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Tan WS, Rong E, Dry I, Lillico S, Law A, Digard P, Whitelaw B, Dalziel RG. Validation of Candidate Host Cell Entry Factors for Bovine Herpes Virus Type-1 Based on a Genome-Wide CRISPR Knockout Screen. Viruses 2024; 16:297. [PMID: 38400072 PMCID: PMC10893506 DOI: 10.3390/v16020297] [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: 12/08/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
To identify host factors that affect Bovine Herpes Virus Type 1 (BoHV-1) infection we previously applied a genome wide CRISPR knockout screen targeting all bovine protein coding genes. By doing so we compiled a list of both pro-viral and anti-viral proteins involved in BoHV-1 replication. Here we provide further analysis of those that are potentially involved in viral entry into the host cell. We first generated single cell knockout clones deficient in some of the candidate genes for validation. We provide evidence that Polio Virus Receptor-related protein (PVRL2) serves as a receptor for BoHV-1, mediating more efficient entry than the previously identified Polio Virus Receptor (PVR). By knocking out two enzymes that catalyze HSPG chain elongation, HST2ST1 and GLCE, we further demonstrate the significance of HSPG in BoHV-1 entry. Another intriguing cluster of candidate genes, COG1, COG2 and COG4-7 encode six subunits of the Conserved Oligomeric Golgi (COG) complex. MDBK cells lacking COG6 produced fewer but bigger plaques compared to control cells, suggesting more efficient release of newly produced virions from these COG6 knockout cells, due to impaired HSPG biosynthesis. We further observed that viruses produced by the COG6 knockout cells consist of protein(s) with reduced N-glycosylation, potentially explaining their lower infectivity. To facilitate candidate validation, we also detailed a one-step multiplex CRISPR interference (CRISPRi) system, an orthogonal method to KO that enables quick and simultaneous deployment of three CRISPRs for efficient gene inactivation. Using CRISPR3i, we verified eight candidates that have been implicated in the synthesis of surface heparan sulfate proteoglycans (HSPGs). In summary, our experiments confirmed the two receptors PVR and PVRL2 for BoHV-1 entry into the host cell and other factors that affect this process, likely through the direct or indirect roles they play during HSPG synthesis and glycosylation of viral proteins.
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Affiliation(s)
- Wenfang Spring Tan
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
| | - Enguang Rong
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
| | - Inga Dry
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
| | - Simon Lillico
- Division of Functional Genetics and Development, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK; (S.L.); (B.W.)
- Centre for Tropical Livestock Genetics and Health, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK
| | - Andy Law
- Division of Genetics and Genomics, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK;
| | - Paul Digard
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
| | - Bruce Whitelaw
- Division of Functional Genetics and Development, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK; (S.L.); (B.W.)
- Division of Genetics and Genomics, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK;
| | - Robert G. Dalziel
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
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Zheng Q, Li M, Qiu Y, Yang J, Cao Y. Overexpression of SLC35F2 is a potential prognostic biomarker for lung adenocarcinoma. Heliyon 2024; 10:e23828. [PMID: 38187235 PMCID: PMC10767229 DOI: 10.1016/j.heliyon.2023.e23828] [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: 03/29/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Objective To explore the potential clinical and prognostic significance of Homo sapiens solute carrier family 35 member F2 (SLC35F2) in the context of lung adenocarcinoma (LUAD). Methods The expression pattern of SLC35F2 in LUAD tissues and normal tissues was analyzed in The Cancer Genome Atlas (TCGA) datasets and validated in 12 pairs of fresh clinical LUAD tissues and their corresponding adjacent normal tissues using quantitative real-time PCR (qRT-PCR) and western blotting. Immunohistochemistry (IHC) was used to assess the protein expression of SLC35F2 in 60 paraffin-embedded LUAD tissues, and its associations with clinicopathological parameters were further examined. The prognostic significance of SLC35F2 mRNA expression was also evaluated using the Kaplan-Meier method, and Cox regression models in LUAD patients from the TCGA database. The potential utility of SLC35F2 as an indicator of recurrence or metastasis was explored through the follow-up of selected clinical LUAD cases. Lastly, gene set enrichment analysis (GSEA) was conducted to investigate the underlying biological mechanisms and signaling pathways. Results Bioinformatics analysis utilizing the TCGA database indicated that SLC35F2 mRNA exhibited heightened expression in LUAD tissues when compared to normal tissues. These findings were further substantiated through the examination of 12 pairs of clinical LUAD tissues and their corresponding adjacent normal tissues, employing qRT-PCR and western blotting techniques. IHC results from a cohort of 60 LUAD patients demonstrated an up-regulation of SLC35F2 in 38 out of 60 individuals (63.3 %), which exhibited a significant correlation with tumor size, lymph node metastasis, and clinical stage (all P < 0.05). Both the Kaplan-Meier curve and the Cox proportional hazard analyses indicated a strong association between the up-regulation of SLC35F2 mRNA expression and unfavorable overall survival (OS) in patients with LUAD, as observed in the TCGA datasets (P < 0.05). The follow-up findings from select clinical LUAD cases provided evidence that the expression of SLC35F2 could serve as a dependable biomarker for monitoring the recurrence or metastasis. Additionally, the GSEA highlighted the enrichment of apoptosis, adhesion, small cell lung cancer (SCLC), and p53 signaling pathways in the subgroup of LUAD patients with elevated SLC35F2 expression. Conclusion SLC35F2 exhibited an up-regulated in both mRNA and protein expression, rendering it a valuable independent prognostic indicator for patients diagnosed with LUAD.
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Affiliation(s)
- Qingzhu Zheng
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Mingjie Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Yingkun Qiu
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Jiahao Yang
- Department of Laboratory Medicine, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, 350004, China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
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Sun L, Zhang Y, Li W, Zhang J, Zhang Y. Mucin Glycans: A Target for Cancer Therapy. Molecules 2023; 28:7033. [PMID: 37894512 PMCID: PMC10609567 DOI: 10.3390/molecules28207033] [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: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Mucin glycans are an important component of the mucus barrier and a vital defence against physical and chemical damage as well as pathogens. There are 20 mucins in the human body, which can be classified into secreted mucins and transmembrane mucins according to their distributions. The major difference between them is that secreted mucins do not have transmembrane structural domains, and the expression of each mucin is organ and cell-specific. Under physiological conditions, mucin glycans are involved in the composition of the mucus barrier and thus protect the body from infection and injury. However, abnormal expression of mucin glycans can lead to the occurrence of diseases, especially cancer, through various mechanisms. Therefore, targeting mucin glycans for the diagnosis and treatment of cancer has always been a promising research direction. Here, we first summarize the main types of glycosylation (O-GalNAc glycosylation and N-glycosylation) on mucins and the mechanisms by which abnormal mucin glycans occur. Next, how abnormal mucin glycans contribute to cancer development is described. Finally, we summarize MUC1-based antibodies, vaccines, radio-pharmaceuticals, and CAR-T therapies using the best characterized MUC1 as an example. In this section, we specifically elaborate on the recent new cancer therapy CAR-M, which may bring new hope to cancer patients.
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Affiliation(s)
- Lingbo Sun
- Medical College of Yan'an University, Yan'an University, Yan'an 716000, China
| | - Yuhan Zhang
- Medical College of Yan'an University, Yan'an University, Yan'an 716000, China
| | - Wenyan Li
- Medical College of Yan'an University, Yan'an University, Yan'an 716000, China
| | - Jing Zhang
- Medical College of Yan'an University, Yan'an University, Yan'an 716000, China
| | - Yuecheng Zhang
- Key Laboratory of Analytical Technology and Detection of Yan'an, College of Chemistry and Chemical Engineering, Yan'an University, Yan'an 716000, China
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Baltussen TJ, van Rhijn N, Coolen JP, Dijksterhuis J, Verweij PE, Bromley MJ, Melchers WJ. The C 2H 2 transcription factor SltA is required for germination and hyphal development in Aspergillus fumigatus. mSphere 2023; 8:e0007623. [PMID: 37260230 PMCID: PMC10449517 DOI: 10.1128/msphere.00076-23] [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: 02/09/2023] [Accepted: 03/23/2023] [Indexed: 06/02/2023] Open
Abstract
Germination of inhaled Aspergillus fumigatus conidia is a necessary sequitur for infection. Germination of conidia starts with the breaking of dormancy, which is initiated by an increase of the cellular perimeter in a process termed isotropic growth. This swelling phase is followed by polarized growth, resulting in the formation of a germ tube. The multinucleate tubular cells exhibit tip growth from the hyphae, after which lateral branches emerge to form the mycelial network. The regulatory mechanisms governing conidial germination are not well defined. In this study, we identified a novel role for the transcription factor SltA in the orchestration of germination and hyphal development. Conidia lacking sltA fail to appropriately regulate isotropic growth and begin to swell earlier and subsequently switch to polarized growth faster. Additionally, hyphal development is distorted in a ∆sltA isolate as hyphae are hyper-branching and wider, and show branching at the apical tip. ∆sltA conidia are more tolerant to cell wall stressors on minimal medium compared to the wild-type (WT) strain. A transcriptome analysis of different stages of early growth was carried out to assess the regulatory role of SltA. Null mutants generated for three of the most dysregulated genes showed rapid germ tube emergence. Distinct from the phenotype observed for ∆sltA, conidia from these strains lacked defects in isotropic growth, but switched to polarized growth faster. Here, we characterize and describe several genes in the regulon of SltA, highlighting the complex nature of germination.IMPORTANCEAspergillus fumigatus is the main human fungal pathogen causing aspergillosis. For this fungus, azoles are the most commonly used antifungal drugs for treatment of aspergillosis. However, the prevalence of azole resistance is alarmingly increasing and linked with elevated mortality. Germination of conidia is crucial within its asexual life cycle and plays a critical role during the infection in the human host. Precluding germination could be a promising strategy considering the role of germination in Aspergillus spp. pathogenicity. Here, we identify a novel role for SltA in appropriate maintenance of dormancy, germination, and hyphal development. Three genes in the regulon of SltA were also essential for appropriate germination of conidia. With an expanding knowledge of germination and its different morphotypes, more advances can be made toward potential anti-germination targets for therapy.
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Affiliation(s)
- Tim J.H. Baltussen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Norman van Rhijn
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jordy P.M. Coolen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael J. Bromley
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Willem J.G. Melchers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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5
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Blois L, de Miguel M, Bert P, Girollet N, Ollat N, Rubio B, Segura V, Voss‐Fels KP, Schmid J, Marguerit E. Genetic structure and first genome-wide insights into the adaptation of a wild relative of grapevine, Vitis berlandieri. Evol Appl 2023; 16:1184-1200. [PMID: 37360024 PMCID: PMC10286229 DOI: 10.1111/eva.13566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis, including V. berlandieri. The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of V. berlandieri and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild V. berlandieri plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome-environment association analysis (GEA). De novo long-read whole-genome sequencing was performed on V. berlandieri and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.
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Affiliation(s)
- Louis Blois
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
- Department of Grapevine BreedingGeisenheim UniversityGeisenheimGermany
| | - Marina de Miguel
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Pierre‐François Bert
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Nabil Girollet
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Nathalie Ollat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Bernadette Rubio
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Vincent Segura
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Kai P. Voss‐Fels
- Department of Grapevine BreedingGeisenheim UniversityGeisenheimGermany
| | - Joachim Schmid
- Department of Grapevine BreedingGeisenheim UniversityGeisenheimGermany
| | - Elisa Marguerit
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
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Premageetha GTR, Dhanabalan K, Bose S, Manjunath L, Joseph D, Paz A, Grandfield S, Nayak V, Bredeston LM, Abramson J, Ramaswamy S. Biochemical characterization of a GDP-mannose transporter from Chaetomium thermophilum. PLoS One 2023; 18:e0280975. [PMID: 37079572 PMCID: PMC10118193 DOI: 10.1371/journal.pone.0280975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
Nucleotide Sugar Transporters (NSTs) belong to the SLC35 family (human solute carrier) of membrane transport proteins and are crucial components of the glycosylation machinery. NSTs are localized in the ER and Golgi apparatus membranes, where they accumulate nucleotide sugars from the cytosol for subsequent polysaccharide biosynthesis. Loss of NST function impacts the glycosylation of cell surface molecules. Mutations in NSTs cause several developmental disorders, immune disorders, and increased susceptibility to infection. Atomic resolution structures of three NSTs have provided a blueprint for a detailed molecular interpretation of their biochemical properties. In this work, we have identified, cloned, and expressed 18 members of the SLC35 family from various eukaryotic organisms in Saccharomyces cerevisiae. Out of 18 clones, we determined Vrg4 from Chaetomium thermophilum (CtVrg4) is a GDP-mannose transporter with an enhanced melting point temperature (Tm) of 56.9°C, which increases with the addition of substrates, GMP and GDP-mannose. In addition, we report-for the first time-that the CtVrg4 shows an affinity to bind to phosphatidylinositol lipids.
