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Dangat Y, Freindorf M, Kraka E. Mechanistic Insights into S-Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study. J Am Chem Soc 2024; 146:145-158. [PMID: 38055807 DOI: 10.1021/jacs.3c06397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Ceroid lipofuscinosis neuronal protein 5 (Cln5) is encoded by the CLN5 gene. The genetic variants of this gene are associated with the CLN5 form of Batten disease. Recently, the first crystal structure of Cln5 was reported. Cln5 shows cysteine palmitoyl thioesterase S-depalmitoylation activity, which was explored via fluorescent emission spectroscopy utilizing the fluorescent probe DDP-5. In this work, the mechanism of the reaction between Cln5 and DDP-5 was studied computationally by applying a QM/MM methodology at the ωB97X-D/6-31G(d,p):AMBER level. The results of our study clearly demonstrate the critical role of the catalytic triad Cys280-His166-Glu183 in S-depalmitoylation activity. This is evidenced through a comparison of the pathways catalyzed by the Cys280-His166-Glu183 triad and those with only Cys280 involved. The computed reaction barriers are in agreement with the catalytic efficiency. The calculated Gibb's free-energy profile suggests that S-depalmitoylation is a rate-limiting step compared to the preceding S-palmitoylation, with barriers of 26.1 and 25.3 kcal/mol, respectively. The energetics were complemented by monitoring the fluctuations in the electron density distribution through NBO charges and bond strength alterations via local mode stretching force constants during the catalytic pathways. This comprehensive protocol led to a more holistic picture of the reaction mechanism at the atomic level. It forms the foundation for future studies on the effects of gene mutations on both the S-palmitoylation and S-depalmitoylation steps, providing valuable data for the further development of enzyme replacement therapy, which is currently the only FDA-approved therapy for childhood neurodegenerative diseases, including Batten disease.
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Affiliation(s)
- Yuvraj Dangat
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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2
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Himmelreich N, Kikul F, Zdrazilova L, Honzik T, Hecker A, Poschet G, Lüchtenborg C, Brügger B, Strahl S, Bürger F, Okun JG, Hansikova H, Thiel C. Complex metabolic disharmony in PMM2-CDG paves the way to new therapeutic approaches. Mol Genet Metab 2023; 139:107610. [PMID: 37245379 DOI: 10.1016/j.ymgme.2023.107610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
PMM2-CDG is the most common defect among the congenital disorders of glycosylation. In order to investigate the effect of hypoglycosylation on important cellular pathways, we performed extensive biochemical studies on skin fibroblasts of PMM2-CDG patients. Among others, acylcarnitines, amino acids, lysosomal proteins, organic acids and lipids were measured, which all revealed significant abnormalities. There was an increased expression of acylcarnitines and amino acids associated with increased amounts of calnexin, calreticulin and protein-disulfid-isomerase in combination with intensified amounts of ubiquitinylated proteins. Lysosomal enzyme activities were widely decreased as well as citrate and pyruvate levels indicating mitochondrial dysfunction. Main lipid classes such as phosphatidylethanolamine, cholesterol or alkyl-phosphatidylcholine, as well as minor lipid species like hexosylceramide, lysophosphatidylcholines or phosphatidylglycerol, were abnormal. Biotinidase and catalase activities were severely reduced. In this study we discuss the impact of metabolite abnormalities on the phenotype of PMM2-CDG. In addition, based on our data we propose new and easy-to-implement therapeutic approaches for PMM2-CDG patients.
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Affiliation(s)
- Nastassja Himmelreich
- Centre for Child and Adolescent Medicine, Department I, Heidelberg University, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Frauke Kikul
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Lucie Zdrazilova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Tomáš Honzik
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Andreas Hecker
- Centre for Child and Adolescent Medicine, Department I, Heidelberg University, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Plant Molecular Biology, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Christian Lüchtenborg
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Friederike Bürger
- Centre for Child and Adolescent Medicine, Department I, Heidelberg University, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Jürgen G Okun
- Centre for Child and Adolescent Medicine, Department I, Heidelberg University, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Hana Hansikova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Christian Thiel
- Centre for Child and Adolescent Medicine, Department I, Heidelberg University, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany.
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3
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Miao SB, Guo H, Kong DX, Zhao YY, Pan SH, Jiang Y, Gao X, Wu XH. Case report: Analysis of novel compound heterozygous TPP1 variants in a Chinese patient with neuronal ceroid lipofuscinosis type 2. Front Genet 2022; 13:937485. [PMID: 36118858 PMCID: PMC9471087 DOI: 10.3389/fgene.2022.937485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Neuronal ceroid lipofuscinosis type 2 (CLN2) is an autosomal recessive neurodegenerative disease caused by variants in the TPP1 gene that lead to the deficiency of the lysosomal enzyme tripeptidyl peptidase I (TPP1) activity. Herein, we report a rare case of CLN2 caused by two novel variants of TPP1. The patient presented with seizures at onset, followed by progressive cognitive impairment, motor decline, and vision loss. Novel compound heterozygous variants, c.544_545del and c.230-3C>G, in TPP1 were identified by whole-exome sequencing. The variant assessment showed that the c.544_545del is a frameshift variant mediating mRNA decay and that c.230-3C>G is a splice variant generating aberrantly spliced TPP1 mRNA, as confirmed by a Splicing Reporter Minigene assay. In conclusion, clinical history, variant assessment, and molecular analyses demonstrate that the novel compound heterozygous variants are responsible for CLN2 disease in this patient. This study expands the mutation spectrum of TPP1.
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Affiliation(s)
- Sui-Bing Miao
- Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Institute of Reproductive Medicine of Shijiazhuang, The Fourth Hospital of Shijiazhuang Affiliated to Hebei Medical University, Shijiazhuang, China
| | - Hui Guo
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Hebei Medical University Shijiazhuang, Shijiazhuang, China
| | - De-Xian Kong
- Department of Endocrinology, The Fourth Affiliated Hospital of Hebei Medical University Shijiazhuang, Shijiazhuang, China
| | - Yuan-Yuan Zhao
- Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Institute of Reproductive Medicine of Shijiazhuang, The Fourth Hospital of Shijiazhuang Affiliated to Hebei Medical University, Shijiazhuang, China
| | - Shu-Hong Pan
- Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Institute of Reproductive Medicine of Shijiazhuang, The Fourth Hospital of Shijiazhuang Affiliated to Hebei Medical University, Shijiazhuang, China
| | - Yan Jiang
- Center of Reproductive Medicine, The Fourth Hospital of Shijiazhuang Affiliated to Hebei Medical University, Shijiazhuang, China
| | - Xing Gao
- Center of Reproductive Medicine, The Fourth Hospital of Shijiazhuang Affiliated to Hebei Medical University, Shijiazhuang, China
| | - Xiao-Hua Wu
- Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Institute of Reproductive Medicine of Shijiazhuang, The Fourth Hospital of Shijiazhuang Affiliated to Hebei Medical University, Shijiazhuang, China
- *Correspondence: Xiao-Hua Wu,
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4
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Oda K, Dunn BM, Wlodawer A. Serine-Carboxyl Peptidases, Sedolisins: From Discovery to Evolution. Biochemistry 2022; 61:1643-1664. [PMID: 35862020 DOI: 10.1021/acs.biochem.2c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sedolisin is a proteolytic enzyme, listed in the peptidase database MEROPS as a founding member of clan SB, family S53. This enzyme, although active at low pH, was originally shown not to be inhibited by an aspartic peptidase specific inhibitor, S-PI (pepstatin Ac). In this Perspective, the S53 family is described from the moment of original identification to evolution. The representative enzymes of the family are sedolisin, kumamolisin, and TPP-1. They exhibit the following unique features. (1) The fold of the molecule is similar to that of subtilisin, but the catalytic residues consist of a triad, Ser/Glu/Asp, that is unlike the Ser/His/Asp triad of subtilisin. (2) The molecule is expressed as a pro-form composed of the amino-terminal prosegment and the active domain. Additionally, some members of this family have an additional, carboxy-terminal prosegment. (3) Their optimum pH for activity is in the acidic region, not in the neutral to alkaline region where subtilisin is active. (4) Their distribution in nature is very broad across the three kingdoms of life. (5) Some of these enzymes from fungi and bacteria are pathogens to plants. (6) Some of them have significant potential applications for industry. (7) The lack of a TPP-1 gene in human brain is the cause of incurable juvenile neuronal ceroid lipofuscinosis (Batten's disease).
