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Martina CE, Crowe JE, Meiler J. Glycan masking in vaccine design: Targets, immunogens and applications. Front Immunol 2023; 14:1126034. [PMID: 37033915 PMCID: PMC10076883 DOI: 10.3389/fimmu.2023.1126034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023] Open
Abstract
Glycan masking is a novel technique in reverse vaccinology in which sugar chains (glycans) are added on the surface of immunogen candidates to hide regions of low interest and thus focus the immune system on highly therapeutic epitopes. This shielding strategy is inspired by viruses such as influenza and HIV, which are able to escape the immune system by incorporating additional glycosylation and preventing the binding of therapeutic antibodies. Interestingly, the glycan masking technique is mainly used in vaccine design to fight the same viruses that naturally use glycans to evade the immune system. In this review we report the major successes obtained with the glycan masking technique in epitope-focused vaccine design. We focus on the choice of the target antigen, the strategy for immunogen design and the relevance of the carrier vector to induce a strong immune response. Moreover, we will elucidate the different applications that can be accomplished with glycan masking, such as shifting the immune response from hyper-variable epitopes to more conserved ones, focusing the response on known therapeutic epitopes, broadening the response to different viral strains/sub-types and altering the antigen immunogenicity to elicit higher or lower immune response, as desired.
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Affiliation(s)
- Cristina E. Martina
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
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2
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Lisacek F, Tiemeyer M, Mazumder R, Aoki-Kinoshita KF. Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance. JACS AU 2023; 3:4-12. [PMID: 36711080 PMCID: PMC9875223 DOI: 10.1021/jacsau.2c00477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 06/18/2023]
Abstract
The GlySpace Alliance was formed in 2018 among the principal investigators of three major glycoscience portals: Glyco@Expasy, GlyCosmos, and GlyGen, representing Europe, Asia, and the United States, respectively. While each of these portals has its unique user interface, the aim is to provide the same basic data set of glycan-related omics data. These portals will be introduced with the aim to enable users to find their target information in the most efficient manner, in particular, in terms of the chemical structures of glycans and their functions.
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Affiliation(s)
- Frederique Lisacek
- Proteome
Informatics Group, SIB Swiss Institute of Bioinformatics, University of Geneva, Geneva CH-1227, Switzerland
- Computer
Science Department & Section of Biology, University of Geneva, Geneva CH-1227, Switzerland
| | - Michael Tiemeyer
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Raja Mazumder
- George
Washington University, Washington, District of Columbia 20037, United States
| | - Kiyoko F. Aoki-Kinoshita
- Glycan
and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo 192-8577, Japan
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3
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Liu Y, Huang Y, Zhu R, Farag MA, Capanoglu E, Zhao C. Structural elucidation approaches in carbohydrates: A comprehensive review on techniques and future trends. Food Chem 2023; 400:134118. [DOI: 10.1016/j.foodchem.2022.134118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
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4
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Yu K, Wang Y, Zheng Y, Liu Z, Zhang Q, Wang S, Zhao Q, Zhang X, Li X, Xu RH, Liu ZX. qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast. Nucleic Acids Res 2022; 51:D479-D487. [PMID: 36165955 PMCID: PMC9825568 DOI: 10.1093/nar/gkac820] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/26/2022] [Accepted: 09/14/2022] [Indexed: 01/29/2023] Open
Abstract
Post-translational modifications (PTMs) are critical molecular mechanisms that regulate protein functions temporally and spatially in various organisms. Since most PTMs are dynamically regulated, quantifying PTM events under different states is crucial for understanding biological processes and diseases. With the rapid development of high-throughput proteomics technologies, massive quantitative PTM proteome datasets have been generated. Thus, a comprehensive one-stop data resource for surfing big data will benefit the community. Here, we updated our previous phosphorylation dynamics database qPhos to the qPTM (http://qptm.omicsbio.info). In qPTM, 11 482 553 quantification events among six types of PTMs, including phosphorylation, acetylation, glycosylation, methylation, SUMOylation and ubiquitylation in four different organisms were collected and integrated, and the matched proteome datasets were included if available. The raw mass spectrometry based false discovery rate control and the recurrences of identifications among datasets were integrated into a scoring system to assess the reliability of the PTM sites. Browse and search functions were improved to facilitate users in swiftly and accurately acquiring specific information. The results page was revised with more abundant annotations, and time-course dynamics data were visualized in trend lines. We expected the qPTM database to be a much more powerful and comprehensive data repository for the PTM research community.
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Affiliation(s)
| | | | | | | | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Siyu Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaolong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaoxing Li
- Precision Medicine Institute, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Rui-Hua Xu
- Correspondence may also be addressed to Rui-Hua Xu. Tel: +86 20 8734 3228; Fax: +86 20 8734 3392;
| | - Ze-Xian Liu
- To whom correspondence should be addressed. Tel: +86 20 8734 2025; Fax: +86 20 8734 2522;
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5
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Aoki-Kinoshita KF. Functions of Glycosylation and Related Web Resources for Its Prediction. Methods Mol Biol 2022; 2499:135-144. [PMID: 35696078 DOI: 10.1007/978-1-0716-2317-6_6] [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: 06/15/2023]
Abstract
Glycosylation involves the attachment of carbohydrate sugar chains, or glycans, onto an amino acid residue of a protein. These glycans are often branched structures and serve to modulate the function of proteins. Glycans are synthesized through a complex process of enzymatic reactions that occur in the Golgi apparatus in mammalian systems. Because there is currently no sequencer for glycans, technologies such as mass spectrometry is used to characterize glycans in a biological sample to ascertain its glycome. This is a tedious process that requires high levels of expertise and equipment. Thus, the enzymes that work on glycans, called glycogenes or glycoenzymes, have been studied to better understand glycan function. With the development of glycan-related databases and a glycan repository, bioinformatics approaches have attempted to predict the glycosylation pathway and the glycosylation sites on proteins. This chapter introduces these methods and related Web resources for understanding glycan function.
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6
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Glycoinformatics Tools for Comprehensive Characterization of Glycans Enzymatically Released from Proteins. Methods Mol Biol 2021. [PMID: 34611862 DOI: 10.1007/978-1-0716-1685-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Glycosylation is important in biology, contributing to both protein conformation and function. Structurally, glycosylation is complex and diverse. This complexity is reflected in the topology, composition, monosaccharide linkages, and isomerism of each oligosaccharide. Glycoanalytics is a discipline that addresses the understanding and characterization of this complexity and its correlation with biology. It includes analytical steps such as sample preparation, instrument measurements, and data analyses. Of these, data analysis has emerged as a critical bottleneck because data collection has increasingly become high-throughput. This has resulted in data-rich workflows that lack rapid and automated data analytics. To address this issue, the field has been developing software for interpretation of quantitative glycomics studies. Here, we describe a protocol using available informatics tools for analysis of data from analysis of released glycans using high-/ultraperformance liquid chromatography (H/UPLC) coupled with mass spectrometry (MS).
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Zhang C, Cai M, Chen S, Zhang F, Cui T, Xue Z, Wang W, Zhang B, Liu X. The consensus N glyco -X-S/T motif and a previously unknown N glyco -N-linked glycosylation are necessary for growth and pathogenicity of Phytophthora. Environ Microbiol 2021; 23:5147-5163. [PMID: 33728790 DOI: 10.1111/1462-2920.15468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Asparagine (Asn, N)-linked glycosylation within Nglyco -X-S/T; X ≠ P motif is a ubiquitously distributed post-translational modification that participates in diverse cellular processes. In this work, N-glycosylation inhibitor was shown to prevent Phytophthora sojae growth, suggesting that N-glycosylation is necessary for oomycete development. We conducted a glycoproteomic analysis of P. sojae to identify and map N-glycosylated proteins and to quantify differentially expressed glycoproteins associated with mycelia, asexual cyst, and sexual oospore developmental stages. A total of 355 N-glycosylated proteins was found, containing 496 glycosites, potentially involved in glycan degradation, carbon metabolism, glycolysis, or other metabolic pathways. Through PNGase F deglycosylation assays and site-directed mutagenesis of a GPI transamidase protein (GPI16) upregulated in cysts and a heat shock protein 70 (HSP70) upregulated in oospores, we demonstrated that both proteins were N-glycosylated and that the Nglyco -N motif is a target site for asparagine - oligosaccharide linkage. Glycosite mutations of Asn 94 Nglyco -X-S/T in the GPI16 led to impaired cyst germination and pathogenicity, while mutation of the previously unknown Asn 270 Nglyco -N motif in HSP70 led to decreased oospore production. In addition to providing a map of the oomycete N-glycoproteome, this work confirms that P. sojae has evolved multiple N-glycosylation motifs essential for growth.
