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Halim A, Anonsen JH. Microbial glycoproteomics. Curr Opin Struct Biol 2017; 44:143-150. [PMID: 28365498 DOI: 10.1016/j.sbi.2017.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/24/2017] [Accepted: 03/06/2017] [Indexed: 02/02/2023]
Abstract
Mass spectrometry-based "-omics" technologies are important tools for global and detailed mapping of post-translational modifications. Protein glycosylation is an abundant and important post translational modification widespread throughout all domains of life. Characterization of glycoproteins, including identification of glycan structure and components, their attachment sites and protein carriers, remains challenging. However, recent advances in glycoproteomics, a subbranch that studies and categorizes protein glycosylations, have greatly expanded the known protein glycosylation space and research in this area is rapidly accelerating. Here, we review recent developments in glycoproteomic technologies with a special focus on microbial protein glycosylation.
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Affiliation(s)
- Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
| | - Jan Haug Anonsen
- Center for Integrative Microbial Evolution, The Mass Spectrometry and Proteomics Unit, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway.
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52
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Development of data-independent acquisition workflows for metabolomic analysis on a quadrupole-orbitrap platform. Talanta 2017; 164:128-136. [DOI: 10.1016/j.talanta.2016.11.048] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/15/2016] [Accepted: 11/20/2016] [Indexed: 12/13/2022]
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53
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Anjo SI, Santa C, Manadas B. SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600278] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Sandra Isabel Anjo
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Faculty of Sciences and Technology; University of Coimbra; Coimbra Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Institute for Interdisciplinary Research (III); University of Coimbra; Coimbra Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
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54
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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55
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Yeo KB, Chrysanthopoulos PK, Nouwens AS, Marcellin E, Schulz BL. High-performance targeted mass spectrometry with precision data-independent acquisition reveals site-specific glycosylation macroheterogeneity. Anal Biochem 2016; 510:106-113. [DOI: 10.1016/j.ab.2016.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 12/13/2022]
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56
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Kerr ED, Schulz BL. Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation. PeerJ 2016; 4:e2271. [PMID: 27602264 PMCID: PMC4991886 DOI: 10.7717/peerj.2271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 06/29/2016] [Indexed: 01/01/2023] Open
Abstract
Vegemite is an iconic Australian food spread made from spent brewers' yeast extract, which has been reported to be used as an ingredient in illegal home brewing. In this study, we tested the utility of Vegemite and the similar spread Marmite in promoting fermentation. We could not culture microorganisms from either Vegemite or Marmite, consistent with these food-grade spreads being essentially sterile. To test if the addition of Vegemite or Marmite could assist in fermentation when additional viable yeast was also present, solutions containing glucose and a range of concentrations of either Vegemite or Marmite were inoculated with brewers' yeast. No fermentation occurred in any condition without addition of extra brewer's yeast. Fermentation did not occur when yeast was inoculated into solutions containing only glucose, but progressed efficiently with when Vegemite or Marmite was also added. Gas Chromatography confirmed that ethanol was present at ∼3% v/v post-fermentation in all samples which contained glucose, Vegemite or Marmite, and brewers' yeast. Trace amounts of methanol were also detected. Mass spectrometry proteomics identified abundant intracellular yeast proteins and barley proteins in Vegemite and Marmite, and abundant secreted yeast proteins from actively growing yeast in those samples to which extra brewers' yeast had been added. We estimate that the real-world cost of home brewed "Vegemite Beer" would be very low. Our results show that Vegemite or other yeast extract spreads could provide cheap and readily available sources of nutrient supplementation to increase the efficiency of fermentation in home brewing or other settings.
