1
|
Tkalec KI, Hayes AJ, Lim KS, Lewis JM, Davies MR, Scott NE. Glycan-Tailored Glycoproteomic Analysis Reveals Serine is the Sole Residue Subjected to O-Linked Glycosylation in Acinetobacter baumannii. J Proteome Res 2024. [PMID: 38850255 DOI: 10.1021/acs.jproteome.4c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
Protein glycosylation is a ubiquitous process observed across all domains of life. Within the human pathogen Acinetobacter baumannii, O-linked glycosylation is required for virulence; however, the targets and conservation of glycosylation events remain poorly defined. In this work, we expand our understanding of the breadth and site specificity of glycosylation within A. baumannii by demonstrating the value of strain specific glycan electron-transfer/higher-energy collision dissociation (EThcD) triggering for bacterial glycoproteomics. By coupling tailored EThcD-triggering regimes to complementary glycopeptide enrichment approaches, we assessed the observable glycoproteome of three A. baumannii strains (ATCC19606, BAL062, and D1279779). Combining glycopeptide enrichment techniques including ion mobility (FAIMS), metal oxide affinity chromatography (titanium dioxide), and hydrophilic interaction liquid chromatography (ZIC-HILIC), as well as the use of multiple proteases (trypsin, GluC, pepsin, and thermolysis), we expand the known A. baumannii glycoproteome to 33 unique glycoproteins containing 42 glycosylation sites. We demonstrate that serine is the sole residue subjected to glycosylation with the substitution of serine for threonine abolishing glycosylation in model glycoproteins. An A. baumannii pan-genome built from 576 reference genomes identified that serine glycosylation sites are highly conserved. Combined this work expands our knowledge of the conservation and site specificity of A. baumannii O-linked glycosylation.
Collapse
Affiliation(s)
- Kristian I Tkalec
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Kataleen S Lim
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jessica M Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| |
Collapse
|
2
|
Bortel P, Piga I, Koenig C, Gerner C, Martinez-Val A, Olsen JV. Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics. Mol Cell Proteomics 2024; 23:100754. [PMID: 38548019 PMCID: PMC11087715 DOI: 10.1016/j.mcpro.2024.100754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-bead phosphoproteomics sample preparation with a focus on low-input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores, and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample, and loading buffer volumes allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 μg of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA).
Collapse
Affiliation(s)
- Patricia Bortel
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
| | - Ilaria Piga
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Claire Koenig
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christopher Gerner
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Ana Martinez-Val
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
3
|
Heo S, Kang T, Bygrave AM, Larsen MR, Huganir RL. Experience-Induced Remodeling of the Hippocampal Post-synaptic Proteome and Phosphoproteome. Mol Cell Proteomics 2023; 22:100661. [PMID: 37806341 PMCID: PMC10652125 DOI: 10.1016/j.mcpro.2023.100661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023] Open
Abstract
The postsynaptic density (PSD) of excitatory synapses contains a highly organized protein network with thousands of proteins and is a key node in the regulation of synaptic plasticity. To gain new mechanistic insight into experience-induced changes in the PSD, we examined the global dynamics of the hippocampal PSD proteome and phosphoproteome in mice following four different types of experience. Mice were trained using an inhibitory avoidance (IA) task and hippocampal PSD fractions were isolated from individual mice to investigate molecular mechanisms underlying experience-dependent remodeling of synapses. We developed a new strategy to identify and quantify the relatively low level of site-specific phosphorylation of PSD proteome from the hippocampus, by using a modified iTRAQ-based TiSH protocol. In the PSD, we identified 3938 proteins and 2761 phosphoproteins in the sequential strategy covering a total of 4968 unique protein groups (at least two peptides including a unique peptide). On the phosphoproteins, we identified a total of 6188 unambiguous phosphosites (75%
Collapse
Affiliation(s)
- Seok Heo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland, USA
| | - Taewook Kang
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Alexei M Bygrave
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland, USA
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
| | - Richard L Huganir
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland, USA.
| |
Collapse
|
4
|
Huang D, Leng Y, Zhang X, Xing M, Ying W, Gao X. Serial and multi-level proteome analysis for microscale protein samples. J Proteomics 2023; 288:104993. [PMID: 37619946 DOI: 10.1016/j.jprot.2023.104993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Post-translational modifications (PTMs), such as phosphorylation and ubiquitination, play key roles in signal transduction and protein homeostasis. The crosstalk of PTMs greatly expands the components of proteome and protein functions. Multi-level proteome analysis, which involves proteome investigations of total lysate and PTMs in this context, provides a comprehensive approach to explore the PTM crosstalk of a biological system under diverse disturbances. However, multi-level proteome practice remains technically challenging. Here we intended to build a strategy for multi-level proteome analysis, in which we focus on the serial profiling the total proteome, ubiquitinome and phosphoproteome from the microscale of starting material. We started by evaluating five common lysis buffers and found that the sodium deoxycholate buffer provided the best overall performance. We then developed an approach for serial enrichment and profiling of the multi-level proteome. To expand the depth of identification, we customized the variable windows to perform data-independent acquisition (DIA) sequencing for each proteome. In total, we identified 6465 proteins, ∼20,000 GlyGly sites (class 1), and ∼ 19,000 phosphosites (class 1) sequentially using 1 mg of HeLa digest by three DIA measurements. We applied this strategy to analyze MG132-treated HeLa cells and observed the crosstalk between ubiquitination and phosphorylation. Our method can be referenced for other multi-level proteome studies with microscale samples. SIGNIFICANCE: Lysis buffer containing sodium deoxycholate provided the best overall performance in multi-level proteome analysis. One step of ubiquitination enrichment before phosphorylation enrichment does not reduce the reproducibility of phosphoproteome. Customized isolation windows were established for DIA analysis on each level of proteome. Combined the serial enrichment approach and the customized single-shot DIA method enabled the multi-level proteome of microscale protein samples.
Collapse
Affiliation(s)
- Dongying Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yeye Leng
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiangye Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Meining Xing
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wantao Ying
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
| | - Xiaoxia Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| |
Collapse
|
5
|
Huang H, Drici L, Lassen PS, Palmisano G, Larsen MR. TiCPG - a strategy for the simultaneous enrichment of reversibly modified cysteine peptides, phosphopeptides, and sialylated N-Glycopeptides to study cytokines stimulated beta-cells. J Proteomics 2023; 273:104796. [PMID: 36538968 DOI: 10.1016/j.jprot.2022.104796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022]
Abstract
Diverse post-translational modifications (PTMs) regulate protein function and interaction to fine-tune biological processes. Reversible phosphorylation, cysteines (Cys) modifications, and N-linked glycosylation are all essentially involved in cellular signaling pathways, such as those initiated by the action of pro-inflammatory cytokines, which can induce pancreatic β-cell death and diabetes. Here we have developed a novel strategy for the simultaneous and comprehensive characterization of the proteome and three PTMs including reversibly modified Cysteines (rmCys), phosphorylation, and sialylated N-linked glycosylation from low amount of sample material. This strategy, termed TiCPG, is based on a combination of chemical labeling and titanium dioxide (TiO2) chromatography. We applied the TiCPG strategy to study the proteome and the three PTMs changes in β-cells subject to pro-inflammatory cytokines stimulation. It enabled quantitative analysis of 8346 rmCys sites, 10,321 phosphosites and 962 sialylated N-glycosites from 5496 proteins. Significant regulation was found on 100 proteins at the expression level, while 3020 PTM peptide isoforms from 1468 proteins were significantly regulated. The three PTMs were involved in cytokine mediated β-cell apoptosis, such as the NFκB and the inducible NO synthase signaling pathways. Overall, the TiCPG strategy is a cheap, straightforward, and powerful tool for studies targeting the three PTMs described above. SIGNIFICANCE: The present study presents a fast and easy method for quantitative assessment of the proteome and three PTMs from minimal amount of sample material. This simple method provides comprehensive and significant knowledge on biological systems and cellular signaling with relatively low analysis time, suitable for younger researchers and researchers that do not have direct access to LC-MSMS in their laboratories. From sub-milligram amount of material, we were able to map known cellular signaling events of proinflammatory cytokine effect on beta-cells and to discover novel PTMs involved in several known signaling pathways.
Collapse
Affiliation(s)
- Honggang Huang
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Lylia Drici
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Pernille S Lassen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Giuseppe Palmisano
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; Departament of Parasitology, Institute of Biomedical Sciences - University of São Paulo, Avenida Prof. Lineu Prestes, 1374 - Edifício Biomédicas II, Cidade Universitária "Armando Salles Oliveira" - CEP, 05508-000 São Paulo, Brazil
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| |
Collapse
|
6
|
Shang D, Chen C, Dong X, Cui Y, Qiao Z, Li X, Liang X. Simultaneous enrichment and sequential separation of glycopeptides and phosphopeptides with poly-histidine functionalized microspheres. Front Bioeng Biotechnol 2022; 10:1011851. [PMID: 36277408 PMCID: PMC9582455 DOI: 10.3389/fbioe.2022.1011851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Protein phosphorylation and glycosylation coordinately regulate numerous complex biological processes. However, the main methods to simultaneously enrich them are based on the coordination interactions or Lewis acid-base interactions, which suffer from low coverage of target molecules due to strong intermolecular interactions. Here, we constructed a poly-histidine modified silica (SiO2@Poly-His) microspheres-based method for the simultaneous enrichment, sequential elution and analysis of phosphopeptides and glycopeptides. The SiO2@Poly-His microspheres driven by hydrophilic interactions and multiple hydrogen bonding interactions exhibited high selectivity and coverage for simultaneous enrichment of phosphopeptides and glycopeptides from 1,000 molar folds of bovine serum albumin interference. Furthermore, “on-line deglycosylation” strategy allows sequential elution of phosphopeptides and glycopeptides, protecting phosphopeptides from hydrolysis during deglycosylation and improving the coverage of phosphopeptides. The application of our established method to HT29 cell lysates resulted in a total of 1,601 identified glycopeptides and 694 identified phosphopeptides, which were 1.2-fold and 1.5-fold higher than those obtained from the co-elution strategy, respectively. The SiO2@Poly-His based simultaneous enrichment and sequential separation strategy might have great potential in co-analysis of PTMs-proteomics of biological and clinic samples.