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Affiliation(s)
- Can Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Meng Cai
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Shanshan Chen
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Fan Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Tongshan Cui
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Zhaolin Xue
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Weizhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Borui Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
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Nagai-Okatani C, Zou X, Fujita N, Sogabe I, Arakawa K, Nagai M, Angata K, Zhang Y, Aoki-Kinoshita KF, Kuno A. LM-GlycomeAtlas Ver. 2.0: An Integrated Visualization for Lectin Microarray-based Mouse Tissue Glycome Mapping Data with Lectin Histochemistry. J Proteome Res 2021; 20:2069-2075. [PMID: 33657805 DOI: 10.1021/acs.jproteome.0c00907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Laser microdissection-assisted lectin microarray has been used to obtain quantitative and qualitative information on glycans on proteins expressed in microscopic regions of formalin-fixed paraffin-embedded tissue sections. For the effective visualization of this "tissue glycome mapping" data, a novel online tool, LM-GlycomeAtlas (https://glycosmos.org/lm_glycomeatlas/index), was launched in the freely available glycoscience portal, the GlyCosmos Portal (https://glycosmos.org). In LM-GlycomeAtlas Version 1.0, nine tissues from normal mice were used to provide one data set of glycomic profiles. Here we introduce an updated version of LM-GlycomeAtlas, which includes more spatial information. We designed it to deposit multiple data sets of glycomic profiles with high-resolution histological images, which included staining images with multiple lectins on the array. The additionally implemented interfaces allow users to display multiple histological images of interest (e.g., diseased and normal mice), thereby facilitating the evaluation of tissue glycomic profiling and glyco-pathological analysis. Using these updated interfaces, 451 glycomic profiling data and 42 histological images obtained from 14 tissues of normal and diseased mice were successfully visualized. By easy integration with other tools for glycoproteomic data and protein glycosylation machinery, LM-GlycomeAtlas will be one of the most valuable open resources that contribute to both glycoscience and proteomics communities.
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Affiliation(s)
- Chiaki Nagai-Okatani
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Xia Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Noriaki Fujita
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Isami Sogabe
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Kouiti Arakawa
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Misugi Nagai
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Kiyohiko Angata
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kiyoko F Aoki-Kinoshita
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics. Int J Mol Sci 2020; 21:ijms21186727. [PMID: 32937895 PMCID: PMC7556027 DOI: 10.3390/ijms21186727] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
Glycosylation plays critical roles in various biological processes and is closely related to diseases. Deciphering the glycocode in diverse cells and tissues offers opportunities to develop new disease biomarkers and more effective recombinant therapeutics. In the past few decades, with the development of glycobiology, glycomics, and glycoproteomics technologies, a large amount of glycoscience data has been generated. Subsequently, a number of glycobiology databases covering glycan structure, the glycosylation sites, the protein scaffolds, and related glycogenes have been developed to store, analyze, and integrate these data. However, these databases and tools are not well known or widely used by the public, including clinicians and other researchers who are not in the field of glycobiology, but are interested in glycoproteins. In this study, the representative databases of glycan structure, glycoprotein, glycan-protein interactions, glycogenes, and the newly developed bioinformatic tools and integrated portal for glycoproteomics are reviewed. We hope this overview could assist readers in searching for information on glycoproteins of interest, and promote further clinical application of glycobiology.
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Angata K, Sawaki H, Tsujikawa S, Ocho M, Togayachi A, Narimatsu H. Glycogene Expression Profiling of Hepatic Cells by RNA-Seq Analysis for Glyco-Biomarker Identification. Front Oncol 2020; 10:1224. [PMID: 32850363 PMCID: PMC7402167 DOI: 10.3389/fonc.2020.01224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/15/2020] [Indexed: 01/01/2023] Open
Abstract
Glycans are primarily generated by “glycogenes,” which consist of more than 200 genes for glycosynthesis, including sugar-nucleotide synthases, sugar-nucleotide transporters, and glycosyltransferases. Measuring the expression level of glycogenes is one of the approaches to analyze the glycomes of particular biological and clinical samples. To develop an effective strategy for identifying the glycosylated biomarkers, we performed transcriptome analyses using quantitative real-time polymerase chain reaction (qRT-PCR) arrays and RNA sequencing (RNA-Seq). First, we measured and analyzed the transcriptome from the primary culture of human liver cells and hepatocarcinoma cells using RNA-Seq. This analysis revealed similar but distinctive expression profiles of glycogenes among hepatic cells as indicated by the qRT-PCR arrays, which determined a copy number of 186 glycogenes. Both data sets indicated that altered expression of glycosyltransferases affect the glycosylation of particular glycoproteins, which is consistent with the mass analysis data. Moreover, RNA-Seq analysis can uncover mutations in glycogenes and search differently expressed genes out of more than 50,000 distinct human gene transcripts including candidate biomarkers that were previously reported for hepatocarcinoma cells. Identification of candidate glyco-biomarkers from the expression profile of the glycogenes and proteins from liver cancer tissues available from public database emphasized the possibility that even though the expression level of biomarkers might not be altered, the expression of the glycogenes modifying biomarkers, generating glyco-biomarkers, might be different. Pathway analysis revealed that ~20% of the glycogenes exhibited different expression levels in normal and cancer cells. Thus, transcriptome analyses using both qRT-PCR array and RNA-Seq in combination with glycome and glycoproteome analyses can be advantageous to identify “glyco-biomarkers” by reinforcing information at the expression levels of both glycogenes and proteins.
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Affiliation(s)
- Kiyohiko Angata
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiromichi Sawaki
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Shigeko Tsujikawa
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Makoto Ocho
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Akira Togayachi
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hisashi Narimatsu
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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Chen XL, Liu C, Tang B, Ren Z, Wang GL, Liu W. Quantitative proteomics analysis reveals important roles of N-glycosylation on ER quality control system for development and pathogenesis in Magnaporthe oryzae. PLoS Pathog 2020; 16:e1008355. [PMID: 32092131 PMCID: PMC7058352 DOI: 10.1371/journal.ppat.1008355] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/05/2020] [Accepted: 01/27/2020] [Indexed: 11/27/2022] Open
Abstract
Genetic studies have shown essential functions of N-glycosylation during infection of the plant pathogenic fungi, however, systematic roles of N-glycosylation in fungi is still largely unknown. Biological analysis demonstrated N-glycosylated proteins were widely present at different development stages of Magnaporthe oryzae and especially increased in the appressorium and invasive hyphae. A large-scale quantitative proteomics analysis was then performed to explore the roles of N-glycosylation in M. oryzae. A total of 559 N-glycosites from 355 proteins were identified and quantified at different developmental stages. Functional classification to the N-glycosylated proteins revealed N-glycosylation can coordinate different cellular processes for mycelial growth, conidium formation, and appressorium formation. N-glycosylation can also modify key components in N-glycosylation, O-glycosylation and GPI anchor pathways, indicating intimate crosstalk between these pathways. Interestingly, we found nearly all key components of the endoplasmic reticulum quality control (ERQC) system were highly N-glycosylated in conidium and appressorium. Phenotypic analyses to the gene deletion mutants revealed four ERQC components, Gls1, Gls2, GTB1 and Cnx1, are important for mycelial growth, conidiation, and invasive hyphal growth in host cells. Subsequently, we identified the Gls1 N-glycosite N497 was important for invasive hyphal growth and partially required for conidiation, but didn’t affect colony growth. Mutation of N497 resulted in reduction of Gls1 in protein level, and localization from ER into the vacuole, suggesting N497 is important for protein stability of Gls1. Our study showed a snapshot of the N-glycosylation landscape in plant pathogenic fungi, indicating functions of this modification in cellular processes, developments and pathogenesis. The fungal pathogen Magnaporthe oryzae can cause rice blast and wheat blast diseases, which threatens worldwide food production. During infection, M. oryzae follows a sequence of distinct developmental stages adapted to survival and invasion of the host environment. M. oryzae attaches onto the host by the conidium, and then develops an appressorium to breach the host cuticle. After penetrating, it forms invasive hyphae to quickly spread in the host cells. Numerous genetic studies have focused on the mechanisms underlying each step in the infection process, but systemic approaches are needed for a broader, integrated understanding of regulatory events during M. oryzae pathogenesis. Many infection-related signaling events are regulated through post-translational protein modifications within the pathogen. N-linked glycosylation, in which a glycan moiety is added to the amide group of an asparagine residue, is an abundant modification known to be essential for M. oryzae infection. In this study, we employed a quantitative proteomics analysis to unravel the overall regulatory mechanisms of N-glycosylation at different developmental stages of M. oryzae. We detected changes in N-glycosylation levels at 559 glycosylated residues (N-glycosites) in 355 proteins during different stages, and determined that the ER quality control system is elaborately regulated by N-glycosylation. The insights gained will help us to better understand the regulatory mechanisms of infection in pathogenic fungi. These findings may be also important for developing novel strategies for fungal disease control.
