1
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Hadjineophytou C, Loh E, Koomey M, Scott NE. Combining FAIMS based glycoproteomics and DIA proteomics reveals widespread proteome alterations in response to glycosylation occupancy changes in Neisseria gonorrhoeae. Proteomics 2024; 24:e2300496. [PMID: 38361220 DOI: 10.1002/pmic.202300496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024]
Abstract
Protein glycosylation is increasingly recognized as a common protein modification across bacterial species. Within the Neisseria genus O-linked protein glycosylation is conserved yet closely related Neisseria species express O-oligosaccharyltransferases (PglOs) with distinct targeting activities. Within this work, we explore the targeting capacity of different PglOs using Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) fractionation and Data-Independent Acquisition (DIA) to allow the characterization of the impact of changes in glycosylation on the proteome of Neisseria gonorrhoeae. We demonstrate FAIMS expands the known glycoproteome of wild type N. gonorrhoeae MS11 and enables differences in glycosylation to be assessed across strains expressing different pglO allelic chimeras with unique substrate targeting activities. Combining glycoproteomic insights with DIA proteomics, we demonstrate that alterations within pglO alleles have widespread impacts on the proteome of N. gonorrhoeae. Examination of peptides known to be targeted by glycosylation using DIA analysis supports alterations in glycosylation occupancy occurs independently of changes in protein levels and that the occupancy of glycosylation is generally low on most glycoproteins. This work thus expands our understanding of the N. gonorrhoeae glycoproteome and the roles that pglO allelic variation may play in governing genus-level protein glycosylation.
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Affiliation(s)
- Chris Hadjineophytou
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- Clinical Microbiology, BioClinicum, Karolinska University Hospital, Solna, Sweden
| | - Edmund Loh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- Clinical Microbiology, BioClinicum, Karolinska University Hospital, Solna, Sweden
| | - Michael Koomey
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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2
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Yammine M, Bray F, Flament S, Picavet A, Lacroix JM, Poilpré E, Mouly I, Rolando C. Reliable Approach for Pure Yeast Cell Wall Protein Isolation from Saccharomyces cerevisiae Yeast Cells. ACS OMEGA 2022; 7:29702-29713. [PMID: 36061670 PMCID: PMC9435031 DOI: 10.1021/acsomega.2c02176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Saccharomyces cerevisiae yeast is a fungus presenting a peripheral organelle called the cell wall. The cell wall protects the yeast cell from stress and provides means for communication with the surrounding environment. It has a complex molecular structure, composed of an internal part of cross-linked polysaccharides and an external part of mannoproteins. These latter are very interesting owing to their functional properties, dependent on their molecular features with massive mannosylations. Therefore, the molecular characterization of mannoproteins is a must relying on the optimal isolation and preparation of the cell wall fraction. Multiple methods are well reported for yeast cell wall isolation. The most applied one consists of yeast cell lysis by mechanical disruption. However, applying this classical approach to S288C yeast cells showed considerable contamination with noncell wall proteins, mainly comprising mitochondrial proteins. Herein, we tried to further purify the yeast cell wall preparation by two means: ultracentrifugation and Triton X-100 addition. While the first strategy showed limited outcomes in mitochondrial protein removal, the second strategy showed optimal results when Triton X-100 was added at 5%, allowing the identification of more mannoproteins and significantly enriching their amounts. This promising method could be reliably implemented on the lab scale for identification of mannoproteins and molecular characterization and industrial processes for "pure" cell wall isolation.
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Affiliation(s)
- Marie Yammine
- Univ.
Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse,
l’Analyse et la Protéomique, F-59000 Lille, France
- Lesaffre
international, Research and Development department, 77 rue de Menin, F-59520 Marquette-lez-Lille, France
| | - Fabrice Bray
- Univ.
Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse,
l’Analyse et la Protéomique, F-59000 Lille, France
| | - Stéphanie Flament
- Univ.
Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse,
l’Analyse et la Protéomique, F-59000 Lille, France
| | - Antoine Picavet
- Lesaffre
international, Research and Development department, 77 rue de Menin, F-59520 Marquette-lez-Lille, France
| | - Jean-Marie Lacroix
- Univ.
