51
|
Yin K, Tong M, Sun F, Wu R. Quantitative Structural Proteomics Unveils the Conformational Changes of Proteins under the Endoplasmic Reticulum Stress. Anal Chem 2022; 94:13250-13260. [PMID: 36108266 PMCID: PMC9789690 DOI: 10.1021/acs.analchem.2c03076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein structures are decisive for their activities and interactions with other molecules. Global analysis of protein structures and conformational changes cannot be achieved by commonly used abundance-based proteomics. Here, we integrated cysteine covalent labeling, selective enrichment, and quantitative proteomics to study protein structures and structural changes on a large scale. This method was applied to globally investigate protein structures in HEK293T cells and protein structural changes in the cells with the tunicamycin (Tm)-induced endoplasmic reticulum (ER) stress. We quantified several thousand cysteine residues, which contain unprecedented and valuable information of protein structures. Combining this method with pulsed stable isotope labeling by amino acids in cell culture, we further analyzed the folding state differences between pre-existing and newly synthesized proteins in cells under the Tm treatment. Besides newly synthesized proteins, unexpectedly, many pre-existing proteins were found to become unfolded upon ER stress, especially those related to gene transcription and protein translation. Furthermore, the current results reveal that N-glycosylation plays a more important role in the folding process of the tertiary and quaternary structures than the secondary structures for newly synthesized proteins. Considering the importance of cysteine in protein structures, this method can be extensively applied in the biological and biomedical research fields.
Collapse
Affiliation(s)
- Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ming Tong
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
52
|
Griffin ME, Hsieh-Wilson LC. Tools for mammalian glycoscience research. Cell 2022; 185:2657-2677. [PMID: 35809571 PMCID: PMC9339253 DOI: 10.1016/j.cell.2022.06.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Cellular carbohydrates or glycans are critical mediators of biological function. Their remarkably diverse structures and varied activities present exciting opportunities for understanding many areas of biology. In this primer, we discuss key methods and recent breakthrough technologies for identifying, monitoring, and manipulating glycans in mammalian systems.
Collapse
Affiliation(s)
- Matthew E. Griffin
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Linda C. Hsieh-Wilson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 92115, USA,Correspondence: (L.C.H.W.)
| |
Collapse
|
53
|
Cao P, Yang X, Liu D, Ye S, Yang W, Xie Z, Lei X. Research progress of
PD‐L1
non‐glycosylation in cancer immunotherapy. Scand J Immunol 2022. [DOI: 10.1111/sji.13205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pu Cao
- School of Pharmacy, Hengyang Medical College, University of South China Hengyang Hunan P.R. China
| | - Xiaoyan Yang
- School of Pharmacy, Hengyang Medical College, University of South China Hengyang Hunan P.R. China
| | - Daquan Liu
- School of Pharmacy, Hengyang Medical College, University of South China Hengyang Hunan P.R. China
| | - Simin Ye
- School of Pharmacy, Hengyang Medical College, University of South China Hengyang Hunan P.R. China
| | - Wei Yang
- School of Pharmacy, Hengyang Medical College, University of South China Hengyang Hunan P.R. China
| | - Zhizhong Xie
- School of Pharmacy, Hengyang Medical College, University of South China Hengyang Hunan P.R. China
| | - Xiaoyong Lei
- School of Pharmacy, Hengyang Medical College, University of South China Hengyang Hunan P.R. China
- The Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China Hengyang Hunan P.R. China
| |
Collapse
|
54
|
Herrera-Estala AL, Fuentes-Garibay JA, Guerrero-Olazarán M, Viader-Salvadó JM. Low specific growth rate and temperature in fed-batch cultures of a beta-propeller phytase producing Pichia pastoris strain under GAP promoter trigger increased KAR2 and PSA1-1 gene expression yielding enhanced extracellular productivity. J Biotechnol 2022; 352:59-67. [PMID: 35618082 DOI: 10.1016/j.jbiotec.2022.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/30/2023]
Abstract
Previously, we showed that the methylotrophic yeast Pichia pastoris (syn. Komagataella phaffii) could produce and secrete the beta-propeller phytase FTEII in an active form under the control of the AOX1 promoter and methanol as the inductor. In this work, we engineered P. pastoris strains to construct a constitutive P. pastoris expression system (GAP promoter) and extracellularly produce the phytase FTEII. We optimized the culture conditions to increase the extracellular volumetric phytase productivity (Qp) and evaluated the impact of the optimization process on the physiological response of the host. Moreover, we analyzed the expression levels of the FTEII gene and endogenous genes for P. pastoris cells in cultures with the lowest and highest Qp to understand which processes (from heterologous gene expression to protein secretion) might be responsible for the increase in Qp. The results indicate that a low specific growth rate and temperature in the fed-batch phase increases the Qp, which was correlated with an upregulation of the KAR2 and PSA1-1/MPG1 genes rather than increased heterologous gene transcription.
Collapse
Affiliation(s)
- Ana Lucía Herrera-Estala
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Biológicas, Instituto de Biotecnología, 66455 San Nicolás de los Garza, N.L., Mexico
| | - José Antonio Fuentes-Garibay
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Biológicas, Instituto de Biotecnología, 66455 San Nicolás de los Garza, N.L., Mexico
| | - Martha Guerrero-Olazarán
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Biológicas, Instituto de Biotecnología, 66455 San Nicolás de los Garza, N.L., Mexico
| | - José María Viader-Salvadó
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Biológicas, Instituto de Biotecnología, 66455 San Nicolás de los Garza, N.L., Mexico.
| |
Collapse
|
55
|
Gao Z, He Y, He Q, Wei W, Luo Y, Ma Z, Chen W, Chu F, Zhang S, Liu Y, Pan Y. Multidimensional identification of disaccharide isomers based on non-covalent complexes and tandem mass spectrometry. Talanta 2022; 249:123674. [PMID: 35717753 DOI: 10.1016/j.talanta.2022.123674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/26/2022]
Abstract
Glycans are the most abundant organic polymers in nature. They are essential to living organisms and regulate a wide range of biological functions. However, mass spectrometry-based identification of glycan isomers remains challenging due to the complexity of their structures including their complex compositions, linkages, and anomeric configurations. In this study, two novel complex ions, the mononuclear copper-bound dimeric ions [(Cu2+)(A)(L-His)-H]+ and the mononuclear copper-bound quaternary ions [(Cu2+)(A)(L-Ser)3-H]+ (where A denotes a disaccharide, and L-Ser/His denotes l-serine/histidine), were designed for the collision-induced dissociation-based identification and relative quantification of 14 disaccharide isomers. When the unique fragmentation patterns of the above two types of complex ions were mapped into a three-dimensional vector, all the isomers were completely distinguished. Of note, the established method is able to identify mixtures of linkage isomers only using tandem mass spectrometry based on linkage-specific fragment ions of histidine-based complex ions. Finally, the method was successfully applied to the identification and relative quantification of two disaccharide isomers (lactose and sucrose) in dairy beverages. In conclusion, the established method is sensitive to subtle structural differences in disaccharide isomers and has the potential to be used for the differentiation of various glycans.
Collapse
Affiliation(s)
- Zhan Gao
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yuwen He
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Quan He
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Wei Wei
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yuanqing Luo
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Zihan Ma
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Weiwei Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Fengjian Chu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, 310027, PR China
| | - Shuheng Zhang
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yaqin Liu
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China.
| |
Collapse
|
56
|
Cheng J, Xia L, Hao X, Gan F, Bai Y, Zhang C, Mao Y, Zhu Y, Pu Q, Park DW, Tavolari S, Mei J, Chen Y, Deng S, Liu L. Targeting STT3A produces an anti-tumor effect in lung adenocarcinoma by blocking the MAPK and PI3K/AKT signaling pathway. Transl Lung Cancer Res 2022; 11:1089-1107. [PMID: 35832442 PMCID: PMC9271429 DOI: 10.21037/tlcr-22-396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/17/2022] [Indexed: 02/05/2023]
Abstract
Background Glycosylation is crucial for the stability and biological functions of proteins. The aberrant glycosylation of critical proteins plays an important role in multiple cancers, including lung adenocarcinoma (LUAD). STT3 oligosaccharyltransferase complex catalytic subunit A (STT3A) is a major isoform of N-linked glycosyltransferase that catalyzes the glycosylation of various proteins. However, the functions of STT3A in LUAD are still unclear. Methods The expression profiles of STT3A were initially analyzed in public data sets and then validated by quantitative real-time polymerase chain reaction, Western blot and immunohistochemistry assays in clinical LUAD samples. The overall survival (OS) between patients with high and low STT3A expression was compared using a Kaplan-Meier curve with a log-rank analysis. STT3A was knocked-out using CRISPR/Cas9 and inhibited by NGI-1. Cell Counting Kit-8, colony formation assay, wound-healing, transwell assay, and flow cytometry were performed to assess the cellular functions of STT3A in vitro. A mice xenograft model was established to investigate the effects of STT3A on tumor growth in vivo. Further, the downstream signaling pathways of STT3A were screened by mass spectrometry with a bioinformatics analysis, and the activation of the target pathways were subsequently validated by Western blot. Results The expression of STT3A was frequently upregulated in LUAD tissues than normal lung tissues. The high expression of STT3A was significantly associated with poor OS in LUAD patients. The knockout or inhibition of STT3A suppressed proliferation, migration, and invasion, and arrested the cell cycle of LUAD cell lines in vitro. Similarly, the knockout or inhibition of STT3A suppressed tumor growth in vivo. In terms of molecular mechanism, STT3A may promote LUAD progression by activating the mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-kinase and protein kinase B (PI3K/AKT) pathways and regulating the epithelial-mesenchymal transition. Conclusions STT3A promotes LUAD progression via the MAPK and PI3K/AKT signaling pathways and could serve as a novel prognostic biomarker and potential therapeutic target for LUAD patients.
Collapse
Affiliation(s)
- Jiahan Cheng
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Liang Xia
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaohu Hao
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Fanyi Gan
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yuquan Bai
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Chuanfen Zhang
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yunke Zhu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Qiang Pu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Dong Won Park
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Simona Tavolari
- Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria of Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Jiandong Mei
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yaohui Chen
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Senyi Deng
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lunxu Liu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
57
|
Xue Y, Meng JG, Jia PF, Zhang ZR, Li HJ, Yang WC. POD1-SUN-CRT3 chaperone complex guards the ER sorting of LRR receptor kinases in Arabidopsis. Nat Commun 2022; 13:2703. [PMID: 35577772 PMCID: PMC9110389 DOI: 10.1038/s41467-022-30179-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
Abstract
Protein sorting in the secretory pathway is essential for cellular compartmentalization and homeostasis in eukaryotic cells. The endoplasmic reticulum (ER) is the biosynthetic and folding factory of secretory cargo proteins. The cargo transport from the ER to the Golgi is highly selective, but the molecular mechanism for the sorting specificity is unclear. Here, we report that three ER membrane localized proteins, SUN3, SUN4 and SUN5, regulate ER sorting of leucine-rich repeat receptor kinases (LRR-RKs) to the plasma membrane. The triple mutant sun3/4/5 displays mis-sorting of these cargo proteins to acidic compartments and therefore impairs the growth of pollen tubes and the whole plant. Furthermore, the extracellular LRR domain of LRR-RKs is responsible for the correct sorting. Together, this study reports a mechanism that is important for the sorting of cell surface receptors. Cargo transport from the ER to the Golgi is highly selective. Here the authors identify three secretory pathway localized proteins that regulate ER sorting of receptor kinases in Arabidopsis and are required to support pollen tube growth.
