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Her J, Zheng H, Bunting SF. RNF4 sustains Myc-driven tumorigenesis by facilitating DNA replication. J Clin Invest 2024; 134:e167419. [PMID: 38530355 PMCID: PMC11093604 DOI: 10.1172/jci167419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/20/2024] [Indexed: 03/27/2024] Open
Abstract
The mammalian SUMO-targeted E3 ubiquitin ligase Rnf4 has been reported to act as a regulator of DNA repair, but the importance of RNF4 as a tumor suppressor has not been tested. Using a conditional-knockout mouse model, we deleted Rnf4 in the B cell lineage to test the importance of RNF4 for growth of somatic cells. Although Rnf4-conditional-knockout B cells exhibited substantial genomic instability, Rnf4 deletion caused no increase in tumor susceptibility. In contrast, Rnf4 deletion extended the healthy lifespan of mice expressing an oncogenic c-myc transgene. Rnf4 activity is essential for normal DNA replication, and in its absence, there was a failure in ATR-CHK1 signaling of replication stress. Factors that normally mediate replication fork stability, including members of the Fanconi anemia gene family and the helicases PIF1 and RECQL5, showed reduced accumulation at replication forks in the absence of RNF4. RNF4 deficiency also resulted in an accumulation of hyper-SUMOylated proteins in chromatin, including members of the SMC5/6 complex, which contributes to replication failure by a mechanism dependent on RAD51. These findings indicate that RNF4, which shows increased expression in multiple human tumor types, is a potential target for anticancer therapy, especially in tumors expressing c-myc.
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Affiliation(s)
- Joonyoung Her
- Department of Molecular Biology and Biochemistry and
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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2
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Ahn G, Riley NM, Kamber RA, Wisnovsky S, Moncayo von Hase S, Bassik MC, Banik SM, Bertozzi CR. Elucidating the cellular determinants of targeted membrane protein degradation by lysosome-targeting chimeras. Science 2023; 382:eadf6249. [PMID: 37856615 PMCID: PMC10766146 DOI: 10.1126/science.adf6249] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 08/31/2023] [Indexed: 10/21/2023]
Abstract
Targeted protein degradation can provide advantages over inhibition approaches in the development of therapeutic strategies. Lysosome-targeting chimeras (LYTACs) harness receptors, such as the cation-independent mannose 6-phosphate receptor (CI-M6PR), to direct extracellular proteins to lysosomes. In this work, we used a genome-wide CRISPR knockout approach to identify modulators of LYTAC-mediated membrane protein degradation in human cells. We found that disrupting retromer genes improved target degradation by reducing LYTAC recycling to the plasma membrane. Neddylated cullin-3 facilitated LYTAC-complex lysosomal maturation and was a predictive marker for LYTAC efficacy. A substantial fraction of cell surface CI-M6PR remains occupied by endogenous M6P-modified glycoproteins. Thus, inhibition of M6P biosynthesis increased the internalization of LYTAC-target complexes. Our findings inform design strategies for next-generation LYTACs and elucidate aspects of cell surface receptor occupancy and trafficking.
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Affiliation(s)
- Green Ahn
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Nicholas M. Riley
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Roarke A. Kamber
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Simon Wisnovsky
- Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Salvador Moncayo von Hase
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Michael C. Bassik
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Steven M. Banik
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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3
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Dang Do AN, Sleat DE, Campbell K, Johnson NL, Zheng H, Wassif CA, Dale RK, Porter FD. Cerebrospinal Fluid Protein Biomarker Discovery in CLN3. J Proteome Res 2023; 22:2493-2508. [PMID: 37338096 PMCID: PMC11095826 DOI: 10.1021/acs.jproteome.3c00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Syndromic CLN3-Batten is a fatal, pediatric, neurodegenerative disease caused by variants in CLN3, which encodes the endolysosomal transmembrane CLN3 protein. No approved treatment for CLN3 is currently available. The protracted and asynchronous disease presentation complicates the evaluation of potential therapies using clinical disease progression parameters. Biomarkers as surrogates to measure the progression and effect of potential therapeutics are needed. We performed proteomic discovery studies using cerebrospinal fluid (CSF) samples from 28 CLN3-affected and 32 age-similar non-CLN3 individuals. Proximal extension assay (PEA) of 1467 proteins and untargeted data-dependent mass spectrometry [MS; MassIVE FTP server (ftp://MSV000090147@massive.ucsd.edu)] were used to generate orthogonal lists of protein marker candidates. At an adjusted p-value of <0.1 and threshold CLN3/non-CLN3 fold-change ratio of 1.5, PEA identified 54 and MS identified 233 candidate biomarkers. Some of these (NEFL, CHIT1) have been previously linked with other neurologic conditions. Others (CLPS, FAM217B, QRICH2, KRT16, ZNF333) appear to be novel. Both methods identified 25 candidate biomarkers, including CHIT1, NELL1, and ISLR2 which had absolute fold-change ratios >2. NELL1 and ISLR2 regulate axonal development in neurons and are intriguing new candidates for further investigation in CLN3. In addition to identifying candidate proteins for CLN3 research, this study provides a comparison of two large-scale proteomic discovery methods in CSF.
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Affiliation(s)
- An N. Dang Do
- Unit on Cellular Stress in Development and Diseases, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David E. Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
- Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Kiersten Campbell
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nicholas L. Johnson
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Christopher A. Wassif
- Section on Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Forbes D. Porter
- Section on Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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4
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Calcagni' A, Staiano L, Zampelli N, Minopoli N, Herz NJ, Di Tullio G, Huynh T, Monfregola J, Esposito A, Cirillo C, Bajic A, Zahabiyon M, Curnock R, Polishchuk E, Parkitny L, Medina DL, Pastore N, Cullen PJ, Parenti G, De Matteis MA, Grumati P, Ballabio A. Loss of the batten disease protein CLN3 leads to mis-trafficking of M6PR and defective autophagic-lysosomal reformation. Nat Commun 2023; 14:3911. [PMID: 37400440 DOI: 10.1038/s41467-023-39643-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
Batten disease, one of the most devastating types of neurodegenerative lysosomal storage disorders, is caused by mutations in CLN3. Here, we show that CLN3 is a vesicular trafficking hub connecting the Golgi and lysosome compartments. Proteomic analysis reveals that CLN3 interacts with several endo-lysosomal trafficking proteins, including the cation-independent mannose 6 phosphate receptor (CI-M6PR), which coordinates the targeting of lysosomal enzymes to lysosomes. CLN3 depletion results in mis-trafficking of CI-M6PR, mis-sorting of lysosomal enzymes, and defective autophagic lysosomal reformation. Conversely, CLN3 overexpression promotes the formation of multiple lysosomal tubules, which are autophagy and CI-M6PR-dependent, generating newly formed proto-lysosomes. Together, our findings reveal that CLN3 functions as a link between the M6P-dependent trafficking of lysosomal enzymes and lysosomal reformation pathway, explaining the global impairment of lysosomal function in Batten disease.
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Affiliation(s)
- Alessia Calcagni'
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
| | - Leopoldo Staiano
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Institute for Genetic and Biomedical Research, National Research Council (CNR), Milan, Italy
| | | | - Nadia Minopoli
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Niculin J Herz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Tuong Huynh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Alessandra Esposito
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- SSM School for Advanced Studies, Federico II University, Naples, Italy
| | - Carmine Cirillo
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Aleksandar Bajic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Mahla Zahabiyon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Rachel Curnock
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Luke Parkitny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Diego Luis Medina
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Nunzia Pastore
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Giancarlo Parenti
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Andrea Ballabio
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy.
- SSM School for Advanced Studies, Federico II University, Naples, Italy.
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5
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Chen J, Soni RK, Xu Y, Simoes S, Liang FX, DeFreitas L, Hwang R, Montesinos J, Lee JH, Area-Gomez E, Nandakumar R, Vardarajan B, Marquer C. Juvenile CLN3 disease is a lysosomal cholesterol storage disorder: similarities with Niemann-Pick type C disease. EBioMedicine 2023; 92:104628. [PMID: 37245481 PMCID: PMC10227369 DOI: 10.1016/j.ebiom.2023.104628] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/30/2023] [Accepted: 05/10/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND The most common form of neuronal ceroid lipofuscinosis (NCL) is juvenile CLN3 disease (JNCL), a currently incurable neurodegenerative disorder caused by mutations in the CLN3 gene. Based on our previous work and on the premise that CLN3 affects the trafficking of the cation-independent mannose-6 phosphate receptor and its ligand NPC2, we hypothesised that dysfunction of CLN3 leads to the aberrant accumulation of cholesterol in the late endosomes/lysosomes (LE/Lys) of JNCL patients' brains. METHODS An immunopurification strategy was used to isolate intact LE/Lys from frozen autopsy brain samples. LE/Lys isolated from samples of JNCL patients were compared with age-matched unaffected controls and Niemann-Pick Type C (NPC) disease patients. Indeed, mutations in NPC1 or NPC2 result in the accumulation of cholesterol in LE/Lys of NPC disease samples, thus providing a positive control. The lipid and protein content of LE/Lys was then analysed using lipidomics and proteomics, respectively. FINDINGS Lipid and protein profiles of LE/Lys isolated from JNCL patients were profoundly altered compared to controls. Importantly, cholesterol accumulated in LE/Lys of JNCL samples to a comparable extent than in NPC samples. Lipid profiles of LE/Lys were similar in JNCL and NPC patients, except for levels of bis(monoacylglycero)phosphate (BMP). Protein profiles detected in LE/Lys of JNCL and NPC patients appeared identical, except for levels of NPC1. INTERPRETATION Our results support that JNCL is a lysosomal cholesterol storage disorder. Our findings also support that JNCL and NPC disease share pathogenic pathways leading to aberrant lysosomal accumulation of lipids and proteins, and thus suggest that the treatments available for NPC disease may be beneficial to JNCL patients. This work opens new avenues for further mechanistic studies in model systems of JNCL and possible therapeutic interventions for this disorder. FUNDING San Francisco Foundation.
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Affiliation(s)
- Jacinda Chen
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, New York City, NY 10032, USA
| | - Yimeng Xu
- Biomarkers Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Sabrina Simoes
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Feng-Xia Liang
- Microscopy Core Laboratory of Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York City, NY 10016, USA
| | - Laura DeFreitas
- Biomarkers Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Robert Hwang
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Jorge Montesinos
- Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Joseph H Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA; G. H. Sergievsky Center, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Epidemiology, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Estela Area-Gomez
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA; Institute of Human Nutrition, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Renu Nandakumar
- Biomarkers Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA; G. H. Sergievsky Center, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Catherine Marquer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, NY 10032, USA.