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Affiliation(s)
- Gowtham Thambra Rajan Premageetha
- Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - KanagaVijayan Dhanabalan
- Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Lavanyaa Manjunath
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Deepthi Joseph
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Aviv Paz
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Samuel Grandfield
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Vinod Nayak
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Luis M. Bredeston
- Departamento de Química Biológica-IQUIFIB, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires-CONICET, Ciudad Autónoma de Buenos Aires, Junín, Argentina
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Subramanian Ramaswamy
- Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
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Gan Y, Wei Z, Liu C, Li G, Feng Y, Deng Y. Solute carrier transporter disease and developmental and epileptic encephalopathy. Front Neurol 2022; 13:1013903. [PMID: 36419532 PMCID: PMC9676364 DOI: 10.3389/fneur.2022.1013903] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/07/2022] [Indexed: 09/14/2023] Open
Abstract
The International League Against Epilepsy officially revised its classification in 2017, which amended "epileptic encephalopathy" to "developmental and epileptic encephalopathy". With the development of genetic testing technology, an increasing number of genes that cause developmental and epileptic encephalopathies are being identified. Among these, solute transporter dysfunction is part of the etiology of developmental and epileptic encephalopathies. Solute carrier transporters play an essential physiological function in the human body, and their dysfunction is associated with various human diseases. Therefore, in-depth studies of developmental and epileptic encephalopathies caused by solute carrier transporter dysfunction can help develop new therapeutic modalities to facilitate the treatment of refractory epilepsy and improve patient prognosis. In this article, the concept of transporter protein disorders is first proposed, and nine developmental and epileptic encephalopathies caused by solute carrier transporter dysfunction are described in detail in terms of pathogenesis, clinical manifestations, ancillary tests, and precise treatment to provide ideas for the precise treatment of epilepsy.
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Affiliation(s)
- Yajing Gan
- Department of Neurology, Epilepsy Center of Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Zihan Wei
- Department of Neurology, Epilepsy Center of Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Chao Liu
- Department of Neurology, Epilepsy Center of Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Guoyan Li
- Department of Neurology, Epilepsy Center of Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yan Feng
- Department of Neurology, Epilepsy Center of Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yanchun Deng
- Department of Neurology, Epilepsy Center of Xijing Hospital, Fourth Military Medical University, Xi'an, China
- Xijing Institute of Epilepsy and Encephalopathy, Xi'an, China
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Delivery of Nucleotide Sugars to the Mammalian Golgi: A Very Well (un)Explained Story. Int J Mol Sci 2022; 23:ijms23158648. [PMID: 35955785 PMCID: PMC9368800 DOI: 10.3390/ijms23158648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022] Open
Abstract
Nucleotide sugars (NSs) serve as substrates for glycosylation reactions. The majority of these compounds are synthesized in the cytoplasm, whereas glycosylation occurs in the endoplasmic reticulum (ER) and Golgi lumens, where catalytic domains of glycosyltransferases (GTs) are located. Therefore, translocation of NS across the organelle membranes is a prerequisite. This process is thought to be mediated by a group of multi-transmembrane proteins from the SLC35 family, i.e., nucleotide sugar transporters (NSTs). Despite many years of research, some uncertainties/inconsistencies related with the mechanisms of NS transport and the substrate specificities of NSTs remain. Here we present a comprehensive review of the NS import into the mammalian Golgi, which consists of three major parts. In the first part, we provide a historical view of the experimental approaches used to study NS transport and evaluate the most important achievements. The second part summarizes various aspects of knowledge concerning NSTs, ranging from subcellular localization up to the pathologies related with their defective function. In the third part, we present the outcomes of our research performed using mammalian cell-based models and discuss its relevance in relation to the general context.
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Paeniclostridium sordellii hemorrhagic toxin targets TMPRSS2 to induce colonic epithelial lesions. Nat Commun 2022; 13:4331. [PMID: 35882856 PMCID: PMC9321280 DOI: 10.1038/s41467-022-31994-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/12/2022] [Indexed: 12/21/2022] Open
Abstract
Hemorrhagic toxin (TcsH) is an important exotoxin produced by Paeniclostridium sordellii, but the exact role of TcsH in the pathogenesis remains unclear, partly due to the lack of knowledge of host receptor(s). Here, we carried out two genome-wide CRISPR/Cas9 screens parallelly with TcsH and identified cell surface fucosylation and TMPRSS2 as host factors contributing to the binding and entry of TcsH. Genetic deletion of either fucosylation biosynthesis enzymes or TMPRSS2 in the cells confers resistance to TcsH intoxication. Interestingly, TMPRSS2 and fucosylated glycans can mediate the binding/entry of TcsH independently, thus serving as redundant receptors. Both TMPRSS2 and fucosylation recognize TcsH through its CROPs domain. By using Tmprss2‒/‒ mice, we show that Tmprss2 is important for TcsH-induced systematic toxicity and colonic epithelial lesions. These findings reveal the importance of TMPRSS2 and surface fucosylation in TcsH actions and further provide insights into host recognition mechanisms for large clostridial toxins. Paeniclostridium sordellii is an opportunistic pathogen that can occur and be fatal in women undergoing abortion or childbirth. The pathogenesis of a hemorrhagic toxin, TcsH, produced by this bacteria, remains unknown. Here, authors carry out genome-wide screens to identify pathologically relevant host factors of TcsH.
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Kot M, Mazurkiewicz E, Wiktor M, Wiertelak W, Mazur AJ, Rahalevich A, Olczak M, Maszczak-Seneczko D. SLC35A2 Deficiency Promotes an Epithelial-to-Mesenchymal Transition-like Phenotype in Madin–Darby Canine Kidney Cells. Cells 2022; 11:cells11152273. [PMID: 35892570 PMCID: PMC9331475 DOI: 10.3390/cells11152273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
In mammalian cells, SLC35A2 delivers UDP–galactose for galactosylation reactions that take place predominantly in the Golgi lumen. Mutations in the corresponding gene cause a subtype of a congenital disorder of glycosylation (SLC35A2-CDG). Although more and more patients are diagnosed with SLC35A2-CDG, the link between defective galactosylation and disease symptoms is not fully understood. According to a number of reports, impaired glycosylation may trigger the process of epithelial-to-mesenchymal transition (EMT). We therefore examined whether the loss of SLC35A2 activity would promote EMT in a non-malignant epithelial cell line. For this purpose, we knocked out the SLC35A2 gene in Madin–Darby canine kidney (MDCK) cells. The resulting clones adopted an elongated, spindle-shaped morphology and showed impaired cell–cell adhesion. Using qPCR and western blotting, we revealed down-regulation of E-cadherin in the knockouts, while the fibronectin and vimentin levels were elevated. Moreover, the knockout cells displayed reorganization of vimentin intermediate filaments and altered subcellular distribution of a vimentin-binding protein, formiminotransferase cyclodeaminase (FTCD). Furthermore, depletion of SLC35A2 triggered Golgi compaction. Finally, the SLC35A2 knockouts displayed increased motility and invasiveness. In conclusion, SLC35A2-deficient MDCK cells showed several hallmarks of EMT. Our findings point to a novel role for SLC35A2 as a gatekeeper of the epithelial phenotype.
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Affiliation(s)
- Magdalena Kot
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.K.); (E.M.); (A.J.M.)
| | - Ewa Mazurkiewicz
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.K.); (E.M.); (A.J.M.)
| | - Maciej Wiktor
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
| | - Wojciech Wiertelak
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
| | - Antonina Joanna Mazur
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.K.); (E.M.); (A.J.M.)
| | - Andrei Rahalevich
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
| | - Mariusz Olczak
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
| | - Dorota Maszczak-Seneczko
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
- Correspondence:
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11
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Colville C, Alcaraz AJ, Green D, Park B, Xia J, Soufan O, Hruṧka P, Potěšil D, Zdráhal Z, Crump D, Basu N, Hogan N, Hecker M. Characterizing toxicity pathways of fluoxetine to predict adverse outcomes in adult fathead minnows (Pimephales promelas). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152747. [PMID: 35026279 DOI: 10.1016/j.scitotenv.2021.152747] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/24/2021] [Indexed: 05/17/2023]
Abstract
Current ecotoxicity testing programs are impeded as they predominantly rely on slow and expensive animal tests measuring adverse outcomes. Therefore, new approach methodologies (NAMs) increasingly involve short-term mechanistic assays that employ molecular endpoints to predict adverse outcomes of regulatory relevance. This study aimed to elucidate the application of NAMs in adult fathead minnows using fluoxetine (FLX) as a model compound. Fish were exposed to three FLX concentrations (measured: 2.42, 10.7, and 56.7 μgL-1) and a control. After 96 h, molecular toxicity signatures were characterized using proteomics and transcriptomics analyses in livers and brains of a sub-set of fish. The remaining fish were sampled at 21 days and assessed for liver histopathology and morphometric measurements. Fecundity was monitored throughout the study. In the livers, 56.7 μgL-1 FLX caused enrichment of PPAR signaling in the proteome and fatty acid-related pathways in the transcriptome, potential upstream responses that led to lipid-type vacuolation of hepatocytes, observed via histopathology. Upregulated genes in the brain suggested alterations in serotonin-related signaling processes and reproductive behaviour, which may explain the observed significant decrease in fecundity. While the relationships between molecular responses and adverse outcomes remain complex, this research provided important insights into the mechanistic toxicity of FLX.
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Affiliation(s)
- Carly Colville
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Alper James Alcaraz
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Derek Green
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Bradley Park
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Othman Soufan
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada; Computer Science Department, St. Francis Xavier University, Antigonish, NS B2G 2W5, Canada
| | - Pavel Hruṧka
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic; RECETOX, Masaryk University, Brno 625 00, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, ON K1A 0H3, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Natacha Hogan
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 5C8, Canada.
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12
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Jiang T, Yang J, Yang H, Chen W, Ji K, Xu Y, Yu L. SLC35B4 Stabilizes c-MYC Protein by O-GlcNAcylation in HCC. Front Pharmacol 2022; 13:851089. [PMID: 35308201 PMCID: PMC8924407 DOI: 10.3389/fphar.2022.851089] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 01/15/2023] Open
Abstract
UDP-GlcNAc is a sugar substrate necessary for the O-GlcNAcylation of proteins. SLC35B4 is one of the nucleotide sugar transporters that transport UDP-GlcNAc and UDP-xylose into the endoplasmic reticulum and Golgi apparatus for glycosylation. The roles of SLC35B4 in hepatocellular carcinoma (HCC) tumorigenesis remain unknown. We find that the expression levels of SLC35B4 are higher in HCC tissues than adjacent non-tumor tissues. SLC35B4 is important for the proliferation and tumorigenesis of HCC cells. Mechanistically, SLC35B4 is important for the O-GlcNAc modification of c-Myc and thus the stabilization of c-Myc, which is required for HCC tumorigenesis. Therefore, SLC35B4 is a promising therapeutic target for treating HCC.
