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Lu J, Feng Y, Zhou Y, Xiao Z, Yang Z, Li J, Cai H, Wang J. DPM2 serve as novel oncogene and prognostic marker transactivated by ESR1 in breast cancer. ENVIRONMENTAL TOXICOLOGY 2024; 39:1737-1746. [PMID: 38050961 DOI: 10.1002/tox.24059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023]
Abstract
Breast cancer (BRCA) is the most common malignancies worldwide with increasing rate. Dolichol phosphate mannose synthase (DPMS) is a critical mannosyltransferase involved in the posttranslational modification of proteins. At present, there is limited knowledge regarding the function of DPMS in breast cancer. In this study, silica analysis in multiple datasets found that dolichyl-phosphate mannosyltransferase subunit 2 (DPM2) is an unfavorable prognostic marker, suggesting its oncogenic role. Cell counting kit-8 and apoptosis assays show that DPM2-silenced cancer cells exhibit decreased growth potential and enhanced cell death rate. Further, transwell and wound healing assays show reduced invasion and migration capabilities in DPM2 knockdown groups, xenograft nude mice model demonstrated smaller tumor volume in DPM2 silenced BC cells. Then, the underlying downstream mechanism of DPM2 in BC was predicted and analyzed, highlighting classical tumorigenic pathways like JAK/STAT signaling pathway and oxidative phosphorylation activated in the cancer group. Finally, ChIP-seq analysis, expression correlation analysis, inhibitor treatment, and dual luciferase assays show that DPM2 is transcriptionally activated by estrogen receptor1 (ESR1). The results show that high expression of DPM2 mRNA is significantly correlated with shorter overall survival (OS) and disease-free survival (DFS) in breast cancer patients, and in vitro knockdown of DPM2 can significantly inhibit the malignant phenotypes of cells, including proliferation, invasion, migration, and apoptosis. These results suggest that DPM2 may play an important role in breast cancer. Altogether, we first uncovered the tumorigenic and prognostic role of DPM2 in breast cancer, cellular assays, and bioinformatics analysis highlighted DPM2 as oncogene via inhibited cancer-related signaling pathways in breast cancer. Besides, DPM2 is transcriptionally activated by ESR1, the signaling axis of ESR1/DPM2 provides a new strategy for BC-targeted therapy.
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Affiliation(s)
- Jiahao Lu
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
| | - Yuejiao Feng
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
| | - Yiting Zhou
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Jiangsu, China
| | - Zengyou Xiao
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
| | - Zean Yang
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
| | - Jiaxian Li
- Department Surgery, Putuo Hospital, University of Traditional Chinese Medicine in Shanghai, Shanghai, China
| | - Han Cai
- Department Surgery, Putuo Hospital, University of Traditional Chinese Medicine in Shanghai, Shanghai, China
| | - Jie Wang
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
- Department Surgery, Putuo Hospital, University of Traditional Chinese Medicine in Shanghai, Shanghai, China
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2
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Sakson R, Beedgen L, Bernhard P, Alp KM, Lübbehusen N, Röth R, Niesler B, Luzarowski M, Shevchuk O, Mayer MP, Thiel C, Ruppert T. Targeted Proteomics Reveals Quantitative Differences in Low-Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation. Int J Mol Sci 2024; 25:1191. [PMID: 38256263 PMCID: PMC10816918 DOI: 10.3390/ijms25021191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Protein glycosylation is an essential post-translational modification in all domains of life. Its impairment in humans can result in severe diseases named congenital disorders of glycosylation (CDGs). Most of the glycosyltransferases (GTs) responsible for proper glycosylation are polytopic membrane proteins that represent challenging targets in proteomics. We established a multiple reaction monitoring (MRM) assay to comprehensively quantify GTs involved in the processes of N-glycosylation and O- and C-mannosylation in the endoplasmic reticulum. High robustness was achieved by using an enriched membrane protein fraction of isotopically labeled HEK 293T cells as an internal protein standard. The analysis of primary skin fibroblasts from eight CDG type I patients with impaired ALG1, ALG2, and ALG11 genes, respectively, revealed a substantial reduction in the corresponding protein levels. The abundance of the other GTs, however, remained unchanged at the transcript and protein levels, indicating that there is no fail-safe mechanism for the early steps of glycosylation in the endoplasmic reticulum. The established MRM assay was shared with the scientific community via the commonly used open source Skyline software environment, including Skyline Batch for automated data analysis. We demonstrate that another research group could easily reproduce all analysis steps, even while using different LC-MS hardware.
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Affiliation(s)
- Roman Sakson
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg University, 69120 Heidelberg, Germany
| | - Lars Beedgen
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Patrick Bernhard
- Institute for Surgical Pathology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - K. Merve Alp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Nicole Lübbehusen
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Ralph Röth
- nCounter Core Facility, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Beate Niesler
- nCounter Core Facility, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Marcin Luzarowski
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Olga Shevchuk
- Department of Immunodynamics, Institute of Experimental Immunology and Imaging, University Hospital Essen, 45147 Essen, Germany
| | - Matthias P. Mayer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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Liu J, Liu Y, Yang C, Liu J, Hao J. Comprehensive analysis for the immune related biomarkers of platinum-based chemotherapy in ovarian cancer. Transl Oncol 2023; 37:101762. [PMID: 37619523 PMCID: PMC10458992 DOI: 10.1016/j.tranon.2023.101762] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/26/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is one of the most lethal gynecological malignancies. This study aimed to identify biomarkers that were sensitive to platinum-based chemotherapeutic agents and can be used in immunotherapy and explore the importance of their mechanisms of action. METHODS RNA-seq profiles and clinicopathological data for OC samples were obtained from The Cancer Genome Atlas (TCGA) and cBioPortal platform, respectively. Platinum-sensitive and platinum-resistant OC samples in the TCGA cohort were selected based on the clinical information. RNA-seq data for 70 OC samples withSingle-sample gene set enrichment analysis (ssGSEA) and unsupervised clustering were used to classify OC patients from the TCGA cohort into clusters with different proportions of infiltrating immune cells. ESTIMATE analysis was used to assess the immune landscape among clusters. Differential expression, univariate Cox regression, and LASSO regression analyses were performed to construct prognostic model. Spearman correlation analysis was conducted to investigate the correlations among immune checkpoint inhibitors (ICIs) and risk score, half-maximal drug inhibitory concentration (IC50) and risk score. RESULTS Using ssGSEA and unsupervised clustering, OC samples were divided into two clusters with different immune cell infiltration. Then, 1715 differentially expressed immune-related genes (DEIRGs) were identified between two clusters, 984 differentially expressed platinum-sensitive related genes (DEPSRGs) between 149 platinum-sensitive and 63 platinum-resistant OC samples were identified, and 5384 differentially expressed genes (DEGs) between 380 OC and 194 normal samples were detected from the TCGA cohort. Six biomarkers (GMPPB, SRPK1, STC1, PRSS16, HPDL, and SPTSSB) were detected to establish a prognostic model. The OC patients in the TCGA cohort were classified into high- and low-risk groups. The receive operating characteristic (ROC) curve was plotted and demonstrated that the prognostic model performed well with the area under ROC curve (AUC) greater than 0.6. The expressions of 5 ICIs, including CD200, TNFRSF18, CD160, CD200R1, and CD274 (PD-L1), were significantly different between two risk groups, and the risk score was significant negative associated with CTLA4, TNFRSF4, TNFRSF18, and CD274. Moreover, there were significant differences in IC50 of 10 chemo drugs between two risk groups, patients in the high-risk group could be more resistant to po0tinib, dasatinib, and neratinib. CONCLUSION In summary, this study constructed a novel prognostic model based on six prognostic biomarkers, including GMPPB, SRPK1, STC1, PRSS16, HPDL, and SPTSSB, which can be utilized for predicting the prognosis of OC patients. These biomarkers were the potential therapeutic targets.
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Affiliation(s)
- Jiao Liu
- Department of Gynecology, Benxi Central Hospital, Benxi 117000, Liaoning Province, China
| | - Yaoyao Liu
- Department of Gynecology, Benxi Central Hospital, Benxi 117000, Liaoning Province, China
| | - Chunjiao Yang
- Department of Radiotheropy, Benxi Central Hospital, Benxi 117000, Liaoning Province, China
| | - Jingjing Liu
- Department of Gynecology, Benxi Central Hospital, Benxi 117000, Liaoning Province, China
| | - Jiaxin Hao
- Department of Orthopedics, Benxi Central Hospital, Benxi 117000, Liaoning Province, China.
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GDP-Mannose Pyrophosphorylase B ( GMPPB)-Related Disorders. Genes (Basel) 2023; 14:genes14020372. [PMID: 36833299 PMCID: PMC9956253 DOI: 10.3390/genes14020372] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
GDP-mannose pyrophosphorylase B (GMPPB) is a cytoplasmic protein that catalyzes the formation of GDP-mannose. Impaired GMPPB function reduces the amount of GDP-mannose available for the O-mannosylation of α-dystroglycan (α-DG) and ultimately leads to disruptions of the link between α-DG and extracellular proteins, hence dystroglycanopathy. GMPPB-related disorders are inherited in an autosomal recessive manner and caused by mutations in either a homozygous or compound heterozygous state. The clinical spectrum of GMPPB-related disorders spans from severe congenital muscular dystrophy (CMD) with brain and eye abnormalities to mild forms of limb-girdle muscular dystrophy (LGMD) to recurrent rhabdomyolysis without overt muscle weakness. GMPPB mutations can also lead to the defect of neuromuscular transmission and congenital myasthenic syndrome due to altered glycosylation of the acetylcholine receptor subunits and other synaptic proteins. Such impairment of neuromuscular transmission is a unique feature of GMPPB-related disorders among dystroglycanopathies. LGMD is the most common phenotypic presentation, characterized by predominant proximal weakness involving lower more than upper limbs. Facial, ocular, bulbar, and respiratory muscles are largely spared. Some patients demonstrate fluctuating fatigable weakness suggesting neuromuscular junction involvement. Patients with CMD phenotype often also have structural brain defects, intellectual disability, epilepsy, and ophthalmic abnormalities. Creatine kinase levels are typically elevated, ranging from 2 to >50 times the upper limit of normal. Involvement of the neuromuscular junction is demonstrated by the decrement in the compound muscle action potential amplitude on low-frequency (2-3 Hz) repetitive nerve stimulation in proximal muscles but not in facial muscles. Muscle biopsies typically show myopathic changes with variable degrees of reduced α-DG expression. Higher mobility of β-DG on Western blotting represents a specific feature of GMPPB-related disorders, distinguishing it from other α-dystroglycanopathies. Patients with clinical and electrophysiologic features of neuromuscular transmission defect can respond to acetylcholinesterase inhibitors alone or combined with 3,4 diaminopyridine or salbutamol.
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Zhao P, Hu Y, Hu J, Li C, Huang Y, Zhang L, Luo S, Zhu H, Jiang J, He X. Identification and characterization of a new variation in DPM2 gene in two Chinese siblings with mild intellectual impairment. Front Genet 2023; 14:930692. [PMID: 37152991 PMCID: PMC10154465 DOI: 10.3389/fgene.2023.930692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction: Congenital disorders of glycosylation (CDGs) are a genetically heterogeneous group of metabolic disorders caused by abnormal protein or lpid glycosylation. DPM2 is one subunit of a heterotrimeric complex for dolichol-phosphatemannose synthase (DPMS), a key enzyme in glycosylation, and only four patients with DPM2-CDG have been reported. Methods: Whole-exome sequencing (WES) was performed in a Chinese family having two siblings with a mild form of DPM2-CDG with developmental delay, mild intellectual disability, hypotonia, and increased serum creatine kinase. Sanger sequencing was used to validate the variants identified in the siblings and their parents. In vitro functional study was performed. Results: A homozygous mutation, c.197G>A (p.Gly66Glu) in exon 4 of DPM2 (NM_003863) was identified by whole exome sequencing (WES). In vitro functional analysis demonstrated that this variant increased the expression level of DPM2 protein and western blot revealed a significant decrease in ICAM1, a universal biomarker for hypoglycosylation in patients with CDG, suggesting abnormal N-linked glycosylation. We also reviewed the 4 previously reported patients carrying homozygous or compound heterozygous variants of DMP2 gene, and found that patients with variants within the region encoding the first domain had more severe clinical symptoms than those with variants within the second domain. However, the actual genotype-phenotype relationship needs more study. Discussion: Overall, our study broadens the variant spectrum of DPM2 gene, attempts to explain the different phenotypes in patients with different DPM2 variants, and emphasizes the need of further functional studies to understand the underlying pathophysiology of the phenotypic heterogeneity.
