1
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Suzuki T, Fujihira H. NGLY1: A fascinating, multifunctional molecule. Biochim Biophys Acta Gen Subj 2024; 1868:130379. [PMID: 37951368 DOI: 10.1016/j.bbagen.2023.130379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/04/2023] [Indexed: 11/14/2023]
Abstract
NGLY1, a cytoplasmic de-N-glycosylating enzyme is well conserved among eukaryotes. This enzyme has attracted considerable attention after mutations on the NGLY1 gene were found to cause a rare genetic disorder called NGLY1 deficiency. Recent explosive progress in NGLY1 research has revealed multi-functional aspects of this protein.
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Affiliation(s)
- Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan.
| | - Haruhiko Fujihira
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
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2
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Okamoto N, Maeda M, Yamamoto C, Kodama R, Sugimoto K, Shinozaki Y, Ezura H, Kimura Y. Construction of tomato plants with suppressed endo-β-N-acetylglucosaminidase activity using CRISPR-Cas9 mediated genome editing. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 190:203-211. [PMID: 36130423 DOI: 10.1016/j.plaphy.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/27/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
High mannose-type free N-glycans with a single N-acetyl-D-glucosamine (GlcNAc) residue at the reducing end (GN1-HMT-FNGs) are produced by cytosolic endo-β-N-acetylglucosaminidase (EC:3.2.1.96) (ENGase) and are ubiquitous in differentiating and growing plant cells. To elucidate the physiological functions of HMT-FNGs in plants, we identified the ENGase gene in tomato (Solyc06g050930) and detected ENGase activity and increased production of GN1-HMT-FNGs during tomato fruit maturation. However, the precise role of GN1-HMT-FNGs in fruit maturation remains unclear. In this study, we established tomato ENGase mutants with suppressed ENGase activity via CRISPR/Cas9 genome editing technology. DNA sequencing of the Δeng mutants (T0 and T1 generations) revealed that they had the same mutations in the genomic DNA around the target sequences. Three null CRISPR/Cas9 segregant plants of the T1 generation (Δeng1-2, -22, and -26) were used to measure ENGase activity and analyze the structural features of HMT-FNGs in the leaves. The Δeng mutants did not exhibit ENGase activity and produced GN2-HMT-FNGs bearing tow GlcNAc residues at the reducing end side instead of GN1-HMT-FNGs. The Δeng mutants lack the N-terminal region of ENGase, indicating that the N-terminal region is important for full ENGase activity. The fruits of Δeng mutants (T2 generation) also showed loss of ENGase activity and similar structural features of HMT-FNGs of the T1 generation. However, there was no significant difference in fruit maturation between the T2 generation of the Δeng mutants and the wild type. The Δeng mutants rich in GN2-HMT-FNGs could be offered as a new tomato that is different from wild type containing GN1-HMT-FNGs.
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Affiliation(s)
- Naoko Okamoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Chiharu Yamamoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Reo Kodama
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Koichi Sugimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yoshihito Shinozaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
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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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Na HJ, Abramowitz LK, Hanover JA. Cytosolic O-GlcNAcylation and PNG1 maintain Drosophila gut homeostasis by regulating proliferation and apoptosis. PLoS Genet 2022; 18:e1010128. [PMID: 35294432 PMCID: PMC8959174 DOI: 10.1371/journal.pgen.1010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/28/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022] Open
Abstract
Tissue homeostasis requires a delicate balance between stem cell self-renewal, proliferation, and differentiation. Essential to this process is glycosylation, with both intra-and extra-cellular glycosylation being required for stem cell homeostasis. However, it remains unknown how intracellular glycosylation, O-GlcNAcylation, interfaces with cellular components of the extracellular glycosylation machinery, like the cytosolic N-glycanase NGLY1. In this study, we utilize the Drosophila gut and uncover a pathway in which O-GlcNAcylation cooperates with the NGLY1 homologue PNG1 to regulate proliferation in intestinal stem cells (ISCs) and apoptosis in differentiated enterocytes. Further, the CncC antioxidant signaling pathway and ENGase, an enzyme involved in the processing of free oligosaccharides in the cytosol, interact with O-GlcNAc and PNG1 through regulation of protein aggregates to contribute to gut maintenance. These findings reveal a complex coordinated regulation between O-GlcNAcylation and the cytosolic glycanase PNG1 critical to balancing proliferation and apoptosis to maintain gut homeostasis. Understanding glycosylation is of great importance as changes in both intra- and extra-cellular glycosylation have been well documented in diseases. However, it remains relatively unclear how intracellular glycosylation, O-GlcNAcylation, interfaces with the cellular machinery of extracellular glycosylation. In this study, we seek to understand how coordination between a cytosolic N-glycanase, NGLY1, and intracellular glycosylation, is utilized during stem cell proliferation. Using the Drosophila gut as a model system, our data showed O-GlcNAcylation and the Drosophila homologue of NGY1, PNG1, have key roles in both progenitor and differentiated cells that contribute to tissue homeostasis. Further, the CncC antioxidant signaling pathway and ENGase, an enzyme involved in the processing of free oligosaccharides in the cytosol, interact with O-GlcNAc and PNG1 through regulation of protein aggregates to contribute to gut maintenance. Our study suggests that alterations in O-GlcNAc and NGLY1 could be future targets utilized as therapeutics for nutrient-sensitive stem cell-derived diseases such as cancer.