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Affiliation(s)
- Tao Jiang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jinghong Yang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Huohong Yang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wancheng Chen
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Kaiyuan Ji
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yang Xu
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Cardiology, Cardiovascular Key Lab of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Lili Yu
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
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13
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Gao Y, Xiong X, Wang H, Wang J, Bi Y, Yan Y, Cao Z, Li D, Song F. Ero1-Pdi1 module-catalysed dimerization of a nucleotide sugar transporter, FonNst2, regulates virulence of Fusarium oxysporum on watermelon. Environ Microbiol 2021; 24:1200-1220. [PMID: 34587346 DOI: 10.1111/1462-2920.15789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/23/2021] [Indexed: 11/29/2022]
Abstract
Fusarium oxysporum f. sp. niveum (Fon) is a soil-borne fungus causing vascular Fusarium wilt on watermelon; however, the molecular network regulating Fon virulence remains to be elucidated. Here, we report the function and mechanism of nucleotide sugar transporters (Nsts) in Fon. Fon genome harbours nine FonNst genes with distinct functions in vegetative growth, asexual production, cell wall stress response and virulence. FonNst2 and FonNst3 are required for full virulence of Fon on watermelon and FonNst2 is mainly involved in fungal colonization of the plant tissues. FonNst2 and FonNst3 form homo- or hetero-dimers but function independently in Fon virulence. FonNst2, which has UDP-galactose transporter activity in yeast, interacts with FonEro1 and FonPdi1, both of which are required for full virulence of Fon. FonNst2, FonPdi1 and FonEro1 target to endoplasmic reticulum (ER) and are essential for ER homeostasis and function. FonEro1-FonPdi1 module catalyses the dimerization of FonNst2, which is critical for Fon virulence. Undimerized FonNst2 is unstable and degraded via ER-associated protein degradation in vivo. These data demonstrate that FonEro1-FonPdi1 module-catalysed dimerization of FonNst2 is critical for Fon virulence on watermelon and provide new insights into the regulation of virulence in plant fungal pathogens via disulfide bond formation of key pathogenicity factors.
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Affiliation(s)
- Yizhou Gao
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaohui Xiong
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Hui Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiajing Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yan Bi
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yuqing Yan
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhongye Cao
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Dayong Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fengming Song
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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14
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Li D, Mukhopadhyay S. A three-pocket model for substrate coordination and selectivity by the nucleotide sugar transporters SLC35A1 and SLC35A2. J Biol Chem 2021; 297:101069. [PMID: 34384782 PMCID: PMC8411240 DOI: 10.1016/j.jbc.2021.101069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 10/25/2022] Open
Abstract
The CMP-sialic acid transporter SLC35A1 and UDP-galactose transporter SLC35A2 are two well-characterized nucleotide sugar transporters with distinctive substrate specificities. Mutations in either induce congenital disorders of glycosylation. Despite the biomedical relevance, mechanisms of substrate specificity are unclear. To address this critical issue, we utilized a structure-guided mutagenesis strategy and assayed a series of SLC35A2 and SLC35A1 mutants using a rescue approach. Our results suggest that three pockets in the central cavity of each transporter provide substrate specificity. The pockets comprise (1) nucleobase (residues E52, K55, and Y214 of SLC35A1; E75, K78, N235, and G239 of SLC35A2); (2) middle (residues Q101, N102, and T260 of SLC35A1; Q125, N126, Q129, Y130, and Q278 of SLC35A2); and (3) sugar (residues K124, T128, S188, and K272 of SLC35A1; K148, T152, S213, and K297 of SLC35A2) pockets. Within these pockets, two components appear to be especially critical for substrate specificity. Y214 (for SLC35A1) and G239 (for SLC35A2) in the nucleobase pocket appear to discriminate cytosine from uracil. Furthermore, Q129 and Q278 of SLC35A2 in the middle pocket appear to interact specifically with the β-phosphate of UDP while the corresponding A105 and A253 residues in SLC35A1 do not interact with CMP, which lacks a β-phosphate. Overall, our findings contribute to a molecular understanding of substrate specificity and coordination in SLC35A1 and SLC35A2, and have important implications for the understanding and treatment of diseases associated with mutations or dysregulations of these two transporters.
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Affiliation(s)
- Danyang Li
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX 78712
| | - Somshuvra Mukhopadhyay
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX 78712.
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15
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Wiktor M, Wiertelak W, Maszczak-Seneczko D, Balwierz PJ, Szulc B, Olczak M. Identification of novel potential interaction partners of UDP-galactose (SLC35A2), UDP-N-acetylglucosamine (SLC35A3) and an orphan (SLC35A4) nucleotide sugar transporters. J Proteomics 2021; 249:104321. [PMID: 34242836 DOI: 10.1016/j.jprot.2021.104321] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Nucleotide sugar transporters (NSTs) are ER and Golgi-resident members of the solute carrier 35 (SLC35) family which supply substrates for glycosylation by exchanging lumenal nucleotide monophosphates for cytosolic nucleotide sugars. Defective NSTs have been associated with congenital disorders of glycosylation (CDG), however, molecular basis of many types of CDG remains poorly characterized. To better understand the biology of NSTs, we identified potential interaction partners of UDP-galactose transporter (SLC35A2), UDP-N-acetylglucosamine transporter (SLC35A3) and an orphan nucleotide sugar transporter SLC35A4 of to date unassigned specificity. For this purpose, each of the SLC35A2-A4 proteins was used as a bait in four independent pull-down experiments and the identity of the immunoprecipitated material was discovered using MS techniques. From the candidate list obtained, we selected a few for which the interaction was confirmed in vitro using the NanoBiT system, a split luciferase-based luminescent technique. NSTs have been shown to interact with two ATPases (ATP2A2, ATP2C1), Golgi pH regulator B (GPR89B) and calcium channel (TMCO1), which may reflect the regulation of glycosylation by ion homeostasis, and with basigin (BSG). Our findings provide a starting point for the NST interaction network discovery in order to better understand how glycosylation is regulated and linked to other cellular processes. SIGNIFICANCE: Despite the facts that nucleotide sugar transporters are a key component of the protein glycosylation machinery, and deficiencies in their activity underlie serious metabolic diseases, biology, function and regulation of these essential proteins remain enigmatic. In this study we have advanced the field by identifying sets of new potential interaction partners for UDP-galactose transporter (SLC35A2), UDP-N-acetylglucosamine transporter (SLC35A3) and an orphan transporter SLC35A4 of yet undefined role. Several of these new interactions were additionally confirmed in vitro using the NanoBiT system, a split luciferase complementation assay. This work is also significant in that it addresses the overall challenge of discovering membrane protein interaction partners by a detailed comparison of 4 different co-immunoprecipitation strategies and by custom sample preparation and data processing workflows.
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Affiliation(s)
- Maciej Wiktor
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
| | - Wojciech Wiertelak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
| | | | - Piotr Jan Balwierz
- Computational Regulatory Genomics, MRC-London Institute of Medical Sciences, London, United Kingdom.
| | - Bożena Szulc
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
| | - Mariusz Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
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16
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Inhibition of CMP-sialic acid transport by endogenous 5-methyl CMP. PLoS One 2021; 16:e0249905. [PMID: 34081697 PMCID: PMC8174729 DOI: 10.1371/journal.pone.0249905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/26/2021] [Indexed: 12/03/2022] Open
Abstract
Nucleotide-sugar transporters (NSTs) transport nucleotide-sugar conjugates into the Golgi lumen where they are then used in the synthesis of glycans. We previously reported crystal structures of a mammalian NST, the CMP-sialic acid transporter (CST) (Ahuja and Whorton 2019). These structures elucidated many aspects of substrate recognition, selectivity, and transport; however, one fundamental unaddressed question is how the transport activity of NSTs might be physiologically regulated as a means to produce the vast diversity of observed glycan structures. Here, we describe the discovery that an endogenous methylated form of cytidine monophosphate (m5CMP) binds and inhibits CST. The presence of m5CMP in cells results from the degradation of RNA that has had its cytosine bases post-transcriptionally methylated through epigenetic processes. Therefore, this work not only demonstrates that m5CMP represents a novel physiological regulator of CST, but it also establishes a link between epigenetic control of gene expression and regulation of glycosylation.
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17
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The promiscuous binding pocket of SLC35A1 ensures redundant transport of CDP-ribitol to the Golgi. J Biol Chem 2021; 296:100789. [PMID: 34015330 PMCID: PMC8192872 DOI: 10.1016/j.jbc.2021.100789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 01/23/2023] Open
Abstract
The glycoprotein α-dystroglycan helps to link the intracellular cytoskeleton to the extracellular matrix. A unique glycan structure attached to this protein is required for its interaction with extracellular matrix proteins such as laminin. Up to now, this is the only mammalian glycan known to contain ribitol phosphate groups. Enzymes in the Golgi apparatus use CDP-ribitol to incorporate ribitol phosphate into the glycan chain of α-dystroglycan. Since CDP-ribitol is synthesized in the cytoplasm, we hypothesized that an unknown transporter must be required for its import into the Golgi apparatus. We discovered that CDP-ribitol transport relies on the CMP-sialic acid transporter SLC35A1 and the transporter SLC35A4 in a redundant manner. These two transporters are closely related, but bulky residues in the predicted binding pocket of SLC35A4 limit its size. We hypothesized that the large binding pocket SLC35A1 might accommodate the bulky CMP-sialic acid and the smaller CDP-ribitol, whereas SLC35A4 might only accept CDP-ribitol. To test this, we expressed SLC35A1 with mutations in its binding pocket in SLC35A1 KO cell lines. When we restricted the binding site of SLC35A1 by introducing the bulky residues present in SLC35A4, the mutant transporter was unable to support sialylation of proteins in cells but still supported ribitol phosphorylation. This demonstrates that the size of the binding pocket determines the substrate specificity of SLC35A1, allowing a variety of cytosine nucleotide conjugates to be transported. The redundancy with SLC35A4 also explains why patients with SLC35A1 mutations do not show symptoms of α-dystroglycan deficiency.
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18
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The Lst Sialyltransferase of Neisseria gonorrhoeae Can Transfer Keto-Deoxyoctanoate as the Terminal Sugar of Lipooligosaccharide: a Glyco-Achilles Heel That Provides a New Strategy for Vaccines to Prevent Gonorrhea. mBio 2021; 12:mBio.03666-20. [PMID: 33758087 PMCID: PMC8092323 DOI: 10.1128/mbio.03666-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The lipooligosaccharide (LOS) of Neisseria gonorrhoeae plays key roles in pathogenesis and is composed of multiple possible glycoforms. These glycoforms are generated by the process of phase variation and by differences in the glycosyltransferase gene content of particular strains. LOS glycoforms of N. gonorrhoeae can be terminated with an N-acetylneuraminic acid (Neu5Ac), which imparts resistance to the bactericidal activity of serum. However, N. gonorrhoeae cannot synthesize the CMP-Neu5Ac required for LOS biosynthesis and must acquire it from the host. In contrast, Neisseria meningitidis can synthesize endogenous CMP-Neu5Ac, the donor molecule for Neu5Ac, which is a component of some meningococcal capsule structures. Both species have an almost identical LOS sialyltransferase, Lst, that transfers Neu5Ac from CMP-Neu5Ac to the terminus of LOS. Lst is homologous to the LsgB sialyltransferase of nontypeable Haemophilus influenzae (NTHi). Studies in NTHi have demonstrated that LsgB can transfer keto-deoxyoctanoate (KDO) from CMP-KDO to the terminus of LOS in place of Neu5Ac. Here, we show that Lst can also transfer KDO to LOS in place of Neu5Ac in both N. gonorrhoeae and N. meningitidis Consistent with access to the pool of CMP-KDO in the cytoplasm, we present data indicating that Lst is localized in the cytoplasm. Lst has previously been reported to be localized on the outer membrane. We also demonstrate that KDO is expressed as a terminal LOS structure in vivo in samples from infected women and further show that the anti-KDO monoclonal antibody 6E4 can mediate opsonophagocytic killing of N. gonorrhoeae Taken together, these studies indicate that KDO expressed on gonococcal LOS represents a new antigen for the development of vaccines against gonorrhea.IMPORTANCE The emergence of multidrug-resistant N. gonorrhoeae strains that are resistant to available antimicrobials is a current health emergency, and no vaccine is available to prevent gonococcal infection. Lipooligosaccharide (LOS) is one of the major virulence factors of N. gonorrhoeae The sialic acid N-acetylneuraminic acid (Neu5Ac) is present as the terminal glycan on LOS in N. gonorrhoeae In this study, we made an unexpected discovery that KDO can be incorporated as the terminal glycan on LOS of N. gonorrhoeae by the alpha-2,3-sialyltransferase Lst. We showed that N. gonorrhoeae express KDO on LOS in vivo and that the KDO-specific monoclonal antibody 6E4 can direct opsonophagocytic killing of N. gonorrhoeae These data support further development of KDO-LOS structures as vaccine antigens for the prevention of infection by N. gonorrhoeae.
