1
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Ozhelvaci F, Steczkiewicz K. Identification and Classification of Papain-like Cysteine Proteinases. J Biol Chem 2023:104801. [PMID: 37164157 DOI: 10.1016/j.jbc.2023.104801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Papain-like cysteine peptidases form a big and highly diverse superfamily of proteins involved in many important biological functions, such as protein turnover, deubiquitination, tissue remodeling, blood clotting, virulence, defense, and cell wall remodeling. High sequence and structure diversity observed within these proteins hinders their comprehensive classification as well as the identification of new representatives. Moreover, in general protein databases, many families already classified as papain-like lack details regarding their mechanism of action or biological function. Here, we use transitive remote homology searches and 3D modeling to newly classify 21 families to the papain-like cysteine peptidase superfamily. We attempt to predict their biological function, and provide structural chacterization of 89 protein clusters defined based on sequence similarity altogether spanning 106 papain-like families. Moreover, we systematically discuss observed diversity in sequences, structures, and catalytic sites. Eventually, we expand the list of human papain-related proteins by seven representatives, including dopamine receptor-interacting protein (DRIP1) as potential deubiquitinase, and centriole duplication regulating CEP76 as retaining catalytically active peptidase-like domain. The presented results not only provide structure-based rationales to already existing peptidase databases but also may inspire further experimental research focused on peptidase-related biological processes.
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Affiliation(s)
- Fatih Ozhelvaci
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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2
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Walber S, Partalidou G, Gerling‐Driessen UIM. NGLY1 Deficiency: A Rare Genetic Disorder Unlocks Therapeutic Potential for Common Diseases. Isr J Chem 2022. [DOI: 10.1002/ijch.202200068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Simon Walber
- Institute of Organic and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf Germany
| | - Georgia Partalidou
- Institute of Organic and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf Germany
| | - Ulla I. M. Gerling‐Driessen
- Institute of Organic and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf Germany
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3
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Miao X, Wu J, Chen H, Lu G. Comprehensive Analysis of the Structure and Function of Peptide:N-Glycanase 1 and Relationship with Congenital Disorder of Deglycosylation. Nutrients 2022; 14:nu14091690. [PMID: 35565658 PMCID: PMC9102325 DOI: 10.3390/nu14091690] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 02/01/2023] Open
Abstract
The cytosolic PNGase (peptide:N-glycanase), also known as peptide-N4-(N-acetyl-β-glucosaminyl)-asparagine amidase, is a well-conserved deglycosylation enzyme (EC 3.5.1.52) which catalyzes the non-lysosomal hydrolysis of an N(4)-(acetyl-β-d-glucosaminyl) asparagine residue (Asn, N) into a N-acetyl-β-d-glucosaminyl-amine and a peptide containing an aspartate residue (Asp, D). This enzyme (NGLY1) plays an essential role in the clearance of misfolded or unassembled glycoproteins through a process named ER-associated degradation (ERAD). Accumulating evidence also points out that NGLY1 deficiency can cause an autosomal recessive (AR) human genetic disorder associated with abnormal development and congenital disorder of deglycosylation. In addition, the loss of NGLY1 can affect multiple cellular pathways, including but not limited to NFE2L1 pathway, Creb1/Atf1-AQP pathway, BMP pathway, AMPK pathway, and SLC12A2 ion transporter, which might be the underlying reasons for a constellation of clinical phenotypes of NGLY1 deficiency. The current comprehensive review uncovers the NGLY1’ssdetailed structure and its important roles for participation in ERAD, involvement in CDDG and potential treatment for NGLY1 deficiency.
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Affiliation(s)
- Xiangguang Miao
- Queen Mary School, Nanchang University, No. 1299 Xuefu Avenue, Honggutan New District, Nanchang 330036, China;
| | - Jin Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People’s Hospital, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China;
- Deyang Key Laboratory of Tumor Molecular Research, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China
- Department of Molecular & Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Hongping Chen
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang 330006, China
- Correspondence: (H.C.); (G.L.); Tel.: +86-188-0147-4087 (G.L.)
| | - Guanting Lu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People’s Hospital, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China;
- Deyang Key Laboratory of Tumor Molecular Research, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China
- Correspondence: (H.C.); (G.L.); Tel.: +86-188-0147-4087 (G.L.)