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Affiliation(s)
- Peiwei Zhao
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanqiu Hu
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Hu
- Rehabilitation Department, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Li
- Department of Neuroelectrophysiology, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yufeng Huang
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Zhang
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sukun Luo
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongmin Zhu
- Rehabilitation Department, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Hongmin Zhu, ; Jun Jiang, ; Xuelian He,
| | - Jun Jiang
- Department of Neuroelectrophysiology, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Hongmin Zhu, ; Jun Jiang, ; Xuelian He,
| | - Xuelian He
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Hongmin Zhu, ; Jun Jiang, ; Xuelian He,
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Jutzi JS, Marneth AE, Ciboddo M, Guerra-Moreno A, Jiménez-Santos MJ, Kosmidou A, Dressman JW, Liang H, Hamel R, Lozano P, Rumi E, Doench JG, Gotlib J, Krishnan A, Elf S, Al-Shahrour F, Mullally A. Whole-genome CRISPR screening identifies N-glycosylation as a genetic and therapeutic vulnerability in CALR-mutant MPNs. Blood 2022; 140:1291-1304. [PMID: 35763665 PMCID: PMC9479036 DOI: 10.1182/blood.2022015629] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/10/2022] [Indexed: 01/13/2023] Open
Abstract
Calreticulin (CALR) mutations are frequent, disease-initiating events in myeloproliferative neoplasms (MPNs). Although the biological mechanism by which CALR mutations cause MPNs has been elucidated, there currently are no clonally selective therapies for CALR-mutant MPNs. To identify unique genetic dependencies in CALR-mutant MPNs, we performed a whole-genome clustered regularly interspaced short palindromic repeats (CRISPR) knockout depletion screen in mutant CALR-transformed hematopoietic cells. We found that genes in the N-glycosylation pathway (among others) were differentially depleted in mutant CALR-transformed cells as compared with control cells. Using a focused pharmacological in vitro screen targeting unique vulnerabilities uncovered in the CRISPR screen, we found that chemical inhibition of N-glycosylation impaired the growth of mutant CALR-transformed cells, through a reduction in MPL cell surface expression. We treated Calr-mutant knockin mice with the N-glycosylation inhibitor 2-deoxy-glucose (2-DG) and found a preferential sensitivity of Calr-mutant cells to 2-DG as compared with wild-type cells and normalization of key MPNs disease features. To validate our findings in primary human cells, we performed megakaryocyte colony-forming unit (CFU-MK) assays. We found that N-glycosylation inhibition significantly reduced CFU-MK formation in patient-derived CALR-mutant bone marrow as compared with bone marrow derived from healthy donors. In aggregate, our findings advance the development of clonally selective treatments for CALR-mutant MPNs.
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Affiliation(s)
- Jonas S Jutzi
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Anna E Marneth
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Michele Ciboddo
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- The Ben May Department for Cancer Research, University of Chicago, Chicago, IL
| | - Angel Guerra-Moreno
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - María José Jiménez-Santos
- Bioinformatics Unit, Structural Biology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Anastasia Kosmidou
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - James W Dressman
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, SC
| | - Hongyan Liang
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, SC
| | - Rebecca Hamel
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- RWTH Aachen University, Aachen, Germany
| | - Patricia Lozano
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elisa Rumi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Hematology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia, Italy
| | | | - Jason Gotlib
- Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Anandi Krishnan
- Department of Pathology, Stanford Cancer Institute, Stanford University School of Medicine, Palo Alto, CA; and
| | - Shannon Elf
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- The Ben May Department for Cancer Research, University of Chicago, Chicago, IL
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Structural Biology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ann Mullally
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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7
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Uehara I, Kajita M, Tanimura A, Hida S, Onda M, Naito Z, Taki S, Tanaka N. 2-Deoxy-d-glucose induces deglycosylation of proinflammatory cytokine receptors and strongly reduces immunological responses in mouse models of inflammation. Pharmacol Res Perspect 2022; 10:e00940. [PMID: 35212163 PMCID: PMC8873284 DOI: 10.1002/prp2.940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/14/2022] Open
Abstract
Anti‐proinflammatory cytokine therapies against interleukin (IL)‐6, tumor necrosis factor (TNF)‐α, and IL‐1 are major advancements in treating inflammatory diseases, especially rheumatoid arthritis. Such therapies are mainly performed by injection of antibodies against cytokines or cytokine receptors. We initially found that the glycolytic inhibitor 2‐deoxy‐d‐glucose (2‐DG), a simple monosaccharide, attenuated cellular responses to IL‐6 by inhibiting N‐linked glycosylation of the IL‐6 receptor gp130. Aglycoforms of gp130 did not bind to IL‐6 or activate downstream intracellular signals that included Janus kinases. 2‐DG completely inhibited dextran sodium sulfate‐induced colitis, a mouse model for inflammatory bowel disease, and alleviated laminarin‐induced arthritis in the SKG mouse, an experimental model for human rheumatoid arthritis. These diseases have been shown to be partially dependent on IL‐6. We also found that 2‐DG inhibited signals for other proinflammatory cytokines such as TNF‐α, IL‐1β, and interferon ‐γ, and accordingly, prevented death by another inflammatory disease, lipopolysaccharide (LPS) shock. Furthermore, 2‐DG prevented LPS shock, a model for a cytokine storm, and LPS‐induced pulmonary inflammation, a model for acute respiratory distress syndrome of coronavirus disease 2019 (COVID‐19). These results suggest that targeted therapies that inhibit cytokine receptor glycosylation are effective for treatment of various inflammatory diseases.
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Affiliation(s)
- Ikuno Uehara
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Mitsuko Kajita
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Atsuko Tanimura
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Shigeaki Hida
- Department of Molecular and Cellular Health Sciences, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Munehiko Onda
- Department of Pathology, Integrative Oncological Pathology, Nippon Medical School, Tokyo, Japan
| | - Zenya Naito
- Department of Pathology, Integrative Oncological Pathology, Nippon Medical School, Tokyo, Japan
| | - Shinsuke Taki
- Department of Molecular and Cellular Immunology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Nobuyuki Tanaka
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
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8
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Hang J, Wang J, Lu M, Xue Y, Qiao J, Tao L. Protein O-mannosylation across kingdoms and related diseases: From glycobiology to glycopathology. Biomed Pharmacother 2022; 148:112685. [PMID: 35149389 DOI: 10.1016/j.biopha.2022.112685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
The post-translational glycosylation of proteins by O-linked α-mannose is conserved from bacteria to humans. Due to advances in high-throughput mass spectrometry-based approaches, a variety of glycoproteins are identified to be O-mannosylated. Various proteins with O-mannosylation are involved in biological processes, providing essential necessity for proper growth and development. In this review, we summarize the process and regulation of O-mannosylation. The multi-step O-mannosylation procedures are quite dynamic and complex, especially when considering the structural and functional inspection of the involved enzymes. The widely studied O-mannosylated proteins in human include α-Dystroglycan (α-DG), cadherins, protocadherins, and plexin, and their aberrant O-mannosylation are associated with many diseases. In addition, O-mannosylation also contributes to diverse functions in lower eukaryotes and prokaryotes. Finally, we present the relationship between O-mannosylation and gut microbiota (GM), and elucidate that O-mannosylation in microbiome is of great importance in the dynamic balance of GM. Our study provides an overview of the processes of O-mannosylation in mammalian cells and other organisms, and also associated regulated enzymes and biological functions, which could contribute to the understanding of newly discovered O-mannosylated glycoproteins.
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Affiliation(s)
- Jing Hang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Jinpeng Wang
- Department of Orthopedics, First Hospital of China Medical University, Shenyang 110001, China
| | - Minzhen Lu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yuchuan Xue
- The First Department of Clinical Medicine, China Medical University, Shenyang 110001, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China.
| | - Lin Tao
- Department of Orthopedics, First Hospital of China Medical University, Shenyang 110001, China.
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Liu Q, Zhang MY, Zhao B, Chen Y, Jiang W, Geng XL, Wang Q. Diagnostic Value of Circulating Antigens in the Serum of Piglets with Experimental Acute Toxoplasmosis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:697-706. [PMID: 35022274 DOI: 10.4049/jimmunol.2100640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Toxoplasmosis, caused by Toxoplasma gondii, an apicomplexan parasite, infects all warm-blooded animals, including a third of the human population. Laboratory diagnosis of acute toxoplasmosis is based on the detection of anti-T. gondii IgM and IgG and T. gondii nucleic acid; however, these assays have certain limitations. Circulating Ags (CAgs) are reliable diagnostic indicators of acute infection. In this study, we established a model of acute T. gondii infection in Large White pigs. CAg levels peaked between 3 and 5 d after inoculation, and 28 CAgs were identified using an immunoprecipitation-shotgun approach, among which dolichol-phosphate-mannose synthase family protein (TgDPM), C3HC zinc finger-like protein (TgZFLP3), and ribosomal protein RPL7 (TgRPL7) were selected to further investigate their value in the diagnosis of acute toxoplasmosis. Immunofluorescence assays revealed that TgDPM and TgRPL7 were localized in the membrane surface, while TgZFLP3 was localized in the apical end. Western blotting revealed the presence of the three proteins in the serum during acute infection. Indirect ELISA results indicate that TgZFLP3 is likely to be a novel candidate for the diagnosis of acute toxoplasmosis. However, these three proteins may not be useful as candidate vaccines against toxoplasmosis owing to their low protective ability. In addition, deletion of the zflp3 gene partially attenuated virulence in Kunming mice. Collectively, we identified 28 CAgs in the serum of piglets with experimental acute toxoplasmosis and confirmed that TgZFLP3 is a potential biomarker for acute T. gondii infection. The results of this study provide data to improve the detection efficiency of acute toxoplasmosis.
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Affiliation(s)
- Qi Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Man-Yu Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Bing Zhao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Yun Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Wei Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Xiao-Ling Geng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Quan Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
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10
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Separovich RJ, Wong MW, Bartolec TK, Hamey JJ, Wilkins MR. Site-specific phosphorylation of histone H3K36 methyltransferase Set2p and demethylase Jhd1p is required for stress responses in Saccharomyces cerevisiae. J Mol Biol 2022; 434:167500. [DOI: 10.1016/j.jmb.2022.167500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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11
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Li M, Zhu P, Huang Z, Huang Y, Lv X, Zheng Q, Zhu Z, Fan Z, Yang Y, Shi P. Aspirin damages the cell wall of Saccharomyces cerevisiae by inhibiting the expression and activity of dolichol-phosphate mannose synthase 1. FEBS Lett 2022; 596:369-380. [PMID: 35028934 DOI: 10.1002/1873-3468.14283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/04/2021] [Accepted: 12/12/2021] [Indexed: 11/10/2022]
Abstract
Aspirin is a commonly used anti-inflammatory, analgesic and antithrombotic drug. It has attracted attention due to its potential antifungal therapeutic effect; however, the molecular mechanism is poorly understood. Here, the effects of aspirin on the cell wall of Saccharomyces cerevisiae were explored. We observed by scanning electron microscopy that aspirin could damage the cell wall ultrastructure. Meanwhile, a cellular surface hydrophobicity (CSH) assay showed that aspirin increased the hydrophobicity of the yeast cell surface. A drug sensitivity assay indicated that the overexpression of dolichol phosphate mannose synthase 1 (DPM1) reversed the cell wall damage and decreased the CSH induced by aspirin. Importantly, aspirin decreased the expression and enzyme activity of DPM1 in S. cerevisiae. Molecular docking results demonstrated that aspirin could directly bind to the Ser141 site of DPM1. Similarly, we found that aspirin damaged the cell wall and inhibited the expression of DPM1 in Candida albicans. These findings improve the current understanding of the action mode of aspirin and provide new strategies for antifungal drug design.
