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Demontis GC, Pezzini F, Margari E, Bianchi M, Longoni B, Doccini S, Lalowski MM, Santorelli FM, Simonati A. Electrophysiological Profile Remodeling via Selective Suppression of Voltage-Gated Currents by CLN1/PPT1 Overexpression in Human Neuronal-Like Cells. Front Cell Neurosci 2020; 14:569598. [PMID: 33390903 PMCID: PMC7772423 DOI: 10.3389/fncel.2020.569598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022] Open
Abstract
CLN1 disease (OMIM #256730) is an inherited neurological disorder of early childhood with epileptic seizures and premature death. It is associated with mutations in CLN1 coding for Palmitoyl-Protein Thioesterase 1 (PPT1), a lysosomal enzyme which affects the recycling and degradation of lipid-modified (S-acylated) proteins by removing palmitate residues. Transcriptomic evidence from a neuronal-like cellular model derived from differentiated SH-SY5Y cells disclosed the potential negative roles of CLN1 overexpression, affecting the elongation of neuronal processes and the expression of selected proteins of the synaptic region. Bioinformatic inquiries of transcriptomic data pinpointed a dysregulated expression of several genes coding for proteins related to voltage-gated ion channels, including subunits of calcium and potassium channels (VGCC and VGKC). In SH-SY5Y cells overexpressing CLN1 (SH-CLN1 cells), the resting potential and the membrane conductance in the range of voltages close to the resting potential were not affected. However, patch-clamp recordings indicated a reduction of Ba2+ currents through VGCC of SH-CLN1 cells; Ca2+ imaging revealed reduced Ca2+ influx in the same cellular setting. The results of the biochemical and morphological investigations of CACNA2D2/α2δ-2, an accessory subunit of VGCC, were in accordance with the downregulation of the corresponding gene and consistent with the hypothesis that a lower number of functional channels may reach the plasma membrane. The combined use of 4-AP and NS-1643, two drugs with opposing effects on Kv11 and Kv12 subfamilies of VGKC coded by the KCNH gene family, provides evidence for reduced functional Kv12 channels in SH-CLN1 cells, consistent with transcriptomic data indicating the downregulation of KCNH4. The lack of compelling evidence supporting the palmitoylation of many ion channels subunits investigated in this study stimulates inquiries about the role of PPT1 in the trafficking of channels to the plasma membrane. Altogether, these results indicate a reduction of functional voltage-gated ion channels in response to CLN1/PPT1 overexpression in differentiated SH-SY5Y cells and provide new insights into the altered neuronal excitability which may underlie the severe epileptic phenotype of CLN1 disease. It remains to be shown if remodeling of such functional channels on plasma membrane can occur as a downstream effect of CLN1 disease.
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Affiliation(s)
| | - Francesco Pezzini
- Neurology (Child Neurology and Neuropathology), Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Elisa Margari
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Marzia Bianchi
- Research Unit for Multi-factorial Diseases, Obesity and Diabetes, Bambino Gesù Children's Hospital Istituto di Ricerca e Cura a Carattere Scientifico, Rome, Italy
| | - Biancamaria Longoni
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Stefano Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Istituto di Ricerca e Cura a Carattere Scientifico Stella Maris Foundation, Pisa, Italy
| | - Maciej Maurycy Lalowski
- Medicum, Biochemistry/Developmental Biology and HiLIFE-Helsinki Institute of Life Science, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Filippo Maria Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Istituto di Ricerca e Cura a Carattere Scientifico Stella Maris Foundation, Pisa, Italy
| | - Alessandro Simonati
- Neurology (Child Neurology and Neuropathology), Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
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52
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Abstract
Protein S-acylation (commonly known as palmitoylation) is a widespread reversible lipid modification, which plays critical roles in regulating protein localization, activity, stability, and complex formation. The deregulation of protein S-acylation contributes to many diseases such as cancer and neurodegenerative disorders. The past decade has witnessed substantial progress in proteomic analysis of protein S-acylation, which significantly advanced our understanding of S-acylation biology. In this review, we summarized the techniques for the enrichment of S-acylated proteins or peptides, critically reviewed proteomic studies of protein S-acylation at eight different levels, and proposed major challenges for the S-acylproteomics field. In summary, proteome-scale analysis of protein S-acylation comes of age and will play increasingly important roles in discovering new disease mechanisms, biomarkers, and therapeutic targets.
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Affiliation(s)
- Yang Wang
- Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States
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53
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Sanders SS, Hernandez LM, Soh H, Karnam S, Walikonis RS, Tzingounis AV, Thomas GM. The palmitoyl acyltransferase ZDHHC14 controls Kv1-family potassium channel clustering at the axon initial segment. eLife 2020; 9:56058. [PMID: 33185190 PMCID: PMC7685708 DOI: 10.7554/elife.56058] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 11/12/2020] [Indexed: 01/02/2023] Open
Abstract
The palmitoyl acyltransferase (PAT) ZDHHC14 is highly expressed in the hippocampus and is the only PAT predicted to bind Type-I PDZ domain-containing proteins. However, ZDHHC14’s neuronal roles are unknown. Here, we identify the PDZ domain-containing Membrane-associated Guanylate Kinase (MaGUK) PSD93 as a direct ZDHHC14 interactor and substrate. PSD93, but not other MaGUKs, localizes to the axon initial segment (AIS). Using lentiviral-mediated shRNA knockdown in rat hippocampal neurons, we find that ZDHHC14 controls palmitoylation and AIS clustering of PSD93 and also of Kv1 potassium channels, which directly bind PSD93. Neurodevelopmental expression of ZDHHC14 mirrors that of PSD93 and Kv1 channels and, consistent with ZDHHC14’s importance for Kv1 channel clustering, loss of ZDHHC14 decreases outward currents and increases action potential firing in hippocampal neurons. To our knowledge, these findings identify the first neuronal roles and substrates for ZDHHC14 and reveal a previously unappreciated role for palmitoylation in control of neuronal excitability.
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Affiliation(s)
- Shaun S Sanders
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, United States
| | - Luiselys M Hernandez
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, United States
| | - Heun Soh
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, United States
| | - Santi Karnam
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, United States
| | - Randall S Walikonis
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, United States
| | | | - Gareth M Thomas
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, United States.,Department of Anatomy and Cell Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, United States
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Collura KM, Niu J, Sanders SS, Montersino A, Holland SM, Thomas GM. The palmitoyl acyltransferases ZDHHC5 and ZDHHC8 are uniquely present in DRG axons and control retrograde signaling via the Gp130/JAK/STAT3 pathway. J Biol Chem 2020; 295:15427-15437. [PMID: 32958558 PMCID: PMC7667964 DOI: 10.1074/jbc.ra120.013815] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Palmitoylation, the modification of proteins with the lipid palmitate, is a key regulator of protein targeting and trafficking. However, knowledge of the roles of specific palmitoyl acyltransferases (PATs), which catalyze palmitoylation, is incomplete. For example, little is known about which PATs are present in neuronal axons, although long-distance trafficking of palmitoyl-proteins is important for axon integrity and for axon-to-soma retrograde signaling, a process critical for axon development and for responses to injury. Identifying axonally targeted PATs might thus provide insights into multiple aspects of axonal biology. We therefore comprehensively determined the subcellular distribution of mammalian PATs in dorsal root ganglion (DRG) neurons and, strikingly, found that only two PATs, ZDHHC5 and ZDHHC8, were enriched in DRG axons. Signals via the Gp130/JAK/STAT3 and DLK/JNK pathways are important for axonal injury responses, and we found that ZDHHC5 and ZDHHC8 were required for Gp130/JAK/STAT3, but not DLK/JNK, axon-to-soma signaling. ZDHHC5 and ZDHHC8 robustly palmitoylated Gp130 in cotransfected nonneuronal cells, supporting the possibility that Gp130 is a direct ZDHHC5/8 substrate. In DRG neurons, Zdhhc5/8 shRNA knockdown reduced Gp130 palmitoylation and even more markedly reduced Gp130 surface expression, potentially explaining the importance of these PATs for Gp130-dependent signaling. Together, these findings provide new insights into the subcellular distribution and roles of specific PATs and reveal a novel mechanism by which palmitoylation controls axonal retrograde signaling.
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Affiliation(s)
- Kaitlin M Collura
- Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair), Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Jingwen Niu
- Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair), Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Shaun S Sanders
- Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair), Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Audrey Montersino
- Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair), Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Sabrina M Holland
- Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair), Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Gareth M Thomas
- Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair), Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA; Department of Anatomy and Cell Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA.
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55
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Jin J, Zhi X, Wang X, Meng D. Protein palmitoylation and its pathophysiological relevance. J Cell Physiol 2020; 236:3220-3233. [PMID: 33094504 DOI: 10.1002/jcp.30122] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/25/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022]
Abstract
Protein palmitoylation, in which C16 fatty acid chains are attached to cysteine residues via a reversible thioester linkage, is one of the most common lipid modifications and plays important roles in regulating protein stability, subcellular localization, membrane trafficking, interactions with effector proteins, enzymatic activity, and a variety of other cellular processes. Moreover, the unique reversibility of palmitoylation allows proteins to be rapidly shuttled between biological membranes and cytoplasmic substrates in a process usually controlled by a member of the DHHC family of protein palmitoyl transferases (PATs). Notably, mutations in PATs are closely related to a variety of human diseases, such as cancer, neurological disorders, and immune deficiency conditions. In addition to PATs, intracellular palmitoylation dynamics are also regulated by the interplay between distinct posttranslational modifications, including ubiquitination and phosphorylation. Understanding the specific mechanisms of palmitoylation may reveal novel potential therapeutic targets for many human diseases.