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Bonduelle T, Hartlieb T, Baldassari S, Sim NS, Kim SH, Kang HC, Kobow K, Coras R, Chipaux M, Dorfmüller G, Adle-Biassette H, Aronica E, Lee JH, Blumcke I, Baulac S. Frequent SLC35A2 brain mosaicism in mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE). Acta Neuropathol Commun 2021; 9:3. [PMID: 33407896 PMCID: PMC7788938 DOI: 10.1186/s40478-020-01085-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Focal malformations of cortical development (MCD) are linked to somatic brain mutations occurring during neurodevelopment. Mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE) is a newly recognized clinico-pathological entity associated with pediatric drug-resistant focal epilepsy, and amenable to neurosurgical treatment. MOGHE is histopathologically characterized by clusters of increased oligodendroglial cell densities, patchy zones of hypomyelination, and heterotopic neurons in the white matter. The molecular etiology of MOGHE remained unknown so far. We hypothesized a contribution of mosaic brain variants and performed deep targeted gene sequencing on 20 surgical MOGHE brain samples from a single-center cohort of pediatric patients. We identified somatic pathogenic SLC35A2 variants in 9/20 (45%) patients with mosaic rates ranging from 7 to 52%. SLC35A2 encodes a UDP-galactose transporter, previously implicated in other malformations of cortical development (MCD) and a rare type of congenital disorder of glycosylation. To further clarify the histological features of SLC35A2-brain tissues, we then collected 17 samples with pathogenic SLC35A2 variants from a multicenter cohort of MCD cases. Histopathological reassessment including anti-Olig2 staining confirmed a MOGHE diagnosis in all cases. Analysis by droplet digital PCR of pools of microdissected cells from one MOGHE tissue revealed a variant enrichment in clustered oligodendroglial cells and heterotopic neurons. Through an international consortium, we assembled an unprecedented series of 26 SLC35A2-MOGHE cases providing evidence that mosaic SLC35A2 variants, likely occurred in a neuroglial progenitor cell during brain development, are a genetic marker for MOGHE.
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20
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Novel Insights into Selected Disease-Causing Mutations within the SLC35A1 Gene Encoding the CMP-Sialic Acid Transporter. Int J Mol Sci 2020; 22:ijms22010304. [PMID: 33396746 PMCID: PMC7795627 DOI: 10.3390/ijms22010304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/13/2020] [Accepted: 12/24/2020] [Indexed: 02/05/2023] Open
Abstract
Congenital disorders of glycosylation (CDG) are a group of rare genetic and metabolic diseases caused by alterations in glycosylation pathways. Five patients bearing CDG-causing mutations in the SLC35A1 gene encoding the CMP-sialic acid transporter (CST) have been reported to date. In this study we examined how specific mutations in the SLC35A1 gene affect the protein’s properties in two previously described SLC35A1-CDG cases: one caused by a substitution (Q101H) and another involving a compound heterozygous mutation (T156R/E196K). The effects of single mutations and the combination of T156R and E196K mutations on the CST’s functionality was examined separately in CST-deficient HEK293T cells. As shown by microscopic studies, none of the CDG-causing mutations affected the protein’s proper localization in the Golgi apparatus. Cellular glycophenotypes were characterized using lectins, structural assignment of N- and O-glycans and analysis of glycolipids. Single Q101H, T156R and E196K mutants were able to partially restore sialylation in CST-deficient cells, and the deleterious effect of a single T156R or E196K mutation on the CST functionality was strongly enhanced upon their combination. We also revealed differences in the ability of CST variants to form dimers. The results of this study improve our understanding of the molecular background of SLC35A1-CDG cases.
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21
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Haouari W, Dubail J, Lounis-Ouaras S, Prada P, Bennani R, Roseau C, Huber C, Afenjar A, Colin E, Vuillaumier-Barrot S, Seta N, Foulquier F, Poüs C, Cormier-Daire V, Bruneel A. Serum bikunin isoforms in congenital disorders of glycosylation and linkeropathies. J Inherit Metab Dis 2020; 43:1349-1359. [PMID: 32700771 DOI: 10.1002/jimd.12291] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022]
Abstract
Bikunin (Bkn) isoforms are serum chondroitin sulfate (CS) proteoglycans synthesized by the liver. They include two light forms, that is, the Bkn core protein and the Bkn linked to the CS chain (urinary trypsin inhibitor [UTI]), and two heavy forms, that is, pro-α-trypsin inhibitor and inter-α-trypsin inhibitor, corresponding to UTI esterified by one or two heavy chains glycoproteins, respectively. We previously showed that the Western-blot analysis of the light forms could allow the fast and easy detection of patients with linkeropathy, deficient in enzymes involved in the synthesis of the initial common tetrasaccharide linker of glycosaminoglycans. Here, we analyzed all serum Bkn isoforms in a context of congenital disorders of glycosylation (CDG) and showed very specific abnormal patterns suggesting potential interests for their screening and diagnosis. In particular, genetic deficiencies in V-ATPase (ATP6V0A2-CDG, CCDC115-CDG, ATP6AP1-CDG), in Golgi manganese homeostasis (TMEM165-CDG) and in the N-acetyl-glucosamine Golgi transport (SLC35A3-CDG) all share specific abnormal Bkn patterns. Furthermore, for each studied linkeropathy, we show that the light abnormal Bkn could be further in-depth characterized by two-dimensional electrophoresis. Moreover, besides being interesting as a specific biomarker of both CDG and linkeropathies, Bkn isoforms' analyses can provide new insights into the pathophysiology of the aforementioned diseases.
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Affiliation(s)
- Walid Haouari
- INSERM UMR1193, Université Paris-Saclay, Châtenay-Malabry, France
| | - Johanne Dubail
- Department of Clinical Genetics and Reference Centre for Constitutional Bone Diseases, INSERM U1163, Université de Paris, Imagine Institute, Necker-Enfants Malades Hospital, AP-HP, Paris, France
| | - Samra Lounis-Ouaras
- INSERM UMR1193, Université Paris-Saclay, Châtenay-Malabry, France
- AP-HP, Biochimie-Hormonologie, Hôpital Antoine Béclère, Clamart, France
| | - Pierre Prada
- AP-HP, Biochimie Métabolique et Cellulaire, Hôpital Bichat-Claude Bernard, Paris, France
| | - Rizk Bennani
- AP-HP, Biochimie Métabolique et Cellulaire, Hôpital Bichat-Claude Bernard, Paris, France
| | - Charles Roseau
- INSERM UMR1193, Université Paris-Saclay, Châtenay-Malabry, France
| | - Céline Huber
- Department of Clinical Genetics and Reference Centre for Constitutional Bone Diseases, INSERM U1163, Université de Paris, Imagine Institute, Necker-Enfants Malades Hospital, AP-HP, Paris, France
| | - Alexandra Afenjar
- Département de Génétique et Embryologie Médicale, Sorbonne Universités, Centre de Référence Malformations et Maladies Congénitales du Cervelet et Déficiences Intellectuelles de Causes Rares, Hôpital Trousseau, AP-HP, Paris, France
| | - Estelle Colin
- Department of Biochemistry and Genetics, University Hospital, Angers, France
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers, France
| | | | - Nathalie Seta
- AP-HP, Biochimie Métabolique et Cellulaire, Hôpital Bichat-Claude Bernard, Paris, France
- Université de Paris, Paris, France
| | - François Foulquier
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Christian Poüs
- INSERM UMR1193, Université Paris-Saclay, Châtenay-Malabry, France
- AP-HP, Biochimie-Hormonologie, Hôpital Antoine Béclère, Clamart, France
| | - Valérie Cormier-Daire
- Department of Clinical Genetics and Reference Centre for Constitutional Bone Diseases, INSERM U1163, Université de Paris, Imagine Institute, Necker-Enfants Malades Hospital, AP-HP, Paris, France
| | - Arnaud Bruneel
- INSERM UMR1193, Université Paris-Saclay, Châtenay-Malabry, France
- AP-HP, Biochimie Métabolique et Cellulaire, Hôpital Bichat-Claude Bernard, Paris, France
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22
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Ma C, Takeuchi H, Hao H, Yonekawa C, Nakajima K, Nagae M, Okajima T, Haltiwanger RS, Kizuka Y. Differential Labeling of Glycoproteins with Alkynyl Fucose Analogs. Int J Mol Sci 2020; 21:ijms21176007. [PMID: 32825463 PMCID: PMC7503990 DOI: 10.3390/ijms21176007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022] Open
Abstract
Fucosylated glycans critically regulate the physiological functions of proteins and cells. Alterations in levels of fucosylated glycans are associated with various diseases. For detection and functional modulation of fucosylated glycans, chemical biology approaches using fucose (Fuc) analogs are useful. However, little is known about how efficiently each unnatural Fuc analog is utilized by enzymes in the biosynthetic pathway of fucosylated glycans. We show here that three clickable Fuc analogs with similar but distinct structures labeled cellular glycans with different efficiency and protein specificity. For instance, 6-alkynyl (Alk)-Fuc modified O-Fuc glycans much more efficiently than 7-Alk-Fuc. The level of GDP-6-Alk-Fuc produced in cells was also higher than that of GDP-7-Alk-Fuc. Comprehensive in vitro fucosyltransferase assays revealed that 7-Alk-Fuc is commonly tolerated by most fucosyltransferases. Surprisingly, both protein O-fucosyltransferases (POFUTs) could transfer all Fuc analogs in vitro, likely because POFUT structures have a larger space around their Fuc binding sites. These findings demonstrate that labeling and detection of fucosylated glycans with Fuc analogs depend on multiple cellular steps, including conversion to GDP form, transport into the ER or Golgi, and utilization by each fucosyltransferase, providing insights into design of novel sugar analogs for specific detection of target glycans or inhibition of their functions.
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Affiliation(s)
- Chenyu Ma
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8550, Japan; (C.M.); (H.T.); (T.O.)
| | - Hideyuki Takeuchi
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8550, Japan; (C.M.); (H.T.); (T.O.)
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Huilin Hao
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (H.H.); (R.S.H.)
| | - Chizuko Yonekawa
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan;
| | - Kazuki Nakajima
- Center for Research Promotion and Support, Fujita Health University, Toyoake 470-1192, Japan;
| | - Masamichi Nagae
- Department of Molecular Immunology, Research Institute for Microbial Disease, Osaka University, Suita 565-0871, Japan;
- Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan
| | - Tetsuya Okajima
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8550, Japan; (C.M.); (H.T.); (T.O.)
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Robert S. Haltiwanger
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (H.H.); (R.S.H.)
| | - Yasuhiko Kizuka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan;
- Institute for Glyco-Core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
- Correspondence: ; Tel.: +81-58-293-3356
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23
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Kotidis P, Kontoravdi C. Harnessing the potential of artificial neural networks for predicting protein glycosylation. Metab Eng Commun 2020; 10:e00131. [PMID: 32489858 PMCID: PMC7256630 DOI: 10.1016/j.mec.2020.e00131] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/16/2022] Open
Abstract
Kinetic models offer incomparable insight on cellular mechanisms controlling protein glycosylation. However, their ability to reproduce site-specific glycoform distributions depends on accurate estimation of a large number of protein-specific kinetic parameters and prior knowledge of enzyme and transport protein levels in the Golgi membrane. Herein we propose an artificial neural network (ANN) for protein glycosylation and apply this to four recombinant glycoproteins produced in Chinese hamster ovary (CHO) cells, two monoclonal antibodies and two fusion proteins. We demonstrate that the ANN model accurately predicts site-specific glycoform distributions of up to eighteen glycan species with an average absolute error of 1.1%, correctly reproducing the effect of metabolic perturbations as part of a hybrid, kinetic/ANN, glycosylation model (HyGlycoM), as well as the impact of manganese supplementation and glycosyltransferase knock out experiments as a stand-alone machine learning algorithm. These results showcase the potential of machine learning and hybrid approaches for rapidly developing performance-driven models of protein glycosylation.
