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Nguyen HP, Liu E, Le AQ, Lamsal M, Misra J, Srivastava S, Hemavathy H, Kapur R, Zaid MA, Abonour R, Zhang J, Wek RC, Walker BA, Tran NT. The oligosaccharyltransferase complex is an essential component of multiple myeloma plasma cells. MOLECULAR THERAPY. ONCOLOGY 2025; 33:200964. [PMID: 40200920 PMCID: PMC11978334 DOI: 10.1016/j.omton.2025.200964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 02/03/2025] [Accepted: 03/05/2025] [Indexed: 04/10/2025]
Abstract
Multiple myeloma (MM) is an incurable malignancy characterized by mutated plasma cell clonal expansion in the bone marrow, leading to severe clinical symptoms. Thus, identifying new therapeutic targets for MM is crucial. We identified the oligosaccharyltransferase (OST) complex as a novel vulnerability in MM cells. Elevated expression of this complex is associated with relapsed, high-risk MM, and poor prognosis. Disrupting the OST complex suppressed MM cell growth, induced cell-cycle arrest, and apoptosis. Combined inhibition with bortezomib synergistically eliminated MM cells in vitro and in vivo, via suppressing genes related to bortezomib-resistant phenotypes. Mechanistically, OST complex disruption downregulated MM pathological pathways (mTORC1 pathway, glycolysis, MYC targets, and cell cycle) and induced TRAIL-mediated apoptosis. Notably, MYC translation was robustly suppressed upon inhibiting the OST complex. Collectively, the OST complex presents a novel target for MM treatment, and combining its inhibition with bortezomib offers a promising approach for relapsed MM patients.
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Affiliation(s)
- Hong Phuong Nguyen
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Anh Quynh Le
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mahesh Lamsal
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jagannath Misra
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sankalp Srivastava
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Harikrishnan Hemavathy
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Reuben Kapur
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mohammad Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Ji Zhang
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ronald C. Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brian A. Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Ngoc Tung Tran
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
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Gaur D, Acquaviva B, Wohlever ML. An Msp1-Protease Chimera Captures Transient AAA+ Interactions and Unveils Ost4 Mislocalization Errors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.31.646376. [PMID: 40236206 PMCID: PMC11996533 DOI: 10.1101/2025.03.31.646376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Membrane protein homeostasis (proteostasis) is essential for maintaining the integrity of eukaryotic organelles. Msp1 is a membrane anchored AAA+ (ATPase Associated with cellular Activities) protein that maintains mitochondrial proteostasis by extracting aberrant proteins from the outer mitochondrial membrane. A comprehensive understanding of the physiological roles of Msp1 has been hindered because AAA+ proteins interact with substrates transiently and common strategies to stabilize this interaction lead to undesirable mitochondrial phenotypes. To circumvent these drawbacks, we fused catalytically active Msp1 to the inactivated protease domain of the AAA+ protease Yme1. The resulting chimera sequesters substrates in the catalytically inactive degradation chamber formed by the protease domain. We performed mass spectrometry analysis with the Msp1-protease chimera and identified the signal anchored protein Ost4 as a novel Msp1 substrate. Topology experiments show that Ost4 adopts mixed orientations when mislocalized to mitochondria and that Msp1 extracts mislocalized Ost4 regardless of orientation. Together, this work develops new tools for capturing transient interactions with AAA+ proteins, identifies new Msp1 substrates, and shows a surprising error in targeting of Ost4.
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Veluri R, Pollin G, Wagenknecht JB, Urrutia R, Zimmermann MT. An Integrative Multitiered Computational Analysis for Better Understanding the Structure and Function of 85 Miniproteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.31.635936. [PMID: 39974886 PMCID: PMC11838408 DOI: 10.1101/2025.01.31.635936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Background Miniproteins, defined as polypeptides containing fewer than 50 amino acids, have recently elicited significant interest due to an emerging understanding of their diverse roles in fundamental biological processes. In addition, miniprotein dysregulation underlies human diseases and is a significant focus for biotechnology and drug development. Notably, the human genome project revealed the existence of many novel miniproteins, most of which remain uncharacterized. This study reports an approach for analyzing and scoring previously uncharacterized miniproteins by integrating knowledge from classic sequence-based bioinformatics, computational biophysics, and system biology annotations. Our results demonstrate that these approaches provide novel information on the structure-function relationship of these molecules with a particular focus on their biomedical relevance. Methods We identified 85 human miniproteins using a simple multi-tier approach. First, we performed a sequence-based analysis of these proteins using several algorithms to identify regions of structural and functional importance. Protein-protein interactions and gene ontology annotations were used to analyze miniprotein function. Then, we predicted miniprotein three-dimensional structures using AI-based methods and peptide modeling to determine their relative yields for these understudied polymers. Subsequently, we used several computational biophysics methods and structure-based calculations to annotate and evaluate results from both algorithms. Results We find several relations between predicted structure and functional properties to assign these proteins to several groups with similar properties. Sequence-based analysis leads us to identify motifs and residues that link structure-to-function for most of these proteins. We suggest novel miniprotein functions, such as thymosin beta proteins regulating the shelterin complex through TERF1 and POT1 interactions, FAM86JP and FAM66E participating in endocytic processes, and BAGE1 influencing chromatin remodeling through interaction with nuclear proteins. Further, known functions of miniproteins, such as STRIT1, STMP1, and SLN, were supported. Finally, structure-based scoring led us to build 3D models that provided complementary information to ontologies. We identify that structural propensity is not strictly dependent on polymer length. In fact, in this dataset, peptide-based algorithms may have advantages over AI-based algorithms for certain groups of miniproteins. Conclusion This analytic approach and resulting identification and annotation of miniproteins adds much to what is currently known about miniproteins. Our determination of novel properties of miniproteins bears significant mechanistic and biomedical relevance. We propose novel functions of miniproteins, which expands our understanding of their potential roles in cellular processes. And, we practically identify which sequence and structure-based tools provide the most information, aiding future studies of miniproteins.