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0245, United States
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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5
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Kallak TK, Fransson E, Bränn E, Berglund H, Lager S, Comasco E, Lyle R, Skalkidou A. Maternal prenatal depressive symptoms and toddler behavior: an umbilical cord blood epigenome-wide association study. Transl Psychiatry 2022; 12:186. [PMID: 35513368 PMCID: PMC9072531 DOI: 10.1038/s41398-022-01954-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/09/2022] Open
Abstract
Children of mothers with prenatal depressive symptoms (PND) have a higher risk of behavioral problems; fetal programming through DNA methylation is a possible underlying mechanism. This study investigated DNA methylation in cord blood to identify possible "at birth" signatures that may indicate susceptibility to behavioral problems at 18 months of age. Cord blood was collected from 256 children of mothers who had self-reported on symptoms of depression during pregnancy and the behavior of their child at 18 months of age. Whole genome DNA methylation was assessed using Illumina MethylationEPIC assay. The mother and child pairs were categorized into four groups, based on both self-reported depressive symptoms, PND or Healthy control (HC), and scores from the Child Behavior checklist (high or low for internalizing, externalizing, and total scores). Adjustments were made for batch effects, cell-type, and clinical covariates. Differentially methylated sites were identified using Kruskal-Wallis test, and Benjamini-Hochberg adjusted p values < 0.05 were considered significant. The analysis was also stratified by sex of the child. Among boys, we observed higher and correlated DNA methylation of one CpG-site in the promoter region of TPP1 in the HC group, with high externalizing scores compared to HC with low externalizing scores. Boys in the PND group showed lower DNA methylation in NUDT15 among those with high, compared to low, internalizing scores; the DNA methylation levels of CpGs in this gene were positively correlated with the CBCL scores. Hence, the differentially methylated CpG sites could be of interest for resilience, regardless of maternal mental health during pregnancy. The findings are in a relatively healthy study cohort, thus limiting the possibility of detecting strong effects associated with behavioral difficulties. This is the first investigation of cord blood DNA methylation signs of fetal programming of PND on child behavior at 18 months of age and thus calls for independent replications.
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Affiliation(s)
| | - Emma Fransson
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Emma Bränn
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Hanna Berglund
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Susanne Lager
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Erika Comasco
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Robert Lyle
- Department of Medical Genetics and Norwegian Sequencing Centre (NSC), Oslo University Hospital, Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alkistis Skalkidou
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
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Luebben AV, Bender D, Becker S, Crowther LM, Erven I, Hofmann K, Söding J, Klemp H, Bellotti C, Stäuble A, Qiu T, Kathayat RS, Dickinson BC, Gärtner J, Sheldrick GM, Krätzner R, Steinfeld R. Cln5 represents a new type of cysteine-based S-depalmitoylase linked to neurodegeneration. SCIENCE ADVANCES 2022; 8:eabj8633. [PMID: 35427157 PMCID: PMC9012467 DOI: 10.1126/sciadv.abj8633] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 03/01/2022] [Indexed: 05/26/2023]
Abstract
Genetic CLN5 variants are associated with childhood neurodegeneration and Alzheimer's disease; however, the molecular function of ceroid lipofuscinosis neuronal protein 5 (Cln5) is unknown. We solved the Cln5 crystal structure and identified a region homologous to the catalytic domain of members of the N1pC/P60 superfamily of papain-like enzymes. However, we observed no protease activity for Cln5; and instead, we discovered that Cln5 and structurally related PPPDE1 and PPPDE2 have efficient cysteine palmitoyl thioesterase (S-depalmitoylation) activity using fluorescent substrates. Mutational analysis revealed that the predicted catalytic residues histidine-166 and cysteine-280 are critical for Cln5 thioesterase activity, uncovering a new cysteine-based catalytic mechanism for S-depalmitoylation enzymes. Last, we found that Cln5-deficient neuronal progenitor cells showed reduced thioesterase activity, confirming live cell function of Cln5 in setting S-depalmitoylation levels. Our results provide new insight into the function of Cln5, emphasize the importance of S-depalmitoylation in neuronal homeostasis, and disclose a new, unexpected enzymatic function for the N1pC/P60 superfamily of proteins.
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Affiliation(s)
- Anna V. Luebben
- Institute of Inorganic Chemistry, University of
Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Daniel Bender
- Department of Pediatric Neurology, University
Children’s Hospital Zürich, University of Zurich,
Steinwiesstrasse 75, 8032 Zürich, Switzerland
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max
Planck Institute for Biophysical Chemistry, Fassberg 11, 37077
Göttingen, Germany
| | - Lisa M. Crowther
- Department of Pediatric Neurology, University
Children’s Hospital Zürich, University of Zurich,
Steinwiesstrasse 75, 8032 Zürich, Switzerland
| | - Ilka Erven
- Institute for Genetics, University of Cologne,
Zülpicher Str.47a, 50674 Cologne, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne,
Zülpicher Str.47a, 50674 Cologne, Germany
| | - Johannes Söding
- Quantitative Biology and Bioinformatics and
Department of Molecular Biology, Max-Planck Institute for Biophysical Chemistry,
Am Fassberg 11, 37077 Göttingen, Germany
| | - Henry Klemp
- Department of Pediatrics and Adolescent Medicine,
Division of Pediatric Neurology, University of Göttingen,
Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Cristina Bellotti
- Department of Pediatric Neurology, University
Children’s Hospital Zürich, University of Zurich,
Steinwiesstrasse 75, 8032 Zürich, Switzerland
| | - Andreas Stäuble
- Department of Pediatric Neurology, University
Children’s Hospital Zürich, University of Zurich,
Steinwiesstrasse 75, 8032 Zürich, Switzerland
| | - Tian Qiu
- Department of Chemistry, University of Chicago,
Chicago, IL, USA
| | | | | | - Jutta Gärtner
- Department of Pediatrics and Adolescent Medicine,
Division of Pediatric Neurology, University of Göttingen,
Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - George M. Sheldrick
- Institute of Inorganic Chemistry, University of
Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Ralph Krätzner
- Department of Pediatrics and Adolescent Medicine,
Division of Pediatric Neurology, University of Göttingen,
Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Robert Steinfeld
- Department of Pediatric Neurology, University
Children’s Hospital Zürich, University of Zurich,
Steinwiesstrasse 75, 8032 Zürich, Switzerland
- Department of Pediatrics and Adolescent Medicine,
Division of Pediatric Neurology, University of Göttingen,
Robert-Koch-Strasse 40, 37075 Göttingen, Germany
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7
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Bakshi T, Pham D, Kaur R, Sun B. Hidden Relationships between N-Glycosylation and Disulfide Bonds in Individual Proteins. Int J Mol Sci 2022; 23:ijms23073742. [PMID: 35409101 PMCID: PMC8998389 DOI: 10.3390/ijms23073742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
N-Glycosylation (NG) and disulfide bonds (DBs) are two prevalent co/post-translational modifications (PTMs) that are often conserved and coexist in membrane and secreted proteins involved in a large number of diseases. Both in the past and in recent times, the enzymes and chaperones regulating these PTMs have been constantly discovered to directly interact with each other or colocalize in the ER. However, beyond a few model proteins, how such cooperation affects N-glycan modification and disulfide bonding at selective sites in individual proteins is largely unknown. Here, we reviewed the literature to discover the current status in understanding the relationships between NG and DBs in individual proteins. Our results showed that more than 2700 human proteins carry both PTMs, and fewer than 2% of them have been investigated in the associations between NG and DBs. We summarized both these proteins with the reported relationships in the two PTMs and the tools used to discover the relationships. We hope that, by exposing this largely understudied field, more investigations can be encouraged to unveil the hidden relationships of NG and DBs in the majority of membranes and secreted proteins for pathophysiological understanding and biotherapeutic development.
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Affiliation(s)
- Tania Bakshi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - David Pham
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Raminderjeet Kaur
- Faculty of Health Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Bingyun Sun
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Correspondence:
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8
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Storey CL, Williams RSB, Fisher PR, Annesley SJ. Dictyostelium discoideum: A Model System for Neurological Disorders. Cells 2022; 11:cells11030463. [PMID: 35159273 PMCID: PMC8833889 DOI: 10.3390/cells11030463] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
Background: The incidence of neurological disorders is increasing due to population growth and extended life expectancy. Despite advances in the understanding of these disorders, curative strategies for treatment have not yet eventuated. In part, this is due to the complexities of the disorders and a lack of identification of their specific underlying pathologies. Dictyostelium discoideum has provided a useful, simple model to aid in unraveling the complex pathological characteristics of neurological disorders including Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, neuronal ceroid lipofuscinoses and lissencephaly. In addition, D. discoideum has proven to be an innovative model for pharmaceutical research in the neurological field. Scope of review: This review describes the contributions of D. discoideum in the field of neurological research. The continued exploration of proteins implicated in neurological disorders in D. discoideum may elucidate their pathological roles and fast-track curative therapeutics.