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4
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NGLY1 Deficiency, a Congenital Disorder of Deglycosylation: From Disease Gene Function to Pathophysiology. Cells 2022; 11:cells11071155. [PMID: 35406718 PMCID: PMC8997433 DOI: 10.3390/cells11071155] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
N-Glycanase 1 (NGLY1) is a cytosolic enzyme involved in removing N-linked glycans of misfolded N-glycoproteins and is considered to be a component of endoplasmic reticulum-associated degradation (ERAD). The 2012 identification of recessive NGLY1 mutations in a rare multisystem disorder has led to intense research efforts on the roles of NGLY1 in animal development and physiology, as well as the pathophysiology of NGLY1 deficiency. Here, we present a review of the NGLY1-deficient patient phenotypes, along with insights into the function of this gene from studies in rodent and invertebrate animal models, as well as cell culture and biochemical experiments. We will discuss critical processes affected by the loss of NGLY1, including proteasome bounce-back response, mitochondrial function and homeostasis, and bone morphogenetic protein (BMP) signaling. We will also cover the biologically relevant targets of NGLY1 and the genetic modifiers of NGLY1 deficiency phenotypes in animal models. Together, these discoveries and disease models have provided a number of avenues for preclinical testing of potential therapeutic approaches for this disease.
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5
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Kariminejad A, Shakiba M, Shams M, Namiranian P, Eghbali M, Talebi S, Makvand M, Jaeken J, Najmabadi H, Hennekam RC. NGLY1 deficiency: Novel variants and literature review. Eur J Med Genet 2021; 64:104146. [PMID: 33497766 DOI: 10.1016/j.ejmg.2021.104146] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 12/05/2020] [Accepted: 01/20/2021] [Indexed: 01/26/2023]
Abstract
NGLY1 deficiency is a recently described autosomal recessive disorder, involved in deglycosylation of proteins, and for that reason grouped as the congenital disorders of deglycosylation together with the lysosomal storage disorders. The typical phenotype is characterized by intellectual disability, liver malfunctioning, muscular hypotonia, involuntary movements, and decreased or absent tear production. Liver biopsy demonstrates vacuolar amorphous cytoplasmic storage material. NGLY1 deficiency is caused by bi-allelic variants in NGLY1 which catalyzes protein deglycosylation. We describe five patients from two families with NGLY1 deficiency due to homozygosity for two novel NGLY1 variants, and compare their findings to those of earlier reported patients. The typical features of the disorder are present in a limited way, and there is intra-familial variability. In addition in one of the families the muscle atrophy and posture abnormalities are marked. These can be explained either as variability of the phenotype or as sign of slowly progression of features as the present affected individuals are older than earlier reported patients.
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Affiliation(s)
| | - Marjan Shakiba
- Pediatric Endocrinology and Metabolism Department, Mofid Children Hospital, Shahid Beheshti, University of Medical Science, Tehran, Iran
| | - Mehrvash Shams
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Parva Namiranian
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Maryam Eghbali
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Said Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran.