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Affiliation(s)
- Xiao-Lin Chen
- The Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Caiyun Liu
- The Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bozeng Tang
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
| | - Zhiyong Ren
- The Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Guo-Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, United States of America
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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12
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Progress in Monolithic Column-based Separation and Enrichment of Glycoproteins. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(19)61207-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Abrahams JL, Taherzadeh G, Jarvas G, Guttman A, Zhou Y, Campbell MP. Recent advances in glycoinformatic platforms for glycomics and glycoproteomics. Curr Opin Struct Biol 2019; 62:56-69. [PMID: 31874386 DOI: 10.1016/j.sbi.2019.11.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022]
Abstract
Protein glycosylation is the most complex and prevalent post-translation modification in terms of the number of proteins modified and the diversity generated. To understand the functional roles of glycoproteins it is important to gain an insight into the repertoire of oligosaccharides present. The comparison and relative quantitation of glycoforms combined with site-specific identification and occupancy are necessary steps in this direction. Computational platforms have continued to mature assisting researchers with the interpretation of such glycomics and glycoproteomics data sets, but frequently support dedicated workflows and users rely on the manual interpretation of data to gain insights into the glycoproteome. The growth of site-specific knowledge has also led to the implementation of machine-learning algorithms to predict glycosylation which is now being integrated into glycoproteomics pipelines. This short review describes commercial and open-access databases and software with an emphasis on those that are actively maintained and designed to support current analytical workflows.
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Affiliation(s)
- Jodie L Abrahams
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Ghazaleh Taherzadeh
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Gabor Jarvas
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary; Horváth Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Andras Guttman
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary; Horváth Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; SCIEX, Brea, CA, USA
| | - Yaoqi Zhou
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Matthew P Campbell
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia.
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Feyertag F, Berninsone PM, Alvarez-Ponce D. N-glycoproteins exhibit a positive expression level-evolutionary rate correlation. J Evol Biol 2019; 32:390-394. [PMID: 30697857 DOI: 10.1111/jeb.13420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 12/22/2022]
Abstract
The different proteins of any proteome evolve at enormously different rates. One of the primary factors influencing rates of protein evolution is expression level, with highly expressed proteins tending to evolve at slow rates. This phenomenon, known as the expression level-evolutionary rate (E-R) anticorrelation, has been attributed to the abundance-dependent deleterious effects of misfolding or misinteraction. We have recently shown that secreted proteins either lack an E-R anticorrelation or exhibit a significantly reduced E-R anticorrelation. This effect may be due to the strict quality control to which secreted proteins are subject in the endoplasmic reticulum (which is expected to reduce the rate of misfolding and its deleterious effects) or to their extracellular location (expected to reduce the rate of misinteraction and its deleterious effects). Among secreted proteins, N-glycosylated ones are under particularly strong quality control. Here, we investigate how N-linked glycosylation affects the E-R anticorrelation. Strikingly, we observe a positive E-R correlation among N-glycosylated proteins. That is, N-glycoproteins that are highly expressed evolve at faster rates than lowly expressed N-glycoproteins, in contrast to what is observed among intracellular proteins.
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Affiliation(s)
- Felix Feyertag
- Department of Biology, University of Nevada, Reno, Reno, Nevada
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15
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Ikegami T. Hydrophilic interaction chromatography for the analysis of biopharmaceutical drugs and therapeutic peptides: A review based on the separation characteristics of the hydrophilic interaction chromatography phases. J Sep Sci 2019; 42:130-213. [DOI: 10.1002/jssc.201801074] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/17/2018] [Accepted: 11/18/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tohru Ikegami
- Faculty of Molecular Chemistry and Engineering; Kyoto Institute of Technology; Kyoto Japan
- Institute of Pharmaceutical Sciences; Pharmaceutical (Bio-) Analysis; Eberhard-Karls Universität Tübingen; Tübingen Germany
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16
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Clarke WR, Amundadottir L, James MA. CLPTM1L/CRR9 ectodomain interaction with GRP78 at the cell surface signals for survival and chemoresistance upon ER stress in pancreatic adenocarcinoma cells. Int J Cancer 2019; 144:1367-1378. [PMID: 30468251 DOI: 10.1002/ijc.32012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 09/24/2018] [Accepted: 11/09/2018] [Indexed: 12/15/2022]
Abstract
Altered regulation of endoplasmic reticulum (ER) homeostasis has been implicated in many cancers and has recently become a therapeutic and chemosensitization target of interest. We have identified Cleft Lip and Palate Transmembrane 1-Like (CLPTM1L)/Cisplatin Resistance Related Protein 9 (CRR9) as an ER stress related mediator of cytoprotection in pancreatic cancer. We recently demonstrated that CLPTM1L is highly expressed in pancreatic ductal adenocarcinoma and associated with poor outcome. Furthermore, we have discovered that CLPTM1L interacts with phosphoinositol-3-kinase-alpha at the tumor cell surface and causes up-regulation of Bcl-xL and pAkt mediated survival signaling. Here, we demonstrate surface relocalization and survival signaling by CLPTM1L triggered by endoplasmic reticular (ER) stress. We demonstrate the interaction of CLPTM1L with the central ER stress survival mediator, Glucose Regulated Protein 78 (GRP78)/Binding Immunoglobulin Protein (BiP) and PI3K-alpha /p110α. This interaction and surface relocalization of CLPTM1L and GRP78 is induced by ER stress, including that caused by treatment with gemcitabine. We demonstrate that the extracellular loop of CLPTM1L is required for gemcitabine resistance and interaction with GRP78. This interaction and the chemoresistance effect conferred by this pathway is targetable with our recently developed inhibitory CLPTM1L antibodies, which may represent novel modalities of chemosensitization and treatment of pancreatic adenocarcinoma. Anchorage independent growth, GRP78-mediated chemoresistance, and Akt phosphorylation were abrogated by inhibition of CLPTM1L. These findings demonstrate a novel and potentially targetable mechanism of cytoprotection and chemoresistance in pancreatic tumors.
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Affiliation(s)
- William R Clarke
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Laufey Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland, USA
| | - Michael A James
- Department of Surgery, Division of Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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17
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Characterization and comparison of whey N-glycoproteomes from human and bovine colostrum and mature milk. Food Chem 2018; 276:266-273. [PMID: 30409594 DOI: 10.1016/j.foodchem.2018.09.174] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/21/2018] [Accepted: 09/30/2018] [Indexed: 12/27/2022]
Abstract
Milk glycoproteins are crucial nutrients with a variety of functions. However, whey N-glycoproteomes in human and bovine milks have not been characterized during lactation. Herein, using lectin enrichment and liquid chromatography tandem mass spectrometry, 68, 58, 100, and 98 N-glycoproteins were identified in human colostrum and mature milk as well as bovine colostrum and mature milk whey. Gene Ontology and KEGG pathway analyses were used to elucidate the biological functions of whey N-glycoproteins in human and bovine colostrum and mature milks. Whey N-glycoproteomes differed dramatically between human and bovine milks and across lactation stages. The conserved and specific whey N-glycoproteins in all four sample types were also determined. Our results improve understanding of the properties and biological functions of whey N-glycoproteins in human and bovine milk and colostra, and provide insight into the potential application of some N-glycoproteins in infant formulae at different stages of development.
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18
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Ednie AR, Deng W, Yip KP, Bennett ES. Reduced myocyte complex N-glycosylation causes dilated cardiomyopathy. FASEB J 2018; 33:1248-1261. [PMID: 30138037 DOI: 10.1096/fj.201801057r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein glycosylation is an essential posttranslational modification that affects a myriad of physiologic processes. Humans with genetic defects in glycosylation, which result in truncated glycans, often present with significant cardiac deficits. Acquired heart diseases and their associated risk factors were also linked to aberrant glycosylation, highlighting its importance in human cardiac disease. In both cases, the link between causation and corollary remains enigmatic. The glycosyltransferase gene, mannosyl (α-1,3-)-glycoprotein β-1,2- N-acetylglucosaminyltransferase (Mgat1), whose product, N-acetylglucosaminyltransferase 1 (GlcNAcT1) is necessary for the formation of hybrid and complex N-glycan structures in the medial Golgi, was shown to be at reduced levels in human end-stage cardiomyopathy, thus making Mgat1 an attractive target for investigating the role of hybrid/complex N-glycosylation in cardiac pathogenesis. Here, we created a cardiomyocyte-specific Mgat1 knockout (KO) mouse to establish a model useful in exploring the relationship between hybrid/complex N-glycosylation and cardiac function and disease. Biochemical and glycomic analyses showed that Mgat1KO cardiomyocytes produce predominately truncated N-glycan structures. All Mgat1KO mice died significantly younger than control mice and demonstrated chamber dilation and systolic dysfunction resembling human dilated cardiomyopathy (DCM). Data also indicate that a cardiomyocyte L-type voltage-gated Ca2+ channel (Cav) subunit (α2δ1) is a GlcNAcT1 target, and Mgat1KO Cav activity is shifted to more-depolarized membrane potentials. Consistently, Mgat1KO cardiomyocyte Ca2+ handling is altered and contraction is dyssynchronous compared with controls. The data demonstrate that reduced hybrid/complex N-glycosylation contributes to aberrant cardiac function at whole-heart and myocyte levels drawing a direct link between altered glycosylation and heart disease. Thus, the Mgat1KO provides a model for investigating the relationship between systemic reductions in glycosylation and cardiac disease, showing that clinically relevant changes in cardiomyocyte hybrid/complex N-glycosylation are sufficient to cause DCM and early death.-Ednie, A. R., Deng, W., Yip, K.-P., Bennett, E. S. Reduced myocyte complex N-glycosylation causes dilated cardiomyopathy.