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Affiliation(s)
- Reethika Veluri
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- School of Medicine, Saint Louis University, Saint Louis, Missouri, USA
| | - Gareth Pollin
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jessica B. Wagenknecht
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul Urrutia
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael T. Zimmermann
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Data Science Institute, Medical College of Wisconsin, Milwaukee, WI, USA
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Ezell KM, Furuta Y, Oglesbee D, Pivnick EK, Rinker D, Sheehan JH, Tinker RJ, Hamid R, Cogan JD, Rives L, Neumann S, Corner B, Koziura M, Phillips JA, the Undiagnosed Diseases Network. Review and metabolomic profiling of unsolved case reveals newly reported autosomal dominant congenital disorder of glycosylation, type Iw formerly thought to only be an autosomal recessive condition. Mol Genet Metab Rep 2024; 41:101145. [PMID: 39435313 PMCID: PMC11491968 DOI: 10.1016/j.ymgmr.2024.101145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 09/20/2024] [Accepted: 09/24/2024] [Indexed: 10/23/2024] Open
Abstract
Autosomal dominant congenital disorder of glycosylation (CDG) type Iw (OMIM# 619714) is caused by a heterozygous mutation in the STT3A gene. Most CDGs have an autosomal recessive (AR) mode of inheritance, but several cases with an autosomal dominant (AD) form of an AR CDG have been recently identified. This report describes a 17-year-old male who was referred to the Undiagnosed Diseases Network (UDN) with a history of macrocephaly, failure to thrive, short stature, epilepsy, autism, attention-deficit/hyperactivity disorder, mild developmental delay, intermittent hypotonia, dysmorphic features, and mildly enlarged aortic root. Trio exome sequencing was negative. His biochemical workup included normal plasma amino acids, ammonia, acylcarnitine profile and urine organic and amino acids. His UDN genome sequencing (GS) identified a previously unreported de novo STT3A variant (c.1631A > G: p.Asn544Ser). This variant removes a glycosylation site and was predicted to be destabilizing by structural biology modeling. The patient was formally diagnosed by the UDN Metabolomics Core as having an abnormal transferrin profile indicative of CDG type Iw through metabolomic profiling. We report here an affected male with phenotypic, molecular, and metabolic findings consistent with CDG type Iw due to a heterozygous STT3A variant. This case highlights the importance of further testing of individuals with the phenotypic and metabolic findings of an AR disorder who are heterozygous for a single disease-causing allele and can be shown to have a new AD form of the disorder that represents clinical heterogeneity.
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Affiliation(s)
- Kimberly M. Ezell
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yutaka Furuta
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Eniko K. Pivnick
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - David Rinker
- Department of Biological Sciences, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jonathan H. Sheehan
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Rory J. Tinker
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rizwan Hamid
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joy D. Cogan
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lynette Rives
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Serena Neumann
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian Corner
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary Koziura
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A. Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - the Undiagnosed Diseases Network
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Biological Sciences, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
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Jin X, Xu W, Wu Q, Huang C, Song Y, Lian J. Detecting early-warning biomarkers associated with heart-exosome genetic-signature for acute myocardial infarction: A source-tracking study of exosome. J Cell Mol Med 2024; 28:e18334. [PMID: 38661439 PMCID: PMC11044819 DOI: 10.1111/jcmm.18334] [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: 11/10/2023] [Revised: 03/14/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
The genetic information of plasma total-exosomes originating from tissues have already proven useful to assess the severity of coronary artery diseases (CAD). However, plasma total-exosomes include multiple sub-populations secreted by various tissues. Only analysing the genetic information of plasma total-exosomes is perturbed by exosomes derived from other organs except the heart. We aim to detect early-warning biomarkers associated with heart-exosome genetic-signatures for acute myocardial infarction (AMI) by a source-tracking analysis of plasma exosome. The source-tracking of AMI plasma total-exosomes was implemented by deconvolution algorithm. The final early-warning biomarkers associated with heart-exosome genetic-signatures for AMI was identified by integration with single-cell sequencing, weighted gene correction network and machine learning analyses. The correlation between biomarkers and clinical indicators was validated in impatient cohort. A nomogram was generated using early-warning biomarkers for predicting the CAD progression. The molecular subtypes landscape of AMI was detected by consensus clustering. A higher fraction of exosomes derived from spleen and blood cells was revealed in plasma exosomes, while a lower fraction of heart-exosomes was detected. The gene ontology revealed that heart-exosomes genetic-signatures was associated with the heart development, cardiac function and cardiac response to stress. We ultimately identified three genes associated with heart-exosomes defining early-warning biomarkers for AMI. The early-warning biomarkers mediated molecular clusters presented heterogeneous metabolism preference in AMI. Our study introduced three early-warning biomarkers associated with heart-exosome genetic-signatures, which reflected the genetic information of heart-exosomes carrying AMI signals and provided new insights for exosomes research in CAD progression and prevention.