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6
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Zhang W, Yang X, Li Y, Yu L, Zhang B, Zhang J, Cho WJ, Venkatarangan V, Chen L, Burugula BB, Bui S, Wang Y, Duan C, Kitzman JO, Li M. GCAF(TMEM251) regulates lysosome biogenesis by activating the mannose-6-phosphate pathway. Nat Commun 2022; 13:5351. [PMID: 36096887 PMCID: PMC9468337 DOI: 10.1038/s41467-022-33025-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
The mannose-6-phosphate (M6P) biosynthetic pathway for lysosome biogenesis has been studied for decades and is considered a well-understood topic. However, whether this pathway is regulated remains an open question. In a genome-wide CRISPR/Cas9 knockout screen, we discover TMEM251 as the first regulator of the M6P modification. Deleting TMEM251 causes mistargeting of most lysosomal enzymes due to their loss of M6P modification and accumulation of numerous undigested materials. We further demonstrate that TMEM251 localizes to the Golgi and is required for the cleavage and activity of GNPT, the enzyme that catalyzes M6P modification. In zebrafish, TMEM251 deletion leads to severe developmental defects including heart edema and skeletal dysplasia, which phenocopies Mucolipidosis Type II. Our discovery provides a mechanism for the newly discovered human disease caused by TMEM251 mutations. We name TMEM251 as GNPTAB cleavage and activity factor (GCAF) and its related disease as Mucolipidosis Type V.
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Affiliation(s)
- Weichao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yingxiang Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Linchen Yu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bokai Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianchao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Woo Jung Cho
- BRCF Microscopy Core, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Varsha Venkatarangan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Liang Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bala Bharathi Burugula
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sarah Bui
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Cunming Duan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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7
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Linhorst A, Lübke T. The Human Ntn-Hydrolase Superfamily: Structure, Functions and Perspectives. Cells 2022; 11:cells11101592. [PMID: 35626629 PMCID: PMC9140057 DOI: 10.3390/cells11101592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
N-terminal nucleophile (Ntn)-hydrolases catalyze the cleavage of amide bonds in a variety of macromolecules, including the peptide bond in proteins, the amide bond in N-linked protein glycosylation, and the amide bond linking a fatty acid to sphingosine in complex sphingolipids. Ntn-hydrolases are all sharing two common hallmarks: Firstly, the enzymes are synthesized as inactive precursors that undergo auto-proteolytic self-activation, which, as a consequence, reveals the active site nucleophile at the newly formed N-terminus. Secondly, all Ntn-hydrolases share a structural consistent αββα-fold, notwithstanding the total lack of amino acid sequence homology. In humans, five subclasses of the Ntn-superfamily have been identified so far, comprising relevant members such as the catalytic active subunits of the proteasome or a number of lysosomal hydrolases, which are often associated with lysosomal storage diseases. This review gives an updated overview on the structural, functional, and (patho-)physiological characteristics of human Ntn-hydrolases, in particular.
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8
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Klarić TS, Lauc G. The dynamic brain N-glycome. Glycoconj J 2022; 39:443-471. [PMID: 35334027 DOI: 10.1007/s10719-022-10055-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/27/2022] [Accepted: 03/09/2022] [Indexed: 01/17/2023]
Abstract
The attachment of carbohydrates to other macromolecules, such as proteins or lipids, is an important regulatory mechanism termed glycosylation. One subtype of protein glycosylation is asparagine-linked glycosylation (N-glycosylation) which plays a key role in the development and normal functioning of the vertebrate brain. To better understand the role of N-glycans in neurobiology, it's imperative we analyse not only the functional roles of individual structures, but also the collective impact of large-scale changes in the brain N-glycome. The systematic study of the brain N-glycome is still in its infancy and data are relatively scarce. Nevertheless, the prevailing view has been that the neuroglycome is inherently restricted with limited capacity for variation. The development of improved methods for N-glycomics analysis of brain tissue has facilitated comprehensive characterisation of the complete brain N-glycome under various experimental conditions on a larger scale. Consequently, accumulating data suggest that it's more dynamic than previously recognised and that, within a general framework, it has a given capacity to change in response to both intrinsic and extrinsic stimuli. Here, we provide an overview of the many factors that can alter the brain N-glycome, including neurodevelopment, ageing, diet, stress, neuroinflammation, injury, and disease. Given this emerging evidence, we propose that the neuroglycome has a hitherto underappreciated plasticity and we discuss the therapeutic implications of this regarding the possible reversal of pathological changes via interventions. We also briefly review the merits and limitations of N-glycomics as an analytical method before reflecting on some of the outstanding questions in the field.
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Affiliation(s)
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
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9
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Li Y, Tian X, Zhang Q, Yan C, Han Y. A novel function of CREG in metabolic disorders. MEDICAL REVIEW (BERLIN, GERMANY) 2021; 1:18-22. [PMID: 37724076 PMCID: PMC10388757 DOI: 10.1515/mr-2021-0031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/13/2021] [Indexed: 09/20/2023]
Abstract
Metabolic disorders are public health problems that require prevention and new efficient drugs for treatment. Cellular repressor of E1A-stimulated genes (CREG) is ubiquitously expressed in mature tissues and cells in mammals and plays a critical role in keeping cells or tissues in a mature, homeostatic state. Recently, CREG turns to be an important mediator in the development of metabolic disorders. Here in this review, we briefly discuss the structure and molecular regulation of CREG along with the therapeutic strategy to combat the metabolic disorders.
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Affiliation(s)
- Yang Li
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China
| | - Xiaoxiang Tian
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China
| | - Quanyu Zhang
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China
| | - Chenghui Yan
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China
| | - Yaling Han
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning, China
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10
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Abstract
Lysosomes are the main degradative organelles of almost all eukaryotic cells. They fulfil a crucial function in cellular homeostasis, and impairments in lysosomal function are connected to a continuously increasing number of pathological conditions. In recent years, lysosomes are furthermore emerging as control centers of cellular metabolism, and major regulators of cellular signaling were shown to be activated at the lysosomal surface. To date, >300 proteins were demonstrated to be located in/at the lysosome, and the lysosomal proteome and interactome is constantly growing. For the identification of these proteins, and their involvement in cellular mechanisms or disease progression, mass spectrometry (MS)-based proteomics has proven its worth in a large number of studies. In this review, we are recapitulating the application of MS-based approaches for the investigation of the lysosomal proteome, and their application to a diverse set of research questions. Numerous strategies were applied for the enrichment of lysosomes or lysosomal proteins and their identification by MS-based methods. This allowed for the characterization of the lysosomal proteome, the investigation of lysosome-related disorders, the utilization of lysosomal proteins as biomarkers for diseases, and the characterization of lysosome-related cellular mechanisms. While these >60 studies provide a comprehensive picture of the lysosomal proteome across several model organisms and pathological conditions, various proteomics approaches have not been applied to lysosomes yet, and a large number of questions are still left unanswered.
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Affiliation(s)
- Pathma Muthukottiappan
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Nussallee 11, 53115 Bonn, Germany.
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Nussallee 11, 53115 Bonn, Germany.
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11
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Tuermer A, Mausbach S, Kaade E, Damme M, Sylvester M, Gieselmann V, Thelen M. CLN6 deficiency causes selective changes in the lysosomal protein composition. Proteomics 2021; 21:e2100043. [PMID: 34432360 DOI: 10.1002/pmic.202100043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/31/2021] [Accepted: 08/17/2021] [Indexed: 11/06/2022]
Abstract
Neuronal ceroid lipofuscinoses (NCLs) collectively account for the highest prevalence of inherited neurodegenerative diseases in childhood. This disease group is classified by the deposition of similar autofluorescence storage material in lysosomes that is accompanied by seizures, blindness and premature mortality in later disease stages. Defects in several genes affecting various proteins lead to NCL, one of them being CLN6, a transmembrane protein resident in the endoplasmic reticulum. Dysfunctionality of CLN6 causes variant late infantile NCL (vLINCL). The function of CLN6 and how its deficiency affects lysosomal integrity remains unknown. In this work, we performed a comparative proteomic analysis of isolated lysosomal fractions from liver tissue of nclf mice, a natural mouse model displaying a similar disease course than its human counterpart. We could identify a drastic reduction in the protein amounts of selected lysosomal proteins, amongst them several members of the NCL protein family. Most of these proteins were N-glycosylated, soluble hydrolases and their reduction in protein levels was verified by western blotting and enzymatic assays. Hereby we could directly link Cln6 dysfunction to changes in the lysosomal compartment and to other NCL forms.
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Affiliation(s)
- Andreas Tuermer
- Institute of Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, North Rhine-Westphalia, Germany
| | - Simone Mausbach
- Institute of Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, North Rhine-Westphalia, Germany
| | - Edgar Kaade
- Institute of Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, North Rhine-Westphalia, Germany
| | - Markus Damme
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | - Marc Sylvester
- Institute of Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, North Rhine-Westphalia, Germany
| | - Volkmar Gieselmann
- Institute of Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, North Rhine-Westphalia, Germany
| | - Melanie Thelen
- Institute of Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, North Rhine-Westphalia, Germany
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12
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Beletskiy A, Chesnokova E, Bal N. Insulin-Like Growth Factor 2 As a Possible Neuroprotective Agent and Memory Enhancer-Its Comparative Expression, Processing and Signaling in Mammalian CNS. Int J Mol Sci 2021; 22:ijms22041849. [PMID: 33673334 PMCID: PMC7918606 DOI: 10.3390/ijms22041849] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
A number of studies performed on rodents suggest that insulin-like growth factor 2 (IGF-2) or its analogs may possibly be used for treating some conditions like Alzheimer’s disease, Huntington’s disease, autistic spectrum disorders or aging-related cognitive impairment. Still, for translational research a comparative knowledge about the function of IGF-2 and related molecules in model organisms (rats and mice) and humans is necessary. There is a number of important differences in IGF-2 signaling between species. In the present review we emphasize species-specific patterns of IGF-2 expression in rodents, humans and some other mammals, using, among other sources, publicly available transcriptomic data. We provide a detailed description of Igf2 mRNA expression regulation and pre-pro-IGF-2 protein processing in different species. We also summarize the function of IGF-binding proteins. We describe three different receptors able to bind IGF-2 and discuss the role of IGF-2 signaling in learning and memory, as well as in neuroprotection. We hope that comprehensive understanding of similarities and differences in IGF-2 signaling between model organisms and humans will be useful for development of more effective medicines targeting IGF-2 receptors.