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Affiliation(s)
- Ming Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Pan Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Zhiwei Huang
- Key Lab of Science & Technology of Eco-textile, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China
| | - Yunxia Huang
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xiaoguang Lv
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Qiaoqiao Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Ziting Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Zheyu Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Youjun Yang
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ping Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
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12
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El-Samadony HA, Mekky HM, Ghetas AM, Saad AS. Molecular characterization of some isolates of rabbit viral hemorrhagic disease (VHD) in Egypt from 2014 to 2019. J Adv Vet Anim Res 2021; 8:396-403. [PMID: 34722738 PMCID: PMC8520161 DOI: 10.5455/javar.2021.h528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/03/2022] Open
Abstract
Objective Rabbit viral hemorrhagic disease (VHD) is a transmittable and lethal viral illness of rabbits. In this study, genetic identification and genetic analysis of the rabbit hemorrhagic disease virus (RHDV) was made in three governorates in Egypt from 2014 to 2019. Materials and Methods Livers from 18 freshly dead rabbits, which was guessed to be VHD epidemics in Egypt (Giza, Menofia, and Fayoum governorates) from 2014 to 2019, were examined for RHDV. The examination was based on the hemagglutination assay (HA) test against different mammalian (human O-type and sheep) and avian (chicken and pigeon) erythrocytes, reverse transcriptase-polymerase chain reaction (RT-PCR), and sequencing of the segment of VP60. Results 33% of the examined samples' virus titers were 5 log2 to 8 log2 hemagglutination of human O-type erythrocytes when compared to 28%, 11%, and 28% of sheep, chicken, and pigeon erythrocytes, respectively. Four RHDV isolates out of eight RT-PCR positives were sequenced and phylogenetically analyzed. Sequenced isolates were designed and submitted to GenBank with accession numbers MN904506, MN904507, MN904508, and MN904509. These four RHDV isolates were related to classic G3 (GI.1d/RHDV). Twelve amino acid differences were detected between the vaccine strain sequence (Giza-2006) and RHDV isolates. Amino acid differences at 416, 423, and 476 positions seem interesting as they changed polarity that could change the protein structure and affect host interaction. Conclusions There is antigenic variation between circulating RHVD strains and the vaccinal strain. This may be the leading cause of vaccination failure and may increase the need to check out the vaccination program against RHVD.
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Affiliation(s)
| | - Hoda Mohammed Mekky
- Poultry Diseases Department, Veterinary Research Division, National Research Centre, Giza, Egypt
| | - Aly Mohammed Ghetas
- Poultry Diseases Department, Veterinary Research Division, National Research Centre, Giza, Egypt
| | - Aalaa Samir Saad
- Food Hygiene Department, Animal Health Research Institute, ARC, Giza, Egypt
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13
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Thakor JM, Parmar G, Mistry KN, Gang S, Rank DN, Joshi CG. Mutational landscape of TRPC6, WT1, LMX1B, APOL1, PTPRO, PMM2, LAMB2 and WT1 genes associated with Steroid resistant nephrotic syndrome. Mol Biol Rep 2021; 48:7193-7201. [PMID: 34546508 DOI: 10.1007/s11033-021-06711-4] [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: 07/24/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Nephrotic syndrome appears as a group of symptoms like proteinuria, edema and hyperlipidemia. Identification of monogenic forms revealed the physiology and pathogenesis of the SRNS. METHODS AND RESULTS We performed Illumina panel sequencing of seven genes in 90 Indian patients to determine the role of these genetic mutations in nephrotic syndrome prognosis. Samtool was used for variants calling, and SnpEff and Snpsift did variants annotation. Clinical significance and variant classification were performed by the ClinVar database. In SSNS and SRNS patients, we found 0.78% pathogenic and 3.41% likely pathogenic mutations. Pathogenic mutations were found in LAMB2, LMX1B and WT1 genes, while likely pathogenic mutations were found in (6/13) LAMB2, (2/13) LMX1B, (2/13) TRPC6, (2/13) PTPRO and (1/13) PMM2 genes. Approximately 46% likely pathogenic mutations were contributed to the LAMB2 gene in SSNS and SRNS patients. We also detect 30 VUS (variants of uncertain significance), which were found (17/30) pathogenic and (13/30) likely pathogenic by different prediction tools. CONCLUSIONS Multigene panels were used for genetic screening of heterogeneous disorders like nephrotic syndrome in the Indian population. We found pathogenic, likely pathogenic and certain VUS, which were responsible for the pathogenesis of the disease. Therefore, mutational analysis of SSNS and SRNS is necessary to avoid adverse effects of corticosteroids, modify the intensity of immunosuppressing agents, and prevent the disease's progression.
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Affiliation(s)
- Jinal M Thakor
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, ADIT Campus, New Vallabh Vidyanagar, 388121, Anand, Gujarat, India
| | - Glory Parmar
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, ADIT Campus, New Vallabh Vidyanagar, 388121, Anand, Gujarat, India
| | - Kinnari N Mistry
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, ADIT Campus, New Vallabh Vidyanagar, 388121, Anand, Gujarat, India.
| | - Sishir Gang
- Muljibhai Patel Urological Hospital, Dr. V.V. Desai Road, Nadiad, 387001, Gujarat, India
| | - Dharamshibhai N Rank
- Department of Animal Breeding and Genetics, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, 388110, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, 388110, Gujarat, India
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14
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A founder mutation in the GMPPB gene [c.1000G > A (p.Asp334Asn)] causes a mild form of limb-girdle muscular dystrophy/congenital myasthenic syndrome (LGMD/CMS) in South Indian patients. Neurogenetics 2021; 22:271-285. [PMID: 34333724 DOI: 10.1007/s10048-021-00658-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Twelve patients from seven unrelated South Indian families with a limb-girdle muscular dystrophy-congenital myasthenic syndrome (LGMD/CMS) phenotype and recessive inheritance underwent deep clinical phenotyping, electrophysiological evaluation, muscle histopathology, and next-generation sequencing/Sanger sequencing-based identification of the genetic defect. Homozygosity mapping was performed using high-throughput genome-wide genotyping for mapping the mutation and to evaluate the founder effect. The age of disease onset among patients ranged from childhood to 40 years of age. The key clinical manifestations observed were progressive fatigable limb-girdle weakness, muscle hypertrophy/atrophy, and preferential weakness in a dystrophic pattern. The ages at last follow-up ranged from 30 to 64 years; nine were independently ambulant, two required assistance, and one was wheelchair-bound. Lower limb muscle MRI showed varying degrees of fat replacement in the glutei, hamstrings, anterior leg muscles, and medial gastrocnemius. All patients showed significant decrement on repetitive nerve stimulation (RNS). Muscle biopsy in 7 patients revealed varying degrees of dystrophic and neurogenic changes. Treatment with pyridostigmine and/or salbutamol resulted in variable improvement in 10 patients. Genetic analysis showed an identical homozygous GMPPB mutation c.1000G > A (p.Asp334Asn) in all affected patients. A region of homozygosity (6Mbp) was observed flanking the c.1000G > A change in carrier chromosomes. This study identifies c.1000G > A in GMPPB as a common founder mutation in an ethnic community of South Indian descent with milder yet variable degree of clinical presentation of GMPPB-associated LGMD-CMS.
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15
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Jiang M, Wang P, Xu L, Ye X, Fan H, Cheng J, Chen J. In silico analysis of glycosyltransferase 2 family genes in duckweed ( Spirodela polyrhiza) and its role in salt stress tolerance. Open Life Sci 2021; 16:583-593. [PMID: 34179502 PMCID: PMC8216227 DOI: 10.1515/biol-2021-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/27/2021] [Accepted: 05/22/2021] [Indexed: 11/15/2022] Open
Abstract
Plant glycosyltransferase 2 (GT2) family genes are involved in plant abiotic stress tolerance. However, the roles of GT2 genes in the abiotic resistance in freshwater plants are largely unknown. We identified seven GT2 genes in duckweed, remarkably more than those in the genomes of Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, Nymphaea tetragona, Persea americana, Zostera marina, and Ginkgo biloba, suggesting a significant expansion of this family in the duckweed genome. Phylogeny resolved the GT2 family into two major clades. Six duckweed genes formed an independent subclade in Clade I, and the other was clustered in Clade II. Gene structure and protein domain analysis showed that the lengths of the seven duckweed GT2 genes were varied, and the majority of GT2 genes harbored two conserved domains, PF04722.12 and PF00535.25. The expression of all Clade I duckweed GT2 genes was elevated at 0 h after salt treatment, suggesting a common role of these genes in rapid response to salt stress. The gene Sp01g00794 was highly expressed at 12 and 24 h after salt treatment, indicating its association with salt stress resilience. Overall, these results are essential for studies on the molecular mechanisms in stress response and resistance in aquatic plants.
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Affiliation(s)
- Mingliang Jiang
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
| | - Ligang Xu
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
| | - Hongxiang Fan
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Junxiang Cheng
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jinting Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
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16
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Bai L, Li H. Protein N-glycosylation and O-mannosylation are catalyzed by two evolutionarily related GT-C glycosyltransferases. Curr Opin Struct Biol 2021; 68:66-73. [PMID: 33445129 PMCID: PMC8222153 DOI: 10.1016/j.sbi.2020.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
The structural folds of glycosyltransferases are categorized into three superfamilies: GT-A, GT-B, and GT-C. Few structures of GT-C fold existed in the Protein Data Bank prior to the recent advent of high-resolution cryo-EM, because the glycosyltransferases are large membrane proteins that are difficult to crystallize. The use of cryo-EM has resulted in the structures of several key GT-C glycosyltransferases. Here we summarize the latest structural features of and mechanistic insights into these membrane enzyme complexes.
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Affiliation(s)
- Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing 100083, PR China.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, United States.
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17
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Wingo TS, Liu Y, Gerasimov ES, Gockley J, Logsdon BA, Duong DM, Dammer EB, Lori A, Kim PJ, Ressler KJ, Beach TG, Reiman EM, Epstein MP, De Jager PL, Lah JJ, Bennett DA, Seyfried NT, Levey AI, Wingo AP. Brain proteome-wide association study implicates novel proteins in depression pathogenesis. Nat Neurosci 2021; 24:810-817. [PMID: 33846625 PMCID: PMC8530461 DOI: 10.1038/s41593-021-00832-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 03/04/2021] [Indexed: 02/01/2023]
Abstract
Depression is a common condition, but current treatments are only effective in a subset of individuals. To identify new treatment targets, we integrated depression genome-wide association study (GWAS) results (N = 500,199) with human brain proteomes (N = 376) to perform a proteome-wide association study of depression followed by Mendelian randomization. We identified 19 genes that were consistent with being causal in depression, acting via their respective cis-regulated brain protein abundance. We replicated nine of these genes using an independent depression GWAS (N = 307,353) and another human brain proteomic dataset (N = 152). Eleven of the 19 genes also had cis-regulated mRNA levels that were associated with depression, based on integration of the depression GWAS with human brain transcriptomes (N = 888). Meta-analysis of the discovery and replication proteome-wide association study analyses identified 25 brain proteins consistent with being causal in depression, 20 of which were not previously implicated in depression by GWAS. Together, these findings provide promising brain protein targets for further mechanistic and therapeutic studies.