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Affiliation(s)
- Andrew R Ednie
- Department of Neuroscience, Cell Biology, and Physiology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.,College of Science and Mathematics, Wright State University, Dayton, Ohio, USA; and
| | - Wei Deng
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Kay-Pong Yip
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Eric S Bennett
- Department of Neuroscience, Cell Biology, and Physiology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.,College of Science and Mathematics, Wright State University, Dayton, Ohio, USA; and
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19
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Dange MC, Bhonsle HS, Godbole RK, More SK, Bane SM, Kulkarni MJ, Kalraiya RD. Mass spectrometry based identification of galectin-3 interacting proteins potentially involved in lung melanoma metastasis. MOLECULAR BIOSYSTEMS 2018; 13:2303-2309. [PMID: 28875213 DOI: 10.1039/c7mb00260b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adhesive interactions between molecules on tumor cells and those on target organs play a key role in organ specific metastasis. Poly-N-acetyl-lactosamine (polyLacNAc) substituted N-oligosaccharides on melanoma cell surface glycoproteins promote lung specific metastasis via galectin-3 by facilitating their arrest and extravasation. This study reports the identification and characterization of galectin-3 interacting proteins using a combination of galectin-3 sepharose affinity and leucoagglutinating phytohemagglutinin (L-PHA) columns. A total of 83 proteins were identified as galectin-3 interacting glycoproteins, of which 35 were constituents of the L-PHA bound fraction, suggesting that these proteins carry polyLacNAc substituted β1,6 branched N-glycans. The identities of some of these proteins, like LAMP-1, LAMP-3, basigin, embigin, and α5 and β1 Integrin, have been confirmed by western blotting, and functional relevance with respect to metastatic properties has been established.
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Affiliation(s)
- Manohar C Dange
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Sector 22, Kharghar, Navi Mumbai 410210, India
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20
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Togayachi A, Tomioka A, Fujita M, Sukegawa M, Noro E, Takakura D, Miyazaki M, Shikanai T, Narimatsu H, Kaji H. Identification of Poly-N-Acetyllactosamine-Carrying Glycoproteins from HL-60 Human Promyelocytic Leukemia Cells Using a Site-Specific Glycome Analysis Method, Glyco-RIDGE. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1138-1152. [PMID: 29675740 PMCID: PMC6004004 DOI: 10.1007/s13361-018-1938-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 05/15/2023]
Abstract
To elucidate the relationship between the protein function and the diversity and heterogeneity of glycans conjugated to the protein, glycosylation sites, glycan variation, and glycan proportions at each site of the glycoprotein must be analyzed. Glycopeptide-based structural analysis technology using mass spectrometry has been developed; however, complicated analyses of complex spectra obtained by multistage fragmentation are necessary, and sensitivity and throughput of the analyses are low. Therefore, we developed a liquid chromatography/mass spectrometry (MS)-based glycopeptide analysis method to reveal the site-specific glycome (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE). This method used accurate masses and retention times of glycopeptides, without requiring MS2, and could be applied to complex mixtures. To increase the number of identified peptide, fractionation of sample glycopeptides for reduction of sample complexity is required. Therefore, in this study, glycopeptides were fractionated into four fractions by hydrophilic interaction chromatography, and each fraction was analyzed using the Glyco-RIDGE method. As a result, many glycopeptides having long glycans were enriched in the highest hydrophilic fraction. Based on the monosaccharide composition, these glycans were thought to be poly-N-acetyllactosamine (polylactosamine [pLN]), and 31 pLN-carrier proteins were identified in HL-60 cells. Gene ontology enrichment analysis revealed that pLN carriers included many molecules related to signal transduction, receptors, and cell adhesion. Thus, these findings provided important insights into the analysis of the glycoproteome using our novel Glyco-RIDGE method. Graphical Abstract ᅟ.
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Affiliation(s)
- Akira Togayachi
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Azusa Tomioka
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Mika Fujita
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Masako Sukegawa
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Erika Noro
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Daisuke Takakura
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Michiyo Miyazaki
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Toshihide Shikanai
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Hisashi Narimatsu
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
| | - Hiroyuki Kaji
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
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21
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Xiao H, Chen W, Smeekens JM, Wu R. An enrichment method based on synergistic and reversible covalent interactions for large-scale analysis of glycoproteins. Nat Commun 2018; 9:1692. [PMID: 29703890 PMCID: PMC5923262 DOI: 10.1038/s41467-018-04081-3] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 03/28/2018] [Indexed: 01/28/2023] Open
Abstract
Protein glycosylation is ubiquitous in biological systems and essential for cell survival. However, the heterogeneity of glycans and the low abundance of many glycoproteins complicate their global analysis. Chemical methods based on reversible covalent interactions between boronic acid and glycans have great potential to enrich glycopeptides, but the binding affinity is typically not strong enough to capture low-abundance species. Here, we develop a strategy using dendrimer-conjugated benzoboroxole to enhance the glycopeptide enrichment. We test the performance of several boronic acid derivatives, showing that benzoboroxole markedly increases glycopeptide coverage from human cell lysates. The enrichment is further improved by conjugating benzoboroxole to a dendrimer, which enables synergistic benzoboroxole–glycan interactions. This robust and simple method is highly effective for sensitive glycoproteomics analysis, especially capturing low-abundance glycopeptides. Importantly, the enriched glycopeptides remain intact, making the current method compatible with mass-spectrometry-based approaches to identify glycosylation sites and glycan structures. Understanding the functions of protein glycosylation critically depends on methods to efficiently enrich glycoproteins from complex samples. Here, the authors develop a strategy using dendrimer-conjugated benzoboroxole to enhance glycopeptide enrichment, providing the basis for more comprehensive glycoprotein analyses.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Weixuan Chen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Johanna M Smeekens
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA. .,The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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22
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Fang P, Wang XJ, Xue Y, Liu MQ, Zeng WF, Zhang Y, Zhang L, Gao X, Yan GQ, Yao J, Shen HL, Yang PY. In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins. Oncotarget 2018; 7:38796-38809. [PMID: 27259237 PMCID: PMC5122430 DOI: 10.18632/oncotarget.9737] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/26/2016] [Indexed: 01/16/2023] Open
Abstract
N-glycosylation is one of the most prominent and abundant posttranslational modifications of proteins. It is estimated that over 50% of mammalian proteins undergo glycosylation. However, the analysis of N-glycoproteins has been limited by the available analytical technology. In this study, we comprehensively mapped the N-glycosylation sites in the mouse brain proteome by combining complementary methods, which included seven protease treatments, four enrichment techniques and two fractionation strategies. Altogether, 13492 N-glycopeptides containing 8386 N-glycosylation sites on 3982 proteins were identified. After evaluating the performance of the above methods, we proposed a simple and efficient workflow for large-scale N-glycosylation site mapping. The optimized workflow yielded 80% of the initially identified N-glycosylation sites with considerably less effort. Analysis of the identified N-glycoproteins revealed that many of the mouse brain proteins are N-glycosylated, including those proteins in critical pathways for nervous system development and neurological disease. Additionally, several important biomarkers of various diseases were found to be N-glycosylated. These data confirm that N-glycosylation is important in both physiological and pathological processes in the brain, and provide useful details about numerous N-glycosylation sites in brain proteins.
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Affiliation(s)
- Pan Fang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xin-Jian Wang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Yu Xue
- Department of Chemistry, Fudan University, Shanghai, China
| | - Ming-Qi Liu
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wen-Feng Zeng
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Yang Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lei Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xing Gao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guo-Quan Yan
- Department of Chemistry, Fudan University, Shanghai, China
| | - Jun Yao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hua-Li Shen
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Peng-Yuan Yang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China.,Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai, China
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23
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Cao X, Kang S, Yang M, Li W, Wu S, Han H, Meng L, Wu R, Yue X. Quantitative N-glycoproteomics of milk fat globule membrane in human colostrum and mature milk reveals changes in protein glycosylation during lactation. Food Funct 2018; 9:1163-1172. [DOI: 10.1039/c7fo01796k] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The present study profiled the N-glycoproteome and quantified the changes of N-glycosylation site occupancy of MFGM proteins during lactation.