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Affiliation(s)
- Jiayu Jin
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, Fudan University, Shanghai, China
| | - Xiuling Zhi
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, Fudan University, Shanghai, China
| | - Xinhong Wang
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, Fudan University, Shanghai, China
| | - Dan Meng
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, Fudan University, Shanghai, China
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Shimell JJ, Shah BS, Cain SM, Thouta S, Kuhlmann N, Tatarnikov I, Jovellar DB, Brigidi GS, Kass J, Milnerwood AJ, Snutch TP, Bamji SX. The X-Linked Intellectual Disability Gene Zdhhc9 Is Essential for Dendrite Outgrowth and Inhibitory Synapse Formation. Cell Rep 2020; 29:2422-2437.e8. [PMID: 31747610 DOI: 10.1016/j.celrep.2019.10.065] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/09/2019] [Accepted: 10/13/2019] [Indexed: 11/29/2022] Open
Abstract
Palmitoylation is a reversible post-translational lipid modification that facilitates vesicular transport and subcellular localization of modified proteins. This process is catalyzed by ZDHHC enzymes that are implicated in several neurological and neurodevelopmental disorders. Loss-of-function mutations in ZDHHC9 have been identified in patients with X-linked intellectual disability (XLID) and associated with increased epilepsy risk. Loss of Zdhhc9 function in hippocampal cultures leads to shorter dendritic arbors and fewer inhibitory synapses, altering the ratio of excitatory-to-inhibitory inputs formed onto Zdhhc9-deficient cells. While Zdhhc9 promotes dendrite outgrowth through the palmitoylation of the GTPase Ras, it promotes inhibitory synapse formation through the palmitoylation of another GTPase, TC10. Zdhhc9 knockout mice exhibit seizure-like activity together with increased frequency and amplitude of both spontaneous and miniature excitatory and inhibitory postsynaptic currents. These findings present a plausible mechanism for how the loss of ZDHHC9 function may contribute to XLID and epilepsy.
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Affiliation(s)
- Jordan J Shimell
- Department of Cellular and Physiological Sciences, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Bhavin S Shah
- Department of Cellular and Physiological Sciences, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Stuart M Cain
- Michael Smith Laboratories, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Samrat Thouta
- Michael Smith Laboratories, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Naila Kuhlmann
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Igor Tatarnikov
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - D Blair Jovellar
- Department of Cellular and Physiological Sciences, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - G Stefano Brigidi
- Department of Cellular and Physiological Sciences, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jennifer Kass
- Michael Smith Laboratories, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Austen J Milnerwood
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Terrance P Snutch
- Michael Smith Laboratories, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Shernaz X Bamji
- Department of Cellular and Physiological Sciences, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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57
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Zhang H, Li X, Ma C, Wang K, Zhou J, Chen J, Wang Y, Shi Y. Fine-mapping of ZDHHC2 identifies risk variants for schizophrenia in the Han Chinese population. Mol Genet Genomic Med 2020; 8:e1190. [PMID: 32180374 PMCID: PMC7336764 DOI: 10.1002/mgg3.1190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 02/05/2020] [Accepted: 02/05/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND ZDHHC2 is a member of the DHHC protein family, mediating palmitoylation of postsynaptic density-95 (PSD-95) and A-kinase-anchoring protein 79/150 (AKAP79/150). Genome-wide association studies (GWASs) have identified ZDHHC2 as a candidate gene for schizophrenia (SCZ). We aimed to fine-map variants of ZDHHC2 conferring risk to SCZ in the Han Chinese population. METHODS Targeted sequencing of whole-exome sequences including untranslated regions (UTRs) along with neighboring regions in 1,827 schizophrenic patients and 1,004 normal controls of Han Chinese origin. RESULTS A total of 123 variants, including five common and 118 rare variants, were identified. Among common variants, rs73198534, rs530313445, and rs74406481 were significantly associated with SCZ. Nine nonsynonymous rare variants, p.Glu96fs, p.Arg127X, p.Val145Ile, p.Ala177Thr, p.Arg269Gln, p.Asn312His, p.Glu319Lys, p.Gln340X, and p.Ile347Val, identified only in patients; eight are located in the important domains, including two stop-gain variants. The 3D structural analysis and functional prediction revealed that all these eight variants may affect AMPAR expression or function, and influence the synaptic plasticity by regulating the palmitoylation of PSD95 and AKAP79/150. CONCLUSION Our results first show strong supportive evidences of the association between the ZDHHC2 and SCZ, and also provide a fine-mapping of variants of this gene in Han Chinese SCZ patients.
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Affiliation(s)
- Han Zhang
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationCollaborative Innovation Center for Brain ScienceShanghai Jiao Tong UniversityShanghaiChina
| | - Xiuli Li
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationCollaborative Innovation Center for Brain ScienceShanghai Jiao Tong UniversityShanghaiChina
| | - Chuanchuan Ma
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationCollaborative Innovation Center for Brain ScienceShanghai Jiao Tong UniversityShanghaiChina
| | - Ke Wang
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationCollaborative Innovation Center for Brain ScienceShanghai Jiao Tong UniversityShanghaiChina
| | - Juan Zhou
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationCollaborative Innovation Center for Brain ScienceShanghai Jiao Tong UniversityShanghaiChina
| | - Jianhua Chen
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationCollaborative Innovation Center for Brain ScienceShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic DisordersShanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yonggang Wang
- Department of NeurologyBeijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Yongyong Shi
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationCollaborative Innovation Center for Brain ScienceShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic DisordersShanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Sleep Disordered BreathingShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
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58
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Mariscal J, Vagner T, Kim M, Zhou B, Chin A, Zandian M, Freeman MR, You S, Zijlstra A, Yang W, Di Vizio D. Comprehensive palmitoyl-proteomic analysis identifies distinct protein signatures for large and small cancer-derived extracellular vesicles. J Extracell Vesicles 2020; 9:1764192. [PMID: 32944167 PMCID: PMC7448892 DOI: 10.1080/20013078.2020.1764192] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/19/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Extracellular vesicles (EVs) are membrane-enclosed particles that play an important role in cancer progression and have emerged as a promising source of circulating biomarkers. Protein S-acylation, frequently called palmitoylation, has been proposed as a post-translational mechanism that modulates the dynamics of EV biogenesis and protein cargo sorting. However, technical challenges have limited large-scale profiling of the whole palmitoyl-proteins of EVs. We successfully employed a novel approach that combines low-background acyl-biotinyl exchange (LB-ABE) with label-free proteomics to analyse the palmitoyl-proteome of large EVs (L-EVs) and small EVs (S-EVs) from prostate cancer cells. Here we report the first palmitoyl-protein signature of EVs, and demonstrate that L- and S-EVs harbour proteins associated with distinct biological processes and subcellular origin. We identified STEAP1, STEAP2, and ABCC4 as prostate cancer-specific palmitoyl-proteins abundant in both EV populations. Importantly, localization of the above proteins in EVs was reduced upon inhibition of palmitoylation in the producing cells. Our results suggest that this post-translational modification may play a role in the sorting of the EV-bound secretome and possibly enable selective detection of disease biomarkers.
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Affiliation(s)
- Javier Mariscal
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tatyana Vagner
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Minhyung Kim
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bo Zhou
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Chin
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mandana Zandian
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael R. Freeman
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Sungyong You
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andries Zijlstra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Yang
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Dolores Di Vizio
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Philippe JM, Jenkins PM. Spatial organization of palmitoyl acyl transferases governs substrate localization and function. Mol Membr Biol 2020; 35:60-75. [PMID: 31969037 DOI: 10.1080/09687688.2019.1710274] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein palmitoylation is a critical posttranslational modification that regulates protein trafficking, localization, stability, sorting and function. In mammals, addition of this lipid modification onto proteins is mediated by a family of 23 palmitoyl acyl transferases (PATs). PATs often palmitoylate substrates in a promiscuous manner, precluding our understanding of how these enzymes achieve specificity for their substrates. Despite generous efforts to identify consensus motifs defining PAT-substrate specificity, it remains to be determined whether additional factors beyond interaction motifs, such as local palmitoylation, participate in PAT-substrate selection. In this review, we emphasize the role of local palmitoylation, in which substrates are palmitoylated and trapped in the same subcellular compartments as their PATs, as a mechanism of enzyme-substrate specificity. We focus here on non-Golgi-localized PATs, as physical proximity to their substrates enables them to engage in local palmitoylation, compared to Golgi PATs, which often direct trafficking of their substrates elsewhere. PAT subcellular localization may be an under-recognized, yet important determinant of PAT-substrate specificity that may work in conjunction or completely independently of interaction motifs. We also discuss some current hypotheses about protein motifs that contribute to localization of non-Golgi-localized PATs, important for the downstream targeting of their substrates.
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Affiliation(s)
- Julie M Philippe
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Paul M Jenkins
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Psychiatry, University of Michigan Medical School, Ann Arbor, MI, USA
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Salaun C, Greaves J, Tomkinson NCO, Chamberlain LH. The linker domain of the SNARE protein SNAP25 acts as a flexible molecular spacer that ensures efficient S-acylation. J Biol Chem 2020; 295:7501-7515. [PMID: 32317281 PMCID: PMC7247313 DOI: 10.1074/jbc.ra120.012726] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/15/2020] [Indexed: 12/14/2022] Open
Abstract
S-Acylation of the SNARE protein SNAP25 (synaptosome-associated protein of 25 kDa) is mediated by a subset of Golgi zinc finger DHHC-type palmitoyltransferase (zDHHC) enzymes, particularly zDHHC17. The ankyrin repeat domain of zDHHC17 interacts with a short linear motif known as the zDHHC ankyrin repeat-binding motif (zDABM) in SNAP25 (112VVASQP117), which is downstream of its S-acylated, cysteine-rich domain (85CGLCVCPC92). Here, we investigated the importance of a flexible linker region (amino acids 93-111, referred to hereafter as the "mini-linker" region) that separates the zDABM and S-acylated cysteines in SNAP25. Shortening the mini-linker did not affect the SNAP25-zDHHC17 interaction but blocked S-acylation. Insertion of additional flexible glycine-serine repeats had no effect on S-acylation, but extended and rigid alanine-proline repeats perturbed it. A SNAP25 mutant in which the mini-linker region was substituted with a flexible glycine-serine linker of the same length underwent efficient S-acylation. Furthermore, this mutant displayed the same intracellular localization as WT SNAP25, indicating that the amino acid composition of the mini-linker is not important for SNAP25 localization. Using the results of previous peptide array experiments, we generated a SNAP25 mutant predicted to have a higher-affinity zDABM. This mutant interacted with zDHHC17 more strongly but was S-acylated with reduced efficiency in HEK293T cells, implying that a lower-affinity interaction of the SNAP25 zDABM with zDHHC17 is optimal for S-acylation efficiency. These results show that amino acids 93-111 in SNAP25 act as a flexible molecular spacer that ensures efficient coupling of the SNAP25-zDHHC17 interaction and S-acylation of SNAP25.
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Affiliation(s)
- Christine Salaun
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom.
| | - Jennifer Greaves
- Faculty of Health and Life Sciences, Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom.