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Affiliation(s)
- Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane , Queensland , Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane , Queensland , Australia
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57
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Peak IR, Chen A, Jen FEC, Jennings C, Schulz BL, Saunders NJ, Khan A, Seifert HS, Jennings MP. Neisseria meningitidis Lacking the Major Porins PorA and PorB Is Viable and Modulates Apoptosis and the Oxidative Burst of Neutrophils. J Proteome Res 2016; 15:2356-65. [PMID: 26562068 DOI: 10.1021/acs.jproteome.5b00938] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The bacterial pathogen Neisseria meningitidis expresses two major outer-membrane porins. PorA expression is subject to phase-variation (high frequency, random, on-off switching), and both PorA and PorB are antigenically variable between strains. PorA expression is variable and not correlated with meningococcal colonisation or invasive disease, whereas all naturally-occurring strains express PorB suggesting strong selection for expression. We have generated N. meningitidis strains lacking expression of both major porins, demonstrating that they are dispensable for bacterial growth in vitro. The porAB mutant strain has an exponential growth rate similar to the parental strain, as do the single porA or porB mutants, but the porAB mutant strain does not reach the same cell density in stationary phase. Proteomic analysis suggests that the double mutant strain exhibits compensatory expression changes in proteins associated with cellular redox state, energy/nutrient metabolism, and membrane stability. On solid media, there is obvious growth impairment that is rescued by addition of blood or serum from mammalian species, particularly heme. These porin mutants are not impaired in their capacity to inhibit both staurosporine-induced apoptosis and a phorbol 12-myristate 13-acetate-induced oxidative burst in human neutrophils suggesting that the porins are not the only bacterial factors that can modulate these processes in host cells.
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Affiliation(s)
- Ian R Peak
- School of Medical Science, Gold Coast Campus, Griffith University , Southport, QLD 4222, Australia.,Institute for Glycomics, Gold Coast Campus, Griffith University , Southport, QLD 4222, Australia
| | - Adrienne Chen
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Freda E-C Jen
- Institute for Glycomics, Gold Coast Campus, Griffith University , Southport, QLD 4222, Australia
| | - Courtney Jennings
- Institute for Glycomics, Gold Coast Campus, Griffith University , Southport, QLD 4222, Australia
| | - Benjamin L Schulz
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Brisbane, QLD 4072, Australia
| | - Nigel J Saunders
- Centre for Systems and Synthetic Biology, Brunel University , Uxbridge, Middlesex UB8 3PH, U.K
| | - Arshad Khan
- Centre for Systems and Synthetic Biology, Brunel University , Uxbridge, Middlesex UB8 3PH, U.K
| | - H Steven Seifert
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Michael P Jennings
- Institute for Glycomics, Gold Coast Campus, Griffith University , Southport, QLD 4222, Australia
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58
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Thaysen-Andersen M, Packer NH, Schulz BL. Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease. Mol Cell Proteomics 2016; 15:1773-90. [PMID: 26929216 PMCID: PMC5083109 DOI: 10.1074/mcp.o115.057638] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/09/2016] [Indexed: 12/21/2022] Open
Abstract
The glycoproteome remains severely understudied because of significant analytical challenges associated with glycoproteomics, the system-wide analysis of intact glycopeptides. This review introduces important structural aspects of protein N-glycosylation and summarizes the latest technological developments and applications in LC-MS/MS-based qualitative and quantitative N-glycoproteomics. These maturing technologies provide unique structural insights into the N-glycoproteome and its synthesis and regulation by complementing existing methods in glycoscience. Modern glycoproteomics is now sufficiently mature to initiate efforts to capture the molecular complexity displayed by the N-glycoproteome, opening exciting opportunities to increase our understanding of the functional roles of protein N-glycosylation in human health and disease.