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Affiliation(s)
- Xueyan Cao
- College of Food Science
- Shenyang Agricultural University
- Shenyang 110161
- PR China
| | - Shimo Kang
- College of Food Science
- Shenyang Agricultural University
- Shenyang 110161
- PR China
| | - Mei Yang
- College of Food Science
- Shenyang Agricultural University
- Shenyang 110161
- PR China
| | - Weixuan Li
- College of Food Science
- Shenyang Agricultural University
- Shenyang 110161
- PR China
| | - Shangyi Wu
- College of Food Science
- Shenyang Agricultural University
- Shenyang 110161
- PR China
| | - Hongjiao Han
- College of Food Science
- Shenyang Agricultural University
- Shenyang 110161
- PR China
| | - Lingshuai Meng
- College of Food Science
- Shenyang Agricultural University
- Shenyang 110161
- PR China
| | - Rina Wu
- College of Food Science
- Shenyang Agricultural University
- Shenyang 110161
- PR China
| | - Xiqing Yue
- College of Food Science
- Shenyang Agricultural University
- Shenyang 110161
- PR China
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24
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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25
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Campbell MP. A Review of Software Applications and Databases for the Interpretation of Glycopeptide Data. TRENDS GLYCOSCI GLYC 2017. [DOI: 10.4052/tigg.1601.1e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Identification of PNGase-dependent ERAD substrates in Saccharomyces cerevisiae. Biochem J 2016; 473:3001-12. [DOI: 10.1042/bcj20160453] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 07/18/2016] [Indexed: 12/24/2022]
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) is a proteolytic pathway for handling misfolded or improperly assembled proteins that are synthesized in the ER. Cytoplasmic peptide:N-glycanase (PNGase) is a deglycosylating enzyme that cleaves N-glycans that are attached to ERAD substrates. While the critical roles of N-glycans in monitoring the folding status of carrier proteins in the ER lumen are relatively well understood, the physiological role of PNGase-mediated deglycosylation in the cytosol remained poorly understood. We report herein the identification of endogenous substrates for the cytoplasmic PNGase in Saccharomyces cerevisiae. Using an isotope-coded glycosylation site-specific tagging (IGOT) method-based LC/MS analysis, 11 glycoproteins were specifically detected in the cytosol of PNGase-deletion cells (png1Δ). Among these molecules, at least five glycoproteins were clearly identified as ERAD substrates in vivo. Moreover, four out of the five proteins were found to be either deglycosylated by PNGase in vivo or the overall degradation was delayed in a png1Δ mutant. Our results clearly indicate that the IGOT method promises to be a powerful tool for the identification of endogenous substrates for the cytoplasmic PNGase.
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27
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Yang Y, Zheng N, Wang W, Zhao X, Zhang Y, Han R, Ma L, Zhao S, Li S, Guo T, Zang C, Wang J. N-glycosylation proteomic characterization and cross-species comparison of milk fat globule membrane proteins from mammals. Proteomics 2016; 16:2792-2800. [PMID: 27539975 DOI: 10.1002/pmic.201500361] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 04/09/2016] [Accepted: 08/12/2016] [Indexed: 12/21/2022]
Abstract
Glycosylation of proteins has been implicated in various biological functions and has received much attention; however, glycoprotein components and inter-species complexity have not yet been elucidated fully in milk proteins. N-linked glycosylation sites and glycoproteins in milk fat globule membrane (MFGM) fractions were investigated by combining N-glycosylated peptides enrichment and high-accuracy Q Exactive identification, to map the N-glycoproteome profiles in Holstein and Jersey cows, buffaloes, yaks, goats, camels, horses, and humans. A total of 399 N-glycoproteins with 677 glycosylation sites were identified in the MFGM fractions of the studied mammals. Most glycosylation sites in humans were classified as known and those in the other studied mammals as unknown, according to Swiss-Prot annotations. Functionally, most of the identified glycoproteins were associated with the 'response to stimulus' GO category. N-glycosylated protein components of MFGM fractions from Holstein and Jersey cows, buffaloes, yaks, and goats were more similar to each other compared with those of camels, horses and human. The findings increased the number of known N-glycosylation sites in the milk from dairy animal species, revealed the complexity of the MFGM glycoproteome, and provided useful information to further explore the mechanism of MFGM glycoproteins biosynthesis among the studied mammals.
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Affiliation(s)
- Yongxin Yang
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Nan Zheng
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiyu Wang
- The High School affiliated to Renmin University of China, Beijing, China
| | - Xiaowei Zhao
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yangdong Zhang
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rongwei Han
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lu Ma
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengguo Zhao
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Songli Li
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tongjun Guo
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changjiang Zang
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqi Wang
- Ministry of Agriculture-Milk Risk Assessment Laboratory, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Lindsey ML, Hall ME, Harmancey R, Ma Y. Adapting extracellular matrix proteomics for clinical studies on cardiac remodeling post-myocardial infarction. Clin Proteomics 2016; 13:19. [PMID: 27651752 PMCID: PMC5024439 DOI: 10.1186/s12014-016-9120-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/15/2016] [Indexed: 01/16/2023] Open
Abstract
Following myocardial infarction (MI), the left ventricle (LV) undergoes a series of cardiac wound healing responses that involve stimulation of robust inflammation to clear necrotic myocytes and tissue debris and induction of extracellular matrix (ECM) protein synthesis to generate a scar. Proteomic strategies provide us with a means to index the ECM proteins expressed in the LV, quantify amounts, determine functions, and explore interactions. This review will focus on the efforts taken in the proteomics research field that have expanded our understanding of post-MI LV remodeling, concentrating on the strengths and limitations of different proteomic approaches to glean information that is specific to ECM turnover in the post-MI setting. We will discuss how recent advances in sample preparation and labeling protocols increase our successes at detecting components of the cardiac ECM proteome. We will summarize how proteomic approaches, focusing on the ECM compartment, have progressed over time to current gel-free methods using decellularized fractions or labeling strategies that will be useful for clinical applications. This review will provide an overview of how cardiac ECM proteomics has evolved over the last decade and will provide insight into future directions that will drive forward our understanding of cardiac ECM turnover in the post-MI LV.
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Affiliation(s)
- Merry L Lindsey
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA ; Division of Cardiology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS USA ; Research Service, G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, MS USA
| | - Michael E Hall
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA ; Division of Cardiology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS USA
| | - Romain Harmancey
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA
| | - Yonggang Ma
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA
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29
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Hydrogen-bond interaction assisted branched copolymer HILIC material for separation and N-glycopeptides enrichment. Talanta 2016; 158:361-367. [DOI: 10.1016/j.talanta.2016.05.034] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 05/09/2016] [Accepted: 05/13/2016] [Indexed: 11/22/2022]
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30
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Walsh I, Zhao S, Campbell M, Taron CH, Rudd PM. Quantitative profiling of glycans and glycopeptides: an informatics' perspective. Curr Opin Struct Biol 2016; 40:70-80. [PMID: 27522273 DOI: 10.1016/j.sbi.2016.07.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/25/2016] [Accepted: 07/30/2016] [Indexed: 12/16/2022]
Abstract
Experimental techniques to identify and quantify glycan structures in a given sample are continuously improving. However, as they advance data analysis and annotation seems to become more complex. To address this issue, much progress has been made in developing software for interpretation of quantitative glycan profiles. Here, we focus on these informatics tools for high/ultra performance liquid chromatography (H/UPLC), mass spectrometry (MS), tandem mass spectrometry (MSn) and combinations thereof. Software for biomarker discovery, pathway, genomic and disease analysis and a final note on some future prospects for glycoinformatics are also mentioned.
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Affiliation(s)
- Ian Walsh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore; New England Biolabs, Ipswich, MA, United States
| | - Sophie Zhao
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Matthew Campbell
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Pauline M Rudd
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore; National Institute for Bioprocessing Research & Training, Dublin, Ireland.
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31
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Karabulut NP, Frishman D. Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites. PLoS One 2016; 11:e0157896. [PMID: 27332813 PMCID: PMC4917084 DOI: 10.1371/journal.pone.0157896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 06/07/2016] [Indexed: 01/22/2023] Open
Abstract
Phosphorylation is the most widespread and well studied reversible posttranslational modification. Discovering tissue-specific preferences of phosphorylation sites is important as phosphorylation plays a role in regulating almost every cellular activity and disease state. Here we present a comprehensive analysis of global and tissue-specific sequence and structure properties of phosphorylation sites utilizing recent proteomics data. We identified tissue-specific motifs in both sequence and spatial environments of phosphorylation sites. Target site preferences of kinases across tissues indicate that, while many kinases mediate phosphorylation in all tissues, there are also kinases that exhibit more tissue-specific preferences which, notably, are not caused by tissue-specific kinase expression. We also demonstrate that many metabolic pathways are differentially regulated by phosphorylation in different tissues.