Lille, CNRS, UMR 8765, UGSF, Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Emmanuel Poilpré
- Lesaffre
international, Research and Development department, 77 rue de Menin, F-59520 Marquette-lez-Lille, France
| | - Isabelle Mouly
- Lesaffre
international, Research and Development department, 77 rue de Menin, F-59520 Marquette-lez-Lille, France
| | - Christian Rolando
- Univ.
Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse,
l’Analyse et la Protéomique, F-59000 Lille, France
- Shrieking
sixties, 1-3 Allée
Lavoisier, F-59650 Villeneuve-d’Ascq, France
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3
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Neuhaus JD, Wild R, Eyring J, Irobalieva RN, Kowal J, Lin CW, Locher KP, Aebi M. Functional analysis of Ost3p and Ost6p containing yeast oligosaccharyltransferases. Glycobiology 2021; 31:1604-1615. [PMID: 34974622 DOI: 10.1093/glycob/cwab084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 07/14/2021] [Accepted: 08/05/2021] [Indexed: 11/14/2022] Open
Abstract
The oligosaccharyltransferase (OST) is the central enzyme in the N-glycosylation pathway. It transfers a defined oligosaccharide from a lipid-linker onto the asparagine side chain of proteins. The yeast OST consists of eight subunits and exists in two catalytically distinct isoforms that differ in one subunit, Ost3p or Ost6p. The cryo-electron microscopy structure of the Ost6p containing complex was found to be highly similar to the Ost3p containing OST. OST enzymes with altered Ost3p/Ost6p subunits were generated and functionally analyzed. The three C-terminal transmembrane helices were responsible for the higher turnover-rate of the Ost3p vs. the Ost6p containing enzyme in vitro and the more severe hypoglycosylation in Ost3p lacking strains in vivo. Glycosylation of specific OST target sites required the N-terminal thioredoxin domain of Ost3p or Ost6p. This Ost3p/Ost6p dependence was glycosylation site but not protein specific. We concluded that the Ost3p/Ost6p subunits modulate the catalytic activity of OST and provide additional specificity for OST substrate recognition.
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Affiliation(s)
- Julia D Neuhaus
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Rebekka Wild
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.,Institut de Biologie Structurale, CNRS, CEA, Université Grenoble-Alpes, 38000 Grenoble, France
| | - Jillianne Eyring
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Rossitza N Irobalieva
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Julia Kowal
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Chia-Wei Lin
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.,Functional Genomic Center Zurich, 8057 Zurich, Switzerland
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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4
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Fenech EJ, Ben-Dor S, Schuldiner M. Double the Fun, Double the Trouble: Paralogs and Homologs Functioning in the Endoplasmic Reticulum. Annu Rev Biochem 2021; 89:637-666. [PMID: 32569522 DOI: 10.1146/annurev-biochem-011520-104831] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of eukaryotic genomes has been propelled by a series of gene duplication events, leading to an expansion in new functions and pathways. While duplicate genes may retain some functional redundancy, it is clear that to survive selection they cannot simply serve as a backup but rather must acquire distinct functions required for cellular processes to work accurately and efficiently. Understanding these differences and characterizing gene-specific functions is complex. Here we explore different gene pairs and families within the context of the endoplasmic reticulum (ER), the main cellular hub of lipid biosynthesis and the entry site for the secretory pathway. Focusing on each of the ER functions, we highlight specificities of related proteins and the capabilities conferred to cells through their conservation. More generally, these examples suggest why related genes have been maintained by evolutionary forces and provide a conceptual framework to experimentally determine why they have survived selection.