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Affiliation(s)
- Xiaojun Jin
- The Affiliated Lihuili Hospital of Ningbo UniversityHealth Science Center, Ningbo UniversityNingboZhejiangChina
| | - Weifeng Xu
- The Affiliated Lihuili Hospital of Ningbo UniversityHealth Science Center, Ningbo UniversityNingboZhejiangChina
| | - Qiaoping Wu
- The Affiliated Lihuili Hospital of Ningbo UniversityHealth Science Center, Ningbo UniversityNingboZhejiangChina
| | - Chen Huang
- Department of GeneticsThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Yongfei Song
- The Affiliated Lihuili Hospital of Ningbo UniversityHealth Science Center, Ningbo UniversityNingboZhejiangChina
| | - Jiangfang Lian
- The Affiliated Lihuili Hospital of Ningbo UniversityHealth Science Center, Ningbo UniversityNingboZhejiangChina
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Kuchynsky K, Stevens P, Hite A, Xie W, Diop K, Tang S, Pietrzak M, Khan S, Walter B, Purmessur D. Transcriptional profiling of human cartilage endplate cells identifies novel genes and cell clusters underlying degenerated and non-degenerated phenotypes. Arthritis Res Ther 2024; 26:12. [PMID: 38173036 PMCID: PMC10763221 DOI: 10.1186/s13075-023-03220-6] [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: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Low back pain is a leading cause of disability worldwide and is frequently attributed to intervertebral disc (IVD) degeneration. Though the contributions of the adjacent cartilage endplates (CEP) to IVD degeneration are well documented, the phenotype and functions of the resident CEP cells are critically understudied. To better characterize CEP cell phenotype and possible mechanisms of CEP degeneration, bulk and single-cell RNA sequencing of non-degenerated and degenerated CEP cells were performed. METHODS Human lumbar CEP cells from degenerated (Thompson grade ≥ 4) and non-degenerated (Thompson grade ≤ 2) discs were expanded for bulk (N=4 non-degenerated, N=4 degenerated) and single-cell (N=1 non-degenerated, N=1 degenerated) RNA sequencing. Genes identified from bulk RNA sequencing were categorized by function and their expression in non-degenerated and degenerated CEP cells were compared. A PubMed literature review was also performed to determine which genes were previously identified and studied in the CEP, IVD, and other cartilaginous tissues. For single-cell RNA sequencing, different cell clusters were resolved using unsupervised clustering and functional annotation. Differential gene expression analysis and Gene Ontology, respectively, were used to compare gene expression and functional enrichment between cell clusters, as well as between non-degenerated and degenerated CEP samples. RESULTS Bulk RNA sequencing revealed 38 genes were significantly upregulated and 15 genes were significantly downregulated in degenerated CEP cells relative to non-degenerated cells (|fold change| ≥ 1.5). Of these, only 2 genes were previously studied in CEP cells, and 31 were previously studied in the IVD and other cartilaginous tissues. Single-cell RNA sequencing revealed 11 unique cell clusters, including multiple chondrocyte and progenitor subpopulations with distinct gene expression and functional profiles. Analysis of genes in the bulk RNA sequencing dataset showed that progenitor cell clusters from both samples were enriched in "non-degenerated" genes but not "degenerated" genes. For both bulk- and single-cell analyses, gene expression and pathway enrichment analyses highlighted several pathways that may regulate CEP degeneration, including transcriptional regulation, translational regulation, intracellular transport, and mitochondrial dysfunction. CONCLUSIONS This thorough analysis using RNA sequencing methods highlighted numerous differences between non-degenerated and degenerated CEP cells, the phenotypic heterogeneity of CEP cells, and several pathways of interest that may be relevant in CEP degeneration.
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Affiliation(s)
- Kyle Kuchynsky
- Department of Biomedical Engineering, The Ohio State University, 3016 Fontana Laboratories, 140 W. 19th Ave, Columbus, OH, 43210, USA
| | - Patrick Stevens
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Amy Hite
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - William Xie
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Khady Diop
- Department of Biomedical Engineering, The Ohio State University, 3016 Fontana Laboratories, 140 W. 19th Ave, Columbus, OH, 43210, USA
| | - Shirley Tang
- Department of Biomedical Engineering, The Ohio State University, 3016 Fontana Laboratories, 140 W. 19th Ave, Columbus, OH, 43210, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Safdar Khan
- Department of Orthopaedics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Benjamin Walter
- Department of Biomedical Engineering, The Ohio State University, 3016 Fontana Laboratories, 140 W. 19th Ave, Columbus, OH, 43210, USA
| | - Devina Purmessur
- Department of Biomedical Engineering, The Ohio State University, 3016 Fontana Laboratories, 140 W. 19th Ave, Columbus, OH, 43210, USA.
- Department of Orthopaedics, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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Song J, Huang F, Chen L, Feng K, Jian F, Huang T, Cai YD. Identification of methylation signatures associated with CAR T cell in B-cell acute lymphoblastic leukemia and non-hodgkin’s lymphoma. Front Oncol 2022; 12:976262. [PMID: 36033519 PMCID: PMC9402909 DOI: 10.3389/fonc.2022.976262] [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: 06/23/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
CD19-targeted CAR T cell immunotherapy has exceptional efficacy for the treatment of B-cell malignancies. B-cell acute lymphocytic leukemia and non-Hodgkin’s lymphoma are two common B-cell malignancies with high recurrence rate and are refractory to cure. Although CAR T-cell immunotherapy overcomes the limitations of conventional treatments for such malignancies, failure of treatment and tumor recurrence remain common. In this study, we searched for important methylation signatures to differentiate CAR-transduced and untransduced T cells from patients with acute lymphoblastic leukemia and non-Hodgkin’s lymphoma. First, we used three feature ranking methods, namely, Monte Carlo feature selection, light gradient boosting machine, and least absolute shrinkage and selection operator, to rank all methylation features in order of their importance. Then, the incremental feature selection method was adopted to construct efficient classifiers and filter the optimal feature subsets. Some important methylated genes, namely, SERPINB6, ANK1, PDCD5, DAPK2, and DNAJB6, were identified. Furthermore, the classification rules for distinguishing different classes were established, which can precisely describe the role of methylation features in the classification. Overall, we applied advanced machine learning approaches to the high-throughput data, investigating the mechanism of CAR T cells to establish the theoretical foundation for modifying CAR T cells.