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Affiliation(s)
- Nermin Pinar Karabulut
- Department of Genome Oriented Bioinformatics, Technische Universität München, Freising, Germany
| | - Dmitrij Frishman
- Department of Genome Oriented Bioinformatics, Technische Universität München, Freising, Germany
- Helmholtz Zentrum Munich; German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
- St Petersburg State Polytechnical University, St Petersburg, Russia
- * E-mail:
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32
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Yu L, He H, Hu Z, Ma Z. Comprehensive quantification of N-glycoproteome in Fusarium graminearum reveals intensive glycosylation changes against fungicide. J Proteomics 2016; 142:82-90. [DOI: 10.1016/j.jprot.2016.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/10/2016] [Accepted: 05/09/2016] [Indexed: 11/28/2022]
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33
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Ducret A, Kux van Geijtenbeek S, Röder D, Simon S, Chin D, Berrera M, Gruenbaum L, Ji C, Cutler P. Identification of six cell surface proteins for specific liver targeting. Proteomics Clin Appl 2016; 9:651-61. [PMID: 26097162 DOI: 10.1002/prca.201400194] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/27/2015] [Accepted: 06/08/2015] [Indexed: 01/09/2023]
Abstract
PURPOSE Cell surface proteins are the primary means for a cell to sense and interact with its environment and their dysregulation has been linked to numerous diseases. In particular, the identification of proteins specific to a single tissue type or to a given disease phenotype may enable the characterization of novel therapeutic targets. We tested here the feasibility of a cell surface proteomics approach to identify pertinent markers directly in a clinically relevant tissue. EXPERIMENTAL DESIGN We analyzed the cell surface proteome of freshly isolated primary heptatocytes using a glycocapture-specific approach combined with a robust bioinformatics filtering. RESULTS Using primary lung epithelial cell cultures as negative controls, we identified 32 hepatocyte-specific cell surface proteins candidates. We used mRNA expression to select six markers that may provide adequate specificity for targeting therapeutics to the liver. CONCLUSIONS AND CLINICAL RELEVANCE We demonstrate the feasibility and the importance of conducting such studies directly in a clinically relevant tissue. In particular, the cell surface proteome of freshly isolated hepatocytes differed substantially from cultured cell lines.
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Affiliation(s)
- Axel Ducret
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Sabine Kux van Geijtenbeek
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Daniel Röder
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Sandrine Simon
- Drug Disposition and Safety, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Daniel Chin
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Marco Berrera
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Lore Gruenbaum
- Translational Medicine - Infectious Diseases, Pharma Research and Early Development (pRED), Roche Innovation Center New York, New York, NY, USA
| | - Changhua Ji
- External Alliances and Portfolio Management, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Shanghai, Pudong, Shanghai, P. R. China
| | - Paul Cutler
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
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34
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Identification, Quantification, and Site Localization of Protein Posttranslational Modifications via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:345-382. [PMID: 27975226 DOI: 10.1007/978-3-319-41448-5_17] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Posttranslational modifications (PTMs) are important biochemical processes for regulating various signaling pathways and determining specific cell fate. Mass spectrometry (MS)-based proteomics has been developed extensively in the past decade and is becoming the standard approach for systematic characterization of different PTMs on a global scale. In this chapter, we will explain the biological importance of various PTMs, summarize key innovations in PTMs enrichment strategies, high-performance liquid chromatography (HPLC)-based fractionation approaches, mass spectrometry detection methods, and lastly bioinformatic tools for PTMs related data analysis. With great effort in recent years by the proteomics community, highly efficient enriching methods and comprehensive resources have been developed. This chapter will specifically focus on five major types of PTMs; phosphorylation, glycosylation, ubiquitination/sumosylation, acetylation, and methylation.
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35
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Takakura D, Tada M, Kawasaki N. Membrane glycoproteomics of fetal lung fibroblasts using LC/MS. Proteomics 2015; 16:47-59. [PMID: 26439794 DOI: 10.1002/pmic.201500003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 07/29/2015] [Accepted: 09/28/2015] [Indexed: 11/05/2022]
Abstract
Some aberrant N-glycosylations are being used as tumor markers, and glycoproteomics is expected to provide novel diagnosis markers and targets of drug developments. However, one has trouble in mass spectrometric glycoproteomics of membrane fraction because of lower intensity of glycopeptides in the existence of surfactants. Previously, we developed a glycopeptide enrichment method by acetone precipitation, and it was successfully applied to human serum glycoproteomics. In this study, we confirmed that this method is useful to remove the surfactants and applicable to membrane glycoproteomics. The glycoproteomic approach to the human fetal lung fibroblasts membrane fraction resulted in the identification of over 272 glycoforms on 63 sites of the 44 glycoproteins. According to the existing databases, the structural features on 41 sites are previously unreported. The most frequently occurring forms at N-glycosylation site were high-mannose type containing nine mannose residues (M9) and monosialo-fucosylated biantennary oligosaccharides. Several unexpected N-glycans, such as fucosylated complex-type and fucosylated high-mannose and/or fucosylated pauci-mannose types were found in ER and lysosome proteins. Our method provides new insights into transport, biosynthesis, and degradation of glycoproteins.
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Affiliation(s)
- Daisuke Takakura
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Minoru Tada
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Setagaya-ku, Tokyo, Japan
| | - Nana Kawasaki
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
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36
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Noro E, Togayachi A, Sato T, Tomioka A, Fujita M, Sukegawa M, Suzuki N, Kaji H, Narimatsu H. Large-Scale Identification of N-Glycan Glycoproteins Carrying Lewis x and Site-Specific N-Glycan Alterations in Fut9 Knockout Mice. J Proteome Res 2015; 14:3823-34. [PMID: 26244810 DOI: 10.1021/acs.jproteome.5b00178] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The Lewis x (Le(x)) structure (Galβ1-4(Fucα1-3)GlcNAc-R) is a carbohydrate epitope comprising the stage-specific embryonic antigen-1 (SSEA-1) and CD15, and it is synthesized by α1,3-fucosyltransferase 9 (Fut9). Fut9 is expressed specifically in the stomach, kidney, brain, and in leukocytes, suggesting a specific function in these tissues. In this study, the N-linked glycan mass spectrometry profile of wild-type mouse kidney glycoproteins revealed the presence of abundant terminal fucoses, which were lost following knockout of the Fut9 gene; the terminal fucose was therefore concluded to be Le(x). These results suggested that Le(x) presence is widespread rather than being limited to specific proteins. We endeavored to comprehensively identify the Le(x) carriers in the mouse kidney. Glycopeptides carrying fucosylated glycans were collected by Aleuria aurantia lectin (AAL) affinity chromatography from kidney homogenates of wild-type and Fut9 knockout mice. The site-specific N-glycomes on the glycopeptides were subsequently analyzed by adopting a new glycoproteomic technology composed of dissociation-independent assignment of glycopeptide signals and accurate mass-based prediction of the N-glycome on the glycopeptides. Our analyses demonstrated that 24/32 glycoproteins contained the Le(x) N-glycan structure in wild-type kidney; of these, Le(x) was lost from 21 in the knockout mice. This is the first report of large-scale identification of Le(x)-carrying glycoproteins from a native sample based on the site-specific glycome analysis.
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Affiliation(s)
- Erika Noro
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan.,Department of Biomolecular Function, Doctoral Program in Life System Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
| | - Akira Togayachi
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Takashi Sato
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Azusa Tomioka
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Mika Fujita
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Masako Sukegawa
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Nami Suzuki
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Hiroyuki Kaji
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Hisashi Narimatsu
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan.,Department of Biomolecular Function, Doctoral Program in Life System Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
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37
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Tissue-specific sequence and structural environments of lysine acetylation sites. J Struct Biol 2015; 191:39-48. [DOI: 10.1016/j.jsb.2015.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 11/22/2022]
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38
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Sugahara D, Tomioka A, Sato T, Narimatsu H, Kaji H. Large-scale identification of secretome glycoproteins recognized by Wisteria floribunda
agglutinin: A glycoproteomic approach to biomarker discovery. Proteomics 2015; 15:2921-33. [DOI: 10.1002/pmic.201400443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 01/27/2015] [Accepted: 04/24/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Daisuke Sugahara
- Research Center for Medical Glycoscience (RCMG); National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Japan
| | - Azusa Tomioka
- Research Center for Medical Glycoscience (RCMG); National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Japan
| | - Takashi Sato
- Research Center for Medical Glycoscience (RCMG); National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Japan
| | - Hisashi Narimatsu
- Research Center for Medical Glycoscience (RCMG); National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Japan
| | - Hiroyuki Kaji
- Research Center for Medical Glycoscience (RCMG); National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Japan
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39
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Tian Y, Koganti T, Yao Z, Cannon P, Shah P, Pietrovito L, Modesti A, Aiyetan P, DeLeon-Pennell K, Ma Y, Halade GV, Hicks C, Zhang H, Lindsey ML. Cardiac extracellular proteome profiling and membrane topology analysis using glycoproteomics. Proteomics Clin Appl 2015; 8:595-602. [PMID: 24920555 DOI: 10.1002/prca.201400009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/23/2014] [Accepted: 06/06/2014] [Indexed: 01/23/2023]
Abstract
PURPOSE Extracellular proteins are easily accessible, which presents a subproteome of molecular targets that have high diagnostic and therapeutic potential. Efforts have been made to catalog the cardiac extracellular matridome and analyze the topology of identified proteins for the design of therapeutic targets. Although many bioinformatics tools have been developed to predict protein topology, topology has been experimentally validated for only a very small portion of membrane proteins. The aim of this study was to use a glycoproteomics and MS approach to identify glycoproteins in the extracellular matridome of the infarcted left ventricle (LV) and provide experimental evidence for topological determination. EXPERIMENTAL DESIGN Glycoproteomics analysis was performed on eight biological replicates of LV samples from wild-type mice at 7 days following myocardial infarction using SPE of glycopeptides, followed by mass spectrometric identification of N-linked glycosylation sites for topology assessment. RESULTS We identified hundreds of glycoproteins, and the identified N-glycosylation sites provide novel information on the correct topology for membrane proteins present in the infarct setting. CONCLUSIONS AND CLINICAL RELEVANCE Our data provide the foundation for future studies of the LV infarct extracellular matridome, which may facilitate the discovery of drug targets and biomarkers.