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Affiliation(s)
- Morten Thaysen-Andersen
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia;
| | - Nicolle H Packer
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Benjamin L Schulz
- §School of Chemistry & Molecular Biosciences, St Lucia, The University of Queensland, Brisbane, QLD, Australia
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59
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Zacchi LF, Schulz BL. SWATH-MS Glycoproteomics Reveals Consequences of Defects in the Glycosylation Machinery. Mol Cell Proteomics 2016; 15:2435-47. [PMID: 27094473 DOI: 10.1074/mcp.m115.056366] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 12/16/2022] Open
Abstract
Glycan macro- and microheterogeneity have profound impacts on protein folding and function. This heterogeneity can be regulated by physiological or environmental factors. However, unregulated heterogeneity can lead to disease, and mutations in the glycosylation process cause a growing number of Congenital Disorders of Glycosylation. We systematically studied how mutations in the N-glycosylation pathway lead to defects in mature proteins using all viable Saccharomyces cerevisiae strains with deletions in genes encoding Endoplasmic Reticulum lumenal mannosyltransferases (Alg3, Alg9, and Alg12), glucosyltransferases (Alg6, Alg8, and Die2/Alg10), or oligosaccharyltransferase subunits (Ost3, Ost5, and Ost6). To measure the changes in glycan macro- and microheterogeneity in mature proteins caused by these mutations we developed a SWATH-mass spectrometry glycoproteomics workflow. We measured glycan structures and occupancy on mature cell wall glycoproteins, and relative protein abundance, in the different mutants. All mutants showed decreased glycan occupancy and altered cell wall proteomes compared with wild-type cells. Mutations in earlier mannosyltransferase or glucosyltransferase steps of glycan biosynthesis had stronger hypoglycosylation phenotypes, but glucosyltransferase defects were more severe. ER mannosyltransferase mutants displayed substantial global changes in glycan microheterogeneity consistent with truncations in the glycan transferred to protein in these strains. Although ER glucosyltransferase and oligosaccharyltransferase subunit mutants broadly showed no change in glycan structures, ost3Δ cells had shorter glycan structures at some sites, consistent with increased protein quality control mannosidase processing in this severely hypoglycosylating mutant. This method allows facile relative quantitative glycoproteomics, and our results provide insights into global regulation of site-specific glycosylation.
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Affiliation(s)
- Lucia F Zacchi
- From the ‡School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia; §Fundación Instituto Leloir, Avenida Patricias Argentinas 435, Ciudad Autónoma de Buenos Aires, 1405, Argentina
| | - Benjamin L Schulz
- From the ‡School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia;
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60
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Agarwal A, Bertolla RP, Samanta L. Sperm proteomics: potential impact on male infertility treatment. Expert Rev Proteomics 2016; 13:285-96. [DOI: 10.1586/14789450.2016.1151357] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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61
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62
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Zacchi LF, Schulz BL. N-glycoprotein macroheterogeneity: biological implications and proteomic characterization. Glycoconj J 2015; 33:359-76. [DOI: 10.1007/s10719-015-9641-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/04/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
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63
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Lin Q, Lim HSR, Lin HL, Tan HT, Lim TK, Cheong WK, Cheah PY, Tang CL, Chow PKH, Chung MCM. Analysis of colorectal cancer glyco-secretome identifies laminin β-1 (LAMB1) as a potential serological biomarker for colorectal cancer. Proteomics 2015; 15:3905-20. [PMID: 26359947 DOI: 10.1002/pmic.201500236] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/20/2015] [Accepted: 09/08/2015] [Indexed: 12/12/2022]
Abstract
The high mortality rate in colorectal cancer is mostly ascribed to metastasis, but the only clinical biomarker available for disease monitoring and prognosis is the carcinoembryonic antigen (CEA). However, the prognostic utility of CEA remains controversial. In an effort to identify novel biomarkers that could be potentially translated for clinical use, we collected the secretomes from the colon adenocarcinoma cell line HCT-116 and its metastatic derivative, E1, using the hollow fiber culture system, and utilized the multilectin affinity chromatography approach to enrich for the secreted glycoproteins (glyco-secretome). The HCT-116 and E1 glyco-secretomes were compared using the label-free quantitative SWATH-MS technology, and a total of 149 glycoproteins were differentially secreted in E1 cells. Among these glycoproteins, laminin β-1 (LAMB1), a glycoprotein not previously known to be secreted in colorectal cancer cells, was observed to be oversecreted in E1 cells. In addition, we showed that LAMB1 levels were significantly higher in colorectal cancer patient serum samples as compared to healthy controls when measured using ELISA. ROC analyses indicated that LAMB1 performed better than CEA at discriminating between colorectal cancer patients from controls. Moreover, the diagnostic performance was further improved when LAMB1 was used in combination with CEA.
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Affiliation(s)
- Qifeng Lin
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hannah S R Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Hui Ling Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Wai Kit Cheong
- Division of Colorectal Surgery, National University Hospital, Singapore.,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Duke-NUS Graduate Medical School, National University of Singapore, Singapore
| | - Choong Leong Tang
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Pierce K H Chow
- Department of General Surgery, Singapore General Hospital, Singapore.,Department of Surgical Oncology, National Cancer Centre, Singapore.,Centre for Quantitative Medicine, Duke-NUS Graduate Medical School, National University of Singapore, Singapore
| | - Maxey C M Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
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