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Affiliation(s)
- Jiwei Song
- College of Life Science, Changchun Sci-Tech University, Shuangyang, China
| | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Fangfang Jian
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Tao Huang, ; Yu-Dong Cai,
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Squalene through Its Post-Squalene Metabolites Is a Modulator of Hepatic Transcriptome in Rabbits. Int J Mol Sci 2022; 23:ijms23084172. [PMID: 35456988 PMCID: PMC9031321 DOI: 10.3390/ijms23084172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
Squalene is a natural bioactive triterpene and an important intermediate in the biosynthesis of sterols. To assess the effect of this compound on the hepatic transcriptome, RNA-sequencing was carried out in two groups of male New Zealand rabbits fed either a diet enriched with 1% sunflower oil or the same diet with 0.5% squalene for 4 weeks. Hepatic lipids, lipid droplet area, squalene, and sterols were also monitored. The Squalene administration downregulated 9 transcripts and upregulated 13 transcripts. The gene ontology of transcripts fitted into the following main categories: transporter of proteins and sterols, lipid metabolism, lipogenesis, anti-inflammatory and anti-cancer properties. When the results were confirmed by RT-qPCR, rabbits receiving squalene displayed significant hepatic expression changes of LOC100344884 (PNPLA3), GCK, TFCP2L1, ASCL1, ACSS2, OST4, FAM91A1, MYH6, LRRC39, LOC108176846, GLT1D1 and TREH. A squalene-enriched diet increased hepatic levels of squalene, lanosterol, dihydrolanosterol, lathosterol, zymostenol and desmosterol. Strong correlations were found among specific sterols and some squalene-changed transcripts. Incubation of the murine AML12 hepatic cell line in the presence of lanosterol, dihydrolanosterol, zymostenol and desmosterol reproduced the observed changes in the expressions of Acss2, Fam91a1 and Pnpla3. In conclusion, these findings indicate that the squalene and post-squalene metabolites play important roles in hepatic transcriptional changes required to protect the liver against malfunction.
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Patel C, Saad H, Shenkman M, Lederkremer GZ. Oxidoreductases in Glycoprotein Glycosylation, Folding, and ERAD. Cells 2020; 9:cells9092138. [PMID: 32971745 PMCID: PMC7563561 DOI: 10.3390/cells9092138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
N-linked glycosylation and sugar chain processing, as well as disulfide bond formation, are among the most common post-translational protein modifications taking place in the endoplasmic reticulum (ER). They are essential modifications that are required for membrane and secretory proteins to achieve their correct folding and native structure. Several oxidoreductases responsible for disulfide bond formation, isomerization, and reduction have been shown to form stable, functional complexes with enzymes and chaperones that are involved in the initial addition of an N-glycan and in folding and quality control of the glycoproteins. Some of these oxidoreductases are selenoproteins. Recent studies also implicate glycan machinery–oxidoreductase complexes in the recognition and processing of misfolded glycoproteins and their reduction and targeting to ER-associated degradation. This review focuses on the intriguing cooperation between the glycoprotein-specific cell machineries and ER oxidoreductases, and highlights open questions regarding the functions of many members of this large family.
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Affiliation(s)
- Chaitanya Patel
- The Shmunis School of Biomedicine and Cancer Research, Cell Biology Division, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (C.P.); (H.S.); (M.S.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haddas Saad
- The Shmunis School of Biomedicine and Cancer Research, Cell Biology Division, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (C.P.); (H.S.); (M.S.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marina Shenkman
- The Shmunis School of Biomedicine and Cancer Research, Cell Biology Division, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (C.P.); (H.S.); (M.S.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gerardo Z. Lederkremer
- The Shmunis School of Biomedicine and Cancer Research, Cell Biology Division, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (C.P.); (H.S.); (M.S.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence:
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10
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Steinberg R, Origi A, Natriashvili A, Sarmah P, Licheva M, Walker PM, Kraft C, High S, Luirink J, Shi WQ, Helmstädter M, Ulbrich MH, Koch HG. Posttranslational insertion of small membrane proteins by the bacterial signal recognition particle. PLoS Biol 2020; 18:e3000874. [PMID: 32997663 PMCID: PMC7549839 DOI: 10.1371/journal.pbio.3000874] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/12/2020] [Accepted: 09/02/2020] [Indexed: 01/05/2023] Open
Abstract
Small membrane proteins represent a largely unexplored yet abundant class of proteins in pro- and eukaryotes. They essentially consist of a single transmembrane domain and are associated with stress response mechanisms in bacteria. How these proteins are inserted into the bacterial membrane is unknown. Our study revealed that in Escherichia coli, the 27-amino-acid-long model protein YohP is recognized by the signal recognition particle (SRP), as indicated by in vivo and in vitro site-directed cross-linking. Cross-links to SRP were also observed for a second small membrane protein, the 33-amino-acid-long YkgR. However, in contrast to the canonical cotranslational recognition by SRP, SRP was found to bind to YohP posttranslationally. In vitro protein transport assays in the presence of a SecY inhibitor and proteoliposome studies demonstrated that SRP and its receptor FtsY are essential for the posttranslational membrane insertion of YohP by either the SecYEG translocon or by the YidC insertase. Furthermore, our data showed that the yohP mRNA localized preferentially and translation-independently to the bacterial membrane in vivo. In summary, our data revealed that YohP engages an unique SRP-dependent posttranslational insertion pathway that is likely preceded by an mRNA targeting step. This further highlights the enormous plasticity of bacterial protein transport machineries.