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61
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Hayashi T. Post-translational palmitoylation of ionotropic glutamate receptors in excitatory synaptic functions. Br J Pharmacol 2020; 178:784-797. [PMID: 32159240 DOI: 10.1111/bph.15050] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/07/2020] [Accepted: 03/05/2020] [Indexed: 12/17/2022] Open
Abstract
In the mammalian CNS, glutamate is the major excitatory neurotransmitter. Ionotropic glutamate receptors (iGluRs) are responsible for the glutamate-mediated postsynaptic excitation of neurons. Regulation of glutamatergic synapses is critical for higher brain functions including neural communication, memory formation, learning, emotion, and behaviour. Many previous studies have shown that post-translational protein S-palmitoylation, the only reversible covalent attachment of lipid to protein, regulates synaptic expression, intracellular localization, and membrane trafficking of iGluRs and their scaffolding proteins in neurons. This modification mechanism is extremely conserved in the vertebrate lineages. The failure of appropriate palmitoylation-dependent regulation of iGluRs leads to hyperexcitability that reduces the maintenance of network stability, resulting in brain disorders, such as epileptic seizures. This review summarizes advances in the study of palmitoylation of iGluRs, especially AMPA receptors and NMDA receptors, and describes the current understanding of palmitoylation-dependent regulation of excitatory glutamatergic synapses. LINKED ARTICLES: This article is part of a themed issue on Neurochemistry in Japan. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.4/issuetoc.
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Affiliation(s)
- Takashi Hayashi
- Section of Cellular Biochemistry, Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
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62
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Ticho AL, Malhotra P, Manzella CR, Dudeja PK, Saksena S, Gill RK, Alrefai WA. S-acylation modulates the function of the apical sodium-dependent bile acid transporter in human cells. J Biol Chem 2020; 295:4488-4497. [PMID: 32071081 DOI: 10.1074/jbc.ra119.011032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/06/2020] [Indexed: 01/16/2023] Open
Abstract
The ileal apical sodium-dependent bile acid transporter (ASBT) is crucial for the enterohepatic circulation of bile acids. ASBT function is rapidly regulated by several posttranslational modifications. One reversible posttranslational modification is S-acylation, involving the covalent attachment of fatty acids to cysteine residues in proteins. However, whether S-acylation affects ASBT function and membrane expression has not been determined. Using the acyl resin-assisted capture method, we found that the majority of ASBT (∼80%) was S-acylated in ileal brush border membrane vesicles from human organ donors, as well as in HEK293 cells stably transfected with ASBT (2BT cells). Metabolic labeling with alkyne-palmitic acid (100 μm for 15 h) also showed that ASBT is S-acylated in 2BT cells. Incubation with the acyltransferase inhibitor 2-bromopalmitate (25 μm for 15 h) significantly reduced ASBT S-acylation, function, and levels on the plasma membrane. Treatment of 2BT cells with saturated palmitic acid (100 μm for 15 h) increased ASBT function, whereas treatment with unsaturated oleic acid significantly reduced ASBT function. Metabolic labeling with alkyne-oleic acid (100 μm for 15 h) revealed that oleic acid attaches to ASBT, suggesting that unsaturated fatty acids may decrease ASBT's function via a direct covalent interaction with ASBT. We also identified Cys-314 as a potential S-acylation site. In conclusion, these results provide evidence that S-acylation is involved in the modulation of ASBT function. These findings underscore the potential for unsaturated fatty acids to reduce ASBT function, which may be useful in disorders in which bile acid toxicity is implicated.
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Affiliation(s)
- Alexander L Ticho
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Illinois 60612-7332
| | - Pooja Malhotra
- Division of Gastroenterology and Hepatology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Illinois 60612-7332
| | - Christopher R Manzella
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Illinois 60612-7332
| | - Pradeep K Dudeja
- Division of Gastroenterology and Hepatology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Illinois 60612-7332.,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
| | - Seema Saksena
- Division of Gastroenterology and Hepatology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Illinois 60612-7332.,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
| | - Ravinder K Gill
- Division of Gastroenterology and Hepatology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Illinois 60612-7332
| | - Waddah A Alrefai
- Division of Gastroenterology and Hepatology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Illinois 60612-7332 .,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
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63
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Stix R, Song J, Banerjee A, Faraldo-Gómez JD. DHHC20 Palmitoyl-Transferase Reshapes the Membrane to Foster Catalysis. Biophys J 2019; 118:980-988. [PMID: 31858978 DOI: 10.1016/j.bpj.2019.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/22/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
Cysteine palmitoylation, a form of S-acylation, is a key posttranslational modification in cellular signaling. This type of reversible lipidation occurs in both plasma and organellar membranes, and is catalyzed by a family of integral membrane proteins known as DHHC acyltransferases. The first step in the S-acylation process is the recognition of free acyl coenzyme A (acyl-CoA) from the lipid bilayer. The DHHC enzyme then becomes autoacylated at a site defined by a conserved Asp-His-His-Cys motif. This reaction entails ionization of the catalytic Cys. Intriguingly, in known DHHC structures, this catalytic Cys appears to be exposed to the hydrophobic interior of the lipid membrane, which would be highly unfavorable for a negatively charged nucleophile, thus hindering autoacylation. Here, we use biochemical and computational methods to reconcile these seemingly contradictory facts. First, we experimentally demonstrate that human DHHC20 is active when reconstituted in POPC nanodiscs. Microsecond-long all-atom molecular dynamics simulations are then calculated for human DHHC20 and for different acyl-CoA forms, also in a POPC membrane. Strikingly, we observe that human DHHC20 induces a drastic deformation in the membrane, particularly on the cytoplasmic side, where autoacylation occurs. As a result, the catalytic Cys becomes hydrated and optimally positioned to encounter the cleavage site in acyl-CoA. In summary, we hypothesize that DHHC enzymes locally reshape the membrane to foster a morphology that is specifically adapted for acyl-CoA recognition and autoacylation.
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Affiliation(s)
- Robyn Stix
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland; Unit on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - James Song
- Unit on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Anirban Banerjee
- Unit on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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64
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Karouzaki S, Peta C, Tsirimonaki E, Mangoura D. PKCε-dependent H-Ras activation encompasses the recruitment of the RasGEF SOS1 and of the RasGAP neurofibromin in the lipid rafts of embryonic neurons. Neurochem Int 2019; 131:104582. [PMID: 31629778 DOI: 10.1016/j.neuint.2019.104582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/27/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023]
Abstract
The spatial organization of plasma membrane proteins is a key factor in the generation of distinct signal outputs, especially for PKC/Ras/ERK signalling. Regulation of activation of the membrane-bound Ras, critical for neuronal differentiation and highly specialized functions, is controlled by exchanges in nucleotides catalyzed by nucleotide exchange factors (GEFs) for GTP loading and Ras activation, and by Ras GTPase Activated Proteins (RasGAPs) that lead to activation of the intrinsic GTPase activity of Ras and thus its inactivation. PKCs are potent Ras activators yet the mechanistic details of these interactions, or the involvement of specific PKC isoforms are now beginning to be addressed. Even less known is the topology where RasGAPs terminate Ras activation. Towards this aim, we isolated lipid rafts from chick embryo neural tissue and primary neuronal cultures when PKCε is the prominent isoform and in combination with in vitro kinase assays, we now show that, in response the PKCε-specific activating peptide ψεRACK, an activated PKCε is recruited to lipid rafts; similar mobility was established when PKCε was physiologically activated with the Cannabinoid receptor 1 (CB1) agonist methanandamide. Activation of H-Ras for both agents was then established for the first time using in vivo RasGAP activity assays, which showed similar temporal profiles of activation and lateral mobility. Moreover, we found that the GEF SOS1, and the major neuronal RasGAP neurofibromin, a specific PKCε substrate, were both transiently significantly enriched in the rafts. Finally, our in silico analysis revealed a highly probable, conserved palmitoylation site adjacent to a CARC motif on neurofibromin, both of which are included only in the RasGAP related domain type I (GRDI) with the known high H-RasGAP activity. Taken together, these results suggest that PKCε activation regulates the spatial plasma membrane enrichments of both SOS1 and neurofibromin, thus controlling the output of activated H-Ras available for downstream signalling in neurons.
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Affiliation(s)
- Sophia Karouzaki
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Efesiou, Athens, 11527, Greece
| | - Charoula Peta
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Efesiou, Athens, 11527, Greece
| | - Emmanouella Tsirimonaki
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Efesiou, Athens, 11527, Greece
| | - Dimitra Mangoura
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Efesiou, Athens, 11527, Greece.
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65
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Amaravadi RK, Kimmelman AC, Debnath J. Targeting Autophagy in Cancer: Recent Advances and Future Directions. Cancer Discov 2019; 9:1167-1181. [PMID: 31434711 DOI: 10.1158/2159-8290.cd-19-0292] [Citation(s) in RCA: 525] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/31/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022]
Abstract
Autophagy, a multistep lysosomal degradation pathway that supports nutrient recycling and metabolic adaptation, has been implicated as a process that regulates cancer. Although autophagy induction may limit the development of tumors, evidence in mouse models demonstrates that autophagy inhibition can limit the growth of established tumors and improve response to cancer therapeutics. Certain cancer genotypes may be especially prone to autophagy inhibition. Different strategies for autophagy modulation may be needed depending on the cancer context. Here, we review new advances in the molecular control of autophagy, the role of selective autophagy in cancer, and the role of autophagy within the tumor microenvironment and tumor immunity. We also highlight clinical efforts to repurpose lysosomal inhibitors, such as hydroxychloroquine, as anticancer agents that block autophagy, as well as the development of more potent and specific autophagy inhibitors for cancer treatment, and review future directions for autophagy research. SIGNIFICANCE: Autophagy plays a complex role in cancer, but autophagy inhibition may be an effective therapeutic strategy in advanced cancer. A deeper understanding of autophagy within the tumor microenvironment has enabled the development of novel inhibitors and clinical trial strategies. Challenges and opportunities remain to identify patients most likely to benefit from this approach.