Collapse
|
58
|
Yu H, Li M, Wen X, Yang J, Liang X, Li X, Bao X, Shu J, Ren X, Chen W, Li Z, Li Y. Elevation of α-1,3 fucosylation promotes the binding ability of TNFR1 to TNF-α and contributes to osteoarthritic cartilage destruction and apoptosis. Arthritis Res Ther 2022; 24:93. [PMID: 35488351 PMCID: PMC9052622 DOI: 10.1186/s13075-022-02776-z] [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: 02/05/2022] [Accepted: 04/09/2022] [Indexed: 12/04/2022] Open
Abstract
Background Osteoarthritis (OA) is the most common form of arthritis and is characterized by the degradation of articular cartilage and inflammation of the synovial membrane. Fucosylation is an important feature of protein N/O-glycosylation and is involved in a variety of pathological processes, including inflammation and cancer. However, whether fucosylation impacts the OA pathological process is unknown. Methods Total proteins were extracted from cartilage samples obtained from patients with OA (n = 11) and OA rabbit models at different time points (n = 12). OA-associated abnormal glycopatterns were evaluated by lectin microarrays and lectin blots. The expression of fucosyltransferases involved in the synthesis of α-1,3 fucosylation was assessed by semi-qPCR. The synthesis of α-1,3 fucosylation mediated by FUT10 was interrupted by the transfection of siRNA, and the effect of α-1,3 fucosylation on OA-associated events was assessed. Then, immunoprecipitation and lectin blotting were used to investigate the relationship between the α-1,3 fucosylation level of tumor necrosis factor receptor superfamily member 1A (TNFR1) and OA. Finally, a TNFR1 antibody microarray was fabricated to evaluate the effect of α-1,3 fucosylation on the ability of TNFR1 to bind to tumor necrosis factor-α (TNF-α). Results Elevated α-1,3 fucosylation was observed in cartilage from OA patients, rabbit models, and chondrocytes induced by TNF-α (fold change> 2, p< 0.01). Our results and the GEO database indicated that the overexpression of FUT10 contributed to this alteration. Silencing the expression of FUT10 impaired the ability of TNFR1 to bind to TNF-α, impeded activation of the NF-κB and P38/JNK-MAPK pathways, and eventually retarded extracellular matrix (ECM) degradation, senescence, and apoptosis in chondrocytes exposed to TNF-α. Conclusion The elevation of α-1,3 fucosylation is not only a characteristic of OA but also impacts the OA pathological process. Our work provides a new positive feedback loop of “inflammation conditions/TNF-α/FUT10/α-1,3 fucosylation of TNFR1/NF-κB and P38/JNK-MAPK pathways/proinflammatory processes” that contributes to ECM degradation and chondrocyte apoptosis. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-022-02776-z.
Collapse
Affiliation(s)
- Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an, 710069, Shaanxi Province, China
| | - Mingxiu Li
- The Second Clinical Medical College of Shaanxi University of Chinese Medicine, Xianyang, China
| | - Xiaodong Wen
- Department of Foot and Ankle Surgery, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Road, Xi'an, 710054, Shaanxi Province, China
| | - Jie Yang
- Department of Foot and Ankle Surgery, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Road, Xi'an, 710054, Shaanxi Province, China
| | - Xiaojun Liang
- Department of Foot and Ankle Surgery, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Road, Xi'an, 710054, Shaanxi Province, China
| | - Xia Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an, 710069, Shaanxi Province, China
| | - Xiaojuan Bao
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an, 710069, Shaanxi Province, China
| | - Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an, 710069, Shaanxi Province, China
| | - Xiameng Ren
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an, 710069, Shaanxi Province, China
| | - Wentian Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an, 710069, Shaanxi Province, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an, 710069, Shaanxi Province, China.
| | - Yi Li
- Department of Foot and Ankle Surgery, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Road, Xi'an, 710054, Shaanxi Province, China.
| |
Collapse
|
59
|
Torres M, Hussain H, Dickson AJ. The secretory pathway - the key for unlocking the potential of Chinese hamster ovary cell factories for manufacturing therapeutic proteins. Crit Rev Biotechnol 2022; 43:628-645. [PMID: 35465810 DOI: 10.1080/07388551.2022.2047004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mammalian cell factories (in particular the CHO cell system) have been crucial in the rise of biopharmaceuticals. Mammalian cells have compartmentalized organelles where intricate networks of proteins manufacture highly sophisticated biopharmaceuticals in a specialized production pipeline - the secretory pathway. In the bioproduction context, the secretory pathway functioning is key for the effectiveness of cell factories to manufacture these life-changing medicines. This review describes the molecular components and events involved in the secretory pathway, and provides a comprehensive summary of the intracellular steps limiting the production of therapeutic proteins as well as the achievements in engineering CHO cell secretory machinery. We also consider antibody-producing plasma cells (so called "professional" secretory cells) to explore the mechanisms underpinning their unique secretory function/features. Such understandings offer the potential to further enhancement of the current CHO cell production platforms for manufacturing next generation of biopharmaceuticals.
Collapse
Affiliation(s)
- Mauro Torres
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK.,Department of Chemical Engineering and Analytical Science, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
| | - Hirra Hussain
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK.,Department of Chemical Engineering and Analytical Science, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
| | - Alan J Dickson
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK.,Department of Chemical Engineering and Analytical Science, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
| |
Collapse
|
60
|
Sea Cucumber Body Vesicular Syndrome Is Driven by the Pond Water Microbiome via an Altered Gut Microbiota. mSystems 2022; 7:e0135721. [PMID: 35418244 PMCID: PMC9239130 DOI: 10.1128/msystems.01357-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Apostichopus japonicus (sea cucumber) is one of the most valuable aquaculture species in China; however, different diseases can limit its economic development. Recently, a novel disease, body vesicular syndrome (BVS), was observed in A. japonicus aquaculture. Diseased animals displayed no obvious phenotypic characteristics; however, after boiling at the postharvest stage, blisters, lysis, and body ruptures appeared. In this study, a multiomics strategy incorporating analysis of the gut microbiota, the pond microbiome, and A. japonicus genotype was established to investigate BVS. Detailed analyses of differentially expressed proteins (DEPs) and metabolites suggested that changes in cell adhesion structures, caused by disordered fatty acid β-oxidation mediated by vitamin B5 deficiency, could be a putative BVS mechanism. Furthermore, intestinal dysbacteriosis due to microbiome variations in pond water was considered a potential reason for vitamin B5 deficiency. Our BVS index, based on biomarkers identified from the A. japonicus gut microbiota, was a useful tool for BVS diagnosis. Finally, vitamin B5 supplementation was successfully used to treat BVS, suggesting an association with BVS etiology. IMPORTANCE Body vesicular syndrome (BVS) is a novel disease in sea cucumber aquaculture. As no phenotypic features are visible, BVS is difficult to confirm during aquaculture and postharvest activities, until animals are boiled. Therefore, BVS could lead to severe economic losses compared with other diseases in sea cucumber aquaculture. In this study, for the first time, we systematically investigated BVS pathogenesis and proposed an effective treatment for the condition. Moreover, based on the gut microbiota, we established a noninvasive diagnostic method for BVS in sea cucumber.
Collapse
|
61
|
Riccio A, Santopolo S, Rossi A, Piacentini S, Rossignol JF, Santoro MG. Impairment of SARS-CoV-2 spike glycoprotein maturation and fusion activity by nitazoxanide: an effect independent of spike variants emergence. Cell Mol Life Sci 2022; 79:227. [PMID: 35391601 PMCID: PMC8989121 DOI: 10.1007/s00018-022-04246-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/03/2022] [Accepted: 03/11/2022] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2, the causative agent of COVID-19, has caused an unprecedented global health crisis. The SARS-CoV-2 spike, a surface-anchored trimeric class-I fusion glycoprotein essential for viral entry, represents a key target for developing vaccines and therapeutics capable of blocking virus invasion. The emergence of SARS-CoV-2 spike variants that facilitate virus spread and may affect vaccine efficacy highlights the need to identify novel antiviral strategies for COVID-19 therapy. Here, we demonstrate that nitazoxanide, an antiprotozoal agent with recognized broad-spectrum antiviral activity, interferes with SARS-CoV-2 spike maturation, hampering its terminal glycosylation at an endoglycosidase H-sensitive stage. Engineering multiple SARS-CoV-2 variant-pseudoviruses and utilizing quantitative cell–cell fusion assays, we show that nitazoxanide-induced spike modifications hinder progeny virion infectivity as well as spike-driven pulmonary cell–cell fusion, a critical feature of COVID-19 pathology. Nitazoxanide, being equally effective against the ancestral SARS-CoV-2 Wuhan-spike and different emerging variants, including the Delta variant of concern, may represent a useful tool in the fight against COVID-19 infections.
Collapse
Affiliation(s)
- Anna Riccio
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Santopolo
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Antonio Rossi
- Institute of Translational Pharmacology, CNR, Rome, Italy
| | - Sara Piacentini
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - M Gabriella Santoro
- Department of Biology, University of Rome Tor Vergata, Rome, Italy. .,Institute of Translational Pharmacology, CNR, Rome, Italy.
| |
Collapse
|
62
|
Glyco-Decipher enables glycan database-independent peptide matching and in-depth characterization of site-specific N-glycosylation. Nat Commun 2022; 13:1900. [PMID: 35393418 PMCID: PMC8990002 DOI: 10.1038/s41467-022-29530-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/16/2022] [Indexed: 12/20/2022] Open
Abstract
Glycopeptides with unusual glycans or poor peptide backbone fragmentation in tandem mass spectrometry are unaccounted for in typical site-specific glycoproteomics analysis and thus remain unidentified. Here, we develop a glycoproteomics tool, Glyco-Decipher, to address these issues. Glyco-Decipher conducts glycan database-independent peptide matching and exploits the fragmentation pattern of shared peptide backbones in glycopeptides to improve the spectrum interpretation. We benchmark Glyco-Decipher on several large-scale datasets, demonstrating that it identifies more peptide-spectrum matches than Byonic, MSFragger-Glyco, StrucGP and pGlyco 3.0, with a 33.5%-178.5% increase in the number of identified glycopeptide spectra. The database-independent and unbiased profiling of attached glycans enables the discovery of 164 modified glycans in mouse tissues, including glycans with chemical or biological modifications. By enabling in-depth characterization of site-specific protein glycosylation, Glyco-Decipher is a promising tool for advancing glycoproteomics analysis in biological research. Poor peptide fragmentation and unusual glycan structures limit mass spectrometry-based analysis of intact N-glycopeptides. Here, the authors develop Glyco-Decipher, a glycan-independent peptide search tool, to tackle these issues and improve the coverage of site-specific glycan analysis.
Collapse
|
63
|
Christianson JC, Carvalho P. Order through destruction: how ER-associated protein degradation contributes to organelle homeostasis. EMBO J 2022; 41:e109845. [PMID: 35170763 PMCID: PMC8922271 DOI: 10.15252/embj.2021109845] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 12/24/2022] Open
Abstract
The endoplasmic reticulum (ER) is a large, dynamic, and multifunctional organelle. ER protein homeostasis is essential for the coordination of its diverse functions and depends on ER-associated protein degradation (ERAD). The latter process selects target proteins in the lumen and membrane of the ER, promotes their ubiquitination, and facilitates their delivery into the cytosol for degradation by the proteasome. Originally characterized for a role in the degradation of misfolded proteins and rate-limiting enzymes of sterol biosynthesis, the many branches of ERAD now appear to control the levels of a wider range of substrates and influence more broadly the organization and functions of the ER, as well as its interactions with adjacent organelles. Here, we discuss recent mechanistic advances in our understanding of ERAD and of its consequences for the regulation of ER functions.