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Affiliation(s)
- Yuan Tian
- San Antonio Cardiovascular Proteomics Center, San Antonio, TX, USA; Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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40
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Sok Hwee Cheow E, Hwan Sim K, de Kleijn D, Neng Lee C, Sorokin V, Sze SK. Simultaneous Enrichment of Plasma Soluble and Extracellular Vesicular Glycoproteins Using Prolonged Ultracentrifugation-Electrostatic Repulsion-hydrophilic Interaction Chromatography (PUC-ERLIC) Approach. Mol Cell Proteomics 2015; 14:1657-71. [PMID: 25862729 DOI: 10.1074/mcp.o114.046391] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 12/16/2022] Open
Abstract
Plasma glycoproteins and extracellular vesicles represent excellent sources of disease biomarkers, but laboratory detection of these circulating structures are limited by their relatively low abundance in complex biological fluids. Although intensive research has led to the development of effective methods for the enrichment and isolation of either plasma glycoproteins or extracellular vesicles from clinical materials, at present it is not possible to enrich both structures simultaneously from individual patient sample, a method that affords the identification of biomarker combinations from both entities for the prediction of clinical outcomes will be clinically useful. We have therefore developed an enrichment method for use in mass spectrometry-based proteomic profiling that couples prolonged ultracentrifugation with electrostatic repulsion-hydrophilic interaction chromatography, to facilitate the recovery of both glycoproteins and extracellular vesicles from nondepleted human plasma. Following prolonged ultracentrifugation, plasma glycoproteins and extracellular vesicles were concentrated as a yellow suspension, and simultaneous analyses of low abundant secretory and vesicular glycoproteins was achieved in a single LC-MS/MS run. Using this systematic prolonged ultracentrifugation-electrostatic repulsion-hydrophilic interaction chromatography approach, we identified a total of 127 plasma glycoproteins at a high level of confidence (FDR ≤ 1%), including 48 glycoproteins with concentrations ranging from pg to ng/ml. The novel enrichment method we report should facilitate future human plasma-based proteome and glycoproteome that will identify novel biomarkers, or combinations of secreted and vesicle-derived biomarkers, that can be used to predict clinical outcomes in human patients.
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Affiliation(s)
- Esther Sok Hwee Cheow
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Kae Hwan Sim
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Dominique de Kleijn
- §Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, and Cardiovascular Research Institute, Singapore 119228; ¶Experimental Cardiology Laboratory, Cardiology, University Medical Center Utrecht, the Netherlands & Interuniversity Cardiovascular Institute of the Netherlands, Utrecht, the Netherlands
| | - Chuen Neng Lee
- §Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, and Cardiovascular Research Institute, Singapore 119228; ‖National University Heart Centre, Department of Cardiac, Thoracic and Vascular Surgery, Singapore 119228; **Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Vitaly Sorokin
- §Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, and Cardiovascular Research Institute, Singapore 119228; ‖National University Heart Centre, Department of Cardiac, Thoracic and Vascular Surgery, Singapore 119228; **Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Siu Kwan Sze
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551;
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41
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Ranzinger R, Aoki-Kinoshita KF, Campbell MP, Kawano S, Lütteke T, Okuda S, Shinmachi D, Shikanai T, Sawaki H, Toukach P, Matsubara M, Yamada I, Narimatsu H. GlycoRDF: an ontology to standardize glycomics data in RDF. Bioinformatics 2015; 31:919-25. [PMID: 25388145 PMCID: PMC4380026 DOI: 10.1093/bioinformatics/btu732] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/12/2014] [Accepted: 10/28/2014] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. RESULTS An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. AVAILABILITY AND IMPLEMENTATION The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/).
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Affiliation(s)
- Rene Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Kiyoko F Aoki-Kinoshita
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Matthew P Campbell
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Shin Kawano
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Thomas Lütteke
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Shujiro Okuda
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Daisuke Shinmachi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Toshihide Shikanai
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Hiromichi Sawaki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Philip Toukach
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Masaaki Matsubara
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Issaku Yamada
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
| | - Hisashi Narimatsu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan
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42
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Goldman R, Sanda M. Targeted methods for quantitative analysis of protein glycosylation. Proteomics Clin Appl 2015; 9:17-32. [PMID: 25522218 PMCID: PMC5780646 DOI: 10.1002/prca.201400152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/15/2014] [Accepted: 12/11/2014] [Indexed: 12/17/2022]
Abstract
Quantification of proteins by LC-MS/MS-MRM has become a standard method with broad projected clinical applicability. MRM quantification of protein modifications is, however, far less utilized, especially in the case of glycoproteins. This review summarizes current methods for quantitative analysis of protein glycosylation with a focus on MRM methods. We describe advantages of this quantitative approach, analytical parameters that need to be optimized to achieve reliable measurements, and point out the limitations. Differences between major classes of N- and O-glycopeptides are described and class-specific glycopeptide assays are demonstrated.
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Affiliation(s)
- Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
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43
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Maeda M, Fujita N, Suzuki Y, Sawaki H, Shikanai T, Narimatsu H. JCGGDB: Japan Consortium for Glycobiology and Glycotechnology Database. Methods Mol Biol 2015; 1273:161-179. [PMID: 25753710 DOI: 10.1007/978-1-4939-2343-4_12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The biological significance of glycans has been widely studied and reported in the past. However, most achievements of our predecessors are not readily available in existing databases. JCGGDB is a meta-database involving 15 original databases in AIST and 5 cooperative databases in alliance with JCGG: Japan Consortium for Glycobiology and Glycotechnology. It centers on a glycan structure database and accumulates information such as glycan preferences of lectins, glycosylation sites in proteins, and genes related to glycan syntheses from glycoscience and related fields. This chapter illustrates how to use three major search interfaces (Keyword Search, Structure Search, and GlycoChem Explorer) available in JCGGDB to search across multiple databases.
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Affiliation(s)
- Masako Maeda
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
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44
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Akiyoshi S, Nomura KH, Dejima K, Murata D, Matsuda A, Kanaki N, Takaki T, Mihara H, Nagaishi T, Furukawa S, Ando KG, Yoshina S, Mitani S, Togayachi A, Suzuki Y, Shikanai T, Narimatsu H, Nomura K. RNAi screening of human glycogene orthologs in the nematode Caenorhabditis elegans and the construction of the C. elegans glycogene database. Glycobiology 2015; 25:8-20. [PMID: 25091817 PMCID: PMC4245905 DOI: 10.1093/glycob/cwu080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 07/16/2014] [Accepted: 07/30/2014] [Indexed: 12/16/2022] Open
Abstract
In this study, we selected 181 nematode glycogenes that are orthologous to human glycogenes and examined their RNAi phenotypes. The results are deposited in the Caenorhabditis elegans Glycogene Database (CGGDB) at AIST, Tsukuba, Japan. The most prominent RNAi phenotypes observed are disruptions of cell cycle progression in germline mitosis/meiosis and in early embryonic cell mitosis. Along with the previously reported roles of chondroitin proteoglycans, glycosphingolipids and GPI-anchored proteins in cell cycle progression, we show for the first time that the inhibition of the functions of N-glycan synthesis genes (cytoplasmic alg genes) resulted in abnormal germline formation, ER stress and small body size phenotypes. The results provide additional information on the roles of glycoconjugates in the cell cycle progression mechanisms of germline and embryonic cells.