Collapse
Affiliation(s)
- Danyi Shang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuefang Dong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China
| | - Yun Cui
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Zichun Qiao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
- *Correspondence: Xiuling Li, ; Xinmiao Liang,
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
- *Correspondence: Xiuling Li, ; Xinmiao Liang,
| |
Collapse
|
7
|
Li J, Zhang J, Xu M, Yang Z, Yue S, Zhou W, Gui C, Zhang H, Li S, Wang PG, Yang S. Advances in glycopeptide enrichment methods for the analysis of protein glycosylation over the past decade. J Sep Sci 2022; 45:3169-3186. [PMID: 35816156 DOI: 10.1002/jssc.202200292] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/16/2022] [Accepted: 07/01/2022] [Indexed: 11/12/2022]
Abstract
Advances in bioanalytical technology have accelerated the analysis of complex protein glycosylation, which is beneficial to understanding glycosylation in drug discovery and disease diagnosis. Due to its biological uniqueness in the course of disease occurrence and development, disease-specific glycosylation requires quantitative characterization of protein glycosylation. We provide a comprehensive review of recent advances in glycosylation analysis, including workflows for glycoprotein digestion, glycopeptide separation and enrichment, and mass-spectrometry sequencing. We specifically focus on different strategies for glycopeptide enrichment through physical interaction, chemical oxidation, or metabolic labeling of intact glycopeptides. The recent advances and challenges of O-glycosylation analysis are presented, and the development of improved enrichment methods combining different proteases to analyze O-glycosylation is also proposed. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Jiajia Li
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Jie Zhang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Mingming Xu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Zeren Yang
- AstraZeneca, Medimmune Ct, Frederick, MD, 21703, USA
| | - Shuang Yue
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Wanlong Zhou
- U.S. Food and Drug Administration, Forensic Chemistry Center, Cincinnati, OH, 45237, USA
| | - Chunshan Gui
- Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Haiyang Zhang
- Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Shuwei Li
- Nanjing Apollomics Biotech, Inc., Nanjing, Jiangsu, 210033, China
| | - Perry G Wang
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740, USA
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China.,Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| |
Collapse
|
8
|
Yi L, Fu M, Shao Y, Tang K, Yan Y, Ding CF. Bifunctional super-hydrophilic mesoporous nanocomposite: a novel nanoprobe for investigation of glycosylation and phosphorylation in Alzheimer's disease. J Chromatogr A 2022; 1676:463236. [PMID: 35709605 DOI: 10.1016/j.chroma.2022.463236] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 10/18/2022]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disease. Abnormal glycosylation and phosphorylation modification in AD may be closely related to its pathology. It is of substantial practical significance to simultaneously investigate the roles of phosphorylation and glycosylation in AD. In this work, a bifunctional super-hydrophilic mesoporous nanocomposite (denoted mTiO2@AuCG) was prepared, which combined hydrophilic interaction chromatography (HILIC) and metal oxide affinity chromatography (MOAC) enrichment strategies to enrich phosphopeptides and glycopeptides, respectively or simultaneously. The mTiO2@AuCG exhibited excellent performance on the high-efficiency enrichment of glycopeptides (selectivity, 5000:1 molar ratios of BSA/HRP; sensitivity, 0.1 fmol HRP; satisfactory recovery rate; loading capacity, 200 mg/g) and phosphopeptides (selectivity, 1000:1 molar ratios of BSA/β-casein; sensitivity, 0.2 fmol β-casein; satisfactory recovery rate; loading capacity, 200 mg/g). Using these advantages, after single-step enrichment of mTiO2@AuCG, a total of 209 glycopeptides related to 93 glycoproteins, and 17 phosphopeptides related to 13 phosphoproteins were detected from normal human serum. By contrast, 167 glycopeptides related to 88 glycoproteins, and 14 phosphopeptides related to 12 phosphoproteins were found in AD serum.
Collapse
Affiliation(s)
- Linhua Yi
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Mengyao Fu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yifan Shao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Keqi Tang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| |
Collapse
|
9
|
He Y, Zheng Q, Huang H, Ji Y, Lin Z. Synergistic synthesis of hydrophilic hollow zirconium organic frameworks for simultaneous recognition and capture of phosphorylated and glycosylated peptides. Anal Chim Acta 2022; 1198:339552. [DOI: 10.1016/j.aca.2022.339552] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 11/26/2022]
|
10
|
Melo-Braga MND, Moreira RDS, Gervásio JHDB, Felicori LF. Overview of protein posttranslational modifications in Arthropoda venoms. J Venom Anim Toxins Incl Trop Dis 2022; 28:e20210047. [PMID: 35519418 PMCID: PMC9036706 DOI: 10.1590/1678-9199-jvatitd-2021-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/27/2021] [Indexed: 11/22/2022] Open
|
11
|
Alghamdi M, Alamry SA, Bahlas SM, Uversky VN, Redwan EM. Circulating extracellular vesicles and rheumatoid arthritis: a proteomic analysis. Cell Mol Life Sci 2021; 79:25. [PMID: 34971426 PMCID: PMC11072894 DOI: 10.1007/s00018-021-04020-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
Circulating extracellular vesicles (EVs) are membrane-bound nanoparticles secreted by most cells for intracellular communication and transportation of biomolecules. EVs carry proteins, lipids, nucleic acids, and receptors that are involved in human physiology and pathology. EV cargo is variable and highly related to the type and state of the cellular origin. Three subtypes of EVs have been identified: exosomes, microvesicles, and apoptotic bodies. Exosomes are the smallest and the most well-studied class of EVs that regulate different biological processes and participate in several diseases, such as cancers and autoimmune diseases. Proteomic analysis of exosomes succeeded in profiling numerous types of proteins involved in disease development and prognosis. In rheumatoid arthritis (RA), exosomes revealed a potential function in joint inflammation. These EVs possess a unique function, as they can transfer specific autoantigens and mediators between distant cells. Current proteomic data demonstrated that exosomes could provide beneficial effects against autoimmunity and exert an immunosuppressive action, particularly in RA. Based on these observations, effective therapeutic strategies have been developed for arthritis and other inflammatory disorders.
Collapse
Affiliation(s)
- Mohammed Alghamdi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
- Laboratory Department, University Medical Services Center, King Abdulaziz University, P.O. Box 80200, Jeddah, 21589, Saudi Arabia
| | - Sultan Abdulmughni Alamry
- Immunology Diagnostic Laboratory Department, King Abdulaziz University Hospital, P.O Box 80215, Jeddah, 21589, Saudi Arabia
| | - Sami M Bahlas
- Department of Internal Medicine, Faculty of Medicine, King Abdulaziz University, P.O. Box 80215, Jeddah, 21589, Saudi Arabia
| | - Vladimir N Uversky
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Elrashdy M Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, 21934, Alexandria, Egypt.
| |
Collapse
|
12
|
Chen YJ, Yen TC, Lin YH, Chen YL, Khoo KH, Chen YJ. ZIC-cHILIC-Based StageTip for Simultaneous Glycopeptide Enrichment and Fractionation toward Large-Scale N-Sialoglycoproteomics. Anal Chem 2021; 93:15931-15940. [PMID: 34780171 DOI: 10.1021/acs.analchem.1c03224] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Alterations of protein glycosylation are closely related with pathophysiological regulation. Due to the structural macro- and microheterogeneity, low stoichiometry, and low ionization efficiency of glycopeptides, high-performance tools to enrich glycopeptides, especially the negatively charged and labile sialoglycopeptides, are essential to enhance the identification of the underexplored glycoproteome. Here, we present the first implementation of zwitterionic hydrophilic interaction chromatography with the exposed choline group (ZIC-cHILIC) in StageTip for simultaneous enrichment and fractionation of intact glycopeptides. In a model study using lung cancer cells, early elution by a high percentage of acetonitrile prominently prefilters nonglycopeptides, facilitating high enrichment specificity for glycopeptides (92-96%) and sialoglycopeptides (77-89%) in the subsequent hydrophilic fractions. The stepwise elution shows a high glycopeptide fractionation efficiency by a <10% overlap of glycopeptides between adjacent fractions. Most importantly, the ZIC-cHILIC stepwise strategy demonstrated good reproducibility (>80% in triplicate analysis) as well as superior coverage of 4.6- to 12.0-fold and 2.1- to 35.6-fold more glycopeptides and sialoglycopeptides compared to conventional TiO2 and ZIC-HILIC, respectively. To the best of our knowledge, the result with 2742 sialoglycopeptides among 7367 unique glycopeptides and 166 glycans from 2434 N-glycosites of 1118 glycoproteins (Byonic score > 100) provides one of the deepest glycoproteomic profiles in single-cell type. Without the immunoprecipitation step, the large-scale glycoproteomic atlas also reveals site-specific glycosylation of many druggable receptor proteins, such as EGFR, MET, ERBB2, ERBB3, AXL, and IGF1R. The demonstrated high enrichment specificity and identification depth show that stepwise ZIC-cHILIC is an efficient method to explore the under-represented sialoglycoproteome.