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Affiliation(s)
- Claire Louise Storey
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora 3086, Australia; (C.L.S.); (P.R.F.)
| | - Robin Simon Brooke Williams
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK;
| | - Paul Robert Fisher
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora 3086, Australia; (C.L.S.); (P.R.F.)
| | - Sarah Jane Annesley
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora 3086, Australia; (C.L.S.); (P.R.F.)
- Correspondence: ; Tel.: +61-394-791-412
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Abstract
The neuronal ceroid lipofuscinoses (NCLs), collectively known as Batten disease, are a group of neurological diseases that affect all ages and ethnicities worldwide. There are 13 different subtypes of NCL, each caused by a mutation in a distinct gene. The NCLs are characterized by the accumulation of undigestible lipids and proteins in various cell types. This leads to progressive neurodegeneration and clinical symptoms including vision loss, progressive motor and cognitive decline, seizures, and premature death. These diseases have commonly been characterized by lysosomal defects leading to the accumulation of undigestible material but further research on the NCLs suggests that altered protein secretion may also play an important role. This has been strengthened by recent work in biomedical model organisms, including Dictyostelium discoideum, mice, and sheep. Research in D. discoideum has reported the extracellular localization of some NCL-related proteins and the effects of NCL-related gene loss on protein secretion during unicellular growth and multicellular development. Aberrant protein secretion has also been observed in mammalian models of NCL, which has allowed examination of patient-derived cerebrospinal fluid and urine for potential diagnostic and prognostic biomarkers. Accumulated evidence links seven of the 13 known NCL-related genes to protein secretion, suggesting that altered secretion is a common hallmark of multiple NCL subtypes. This Review highlights the impact of altered protein secretion in the NCLs, identifies potential biomarkers of interest and suggests that future work in this area can provide new therapeutic insight. Summary: This Review discusses work in different model systems and humans, examining the impact of altered protein secretion in the neuronal ceroid lipofuscinoses group of diseases to provide novel therapeutic insights.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Life & Health Sciences Building, 1600 West Bank Drive, Peterborough, Ontario K9L 0G2, Canada
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10
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Ma L, Prada AM, Schmidt M, Morrow EM. Generation of pathogenic TPP1 mutations in human stem cells as a model for neuronal ceroid lipofuscinosis type 2 disease. Stem Cell Res 2021; 53:102323. [PMID: 33845243 PMCID: PMC9173593 DOI: 10.1016/j.scr.2021.102323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/19/2021] [Accepted: 03/28/2021] [Indexed: 01/22/2023] Open
Abstract
Neuronal ceroid lipofuscinosis type 2 (CLN2 disease) is an autosomal recessive neurodegenerative disorder generally with onset at 2 to 4 years of age and characterized by seizures, loss of vision, progressive motor and mental decline, and premature death. CLN2 disease is caused by loss-of-function mutations in the tripeptidyl peptidase 1 (TPP1) gene leading to deficiency in TPP1 enzyme activity. Approximately 60% of patients have one of two pathogenic variants (c.509–1G > C or c.622C > T [p.(Arg208*)]). In order to generate a human stem cell model of CLN2 disease, we used CRISPR/Cas9-mediated knock-in technology to introduce these mutations in a homozygous state into H9 human embryonic stem cells. Heterozygous lines of the c.622C > T (p.(Arg208*)) mutation were also generated, which included a heterozygous mutant with a wild-type allele and different compound heterozygous coding mutants resulting from indels on one allele. We describe the methodology that led to the generation of the lines and provide data on the initial validation and characterization of these CLN2 disease models. Notably, both mutant lines (c.509–1G > C and c.622C > T [p.(Arg208*)]) in the homozygous state were shown to have reduced or absent protein, respectively, and deficiency of TPP1 enzyme activity. These models, which we have made available for wide-spread sharing, will be useful for future studies of molecular and cellular mechanisms underlying CLN2 disease and for therapeutic development.
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Affiliation(s)
- Li Ma
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, Rhode Island 02912, USA
| | - Adriana M Prada
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, Rhode Island 02912, USA
| | - Michael Schmidt
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, Rhode Island 02912, USA; Hassenfeld Child Health Innovation Institute, Brown University, Providence, Rhode Island 02912, USA
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, Rhode Island 02912, USA; Hassenfeld Child Health Innovation Institute, Brown University, Providence, Rhode Island 02912, USA.
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11
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Amadori E, Scala M, Cereda GS, Vari MS, Marchese F, Di Pisa V, Mancardi MM, Giacomini T, Siri L, Vercellino F, Serino D, Orsini A, Bonuccelli A, Bagnasco I, Papa A, Minetti C, Cordelli DM, Striano P. Targeted re-sequencing for early diagnosis of genetic causes of childhood epilepsy: the Italian experience from the 'beyond epilepsy' project. Ital J Pediatr 2020; 46:92. [PMID: 32631363 PMCID: PMC7339579 DOI: 10.1186/s13052-020-00860-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/01/2020] [Indexed: 01/12/2023] Open
Abstract
Background Childhood epilepsies are a heterogeneous group of conditions differing in diagnostic criteria, management, and outcome. Late-infantile neuronal ceroid lipofuscinosis type 2 (CLN2) is a neurodegenerative condition caused by biallelic TPP1 variants. This disorder presents with subtle and relatively non-specific symptoms, mimicking those observed in more common paediatric epilepsies and followed by rapid psychomotor deterioration and drug-resistant epilepsy. A prompt diagnosis is essential to adopt appropriate treatment and disease management strategies. Methods This is a prospective, multicentre study on the efficiency of targeted re-sequencing in the early identification of the genetic causes of childhood epilepsy, with particular regard to CLN2. After phenotypic characterization, a 283-gene Next Generation Sequencing panel was performed in 21 Italian children with neurodevelopmental abnormalities, aged between 24 and 60 months, experiencing first unprovoked seizure after 2 years of age. Results The average age at enrolment was 39.9 months, with a mean age at seizure onset of 30.9 months and a mean time interval between seizure onset and targeted resequencing of 9 months. Genetic confirmation was achieved in 4 out of 21 patients, with a diagnostic yield of 19%. In one case, the homozygous splice acceptor variant c.509-1G > C in TPP1 was identified, leading to a CLN2 diagnosis. Three pathogenic variants in MECP2 were also detected in three patients, including the frameshift variant c.1157_1186delinsA (p.Leu386Hisfs*9) in a girl with negative single gene sequencing. Variants of unknown significance (VUS) were found in 11 out of 21 (52.4%) individuals, whereas no clinically significant variants were observed in the remaining 6 subjects. Conclusions Our findings support the efficacy of target re-sequencing in the identification of the genetic causes of childhood epilepsy and suggest that this technique might prove successful in the early detection of CLN2 as well as other neurodevelopmental conditions.
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Affiliation(s)
- Elisabetta Amadori
- Pediatric Neurology and Muscular Diseases Unit, IRCCS 'G. Gaslini' Institute, 16147, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Marcello Scala
- Pediatric Neurology and Muscular Diseases Unit, IRCCS 'G. Gaslini' Institute, 16147, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Giulia Sofia Cereda
- Pediatric Neurology and Muscular Diseases Unit, IRCCS 'G. Gaslini' Institute, 16147, Genoa, Italy
| | - Maria Stella Vari
- Pediatric Neurology and Muscular Diseases Unit, IRCCS 'G. Gaslini' Institute, 16147, Genoa, Italy
| | - Francesca Marchese
- Pediatric Neurology and Muscular Diseases Unit, IRCCS 'G. Gaslini' Institute, 16147, Genoa, Italy
| | - Veronica Di Pisa
- Child Neurology and Psychiatry Unit, Department of Medical and Surgical Sciences (DIMEC), S. Orsola Hospital, University of Bologna, Bologna, Italy
| | - Maria Margherita Mancardi
- Child Neuropsychiatry Unit, Epilepsy Centre, Department of Clinical and Surgical Neurosciences and Rehabilitation, IRCSS 'G. Gaslini' Institute, Genoa, Italy
| | - Thea Giacomini
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Child Neuropsychiatry Unit, Epilepsy Centre, Department of Clinical and Surgical Neurosciences and Rehabilitation, IRCSS 'G. Gaslini' Institute, Genoa, Italy
| | - Laura Siri
- Child Neuropsychiatry Unit, IRCSS 'G. Gaslini' Institute, Genoa, Italy
| | - Fabiana Vercellino
- Department of Child Neurology and Psychiatry, Cesare Arrigo Hospital, Alessandria, Italy
| | - Domenico Serino
- Department of Paediatric Neurology, Royal Aberdeen Children's Hospital, Aberdeen, UK.,Child Neurology and Psychiatry Unit, ASL CN1, Cuneo, Italy
| | - Alessandro Orsini
- Pediatric Neurology, Pediatric Department, Azienda Ospedaliera Universitaria Pisana, University of Pisa, Pisa, Italy
| | - Alice Bonuccelli
- Pediatric Neurology, Pediatric Department, Azienda Ospedaliera Universitaria Pisana, University of Pisa, Pisa, Italy
| | - Irene Bagnasco
- Division of Child Neuropsychiatry, Martini Hospital, via Tofane 71, 10141, Torino, Italy
| | - Amanda Papa
- Department of Child Neuropsychiatry, AOU Maggiore della Carita, Novara, Italy
| | - Carlo Minetti
- Pediatric Neurology and Muscular Diseases Unit, IRCCS 'G. Gaslini' Institute, 16147, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Duccio Maria Cordelli
- Child Neurology and Psychiatry Unit, Department of Medical and Surgical Sciences (DIMEC), S. Orsola Hospital, University of Bologna, Bologna, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS 'G. Gaslini' Institute, 16147, Genoa, Italy. .,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.