| | - Mina Makvand
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Jaak Jaeken
- Department of Development and Regeneration, Center for Metabolic Diseases, KU Leuven, Leuven, Belgium
| | - Hossein Najmabadi
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran; Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Raoul C Hennekam
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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6
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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7
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Waheed R, El Asely AM, Bakery H, El-Shawarby R, Abuo-Salem M, Abdel-Aleem N, Malhat F, Khafaga A, Abdeen A. Thermal stress accelerates mercury chloride toxicity in Oreochromis niloticus via up-regulation of mercury bioaccumulation and HSP70 mRNA expression. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137326. [PMID: 32092518 DOI: 10.1016/j.scitotenv.2020.137326] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 05/22/2023]
Abstract
Mercury (Hg) is an environmental pollutant that threatens aquatic life. Many environmental factors, including water temperature, are reported to influence the toxicity of dissolved chemicals in the aquatic ecosystem. Therefore, we investigated the impact of thermal stress on Hg-induced subchronic toxicity in Nile tilapia (Oreochromis niloticus). Fish were randomly allocated into five groups. Group I served as the control and kept at 25 °C. Groups II, III, IV, and V were reared at 25, 28, 31, and 34 °C, respectively, and co-exposed to HgCl2 (1/10 LC50) for 42 days. Blood and tissue samples were collected after 21 and 42 days. All HgCl2-exposed groups exhibited significant elevations in serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), urea, and creatinine, along with decreases in the serum total protein and albumin. In addition, marked reductions in antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSPx), were observed. Remarkable increases in Hg tissue concentrations were detected along with increases in heat shock protein (HSP) 70 mRNA expression. Interestingly, the patterns data that were recorded were more coincident with the water temperature than the period of exposure. In conclusion, water temperature and exposure period are two crucial factors modulating HgCl2-induced toxicity and bioaccumulation in Nile tilapia. Our findings provide new insights concerning the impact of thermal stress as an environmental factor on Hg toxicity and bioaccumulation in Nile tilapia and, in turn, on fish and fish consumer health.
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Affiliation(s)
- Rania Waheed
- Teaching Hospital, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Amel M El Asely
- Department of Aquatic Animals Diseases and Management, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Hatem Bakery
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Ragab El-Shawarby
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Mohamed Abuo-Salem
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Nabila Abdel-Aleem
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Farag Malhat
- Pesticide Residues and Environmental Pollution Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, Dokki, Giza 12618, Egypt
| | - Asmaa Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina 22758, Egypt
| | - Ahmed Abdeen
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt.
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8
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Novel NGLY1 gene variants in Chinese children with global developmental delay, microcephaly, hypotonia, hypertransaminasemia, alacrimia, and feeding difficulty. J Hum Genet 2020; 65:387-396. [PMID: 31965062 DOI: 10.1038/s10038-019-0719-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 11/09/2022]
Abstract
NGLY1 deficiency is the first and only autosomal recessive congenital disorder of N-linked deglycosylation (NGLY1-CDDG). To date, no patients with NGLY1 deficiency has been reported from mainland China or East Asia in English literature. Here, we present six patients with a diagnosis of NGLY1-CDDG on the basis of clinical phenotype, genetic testing, and functional studies. We retrospectively analyzed clinical phenotypes and NGLY1 genotypes of six cases from four families. Informed consent was obtained for diagnosis and treatment. In-silico tools and in vitro enzyme activity assays were used to determine pathogenicity of NGLY1 varaints. All patients had typical features of NGLY1-CDDG, including global developmental delay, microcephaly, hypotonia, hypertransaminasemia, alacrimia, and feeding difficulty. Dysmorphic features found in our patients include flat nasal bridge, loose and hollow cheeks, short stature, malnutrition, and ptosis. Pachylosis could be a novel cutaneous feature that may be explained by lack of sweat. We found three novel variants, including one missense (c.982C > G/p.Arg328Gly), one splice site (c.1003+3A > G), and one frame-shift (c.1637-1652delCATCTTTTGCTTATAT/p.Ser546PhefsTer) variant. All mutations were predicted to be disease causing with in-silico prediction tools, and affected at least one feature of gene splicing. Protein modeling showed missense variants may affect covalent bonding within the protein structure, or interrupt active/binding amino-acid residues. In vitro studies indicated that proteins carrying missense variants (p.Arg328Gly and p.Tyr342Cys) lost the enzyme activity. We expanded clinical phenotype and genetic mutation spectrum of NGLY1-CDDG by reporting six cases, three novel variants, and novel clinical features from mainland China.