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Affiliation(s)
- Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
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5
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Honer J, Niemeyer KM, Fercher C, Diez Tissera AL, Jaberolansar N, Jafrani YMA, Zhou C, Caramelo JJ, Shewan AM, Schulz BL, Brodsky JL, Zacchi LF. TorsinA folding and N-linked glycosylation are sensitive to redox homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119073. [PMID: 34062155 PMCID: PMC8889903 DOI: 10.1016/j.bbamcr.2021.119073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 01/03/2023]
Abstract
The Endoplasmic Reticulum (ER) is responsible for the folding and post-translational modification of secretory proteins, as well as for triaging misfolded proteins. During folding, there is a complex yet only partially understood interplay between disulfide bond formation, which is an enzyme catalyzed event in the oxidizing environment of the ER, along with other post-translational modifications (PTMs) and chaperone-supported protein folding. Here, we used the glycoprotein torsinA as a model substrate to explore the impact of ER redox homeostasis on PTMs and protein biogenesis. TorsinA is a AAA+ ATPase with unusual oligomeric properties and controversial functions. The deletion of a C-terminal glutamic acid residue (∆E) is associated with the development of Early-Onset Torsion Dystonia, a severe movement disorder. TorsinA differs from other AAA+ ATPases since it is an ER resident, and as a result of its entry into the ER torsinA contains two N-linked glycans and at least one disulfide bond. The role of these PTMs on torsinA biogenesis and function and the identity of the enzymes that catalyze them are poorly defined. Using a yeast torsinA expression system, we demonstrate that a specific protein disulfide isomerase, Pdi1, affects the folding and N-linked glycosylation of torsinA and torsinA∆E in a redox-dependent manner, suggesting that the acquisition of early torsinA folding intermediates is sensitive to perturbed interactions between Cys residues and the quality control machinery. We also highlight the role of specific Cys residues during torsinA biogenesis and demonstrate that torsinA∆E is more sensitive than torsinA when these Cys residues are mutated.
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Affiliation(s)
- Jonas Honer
- Department of Biological Sciences, A320 Langley Hall, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Katie M Niemeyer
- Department of Biological Sciences, A320 Langley Hall, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Christian Fercher
- Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Ana L Diez Tissera
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), 1405 Buenos Aires, Argentina
| | - Noushin Jaberolansar
- Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yohaann M A Jafrani
- Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Chun Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Julio J Caramelo
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), 1405 Buenos Aires, Argentina
| | - Annette M Shewan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Benjamin L Schulz
- Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Jeffrey L Brodsky
- Department of Biological Sciences, A320 Langley Hall, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Lucía F Zacchi
- Department of Biological Sciences, A320 Langley Hall, University of Pittsburgh, Pittsburgh, PA 15260, United States of America; Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia; Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), 1405 Buenos Aires, Argentina; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia.
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6
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Eyring J, Lin CW, Ngwa EM, Boilevin J, Pesciullesi G, Locher KP, Darbre T, Reymond JL, Aebi M. Substrate specificities and reaction kinetics of the yeast oligosaccharyltransferase isoforms. J Biol Chem 2021; 296:100809. [PMID: 34023382 PMCID: PMC8191290 DOI: 10.1016/j.jbc.2021.100809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Oligosaccharyltransferase (OST) catalyzes the central step in N-linked protein glycosylation, the transfer of a preassembled oligosaccharide from its lipid carrier onto asparagine residues of secretory proteins. The prototypic hetero-octameric OST complex from the yeast Saccharomyces cerevisiae exists as two isoforms that contain either Ost3p or Ost6p, both noncatalytic subunits. These two OST complexes have different protein substrate specificities in vivo. However, their detailed biochemical mechanisms and the basis for their different specificities are not clear. The two OST complexes were purified from genetically engineered strains expressing only one isoform. The kinetic properties and substrate specificities were characterized using a quantitative in vitro glycosylation assay with short peptides and different synthetic lipid-linked oligosaccharide (LLO) substrates. We found that the peptide sequence close to the glycosylation sequon affected peptide affinity and turnover rate. The length of the lipid moiety affected LLO affinity, while the lipid double-bond stereochemistry had a greater influence on LLO turnover rates. The two OST complexes had similar affinities for both the peptide and LLO substrates but showed significantly different turnover rates. These data provide the basis for a functional analysis of the Ost3p and Ost6p subunits.
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Affiliation(s)
- Jillianne Eyring
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Chia-Wei Lin
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland; Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Elsy Mankah Ngwa
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Jérémy Boilevin
- Department of Chemistry and Biochemistry, University of Berne, Bern, Switzerland
| | - Giorgio Pesciullesi
- Department of Chemistry and Biochemistry, University of Berne, Bern, Switzerland
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Berne, Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Bern, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.