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12
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Boon L, Ugarte-Berzal E, Vandooren J, Opdenakker G. Protease propeptide structures, mechanisms of activation, and functions. Crit Rev Biochem Mol Biol 2020; 55:111-165. [PMID: 32290726 DOI: 10.1080/10409238.2020.1742090] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteases are a diverse group of hydrolytic enzymes, ranging from single-domain catalytic molecules to sophisticated multi-functional macromolecules. Human proteases are divided into five mechanistic classes: aspartate, cysteine, metallo, serine and threonine proteases, based on the catalytic mechanism of hydrolysis. As a protective mechanism against uncontrolled proteolysis, proteases are often produced and secreted as inactive precursors, called zymogens, containing inhibitory N-terminal propeptides. Protease propeptide structures vary considerably in length, ranging from dipeptides and propeptides of about 10 amino acids to complex multifunctional prodomains with hundreds of residues. Interestingly, sequence analysis of the different protease domains has demonstrated that propeptide sequences present higher heterogeneity compared with their catalytic domains. Therefore, we suggest that protease inhibition targeting propeptides might be more specific and have less off-target effects than classical inhibitors. The roles of propeptides, besides keeping protease latency, include correct folding of proteases, compartmentalization, liganding, and functional modulation. Changes in the propeptide sequence, thus, have a tremendous impact on the cognate enzymes. Small modifications of the propeptide sequences modulate the activity of the enzymes, which may be useful as a therapeutic strategy. This review provides an overview of known human proteases, with a focus on the role of their propeptides. We review propeptide functions, activation mechanisms, and possible therapeutic applications.
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Affiliation(s)
- Lise Boon
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Immunobiology, KU Leuven, Leuven, Belgium
| | - Estefania Ugarte-Berzal
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Immunobiology, KU Leuven, Leuven, Belgium
| | - Jennifer Vandooren
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Immunobiology, KU Leuven, Leuven, Belgium
| | - Ghislain Opdenakker
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Immunobiology, KU Leuven, Leuven, Belgium
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13
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Collier AM, Nemtsova Y, Kuber N, Banach-Petrosky W, Modak A, Sleat DE, Nanda V, Lobel P. Lysosomal protein thermal stability does not correlate with cellular half-life: global observations and a case study of tripeptidyl-peptidase 1. Biochem J 2020; 477:727-745. [PMID: 31957806 PMCID: PMC8442665 DOI: 10.1042/bcj20190874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/16/2022]
Abstract
Late-infantile neuronal ceroid lipofuscinosis (LINCL) is a neurodegenerative lysosomal storage disorder caused by mutations in the gene encoding the protease tripeptidyl-peptidase 1 (TPP1). Progression of LINCL can be slowed or halted by enzyme replacement therapy, where recombinant human TPP1 is administered to patients. In this study, we utilized protein engineering techniques to increase the stability of recombinant TPP1 with the rationale that this may lengthen its lysosomal half-life, potentially increasing the potency of the therapeutic protein. Utilizing multiple structure-based methods that have been shown to increase the stability of other proteins, we have generated and evaluated over 70 TPP1 variants. The most effective mutation, R465G, increased the melting temperature of TPP1 from 55.6°C to 64.4°C and increased its enzymatic half-life at 60°C from 5.4 min to 21.9 min. However, the intracellular half-life of R465G and all other variants tested in cultured LINCL patient-derived lymphoblasts was similar to that of WT TPP1. These results provide structure/function insights into TPP1 and indicate that improving in vitro thermal stability alone is insufficient to generate TPP1 variants with improved physiological stability. This conclusion is supported by a proteome-wide analysis that indicates that lysosomal proteins have higher melting temperatures but also higher turnover rates than proteins of other organelles. These results have implications for similar efforts where protein engineering approaches, which are frequently evaluated in vitro, may be considered for improving the physiological properties of proteins, particularly those that function in the lysosomal environment.
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Affiliation(s)
- Aaron M. Collier
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Yuliya Nemtsova
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Narendra Kuber
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | | | - Anurag Modak
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - David E. Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
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14
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Gardner E, Bailey M, Schulz A, Aristorena M, Miller N, Mole SE. Mutation update: Review of TPP1 gene variants associated with neuronal ceroid lipofuscinosis CLN2 disease. Hum Mutat 2019; 40:1924-1938. [PMID: 31283065 PMCID: PMC6851559 DOI: 10.1002/humu.23860] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 01/03/2023]
Abstract
Neuronal ceroid lipofuscinosis type 2 (CLN2 disease) is an autosomal recessive condition caused by variants in the TPP1 gene, leading to deficient activity of the lysosomal enzyme tripeptidyl peptidase I (TPP1). We update on the spectrum of TPP1 variants associated with CLN2 disease, comprising 131 unique variants from 389 individuals (717 alleles) collected from the literature review, public databases, and laboratory communications. Previously unrecorded individuals were added to the UCL TPP1‐specific database. Two known pathogenic variants, c.509–1 G>C and c.622 C>T (p.(Arg208*)), collectively occur in 60% of affected individuals in the sample, and account for 50% of disease‐associated alleles. At least 86 variants (66%) are private to single families. Homozygosity occurs in 45% of individuals where both alleles are known (87% of reported individuals). Atypical CLN2 disease, TPP1 enzyme deficiency with disease onset and/or progression distinct from classic late‐infantile CLN2, represents 13% of individuals recorded with associated phenotype. NCBI ClinVar currently holds records for 37% of variants collected here. Effective CLN2 disease management requires early diagnosis; however, irreversible neurodegeneration occurs before a diagnosis is typically reached at age 5. Timely classification and public reporting of TPP1 variants is essential as molecular testing increases in use as a first‐line diagnostic test for pediatric‐onset neurological disease.
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Affiliation(s)
- Emily Gardner
- UCL MRC Laboratory for Molecular Cell Biology and UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Mitch Bailey
- Global Scientific Affairs, BioMarin Pharmaceutical Inc, Novato, California
| | - Angela Schulz
- Department of Paediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mikel Aristorena
- UCL MRC Laboratory for Molecular Cell Biology and UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Nicole Miller
- Global Scientific Affairs, BioMarin Pharmaceutical Inc, Novato, California
| | - Sara E Mole
- UCL MRC Laboratory for Molecular Cell Biology and UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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15
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Orts F, Ten Have A. Structure-function analysis of Sedolisins: evolution of tripeptidyl peptidase and endopeptidase subfamilies in fungi. BMC Bioinformatics 2018; 19:464. [PMID: 30514213 PMCID: PMC6278154 DOI: 10.1186/s12859-018-2404-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Sedolisins are acid proteases that are related to the basic subtilisins. They have been identified in all three superkingdoms but are not ubiquitous, although fungi that secrete acids as part of their lifestyle can have up to six paralogs. Both TriPeptidyl Peptidase (TPP) and endopeptidase activity have been identified and it has been suggested that these correspond to separate subfamilies. Results We studied eukaryotic sedolisins by computational analysis. A maximum likelihood tree shows one major clade containing non-fungal sequences only and two major as well as two minor clades containing only fungal sequences. One of the major fungal clades contains all known TPPs whereas the other contains characterized endosedolisins. We identified four Cluster Specific Inserts (CSIs) in endosedolisins, of which CSIs 1, 3 and 4 appear as solvent exposed according to structure modeling. Part of CSI2 is exposed but a short stretch forms a novel and partially buried α-helix that induces a conformational change near the binding pocket. We also identified a total of 15 specificity determining positions (SDPs) of which five, identified in two independent analyses, form highly connected SDP sub-networks. Modeling of virtual mutants suggests a key role for the W307A or F307A substitution. The remaining four key SDPs physically interact at the interface of the catalytic domain and the enzyme’s prosegment. Modeling of virtual mutants suggests these SDPs are indeed required to compensate the conformational change induced by CSI2 and the A307. One of the two small fungal clades concerns a subfamily that contains 213 sequences, is mostly similar to the major TPP subfamily but differs, interestingly, in position 307, showing mostly isoleucine and threonine. Conclusions Analysis confirms there are at least two sedolisin subfamilies in fungi: TPPs and endopeptidases, and suggests a third subfamily with unknown characteristics. Sequence and functional diversification was centered around buried SDP307 and resulted in a conformational change of the pocket. Mutual Information network analysis forms a useful instrument in the corroboration of predicted SDPs. Electronic supplementary material The online version of this article (10.1186/s12859-018-2404-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Facundo Orts
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina
| | - Arjen Ten Have
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina.