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9
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Tomlin F, Gerling-Driessen UIM, Liu YC, Flynn RA, Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR. Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity. ACS CENTRAL SCIENCE 2017; 3:1143-1155. [PMID: 29202016 PMCID: PMC5704294 DOI: 10.1021/acscentsci.7b00224] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Indexed: 05/06/2023]
Abstract
Proteasome inhibitors are used to treat blood cancers such as multiple myeloma (MM) and mantle cell lymphoma. The efficacy of these drugs is frequently undermined by acquired resistance. One mechanism of proteasome inhibitor resistance may involve the transcription factor Nuclear Factor, Erythroid 2 Like 1 (NFE2L1, also referred to as Nrf1), which responds to proteasome insufficiency or pharmacological inhibition by upregulating proteasome subunit gene expression. This "bounce-back" response is achieved through a unique mechanism. Nrf1 is constitutively translocated into the ER lumen, N-glycosylated, and then targeted for proteasomal degradation via the ER-associated degradation (ERAD) pathway. Proteasome inhibition leads to accumulation of cytosolic Nrf1, which is then processed to form the active transcription factor. Here we show that the cytosolic enzyme N-glycanase 1 (NGLY1, the human PNGase) is essential for Nrf1 activation in response to proteasome inhibition. Chemical or genetic disruption of NGLY1 activity results in the accumulation of misprocessed Nrf1 that is largely excluded from the nucleus. Under these conditions, Nrf1 is inactive in regulating proteasome subunit gene expression in response to proteasome inhibition. Through a small molecule screen, we identified a cell-active NGLY1 inhibitor that disrupts the processing and function of Nrf1. The compound potentiates the cytotoxicity of carfilzomib, a clinically used proteasome inhibitor, against MM and T cell-derived acute lymphoblastic leukemia (T-ALL) cell lines. Thus, NGLY1 inhibition prevents Nrf1 activation and represents a new therapeutic approach for cancers that depend on proteasome homeostasis.
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Affiliation(s)
- Frederick
M. Tomlin
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | | | - Yi-Chang Liu
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ryan A. Flynn
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Janakiram R. Vangala
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Christian S. Lentz
- Department
of Pathology, Stanford University School
of Medicine, 300 Pasteur
Drive, Stanford, California 94305, United States
| | - Sandra Clauder-Muenster
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Petra Jakob
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - William F. Mueller
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Diana Ordoñez-Rueda
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Malte Paulsen
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Naoko Matsui
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Deirdre Foley
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Agnes Rafalko
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Tadashi Suzuki
- Glycometabolome
Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Matthew Bogyo
- Department
of Pathology, Stanford University School
of Medicine, 300 Pasteur
Drive, Stanford, California 94305, United States
- Department
of Microbiology and Immunology, Stanford
University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Lars M. Steinmetz
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
- Department
of Genetics, School of Medicine, Stanford
University, Stanford, California 94305, United States
| | - Senthil K. Radhakrishnan
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Carolyn R. Bertozzi
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
- E-mail:
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10
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Ipe J, Swart M, Burgess KS, Skaar TC. High-Throughput Assays to Assess the Functional Impact of Genetic Variants: A Road Towards Genomic-Driven Medicine. Clin Transl Sci 2017; 10:67-77. [PMID: 28213901 PMCID: PMC5355973 DOI: 10.1111/cts.12440] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/03/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
- J Ipe
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
| | - M Swart
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
| | - KS Burgess
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
- Indiana University School of MedicineDepartment of Pharmacology and ToxicologyIndianapolisIndianaUSA
| | - TC Skaar
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
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11
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The cytoplasmic peptide:N-glycanase (NGLY1) - Structure, expression and cellular functions. Gene 2015; 577:1-7. [PMID: 26611529 DOI: 10.1016/j.gene.2015.11.021] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 11/23/2022]
Abstract
NGLY1/Ngly1 is a cytosolic peptide:N-glycanase, i.e. de-N-glycosylating enzyme acting on N-glycoproteins in mammals, generating free, unconjugated N-glycans and deglycosylated peptides in which the N-glycosylated asparagine residues are converted to aspartates. This enzyme is known to be involved in the quality control system for the newly synthesized glycoproteins in the endoplasmic reticulum (ER). In this system, misfolded (glyco)proteins are retrotranslocated to the cytosol, where the 26S proteasomes play a central role in degrading the proteins: a process referred to as ER-associated degradation or ERAD in short. PNGase-mediated deglycosylation is believed to facilitate the efficient degradation of some misfolded glycoproteins. Human patients harboring mutations of NGLY1 gene (NGLY1-deficiency) have recently been discovered, clearly indicating the functional importance of this enzyme. This review summarizes the current state of our knowledge on NGLY1 and its gene product in mammalian cells.