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Affiliation(s)
- Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Ana Natriashvili
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Pinku Sarmah
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Princess M. Walker
- Department of Chemistry, Ball State University, Muncie, Indiana, United States of America
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Stephen High
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Joen Luirink
- Molecular Microbiology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Wei. Q. Shi
- Department of Chemistry, Ball State University, Muncie, Indiana, United States of America
| | - Martin Helmstädter
- Internal Medicine IV, Department of Medicine, Medical Center − University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian H. Ulbrich
- Internal Medicine IV, Department of Medicine, Medical Center − University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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11
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Knopf JD, Landscheidt N, Pegg CL, Schulz BL, Kühnle N, Chao CW, Huck S, Lemberg MK. Intramembrane protease RHBDL4 cleaves oligosaccharyltransferase subunits to target them for ER-associated degradation. J Cell Sci 2020; 133:jcs243790. [PMID: 32005703 DOI: 10.1242/jcs.243790] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/21/2020] [Indexed: 08/31/2023] Open
Abstract
The endoplasmic reticulum (ER)-resident intramembrane rhomboid protease RHBDL4 generates metastable protein fragments and together with the ER-associated degradation (ERAD) machinery provides a clearance mechanism for aberrant and surplus proteins. However, the endogenous substrate spectrum and with that the role of RHBDL4 in physiological ERAD is mainly unknown. Here, we use a substrate trapping approach in combination with quantitative proteomics to identify physiological RHBDL4 substrates. This revealed oligosaccharyltransferase (OST) complex subunits such as the catalytic active subunit STT3A as substrates for the RHBDL4-dependent ERAD pathway. RHBDL4-catalysed cleavage inactivates OST subunits by triggering dislocation into the cytoplasm and subsequent proteasomal degradation. RHBDL4 thereby controls the abundance and activity of OST, suggesting a novel link between the ERAD machinery and glycosylation tuning.
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Affiliation(s)
- Julia D Knopf
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Nina Landscheidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Nathalie Kühnle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Chao-Wei Chao
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Simon Huck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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12
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Tamana S, Promponas VJ. An updated view of the oligosaccharyltransferase complex in Plasmodium. Glycobiology 2019; 29:385-396. [PMID: 30835280 DOI: 10.1093/glycob/cwz011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 01/27/2019] [Accepted: 03/04/2019] [Indexed: 12/18/2022] Open
Abstract
Despite the controversy regarding the importance of protein N-linked glycosylation in species of the genus Plasmodium, genes potentially encoding core subunits of the oligosaccharyltransferase (OST) complex have already been characterized in completely sequenced genomes of malaria parasites. Nevertheless, the currently established notion is that only four out of eight subunits of the OST complex-which is considered conserved across eukaryotes-are present in Plasmodium species. In this study, we carefully conduct computational analysis to provide unequivocal evidence that all components of the OST complex, with the exception of Swp1/Ribophorin II, can be reliably identified within completely sequenced plasmodial genomes. In fact, most of the subunits currently considered as absent from Plasmodium refer to uncharacterized protein sequences already existing in sequence databases. Interestingly, the main reason why the unusually short Ost4 subunit (36 residues long in yeast) has not been identified so far in plasmodia (and possibly other species) is the failure of gene-prediction pipelines to detect such a short coding sequence. We further identify elusive OST subunits in select protist species with completely sequenced genomes. Thus, our work highlights the necessity of a systematic approach towards the characterization of OST subunits across eukaryotes. This is necessary both for obtaining a concrete picture of the evolution of the OST complex but also for elucidating its possible role in eukaryotic pathogens.
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Affiliation(s)
- Stella Tamana
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, CY, Nicosia, Cyprus
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, CY, Nicosia, Cyprus
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13
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Ramírez AS, Kowal J, Locher KP. Cryo–electron microscopy structures of human oligosaccharyltransferase complexes OST-A and OST-B. Science 2019; 366:1372-1375. [DOI: 10.1126/science.aaz3505] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Abstract
Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan onto secretory proteins in the endoplasmic reticulum. Mammals express two distinct OST complexes that act in a cotranslational (OST-A) or posttranslocational (OST-B) manner. Here, we present high-resolution cryo–electron microscopy structures of human OST-A and OST-B. Although they have similar overall architectures, structural differences in the catalytic subunits STT3A and STT3B facilitate contacts to distinct OST subunits, DC2 in OST-A and MAGT1 in OST-B. In OST-A, interactions with TMEM258 and STT3A allow ribophorin-I to form a four-helix bundle that can bind to a translating ribosome, whereas the equivalent region is disordered in OST-B. We observed an acceptor peptide and dolichylphosphate bound to STT3B, but only dolichylphosphate in STT3A, suggesting distinct affinities of the two OST complexes for protein substrates.
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Affiliation(s)
- Ana S. Ramírez
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland
| | - Julia Kowal
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland
| | - Kaspar P. Locher
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland
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14
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Harada Y, Ohkawa Y, Kizuka Y, Taniguchi N. Oligosaccharyltransferase: A Gatekeeper of Health and Tumor Progression. Int J Mol Sci 2019; 20:ijms20236074. [PMID: 31810196 PMCID: PMC6929149 DOI: 10.3390/ijms20236074] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 02/06/2023] Open
Abstract
Oligosaccharyltransferase (OST) is a multi-span membrane protein complex that catalyzes the addition of glycans to selected Asn residues within nascent polypeptides in the lumen of the endoplasmic reticulum. This process, termed N-glycosylation, is a fundamental post-translational protein modification that is involved in the quality control, trafficking of proteins, signal transduction, and cell-to-cell communication. Given these crucial roles, N-glycosylation is essential for homeostasis at the systemic and cellular levels, and a deficiency in genes that encode for OST subunits often results in the development of complex genetic disorders. A growing body of evidence has also demonstrated that the expression of OST subunits is cell context-dependent and is frequently altered in malignant cells, thus contributing to tumor cell survival and proliferation. Importantly, a recently developed inhibitor of OST has revealed this enzyme as a potential target for the treatment of incurable drug-resistant tumors. This review summarizes our current knowledge regarding the functions of OST in the light of health and tumor progression, and discusses perspectives on the clinical relevance of inhibiting OST as a tumor treatment.