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13
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Parenti G, Medina DL, Ballabio A. The rapidly evolving view of lysosomal storage diseases. EMBO Mol Med 2021; 13:e12836. [PMID: 33459519 PMCID: PMC7863408 DOI: 10.15252/emmm.202012836] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022] Open
Abstract
Lysosomal storage diseases are a group of metabolic disorders caused by deficiencies of several components of lysosomal function. Most commonly affected are lysosomal hydrolases, which are involved in the breakdown and recycling of a variety of complex molecules and cellular structures. The understanding of lysosomal biology has progressively improved over time. Lysosomes are no longer viewed as organelles exclusively involved in catabolic pathways, but rather as highly dynamic elements of the autophagic-lysosomal pathway, involved in multiple cellular functions, including signaling, and able to adapt to environmental stimuli. This refined vision of lysosomes has substantially impacted on our understanding of the pathophysiology of lysosomal disorders. It is now clear that substrate accumulation triggers complex pathogenetic cascades that are responsible for disease pathology, such as aberrant vesicle trafficking, impairment of autophagy, dysregulation of signaling pathways, abnormalities of calcium homeostasis, and mitochondrial dysfunction. Novel technologies, in most cases based on high-throughput approaches, have significantly contributed to the characterization of lysosomal biology or lysosomal dysfunction and have the potential to facilitate diagnostic processes, and to enable the identification of new therapeutic targets.
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Affiliation(s)
- Giancarlo Parenti
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Diego L Medina
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,SSM School for Advanced Studies, Federico II University, Naples, Italy
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14
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Best HL, Clare AJ, McDonald KO, Wicky HE, Hughes SM. An altered secretome is an early marker of the pathogenesis of CLN6 Batten disease. J Neurochem 2021; 157:764-780. [PMID: 33368303 DOI: 10.1111/jnc.15285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/20/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022]
Abstract
Neuronal ceroid lipofuscinoses (NCLs) are a group of inherited childhood neurodegenerative disorders. In addition to the accumulation of auto-fluorescent storage material in lysosomes, NCLs are largely characterised by region-specific neuroinflammation that can predict neuron loss. These phenotypes suggest alterations in the extracellular environment-making the secretome an area of significant interest. This study investigated the secretome in the CLN6 (ceroid-lipofuscinosis neuronal protein 6) variant of NCL. To investigate the CLN6 secretome, we co-cultured neurons and glia isolated from Cln6nclf or Cln6± mice, and utilised mass spectrometry to compare protein constituents of conditioned media. The significant changes noted in cathepsin enzymes, were investigated further via western blotting and enzyme activity assays. Viral-mediated gene therapy was used to try and rescue the wild-type phenotype and restore the secretome-both in vitro in co-cultures and in vivo in mouse plasma. In Cln6nclf cells, proteomics revealed a marked increase in catabolic and cytoskeletal-associated proteins-revealing new similarities between the pathogenic signatures of NCLs with other neurodegenerative disorders. These changes were, in part, corrected by gene therapy intervention, suggesting these proteins as candidate in vitro biomarkers. Importantly, these in vitro changes show promise for in vivo translation, with Cathepsin L (CTSL) activity reduced in both co-cultures and Cln6nclf plasma samples post gene-therapy. This work suggests the secretome plays a role in CLN6 pathogenesis and highlights its potential use as an in vitro model. Proteomic changes present a list of candidate biomarkers for monitoring disease and assessing potential therapeutics in future studies.
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Affiliation(s)
- Hannah L Best
- Department of Biochemistry, School of Biomedical Sciences, Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Alison J Clare
- Department of Biochemistry, School of Biomedical Sciences, Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Kirstin O McDonald
- Department of Biochemistry, School of Biomedical Sciences, Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Hollie E Wicky
- Department of Biochemistry, School of Biomedical Sciences, Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Stephanie M Hughes
- Department of Biochemistry, School of Biomedical Sciences, Brain Health Research Centre, University of Otago, Dunedin, New Zealand
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15
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Lysosomal sulfatases: a growing family. Biochem J 2020; 477:3963-3983. [PMID: 33120425 DOI: 10.1042/bcj20200586] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023]
Abstract
Sulfatases constitute a family of enzymes that specifically act in the hydrolytic degradation of sulfated metabolites by removing sulfate monoesters from various substrates, particularly glycolipids and glycosaminoglycans. A common essential feature of all known eukaryotic sulfatases is the posttranslational modification of a critical cysteine residue in their active site by oxidation to formylglycine (FGly), which is mediated by the FGly-generating enzyme in the endoplasmic reticulum and is indispensable for catalytic activity. The majority of the so far described sulfatases localize intracellularly to lysosomes, where they act in different catabolic pathways. Mutations in genes coding for lysosomal sulfatases lead to an accumulation of the sulfated substrates in lysosomes, resulting in impaired cellular function and multisystemic disorders presenting as lysosomal storage diseases, which also cover the mucopolysaccharidoses and metachromatic leukodystrophy. Bioinformatics analysis of the eukaryotic genomes revealed, besides the well described and long known disease-associated sulfatases, additional genes coding for putative enzymes with sulfatases activity, including arylsulfatase G as well as the arylsulfatases H, I, J and K, respectively. In this article, we review current knowledge about lysosomal sulfatases with a special focus on the just recently characterized family members arylsulfatase G and arylsulfatase K.
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16
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Ponnaiyan S, Akter F, Singh J, Winter D. Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics. Sci Data 2020; 7:68. [PMID: 32103020 PMCID: PMC7044164 DOI: 10.1038/s41597-020-0399-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/23/2020] [Indexed: 11/09/2022] Open
Abstract
Lysosomes are the main degradative organelles of cells and involved in a variety of processes including the recycling of macromolecules, storage of compounds, and metabolic signaling. Despite an increasing interest in the proteomic analysis of lysosomes, no systematic study of sample preparation protocols for lysosome enriched fractions has been performed to date. In the current study, we used samples enriched for lysosomes by paramagnetic nanoparticles and systematically evaluated experimental parameters for the analysis of the lysosomal proteome. This includes different approaches for the concentration of lysosome-containing fractions; desalting of samples by solid phase extraction; fractionation of peptide samples; and different gradient lengths for LC-MS/MS analyses of unfractionated samples by data dependent and data independent acquisition. Furthermore, we evaluated four different digestion methods including filter aided sample preparation (FASP), in-gel digestion, and in-solution digestion using either RapiGest or urea. Using the combined data, we generated a benchmark lysosomal proteome data set for mouse embryonic fibroblasts as well as a spectral library for the analysis of lysosomes by data independent acquisition.
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Affiliation(s)
- Srigayatri Ponnaiyan
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Fatema Akter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany
- Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Jasjot Singh
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany.
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17
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Sun M, Luong G, Plastikwala F, Sun Y. Control of Rab7a activity and localization through endosomal type Igamma PIP 5-kinase is required for endosome maturation and lysosome function. FASEB J 2019; 34:2730-2748. [PMID: 31908013 DOI: 10.1096/fj.201901830r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/22/2019] [Accepted: 12/08/2019] [Indexed: 02/06/2023]
Abstract
The small GTPase Ras-related protein Rab-7a (Rab7a) serves as a key organizer of the endosomal-lysosomal system. However, molecular mechanisms controlling Rab7a activation levels and subcellular translocation are still poorly defined. Here, we demonstrate that type Igamma phosphatidylinositol phosphate 5-kinase i5 (PIPKIγi5), an endosome-localized enzyme that produces phosphatidylinositol 4,5-bisphosphate, directly interacts with Rab7a and plays critical roles in the control of the endosomal-lysosomal system. The loss of PIPKIγi5 blocks Rab7a recruitment to early endosomes, which prevents the maturation of early to late endosomes. PIPKIγi5 loss disturbs retromer complex connection with Rab7a, which blocks the retrograde sorting of Cation-independent Mannose 6-Phosphate Receptor from late endosomes. This leads to the decreased sorting of hydrolases to lysosomes and reduces the autophagic degradation. By modulating the retromer-Rab7a connection, PIPKIγi5 is also required for the recruitment of the GTPase-activating protein TBC1 domain family member 5 to late endosomes, which controls the conversion of Rab7a from the active state to the inactive state. Thus, PIPKIγi5 is critical for the modulation of Rab7a activity, localization, and function in the endosomal-lysosomal system.
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Affiliation(s)
- Ming Sun
- Philips Institute for Oral Health Research, School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Gary Luong
- Philips Institute for Oral Health Research, School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Faiz Plastikwala
- Philips Institute for Oral Health Research, School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Yue Sun
- Philips Institute for Oral Health Research, School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
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18
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Sleat DE, Wiseman JA, El-Banna M, Zheng H, Zhao C, Soherwardy A, Moore DF, Lobel P. Analysis of Brain and Cerebrospinal Fluid from Mouse Models of the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Changes in the Lysosomal Proteome. Mol Cell Proteomics 2019; 18:2244-2261. [PMID: 31501224 PMCID: PMC6823856 DOI: 10.1074/mcp.ra119.001587] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/06/2019] [Indexed: 01/06/2023] Open
Abstract
Treatments are emerging for the neuronal ceroid lipofuscinoses (NCLs), a group of similar but genetically distinct lysosomal storage diseases. Clinical ratings scales measure long-term disease progression and response to treatment but clinically useful biomarkers have yet to be identified in these diseases. We have conducted proteomic analyses of brain and cerebrospinal fluid (CSF) from mouse models of the most frequently diagnosed NCL diseases: CLN1 (infantile NCL), CLN2 (classical late infantile NCL) and CLN3 (juvenile NCL). Samples were obtained at different stages of disease progression and proteins quantified using isobaric labeling. In total, 8303 and 4905 proteins were identified from brain and CSF, respectively. We also conduced label-free analyses of brain proteins that contained the mannose 6-phosphate lysosomal targeting modification. In general, we detect few changes at presymptomatic timepoints but later in disease, we detect multiple proteins whose expression is significantly altered in both brain and CSF of CLN1 and CLN2 animals. Many of these proteins are lysosomal in origin or are markers of neuroinflammation, potentially providing clues to underlying pathogenesis and providing promising candidates for further validation.
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Affiliation(s)
- David E Sleat
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854; Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, NJ 08854.
| | | | - Mukarram El-Banna
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854
| | - Amenah Soherwardy
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854
| | - Dirk F Moore
- Department of Biostatistics, School of Public Health, Rutgers - The State University of New Jersey, Piscataway, NJ 08854
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854; Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, NJ 08854.