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16
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Untargeted Metabolite Profiling of Cerebrospinal Fluid Uncovers Biomarkers for Severity of Late Infantile Neuronal Ceroid Lipofuscinosis (CLN2, Batten Disease). Sci Rep 2018; 8:15229. [PMID: 30323181 PMCID: PMC6189193 DOI: 10.1038/s41598-018-33449-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Late infantile neuronal ceroid lipofuscinosis (CLN2 disease) is a rare lysosomal storage disorder caused by a monogenetic deficiency of tripeptidyl peptidase-1 (TPP1). Despite knowledge that lipofuscin is the hallmark disease product, the relevant TPP1 substrate and its role in neuronal physiology/pathology is unknown. We hypothesized that untargeted metabolite profiling of cerebrospinal fluid (CSF) could be used as an effective tool to identify disease-associated metabolic disruptions in CLN2 disease, offering the potential to identify biomarkers that inform on disease severity and progression. Accordingly, a mass spectrometry-based untargeted metabolite profiling approach was employed to differentiate CSF from normal vs. CLN2 deficient individuals. Of 1,433 metabolite features surveyed, 29 linearly correlated with currently employed disease severity scores. With tandem mass spectrometry 8 distinct metabolite identities were structurally confirmed based on retention time and fragmentation pattern matches, vs. standards. These putative CLN2 biomarkers include 7 acetylated species - all attenuated in CLN2 compared to controls. Because acetate is the major bioenergetic fuel for support of mitochondrial respiration, deficient acetylated species in CSF suggests a brain energy defect that may drive neurodegeneration. Targeted analysis of these metabolites in CSF of CLN2 patients offers a powerful new approach for monitoring CLN2 disease progression and response to therapy.
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17
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Fayer EL, Gilliland WM, Ramsey JM, Allbritton NL, Waters ML. N-Gemini peptides: cytosolic protease resistance via N-terminal dimerization of unstructured peptides. Chem Commun (Camb) 2017; 54:204-207. [PMID: 29230440 DOI: 10.1039/c7cc06819k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe a synthetically simple strategy for increasing the lifetime of unstructured peptides in cytosolic environment via dimerization at the N-terminus to block threading into the catalytic cleft of cytosolic proteases. We establish this approach with kinase substrates, allowing for phosphorylation in cells as a demonstration of protease resistance.
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Affiliation(s)
- Effrat L Fayer
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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18
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Stumpf M, Müller R, Gaßen B, Wehrstedt R, Fey P, Karow MA, Eichinger L, Glöckner G, Noegel AA. A tripeptidyl peptidase 1 is a binding partner of the Golgi pH regulator (GPHR) in Dictyostelium. Dis Model Mech 2017; 10:897-907. [PMID: 28546289 PMCID: PMC5536908 DOI: 10.1242/dmm.029280] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/17/2017] [Indexed: 02/02/2023] Open
Abstract
Mutations in tripeptidyl peptidase 1 (TPP1) have been associated with late infantile neuronal ceroid lipofuscinosis (NCL), a neurodegenerative disorder. TPP1 is a lysosomal serine protease, which removes tripeptides from the N-terminus of proteins and is composed of an N-terminal prodomain and a catalytic domain. It is conserved in mammals, amphibians, fish and the amoeba Dictyostelium discoideum. D. discoideum harbors at least six genes encoding TPP1, tpp1A to tpp1F. We identified TPP1F as binding partner of Dictyostelium GPHR (Golgi pH regulator), which is an evolutionarily highly conserved intracellular transmembrane protein. A region encompassing the DUF3735 (GPHR_N) domain of GPHR was responsible for the interaction. In TPP1F, the binding site is located in the prodomain of the protein. The tpp1F gene is transcribed throughout development and translated into a polypeptide of ∼65 kDa. TPP1 activity was demonstrated for TPP1F-GFP immunoprecipitated from D. discoideum cells. Its activity could be inhibited by addition of the recombinant DUF3735 domain of GPHR. Knockout tpp1F mutants did not display any particular phenotype, and TPP1 activity was not abrogated, presumably because tpp1B compensates as it has the highest expression level of all the TPP1 genes during growth. The GPHR interaction was not restricted to TPP1F but occurred also with TPP1B. As previous reports show that the majority of the TPP1 mutations in NCL resulted in reduction or loss of enzyme activity, we suggest that Dicyostelium could be used as a model system in which to test new reagents that could affect the activity of the protein and ameliorate the disease. Summary: Interaction of Dictyostelium tripeptidyl peptidase 1 with GPHR could be relevant for studies of the human enzyme, which is associated with a neurodegenerative disorder.
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Affiliation(s)
- Maria Stumpf
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Rolf Müller
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Berthold Gaßen
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Regina Wehrstedt
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Petra Fey
- Dicty Base, Northwestern University, Biomedical Informatics Center and Center for Genetic Medicine, Chicago, IL 60611, USA
| | - Malte A Karow
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Ludwig Eichinger
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Gernot Glöckner
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Angelika A Noegel
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
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19
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Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases. Int J Mol Sci 2016; 17:ijms17121969. [PMID: 27898009 PMCID: PMC5187769 DOI: 10.3390/ijms17121969] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 02/06/2023] Open
Abstract
Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications.
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Kondo MY, Gouvea IE, Okamoto DN, Santos JAN, Souccar C, Oda K, Juliano L, Juliano MA. Analysis of catalytic properties of tripeptidyl peptidase I (TTP-I), a serine carboxyl lysosomal protease, and its detection in tissue extracts using selective FRET peptide substrate. Peptides 2016; 76:80-6. [PMID: 26775801 DOI: 10.1016/j.peptides.2016.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/01/2016] [Accepted: 01/10/2016] [Indexed: 11/30/2022]
Abstract
Tripeptidyl peptidase I (TPP-I), also named ceroid lipofuscinosis 2 protease (CLN2p), is a serine carboxyl lysosomal protease involved in neurodegenerative diseases, and has both tripeptidyl amino- and endo- peptidase activities under different pH conditions. We developed fluorescence resonance energy transfer (FRET) peptides using tryptophan (W) as the fluorophore to study TPP-I hydrolytic properties based on previous detailed substrate specificity study (Tian Y. et al., J. Biol. Chem. 2006, 281:6559-72). Tripeptidyl amino peptidase activity is enhanced by the presence of amino acids in the prime side and the peptide NH2-RWFFIQ-EDDnp is so far the best substrate described for TPP-I. The hydrolytic parameters of this peptide and its analogues indicated that the S4 subsite of TPP-I is occluded and there is an electrostatic interaction of the positively charged substrate N-terminus amino group and a negative locus in the region of the enzyme active site. KCl activated TPP-I in contrast to the inhibition by Ca(2+) and NaCl. Solvent kinetic isotope effects (SKIEs) show the importance of the free N-terminus amino group of the substrates, whose absence results in a more complex solvent-dependent enzyme: substrate interaction and catalytic process. Like pure TPP-I, rat spleen and kidney homogenates cleaved NH2-RWFFIQ-EDDnp only at F-F bond and is not inhibited by pepstatin, E-64, EDTA or PMSF. The selectivity of NH2-RWFFIQ-EDDnp to TPP-I was also demonstrated by the 400 times higher k(cat)/K(M) compared to generally used substrate, NH2-AAF-MCA and by its resistance to hydrolysis by cathepsin D that is present in high levels in kidneys.
