PMC10847051 DOI: 10.1083/jcb.202307094] [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: 07/20/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Endosomes are specialized organelles that function in the secretory and endocytic protein sorting pathways. Endocytosed cell surface receptors and transporters destined for lysosomal degradation are sorted into intraluminal vesicles (ILVs) at endosomes by endosomal sorting complexes required for transport (ESCRT) proteins. The endosomes (multivesicular bodies, MVBs) then fuse with the lysosome. During endosomal maturation, the number of ILVs increases, but the size of endosomes does not decrease despite the consumption of the limiting membrane during ILV formation. Vesicle-mediated trafficking is thought to provide lipids to support MVB biogenesis. However, we have uncovered an unexpected contribution of a large bridge-like lipid transfer protein, Vps13, in this process. Here, we reveal that Vps13-mediated lipid transfer at ER-endosome contact sites is required for the ESCRT pathway. We propose that Vps13 may play a critical role in supplying lipids to the endosome, ensuring continuous ESCRT-mediated sorting during MVB biogenesis.
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Affiliation(s)
- Sho W. Suzuki
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Matthew West
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Yichen Zhang
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jenny S. Fan
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Rachel T. Roberts
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Greg Odorizzi
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Scott D. Emr
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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6
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Ghodsinezhad V, Ghoreishi A, Rohani M, Dadfar M, Mohammadzadeh A, Rostami A, Rahimi H. Identification of four novel mutations in VSP13A in Iranian patients with Chorea-acanthocytosis (ChAc). Mol Genet Genomics 2024; 299:39. [PMID: 38519717 DOI: 10.1007/s00438-024-02111-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: 09/07/2023] [Accepted: 01/13/2024] [Indexed: 03/25/2024]
Abstract
Chorea-acanthocytosis (ChAc) is a rare autosomal recessive neurodegenerative disorder characterized by a variety of involuntary movements, predominantly chorea, and the presence of acanthocytosis in peripheral blood smears. ChAc is caused by mutations in the vacuolar protein sorting-associated protein 13A (VPS13A) gene. The aim of the present study was to conduct a clinical and genetic analysis of five patients with suspected ChAc in Iran. This study included five patients who were referred to the genetic department of the Endocrinology and Metabolism Research Institute between 2020 and 2022, with a suspicion of ChAc. Clinical features and the presence of characteristic MRI findings were evaluated in the patients. Whole-exome sequencing (WES) followed by Sanger sequencing was employed to identify the disease-causing variants. The functional effects of novel mutations were analyzed by specific bioinformatics prediction tools. WES and data analysis revealed the presence of five distinct VPS13A mutations in the patients, four of which were novel. These included one nonsense mutation (p.L984X), and three splice site mutations (c.755-1G>A, c.144+1 G>C, c.2512+1G>A). All mutations were validated by Sanger sequencing, and in silico analysis predicted that all mutations were pathogenic. This study provides the first molecular genetic characteristics of Iranian patients with ChAc, identifying four novel mutations in the VPS13A gene. These findings expand the VPS13A variants spectrum and confirm the clinical variability in ChAc patients.
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Affiliation(s)
- Vadieh Ghodsinezhad
- Department of Genetics and Molecular Medicine, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Abdoreza Ghoreishi
- Department of Neurology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammad Rohani
- Department of Neurology, Rasoul Akram Hospital, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahdi Dadfar
- Skull Base Research Center, Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Akbar Mohammadzadeh
- Department of Genetics and Molecular Medicine, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Ali Rostami
- Department of Pharmacology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
- Texas Biomedical Research Institute, San Antonio, TX, USA.
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7
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Durant M, Mucelli X, Huang LS. Meiotic Cytokinesis in Saccharomyces cerevisiae: Spores That Just Need Closure. J Fungi (Basel) 2024; 10:132. [PMID: 38392804 PMCID: PMC10890087 DOI: 10.3390/jof10020132] [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: 01/12/2024] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, sporulation occurs during starvation of a diploid cell and results in the formation of four haploid spores forming within the mother cell ascus. Meiosis divides the genetic material that is encapsulated by the prospore membrane that grows to surround the haploid nuclei; this membrane will eventually become the plasma membrane of the haploid spore. Cellularization of the spores occurs when the prospore membrane closes to capture the haploid nucleus along with some cytoplasmic material from the mother cell, and thus, closure of the prospore membrane is the meiotic cytokinetic event. This cytokinetic event involves the removal of the leading-edge protein complex, a complex of proteins that localizes to the leading edge of the growing prospore membrane. The development and closure of the prospore membrane must be coordinated with other meiotic exit events such as spindle disassembly. Timing of the closure of the prospore membrane depends on the meiotic exit pathway, which utilizes Cdc15, a Hippo-like kinase, and Sps1, an STE20 family GCKIII kinase, acting in parallel to the E3 ligase Ama1-APC/C. This review describes the sporulation process and focuses on the development of the prospore membrane and the regulation of prospore membrane closure.
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Affiliation(s)
- Matthew Durant
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Xheni Mucelli
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Linda S Huang
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
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8
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Strawn G, Wong RWK, Young BP, Davey M, Nislow C, Conibear E, Loewen CJR, Mayor T. Genome-wide screen identifies new set of genes for improved heterologous laccase expression in Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:36. [PMID: 38287338 PMCID: PMC10823697 DOI: 10.1186/s12934-024-02298-0] [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: 07/12/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024] Open
Abstract
The yeast Saccharomyces cerevisiae is widely used as a host cell for recombinant protein production due to its fast growth, cost-effective culturing, and ability to secrete large and complex proteins. However, one major drawback is the relatively low yield of produced proteins compared to other host systems. To address this issue, we developed an overlay assay to screen the yeast knockout collection and identify mutants that enhance recombinant protein production, specifically focusing on the secretion of the Trametes trogii fungal laccase enzyme. Gene ontology analysis of these mutants revealed an enrichment of processes including vacuolar targeting, vesicle trafficking, proteolysis, and glycolipid metabolism. We confirmed that a significant portion of these mutants also showed increased activity of the secreted laccase when grown in liquid culture. Notably, we found that the combination of deletions of OCA6, a tyrosine phosphatase gene, along with PMT1 or PMT2, two genes encoding ER membrane protein-O-mannosyltransferases involved in ER quality control, and SKI3, which encode for a component of the SKI complex responsible for mRNA degradation, further increased secreted laccase activity. Conversely, we also identified over 200 gene deletions that resulted in decreased secreted laccase activity, including many genes that encode for mitochondrial proteins and components of the ER-associated degradation pathway. Intriguingly, the deletion of the ER DNAJ co-chaperone gene SCJ1 led to almost no secreted laccase activity. When we expressed SCJ1 from a low-copy plasmid, laccase secretion was restored. However, overexpression of SCJ1 had a detrimental effect, indicating that precise dosing of key chaperone proteins is crucial for optimal recombinant protein expression. This study offers potential strategies for enhancing the overall yield of recombinant proteins and provides new avenues for further research in optimizing protein production systems.
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Affiliation(s)
- Garrett Strawn
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Ryan W K Wong
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Barry P Young
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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9
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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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10
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Ditzel RM, Walker RH, Nirenberg MJ, Tetlow AM, Farrell K, Lind-Watson KJ, Thorn EL, Dangoor DK, Gordon R, De Sanctis C, Barton B, Karp BI, Kirby A, Lett DJ, Mente K, Simon DK, Velayos-Baeza A, Miltenberger-Miltenyi G, Humphrey J, Crary JF. An Autopsy Series of Seven Cases of VPS13A Disease (Chorea-Acanthocytosis). Mov Disord 2023; 38:2163-2172. [PMID: 37670483 PMCID: PMC10841393 DOI: 10.1002/mds.29589] [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: 05/22/2023] [Revised: 07/29/2023] [Accepted: 08/04/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Vacuolar protein sorting 13 homolog A (VPS13A) disease, historically known as chorea-acanthocytosis, is a rare neurodegenerative disorder caused by biallelic mutations in VPS13A, usually resulting in reduced or absent levels of its protein product, VPS13A. VPS13A localizes to contact sites between subcellular organelles, consistent with its recently identified role in lipid transfer between membranes. Mutations are associated with neuronal loss in the striatum, most prominently in the caudate nucleus, and associated marked astrogliosis. There are no other known disease-specific cellular changes (eg, protein aggregation), but autopsy reports to date have been limited, often lacking genetic or biochemical diagnostic confirmation. OBJECTIVE The goal of this study was to characterize neuropathological findings in the brains of seven patients with VPS13A disease (chorea-acanthocytosis). METHODS In this study, we collected brain tissues and clinical data from seven cases of VPS13A for neuropathological analysis. The clinical diagnosis was confirmed by the presence of VPS13A mutations and/or immunoblot showing the loss or reduction of VPS13A protein. Tissues underwent routine, special, and immunohistochemical staining focused on neurodegeneration. Electron microscopy was performed in one case. RESULTS Gross examination showed severe striatal atrophy. Microscopically, there was neuronal loss and astrogliosis in affected regions. Luxol fast blue staining showed variable lipid accumulation with diverse morphology, which was further characterized by electron microscopy. In some cases, rare degenerating p62- and ubiquitin-positive cells were present in affected regions. Calcifications were present in four cases, being extensive in one. CONCLUSIONS We present the largest autopsy series of biochemically and genetically confirmed VPS13A disease and identify novel histopathological findings implicating abnormal lipid accumulation. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Ricky M. Ditzel
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruth H. Walker
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - Melissa J. Nirenberg
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - Amber M. Tetlow
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kurt Farrell
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kourtni J. Lind-Watson
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma L. Thorn
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Diana K. Dangoor
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ronald Gordon
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Claudia De Sanctis
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brandon Barton
- Rush University Medical Center, Chicago, Illinois, USA
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Barbara I. Karp
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Alana Kirby
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Debra J. Lett
- Newcastle Brain Tissue Resource, Newcastle University, Newcastle, UK
| | - Karin Mente
- Departments of Neurology and Pathology, Case Western Reserve University, Cleveland, OH, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland OH, USA
| | - David K. Simon
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Antonio Velayos-Baeza
- Department of Physiology, Anatomy, and Genetics, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gabriel Miltenberger-Miltenyi
- Laboratório de Genética, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
- Reference Center on Lysosomal Storage Diseases, Hospital Senhora da Oliveira, Guimarães, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Jack Humphrey
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F. Crary
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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11
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Shnaider TA, Khabarova AA, Morozova KN, Yunusova AM, Yakovleva SA, Chvileva AS, Wolf ER, Kiseleva EV, Grigor'eva EV, Voinova VY, Lagarkova MA, Pomerantseva EA, Musatova EV, Smirnov AV, Smirnova AV, Stoklitskaya DS, Arefieva TI, Larina DA, Nikitina TV, Pristyazhnyuk IE. Ultrastructural Abnormalities in Induced Pluripotent Stem Cell-Derived Neural Stem Cells and Neurons of Two Cohen Syndrome Patients. Cells 2023; 12:2702. [PMID: 38067130 PMCID: PMC10705360 DOI: 10.3390/cells12232702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/12/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Cohen syndrome is an autosomal recessive disorder caused by VPS13B (COH1) gene mutations. This syndrome is significantly underdiagnosed and is characterized by intellectual disability, microcephaly, autistic symptoms, hypotension, myopia, retinal dystrophy, neutropenia, and obesity. VPS13B regulates intracellular membrane transport and supports the Golgi apparatus structure, which is critical for neuron formation. We generated induced pluripotent stem cells from two patients with pronounced manifestations of Cohen syndrome and differentiated them into neural stem cells and neurons. Using transmission electron microscopy, we documented multiple new ultrastructural changes associated with Cohen syndrome in the neuronal cells. We discovered considerable disturbances in the structure of some organelles: Golgi apparatus fragmentation and swelling, endoplasmic reticulum structural reorganization, mitochondrial defects, and the accumulation of large autophagosomes with undigested contents. These abnormalities underline the ultrastructural similarity of Cohen syndrome to many neurodegenerative diseases. The cell models that we developed based on patient-specific induced pluripotent stem cells can serve to uncover not only neurodegenerative processes, but the causes of intellectual disability in general.