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7
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Phoomak C, Cui W, Hayman TJ, Yu SH, Zhao P, Wells L, Steet R, Contessa JN. The translocon-associated protein (TRAP) complex regulates quality control of N-linked glycosylation during ER stress. SCIENCE ADVANCES 2021; 7:eabc6364. [PMID: 33523898 PMCID: PMC7810369 DOI: 10.1126/sciadv.abc6364] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/24/2020] [Indexed: 05/04/2023]
Abstract
Asparagine (N)-linked glycosylation is required for endoplasmic reticulum (ER) homeostasis, but how this co- and posttranslational modification is maintained during ER stress is unknown. Here, we introduce a fluorescence-based strategy to detect aberrant N-glycosylation in individual cells and identify a regulatory role for the heterotetrameric translocon-associated protein (TRAP) complex. Unexpectedly, cells with knockout of SSR3 or SSR4 subunits restore N-glycosylation over time concurrent with a diminished ER stress transcriptional signature. Activation of ER stress or silencing of the ER chaperone BiP exacerbates or rescues the glycosylation defects, respectively, indicating that SSR3 and SSR4 enable N-glycosylation during ER stress. Protein levels of the SSR3 subunit are ER stress and UBE2J1 dependent, revealing a mechanism that coordinates upstream N-glycosylation proficiency with downstream ER-associated degradation and proteostasis. The fidelity of N-glycosylation is not static in both nontransformed and tumor cells, and the TRAP complex regulates ER glycoprotein quality control under conditions of stress.
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Affiliation(s)
- Chatchai Phoomak
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Wei Cui
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Thomas J Hayman
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Seok-Ho Yu
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Peng Zhao
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30601, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30601, USA
| | | | - Joseph N Contessa
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA
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8
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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9
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Pegg CL, Zacchi LF, Recinos DR, Howard CB, Schulz BL. Identification of novel glycosylation events on human serum-derived factor IX. Glycoconj J 2020; 37:471-483. [PMID: 32378017 DOI: 10.1007/s10719-020-09922-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/06/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Human Factor IX is a highly post-translationally modified protein that is an important clotting factor in the blood coagulation cascade. Functional deficiencies in Factor IX result in the bleeding disorder haemophilia B, which is treated with plasma-derived or recombinant Factor IX concentrates. Here, we investigated the post-translational modifications of human serum-derived Factor IX and report previously undescribed O-linked monosaccharide compositions at serine 141 and a novel site of glycosylation. At serine 141 we observed two monosaccharide compositions, with HexNAc1Hex1NeuAc2 dominant and a low level of HexNAc1Hex1NeuAc1. This O-linked site lies N-terminal to the first cleavage site for the activation peptide, an important region of the protein that is removed to activate Factor IX. The novel site is an N-linked site in the serine protease domain with low occupancy in a non-canonical consensus motif at asparagine 258, observed with a HexNAc4Hex5NeuAc2 monosaccharide composition attached. This is the first reported instance of a site of modification in the serine protease domain. The description of these glycosylation events provides a basis for future functional studies and contributes to structural characterisation of native Factor IX for the production of effective therapeutic biosimilars and biobetters.
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Affiliation(s)
- Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Lucia F Zacchi
- Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dinora Roche Recinos
- Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Christopher B Howard
- Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia. .,Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia.
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10
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Zhou C, Schulz BL. Glycopeptide variable window SWATH for improved data independent acquisition glycoprotein analysis. Anal Biochem 2020; 597:113667. [PMID: 32119847 DOI: 10.1016/j.ab.2020.113667] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 01/06/2023]
Abstract
N-glycosylation plays an essential role in regulating protein folding and function in eukaryotic cells. Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH) has proven useful as a data independent acquisition (DIA) MS method for analysis of glycoproteins and their glycan modifications. By separating the entire m/z range into consecutive isolation windows, DIA-MS allows comprehensive MS data acquisition and high-sensitivity detection of molecules of interest. Variable width DIA windows allow optimal analyte measurement, as peptide ions are not evenly distributed across the full m/z range. However, the m/z distribution of glycopeptides is different to that of unmodified peptides because of their large glycan structures. Here, we improved the performance of DIA glycoproteomics by using variable width windows optimized for glycopeptides. This method allocates narrow windows at m/z ranges rich in glycopeptides, improving analytical specificity and performance. We show that related glycoforms must fall in separate windows to allow accurate glycopeptide measurement. We demonstrate the utility of the method by comparing the cell wall glycoproteomes of wild-type and N-glycan biosynthesis deficient yeast and showing improved measurement of glycopeptides with different glycan structures. Our results highlight the importance of appropriately optimized DIA methods for measurement of post-translationally modified peptides.