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Affiliation(s)
- Marcia Y Kondo
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Iuri E Gouvea
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Débora N Okamoto
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Jorge A N Santos
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Caden Souccar
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - Luiz Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Maria A Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil.
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Huang L, Pike D, Sleat DE, Nanda V, Lobel P. Potential pitfalls and solutions for use of fluorescent fusion proteins to study the lysosome. PLoS One 2014; 9:e88893. [PMID: 24586430 PMCID: PMC3931630 DOI: 10.1371/journal.pone.0088893] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 01/13/2014] [Indexed: 01/06/2023] Open
Abstract
Use of fusion protein tags to investigate lysosomal proteins can be complicated by the acidic, protease-rich environment of the lysosome. Potential artifacts include degradation or release of the tag and acid quenching of fluorescence. Tagging can also affect protein folding, glycosylation and/or trafficking. To specifically investigate the use of fluorescent tags to reveal lysosomal localization, we tested mCherry derivatives as C-terminal tags for Niemann-Pick disease type C protein 2 (NPC2), a luminal lysosomal protein. Full-length mCherry was released from the NPC2 chimera while deletion of the 11 N-terminal residues of mCherry generated a cleavage-resistant (cr) fluorescent variant. Insertion of proline linkers between NPC2 and crmCherry had little effect while Gly-Ser linkers promoted cleavage. The NPC2-crmCherry fusion was targeted to the lysosome and restored function in NPC2-deficient cells. Fusion of crmCherry to known and candidate lysosomal proteins revealed that the linkers had different effects on lysosomal localization. Direct fusion of crmCherry impaired mannose 6-phosphorylation and lysosomal targeting of the lysosomal protease tripeptidyl peptidase I (TPP1), while insertion of linkers corrected the defects. Molecular modeling suggested structural bases for the effects of different linkers on NPC2 and TPP1 fusion proteins. While mCherry fusion proteins can be useful tools for studying the lysosome and related organelles, our findings underscore the potential artifacts associated with such applications.
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Affiliation(s)
- Ling Huang
- . Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Pharmacology Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
| | - Douglas Pike
- . Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
| | - David E. Sleat
- . Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
| | - Vikas Nanda
- . Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
| | - Peter Lobel
- . Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
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Gruene T. mrtailor: a tool for PDB-file preparation for the generation of external restraints. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1861-3. [PMID: 23999309 DOI: 10.1107/s090744491301648x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 06/13/2013] [Indexed: 11/11/2022]
Abstract
Model building starting from, for example, a molecular-replacement solution with low sequence similarity introduces model bias, which can be difficult to detect, especially at low resolution. The program mrtailor removes low-similarity regions from a template PDB file according to sequence similarity between the target sequence and the template sequence and maps the target sequence onto the PDB file. The modified PDB file can be used to generate external restraints for low-resolution refinement with reduced model bias and can be used as a starting point for model building and refinement. The program can call ProSMART [Nicholls et al. (2012), Acta Cryst. D68, 404-417] directly in order to create external restraints suitable for REFMAC5 [Murshudov et al. (2011), Acta Cryst. D67, 355-367]. Both a command-line version and a GUI exist.
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Affiliation(s)
- Tim Gruene
- Department of Structural Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
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23
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Miller JN, Chan CH, Pearce DA. The role of nonsense-mediated decay in neuronal ceroid lipofuscinosis. Hum Mol Genet 2013; 22:2723-34. [PMID: 23539563 DOI: 10.1093/hmg/ddt120] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Neuronal ceroid lipofuscinosis (NCL), commonly referred to as Batten disease, is a group of autosomal recessive neurodegenerative diseases of childhood characterized by seizures, blindness, motor and cognitive decline and premature death. Currently, there are over 400 known mutations in 14 different genes, leading to five overlapping clinical variants of NCL. A large portion of these mutations lead to premature stop codons (PTCs) and are predicted to predispose mRNA transcripts to nonsense-mediated decay (NMD). Nonsense-mediated decay is associated with a number of other genetic diseases and is an important regulator of disease pathogenesis. We contend that NMD targets PTCs in NCL gene transcripts for degradation. A number of PTC mutations in CLN1, CLN2 and CLN3 lead to a significant decrease in mRNA transcripts and a corresponding decrease in protein levels and function in patient-derived lymphoblast cell lines. Inhibiting NMD leads to an increased transcript level, and where protein function is known, increased activity. Treatment with read-through drugs also leads to increased protein function. Thus, NMD provides a promising therapeutic target that would allow read-through of transcripts to enhance protein function and possibly ameliorate Batten disease pathogenesis.
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Affiliation(s)
- Jake N Miller
- Sanford Children’s Health Research Center, Sanford Research/USD, Sioux Falls, SD 57104, USA
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24
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Sun Y, Almomani R, Breedveld GJ, Santen GWE, Aten E, Lefeber DJ, Hoff JI, Brusse E, Verheijen FW, Verdijk RM, Kriek M, Oostra B, Breuning MH, Losekoot M, den Dunnen JT, van de Warrenburg BP, Maat-Kievit AJA. Autosomal recessive spinocerebellar ataxia 7 (SCAR7) is caused by variants in TPP1, the gene involved in classic late-infantile neuronal ceroid lipofuscinosis 2 disease (CLN2 disease). Hum Mutat 2013; 34:706-13. [PMID: 23418007 DOI: 10.1002/humu.22292] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/31/2013] [Indexed: 01/15/2023]
Abstract
Spinocerebellar ataxias are phenotypically, neuropathologically, and genetically heterogeneous. The locus of autosomal recessive spinocerebellar ataxia type 7 (SCAR7) was previously linked to chromosome band 11p15. We have identified TPP1 as the causative gene for SCAR7 by exome sequencing. A missense and a splice site variant in TPP1, cosegregating with the disease, were found in a previously described SCAR7 family and also in another patient with a SCAR7 phenotype. TPP1, encoding the tripeptidyl-peptidase 1 enzyme, is known as the causative gene for late infantile neuronal ceroid lipofuscinosis disease 2 (CLN2 disease). CLN2 disease is characterized by epilepsy, loss of vision, ataxia, and a rapidly progressive course, leading to early death. SCAR7 patients showed ataxia and low activity of tripeptidyl-peptidase 1, but no ophthalmologic abnormalities or epilepsy. Also, the slowly progressive evolution of the disease until old age and absence of ultra structural curvilinear profiles is different from the known CLN2 phenotypes. Our findings now expand the phenotypes related to TPP1-variants to SCAR7. In spite of the limited sample size and measurements, a putative genotype-phenotype correlation may be drawn: we hypothesize that loss of function variants abolishing TPP1 enzyme activity lead to CLN2 disease, whereas variants that diminish TPP1 enzyme activity lead to SCAR7.
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Affiliation(s)
- Yu Sun
- Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
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25
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Yao J, Xu Q, Guo H. QM/MM and free-energy simulations of deacylation reaction catalysed by sedolisin, a serine-carboxyl peptidase. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.714467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Kohan R, Noelia Carabelos M, Xin W, Sims K, Guelbert N, Adriana Cismondi I, Pons P, Alonso GI, Troncoso M, Witting S, Pearce DA, de Kremer RD, Oller-Ramírez AM, de Halac IN. Neuronal ceroid lipofuscinosis type CLN2: a new rationale for the construction of phenotypic subgroups based on a survey of 25 cases in South America. Gene 2013; 516:114-21. [PMID: 23266810 PMCID: PMC3855401 DOI: 10.1016/j.gene.2012.12.058] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/03/2012] [Indexed: 11/18/2022]
Abstract
Tripeptidyl-peptidase 1 (TPP1) null or residual activity occurs in neuronal ceroid lipofuscinosis (NCL) with underlying TPP1/CLN2 mutations. A survey of 25 South American CLN2 affected individuals enabled the differentiation of two phenotypes: classical late-infantile and variant juvenile, each in approximately 50% of patients, with residual TPP1 activity occurring in approximately 32%. Each individual was assigned to one of three subgroups: (I) n=11, null TPP1 activity in leukocytes; (II) n=8, residual TPP1 activity of 0.60-15.85 nmol/h/mg (nr 110-476); (III) n=6, activity not measured in leukocytes. Curvilinear bodies (CB) appeared in almost all studied CLN2 subjects; the only exceptions occurred in cases of subgroup II: two individuals had combined CBs/fingerprints (FPs), and one case had pure FPs. There were 15 mutations (4 first published in this paper, 3 previously observed in South America by our group, and 8 previously observed by others). In subgroup I, mutations were either missense or nonsense; in subgroups II and III, mutations prevailed at the non-conserved intronic site, c.887-10A>G (intron 7), and to a lesser extent at c.89+5G>C (intron 2), in heterozygous combinations. Grouping phenotypically and genetically known individuals on the basis of TPP1 activity supported the concept that residual enzyme activity underlies a protracted disease course. The prevalence of intronic mutations at non-conserved sites in subgroup II individuals indicates that some alternative splicing might allow some residual TPP1 activity.