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19
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Park JK, Kim KY, Sim YW, Kim YI, Kim JK, Lee C, Han J, Kim CU, Lee JE, Park S. Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder. IUCRJ 2019; 6:729-739. [PMID: 31316816 PMCID: PMC6608618 DOI: 10.1107/s2052252519007668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
Ependymin was first discovered as a predominant protein in brain extracellular fluid in fish and was suggested to be involved in functions mostly related to learning and memory. Orthologous proteins to ependymin called ependymin-related proteins (EPDRs) have been found to exist in various tissues from sea urchins to humans, yet their functional role remains to be revealed. In this study, the structures of EPDR1 from frog, mouse and human were determined and analyzed. All of the EPDR1s fold into a dimer using a monomeric subunit that is mostly made up of two stacking antiparallel β-sheets with a curvature on one side, resulting in the formation of a deep hydrophobic pocket. All six of the cysteine residues in the monomeric subunit participate in the formation of three intramolecular disulfide bonds. Other interesting features of EPDR1 include two asparagine residues with glycosylation and a Ca2+-binding site. The EPDR1 fold is very similar to the folds of bacterial VioE and LolA/LolB, which also use a similar hydrophobic pocket for their respective functions as a hydrophobic substrate-binding enzyme and a lipoprotein carrier, respectively. A further fatty-acid binding assay using EPDR1 suggests that it indeed binds to fatty acids, presumably via this pocket. Additional interactome analysis of EPDR1 showed that EPDR1 interacts with insulin-like growth factor 2 receptor and flotillin proteins, which are known to be involved in protein and vesicle translocation.
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Affiliation(s)
- Jeong Kuk Park
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Keon Young Kim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Yeo Won Sim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Yong-In Kim
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - Jin Kyun Kim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Cheol Lee
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jeongran Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - J. Eugene Lee
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - SangYoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
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20
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HIV Infection Induces Extracellular Cathepsin B Uptake and Damage to Neurons. Sci Rep 2019; 9:8006. [PMID: 31142756 PMCID: PMC6541605 DOI: 10.1038/s41598-019-44463-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 04/23/2019] [Indexed: 01/22/2023] Open
Abstract
HIV-associated neurocognitive disorders prevail in 20-50 percent of infected individuals. Macrophages transmigrate through the blood brain barrier during HIV-1 infection, triggering neuronal dysfunction. HIV-infected macrophages secrete cathepsin B (CATB), and serum amyloid p component (SAPC), inducing neuronal apoptosis by an unknown mechanism. We hypothesized that HIV infection facilitates CATB/SAPC secretion from macrophages followed by neuronal internalization, promoting dysfunction. SK-N-SH neuronal cells were exposed to active recombinant histidine-tagged cathepsin B (His-CATB). His-CATB entry was tracked by intracellular flow cytometry, and neuronal dysfunction was verified by western blot. Macrophage-derived extracellular vesicles (EVs) were tested for the presence of CATB and SAPC. Neurons internalized His-CATB, an effect that was partially decreased by pre-treatment with anti-CATB antibody. Pre-treatment with CATB and SAPC antibodies decreased cleavage of caspase-3 and restored synaptophysin in neurons. Neurons exposed to macrophage-conditioned media differentially internalized His-CATB, dependent on the HIV replication levels. Finally, CATB and SAPC were secreted in EVs. We report for the first time that CATB is secreted from macrophages both free and in EVs, and is internalized by neurons. Moreover, HIV-replication levels modulate the amount of CATB neuronal uptake, and neuronal dysfunction can be decreased with CATB antibodies. In conclusion, the CATB/SAPC complex represents a novel target against HIV-associated neurocognitive disorders.
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21
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Zhao W, Su J, Wang Y, Qian T, Liu Y. Functional importance of palmitoyl protein thioesterase 1 (PPT1) expression by Sertoli cells in mediating cholesterol metabolism and maintenance of sperm quality. Mol Reprod Dev 2019; 86:984-998. [PMID: 31134714 DOI: 10.1002/mrd.23173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/23/2019] [Accepted: 05/01/2019] [Indexed: 12/13/2022]
Abstract
Sertoli cells are a type of nurse cell in the seminiferous epithelium that are crucial for sustaining spermatogenesis by extending nutritional and energy support to the developing germ cells. Dysfunction of Sertoli cells could cause disordered spermatogenesis and reduced fertility in males. In this study, we focused on the expression and function of palmitoyl protein thioesterase 1 (PPT1), a lysosomal depalmitoylating enzyme, in Sertoli cells. Here, we show that PPT1 expression in Sertoli cells is responsive to cholesterol treatment and that specific knockout of Ppt1 in Sertoli cells causes male subfertility associated with poor sperm quality and a high ratio of sperm deformity. Specifically, Ppt1 deficiency leads to poor cell variably accompanied with abnormal lysosome accumulation and increased cholesterol levels in Sertoli cells. Further, Ppt1 deficiency results in poor adhesion of developing germ cells to Sertoli cells in the seminiferous epithelium, which is likely to be responsible for the reduced male fertility as a consequence of declines in sperm count and motility as well as a high incidence of sperm head deformity. In summary, PPT1 affects sperm quality and male fertility through regulating lysosomal function and cholesterol metabolism in Sertoli cells.
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Affiliation(s)
- Wenzhen Zhao
- Department of Histology and Embryology, School of Basic Medical Science, Dali University, Yunnan, China.,Institute of Reproductive Medicine, Dali University, Yunnan, China
| | - Juan Su
- Department of Physiology and Pathophysiology, School of Basic Medical Science, Dali University, Yunnan, China
| | - Yuntao Wang
- Department of Histology and Embryology, School of Basic Medical Science, Dali University, Yunnan, China
| | - Tijun Qian
- Vector Laboratory, Institute of Pathogens and Vectors, Dali University, Yunnan, China
| | - Yue Liu
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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22
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Wei Y, Xiong ZJ, Li J, Zou C, Cairo CW, Klassen JS, Privé GG. Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters. Commun Biol 2019; 2:52. [PMID: 30729188 PMCID: PMC6363788 DOI: 10.1038/s42003-018-0262-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/11/2018] [Indexed: 01/01/2023] Open
Abstract
EPDR1, a member of the ependymin-related protein family, is a relatively uncharacterized protein found in the lysosomes and secretomes of most vertebrates. Despite having roles in human disease and health, the molecular functions of EPDR1 remain unknown. Here, we present crystal structures of human EPDR1 and reveal that the protein adopts a fold previously seen only in bacterial proteins related to the LolA lipoprotein transporter. EPDR1 forms a homodimer with an overall shape resembling a half-shell with two non-overlapping hydrophobic grooves on the flat side of the hemisphere. EPDR1 can interact with membranes that contain negatively charged lipids, including BMP and GM1, and we suggest that EPDR1 may function as a lysosomal activator protein or a lipid transporter. A phylogenetic analysis reveals that the fold is more widely distributed than previously suspected, with representatives identified in all branches of cellular life.
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Affiliation(s)
- Yong Wei
- Princess Margaret Cancer Centre, Toronto, M5G 1L7 ON Canada
| | - Zi Jian Xiong
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Jun Li
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - Chunxia Zou
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - Gilbert G. Privé
- Princess Margaret Cancer Centre, Toronto, M5G 1L7 ON Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8 ON Canada
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7 ON Canada
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23
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Mukherjee AB, Appu AP, Sadhukhan T, Casey S, Mondal A, Zhang Z, Bagh MB. Emerging new roles of the lysosome and neuronal ceroid lipofuscinoses. Mol Neurodegener 2019; 14:4. [PMID: 30651094 PMCID: PMC6335712 DOI: 10.1186/s13024-018-0300-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/04/2018] [Indexed: 12/04/2022] Open
Abstract
Neuronal Ceroid Lipofuscinoses (NCLs), commonly known as Batten disease, constitute a group of the most prevalent neurodegenerative lysosomal storage disorders (LSDs). Mutations in at least 13 different genes (called CLNs) cause various forms of NCLs. Clinically, the NCLs manifest early impairment of vision, progressive decline in cognitive and motor functions, seizures and a shortened lifespan. At the cellular level, all NCLs show intracellular accumulation of autofluorescent material (called ceroid) and progressive neuron loss. Despite intense studies the normal physiological functions of each of the CLN genes remain poorly understood. Consequently, the development of mechanism-based therapeutic strategies remains challenging. Endolysosomal dysfunction contributes to pathogenesis of virtually all LSDs. Studies within the past decade have drastically changed the notion that the lysosomes are merely the terminal degradative organelles. The emerging new roles of the lysosome include its central role in nutrient-dependent signal transduction regulating metabolism and cellular proliferation or quiescence. In this review, we first provide a brief overview of the endolysosomal and autophagic pathways, lysosomal acidification and endosome-lysosome and autophagosome-lysosome fusions. We emphasize the importance of these processes as their dysregulation leads to pathogenesis of many LSDs including the NCLs. We also describe what is currently known about each of the 13 CLN genes and their products and how understanding the emerging new roles of the lysosome may clarify the underlying pathogenic mechanisms of the NCLs. Finally, we discuss the current and emerging therapeutic strategies for various NCLs.
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Affiliation(s)
- Anil B. Mukherjee
- Section on Developmental Genetics, Program on Endocrinology and Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892-1830 USA
| | - Abhilash P. Appu
- Section on Developmental Genetics, Program on Endocrinology and Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892-1830 USA
| | - Tamal Sadhukhan
- Section on Developmental Genetics, Program on Endocrinology and Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892-1830 USA
| | - Sydney Casey
- Section on Developmental Genetics, Program on Endocrinology and Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892-1830 USA
| | - Avisek Mondal
- Section on Developmental Genetics, Program on Endocrinology and Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892-1830 USA
| | - Zhongjian Zhang
- Section on Developmental Genetics, Program on Endocrinology and Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892-1830 USA
- Present address: Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003 Henan China
| | - Maria B. Bagh
- Section on Developmental Genetics, Program on Endocrinology and Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892-1830 USA
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24
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Sleat DE, Tannous A, Sohar I, Wiseman JA, Zheng H, Qian M, Zhao C, Xin W, Barone R, Sims KB, Moore DF, Lobel P. Proteomic Analysis of Brain and Cerebrospinal Fluid from the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Potential Biomarkers. J Proteome Res 2017; 16:3787-3804. [PMID: 28792770 DOI: 10.1021/acs.jproteome.7b00460] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Clinical trials have been conducted for the neuronal ceroid lipofuscinoses (NCLs), a group of neurodegenerative lysosomal diseases that primarily affect children. Whereas clinical rating systems will evaluate long-term efficacy, biomarkers to measure short-term response to treatment would be extremely valuable. To identify candidate biomarkers, we analyzed autopsy brain and matching CSF samples from controls and three genetically distinct NCLs due to deficiencies in palmitoyl protein thioesterase 1 (CLN1 disease), tripeptidyl peptidase 1 (CLN2 disease), and CLN3 protein (CLN3 disease). Proteomic and biochemical methods were used to analyze lysosomal proteins, and, in general, we find that changes in protein expression compared with control were most similar between CLN2 disease and CLN3 disease. This is consistent with previous observations of biochemical similarities between these diseases. We also conducted unbiased proteomic analyses of CSF and brain using isobaric labeling/quantitative mass spectrometry. Significant alterations in protein expression were identified in each NCL, including reduced STXBP1 in CLN1 disease brain. Given the confounding variable of post-mortem changes, additional validation is required, but this study provides a useful starting set of candidate NCL biomarkers for further evaluation.