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Affiliation(s)
- Chun Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, 4072, Queensland, Australia; Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, Queensland, Australia.
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11
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Midorikawa R, Takakura D, Morise J, Wakazono Y, Kawasaki N, Oka S, Takamiya K. Monitoring the glycosylation of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate-type glutamate receptors using specific antibodies reveals a novel regulatory mechanism of N-glycosylation occupancy by molecular chaperones in mice. J Neurochem 2020; 153:567-585. [PMID: 31958346 DOI: 10.1111/jnc.14964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 01/11/2023]
Abstract
In the mammalian nervous system, protein N-glycosylation plays an important role in neuronal physiology. In this study, we performed a comprehensive N-glycosylation analysis of mouse GluA1, one of the major subunits of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate type glutamate receptor, which possesses six potential N-glycosylation sites in the N-terminal domain. By mass spectrometry-based analysis, we identified the N-glycoforms and semiquantitatively determined the site-specific N-glycosylation occupancy of GluA1. In addition, only the N401-glycosylation site demonstrated incomplete N-glycosylation occupancy. Therefore, we generated a peptide antibody that specifically detects the N401-glycan-free form to precisely quantify N401-glycosylation occupancy. Using this antibody, we clarified that N401 occupancy varies between cell types and increases in an age-dependent manner in mouse forebrains. To address the regulatory mechanism of N401-glycosylation, binding proteins of GluA1 around the N401 site were screened. HSP70 family proteins, including Bip, were identified as candidates. Bip has been known as a molecular chaperone that plays a key role in protein folding in the ER (endoplasmic reticulum). To examine the involvement of Bip in N401-glycosylation, the effect of Bip over-expression on N401 occupancy was evaluated in HEK293T cells, and the results demonstrated Bip increases the N401 glycan-free form by mediating selective prolongation of its protein half-life. Taken together, we propose that the N401-glycosite of GluA1 receives a unique control of modification, and we also propose a novel N-glycosylation occupancy regulatory mechanism by Bip that might be associated with α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate receptors function in the brain.
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Affiliation(s)
- Ryosuke Midorikawa
- Department of Neuroscience, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
| | - Daisuke Takakura
- Project for Utilizing Glycans in the Development of Innovative Drug Discovery Technologies, Shinanomachi Research Park, Keio University School of Medicine, Tokyo, Japan
| | - Jyoji Morise
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihiko Wakazono
- Department of Neuroscience, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
| | - Nana Kawasaki
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Shogo Oka
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kogo Takamiya
- Department of Neuroscience, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
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12
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Kajiwara S, Yamada R, Matsumoto T, Ogino H. N-linked glycosylation of thermostable lipase from Bacillus thermocatenulatus to improve organic solvent stability. Enzyme Microb Technol 2020; 132:109416. [DOI: 10.1016/j.enzmictec.2019.109416] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/31/2019] [Accepted: 08/22/2019] [Indexed: 01/14/2023]
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13
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Shrimal S, Cherepanova NA, Mandon EC, Venev SV, Gilmore R. Asparagine-linked glycosylation is not directly coupled to protein translocation across the endoplasmic reticulum in Saccharomyces cerevisiae. Mol Biol Cell 2019; 30:2626-2638. [PMID: 31433728 PMCID: PMC6761772 DOI: 10.1091/mbc.e19-06-0330] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Mammalian cells express two oligosaccharyltransferase complexes, STT3A and STT3B, that have distinct roles in N-linked glycosylation. The STT3A complex interacts directly with the protein translocation channel to mediate glycosylation of proteins using an N-terminal-to-C-terminal scanning mechanism. N-linked glycosylation of proteins in budding yeast has been assumed to be a cotranslational reaction. We have compared glycosylation of several glycoproteins in yeast and mammalian cells. Prosaposin, a cysteine-rich protein that contains STT3A-dependent glycosylation sites, is poorly glycosylated in yeast cells and STT3A-deficient human cells. In contrast, a protein with extreme C-terminal glycosylation sites was efficiently glycosylated in yeast by a posttranslocational mechanism. Posttranslocational glycosylation was also observed for carboxypeptidase Y-derived reporter proteins that contain closely spaced acceptor sites. A comparison of two recent protein structures indicates that the yeast OST is unable to interact with the yeast heptameric Sec complex via an evolutionarily conserved interface due to occupation of the OST binding site by the Sec63 protein. The efficiency of glycosylation in yeast is not enhanced for proteins that are translocated by the Sec61 or Ssh1 translocation channels instead of the Sec complex. We conclude that N-linked glycosylation and protein translocation are not directly coupled in yeast cells.