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Affiliation(s)
- Hyun-jin Na
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lara K. Abramowitz
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John A. Hanover
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Shirai S, Uemura R, Maeda M, Kajiura H, Misaki R, Fujiyama K, Kimura Y. Direct evidence of cytosolic PNGase activity in Arabidopsis thaliana: in vitro assay system for plant cPNGase activity. Biosci Biotechnol Biochem 2021; 85:1460-1463. [PMID: 33724383 DOI: 10.1093/bbb/zbab047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/02/2021] [Indexed: 11/12/2022]
Abstract
Cytosolic peptide:N-glycanase (cPNGase), which occurs ubiquitously in eukaryotic cells, is involved in the de-N-glycosylation of misfolded glycoproteins in the protein quality control system. In this study, we aimed to provide direct evidence of plant cPNGase activity against a denatured glycoprotein using a crude extract prepared from a mutant line of Arabidopsis thaliana lacking 2 acidic PNGase genes.
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Affiliation(s)
- Sahoko Shirai
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Ryota Uemura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Hiroyuki Kajiura
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Ryo Misaki
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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Maeda M, Okamoto N, Araki N, Kimura Y. Purification, Characterization, and Gene Expression of Rice Endo-β- N-Acetylglucosaminidase, Endo-Os. FRONTIERS IN PLANT SCIENCE 2021; 12:647684. [PMID: 34447396 PMCID: PMC8382983 DOI: 10.3389/fpls.2021.647684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
In the endoplasmic reticulum-associated degradation system of plant and animal cells, high-mannose type free N-glycans (HMT-FNGs) are produced from misfolded glycoproteins prior to proteasomal degradation, and two enzymes, cytosolic peptide:N-glycanase (cPNGase) and endo-β-N-acetylglucosaminidase (endo-β-GlcNAc-ase), are involved in the deglycosylation. Although the physiological functions of these FNGs in plant growth and development remain to be elucidated, detailed characterization of cPNGase and endo-β-GlcNAc-ase is required. In our previous work, we described the purification, characterization, and subcellular distribution of some plant endo-β-GlcNAc-ases and preliminarily reported the gene information of rice endo-β-GlcNAc-ase (Endo-Os). Furthermore, we analyzed the changes in gene expression of endo-β-GlcNAc-ase during tomato fruit maturation and constructed a mutant line of Arabidopsis thaliana, in which the two endo-β-GlcNAc-ase genes were knocked-out based on the Endo-Os gene. In this report, we describe the purification, characterization, amino acid sequence, and gene cloning of Endo-Os in detail. Purified Endo-Os, with an optimal pH of 6.5, showed high activity for high-mannose type N-glycans bearing the Manα1-2Manα1-3Manβ1 unit; this substrate specificity was almost the same as that of other plant endo-β-GlcNAc-ases, suggesting that Endo-Os plays a critical role in the production of HTM-FNGs in the cytosol. Electrospray ionization-mass spectrometry analysis of the tryptic peptides revealed 17 internal amino acid sequences, including the C terminus; the N-terminal sequence could not be identified due to chemical modification. These internal amino acid sequences were consistent with the amino acid sequence (UniProt ID: Q5W6R1) deduced from the Oryza sativa cDNA clone AK112067 (gene ID: Os05g0346500). Recombinant Endo-Os expressed in Escherichia coli using cDNA showed the same enzymatic properties as those of native Endo-Os.
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Affiliation(s)
- Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Naoko Okamoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Norie Araki
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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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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Hou K, Wang Y, Tao MQ, Jahan MS, Shu S, Sun J, Guo SR. Characterization of the CsPNG1 gene from cucumber and its function in response to salinity stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 150:140-150. [PMID: 32142987 DOI: 10.1016/j.plaphy.2020.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/07/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
Peptide: N-glycanase (PNGase; EC 3.5.1.52) is a deglycosylation enzyme that is responsible for deglycosylating misfolded glycoproteins in the endoplasmic reticulum. However, the role of PNGase in plants is largely unknown. Here, we cloned and characterized the function of peptide: N-glycanase (CsPNG1) from cucumber. The amino acid encoded by CsPNG1 gene contained a typical transglutaminase (TGase) catalytic triad domain and belonged to the "TGase superfamily". Subcellular localization showed that CsPNG1 was located in the cell membrane and nucleus. Promoter sequence analysis and qPCR tests showed that CsPNG1 could respond to a variety of abiotic stresses and hormone treatments. Yeast one-hybrid assays revealed the interaction between the transcription factor CsGT-3b and CsPNG1 promoter. Importantly, overexpression of CsPNG1 in tobacco increased the tolerance to salt stress of transgenic plants. In addition, CsPNG1 interacted with CsRAD23 family proteins and the C-terminal UBA domain of CsRAD23 protein was responsible for binding to CsPNG1, indicating that CsPNG1 was involved in the ER-associated degradation pathway (ERAD). Taken together, our study demonstrated that CsPNG1 plays a positive role in improving plant salt tolerance, and these findings might provide a basis for further functional analysis of CsPNG1 genes in abiotic stress and ERAD.