Collapse
Affiliation(s)
- Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ta-Chi Yen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Hsien Lin
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yan-Lin Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
13
|
Abstract
![]()
Protein phosphorylation
in prokaryotes has gained more
attention in recent years as several
studies linked it to regulatory and signaling functions, indicating
importance similar to protein phosphorylation in eukaryotes. Studies
on bacterial phosphorylation have so far been conducted using manual
or HPLC-supported phosphopeptide enrichment, whereas automation of
phosphopeptide enrichment has been established in eukaryotes, allowing
for high-throughput sampling. To facilitate the prospect of studying
bacterial phosphorylation on a systems level, we here established
an automated Ser/Thr/Tyr phosphopeptide enrichment workflow on the
Agilent AssayMap platform. We present optimized buffer conditions
for TiO2 and Fe(III)-NTA-IMAC cartridge-based enrichment
and the most advantageous, species-specific loading amounts for Streptococcus pyogenes, Listeria monocytogenes, and Bacillus subtilis. For higher
sample amounts (≥250 μg), we observed superior performance
of the Fe(III)-NTA cartridges, whereas for lower sample amounts (≤100
μg), TiO2-based enrichment is equally efficient.
Both cartridges largely enriched the same set of phosphopeptides,
suggesting no improvement of peptide yield by the complementary use
of the two cartridges. Our data represent, to the best of our knowledge,
the largest phosphoproteome identified in a single study for each
of these bacteria.
Collapse
Affiliation(s)
- Marlène S Birk
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | | |
Collapse
|
14
|
Chen C, Zhang X, Dong X, Zhou H, Li X, Liang X. TiO 2 Simultaneous Enrichment, On-Line Deglycosylation, and Sequential Analysis of Glyco- and Phosphopeptides. Front Chem 2021; 9:703176. [PMID: 34458235 PMCID: PMC8385670 DOI: 10.3389/fchem.2021.703176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023] Open
Abstract
Reversible protein glycosylation and phosphorylation tightly modulate important cellular processes and are closely involved in pathological processes in a crosstalk dependent manner. Because of their significance and low abundances of glyco- and phosphopeptides, several strategies have been developed to simultaneously enrich and co-elute glyco- and phosphopeptides. However, the co-existence of deglycosylated peptides and phosphopeptides aggravates the mass spectrometry analysis. Herein we developed a novel strategy to analyze glyco- and phosphopeptides based on simultaneous enrichment with TiO2, on-line deglycosylation and collection of deglycosylated peptides, and subsequent elution of phosphopeptides. To optimize on-line deglycosylation conditions, the solution pH, buffer types and concentrations, and deglycosylation time were investigated. The application of this novel strategy to 100 μg mouse brain resulted in 355 glycopeptides and 1,975 phosphopeptides, which were 2.5 and 1.4 folds of those enriched with the reported method. This study will expand the application of TiO2 and may shed light on simultaneously monitoring protein multiple post-translational modifications.
Collapse
Affiliation(s)
- Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xuefang Dong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Han Zhou
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| |
Collapse
|
15
|
Decoding post translational modification crosstalk with proteomics. Mol Cell Proteomics 2021; 20:100129. [PMID: 34339852 PMCID: PMC8430371 DOI: 10.1016/j.mcpro.2021.100129] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/06/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modification (PTM) of proteins allows cells to regulate protein functions, transduce signals and respond to perturbations. PTMs expand protein functionality and diversity, which leads to increased proteome complexity. PTM crosstalk describes the combinatorial action of multiple PTMs on the same or on different proteins for higher order regulation. Here we review how recent advances in proteomic technologies, mass spectrometry instrumentation, and bioinformatics spurred the proteome-wide identification of PTM crosstalk through measurements of PTM sites. We provide an overview of the basic modes of PTM crosstalk, the proteomic methods to elucidate PTM crosstalk, and approaches that can inform about the functional consequences of PTM crosstalk. Description of basic modules and different modes of PTM crosstalk. Overview of current proteomic methods to identify and infer PTM crosstalk. Discussion of large-scale approaches to characterize functional PTM crosstalk. Future directions and potential proteomic methods for elucidating PTM crosstalk.
Collapse
|
16
|
Matthies I, Abrahams JL, Jensen P, Oliveira T, Kolarich D, Larsen MR. N-Glycosylation in isolated rat nerve terminals. Mol Omics 2021; 17:517-532. [PMID: 34106099 DOI: 10.1039/d0mo00044b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-linked glycosylation is a ubiquitous protein modification that is capable of modulating protein structure, function and interactions. Many proteins in the brain associated with the synapse and important for synaptic transmission are highly glycosylated and their glycosylation could be important for learning and memory related molecular processes and synaptic plasticity. In the present study, we extend the knowledge of the synaptic glycome and glycoproteome by performing glycan- and intact glycopeptide-focused analyses of isolated rat nerve terminals (synaptosomes) by LC-MS/MS. Overall, glycomics identified a total of 41 N-glycans in isolated synaptosomes. Sialylated N-glycans represented only 7% of the total abundance of the rat synaptosome N-glycome with oligomannose, neutral hybrid and complex type N-glycans being the most abundant structures. Using detergent extraction of the active zone proteins from the synaptosomes revealed a change in the active zone glycan abundance in comparison with the rest of the synaptosome glycan content. Characterization of intact sialylated N-linked glycopeptides enriched by titanium dioxide chromatography revealed more than 85% selectivity of sialylated species and the presence of NeuGc on active zone proteins. In addition, both disialic and trisialic acid modified glycans were present on synaptic glycoproteins, although oxonium ion profiling revealed that trisialic units were only present on glycoproteins in the detergent soluble fraction. However, correct identification of intact sialylated N-linked glycopeptides using the Byonic program failed, most likely due to the lack of peptide backbone fragmentation during tandem mass spectrometry.
Collapse
Affiliation(s)
- Inga Matthies
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
| | | | | | | | | | | |
Collapse
|
17
|
Yue X, Qin H, Chen Y, Fang Z, Liu L, Zhu H, Liu X, Zhou J, Tian K, Qiao X, Ye M. Highly Efficient Enrichment of O-GalNAc Glycopeptides by Using Immobilized Metal Ion Affinity Chromatography. Anal Chem 2021; 93:7579-7587. [PMID: 34009939 DOI: 10.1021/acs.analchem.0c05236] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Proteomics analysis of O-GalNAc glycosylation is important for the screening of biomarkers and the assessment of therapeutic responses. However, its analysis still faces challenges due to the poor performance of currently available enrichment methods. In this study, an enrichment method was established on the basis of Ti-IMAC(IV) materials, which could enrich the intact O-GalNAc glycopeptides via both the hydrophilic interaction and affinity interaction. This method enabled nearly 200 intact O-GalNAc glycopeptides identified from only 0.1 μL of human serum. This was nearly 2-fold different from that of the HILIC method. An in-depth analysis of the O-GalNAc glycosylation was performed, and 2093 intact glycopeptides were identified from 7.2 μL of human serum samples. This is the largest O-GalNAc glycosylation database of human serum from a trace amount of sample. Furthermore, 52 significantly changed intact O-GalNAc glycopeptides were determined by the quantitative analysis of hepatocellular carcinoma (HCC) and control serum samples, indicating the potential applications of this enrichment method in biomarker discovery.
Collapse
Affiliation(s)
- Xuyang Yue
- College of Pharmacy, Hebei Province Key Laboratory of Analytical Science & Technology, MOE Key Laboratory of Medicinal Chemistry & Molecular Diagnosis, Hebei University, Baoding 071002, China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luyao Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - He Zhu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Jiahua Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kailu Tian
- College of Pharmacy, Hebei Province Key Laboratory of Analytical Science & Technology, MOE Key Laboratory of Medicinal Chemistry & Molecular Diagnosis, Hebei University, Baoding 071002, China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoqiang Qiao
- College of Pharmacy, Hebei Province Key Laboratory of Analytical Science & Technology, MOE Key Laboratory of Medicinal Chemistry & Molecular Diagnosis, Hebei University, Baoding 071002, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| |
Collapse
|
18
|
Siino V, Jensen P, James P, Vasto S, Amato A, Mulè F, Accardi G, Larsen MR. Obesogenic Diets Cause Alterations on Proteins and Theirs Post-Translational Modifications in Mouse Brains. Nutr Metab Insights 2021; 14:11786388211012405. [PMID: 34017182 PMCID: PMC8114309 DOI: 10.1177/11786388211012405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/13/2021] [Indexed: 11/17/2022] Open
Abstract
Obesity constitutes a major global health threat and is associated with a variety of diseases ranging from metabolic and cardiovascular disease, cancer to neurodegeneration. The hallmarks of neurodegeneration include oxidative stress, proteasome impairment, mitochondrial dysfunction and accumulation of abnormal protein aggregates as well as metabolic alterations. As an example, in post-mortem brain of patients with Alzheimer’s disease (AD), several studies have reported reduction of insulin, insulin-like growth factor 1 and insulin receptor and an increase in tau protein and glycogen-synthase kinase-3β compared to healthy controls suggesting an impairment of metabolism in the AD patient’s brain. Given these lines of evidence, in the present study we investigated brains of mice treated with 2 obesogenic diets, high-fat diet (HFD) and high-glycaemic diet (HGD), compared to mice fed with a standard diet (SD) employing a quantitative mass spectrometry-based approach. Moreover, post-translational modified proteins (phosphorylated and N-linked glycosylated) were studied. The aim of the study was to identify proteins present in the brain that are changing their expression based on the diet given to the mice. We believed that some of these changes would highlight pathways and molecular mechanisms that could link obesity to brain impairment. The results showed in this study suggest that, together with cytoskeletal proteins, mitochondria and metabolic proteins are changing their post-translational status in brains of obese mice. Specifically, proteins involved in metabolic pathways and in mitochondrial functions are mainly downregulated in mice fed with obesogenic diets compared to SD. These changes suggest a reduced metabolism and a lower activity of mitochondria in obese mice. Some of these proteins, such as PGM1 and MCT1 have been shown to be involved in brain impairment as well. These results might shed light on the well-studied correlation between obesity and brain damage. The results presented here are in agreement with previous findings and aim to open new perspectives on the connection between diet-induced obesity and brain impairment.