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24
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Ukaegbu OI, DeMeester KE, Liang H, Brown AR, Jones ZS, Grimes CL. Utility of bacterial peptidoglycan recycling enzymes in the chemoenzymatic synthesis of valuable UDP sugar substrates. Methods Enzymol 2020; 638:1-26. [PMID: 32416908 DOI: 10.1016/bs.mie.2020.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Uridine diphosphate (UDP) sugars are essential precursors for glycosylation reactions in all forms of life. Reactions that transfer the carbohydrate from the UDP donor are catalyzed by glycosyltransferases (Gtfs). While the stereochemistry and negative physiological charge of UDP-sugars are essential for their biochemical function in the cell, these characteristics make them challenging molecules to synthesize and purify on scale in the laboratory. This chapter focuses on the utilization of a chemoenzymatic synthesis of muramyl UDP-sugars, key building blocks in the bacterial cell peptidoglycan. A scalable strategy to obtain UDP-N-acetyl muramic acid derivatives (UDP-NAM), the first committed intermediate used solely in peptidoglycan biosynthesis, is described herein. This methodology utilizes two enzymes involving the cell wall recycling enzymes MurNAc/GlcNAc anomeric kinase (AmgK) and NAM α-1-phosphate uridylyl transferase (MurU), respectively. The promiscuity of these enzymes allows for the unique chemical functionality to be embedded in bacterial peptidoglycan both in vitro and in whole bacterial cells for subsequent structural and functional studies of this important biopolymer.
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Affiliation(s)
- Ophelia I Ukaegbu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Kristen E DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Ashley R Brown
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Zachary S Jones
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States.
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25
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Cahill J, Ahuja S, Whorton MR. In vitro Measurement of CMP-Sialic Acid Transporter Activity in Reconstituted Proteoliposomes. Bio Protoc 2020; 10:e3551. [PMID: 33659525 DOI: 10.21769/bioprotoc.3551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/13/2020] [Accepted: 02/19/2020] [Indexed: 01/09/2023] Open
Abstract
Nucleotide-sugar transporters (NSTs) facilitate eukaryotic cellular glycosylation by transporting nucleotide-sugar conjugates into the Golgi lumen and endoplasmic reticulum for use by glycosyltransferases, while also transferring nucleotide monophosphate byproducts to the cytoplasm. Mutations in this family of proteins can cause a number of significant cellular pathologies, and wild type members can act as virulence factors for many parasites and fungi. Here, we describe an in vitro assay to measure the transport activity of the CMP-sialic acid transporter (CST), one of seven NSTs found in mammals. While in vitro transport assays have been previously described for CST, these studies failed to account for the fact that 1) commercially available stocks of CMP-sialic acid (CMP-Sia) are composed of ~10% of the higher-affinity CMP and 2) CMP-Sia is hydrolyzed into CMP and sialic acid in aqueous solutions. Herein we describe a method for treating CMP-Sia with a nonselective phosphatase, Antarctic phosphatase, to convert all free CMP to cytidine. This allows us to accurately measure substrate affinities and transport kinetics for purified CST reconstituted into proteoliposomes.
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Affiliation(s)
- James Cahill
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, USA
| | - Shivani Ahuja
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, USA
| | - Matthew R Whorton
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, USA
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26
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Zhang W, Tang X, Yang Y, Zhang X, Zhang X. Elevated pCO 2 Level Affects the Extracellular Polymer Metabolism of Phaeodactylum tricornutum. Front Microbiol 2020; 11:339. [PMID: 32194534 PMCID: PMC7064563 DOI: 10.3389/fmicb.2020.00339] [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: 11/07/2019] [Accepted: 02/17/2020] [Indexed: 01/08/2023] Open
Abstract
Extracellular polymeric substances (EPS) play an important role in diatom physiology and carbon biogeochemical cycling in marine ecosystems. Both the composition and yield of EPS in diatom cells can vary with environmental changes. However, information on intracellular pathways and controls of both biochemical and genetic of EPS is limited. Further, how such changes would affect their critical ecological roles in marine systems is also unclear. Here, we evaluated the physiological characteristics, EPS yields, EPS compositions, and gene expression levels of Phaeodactylum tricornutum under elevated pCO2 levels. Genes and pathways related to EPS metabolism in P. tricornutum were identified. Carbohydrate yields in different EPS fractions increased with elevated pCO2 exposure. Although the proportions of monosaccharide sugars among total sugars did not change, higher abundances of uronic acid were observed under high pCO2 conditions, suggesting the alterations of EPS composition. Elevated pCO2 increased PSII light energy conversion efficiency and carbon sequestration efficiency. The up-regulation of most genes involved in carbon fixation pathways led to increased growth and EPS release. RNA-Seq analysis revealed a number of genes and divergent alleles related to EPS production that were up-regulated by elevated pCO2 levels. Nucleotide diphosphate (NDP)-sugar activation and accelerated glycosylation could be responsible for more EPS responding to environmental signals. Further, NDP-sugar transporters exhibited increased expression levels, suggesting roles in EPS over-production. Overall, these results provide critical data for understanding the mechanisms of EPS production in diatoms and evaluating the metabolic plasticity of these organisms in response to environmental changes.
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Affiliation(s)
- Wei Zhang
- Department of Marine Ecology, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuexi Tang
- Department of Marine Ecology, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory of Oceanology for Marine Science and Technology, Qingdao, China
| | - Yingying Yang
- Department of Marine Ecology, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xin Zhang
- Department of Marine Ecology, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinxin Zhang
- Department of Marine Ecology, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory of Oceanology for Marine Science and Technology, Qingdao, China
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27
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Saeui CT, Cho KC, Dharmarha V, Nairn AV, Galizzi M, Shah SR, Gowda P, Park M, Austin M, Clarke A, Cai E, Buettner MJ, Ariss R, Moremen KW, Zhang H, Yarema KJ. Cell Line-, Protein-, and Sialoglycosite-Specific Control of Flux-Based Sialylation in Human Breast Cells: Implications for Cancer Progression. Front Chem 2020; 8:13. [PMID: 32117864 PMCID: PMC7013041 DOI: 10.3389/fchem.2020.00013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
Sialylation, a post-translational modification that impacts the structure, activity, and longevity of glycoproteins has been thought to be controlled primarily by the expression of sialyltransferases (STs). In this report we explore the complementary impact of metabolic flux on sialylation using a glycoengineering approach. Specifically, we treated three human breast cell lines (MCF10A, T-47D, and MDA-MB-231) with 1,3,4-O-Bu3ManNAc, a "high flux" metabolic precursor for the sialic acid biosynthetic pathway. We then analyzed N-glycan sialylation using solid phase extraction of glycopeptides (SPEG) mass spectrometry-based proteomics under conditions that selectively captured sialic acid-containing glycopeptides, referred to as "sialoglycosites." Gene ontology (GO) analysis showed that flux-based changes to sialylation were broadly distributed across classes of proteins in 1,3,4-O-Bu3ManNAc-treated cells. Only three categories of proteins, however, were "highly responsive" to flux (defined as two or more sialylation changes of 10-fold or greater). Two of these categories were cell signaling and cell adhesion, which reflect well-known roles of sialic acid in oncogenesis. A third category-protein folding chaperones-was unexpected because little precedent exists for the role of glycosylation in the activity of these proteins. The highly flux-responsive proteins were all linked to cancer but sometimes as tumor suppressors, other times as proto-oncogenes, or sometimes both depending on sialylation status. A notable aspect of our analysis of metabolically glycoengineered breast cells was decreased sialylation of a subset of glycosites, which was unexpected because of the increased intracellular levels of sialometabolite "building blocks" in the 1,3,4-O-Bu3ManNAc-treated cells. Sites of decreased sialylation were minor in the MCF10A (<25% of all glycosites) and T-47D (<15%) cells but dominated in the MDA-MB-231 line (~60%) suggesting that excess sialic acid could be detrimental in advanced cancer and cancer cells can evolve mechanisms to guard against hypersialylation. In summary, flux-driven changes to sialylation offer an intriguing and novel mechanism to switch between context-dependent pro- or anti-cancer activities of the several oncoproteins identified in this study. These findings illustrate how metabolic glycoengineering can uncover novel roles of sialic acid in oncogenesis.
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Affiliation(s)
- Christopher T Saeui
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Kyung-Cho Cho
- Department of Pathology, The Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Vrinda Dharmarha
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Alison V Nairn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Melina Galizzi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Sagar R Shah
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Prateek Gowda
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Marian Park
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Melissa Austin
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Amelia Clarke
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Edward Cai
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Matthew J Buettner
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Ryan Ariss
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Kevin J Yarema
- Department of Biomedical Engineering, Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States.,Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD, United States.,Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, United States
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28
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Li D, Mukhopadhyay S. Functional analyses of the UDP-galactose transporter SLC35A2 using the binding of bacterial Shiga toxins as a novel activity assay. Glycobiology 2020; 29:490-503. [PMID: 30834435 DOI: 10.1093/glycob/cwz016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 01/13/2023] Open
Abstract
SLC35A2 transports UDP-galactose from the cytosol to the lumen of the Golgi apparatus and endoplasmic reticulum for glycosylation. Mutations in SLC35A2 induce a congenital disorder of glycosylation. Despite the biomedical relevance, mechanisms of transport via SLC35A2 and the impact of disease-associated mutations on activity are unclear. To address these issues, we generated a predicted structure of SLC35A2 and assayed for the effects of a set of structural and disease-associated mutations. Activity assays were performed using a rescue approach in ΔSLC35A2 cells and took advantage of the fact that SLC35A2 is required for expression of the glycosphingolipid globotriaosylceramide (Gb3), the cell surface receptor for Shiga toxin 1 (STx1) and 2 (STx2). The N- and C-terminal cytoplasmic loops of SLC35A2 were dispensable for activity, but two critical glycine (Gly-202 and Gly-214) and lysine (Lys-78 and Lys-297) residues in transmembrane segments were required. Residues corresponding to Gly-202 and Gly-214 in the related transporter SLC35A1 form a substrate-translocating channel, suggesting that a similar mechanism may be involved in SLC35A2. Among the eight disease-associated mutations tested, SLC35A2 function was completely inhibited by two (S213F and G282R) and partially inhibited by three (R55L, G266V, and S304P), providing a straight-forward mechanism of disease. Interestingly, the remaining three (V331I, V258M, and Y267C) did not impact SLC35A2 function, suggesting that complexities beyond loss of transporter activity may underlie disease due to these mutations. Overall, our results provide new insights into the mechanisms of transport of SLC35A2 and improve understanding of the relationship between SLC35A2 mutations and disease.
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Affiliation(s)
- Danyang Li
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - Somshuvra Mukhopadhyay
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX, USA
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29
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Wiertelak W, Sosicka P, Olczak M, Maszczak-Seneczko D. Analysis of homologous and heterologous interactions between UDP-galactose transporter and beta-1,4-galactosyltransferase 1 using NanoBiT. Anal Biochem 2020; 593:113599. [PMID: 32004544 DOI: 10.1016/j.ab.2020.113599] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 12/17/2022]
Abstract
Split luciferase complementation assay is one of the approaches enabling identification and analysis of protein-protein interactions in vivo. The NanoBiT technology is the most recent improvement of this strategy. Nucleotide sugar transporters and glycosyltransferases of the Golgi apparatus are the key players in glycosylation. Here we demonstrate the applicability of the NanoBiT system for studying homooligomerization of these proteins. We also report and discuss a novel heterologous interaction between UDP-galactose transporter and beta-1,4-galactosyltransferase 1.
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Affiliation(s)
- Wojciech Wiertelak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383, Wroclaw, Poland
| | - Paulina Sosicka
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Mariusz Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383, Wroclaw, Poland
| | - Dorota Maszczak-Seneczko
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383, Wroclaw, Poland.
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30
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Stach CS, McCann MG, O’Brien CM, Le TS, Somia N, Chen X, Lee K, Fu HY, Daoutidis P, Zhao L, Hu WS, Smanski M. Model-Driven Engineering of N-Linked Glycosylation in Chinese Hamster Ovary Cells. ACS Synth Biol 2019; 8:2524-2535. [PMID: 31596566 DOI: 10.1021/acssynbio.9b00215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chinese hamster ovary (CHO) cells are used for industrial production of protein-based therapeutics (i.e., "biologics"). Here we describe a method for combining systems-level kinetic models with a synthetic biology platform for multigene overexpression to rationally perturb N-linked glycosylation. Specifically, we sought to increase galactose incorporation on a secreted Immunoglobulin G (IgG) protein. We rationally design, build, and test a total of 23 transgenic cell pools that express single or three-gene glycoengineering cassettes comprising a total of 100 kilobases of engineered DNA sequence. Through iterative engineering and model refinement, we rationally increase the fraction of bigalactosylated glycans five-fold from 11.9% to 61.9% and simultaneously decrease the glycan heterogeneity on the secreted IgG. Our approach allows for rapid hypothesis testing and identification of synergistic behavior from genetic perturbations by bridging systems and synthetic biology.