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Affiliation(s)
- Kun Hou
- College of Horticulture/Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yu Wang
- College of Horticulture/Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Mei-Qi Tao
- College of Horticulture/Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Mohammad Shah Jahan
- College of Horticulture/Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China; Department of Horticulture, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh
| | - Sheng Shu
- College of Horticulture/Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China; Suqian Academy of Protected Horticulture, Nanjing Agricultural University, Suqian, Jiangsu, China
| | - Jin Sun
- College of Horticulture/Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China; Suqian Academy of Protected Horticulture, Nanjing Agricultural University, Suqian, Jiangsu, China
| | - Shi-Rong Guo
- College of Horticulture/Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China; Suqian Academy of Protected Horticulture, Nanjing Agricultural University, Suqian, Jiangsu, China.
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Uemura R, Ogura M, Matsumaru C, Akiyama T, Maeda M, Kimura Y. Novel assay system for acidic Peptide:N-glycanase (aPNGase) activity in crude plant extract. Biosci Biotechnol Biochem 2018; 82:1172-1175. [DOI: 10.1080/09168451.2018.1459464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Abstract
Acidic peptide:N-glycanase (aPNGase) plays a pivotal role in plant glycoprotein turnover. For the construction of aPNGase-knockout or -overexpressing plants, a new method to detect the activity in crude plant extracts is required because endogenous peptidases present in the extract hamper enzyme assays using fluorescence-labeled N-glycopeptides as a substrate. In this study, we developed a new method for measuring aPNGase activity in crude extracts from plant materials.
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Affiliation(s)
- Ryota Uemura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
| | - Mikako Ogura
- Faculty of Agriculture, Okayama University , Okayama, Japan
| | - Chihiro Matsumaru
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
| | - Tsuyoshi Akiyama
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
| | - Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
- Faculty of Agriculture, Okayama University , Okayama, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
- Faculty of Agriculture, Okayama University , Okayama, Japan
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Ma Y, Kim SS, Kwag DG, Kim SH, Kim MS, Ryu SH, Lee DH, So JH, Nam BH, Kim YO, An CM, Park JS. High-Level Expression and Purification of Tag-free Peptides Containing Multiple Disulfide Bond in Pichia pastoris. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yunqi Ma
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - So-Sun Kim
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Dong-Geon Kwag
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Seo-Hyun Kim
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Min-Seob Kim
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Seung-Ho Ryu
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Dong-Hoon Lee
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Jae-Hyeong So
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, Aquaculture Industry Department; National Fisheries Research and Development Institute; Busan 619-902 Republic of Korea
| | - Yong-Ok Kim
- Biotechnology Research Division, Aquaculture Industry Department; National Fisheries Research and Development Institute; Busan 619-902 Republic of Korea
| | - Cheul-Min An
- Biotechnology Research Division, Aquaculture Industry Department; National Fisheries Research and Development Institute; Busan 619-902 Republic of Korea
| | - Jang-Su Park
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
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Deglycosylating enzymes acting on N- glycans in fungi: Insights from a genome survey. Biochim Biophys Acta Gen Subj 2017; 1861:2551-2558. [DOI: 10.1016/j.bbagen.2017.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/16/2017] [Accepted: 08/28/2017] [Indexed: 11/19/2022]
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13
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Galeone A, Han SY, Huang C, Hosomi A, Suzuki T, Jafar-Nejad H. Tissue-specific regulation of BMP signaling by Drosophila N-glycanase 1. eLife 2017; 6:27612. [PMID: 28826503 PMCID: PMC5599231 DOI: 10.7554/elife.27612] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 08/03/2017] [Indexed: 12/14/2022] Open
Abstract
Mutations in the human N-glycanase 1 (NGLY1) cause a rare, multisystem congenital disorder with global developmental delay. However, the mechanisms by which NGLY1 and its homologs regulate embryonic development are not known. Here we show that Drosophila Pngl encodes an N-glycanase and exhibits a high degree of functional conservation with human NGLY1. Loss of Pngl results in developmental midgut defects reminiscent of midgut-specific loss of BMP signaling. Pngl mutant larvae also exhibit a severe midgut clearance defect, which cannot be fully explained by impaired BMP signaling. Genetic experiments indicate that Pngl is primarily required in the mesoderm during Drosophila development. Loss of Pngl results in a severe decrease in the level of Dpp homodimers and abolishes BMP autoregulation in the visceral mesoderm mediated by Dpp and Tkv homodimers. Thus, our studies uncover a novel mechanism for the tissue-specific regulation of an evolutionarily conserved signaling pathway by an N-glycanase enzyme. DNA carries the information needed to build and maintain an organism, and units of DNA known as genes contain coded instructions to build other molecules, including enzymes. Sometimes, genes can become faulty and develop mutations that can affect how an embryo develops and lead to diseases. For example, people with mutations in the gene that encodes an enzyme called N-glycanase 1 experience many problems with their nervous system, gut and other organs. Normally, N-glycanase 1 helps the body remove specific sugar molecules from some proteins in the cells, and is also thought to be important during embryonic development. As an embryo develops, its cells undergo a series of transformations, which is regulated by different molecules and signaling pathways. For example, a pathway known as BMP signaling plays an important role in many tissues. Problems with this pathway can lead to many diseases throughout the body, including the gut, where it helps cells to develop. Previous research has shown that fruit flies lacking the gene that codes for an equivalent N-glycanase enzyme (which is called Pngl in flies) cannot develop properly into adults. However, until now it was not known what type of cells need the N-glycanase enzyme in any organism, or if NGLY1 is essential for important signaling pathways like BMP signaling. Now, Galeone et al. have used genetically modified flies to test how losing Pngl affected their development. The results first showed that engineering Pngl-deficient fruit flies to produce the human enzyme eliminated their problems; these flies developed and survived like normal flies. This confirmed that that the human and fly enzymes can perform equivalent roles. Galeone et al. then discovered that Pngl plays two distinct roles in a group of cells that surround the fruit fly’s gut tissue and give rise to the cells that eventually form the muscle layer in the gut. In the larvae, Pngl was required to empty the gut, which is a necessary step before the larvae can develop into an adult. Moreover, Pngl is needed for BMP signaling in the gut, and when flies had the enzyme removed, some parts of their gut could not from properly. This study will provide a framework to improve our understanding of how BMP signaling is regulated in humans. A next step will be to test if some of the symptoms experienced by patients without a working copy of the gene for N-glycanase 1 are caused by a faulty BMP-signaling system in specific tissues. If this is the case, it could provide new opportunities to treat some of these symptoms.