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Affiliation(s)
- Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Yue Liu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | | | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Adriana Lori
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul J Kim
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - Eric M Reiman
- Banner Alzheimer's Institute, Arizona State University and University of Arizona, Phoenix, AZ, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Aliza P Wingo
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA.
- Division of Mental Health, Atlanta VA Medical Center, Decatur, GA, USA.
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18
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Radenkovic S, Fitzpatrick-Schmidt T, Byeon SK, Madugundu AK, Saraswat M, Lichty A, Wong SYW, McGee S, Kubiak K, Ligezka A, Ranatunga W, Zhang Y, Wood T, Friez MJ, Clarkson K, Pandey A, Jones JR, Morava E. Expanding the clinical and metabolic phenotype of DPM2 deficient congenital disorders of glycosylation. Mol Genet Metab 2021; 132:27-37. [PMID: 33129689 PMCID: PMC7855207 DOI: 10.1016/j.ymgme.2020.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/05/2020] [Accepted: 10/10/2020] [Indexed: 12/14/2022]
Abstract
Pathogenic alterations in the DPM2 gene have been previously described in patients with hypotonia, progressive muscle weakness, absent psychomotor development, intractable seizures, and early death. We identified biallelic DPM2 variants in a 23-year-old male with truncal hypotonia, hypertonicity, congenital heart defects, intellectual disability, and generalized muscle wasting. His clinical presentation was much less severe than that of the three previously described patients. This is the second report on this ultra-rare disorder. Here we review the characteristics of previously reported individuals with a defect in the DPM complex while expanding the clinical phenotype of DPM2-Congenital Disorders of Glycosylation. In addition, we offer further insights into the pathomechanism of DPM2-CDG disorder by introducing glycomics and lipidomics analysis.
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Affiliation(s)
- Silvia Radenkovic
- Mayo Clinic, Department of Clinical Genomics, Rochester, MN, USA; Metabolomics Expertise Center, CCB, KU Leuven-VIB, Leuven, Belgium; Laboratory of Hepatology, Department of CHROMETA, KU Leuven, Leuven, Belgium.
| | | | - Seul Kee Byeon
- Mayo Clinic, Department of Laboratory of Medical Pathology, Rochester, MN, USA
| | - Anil K Madugundu
- Mayo Clinic, Department of Laboratory of Medical Pathology, Rochester, MN, USA; Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India; Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mayank Saraswat
- Mayo Clinic, Department of Laboratory of Medical Pathology, Rochester, MN, USA; Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India; Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | | - Sunnie Y W Wong
- Tulane University Medical School, New Orleans, LA, USA; Stanford University, CA, USA
| | | | | | - Anna Ligezka
- Mayo Clinic, Department of Clinical Genomics, Rochester, MN, USA
| | | | - Yuebo Zhang
- Mayo Clinic, Department of Clinical Genomics, Rochester, MN, USA
| | - Tim Wood
- Greenwood Genetic Center, Greenwood, SC, USA
| | | | | | - Akhilesh Pandey
- Mayo Clinic, Department of Laboratory of Medical Pathology, Rochester, MN, USA; Mayo Clinic, Center for Individualized Medicine, Rochester, MN, USA
| | | | - Eva Morava
- Mayo Clinic, Department of Clinical Genomics, Rochester, MN, USA; Mayo Clinic, Department of Laboratory of Medical Pathology, Rochester, MN, USA
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19
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Abstract
N-glycosylation is a highly conserved glycan modification, and more than 7000 proteins are N-glycosylated in humans. N-glycosylation has many biological functions such as protein folding, trafficking, and signal transduction. Thus, glycan modification to proteins is profoundly involved in numerous physiological and pathological processes. The N-glycan precursor is biosynthesized in the endoplasmic reticulum (ER) from dolichol phosphate by sequential enzymatic reactions to generate the dolichol-linked oligosaccharide composed of 14 sugar residues, Glc3Man9GlcNAc2. The oligosaccharide is then en bloc transferred to the consensus sequence N-X-S/T (X represents any amino acid except proline) of nascent proteins. Subsequently, the N-glycosylated nascent proteins enter the folding step, in which N-glycans contribute largely to attaining the correct protein fold by recruiting the lectin-like chaperones, calnexin, and calreticulin. Despite the N-glycan-dependent folding process, some glycoproteins do not fold correctly, and these misfolded glycoproteins are destined to degradation by proteasomes in the cytosol. Properly folded proteins are transported to the Golgi, and N-glycans undergo maturation by the sequential reactions of glycosidases and glycosyltransferases, generating complex-type N-glycans. N-Acetylglucosaminyltransferases (GnT-III, GnT-IV, and GnT-V) produce branched N-glycan structures, affording a higher complexity to N-glycans. In this chapter, we provide an overview of the biosynthetic pathway of N-glycans in the ER and Golgi.
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20
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Mikkola S. Nucleotide Sugars in Chemistry and Biology. Molecules 2020; 25:E5755. [PMID: 33291296 PMCID: PMC7729866 DOI: 10.3390/molecules25235755] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleotide sugars have essential roles in every living creature. They are the building blocks of the biosynthesis of carbohydrates and their conjugates. They are involved in processes that are targets for drug development, and their analogs are potential inhibitors of these processes. Drug development requires efficient methods for the synthesis of oligosaccharides and nucleotide sugar building blocks as well as of modified structures as potential inhibitors. It requires also understanding the details of biological and chemical processes as well as the reactivity and reactions under different conditions. This article addresses all these issues by giving a broad overview on nucleotide sugars in biological and chemical reactions. As the background for the topic, glycosylation reactions in mammalian and bacterial cells are briefly discussed. In the following sections, structures and biosynthetic routes for nucleotide sugars, as well as the mechanisms of action of nucleotide sugar-utilizing enzymes, are discussed. Chemical topics include the reactivity and chemical synthesis methods. Finally, the enzymatic in vitro synthesis of nucleotide sugars and the utilization of enzyme cascades in the synthesis of nucleotide sugars and oligosaccharides are briefly discussed.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, 20014 Turku, Finland
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21
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Piłsyk S, Perlinska-Lenart U, Janik A, Gryz E, Ajchler-Adamska M, Kruszewska JS. Yil102c-A is a Functional Homologue of the DPMII Subunit of Dolichyl Phosphate Mannose Synthase in Saccharomyces cerevisiae. Int J Mol Sci 2020; 21:E8938. [PMID: 33255655 PMCID: PMC7728079 DOI: 10.3390/ijms21238938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 11/30/2022] Open
Abstract
In a wide range of organisms, dolichyl phosphate mannose (DPM) synthase is a complex of tree proteins Dpm1, Dpm2, and Dpm3. However, in the yeast Saccharomyces cerevisiae, it is believed to be a single Dpm1 protein. The function of Dpm3 is performed in S. cerevisiae by the C-terminal transmembrane domain of the catalytic subunit Dpm1. Until present, the regulatory Dpm2 protein has not been found in S. cerevisiae. In this study, we show that, in fact, the Yil102c-A protein interacts directly with Dpm1 in S. cerevisiae and influences its DPM synthase activity. Deletion of the YIL102c-A gene is lethal, and this phenotype is reversed by the dpm2 gene from Trichoderma reesei. Functional analysis of Yil102c-A revealed that it also interacts with glucosylphosphatidylinositol-N-acetylglucosaminyl transferase (GPI-GnT), similar to DPM2 in human cells. Taken together, these results show that Yil102c-A is a functional homolog of DPMII from T. reesei and DPM2 from humans.
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Affiliation(s)
| | | | | | | | | | - Joanna S. Kruszewska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (S.P.); (U.P.-L.); (A.J.); (E.G.); (M.A.-A.)
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Li M, Xia S, Shi P. DPM1 expression as a potential prognostic tumor marker in hepatocellular carcinoma. PeerJ 2020; 8:e10307. [PMID: 33282554 PMCID: PMC7694566 DOI: 10.7717/peerj.10307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
Background Altered glycosylation of proteins contributes to tumor progression. Dolichol phosphate mannose synthase (DPMS), an essential mannosyltransferase, plays a central role in post-translational modification of proteins, including N-linked glycoproteins, O-mannosylation, C-mannosylation and glycosylphosphatidylinositol anchors synthesis. Little is known about the function of DPMS in liver cancer. Methods The study explored the roles of DPMS in the prognosis of hepatocellular carcinoma using UALCAN, Human Protein Atlas, GEPIA, cBioPortal and Metascape databases. The mRNA expressions of DPM1/2/3 also were detected by quantitative real-time PCR experiments in vitro. Results The transcriptional and proteinic expressions of DPM1/2/3 were both over-expressed in patients with hepatocellular carcinoma. Over-expressions of DPMS were discovered to be dramatically associated with clinical cancer stages and pathological tumor grades in hepatocellular carcinoma patients. In addition, higher mRNA expressions of DPM1/2/3 were found to be significantly related to shorter overall survival in liver cancer patients. Futhermore, high genetic alteration rate of DPMS (41%) was also observed in patients with liver cancer, and genetic alteration in DPMS was associated with shorter overall survival in hepatocellular carcinoma patients. We also performed quantitative real-time PCR experiments in human normal hepatocytes and hepatoma cells to verify the expressions of DPM1/2/3 and results showed that the expression of DPM1 was significantly increased in hepatoma cells SMMC-7721 and HepG2. Conclusions Taken together, these results suggested that DPM1 could be a potential prognostic biomarker for survivals of hepatocellular carcinoma patients.
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Affiliation(s)
- Ming Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Shengli Xia
- Department of Orthopedics, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Ping Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Chao Q, Ding Y, Chen ZH, Xiang MH, Wang N, Gao XD. Recent Progress in Chemo-Enzymatic Methods for the Synthesis of N-Glycans. Front Chem 2020; 8:513. [PMID: 32612979 PMCID: PMC7309569 DOI: 10.3389/fchem.2020.00513] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/18/2020] [Indexed: 01/06/2023] Open
Abstract
Asparagine (N)-linked glycosylation is one of the most common co- and post-translational modifications of both intra- and extracellularly distributing proteins, which directly affects their biological functions, such as protein folding, stability and intercellular traffic. Production of the structural well-defined homogeneous N-glycans contributes to comprehensive investigation of their biological roles and molecular basis. Among the various methods, chemo-enzymatic approach serves as an alternative to chemical synthesis, providing high stereoselectivity and economic efficiency. This review summarizes some recent advances in the chemo-enzymatic methods for the production of N-glycans, including the preparation of substrates and sugar donors, and the progress in the glycosyltransferases characterization which leads to the diversity of N-glycan synthesis. We discuss the bottle-neck and new opportunities in exploiting the chemo-enzymatic synthesis of N-glycans based on our research experiences. In addition, downstream applications of the constructed N-glycans, such as automation devices and homogeneous glycoproteins synthesis are also described.