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Affiliation(s)
- Ravi K Amaravadi
- Abramson Cancer Center and the Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Alec C Kimmelman
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Jayanta Debnath
- Department of Pathology, University of California, San Francisco, California
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66
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Shah BS, Shimell JJ, Bamji SX. Regulation of dendrite morphology and excitatory synapse formation by zDHHC15. J Cell Sci 2019; 132:jcs.230052. [PMID: 31189538 PMCID: PMC6633394 DOI: 10.1242/jcs.230052] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/28/2019] [Indexed: 12/11/2022] Open
Abstract
Protein palmitoylation is the most common post-translational lipid modification in the brain and is mediated by a family of 24 zDHHC enzymes. There has been growing interest in zDHHCs due to mounting evidence that these enzymes play key roles in the development and function of neuronal connections, and the fact that a number of zDHHCs have been associated with neurodevelopmental and neurodegenerative diseases. Loss-of-function variants in several zDHHCs, including zDHHC15, have been identified in patients with intellectual disabilities; however, the function of zDHHC15 in the brain has not been well studied. Here, we demonstrate that knocking down zDHHC15 in primary rat hippocampal cultures reduces dendritic outgrowth and arborization, as well as spine maturation. Moreover, knockdown of zDHHC15 reduces palmitoylation of PSD-95 and its trafficking into dendrites, resulting in an overall decrease in the density of excitatory synapses being formed onto mutant cells. Summary: Disruption of zDHHC15 function in primary hippocampal cultures reduces dendritic outgrowth, spine maturation, excitatory synapse density and trafficking of PSD-95 into dendrites.
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Affiliation(s)
- Bhavin S Shah
- Department of Cellular & Physiological Sciences & the Brain Research Centre, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., V6T-1Z3, Canada
| | - Jordan J Shimell
- Department of Cellular & Physiological Sciences & the Brain Research Centre, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., V6T-1Z3, Canada
| | - Shernaz X Bamji
- Department of Cellular & Physiological Sciences & the Brain Research Centre, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., V6T-1Z3, Canada
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67
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AMPAR Palmitoylation Tunes Synaptic Strength: Implications for Synaptic Plasticity and Disease. J Neurosci 2019; 39:5040-5043. [PMID: 31243093 DOI: 10.1523/jneurosci.0055-19.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 11/21/2022] Open
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68
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Cell contact and Nf2/Merlin-dependent regulation of TEAD palmitoylation and activity. Proc Natl Acad Sci U S A 2019; 116:9877-9882. [PMID: 31043565 DOI: 10.1073/pnas.1819400116] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Hippo pathway is involved in regulating contact inhibition of proliferation and organ size control and responds to various physical and biochemical stimuli. It is a kinase cascade that negatively regulates the activity of cotranscription factors YAP and TAZ, which interact with DNA binding transcription factors including TEAD and activate the expression of target genes. In this study, we show that the palmitoylation of TEAD, which controls the activity and stability of TEAD proteins, is actively regulated by cell density independent of Lats, the key kinase of the Hippo pathway. The expression of fatty acid synthase and acetyl-CoA carboxylase involved in de novo biosynthesis of palmitate is reduced by cell density in an Nf2/Merlin-dependent manner. Depalmitoylation of TEAD is mediated by depalmitoylases including APT2 and ABHD17A. Palmitoylation-deficient TEAD4 mutant is unstable and degraded by proteasome through the activity of the E3 ubiquitin ligase CHIP. These findings show that TEAD activity is tightly controlled through the regulation of palmitoylation and stability via the orchestration of FASN, depalmitoylases, and E3 ubiquitin ligase in response to cell contact.
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69
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Sanders SS, De Simone FI, Thomas GM. mTORC1 Signaling Is Palmitoylation-Dependent in Hippocampal Neurons and Non-neuronal Cells and Involves Dynamic Palmitoylation of LAMTOR1 and mTOR. Front Cell Neurosci 2019; 13:115. [PMID: 31001086 PMCID: PMC6454084 DOI: 10.3389/fncel.2019.00115] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/08/2019] [Indexed: 11/13/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) Complex 1 (mTORC1) controls growth and proliferation of non-neuronal cells, while during neuronal development mTORC1 responds to glutamate and neurotrophins to promote neuronal migration and dendritic arborization. Recent studies reveal that mTORC1 signaling complexes are assembled on lysosomal membranes, but how mTORC1 membrane targeting is regulated is not fully clear. Our examination of palmitoyl-proteomic databases and additional bioinformatic analyses revealed that several mTORC1 proteins are predicted to undergo covalent modification with the lipid palmitate. This process, palmitoylation, can dynamically target proteins to specific membranes but its roles in mTORC1 signaling are not well described. Strikingly, we found that acute pharmacological inhibition of palmitoylation prevents amino acid-dependent mTORC1 activation in HEK293T cells and brain-derived neurotrophic factor (BDNF)-dependent mTORC1 activation in hippocampal neurons. We sought to define the molecular basis for this finding and found that the mTORC1 proteins LAMTOR1 and mTOR itself are directly palmitoylated, while several other mTORC1 proteins are not palmitoylated, despite strong bioinformatic prediction. Interestingly, palmitoylation of LAMTOR1, whose anchoring on lysosomal membranes is important for mTORC1 signaling, was rapidly increased prior to mTORC1 activation. In contrast, mTOR palmitoylation was decreased by stimuli that activate mTORC1. These findings reveal that specific key components of the mTOR pathway are dynamically palmitoylated, suggesting that palmitoylation is not merely permissive for mTOR activation but is instead actively involved in mTORC1-dependent signaling.
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Affiliation(s)
- Shaun S Sanders
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Francesca I De Simone
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Gareth M Thomas
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States.,Department of Anatomy and Cell Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
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70
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Strassburger K, Kang E, Teleman AA. Drosophila ZDHHC8 palmitoylates scribble and Ras64B and controls growth and viability. PLoS One 2019; 14:e0198149. [PMID: 30735487 PMCID: PMC6368284 DOI: 10.1371/journal.pone.0198149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Abstract
Palmitoylation is an important posttranslational modification regulating diverse cellular functions. Consequently, aberrant palmitoylation can lead to diseases such as neuronal disorders or cancer. In humans there are roughly one hundred times more palmitoylated proteins than enzymes catalyzing palmitoylation (palmitoyltransferases). Therefore, it is an important challenge to establish the links between palmitoyltransferases and their targets. From publicly available data, we find that expression of human ZDHHC8 correlates significantly with cancer survival. To elucidate the organismal function of ZDHHC8, we study the Drosophila ortholog of hZDHHC8, CG34449/dZDHHC8. Knockdown of dZDHHC8 causes tissue overgrowth while dZDHHC8 mutants are larval lethal. We provide a list of 159 palmitoylated proteins in Drosophila and present data suggesting that scribble and Ras64B are targets of dZDHHC8.
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Affiliation(s)
- Katrin Strassburger
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | - Evangeline Kang
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | - Aurelio A. Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
- * E-mail:
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71
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Matt L, Kim K, Chowdhury D, Hell JW. Role of Palmitoylation of Postsynaptic Proteins in Promoting Synaptic Plasticity. Front Mol Neurosci 2019; 12:8. [PMID: 30766476 PMCID: PMC6365469 DOI: 10.3389/fnmol.2019.00008] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/10/2019] [Indexed: 12/19/2022] Open
Abstract
Many postsynaptic proteins undergo palmitoylation, the reversible attachment of the fatty acid palmitate to cysteine residues, which influences trafficking, localization, and protein interaction dynamics. Both palmitoylation by palmitoyl acyl transferases (PAT) and depalmitoylation by palmitoyl-protein thioesterases (PPT) is regulated in an activity-dependent, localized fashion. Recently, palmitoylation has received attention for its pivotal contribution to various forms of synaptic plasticity, the dynamic modulation of synaptic strength in response to neuronal activity. For instance, palmitoylation and depalmitoylation of the central postsynaptic scaffold protein postsynaptic density-95 (PSD-95) is important for synaptic plasticity. Here, we provide a comprehensive review of studies linking palmitoylation of postsynaptic proteins to synaptic plasticity.
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Affiliation(s)
- Lucas Matt
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Tübingen, Germany
| | - Karam Kim
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Dhrubajyoti Chowdhury
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Johannes W Hell
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
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72
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Progress in targeting RAS with small molecule drugs. Biochem J 2019; 476:365-374. [PMID: 30705085 DOI: 10.1042/bcj20170441] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 01/01/2023]
Abstract
RAS proteins have traditionally been deemed undruggable, as they do not possess an active site to which small molecules could bind but small molecules that target one form of oncogenic RAS, KRAS G12C, are already in preclinical and clinical trials, and several other compounds that bind to different RAS proteins at distinct sites are in earlier stage evaluation. KRAS is the major clinical target, as it is by far the most significant form of RAS in terms of cancer incidence. Unfortunately, KRAS exists in two isoforms, each with unique biochemical properties. This complicates efforts to target KRAS specifically. KRAS is also a member of a family of closely related proteins, which share similar effector-binding regions and G-domains, further increasing the challenge of specificity. Nevertheless, progress is being made, driven by new drug discovery technologies and creative science.
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73
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Kathayat RS, Dickinson BC. Measuring S-Depalmitoylation Activity In Vitro and In Live Cells with Fluorescent Probes. Methods Mol Biol 2019; 2009:99-109. [PMID: 31152398 PMCID: PMC7240838 DOI: 10.1007/978-1-4939-9532-5_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
S-palmitoylation is a reversible lipid posttranslational modification (PTM) that can mediate protein localization, trafficking, interaction with membranes, and a host of other biophysical characteristics. Over the past decade, a suite of chemoproteomic strategies have uncovered the breadth of S-palmitoylation, revealing widespread susceptibility to modification by this PTM throughout the human proteome. A focal point of research toward understanding the role of S-palmitoylation in varied cellular processes has focused on understanding how "writer" and "eraser" proteins function together to control the levels of S-palmitoylation of target proteins. The spatial and temporal regulation of S-palmitoylation by its "erasers"-acyl protein thioesterases (APTs)-is not fully understood. Tools which enable monitoring of the activity levels of the APTs in real-time in live cells illuminate how spatial control of these enzymes redecorate the lipidation state of the local proteome. To this end, we have developed fluorescence-based depalmitoylation probes (DPPs), which report S-depalmitoylase activity in live cells. Using DPPs, we have demonstrated that S-depalmitoylase activity changes in response to growth factor stimulation, unveiling potential regulation of cell growth and metabolism by APTs. Additionally, we recently discovered APTs in mitochondria using targeted DPPs, indicating new roles for S-depalmitoylation in this critical cellular compartment. Here, we present detailed protocols on how to carry out in vitro S-depalmitoylase activity assays and live cell fluorescence imaging employing the growing DPP toolbox.