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Affiliation(s)
- Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Elisabet C Mandon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Sergey V Venev
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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14
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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.
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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
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15
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Cherepanova NA, Venev SV, Leszyk JD, Shaffer SA, Gilmore R. Quantitative glycoproteomics reveals new classes of STT3A- and STT3B-dependent N-glycosylation sites. J Cell Biol 2019; 218:2782-2796. [PMID: 31296534 PMCID: PMC6683751 DOI: 10.1083/jcb.201904004] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 11/24/2022] Open
Abstract
Cherepanova et al. provide quantitative glycoproteomic analyses of human cells that lack either the STT3A or STT3B oligosaccharyltransferase (OST) complex, revealing new classes of STT3A- and STT3B-dependent glycosylation sites and indicating how cooperation between the OST complexes maximizes acceptor site occupancy in cellular glycoproteins. Human cells express two oligosaccharyltransferase complexes (STT3A and STT3B) with partially overlapping functions. The STT3A complex interacts directly with the protein translocation channel to mediate cotranslational glycosylation, while the STT3B complex can catalyze posttranslocational glycosylation. We used a quantitative glycoproteomics procedure to compare glycosylation of roughly 1,000 acceptor sites in wild type and mutant cells. Analysis of site occupancy data disclosed several new classes of STT3A-dependent acceptor sites including those with suboptimal flanking sequences and sites located within cysteine-rich protein domains. Acceptor sites located in short loops of multi-spanning membrane proteins represent a new class of STT3B-dependent site. Remarkably, the lumenal ER chaperone GRP94 was hyperglycosylated in STT3A-deficient cells, bearing glycans on five silent sites in addition to the normal glycosylation site. GRP94 was also hyperglycosylated in wild-type cells treated with ER stress inducers including thapsigargin, dithiothreitol, and NGI-1.
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Affiliation(s)
- Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Sergey V Venev
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA
| | - John D Leszyk
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
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16
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Shrimal S, Gilmore R. Oligosaccharyltransferase structures provide novel insight into the mechanism of asparagine-linked glycosylation in prokaryotic and eukaryotic cells. Glycobiology 2019; 29:288-297. [PMID: 30312397 DOI: 10.1093/glycob/cwy093] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/26/2018] [Accepted: 10/09/2018] [Indexed: 11/12/2022] Open
Abstract
Asparagine-linked (N-linked) glycosylation is one of the most common protein modification reactions in eukaryotic cells, occurring upon the majority of proteins that enter the secretory pathway. X-ray crystal structures of the single subunit OSTs from eubacterial and archaebacterial organisms revealed the location of donor and acceptor substrate binding sites and provided the basis for a catalytic mechanism. Cryoelectron microscopy structures of the octameric yeast OST provided substantial insight into the organization and assembly of the multisubunit oligosaccharyltransferases. Furthermore, the cryoelectron microscopy structure of a complex consisting of a mammalian OST complex, the protein translocation channel and a translating ribosome revealed new insight into the mechanism of cotranslational glycosylation.