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Affiliation(s)
| | | | | | | | - Ning Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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24
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Abstract
Objective: To summarize the abnormal location of FLT3 caused by different glycosylation status which further leads to the distinguishing signaling pathways and discuss targeting on FLT3 glycosylation by drugs reported in recent literatures. Methods: We review FLT3 glycosylation in endoplasmic reticulum. The abnormal signal of mutant FLT3 with different glycosylation status is discussed. We also address potential FLT3 glycosylation-targeting strategies for the treatment. Results: Inhibition of FLT3 mutant cells by drugs reported in recent literatures involves the influence of glycosylation of FLT3: 2-deoxy-D-glucose, Tunicamycin and Fluvastatin are reported to inhibit N-glycosylation of FLT3; Pim-1 inhibitors are proved to block the inhibition of Pim-1 on FLT3 Oglycosylation; HSP90 inhibitors and Tyrosine Kinase Inhibitors are shown to increase fully glycosylated form of FLT3. Discussion: The FMS-like tyrosine kinase 3 (FLT3) gene expressed only in CD34+ progenitor cells in bone marrow is located on chromosome 13q12 encoding FLT3 protein. FLT3 is initially synthesized as a 110 KD protein, which glycosylated in the endoplasmic reticulum to a 130 KD immature protein rich in mannose, and further processed into a mature 160 KD protein in the Golgi apparatus, which could be transferred to the cell surface. Therapy targeting on FLT3 glycosylation is a promising direction for AML treatment. Conclusions: The abnormal location of FLT3 caused by different glycosylation status leads to the distinguishing signaling pathways. Targeting on FLT3 glycosylation may provide a new perspective for therapeutic strategies. Abbreviations: ABCG2: ATP-binding cassette transporter breast cancer resistance protein; ATF: activating transcription factor; AML: acute myeloid leukemia; CHOP: CCAAT-enhancer-binding protein homologous protein; 2-DG: 2-deoxy-D-glucose; EFS: event free survival; EPO: erythropoietin; EPOR: erythropoietin receptor; ERS: endoplasmic reticulum stress; FLT3: FMS-like tyrosine kinase 3; GPI: glycosylphosphatidylinositol; HSP: heat shock protein; ITD: internal tandem duplication; IRE1a: inositol-requiring enzyme 1 alpha; JNK: c-Jun N-terminal kinase; JMD: juxtamembrane domain; JAK: janus kinase; MAPK/ERK: mitogen activated protein kinase/extracellular signal-regulated protein kinase; OS: overall survival; PI3K/AKT: phosphatidylinositide 3-kinases/protein kinase B; PERK: RNA-activated protein kinase-like endoplasmic reticulum kinase; Pgp: P-glycoprotein; PTX3: human pentraxin-3; STAT: signal transducer and activator of transcriptions; TKD: tyrosine-kinase domain; TKI: tyrosine kinase inhibitor; TM: Tunicamycin; UPR: unfolded protein reaction.
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Affiliation(s)
- Xiaoli Hu
- Department of Hematology, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai , People's Republic of China
| | - Fangyuan Chen
- Department of Hematology, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai , People's Republic of China
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Labeau A, Simon-Loriere E, Hafirassou ML, Bonnet-Madin L, Tessier S, Zamborlini A, Dupré T, Seta N, Schwartz O, Chaix ML, Delaugerre C, Amara A, Meertens L. A Genome-Wide CRISPR-Cas9 Screen Identifies the Dolichol-Phosphate Mannose Synthase Complex as a Host Dependency Factor for Dengue Virus Infection. J Virol 2020; 94:e01751-19. [PMID: 31915280 PMCID: PMC7081898 DOI: 10.1128/jvi.01751-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/20/2019] [Indexed: 12/24/2022] Open
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no specific therapies are available. Like other viruses, DENV relies heavily on the host cellular machinery for productive infection. In this study, we performed a genome-wide CRISPR-Cas9 screen using haploid HAP1 cells to identify host genes important for DENV infection. We identified DPM1 and -3, two subunits of the endoplasmic reticulum (ER) resident dolichol-phosphate mannose synthase (DPMS) complex, as host dependency factors for DENV and other related flaviviruses, such as Zika virus (ZIKV). The DPMS complex catalyzes the synthesis of dolichol-phosphate mannose (DPM), which serves as mannosyl donor in pathways leading to N-glycosylation, glycosylphosphatidylinositol (GPI) anchor biosynthesis, and C- or O-mannosylation of proteins in the ER lumen. Mutation in the DXD motif of DPM1, which is essential for its catalytic activity, abolished DPMS-mediated DENV infection. Similarly, genetic ablation of ALG3, a mannosyltransferase that transfers mannose to lipid-linked oligosaccharide (LLO), rendered cells poorly susceptible to DENV. We also established that in cells deficient for DPMS activity, viral RNA amplification is hampered and truncated oligosaccharides are transferred to the viral prM and E glycoproteins, affecting their proper folding. Overall, our study provides new insights into the host-dependent mechanisms of DENV infection and supports current therapeutic approaches using glycosylation inhibitors to treat DENV infection.IMPORTANCE Dengue disease, which is caused by dengue virus (DENV), has emerged as the most important mosquito-borne viral disease in humans and is a major global health concern. DENV encodes only few proteins and relies on the host cell machinery to accomplish its life cycle. The identification of the host factors important for DENV infection is needed to propose new targets for antiviral intervention. Using a genome-wide CRISPR-Cas9 screen, we identified DPM1 and -3, two subunits of the DPMS complex, as important host factors for the replication of DENV as well as other related viruses such as Zika virus. We established that DPMS complex plays dual roles during viral infection, both regulating viral RNA replication and promoting viral structural glycoprotein folding/stability. These results provide insights into the host molecules exploited by DENV and other flaviviruses to facilitate their life cycle.
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Affiliation(s)
- Athena Labeau
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | | | - Mohamed-Lamine Hafirassou
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Lucie Bonnet-Madin
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Sarah Tessier
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Alessia Zamborlini
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thierry Dupré
- Laboratoire de Biochimie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Nathalie Seta
- Laboratoire de Biochimie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Olivier Schwartz
- Institut Pasteur, Virus and Immunity Unit, CNRS-UMR3569, Paris, France
| | - Marie-Laure Chaix
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
- Laboratoire de Virologie et Département des Maladies Infectieuses, Hôpital Saint-Louis, APHP, Paris, France
| | - Constance Delaugerre
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
- Laboratoire de Virologie et Département des Maladies Infectieuses, Hôpital Saint-Louis, APHP, Paris, France
| | - Ali Amara
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Laurent Meertens
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
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Qi R, Zhu J, Miao Q, Tang A, Dong D, Wang X, Liu G. Bioinformatics analysis of capsid protein of different subtypes rabbit hemorrhagic disease virus. BMC Vet Res 2019; 15:423. [PMID: 31775738 PMCID: PMC6882040 DOI: 10.1186/s12917-019-2161-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/29/2019] [Indexed: 11/10/2022] Open
Abstract
Background Rabbit Hemorrhagic Disease Virus (RHDV) belongs to the Caliciviridae family, is a highly lethal pathogen to rabbits. Increasing numbers of studies have demonstrated the existence of antigenic variation in RHDV, leading to the emergence of a new RHDV isolate (RHDVb). However, the underlying factors determining the emergence of the new RHDV and its unpredictable epidemiology remain unclear. To investigate these issues, we selected more than 184 partial and/or complete genome sequences of RHDV from GenBank and analyzed their phylogenetic relationships, divergence, and predicted protein modification sites. Results Phylogenetic analysis showed that classic RHDV isolates, RHDVa, and RHDVb formed different clades. It’s interesting to note that RHDVa being more closely related to classic RHDV than RHDVb, while RHDVb had a closer genetic relationship to Rabbit Calicivirus (RCV) than to classic RHDV isolates. Moreover, divergence analysis suggested that the accumulation of amino acid (aa) changes might be a consequence of adaptive diversification of capsid protein (VP60) during the division between classical RHDV, RHDVa, RHDVb, and RCV. Notably, the prediction of N-glycosylation sites suggested that RHDVb subtypes had two unique N-glycosylation sites (aa 301, 362) but lacked three other N-glycosylation sites (aa 45, 308, 474) displayed in classic RHDV and RHDVa VP60 implying this divergence of N-glycosylation sites in RHDV might affect viral virulence. Analysis of phosphorylation sites also indicated that some phosphorylation sites in RHDVa and RHDVb differed from those in classic RHDV, potentially related to antigenic variation in RHDV. Conclusion The genetic relationship between RHDVb and RCV was closer than classic RHDV isolates. Moreover, compared to RHDV and RHDVa, RHDVb had two unique N-glycosylation sites but lacked three sites, which might affect the virulence of RHDV. These results may provide new clues for further investigations of the origin of new types of RHDV and the mechanisms of genetic variation in RHDV.
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Affiliation(s)
- Ruibin Qi
- Innovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China
| | - Jie Zhu
- Innovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China
| | - Qiuhong Miao
- Innovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China
| | - Aoxing Tang
- Innovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China
| | - Dandan Dong
- Innovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China
| | - Xiaoxue Wang
- Innovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China
| | - Guangqing Liu
- Innovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China.
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Entova S, Guan Z, Imperiali B. Investigation of the conserved reentrant membrane helix in the monotopic phosphoglycosyl transferase superfamily supports key molecular interactions with polyprenol phosphate substrates. Arch Biochem Biophys 2019; 675:108111. [PMID: 31563509 PMCID: PMC6909930 DOI: 10.1016/j.abb.2019.108111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 01/10/2023]
Abstract
Long-chain polyprenol phosphates feature in membrane-associated glycoconjugate biosynthesis pathways across domains of life. These unique amphiphilic molecules are best known as substrates of polytopic membrane proteins, including polyprenol-phosphate phosphoglycosyl and glycosyl transferases, and as components of more complex substrates. The linear polyprenols are constrained by double bond geometry and lend themselves well to interactions with polytopic membrane proteins, in which multiple transmembrane helices form a rich landscape for interactions. Recently, a new superfamily of monotopic phosphoglycosyl transferase enzymes has been identified that interacts with polyprenol phosphate substrates via a single reentrant membrane helix. Intriguingly, despite the dramatic differences in their membrane-interaction domains, both polytopic and monotopic enzymes similarly favor a unique cis/trans geometry in their polyprenol phosphate substrates. Herein, we present a multipronged biochemical and biophysical study of PglC, a monotopic phosphoglycosyl transferase that catalyzes the first membrane-committed step in N-linked glycoprotein biosynthesis in Campylobacter jejuni. We probe the significance of polyprenol phosphate geometry both in mediating substrate binding to PglC and in modulating the local membrane environment. Geometry is found to be important for binding to PglC; a conserved proline residue in the reentrant membrane helix is determined to drive polyprenol phosphate recognition and specificity. Pyrene fluorescence studies show that polyprenol phosphates at physiologically-relevant levels increase the disorder of the local lipid bilayer; however, this effect is confined to polyprenol phosphates with specific isoprene geometries. The molecular insights from this study may shed new light on the interactions of polyprenol phosphates with diverse membrane-associated proteins in glycoconjugate biosynthesis.
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Affiliation(s)
- Sonya Entova
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA.
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, 10 Duke Medicine Circle, Durham, NC, 27710, USA.
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Bai L, Kovach A, You Q, Kenny A, Li H. Structure of the eukaryotic protein O-mannosyltransferase Pmt1-Pmt2 complex. Nat Struct Mol Biol 2019; 26:704-711. [PMID: 31285605 PMCID: PMC6684406 DOI: 10.1038/s41594-019-0262-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/29/2019] [Indexed: 12/24/2022]
Abstract
In eukaryotes, a nascent peptide entering the endoplasmic reticulum (ER) is scanned by two Sec61-translocon-associated large membrane machines for protein N-glycosylation and protein O-mannosylation, respectively. While the structure of the eight-protein oligosaccharyltransferase complex has been determined recently, the structures of mannosyltransferases of the PMT family, which are an integral part of ER protein homeostasis, are still unknown. Here we report cryo-EM structures of the S. cerevisiae Pmt1–Pmt2 complex bound to a donor and an acceptor peptide at 3.2-Å resolution, showing that each subunit contains 11 transmembrane helices and a lumenal β-trefoil fold termed the MIR domain. The structures reveal the substrate recognition model and confirm an inverting mannosyl-transferring reaction mechanism by the enzyme complex. Furthermore, we found that the transmembrane domains of Pmt1 and Pmt2 share a structural fold with the catalytic subunits of oligosaccharyltransferases, confirming a previously proposed evolutionary relationship between protein O-mannosylation and protein N-glycosylation.