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74
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Detection of S-palmitoylated Proteins in Mouse Heart Tissue Based on Different Precipitation Methods. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(18)61134-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rudd AK, Brea RJ, Devaraj NK. Amphiphile-Mediated Depalmitoylation of Proteins in Living Cells. J Am Chem Soc 2018; 140:17374-17378. [PMID: 30516377 DOI: 10.1021/jacs.8b10806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Post-translational S-palmitoylation plays a central role in protein localization, trafficking, stability, aggregation, and cell signaling. Dysregulation of palmitoylation pathways in cells can alter protein function and is the cause of several diseases. Considering the biological and clinical importance of S-palmitoylation, tools for direct, in vivo modulation of this lipid modification would be extremely valuable. Here, we describe a method for the cleavage of native S-palmitoyl groups from proteins in living cells. Using a cell permeable, cysteine-functionalized amphiphile, we demonstrate the direct depalmitoylation of cellular proteins. We show that amphiphile-mediated depalmitoylation (AMD) can effectively cleave S-palmitoyl groups from the native GTPase HRas and successfully depalmitoylate mislocalized proteins in an infantile neuronal ceroid lipofuscinosis (INCL) disease model. AMD enables direct and facile depalmitoylation of proteins in live cells and has potential therapeutic applications for diseases such as INCL, where native protein thioesterase activity is deficient.
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Affiliation(s)
- Andrew K Rudd
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Roberto J Brea
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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76
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Spinelli M, Fusco S, Grassi C. Nutrient-Dependent Changes of Protein Palmitoylation: Impact on Nuclear Enzymes and Regulation of Gene Expression. Int J Mol Sci 2018; 19:ijms19123820. [PMID: 30513609 PMCID: PMC6320809 DOI: 10.3390/ijms19123820] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/22/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022] Open
Abstract
Diet is the main environmental stimulus chronically impinging on the organism throughout the entire life. Nutrients impact cells via a plethora of mechanisms including the regulation of both protein post-translational modifications and gene expression. Palmitoylation is the most-studied protein lipidation, which consists of the attachment of a molecule of palmitic acid to residues of proteins. S-palmitoylation is a reversible cysteine modification finely regulated by palmitoyl-transferases and acyl-thioesterases that is involved in the regulation of protein trafficking and activity. Recently, several studies have demonstrated that diet-dependent molecules such as insulin and fatty acids may affect protein palmitoylation. Here, we examine the role of protein palmitoylation on the regulation of gene expression focusing on the impact of this modification on the activity of chromatin remodeler enzymes, transcription factors, and nuclear proteins. We also discuss how this physiological phenomenon may represent a pivotal mechanism underlying the impact of diet and nutrient-dependent signals on human diseases.
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Affiliation(s)
- Matteo Spinelli
- Institute of Human Physiology, Università Cattolica del Sacro Cuore, Rome 00168, Italy.
| | - Salvatore Fusco
- Institute of Human Physiology, Università Cattolica del Sacro Cuore, Rome 00168, Italy.
- Fondazione Policlinico Universitario A. Gemelli IRCSS, Rome 00168, Italy.
| | - Claudio Grassi
- Institute of Human Physiology, Università Cattolica del Sacro Cuore, Rome 00168, Italy.
- Fondazione Policlinico Universitario A. Gemelli IRCSS, Rome 00168, Italy.
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77
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Ahearn I, Zhou M, Philips MR. Posttranslational Modifications of RAS Proteins. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031484. [PMID: 29311131 DOI: 10.1101/cshperspect.a031484] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The three human RAS genes encode four proteins that play central roles in oncogenesis by acting as binary molecular switches that regulate signaling pathways for growth and differentiation. Each is subject to a set of posttranslational modifications (PTMs) that modify their activity or are required for membrane targeting. The enzymes that catalyze the various PTMs are potential targets for anti-RAS drug discovery. The PTMs of RAS proteins are the focus of this review.
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Affiliation(s)
- Ian Ahearn
- Department of Medicine, Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016
| | - Mo Zhou
- Department of Medicine, Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016
| | - Mark R Philips
- Department of Medicine, Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016
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78
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Ko PJ, Dixon SJ. Protein palmitoylation and cancer. EMBO Rep 2018; 19:embr.201846666. [PMID: 30232163 DOI: 10.15252/embr.201846666] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/24/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Protein S-palmitoylation is a reversible post-translational modification that alters the localization, stability, and function of hundreds of proteins in the cell. S-palmitoylation is essential for the function of both oncogenes (e.g., NRAS and EGFR) and tumor suppressors (e.g., SCRIB, melanocortin 1 receptor). In mammalian cells, the thioesterification of palmitate to internal cysteine residues is catalyzed by 23 Asp-His-His-Cys (DHHC)-family palmitoyl S-acyltransferases while the removal of palmitate is catalyzed by serine hydrolases, including acyl-protein thioesterases (APTs). These enzymes modulate the function of important oncogenes and tumor suppressors and often display altered expression patterns in cancer. Targeting S-palmitoylation or the enzymes responsible for palmitoylation dynamics may therefore represent a candidate therapeutic strategy for certain cancers.
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Affiliation(s)
- Pin-Joe Ko
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA, USA
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79
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Romancino DP, Buffa V, Caruso S, Ferrara I, Raccosta S, Notaro A, Campos Y, Noto R, Martorana V, Cupane A, Giallongo A, d'Azzo A, Manno M, Bongiovanni A. Palmitoylation is a post-translational modification of Alix regulating the membrane organization of exosome-like small extracellular vesicles. Biochim Biophys Acta Gen Subj 2018; 1862:2879-2887. [PMID: 30251702 DOI: 10.1016/j.bbagen.2018.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/04/2018] [Accepted: 09/06/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Virtually all cell types have the capacity to secrete nanometer-sized extracellular vesicles, which have emerged in recent years as potent signal transducers and cell-cell communicators. The multifunctional protein Alix is a bona fide exosomal regulator and skeletal muscle cells can release Alix-positive nano-sized extracellular vesicles, offering a new paradigm for understanding how myofibers communicate within skeletal muscle and with other organs. S-palmitoylation is a reversible lipid post-translational modification, involved in different biological processes, such as the trafficking of membrane proteins, achievement of stable protein conformations, and stabilization of protein interactions. METHODS Here, we have used an integrated biochemical-biophysical approach to determine whether S-palmitoylation contributes to the regulation of extracellular vesicle production in skeletal muscle cells. RESULTS We ascertained that Alix is S-palmitoylated and that this post-translational modification influences its protein-protein interaction with CD9, a member of the tetraspanin protein family. Furthermore, we showed that the structural organization of the lipid bilayer of the small (nano-sized) extracellular vesicle membrane with altered palmitoylation is qualitatively different compared to mock control vesicles. CONCLUSIONS We propose that S-palmitoylation regulates the function of Alix in facilitating the interactions among extracellular vesicle-specific regulators and maintains the proper structural organization of exosome-like extracellular vesicle membranes. GENERAL SIGNIFICANCE Beyond its biological relevance, our study also provides the means for a comprehensive structural characterization of EVs.
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Affiliation(s)
- Daniele P Romancino
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR) of Italy, Palermo, Italy
| | - Valentina Buffa
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR) of Italy, Palermo, Italy
| | - Stefano Caruso
- UMR-1162, Functional Genomics of Solid Tumors, Inserm, Paris 1162, France
| | - Ines Ferrara
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR) of Italy, Palermo, Italy
| | - Samuele Raccosta
- Institute of Biophysics (IBF), National Research Council (CNR) of Italy, Palermo, Italy
| | - Antonietta Notaro
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR) of Italy, Palermo, Italy
| | - Yvan Campos
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rosina Noto
- Institute of Biophysics (IBF), National Research Council (CNR) of Italy, Palermo, Italy
| | - Vincenzo Martorana
- Institute of Biophysics (IBF), National Research Council (CNR) of Italy, Palermo, Italy
| | - Antonio Cupane
- Department of Physics and Chemistry, University of Palermo, Italy
| | - Agata Giallongo
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR) of Italy, Palermo, Italy
| | - Alessandra d'Azzo
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mauro Manno
- Institute of Biophysics (IBF), National Research Council (CNR) of Italy, Palermo, Italy
| | - Antonella Bongiovanni
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR) of Italy, Palermo, Italy.
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80
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Batista CM, Kessler RL, Eger I, Soares MJ. Treatment of Trypanosoma cruzi with 2-bromopalmitate alters morphology, endocytosis, differentiation and infectivity. BMC Cell Biol 2018; 19:19. [PMID: 30170543 PMCID: PMC6119340 DOI: 10.1186/s12860-018-0170-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Abstract
Background The palmitate analogue 2-bromopalmitate (2-BP) is a non-selective membrane tethered cysteine alkylator of many membrane-associated enzymes that in the last years emerged as a general inhibitor of protein S-palmitoylation. Palmitoylation is a post-translational protein modification that adds palmitic acid to a cysteine residue through a thioester linkage, promoting membrane localization, protein stability, regulation of enzymatic activity, and the epigenetic regulation of gene expression. Little is known on such important process in the pathogenic protozoan Trypanosoma cruzi, the etiological agent of Chagas disease. Results The effect of 2-BP was analyzed on different developmental forms of Trypanosoma cruzi. The IC50/48 h value for culture epimastigotes was estimated as 130 μM. The IC50/24 h value for metacyclic trypomastigotes was 216 nM, while for intracellular amastigotes it was 242 μM and for cell derived trypomasigotes was 262 μM (IC50/24 h). Our data showed that 2-BP altered T. cruzi: 1) morphology, as assessed by bright field, scanning and transmission electron microscopy; 2) mitochondrial membrane potential, as shown by flow cytometry after incubation with rhodamine-123; 3) endocytosis, as seen after incubation with transferrin or albumin and analysis by flow cytometry/fluorescence microscopy; 4) in vitro metacyclogenesis; and 5) infectivity, as shown by host cell infection assays. On the other hand, lipid stress by incubation with palmitate did not alter epimastigote growth, metacyclic trypomastigotes viability or trypomastigote infectivity. Conclusion Our results indicate that 2-BP inhibits key cellular processes of T. cruzi that may be regulated by palmitoylation of vital proteins and suggest a metacyclic trypomastigote unique target dependency during the parasite development. Electronic supplementary material The online version of this article (10.1186/s12860-018-0170-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cassiano Martin Batista
- Laboratory of Cell Biology, Carlos Chagas Institute/Fiocruz-PR, 81310-020 Curitiba, Paraná, Brazil
| | - Rafael Luis Kessler
- Laboratory of Functional Genomics, Carlos Chagas Institute/Fiocruz-PR, 81310-020 Curitiba, Paraná, Brazil.,Mammalian Cell Biotechnology Laboratory, Molecular Biology Institute of Paraná (IBMP), 81310-020 Curitiba, Paraná, Brazil
| | - Iriane Eger
- Department of General Biology, State University of Ponta Grossa, 84010-290 Ponta Grossa, Paraná, Brazil
| | - Maurilio José Soares
- Laboratory of Cell Biology, Carlos Chagas Institute/Fiocruz-PR, 81310-020 Curitiba, Paraná, Brazil.