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Affiliation(s)
- Antonio Galeone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Seung Yeop Han
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Chengcheng Huang
- Glycometabolome Team, RIKEN Global Research Cluster, Saitama, Japan
| | - Akira Hosomi
- Glycometabolome Team, RIKEN Global Research Cluster, Saitama, Japan
| | - Tadashi Suzuki
- Glycometabolome Team, RIKEN Global Research Cluster, Saitama, Japan
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Program in Developmental Biology, Baylor College of Medicine, Houston, United States
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14
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Fujihira H, Masahara-Negishi Y, Tamura M, Huang C, Harada Y, Wakana S, Takakura D, Kawasaki N, Taniguchi N, Kondoh G, Yamashita T, Funakoshi Y, Suzuki T. Lethality of mice bearing a knockout of the Ngly1-gene is partially rescued by the additional deletion of the Engase gene. PLoS Genet 2017; 13:e1006696. [PMID: 28426790 PMCID: PMC5398483 DOI: 10.1371/journal.pgen.1006696] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/15/2017] [Indexed: 11/25/2022] Open
Abstract
The cytoplasmic peptide:N-glycanase (Ngly1 in mammals) is a de-N-glycosylating enzyme that is highly conserved among eukaryotes. It was recently reported that subjects harboring mutations in the NGLY1 gene exhibited severe systemic symptoms (NGLY1-deficiency). While the enzyme obviously has a critical role in mammals, its precise function remains unclear. In this study, we analyzed Ngly1-deficient mice and found that they are embryonic lethal in C57BL/6 background. Surprisingly, the additional deletion of the gene encoding endo-β-N-acetylglucosaminidase (Engase), which is another de-N-glycosylating enzyme but leaves a single GlcNAc at glycosylated Asn residues, resulted in the partial rescue of the lethality of the Ngly1-deficient mice. Additionally, we also found that a change in the genetic background of C57BL/6 mice, produced by crossing the mice with an outbred mouse strain (ICR) could partially rescue the embryonic lethality of Ngly1-deficient mice. Viable Ngly1-deficient mice in a C57BL/6 and ICR mixed background, however, showed a very severe phenotype reminiscent of the symptoms of NGLY1-deficiency subjects. Again, many of those defects were strongly suppressed by the additional deletion of Engase in the C57BL/6 and ICR mixed background. The defects observed in Ngly1/Engase-deficient mice (C57BL/6 background) and Ngly1-deficient mice (C57BL/6 and ICR mixed background) closely resembled some of the symptoms of patients with an NGLY1-deficiency. These observations strongly suggest that the Ngly1- or Ngly1/Engase-deficient mice could serve as a valuable animal model for studies related to the pathogenesis of the NGLY1-deficiency, and that cytoplasmic ENGase represents one of the potential therapeutic targets for this genetic disorder. Ngly1 is a cytoplasmic de-N-glycosylating enzyme that is ubiquitously found in eukaryotes. This enzyme is involved in a process referred to as endoplasmic reticulum-associated degradation (ERAD), one of the quality control mechanisms for newly synthesized proteins. A genetic disorder, NGLY1-deficiency, caused by mutations in the NGLY1 gene has recently been discovered. However, the precise mechanism for the pathogenesis of this devastating disease continues to remain unclear. We report herein that Ngly1-deficient mice are embryonically lethal in a C57BL/6 background. Surprisingly, the lethality was suppressed by crossing the mice with an outbred mouse strain (ICR), suggesting that the phenotypic consequence of Ngly1 is greatly influenced by their genetic background. In both cases, the additional deletion of Engase in Ngly1-deficient mice could strongly mitigate the phenotypes. Interestingly, the remaining defects in Ngly1-deficient or Ngly1/Engase-deficient mice were reminiscent of the symptoms of subjects with an NGLY1-deficiency. Our results clearly point to the importance of Ngly1 in mammals and show that the inhibition of ENGase represents an effective therapy for treating an NGLY1-deficiency. Most importantly, the mice described herein could serve as valuable viable model mice for studies related to the pathophysiology of an NGLY1-deficiency.