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Affiliation(s)
- Lin Bai
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Amanda Kovach
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Qinglong You
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Alanna Kenny
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Huilin Li
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA.
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29
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Kanagawa M, Toda T. Muscular Dystrophy with Ribitol-Phosphate Deficiency: A Novel Post-Translational Mechanism in Dystroglycanopathy. J Neuromuscul Dis 2019; 4:259-267. [PMID: 29081423 PMCID: PMC5701763 DOI: 10.3233/jnd-170255] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Muscular dystrophy is a group of genetic disorders characterized by progressive muscle weakness. In the early 2000s, a new classification of muscular dystrophy, dystroglycanopathy, was established. Dystroglycanopathy often associates with abnormalities in the central nervous system. Currently, at least eighteen genes have been identified that are responsible for dystroglycanopathy, and despite its genetic heterogeneity, its common biochemical feature is abnormal glycosylation of alpha-dystroglycan. Abnormal glycosylation of alpha-dystroglycan reduces its binding activities to ligand proteins, including laminins. In just the last few years, remarkable progress has been made in determining the sugar chain structures and gene functions associated with dystroglycanopathy. The normal sugar chain contains tandem structures of ribitol-phosphate, a pentose alcohol that was previously unknown in humans. The dystroglycanopathy genes fukutin, fukutin-related protein (FKRP), and isoprenoid synthase domain-containing protein (ISPD) encode essential enzymes for the synthesis of this structure: fukutin and FKRP transfer ribitol-phosphate onto sugar chains of alpha-dystroglycan, and ISPD synthesizes CDP-ribitol, a donor substrate for fukutin and FKRP. These findings resolved long-standing questions and established a disease subgroup that is ribitol-phosphate deficient, which describes a large population of dystroglycanopathy patients. Here, we review the history of dystroglycanopathy, the properties of the sugar chain structure of alpha-dystroglycan, dystroglycanopathy gene functions, and therapeutic strategies.
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Affiliation(s)
- Motoi Kanagawa
- Division of Neurology/Molecular Brain Science, Kobe University Graduate School of Medicine, Chuo-ku, Kobe, Japan
| | - Tatsushi Toda
- Division of Neurology/Molecular Brain Science, Kobe University Graduate School of Medicine, Chuo-ku, Kobe, Japan.,Department of Neurology, Division of Neuroscience, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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30
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Gryz E, Perlińska-Lenart U, Gawarecka K, Jozwiak A, Piłsyk S, Lipko A, Jemiola-Rzeminska M, Bernat P, Muszewska A, Steczkiewicz K, Ginalski K, Długoński J, Strzalka K, Swiezewska E, Kruszewska JS. Poly-Saturated Dolichols from Filamentous Fungi Modulate Activity of Dolichol-Dependent Glycosyltransferase and Physical Properties of Membranes. Int J Mol Sci 2019; 20:ijms20123043. [PMID: 31234450 PMCID: PMC6628320 DOI: 10.3390/ijms20123043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 11/17/2022] Open
Abstract
Mono-saturated polyprenols (dolichols) have been found in almost all Eukaryotic cells, however, dolichols containing additional saturated bonds at the ω-end, have been identified in A. fumigatus and A. niger. Here we confirm using an LC-ESI-QTOF-MS analysis, that poly-saturated dolichols are abundant in other filamentous fungi, Trichoderma reesei, A. nidulans and Neurospora crassa, while the yeast Saccharomyces cerevisiae only contains the typical mono-saturated dolichols. We also show, using differential scanning calorimetry (DSC) and fluorescence anisotropy of 1,6-diphenyl-l,3,5-hexatriene (DPH) that the structure of dolichols modulates the properties of membranes and affects the functioning of dolichyl diphosphate mannose synthase (DPMS). The activity of this enzyme from T. reesei and S. cerevisiae was strongly affected by the structure of dolichols. Additionally, the structure of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) model membranes was more strongly disturbed by the poly-saturated dolichols from Trichoderma than by the mono-saturated dolichols from yeast. By comparing the lipidome of filamentous fungi with that from S. cerevisiae, we revealed significant differences in the PC/PE ratio and fatty acids composition. Filamentous fungi differ from S. cerevisiae in the lipid composition of their membranes and the structure of dolichols. The structure of dolichols profoundly affects the functioning of dolichol-dependent enzyme, DPMS.
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Affiliation(s)
- Elżbieta Gryz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Urszula Perlińska-Lenart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Katarzyna Gawarecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Adam Jozwiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Agata Lipko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Malgorzata Jemiola-Rzeminska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.
| | - Przemysław Bernat
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
| | - Jerzy Długoński
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.
| | - Kazimierz Strzalka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Joanna S Kruszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
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31
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Allen KN, Imperiali B. Structural and mechanistic themes in glycoconjugate biosynthesis at membrane interfaces. Curr Opin Struct Biol 2019; 59:81-90. [PMID: 31003021 DOI: 10.1016/j.sbi.2019.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 12/29/2022]
Abstract
Peripheral and integral membrane proteins feature in stepwise assembly of complex glycans and glycoconjugates. Catalysis on membrane-bound substrates features challenges with substrate solubility and active-site accessibility. However, advantages in enzyme and substrate orientation and control of lateral membrane diffusion provide order to the multistep processes. Recent glycosyltransferase (GT) studies show that substrate diversity is met by the selection of folds which do not converge upon a common mechanism. Examples of polyprenol phosphate phosphoglycosyl transferases (PGTs) highlight that divergent fold families catalyze the same reaction with different mechanisms. Lipid A biosynthesis enzymes illustrate that variations on the robust Rossmann fold allow substrate diversity. Improved understanding of GT and PGT structure and function holds promise for better function prediction and improvement of therapeutic inhibitory ligands.
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Affiliation(s)
- Karen N Allen
- Department of Chemistry, Boston University, Boston, MA 02215, United States; Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA 02118, United States.
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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32
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Kim E, Dede M, Lenoir WF, Wang G, Srinivasan S, Colic M, Hart T. A network of human functional gene interactions from knockout fitness screens in cancer cells. Life Sci Alliance 2019; 2:2/2/e201800278. [PMID: 30979825 PMCID: PMC6464042 DOI: 10.26508/lsa.201800278] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/12/2022] Open
Abstract
The function of human genes can be strongly inferred from their knockout fitness profiles across hundreds of CRISPR screens, illuminating the modular organization of the cell. Genetic interactions mediate the emergence of phenotype from genotype. The systematic survey of genetic interactions in yeast showed that genes operating in the same biological process have highly correlated genetic interaction profiles, and this observation has been exploited to infer gene function in model organisms. Such assays of digenic perturbations in human cells are also highly informative, but are not scalable, even with CRISPR-mediated methods. As an alternative, we developed an indirect method of deriving functional interactions. We show that genes having correlated knockout fitness profiles across diverse, non-isogenic cell lines are analogous to genes having correlated genetic interaction profiles across isogenic query strains and similarly imply shared biological function. We constructed a network of genes with correlated fitness profiles across 276 high-quality CRISPR knockout screens in cancer cell lines into a “coessentiality network,” with up to 500-fold enrichment for co-functional gene pairs, enabling strong inference of gene function and highlighting the modular organization of the cell.
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Affiliation(s)
- Eiru Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Walter F Lenoir
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanjana Srinivasan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Medina Colic
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA .,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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33
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Wen L, Edmunds G, Gibbons C, Zhang J, Gadi MR, Zhu H, Fang J, Liu X, Kong Y, Wang PG. Toward Automated Enzymatic Synthesis of Oligosaccharides. Chem Rev 2018; 118:8151-8187. [DOI: 10.1021/acs.chemrev.8b00066] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Liuqing Wen
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Garrett Edmunds
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Christopher Gibbons
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jiabin Zhang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Madhusudhan Reddy Gadi
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Hailiang Zhu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Junqiang Fang
- National Glycoengineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Xianwei Liu
- National Glycoengineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Yun Kong
- National Glycoengineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Peng George Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- National Glycoengineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
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34
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Kanagawa M, Toda T. Ribitol-phosphate—a newly identified posttranslational glycosylation unit in mammals: structure, modification enzymes and relationship to human diseases. J Biochem 2018; 163:359-369. [DOI: 10.1093/jb/mvy020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/23/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Motoi Kanagawa
- Division of Molecular Brain Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Tatsushi Toda
- Division of Molecular Brain Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
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35
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Citro V, Cimmaruta C, Liguori L, Viscido G, Cubellis MV, Andreotti G. A mutant of phosphomannomutase1 retains full enzymatic activity, but is not activated by IMP: Possible implications for the disease PMM2-CDG. PLoS One 2017; 12:e0189629. [PMID: 29261720 PMCID: PMC5736207 DOI: 10.1371/journal.pone.0189629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/29/2017] [Indexed: 11/18/2022] Open
Abstract
The most frequent disorder of glycosylation, PMM2-CDG, is caused by a deficiency of phosphomannomutase activity. In humans two paralogous enzymes exist, both of them require mannose 1,6-bis-phosphate or glucose 1,6-bis-phosphate as activators, but only phospho-mannomutase1 hydrolyzes bis-phosphate hexoses. Mutations in the gene encoding phosphomannomutase2 are responsible for PMM2-CDG. Although not directly causative of the disease, the role of the paralogous enzyme in the disease should be clarified. Phosphomannomutase1 could have a beneficial effect, contributing to mannose 6-phosphate isomerization, or a detrimental effect, hydrolyzing the bis-phosphate hexose activator. A pivotal role in regulating mannose-1phosphate production and ultimately protein glycosylation might be played by inosine monophosphate that enhances the phosphatase activity of phosphomannomutase1. In this paper we analyzed human phosphomannomutases by conventional enzymatic assays as well as by novel techniques such as 31P-NMR and thermal shift assay. We characterized a triple mutant of phospomannomutase1 that retains mutase and phosphatase activity, but is unable to bind inosine monophosphate.
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Affiliation(s)
- Valentina Citro
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
| | | | - Ludovica Liguori
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, Italy
- Dipartimento di scienze e tecnologie ambientali, biologiche e farmaceutiche, Università della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Gaetano Viscido
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, Italy
- * E-mail:
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36
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Morgan MB, Edge SE, Venn AA, Jones RJ. Developing transcriptional profiles in Orbicella franksi exposed to copper: Characterizing responses associated with a spectrum of laboratory-controlled environmental conditions. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 189:60-76. [PMID: 28599170 DOI: 10.1016/j.aquatox.2017.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/23/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Michael B Morgan
- Department of Biology, Berry College, School of Mathematics and Natural Sciences, 2277 Martha Berry Hwy, Mount Berry, GA, 30149, USA.
| | - Sara E Edge
- Hawaii Pacific University, 45-045 Kamehameha Hwy, Kaneohe, HI, 96744, USA
| | - Alexander A Venn
- Marine Biology Department et Laboratoire International Associé 647 "BIOSENSIB", Centre Scientifique de Monaco, 8 Quai Antoine 1er, MC98000, Monaco
| | - Ross J Jones
- Australian Institute of Marine Science (AIMS), Perth, 6009, Australia
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37
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Gandini R, Reichenbach T, Tan TC, Divne C. Structural basis for dolichylphosphate mannose biosynthesis. Nat Commun 2017; 8:120. [PMID: 28743912 PMCID: PMC5526996 DOI: 10.1038/s41467-017-00187-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 06/06/2017] [Indexed: 12/21/2022] Open
Abstract
Protein glycosylation is a critical protein modification. In biogenic membranes of eukaryotes and archaea, these reactions require activated mannose in the form of the lipid conjugate dolichylphosphate mannose (Dol-P-Man). The membrane protein dolichylphosphate mannose synthase (DPMS) catalyzes the reaction whereby mannose is transferred from GDP-mannose to the dolichol carrier Dol-P, to yield Dol-P-Man. Failure to produce or utilize Dol-P-Man compromises organism viability, and in humans, several mutations in the human dpm1 gene lead to congenital disorders of glycosylation (CDG). Here, we report three high-resolution crystal structures of archaeal DPMS from Pyrococcus furiosus, in complex with nucleotide, donor, and glycolipid product. The structures offer snapshots along the catalytic cycle, and reveal how lipid binding couples to movements of interface helices, metal binding, and acceptor loop dynamics to control critical events leading to Dol-P-Man synthesis. The structures also rationalize the loss of dolichylphosphate mannose synthase function in dpm1-associated CDG. The generation of glycolipid dolichylphosphate mannose (Dol-P-Man) is a critical step for protein glycosylation and GPI anchor synthesis. Here the authors report the structure of dolichylphosphate mannose synthase in complex with bound nucleotide and donor to provide insight into the mechanism of Dol-P-Man synthesis.