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Affiliation(s)
| | | | | | | | | | - Xinning Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
| | | | | | | | - Liang Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
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Lee DJ, O'Donnell H, Routier FH, Tiralongo J, Haselhorst T. Glycobiology of Human Fungal Pathogens: New Avenues for Drug Development. Cells 2019; 8:cells8111348. [PMID: 31671548 PMCID: PMC6912366 DOI: 10.3390/cells8111348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 12/20/2022] Open
Abstract
Invasive fungal infections (IFI) are an increasing threat to the developing world, with fungal spores being ubiquitous and inhaled every day. Some fungal species are commensal organisms that are part of the normal human microbiota, and, as such, do not pose a threat to the immune system. However, when the natural balance of this association is disturbed or the host's immune system is compromised, these fungal pathogens overtake the organism, and cause IFI. To understand the invasiveness of these pathogens and to address the growing problem of IFI, it is essential to identify the cellular processes of the invading organism and their virulence. In this review, we will discuss the prevalence and current options available to treat IFI, including recent reports of drug resistance. Nevertheless, the main focus of this review is to describe the glycobiology of human fungal pathogens and how various components of the fungal cell wall, particularly cell wall polysaccharides and glycoconjugates, are involved in fungal pathogenicity, their biosynthesis and how they can be potentially exploited to develop novel antifungal treatment options. We will specifically describe the nucleotide sugar transporters (NSTs) that are important in fungal survival and suggest that the inhibition of fungal NSTs may potentially be useful to prevent the establishment of fungal infections.
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Affiliation(s)
- Danielle J Lee
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland, 4222, Australia; Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Nikolai-Fuchs Strasse 1, 30625 Hannover, Germany.
| | - Holly O'Donnell
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland, 4222, Australia; Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Nikolai-Fuchs Strasse 1, 30625 Hannover, Germany.
| | - Françoise H Routier
- Department of Clinical Biochemistry OE4340, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Nikolai-Fuchs Strasse 1, 30625 Hannover, Germany.
| | - Joe Tiralongo
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland, 4222, Australia; Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Nikolai-Fuchs Strasse 1, 30625 Hannover, Germany.
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland, 4222, Australia; Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Nikolai-Fuchs Strasse 1, 30625 Hannover, Germany.
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Parker JL, Corey RA, Stansfeld PJ, Newstead S. Structural basis for substrate specificity and regulation of nucleotide sugar transporters in the lipid bilayer. Nat Commun 2019; 10:4657. [PMID: 31604945 PMCID: PMC6789118 DOI: 10.1038/s41467-019-12673-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/24/2019] [Indexed: 01/21/2023] Open
Abstract
Nucleotide sugars are the activated form of monosaccharides used by glycosyltransferases during glycosylation. In eukaryotes the SLC35 family of solute carriers are responsible for their selective uptake into the Endoplasmic Reticulum or Golgi apparatus. The structure of the yeast GDP-mannose transporter, Vrg4, revealed a requirement for short chain lipids and a marked difference in transport rate between the nucleotide sugar and nucleoside monophosphate, suggesting a complex network of regulatory elements control transport into these organelles. Here we report the crystal structure of the GMP bound complex of Vrg4, revealing the molecular basis for GMP recognition and transport. Molecular dynamics, combined with biochemical analysis, reveal a lipid mediated dimer interface and mechanism for coordinating structural rearrangements during transport. Together these results provide further insight into how SLC35 family transporters function within the secretory pathway and sheds light onto the role that membrane lipids play in regulating transport across the membrane.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, The University of Warwick, Coventry, CV4 7AL, UK.
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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Tax G, Lia A, Santino A, Roversi P. Modulation of ERQC and ERAD: A Broad-Spectrum Spanner in the Works of Cancer Cells? JOURNAL OF ONCOLOGY 2019; 2019:8384913. [PMID: 31662755 PMCID: PMC6791201 DOI: 10.1155/2019/8384913] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022]
Abstract
Endoplasmic reticulum glycoprotein folding quality control (ERQC) and ER-associated degradation (ERAD) preside over cellular glycoprotein secretion and maintain steady glycoproteostasis. When cells turn malignant, cancer cell plasticity is affected and supported either by point mutations, preferential isoform selection, altered expression levels, or shifts to conformational equilibria of a secreted glycoprotein. Such changes are crucial in mediating altered extracellular signalling, metabolic behavior, and adhesion properties of cancer cells. It is therefore conceivable that interference with ERQC and/or ERAD can be used to selectively damage cancers. Indeed, inhibitors of the late stages of ERAD are already in the clinic against cancers such as multiple myeloma. Here, we review recent advances in our understanding of the complex relationship between glycoproteostasis and cancer biology and discuss the potential of ERQC and ERAD modulators for the selective targeting of cancer cell plasticity.
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Affiliation(s)
- Gábor Tax
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, UK
| | - Andrea Lia
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, UK
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, I-73100 Lecce, Italy
| | - Angelo Santino
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, I-73100 Lecce, Italy
| | - Pietro Roversi
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, UK
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Han J, Perez JT, Chen C, Li Y, Benitez A, Kandasamy M, Lee Y, Andrade J, tenOever B, Manicassamy B. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication. Cell Rep 2019; 23:596-607. [PMID: 29642015 PMCID: PMC5939577 DOI: 10.1016/j.celrep.2018.03.045] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 01/24/2018] [Accepted: 03/10/2018] [Indexed: 11/13/2022] Open
Abstract
The emergence of influenza A viruses (IAVs) from zoonotic reservoirs poses a great threat to human health. As seasonal vaccines are ineffective against zoonotic strains, and newly transmitted viruses can quickly acquire drug resistance, there remains a need for host-directed therapeutics against IAVs. Here, we performed a genome-scale CRISPR/Cas9 knockout screen in human lung epithelial cells with a human isolate of an avian H5N1 strain. Several genes involved in sialic acid biosynthesis and related glycosylation pathways were highly enriched post-H5N1 selection, including SLC35A1, a sialic acid transporter essential for IAV receptor expression and thus viral entry. Importantly, we have identified capicua (CIC) as a negative regulator of cell-intrinsic immunity, as loss of CIC resulted in heightened antiviral responses and restricted replication of multiple viruses. Therefore, our study demonstrates that the CRISPR/Cas9 system can be utilized for the discovery of host factors critical for the replication of intracellular pathogens.
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Affiliation(s)
- Julianna Han
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Jasmine T Perez
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Cindy Chen
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Yan Li
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA
| | - Asiel Benitez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Republic of Korea
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA
| | - Benjamin tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Balaji Manicassamy
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA.
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Li Q, Xie Y, Wong M, Lebrilla CB. Characterization of Cell Glycocalyx with Mass Spectrometry Methods. Cells 2019; 8:E882. [PMID: 31412618 PMCID: PMC6721671 DOI: 10.3390/cells8080882] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023] Open
Abstract
The cell membrane plays an important role in protecting the cell from its extracellular environment. As such, extensive work has been devoted to studying its structure and function. Crucial intercellular processes, such as signal transduction and immune protection, are mediated by cell surface glycosylation, which is comprised of large biomolecules, including glycoproteins and glycosphingolipids. Because perturbations in glycosylation could result in dysfunction of cells and are related to diseases, the analysis of surface glycosylation is critical for understanding pathogenic mechanisms and can further lead to biomarker discovery. Different mass spectrometry-based techniques have been developed for glycan analysis, ranging from highly specific, targeted approaches to more comprehensive profiling studies. In this review, we summarized the work conducted for extensive analysis of cell membrane glycosylation, particularly those employing liquid chromatography with mass spectrometry (LC-MS) in combination with various sample preparation techniques.
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Affiliation(s)
- Qiongyu Li
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Yixuan Xie
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA 95616, USA.
- Department of Biochemistry, University of California, Davis, CA 95616, USA.
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Hadley B, Litfin T, Day CJ, Haselhorst T, Zhou Y, Tiralongo J. Nucleotide Sugar Transporter SLC35 Family Structure and Function. Comput Struct Biotechnol J 2019; 17:1123-1134. [PMID: 31462968 PMCID: PMC6709370 DOI: 10.1016/j.csbj.2019.08.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/05/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
The covalent attachment of sugars to growing glycan chains is heavily reliant on a specific family of solute transporters (SLC35), the nucleotide sugar transporters (NSTs) that connect the synthesis of activated sugars in the nucleus or cytosol, to glycosyltransferases that reside in the lumen of the endoplasmic reticulum (ER) and/or Golgi apparatus. This review provides a timely update on recent progress in the NST field, specifically we explore several NSTs of the SLC35 family whose substrate specificity and function have been poorly understood, but where recent significant progress has been made. This includes SLC35 A4, A5 and D3, as well as progress made towards understanding the association of SLC35A2 with SLC35A3 and how this relates to their potential regulation, and how the disruption to the dilysine motif in SLC35B4 causes mislocalisation, calling into question multisubstrate NSTs and their subcellular localisation and function. We also report on the recently described first crystal structure of an NST, the SLC35D2 homolog Vrg-4 from yeast. Using this crystal structure, we have generated a new model of SLC35A1, (CMP-sialic acid transporter, CST), with structural and mechanistic predictions based on all known CST-related data, and includes an overview of reported mutations that alter transport and/or substrate recognition (both de novo and site-directed). We also present a model of the CST-del177 isoform that potentially explains why the human CST isoform remains active while the hamster CST isoform is inactive, and we provide a possible alternate access mechanism that accounts for the CST being functional as either a monomer or a homodimer. Finally we provide an update on two NST crystal structures that were published subsequent to the submission and during review of this report.
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Affiliation(s)
- Barbara Hadley
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Thomas Litfin
- School of Information and Communication Technology, Griffith University, Gold Coast Campus, Queensland 4212, Australia
| | - Chris J. Day
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
- School of Information and Communication Technology, Griffith University, Gold Coast Campus, Queensland 4212, Australia
| | - Joe Tiralongo
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
- Corresponding author.
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Miyamoto S, Nakashima M, Ohashi T, Hiraide T, Kurosawa K, Yamamoto T, Takanashi J, Osaka H, Inoue K, Miyazaki T, Wada Y, Okamoto N, Saitsu H. A case of de novo splice site variant in SLC35A2 showing developmental delays, spastic paraplegia, and delayed myelination. Mol Genet Genomic Med 2019; 7:e814. [PMID: 31231989 PMCID: PMC6687661 DOI: 10.1002/mgg3.814] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Congenital disorders of glycosylation (CDGs) are genetic diseases caused by pathogenic variants of genes involved in protein or lipid glycosylation. De novo variants in the SLC35A2 gene, which encodes a UDP-galactose transporter, are responsible for CDGs with an X-linked dominant manner. Common symptoms related to SLC35A2 variants include epilepsy, psychomotor developmental delay, hypotonia, abnormal facial and skeletal features, and various magnetic resonance imaging (MRI) findings. METHODS Whole-exome sequencing was performed on the patient's DNA, and candidate variants were confirmed by Sanger sequencing. cDNA analysis was performed to assess the effect of the splice site variant using peripheral leukocytes. The X-chromosome inactivation pattern was studied using the human androgen receptor assay. RESULTS We identified a de novo splice site variant in SLC35A2 (NM_005660.2: c.274+1G>A) in a female patient who showed severe developmental delay, spastic paraplegia, mild cerebral atrophy, and delayed myelination on MRI, but no seizures. The variant led to an aberrant splicing resulting in an in-frame 33-bp insertion, which caused an 11-amino acid insertion in the presumptive cytoplasmic loop. X-inactivation pattern was random. Partial loss of galactose and sialic acid of the N-linked glycans of serum transferrin was observed. CONCLUSION This case would expand the phenotypic spectrum of SLC35A2-related disorders to delayed myelination with spasticity and no seizures.