Collapse
Affiliation(s)
- John C Christianson
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesBotnar Research CentreUniversity of OxfordOxfordUK
| | - Pedro Carvalho
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| |
Collapse
|
64
|
(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants. Life (Basel) 2022; 12:life12020324. [PMID: 35207610 PMCID: PMC8874572 DOI: 10.3390/life12020324] [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: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants.
Collapse
|
65
|
Hang J, Wang J, Lu M, Xue Y, Qiao J, Tao L. Protein O-mannosylation across kingdoms and related diseases: From glycobiology to glycopathology. Biomed Pharmacother 2022; 148:112685. [PMID: 35149389 DOI: 10.1016/j.biopha.2022.112685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
The post-translational glycosylation of proteins by O-linked α-mannose is conserved from bacteria to humans. Due to advances in high-throughput mass spectrometry-based approaches, a variety of glycoproteins are identified to be O-mannosylated. Various proteins with O-mannosylation are involved in biological processes, providing essential necessity for proper growth and development. In this review, we summarize the process and regulation of O-mannosylation. The multi-step O-mannosylation procedures are quite dynamic and complex, especially when considering the structural and functional inspection of the involved enzymes. The widely studied O-mannosylated proteins in human include α-Dystroglycan (α-DG), cadherins, protocadherins, and plexin, and their aberrant O-mannosylation are associated with many diseases. In addition, O-mannosylation also contributes to diverse functions in lower eukaryotes and prokaryotes. Finally, we present the relationship between O-mannosylation and gut microbiota (GM), and elucidate that O-mannosylation in microbiome is of great importance in the dynamic balance of GM. Our study provides an overview of the processes of O-mannosylation in mammalian cells and other organisms, and also associated regulated enzymes and biological functions, which could contribute to the understanding of newly discovered O-mannosylated glycoproteins.
Collapse
Affiliation(s)
- Jing Hang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Jinpeng Wang
- Department of Orthopedics, First Hospital of China Medical University, Shenyang 110001, China
| | - Minzhen Lu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yuchuan Xue
- The First Department of Clinical Medicine, China Medical University, Shenyang 110001, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China.
| | - Lin Tao
- Department of Orthopedics, First Hospital of China Medical University, Shenyang 110001, China.
| |
Collapse
|
66
|
Smith MJ, Pastor L, Newman JR, Concannon P. Genetic Control of Splicing at SIRPG Modulates Risk of Type 1 Diabetes. Diabetes 2022; 71:350-358. [PMID: 34799406 PMCID: PMC8914281 DOI: 10.2337/db21-0194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023]
Abstract
Signal regulatory protein SIRPγ (CD172G) is expressed on the surface of lymphocytes, where it acts by engaging its ligand, CD47. SIRPG, which encodes SIRPγ, contains a nonsynonymous coding variant, rs6043409, which is significantly associated with risk for type 1 diabetes. SIRPG produces multiple transcript isoforms via alternative splicing, all encoding potentially functional proteins. We show that rs6043409 alters a predicted exonic splicing enhancer, resulting in significant shifts in the distribution of SIRPG transcript isoforms. All of these transcript isoforms produced protein upon transient expression in vitro. However, CRISPR/Cas9 targeting of one of the alternatively spliced exons in SIRPG eliminated all SIRPγ expression in Jurkat T cells. These targeted cells formed fewer cell-cell conjugates with each other than with wild-type Jurkat cells, expressed reduced levels of genes associated with CD47 signaling, and had significantly increased levels of cell-surface CD47. In primary CD4+ and CD8+ T cells, cell-surface SIRPγ levels in response to anti-CD3 stimulation varied quantitatively by rs6043409 genotype. Our results suggest that SIRPG is the most likely causative gene for type 1 diabetes risk in the 20p13 region and highlight the role of alternative splicing in lymphocytes in mediating the genetic risk for autoimmunity.
Collapse
Affiliation(s)
- Morgan J. Smith
- Biomedical Sciences Training Program, University of Florida College of Medicine, Gainesville, FL
- University of Florida Genetics Institute, Gainesville, FL
| | - Lucia Pastor
- University of Florida Genetics Institute, Gainesville, FL
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL
| | - Jeremy R.B. Newman
- University of Florida Genetics Institute, Gainesville, FL
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL
| | - Patrick Concannon
- University of Florida Genetics Institute, Gainesville, FL
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL
- Corresponding author: Patrick Concannon,
| |
Collapse
|
67
|
Spillings BL, Day CJ, Garcia-Minambres A, Aggarwal A, Condon ND, Haselhorst T, Purcell DFJ, Turville SG, Stow JL, Jennings MP, Mak J. Host glycocalyx captures HIV proximal to the cell surface via oligomannose-GlcNAc glycan-glycan interactions to support viral entry. Cell Rep 2022; 38:110296. [PMID: 35108536 DOI: 10.1016/j.celrep.2022.110296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/18/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Here, we present ultrastructural analyses showing that incoming HIV are captured near the lymphocyte surface in a virion-glycan-dependent manner. Biophysical analyses show that removal of either virion- or cell-associated N-glycans impairs virus-cell binding, and a similar glycan-dependent relationship is observed between purified HIV envelope (Env) and primary T cells. Trimming of N-glycans from either HIV or Env does not inhibit protein-protein interactions. Glycan arrays reveal HIV preferentially binds to N-acetylglucosamine and mannose. Interfering with these glycan-based interactions reduces HIV infectivity. These glycan interactions are distinct from previously reported glycan-lectin and non-specific electrostatic charge-based interactions. Specific glycan-glycan-mediated attachment occurs prior to virus entry and enhances efficiency of infection. Binding and fluorescent imaging data support glycan-glycan interactions as being responsible, at least in part, for initiating contact between HIV and the host cell, prior to viral Env-cellular CD4 engagement.
Collapse
Affiliation(s)
- Belinda L Spillings
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Christopher J Day
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | | | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicholas D Condon
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Damian F J Purcell
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jennifer L Stow
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia.
| | - Johnson Mak
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia; School of Medicine, Deakin University, Geelong, VIC 3216, Australia.
| |
Collapse
|
68
|
Improving Protein Quantity and Quality—The Next Level of Plant Molecular Farming. Int J Mol Sci 2022; 23:ijms23031326. [PMID: 35163249 PMCID: PMC8836236 DOI: 10.3390/ijms23031326] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/15/2022] Open
Abstract
Plants offer several unique advantages in the production of recombinant pharmaceuticals for humans and animals. Although numerous recombinant proteins have been expressed in plants, only a small fraction have been successfully put into use. The hugely distinct expression systems between plant and animal cells frequently cause insufficient yield of the recombinant proteins with poor or undesired activity. To overcome the issues that greatly constrain the development of plant-produced pharmaceuticals, great efforts have been made to improve expression systems and develop alternative strategies to increase both the quantity and quality of the recombinant proteins. Recent technological revolutions, such as targeted genome editing, deconstructed vectors, virus-like particles, and humanized glycosylation, have led to great advances in plant molecular farming to meet the industrial manufacturing and clinical application standards. In this review, we discuss the technological advances made in various plant expression platforms, with special focus on the upstream designs and milestone achievements in improving the yield and glycosylation of the plant-produced pharmaceutical proteins.
Collapse
|
69
|
Sim HJ, Cho C, Kim HE, Hong JY, Song EK, Kwon KY, Jang DG, Kim SJ, Lee HS, Lee C, Kwon T, Yang S, Park TJ. Augmented ERAD (ER-associated degradation) activity in chondrocytes is necessary for cartilage development and maintenance. SCIENCE ADVANCES 2022; 8:eabl4222. [PMID: 35061535 PMCID: PMC8782459 DOI: 10.1126/sciadv.abl4222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/29/2021] [Indexed: 05/28/2023]
Abstract
Chondrocytes secrete massive extracellular matrix (ECM) molecules that are produced, folded, and modified in the endoplasmic reticulum (ER). Thus, the ER-associated degradation (ERAD) complex-which removes misfolded and unfolded proteins to maintain proteostasis in the ER- plays an indispensable role in building and maintaining cartilage. Here, we examined the necessity of the ERAD complex in chondrocytes for cartilage formation and maintenance. We show that ERAD gene expression is exponentially increased during chondrogenesis, and disruption of ERAD function causes severe chondrodysplasia in developing embryos and loss of adult articular cartilage. ERAD complex malfunction also causes abnormal accumulation of cartilage ECM molecules and subsequent chondrodysplasia. ERAD gene expression is decreased in damaged cartilage from patients with osteoarthritis (OA), and disruption of ERAD function in articular cartilage leads to cartilage destruction in a mouse OA model.
Collapse
Affiliation(s)
- Hyo Jung Sim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Chanmi Cho
- Department of Pharmacology, Ajou University School of Medicine, Suwon 16499, Korea
- Department of Biomedical Sciences, Graduate School, Ajou University, Suwon 16499, Korea
- CIRNO, Sungkyunkwan University, Suwon 16419, Korea
- Degenerative Inter Diseases Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Ha Eun Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Ju Yeon Hong
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Eun Kyung Song
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Keun Yeong Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Dong Gil Jang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Seok-Jung Kim
- Department of Orthopaedic Surgery, Uijeongbu St. Mary’s Hospital, Catholic University of Korea College of Medicine, Uijeongbu 11765, Korea
| | - Hyun-Shik Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Changwook Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Taejoon Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Siyoung Yang
- Department of Pharmacology, Ajou University School of Medicine, Suwon 16499, Korea
- Department of Biomedical Sciences, Graduate School, Ajou University, Suwon 16499, Korea
- CIRNO, Sungkyunkwan University, Suwon 16419, Korea
- Degenerative Inter Diseases Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Tae Joo Park
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| |
Collapse
|
70
|
Yin X, Konishi T, Horikawa K, Tanaka R, Togo Y, Noda T, Hosoi M, Tsuchida M, Kunoh T, Wada S, Nakamura T, Tsuda E, Sasaki R, Mizukami T, Hasegawa M. Structure and Function of Potential Glycosylation Sites of Dynactin-Associated Protein dynAP. Mol Biotechnol 2022; 64:611-620. [PMID: 35022995 DOI: 10.1007/s12033-021-00435-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 12/01/2021] [Indexed: 11/28/2022]
Abstract
Overexpression of human dynactin-associated protein (dynAP) transforms NIH3T3 cells. DynAP is a single-pass transmembrane protein with a carboxy-terminal region (amino acids 135-210) exposed to the outside of the cell possessing one potential N-glycosylation site (position 143) and a distal C-terminal region (residues 173-210) harboring a Thr/Ser-rich (T/S) cluster that may be O-glycosylated. In SDS-PAGE, dynAP migrates anomalously at ~ 45 kDa, much larger than expected (22.5 kDa) based on the amino acid composition. Using dynAP mutants, we herein showed that the T/S cluster region is responsible for the anomalous migration. The T/S cluster region is required for transport to the cytoplasmic membrane and cell transformation. We produced and purified the extracellular fragment (dynAP135-210) in secreted form and analyzed the attached glycans. Asn143 displayed complex-type glycosylation, suggesting that oligosaccharide transferase may recognize the NXT/S sequon in the secretory form, but not clearly in full-length dynAP. Core I-type O-glycosylation (Gal-GalNAc) was observed, but the mass spectrometry signal was weak, clearly indicating that further studies are needed to elucidate modifications in this region.