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12
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Weng Y, Sui Z, Jiang H, Shan Y, Chen L, Zhang S, Zhang L, Zhang Y. Releasing N-glycan from peptide N-terminus by N-terminal succinylation assisted enzymatic deglycosylation. Sci Rep 2015; 5:9770. [PMID: 25902405 PMCID: PMC4405948 DOI: 10.1038/srep09770] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/18/2015] [Indexed: 01/13/2023] Open
Abstract
Due to the important roles of N-glycoproteins in various biological processes, the global N-glycoproteome analysis has been paid much attention. However, by current strategies for N-glycoproteome profiling, peptides with glycosylated Asn at N-terminus (PGANs), generated by protease digestion, could hardly be identified, due to the poor deglycosylation capacity by enzymes. However, theoretically, PGANs occupy 10% of N-glycopeptides in the typical tryptic digests. Therefore, in this study, we developed a novel strategy to identify PGANs by releasing N-glycans through the N-terminal site-selective succinylation assisted enzymatic deglycosylation. The obtained PGANs information is beneficial to not only achieve the deep coverage analysis of glycoproteomes, but also discover the new biological functions of such modification.
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Affiliation(s)
- Yejing Weng
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Jiang
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichu Shan
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lingfan Chen
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shen Zhang
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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13
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Yan Q, Li XP, Tumer NE. Wild type RTA and less toxic variants have distinct requirements for Png1 for their depurination activity and toxicity in Saccharomyces cerevisiae. PLoS One 2014; 9:e113719. [PMID: 25436896 PMCID: PMC4250064 DOI: 10.1371/journal.pone.0113719] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 10/30/2014] [Indexed: 01/29/2023] Open
Abstract
Ricin A chain (RTA) undergoes retrograde trafficking and is postulated to use components of the endoplasmic reticulum (ER) associated degradation (ERAD) pathway to enter the cytosol to depurinate ribosomes. However, it is not known how RTA evades degradation by the proteasome after entry into the cytosol. We observed two distinct trafficking patterns among the precursor forms of wild type RTA and nontoxic variants tagged with enhanced green fluorescent protein (EGFP) at their C-termini in yeast. One group, which included wild type RTA, underwent ER-to-vacuole transport, while another group, which included the G83D variant, formed aggregates in the ER and was not transported to the vacuole. Peptide: N-glycanase (Png1), which catalyzes degradation of unfolded glycoproteins in the ERAD pathway affected depurination activity and toxicity of wild type RTA and G83D variant differently. PreG83D variant was deglycosylated by Png1 on the ER membrane, which reduced its depurination activity and toxicity by promoting its degradation. In contrast, wild type preRTA was deglycosylated by the free pool of Png1 in the cytosol, which increased its depurination activity, possibly by preventing its degradation. These results indicate that wild type RTA has a distinct requirement for Png1 compared to the G83D variant and is deglycosylated by Png1 in the cytosol as a possible strategy to avoid degradation by the ERAD pathway to reach the ribosome.