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Affiliation(s)
- Romina Kohan
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
- Facultad de Odontología, Universidad Nacional de Córdoba. Haya de la Torre s/n, (5000) Córdoba, Argentina
- Secretaría de Ciencia y Tecnología (SECyT), Universidad Nacional de Córdoba. Juan Filloy s/n, (5000) Córdoba, Argentina
| | - María Noelia Carabelos
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Winnie Xin
- Massachussets General Hospital, Neurogenetics DNA Diagnostic Laboratory, Simches Research Building, 5 300, 185 Cambridge St., Boston, Massachussets 02114, USA
| | - Katherine Sims
- Massachussets General Hospital, Neurogenetics DNA Diagnostic Laboratory, Simches Research Building, 5 300, 185 Cambridge St., Boston, Massachussets 02114, USA
| | - Norberto Guelbert
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Inés Adriana Cismondi
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
- Massachussets General Hospital, Neurogenetics DNA Diagnostic Laboratory, Simches Research Building, 5 300, 185 Cambridge St., Boston, Massachussets 02114, USA
| | - Patricia Pons
- Centro de Microscopía Electrónica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Haya de la Torre esq. Enrique Barros, 1° piso, (5000) Córdoba, Argentina
| | - Graciela Irene Alonso
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Mónica Troncoso
- Servicio de Neuropsiquiatría Infantil. Hospital Clínico San Borja Arriarán, Avenida Santa Rosa 1234, Santiago, Chile
| | - Scarlet Witting
- Servicio de Neuropsiquiatría Infantil. Hospital Clínico San Borja Arriarán, Avenida Santa Rosa 1234, Santiago, Chile
| | - David A. Pearce
- Sanford Childrens Health Research Center, Sanford Research/USD, Sioux Falls, South Dakota, USA
| | - Raquel Dodelson de Kremer
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Ana María Oller-Ramírez
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Inés Noher de Halac
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Av. Rivadavia 1917, C1033AAJ CABA, Argentina
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27
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Vidal-Donet JM, Cárcel-Trullols J, Casanova B, Aguado C, Knecht E. Alterations in ROS activity and lysosomal pH account for distinct patterns of macroautophagy in LINCL and JNCL fibroblasts. PLoS One 2013; 8:e55526. [PMID: 23408996 PMCID: PMC3567113 DOI: 10.1371/journal.pone.0055526] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/27/2012] [Indexed: 12/21/2022] Open
Abstract
Neuronal ceroid lipofuscinoses (NCL) are lysosomal storage disorders characterized by the accumulation of lipofuscin within lysosomes. Late infantile (LINCL) and juvenile (JNCL) are their most common forms and are caused by loss-of-function mutations in tripeptidyl peptidase 1 (TPP1), a lysosomal endopeptidase, and CLN3 protein (CLN3p), whose location and function is still controversial. LINCL patients suffer more severely from NCL consequences than JNCL patients, in spite of having in common an abnormal accumulation of material with a similar composition in the lysosomes. To identify distinctive characteristics that could explain the differences in the severity of LINCL and JNCL pathologies, we compared the protein degradation mechanisms in patientś fibroblasts. Pulse-chase experiments show a significant decrease in protein degradation by macroautophagy in fibroblasts bearing TPP1 (CLN2) and CLN3p (CLN3) mutations. In CLN2 fibroblasts, LC3-II levels and other procedures indicate an impaired formation of autophagosomes, which confirms the pulse-chase experiments. This defect is linked to an accumulation of reactive oxygen species (ROS), an upregulation of the Akt-mTOR signalling pathway and increased activities of the p38α and ERK1/2 MAPKs. In CLN3 fibroblasts, LC3-II analysis indicates impairment in autophagosome maturation and there is also a defect in fluid phase endocytosis, two alterations that can be related to an observed increase of 0.5 units in lysosomal pH. CLN3 fibroblasts also accumulate ROS but to a lower extent than CLN2. TPP1 activity is completely abrogated in CLN2 and partially diminished in CLN3 fibroblasts. TPP1 cleaves small hydrophobic proteins like subunit c of mitochondrial ATP synthase and the lack or a lower activity of this enzyme can contribute to lipofuscin accumulation. These alterations in TPP1 activity lead to an increased ROS production, especially in CLN2 in which it is aggravated by a decrease in catalase activity. This could explain the earlier appearance of the symptoms in the LINCL form.
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Affiliation(s)
| | - Jaime Cárcel-Trullols
- Laboratory of Cellular Biology, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | | | - Carmen Aguado
- Laboratory of Cellular Biology, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Erwin Knecht
- Laboratory of Cellular Biology, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
- * E-mail:
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28
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Thorn A, Steinfeld R, Ziegenbein M, Grapp M, Hsiao HH, Urlaub H, Sheldrick GM, Gärtner J, Krätzner R. Structure and activity of the only human RNase T2. Nucleic Acids Res 2012; 40:8733-42. [PMID: 22735700 PMCID: PMC3458558 DOI: 10.1093/nar/gks614] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mutations in the gene of human RNase T2 are associated with white matter disease of the human brain. Although brain abnormalities (bilateral temporal lobe cysts and multifocal white matter lesions) and clinical symptoms (psychomotor impairments, spasticity and epilepsy) are well characterized, the pathomechanism of RNase T2 deficiency remains unclear. RNase T2 is the only member of the Rh/T2/S family of acidic hydrolases in humans. In recent years, new functions such as tumor suppressing properties of RNase T2 have been reported that are independent of its catalytic activity. We determined the X-ray structure of human RNase T2 at 1.6 Å resolution. The α+β core fold shows high similarity to those of known T2 RNase structures from plants, while, in contrast, the external loop regions show distinct structural differences. The catalytic features of RNase T2 in presence of bivalent cations were analyzed and the structural consequences of known clinical mutations were investigated. Our data provide further insight into the function of human RNase T2 and may prove useful in understanding its mode of action independent of its enzymatic activity.
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Affiliation(s)
- Andrea Thorn
- Department of Structural Chemistry, University of Göttingen, 37075 Göttingen, Germany
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29
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Oda K. New families of carboxyl peptidases: serine-carboxyl peptidases and glutamic peptidases. J Biochem 2011; 151:13-25. [PMID: 22016395 DOI: 10.1093/jb/mvr129] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Peptidases or proteinases are now classified into seven families based on the nature of the catalytic residues [MEROPS-the peptidase database (http://merops.sanger.ac.uk/)]. They are aspartic- (first described in 1993), cysteine- (1993), serine- (1993) metallo- (1993), threonine- (1997), glutamic- (2004) and asparagine-peptidase (2010). By using an S-PI (pepstatin Ac) as a probe, a new subfamily of serine peptidase, serine-carboxyl peptidase (sedolisin) was discovered in 2001. In addition, the sixth family of peptidase, glutamic peptidase (eqolisin) was also discovered in 2004. The former peptidase is widely distributed in nature from archea to mammals, including humans. One of these enzymes is related to a human fatal hereditable disease, Batten disease. In contrast, the distribution of the latter peptidases is limited, with most of them found in human or plant pathogenic fungi. One such enzyme was isolated from a fungal infection in an HIV-infected patient. In this review, the background of the findings, and crystal structures, catalytic mechanisms, substrates specificities and distribution of the new peptidase families are described.