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Affiliation(s)
- Sachiko Miyamoto
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
| | - Mitsuko Nakashima
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
| | - Tsukasa Ohashi
- Department of PediatricsNiigata University Medical and Dental HospitalNiigataJapan
| | - Takuya Hiraide
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
| | - Kenji Kurosawa
- Division of Medical GeneticsKanagawa Children's Medical CenterYokohamaJapan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical SciencesTokyoJapan
| | - Junichi Takanashi
- Department of Pediatrics and Pediatric NeurologyTokyo Women's Medical University, Yachiyo Medical CenterYachiyoJapan
| | - Hitoshi Osaka
- Department of PediatricsJichi Medical UniversityTochigiJapan
| | - Ken Inoue
- Department of Mental Retardation & Birth Defect ResearchNational Institute of NeuroscienceNational Center of Neurology & PsychiatryJapan
| | - Takehiro Miyazaki
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
| | - Yoshinao Wada
- Department of Molecular MedicineOsaka Women's and Children's HospitalOsakaJapan
| | - Nobuhiko Okamoto
- Department of Molecular MedicineOsaka Women's and Children's HospitalOsakaJapan
- Department of Medical GeneticsOsaka Women's and Children's HospitalOsakaJapan
| | - Hirotomo Saitsu
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
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38
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Kang DG, Kim CS, Cha HJ. Coexpression of CMP-sialic acid transporter reduces N-glycolylneuraminic acid levels of recombinant glycoproteins in Chinese hamster ovary cells. Biotechnol Bioeng 2019; 116:2815-2822. [PMID: 31317538 DOI: 10.1002/bit.27122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 01/17/2023]
Abstract
Recombinant glycoproteins expressed in Chinese hamster ovary (CHO) cells contain two forms of sialic acids; N-acetylneuraminic acid (Neu5Ac) as a major type and N-glycolylneuraminic acid (Neu5Gc) as a minor type. The Neu5Gc glycan moieties in therapeutic glycoproteins can elicit immune responses because they do not exist in human. In the present work, to reduce Neu5Gc levels of recombinant glycoproteins from CHO cell cultures, we coexpressed cytidine-5'-monophosphate-sialic acid transporter (CMP-SAT) that is an antiporter and transports cytosolic CMP-sialic acids (both forms) into Golgi lumen. When human erythropoietin was used as a target human glycoprotein, coexpression of CMP-SAT resulted in a significant decrease of Neu5Gc level by 41.4% and a notable increase of Neu5Ac level by 21.2%. This result could be reasonably explained by our hypothesis that the turnover rate of Neu5Ac to Neu5Gc catalyzed by CMP-Neu5Ac hydroxylase would be reduced through facilitated transportation of Neu5Ac into Golgi apparatus by coexpression of CMP-SAT. We confirmed the effects of CMP-SAT coexpression on the decrease of Neu5Gc level and the increase of Neu5Ac level using another glycoprotein human DNase I. Therefore, CMP-SAT coexpression might be an effective strategy to reduce the levels of undesired Neu5Gc in recombinant therapeutic glycoproteins from CHO cell cultures.
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Affiliation(s)
- Dong Gyun Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Korea
| | - Chang Sup Kim
- School of Chemistry and Biochemistry, Yeungnam University, Gyeongsan, Korea
| | - Hyung Joon Cha
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Korea
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39
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Masukagami Y, Nijagal B, Mahdizadeh S, Tseng CW, Dayalan S, Tivendale KA, Markham PF, Browning GF, Sansom FM. A combined metabolomic and bioinformatic approach to investigate the function of transport proteins of the important pathogen Mycoplasma bovis. Vet Microbiol 2019; 234:8-16. [PMID: 31213276 DOI: 10.1016/j.vetmic.2019.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/05/2023]
Abstract
Mycoplasma bovis is an economically important pathogen of the cattle industry worldwide, and there is an urgent need for a more effective vaccine to control the diseases caused by this organism. Although the M. bovis genome sequence is available, very few gene functions of M. bovis have been experimentally determined, and a better understanding of the genes involved in pathogenesis are required for vaccine development. In this study, we compared the metabolite profiles of wild type M. bovis to a number of strains that each contained a transposon insertion into a putative transporter gene. Transport systems are thought to play an important role in survival of mycoplasmas, as they rely on the host for many nutrients. We also performed 13C-stable isotope labelling on strains with transposon insertions into putative glycerol transporters. Integration of metabolomic and bioinformatic analyses revealed unexpected results (when compared to genome annotation) for two mutants, with a putative amino acid transporter (MBOVPG45_0533) appearing more likely to transport nucleotide sugars, and a second mutant, a putative dicarboxylate/amino acid:cation (Na+ or H+) symporter (DAACS), more likely to function as a biopterin/folate transporter. This study also highlighted the apparent redundancy in some transport and metabolic pathways, such as the glycerol transport systems, even in an organism with a reduced genome. Overall, this study highlights the value of metabolomics for revealing the likely function of a number of transporters of M. bovis.
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Affiliation(s)
- Yumiko Masukagami
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Brunda Nijagal
- Metabolomics Australia, The Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Victoria, Australia
| | - Sara Mahdizadeh
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Chi-Wen Tseng
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, The Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kelly A Tivendale
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Philip F Markham
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Fiona M Sansom
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
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40
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Hyaluronan as tunable drug delivery system. Adv Drug Deliv Rev 2019; 146:83-96. [PMID: 31421148 DOI: 10.1016/j.addr.2019.08.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 08/08/2019] [Accepted: 08/12/2019] [Indexed: 12/15/2022]
Abstract
The hyaluronan (HA) polymer is an important macromolecule of extracellular matrix with remarkable structure and functions: it is a linear and unbranched polymer without sulphate or phosphate groups and has key role in several biological processes in mammals. It is ubiquitous in mammalian tissues with several and specific functions, influencing cell proliferation and migration as well as angiogenesis and inflammation. To exert these important functions in tissues HA modifies the concentration and size. Considering this HA content in tissues is carefully controlled by different mechanisms including covalent modification of the synthetic enzymes and epigenetic control of their gene expression. The function of HA is also critical in several pathologies including cancer, diabetes and chronic inflammation. Among these biological roles, the structural properties of HA allow to use this polymer in regenerative medicine including cosmetics and drug delivery. HA takes advantage from its capacity to form gels even at concentration of 1% producing scaffolds with very intriguing mechanical properties. These hydrogels are useful in regenerative medicine as biocompatible material for advanced therapeutic uses. In this review we highlight the biological aspects of HA addressing the mechanisms controlling the HA content in tissues and its role as drug delivery system.
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41
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Structural basis for the delivery of activated sialic acid into Golgi for sialyation. Nat Struct Mol Biol 2019; 26:415-423. [PMID: 31133698 DOI: 10.1038/s41594-019-0225-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/09/2019] [Indexed: 01/08/2023]
Abstract
The decoration of secretory glycoproteins and glycolipids with sialic acid is critical to many physiological and pathological processes. Sialyation is dependent on a continuous supply of sialic acid into Golgi organelles in the form of CMP-sialic acid. Translocation of CMP-sialic acid into Golgi is carried out by the CMP-sialic acid transporter (CST). Mutations in human CST are linked to glycosylation disorders, and CST is important for glycopathway engineering, as it is critical for sialyation efficiency of therapeutic glycoproteins. The mechanism of how CMP-sialic acid is recognized and translocated across Golgi membranes in exchange for CMP is poorly understood. Here we have determined the crystal structure of a Zea mays CST in complex with CMP. We conclude that the specificity of CST for CMP-sialic acid is established by the recognition of the nucleotide CMP to such an extent that they are mechanistically capable of both passive and coupled antiporter activity.
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Ahuja S, Whorton MR. Structural basis for mammalian nucleotide sugar transport. eLife 2019; 8:45221. [PMID: 30985278 PMCID: PMC6508934 DOI: 10.7554/elife.45221] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/13/2019] [Indexed: 12/12/2022] Open
Abstract
Nucleotide-sugar transporters (NSTs) are critical components of the cellular glycosylation machinery. They transport nucleotide-sugar conjugates into the Golgi lumen, where they are used for the glycosylation of proteins and lipids, and they then subsequently transport the nucleotide monophosphate byproduct back to the cytoplasm. Dysregulation of human NSTs causes several debilitating diseases, and NSTs are virulence factors for many pathogens. Here we present the first crystal structures of a mammalian NST, the mouse CMP-sialic acid transporter (mCST), in complex with its physiological substrates CMP and CMP-sialic acid. Detailed visualization of extensive protein-substrate interactions explains the mechanisms governing substrate selectivity. Further structural analysis of mCST’s unique lumen-facing partially-occluded conformation, coupled with the characterization of substrate-induced quenching of mCST’s intrinsic tryptophan fluorescence, reveals the concerted conformational transitions that occur during substrate transport. These results provide a framework for understanding the effects of disease-causing mutations and the mechanisms of this diverse family of transporters. The cells in our body are tiny machines which, amongst other things, produce proteins. One of the production steps involves a compartment in the cell called the Golgi, where proteins are tagged and packaged before being sent to their final destination. In particular, sugars can be added onto an immature protein to help to fold it, stabilize it, and to affect how it works. Before sugars can be attached to a protein, they need to be ‘activated’ outside of the Golgi by attaching to a small molecule known as a nucleotide. Then, these ‘nucleotide-sugars’ are ferried across the Golgi membrane and inside the compartment by nucleotide-sugar transporters, or NSTs. Humans have seven different kinds of NSTs, each responsible for helping specific types of nucleotide-sugars cross the Golgi membrane. Changes in NSTs are linked to several human diseases, including certain types of epilepsy; these proteins are also important for dangerous microbes to be able to infect cells. Yet, scientists know very little about how the transporters recognize their cargo, and how they transport it. To shed light on these questions, Ahuja and Whorton set to uncover for the first time the 3D structure of a mammalian NST using a method known as X-ray crystallography. This revealed how nearly every component of this transporter is arranged when the protein is bound to two different molecules: a specific nucleotide, or a type of nucleotide-sugar. The results help to understand how changes in certain components of the NST can lead to a problem in the way the protein works. Ultimately, this knowledge may be useful to prevent diseases linked to faulty NSTs, or to stop microbes from using the transporters to their own advantage.
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Affiliation(s)
- Shivani Ahuja
- Vollum Institute, Oregon Health & Science University, Portland, United States
| | - Matthew R Whorton
- Vollum Institute, Oregon Health & Science University, Portland, United States
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Parker JL, Newstead S. Gateway to the Golgi: molecular mechanisms of nucleotide sugar transporters. Curr Opin Struct Biol 2019; 57:127-134. [PMID: 30999236 DOI: 10.1016/j.sbi.2019.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/09/2019] [Accepted: 03/12/2019] [Indexed: 12/16/2022]
Abstract
The Golgi apparatus plays a central role in the secretory pathway as a hub for posttranslational modification, protein sorting and quality control. To date, there is little structural or biochemical information concerning the function of transporters that reside within this organelle. The SLC35 family of nucleotide sugar transporters link the synthesis of activated sugar molecules and sulfate in the cytoplasm, with the luminal transferases that catalyse their attachment to proteins and lipids during glycosylation and sulfation. A recent crystal structure of the GDP-mannose transporter has revealed key sequence motifs that direct ligand recognition and transport. Further biochemical studies unexpectedly found a requirement for short chain lipids in activating the transporter, suggesting a possible route for transport regulation within the Golgi.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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Ma QJ, Sun MH, Kang H, Lu J, You CX, Hao YJ. A CIPK protein kinase targets sucrose transporter MdSUT2.2 at Ser 254 for phosphorylation to enhance salt tolerance. PLANT, CELL & ENVIRONMENT 2019; 42:918-930. [PMID: 29791976 DOI: 10.1111/pce.13349] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/17/2018] [Accepted: 05/17/2018] [Indexed: 05/18/2023]
Abstract
Soil salinity is one of the major abiotic stressors that negatively affect crop growth and yield. Salt stress can regulate antioxidants and the accumulation of osmoprotectants. In the study, a sucrose transporter MdSUT2.2 was identified in apple. Overexpression of MdSUT2.2 gene increased salt tolerance in the transgenic apple, compared with the WT control "Gala." In addition, it was found that protein MdSUT2.2 was phosphorylated at Ser254 site in response to salt. A DUAL membrane yeast hybridization system through an apple cDNA library demonstrated that a protein kinase MdCIPK13 interacted with MdSUT2.2. A series of transgenic analysis in apple calli showed that MdCIPK13 was required for the salt-induced phosphorylation of MdSUT2.2 protein and enhanced its stability and transport activity. Finally, it was found that MdCIPK13 improved salt resistance in an MdSUT2.2-dependent manner. These findings had enriched our understanding of the molecular mechanisms underlying abiotic stress.