Collapse
Affiliation(s)
- Xiaobo Yin
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Takayuki Konishi
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Kazuo Horikawa
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Ryota Tanaka
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Yuki Togo
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Takanori Noda
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Miho Hosoi
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan.,Frontier Pharma, 1281-8 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Mie Tsuchida
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan.,Frontier Pharma, 1281-8 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Tatsuki Kunoh
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Shuichi Wada
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Toshinobu Nakamura
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Eisuke Tsuda
- Specialty Medicine Research Laboratories 1, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Ryuzo Sasaki
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan.,Frontier Pharma, 1281-8 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Tamio Mizukami
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan.,Frontier Pharma, 1281-8 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Makoto Hasegawa
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan.
| |
Collapse
|
71
|
West B, Wood AJ, Ungar D. Computational Modeling of Glycan Processing in the Golgi for Investigating Changes in the Arrangements of Biosynthetic Enzymes. Methods Mol Biol 2022; 2370:209-222. [PMID: 34611871 DOI: 10.1007/978-1-0716-1685-7_10] [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] [Indexed: 06/13/2023]
Abstract
Modeling glycan biosynthesis is becoming increasingly important due to the far-reaching implications that glycosylation can exhibit, from pathologies to biopharmaceutical manufacturing. Here we describe a stochastic simulation approach, to overcome the deterministic nature of previous models, that aims to simulate the action of glycan modifying enzymes to produce a glycan profile. This is then coupled with an approximate Bayesian computation methodology to systematically fit to empirical data in order to determine which set of parameters adequately describes the organization of enzymes within the Golgi. The model is described in detail along with a proof of concept and therapeutic applications.
Collapse
Affiliation(s)
- Ben West
- Department of Biology, University of York, York, UK
| | - A Jamie Wood
- Departments of Biology and Mathematics, University of York, York, UK
| | - Daniel Ungar
- Department of Biology, University of York, York, UK.
| |
Collapse
|
72
|
Indraratna AD, Everest-Dass A, Skropeta D, Sanderson-Smith M. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6519265. [PMID: 35104861 PMCID: PMC9075583 DOI: 10.1093/femsre/fuac001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/29/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
Host carbohydrates, or glycans, have been implicated in the pathogenesis of many bacterial infections. Group A Streptococcus (GAS) is a Gram-positive bacterium that readily colonises the skin and oropharynx, and is a significant cause of mortality in humans. While the glycointeractions orchestrated by many other pathogens are increasingly well-described, the understanding of the role of human glycans in GAS disease remains incomplete. Although basic investigation into the mechanisms of GAS disease is ongoing, several glycointeractions have been identified and are examined herein. The majority of research in this context has focussed on bacterial adherence, however, glycointeractions have also been implicated in carbohydrate metabolism; evasion of host immunity; biofilm adaptations; and toxin-mediated haemolysis. The involvement of human glycans in these diverse avenues of pathogenesis highlights the clinical value of understanding glycointeractions in combatting GAS disease.
Collapse
Affiliation(s)
- Anuk D Indraratna
- Illawarra Health and Medical Research Institute, Northfields Ave, Keiraville New South Wales 2522, Australia
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong, Northfields Avenue, Keiraville, New South Wales, 2522, Australia
| | - Arun Everest-Dass
- Institute for Glycomics, Griffith University, Gold Coast Campus, Parklands Drive, Southport, Queensland, 4215, Australia
| | - Danielle Skropeta
- Illawarra Health and Medical Research Institute, Northfields Ave, Keiraville New South Wales 2522, Australia
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong, Northfields Avenue, Keiraville, New South Wales, 2522, Australia
| | - Martina Sanderson-Smith
- Corresponding author: Illawarra Health and Medical Research Institute, Bld 32, University of Wollongong, Northfields Avenue, Keiraville, New South Wales, 2522, Australia. Tel: +61 2 42981935; E-mail:
| |
Collapse
|
73
|
Abstract
The web application O-Glycologue provides an online simulation of the biosynthetic enzymes of O-linked glycosylation, using a knowledge-based system described previously. Glycans can be imported in GlycoCT condensed format, or else as IUPAC condensed names, and passed as substrates to the enzymes, which are modeled as regular-expression-based substitutions on strings. The resulting networks of reactions can be exported as SBML. The effects of knocking out different sets of enzyme activities can be compared. A method is provided for predicting the enzymes required to produce a given substrate, using an O-glycan from human gastric mucin as an example. The system has been adapted to other systems of glycosylation enzymes, and an application to ganglioside oligosaccharide synthesis is demonstrated. O-Glycologue is available at https://glycologue.org/o/ .
Collapse
|
74
|
Nowakowska-Gołacka J, Czapiewska J, Sominka H, Sowa-Rogozińska N, Słomińska-Wojewódzka M. EDEM1 Regulates Amyloid Precursor Protein (APP) Metabolism and Amyloid-β Production. Int J Mol Sci 2021; 23:ijms23010117. [PMID: 35008544 PMCID: PMC8745108 DOI: 10.3390/ijms23010117] [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: 11/12/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Endoplasmic reticulum (ER) degradation-enhancing α-mannosidase-like protein 1 (EDEM1) is a quality control factor directly involved in the endoplasmic reticulum-associated degradation (ERAD) process. It recognizes terminally misfolded proteins and directs them to retrotranslocation which is followed by proteasomal degradation in the cytosol. The amyloid-β precursor protein (APP) is synthesized and N-glycosylated in the ER and transported to the Golgi for maturation before being delivered to the cell surface. The amyloidogenic cleavage pathway of APP leads to production of amyloid-β (Aβ), deposited in the brains of Alzheimer’s disease (AD) patients. Here, using biochemical methods applied to human embryonic kidney, HEK293, and SH-SY5Y neuroblastoma cells, we show that EDEM1 is an important regulatory factor involved in APP metabolism. We find that APP cellular levels are significantly reduced after EDEM1 overproduction and are increased in cells with downregulated EDEM1. We also report on EDEM1-dependent transport of APP from the ER to the cytosol that leads to proteasomal degradation of APP. EDEM1 directly interacts with APP. Furthermore, overproduction of EDEM1 results in decreased Aβ40 and Aβ42 secretion. These findings indicate that EDEM1 is a novel regulator of APP metabolism through ERAD.
Collapse
|
75
|
Capraz T, Kienzl NF, Laurent E, Perthold JW, Föderl-Höbenreich E, Grünwald-Gruber C, Maresch D, Monteil V, Niederhöfer J, Wirnsberger G, Mirazimi A, Zatloukal K, Mach L, Penninger JM, Oostenbrink C, Stadlmann J. Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor. eLife 2021; 10:e73641. [PMID: 34927585 PMCID: PMC8730730 DOI: 10.7554/elife.73641] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/17/2021] [Indexed: 11/17/2022] Open
Abstract
Infection and viral entry of SARS-CoV-2 crucially depends on the binding of its Spike protein to angiotensin converting enzyme 2 (ACE2) presented on host cells. Glycosylation of both proteins is critical for this interaction. Recombinant soluble human ACE2 can neutralize SARS-CoV-2 and is currently undergoing clinical tests for the treatment of COVID-19. We used 3D structural models and molecular dynamics simulations to define the ACE2 N-glycans that critically influence Spike-ACE2 complex formation. Engineering of ACE2 N-glycosylation by site-directed mutagenesis or glycosidase treatment resulted in enhanced binding affinities and improved virus neutralization without notable deleterious effects on the structural stability and catalytic activity of the protein. Importantly, simultaneous removal of all accessible N-glycans from recombinant soluble human ACE2 yields a superior SARS-CoV-2 decoy receptor with promise as effective treatment for COVID-19 patients.
Collapse
Affiliation(s)
- Tümay Capraz
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Nikolaus F Kienzl
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Elisabeth Laurent
- Institute of Molecular Biotechnology, Department of Biotechnology and Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Jan W Perthold
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | | | - Clemens Grünwald-Gruber
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Daniel Maresch
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Vanessa Monteil
- Karolinska Institute, Department of Laboratory MedicineStockholmSweden
| | | | | | - Ali Mirazimi
- Karolinska Institute, Department of Laboratory MedicineStockholmSweden
- National Veterinary InstituteUppsalaSweden
| | - Kurt Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University of GrazGrazAustria
| | - Lukas Mach
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Josef M Penninger
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. BohrViennaAustria
- Department of Medical Genetics, Life Sciences Institute, University of British ColumbiaVancouverCanada
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Johannes Stadlmann
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life SciencesViennaAustria
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. BohrViennaAustria
| |
Collapse
|
76
|
Mustafa G, Komatsu S. Plant proteomic research for improvement of food crops under stresses: a review. Mol Omics 2021; 17:860-880. [PMID: 34870299 DOI: 10.1039/d1mo00151e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crop improvement approaches have been changed due to technological advancements in traditional plant-breeding methods. Abiotic and biotic stresses limit plant growth and development, which ultimately lead to reduced crop yield. Proteins encoded by genomes have a considerable role in the endurance and adaptation of plants to different environmental conditions. Biotechnological applications in plant breeding depend upon the information generated from proteomic studies. Proteomics has a specific advantage to contemplate post-translational modifications, which indicate the functional effects of protein modifications on crop production. Subcellular proteomics helps in exploring the precise cellular responses and investigating the networking among subcellular compartments during plant development and biotic/abiotic stress responses. Large-scale mass spectrometry-based plant proteomic studies with a more comprehensive overview are now possible due to dramatic improvements in mass spectrometry, sample preparation procedures, analytical software, and strengthened availability of genomes for numerous plant species. Development of stress-tolerant or resilient crops is essential to improve crop productivity and growth. Use of high throughput techniques with advanced instrumentation giving efficient results made this possible. In this review, the role of proteomic studies in identifying the stress-response processes in different crops is summarized. Advanced techniques and their possible utilization on plants are discussed in detail. Proteomic studies accelerate marker-assisted genetic augmentation studies on crops for developing high yielding stress-tolerant lines or varieties under stresses.
Collapse
Affiliation(s)
- Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
| |
Collapse
|
77
|
Toustou C, Walet-Balieu ML, Kiefer-Meyer MC, Houdou M, Lerouge P, Foulquier F, Bardor M. Towards understanding the extensive diversity of protein N-glycan structures in eukaryotes. Biol Rev Camb Philos Soc 2021; 97:732-748. [PMID: 34873817 PMCID: PMC9300197 DOI: 10.1111/brv.12820] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 11/04/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022]
Abstract
N‐glycosylation is an important post‐translational modification of proteins that has been highly conserved during evolution and is found in Eukaryota, Bacteria and Archaea. In eukaryotes, N‐glycan processing is sequential, involving multiple specific steps within the secretory pathway as proteins travel through the endoplasmic reticulum and the Golgi apparatus. In this review, we first summarize the different steps of the N‐glycan processing and further describe recent findings regarding the diversity of N‐glycan structures in eukaryotic clades. This comparison allows us to explore the different regulation mechanisms of N‐glycan processing among eukaryotic clades. Recent findings regarding the regulation of protein N‐glycosylation are highlighted, especially the regulation of the biosynthesis of complex‐type N‐glycans through manganese and calcium homeostasis and the specific role of transmembrane protein 165 (TMEM165) for which homologous sequences have been identified in several eukaryotic clades. Further research will be required to characterize the function of TMEM165 homologous sequences in different eukaryotic clades.