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Affiliation(s)
- Rosaria Gandini
- School of Biotechnology, KTH Royal Institute of Technology, S-10691, Stockholm, Sweden
| | - Tom Reichenbach
- School of Biotechnology, KTH Royal Institute of Technology, S-10691, Stockholm, Sweden
| | - Tien-Chye Tan
- School of Biotechnology, KTH Royal Institute of Technology, S-10691, Stockholm, Sweden
| | - Christina Divne
- School of Biotechnology, KTH Royal Institute of Technology, S-10691, Stockholm, Sweden.
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38
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Balcin H, Palmio J, Penttilä S, Nennesmo I, Lindfors M, Solders G, Udd B. Late-onset limb-girdle muscular dystrophy caused by GMPPB mutations. Neuromuscul Disord 2017; 27:627-630. [DOI: 10.1016/j.nmd.2017.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/26/2017] [Accepted: 04/13/2017] [Indexed: 11/29/2022]
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39
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Knocking Down the Expression of GMPase Gene OsVTC1-1 Decreases Salt Tolerance of Rice at Seedling and Reproductive Stages. PLoS One 2016; 11:e0168650. [PMID: 27992560 PMCID: PMC5167552 DOI: 10.1371/journal.pone.0168650] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 12/04/2016] [Indexed: 12/25/2022] Open
Abstract
Salinity is a severe environmental stress that greatly impairs production of crops worldwide. Previous studies have shown that GMPase plays an important role in tolerance of plants to salt stress at vegetative stage. However, the function of GMPase in plant responses to salt stress at reproductive stage remains unclear. Studies have shown that heterologous expression of rice GMPase OsVTC1-1 enhanced salt tolerance of tobacco seedlings, but the native role of OsVTC1-1 in salt stress tolerance of rice is unknown. To illustrate the native function of GMPase in response of rice to salt stress, OsVTC1-1 expression was suppressed using RNAi-mediated gene silencing. Suppressing OsVTC1-1 expression obviously decreased salt tolerance of rice varieties at vegetative stage. Intriguingly, grain yield of OsVTC1-1 RNAi rice was also significantly reduced under salt stress, indicating that OsVTC1-1 plays an important role in salt tolerance of rice at both seedling and reproductive stages. OsVTC1-1 RNAi rice accumulated more ROS under salt stress, and supplying exogenous ascorbic acid restored salt tolerance of OsVTC1-1 RNAi lines, suggesting that OsVTC1-1 is involved in salt tolerance of rice through the biosynthesis regulation of ascorbic acid. Altogether, results of present study showed that rice GMPase gene OsVTC1-1 plays a critical role in salt tolerance of rice at both vegetative and reproductive stages through AsA scavenging of excess ROS.
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40
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Bouchet-Séraphin C, Chelbi-Viallon M, Vuillaumier-Barrot S, Seta N. [Genes of alpha-dystroglycanopathies in 2016]. Med Sci (Paris) 2016; 32 Hors série n°2:40-45. [PMID: 27869076 DOI: 10.1051/medsci/201632s210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Céline Bouchet-Séraphin
- AP-HP, Hôpital Bichat Claude Bernard, Service de Biochimie, 75018 Paris, France - AP-HP, Hôpital Bichat Claude Bernard, Département de Génétique, 75018 Paris, France
| | | | - S Vuillaumier-Barrot
- AP-HP, Hôpital Bichat Claude Bernard, Service de Biochimie, 75018 Paris, France - AP-HP, Hôpital Bichat Claude Bernard, Département de Génétique, 75018 Paris, France - Inserm U733, Faculté Bichat, 75018 Paris, France
| | - N Seta
- AP-HP, Hôpital Bichat Claude Bernard, Service de Biochimie, 75018 Paris, France - Université Paris Descartes, 75006 Paris, France
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41
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Lombard J. The multiple evolutionary origins of the eukaryotic N-glycosylation pathway. Biol Direct 2016; 11:36. [PMID: 27492357 PMCID: PMC4973528 DOI: 10.1186/s13062-016-0137-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/26/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The N-glycosylation is an essential protein modification taking place in the membranes of the endoplasmic reticulum (ER) in eukaryotes and the plasma membranes in archaea. It shares mechanistic similarities based on the use of polyisoprenol lipid carriers with other glycosylation pathways involved in the synthesis of bacterial cell wall components (e.g. peptidoglycan and teichoic acids). Here, a phylogenomic analysis was carried out to examine the validity of rival hypotheses suggesting alternative archaeal or bacterial origins to the eukaryotic N-glycosylation pathway. RESULTS The comparison of several polyisoprenol-based glycosylation pathways from the three domains of life shows that most of the implicated proteins belong to a limited number of superfamilies. The N-glycosylation pathway enzymes are ancestral to the eukaryotes, but their origins are mixed: Alg7, Dpm and maybe also one gene of the glycosyltransferase 1 (GT1) superfamily and Stt3 have proteoarchaeal (TACK superphylum) origins; alg2/alg11 may have resulted from the duplication of the original GT1 gene; the lumen glycosyltransferases were probably co-opted and multiplied through several gene duplications during eukaryogenesis; Alg13/Alg14 are more similar to their bacterial homologues; and Alg1, Alg5 and a putative flippase have unknown origins. CONCLUSIONS The origin of the eukaryotic N-glycosylation pathway is not unique and less straightforward than previously thought: some basic components likely have proteoarchaeal origins, but the pathway was extensively developed before the eukaryotic diversification through multiple gene duplications, protein co-options, neofunctionalizations and even possible horizontal gene transfers from bacteria. These results may have important implications for our understanding of the ER evolution and eukaryogenesis. REVIEWERS This article was reviewed by Pr. Patrick Forterre and Dr. Sergei Mekhedov (nominated by Editorial Board member Michael Galperin).
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Affiliation(s)
- Jonathan Lombard
- National Evolutionary Synthesis Center, 2024 W. Main Street Suite A200, Durham, NC, 27705, USA.
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
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42
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Rush JS. Role of Flippases in Protein Glycosylation in the Endoplasmic Reticulum. Lipid Insights 2016; 8:45-53. [PMID: 26917968 PMCID: PMC4762491 DOI: 10.4137/lpi.s31784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 12/21/2022] Open
Abstract
Glycosylation is essential to the synthesis, folding, and function of glycoproteins in eukaryotes. Proteins are co- and posttranslationally modified by a variety of glycans in the endoplasmic reticulum (ER); modifications include C- and O-mannosylation, N-glycosylation, and the addition of glycosylphosphatidylinositol membrane anchors. Protein glycosylation in the ER of eukaryotes involves enzymatic steps on both the cytosolic and lumenal surfaces of the ER membrane. The glycans are first assembled as precursor glycolipids, on the cytosolic surface of the ER, which are tethered to the membrane by attachment to a long-chain polyisoprenyl phosphate (dolichol) containing a reduced α-isoprene. The lipid-anchored building blocks then migrate transversely (flip) across the ER membrane to the lumenal surface, where final assembly of the glycan is completed. This strategy allows the cell to export high-energy biosynthetic intermediates as lipid-bound glycans, while constraining the glycosyl donors to the site of assembly on the membrane surface. This review focuses on the flippases that participate in protein glycosylation in the ER.
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Affiliation(s)
- Jeffrey S Rush
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, USA
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43
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Ardiccioni C, Clarke OB, Tomasek D, Issa HA, von Alpen DC, Pond HL, Banerjee S, Rajashankar KR, Liu Q, Guan Z, Li C, Kloss B, Bruni R, Kloppmann E, Rost B, Manzini MC, Shapiro L, Mancia F. Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis. Nat Commun 2016; 7:10175. [PMID: 26729507 PMCID: PMC4728340 DOI: 10.1038/ncomms10175] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/11/2015] [Indexed: 11/08/2022] Open
Abstract
The attachment of a sugar to a hydrophobic polyisoprenyl carrier is the first step for all extracellular glycosylation processes. The enzymes that perform these reactions, polyisoprenyl-glycosyltransferases (PI-GTs) include dolichol phosphate mannose synthase (DPMS), which generates the mannose donor for glycosylation in the endoplasmic reticulum. Here we report the 3.0 Å resolution crystal structure of GtrB, a glucose-specific PI-GT from Synechocystis, showing a tetramer in which each protomer contributes two helices to a membrane-spanning bundle. The active site is 15 Å from the membrane, raising the question of how water-soluble and membrane-embedded substrates are brought into apposition for catalysis. A conserved juxtamembrane domain harbours disease mutations, which compromised activity in GtrB in vitro and in human DPM1 tested in zebrafish. We hypothesize a role of this domain in shielding the polyisoprenyl-phosphate for transport to the active site. Our results reveal the basis of PI-GT function, and provide a potential molecular explanation for DPM1-related disease.
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Affiliation(s)
- Chiara Ardiccioni
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Oliver B. Clarke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - David Tomasek
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Habon A. Issa
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Desiree C. von Alpen
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Heather L. Pond
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Surajit Banerjee
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Qun Liu
- New York Structural Biology Center, X4 Beamlines, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chijun Li
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York 10027, USA
| | - Renato Bruni
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York 10027, USA
| | - Edda Kloppmann
- Department of Informatics, Bioinformatics and Computational Biology, Garching 85748, Germany
- Institute for Advanced Study (TUM-IAS), TUM (Technische Universität München), Garching 85748, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology, Garching 85748, Germany
- Institute for Advanced Study (TUM-IAS), TUM (Technische Universität München), Garching 85748, Germany
| | - M. Chiara Manzini
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
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44
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Xu C, Ng DTW. Glycosylation-directed quality control of protein folding. Nat Rev Mol Cell Biol 2015; 16:742-52. [PMID: 26465718 DOI: 10.1038/nrm4073] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane-bound and soluble proteins of the secretory pathway are commonly glycosylated in the endoplasmic reticulum. These adducts have many biological functions, including, notably, their contribution to the maturation of glycoproteins. N-linked glycans are of oligomeric structure, forming configurations that provide blueprints to precisely instruct the folding of protein substrates and the quality control systems that scrutinize it. O-linked mannoses are simpler in structure and were recently found to have distinct functions in protein quality control that do not require the complex structure of N-linked glycans. Together, recent studies reveal the breadth and sophistication of the roles of these glycan-directed modifications in protein biogenesis.