Collapse
Affiliation(s)
| | - Pia Jensen
- Department of Biochemistry and Molecular Biology, PR Group, University of Southern Denmark, Odense, Denmark
| | - Peter James
- Department of Immunotechnology, Lund University, Sweden.,Turku Centre for Biotechnology and Åbo Academy University, Turku, Finland
| | - Sonya Vasto
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.,Institute of Biomedicine and Molecular Immunology 'Alberto Monroy' CNR, Palermo, Italy
| | - Antonella Amato
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Flavia Mulè
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Giulia Accardi
- Department of Biopathology and Medical biotechnologies Pathobiology and Medical Biotechnologies, University of Palermo, Palermo, Italy
| | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology, PR Group, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
19
|
Macedo-da-Silva J, Santiago VF, Rosa-Fernandes L, Marinho CRF, Palmisano G. Protein glycosylation in extracellular vesicles: Structural characterization and biological functions. Mol Immunol 2021; 135:226-246. [PMID: 33933815 DOI: 10.1016/j.molimm.2021.04.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023]
Abstract
Extracellular vesicles (EVs) are lipid bilayer-enclosed particles involved in intercellular communication, delivery of biomolecules from donor to recipient cells, cellular disposal and homeostasis, potential biomarkers and drug carriers. The content of EVs includes DNA, lipids, metabolites, proteins, and microRNA, which have been studied in various diseases, such as cancer, diabetes, pregnancy, neurodegenerative, and cardiovascular disorders. EVs are enriched in glycoconjugates and exhibit specific glycosignatures. Protein glycosylation is a co- and post-translational modification (PTM) that plays an important role in the expression and function of exosomal proteins. N- and O-linked protein glycosylation has been mapped in exosomal proteins. The purpose of this review is to highlight the importance of glycosylation in EVs proteins. Initially, we describe the main PTMs in EVs with a focus on glycosylation. Then, we explore glycan-binding proteins describing the main findings of studies that investigated the glycosylation of EVs in cancer, pregnancy, infectious diseases, diabetes, mental disorders, and animal fluids. We have highlighted studies that have developed innovative methods for studying the content of EVs. In addition, we present works related to lipid glycosylation. We explored the content of studies deposited in public databases, such as Exocarta and Vesiclepedia. Finally, we discuss analytical methods for structural characterization of glycoconjugates and present an overview of the critical points of the study of glycosylation EVs, as well as perspectives in this field.
Collapse
Affiliation(s)
- Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Verônica F Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil.
| |
Collapse
|
20
|
Wang X, Ma T, Yu H, Chen Z, Zhu B, Chen W, Sun S, Li Z. Purification of sialoglycoproteins from bovine milk using serotonin-functionalized magnetic particles and their application against influenza A virus. Food Funct 2021; 11:6911-6920. [PMID: 32691813 DOI: 10.1039/d0fo01447h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sialylation is involved in receptor-ligand interactions, communication between cells, and host-pathogen interactions and it is involved in the ability of glycoproteins of bovine milk to inhibit the influenza A virus (IAV). The present paper describes a simple and efficient method to isolate sialoglycoproteins from bovine milk using serotonin-magnetic particle conjugates. Then, the isolated glycoproteins were analysed by lectin blotting and LC-MS/MS. The N-glycans on isolated glycoproteins were characterized by MALDI-TOF/TOF-MS. The role of the isolated sialoglycoproteins against IAV was validated in vitro. As a result, there were 91 proteins and 17 sialylated N-glycans to be identified. The isolated proteins have ability to inhibit attachment of IAV mimics to MDCK cells. However, the role of inhibition was abolished when the sialic acid moieties were destroyed. This method could provide useful information for the large-scale production of sialoglycoproteins from bovine milk against IAV.
Collapse
Affiliation(s)
- Xilong Wang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Tianran Ma
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhuo Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Bojing Zhu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Wentian Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Shisheng Sun
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, China.
| |
Collapse
|
21
|
Comprehensive Protocol to Simultaneously Study Protein Phosphorylation, Acetylation, and N-Linked Sialylated Glycosylation. Methods Mol Biol 2021. [PMID: 33420984 DOI: 10.1007/978-1-0716-1186-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Abstract
Posttranslational modifications (PTMs) such as phosphorylation, acetylation, and glycosylation are an essential regulatory mechanism of protein function and interaction, and they are associated with a wide range of biological processes. Since most PTMs alter the molecular mass of a protein, mass spectrometry (MS) is the ideal analytical tool for studying various PTMs. However, PTMs are often present in substoichiometric levels, and therefore their unmodified counterpart often suppresses their signal in MS. Consequently, PTM analysis by MS is a challenging task, requiring highly specialized and sensitive PTM-specific enrichment methods. Currently, several methods have been implemented for PTM enrichment, and each of them has its drawbacks and advantages as they differ in selectivity and specificity toward specific protein modifications. Unfortunately, for the vast majority of more than 400 known modifications, we have no or poor tools for selective enrichment.Here, we describe a comprehensive workflow to simultaneously study phosphorylation, acetylation, and N-linked sialylated glycosylation from the same biological sample. The protocol involves an initial titanium dioxide (TiO2) step to enrich for phosphopeptides and sialylated N-linked glycopeptides followed by glycan release and post-fractionation using sequential elution from immobilized metal affinity chromatography (SIMAC) to separate mono-phosphorylated and deglycosylated peptides from multi-phosphorylated ones. The IMAC flow-through and acidic elution are subsequently subjected to a next round of TiO2 enrichment for further separation of mono-phosphopeptides from deglycosylated peptides. Furthermore, the lysine-acetylated peptides present in the first TiO2 flow-through fraction are enriched by immunoprecipitation (IP) after peptide cleanup. Finally, the samples are fractionated by high pH reversed phase chromatography (HpH) or hydrophilic interaction liquid chromatography (HILIC ) to reduce sample complexity and increase the coverage in the subsequent LC-MS /MS analysis. This allows the analysis of multiple types of modifications from the same highly complex biological sample without decreasing the quality of each individual PTM study.
Collapse
|
22
|
Sheng Q, Xue C, Zhou Y, Li J, Yuan H, Ke Y, Lan M. Synthesis of Al 3+-doping-TiO 2 monodisperse microspheres and their application for phosphopeptides and glycopeptides enrichment. Talanta 2021; 223:121715. [PMID: 33298258 DOI: 10.1016/j.talanta.2020.121715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 11/26/2022]
Abstract
Glycosylation and phosphorylation are two of the most common and important post-translational modifications (PTMs) of proteins, which play critical roles in regulating a variety of complex biological processes and involvement in many diseases. Due to the low abundance of phosphopeptides and glycopeptides, highly selective enrichment methods are crucial to the identification of protein phosphorylation and glycosylation by mass spectrometry (MS). Here, monodisperse uniform Al3+-doping-TiO2 mixed oxide microspheres were easily synthesized. The morphology was controlled by a sol-gel method, during the hydrothermal treatment. The obtained microspheres with uniform particle size distribution (about 1-2 μm),high surface area and improved pore structures, were characterized by SEM, TEM, XRD and N2 adsorption-desorption isotherms. Al3+-doping-TiO2 was applied in enriching glycopeptides and phosphopeptides respectively or simultaneously by using different enrichment conditions, achieving selective enrichment of glycopeptides and phosphopeptides. 20 glycopeptides and 25 phosphopeptides enriched from the tryptic digest mixtures of human serum immunoglobulin G (IgG) and α-casein (molar ratio of 1:1) were obviously observed with greatly improved signal-to-noise (S/N) ratio. Meanwhile, the enrichment results of non-fat milk and human serum also show the enrichment selectivity from complex biological samples. This study will provide a novel insight for selective enrichment of glycopeptides and phosphopeptides in post-translational modification proteomics research.
Collapse
Affiliation(s)
- Qianying Sheng
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Chenli Xue
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yang Zhou
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Junyan Li
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Huihui Yuan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yanxiong Ke
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, PR China.
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.
| |
Collapse
|
23
|
Petrović T, Trbojević-Akmačić I. Lectin and Liquid Chromatography-Based Methods for Immunoglobulin (G) Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:29-72. [PMID: 34687007 DOI: 10.1007/978-3-030-76912-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Immunoglobulin (Ig) glycosylation has been shown to dramatically affect its structure and effector functions. Ig glycosylation changes have been associated with different diseases and show a promising biomarker potential for diagnosis and prognosis of disease advancement. On the other hand, therapeutic biomolecules based on structural and functional features of Igs demand stringent quality control during the production process to ensure their safety and efficacy. Liquid chromatography (LC) and lectin-based methods are routinely used in Ig glycosylation analysis complementary to other analytical methods, e.g., mass spectrometry and capillary electrophoresis. This chapter covers analytical approaches based on LC and lectins used in low- and high-throughput N- and O-glycosylation analysis of Igs, with the focus on immunoglobulin G (IgG) applications. General principles and practical examples of the most often used LC methods for Ig purification are described, together with typical workflows for N- and O-glycan analysis on the level of free glycans, glycopeptides, subunits, or intact Igs. Lectin chromatography is a historical approach for the analysis of lectin-carbohydrate interactions and glycoprotein purification but is still being used as a valuable tool in Igs purification and glycan analysis. On the other hand, lectin microarrays have found their application in the rapid screening of glycan profiles on intact proteins.
Collapse
Affiliation(s)
- Tea Petrović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | | |
Collapse
|
24
|
Silbern I, Fang P, Ji Y, Christof L, Urlaub H, Pan KT. Relative Quantification of Phosphorylated and Glycosylated Peptides from the Same Sample Using Isobaric Chemical Labelling with a Two-Step Enrichment Strategy. Methods Mol Biol 2021; 2228:185-203. [PMID: 33950492 DOI: 10.1007/978-1-0716-1024-4_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Post-translational modifications (PTMs) are essential for the regulation of all cellular processes. The interplay of various PTMs on a single protein or different proteins comprises a complexity that we are far from understanding in its entirety. Reliable strategies for the enrichment and accurate quantification of PTMs are needed to study as many PTMs on proteins as possible. In this protocol we present a liquid chromatography-tandem mass spectrometry (LC/MS/MS)-based workflow that enables the enrichment and quantification of phosphorylated and N-glycosylated peptides from the same sample. After extraction and digestion of proteins, we label the peptides with stable isotope-coded tandem mass tags (TMTs) and enrich N-glycopeptides and phosphopeptides by using zwitterionic hydrophilic interaction chromatography (ZIC-HILIC) and titanium dioxide (TiO2) beads, respectively. Labelled and enriched N-glycopeptides and phosphopeptides are further separated by high pH (basic) reversed-phase chromatography and analyzed by LC/MS/MS. The enrichment strategies, together with quantification of two different PTM types from the same sample, allow investigation of the interplay of those two PTMs, which are important for signal transduction inside the cell (phosphorylation), as well as for messaging between cells through decoration of the cellular surface (glycosylation).