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Affiliation(s)
- Qi-Jun Ma
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai Region, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Mei-Hong Sun
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai Region, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Hui Kang
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai Region, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jing Lu
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai Region, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai Region, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yu-Jin Hao
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai Region, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
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Morrin ST, Owens RA, Le Berre M, Gerlach JQ, Joshi L, Bode L, Irwin JA, Hickey RM. Interrogation of Milk-Driven Changes to the Proteome of Intestinal Epithelial Cells by Integrated Proteomics and Glycomics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1902-1917. [PMID: 30663306 DOI: 10.1021/acs.jafc.8b06484] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bovine colostrum is a rich source of bioactive components which are important in the development of the intestine, in stimulating gut structure and function and in preparing the gut surface for subsequent colonization of microbes. What is not clear, however, is how colostrum may affect the repertoire of receptors and membrane proteins of the intestinal surface and the post-translational modifications associated with them. In the present work, we aimed to characterize the surface receptor and glycan profile of human HT-29 intestinal cells after exposure to a bovine colostrum fraction (BCF) by means of proteomic and glycomic analyses. Integration of label-free quantitative proteomic analysis and lectin array profiles confirmed that BCF exposure results in changes in the levels of glycoproteins present at the cell surface and also changes to their glycosylation pattern. This study contributes to our understanding of how milk components may regulate intestinal cells and prime them for bacterial interaction.
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Affiliation(s)
- Sinead T Morrin
- Teagasc Food Research Centre , Moorepark , Fermoy, P61C996 , County Cork , Ireland
- Veterinary Sciences Centre, School of Veterinary Medicine , University College Dublin , Belfield, Dublin 4, D04 V1W8 , Ireland
| | - Rebecca A Owens
- Department of Biology , Maynooth University , Maynooth , W23 F2H6 , County Kildare , Ireland
| | - Marie Le Berre
- Glycoscience Group, Advanced Glycoscience Research Cluster, National Centre for Biomedical Engineering Science , National University of Ireland Galway , H91TK33 , Galway , Ireland
| | - Jared Q Gerlach
- Glycoscience Group, Advanced Glycoscience Research Cluster, National Centre for Biomedical Engineering Science , National University of Ireland Galway , H91TK33 , Galway , Ireland
| | - Lokesh Joshi
- Glycoscience Group, Advanced Glycoscience Research Cluster, National Centre for Biomedical Engineering Science , National University of Ireland Galway , H91TK33 , Galway , Ireland
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence , University of California, San Diego , La Jolla , California 92093 , United States
| | - Jane A Irwin
- Veterinary Sciences Centre, School of Veterinary Medicine , University College Dublin , Belfield, Dublin 4, D04 V1W8 , Ireland
| | - Rita M Hickey
- Teagasc Food Research Centre , Moorepark , Fermoy, P61C996 , County Cork , Ireland
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46
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Sosicka P, Bazan B, Maszczak-Seneczko D, Shauchuk Y, Olczak T, Olczak M. SLC35A5 Protein-A Golgi Complex Member with Putative Nucleotide Sugar Transport Activity. Int J Mol Sci 2019; 20:ijms20020276. [PMID: 30641943 PMCID: PMC6359379 DOI: 10.3390/ijms20020276] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/18/2018] [Accepted: 01/07/2019] [Indexed: 12/12/2022] Open
Abstract
Solute carrier family 35 member A5 (SLC35A5) is a member of the SLC35A protein subfamily comprising nucleotide sugar transporters. However, the function of SLC35A5 is yet to be experimentally determined. In this study, we inactivated the SLC35A5 gene in the HepG2 cell line to study a potential role of this protein in glycosylation. Introduced modification affected neither N- nor O-glycans. There was also no influence of the gene knock-out on glycolipid synthesis. However, inactivation of the SLC35A5 gene caused a slight increase in the level of chondroitin sulfate proteoglycans. Moreover, inactivation of the SLC35A5 gene resulted in the decrease of the uridine diphosphate (UDP)-glucuronic acid, UDP-N-acetylglucosamine, and UDP-N-acetylgalactosamine Golgi uptake, with no influence on the UDP-galactose transport activity. Further studies demonstrated that SLC35A5 localized exclusively to the Golgi apparatus. Careful insight into the protein sequence revealed that the C-terminus of this protein is extremely acidic and contains distinctive motifs, namely DXEE, DXD, and DXXD. Our studies show that the C-terminus is directed toward the cytosol. We also demonstrated that SLC35A5 formed homomers, as well as heteromers with other members of the SLC35A protein subfamily. In conclusion, the SLC35A5 protein might be a Golgi-resident multiprotein complex member engaged in nucleotide sugar transport.
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Affiliation(s)
- Paulina Sosicka
- Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland.
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Bożena Bazan
- Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland.
| | - Dorota Maszczak-Seneczko
- Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland.
| | - Yauhen Shauchuk
- Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland.
| | - Teresa Olczak
- Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland.
| | - Mariusz Olczak
- Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland.
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47
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Sumit M, Dolatshahi S, Chu AHA, Cote K, Scarcelli JJ, Marshall JK, Cornell RJ, Weiss R, Lauffenburger DA, Mulukutla BC, Figueroa B. Dissecting N-Glycosylation Dynamics in Chinese Hamster Ovary Cells Fed-batch Cultures using Time Course Omics Analyses. iScience 2019; 12:102-120. [PMID: 30682623 PMCID: PMC6352710 DOI: 10.1016/j.isci.2019.01.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 12/24/2022] Open
Abstract
N-linked glycosylation affects the potency, safety, immunogenicity, and pharmacokinetic clearance of several therapeutic proteins including monoclonal antibodies. A robust control strategy is needed to dial in appropriate glycosylation profile during the course of cell culture processes accurately. However, N-glycosylation dynamics remains insufficiently understood owing to the lack of integrative analyses of factors that influence the dynamics, including sugar nucleotide donors, glycosyltransferases, and glycosidases. Here, an integrative approach involving multi-dimensional omics analyses was employed to dissect the temporal dynamics of glycoforms produced during fed-batch cultures of CHO cells. Several pathways including glycolysis, tricarboxylic citric acid cycle, and nucleotide biosynthesis exhibited temporal dynamics over the cell culture period. The steps involving galactose and sialic acid addition were determined as temporal bottlenecks. Our results show that galactose, and not manganese, is able to mitigate the temporal bottleneck, despite both being known effectors of galactosylation. Furthermore, sialylation is limited by the galactosylated precursors and autoregulation of cytidine monophosphate-sialic acid biosynthesis. Major glycosylated species exhibit temporal dynamics during fed-batch processes Key metabolic pathways linked to N-glycosylation exhibit significant temporal dynamics Dynamics in nucleotide sugar donors (NSDs) directly influences glycoform heterogeneity Glycoform heterogeneity can be mitigated by supplementing NSD biosynthetic precursors
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Affiliation(s)
- Madhuresh Sumit
- Culture Process Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Sepideh Dolatshahi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - An-Hsiang Adam Chu
- Analytical Research and Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Kaffa Cote
- Analytical Research and Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - John J Scarcelli
- Cell Line Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Jeffrey K Marshall
- Analytical Research and Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Richard J Cornell
- Analytical Research and Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bhanu Chandra Mulukutla
- Culture Process Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA.
| | - Bruno Figueroa
- Culture Process Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
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48
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Hyaluronan: Structure, Metabolism, and Biological Properties. BIOLOGICALLY-INSPIRED SYSTEMS 2019. [DOI: 10.1007/978-3-030-12919-4_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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OhAinle M, Helms L, Vermeire J, Roesch F, Humes D, Basom R, Delrow JJ, Overbaugh J, Emerman M. A virus-packageable CRISPR screen identifies host factors mediating interferon inhibition of HIV. eLife 2018; 7:e39823. [PMID: 30520725 PMCID: PMC6286125 DOI: 10.7554/elife.39823] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/13/2018] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN) inhibits HIV replication by inducing antiviral effectors. To comprehensively identify IFN-induced HIV restriction factors, we assembled a CRISPR sgRNA library of Interferon Stimulated Genes (ISGs) into a modified lentiviral vector that allows for packaging of sgRNA-encoding genomes in trans into budding HIV-1 particles. We observed that knockout of Zinc Antiviral Protein (ZAP) improved the performance of the screen due to ZAP-mediated inhibition of the vector. A small panel of IFN-induced HIV restriction factors, including MxB, IFITM1, Tetherin/BST2 and TRIM5alpha together explain the inhibitory effects of IFN on the CXCR4-tropic HIV-1 strain, HIV-1LAI, in THP-1 cells. A second screen with a CCR5-tropic primary strain, HIV-1Q23.BG505, described an overlapping, but non-identical, panel of restriction factors. Further, this screen also identifies HIV dependency factors. The ability of IFN-induced restriction factors to inhibit HIV strains to replicate in human cells suggests that these human restriction factors are incompletely antagonized. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Molly OhAinle
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Louisa Helms
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Jolien Vermeire
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Ferdinand Roesch
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Daryl Humes
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Ryan Basom
- Genomics and Bioinformatics Shared ResourceFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared ResourceFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Julie Overbaugh
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Michael Emerman
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
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50
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Sim NS, Seo Y, Lim JS, Kim WK, Son H, Kim HD, Kim S, An HJ, Kang HC, Kim SH, Kim DS, Lee JH. Brain somatic mutations in SLC35A2 cause intractable epilepsy with aberrant N-glycosylation. Neurol Genet 2018; 4:e294. [PMID: 30584598 PMCID: PMC6283456 DOI: 10.1212/nxg.0000000000000294] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/03/2018] [Indexed: 01/16/2023]
Abstract
OBJECTIVE To identify whether somatic mutations in SLC35A2 alter N-glycan structures in human brain tissues and cause nonlesional focal epilepsy (NLFE) or mild malformation of cortical development (mMCD). METHODS Deep whole exome and targeted sequencing analyses were conducted for matched brain and blood tissues from patients with intractable NLFE and patients with mMCD who are negative for mutations in mTOR pathway genes. Furthermore, tissue glyco-capture and nanoLC/mass spectrometry analysis were performed to examine N-glycosylation in affected brain tissue. RESULTS Six of the 31 (19.3%) study patients exhibited brain-only mutations in SLC35A2 (mostly nonsense and splicing site mutations) encoding a uridine diphosphate (UDP)-galactose transporter. Glycome analysis revealed the presence of an aberrant N-glycan series, including high degrees of N-acetylglucosamine, in brain tissues with SLC35A2 mutations. CONCLUSION Our study suggests that brain somatic mutations in SLC35A2 cause intractable focal epilepsy with NLFE or mMCD via aberrant N-glycosylation in the affected brain.
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Affiliation(s)
- Nam Suk Sim
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Youngsuk Seo
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Jae Seok Lim
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Woo Kyeong Kim
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyeonju Son
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Heung Dong Kim
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Sangwoo Kim
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyun Joo An
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Hoon-Chul Kang
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Se Hoon Kim
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Dong-Seok Kim
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering (N.S.S., J.S.L., W.K.K., J.H.L.), KAIST; Asia Glycomics Reference Site (Y.S., H.J.A.); Graduate School of Analytical Science & Technology (Y.S., H.J.A.), Chungnam National University, Daejeon, Korea; Department of Biomedical System informatics (H.S., S.K.), Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine; Division of Pediatric Neurology (H.D.K., H.C.K.), Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children's Hospital; Epilepsy Research Institute (H.D.K., H.C.K.), Yonsei University College of Medicine; Department of Pathology (S.H.K.), Yonsei University College of Medicine, Seoul, Korea; and Pediatric Neurosurgery (D.S.K.), Severance Children's Hospital, Department of Neurosurgery, Yonsei University College of Medicine, Seoul, South Korea
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