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Affiliation(s)
- Qing Yan
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Xiao-Ping Li
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nilgun E. Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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Suzuki T. The cytoplasmic peptide:N-glycanase (Ngly1)--basic science encounters a human genetic disorder. J Biochem 2014; 157:23-34. [DOI: 10.1093/jb/mvu068] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Bhaskaran SS, Stebbins CE. Structure of the catalytic domain of the Salmonella virulence factor SseI. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1613-21. [PMID: 23151626 PMCID: PMC3498931 DOI: 10.1107/s0907444912039042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/12/2012] [Indexed: 11/15/2022]
Abstract
SseI is secreted into host cells by Salmonella and contributes to the establishment of systemic infections. The crystal structure of the C-terminal domain of SseI has been solved to 1.70 Å resolution, revealing it to be a member of the cysteine protease superfamily with a catalytic triad consisting of Cys178, His216 and Asp231 that is critical to its virulence activities. Structure-based analysis revealed that SseI is likely to possess either acyl hydrolase or acyltransferase activity, placing this virulence factor in the rapidly growing class of enzymes of this family utilized by bacterial pathogens inside eukaryotic cells.
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Affiliation(s)
- Shyam S. Bhaskaran
- Laboratory of Structural Microbiology, The Rockefeller University, New York, NY 10065, USA
| | - C. Erec Stebbins
- Laboratory of Structural Microbiology, The Rockefeller University, New York, NY 10065, USA
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16
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Masahara-Negishi Y, Hosomi A, Della Mea M, Serafini-Fracassini D, Suzuki T. A plant peptide: N-glycanase orthologue facilitates glycoprotein ER-associated degradation in yeast. Biochim Biophys Acta Gen Subj 2012; 1820:1457-62. [PMID: 22659524 DOI: 10.1016/j.bbagen.2012.05.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 05/14/2012] [Accepted: 05/21/2012] [Indexed: 11/16/2022]
Abstract
BACKGROUND The cytoplasmic peptide:N-glycanase (PNGase) is a deglycosylating enzyme involved in the ER-associated degradation (ERAD) process, while ERAD-independent activities are also reported. Previous biochemical analyses indicated that the cytoplasmic PNGase orthologue in Arabidopsis thaliana (AtPNG1) can function as not only PNGase but also transglutaminase, while its in vivo function remained unclarified. METHODS AtPNG1 was expressed in Saccharomyces cerevisiae and its in vivo role on PNGase-dependent ERAD pathway was examined. RESULTS AtPNG1 could facilitate the ERAD through its deglycosylation activity. Moreover, a catalytic mutant of AtPNG1 (AtPNG1(C251A)) was found to significantly impair the ERAD process. This result was found to be N-glycan-dependent, as the AtPNG(C251A) did not affect the stability of the non-glycosylated RTA∆ (ricin A chain non-toxic mutant). Tight interaction between AtPNG1(C251A) and the RTA∆ was confirmed by co-immunoprecipitation analysis. CONCLUSION The plant PNGase facilitates ERAD through its deglycosylation activity, while the catalytic mutant of AtPNG1 impair glycoprotein ERAD by binding to N-glycans on the ERAD substrates. GENERAL SIGNIFICANCE Our studies underscore the functional importance of a plant PNGase orthologue as a deglycosylating enzyme involved in the ERAD.
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Affiliation(s)
- Yuki Masahara-Negishi
- Glycometabolome Team, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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17
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Lakhtin V, Lakhtin M, Alyoshkin V. Lectins of living organisms. The overview. Anaerobe 2011; 17:452-5. [DOI: 10.1016/j.anaerobe.2011.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 06/09/2011] [Indexed: 10/18/2022]
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18
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Dieterle MG, Wiest AE, Plamann M, McCluskey K. Characterization of the temperature-sensitive mutations un-7 and png-1 in Neurospora crassa. PLoS One 2010; 5:e10703. [PMID: 20502699 PMCID: PMC2872674 DOI: 10.1371/journal.pone.0010703] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 04/29/2010] [Indexed: 11/22/2022] Open
Abstract
The model filamentous fungus Neurospora crassa has been studied for over fifty years and many temperature-sensitive mutants have been generated. While most of these have been mapped genetically, many remain anonymous. The mutation in the N. crassa temperature-sensitive lethal mutant un-7 was identified by a complementation based approach as being in the open reading frame designated NCU00651 on linkage group I. Other mutations in this gene have been identified that lead to a temperature-sensitive morphological phenotype called png-1. The mutations underlying un-7 result in a serine to phenylalanine change at position 273 and an isoleucine to valine change at position 390, while the mutation in png-1 was found to result in a serine to leucine change at position 279 although there were other conservative changes in this allele. The overall morphology of the strain carrying the un-7 mutation is compared to strains carrying the png-1 mutation and these mutations are evaluated in the context of other temperature-sensitive mutants in Neurospora.