Collapse
Affiliation(s)
- Ivan Silbern
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Pan Fang
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Yanlong Ji
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Lenz Christof
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany.
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany.
| | - Kuan-Ting Pan
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany.
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany.
| |
Collapse
|
25
|
Bermudez A, Pitteri SJ. Enrichment of Intact Glycopeptides Using Strong Anion Exchange and Electrostatic Repulsion Hydrophilic Interaction Chromatography. Methods Mol Biol 2021; 2271:107-120. [PMID: 33908003 DOI: 10.1007/978-1-0716-1241-5_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glycosylation is a biologically important and complex protein posttranslational modification. The emergence of glycoproteomic technologies to identify and characterize glycans on proteins has the potential to enable a better understanding the role of glycosylation in biology, disease states, and other areas of interest. In particular, the analysis of intact glycopeptides by mass spectrometry allows information about glycan location and composition to be ascertained. However, such analysis is often complicated by extensive glycan diversity and the low abundance of glycopeptides in a complex mixture relative to nonglycosylated peptides. Enrichment of glycopeptides from a protein enzymatic digest is an effective approach to overcome such challenges. In this chapter, we described a glycopeptide enrichment method combining strong anion exchange, electrostatic repulsion, and hydrophilic interaction chromatography (SAX-ERLIC). Following enzymatic digestion of proteins into peptides, SAX-ERLIC is performed by solid phase extraction to enrich glycopeptides from biological samples with subsequent LC-MS/MS analysis. Glycopeptide data generated using the SAX-ERLIC enrichment yields a high number of total and unique glycopeptide identifications which can be mapped back to proteins. The enrichment strategy is robust, easy to perform, and does not require cleavage of glycans prior to LC-MS/MS analysis.
Collapse
Affiliation(s)
- Abel Bermudez
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sharon J Pitteri
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, USA.
| |
Collapse
|
26
|
Geiszler DJ, Kong AT, Avtonomov DM, Yu F, Leprevost FDV, Nesvizhskii AI. PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results. Mol Cell Proteomics 2020; 20:100018. [PMID: 33568339 PMCID: PMC7950090 DOI: 10.1074/mcp.tir120.002216] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/13/2020] [Accepted: 12/01/2020] [Indexed: 01/17/2023] Open
Abstract
Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift that may correspond to a single modification or a combination of several modifications. Here we present PTM-Shepherd, a bioinformatics tool that automates characterization of post-translational modification profiles detected in open searches based on attributes, such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multiexperiment comparisons for studying changes in modification profiles, e.g., in data generated in different laboratories or under different conditions. We demonstrate how PTM-Shepherd improves the analysis of data from formalin-fixed and paraffin-embedded samples, detects extreme underalkylation of cysteine in some data sets, discovers an artifactual modification introduced during peptide synthesis, and uncovers site-specific biases in sample preparation artifacts in a multicenter proteomics profiling study.
Collapse
Affiliation(s)
- Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Andy T Kong
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Dmitry M Avtonomov
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA; Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
| |
Collapse
|
27
|
Chen X, Sun Y, Zhang T, Roepstorff P, Yang F. Comprehensive Analysis of the Proteome and PTMomes of C2C12 Myoblasts Reveals that Sialylation Plays a Role in the Differentiation of Skeletal Muscle Cells. J Proteome Res 2020; 20:222-235. [PMID: 33216553 DOI: 10.1021/acs.jproteome.0c00353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The C2C12 myoblast is a model that has been used extensively to study the process of skeletal muscle differentiation. Proteomics has advanced our understanding of skeletal muscle biology and also the differentiation process of skeletal muscle cells. However, there is still no comprehensive analysis of C2C12 myoblast proteomes, which is important for the understanding of key drivers for the differentiation of skeletal muscle cells. Here, we conducted multidimensional proteome profiling to get a comprehensive analysis of proteomes and PTMomes of C2C12 myoblasts with a TiSH strategy. A total of 8313 protein groups were identified, including 7827 protein groups from nonmodified peptides, 3803 phosphoproteins, and 977 formerly sialylated N-linked glycoproteins. Integrated analysis of proteomic and PTMomic data showed that almost all of the kinases and transcription factors in the muscle cell differentiation pathway were phosphorylated. Further analysis indicated that sialylation might play a role in the differentiation of C2C12 myoblasts. Further functional analysis demonstrated that C2C12 myoblasts showed a decreased level of sialylation during skeletal muscle cell differentiation. Inhibition of sialylation with the sialyltransferase inhibitor 3Fax-Neu5Ac resulted in the lower expression of MHC and suppression of myoblast fusion. In all, these results indicate that sialylation has an effect on the differentiation of skeletal muscle cells.
Collapse
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| | - Yaping Sun
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| | - Tingting Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| |
Collapse
|
28
|
Dawson AR, Wilson GM, Coon JJ, Mehle A. Post-Translation Regulation of Influenza Virus Replication. Annu Rev Virol 2020; 7:167-187. [DOI: 10.1146/annurev-virology-010320-070410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Influenza virus exploits cellular factors to complete each step of viral replication. Yet, multiple host proteins actively block replication. Consequently, infection success depends on the relative speed and efficacy at which both the virus and host use their respective effectors. Post-translational modifications (PTMs) afford both the virus and the host means to readily adapt protein function without the need for new protein production. Here we use influenza virus to address concepts common to all viruses, reviewing how PTMs facilitate and thwart each step of the replication cycle. We also discuss advancements in proteomic methods that better characterize PTMs. Although some effectors and PTMs have clear pro- or antiviral functions, PTMs generally play regulatory roles to tune protein functions, levels, and localization. Synthesis of our current understanding reveals complex regulatory schemes where the effects of PTMs are time and context dependent as the virus and host battle to control infection.
Collapse
Affiliation(s)
- Anthony R. Dawson
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Gary M. Wilson
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Andrew Mehle
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| |
Collapse
|
29
|
Boll I, Jensen P, Schwämmle V, Larsen MR. Depolarization-dependent Induction of Site-specific Changes in Sialylation on N-linked Glycoproteins in Rat Nerve Terminals. Mol Cell Proteomics 2020; 19:1418-1435. [PMID: 32518069 PMCID: PMC8143646 DOI: 10.1074/mcp.ra119.001896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/08/2020] [Indexed: 12/11/2022] Open
Abstract
Synaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show that sialylation of N-linked glycosylation is a novel potential modulator of neurotransmitter release mechanisms by investigating depolarization-dependent changes of formerly sialylated N-linked glycopeptides. We suggest that negatively charged sialic acids can be modulated, similarly to phosphorylation, by the action of sialyltransferases and sialidases thereby changing local structure and function of membrane glycoproteins. We characterized site-specific alteration in sialylation on N-linked glycoproteins in isolated rat nerve terminals after brief depolarization using quantitative sialiomics. We identified 1965 formerly sialylated N-linked glycosites in synaptic proteins and found that the abundances of 430 glycosites changed after 5 s depolarization. We observed changes on essential synaptic proteins such as synaptic vesicle proteins, ion channels and transporters, neurotransmitter receptors and cell adhesion molecules. This study is to our knowledge the first to describe ultra-fast site-specific modulation of the sialiome after brief stimulation of a biological system.
Collapse
Affiliation(s)
- Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Pia Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
| |
Collapse
|
30
|
Tahir M, Arshid S, Fontes B, S. Castro M, Sidoli S, Schwämmle V, Luz IS, Roepstorff P, Fontes W. Phosphoproteomic Analysis of Rat Neutrophils Shows the Effect of Intestinal Ischemia/Reperfusion and Preconditioning on Kinases and Phosphatases. Int J Mol Sci 2020; 21:ijms21165799. [PMID: 32823483 PMCID: PMC7460855 DOI: 10.3390/ijms21165799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/11/2020] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Intestinal ischemia reperfusion injury (iIRI) is a severe clinical condition presenting high morbidity and mortality worldwide. Some of the systemic consequences of IRI can be prevented by applying ischemic preconditioning (IPC), a series of short ischemia/reperfusion events preceding the major ischemia. Although neutrophils are key players in the pathophysiology of ischemic injuries, neither the dysregulation presented by these cells in iIRI nor the protective effect of iIPC have their regulation mechanisms fully understood. Protein phosphorylation, as well as the regulation of the respective phosphatases and kinases are responsible for regulating a large number of cellular functions in the inflammatory response. Moreover, in previous work we found hydrolases and transferases to be modulated in iIR and iIPC, suggesting the possible involvement of phosphatases and kinases in the process. Therefore, in the present study, we analyzed the phosphoproteome of neutrophils from rats submitted to mesenteric ischemia and reperfusion, either submitted or not to IPC, compared to quiescent controls and sham laparotomy. Proteomic analysis was performed by multi-step enrichment of phosphopeptides, isobaric labeling, and LC-MS/MS analysis. Bioinformatics was used to determine phosphosite and phosphopeptide abundance and clustering, as well as kinases and phosphatases sites and domains. We found that most of the phosphorylation-regulated proteins are involved in apoptosis and migration, and most of the regulatory kinases belong to CAMK and CMGC families. An interesting finding revealed groups of proteins that are modulated by iIR, but such modulation can be prevented by iIPC. Among the regulated proteins related to the iIPC protective effect, Vamp8 and Inpp5d/Ship are discussed as possible candidates for control of the iIR damage.