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Affiliation(s)
- Tatiana A Shnaider
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna A Khabarova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ksenia N Morozova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anastasia M Yunusova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sophia A Yakovleva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anastasia S Chvileva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina R Wolf
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena V Kiseleva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Grigor'eva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Viktori Y Voinova
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
- The Mental Health Research Center, Moscow 115522, Russia
| | - Maria A Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | | | | | - Alexander V Smirnov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna V Smirnova
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
| | | | - Tatiana I Arefieva
- National Medical Research Centre of Cardiology Named after Academician E. I. Chazov., Moscow 121552, Russia
| | - Daria A Larina
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
| | - Tatiana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk 634050, Russia
| | - Inna E Pristyazhnyuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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12
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Záhonová K, Füssy Z, Stairs CW, Leger MM, Tachezy J, Čepička I, Roger AJ, Hampl V. Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans. Microb Genom 2023; 9. [PMID: 37994879 DOI: 10.1099/mgen.0.001143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared in silico reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in Entamoeba, probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of Rhizomastix libera, Mastigamoeba abducta and Endolimax sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.
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Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Courtney W Stairs
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Microbiology Research Group, Department of Biology, Lund University, Lund, Sweden
| | - Michelle M Leger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
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13
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Hanna M, Guillén-Samander A, De Camilli P. RBG Motif Bridge-Like Lipid Transport Proteins: Structure, Functions, and Open Questions. Annu Rev Cell Dev Biol 2023; 39:409-434. [PMID: 37406299 DOI: 10.1146/annurev-cellbio-120420-014634] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The life of eukaryotic cells requires the transport of lipids between membranes, which are separated by the aqueous environment of the cytosol. Vesicle-mediated traffic along the secretory and endocytic pathways and lipid transfer proteins (LTPs) cooperate in this transport. Until recently, known LTPs were shown to carry one or a few lipids at a time and were thought to mediate transport by shuttle-like mechanisms. Over the last few years, a new family of LTPs has been discovered that is defined by a repeating β-groove (RBG) rod-like structure with a hydrophobic channel running along their entire length. This structure and the localization of these proteins at membrane contact sites suggest a bridge-like mechanism of lipid transport. Mutations in some of these proteins result in neurodegenerative and developmental disorders. Here we review the known properties and well-established or putative physiological roles of these proteins, and we highlight the many questions that remain open about their functions.
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Affiliation(s)
- Michael Hanna
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrés Guillén-Samander
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
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14
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Banerjee S, Prinz WA. Early steps in the birth of four membrane-bound organelles-Peroxisomes, lipid droplets, lipoproteins, and autophagosomes. Curr Opin Cell Biol 2023; 84:102210. [PMID: 37531895 PMCID: PMC10926090 DOI: 10.1016/j.ceb.2023.102210] [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: 03/13/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023]
Abstract
Membrane-bound organelles allow cells to traffic cargo and separate and regulate metabolic pathways. While many organelles are generated by the growth and division of existing organelles, some can also be produced de novo, often in response to metabolic cues. This review will discuss recent advances in our understanding of the early steps in the de novo biogenesis of peroxisomes, lipid droplets, lipoproteins, and autophagosomes. These organelles play critical roles in cellular lipid metabolism and other processes, and their dysfunction causes or is linked to several human diseases. The de novo biogenesis of these organelles occurs in or near the endoplasmic reticulum membrane. This review summarizes recent progress and highlights open questions.
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Affiliation(s)
- Subhrajit Banerjee
- Dept of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - William A Prinz
- Dept of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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15
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Tan X, Wang X, Liao X, Wang X, Jiang Z, Liang W, Cao C, Gong D, Hu Z, Tian X. Downregulation of VPS13C promotes cisplatin resistance in cervical cancer by upregulating GSTP1. iScience 2023; 26:107315. [PMID: 37520723 PMCID: PMC10372835 DOI: 10.1016/j.isci.2023.107315] [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: 10/07/2022] [Revised: 03/05/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023] Open
Abstract
Cisplatin resistance remains a major obstacle limiting the effectiveness of chemotherapy in cervical cancer. However, the underlying mechanism of cisplatin resistance is still unclear. In this study, we demonstrate that vacuolar protein sorting 13 homolog C (VPS13C) deficiency promotes cisplatin resistance in cervical cancer. Moreover, through an RNA sequencing screen, VPS13C deficiency was identified as negatively correlated with the high expression of glutathione S-transferase pi gene (GSTP1). Mechanistically, loss of VPS13C contributes to cisplatin resistance by influencing the expression of GSTP1 and inhibiting the downstream c-Jun N-terminal kinase (JNK) pathway. In addition, targeting GSTP1 with the inhibitor NBDHEX effectively rescued the cisplatin resistance induced by VPS13C deficiency. Overall, our findings provide insights into the underlying mechanisms of VPS13C in cisplatin resistance and identify VPS13C as a promising candidate for the treatment of chemoresistance in cervical cancer.
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Affiliation(s)
- Xiangyu Tan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430110, China
| | - Xueqian Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430110, China
| | - Xueyao Liao
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, China
| | - Xin Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430110, China
| | - Zhichao Jiang
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, China
| | - Wenjia Liang
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, China
| | - Chen Cao
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, China
| | - Danni Gong
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, China
| | - Zheng Hu
- Department of Gynecologic Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071 Hubei, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan 430071 Hubei, China
- Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan 430071 Hubei, China
| | - Xun Tian
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430110, China
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16
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Enkler L, Szentgyörgyi V, Pennauer M, Prescianotto-Baschong C, Riezman I, Wiesyk A, Avraham RE, Spiess M, Zalckvar E, Kucharczyk R, Riezman H, Spang A. Arf1 coordinates fatty acid metabolism and mitochondrial homeostasis. Nat Cell Biol 2023; 25:1157-1172. [PMID: 37400497 PMCID: PMC10415182 DOI: 10.1038/s41556-023-01180-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/05/2023] [Indexed: 07/05/2023]
Abstract
Lipid mobilization through fatty acid β-oxidation is a central process essential for energy production during nutrient shortage. In yeast, this catabolic process starts in the peroxisome from where β-oxidation products enter mitochondria and fuel the tricarboxylic acid cycle. Little is known about the physical and metabolic cooperation between these organelles. Here we found that expression of fatty acid transporters and of the rate-limiting enzyme involved in β-oxidation is decreased in cells expressing a hyperactive mutant of the small GTPase Arf1, leading to an accumulation of fatty acids in lipid droplets. Consequently, mitochondria became fragmented and ATP synthesis decreased. Genetic and pharmacological depletion of fatty acids phenocopied the arf1 mutant mitochondrial phenotype. Although β-oxidation occurs in both mitochondria and peroxisomes in mammals, Arf1's role in fatty acid metabolism is conserved. Together, our results indicate that Arf1 integrates metabolism into energy production by regulating fatty acid storage and utilization, and presumably organelle contact sites.
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Affiliation(s)
| | | | | | | | - Isabelle Riezman
- Department of Biochemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Aneta Wiesyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Reut Ester Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Howard Riezman
- Department of Biochemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland.