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Affiliation(s)
- Haruhiko Fujihira
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, Saitama, Japan
| | - Yuki Masahara-Negishi
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, Saitama, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, BioResourse Center, RIKEN, Ibaraki, Japan
| | - Chengcheng Huang
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, Saitama, Japan
| | - Yoichiro Harada
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, Saitama, Japan
| | - Shigeharu Wakana
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, BioResourse Center, RIKEN, Ibaraki, Japan
| | - Daisuke Takakura
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan
| | - Nana Kawasaki
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan
| | - Naoyuki Taniguchi
- Disease Glycomics Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, Saitama, Japan
| | - Gen Kondoh
- Laboratory of Integrative Biological Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tadashi Yamashita
- Laboratory of Biochemistry, School of Veterinary Medicine, Azabu University, Kanagawa, Japan
| | - Yoko Funakoshi
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, Saitama, Japan
| | - Tadashi Suzuki
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, Saitama, Japan
- * E-mail:
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15
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Aloisi I, Cai G, Serafini-Fracassini D, Del Duca S. Transglutaminase as polyamine mediator in plant growth and differentiation. Amino Acids 2016; 48:2467-78. [DOI: 10.1007/s00726-016-2235-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/11/2016] [Indexed: 01/23/2023]
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16
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Harada Y, Hirayama H, Suzuki T. Generation and degradation of free asparagine-linked glycans. Cell Mol Life Sci 2015; 72:2509-33. [PMID: 25772500 PMCID: PMC11113800 DOI: 10.1007/s00018-015-1881-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/19/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
Asparagine (N)-linked protein glycosylation, which takes place in the eukaryotic endoplasmic reticulum (ER), is important for protein folding, quality control and the intracellular trafficking of secretory and membrane proteins. It is known that, during N-glycosylation, considerable amounts of lipid-linked oligosaccharides (LLOs), the glycan donor substrates for N-glycosylation, are hydrolyzed to form free N-glycans (FNGs) by unidentified mechanisms. FNGs are also generated in the cytosol by the enzymatic deglycosylation of misfolded glycoproteins during ER-associated degradation. FNGs derived from LLOs and misfolded glycoproteins are eventually merged into one pool in the cytosol and the various glycan structures are processed to a near homogenous glycoform. This article summarizes the current state of our knowledge concerning the formation and catabolism of FNGs.
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Affiliation(s)
- Yoichiro Harada
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Hiroto Hirayama
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Tadashi Suzuki
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
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17
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Hirayama H, Hosomi A, Suzuki T. Physiological and molecular functions of the cytosolic peptide:N-glycanase. Semin Cell Dev Biol 2015; 41:110-20. [DOI: 10.1016/j.semcdb.2014.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 01/04/2023]
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18
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He P, Grotzke JE, Ng BG, Gunel M, Jafar-Nejad H, Cresswell P, Enns GM, Freeze HH. A congenital disorder of deglycosylation: Biochemical characterization of N-glycanase 1 deficiency in patient fibroblasts. Glycobiology 2015; 25:836-44. [PMID: 25900930 DOI: 10.1093/glycob/cwv024] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/14/2015] [Indexed: 01/17/2023] Open
Abstract
N-Glycanase 1, encoded by NGLY1, catalyzes the deglycosylation of misfolded N-linked glycoproteins retrotranslocated into the cytosol. We identified nine cases with mutations in NGLY1. The patients show developmental delay, seizures, peripheral neuropathy, abnormal liver function and alacrima (absence of tears). The mutations in NGLY1 resulted in the absence of N-glycanase 1 protein in patient-derived fibroblasts. Applying a recently established cellular deglycosylation-dependent Venus fluorescence assay, we found that patient fibroblasts had dramatically reduced fluorescence, indicating a pronounced reduction in N-glycanase enzymatic activity. Using this assay, we could find no evidence of other related activities. Our findings reveal that NGLY1 mutations destroy both N-glycanase 1 protein and enzymatic activity.
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Affiliation(s)
- Ping He
- Human Genetics Program, Sanford Children's Health Research Center, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jeff E Grotzke
- Department of Immunobiology, Yale University, School of Medicine, New Haven, CT 06520-8011, USA
| | - Bobby G Ng
- Human Genetics Program, Sanford Children's Health Research Center, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Murat Gunel
- Yale Program on Neurogenetics, Departments of Neurosurgery, Neurobiology and Genetics, Yale University, School of Medicine, New Haven, CT 06510, USA
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter Cresswell
- Department of Immunobiology, Yale University, School of Medicine, New Haven, CT 06520-8011, USA
| | - Gregory M Enns
- Department of Pediatrics, Division of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, CA 94304, USA
| | - Hudson H Freeze
- Human Genetics Program, Sanford Children's Health Research Center, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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19
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Endo-β-N-acetylglucosaminidase forms N-GlcNAc protein aggregates during ER-associated degradation in Ngly1-defective cells. Proc Natl Acad Sci U S A 2015; 112:1398-403. [PMID: 25605922 DOI: 10.1073/pnas.1414593112] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cytoplasmic peptide:N-glycanase (PNGase; Ngly1 in mice) is a deglycosylating enzyme involved in the endoplasmic reticulum (ER)-associated degradation (ERAD) process. The precise role of Ngly1 in the ERAD process, however, remains unclear in mammals. The findings reported herein, using mouse embryonic fibroblast (MEF) cells, that the ablation of Ngly1 causes dysregulation of the ERAD process. Interestingly, not only delayed degradation but also the deglycosylation of a misfolded glycoprotein was observed in Ngly1(-/-) MEF cells. The unconventional deglycosylation reaction was found to be catalyzed by the cytosolic endo-β-N-acetylglucosaminidase (ENGase), generating aggregation-prone N-GlcNAc proteins. The ERAD dysregulation in cells lacking Ngly1 was restored by the additional knockout of ENGase gene. Thus, our study underscores the functional importance of Ngly1 in the ERAD process and provides a potential mechanism underlying the phenotypic consequences of a newly emerging genetic disorder caused by mutation of the human NGLY1 gene.