Collapse
Affiliation(s)
- Muhammad Tahir
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (S.S.); (V.S.); (P.R.)
| | - Samina Arshid
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
- Laboratory of Surgical Physiopathology (LIM-62), Faculty of Medicine, University of São Paulo, São Paulo 01246903, Brazil;
| | - Belchor Fontes
- Laboratory of Surgical Physiopathology (LIM-62), Faculty of Medicine, University of São Paulo, São Paulo 01246903, Brazil;
| | - Mariana S. Castro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
| | - Simone Sidoli
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (S.S.); (V.S.); (P.R.)
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (S.S.); (V.S.); (P.R.)
| | - Isabelle S. Luz
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (S.S.); (V.S.); (P.R.)
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
- Correspondence:
| |
Collapse
|
31
|
Yang SS, Wang C, Yu X, Shang W, Chen DDY, Gu ZY. A hydrophilic two-dimensional titanium-based metal-organic framework nanosheets for specific enrichment of glycopeptides. Anal Chim Acta 2020; 1119:60-67. [DOI: 10.1016/j.aca.2020.04.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/17/2020] [Accepted: 04/25/2020] [Indexed: 11/29/2022]
|
32
|
Zhang Y, Li J, Yu Y, Xie R, Liao H, Zhang B, Chen J. Coupling hydrophilic interaction chromatography materials with immobilized Fe 3+ for phosphopeptide and glycopeptide enrichment and separation. RSC Adv 2020; 10:22176-22182. [PMID: 35516639 PMCID: PMC9054515 DOI: 10.1039/d0ra01048k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/24/2020] [Indexed: 01/05/2023] Open
Abstract
Simultaneous profiling of protein phosphorylation and glycosylation is very important to elucidate the bio-functions of these proteins. However, simultaneous enrichment of glyco- and phosphopeptides is the bottleneck in proteomics because of the low abundance of these species and ion suppression from non-modified peptides in mass spectrometry (MS). In this study, Fe3+ immobilized hydrophilic interaction chromatography (HILIC) materials (termed polySD-SiO2, recently reported in our lab) and polySD-SiO2 in the HILIC mode were employed for the simultaneous enrichment and subsequent separation of glyco- and phosphopeptides. The Fe3+ immobilized polySD-SiO2 could selectively enrich glycopeptides and phosphopeptides and the co-enriched peptides were further fractionated with polySD-SiO2 in the HILIC mode. With the established method, glyco- and phosphopeptides were well enriched and divided into two fractions even from tryptic digests of a-casein, fetuin and BSA at a molar ratio of 1 : 2 : 400. Application of the established method to HeLa cell lysate resulted in a total of 1903 phosphopeptides and 141 glycosylation sites. These results demonstrate that the established method could selectively and simultaneously enrich and fractionate glyco- and phosphopeptides from complex peptide mixtures. Simultaneous profiling of protein phosphorylation and glycosylation is very important to elucidate the bio-functions of these proteins.![]()
Collapse
Affiliation(s)
- Yue Zhang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan 430022 China
| | - Jiyong Li
- Department of Breast and Thyroid Surgery, Huangpi People's Hospital, Jianghan University Wuhan 430300 China
| | - Yuanhang Yu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan 430022 China
| | - Rong Xie
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan 430022 China
| | - Han Liao
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan 430022 China
| | - Bo Zhang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan 430022 China
| | - Jianying Chen
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan 430022 China
| |
Collapse
|
33
|
Abstract
Aspergillus fumigatus is an opportunistic and allergenic pathogenic fungus, responsible for fungal infections in humans. A. fumigatus infections are usually treated with polyenes, azoles, or echinocandins. Echinocandins, such as caspofungin, can inhibit the biosynthesis of the β-1,3-glucan polysaccharide, affecting the integrity of the cell wall and leading to fungal death. In some A. fumigatus strains, caspofungin treatment at high concentrations induces an increase of fungal growth, a phenomenon called the caspofungin paradoxical effect (CPE). Here, we analyze the proteome and phosphoproteome of the A. fumigatus wild-type strain and of mitogen-activated protein kinase (MAPK) mpkA and sakA null mutant strains during CPE (2 μg/ml caspofungin for 1 h). The wild-type proteome showed 75 proteins and 814 phosphopeptides (corresponding to 520 proteins) altered in abundance in response to caspofungin treatment. The ΔmpkA (ΔmpkA caspofungin/wild-type caspofungin) and ΔsakA (ΔsakA caspofungin/wild-type caspofungin) strains displayed 626 proteins and 1,236 phosphopeptides (corresponding to 703 proteins) and 101 proteins and 1,217 phosphopeptides (corresponding to 645 proteins), respectively, altered in abundance. Functional characterization of the phosphopeptides from the wild-type strain exposed to caspofungin showed enrichment for transcription factors, protein kinases, and cytoskeleton proteins. Proteomic analysis of the ΔmpkA and ΔsakA mutants indicated that control of proteins involved in metabolism, such as in production of secondary metabolites, was highly represented in both mutants. Results of functional categorization of phosphopeptides from both mutants were very similar and showed a high number of proteins with decreased phosphorylation of proteins involved in transcriptional control, DNA/RNA binding, cell cycle control, and DNA processing. This report reveals novel transcription factors involved in caspofungin tolerance.IMPORTANCE Aspergillus fumigatus is an opportunistic human-pathogenic fungus causing allergic reactions or systemic infections, such as invasive pulmonary aspergillosis in immunocompromised patients. Caspofungin is an echinocandin that impacts the construction of the fungal cell wall by inhibiting the biosynthesis of the β-1,3-glucan polysaccharide. Caspofungin is a fungistatic drug and is recommended as a second-line therapy for treatment of aspergillosis. Treatment at high concentrations induces an increase of fungal growth, a phenomenon called the caspofungin paradoxical effect (CPE). Collaboration between the mitogen-activated protein kinases (MAPK) of the cell wall integrity (MapkA) and high-osmolarity glycerol (SakA) pathways is essential for CPE. Here, we investigate the global proteome and phosphoproteome of A. fumigatus wild-type, ΔmpkA, and ΔsakA strains upon CPE. This study showed intense cross talk between the two MAPKs for the CPE and identified novel protein kinases and transcription factors possibly important for CPE. Increased understanding of how the modulation of protein phosphorylation may affect the fungal growth in the presence of caspofungin represents an important step in the development of new strategies and methods to combat the fungus inside the host.
Collapse
|
34
|
Bagdonaite I, Pallesen EM, Ye Z, Vakhrushev SY, Marinova IN, Nielsen MI, Kramer SH, Pedersen SF, Joshi HJ, Bennett EP, Dabelsteen S, Wandall HH. O-glycan initiation directs distinct biological pathways and controls epithelial differentiation. EMBO Rep 2020; 21:e48885. [PMID: 32329196 PMCID: PMC7271655 DOI: 10.15252/embr.201948885] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 12/17/2022] Open
Abstract
Post-translational modifications (PTMs) greatly expand the function and potential for regulation of protein activity, and O-glycosylation is among the most abundant and diverse PTMs. Initiation of O-GalNAc glycosylation is regulated by 20 distinct GalNAc-transferases (GalNAc-Ts), and deficiencies in individual GalNAc-Ts are associated with human disease, causing subtle but distinct phenotypes in model organisms. Here, we generate a set of isogenic keratinocyte cell lines lacking either of the three dominant and differentially expressed GalNAc-Ts. Through the ability of keratinocytes to form epithelia, we investigate the phenotypic consequences of the loss of individual GalNAc-Ts. Moreover, we probe the cellular responses through global transcriptomic, differential glycoproteomic, and differential phosphoproteomic analyses. We demonstrate that loss of individual GalNAc-T isoforms causes distinct epithelial phenotypes through their effect on specific biological pathways; GalNAc-T1 targets are associated with components of the endomembrane system, GalNAc-T2 targets with cell-ECM adhesion, and GalNAc-T3 targets with epithelial differentiation. Thus, GalNAc-T isoforms serve specific roles during human epithelial tissue formation.
Collapse
Affiliation(s)
- Ieva Bagdonaite
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Emil Mh Pallesen
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Irina N Marinova
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mathias I Nielsen
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Signe H Kramer
- Cell Biology and Physiology, Department of Science, University of Copenhagen, Copenhagen, Denmark
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Science, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.,School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
35
|
Lu Q, Chen C, Xiong Y, Li G, Zhang X, Zhang Y, Wang D, Zhu Z, Li X, Qing G, Sun T, Liang X. High-Efficiency Phosphopeptide and Glycopeptide Simultaneous Enrichment by Hydrogen Bond–based Bifunctional Smart Polymer. Anal Chem 2020; 92:6269-6277. [DOI: 10.1021/acs.analchem.9b02643] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Qi Lu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
- Research & Development Center, Jushi Group. Co., Ltd, 669 Wenhua Road, Tongxiang 314500, China
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yuting Xiong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Guodong Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yahui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Dongdong Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Zhichao Zhu
- College of Chemistry and Chemical Engineering, Wuhan Textile University, 1 Sunshine Road, Wuhan 430200, China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- College of Chemistry and Chemical Engineering, Wuhan Textile University, 1 Sunshine Road, Wuhan 430200, China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| |
Collapse
|
36
|
Valdés A, Zhao H, Pettersson U, Lind SB. Phosphorylation Time-Course Study of the Response during Adenovirus Type 2 Infection. Proteomics 2020; 20:e1900327. [PMID: 32032466 DOI: 10.1002/pmic.201900327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/22/2020] [Indexed: 12/31/2022]
Abstract
PTMs such as phosphorylations are usually involved in signal transduction pathways. To investigate the temporal dynamics of phosphoproteome changes upon viral infection, a model system of IMR-90 cells infected with human adenovirus type 2 (Ad2) is used in a time-course quantitative analysis combining titanium dioxide (TiO2 ) particle enrichment and SILAC-MS. Quantitative data from 1552 phosphorylated sites clustered the highly altered phosphorylated sites to the signaling by rho family GTPases, the actin cytoskeleton signaling, and the cAMP-dependent protein kinase A signaling pathways. Their activation is especially pronounced at early time post-infection. Changes of several phosphorylated sites involved in the glycolysis pathway, related to the activation of the Warburg effect, point at virus-induced energy production. For Ad2 proteins, 32 novel phosphorylation sites are identified and as many as 52 phosphorylated sites on 17 different Ad2 proteins are quantified, most of them at late time post-infection. Kinase predictions highlighted activation of PKA, CDK1/2, MAPK, and CKII. Overlaps of kinase motif sequences for viral and human proteins are observed, stressing the importance of phosphorylation during Ad2 infection.