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Affiliation(s)
- Yoichiro Harada
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka 541-8567, Japan; (Y.H.); (Y.O.)
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka 541-8567, Japan; (Y.H.); (Y.O.)
| | - Yasuhiko Kizuka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan;
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka 541-8567, Japan; (Y.H.); (Y.O.)
- Correspondence: ; Tel.: +81-6-6945-1181
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15
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Ji Z, Chao T, Zhang C, Liu Z, Hou L, Wang J, Wang A, Wang Y, Zhou J, Xuan R, Wang G, Wang J. Transcriptome Analysis of Dairy Goat Mammary Gland Tissues from Different Lactation Stages. DNA Cell Biol 2019; 38:129-143. [DOI: 10.1089/dna.2018.4349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Chunlan Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Zhaohua Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Lei Hou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Jin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Aili Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Yong Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Jie Zhou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Rong Xuan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
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16
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Wu GQ, Wang JL, Feng RJ, Li SJ, Wang CM. iTRAQ-Based Comparative Proteomic Analysis Provides Insights into Molecular Mechanisms of Salt Tolerance in Sugar Beet ( Beta vulgaris L.). Int J Mol Sci 2018; 19:ijms19123866. [PMID: 30518064 PMCID: PMC6321137 DOI: 10.3390/ijms19123866] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 01/24/2023] Open
Abstract
Salinity is one of the major abiotic stress factors that limit plant growth and crop yield worldwide. To understand the molecular mechanisms and screen the key proteins in response of sugar beet (Beta vulgaris L.) to salt, in the present study, the proteomics of roots and shoots in three-week-old sugar beet plants exposed to 50 mM NaCl for 72 h was investigated by isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technology. The results showed that 105 and 30 differentially expressed proteins (DEPs) were identified in roots and shoots of salt-treated plants compared with untreated plants, respectively. There were 46 proteins up-regulated and 59 proteins down-regulated in roots; and 13 up-regulated proteins and 17 down-regulated proteins found in shoots, respectively. These DEPs were mainly involved in carbohydrate metabolism, energy metabolism, lipid metabolism, biosynthesis of secondary metabolites, transcription, translation, protein folding, sorting, and degradation as well as transport. It is worth emphasizing that some novel salt-responsive proteins were identified, such as PFK5, MDH, KAT2, ACAD10, CYP51, F3H, TAL, SRPR, ZOG, V-H+-ATPase, V-H+-PPase, PIPs, TIPs, and tubulin α-2/β-1 chain. qRT-PCR analysis showed that six of the selected proteins, including BvPIP1-4, BvVP and BvVAP in root and BvTAL, BvURO-D1, and BvZOG in shoot, displayed good correlation between the expression levels of protein and mRNA. These novel proteins provide a good starting point for further research into their functions using genetic or other approaches. These findings should significantly improve the understanding of the molecular mechanisms involved in salt tolerance of sugar beet plants.
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Affiliation(s)
- Guo-Qiang Wu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Jin-Long Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Rui-Jun Feng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Shan-Jia Li
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Chun-Mei Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, CAAS, Lanzhou 730050, China.
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17
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McVeigh P, Cwiklinski K, Garcia-Campos A, Mulcahy G, O'Neill SM, Maule AG, Dalton JP. In silico analyses of protein glycosylating genes in the helminth Fasciola hepatica (liver fluke) predict protein-linked glycan simplicity and reveal temporally-dynamic expression profiles. Sci Rep 2018; 8:11700. [PMID: 30076319 PMCID: PMC6076252 DOI: 10.1038/s41598-018-29673-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/04/2018] [Indexed: 01/05/2023] Open
Abstract
Glycoproteins secreted by helminth parasites are immunogenic and represent appealing components of vaccine preparations. Our poor knowledge of the pathways that mediate protein glycosylation in parasitic flatworms hinders our understanding of how proteins are synthesised and modified, and our ability to target these pathways for parasite control. Here we provide the first detailed description of genes associated with protein glycosylation in a parasitic flatworm, focusing on the genome of the liver fluke (Fasciola hepatica), which is a globally important trematode parasite of humans and their livestock. Using 190 human sequences as search queries against currently available F. hepatica genomes, we identified 149 orthologues with putative roles in sugar uptake or nucleotide sugar synthesis, and an array of glycosyltransferase and glycosidase activities required for protein N- and O-glycosylation. We found appreciable duplication within these orthologues, describing just 87 non-redundant genes when paralogues were excluded. F. hepatica lacks many of the enzymes required to produce complex N- and O-linked glycans, which explains the genomic basis for the structurally simple glycans described by F. hepatica glycomic datasets, and predicts pervasive structural simplicity in the wider glycome. These data provide a foundation for functional genomic interrogation of these pathways with the view towards novel parasite intervention strategies.