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20
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Hosomi A, Suzuki T. Cytoplasmic peptide:N-glycanase cleaves N-glycans on a carboxypeptidase Y mutant during ERAD in Saccharomyces cerevisiae. Biochim Biophys Acta Gen Subj 2014; 1850:612-9. [PMID: 25497214 DOI: 10.1016/j.bbagen.2014.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/07/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Endoplasmic reticulum (ER)-associated degradation (ERAD) is a pathway by which misfolded or improperly assembled proteins in the ER are directed to degradation. The cytoplasmic peptide:N-glycanase (PNGase) is a deglycosylating enzyme that cleaves N-glycans from misfolded glycoproteins during the ERAD process. The mutant form of yeast carboxypeptidase Y (CPY*) is an ERAD model substrate that has been extensively studied in yeast. While a delay in the degradation of CPY* in yeast cells lacking the cytoplasmic PNGase (Png1 in yeast) was evident, the in vivo action of PNGase on CPY* has not been detected. METHODS We constructed new ERAD substrates derived from CPY*, bearing epitope tags at both N- and C-termini and examined the degradation intermediates observed in yeast cells with compromised proteasome activity. RESULTS The occurrence of the PNGase-mediated deglycosylation of intact CPY* and its degradation intermediates was evident. A major endoproteolytic reaction on CPY* appears to occur between amino acid 400 and 404. CONCLUSIONS The findings reported herein clearly indicate that PNGase indeed releases N-glycans from CPY* during the ERAD process in vivo. GENERAL SIGNIFICANCE This report implies that the PNGase-mediated deglycosylation during the ERAD process may occur more abundantly than currently envisaged.
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Affiliation(s)
- Akira Hosomi
- Glycometabolome Team, RIKEN-Max Planck Institute Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tadashi Suzuki
- Glycometabolome Team, RIKEN-Max Planck Institute Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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21
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Polyamines are common players in different facets of plant programmed cell death. Amino Acids 2014; 47:27-44. [PMID: 25399055 DOI: 10.1007/s00726-014-1865-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/29/2014] [Indexed: 01/16/2023]
Abstract
Programmed cell death (PCD) is a process that occurs throughout the life span of every plant life, from initial germination of the seed to the senescence of the plant. It is a normal physiological milestone during the plant's developmental process, but it can also be induced by external factors, including a variety of environmental stresses and as a response to pathogen infections. Changes in the morphology of the nucleus is one of the most noticeable during PCD but all the components of the plant cell (cytoplasm, cytoskeleton and organelles) are involved in this fascinating process. To date, relatively little is known about PCD in plants, but several factors, among which polyamines (PAs) and plant growth regulators, have been shown to play an important role in the initiation and regulation of the process. The role of PAs in plant PCD appears to be multifaceted acting in some instances as pro-survival molecules, whereas in others seem to be implicated in accelerating PCD. The molecular mechanism is still under study. Here we present some PCD plant models, focusing on the role of the enzyme responsible for PA conjugation to proteins: transglutaminase (TGase), an enzyme linked with the process of PCD also in some animal models. The role of PAs and plant TGase in the senescence and PCD in flowers, leaf and the self-incompatibility of pollen will be discussed and examined in depth.
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22
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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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23
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Del Duca S, Serafini-Fracassini D, Cai G. Senescence and programmed cell death in plants: polyamine action mediated by transglutaminase. FRONTIERS IN PLANT SCIENCE 2014; 5:120. [PMID: 24778637 PMCID: PMC3985020 DOI: 10.3389/fpls.2014.00120] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/12/2014] [Indexed: 05/14/2023]
Abstract
Research on polyamines (PAs) in plants laps a long way of about 50 years and many roles have been discovered for these aliphatic cations. PAs regulate cell division, differentiation, organogenesis, reproduction, dormancy-break and senescence, homeostatic adjustments in response to external stimuli and stresses. Nevertheless, the molecular mechanisms of their multiple activities are still matter of research. PAs are present in free and bound forms and interact with several important cell molecules; some of these interactions may occur by covalent linkages catalyzed by transglutaminase (TGase), giving rise to "cationization" or cross-links among specific proteins. Senescence and programmed cell death (PCD) can be delayed by PAs; in order to re-interpret some of these effects and to obtain new insights into their molecular mechanisms, their conjugation has been revised here. The TGase-mediated interactions between proteins and PAs are the main target of this review. After an introduction on the characteristics of this enzyme, on its catalysis and role in PCD in animals, the plant senescence and PCD models in which TGase has been studied, are presented: the corolla of naturally senescing or excised flowers, the leaves senescing, either excised or not, the pollen during self-incompatible pollination, the hypersensitive response and the tuber storage parenchyma during dormancy release. In all the models examined, TGase appears to be involved by a similar molecular mechanism as described during apoptosis in animal cells, even though several substrates are different. Its effect is probably related to the type of PCD, but mostly to the substrate to be modified in order to achieve the specific PCD program. As a cross-linker of PAs and proteins, TGase is an important factor involved in multiple, sometimes controversial, roles of PAs during senescence and PCD.