Collapse
Affiliation(s)
- Alberto Valdés
- Section of Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, 751 24, Sweden.,Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Ctra. Madrid-Barcelona, Km. 33.600, 28871, Alcalá de Henares, Madrid, Spain
| | - Hongxing Zhao
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, 75185, Uppsala, Sweden
| | - Ulf Pettersson
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, 75185, Uppsala, Sweden
| | - Sara Bergström Lind
- Section of Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, 751 24, Sweden
| |
Collapse
|
37
|
Jie J, Liu D, Zou X. A one-pot synthesis of hydrophilic poly(glycerol methacrylate) chitosan for highly selective enrichment of glycopeptides. Chem Commun (Camb) 2020; 56:908-911. [PMID: 31850411 DOI: 10.1039/c9cc08016c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Poly(glycerol methacrylate) chitosan nanospheres were facilely one-pot synthesized. For the first time, poly(glycerol methacrylate) with a highly flexible density of hydrophilic molecules grafted on the surface of chitosan was applied to highly specific enrichment of glycopeptides.
Collapse
Affiliation(s)
- Jianzheng Jie
- Department of Gastrointestinal Surgery, China-Japan Friendship Hospital, 2 Yinghua Dongjie, Chaoyang District, Beijing 100029, China
| | | | | |
Collapse
|
38
|
Mule SN, Saad JS, Fernandes LR, Stolf BS, Cortez M, Palmisano G. Protein glycosylation inLeishmaniaspp. Mol Omics 2020; 16:407-424. [DOI: 10.1039/d0mo00043d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation is a co- and post-translational modification that, inLeishmaniaparasites, plays key roles in vector–parasite–vertebrate host interaction.
Collapse
Affiliation(s)
- Simon Ngao Mule
- GlycoProteomics Laboratory
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo - 05508-000
| | - Joyce Silva Saad
- GlycoProteomics Laboratory
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo - 05508-000
| | - Livia Rosa Fernandes
- GlycoProteomics Laboratory
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo - 05508-000
| | - Beatriz S. Stolf
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo
- Brazil
| | - Mauro Cortez
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo
- Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo - 05508-000
| |
Collapse
|
39
|
Preparation of cotton wool modified with boric acid functionalized titania for selective enrichment of glycopeptides. Talanta 2019; 203:58-64. [DOI: 10.1016/j.talanta.2019.05.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 04/11/2019] [Accepted: 05/10/2019] [Indexed: 01/15/2023]
|
40
|
Chen Z, Huang J, Li L. Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples. Trends Analyt Chem 2019; 118:880-892. [PMID: 31579312 PMCID: PMC6774629 DOI: 10.1016/j.trac.2018.10.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein glycosylation plays a key role in various biological processes and disease-related pathological progression. Mass spectrometry (MS)-based glycoproteomics is a powerful approach that provides a system-wide profiling of the glycoproteome in a high-throughput manner. There have been numerous significant technological advances in this field, including improved glycopeptide enrichment, hybrid fragmentation techniques, emerging specialized software packages, and effective quantitation strategies, as well as more dedicated workflows. With increasingly sophisticated glycoproteomics tools on hand, researchers have extensively adapted this approach to explore different biological systems both in terms of in-depth glycoproteome profiling and comparative glycoproteome analysis. Quantitative glycoproteomics enables researchers to discover novel glycosylation-based biomarkers in various diseases with potential to offer better sensitivity and specificity for disease diagnosis. In this review, we present recent methodological developments in MS-based glycoproteomics and highlight its utility and applications in answering various questions in complex biological systems.
Collapse
Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| |
Collapse
|
41
|
Hacı Mehmet KAYILI, İzzet AVCI, Bekir SALİH. A New titania glyco-purification tip for the fast enrichment and efficient analysis of glycopeptides and glycans by MALDI-TOF-MS. J Pharm Biomed Anal 2019; 174:191-197. [DOI: 10.1016/j.jpba.2019.05.061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/23/2019] [Accepted: 05/26/2019] [Indexed: 01/21/2023]
|
42
|
Chen Z, Huang J, Li L. Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples. Trends Analyt Chem 2019. [PMID: 31579312 DOI: 10.1016/jtrac.2018.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Protein glycosylation plays a key role in various biological processes and disease-related pathological progression. Mass spectrometry (MS)-based glycoproteomics is a powerful approach that provides a system-wide profiling of the glycoproteome in a high-throughput manner. There have been numerous significant technological advances in this field, including improved glycopeptide enrichment, hybrid fragmentation techniques, emerging specialized software packages, and effective quantitation strategies, as well as more dedicated workflows. With increasingly sophisticated glycoproteomics tools on hand, researchers have extensively adapted this approach to explore different biological systems both in terms of in-depth glycoproteome profiling and comparative glycoproteome analysis. Quantitative glycoproteomics enables researchers to discover novel glycosylation-based biomarkers in various diseases with potential to offer better sensitivity and specificity for disease diagnosis. In this review, we present recent methodological developments in MS-based glycoproteomics and highlight its utility and applications in answering various questions in complex biological systems.
Collapse
Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| |
Collapse
|
43
|
Abstract
Glycosylation is one of the most ubiquitous and complex post-translational modifications (PTMs). It plays pivotal roles in various biological processes. Studies at the glycopeptide level are typically considered as a downstream work resulting from enzymatic digested glycoproteins. Less attention has been focused on glycosylated endogenous signaling peptides due to their low abundance, structural heterogeneity and the lack of enabling analytical tools. Here, protocols are presented to isolate and characterize glycosylated neuropeptides utilizing nanoflow liquid chromatography coupled with mass spectrometry (LC-MS). We first demonstrate how to extract neuropeptides from raw tissues and perform further separation/cleanup before MS analysis. Then we describe hybrid MS methods for glycosylated neuropeptide profiling and site-specific analysis. We also include recommendations for data analysis to identify glycosylated neuropeptides in crustaceans where a complete neuropeptide database is still lacking. Other strategies and future directions are discussed to provide readers with alternative approaches and further unravel biological complexity rendered by glycosylation.
Collapse
Affiliation(s)
- Yang Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Qinjingwen Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States; School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States.
| |
Collapse
|
44
|
Xiao H, Sun F, Suttapitugsakul S, Wu R. Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:356-379. [PMID: 30605224 PMCID: PMC6610820 DOI: 10.1002/mas.21586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/27/2018] [Indexed: 05/16/2023]
Abstract
Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.
Collapse
Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| |
Collapse
|
45
|
Hernandez-Valladares M, Wangen R, Berven FS, Guldbrandsen A. Protein Post-Translational Modification Crosstalk in Acute Myeloid Leukemia Calls for Action. Curr Med Chem 2019; 26:5317-5337. [PMID: 31241430 DOI: 10.2174/0929867326666190503164004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/23/2018] [Accepted: 02/01/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Post-translational modification (PTM) crosstalk is a young research field. However, there is now evidence of the extraordinary characterization of the different proteoforms and their interactions in a biological environment that PTM crosstalk studies can describe. Besides gene expression and phosphorylation profiling of acute myeloid leukemia (AML) samples, the functional combination of several PTMs that might contribute to a better understanding of the complexity of the AML proteome remains to be discovered. OBJECTIVE By reviewing current workflows for the simultaneous enrichment of several PTMs and bioinformatics tools to analyze mass spectrometry (MS)-based data, our major objective is to introduce the PTM crosstalk field to the AML research community. RESULTS After an introduction to PTMs and PTM crosstalk, this review introduces several protocols for the simultaneous enrichment of PTMs. Two of them allow a simultaneous enrichment of at least three PTMs when using 0.5-2 mg of cell lysate. We have reviewed many of the bioinformatics tools used for PTM crosstalk discovery as its complex data analysis, mainly generated from MS, becomes challenging for most AML researchers. We have presented several non-AML PTM crosstalk studies throughout the review in order to show how important the characterization of PTM crosstalk becomes for the selection of disease biomarkers and therapeutic targets. CONCLUSION Herein, we have reviewed the advances and pitfalls of the emerging PTM crosstalk field and its potential contribution to unravel the heterogeneity of AML. The complexity of sample preparation and bioinformatics workflows demands a good interaction between experts of several areas.