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Affiliation(s)
- David E Sleat
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences , Piscataway, New Jersey 08854, United States
| | - Abla Tannous
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Istvan Sohar
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Jennifer A Wiseman
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Meiqian Qian
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Winnie Xin
- Neurogenetics DNA Diagnostic Laboratory, Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Rosemary Barone
- Neurogenetics DNA Diagnostic Laboratory, Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Katherine B Sims
- Neurogenetics DNA Diagnostic Laboratory, Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Dirk F Moore
- Department of Biostatistics, School of Public Health, Rutgers - The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences , Piscataway, New Jersey 08854, United States
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25
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Markmann S, Krambeck S, Hughes CJ, Mirzaian M, Aerts JMFG, Saftig P, Schweizer M, Vissers JPC, Braulke T, Damme M. Quantitative Proteome Analysis of Mouse Liver Lysosomes Provides Evidence for Mannose 6-phosphate-independent Targeting Mechanisms of Acid Hydrolases in Mucolipidosis II. Mol Cell Proteomics 2017; 16:438-450. [PMID: 28062798 DOI: 10.1074/mcp.m116.063636] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 12/24/2016] [Indexed: 01/01/2023] Open
Abstract
The efficient receptor-mediated targeting of soluble lysosomal proteins to lysosomes requires the modification with mannose 6-phosphate (M6P) residues. Although the absence of M6P results in misrouting and hypersecretion of lysosomal enzymes in many cells, normal levels of lysosomal enzymes have been reported in liver of patients lacking the M6P-generating phosphotransferase (PT). The identity of lysosomal proteins depending on M6P has not yet been comprehensively analyzed. In this study we purified lysosomes from liver of PT-defective mice and 67 known soluble lysosomal proteins were identified that illustrated quantitative changes using an ion mobility-assisted data-independent label-free LC-MS approach. After validation of various differentially expressed lysosomal components by Western blotting and enzyme activity assays, the data revealed a small number of lysosomal proteins depending on M6P, including neuraminidase 1, cathepsin F, Npc2, and cathepsin L, whereas the majority reach lysosomes by alternative pathways. These data were compared with findings on cultured hepatocytes and liver sinusoid endothelial cells isolated from the liver of wild-type and PT-defective mice. Our findings show that the relative expression, targeting efficiency and lysosomal localization of lysosomal proteins tested in cultured hepatic cells resemble their proportion in isolated liver lysosomes. Hypersecretion of newly synthesized nonphosphorylated lysosomal proteins suggest that secretion-recapture mechanisms contribute to maintain major lysosomal functions in liver.
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Affiliation(s)
- Sandra Markmann
- From the ‡Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,§Waters Corporation, Wilmslow, SK9 4AX, United Kingdom
| | - Svenja Krambeck
- From the ‡Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,§Waters Corporation, Wilmslow, SK9 4AX, United Kingdom
| | | | - Mina Mirzaian
- ¶Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
| | - Johannes M F G Aerts
- ¶Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
| | - Paul Saftig
- ‖Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, 24098 Kiel, Germany
| | - Michaela Schweizer
- **Morphology Unit, Center for Molecular Neurobiology ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Thomas Braulke
- From the ‡Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany;
| | - Markus Damme
- ‖Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, 24098 Kiel, Germany;
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26
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Cell biology of the NCL proteins: What they do and don't do. Biochim Biophys Acta Mol Basis Dis 2015; 1852:2242-55. [PMID: 25962910 DOI: 10.1016/j.bbadis.2015.04.027] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 02/06/2023]
Abstract
The fatal, primarily childhood neurodegenerative disorders, neuronal ceroid lipofuscinoses (NCLs), are currently associated with mutations in 13 genes. The protein products of these genes (CLN1 to CLN14) differ in their function and their intracellular localization. NCL-associated proteins have been localized mostly in lysosomes (CLN1, CLN2, CLN3, CLN5, CLN7, CLN10, CLN12 and CLN13) but also in the Endoplasmic Reticulum (CLN6 and CLN8), or in the cytosol associated to vesicular membranes (CLN4 and CLN14). Some of them such as CLN1 (palmitoyl protein thioesterase 1), CLN2 (tripeptidyl-peptidase 1), CLN5, CLN10 (cathepsin D), and CLN13 (cathepsin F), are lysosomal soluble proteins; others like CLN3, CLN7, and CLN12, have been proposed to be lysosomal transmembrane proteins. In this review, we give our views and attempt to summarize the proposed and confirmed functions of each NCL protein and describe and discuss research results published since the last review on NCL proteins. This article is part of a Special Issue entitled: "Current Research on the Neuronal Ceroid Lipofuscinoses (Batten Disease)".
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27
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Ji IJ, Hua S, Shin DH, Seo N, Hwang JY, Jang IS, Kang MG, Choi JS, An HJ. Spatially-Resolved Exploration of the Mouse Brain Glycome by Tissue Glyco-Capture (TGC) and Nano-LC/MS. Anal Chem 2015; 87:2869-77. [DOI: 10.1021/ac504339t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- In Jung Ji
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Serenus Hua
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Dong Hee Shin
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Nari Seo
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Jae Yun Hwang
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Ik-Soon Jang
- Division
of Life Science, Korea Basic Science Institute, Daejeon 305-764, Korea
| | - Myoung-Goo Kang
- Center
for Cognition and Sociality, Institute for Basic Science, Daejeon 305-764, Korea
| | - Jong-Soon Choi
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
- Division
of Life Science, Korea Basic Science Institute, Daejeon 305-764, Korea
| | - Hyun Joo An
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
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28
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Puissant E, Gilis F, Dogné S, Flamion B, Jadot M, Boonen M. Subcellular trafficking and activity of Hyal-1 and its processed forms in murine macrophages. Traffic 2014; 15:500-15. [PMID: 24502338 DOI: 10.1111/tra.12162] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/04/2014] [Accepted: 02/06/2014] [Indexed: 11/30/2022]
Abstract
The hyaluronidase Hyal-1 is an acid hydrolase that degrades hyaluronic acid (HA), a component of the extracellular matrix. It is often designated as a lysosomal protein. Yet few data are available on its intracellular localization and trafficking. We demonstrate here that in RAW264.7 murine macrophages, Hyal-1 is synthesized as a glycosylated precursor that is only weakly mannose 6-phosphorylated. Nevertheless, this precursor traffics to endosomes, via a mannose 6-phosphate-independent secretion/recapture mechanism that involves the mannose receptor. Once in endosomes, it is processed into a lower molecular mass form that is transported to lysosomes, where its activity could be detected using native gel zymography. Indeed, this activity co-distributed with lysosomal hydrolases in the densest fraction of a self-forming Percoll(TM) density gradient. Moreover, it shifted toward the lower density region, in parallel with those hydrolases, when a decrease of lysosomal density was induced by the endocytosis of sucrose. Interestingly, the activity of the processed form of Hyal-1 was largely underestimated when assayed by zymography after SDS-PAGE and subsequent renaturation of the proteins, by contrast to the full-length protein that could efficiently degrade HA in those conditions. These results suggest that noncovalent associations support the lysosomal activity of Hyal-1.
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Affiliation(s)
- Emeline Puissant
- URPhyM-Laboratoire de Chimie Physiologique, NARILIS, University of Namur, Namur, Belgium
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29
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Petrey AC, de la Motte CA. Hyaluronan, a crucial regulator of inflammation. Front Immunol 2014; 5:101. [PMID: 24653726 PMCID: PMC3949149 DOI: 10.3389/fimmu.2014.00101] [Citation(s) in RCA: 337] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 02/25/2014] [Indexed: 12/30/2022] Open
Abstract
Hyaluronan (HA), a major component of the extracellular matrix (ECM), plays a key role in regulating inflammation. Inflammation is associated with accumulation and turnover of HA polymers by multiple cell types. Increasingly through the years, HA has become recognized as an active participant in inflammatory, angiogenic, fibrotic, and cancer promoting processes. HA and its binding proteins regulate the expression of inflammatory genes, the recruitment of inflammatory cells, the release of inflammatory cytokines, and can attenuate the course of inflammation, providing protection against tissue damage. A growing body of evidence suggests the cell responses are HA molecular weight dependent. HA fragments generated by multiple mechanisms throughout the course of inflammatory pathologies, elicit cellular responses distinct from intact HA. This review focuses on the role of HA in the promotion and resolution of inflammation.