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17
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Kurtović Z, Sandor K, ter Heegde F, Rudjito R, Svensson CI, Palada V. circRNA landscape in dorsal root ganglia from mice with collagen antibody-induced arthritis. NEUROBIOLOGY OF PAIN (CAMBRIDGE, MASS.) 2023; 14:100142. [PMID: 38099281 PMCID: PMC10719524 DOI: 10.1016/j.ynpai.2023.100142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 12/17/2023]
Abstract
Circular RNAs are a novel class of RNA molecules that are covalently closed into a ring structure. They are an epigenetic regulatory mechanism, and their best-studied function is regulation of microRNA activity. As such circular RNAs may be involved in the switch from acute to chronic pain. They have previously been studied in the context of neuropathic pain models, but their importance in inflammation-induced chronic pain models is unexplored. Microarray analysis of dorsal root ganglia collected in the late phase of collagen antibody-induced arthritis (day 59) were used to elucidate the relevance of circular RNAs in the mechanical hypersensitivity caused by this model. 120 circular RNA genes were found to be significantly differentially regulated in female BALB/c mice with collagen antibody-induced arthritis. Six genes were chosen for RT-qPCR analysis in the late (day 54-60) as well as the inflammatory (day 11-12) phase of this model. This validated an increase in circNufip1 expression in the late phase of collagen antibody-induced arthritis. Additionally, it was found that circVps13 and circMicall1 are upregulated in the inflammatory phase. Interestingly, no changes were found in dorsal root ganglia from mice injected with Freund's Complete Adjuvant (day 3) nor mice with spared nerve injury (day 20), despite their similarities to inflammatory and late phase collagen antibody-induced arthritis, respectively. This study provides evidence that mild circular RNA changes occur in dorsal root ganglia of mice with collagen antibody-induced arthritis that are, bioinformatically, predicated to be involved in processes relevant to sensitization.
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Affiliation(s)
- Zerina Kurtović
- Department of Physiology and Pharmacology and Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
- Kancera AB, Karolinska Institutet Science Park, Solna, Sweden
| | - Katalin Sandor
- Department of Physiology and Pharmacology and Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Freija ter Heegde
- Department of Physiology and Pharmacology and Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Resti Rudjito
- Department of Physiology and Pharmacology and Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Camilla I. Svensson
- Department of Physiology and Pharmacology and Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Vinko Palada
- Department of Physiology and Pharmacology and Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
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18
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Miltenberger-Miltenyi G, Jones A, Tetlow AM, Conceição VA, Crary JF, Ditzel RM, Farrell K, Nandakumar R, Barton B, Karp BI, Kirby A, Lett DJ, Mente K, Morgello S, Simon DK, Walker RH. Sphingolipid and Phospholipid Levels Are Altered in Human Brain in Chorea-Acanthocytosis. Mov Disord 2023; 38:1535-1541. [PMID: 37307400 DOI: 10.1002/mds.29445] [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: 10/20/2022] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Chorea-acanthocytosis (ChAc) is associated with mutations of VPS13A, which encodes for chorein, a protein implicated in lipid transport at intracellular membrane contact sites. OBJECTIVES The goal of this study was to establish the lipidomic profile of patients with ChAc. METHODS We analyzed 593 lipid species in the caudate nucleus (CN), putamen, and dorsolateral prefrontal cortex (DLPFC) from postmortem tissues of four patients with ChAc and six patients without ChAc. RESULTS We found increased levels of bis(monoacylglycerol)phosphate, sulfatide, lysophosphatidylserine, and phosphatidylcholine ether in the CN and putamen, but not in the DLPFC, of patients with ChAc. Phosphatidylserine and monoacylglycerol were increased in the CN and N-acyl phosphatidylserine in the putamen. N-acyl serine was decreased in the CN and DLPFC, whereas lysophosphatidylinositol was decreased in the DLPFC. CONCLUSIONS We present the first evidence of altered sphingolipid and phospholipid levels in the brains of patients with ChAc. Our observations are congruent with recent findings in cellular and animal models, and implicate defects of lipid processing in VPS13A disease pathophysiology. © 2023 International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Gabriel Miltenberger-Miltenyi
- Laboratório de Genética, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
- Reference Center on Lysosomal Storage Diseases, Hospital Senhora da Oliveira, Guimarães, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Attila Jones
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Amber M Tetlow
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Neuroscience and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Vasco A Conceição
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - John F Crary
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Neuroscience and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Ricky Michael Ditzel
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Neuroscience and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Kurt Farrell
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Neuroscience and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Renu Nandakumar
- Biomarkers Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York City, New York, USA
| | - Brandon Barton
- Rush University Medical Center, Chicago, Illinois, USA
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Barbara I Karp
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Alana Kirby
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Debra J Lett
- Newcastle Brain Tissue Resource, Newcastle University, Newcastle, United Kingdom
| | - Karin Mente
- Departments of Neurology and Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
| | - Susan Morgello
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - David K Simon
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Ruth H Walker
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- James J. Peters Veterans Affairs Medical Center, Bronx, New York, USA
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19
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Del Vecchio M, Amado L, Cogan AP, Meert E, Rosseels J, Franssens V, Govers SK, Winderickx J, Montoro AG. Multiple tethers of organelle contact sites are involved in α-synuclein toxicity in yeast. Mol Biol Cell 2023; 34:ar84. [PMID: 37074954 PMCID: PMC10398879 DOI: 10.1091/mbc.e23-01-0029] [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: 01/31/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/20/2023] Open
Abstract
The protein α-synuclein (α-syn) is one of the major factors linked to Parkinson's disease, yet how its misfolding and deposition contribute to the pathology remains largely elusive. Recently, contact sites among organelles were implicated in the development of this disease. Here, we used the budding yeast Saccharomyces cerevisiae, in which organelle contact sites have been characterized extensively, as a model to investigate their role in α-syn cytotoxicity. We observed that lack of specific tethers that anchor the endoplasmic reticulum to the plasma membrane resulted in cells with increased resistance to α-syn expression. Additionally, we found that strains lacking two dual-function proteins involved in contact sites, Mdm10 and Vps39, were resistant to the expression of α-syn. In the case of Mdm10, we found that this is related to its function in mitochondrial protein biogenesis and not to its role as a contact site tether. In contrast, both functions of Vps39, in vesicular transport and as a tether of the vacuole-mitochondria contact site, were required to support α-syn toxicity. Overall, our findings support that interorganelle communication through membrane contact sites is highly relevant for α-syn-mediated toxicity.
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Affiliation(s)
- Mara Del Vecchio
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
- Department of Biology, Microbial Systems Cell Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Lucia Amado
- Department of Biology/Chemistry, Cellular Communication Laboratory, Osnabrück University, 49076 Osnabrück, Germany
| | - Alexandra P. Cogan
- Department of Biology/Chemistry, Cellular Communication Laboratory, Osnabrück University, 49076 Osnabrück, Germany
| | - Els Meert
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Joelle Rosseels
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Vanessa Franssens
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Sander K. Govers
- Department of Biology, Microbial Systems Cell Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Joris Winderickx
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Ayelén González Montoro
- Department of Biology/Chemistry, Cellular Communication Laboratory, Osnabrück University, 49076 Osnabrück, Germany
- Center of Cellular Nanoanalytics Osnabrück, 49076 Osnabrück, Germany
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20
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Tornero-Écija A, Zapata-Del-Baño A, Antón-Esteban L, Vincent O, Escalante R. The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5. Life Sci Alliance 2023; 6:e202201852. [PMID: 36977596 PMCID: PMC10053439 DOI: 10.26508/lsa.202201852] [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: 11/25/2022] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Human VPS13 proteins are implicated in severe neurological diseases. These proteins play an important role in lipid transport at membrane contact sites between different organelles. Identification of adaptors that regulate the subcellular localization of these proteins at specific membrane contact sites is essential to understand their function and role in disease. We have identified the sorting nexin SNX5 as an interactor of VPS13A that mediates its association with endosomal subdomains. As for the yeast sorting nexin and Vps13 endosomal adaptor Ypt35, this association involves the VPS13 adaptor-binding (VAB) domain in VPS13A and a PxP motif in SNX5. Notably, this interaction is impaired by mutation of a conserved asparagine residue in the VAB domain, which is also required for Vps13-adaptor binding in yeast and is pathogenic in VPS13D. VPS13A fragments containing the VAB domain co-localize with SNX5, whereas the more C-terminal part of VPS13A directs its localization to the mitochondria. Overall, our results suggest that a fraction of VPS13A localizes to junctions between the endoplasmic reticulum, mitochondria, and SNX5-containing endosomes.
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Affiliation(s)
- Alba Tornero-Écija
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | | | - Laura Antón-Esteban
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Olivier Vincent
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
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21
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Chaudhari S, Ware AP, Jasti DB, Gorthi SP, Acharya LP, Bhat M, Mallya S, Satyamoorthy K. Exome sequencing of choreoacanthocytosis reveals novel mutations in VPS13A and co-mutation in modifier gene(s). Mol Genet Genomics 2023; 298:965-976. [PMID: 37209156 DOI: 10.1007/s00438-023-02032-2] [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: 09/01/2022] [Accepted: 05/04/2023] [Indexed: 05/22/2023]
Abstract
Choreoacanthocytosis, one of the forms of neuroacanthocytosis, is caused by mutations in vacuolar protein sorting-associated protein A (VPS13A), and is often misdiagnosed with other form of neuroacanthocytosis with discrete genetic defects. The phenotypic variations among the patients with VPS13A mutations significantly obfuscates the understanding of the disease and treatment strategies. In this study, two unrelated cases were identified, exhibiting the core phenotype of neuroacanthocytosis but with considerable clinical heterogeneity. Case 1 presented with an additional Parkinsonism phenotype, whereas seizures were evident in case 2. To decipher the genetic basis, whole exome sequencing followed by validation with Sanger sequencing was performed. A known homozygous pathogenic nonsense mutation (c.799C > T; p.R267X) in exon 11 of the VPS13A gene was identified in case 1 that resulted in a truncated protein. A novel missense mutation (c.9263T > G; p.M3088R) in exon 69 of VPS13A identified in case 2 was predicted as pathogenic. In silico analysis of the p.M3088R mutation at the C-terminus of VPS13A suggests a loss of interaction with TOMM40 and may disrupt mitochondrial localization. We also observed an increase in mitochondrial DNA copy numbers in case 2. Mutation analysis revealed benign heterozygous variants in interacting partners of VPS13A such as VAPA in case 1. Our study confirmed the cases as ChAc and identified the novel homozygous variant of VPS13A (c.9263T > G; p.M3088R) within the mutation spectrum of VPS13A-associated ChAc. Furthermore, mutations in VPS13A and co-mutations in its potential interacting partner(s) might contribute to the diverse clinical manifestations of ChAc, which requires further study.