Collapse
Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Jonas Lies vei 87, N-5021 Bergen, Norway.,The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Rebecca Wangen
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Jonas Lies vei 87, N-5021 Bergen, Norway.,The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.,Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Jonas Lies vei 65, N-5021 Bergen, Norway
| | - Frode S Berven
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Astrid Guldbrandsen
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.,Computational Biology Unit, Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Bergen, Thormøhlensgt 55, N-5008 Bergen, Norway
| |
Collapse
|
46
|
Rosa-Fernandes L, Cugola FR, Russo FB, Kawahara R, de Melo Freire CC, Leite PEC, Bassi Stern AC, Angeli CB, de Oliveira DBL, Melo SR, Zanotto PMDA, Durigon EL, Larsen MR, Beltrão-Braga PCB, Palmisano G. Zika Virus Impairs Neurogenesis and Synaptogenesis Pathways in Human Neural Stem Cells and Neurons. Front Cell Neurosci 2019; 13:64. [PMID: 30949028 PMCID: PMC6436085 DOI: 10.3389/fncel.2019.00064] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/11/2019] [Indexed: 11/21/2022] Open
Abstract
Growing evidences have associated Zika virus (ZIKV) infection with congenital malformations, including microcephaly. Nonetheless, signaling mechanisms that promote the disease outcome are far from being understood, affecting the development of suitable therapeutics. In this study, we applied shotgun mass spectrometry (MS)-based proteomics combined with cell biology approaches to characterize altered molecular pathways on human neuroprogenitor cells (NPC) and neurons derived from induced pluripotent stem cells infected by ZIKV-BR strain, obtained from the 2015 Brazilian outbreak. Furthermore, ZIKV-BR infected NPCs showed unique alteration of pathways involved in neurological diseases, cell death, survival and embryonic development compared to ZIKV-AF, showing a human adaptation of the Brazilian viral strain. Besides, infected neurons differentiated from NPC presented an impairment of neurogenesis and synaptogenesis processes. Taken together, these data explain that CNS developmental arrest observed in Congenital Zika Syndrome is beyond neuronal cell death.
Collapse
Affiliation(s)
- Livia Rosa-Fernandes
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Fernanda Rodrigues Cugola
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Fabiele Baldino Russo
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Rebeca Kawahara
- Department of Parasitology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | | | - Paulo Emílio Corrêa Leite
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Carolina Bassi Stern
- Department of Parasitology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Claudia Blanes Angeli
- Department of Parasitology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | | | - Stella Rezende Melo
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | | | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patricia Cristina Baleeiro Beltrão-Braga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
- School of Arts Sciences and Humanities, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
47
|
Kawahara R, Ortega F, Rosa-Fernandes L, Guimarães V, Quina D, Nahas W, Schwämmle V, Srougi M, Leite KRM, Thaysen-Andersen M, Larsen MR, Palmisano G. Distinct urinary glycoprotein signatures in prostate cancer patients. Oncotarget 2018; 9:33077-33097. [PMID: 30237853 PMCID: PMC6145689 DOI: 10.18632/oncotarget.26005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
Novel biomarkers are needed to complement prostate specific antigen (PSA) in prostate cancer (PCa) diagnostic screening programs. Glycoproteins represent a hitherto largely untapped resource with a great potential as specific and sensitive tumor biomarkers due to their abundance in bodily fluids and their dynamic and cancer-associated glycosylation. However, quantitative glycoproteomics strategies to detect potential glycoprotein cancer markers from complex biospecimen are only just emerging. Here, we describe a glycoproteomics strategy for deep quantitative mapping of N- and O-glycoproteins in urine with a view to investigate the diagnostic value of the glycoproteome to discriminate PCa from benign prostatic hyperplasia (BPH), two conditions that remain difficult to clinically stratify. Total protein extracts were obtained, concentrated and digested from urine of six PCa patients (Gleason score 7) and six BPH patients. The resulting peptide mixtures were TMT-labeled and mixed prior to a multi-faceted sample processing including hydrophilic interaction liquid chromatography (HILIC) and titanium dioxide SPE based enrichment, endo-/exoglycosidase treatment and HILIC-HPLC pre-fractionation. The isolated N- and O-glycopeptides were detected and quantified using high resolution mass spectrometry. We accurately quantified 729 N-glycoproteins spanning 1,310 unique N-glycosylation sites and observed 954 and 965 unique intact N- and O-glycopeptides, respectively, across the two disease conditions. Importantly, a panel of 56 intact N-glycopeptides perfectly discriminated PCa and BPH (ROC: AUC = 1). This study has generated a panel of intact glycopeptides that has a potential for PCa detection.
Collapse
Affiliation(s)
- Rebeca Kawahara
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Fabio Ortega
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, LIM55, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Vanessa Guimarães
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, LIM55, São Paulo, Brazil
| | - Daniel Quina
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Willian Nahas
- Instituto do Câncer do Estado de São Paulo, ICESP, São Paulo, Brazil
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Miguel Srougi
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, LIM55, São Paulo, Brazil
| | - Katia R M Leite
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, LIM55, São Paulo, Brazil
| | | | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Giuseppe Palmisano
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, USP, São Paulo, Brazil
| |
Collapse
|
48
|
Zhang Q, Li Z, Wang Y, Zheng Q, Li J. Mass spectrometry for protein sialoglycosylation. MASS SPECTROMETRY REVIEWS 2018; 37:652-680. [PMID: 29228471 DOI: 10.1002/mas.21555] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
Sialic acids are a family of structurally unique and negatively charged nine-carbon sugars, normally found at the terminal positions of glycan chains on glycoproteins and glycolipids. The glycosylation of proteins is a universal post-translational modification in eukaryotic species and regulates essential biological functions, in which the most common sialic acid is N-acetyl-neuraminic acid (2-keto-5-acetamido-3,5-dideoxy-D-glycero-D-galactononulopyranos-1-onic acid) (Neu5NAc). Because of the properties of sialic acids under general mass spectrometry (MS) conditions, such as instability, ionization discrimination, and mixed adducts, the use of MS in the analysis of protein sialoglycosylation is still challenging. The present review is focused on the application of MS related methodologies to the study of both N- and O-linked sialoglycans. We reviewed MS-based strategies for characterizing sialylation by analyzing intact glycoproteins, proteolytic digested glycopeptides, and released glycans. The review concludes with future perspectives in the field.
Collapse
Affiliation(s)
- Qiwei Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Zack Li
- School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
| | - Jianjun Li
- National Research Council Canada, Ottawa, Ontario, Canada
| |
Collapse
|
49
|
Hong Y, Zhao H, Pu C, Zhan Q, Sheng Q, Lan M. Hydrophilic Phytic Acid-Coated Magnetic Graphene for Titanium(IV) Immobilization as a Novel Hydrophilic Interaction Liquid Chromatography-Immobilized Metal Affinity Chromatography Platform for Glyco- and Phosphopeptide Enrichment with Controllable Selectivity. Anal Chem 2018; 90:11008-11015. [PMID: 30136585 DOI: 10.1021/acs.analchem.8b02614] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this work, multifunctional Ti4+-immobilized phytic acid-modified magnetic graphene (denoted as MagG@PEI@PA-Ti4+) nanocomposites were fabricated through a facile route for simultaneous/respective enrichment of N-glyco- and phosphopeptides. Phytic acid (PA), with six phosphate groups, possesses excellent hydrophilicity and metal ion coordination ability, which endowed the MagG@PEI@PA-Ti4+ with combined properties of immobilized metal ion affinity chromatography (IMAC)- and hydrophilic interaction liquid chromatography (HILIC)-based materials. On the basis of the different binding ability of N-glyco- and phosphopeptides on MagG@PEI@PA-Ti4+, the MagG@PEI@PA-Ti4+ nanocomposites could enrich N-glyco- and phosphopeptides simultaneously or respectively by using different enrichment conditions, achieving controllable selective enrichment of N-glyco- and phosphopeptides. The proposed nanocomposites demonstrated an outstanding performance for selective enrichment of N-glycopeptides (selectivity, 1:1000 molar ratios of IgG/BSA; sensitivity, 0.5 fmol/μL IgG; loading capacity, 300 mg g-1; recovery, >90%) and phosphopeptides (selectivity, 1:5000 molar ratios of α-casein/BSA; sensitivity, 0.1 fmol/μL α-casein; loading capacity, 100 mg g-1; recovery, >90%). Taking advantage of these merits, a total of 393 N-glycopeptides derived from 259 glycoproteins and 574 phosphopeptides derived from 341 phosphoproteins were identified from 200 μg of HeLa cell extracts through a single-step enrichment using MagG@PEI@PA-Ti4+.
Collapse
Affiliation(s)
- Yayun Hong
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Hongli Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Chenlu Pu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Qiliang Zhan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Qianying Sheng
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China.,State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| |
Collapse
|
50
|
Stadlmann J, Hoi DM, Taubenschmid J, Mechtler K, Penninger JM. Analysis of PNGase F-Resistant N-Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities. Proteomics 2018; 18:e1700436. [PMID: 29775240 PMCID: PMC6055662 DOI: 10.1002/pmic.201700436] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/27/2018] [Indexed: 11/11/2022]
Abstract
SugarQb (www.imba.oeaw.ac.at/sugarqb) is a freely available collection of computational tools for the automated identification of intact glycopeptides from high-resolution HCD MS/MS datasets in the Proteome Discoverer environment. We report the migration of SugarQb to the latest and free version of Proteome Discoverer 2.1, and apply it to the analysis of PNGase F-resistant N-glycopeptides from mouse embryonic stem cells. The analysis of intact glycopeptides highlights unexpected technical limitations to PNGase F-dependent glycoproteomic workflows at the proteome level, and warrants a critical reinterpretation of seminal datasets in the context of N-glycosylation-site prediction.
Collapse
Affiliation(s)
- Johannes Stadlmann
- Institute of Molecular Biotechnology Austrian Academy of SciencesDr. Bohr Gasse 3A‐1030ViennaAustria
| | - David M. Hoi
- Institute of Molecular PathologyCampus‐Vienna‐Biocenter 1A‐1030ViennaAustria
| | - Jasmin Taubenschmid
- Institute of Molecular Biotechnology Austrian Academy of SciencesDr. Bohr Gasse 3A‐1030ViennaAustria
| | - Karl Mechtler
- Institute of Molecular Biotechnology Austrian Academy of SciencesDr. Bohr Gasse 3A‐1030ViennaAustria
- Institute of Molecular PathologyCampus‐Vienna‐Biocenter 1A‐1030ViennaAustria
| | - Josef M. Penninger
- Institute of Molecular Biotechnology Austrian Academy of SciencesDr. Bohr Gasse 3A‐1030ViennaAustria
| |
Collapse
|