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Affiliation(s)
- Stefano Del Duca
- Department of Biological, Geological and Environmental Sciences (Botany), University of BolognaBologna, Italy
| | | | - Giampiero Cai
- Department of Life Sciences, University of SienaSiena, Italy
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24
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Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, Crimian R, Schoch K, Platt J, Cox R, Bernstein JA, Scavina M, Walter RS, Bibb A, Jones M, Hegde M, Graham BH, Need AC, Oviedo A, Schaaf CP, Boyle S, Butte AJ, Chen R, Chen R, Clark MJ, Haraksingh R, Cowan TM, He P, Langlois S, Zoghbi HY, Snyder M, Gibbs RA, Freeze HH, Goldstein DB. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genet Med 2014; 16:751-8. [PMID: 24651605 DOI: 10.1038/gim.2014.22] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/09/2014] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The endoplasmic reticulum-associated degradation pathway is responsible for the translocation of misfolded proteins across the endoplasmic reticulum membrane into the cytosol for subsequent degradation by the proteasome. To define the phenotype associated with a novel inherited disorder of cytosolic endoplasmic reticulum-associated degradation pathway dysfunction, we studied a series of eight patients with deficiency of N-glycanase 1. METHODS Whole-genome, whole-exome, or standard Sanger sequencing techniques were employed. Retrospective chart reviews were performed in order to obtain clinical data. RESULTS All patients had global developmental delay, a movement disorder, and hypotonia. Other common findings included hypolacrima or alacrima (7/8), elevated liver transaminases (6/7), microcephaly (6/8), diminished reflexes (6/8), hepatocyte cytoplasmic storage material or vacuolization (5/6), and seizures (4/8). The nonsense mutation c.1201A>T (p.R401X) was the most common deleterious allele. CONCLUSION NGLY1 deficiency is a novel autosomal recessive disorder of the endoplasmic reticulum-associated degradation pathway associated with neurological dysfunction, abnormal tear production, and liver disease. The majority of patients detected to date carry a specific nonsense mutation that appears to be associated with severe disease. The phenotypic spectrum is likely to enlarge as cases with a broader range of mutations are detected.
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Affiliation(s)
- Gregory M Enns
- Department of Pediatrics, Division of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Matthew Bainbridge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michael J Gambello
- Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Farah R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Rebecca Crimian
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Julia Platt
- Department of Pediatrics, Division of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Rachel Cox
- Department of Pediatrics, Division of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Division of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Mena Scavina
- Division of Pediatric Neurology, Department of Pediatrics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Rhonda S Walter
- Division of Developmental Medicine, Department of Pediatrics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Audrey Bibb
- Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Melanie Jones
- Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Madhuri Hegde
- Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Brett H Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Anna C Need
- Department of Medicine, Imperial College, London, UK
| | - Angelica Oviedo
- Department of Pathology and Laboratory Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Christian P Schaaf
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA [2] Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Sean Boyle
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Atul J Butte
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Rui Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rong Chen
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Michael J Clark
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Rajini Haraksingh
- Department of Genetics, Stanford University, Stanford, California, USA
| | | | - Tina M Cowan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Ping He
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Huda Y Zoghbi
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA [2] Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA [3] Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Richard A Gibbs
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA [2] Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Hudson H Freeze
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - David B Goldstein
- 1] Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA [2] Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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Liu Y, Li J. Endoplasmic reticulum-mediated protein quality control in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2014; 5:162. [PMID: 24817869 PMCID: PMC4012192 DOI: 10.3389/fpls.2014.00162] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 04/07/2014] [Indexed: 05/19/2023]
Abstract
A correct three-dimensional structure is crucial for the physiological functions of a protein, yet the folding of proteins to acquire native conformation is a fundamentally error-prone process. Eukaryotic organisms have evolved a highly conserved endoplasmic reticulum-mediated protein quality control (ERQC) mechanism to monitor folding processes of secretory and membrane proteins, allowing export of only correctly folded proteins to their physiological destinations, retaining incompletely/mis-folded ones in the ER for additional folding attempts, marking and removing terminally misfolded ones via a unique multiple-step degradation process known as ER-associated degradation (ERAD). Most of our current knowledge on ERQC and ERAD came from genetic and biochemical investigations in yeast and mammalian cells. Recent studies in the reference plant Arabidopsis thaliana uncovered homologous components and similar mechanisms in plants for monitoring protein folding and for retaining, repairing, and removing misfolded proteins. These studies also revealed critical roles of the plant ERQC/ERAD systems in regulating important biochemical/physiological processes, such as abiotic stress tolerance and plant defense. In this review, we discuss our current understanding about the molecular components and biochemical mechanisms of the plant ERQC/ERAD system in comparison to yeast and mammalian systems.