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Affiliation(s)
- Sima Chaudhari
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Akshay Pramod Ware
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Dushyanth Babu Jasti
- Department of Neurology, Kasturba Medical College, Manipal, Karnataka, 576104, India
| | - Sankar Prasad Gorthi
- Department of Neurology, Kasturba Medical College, Manipal, Karnataka, 576104, India
- Department of Neurology, Bharati Hospital and Research Center, Bharati Vidyapeeth (Deemed to be University) Medical College and Hospital, Dhankawadi, Pune, Maharashtra, 411043, India
| | - Lavanya Prakash Acharya
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Manoj Bhat
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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22
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Carmichael RE, Richards DM, Fahimi HD, Schrader M. Organelle Membrane Extensions in Mammalian Cells. BIOLOGY 2023; 12:biology12050664. [PMID: 37237478 DOI: 10.3390/biology12050664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Organelles within eukaryotic cells are not isolated static compartments, instead being morphologically diverse and highly dynamic in order to respond to cellular needs and carry out their diverse and cooperative functions. One phenomenon exemplifying this plasticity, and increasingly gaining attention, is the extension and retraction of thin tubules from organelle membranes. While these protrusions have been observed in morphological studies for decades, their formation, properties and functions are only beginning to be understood. In this review, we provide an overview of what is known and still to be discovered about organelle membrane protrusions in mammalian cells, focusing on the best-characterised examples of these membrane extensions arising from peroxisomes (ubiquitous organelles involved in lipid metabolism and reactive oxygen species homeostasis) and mitochondria. We summarise the current knowledge on the diversity of peroxisomal/mitochondrial membrane extensions, as well as the molecular mechanisms by which they extend and retract, necessitating dynamic membrane remodelling, pulling forces and lipid flow. We also propose broad cellular functions for these membrane extensions in inter-organelle communication, organelle biogenesis, metabolism and protection, and finally present a mathematical model that suggests that extending protrusions is the most efficient way for an organelle to explore its surroundings.
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Affiliation(s)
- Ruth E Carmichael
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - David M Richards
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
- Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, UK
| | - H Dariush Fahimi
- Institute for Anatomy and Cell Biology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Michael Schrader
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, UK
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23
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Cornaro L, Banfi C, Cucinotta M, Colombo L, van Dijk PJ. Asexual reproduction through seeds: the complex case of diplosporous apomixis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2462-2478. [PMID: 36794770 DOI: 10.1093/jxb/erad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/07/2023] [Indexed: 06/06/2023]
Abstract
Apomixis is considered a potentially revolutionary tool to generate high-quality food at a lower cost and shorter developmental time due to clonal seed production through apomeiosis and parthenogenesis. In the diplosporous type of apomixis, meiotic recombination and reduction are circumvented either by avoiding or failing meiosis or by a mitotic-like division. Here, we review the literature on diplospory, from early cytological studies dating back to the late 19th century to recent genetic findings. We discuss diplosporous developmental mechanisms, including their inheritance. Furthermore, we compare the strategies adopted to isolate the genes controlling diplospory with those to produce mutants forming unreduced gametes. Nowadays, the dramatically improved technologies of long-read sequencing and targeted CRISPR/Cas mutagenesis justify the expectation that natural diplospory genes will soon be identified. Their identification will answer questions such as how the apomictic phenotype can be superimposed upon the sexual pathway and how diplospory genes have evolved. This knowledge will contribute to the application of apomixis in agriculture.
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Affiliation(s)
- Letizia Cornaro
- Department of Biosciences, University of Milan, Via Giovanni Celoria 26, 20133, Milano, Italy
| | - Camilla Banfi
- Department of Biosciences, University of Milan, Via Giovanni Celoria 26, 20133, Milano, Italy
| | - Mara Cucinotta
- Department of Biosciences, University of Milan, Via Giovanni Celoria 26, 20133, Milano, Italy
| | - Lucia Colombo
- Department of Biosciences, University of Milan, Via Giovanni Celoria 26, 20133, Milano, Italy
| | - Peter J van Dijk
- KeyGene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands
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24
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Guillén-Samander A, De Camilli P. Endoplasmic Reticulum Membrane Contact Sites, Lipid Transport, and Neurodegeneration. Cold Spring Harb Perspect Biol 2023; 15:a041257. [PMID: 36123033 PMCID: PMC10071438 DOI: 10.1101/cshperspect.a041257] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Endoplasmic Reticulum (ER) is an endomembrane system that plays a multiplicity of roles in cell physiology and populates even the most distal cell compartments, including dendritic tips and axon terminals of neurons. Some of its functions are achieved by a cross talk with other intracellular membranous organelles and with the plasma membrane at membrane contacts sites (MCSs). As the ER synthesizes most membrane lipids, lipid exchanges mediated by lipid transfer proteins at MCSs are a particularly important aspect of this cross talk, which synergizes with the cross talk mediated by vesicular transport. Several mutations of genes that encode proteins localized at ER MCSs result in familial neurodegenerative diseases, emphasizing the importance of the normal lipid traffic within cells for a healthy brain. Here, we provide an overview of such diseases, with a specific focus on proteins that directly or indirectly impact lipid transport.
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Affiliation(s)
- Andrés Guillén-Samander
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland 20815, USA
| | - Pietro De Camilli
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland 20815, USA
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25
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Zare Ashrafi F, Akhtarkhavari T, Fattahi Z, Asadnezhad M, Beheshtian M, Arzhangi S, Najmabadi H, Kahrizi K. Emerging Epidemiological Data on Rare Intellectual Disability Syndromes from Analyzing the Data of a Large Iranian Cohort. ARCHIVES OF IRANIAN MEDICINE 2023; 26:186-197. [PMID: 38301078 PMCID: PMC10685746 DOI: 10.34172/aim.2023.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/25/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Intellectual disability (ID) is a genetically heterogeneous condition, and so far, 1679 human genes have been identified for this phenotype. Countries with a high rate of parental consanguinity, such as Iran, provide an excellent opportunity to identify the remaining novel ID genes, especially those with an autosomal recessive (AR) mode of inheritance. This study aimed to investigate the most prevalent ID genes identified via next-generation sequencing (NGS) in a large ID cohort at the Genetics Research Center (GRC) of the University of Social Welfare and Rehabilitation Sciences. METHODS First, we surveyed the epidemiological data of 619 of 1295 families in our ID cohort, who referred to the Genetics Research Center from all over the country between 2004 and 2021 for genetic investigation via the NGS pipeline. We then compared our data with those of several prominent studies conducted in consanguineous countries. Data analysis, including cohort data extraction, categorization, and comparison, was performed using the R program version 4.1.2. RESULTS We categorized the most common ID genes that were mutated in more than two families into 17 categories. The most common syndromic ID in our cohort was AP4 deficiency syndrome, and the most common non-syndromic autosomal recessive intellectual disability (ARID) gene was ASPM. We identified two unrelated families for the 36 ID genes. We found 14 genes in common between our cohort and the Arab and Pakistani groups, of which three genes (AP4M1, AP4S1, and ADGRG1) were repeated more than once. CONCLUSION To date, there has been no comprehensive targeted NGS platform for the detection of ID genes in our country. Due to the large sample size of our study, our data may provide the initial step toward designing an indigenously targeted NGS platform for the diagnosis of ID, especially common ARID in our population.
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Affiliation(s)
- Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Asadnezhad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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26
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Dall'Armellina F, Stagi M, Swan LE. In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms. Proteins 2023; 91:439-455. [PMID: 36404287 PMCID: PMC10953354 DOI: 10.1002/prot.26446] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/14/2022] [Accepted: 11/03/2022] [Indexed: 11/22/2022]
Abstract
The VPS13 protein family constitutes a novel class of bridge-like lipid transferases. Autosomal recessive inheritance of mutations in VPS13 genes is associated with the development of neurodegenerative diseases in humans. Bioinformatic approaches previously recognized the domain architecture of these proteins. In this study, we model the first ever full-length structures of the four human homologs VPS13A, VPS13B, VPS13C, and VPS13D in association with model membranes, to investigate their lipid transfer ability and potential structural association with membrane leaflets. We analyze the evolutionary conservation and physicochemical properties of these proteins, focusing on conserved C-terminal amphipathic helices that disturb organelle surfaces and that, adjoined, resemble a traditional Venetian gondola. The gondola domains share significant structural homology with lipid droplet surface-binding proteins. We introduce in silico protein-membrane models displaying the mode of association of VPS13A, VPS13B, VPS13C, and VPS13D to donor and target membranes, and present potential models of action for protein-mediated lipid transfer.