Collapse
Affiliation(s)
- Charlotte Toustou
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France
| | - Marie-Laure Walet-Balieu
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France
| | - Marie-Christine Kiefer-Meyer
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France
| | - Marine Houdou
- Univ Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, F-59000, France.,Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Box 802, Leuven, 3000, Belgium
| | - Patrice Lerouge
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France
| | - François Foulquier
- Univ Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, F-59000, France
| | - Muriel Bardor
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France.,Univ Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, F-59000, France
| |
Collapse
|
78
|
Brito A, Dave D, Lampel A, Castro VIB, Kroiss D, Reis RL, Tuttle T, Ulijn RV, Pires RA, Pashkuleva I. Expanding the Conformational Landscape of Minimalistic Tripeptides by Their O-Glycosylation. J Am Chem Soc 2021; 143:19703-19710. [PMID: 34797059 DOI: 10.1021/jacs.1c07592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We report on the supramolecular self-assembly of tripeptides and their O-glycosylated analogues, in which the carbohydrate moiety is coupled to a central serine or threonine flanked by phenylalanine residues. The substitution of serine with threonine introduces differential side-chain interactions, which results in the formation of aggregates with different morphology. O-glycosylation decreases the aggregation propensity because of rebalancing of the π interactions. The glycopeptides form aggregates with reduced stiffness but increased thermal stability. Our results demonstrate that the designed minimalistic glycopeptides retain critical functional features of glycoproteins and therefore are promising tools for elucidation of molecular mechanisms involved in the glycoprotein interactome. They can also serve as an inspiration for the design of functional glycopeptide-based biomaterials.
Collapse
Affiliation(s)
- Alexandra Brito
- 3B's Research Group, I3Bs Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, United States
| | - Dhwanit Dave
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, United States.,Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Ayala Lampel
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, United States
| | - Vânia I B Castro
- 3B's Research Group, I3Bs Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Daniela Kroiss
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, United States.,Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Rui L Reis
- 3B's Research Group, I3Bs Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Tell Tuttle
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, United States.,Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,Ph.D. program in Biochemistry, The Graduate Center of the City University of New York, New York, New York10016, United States
| | - Ricardo A Pires
- 3B's Research Group, I3Bs Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Iva Pashkuleva
- 3B's Research Group, I3Bs Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| |
Collapse
|
79
|
Esmail S, Manolson MF. Advances in understanding N-glycosylation structure, function, and regulation in health and disease. Eur J Cell Biol 2021; 100:151186. [PMID: 34839178 DOI: 10.1016/j.ejcb.2021.151186] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/14/2021] [Accepted: 11/18/2021] [Indexed: 01/17/2023] Open
Abstract
N-linked glycosylation is a post-translational modification crucial for membrane protein folding, stability and other cellular functions. Alteration of membrane protein N-glycans is implicated in wide range of pathological conditions including cancer metastasis, chronic inflammatory diseases, and viral pathogenesis. Even though the roles of N-glycans have been studied extensively, our knowledge of their mechanisms remains unclear due to the lack of detailed structural analysis of the N-glycome. Mapping the N-glycome landscape will open new avenues to explore disease mechanisms and identify novel therapeutic targets. This review discusses the diverse structure of N-linked glycans, the function and regulation of N-glycosylation in health and disease, and ends with a focus on recent approaches to target N-glycans in rheumatoid arthritis and cancer metastasis.
Collapse
Affiliation(s)
- Sally Esmail
- Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada.
| | - Morris F Manolson
- Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| |
Collapse
|
80
|
Hirayama H, Tachida Y, Seino J, Suzuki T. A method for assaying peptide: N-glycanase/N-Glycanase 1 activities in crude extracts using an N-glycosylated cyclopeptide. Glycobiology 2021; 32:110-122. [PMID: 34939090 PMCID: PMC8934141 DOI: 10.1093/glycob/cwab115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/09/2021] [Accepted: 10/31/2021] [Indexed: 11/13/2022] Open
Abstract
Cytosolic peptide: N-glycanase (PNGase; NGLY1), an enzyme responsible for de-glycosylation of N-glycans on glycoproteins, is known to play pivotal roles in a variety of biological processes. In 2012, NGLY1 deficiency, a rare genetic disorder, was reported and since then, more than 100 patients have now been identified worldwide. Patients with this disease exhibit several common symptoms that are caused by the dysfunction of NGLY1. However, correlation between the severity of patient symptoms and the extent of the reduction in NGLY1 activity in these patients remains to be clarified, mainly due to the absence of a facile quantitative assay system for this enzyme, especially in a crude extract as an enzyme source. In this study, a quantitative, non-radioisotope (RI)-based assay method for measuring recombinant NGLY1 activity was established using a BODIPY-labeled asialoglycopeptide (BODIPY-ASGP) derived from hen eggs. With this assay, the activities of 27 recombinant NGLY1 mutants that are associated with the deficiency were examined. It was found that the activities of 3 (R469X, R458fs, and H494fs) out of the 27 recombinant mutant proteins were 30-70 percent of the activities of wild-type NGLY1. We further developed a method for measuring endogenous NGLY1 activity in crude extracts derived from cultured cells, patients' fibroblasts, iPS cells or peripheral blood mononuclear cells (PBMCs), using a glycosylated cyclopeptide (GCP) that exhibited resistance to the endogenous proteases in the extract. Our methods will not only provide new insights into the molecular mechanism responsible for this disease but also promises to be applicable for its diagnosis.
Collapse
Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
| | - Yuriko Tachida
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
| | - Junichi Seino
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
| |
Collapse
|
81
|
Xu Y, Gao Z, Hu R, Wang Y, Wang Y, Su Z, Zhang X, Yang J, Mei M, Ren Y, Li M, Zhou X. PD-L2 glycosylation promotes immune evasion and predicts anti-EGFR efficacy. J Immunother Cancer 2021; 9:jitc-2021-002699. [PMID: 34697216 PMCID: PMC8547513 DOI: 10.1136/jitc-2021-002699] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2021] [Indexed: 12/25/2022] Open
Abstract
Background Combination therapy has been explored for advanced head and neck squamous cell carcinoma (HNSCC) owing to the limited efficacy of anti-epidermal growth factor receptor (EGFR) therapy. Increased expression and glycosylation of immune checkpoint molecules in tumors are responsible for cetuximab therapy refractoriness. The role of programmed death ligand 2 (PD-L2), a ligand of PD-1, in the immune function is unclear. Here, we examined the regulatory mechanism of PD-L2 glycosylation and its role in antitumor immunity and cetuximab therapy. Methods Single-cell RNA sequencing and immunohistochemical staining were used to investigate PD-L2 expression in cetuximab-resistant/sensitive HNSCC tissues. The mechanism of PD-L2 glycosylation regulation was explored in vitro. The effects of PD-L2 glycosylation on immune evasion and cetuximab efficacy were verified in vitro and using mice bearing orthotopic SCC7 tumors. Results The PD-L2 levels were elevated and N-glycosylated in patients with cetuximab-resistant HNSCC. Glycosylated PD-L2 formed a complex with EGFR, which resulted in the activation of EGFR/signal transducer and activator of transcription 3 (STAT3) signaling and decreased the cetuximab binding affinity to EGFR. The N-glycosyltransferase fucosyltransferase (FUT8), a transcriptional target of STAT3, was required for PD-L2 glycosylation. Moreover, glycosylation modification stabilized PD-L2 by blocking ubiquitin-dependent lysosomal degradation, which consequently promoted its binding to PD-1 and immune evasion. Inhibition of PD-L2 glycosylation using Stattic, a specific STAT3 inhibitor, or PD-L2 mutation blocking its binding to FUT8, increased cytotoxic T lymphocyte activity and augmented response to cetuximab. Conclusions Increased expression and glycosylation of PD-L2 in tumors are an important mechanism for cetuximab therapy refractoriness. Thus, the combination of PD-L2 glycosylation inhibition and cetuximab is a potential therapeutic strategy for cancer.
Collapse
Affiliation(s)
- Yiqi Xu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China.,Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Zhenyue Gao
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China.,Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Ruxin Hu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yuqing Wang
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yuhong Wang
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Zheng Su
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Xiaoyue Zhang
- Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Jingxuan Yang
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Mei Mei
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yu Ren
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Min Li
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Xuan Zhou
- Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| |
Collapse
|
82
|
Shen L, Gao J, Wang Y, Li X, Liu H, Zhong Y. Engineering the endoplasmic reticulum secretory pathway in Trichoderma reesei for improved cellulase production. Enzyme Microb Technol 2021; 152:109923. [PMID: 34688089 DOI: 10.1016/j.enzmictec.2021.109923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/18/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
The filamentous fungus Trichoderma reesei is an extraordinarily efficient cell factory of industrial cellulase for production of biofuels and other bio-based products because of its excellent potential to secrete cellulolytic enzymes. Engineering the protein secretory pathway may be a powerful means for efficient protein production. However, it is uncertain whether this engineering approach could improve cellulase production in T. reesei. Herein, the endoplasmic reticulum (ER) secretory pathway was engineered for the production of cellulolytic enzymes by multiple strategies, including: (I) overexpression of the key components of protein folding (Pdi1, Ero1 and BiP); (II) overexpression of the glycosylation-related elements (Gpt1 and Gls2); (III) knockout of the ER mannosidase I (Mns1) encoding gene mns1. By utilizing these ER engineering strategies, the secretion of β-glucosidase was remarkably elevated in the engineered strains, ranging from 29.2 % to 112.5 %. Furthermore, it was found that engineering these components also regulated the ER stress resistance. More importantly, the total cellulase production was increased with varying degrees, which reached a maximum of 149.4 %, using the filter paper assay (FPA) as a characterization method. These results demonstrated that engineering the ER secretory pathway can enhance protein secretion, particularly for cellulase production, which shed light for the development of high-efficient cellulolytic enzymes for economically feasible bioethanol production from lignocellulosic biomass.
Collapse
Affiliation(s)
- Linjing Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Jia Gao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Yifan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Xihai Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Hong Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, PR China
| |
Collapse
|
83
|
Pratama F, Linton D, Dixon N. Genetic and process engineering strategies for enhanced recombinant N-glycoprotein production in bacteria. Microb Cell Fact 2021; 20:198. [PMID: 34649588 PMCID: PMC8518210 DOI: 10.1186/s12934-021-01689-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/25/2021] [Indexed: 11/28/2022] Open
Abstract
Background The production of N-linked glycoproteins in genetically amenable bacterial hosts offers great potential for reduced cost, faster/simpler bioprocesses, greater customisation, and utility for distributed manufacturing of glycoconjugate vaccines and glycoprotein therapeutics. Efforts to optimize production hosts have included heterologous expression of glycosylation enzymes, metabolic engineering, use of alternative secretion pathways, and attenuation of gene expression. However, a major bottleneck to enhance glycosylation efficiency, which limits the utility of the other improvements, is the impact of target protein sequon accessibility during glycosylation. Results Here, we explore a series of genetic and process engineering strategies to increase recombinant N-linked glycosylation, mediated by the Campylobacter-derived PglB oligosaccharyltransferase in Escherichia coli. Strategies include increasing membrane residency time of the target protein by modifying the cleavage site of its secretion signal, and modulating protein folding in the periplasm by use of oxygen limitation or strains with compromised oxidoreductase or disulphide-bond isomerase activity. These approaches achieve up to twofold improvement in glycosylation efficiency. Furthermore, we also demonstrate that supplementation with the chemical oxidant cystine enhances the titre of glycoprotein in an oxidoreductase knockout strain by improving total protein production and cell fitness, while at the same time maintaining higher levels of glycosylation efficiency. Conclusions In this study, we demonstrate that improved protein glycosylation in the heterologous host could be achieved by mimicking the coordination between protein translocation, folding and glycosylation observed in native host such as Campylobacter jejuni and mammalian cells. Furthermore, it provides insight into strain engineering and bioprocess strategies, to improve glycoprotein yield and titre, and to avoid physiological burden of unfolded protein stress upon cell growth. The process and genetic strategies identified herein will inform further optimisation and scale-up of heterologous recombinant N-glycoprotein production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01689-x.