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81
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Zaballa ME, van der Goot FG. The molecular era of protein S-acylation: spotlight on structure, mechanisms, and dynamics. Crit Rev Biochem Mol Biol 2018; 53:420-451. [DOI: 10.1080/10409238.2018.1488804] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- María-Eugenia Zaballa
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - F. Gisou van der Goot
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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82
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Rana MS, Kumar P, Lee CJ, Verardi R, Rajashankar KR, Banerjee A. Fatty acyl recognition and transfer by an integral membrane S-acyltransferase. Science 2018; 359:eaao6326. [PMID: 29326245 PMCID: PMC6317078 DOI: 10.1126/science.aao6326] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/07/2017] [Indexed: 12/11/2022]
Abstract
DHHC (Asp-His-His-Cys) palmitoyltransferases are eukaryotic integral membrane enzymes that catalyze protein palmitoylation, which is important in a range of physiological processes, including small guanosine triphosphatase (GTPase) signaling, cell adhesion, and neuronal receptor scaffolding. We present crystal structures of two DHHC palmitoyltransferases and a covalent intermediate mimic. The active site resides at the membrane-cytosol interface, which allows the enzyme to catalyze thioester-exchange chemistry by using fatty acyl-coenzyme A and explains why membrane-proximal cysteines are candidates for palmitoylation. The acyl chain binds in a cavity formed by the transmembrane domain. We propose a mechanism for acyl chain-length selectivity in DHHC enzymes on the basis of cavity mutants with preferences for shorter and longer acyl chains.
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Affiliation(s)
- Mitra S. Rana
- Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human, Development, National Institutes of Health, Bethesda, MD-20892
| | - Pramod Kumar
- Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human, Development, National Institutes of Health, Bethesda, MD-20892
| | - Chul-Jin Lee
- Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human, Development, National Institutes of Health, Bethesda, MD-20892
| | - Raffaello Verardi
- Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human, Development, National Institutes of Health, Bethesda, MD-20892
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Dept. of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL-60439
| | - Anirban Banerjee
- Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human, Development, National Institutes of Health, Bethesda, MD-20892
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83
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Rebecca VW, Nicastri MC, McLaughlin N, Fennelly C, McAfee Q, Ronghe A, Nofal M, Lim CY, Witze E, Chude CI, Zhang G, Alicea GM, Piao S, Murugan S, Ojha R, Levi SM, Wei Z, Barber-Rotenberg JS, Murphy ME, Mills GB, Lu Y, Rabinowitz J, Marmorstein R, Liu Q, Liu S, Xu X, Herlyn M, Zoncu R, Brady DC, Speicher DW, Winkler JD, Amaravadi RK. A Unified Approach to Targeting the Lysosome's Degradative and Growth Signaling Roles. Cancer Discov 2017; 7:1266-1283. [PMID: 28899863 PMCID: PMC5833978 DOI: 10.1158/2159-8290.cd-17-0741] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/24/2017] [Accepted: 09/06/2017] [Indexed: 01/01/2023]
Abstract
Lysosomes serve dual roles in cancer metabolism, executing catabolic programs (i.e., autophagy and macropinocytosis) while promoting mTORC1-dependent anabolism. Antimalarial compounds such as chloroquine or quinacrine have been used as lysosomal inhibitors, but fail to inhibit mTOR signaling. Further, the molecular target of these agents has not been identified. We report a screen of novel dimeric antimalarials that identifies dimeric quinacrines (DQ) as potent anticancer compounds, which concurrently inhibit mTOR and autophagy. Central nitrogen methylation of the DQ linker enhances lysosomal localization and potency. An in situ photoaffinity pulldown identified palmitoyl-protein thioesterase 1 (PPT1) as the molecular target of DQ661. PPT1 inhibition concurrently impairs mTOR and lysosomal catabolism through the rapid accumulation of palmitoylated proteins. DQ661 inhibits the in vivo tumor growth of melanoma, pancreatic cancer, and colorectal cancer mouse models and can be safely combined with chemotherapy. Thus, lysosome-directed PPT1 inhibitors represent a new approach to concurrently targeting mTORC1 and lysosomal catabolism in cancer.Significance: This study identifies chemical features of dimeric compounds that increase their lysosomal specificity, and a new molecular target for these compounds, reclassifying these compounds as targeted therapies. Targeting PPT1 blocks mTOR signaling in a manner distinct from catalytic inhibitors, while concurrently inhibiting autophagy, thereby providing a new strategy for cancer therapy. Cancer Discov; 7(11); 1266-83. ©2017 AACR.See related commentary by Towers and Thorburn, p. 1218This article is highlighted in the In This Issue feature, p. 1201.
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Affiliation(s)
- Vito W Rebecca
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael C Nicastri
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Noel McLaughlin
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Colin Fennelly
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Quentin McAfee
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amruta Ronghe
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Michel Nofal
- Department of Chemistry and Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Chun-Yan Lim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California
| | - Eric Witze
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Cynthia I Chude
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gao Zhang
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Gretchen M Alicea
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Shengfu Piao
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Rani Ojha
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Samuel M Levi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Julie S Barber-Rotenberg
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maureen E Murphy
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joshua Rabinowitz
- Department of Chemistry and Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Qin Liu
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Shujing Liu
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xiaowei Xu
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California
| | - Donita C Brady
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David W Speicher
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Jeffrey D Winkler
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ravi K Amaravadi
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
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84
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Beck MW, Kathayat RS, Cham CM, Chang EB, Dickinson BC. Michael addition-based probes for ratiometric fluorescence imaging of protein S-depalmitoylases in live cells and tissues. Chem Sci 2017; 8:7588-7592. [PMID: 29568422 PMCID: PMC5848818 DOI: 10.1039/c7sc02805a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/09/2017] [Indexed: 12/31/2022] Open
Abstract
The reversible modification of cysteine residues through thioester formation with palmitate (protein S-palmitoylation) is a prevalent chemical modification that regulates the function, localization, and stability of many proteins. Current methods for monitoring the "erasers" of S-palmitoylation, acyl-protein thioesterases (APTs), rely on destructive proteomic methods or "turn-on" probes, precluding deployment in heterogeneous samples such as primary tissues. To address these challenges, we present the design, synthesis, and biological evaluation of Ratiometric Depalmitoylation Probes (RDPs). RDPs respond to APTs with a robust ratiometric change in fluorescent signal both in vitro and in live cells. Moreover, RDPs can monitor endogenous APT activities in heterogeneous primary human tissues such as colon organoids, presaging the utility of these molecules in uncovering novel roles for APTs in metabolic regulation.
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Affiliation(s)
- Michael W Beck
- Department of Chemistry , The University of Chicago , 5801 South Ellis Avenue , Chicago , Illinois 60637 , USA .
| | - Rahul S Kathayat
- Department of Chemistry , The University of Chicago , 5801 South Ellis Avenue , Chicago , Illinois 60637 , USA .
| | - Candace M Cham
- Department of Medicine , The University of Chicago , 5801 South Ellis Avenue , Chicago , Illinois 60637 , USA
| | - Eugene B Chang
- Department of Medicine , The University of Chicago , 5801 South Ellis Avenue , Chicago , Illinois 60637 , USA
| | - Bryan C Dickinson
- Department of Chemistry , The University of Chicago , 5801 South Ellis Avenue , Chicago , Illinois 60637 , USA .
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85
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Pezzini F, Bianchi M, Benfatto S, Griggio F, Doccini S, Carrozzo R, Dapkunas A, Delledonne M, Santorelli FM, Lalowski MM, Simonati A. The Networks of Genes Encoding Palmitoylated Proteins in Axonal and Synaptic Compartments Are Affected in PPT1 Overexpressing Neuronal-Like Cells. Front Mol Neurosci 2017; 10:266. [PMID: 28878621 PMCID: PMC5572227 DOI: 10.3389/fnmol.2017.00266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/07/2017] [Indexed: 12/13/2022] Open
Abstract
CLN1 disease (OMIM #256730) is an early childhood ceroid-lipofuscinosis associated with mutated CLN1, whose product Palmitoyl-Protein Thioesterase 1 (PPT1) is a lysosomal enzyme involved in the removal of palmitate residues from S-acylated proteins. In neurons, PPT1 expression is also linked to synaptic compartments. The aim of this study was to unravel molecular signatures connected to CLN1. We utilized SH-SY5Y neuroblastoma cells overexpressing wild type CLN1 (SH-p.wtCLN1) and five selected CLN1 patients’ mutations. The cellular distribution of wtPPT1 was consistent with regular processing of endogenous protein, partially detected inside Lysosomal Associated Membrane Protein 2 (LAMP2) positive vesicles, while the mutants displayed more diffuse cytoplasmic pattern. Transcriptomic profiling revealed 802 differentially expressed genes (DEGs) in SH-p.wtCLN1 (as compared to empty-vector transfected cells), whereas the number of DEGs detected in the two mutants (p.L222P and p.M57Nfs*45) was significantly lower. Bioinformatic scrutiny linked DEGs with neurite formation and neuronal transmission. Specifically, neuritogenesis and proliferation of neuronal processes were predicted to be hampered in the wtCLN1 overexpressing cell line, and these findings were corroborated by morphological investigations. Palmitoylation survey identified 113 palmitoylated protein-encoding genes in SH-p.wtCLN1, including 25 ones simultaneously assigned to axonal growth and synaptic compartments. A remarkable decrease in the expression of palmitoylated proteins, functionally related to axonal elongation (GAP43, CRMP1 and NEFM) and of the synaptic marker SNAP25, specifically in SH-p.wtCLN1 cells was confirmed by immunoblotting. Subsequent, bioinformatic network survey of DEGs assigned to the synaptic annotations linked 81 DEGs, including 23 ones encoding for palmitoylated proteins. Results obtained in this experimental setting outlined two affected functional modules (connected to the axonal and synaptic compartments), which can be associated with an altered gene dosage of wtCLN1. Moreover, these modules were interrelated with the pathological effects associated with loss of PPT1 function, similarly as observed in the Ppt1 knockout mice and patients with CLN1 disease.