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Affiliation(s)
| | - Jianming Li
- *Correspondence: Jianming Li, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4085 Natural Science Building, 830 North University, Ann Arbor, MI 48109-1048, USA e-mail:
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Maeda M, Kimura Y. Structural features of free N-glycans occurring in plants and functional features of de-N-glycosylation enzymes, ENGase, and PNGase: the presence of unusual plant complex type N-glycans. FRONTIERS IN PLANT SCIENCE 2014; 5:429. [PMID: 25237315 PMCID: PMC4154441 DOI: 10.3389/fpls.2014.00429] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 08/12/2014] [Indexed: 05/22/2023]
Abstract
Free N-glycans (FNGs) are present at micromolar concentrations in plant cells during their differentiation, growth, and maturation stages. It has been postulated that these FNGs are signaling molecules involved in plant development or fruit ripening. However, the hypothetical biochemical and molecular function of FNGs has not been yet established. The structure of FNGs found ubiquitously in plant tissues such as hypocotyls, leaves, roots, developing seeds, or fruits can be classified into two types: high-mannose type and plant complex type; the former, in most cases, has only one GlcNAc residue at the reducing end (GN1 type), while the latter has the chitobiosyl unit at the reducing end (GN2 type). These findings suggest that endo-β-N-acetylglucosaminidase (ENGase) must be involved in the production of GN1 type FNGs, whereas only peptide:N-glycanase (PNGase) is involved in the production of GN2 type FNGs. It has been hypothesized that cytosolic PNGase (cPNGase) and ENGase in animal cells are involved in the production of high-mannose type FNGs in order to release N-glycans from the misfolded glycoproteins in the protein quality control systems. In the case of plants, it is well known that another type of PNGase, the acidic PNGase (aPNGase) is involved in the production of plant complex type FNGs in an acidic organelle, suggesting the de-N-glycosylation mechanism in plants is different from that in animal cells. To better understand the role of these FNGs in plants, the genes encoding these N-glycan releasing enzymes (ENGase and PNGase) were first identified, and then structure of FNGs in ENGase knocked-out plants were analyzed. These transgenic plants provide new insight into the plant-specific de-N-glycosylation mechanism and putative physiological functions of FNGs. In this review, we focus on the structural features of plant FNGs, as well as functional features of cPNGase/ENGase and plant specific PNGase, and putative functions of FNGs are also discussed.
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Affiliation(s)
| | - Yoshinobu Kimura
- *Correspondence: Yoshinobu Kimura, Functional Glycobiochemistry, Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, Japan e-mail:
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Del Duca S, Faleri C, Iorio RA, Cresti M, Serafini-Fracassini D, Cai G. Distribution of transglutaminase in pear pollen tubes in relation to cytoskeleton and membrane dynamics. PLANT PHYSIOLOGY 2013; 161:1706-21. [PMID: 23396835 PMCID: PMC3613450 DOI: 10.1104/pp.112.212225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Transglutaminases (TGases) are ubiquitous enzymes that take part in a variety of cellular functions. In the pollen tube, cytoplasmic TGases are likely to be involved in the incorporation of primary amines at selected peptide-bound glutamine residues of cytosolic proteins (including actin and tubulin), while cell wall-associated TGases are believed to regulate pollen tube growth. Using immunological probes, we identified TGases associated with different subcellular compartments (cytosol, membranes, and cell walls). Binding of cytosolic TGase to actin filaments was shown to be Ca(2+) dependent. The membrane TGase is likely associated with both Golgi-derived structures and the plasma membrane, suggesting a Golgi-based exocytotic delivery of TGase. Association of TGase with the plasma membrane was also confirmed by immunogold transmission electron microscopy. Immunolocalization of TGase indicated that the enzyme was present in the growing region of pollen tubes and that the enzyme colocalizes with cell wall markers. Bidimensional electrophoresis indicated that different TGase isoforms were present in distinct subcellular compartments, suggesting either different roles or different regulatory mechanisms of enzyme activity. The application of specific inhibitors showed that the distribution of TGase in different subcellular compartments was regulated by both membrane dynamics and cytoskeleton integrity, suggesting that delivery of TGase to the cell wall requires the transport of membranes along cytoskeleton filaments. Taken together, these data indicate that a cytoplasmic TGase interacts with the cytoskeleton, while a different TGase isoform, probably delivered via a membrane/cytoskeleton-based transport system, is secreted in the cell wall of pear (Pyrus communis) pollen tubes, where it might play a role in the regulation of apical growth.
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Cai G, Serafini-Fracassini D, Del Duca S. Regulation of Pollen Tube Growth by Transglutaminase. PLANTS 2013; 2:87-106. [PMID: 27137368 PMCID: PMC4844290 DOI: 10.3390/plants2010087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 02/08/2013] [Accepted: 02/27/2013] [Indexed: 11/23/2022]
Abstract
In pollen tubes, cytoskeleton proteins are involved in many aspects of pollen germination and growth, from the transport of sperm cells to the asymmetrical distribution of organelles to the deposition of cell wall material. These activities are based on the dynamics of the cytoskeleton. Changes to both actin filaments and microtubules are triggered by specific proteins, resulting in different organization levels suitable for the different functions of the cytoskeleton. Transglutaminases are enzymes ubiquitous in all plant organs and cell compartments. They catalyze the post-translational conjugation of polyamines to different protein targets, such as the cytoskeleton. Transglutaminases are suggested to have a general role in the interaction between pollen tubes and the extracellular matrix during fertilization and a specific role during the self-incompatibility response. In such processes, the activity of transglutaminases is enhanced, leading to the formation of cross-linked products (including aggregates of tubulin and actin). Consequently, transglutaminases are suggested to act as regulators of cytoskeleton dynamics. The distribution of transglutaminases in pollen tubes is affected by both membrane dynamics and the cytoskeleton. Transglutaminases are also secreted in the extracellular matrix, where they may take part in the assembly and/or strengthening of the pollen tube cell wall.
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Affiliation(s)
- Giampiero Cai
- Dipartimento di Scienze della Vita, Università degli Studi di Siena, via Mattioli 4, Siena 53100, Italy.
| | - Donatella Serafini-Fracassini
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università degli Studi di Bologna, via Irnerio, Bologna 40126, Italy.
| | - Stefano Del Duca
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università degli Studi di Bologna, via Irnerio, Bologna 40126, Italy.
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