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Affiliation(s)
- Michael G. Dieterle
- Fungal Genetics Stock Center, School of Biological Sciences, University of Missouri- Kansas City, Kansas City, Missouri, United States of America
- Pembroke Hill School, Kansas City, Missouri, United States of America
| | - Aric E. Wiest
- Fungal Genetics Stock Center, School of Biological Sciences, University of Missouri- Kansas City, Kansas City, Missouri, United States of America
| | - Mike Plamann
- Fungal Genetics Stock Center, School of Biological Sciences, University of Missouri- Kansas City, Kansas City, Missouri, United States of America
| | - Kevin McCluskey
- Fungal Genetics Stock Center, School of Biological Sciences, University of Missouri- Kansas City, Kansas City, Missouri, United States of America
- * E-mail:
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19
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Funakoshi Y, Negishi Y, Gergen JP, Seino J, Ishii K, Lennarz WJ, Matsuo I, Ito Y, Taniguchi N, Suzuki T. Evidence for an essential deglycosylation-independent activity of PNGase in Drosophila melanogaster. PLoS One 2010; 5:e10545. [PMID: 20479940 PMCID: PMC2866665 DOI: 10.1371/journal.pone.0010545] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Accepted: 04/12/2010] [Indexed: 12/03/2022] Open
Abstract
Background Peptide:N-glycanase (PNGase) is an enzyme which releases N-linked glycans from glycopeptides/glycoproteins. This enzyme plays a role in the ER-associated degradation (ERAD) pathway in yeast and mice, but the biological importance of this activity remains unknown. Principal Findings In this study, we characterized the ortholog of cytoplasmic PNGases, PNGase-like (Pngl), in Drosophila melanogaster. Pngl was found to have a molecular weight of ∼74K and was mainly localized in the cytosol. Pngl lacks a CXXC motif that is critical for enzymatic activity in other species and accordingly did not appear to possess PNGase activity, though it still retains carbohydrate-binding activity. We generated microdeletions in the Pngl locus in order to investigate the functional importance of this protein in vivo. Elimination of Pngl led to a serious developmental delay or arrest during the larval and pupal stages, and surviving mutant adult males and females were frequently sterile. Most importantly, these phenotypes were rescued by ubiquitous expression of Pngl, clearly indicating that those phenotypic consequences were indeed due to the lack of functional Pngl. Interestingly, a putative “catalytic-inactive” mutant could not rescue the growth-delay phenotype, indicating that a biochemical activity of this protein is important for its biological function. Conclusion Pngl was shown to be inevitable for the proper developmental transition and the biochemical properties other than deglycosylation activity is important for its biological function.