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Affiliation(s)
- Francesco Pezzini
- Neurology (Neuropathology and Child Neurology), Department of Neuroscience, Biomedicine and Movement, University of VeronaVerona, Italy
| | - Marzia Bianchi
- Unit of Muscular and Neurodegenerative Disorders, IRCCS Bambino Gesù Children's HospitalRome, Italy
| | - Salvatore Benfatto
- Functional Genomics Center, Department of Biotechnology, University of VeronaVerona, Italy
| | - Francesca Griggio
- Functional Genomics Center, Department of Biotechnology, University of VeronaVerona, Italy
| | - Stefano Doccini
- Molecular Medicine, IRCCS Stella MarisCalambrone-Pisa, Italy
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, IRCCS Bambino Gesù Children's HospitalRome, Italy
| | - Arvydas Dapkunas
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of HelsinkiHelsinki, Finland
| | - Massimo Delledonne
- Functional Genomics Center, Department of Biotechnology, University of VeronaVerona, Italy
| | | | - Maciej M Lalowski
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of HelsinkiHelsinki, Finland
| | - Alessandro Simonati
- Neurology (Neuropathology and Child Neurology), Department of Neuroscience, Biomedicine and Movement, University of VeronaVerona, Italy
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86
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Hernandez JL, Davda D, Majmudar JD, Won SJ, Prakash A, Choi AI, Martin BR. Correlated S-palmitoylation profiling of Snail-induced epithelial to mesenchymal transition. MOLECULAR BIOSYSTEMS 2017; 12:1799-808. [PMID: 27030425 DOI: 10.1039/c6mb00019c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epithelial cells form spatially-organized adhesion complexes that establish polarity gradients, regulate cell proliferation, and direct wound healing. As cells accumulate oncogenic mutations, these key tumor suppression mechanisms are disrupted, eliminating many adhesion complexes and bypassing contact inhibition. The transcription factor Snail is often expressed in malignant cancers, where it promotes transcriptional reprogramming to drive epithelial-mesenchymal transition (EMT) and establishes a more invasive state. S-Palmitoylation describes the fatty-acyl post-translational modification of cysteine residues in proteins, and is required for membrane anchoring, trafficking, localization and function of hundreds of proteins involved in cell growth, polarity, and signaling. Since Snail-expression disrupts apico-basolateral cell polarity, we asked if Snail-dependent transformation induces proteome-wide changes in S-palmitoylation. MCF10A breast cancer cells were retrovirally transduced with Snail and correlated proteome-wide changes in protein abundance and S-palmitoylation were profiled by using stable isotope labeling in cell culture with amino acid (SILAC) mass spectrometry. This analysis identified increased levels of proteins involved in migration, glycolysis, and cell junction remodeling, and decreased levels of proteins involved in cell adhesion. Overall, protein S-palmitoylation is highly correlated with protein abundance, yet for a subset of proteins, this correlation is uncoupled. These findings suggest that Snail-overexpression affects the S-palmitoylation cycle of some proteins, which may participate in cell polarity and tumor suppression.
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Affiliation(s)
- Jeannie L Hernandez
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Dahvid Davda
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA. and Program in Chemical Biology, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Jaimeen D Majmudar
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Sang Joon Won
- Program in Chemical Biology, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Ashesh Prakash
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Alexandria I Choi
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Brent R Martin
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA. and Program in Chemical Biology, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
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87
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Protein S-palmitoylation in cellular differentiation. Biochem Soc Trans 2017; 45:275-285. [PMID: 28202682 PMCID: PMC5310721 DOI: 10.1042/bst20160236] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 01/01/2023]
Abstract
Reversible protein S-palmitoylation confers spatiotemporal control of protein function by modulating protein stability, trafficking and activity, as well as protein-protein and membrane-protein associations. Enabled by technological advances, global studies revealed S-palmitoylation to be an important and pervasive posttranslational modification in eukaryotes with the potential to coordinate diverse biological processes as cells transition from one state to another. Here, we review the strategies and tools to analyze in vivo protein palmitoylation and interrogate the functions of the enzymes that put on and take off palmitate from proteins. We also highlight palmitoyl proteins and palmitoylation-related enzymes that are associated with cellular differentiation and/or tissue development in yeasts, protozoa, mammals, plants and other model eukaryotes.
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88
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Abstract
It has been estimated that 10% of the human genome encodes proteins that are fatty acylated at cysteine residues. The vast majority of these proteins are modified by members of the DHHC protein family, which carry out their enzymatic function on the cytoplasmic face of cell membranes. The biomedical importance of DHHC proteins is underscored by their association with human disease; unique and essential roles for DHHC proteins have been uncovered using DHHC-deficient mouse models. Accordingly, there is great interest in elucidating the molecular mechanisms that underlie DHHC protein function. In this review, we present recent insights into the structure and function of DHHC enzymes.
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89
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Analysis of the brain palmitoyl-proteome using both acyl-biotin exchange and acyl-resin-assisted capture methods. Sci Rep 2017; 7:3299. [PMID: 28607426 PMCID: PMC5468251 DOI: 10.1038/s41598-017-03562-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 05/02/2017] [Indexed: 11/18/2022] Open
Abstract
Palmitoylation is a reversible post-translational protein modification in which palmitic acid is added to cysteine residues, allowing association with different cellular membranes and subdomains. Recently, techniques have been developed to identify palmitoylation on a proteome-wide scale in order to reveal the full cellular complement of palmitoylated proteins. However, in the studies reported to date, there is considerable variation between the sets of identified palmitoyl-proteins and so there remains some uncertainty over what constitutes the definitive complement of palmitoylated proteins even in well-studied tissues such as brain. To address this issue, we used both acyl-biotin exchange and acyl-resin-assisted capture approaches using rat brain as a common protein source. The palmitoyl-proteins identified from each method by mass spectrometry were then compared with each other and previously published studies. There was generally good agreement between the two methods, although many identifications were unique to one method, indicating that at least some of the variability in published palmitoyl proteomes is due to methodological differences. By combining our new data with previous publications using mammalian cells/tissues, we propose a high confidence set of bona fide palmitoylated proteins in brain and provide a resource to help researchers prioritise candidate palmitoyl-proteins for investigation.
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90
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Magrinelli F, Pezzini F, Moro F, Santorelli FM, Simonati A. Diagnostic methods and emerging treatments for adult neuronal ceroid lipofuscinoses (Kufs disease). Expert Opin Orphan Drugs 2017. [DOI: 10.1080/21678707.2017.1325359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Francesca Magrinelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Francesco Pezzini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Francesca Moro
- Molecular Medicine and Neurogenetics Unit, IRCCS Stella Maris, Pisa, Italy
| | | | - Alessandro Simonati
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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91
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Globa AK, Bamji SX. Protein palmitoylation in the development and plasticity of neuronal connections. Curr Opin Neurobiol 2017; 45:210-220. [PMID: 28366531 DOI: 10.1016/j.conb.2017.02.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/19/2017] [Accepted: 02/28/2017] [Indexed: 01/01/2023]
Abstract
Protein palmitoylation, or the reversible addition of the fatty acid, palmitate, onto substrate proteins, can impact the structure and stability of proteins as well as regulate protein-protein interactions and the trafficking and localization of proteins to cell membranes. This posttranslational modification is mediated by palmitoyl-acyltransferases, consisting of a family of 23 zDHHC proteins in mammals. This review focuses on the subcellular distribution of zDHHC proteins within the neuron and the regulation of zDHHC trafficking and function by synaptic activity. We review recent studies identifying actin binding proteins, cell adhesion molecules and synaptic scaffolding proteins as targets of palmitoylation, and examine the implications of activity-mediated palmitoylation in the establishment and plasticity of neuronal connections.
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Affiliation(s)
- Andrea K Globa
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Shernaz X Bamji
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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92
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Skotte NH, Sanders SS, Singaraja RR, Ehrnhoefer DE, Vaid K, Qiu X, Kannan S, Verma C, Hayden MR. Palmitoylation of caspase-6 by HIP14 regulates its activation. Cell Death Differ 2017; 24:433-444. [PMID: 27911442 PMCID: PMC5344205 DOI: 10.1038/cdd.2016.139] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 10/03/2016] [Accepted: 10/25/2016] [Indexed: 02/06/2023] Open
Abstract
Caspase-6 (CASP6) has an important role in axonal degeneration during neuronal apoptosis and in the neurodegenerative diseases Alzheimer and Huntington disease. Decreasing CASP6 activity may help to restore neuronal function in these and other diseases such as stroke and ischemia, where increased CASP6 activity has been implicated. The key to finding approaches to decrease CASP6 activity is a deeper understanding of the mechanisms regulating CASP6 activation. We show that CASP6 is posttranslationally palmitoylated by the palmitoyl acyltransferase HIP14 and that the palmitoylation of CASP6 inhibits its activation. Palmitoylation of CASP6 is decreased both in Hip14-/- mice, where HIP14 is absent, and in YAC128 mice, a model of Huntington disease, where HIP14 is dysfunctional and where CASP6 activity is increased. Molecular modeling suggests that palmitoylation of CASP6 may inhibit its activation via steric blockage of the substrate-binding groove and inhibition of CASP6 dimerization, both essential for CASP6 function. Our studies identify palmitoylation as a novel CASP6 modification and as a key regulator of CASP6 activity.