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Affiliation(s)
- Filippo Dall'Armellina
- Department of Biochemistry and Systems BiologyInstitute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUK
| | - Massimiliano Stagi
- Department of Biochemistry and Systems BiologyInstitute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUK
| | - Laura E. Swan
- Department of Biochemistry and Systems BiologyInstitute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUK
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27
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Leterme S, Michaud M. Mitochondrial membrane biogenesis: A new pathway for lipid transport mediated by PERK/E-Syt1 complex. J Cell Biol 2023; 222:e202301132. [PMID: 36821089 PMCID: PMC9998955 DOI: 10.1083/jcb.202301132] [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] [Indexed: 02/24/2023] Open
Abstract
Despite decades of extensive research, mitochondrial lipid transport is a process far from fully understood. In this issue, Sassano et al. (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202206008) identified a new complex, composed of E-Syt1 and PERK, which mediates lipid transport at ER-mitochondria contact sites and regulates mitochondrial functions in human cells.
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Affiliation(s)
- Sébastien Leterme
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Université Grenoble Alpes, INRAE, CEA, IRIG, Grenoble, France
| | - Morgane Michaud
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Université Grenoble Alpes, INRAE, CEA, IRIG, Grenoble, France
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28
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Pauly MG, Brüggemann N, Efthymiou S, Grözinger A, Diaw SH, Chelban V, Turchetti V, Vona B, Tadic V, Houlden H, Münchau A, Lohmann K. Not to Miss: Intronic Variants, Treatment, and Review of the Phenotypic Spectrum in VPS13D-Related Disorder. Int J Mol Sci 2023; 24:ijms24031874. [PMID: 36768210 PMCID: PMC9953040 DOI: 10.3390/ijms24031874] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/28/2022] [Indexed: 01/21/2023] Open
Abstract
VPS13D is one of four human homologs of the vacuolar sorting protein 13 gene (VPS13). Biallelic pathogenic variants in the gene are associated with spastic ataxia or spastic paraplegia. Here, we report two patients with intronic pathogenic variants: one patient with early onset severe spastic ataxia and debilitating tremor, which is compound-heterozygous for a canonical (NM_018156.4: c.2237-1G > A) and a non-canonical (NM_018156.4: c.941+3G>A) splice site variant. The second patient carries the same non-canonical splice site variant in the homozygous state and is affected by late-onset spastic paraplegia. We confirmed altered splicing as a result of the intronic variants and demonstrated disturbed mitochondrial integrity. Notably, tremor in the first patient improved significantly by bilateral deep brain stimulation (DBS) in the ventralis intermedius (VIM) nucleus of the thalamus. We also conducted a literature review and summarized the phenotypical spectrum of reported VPS13D-related disorders. Our study underscores that looking for mutations outside the canonical splice sites is important not to miss a genetic diagnosis, especially in disorders with a highly heterogeneous presentation without specific red flags.
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Affiliation(s)
- Martje G. Pauly
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Lübeck, Germany
- Institute of Systems Motor Science, University of Lübeck, 23562 Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Lübeck, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Anne Grözinger
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
| | | | - Viorica Chelban
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Valentina Turchetti
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Barbara Vona
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Vera Tadic
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Lübeck, Germany
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Lübeck, 23562 Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Correspondence:
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29
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Amos C, Xu P, De Camilli P. Erythroid Differentiation Dependent Interaction of VPS13A with XK at the Plasma Membrane of K562 Cells. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231215133. [PMID: 38144430 PMCID: PMC10748539 DOI: 10.1177/25152564231215133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/26/2023]
Abstract
Mutations of the bridge-like lipid transport protein VPS13A and the lipid scramblase XK result in Chorea Acanthocytosis (ChAc) and McLeod syndrome (MLS), respectively, two similar conditions involving neurodegeneration and deformed erythrocytes (acanthocytes). VPS13A binds XK, suggesting a model in which VPS13A forms a lipid transport bridge between the endoplasmic reticulum (ER) and the plasma membrane (PM), where XK resides. However, studies of VPS13A in HeLa and COS7 cells showed that this protein localizes primarily at contacts of the ER with mitochondria. Overexpression of XK in these cells redistributed VPS13A to the biosynthetic XK pool in the ER but not to PM-localized XK. Colocalization of VPS13A with XK at the PM was only observed if overexpressed XK harbored mutations that disengaged its VPS13A-binding site from an intramolecular interaction. As the acanthocytosis phenotype of ChAc and MLS suggests a role of the two proteins in cells of the erythroid lineage, we explored their localization in K562 cells, which differentiate into erythroblasts upon hemin addition. When tagged VPS13A was overexpressed in hemin-treated K562 cells, robust formation of ER-PM contacts positive for VPS13A was observed and their formation was abolished in XK KO cells. ER-PM contacts positive for VPS13A were seldom observed in undifferentiated K562 cells, despite the presence of XK in these cells at concentrations similar to those observed after differentiation. These findings reveal that the interaction of VPS13A with XK at ER-PM contacts requires a permissive state which depends upon cell type and/or functional state of the cell.
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Affiliation(s)
- Chase Amos
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, 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
| | - Peng Xu
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, 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
| | - Pietro De Camilli
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, 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
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Leterme S, Bastien O, Aiese Cigliano R, Amato A, Michaud M. Phylogenetic and Structural Analyses of VPS13 Proteins in Archaeplastida Reveal Their Complex Evolutionary History in Viridiplantae. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231211976. [PMID: 38033810 PMCID: PMC10683392 DOI: 10.1177/25152564231211976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
VPS13 is a lipid transfer protein family conserved among Eukaryotes and playing roles in fundamental processes involving vesicular transport and membrane expansion including autophagy and organelle biogenesis. VPS13 folds into a long hydrophobic tunnel, allowing lipid transport, decorated by distinct domains involved in protein localization and regulation. Whereas VPS13 organization and function have been extensively studied in yeast and mammals, information in organisms originating from primary endosymbiosis is scarce. In the higher plant Arabidopsis thaliana, four paralogs, AtVPS13S, X, M1, and M2, were identified, AtVPS13S playing a role in the regulation of root growth, cell patterning, and reproduction. In this work, we performed phylogenetic, as well as domain and structural modeling of VPS13 proteins in Archaeplastida in order to understand their general organization and evolutionary history. We confirmed the presence of human VPS13B orthologues in some phyla and described two new VPS13 families presenting a particular domain arrangement: VPS13R in Rhodophytes and VPS13Y in Chlorophytes and Streptophytes. By focusing on Viridiplantae, we were able to draw the evolutionary history of these proteins made by multiple gene gains and duplications as well as domain rearrangements. We showed that some Chlorophytes have only three (AtVPS13M, S, Y) whereas some Charophytes have up to six VPS13 paralogs (AtVPS13M1, M2, S, Y, X, B). We also highlighted specific structural features of VPS13M and X paralogs. This study reveals the complex evolution of VPS13 family and opens important perspectives for their functional characterization in photosynthetic organisms.
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Affiliation(s)
- Sébastien Leterme
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Olivier Bastien
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | | | - Alberto Amato
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Morgane Michaud
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
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31
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Huet D, Moreno SNJ. Interorganellar Communication Through Membrane Contact Sites in Toxoplasma Gondii. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231189064. [PMID: 37560622 PMCID: PMC10408353 DOI: 10.1177/25152564231189064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 08/11/2023]
Abstract
Apicomplexan parasites are a group of protists that cause disease in humans and include pathogens like Plasmodium spp., the causative agent of malaria, and Toxoplasma gondii, the etiological agent of toxoplasmosis and one of the most ubiquitous human parasites in the world. Membrane contact sites (MCSs) are widespread structures within eukaryotic cells but their characterization in apicomplexan parasites is only in its very beginnings. Basic biological features of the T. gondii parasitic cycle support numerous organellar interactions, including the transfer of Ca2+ and metabolites between different compartments. In T. gondii, Ca2+ signals precede a series of interrelated molecular processes occurring in a coordinated manner that culminate in the stimulation of key steps of the parasite life cycle. Calcium transfer from the endoplasmic reticulum to other organelles via MCSs would explain the precision, speed, and efficiency that is needed during the lytic cycle of T. gondii. In this short review, we discuss the implications of these structures in cellular signaling, with an emphasis on their potential role in Ca2+ signaling.
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Affiliation(s)
- Diego Huet
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
| | - Silvia N. J. Moreno
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
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32
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Peikert K, Danek A. VPS13 Forum Proceedings: XK, XK-Related and VPS13 Proteins in Membrane Lipid Dynamics. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231156994. [PMID: 37366410 PMCID: PMC10243564 DOI: 10.1177/25152564231156994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 01/23/2023] [Indexed: 06/28/2023]
Abstract
In 2020, the pandemic interrupted the series of biannual International Neuroacanthocytosis Meetings that brought together clinicians, scientists, and patient groups to share research into a small group of devastating genetic diseases that combine both acanthocytosis (deformed red blood cells) and neurodegeneration with movement disorders. This Meeting Report describes talks at the 5th VPS13 Forum in January 2022, one of a series of online meetings held to fill the gap. The meeting addressed the basic biology of two key proteins implicated in chorea-acanthocytosis (mutations in VPS13A) and McLeod syndrome (mutations in XK). In a remarkable confluence of ideas, the speakers described different aspects of a single functional unit that comprises of VPS13A and XK proteins working together. Conditions caused by VPS13 (A-D) gene family mutations and related genes, such as XK, previously footnote knowledge, seem to turn central for a novel disease paradigm: bulk lipid transfer disorders.