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Affiliation(s)
- Aaron C Petrey
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic Foundation , Cleveland, OH , USA
| | - Carol A de la Motte
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic Foundation , Cleveland, OH , USA
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30
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Tribl F, Meyer HE, Marcus K. Analysis of organelles within the nervous system: impact on brain and organelle functions. Expert Rev Proteomics 2014; 5:333-51. [DOI: 10.1586/14789450.5.2.333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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31
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NCL disease mechanisms. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1882-93. [DOI: 10.1016/j.bbadis.2013.05.014] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 01/13/2023]
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32
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Repo H, Kuokkanen E, Oksanen E, Goldman A, Heikinheimo P. Is the bovine lysosomal phospholipase B-like protein an amidase? Proteins 2013; 82:300-11. [PMID: 23934913 DOI: 10.1002/prot.24388] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/17/2013] [Accepted: 07/26/2013] [Indexed: 12/17/2022]
Abstract
The main function of lysosomal proteins is to degrade cellular macromolecules. We purified a novel lysosomal protein to homogeneity from bovine kidneys. By gene annotation, this protein is defined as a bovine phospholipase B-like protein 1 (bPLBD1) and, to better understand its biological function, we solved its structure at 1.9 Å resolution. We showed that bPLBD1 has uniform noncomplex-type N-glycosylation and that it localized to the lysosome. The first step in lysosomal protein transport, the initiation of mannose-6-phosphorylation by a N-acetylglucosamine-1-phosphotransferase, requires recognition of at least two distinct lysines on the protein surface. We identified candidate lysines by analyzing the structural and sequentially conserved N-glycosylation sites and lysines in bPLBD1 and in the homologous mouse PLBD2. Our model suggests that N408 is the primarily phosphorylated glycan, and K358 a key residue for N-acetylglucosamine-1-phosphotransferase recognition. Two other lysines, K334 and K342, provide the required second site for N-acetylglucosamine-1-phosphotransferase recognition. bPLBD1 is an N-terminal nucleophile (Ntn) hydrolase. By comparison with other Ntn-hydrolases, we conclude that the acyl moiety of PLBD1 substrate must be small to fit the putative binding pocket, whereas the space for the rest of the substrate is a large open cleft. Finally, as all the known substrates of Ntn-hydrolases have amide bonds, we suggest that bPLBD1 may be an amidase or peptidase instead of lipase, explaining the difficulty in finding a good substrate for any members of the PLBD family.
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Affiliation(s)
- Heidi Repo
- Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland; Department of Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
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33
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Chapel A, Kieffer-Jaquinod S, Sagné C, Verdon Q, Ivaldi C, Mellal M, Thirion J, Jadot M, Bruley C, Garin J, Gasnier B, Journet A. An extended proteome map of the lysosomal membrane reveals novel potential transporters. Mol Cell Proteomics 2013; 12:1572-88. [PMID: 23436907 PMCID: PMC3675815 DOI: 10.1074/mcp.m112.021980] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 02/01/2013] [Indexed: 12/22/2022] Open
Abstract
Lysosomes are membrane-bound endocytic organelles that play a major role in degrading cell macromolecules and recycling their building blocks. A comprehensive knowledge of the lysosome function requires an extensive description of its content, an issue partially addressed by previous proteomic analyses. However, the proteins underlying many lysosomal membrane functions, including numerous membrane transporters, remain unidentified. We performed a comparative, semi-quantitative proteomic analysis of rat liver lysosome-enriched and lysosome-nonenriched membranes and used spectral counts to evaluate the relative abundance of proteins. Among a total of 2,385 identified proteins, 734 proteins were significantly enriched in the lysosomal fraction, including 207 proteins already known or predicted as endo-lysosomal and 94 proteins without any known or predicted subcellular localization. The remaining 433 proteins had been previously assigned to other subcellular compartments but may in fact reside on lysosomes either predominantly or as a secondary location. Many membrane-associated complexes implicated in diverse processes such as degradation, membrane trafficking, lysosome biogenesis, lysosome acidification, signaling, and nutrient sensing were enriched in the lysosomal fraction. They were identified to an unprecedented extent as most, if not all, of their subunits were found and retained by our screen. Numerous transporters were also identified, including 46 novel potentially lysosomal proteins. We expressed 12 candidates in HeLa cells and observed that most of them colocalized with the lysosomal marker LAMP1, thus confirming their lysosomal residency. This list of candidate lysosomal proteins substantially increases our knowledge of the lysosomal membrane and provides a basis for further characterization of lysosomal functions.
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Affiliation(s)
- Agnès Chapel
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Sylvie Kieffer-Jaquinod
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Corinne Sagné
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Quentin Verdon
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
- §§Graduate School ED 419, Université Paris-Sud 11, Hôpital Bicêtre, F-94276 Le Kremlin Bicêtre France, and
| | - Corinne Ivaldi
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Mourad Mellal
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jaqueline Thirion
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Michel Jadot
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Christophe Bruley
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jérôme Garin
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Bruno Gasnier
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Agnès Journet
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
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34
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Begara-Morales JC, López-Jaramillo FJ, Sánchez-Calvo B, Carreras A, Ortega-Muñoz M, Santoyo-González F, Corpas FJ, Barroso JB. Vinyl sulfone silica: application of an open preactivated support to the study of transnitrosylation of plant proteins by S-nitrosoglutathione. BMC PLANT BIOLOGY 2013; 13:61. [PMID: 23586608 PMCID: PMC3639107 DOI: 10.1186/1471-2229-13-61] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/25/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND S-nitrosylaton is implicated in the regulation of numerous signaling pathways with a diversity of regulatory roles. The high lability of the S-NO bond makes the study of proteins regulated by S-nitrosylation/denitrosylation a challenging task and most studies have focused on already S-nitrosylated proteins. We hypothesize that: i) S-nitrosoglutathione (GSNO) transnitrosylation is a feasible mechanism to account for the physiological S-nitrosylation of rather electropositive sulfur atoms from proteins, ii) affinity chromatography is a suitable approach to isolate proteins that are prone to undergo S-transnitrosylation and iii) vinyl sulfone silica is a suitable chromatographic bead. RESULTS The combination of vinyl sulfone silica with GSNO yielded an affinity resin that withstood high ionic strength without shrinking or deforming and that it was suitable to isolate potential GSNO transnitrosylation target candidates. Fractions eluted at 1500 mM NaCl resulted in a symmetrical peak for both, protein and S-nitrosothiols, supporting the idea of transnitrosylation by GSNO as a selective process that involves strong and specific interactions with the target protein. Proteomic analysis led to the identification of 22 physiological significant enzymes that differ with the tissue analyzed, being regulatory proteins the most abundant group in hypocotyls. The identification of chloroplastidic FBPase, proteasome, GTP-binding protein, heat shock Hsp70, syntaxin, catalase I, thioredoxin peroxidase and cytochrome P450 that have already been reported as S-nitrosylated by other techniques can be considered as internal positive controls that validate our experimental approach. An additional validation was provided by the prediction of the S-nitrosylation sites in 19 of the GSNO transnitrosylation target candidates. CONCLUSIONS Vinyl sulfone silica is an open immobilization support that can be turned ad hoc and in a straightforward manner into an affinity resin. Its potential in omic sciences was successfully put to test in the context of the analysis of post-translational modification by S-nitrosylation with two different tissues: mature pea leaves and embryogenic sunflower hypocotyls. The identified proteins reveal an intriguing overlap among S-nitrosylation and both tyrosine nitration and thioredoxin regulation. Chloroplastidic FBPase is a paradigm of such overlap of post-translational modifications since it is reversible modified by thioredoxin and S-nitrosylation and irreversibly by tyrosine nitration. Our results suggest a complex interrelation among different modulation mechanisms mediated by NO-derived molecules.
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Affiliation(s)
- Juan C Begara-Morales
- Grupo de Señalización Molecular y Sistemas Antioxidantes en Plantas, Unidad Asociada al CSIC (EEZ), Departamento de Bioquímica y Biología Molecular, Universidad de Jaén, de Jaén, Spain
| | | | - Beatriz Sánchez-Calvo
- Grupo de Señalización Molecular y Sistemas Antioxidantes en Plantas, Unidad Asociada al CSIC (EEZ), Departamento de Bioquímica y Biología Molecular, Universidad de Jaén, de Jaén, Spain
| | - Alfonso Carreras
- Grupo de Señalización Molecular y Sistemas Antioxidantes en Plantas, Unidad Asociada al CSIC (EEZ), Departamento de Bioquímica y Biología Molecular, Universidad de Jaén, de Jaén, Spain
| | | | | | - Francisco J Corpas
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Juan B Barroso
- Grupo de Señalización Molecular y Sistemas Antioxidantes en Plantas, Unidad Asociada al CSIC (EEZ), Departamento de Bioquímica y Biología Molecular, Universidad de Jaén, de Jaén, Spain
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Brozzi A, Urbanelli L, Germain PL, Magini A, Emiliani C. hLGDB: a database of human lysosomal genes and their regulation. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat024. [PMID: 23584836 PMCID: PMC3625959 DOI: 10.1093/database/bat024] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lysosomes are cytoplasmic organelles present in almost all eukaryotic cells, which play a fundamental role in key aspects of cellular homeostasis such as membrane repair, autophagy, endocitosis and protein metabolism. The characterization of the genes and enzymes constituting the lysosome represents a central issue to be addressed toward a better understanding of the biology of this organelle. In humans, mutations that cause lysosomal enzyme deficiencies result in >50 different disorders and severe pathologies. So far, many experimental efforts using different methodologies have been carried out to identity lysosomal genes. The Human Lysosome Gene Database (hLGDB) is the first resource that provides a comprehensive and accessible census of the human genes belonging to the lysosomal system. This database was developed by collecting and annotating gene lists from many different sources. References to the studies that have identified each gene are provided together with cross databases gene related information. Special attention has been given to the regulation of the genes through microRNAs and the transcription factor EB. The hLGDB can be easily queried to retrieve, combine and analyze information on different lists of lysosomal genes and their regulation by microRNA (binding sites predicted by five different algorithms). The hLGDB is an open access dynamic project that will permit in the future to collapse in a unique publicly accessible resource all the available biological information about lysosome genes and their regulation. Database URL:http://lysosome.unipg.it/
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Affiliation(s)
- Alessandro Brozzi
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Via del Giochetto, 06123 Perugia, Italy
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36
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Sleat DE, Sun P, Wiseman JA, Huang L, El-Banna M, Zheng H, Moore DF, Lobel P. Extending the mannose 6-phosphate glycoproteome by high resolution/accuracy mass spectrometry analysis of control and acid phosphatase 5-deficient mice. Mol Cell Proteomics 2013; 12:1806-17. [PMID: 23478313 DOI: 10.1074/mcp.m112.026179] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In mammals, most newly synthesized lumenal lysosomal proteins are delivered to the lysosome by the mannose 6-phosphate (Man6P) targeting pathway. Man6P -containing proteins can be affinity-purified and characterized using proteomic approaches, and such studies have led to the discovery of new lysosomal proteins and associated human disease genes. One limitation to this approach is that in most cell types the Man6P modification is rapidly removed by acid phosphatase 5 (ACP5) after proteins are targeted to the lysosome, and thus, some lysosomal proteins may escape detection. In this study, we have extended the analysis of the lysosomal proteome using high resolution/accuracy mass spectrometry to identify and quantify proteins in a combined analysis of control and ACP5-deficient mice. To identify Man6P glycoproteins with limited tissue distribution, we analyzed multiple tissues and used statistical approaches to identify proteins that are purified with high specificity. In addition to 68 known Man6P glycoproteins, 165 other murine proteins were identified that may contain Man6P and may thus represent novel lysosomal residents. For four of these lysosomal candidates, (lactoperoxidase, phospholipase D family member 3, ribonuclease 6, and serum amyloid P component), we demonstrate lysosomal residence based on the colocalization of fluorescent fusion proteins with a lysosomal marker.