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Affiliation(s)
- Paul McVeigh
- Parasitology & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK.
| | - Krystyna Cwiklinski
- Parasitology & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | | | - Grace Mulcahy
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Sandra M O'Neill
- Department of Biotechnology, Dublin City University, Dublin, Ireland
| | - Aaron G Maule
- Parasitology & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - John P Dalton
- Parasitology & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
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18
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Wild R, Kowal J, Eyring J, Ngwa EM, Aebi M, Locher KP. Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation. Science 2018; 359:545-550. [PMID: 29301962 DOI: 10.1126/science.aar5140] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/22/2017] [Indexed: 12/18/2022]
Abstract
Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to glycosylation sites of secretory proteins. Here we describe the atomic structure of yeast OST determined by cryo-electron microscopy, revealing a conserved subunit arrangement. The active site of the catalytic STT3 subunit points away from the center of the complex, allowing unhindered access to substrates. The dolichol-pyrophosphate moiety binds to a lipid-exposed groove of STT3, whereas two noncatalytic subunits and an ordered N-glycan form a membrane-proximal pocket for the oligosaccharide. The acceptor polypeptide site faces an oxidoreductase domain in stand-alone OST complexes or is immediately adjacent to the translocon, suggesting how eukaryotic OSTs efficiently glycosylate a large number of polypeptides before their folding.
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Affiliation(s)
- Rebekka Wild
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Julia Kowal
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Jillianne Eyring
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Elsy M Ngwa
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.
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19
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Kitajima T, Xue W, Liu YS, Wang CD, Liu SS, Fujita M, Gao XD. Construction of green fluorescence protein mutant to monitor STT3B-dependent N-glycosylation. FEBS J 2017; 285:915-928. [PMID: 29282902 DOI: 10.1111/febs.14375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/06/2017] [Accepted: 12/21/2017] [Indexed: 12/21/2022]
Abstract
Oligosaccharyltransferases (OSTs) mediate the en bloc transfer of N-glycan intermediates onto the asparagine residue in glycosylation sequons (N-X-S/T, X≠P). These enzymes are typically heteromeric complexes composed of several membrane-associated subunits, in which STT3 is highly conserved as a catalytic core. Metazoan organisms encode two STT3 genes (STT3A and STT3B) in their genome, resulting in the formation of at least two distinct OST isoforms consisting of shared subunits and complex specific subunits. The STT3A isoform of OST primarily glycosylates substrate polypeptides cotranslationally, whereas the STT3B isoform is involved in cotranslational and post-translocational glycosylation of sequons that are skipped by the STT3A isoform. Here, we describe mutant constructs of monomeric enhanced green fluorescent protein (mEGFP), which are susceptible to STT3B-dependent N-glycosylation. The endoplasmic reticulum-localized mEGFP (ER-mEGFP) mutants contained an N-glycosylation sequon at their C-terminus and exhibited increased fluorescence in response to N-glycosylation. Isoform-specific glycosylation of the constructs was confirmed by using STT3A- or STT3B-knockout cell lines. Among the mutant constructs that we tested, the ER-mEGFP mutant containing the N185 -C186 -T187 sequon was the best substrate for the STT3B isoform in terms of glycosylation efficiency and fluorescence change. Our results suggest that the mutant ER-mEGFP is useful for monitoring STT3B-dependent post-translocational N-glycosylation in cells of interest, such as those from putative patients with a congenital disorder of glycosylation.
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Affiliation(s)
- Toshihiko Kitajima
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wei Xue
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Chun-Di Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Si-Si Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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20
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Hamieh A, Cartier D, Abid H, Calas A, Burel C, Bucharles C, Jehan C, Grumolato L, Landry M, Lerouge P, Anouar Y, Lihrmann I. Selenoprotein T is a novel OST subunit that regulates UPR signaling and hormone secretion. EMBO Rep 2017; 18:1935-1946. [PMID: 28928140 DOI: 10.15252/embr.201643504] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 08/04/2017] [Accepted: 08/09/2017] [Indexed: 12/12/2022] Open
Abstract
Selenoprotein T (SelT) is a recently characterized thioredoxin-like protein whose expression is very high during development, but is confined to endocrine tissues in adulthood where its function is unknown. We report here that SelT is required for adaptation to the stressful conditions of high hormone level production in endocrine cells. Using immunofluorescence and TEM immunogold approaches, we find that SelT is expressed at the endoplasmic reticulum membrane in all hormone-producing pituitary cell types. SelT knockdown in corticotrope cells promotes unfolded protein response (UPR) and ER stress and lowers endoplasmic reticulum-associated protein degradation (ERAD) and hormone production. Using a screen in yeast for SelT-membrane protein interactions, we sort keratinocyte-associated protein 2 (KCP2), a subunit of the protein complex oligosaccharyltransferase (OST). In fact, SelT interacts not only with KCP2 but also with other subunits of the A-type OST complex which are depleted after SelT knockdown leading to POMC N-glycosylation defects. This study identifies SelT as a novel subunit of the A-type OST complex, indispensable for its integrity and for ER homeostasis, and exerting a pivotal adaptive function that allows endocrine cells to properly achieve the maturation and secretion of hormones.