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Affiliation(s)
- Yoko Funakoshi
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN Advanced Science Institute, Wako, Saitama, Japan
- * E-mail: (YF); (TS)
| | - Yuki Negishi
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN Advanced Science Institute, Wako, Saitama, Japan
| | - J. Peter Gergen
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, New York, United States of America
| | - Junichi Seino
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN Advanced Science Institute, Wako, Saitama, Japan
| | - Kumiko Ishii
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN Advanced Science Institute, Wako, Saitama, Japan
| | - William J. Lennarz
- Department of Biochemistry and Cell Biology and Institute for Cell and Developmental Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Ichiro Matsuo
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Gunma, Japan
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan
- Glycotrilogy Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
| | - Naoyuki Taniguchi
- Department of Disease Glycomics, The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
- Disease Glycomics Team, RIKEN Advanced Science Institute, Wako, Saitama, Japan
| | - Tadashi Suzuki
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN Advanced Science Institute, Wako, Saitama, Japan
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
- * E-mail: (YF); (TS)
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Ishiwata A, Lee YJ, Ito Y. Recent advances in stereoselective glycosylation through intramolecular aglycon delivery. Org Biomol Chem 2010; 8:3596-608. [DOI: 10.1039/c004281a] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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21
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Wang S, Xin F, Liu X, Wang Y, An Z, Qi Q, Wang PG. N-terminal deletion of peptide:N-glycanase results in enhanced deglycosylation activity. PLoS One 2009; 4:e8335. [PMID: 20016784 PMCID: PMC2791212 DOI: 10.1371/journal.pone.0008335] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Accepted: 11/25/2009] [Indexed: 11/19/2022] Open
Abstract
Peptide:N-glycanase catalyzes the detachment of N-linked glycan chains from glycopeptides or glycoproteins by hydrolyzing the β-aspartylglucosaminyl bond. Peptide:N-glycanase in yeast binds to Rad23p through its N-terminus. In this study, the complex formed between Peptide:N-glycanase and Rad23p was found to exhibit enhanced deglycosylation activity, which suggests an important role for this enzyme in the misfolded glycoprotein degradation pathway in vivo. To investigate the role of this enzyme in this pathway, we made stepwise deletions of the N-terminal helices of peptide:N-glycanase. Enzymatic analysis of the deletion mutants showed that deletion of the N-terminal H1 helix (Png1p-ΔH1) enhanced the deglycosylation activity of N-glycanase towards denatured glycoproteins. In addition, this mutant exhibited high deglycosylation activity towards native glycoproteins. Dynamic simulations of the wild type and N-terminal H1 deletion mutant implied that Png1p-ΔH1 is more flexible than wild type Png1p. The efficient deglycosylation of Png1p-ΔH1 towards native and non-native glycoproteins offers a potential biotechnological application.
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Affiliation(s)
- Shengjun Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Fengxue Xin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Xiaoyue Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yuxiao Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Zhenyi An
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- National Glycoengineering Research Center, Shandong University, Jinan, China
- * E-mail:
| | - Peng George Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- National Glycoengineering Research Center, Shandong University, Jinan, China
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Maerz S, Funakoshi Y, Negishi Y, Suzuki T, Seiler S. The Neurospora peptide:N-glycanase ortholog PNG1 is essential for cell polarity despite its lack of enzymatic activity. J Biol Chem 2009; 285:2326-32. [PMID: 19940117 DOI: 10.1074/jbc.m109.045302] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Secretory proteins are subjected to a stringent endoplasmic reticulum-based quality control system that distinguishes aberrant from correctly folded proteins. The cytoplasmic peptide:N-glycanase cleaves oligosaccharides from misfolded glycoproteins and prepares them for degradation by the 26 S proteasome. In contrast to abundant in vitro data on its enzymatic function, the in vivo relevance of peptide:N-glycanase activity remains unclear. Here we show that the PNG1 ortholog from the filamentous ascomycete Neurospora crassa is an essential protein, and its deletion results in strong polarity defects. PNG1 and its predicted binding partner RAD23 have distinct functions in N. crassa and are involved in cell wall integrity and DNA repair, respectively. Moreover, wild type PNG1 has substitutions in essential catalytic amino acids, and its deglycosylation activity is lost. These substitutions are conserved in many PNG1 orthologs of the fungal kingdom, implying a so far unrecognized enzyme-independent function of PNG1 that may only become apparent in highly polar cells such as fungal hyphae.
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Affiliation(s)
- Sabine Maerz
- DFG Research Center of Molecular Physiology of the Brain (CMPB), D-37073 Goettingen, Germany
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