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Affiliation(s)
- David E Sleat
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA.
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37
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Kollmann K, Uusi-Rauva K, Scifo E, Tyynelä J, Jalanko A, Braulke T. Cell biology and function of neuronal ceroid lipofuscinosis-related proteins. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1866-81. [PMID: 23402926 DOI: 10.1016/j.bbadis.2013.01.019] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/18/2013] [Accepted: 01/23/2013] [Indexed: 01/17/2023]
Abstract
Neuronal ceroid lipofuscinoses (NCL) comprise a group of inherited lysosomal disorders with variable age of onset, characterized by lysosomal accumulation of autofluorescent ceroid lipopigments, neuroinflammation, photoreceptor- and neurodegeneration. Most of the NCL-related genes encode soluble and transmembrane proteins which localize to the endoplasmic reticulum or to the endosomal/lysosomal compartment and directly or indirectly regulate lysosomal function. Recently, exome sequencing led to the identification of four novel gene defects in NCL patients and a new NCL nomenclature currently comprising CLN1 through CLN14. Although the precise function of most of the NCL proteins remains elusive, comprehensive analyses of model organisms, particularly mouse models, provided new insight into pathogenic mechanisms of NCL diseases and roles of mutant NCL proteins in cellular/subcellular protein and lipid homeostasis, as well as their adaptive/compensatorial regulation at the transcriptional level. This review summarizes the current knowledge on the expression, function and regulation of NCL proteins and their impact on lysosomal integrity. This article is part of a Special Issue entitled: The Neuronal Ceroid Lipofuscinoses or Batten Disease.
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Affiliation(s)
- Katrin Kollmann
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Palmieri M, Impey S, Kang H, di Ronza A, Pelz C, Sardiello M, Ballabio A. Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. Hum Mol Genet 2011; 20:3852-66. [PMID: 21752829 DOI: 10.1093/hmg/ddr306] [Citation(s) in RCA: 696] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In metazoans, lysosomes are the center for the degradation of macromolecules and play a key role in a variety of cellular processes, such as autophagy, exocytosis and membrane repair. Defects of lysosomal pathways are associated with lysosomal storage disorders and with several late onset neurodegenerative diseases. We recently discovered the CLEAR (Coordinated Lysosomal Expression and Regulation) gene network and its master gene transcription factor EB (TFEB), which regulates lysosomal biogenesis and function. Here, we used a combination of genomic approaches, including ChIP-seq (sequencing of chromatin immunoprecipitate) analysis, profiling of TFEB-mediated transcriptional induction, genome-wide mapping of TFEB target sites and recursive expression meta-analysis of TFEB targets, to identify 471 TFEB direct targets that represent essential components of the CLEAR network. This analysis revealed a comprehensive system regulating the expression, import and activity of lysosomal enzymes that control the degradation of proteins, glycosaminoglycans, sphingolipids and glycogen. Interestingly, the CLEAR network appears to be involved in the regulation of additional lysosome-associated processes, including autophagy, exo- and endocytosis, phagocytosis and immune response. Furthermore, non-lysosomal enzymes involved in the degradation of essential proteins such as hemoglobin and chitin are also part of the CLEAR network. Finally, we identified nine novel lysosomal proteins by using the CLEAR network as a tool for prioritizing candidates. This study provides potential therapeutic targets to modulate cellular clearance in a variety of disease conditions.
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Affiliation(s)
- Michela Palmieri
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
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Linterman KS, Palmer DN, Kay GW, Barry LA, Mitchell NL, McFarlane RG, Black MA, Sands MS, Hughes SM. Lentiviral-mediated gene transfer to the sheep brain: implications for gene therapy in Batten disease. Hum Gene Ther 2011; 22:1011-20. [PMID: 21595499 DOI: 10.1089/hum.2011.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The neuronal ceroid lipofuscinoses (NCLs; Batten disease) are inherited neurodegenerative lysosomal storage diseases with common clinical features of blindness and seizures culminating in premature death. Gene-therapy strategies for these diseases depend on whether the missing activity is a secreted lysosomal protein taken up by neighboring cells, or an intramembrane protein that requires careful targeting. Therapies are best developed in animal models with large complex human-like brains. Lentiviral-mediated gene delivery to neural cell cultures from normal sheep and sheep affected with an NCL resulted in green fluorescent protein (GFP) expression in neurons and neuroblasts, more efficiently than in astrocytes. Similar transgene expression was obtained from two constitutive promoters, the viral MND promoter and the human EF1α promoter. In vivo studies showed stable and persistent GFP expression throughout the cell bodies, axons, and dendrites from intracortical injections and indicated ependymal and subependymal transduction. The sheep showed no ill effects from the injections. These data support continuing gene-therapy trials in the sheep models of Batten disease.
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Affiliation(s)
- Kathryn S Linterman
- Department of Biochemistry, School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
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40
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Abstract
Lysosomes are organelles of eukaryotic cells that are critically involved in the degradation of macromolecules mainly delivered by endocytosis and autophagocytosis. Degradation is achieved by more than 60 hydrolases sequestered by a single phospholipid bilayer. The lysosomal membrane facilitates interaction and fusion with other compartments and harbours transport proteins catalysing the export of catabolites, thereby allowing their recycling. Lysosomal proteins have been addressed in various proteomic studies that are compared in this review regarding the source of material, the organelle/protein purification scheme, the proteomic methodology applied and the proteins identified. Distinguishing true constituents of an organelle from co-purifying contaminants is a central issue in subcellular proteomics, with additional implications for lysosomes as being the site of degradation of many cellular and extracellular proteins. Although many of the lysosomal hydrolases were identified by classical biochemical approaches, the knowledge about the protein composition of the lysosomal membrane has remained fragmentary for a long time. Using proteomics many novel lysosomal candidate proteins have been discovered and it can be expected that their functional characterisation will help to understand functions of lysosomes at a molecular level that have been characterised only phenomenologically so far and to generally deepen our understanding of this indispensable organelle.
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Affiliation(s)
- Bernd A Schröder
- Biochemical Institute, Christian-Albrechts University, Kiel, Germany.
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41
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Robinson MS, Sahlender DA, Foster SD. Rapid inactivation of proteins by rapamycin-induced rerouting to mitochondria. Dev Cell 2010; 18:324-31. [PMID: 20159602 PMCID: PMC2845799 DOI: 10.1016/j.devcel.2009.12.015] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 10/28/2009] [Accepted: 12/17/2009] [Indexed: 11/26/2022]
Abstract
We have developed a method for rapidly inactivating proteins with rapamycin-induced heterodimerization. Cells were stably transfected with siRNA-resistant, FKBP-tagged subunits of the adaptor protein (AP) complexes of clathrin-coated vesicles (CCVs), together with an FKBP and rapamycin-binding domain-containing construct with a mitochondrial targeting signal. Knocking down the endogenous subunit with siRNA, and then adding rapamycin, caused the APs to be rerouted to mitochondria within seconds. Rerouting AP-2 to mitochondria effectively abolished clathrin-mediated endocytosis of transferrin. In cells with rerouted AP-1, endocytosed cation-independent mannose 6-phosphate receptor (CIMPR) accumulated in a peripheral compartment, and isolated CCVs had reduced levels of CIMPR, but normal levels of the lysosomal hydrolase DNase II. Both observations support a role for AP-1 in retrograde trafficking. This type of approach, which we call a “knocksideways,” should be widely applicable as a means of inactivating proteins with a time scale of seconds or minutes rather than days.
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Affiliation(s)
- Margaret S Robinson
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, UK.
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42
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Lyly A, von Schantz C, Heine C, Schmiedt ML, Sipilä T, Jalanko A, Kyttälä A. Novel interactions of CLN5 support molecular networking between Neuronal Ceroid Lipofuscinosis proteins. BMC Cell Biol 2009; 10:83. [PMID: 19941651 PMCID: PMC2790443 DOI: 10.1186/1471-2121-10-83] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 11/26/2009] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Neuronal ceroid lipofuscinoses (NCLs) comprise at least eight genetically characterized neurodegenerative disorders of childhood. Despite of genetic heterogeneity, the high similarity of clinical symptoms and pathology of different NCL disorders suggest cooperation between different NCL proteins and common mechanisms of pathogenesis. Here, we have studied molecular interactions between NCL proteins, concentrating specifically on the interactions of CLN5, the protein underlying the Finnish variant late infantile form of NCL (vLINCLFin). RESULTS We found that CLN5 interacts with several other NCL proteins namely, CLN1/PPT1, CLN2/TPP1, CLN3, CLN6 and CLN8. Furthermore, analysis of the intracellular targeting of CLN5 together with the interacting NCL proteins revealed that over-expression of PPT1 can facilitate the lysosomal transport of mutated CLN5FinMajor, normally residing in the ER and in the Golgi complex. The significance of the novel interaction between CLN5 and PPT1 was further supported by the finding that CLN5 was also able to bind the F1-ATPase, earlier shown to interact with PPT1. CONCLUSION We have described novel interactions between CLN5 and several NCL proteins, suggesting a modifying role for these proteins in the pathogenesis of individual NCL disorders. Among these novel interactions, binding of CLN5 to CLN1/PPT1 is suggested to be the most significant one, since over-expression of PPT1 was shown to influence on the intracellular trafficking of mutated CLN5, and they were shown to share a binding partner outside the NCL protein spectrum.