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Affiliation(s)
- Abdallah Hamieh
- Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen-Normandie University UNIROUEN, Inserm, U1239, Mont-Saint-Aignan, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Dorthe Cartier
- Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen-Normandie University UNIROUEN, Inserm, U1239, Mont-Saint-Aignan, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Houssni Abid
- Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen-Normandie University UNIROUEN, Inserm, U1239, Mont-Saint-Aignan, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - André Calas
- Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, University of Bordeaux, Bordeaux, France
| | - Carole Burel
- Institute for Research and Innovation in Biomedicine, Rouen, France.,Glyco-MEV Laboratory, Rouen-Normandie University UNIROUEN, Mont-Saint-Aignan, France
| | - Christine Bucharles
- Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen-Normandie University UNIROUEN, Inserm, U1239, Mont-Saint-Aignan, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Cedric Jehan
- Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen-Normandie University UNIROUEN, Inserm, U1239, Mont-Saint-Aignan, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Luca Grumolato
- Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen-Normandie University UNIROUEN, Inserm, U1239, Mont-Saint-Aignan, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Marc Landry
- Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, University of Bordeaux, Bordeaux, France
| | - Patrice Lerouge
- Institute for Research and Innovation in Biomedicine, Rouen, France.,Glyco-MEV Laboratory, Rouen-Normandie University UNIROUEN, Mont-Saint-Aignan, France
| | - Youssef Anouar
- Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen-Normandie University UNIROUEN, Inserm, U1239, Mont-Saint-Aignan, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Isabelle Lihrmann
- Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen-Normandie University UNIROUEN, Inserm, U1239, Mont-Saint-Aignan, France .,Institute for Research and Innovation in Biomedicine, Rouen, France
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21
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Blomen VA, Májek P, Jae LT, Bigenzahn JW, Nieuwenhuis J, Staring J, Sacco R, van Diemen FR, Olk N, Stukalov A, Marceau C, Janssen H, Carette JE, Bennett KL, Colinge J, Superti-Furga G, Brummelkamp TR. Gene essentiality and synthetic lethality in haploid human cells. Science 2015; 350:1092-6. [PMID: 26472760 DOI: 10.1126/science.aac7557] [Citation(s) in RCA: 618] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 10/01/2015] [Indexed: 12/11/2022]
Abstract
Although the genes essential for life have been identified in less complex model organisms, their elucidation in human cells has been hindered by technical barriers. We used extensive mutagenesis in haploid human cells to identify approximately 2000 genes required for optimal fitness under culture conditions. To study the principles of genetic interactions in human cells, we created a synthetic lethality network focused on the secretory pathway based exclusively on mutations. This revealed a genetic cross-talk governing Golgi homeostasis, an additional subunit of the human oligosaccharyltransferase complex, and a phosphatidylinositol 4-kinase β adaptor hijacked by viruses. The synthetic lethality map parallels observations made in yeast and projects a route forward to reveal genetic networks in diverse aspects of human cell biology.
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Affiliation(s)
- Vincent A Blomen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Lucas T Jae
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Joppe Nieuwenhuis
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Jacqueline Staring
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Roberto Sacco
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Ferdy R van Diemen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Nadine Olk
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Caleb Marceau
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Hans Janssen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. University of Montpellier, Institut de Recherche en Cancérologie de Montpellier Inserm U1194, Institut régional du Cancer Montpellier, 34000 Montpellier, France.
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
| | - Thijn R Brummelkamp
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. Cancer Genomics Center (CGC.nl), Plesmanlaan 121, 1066CX, Amsterdam, Netherlands.
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22
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Xu Y, Bailey UM, Schulz BL. Automated measurement of site-specific N
-glycosylation occupancy with SWATH-MS. Proteomics 2015; 15:2177-86. [DOI: 10.1002/pmic.201400465] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/08/2015] [Accepted: 02/27/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Ying Xu
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Ulla-Maja Bailey
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
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23
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Shrimal S, Cherepanova NA, Gilmore R. Cotranslational and posttranslocational N-glycosylation of proteins in the endoplasmic reticulum. Semin Cell Dev Biol 2014; 41:71-8. [PMID: 25460543 DOI: 10.1016/j.semcdb.2014.11.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022]
Abstract
Asparagine linked glycosylation of proteins is an essential protein modification reaction in most eukaryotic organisms. N-linked oligosaccharides are important for protein folding and stability, biosynthetic quality control, intracellular traffic and the physiological function of many N-glycosylated proteins. In metazoan organisms, the oligosaccharyltransferase is composed of a catalytic subunit (STT3A or STT3B) and a set of accessory subunits. Duplication of the catalytic subunit gene allowed cells to evolve OST complexes that act sequentially to maximize the glycosylation efficiency of the large number of proteins that are glycosylated in metazoan organisms. We will summarize recent progress in understanding the mechanism of (a) cotranslational glycosylation by the translocation channel associated STT3A complex, (b) the role of the STT3B complex in mediating cotranslational or posttranslocational glycosylation of acceptor sites that have been skipped by the STT3A complex, and (c) the role of the oxidoreductase MagT1 in STT3B-dependent glycosylation of cysteine-proximal acceptor sites.
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Affiliation(s)
- Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States
| | - Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States.
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24
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Cherepanova NA, Shrimal S, Gilmore R. Oxidoreductase activity is necessary for N-glycosylation of cysteine-proximal acceptor sites in glycoproteins. ACTA ACUST UNITED AC 2014; 206:525-39. [PMID: 25135935 PMCID: PMC4137057 DOI: 10.1083/jcb.201404083] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Stabilization of protein tertiary structure by disulfides can interfere with glycosylation of acceptor sites (NXT/S) in nascent polypeptides. Here, we show that MagT1, an ER-localized thioredoxin homologue, is a subunit of the STT3B isoform of the oligosaccharyltransferase (OST). The lumenally oriented active site CVVC motif in MagT1 is required for glycosylation of STT3B-dependent acceptor sites including those that are closely bracketed by disulfides or contain cysteine as the internal residue (NCT/S). The MagT1- and STT3B-dependent glycosylation of cysteine-proximal acceptor sites can be reduced by eliminating cysteine residues. The predominant form of MagT1 in vivo is oxidized, which is consistent with transient formation of mixed disulfides between MagT1 and a glycoprotein substrate to facilitate access of STT3B to unmodified acceptor sites. Cotranslational N-glycosylation by the STT3A isoform of the OST, which lacks MagT1, allows efficient modification of acceptor sites in cysteine-rich protein domains before disulfide bond formation. Thus, mammalian cells use two mechanisms to achieve N-glycosylation of cysteine proximal acceptor sites.
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Affiliation(s)
- Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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