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Affiliation(s)
- Kevin Peikert
- Translational Neurodegeneration Section
“Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, University of
Rostock, Rostock, Germany
- Center for Transdisciplinary Neurosciences
Rostock (CTNR), University Medical Center Rostock, Rostock, Germany
- United Neuroscience Campus Lund-Rostock
(UNC), Rostock site, Rostock, Germany
| | - Adrian Danek
- Department of Neurology, University Hospital,
LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases
(Deutsches Zentrum für Neurodegenerative Erkrankungen, DZNE), Research Site Munich, Munich,
Germany
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33
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The Critical Role of Galectin-12 in Modulating Lipid Metabolism in Sebaceous Glands. J Invest Dermatol 2022; 143:913-924.e4. [PMID: 36535362 DOI: 10.1016/j.jid.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022]
Abstract
Sebaceous glands play an important role in maintaining the skin barrier function by producing lipids. Dysregulated lipid production in these glands may contribute to the pathogenesis of human skin diseases. Galectin-12, a member of the β-galactoside‒binding lectin family, is preferentially expressed in adipocytes, where it regulates adipogenesis and functions as an intrinsic negative regulator of lipolysis. It is also expressed by sebocytes and contributes to the proliferation of this cell type. In this study, we show the association between galectin-12 expression and sebocyte differentiation. Galectin-12 knockdown in a human sebocyte cell line reduced lipogenesis and decreased the production of cholesteryl esters, triglycerides, free fatty acids, and cholesterol. Metabolomic analysis of skin surface lipids showed that the levels of the lipids mentioned earlier decreased in sebaceous gland‒specific galectin-12‒knockout mice compared with that in wild-type mice. In addition, galectin-12 positively regulated peroxisome proliferator‒activated receptor-γ transcriptional activity in sebocytes stimulated with fatty acids. Downregulating galectin-12 suppressed the expression of peroxisome proliferator‒activated receptor-γ target genes-acetyl-coenzyme A synthetase 2 gene ACS2 and diacylglycerol O-acyltransferase 1 gene DGAT1-that are required for fatty acid activation and cholesterol and triglyceride biosynthesis. In conclusion, galectin-12 is a positive regulator of sebaceous lipid metabolism with a potential role in the maintenance of skin homeostasis.
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Neuman SD, Levine TP, Bashirullah A. A novel superfamily of bridge-like lipid transfer proteins. Trends Cell Biol 2022; 32:962-974. [PMID: 35491307 PMCID: PMC9588498 DOI: 10.1016/j.tcb.2022.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 01/21/2023]
Abstract
Lipid transfer proteins mediate nonvesicular transport of lipids at membrane contact sites to regulate the lipid composition of organelle membranes. Recently, a new type of bridge-like lipid transfer protein has emerged; these proteins contain a long hydrophobic groove and can mediate bulk transport of lipids between organelles. Here, we review recent insights into the structure of these proteins and identify a repeating modular unit that we propose to name the repeating β-groove (RBG) domain. This new structural understanding conceptually unifies all the RBG domain-containing lipid transfer proteins as members of an RBG protein superfamily. We also examine the biological functions of these lipid transporters in normal physiology and disease and speculate on the evolutionary origins of RBG proteins in bacteria.
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Affiliation(s)
- Sarah D Neuman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA
| | - Tim P Levine
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.
| | - Arash Bashirullah
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA.
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35
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Chhetri G, Ke Y, Wang P, Usman M, Li Y, Sapp E, Wang J, Ghosh A, Islam MA, Wang X, Boudi A, DiFiglia M, Li X. Impaired XK recycling for importing manganese underlies striatal vulnerability in Huntington's disease. J Cell Biol 2022; 221:213461. [PMID: 36099524 PMCID: PMC9475296 DOI: 10.1083/jcb.202112073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/15/2022] [Accepted: 07/29/2022] [Indexed: 02/08/2023] Open
Abstract
Mutant huntingtin, which causes Huntington's disease (HD), is ubiquitously expressed but induces preferential loss of striatal neurons by unclear mechanisms. Rab11 dysfunction mediates homeostatic disturbance of HD neurons. Here, we report that Rab11 dysfunction also underscores the striatal vulnerability in HD. We profiled the proteome of Rab11-positive endosomes of HD-vulnerable striatal cells to look for protein(s) linking Rab11 dysfunction to striatal vulnerability in HD and found XK, which triggers the selective death of striatal neurons in McLeod syndrome. XK was trafficked together with Rab11 and was diminished on the surface of immortalized HD striatal cells and striatal neurons in HD mouse brains. We found that XK participated in transporting manganese, an essential trace metal depleted in HD brains. Introducing dominantly active Rab11 into HD striatal cells improved XK dynamics and increased manganese accumulation in an XK-dependent manner. Our study suggests that impaired Rab11-based recycling of XK onto cell surfaces for importing manganese is a driver of striatal dysfunction in Huntington's disease.
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Affiliation(s)
- Gaurav Chhetri
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yuting Ke
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Ping Wang
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA.,Department of Neurology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Muhammad Usman
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Jing Wang
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Arabinda Ghosh
- Department of Botany, Microbiology Division, Gauhati University, Guwahati, Assam, India
| | - Md Ariful Islam
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaolong Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Xueyi Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
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36
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Park JS, Hu Y, Hollingsworth NM, Miltenberger-Miltenyi G, Neiman AM. Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans. J Cell Sci 2022; 135:jcs260227. [PMID: 35950506 PMCID: PMC9482346 DOI: 10.1242/jcs.260227] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
VPS13 family proteins form conduits between the membranes of different organelles through which lipids are transferred. In humans, there are four VPS13 paralogs, and mutations in the genes encoding each of them are associated with different inherited disorders. VPS13 proteins contain multiple conserved domains. The Vps13 adaptor-binding (VAB) domain binds to adaptor proteins that recruit VPS13 to specific membrane contact sites. This work demonstrates the importance of a different domain in VPS13A function. The pleckstrin homology (PH) domain at the C-terminal region of VPS13A is required to form a complex with the XK scramblase and for the co-localization of VPS13A with XK within the cell. Alphafold modeling was used to predict an interaction surface between VPS13A and XK. Mutations in this region disrupt both complex formation and co-localization of the two proteins. Mutant VPS13A alleles found in patients with VPS13A disease truncate the PH domain. The phenotypic similarities between VPS13A disease and McLeod syndrome caused by mutations in VPS13A and XK, respectively, argue that loss of the VPS13A-XK complex is the basis of both diseases.
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Affiliation(s)
- Jae-Sook Park
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Yiying Hu
- Fish Core Unit, German Center for Neurodegenerative Diseases München (DZNE), 81377 Munich, Germany
- Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Nancy M. Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | | | - Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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37
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A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane. Proc Natl Acad Sci U S A 2022; 119:e2205425119. [PMID: 35994651 PMCID: PMC9436381 DOI: 10.1073/pnas.2205425119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chorea-acanthocytosis (ChAc) and McLeod syndrome are diseases with shared clinical manifestations caused by mutations in VPS13A and XK, respectively. Key features of these conditions are the degeneration of caudate neurons and the presence of abnormally shaped erythrocytes. XK belongs to a family of plasma membrane (PM) lipid scramblases whose action results in exposure of PtdSer at the cell surface. VPS13A is an endoplasmic reticulum (ER)-anchored lipid transfer protein with a putative role in the transport of lipids at contacts of the ER with other membranes. Recently VPS13A and XK were reported to interact by still unknown mechanisms. So far, however, there is no evidence for a colocalization of the two proteins at contacts of the ER with the PM, where XK resides, as VPS13A was shown to be localized at contacts between the ER and either mitochondria or lipid droplets. Here we show that VPS13A can also localize at ER-PM contacts via the binding of its PH domain to a cytosolic loop of XK, that such interaction is regulated by an intramolecular interaction within XK, and that both VPS13A and XK are highly expressed in the caudate neurons. Binding of the PH domain of VPS13A to XK is competitive with its binding to intracellular membranes that mediate other tethering functions of VPS13A. Our findings support a model according to which VPS13A-dependent lipid transfer between the ER and the PM is coupled to lipid scrambling within the PM. They raise the possibility that defective cell surface exposure of PtdSer may be responsible for neurodegeneration.
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38
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Ryoden Y, Nagata S. The XK plasma membrane scramblase and the VPS13A cytosolic lipid transporter for ATP-induced cell death. Bioessays 2022; 44:e2200106. [PMID: 35996795 DOI: 10.1002/bies.202200106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 11/12/2022]
Abstract
Extracellular ATP released from necrotic cells in inflamed tissues activates the P2X7 receptor, stimulates the exposure of phosphatidylserine, and causes cell lysis. Recent findings indicated that XK, a paralogue of XKR8 lipid scramblase, forms a complex with VPS13A at the plasma membrane of T cells. Upon engagement by ATP, an unidentified signal(s) from the P2X7 receptor activates the XK-VPS13A complex to scramble phospholipids, followed by necrotic cell death. P2X7 is expressed highly in CD25+ CD4+ T cells but weakly in CD8+ T cells, suggesting a role of this system in the activation of the immune system to prevent infection. On the other hand, a loss-of-function mutation in XK or VPS13A causes neuroacanthocytosis, indicating the crucial involvement of XK-VPS13A-mediated phospholipid scrambling at plasma membranes in the maintenance of homeostasis in the nervous and red blood cell systems.
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Affiliation(s)
- Yuta Ryoden
- Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Shigekazu Nagata
- Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Japan
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39
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Kim S, Coukos R, Gao F, Krainc D. Dysregulation of organelle membrane contact sites in neurological diseases. Neuron 2022; 110:2386-2408. [PMID: 35561676 PMCID: PMC9357093 DOI: 10.1016/j.neuron.2022.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/21/2022] [Accepted: 04/18/2022] [Indexed: 10/18/2022]
Abstract
The defining evolutionary feature of eukaryotic cells is the emergence of membrane-bound organelles. Compartmentalization allows each organelle to maintain a spatially, physically, and chemically distinct environment, which greatly bolsters individual organelle function. However, the activities of each organelle must be balanced and are interdependent for cellular homeostasis. Therefore, properly regulated interactions between organelles, either physically or functionally, remain critical for overall cellular health and behavior. In particular, neuronal homeostasis depends heavily on the proper regulation of organelle function and cross talk, and deficits in these functions are frequently associated with diseases. In this review, we examine the emerging role of organelle contacts in neurological diseases and discuss how the disruption of contacts contributes to disease pathogenesis. Understanding the molecular mechanisms underlying the formation and regulation of organelle contacts will broaden our knowledge of their role in health and disease, laying the groundwork for the development of new therapies targeting interorganelle cross talk and function.