Collapse
Affiliation(s)
- Fenryco Pratama
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, M1 7DN, UK.,Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.,Microbial Biotechnology Research Group, School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Dennis Linton
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M1 7DN, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, M1 7DN, UK. .,Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| |
Collapse
|
84
|
Naito T, Jingushi K, Ueda K, Tsujikawa K. Azurocidin is loaded into small extracellular vesicles via its N-linked glycosylation and promotes intravasation of renal cell carcinoma cells. FEBS Lett 2021; 595:2522-2532. [PMID: 34418081 DOI: 10.1002/1873-3468.14183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 01/10/2023]
Abstract
Azurocidin (AZU1) is an antimicrobial protein secreted by neutrophils that acts as a chemoattractant for monocytes and macrophages and a permeabilizer of vascular endothelial cells. We previously identified AZU1 to be specifically present in extracellular vesicles (EVs) obtained from renal cell carcinoma (RCC) tissues. Here, we examined the relationship between N-linked glycosylation and AZU1 loading into small EVs (SEVs). Inhibition of N-linked glycosylation by introducing mutations in three glycosylation sites inhibited AZU1 loading into SEVs. Furthermore, SEVs released from AZU1-wild-type cells increased the Ca2+ concentration in endothelial cells and the endothelial permeability, whereas SEVs released from AZU1-mutant cells had no significant effect. Anti-AZU1 antibodies diminished the effect of SEVs on endothelial cell sheets. Collectively, we found that N-linked glycosylation of AZU1 directs its loading into SEVs, thereby enabling AZU1-positive SEVs to function as potent permeabilizers of endothelial cells and leading to enhanced transendothelial migration of RCC cells.
Collapse
Affiliation(s)
- Takuya Naito
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Koji Ueda
- Project for Personalized Cancer Medicine, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| |
Collapse
|
85
|
Martin CE, Murray AS, Sala-Hamrick KE, Mackinder JR, Harrison EC, Lundgren JG, Varela FA, List K. Posttranslational modifications of serine protease TMPRSS13 regulate zymogen activation, proteolytic activity, and cell surface localization. J Biol Chem 2021; 297:101227. [PMID: 34562451 PMCID: PMC8503615 DOI: 10.1016/j.jbc.2021.101227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 12/01/2022] Open
Abstract
TMPRSS13, a member of the type II transmembrane serine protease (TTSP) family, harbors four N-linked glycosylation sites in its extracellular domain. Two of the glycosylated residues are located in the scavenger receptor cysteine-rich (SRCR) protein domain, while the remaining two sites are in the catalytic serine protease (SP) domain. In this study, we examined the role of N-linked glycosylation in the proteolytic activity, autoactivation, and cellular localization of TMPRSS13. Individual and combinatory site-directed mutagenesis of the glycosylated asparagine residues indicated that glycosylation of the SP domain is critical for TMPRSS13 autoactivation and catalytic activity toward one of its protein substrates, the prostasin zymogen. Additionally, SP domain glycosylation-deficient TMPRSS13 displayed impaired trafficking of TMPRSS13 to the cell surface, which correlated with increased retention in the endoplasmic reticulum. Importantly, we showed that N-linked glycosylation was a critical determinant for subsequent phosphorylation of endogenous TMPRSS13. Taken together, we conclude that glycosylation plays an important role in regulating TMPRSS13 activation and activity, phosphorylation, and cell surface localization.
Collapse
Affiliation(s)
- Carly E Martin
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Oncology, Wayne State University, Detroit, Michigan, USA
| | - Andrew S Murray
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Oncology, Wayne State University, Detroit, Michigan, USA; Division of Hematological Malignancies and Cellular Therapy, Duke University, Durham, North Carolina, USA
| | | | - Jacob R Mackinder
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA
| | - Evan C Harrison
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA
| | - Joseph G Lundgren
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Oncology, Wayne State University, Detroit, Michigan, USA
| | - Fausto A Varela
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Karin List
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Oncology, Wayne State University, Detroit, Michigan, USA.
| |
Collapse
|
86
|
Sun Z, Guerriero CJ, Brodsky JL. Substrate ubiquitination retains misfolded membrane proteins in the endoplasmic reticulum for degradation. Cell Rep 2021; 36:109717. [PMID: 34551305 PMCID: PMC8503845 DOI: 10.1016/j.celrep.2021.109717] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/11/2021] [Accepted: 08/25/2021] [Indexed: 11/28/2022] Open
Abstract
To maintain secretory pathway fidelity, misfolded proteins are commonly retained in the endoplasmic reticulum (ER) and selected for ER-associated degradation (ERAD). Soluble misfolded proteins use ER chaperones for retention, but the machinery that restricts aberrant membrane proteins to the ER is unclear. In fact, some misfolded membrane proteins escape the ER and traffic to the lysosome/vacuole. To this end, we describe a model substrate, SZ*, that contains an ER export signal but is also targeted for ERAD. We observe decreased ER retention when chaperone-dependent SZ* ubiquitination is compromised. In addition, appending a linear tetra-ubiquitin motif onto SZ* overrides ER export. By screening known ubiquitin-binding proteins, we then positively correlate SZ* retention with Ubx2 binding. Deletion of Ubx2 also inhibits the retention of another misfolded membrane protein. Our results indicate that polyubiquitination is sufficient to retain misfolded membrane proteins in the ER prior to ERAD. Sun et al. characterize how misfolded membrane proteins are delivered for either ERAD or post-ER degradation in the secretory pathway. By using a model substrate that can access both pathways, they show that substrate retention requires chaperone-dependent substrate ubiquitination and interaction with a conserved ER membrane protein, Ubx2.
Collapse
Affiliation(s)
- Zhihao Sun
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| |
Collapse
|
87
|
Yang L, Gong T, Shen H, Pei J, Zhang L, Zhang Q, Huang Y, Hu Z, Pan Z, Yang P, Lin L, Yu H. Precision N-Glycoproteomic Profiling of Murine Peritoneal Macrophages After Different Stimulations. Front Immunol 2021; 12:722293. [PMID: 34484231 PMCID: PMC8416091 DOI: 10.3389/fimmu.2021.722293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Macrophages are important immune cells that participate in both innate and adaptive immune responses, such as phagocytosis, recognition of molecular patterns, and activation of the immune response. In this study, murine peritoneal macrophages were isolated and then activated by LPS, HSV and VSV. Integrative proteomic and precision N-glycoproteomic profiling were conducted to assess the underlying macrophage activation. We identified a total of 587 glycoproteins, including 1239 glycopeptides, 526 monosaccharide components, and 8326 intact glycopeptides in glycoproteomics, as well as a total of 4496 proteins identified in proteomic analysis. These glycoproteins are widely involved in important biological processes, such as antigen presentation, cytokine production and glycosylation progression. Under the stimulation of the different pathogens, glycoproteins showed a dramatic change. We found that receptors in the Toll-like receptor pathway, such as Tlr2 and CD14, were increased under LPS and HSV stimulation. Glycosylation of those proteins was proven to influence their subcellular locations.
Collapse
Affiliation(s)
- Lujie Yang
- Institutes of Biomedical Sciences & Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Tianqi Gong
- Institutes of Biomedical Sciences & Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Huali Shen
- Institutes of Biomedical Sciences & Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Jiangnan Pei
- Obestetics & Gynecology Hospital, Fudan University, Shanghai, China
| | - Lei Zhang
- Institutes of Biomedical Sciences & Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Quanqing Zhang
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, CA, United States
| | - Yuanyu Huang
- Institutes of Biomedical Sciences & Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Zuojian Hu
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ziyue Pan
- Institutes of Biomedical Sciences & Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Pengyuan Yang
- Institutes of Biomedical Sciences & Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Ling Lin
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, China
| | - Hongxiu Yu
- Institutes of Biomedical Sciences & Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| |
Collapse
|
88
|
Zhang N, Hu X, Chen H, Deng C, Sun N. Specific enrichment and glycosylation discrepancy profiling of cellular exosomes using a dual-affinity probe. Chem Commun (Camb) 2021; 57:6249-6252. [PMID: 34059853 DOI: 10.1039/d1cc01530c] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A hydrophilic probe is employed to enrich exosomes from three kinds of cancer cells by TiO2-phosphate interaction and exosomal glycoproteins by hydrophilic interaction in succession. The probe performs efficiently in both the enrichment processes. And the analytical results confirm that unique exosomal glycoproteins can distinguish parent exosomes from others.
Collapse
Affiliation(s)
- Ning Zhang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China and Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Xufang Hu
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Haolin Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Chunhui Deng
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China and Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Nianrong Sun
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| |
Collapse
|
89
|
Li C, Chi H, Deng S, Wang H, Yao H, Wang Y, Chen D, Guo X, Fang JY, He F, Xu J. THADA drives Golgi residency and upregulation of PD-L1 in cancer cells and provides promising target for immunotherapy. J Immunother Cancer 2021; 9:jitc-2021-002443. [PMID: 34341130 PMCID: PMC8330570 DOI: 10.1136/jitc-2021-002443] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 12/28/2022] Open
Abstract
Background The abnormal upregulation of programmed death-ligand 1 (PD-L1) in cancer cells inhibits T cell-mediated cytotoxicity, but the molecular mechanisms that drive and maintain PD-L1 expression are still incompletely understood. Methods Combined analyses of genomes and proteomics were applied to find potential regulators of PD-L1. In vitro experiments were performed to investigate the regulatory mechanism of PD-L1 by thyroid adenoma associated gene (THADA) using human colorectal cancer (CRC) cells. The prevalence of THADA was analyzed using CRC tissue microarrays by immunohistochemistry. T cell killing assay, programmed cell death 1 binding assay and MC38 transplanted tumor models in C57BL/6 mice were developed to investigate the antitumor effect of THADA. Results THADA is critically required for the Golgi residency of PD-L1, and this non-redundant, coat protein complex II (COPII)-associated mechanism maintains PD-L1 expression in tumor cells. THADA mediated the interaction between PD-L1 as a cargo protein with SEC24A, a module on the COPII trafficking vesicle. Silencing THADA caused absence and endoplasmic reticulum (ER) retention of PD-L1 but not major histocompatibility complex-I, inducing PD-L1 clearance through ER-associated degradation. Targeting THADA substantially enhanced T cell-mediated cytotoxicity, and increased CD8+ T cells infiltration in mouse tumor tissues. Analysis on clinical tissue samples supported a potential role of THADA in upregulating PD-L1 expression in cancer. Conclusions Our data reveal a crucial cellular process for PD-L1 maturation and maintenance in tumor cells, and highlight THADA as a promising target for overcoming PD-L1-dependent immune evasion.