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Affiliation(s)
- Niels H Skotte
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Shaun S Sanders
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Roshni R Singaraja
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine at Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138648, Singapore
| | - Dagmar E Ehrnhoefer
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kuljeet Vaid
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Xiaofan Qiu
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Srinivasaragavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore
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93
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Holland SM, Thomas GM. Roles of palmitoylation in axon growth, degeneration and regeneration. J Neurosci Res 2017; 95:1528-1539. [PMID: 28150429 DOI: 10.1002/jnr.24003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/09/2016] [Accepted: 11/28/2016] [Indexed: 12/11/2022]
Abstract
The protein-lipid modification palmitoylation plays important roles in neurons, but most attention has focused on roles of this modification in the regulation of mature pre- and post-synapses. However, exciting recent findings suggest that palmitoylation is also critical for both the growth and integrity of neuronal axons and plays previously unappreciated roles in conveying axonal anterograde and retrograde signals. Here we review these emerging roles for palmitoylation in the regulation of axons in health and disease. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sabrina M Holland
- Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair)
| | - Gareth M Thomas
- Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair).,Department of Anatomy and Cell Biology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140
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94
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Sanders SS, Parsons MP, Mui KKN, Southwell AL, Franciosi S, Cheung D, Waltl S, Raymond LA, Hayden MR. Sudden death due to paralysis and synaptic and behavioral deficits when Hip14/Zdhhc17 is deleted in adult mice. BMC Biol 2016; 14:108. [PMID: 27927242 PMCID: PMC5142322 DOI: 10.1186/s12915-016-0333-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/16/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Palmitoylation, the addition of palmitate to proteins by palmitoyl acyltransferases (PATs), is an important regulator of synaptic protein localization and function. Many palmitoylated proteins and PATs have been implicated in neuropsychiatric diseases, including Huntington disease, schizophrenia, amyotrophic lateral sclerosis, Alzheimer disease, and X-linked intellectual disability. HIP14/DHHC17 is the most conserved PAT that palmitoylates many synaptic proteins. Hip14 hypomorphic mice have behavioral and synaptic deficits. However, the phenotype is developmental; thus, a model of post-developmental loss of Hip14 was generated to examine the role of HIP14 in synaptic function in the adult. RESULTS Ten weeks after Hip14 deletion (iHip14 Δ/Δ ), mice die suddenly from rapidly progressive paralysis. Prior to death the mice exhibit motor deficits, increased escape response during tests of anxiety, anhedonia, a symptom indicative of depressive-like behavior, and striatal synaptic deficits, including reduced probability of transmitter release and increased amplitude but decreased frequency of spontaneous post-synaptic currents. The mice also have increased brain weight due to microgliosis and astrogliosis in the cortex. CONCLUSIONS Behavioral changes and electrophysiological measures suggest striatal dysfunction in iHip14 Δ/Δ mice, and increased cortical volume due to astrogliosis and microgliosis suggests a novel role for HIP14 in glia. These data suggest that HIP14 is essential for maintenance of life and neuronal integrity in the adult mouse.
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Affiliation(s)
- Shaun S Sanders
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia (UBC), Vancouver, BC, V5Z 4H4, Canada
| | - Matthew P Parsons
- Department of Psychiatry, Brain Research Centre and Djavad Mowafaghian Centre for Brain Health, UBC, Vancouver, BC, V6T 1Z3, Canada
- Present address: Division of Biomedical Sciences, Faculty of Medicine, Memorial University, Newfoundland and Labrador, A1B 3V6, Canada
| | - Katherine K N Mui
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia (UBC), Vancouver, BC, V5Z 4H4, Canada
| | - Amber L Southwell
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia (UBC), Vancouver, BC, V5Z 4H4, Canada
| | - Sonia Franciosi
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia (UBC), Vancouver, BC, V5Z 4H4, Canada
| | - Daphne Cheung
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia (UBC), Vancouver, BC, V5Z 4H4, Canada
| | - Sabine Waltl
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia (UBC), Vancouver, BC, V5Z 4H4, Canada
| | - Lynn A Raymond
- Department of Psychiatry, Brain Research Centre and Djavad Mowafaghian Centre for Brain Health, UBC, Vancouver, BC, V6T 1Z3, Canada
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia (UBC), Vancouver, BC, V5Z 4H4, Canada.
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95
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Reddy KD, Malipeddi J, DeForte S, Pejaver V, Radivojac P, Uversky VN, Deschenes RJ. Physicochemical sequence characteristics that influence S-palmitoylation propensity. J Biomol Struct Dyn 2016; 35:2337-2350. [PMID: 27498722 DOI: 10.1080/07391102.2016.1217275] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Over the past 30 years, several hundred eukaryotic proteins spanning from yeast to man have been shown to be S-palmitoylated. This post-translational modification involves the reversible addition of a 16-carbon saturated fatty acyl chain onto the cysteine residue of a protein where it regulates protein membrane association and distribution, conformation, and stability. However, the large-scale proteome-wide discovery of new palmitoylated proteins has been hindered by the difficulty of identifying a palmitoylation consensus sequence. Using a bioinformatics approach, we show that the enrichment of hydrophobic and basic residues, the cellular context of the protein, and the structural features of the residues surrounding the palmitoylated cysteine all influence the likelihood of palmitoylation. We developed a new palmitoylation predictor that incorporates these identified features, and this predictor achieves a Matthews Correlation Coefficient of .74 using 10-fold cross validation, and significantly outperforms existing predictors on unbiased testing sets. This demonstrates that palmitoylation sites can be predicted with accuracy by taking into account not only physiochemical properties of the modified cysteine and its surrounding residues, but also structural parameters and the subcellular localization of the modified cysteine. This will allow for improved predictions of palmitoylated residues in uncharacterized proteins. A web-based version of this predictor is currently under development.
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Affiliation(s)
- Krishna D Reddy
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA
| | - Jashwanth Malipeddi
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA
| | - Shelly DeForte
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA
| | - Vikas Pejaver
- c Department of Computer Science and Informatics , Indiana University , Bloomington , IN 47405 , USA
| | - Predrag Radivojac
- c Department of Computer Science and Informatics , Indiana University , Bloomington , IN 47405 , USA
| | - Vladimir N Uversky
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA.,b Johnnie B. Byrd Alzheimer's Research Institute , University of South Florida , Tampa , FL 33612 , USA
| | - Robert J Deschenes
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA
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96
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Raymond LA. Striatal synaptic dysfunction and altered calcium regulation in Huntington disease. Biochem Biophys Res Commun 2016; 483:1051-1062. [PMID: 27423394 DOI: 10.1016/j.bbrc.2016.07.058] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/11/2016] [Indexed: 11/30/2022]
Abstract
Synaptic dysfunction and altered calcium homeostasis in the brain is common to many neurodegenerative disorders. Among these, Huntington disease (HD), which is inherited in an autosomal dominant fashion, can serve as a model for investigating these mechanisms. HD generally manifests in middle age as a disorder of movement, mood and cognition. An expanded polymorphic CAG repeat in the HTT gene results in progressive neurodegeneration that impacts striatal spiny projection neurons (SPNs) earliest and most severely. Striatal SPNs receive massive glutamatergic input from cortex and thalamus, and these excitatory synapses are a focus for early changes that can trigger aberrant downstream signaling to disrupt synaptic plasticity and lead to later degeneration. Mitochondrial dysfunction and altered intracellular calcium-induced calcium release and sequestration mechanisms add to the impairments in circuit function that may underlie prodromal cognitive and subtle motor deficits. These mechanisms and implications for developing disease-modifying therapy will be reviewed here.
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Affiliation(s)
- Lynn A Raymond
- Department of Psychiatry and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 4834-2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3.
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97
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Montersino A, Thomas GM. Slippery signaling: Palmitoylation-dependent control of neuronal kinase localization and activity. Mol Membr Biol 2016; 32:179-88. [PMID: 27241460 DOI: 10.1080/09687688.2016.1182652] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Modification of proteins with the lipid palmitate, a process called palmitoylation, is important for the normal function of neuronal cells. However, most attention has focused on how palmitoylation regulates the targeting and trafficking of neurotransmitter receptors and non-enzymatic scaffold proteins. In this review we discuss recent studies that suggest that palmitoylation also plays additional roles in neurons by controlling the localization, interactions and perhaps even the activity of protein kinases that play key roles in physiological neuronal regulation and in neuropathological processes.
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Affiliation(s)
- Audrey Montersino
- a Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair) and
| | - Gareth M Thomas
- a Shriners Hospitals Pediatric Research Center (Center for Neurorehabilitation and Neural Repair) and.,b Department of Anatomy and Cell Biology , Temple University School of Medicine , Philadelphia , PA , USA
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98
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Peng T, Thinon E, Hang HC. Proteomic analysis of fatty-acylated proteins. Curr Opin Chem Biol 2015; 30:77-86. [PMID: 26656971 DOI: 10.1016/j.cbpa.2015.11.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 12/11/2022]
Abstract
Protein fatty-acylation in eukaryotes has been associated with many fundamental biological processes. However, the diversity, abundance and regulatory mechanisms of protein fatty-acylation in vivo remain to be explored. Herein, we review the proteomic analysis of fatty-acylated proteins, with a focus on N-myristoylation and S-palmitoylation. We then highlight major challenges and emerging methods for direct site identification, quantitation, and lipid structure characterization to understand the functions and regulatory mechanisms of fatty-acylated proteins in physiology and disease.
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Affiliation(s)
- Tao Peng
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, United States
| | - Emmanuelle Thinon
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, United States; The Crick Institute, 215 Euston Road, London NW1 2BE, United Kingdom
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, United States.
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99
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Gottlieb CD, Zhang S, Linder ME. The Cysteine-rich Domain of the DHHC3 Palmitoyltransferase Is Palmitoylated and Contains Tightly Bound Zinc. J Biol Chem 2015; 290:29259-69. [PMID: 26487721 DOI: 10.1074/jbc.m115.691147] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Indexed: 11/06/2022] Open
Abstract
DHHC palmitoyltransferases catalyze the addition of the fatty acid palmitate to proteins on the cytoplasmic leaflet of cell membranes. There are 23 members of the highly diverse mammalian DHHC protein family, all of which contain a conserved catalytic domain called the cysteine-rich domain (CRD). DHHC proteins transfer palmitate via a two-step catalytic mechanism in which the enzyme first modifies itself with palmitate in a process termed autoacylation. The enzyme then transfers palmitate from itself onto substrate proteins. The number and location of palmitoylated cysteines in the autoacylated intermediate is unknown. In this study, we present evidence using mass spectrometry that DHHC3 is palmitoylated at the cysteine in the DHHC motif. Mutation of highly conserved CRD cysteines outside the DHHC motif resulted in activity deficits and a structural perturbation revealed by limited proteolysis. Treatment of DHHC3 with chelating agents in vitro replicated both the specific structural perturbations and activity deficits observed in conserved cysteine mutants, suggesting metal ion-binding in the CRD. Using the fluorescent indicator mag-fura-2, the metal released from DHHC3 was identified as zinc. The stoichiometry of zinc binding was measured as 2 mol of zinc/mol of DHHC3 protein. Taken together, our data demonstrate that coordination of zinc ions by cysteine residues within the CRD is required for the structural integrity of DHHC proteins.
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Affiliation(s)
| | - Sheng Zhang
- the Core Proteomics and Mass Spectrometry Facility, Cornell University, Ithaca, New York 14853
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