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Affiliation(s)
- Chengchao Xu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Davis T W Ng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Duke University-National University of Singapore Graduate Medical School, 8 College Road, Singapore 169857
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45
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Rong Y, Nakamura S, Hirata T, Motooka D, Liu YS, He ZA, Gao XD, Maeda Y, Kinoshita T, Fujita M. Genome-Wide Screening of Genes Required for Glycosylphosphatidylinositol Biosynthesis. PLoS One 2015; 10:e0138553. [PMID: 26383639 PMCID: PMC4575048 DOI: 10.1371/journal.pone.0138553] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/01/2015] [Indexed: 01/16/2023] Open
Abstract
Glycosylphosphatidylinositol (GPI) is synthesized and transferred to proteins in the endoplasmic reticulum (ER). GPI-anchored proteins are then transported from the ER to the plasma membrane through the Golgi apparatus. To date, at least 17 steps have been identified to be required for the GPI biosynthetic pathway. Here, we aimed to establish a comprehensive screening method to identify genes involved in GPI biosynthesis using mammalian haploid screens. Human haploid cells were mutagenized by the integration of gene trap vectors into the genome. Mutagenized cells were then treated with a bacterial pore-forming toxin, aerolysin, which binds to GPI-anchored proteins for targeting to the cell membrane. Cells that showed low surface expression of CD59, a GPI-anchored protein, were further enriched for. Gene trap insertion sites in the non-selected population and in the enriched population were determined by deep sequencing. This screening enriched 23 gene regions among the 26 known GPI biosynthetic genes, which when mutated are expected to decrease the surface expression of GPI-anchored proteins. Our results indicate that the forward genetic approach using haploid cells is a useful and powerful technique to identify factors involved in phenotypes of interest.
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Affiliation(s)
- Yao Rong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Tetsuya Hirata
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zeng-An He
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- * E-mail: (XDG); (MF)
| | - Yusuke Maeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- * E-mail: (XDG); (MF)
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Zhang Q, Huang L, Zhang C, Xie P, Zhang Y, Ding S, Xu F. Synthesis and biological activity of polyprenols. Fitoterapia 2015; 106:184-93. [PMID: 26358482 DOI: 10.1016/j.fitote.2015.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 11/26/2022]
Abstract
The polyprenols and their derivatives are highlighted in this study. These lipid linear polymers of isoprenoid residues are widespread in nature from bacteria to human cells. This review primarily presents the synthesis and biological activities of polyprenyl derivatives. Attention is focused on the synthesis and biological activity of dolichols, polyprenyl ester derivatives and polyprenyl amines. Other polyprenyl derivatives, such as oxides of polyprenols, aromatic polyprenols, polyprenyl bromide and polyprenyl sulphates, are mentioned. It is noted that polyprenyl phosphates and polyprenyl-linked glycosylation have better antibacterial, gene therapy and immunomodulating performance, whereas polyprenyl amines have better for antibacterial and antithrombotic activity. Dolichols, polyprenyl acetic esters, polyprenyl phosphates and polyprenyl-linked glycosylation have pharmacological anti-tumour effects. Finally, the postulated prospect of polyprenols and their derivatives are discussed. Further in vivo studies on the above derivatives are needed. The compatibility of polyprenols and their derivatives with other drugs should be studied, and new preparations of polyprenyl derivatives, such as hydrogel glue and release-controlled drugs, are suggested for future research and development.
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Affiliation(s)
- Qiong Zhang
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China; Beijing Forestry University, Beijing 100083, China
| | - Lixin Huang
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China.
| | - Caihong Zhang
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China
| | - Pujun Xie
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China
| | - Yaolei Zhang
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China
| | - Shasha Ding
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu Province 210042, China; National Engineering Lab. for Biomass Chemical Utilization, Key and Open lab. of Forest Chemical Engineering, SFA, Nanjing, Jiangsu Province 210042, China; Key Lab. of Biomass Energy and Material, Nanjing, Jiangsu Province 210042, China
| | - Feng Xu
- Beijing Forestry University, Beijing 100083, China
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Mulcahy MJ, Blattman SB, Barrantes FJ, Lukas RJ, Hawrot E. Resistance to Inhibitors of Cholinesterase 3 (Ric-3) Expression Promotes Selective Protein Associations with the Human α7-Nicotinic Acetylcholine Receptor Interactome. PLoS One 2015; 10:e0134409. [PMID: 26258666 PMCID: PMC4530945 DOI: 10.1371/journal.pone.0134409] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/08/2015] [Indexed: 11/19/2022] Open
Abstract
The α7-nicotinic acetylcholine receptor (α7-nAChR) is a ligand-gated ion channel widely expressed in vertebrates and is associated with numerous physiological functions. As transmembrane ion channels, α7-nAChRs need to be expressed on the surface of the plasma membrane to function. The receptor has been reported to associate with proteins involved with receptor biogenesis, modulation of receptor properties, as well as intracellular signaling cascades and some of these associated proteins may affect surface expression of α7-nAChRs. The putative chaperone resistance to inhibitors of cholinesterase 3 (Ric-3) has been reported to interact with, and enhance the surface expression of, α7-nAChRs. In this study, we identified proteins that associate with α7-nAChRs when Ric-3 is expressed. Using α-bungarotoxin (α-bgtx), we isolated and compared α7-nAChR-associated proteins from two stably transfected, human tumor-derived cell lines: SH-EP1-hα7 expressing human α7-nAChRs and the same cell line further transfected to express Ric-3, SH-EP1-hα7-Ric-3. Mass spectrometric analysis of peptides identified thirty-nine proteins that are associated with α7-nAChRs only when Ric-3 was expressed. Significantly, and consistent with reports of Ric-3 function in the literature, several of the identified proteins are involved in biological processes that may affect nAChR surface expression such as post-translational processing of proteins, protein trafficking, and protein transport. Additionally, proteins affecting the cell cycle, the cytoskeleton, stress responses, as well as cyclic AMP- and inositol triphosphate-dependent signaling cascades were identified. These results illuminate how α-bgtx may be used to isolate and identify α7-nAChRs as well as how the expression of chaperones such as Ric-3 can influence proteins associating with α7-nAChRs. These associating proteins may alter activities of α7-nAChRs to expand their functionally-relevant repertoire as well as to affect biogenesis and membrane trafficking of α7-nAChRs.
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Affiliation(s)
- Matthew J. Mulcahy
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, United States of America
| | - Sydney B. Blattman
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, United States of America
| | - Francisco J. Barrantes
- Laboratory of Molecular Neurobiology, Institute of Biomedical Research, UCA-CONICET, Buenos Aires, Argentina
| | - Ronald J. Lukas
- Division of Neurobiology, Barrow Neurological Institute, Phoenix, Arizona, United States of America
| | - Edward Hawrot
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, United States of America
- * E-mail:
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48
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Evangelista T, Hanna M, Lochmüller H. Congenital Myasthenic Syndromes with Predominant Limb Girdle Weakness. J Neuromuscul Dis 2015; 2:S21-S29. [PMID: 26870666 PMCID: PMC4746746 DOI: 10.3233/jnd-150098] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Congenital myasthenic syndromes are a heterogeneous group of genetically determined disorders characterized by impaired neuromuscular transmission. They usually present from birth to childhood and are characterised by exercise induced weakness and fatigability. Genotype-phenotype correlations are difficult. However, in some patients particular phenotypic aspects may point towards a specific genetic defect. The absence of ptosis and ophthalmoparesis in patients with limb-girdle weakness makes the diagnosis of a neuromuscular transmission defect particularly challenging (LG-CMS). This is illustrated by a well-documented case published by Walton in 1956. The diagnosis of LG-CMS is secured by demonstrating a neuromuscular transmission defect with single fibre EMG or repetitive nerve stimulation, in the absence of auto-antibodies. Ultimately, a genetic test is required to identify the underlying cause and assure counselling and optimization of treatment. LG-CMS are inherited in autosomal recessive traits, and are often associated with mutations in DOK7 and GFPT1, and less frequently with mutations in COLQ, ALG2, ALG14 and DPAGT. Genetic characterization of CMS is of the upmost importance when choosing the adequate treatment. Some of the currently used drugs can either ameliorate or aggravate the symptoms depending on the underlying genetic defect. The drug most frequently used for the treatment of CMS is pyridostigmine an acetylcholinesterase inhibitor. However, pyridostigmine is not effective or is even detrimental in DOK7- and COLQ-related LG-CMS, while beta-adrenergic agonists (ephedrine, salbutamol) show some sustained benefit. Standard clinical trials may be difficult, but standardized follow-up of patients and international collaboration may help to improve the standards of care of these conditions.
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Affiliation(s)
- Teresinha Evangelista
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Newcastle University, Newcastle upon Tyne, UK
| | - Mike Hanna
- UCL MRC Centre for Neuromuscular Disease, Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, United Kingdom
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Newcastle University, Newcastle upon Tyne, UK
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49
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Xu C, Ng DT. O-mannosylation: The other glycan player of ER quality control. Semin Cell Dev Biol 2015; 41:129-34. [DOI: 10.1016/j.semcdb.2015.01.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 01/30/2015] [Indexed: 01/07/2023]
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50
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Cabrera-Serrano M, Ghaoui R, Ravenscroft G, Johnsen RD, Davis MR, Corbett A, Reddel S, Sue CM, Liang C, Waddell LB, Kaur S, Lek M, North KN, MacArthur DG, Lamont PJ, Clarke NF, Laing NG. Expanding the phenotype of GMPPB mutations. ACTA ACUST UNITED AC 2015; 138:836-44. [PMID: 25681410 DOI: 10.1093/brain/awv013] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Dystroglycanopathies are a heterogeneous group of diseases with a broad phenotypic spectrum ranging from severe disorders with congenital muscle weakness, eye and brain structural abnormalities and intellectual delay to adult-onset limb-girdle muscular dystrophies without mental retardation. Most frequently the disease onset is congenital or during childhood. The exception is FKRP mutations, in which adult onset is a common presentation. Here we report eight patients from five non-consanguineous families where next generation sequencing identified mutations in the GMPPB gene. Six patients presented as an adult or adolescent-onset limb-girdle muscular dystrophy, one presented with isolated episodes of rhabdomyolysis, and one as a congenital muscular dystrophy. This report expands the phenotypic spectrum of GMPPB mutations to include limb-girdle muscular dystrophies with adult onset with or without intellectual disability, or isolated rhabdomyolysis.
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Affiliation(s)
- Macarena Cabrera-Serrano
- 1 Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia 2 Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Roula Ghaoui
- 3 Institute for Neuroscience and Muscle Research, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia 4 Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW 2006, Australia 5 Department of Neurology, Royal North Shore Hospital, Sydney, Australia
| | - Gianina Ravenscroft
- 1 Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Russell D Johnsen
- 6 Centre for Comparative Genomics, Murdoch University, Perth, Australia
| | - Mark R Davis
- 7 Department of Diagnostic Genomics, Pathwest Laboratory Medicine WA. Perth, WA, Australia
| | - Alastair Corbett
- 8 Department of Neurology, Concord Repatriation Hospital, and Sydney Medical School, Sydney, Australia
| | - Stephen Reddel
- 8 Department of Neurology, Concord Repatriation Hospital, and Sydney Medical School, Sydney, Australia
| | - Carolyn M Sue
- 5 Department of Neurology, Royal North Shore Hospital, Sydney, Australia
| | - Christina Liang
- 5 Department of Neurology, Royal North Shore Hospital, Sydney, Australia
| | - Leigh B Waddell
- 3 Institute for Neuroscience and Muscle Research, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia 4 Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Simranpreet Kaur
- 3 Institute for Neuroscience and Muscle Research, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Monkol Lek
- 3 Institute for Neuroscience and Muscle Research, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia 4 Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW 2006, Australia 9 Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA 10 Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kathryn N North
- 3 Institute for Neuroscience and Muscle Research, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia 11 Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia 12 Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Daniel G MacArthur
- 9 Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA 10 Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Phillipa J Lamont
- 13 Neurogenetic Unit, Department of Neurology, Royal Perth Hospital, Perth, WA, Australia
| | - Nigel F Clarke
- 3 Institute for Neuroscience and Muscle Research, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia 4 Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Nigel G Laing
- 1 Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
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