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Affiliation(s)
- Kohei Oda
- Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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30
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Xu Q, Yao J, Wlodawer A, Guo H. Clarification of the mechanism of acylation reaction and origin of substrate specificity of the serine-carboxyl peptidase sedolisin through QM/MM free energy simulations. J Phys Chem B 2011; 115:2470-6. [PMID: 21332137 DOI: 10.1021/jp1122294] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical/molecular mechanical (QM/MM) free energy simulations are applied for understanding the mechanism of the acylation reaction catalyzed by sedolisin, a representative serine-carboxyl peptidase, leading to the acyl-enzyme (AE) and first product from the enzyme-catalyzed reaction. One of the interesting questions to be addressed in this work is the origin of the substrate specificity of sedolisin that shows a relatively high activity on the substrates with Glu at P(1) site. It is shown that the bond making and breaking events of the acylation reaction involving a peptide substrate (LLE*FL) seem to be accompanied by local conformational changes, proton transfers as well as the formation of alternative hydrogen bonds. The results of the simulations indicate that the conformational change of Glu at P(1) site and its formation of a low barrier hydrogen bond with Asp-170 (along with the transient proton transfer) during the acylation reaction might play a role in the relatively high specificity for the substrate with Glu at P(1) site. The role of some key residues in the catalysis is confirmed through free energy simulations. Glu-80 is found to act as a general base to accept a proton from Ser-287 during the nucleophilic attack and then as a general acid to protonate the leaving group (N-H of P(1')-Phe) during the cleavage of the scissile peptide bond. Another acidic residue, Asp-170, acts as a general acid catalyst to protonate the carbonyl of P(1)-Glu during the formation of the tetrahedral intermediate and as a general base for the formation of the acyl-enzyme. The energetic results from the free energy simulations support the importance of proton transfer from Asp-170 to the carbonyl of P(1)-Glu in the stabilization of the tetrahedral intermediate and the formation of a low-barrier hydrogen bond between the carboxyl group of P(1)-Glu and Asp-170 in the lowering of the free energy barrier for the cleavage of the peptide bond. Detailed analyses of the proton transfers during acylation are also given.
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Affiliation(s)
- Qin Xu
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 3799, USA
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31
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Xu Q, Li L, Guo H. Understanding the mechanism of deacylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As: insights from QM/MM free energy simulations. J Phys Chem B 2010; 114:10594-600. [PMID: 20734497 DOI: 10.1021/jp102785s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics and free energy simulations are performed to study the process of the deacylation reaction catalyzed by kumamolisin-As, a serine-carboxyl peptidase, and to elucidate the catalytic mechanism. The results given here suggest that Asp-164 acts as a general acid/base catalyst not only for the acylation reaction but also for the deacylation reaction. It is shown that the electrostatic oxyanion hole interactions may be less effective in transition state stabilization for the kumamolisin-As catalyzed reaction compared to the general acid/base mechanism involving the proton transfer from or to Asp-164. The dynamic substrate-assisted catalysis (DSAC) involving His at the P1 site of the substrate is found to be less important for the deacylation reaction than for the acylation reaction in the kumamolisin-As catalyzed reaction. The proton transfer processes during the enzyme-catalyzed process are examined and their role in the catalysis is discussed.
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Affiliation(s)
- Qin Xu
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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32
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Kuizon S, DiMaiuta K, Walus M, Jenkins EC, Kuizon M, Kida E, Golabek AA, Espinoza DO, Pullarkat RK, Junaid MA. A critical tryptophan and Ca2+ in activation and catalysis of TPPI, the enzyme deficient in classic late-infantile neuronal ceroid lipofuscinosis. PLoS One 2010; 5:e11929. [PMID: 20689811 PMCID: PMC2914745 DOI: 10.1371/journal.pone.0011929] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 07/07/2010] [Indexed: 11/18/2022] Open
Abstract
Background Tripeptidyl aminopeptidase I (TPPI) is a crucial lysosomal enzyme that is deficient in the fatal neurodegenerative disorder called classic late-infantile neuronal ceroid lipofuscinosis (LINCL). It is involved in the catabolism of proteins in the lysosomes. Recent X-ray crystallographic studies have provided insights into the structural/functional aspects of TPPI catalysis, and indicated presence of an octahedrally coordinated Ca2+. Methodology Purified precursor and mature TPPI were used to study inhibition by NBS and EDTA using biochemical and immunological approaches. Site-directed mutagenesis with confocal imaging technique identified a critical W residue in TPPI activity, and the processing of precursor into mature enzyme. Principal Findings NBS is a potent inhibitor of the purified TPPI. In mammalian TPPI, W542 is critical for tripeptidyl peptidase activity as well as autocatalysis. Transfection studies have indicated that mutants of the TPPI that harbor residues other than W at position 542 have delayed processing, and are retained in the ER rather than transported to lysosomes. EDTA inhibits the autocatalytic processing of the precursor TPPI. Conclusions/Significance We propose that W542 and Ca2+ are critical for maintaining the proper tertiary structure of the precursor proprotein as well as the mature TPPI. Additionally, Ca2+ is necessary for the autocatalytic processing of the precursor protein into the mature TPPI. We have identified NBS as a potent TPPI inhibitor, which led in delineating a critical role for W542 residue. Studies with such compounds will prove valuable in identifying the critical residues in the TPPI catalysis and its structure-function analysis.
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Affiliation(s)
- Salomon Kuizon
- Department of Developmental Biochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Kathleen DiMaiuta
- Department of Developmental Biochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Marius Walus
- Department of Developmental Neurobiology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Edmund C. Jenkins
- Department of Developmental Biochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Marisol Kuizon
- Department of Developmental Biochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Elizabeth Kida
- Department of Developmental Neurobiology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Adam A. Golabek
- Department of Developmental Neurobiology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Daniel O. Espinoza
- Department of Molecular Biology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Raju K. Pullarkat
- Department of Developmental Biochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Mohammed A. Junaid
- Department of Developmental Biochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- * E-mail:
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Walus M, Kida E, Golabek AA. Functional consequences and rescue potential of pathogenic missense mutations in tripeptidyl peptidase I. Hum Mutat 2010; 31:710-21. [DOI: 10.1002/humu.21251] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Impaired lysosomal trimming of N-linked oligosaccharides leads to hyperglycosylation of native lysosomal proteins in mice with alpha-mannosidosis. Mol Cell Biol 2010; 30:273-83. [PMID: 19884343 DOI: 10.1128/mcb.01143-09] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Alpha-mannosidosis is caused by the genetic defect of the lysosomal alpha-d-mannosidase (LAMAN), which is involved in the breakdown of free alpha-linked mannose-containing oligosaccharides originating from glycoproteins with N-linked glycans, and thus manifests itself in an extensive storage of mannose-containing oligosaccharides. Here we demonstrate in a model of mice with alpha-mannosidosis that native lysosomal proteins exhibit elongated N-linked oligosaccharides as shown by two-dimensional difference gel electrophoresis, deglycosylation assays, and mass spectrometry. The analysis of cathepsin B-derived oligosaccharides revealed a hypermannosylation of glycoproteins in mice with alpha-mannosidosis as indicated by the predominance of extended Man3GlcNAc2 oligosaccharides. Treatment with recombinant human alpha-mannosidase partially corrected the hyperglycosylation of lysosomal proteins in vivo and in vitro. These data clearly demonstrate that LAMAN is involved not only in the lysosomal catabolism of free oligosaccharides but also in the trimming of asparagine-linked oligosaccharides on native lysosomal proteins.
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Guhaniyogi J, Sohar I, Das K, Stock AM, Lobel P. Crystal structure and autoactivation pathway of the precursor form of human tripeptidyl-peptidase 1, the enzyme deficient in late infantile ceroid lipofuscinosis. J Biol Chem 2009; 284:3985-97. [PMID: 19038967 PMCID: PMC2635056 DOI: 10.1074/jbc.m806943200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/07/2008] [Indexed: 11/20/2022] Open
Abstract
Late infantile neuronal ceroid lipofuscinosis is a fatal childhood neurological disorder caused by a deficiency in the lysosomal protease tripeptidyl-peptidase 1 (TPP1). TPP1 represents the only known mammalian member of the S53 family of serine proteases, a group characterized by a subtilisin-like fold, a Ser-Glu-Asp catalytic triad, and an acidic pH optimum. TPP1 is synthesized as an inactive proenzyme (pro-TPP1) that is proteolytically processed into the active enzyme after exposure to low pH in vitro or targeting to the lysosome in vivo. In this study, we describe an endoglycosidase H-deglycosylated form of TPP1 containing four Asn-linked N-acetylglucosamines that is indistinguishable from fully glycosylated TPP1 in terms of autocatalytic processing of the proform and enzymatic properties of the mature protease. The crystal structure of deglycosylated pro-TPP1 was determined at 1.85 angstroms resolution. A large 151-residue C-shaped prodomain makes extensive contacts as it wraps around the surface of the catalytic domain with the two domains connected by a 24-residue flexible linker that passes through the substrate-binding groove. The proenzyme structure reveals suboptimal catalytic triad geometry with its propiece linker partially blocking the substrate-binding site, which together serve to prevent premature activation of the protease. Finally, we have identified numerous processing intermediates and propose a structural model that explains the pathway for TPP1 activation in vitro. These data provide new insights into TPP1 function and represent a valuable resource for constructing improved TPP1 variants for treatment of late infantile neuronal ceroid lipofuscinosis.
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Affiliation(s)
- Jayita Guhaniyogi
- Center for Advanced Biotechnology and Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Jersey, USA
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