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Affiliation(s)
- Soojin Kim
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Robert Coukos
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Fanding Gao
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL 60611, USA.
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40
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Vrijsen S, Vrancx C, Del Vecchio M, Swinnen JV, Agostinis P, Winderickx J, Vangheluwe P, Annaert W. Inter-organellar Communication in Parkinson's and Alzheimer's Disease: Looking Beyond Endoplasmic Reticulum-Mitochondria Contact Sites. Front Neurosci 2022; 16:900338. [PMID: 35801175 PMCID: PMC9253489 DOI: 10.3389/fnins.2022.900338] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/05/2022] [Indexed: 01/13/2023] Open
Abstract
Neurodegenerative diseases (NDs) are generally considered proteinopathies but whereas this may initiate disease in familial cases, onset in sporadic diseases may originate from a gradually disrupted organellar homeostasis. Herein, endolysosomal abnormalities, mitochondrial dysfunction, endoplasmic reticulum (ER) stress, and altered lipid metabolism are commonly observed in early preclinical stages of major NDs, including Parkinson's disease (PD) and Alzheimer's disease (AD). Among the multitude of underlying defective molecular mechanisms that have been suggested in the past decades, dysregulation of inter-organellar communication through the so-called membrane contact sites (MCSs) is becoming increasingly apparent. Although MCSs exist between almost every other type of subcellular organelle, to date, most focus has been put on defective communication between the ER and mitochondria in NDs, given these compartments are critical in neuronal survival. Contributions of other MCSs, notably those with endolysosomes and lipid droplets are emerging, supported as well by genetic studies, identifying genes functionally involved in lysosomal homeostasis. In this review, we summarize the molecular identity of the organelle interactome in yeast and mammalian cells, and critically evaluate the evidence supporting the contribution of disturbed MCSs to the general disrupted inter-organellar homeostasis in NDs, taking PD and AD as major examples.
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Affiliation(s)
- Stephanie Vrijsen
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, Leuven, Belgium
| | - Céline Vrancx
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Mara Del Vecchio
- Laboratory of Functional Biology, Department of Biology, KU Leuven, Heverlee, Belgium
| | - Johannes V. Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
- Johannes V. Swinnen
| | - Patrizia Agostinis
- Laboratory of Cell Death Research and Therapy, VIB-Center for Cancer Research, KU Leuven, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Patrizia Agostinis
| | - Joris Winderickx
- Laboratory of Functional Biology, Department of Biology, KU Leuven, Heverlee, Belgium
- Joris Winderickx
| | - Peter Vangheluwe
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, Leuven, Belgium
- Peter Vangheluwe
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- *Correspondence: Wim Annaert
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41
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Adlakha J, Hong Z, Li P, Reinisch KM. Structural and biochemical insights into lipid transport by VPS13 proteins. J Cell Biol 2022; 221:213104. [PMID: 35357422 PMCID: PMC8978259 DOI: 10.1083/jcb.202202030] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/19/2022] Open
Abstract
VPS13 proteins are proposed to function at contact sites between organelles as bridges for lipids to move directionally and in bulk between organellar membranes. VPS13s are anchored between membranes via interactions with receptors, including both peripheral and integral membrane proteins. Here we present the crystal structure of VPS13s adaptor binding domain (VAB) complexed with a Pro-X-Pro peptide recognition motif present in one such receptor, the integral membrane protein Mcp1p, and show biochemically that other Pro-X-Pro motifs bind the VAB in the same site. We further demonstrate that Mcp1p and another integral membrane protein that interacts directly with human VPS13A, XK, are scramblases. This finding supports an emerging paradigm of a partnership between bulk lipid transport proteins and scramblases. Scramblases can re-equilibrate lipids between membrane leaflets as lipids are removed from or inserted into the cytosolic leaflet of donor and acceptor organelles, respectively, in the course of protein-mediated transport.
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Affiliation(s)
- Jyoti Adlakha
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD
| | - Zhouping Hong
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD
| | - PeiQi Li
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Karin M Reinisch
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD
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42
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The Association of Lipids with Amyloid Fibrils. J Biol Chem 2022; 298:102108. [PMID: 35688209 PMCID: PMC9293637 DOI: 10.1016/j.jbc.2022.102108] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 01/02/2023] Open
Abstract
Amyloid formation continues to be a widely studied area because of its association with numerous diseases, such as Alzheimer’s and Parkinson’s diseases. Despite a large body of work on protein aggregation and fibril formation, there are still significant gaps in our understanding of the factors that differentiate toxic amyloid formation in vivo from alternative misfolding pathways. In addition to proteins, amyloid fibrils are often associated in their cellular context with several types of molecule, including carbohydrates, polyanions, and lipids. This review focuses in particular on evidence for the presence of lipids in amyloid fibrils and the routes by which those lipids may become incorporated. Chemical analyses of fibril composition, combined with studies to probe the lipid distribution around fibrils, provide evidence that in some cases, lipids have a strong association with fibrils. In addition, amyloid fibrils formed in the presence of lipids have distinct morphologies and material properties. It is argued that lipids are an integral part of many amyloid deposits in vivo, where their presence has the potential to influence the nucleation, morphology, and mechanical properties of fibrils. The role of lipids in these structures is therefore worthy of further study.
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43
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Kaminska J, Soczewka P, Rzepnikowska W, Zoladek T. Yeast as a Model to Find New Drugs and Drug Targets for VPS13-Dependent Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23095106. [PMID: 35563497 PMCID: PMC9104724 DOI: 10.3390/ijms23095106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 12/10/2022] Open
Abstract
Mutations in human VPS13A-D genes result in rare neurological diseases, including chorea-acanthocytosis. The pathogenesis of these diseases is poorly understood, and no effective treatment is available. As VPS13 genes are evolutionarily conserved, the effects of the pathogenic mutations could be studied in model organisms, including yeast, where one VPS13 gene is present. In this review, we summarize advancements obtained using yeast. In recent studies, vps13Δ and vps13-I2749 yeast mutants, which are models of chorea-acanthocytosis, were used to screen for multicopy and chemical suppressors. Two of the suppressors, a fragment of the MYO3 and RCN2 genes, act by downregulating calcineurin activity. In addition, vps13Δ suppression was achieved by using calcineurin inhibitors. The other group of multicopy suppressors were genes: FET4, encoding iron transporter, and CTR1, CTR3 and CCC2, encoding copper transporters. Mechanisms of their suppression rely on causing an increase in the intracellular iron content. Moreover, among the identified chemical suppressors were copper ionophores, which require a functional iron uptake system for activity, and flavonoids, which bind iron. These findings point at areas for further investigation in a higher eukaryotic model of VPS13-related diseases and to new therapeutic targets: calcium signalling and copper and iron homeostasis. Furthermore, the identified drugs are interesting candidates for drug repurposing for these diseases.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
- Correspondence:
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Melia TJ, Reinisch KM. A possible role for VPS13-family proteins in bulk lipid transfer, membrane expansion and organelle biogenesis. J Cell Sci 2022; 135:274675. [PMID: 35267021 PMCID: PMC8976877 DOI: 10.1242/jcs.259357] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
At organelle–organelle contact sites, proteins have long been known to facilitate the rapid movement of lipids. Classically, this lipid transport involves the extraction of single lipids into a hydrophobic pocket on a lipid transport protein. Recently, a new class of lipid transporter has been described with physical characteristics that suggest these proteins are likely to function differently. They possess long hydrophobic tracts that can bind many lipids at once and physically span the entire gulf between membranes at contact sites, suggesting that they may act as bridges to facilitate bulk lipid flow. Here, we review what has been learned regarding the structure and function of this class of lipid transporters, whose best characterized members are VPS13 and ATG2 proteins, and their apparent coordination with other lipid-mobilizing proteins on organelle membranes. We also discuss the prevailing hypothesis in the field, that this type of lipid transport may facilitate membrane expansion through the bulk delivery of lipids, as well as other emerging hypotheses and questions surrounding these novel lipid transport proteins. Summary: We discuss emerging roles of VPS13-family proteins in vesicle-independent bulk lipid transport between organelles, the possible functions of such transport and the underlying molecular mechanisms.
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Affiliation(s)
- Thomas J Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Karin M Reinisch
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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Yuan W, Akşit A, de Boer R, Krikken AM, van der Klei IJ. Yeast Vps13 is Crucial for Peroxisome Expansion in Cells With Reduced Peroxisome-ER Contact Sites. Front Cell Dev Biol 2022; 10:842285. [PMID: 35252206 PMCID: PMC8891532 DOI: 10.3389/fcell.2022.842285] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/28/2022] [Indexed: 12/22/2022] Open
Abstract
In the yeast Hansenula polymorpha the peroxisomal membrane protein Pex11 and three endoplasmic reticulum localized proteins of the Pex23 family (Pex23, Pex24 and Pex32) are involved in the formation of peroxisome-ER contact sites. Previous studies suggested that these contacts are involved in non-vesicular lipid transfer and important for expansion of the peroxisomal membrane. The absence of Pex32 results in a severe peroxisomal phenotype, while cells lacking Pex11, Pex23 or Pex24 show milder defects and still are capable to form peroxisomes and grow on methanol. We performed transposon mutagenesis on H. polymorpha pex11 cells and selected mutants that lost the capacity to grow on methanol and are severely blocked in peroxisome formation. This strategy resulted in the identification of Vps13, a highly conserved contact site protein involved in bulk lipid transfer. Our data show that peroxisome formation and function is normal in cells of a vps13 single deletion strain. However, Vps13 is essential for peroxisome biogenesis in pex11. Notably, Vps13 is also required for peroxisome formation in pex23 and pex24 cells. These data suggest that Vps13 is crucial for peroxisome formation in cells with reduced peroxisome-endoplasmic reticulum contact sites and plays a redundant function in lipid transfer from the ER to peroxisomes.