Collapse
Affiliation(s)
- Chushu Li
- Zhongshan-Xuhui Hospital, Institutes of Biomedical Sciences (visiting), Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, China.,Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Chi
- Zhongshan-Xuhui Hospital, Shanghai Xuhui Central Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, China
| | - Shouyan Deng
- Zhongshan-Xuhui Hospital, Institutes of Biomedical Sciences (visiting), Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, China.,Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huanbin Wang
- Zhongshan-Xuhui Hospital, Institutes of Biomedical Sciences (visiting), Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, China
| | - Han Yao
- Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yungang Wang
- Zhongshan-Xuhui Hospital, Shanghai Xuhui Central Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, China
| | - Dawei Chen
- Innomodels Biotechnology (Beijing) Co., Ltd, Beijing, China
| | - Xun Guo
- Innomodels Biotechnology (Beijing) Co., Ltd, Beijing, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fang He
- Zhongshan-Xuhui Hospital, Shanghai Xuhui Central Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, China
| | - Jie Xu
- Zhongshan-Xuhui Hospital, Shanghai Xuhui Central Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, China
| |
Collapse
|
90
|
Reis CA, Tauber R, Blanchard V. Glycosylation is a key in SARS-CoV-2 infection. J Mol Med (Berl) 2021; 99:1023-1031. [PMID: 34023935 PMCID: PMC8140746 DOI: 10.1007/s00109-021-02092-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/29/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 causes the respiratory syndrome COVID-19 and is responsible for the current pandemic. The S protein of SARS-CoV-2-mediating virus binding to target cells and subsequent viral uptake is extensively glycosylated. Here we focus on how glycosylation of both SARS-CoV-2 and target cells crucially impacts SARS-CoV-2 infection at different levels: (1) virus binding and entry to host cells, with glycosaminoglycans of host cells acting as a necessary co-factor for SARS-CoV-2 infection by interacting with the receptor-binding domain of the SARS-CoV-2 spike glycoprotein, (2) innate and adaptive immune response where glycosylation plays both a protective role and contributes to immune evasion by masking of viral polypeptide epitopes and may add to the cytokine cascade via non-fucosylated IgG, and (3) therapy and vaccination where a monoclonal antibody-neutralizing SARS-CoV-2 was shown to interact also with a distinct glycan epitope on the SARS-CoV-2 spike protein. These evidences highlight the importance of ensuring that glycans are considered when tackling this disease, particularly in the development of vaccines, therapeutic strategies and serological testing.
Collapse
Affiliation(s)
- Celso A Reis
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
- IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, 4050-313, Porto, Portugal
| | - Rudolf Tauber
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Véronique Blanchard
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| |
Collapse
|
91
|
Huang J, Jiang B, Liu M, Yang P, Cao W. gQuant, an Automated Tool for Quantitative Glycomic Data Analysis. Front Chem 2021; 9:707738. [PMID: 34395380 PMCID: PMC8355585 DOI: 10.3389/fchem.2021.707738] [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: 05/10/2021] [Accepted: 07/15/2021] [Indexed: 11/25/2022] Open
Abstract
MALDI-MS-based glycan isotope labeling methods have been effectively and widely used for quantitative glycomics. However, interpretation of the data produced by MALDI-MS is inaccurate and tedious because the bioinformatic tools are inadequate. In this work, we present gQuant, an automated tool for MALDI-MS-based glycan isotope labeling data processing. gQuant was designed with a set of dedicated algorithms to improve the efficiency, accuracy and convenience of quantitation data processing. When tested on the reference data set, gQuant showed a fast processing speed, as it was able to search the glycan data of model glycoproteins in a few minutes and reported more results than the manual analysis did. The reported quantitation ratios matched well with the experimental glycan mixture ratios ranging from 1:10 to 10:1. In addition, gQuant is fully open-source and is coded in Python, which is supported by most operating systems, and it has a user-friendly interface. gQuant can be easily adapted by users for specific experimental designs, such as specific glycan databases, different derivatization types and relative quantitation designs and can thus facilitate fast glycomic quantitation for clinical sample analysis using MALDI-MS-based stable isotope labeling.
Collapse
Affiliation(s)
- Jiangming Huang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Biyun Jiang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mingqi Liu
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Pengyuan Yang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Weiqian Cao
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| |
Collapse
|
92
|
Cheng B, Tang Q, Zhang C, Chen X. Glycan Labeling and Analysis in Cells and In Vivo. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:363-387. [PMID: 34314224 DOI: 10.1146/annurev-anchem-091620-091314] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As one of the major types of biomacromolecules in the cell, glycans play essential functional roles in various biological processes. Compared with proteins and nucleic acids, the analysis of glycans in situ has been more challenging. Herein we review recent advances in the development of methods and strategies for labeling, imaging, and profiling of glycans in cells and in vivo. Cellular glycans can be labeled by affinity-based probes, including lectin and antibody conjugates, direct chemical modification, metabolic glycan labeling, and chemoenzymatic labeling. These methods have been applied to label glycans with fluorophores, which enables the visualization and tracking of glycans in cells, tissues, and living organisms. Alternatively, labeling glycans with affinity tags has enabled the enrichment of glycoproteins for glycoproteomic profiling. Built on the glycan labeling methods, strategies enabling cell-selective and tissue-specific glycan labeling and protein-specific glycan imaging have been developed. With these methods and strategies, researchers are now better poised than ever to dissect the biological function of glycans in physiological or pathological contexts.
Collapse
Affiliation(s)
- Bo Cheng
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Che Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| |
Collapse
|
93
|
Luo B, Li G, Li Z, He J, Zhou J, Wu L, Lan F, Wu Y. Construction of a magnetic covalent organic framework with synergistic affinity strategy for enhanced glycopeptide enrichment. J Mater Chem B 2021; 9:6377-6386. [PMID: 34296732 DOI: 10.1039/d1tb01168e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Considering the inherent properties of glycopeptides, such as glycan structure, size, and hydrophilicity, affinity materials possessing suitable functional molecule-glycan interactions, matched channels with size exclusion, and surfaces with hydrophilic interactions are preferred for glycopeptide separation in biological samples. Here, a novel boronic-acid-functionalized magnetic covalent organic framework was prepared through epitaxial growth and multi-ligand strategies. The multi-ligand strategy was firstly employed to prepare functionalized magnetic covalent organic framework without any post-functionalization protocol. Notably, the proposed strategy was found to be time saving, robust, and reproducible. The versatile magnetic covalent organic framework nanocomposite was endowed with phenylboronic acid functional molecules, strong hydrophilic features, mesoporous channels, fast magnetic responsiveness, and a large surface area. Benefitting from multiple affinity interactions, namely, synergistic reversible covalent interactions and hydrophilic affinity interactions, the nanocomposite presented extremely high performance in the recognition of intact N-glycopeptides. The inherent properties endowed the nanocomposite with excellent enrichment performance for N-glycopeptides: excellent selectivity (1 : 2000, IgG/BSA, m/m), an ultralow detection limit (0.05 fmol μL-1), and a good size-exclusion effect (1 : 500, IgG digests/BSA, m/m). More excitingly, a total of 1921 unique intact glycopeptides assigned to 1154 glycoproteins were identified from rat liver tissue; this performance is superior to that of commercial products. Additionally, the nanocomposite was successfully applied to enrich intact glycopeptides of exosomes extracted from healthy individuals and renal failure patients, providing a novel concept for the design of materials using a synergistic affinity strategy for sample preparation in glycoproteomics.
Collapse
Affiliation(s)
- Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | | | | | | | | | | | | | | |
Collapse
|
94
|
Allen JD, Chawla H, Samsudin F, Zuzic L, Shivgan AT, Watanabe Y, He WT, Callaghan S, Song G, Yong P, Brouwer PJM, Song Y, Cai Y, Duyvesteyn HME, Malinauskas T, Kint J, Pino P, Wurm MJ, Frank M, Chen B, Stuart DI, Sanders RW, Andrabi R, Burton DR, Li S, Bond PJ, Crispin M. Site-Specific Steric Control of SARS-CoV-2 Spike Glycosylation. Biochemistry 2021; 60:2153-2169. [PMID: 34213308 PMCID: PMC8262170 DOI: 10.1021/acs.biochem.1c00279] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/18/2021] [Indexed: 02/08/2023]
Abstract
A central tenet in the design of vaccines is the display of native-like antigens in the elicitation of protective immunity. The abundance of N-linked glycans across the SARS-CoV-2 spike protein is a potential source of heterogeneity among the many different vaccine candidates under investigation. Here, we investigate the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compare them against S protein from infectious virus, cultured in Vero cells. We find patterns that are conserved across all samples, and this can be associated with site-specific stalling of glycan maturation that acts as a highly sensitive reporter of protein structure. Molecular dynamics simulations of a fully glycosylated spike support a model of steric restrictions that shape enzymatic processing of the glycans. These results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.
Collapse
Affiliation(s)
- Joel D. Allen
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Himanshi Chawla
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Firdaus Samsudin
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
| | - Lorena Zuzic
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
- Department
of Chemistry, Faculty of Science and Engineering, Manchester Institute
of Biotechnology, The University of Manchester, Manchester M1 7DN, U.K.
| | - Aishwary Tukaram Shivgan
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
- Department
of Biological Sciences, National University
of Singapore, Singapore 117543
| | - Yasunori Watanabe
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Wan-ting He
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Sean Callaghan
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ge Song
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Peter Yong
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Philip J. M. Brouwer
- Department
of Medical Microbiology, Amsterdam UMC,
University of Amsterdam, Amsterdam Infection & Immunity Institute, 1007 MB Amsterdam, The Netherlands
| | - Yutong Song
- Tsinghua-Peking
Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing
Advanced Innovation Center for Structural Biology and Frontier Research
Center for Biological Structure, Beijing 100084, China
| | - Yongfei Cai
- Division
of Molecular Medicine, Boston Children’s
Hospital, 3 Blackfan
Street, Boston, Massachusetts 02115, United States
| | - Helen M. E. Duyvesteyn
- Division
of Structural Biology, University of Oxford,
The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, U.K.
| | - Tomas Malinauskas
- Division
of Structural Biology, University of Oxford,
The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, U.K.
| | - Joeri Kint
- ExcellGene SA, CH1870 Monthey, Switzerland
| | - Paco Pino
- ExcellGene SA, CH1870 Monthey, Switzerland
| | | | - Martin Frank
- Biognos AB, Generatorsgatan
1, 41705 Göteborg, Sweden
| | - Bing Chen
- Division
of Molecular Medicine, Boston Children’s
Hospital, 3 Blackfan
Street, Boston, Massachusetts 02115, United States
- Department
of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, Massachusetts 02115, United States
| | - David I. Stuart
- Division
of Structural Biology, University of Oxford,
The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, U.K.