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Affiliation(s)
| | - Kazuko H Nomura
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi Center Building, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Katsufumi Dejima
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi Center Building, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo 162-8666, Japan
| | - Daisuke Murata
- Graduate School of Systems Life Sciences, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi Center Building, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | | | - Nanako Kanaki
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
| | - Tetsuro Takaki
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
| | - Hiroyuki Mihara
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
| | - Takayuki Nagaishi
- Graduate School of Systems Life Sciences, and Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
| | - Shuhei Furukawa
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
| | - Keiko-Gengyo Ando
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi Center Building, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo 162-8666, Japan
| | - Sawako Yoshina
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo 162-8666, Japan
| | - Shohei Mitani
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi Center Building, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo 162-8666, Japan
| | - Akira Togayachi
- Glycomedicine Technology Research Center (GTRC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Yoshinori Suzuki
- Glycomedicine Technology Research Center (GTRC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Toshihide Shikanai
- Glycomedicine Technology Research Center (GTRC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Hisashi Narimatsu
- Glycomedicine Technology Research Center (GTRC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Kazuya Nomura
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi Center Building, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
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45
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Pan Y, Ma C, Tong W, Fan C, Zhang Q, Zhang W, Tian F, Peng B, Qin W, Qian X. Preparation of Sequence-Controlled Triblock Copolymer-Grafted Silica Microparticles by Sequential-ATRP for Highly Efficient Glycopeptides Enrichment. Anal Chem 2014; 87:656-62. [DOI: 10.1021/ac5034215] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yiting Pan
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
- Chemical
Engineering College, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Cheng Ma
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Wei Tong
- Tianjin
Key Laboratory for Prevention and Control of Occupational and Environmental
Hazards, Logistics College of CAPF, Tianjin 300162, China
| | - Chao Fan
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Qian Zhang
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Wanjun Zhang
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Fang Tian
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Bo Peng
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Weijie Qin
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaohong Qian
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
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46
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Lazar IM, Deng J, Ikenishi F, Lazar AC. Exploring the glycoproteomics landscape with advanced MS technologies. Electrophoresis 2014; 36:225-37. [PMID: 25311661 DOI: 10.1002/elps.201400400] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/28/2014] [Accepted: 09/29/2014] [Indexed: 12/13/2022]
Abstract
The advance of glycoproteomic technologies has offered unique insights into the importance of glycosylation in determining the functional roles of a protein within a cell. Biologically active glycoproteins include the categories of enzymes, hormones, proteins involved in cell proliferation, cell membrane proteins involved in cell-cell recognition, and communication events or secreted proteins, just to name a few. The recent progress in analytical instrumentation, methodologies, and computational approaches has enabled a detailed exploration of glycan structure, connectivity, and heterogeneity, underscoring the staggering complexity of the glycome repertoire in a cell. A variety of approaches involving the use of spectroscopy, MS, separation, microfluidic, and microarray technologies have been used alone or in combination to tackle the glycoproteome challenge, the research results of these efforts being captured in an overwhelming number of annual publications. This work is aimed at reviewing the major developments and accomplishments in the field of glycoproteomics, with focus on the most recent advancements (2012-2014) that involve the use of capillary separations and MS detection.
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Affiliation(s)
- Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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47
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Dobson L, Langó T, Reményi I, Tusnády GE. Expediting topology data gathering for the TOPDB database. Nucleic Acids Res 2014; 43:D283-9. [PMID: 25392424 PMCID: PMC4383934 DOI: 10.1093/nar/gku1119] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Topology Data Bank of Transmembrane Proteins (TOPDB, http://topdb.enzim.ttk.mta.hu) contains experimentally determined topology data of transmembrane proteins. Recently, we have updated TOPDB from several sources and utilized a newly developed topology prediction algorithm to determine the most reliable topology using the results of experiments as constraints. In addition to collecting the experimentally determined topology data published in the last couple of years, we gathered topographies defined by the TMDET algorithm using 3D structures from the PDBTM. Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database. Moreover, a new algorithm was developed to integrate scattered topology data from various publicly available databases and a new method was introduced to measure the reliability of predicted topologies. We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method. Altogether, more than 52 000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database.
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Affiliation(s)
- László Dobson
- 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary
| | - Tamás Langó
- 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary
| | - István Reményi
- 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary
| | - Gábor E Tusnády
- 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary
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48
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Poulin EJ, Powell AE, Wang Y, Li Y, Franklin JL, Coffey RJ. Using a new Lrig1 reporter mouse to assess differences between two Lrig1 antibodies in the intestine. Stem Cell Res 2014; 13:422-30. [PMID: 25460603 DOI: 10.1016/j.scr.2014.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/08/2014] [Accepted: 09/11/2014] [Indexed: 01/01/2023] Open
Abstract
Lrig1 is an intestinal stem cell marker important for epithelial homeostasis. However, the position of the Lrig1(+) population in the intestinal crypt has been debated, largely due to discrepant staining patterns using two Lrig1 antibodies. Here, we set out to decipher the differences between these Lrig1 antibodies to clarify their use for Lrig1-related studies. We confirmed that the commercially available Lrig1-R&D antibody stained the bottom third of the colonic crypt, whereas an independently generated Lrig1-VU antibody recognized a subset of anti-Lrig1-R&D(+) cells. Biochemically, we found that anti-Lrig1-VU recognized a non-glycosylated form of Lrig1; in contrast, anti-Lrig1-R&D recognized both glycosylated and non-glycosylated forms of Lrig1. In addition, we generated a reporter mouse (Lrig1-Apple) as an independent readout of Lrig1 transcriptional activity. Flow cytometry of isolated colonic epithelial cells from Lrig1-Apple mice demonstrated anti-Lrig1-R&D recognized mostly RFP-hi cells, while anti-Lrig1-VU recognized cells that were largely RFP-mid. Of note, by qRT-PCR, Lgr5 was expressed in the RFP-hi population, but not in the RFP-mid population. We conclude that anti-Lrig1-R&D appears to recognize all Lrig1(+) cells, while anti-Lrig1-VU recognizes a subpopulation of Lrig1(+) cells.
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Affiliation(s)
- Emily J Poulin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Anne E Powell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yang Wang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yina Li
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey L Franklin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert J Coffey
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA.
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49
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Ma C, Zhang Q, Qu J, Zhao X, Li X, Liu Y, Wang PG. A precise approach in large scale core-fucosylated glycoprotein identification with low- and high-normalized collision energy. J Proteomics 2014; 114:61-70. [PMID: 25220145 DOI: 10.1016/j.jprot.2014.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/26/2014] [Accepted: 09/02/2014] [Indexed: 01/03/2023]
Abstract
UNLABELLED The core fucosylation (CF) of N-glycoproteins plays important roles in regulating protein functions during biological development, and it has also been shown to be up-regulated in several high metastasis cancer cell lines. Therefore, global profiling and quantitative characterization of CF-glycoproteins may reveal potent biomarkers for clinical applications. However, due to the complex fragmentation pattern of CF-glycopeptides, accurately identifying CF-glycosylation sites via mass spectrometry with high throughput remains a formidable challenge. In this study, we established a precise CF-glycosylation site identification strategy with UHPLC LTQ-Orbitrap Elite under low- and high-normalized collision energy (LHNCE) conditions. To demonstrate the feasibility of LHNCE, the CF-glycopeptides of target proteins in clinical plasma samples were applied and compared as a preliminary demonstration and resulted in the assignment of 357 unique CF-glycosylation sites from 209 CF-glycoproteins. In this study, the largest human plasma CF-glycosylation site database was constructed, and at least three-fold more CF-sites were identified compared to previously published studies. The results further demonstrated that LHNCE provides an important approach for CF-glycoprotein function studies and biomarker screening in cancer research. BIOLOGICAL SIGNIFICANCE Core-fucosylation (CF) is a kind of N-linked glycosylation in which an α1,6-linked fucose is added to the innermost N-acetylglucosamine (GlcNAc) residue. It has been proved that core-fucosylation is involved in regulating biological processes in mammals. Abnormal core-fucosylation has been demonstrated in human pathological processes, such as metastasis. For example, the CF-glycosylation of an α-fetoprotein isoform (AFP-L3) was approved as a biomarker of hepatocellular carcinoma (HCC). In addition, GP73 is also a well-known biomarker and its CF-glycosylation level will increase in liver cancer patients. Therefore, it is crucial to develop a strategy for mapping human CF-glycosylation.
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Affiliation(s)
- Cheng Ma
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Qi Zhang
- Department of Parasitology, Faculty of Biology, Philipps University Marburg, Marburg, Hessen 35043, Germany
| | - Jingyao Qu
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; National Glycoengineering Research Center, The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Xinyuan Zhao
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Xu Li
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Yunpeng Liu
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; National Glycoengineering Research Center, The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Peng George Wang
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; National Glycoengineering Research Center, The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, People's Republic of China.
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50
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Holland A, Ohlendieck K. Comparative profiling of the sperm proteome. Proteomics 2014; 15:632-48. [DOI: 10.1002/pmic.201400032] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/27/2014] [Accepted: 06/02/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Ashling Holland
- Department of Biology; National University of Ireland; Maynooth County Kildare Ireland
| | - Kay Ohlendieck
- Department of Biology; National University of Ireland; Maynooth County Kildare Ireland
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