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Peikert K, Hermann A, Danek A. XK-Associated McLeod Syndrome: Nonhematological Manifestations and Relation to VPS13A Disease. Transfus Med Hemother 2022; 49:4-12. [PMID: 35221863 PMCID: PMC8832239 DOI: 10.1159/000521417] [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: 10/10/2021] [Accepted: 12/03/2021] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND McLeod syndrome (MLS) is an X-linked multisystemic progressive disorder caused by loss of function mutations in the XK gene. The rare blood group phenotype of MLS patients with absent Kx antigen requires the support of specialized transfusion institutions because of the risk of transfusion complications. Acanthocytosis of red blood cells occurs in almost all patients. Nonhematological manifestations of MLS are very similar to those of VPS13A disease (chorea-acanthocytosis), an autosomal-recessive condition. Their shared phenotype apart from acanthocytosis includes movement disorders such as chorea and dystonia, epilepsy, peripheral neuropathy, and muscle involvement, typically with creatine kinase (CK) elevation, cardiomyopathy included. SUMMARY In this review, we describe the nonhematological manifestations of MLS in comparison with those of VPS13A disease. While there are many similarities, differences such as mode of inheritance, sex distribution, age at manifestation, severity of heart involvement, frequency of feeding dystonia or of involuntary head drops may help to distinguish these disorders in the clinic. Immunohematological demonstration of the McLeod-Kell phenotype or detection of pathogenic mutations of XK (or VPS13A, respectively) is the gold standard for distinction. "Neuroacanthocytosis" was often used as an overarching term, but is potentially misleading, as the term does not refer to a defined disease entity. Its use, if continued, must not prevent clinicians to seek a final diagnosis on the basis of molecular findings. The clinical similarity of MLS and VPS13A disease has long suggested some shared pathophysiology. Evidence for molecular interaction between XK, the McLeod protein, and chorein, the VPS13A gene product, has recently been put forward: XK forms a complex with chorein/VPS13A, a bulk lipid transporter located at various membrane contact sites. The exact role of XK in this complex needs to be further elucidated. Impairment of bulk lipid transport appears as the common denominator of both MLS and VPS13A disease. A variety of further conditions may in time be added to the "bulk lipid transport diseases," such as the recently recognized disorders caused by mutations in the VPS13B, VPS13C, and VPS13D genes. KEY MESSAGES (1) Patients diagnosed with the rare red cell McLeod phenotype (McLeod syndrome, MLS) require interdisciplinary collaboration of transfusion medicine specialists, neurologists, and cardiologists for both their hematological and nonhematological disease manifestations. (2) The phenotypical similarity of MLS and VPS13A disease, often leading to either confusion or insufficient diagnostic depth (under the label of "neuroacanthocytosis"), is based on interaction of the respective proteins, XK and chorein, within the cellular machinery for bulk lipid transport. (3) Overall, the term "bulk lipid transport diseases" seems useful for further research on a group of conditions that may not only share pathophysiology, but may also share treatment approaches.
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Affiliation(s)
- Kevin Peikert
- Translational Neurodegeneration Section “Albrecht Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section “Albrecht Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
- DZNE, German Center for Neurodegenerative Diseases, Research Site Rostock/Greifswald, Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Adrian Danek
- Neurologische Klinik und Poliklinik, Ludwig-Maximilians-Universität, Munich, Germany
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Levine TP. Sequence Analysis and Structural Predictions of Lipid Transfer Bridges in the Repeating Beta Groove (RBG) Superfamily Reveal Past and Present Domain Variations Affecting Form, Function and Interactions of VPS13, ATG2, SHIP164, Hobbit and Tweek. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:251525642211343. [PMID: 36571082 PMCID: PMC7613979 DOI: 10.1177/25152564221134328] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Lipid transfer between organelles requires proteins that shield the hydrophobic portions of lipids as they cross the cytoplasm. In the last decade a new structural form of lipid transfer protein (LTP) has been found: long hydrophobic grooves made of beta-sheet that bridge between organelles at membrane contact sites. Eukaryotes have five families of bridge-like LTPs: VPS13, ATG2, SHIP164, Hobbit and Tweek. These are unified into a single superfamily through their bridges being composed of just one domain, called the repeating beta groove (RBG) domain, which builds into rod shaped multimers with a hydrophobic-lined groove and hydrophilic exterior. Here, sequences and predicted structures of the RBG superfamily were analyzed in depth. Phylogenetics showed that the last eukaryotic common ancestor contained all five RBG proteins, with duplicated VPS13s. The current set of long RBG protein appears to have arisen in even earlier ancestors from shorter forms with 4 RBG domains. The extreme ends of most RBG proteins have amphipathic helices that might be an adaptation for direct or indirect bilayer interaction, although this has yet to be tested. The one exception to this is the C-terminus of SHIP164, which instead has a coiled-coil. Finally, the exterior surfaces of the RBG bridges are shown to have conserved residues along most of their length, indicating sites for partner interactions almost all of which are unknown. These findings can inform future cell biological and biochemical experiments.
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Lei Y, Wen X, Klionsky DJ. Vps13 is required for efficient autophagy in Saccharomyces cerevisiae. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:25152564221136388. [PMID: 37151407 PMCID: PMC10162780 DOI: 10.1177/25152564221136388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/14/2022] [Indexed: 05/09/2023]
Abstract
Vps13 is a large, conserved protein that transports lipids between membranes. Its localization at multiple organelle membranes and membrane contact sites suggests its important physiological roles. In addition, the high correlation of mutant VPS13 with certain diseases, especially those involving neurodegeneration, makes this protein of considerable biomedical interest. Taking advantage of the fact that yeasts only have one Vps13 protein, the roles of yeast Vps13 have been well studied. However, whether and how Vps13 functions in macroautophagy/autophagy, a process of degradation of cytoplasmic cargoes, have been elusive questions. In this paper, we investigated the role of Vps13 in both non-selective and selective autophagy and found that this protein participates in non-selective autophagy, reticulophagy and pexophagy, but not mitophagy, and that Vps13 plays a role in the late stage of autophagy.
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Affiliation(s)
- Yuchen Lei
- Life Sciences Institute, and the Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xin Wen
- Life Sciences Institute, and the Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Life Sciences Institute, and the Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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49
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Kaminska J. The PH-like Domain of VPS13 Proteins - a Determinant of Localization to the Golgi Apparatus or to the Plasma Membrane. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:25152564221106024. [PMID: 37366508 PMCID: PMC10243563 DOI: 10.1177/25152564221106024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Mutations in the four human genes VPS13A-D, encoding vacuolar protein sorting 13 (VPS13A-D) proteins, result in developmental or neurodegenerative diseases. Understanding the functioning of VPS13 proteins in physiology and pathology is a hot topic of research. Especially interesting is how VPS13 proteins are localized to specific membrane contact sites and function in lipid transport. Recently, the C-terminal Pleckstrin Homology (PH)-like domains of yeast Vps13 and human VPS13A were found to bind Arf1 GTPase and to phosphoinositol 4,5-bisphosphate. Here, hypotheses on the importance of the dual binding ability of the PH-like domain of VPS13A protein for cell physiology are presented. While yeast Vps13, together with Arf1 GTPase, is important for protein sorting in the Trans Golgi Network (TGN), the localization of VPS13A in TGN is speculated to restrict the binding of VPS13A to the plasma membrane.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish
Academy of Science, Warsaw, Poland
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50
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Adaptative Up-Regulation of PRX2 and PRX5 Expression Characterizes Brain from a Mouse Model of Chorea-Acanthocytosis. Antioxidants (Basel) 2021; 11:antiox11010076. [PMID: 35052580 PMCID: PMC8772732 DOI: 10.3390/antiox11010076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 02/04/2023] Open
Abstract
The peroxiredoxins (PRXs) constitute a ubiquitous antioxidant. Growing evidence in neurodegenerative disorders such as Parkinson’s disease (PD) or Alzheimer’s disease (AD) has highlighted a crucial role for PRXs against neuro-oxidation. Chorea-acanthocytosis/Vps13A disease (ChAc) is a devastating, life-shortening disorder characterized by acanthocytosis, neurodegeneration and abnormal proteostasis. We recently developed a Vps13a−/− ChAc-mouse model, showing acanthocytosis, neurodegeneration and neuroinflammation which could be restored by LYN inactivation. Here, we show in our Vps13a−/− mice protein oxidation, NRF2 activation and upregulation of downstream cytoprotective systems NQO1, SRXN1 and TRXR in basal ganglia. This was associated with upregulation of PRX2/5 expression compared to wild-type mice. PRX2 expression was age-dependent in both mouse strains, whereas only Vps13a−/− PRX5 expression was increased independent of age. LYN deficiency or nilotinib-mediated LYN inhibition improved autophagy in Vps13a−/− mice. In Vps13a−/−; Lyn−/− basal ganglia, absence of LYN resulted in reduced NRF2 activation and down-regulated expression of PRX2/5, SRXN1 and TRXR. Nilotinib treatment of Vps13a−/− mice reduced basal ganglia oxidation, and plasma PRX5 levels, suggesting plasma PRX5 as a possible ChAc biomarker. Our data support initiation of therapeutic Lyn inhibition as promptly as possible after ChAc diagnosis to minimize development of irreversible neuronal damage during otherwise inevitable ChAc progression.
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