- Diamond Light Source Ltd., Harwell Science
& Innovation Campus, Didcot OX11 0DE, U.K.
| | - Rogier W. Sanders
- Department
of Medical Microbiology, Amsterdam UMC,
University of Amsterdam, Amsterdam Infection & Immunity Institute, 1007 MB Amsterdam, The Netherlands
- Department
of Microbiology and Immunology, Weill Medical
College of Cornell University, New York, New York 10065, United States
| | - Raiees Andrabi
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dennis R. Burton
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
- Ragon Institute of Massachusetts General
Hospital, Massachusetts
Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, United States
| | - Sai Li
- Tsinghua-Peking
Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing
Advanced Innovation Center for Structural Biology and Frontier Research
Center for Biological Structure, Beijing 100084, China
| | - Peter J. Bond
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
- Department
of Biological Sciences, National University
of Singapore, Singapore 117543
| | - Max Crispin
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| |
Collapse
|
95
|
SHANG S, DONG H, LI Y, ZHANG W, LI H, QIN W, QIAN X. [Large-scale enrichment and identification of human urinary N-glycoproteins/ N-glycopeptides]. Se Pu 2021; 39:686-694. [PMID: 34227365 PMCID: PMC9421575 DOI: 10.3724/sp.j.1123.2021.01039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Indexed: 11/25/2022] Open
Abstract
N-Glycosylation of proteins, an important post-translational modification in eukaryotic cells, plays an essential role in the regulation of cell adhesion, migration, signal transduction, and apoptosis. Abnormal changes in protein glycosylation are closely related to the occurrence of many critical diseases, including diabetes, tumors, and neurological, kidney, and inflammatory diseases. A non-invasive type of liquid biopsy, urine sampling has the advantage of reducing the complexity of proteomic analysis. This facilitates the design of large-scale and continuous or multi-time point sampling strategies. However, the dynamic range of urinary protein abundance is relatively large, owing to individual differences and physiological conditions. Currently, there is a lack of specialized research on individual differences, physiological fluctuations, and physiological abundance ranges of urinary N-glycoproteins in large healthy populations. Therefore, it is difficult to accurately distinguish individual differences and normal physiological fluctuations from changes caused by disease; this poses a great challenge in disease marker research. Liquid chromatography-mass spectrometry (LC-MS) is an analytical technique widely used for the large-scale profiling of proteomes in biological systems, and the enrichment of N-glycopeptides is a prerequisite for their detection by MS.In this study, we established an approach based on hydrophilic interaction chromatography (HILIC) by optimizing the activation, cleaning, and elution processes of the enrichment method, for instance through the optimization of particle size and solvent composition, and investigated the identification number, selectivity, and stability of N-glycoprotein/N-glycopeptide enrichment under different experimental conditions. We found that N-glycoproteins and N-glycopeptides were highly enriched in a trifluoroacetic acid system with 5-μm filling particles in the HILIC column. On this basis, we analyzed the levels of N-glycoproteins/N-glycopeptides in urine samples. The consistency of N-glycoprotein/N-glycopeptide levels in urine samples taken from the same healthy person for five consecutive days was investigated by correlation analysis. This analysis revealed that the urinary N-glycoproteome of the same healthy person was relatively stable over a short period of time. Next, urinary samples from 20 healthy male volunteers and 20 healthy female volunteers were enriched for N-glycoproteins/N-glycopeptides, which were profiled by MS through qualitative and quantitative analyses. Screening and functional analysis of differential proteins were then carried out. A total of 1016 N-glycoproteins and 2192 N-glycopeptides were identified in the mid-morning urine samples of the 40 healthy volunteers. A label-free quantitation strategy was used to investigate the fluctuation range of the physiologically abundant urinary N-glycopeptides. The abundance of urinary N-glycopeptides spanned across approximately five orders of magnitude. Subsequently, gender differences in the N-glycosylation levels of urinary proteins were also explored in healthy people. Functional analysis of the N-glycoproteins that exhibited gender differences in abundance was performed. Based on multivariate statistical analysis, 206 differentially expressed proteins (p<0.05, fold change (FC)> 4) were identified. In females, we found 175 significantly down-regulated N-glycoproteins and 31 significantly up-regulated N-glycoproteins with respect to males. The expression levels of N-glycopeptides between the two groups suggested a clear gender difference. To investigate the biological processes and functions of these proteins, gene ontology (GO) analysis was performed on the N-glycoproteins/N-glycopeptides differentially expressed between males and females. Metabolic pathway analysis was also carried out based on the kyoto encyclopedia of genes and genomes (KEGG). Differentially expressed N-glycoproteins were mostly associated with platelet degranulation, extracellular region, and ossification. The top three relevant pathways were glycan biosynthesis and metabolism, metabolism of cofactors and vitamins, and lipid metabolism. Overall, sex may be an important factor for urinary N-glycoproteome differences among normal individuals and should be considered in clinical applications. This study provides relevant information regarding the function and mechanisms of the urinary glycoproteome and the screening of clinical biomarkers.
Collapse
Affiliation(s)
- Shiting SHANG
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Hangyan DONG
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Yuanyuan LI
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Wanjun ZHANG
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Hang LI
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Weijie QIN
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Xiaohong QIAN
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| |
Collapse
|
96
|
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.
Collapse
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.
| |
Collapse
|
97
|
Groux-Degroote S, Foulquier F, Cavdarli S, Delannoy P. [Reticular and Golgi glycosylation: Advances and associated diseases]. Med Sci (Paris) 2021; 37:609-617. [PMID: 34180820 DOI: 10.1051/medsci/2021082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycosylation is one of the essential modifications of proteins and lipids. It is carried out mainly in the endoplasmic reticulum and Golgi apparatus, and requires a specific molecular machinery associating several hundreds of glycosyltransferases, glycosidases, transporters and regulating proteins. Modifications of glycosylation are found in numerous diseases, notably in cancers. All types of glycosylation can be affected and this leads to dysfunctions of cellular metabolism. In this review, we present the current knowledge on the regulation of glycosylation mechanisms and illustrate how the alteration of these regulatory mechanisms can lead to abnormal protein and lipid glycosylation, and take part in the development of cancers.
Collapse
Affiliation(s)
- Sophie Groux-Degroote
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de glycobiologie structurale et fonctionnelle, Avenue Mendeleïev, 59655 Villeneuve-d'Ascq, France
| | - François Foulquier
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de glycobiologie structurale et fonctionnelle, Avenue Mendeleïev, 59655 Villeneuve-d'Ascq, France
| | - Sumeyye Cavdarli
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de glycobiologie structurale et fonctionnelle, Avenue Mendeleïev, 59655 Villeneuve-d'Ascq, France
| | - Philippe Delannoy
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de glycobiologie structurale et fonctionnelle, Avenue Mendeleïev, 59655 Villeneuve-d'Ascq, France
| |
Collapse
|
98
|
Gao Z, Li L, Chen W, Ma Z, Li Y, Gao Y, Ding CF, Zhao X, Pan Y. Distinguishment of Glycan Isomers by Trapped Ion Mobility Spectrometry. Anal Chem 2021; 93:9209-9217. [PMID: 34165974 DOI: 10.1021/acs.analchem.1c01461] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The in-depth study of glycan has drawn large research interests since it is one of the main biopolymers on the earth with a variety of biological functions. However, the distinguishment of glycans is still difficult due to the similarity of the monosaccharide building block, the anomer, and the linkage of glycosidic bonds. In this study, four novel and representative copper-bound diastereoisomeric complex ions were simultaneously detected in a single measurement by trapped ion mobility mass spectrometry, including mononuclear copper-bound dimeric ions [(Cu2+)(A)(l-Ser)-H]+ and [(Cu2+)(A)(l-His)-H]+, the mononuclear copper-bound trimeric ion [(Cu2+)(A)(l-Ser)(l-His)-H]+, and the binuclear copper-bound tetrameric ion [(Cu2+)2(A)(l-Ser)2(l-His)-3H]+ (where A denotes an oligosaccharide, and l-Ser and l-His denote l-serine and l-histidine, respectively). By combining the collision cross sections of complex ions, 23 oligosaccharide isomers were successfully distinguished including two pairs of sialylated glycan linkage isomers. In addition, due to the unique dissociation pathways of the trimeric ion, both the relative and absolute quantification of the individual isomer in the mixture could be determined using a mass spectrometry-based kinetic method. Finally, the method established above was successfully applied to the identification and quantification of glycan isomers in dairy beverages and juice. The method in the present study was sensitive to the fine difference of glycan isomers and might have wide applicability in glycoscience.
Collapse
Affiliation(s)
- Zhan Gao
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Lei Li
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, Zhejiang, P. R. China
| | - Weiwei Chen
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Zihan Ma
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Yuan Li
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Yuanji Gao
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Chuan-Fan Ding
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, Zhejiang, P. R. China
| | - Xiaoyong Zhao
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| |
Collapse
|
99
|
Li J, Yu J, Xue W, Huang H, Yan L, Sang F, An S, Zhang J, Wang M, Zhang J, Li H, Cui X, He J, Hu Y. The engineered expression of secreted HSPB5-Fc in CHO cells exhibits cytoprotection in vitro. BMC Biotechnol 2021; 21:39. [PMID: 34126963 PMCID: PMC8204567 DOI: 10.1186/s12896-021-00700-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background HSPB5 is an ATP-independent molecular chaperone that is induced by heat shock or other proteotoxic stresses. HSPB5 is cytoprotective against stress both intracellularly and extracellularly. It acts as a potential therapeutic candidate in ischemia-reperfusion and neurodegenerative diseases. Results In this paper, we constructed a recombinant plasmid that expresses and extracellularly secrets a HSPB5-Fc fusion protein (sHSPB5-Fc) at 0.42 μg/ml in CHO-K1 cells. This sHSPB5-Fc protein contains a Fc-tag at the C-terminal extension of HSPB5, facilitating protein-affinity purification. Our study shows that sHSPB5-Fc inhibits heat-induced aggregation of citrate synthase in a time and dose dependent manner in vitro. Administration of sHSPB5-Fc protects lens epithelial cells against cisplatin- or UVB-induced cell apoptosis. It also decreases GFP-Httex1-Q74 insolubility, and reduces the size and cytotoxicity of GFP-Httex1-Q74 aggregates in PC-12 cells. Conclusion This recombinant sHSPB5-Fc exhibits chaperone activity to protect cells against proteotoxicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00700-y.
Collapse
Affiliation(s)
- Jing Li
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China.,Kaifeng Key Lab for Cataract and Myopia, Institute of Eye Disease, Kaifeng Central Hospital, Kaifeng, China
| | - Jingjing Yu
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Wenxian Xue
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Huili Huang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Longjun Yan
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Fan Sang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Shuangshuang An
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Jing Zhang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Mingli Wang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Jun Zhang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Hui Li
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Xiukun Cui
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Jiang He
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yanzhong Hu
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China. .,Kaifeng Key Lab for Cataract and Myopia, Institute of Eye Disease, Kaifeng Central Hospital, Kaifeng, China. .,Department of Ophthalmology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| |
Collapse
|
100
|
Gao J, Li Q, Li D. Novel Proteome and N-Glycoproteome of the Thermophilic Fungus Chaetomium thermophilum in Response to High Temperature. Front Microbiol 2021; 12:644984. [PMID: 34163440 PMCID: PMC8216556 DOI: 10.3389/fmicb.2021.644984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/22/2021] [Indexed: 11/26/2022] Open
Abstract
Thermophilic fungi are eukaryotic species that grow at high temperatures, but little is known about the underlying basis of thermophily at cell and molecular levels. Here the proteome and N-glycoproteome of Chaetomium thermophilum at varying culture temperatures (30, 50, and 55°C) were studied using hydrophilic interaction liquid chromatography enrichment and high-resolution liquid chromatography–tandem mass spectroscopy analysis. With respect to the proteome, the numbers of differentially expressed proteins were 1,274, 1,374, and 1,063 in T50/T30, T55/T30, and T55/T50, respectively. The upregulated proteins were involved in biological processes, such as protein folding and carbohydrate metabolism. Most downregulated proteins were involved in molecular functions, including structural constituents of the ribosome and other protein complexes. For the N-glycoproteome, the numbers of differentially expressed N-glycoproteins were 160, 176, and 128 in T50/T30, T55/T30, and T55/T50, respectively. The differential glycoproteins were mainly involved in various types of N-glycan biosynthesis, mRNA surveillance pathway, and protein processing in the endoplasmic reticulum. These results indicated that an efficient protein homeostasis pathway plays an essential role in the thermophily of C. thermophilum, and N-glycosylation is involved by affecting related proteins. This is the novel study to reveal thermophilic fungi’s physiological response to high-temperature adaptation using omics analysis, facilitating the exploration of the thermophily mechanism of thermophilic fungi.
Collapse
Affiliation(s)
- Jinpeng Gao
- Department of Mycology, Shandong Agricultural University, Taian, China
| | - Qingchao Li
- Department of Mycology, Shandong Agricultural University, Taian, China
| | - Duochuan Li
- Department of Mycology, Shandong Agricultural University, Taian, China
| |
Collapse
|