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Affiliation(s)
- Annina Lyly
- National Institute for Health and Welfare (THL), Biomedicum Helsinki, Finland and FIMM, Institute for Molecular Medicine in Finland
| | - Carina von Schantz
- National Institute for Health and Welfare (THL), Biomedicum Helsinki, Finland and FIMM, Institute for Molecular Medicine in Finland
| | - Claudia Heine
- National Institute for Health and Welfare (THL), Biomedicum Helsinki, Finland and FIMM, Institute for Molecular Medicine in Finland
| | - Mia-Lisa Schmiedt
- National Institute for Health and Welfare (THL), Biomedicum Helsinki, Finland and FIMM, Institute for Molecular Medicine in Finland
| | - Tessa Sipilä
- National Institute for Health and Welfare (THL), Biomedicum Helsinki, Finland and FIMM, Institute for Molecular Medicine in Finland
| | - Anu Jalanko
- National Institute for Health and Welfare (THL), Biomedicum Helsinki, Finland and FIMM, Institute for Molecular Medicine in Finland
| | - Aija Kyttälä
- National Institute for Health and Welfare (THL), Biomedicum Helsinki, Finland and FIMM, Institute for Molecular Medicine in Finland
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43
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Saftig P, Klumperman J. Lysosome biogenesis and lysosomal membrane proteins: trafficking meets function. Nat Rev Mol Cell Biol 2009; 10:623-35. [PMID: 19672277 DOI: 10.1038/nrm2745] [Citation(s) in RCA: 1155] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lysosomes are the primary catabolic compartments of eukaryotic cells. They degrade extracellular material that has been internalized by endocytosis and intracellular components that have been sequestered by autophagy. In addition, specialized cells contain lysosome-related organelles that store and secrete proteins for cell-type-specific functions. The functioning of a healthy cell is dependent on the proper targeting of newly synthesized lysosomal proteins. Accumulating evidence suggests that there are multiple lysosomal delivery pathways that together allow the regulated and sequential deposition of lysosomal components. The importance of lysosomal trafficking pathways is emphasized by recent findings that reveal new roles for lysosomal membrane proteins in cellular physiology and in an increasing number of diseases that are characterized by defects in lysosome biogenesis.
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Affiliation(s)
- Paul Saftig
- Department of Biochemistry, Christian-Albrechts University, Kiel, Germany.
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44
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Kay GW, Verbeek MM, Furlong JM, Willemsen MAAP, Palmer DN. Neuropeptide changes and neuroactive amino acids in CSF from humans and sheep with neuronal ceroid lipofuscinoses (NCLs, Batten disease). Neurochem Int 2009; 55:783-8. [PMID: 19664668 DOI: 10.1016/j.neuint.2009.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 07/28/2009] [Accepted: 07/29/2009] [Indexed: 01/21/2023]
Abstract
Anomalies in neuropeptides and neuroactive amino acids have been postulated to play a role in neurodegeneration in a variety of diseases including the inherited neuronal ceroid lipofuscinoses (NCLs, Batten disease). These are often indicated by concentration changes in cerebrospinal fluid (CSF). Here we compare CSF neuropeptide concentrations in patients with the classical juvenile CLN3 form of NCL and the classical late infantile CLN2 form with neuropeptide and neuroactive amino acid concentrations in CSF from sheep with the late infantile variant CLN6 form. A marked disease related increase in CSF concentrations of neuron specific enolase and tau protein was noted in the juvenile CLN3 patients but this was not observed in an advanced CLN2 patient nor CLN6 affected sheep. No changes were noted in S-100b, GFAP or MBP in patients or of S-100b, GFAP or IGF-1 in affected sheep. There were no disease related changes in CSF concentrations of the neuroactive amino acids, aspartate, glutamate, serine, glutamine, glycine, taurine and GABA in these sheep. The changes observed in the CLN3 patients may be progressive markers of neurodegeneration, or of underlying metabolic changes perhaps associated with CLN3 specific changes in neuroactive amino acids, as have been postulated. The lack of changes in the CLN2 and CLN6 subjects indicate that these changes are not shared by the CLN2 or CLN6 forms and changes in CSF concentrations of these compounds are unreliable as biomarkers of neurodegeneration in the NCLs in general.
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Affiliation(s)
- Graham W Kay
- Agriculture and Life Sciences Faculty, Lincoln University, Lincoln 7647, New Zealand
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45
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von Schantz C, Kielar C, Hansen SN, Pontikis CC, Alexander NA, Kopra O, Jalanko A, Cooper JD. Progressive thalamocortical neuron loss in Cln5 deficient mice: Distinct effects in Finnish variant late infantile NCL. Neurobiol Dis 2009; 34:308-19. [PMID: 19385065 PMCID: PMC2704904 DOI: 10.1016/j.nbd.2009.02.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Finnish variant LINCL (vLINCL(Fin)) is the result of mutations in the CLN5 gene. To gain insights into the pathological staging of this fatal pediatric disorder, we have undertaken a stereological analysis of the CNS of Cln5 deficient mice (Cln5-/-) at different stages of disease progression. Consistent with human vLINCL(Fin), these Cln5-/- mice displayed a relatively late onset regional atrophy and generalized cortical thinning and synaptic pathology, preceded by early and localized glial responses within the thalamocortical system. However, in marked contrast to other forms of NCL, neuron loss in Cln5-/- mice began in the cortex and only subsequently occurred within thalamic relay nuclei. Nevertheless, as in other NCL mouse models, this progressive thalamocortical neuron loss was still most pronounced within the visual system. These data provide unexpected evidence for a distinctive sequence of neuron loss in the thalamocortical system of Cln5-/- mice, diametrically opposed to that seen in other forms of NCL.
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Affiliation(s)
- Carina von Schantz
- The National Institute for Health and Welfare and FIMM, Institute for Molecular Medicine Finland, Biomedicum Helsinki, Finland
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46
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Sleat DE, Ding L, Wang S, Zhao C, Wang Y, Xin W, Zheng H, Moore DF, Sims KB, Lobel P. Mass spectrometry-based protein profiling to determine the cause of lysosomal storage diseases of unknown etiology. Mol Cell Proteomics 2009; 8:1708-18. [PMID: 19383612 DOI: 10.1074/mcp.m900122-mcp200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Diagnosis of lysosomal storage diseases (LSDs) can be problematic in atypical cases where clinical phenotype may overlap with other genetically distinct disorders. In addition, LSDs may result from mutations in genes not yet implicated in disease. Thus, there are individuals that are diagnosed with apparent LSD based upon clinical criteria where the gene defect remains elusive. The objective of this study was to determine whether comparative proteomics approaches could provide useful insights into such cases. Most LSDs arise from mutations in genes encoding lysosomal proteins that contain mannose 6-phosphate, a carbohydrate modification that acts as a signal for intracellular targeting to the lysosome. We purified mannose 6-phosphorylated proteins by affinity chromatography and estimated relative abundance of individual proteins in the mixture by spectral counting of peptides detected by tandem mass spectrometry. Our rationale was that proteins that are decreased or absent in patients compared with controls could represent candidates for the primary defect, directing biochemical or genetics studies. On a survey of brain autopsy specimens from 23 patients with either confirmed or possible lysosomal disease, this approach identified or validated the genetic basis for disease in eight cases. These results indicate that this protein expression approach is useful for identifying defects in cases of undiagnosed lysosomal disease, and we demonstrated that it can be used with more accessible patient samples, e.g. cultured cells. Furthermore this approach was instrumental in the identification or validation of mutations in two lysosomal proteins, CLN5 and sulfamidase, in the adult form of neuronal ceroid lipofuscinosis.
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Affiliation(s)
- David E Sleat
- Center for Advanced Biotechnology and Medicine, Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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47
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Jalanko A, Braulke T. Neuronal ceroid lipofuscinoses. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2009; 1793:697-709. [DOI: 10.1016/j.bbamcr.2008.11.004] [Citation(s) in RCA: 262] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 11/06/2008] [Accepted: 11/12/2008] [Indexed: 12/26/2022]
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Kollmann K, Damme M, Deuschl F, Kahle J, D’Hooge R, Lüllmann-Rauch R, Lübke T. Molecular characterization and gene disruption of mouse lysosomal putative serine carboxypeptidase 1. FEBS J 2009; 276:1356-69. [DOI: 10.1111/j.1742-4658.2009.06877.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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49
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Lübke T, Lobel P, Sleat DE. Proteomics of the lysosome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1793:625-35. [PMID: 18977398 DOI: 10.1016/j.bbamcr.2008.09.018] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 09/24/2008] [Accepted: 09/30/2008] [Indexed: 01/05/2023]
Abstract
Defects in lysosomal function have been associated with numerous monogenic human diseases typically classified as lysosomal storage diseases. However, there is increasing evidence that lysosomal proteins are also involved in more widespread human diseases including cancer and Alzheimer disease. Thus, there is a continuing interest in understanding the cellular functions of the lysosome and an emerging approach to this is the identification of its constituent proteins by proteomic analyses. To date, the mammalian lysosome has been shown to contain approximately 60 soluble luminal proteins and approximately 25 transmembrane proteins. However, recent proteomic studies based upon affinity purification of soluble components or subcellular fractionation to obtain both soluble and membrane components suggest that there may be many more of both classes of protein resident within this organelle than previously appreciated. Discovery of such proteins has important implications for understanding the function and the dynamics of the lysosome but can also lead the way towards the discovery of the genetic basis for human diseases of hitherto unknown etiology. Here, we describe current approaches to lysosomal proteomics and data interpretation and review the new lysosomal proteins that have recently emerged from such studies.
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Affiliation(s)
- Torben Lübke
- Zentrum Biochemie und Molekulare Zellbiologie, Abteilung Biochemie II, Georg-August Universität Göttingen, 37073 Göttingen, Germany
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50
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Dahms NM, Olson LJ, Kim JJP. Strategies for carbohydrate recognition by the mannose 6-phosphate receptors. Glycobiology 2008; 18:664-78. [PMID: 18621992 DOI: 10.1093/glycob/cwn061] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The two members of the P-type lectin family, the 46 kDa cation-dependent mannose 6-phosphate receptor (CD-MPR) and the 300 kDa cation-independent mannose 6-phosphate receptor (CI-MPR), are ubiquitously expressed throughout the animal kingdom and are distinguished from all other lectins by their ability to recognize phosphorylated mannose residues. The best-characterized function of the MPRs is their ability to direct the delivery of approximately 60 different newly synthesized soluble lysosomal enzymes bearing mannose 6-phosphate (Man-6-P) on their N-linked oligosaccharides to the lysosome. In addition to its intracellular role in lysosome biogenesis, the CI-MPR, but not the CD-MPR, participates in a number of other biological processes by interacting with various molecules at the cell surface. The list of extracellular ligands recognized by this multifunctional receptor has grown to include a diverse spectrum of Man-6-P-containing proteins as well as several non-Man-6-P-containing ligands. Recent structural studies have given us a clearer view of how these two receptors use related, but yet distinct, approaches in the recognition of phosphomannosyl residues.
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Affiliation(s)
- Nancy M Dahms
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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