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Affiliation(s)
- Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, USA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, USA
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17
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Berg P, McConnell EW, Hicks LM, Popescu SC, Popescu GV. Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics. BMC Bioinformatics 2019; 20:102. [PMID: 30871482 PMCID: PMC6419331 DOI: 10.1186/s12859-019-2619-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM) analysis like reversible cysteine oxidation are evaluated. The paper proposes a pipeline based on the R programming language to analyze PTMs from peptide-centric label-free quantitative proteomics data. RESULTS Our methodology includes variance stabilization, normalization, and missing data imputation to account for the large dynamic range of PTM measurements. It also corrects biases from an enrichment protocol and reduces the random and systematic errors associated with label-free quantification. The performance of the methodology is tested by performing proteome-wide differential PTM quantitation using linear models analysis (limma). We objectively compare two imputation methods along with significance testing when using multiple-imputation for missing data. CONCLUSION Identifying PTMs in large-scale datasets is a problem with distinct characteristics that require new methods for handling missing data imputation and differential proteome analysis. Linear models in combination with multiple-imputation could significantly outperform a t-test-based decision method.
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Affiliation(s)
- Philip Berg
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA
| | - Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - George V Popescu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA. .,The National Institute for Laser, Plasma & Radiation Physics, Bucharest, Romania.
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18
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Abstract
Flocculation is one of the most important characteristics of brewing yeast as it allows for the easy and cheap removal of cells after fermentation. The genes responsible for both the Flo1 and NewFlo flocculation phenotypes are well characterized. However, the relationship between Flo protein abundance and flocculation efficiency is poorly understood. In this present study, we used mass spectrometry proteomics to compare the cell wall and whole cell proteomes of commercial yeast strains with diverse flocculation behaviors. We found that the relative abundance of Flo1/5 or Flo10 in the cell wall was correlated with the ability of these yeast strains to flocculate. Analysis of whole cell proteomes identified differences in the proteomes of yeast strains and identified the potential for high metabolic diversity. Characterization of the cell wall and whole cell proteomes during fermentation showed high levels of Flo10 in cells that settled early during fermentation. Our data reveal the diversity of the cell wall and global proteomes of brewing yeast, highlighting the potential biochemical diversity present in yeast that can be utilized in the production of fermented beverages.
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19
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Aviram N, Schuldiner M. Targeting and translocation of proteins to the endoplasmic reticulum at a glance. J Cell Sci 2018; 130:4079-4085. [PMID: 29246967 DOI: 10.1242/jcs.204396] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The evolutionary emergence of organelles was a defining process in diversifying biochemical reactions within the cell and enabling multicellularity. However, compartmentalization also imposed a great challenge-the need to import proteins synthesized in the cytosol into their respective sites of function. For example, one-third of all genes encode for proteins that must be targeted and translocated into the endoplasmic reticulum (ER), which serves as the entry site to the majority of endomembrane compartments. Decades of research have set down the fundamental principles of how proteins get from the cytosol into the ER, and recent studies have brought forward new pathways and additional regulators enabling better definition of the rules governing substrate recognition. In this Cell Science at a Glance article and the accompanying poster, we give an overview of our current understanding of the multifaceted and regulated processes of protein targeting and translocation to the ER.
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Affiliation(s)
- Naama Aviram
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 7610001
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 7610001
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20
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Harada Y. The Early Stages of Asparagine-Linked Glycosylation. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1807.2e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yoichiro Harada
- Department of Systems Biology in Thromboregulation, Kagoshima University Graduate School of Medical and Dental Sciences
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21
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Harada Y. The Early Stages of Asparagine-Linked Glycosylation. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1807.2j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yoichiro Harada
- Department of Systems Biology in Thromboregulation, Kagoshima University Graduate School of Medical and Dental Sciences
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22
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Synthesis and use of 6,6,6-trifluoro-L-fucose to block core-fucosylation in hybridoma cell lines. Carbohydr Res 2018; 465:4-9. [PMID: 29874559 DOI: 10.1016/j.carres.2018.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/17/2018] [Accepted: 05/19/2018] [Indexed: 01/18/2023]
Abstract
Many monoclonal antibodies (mAbs) used in cancer immunotherapy mediate tumour cell lysis by recruiting natural killer (NK) cells; a phenomenon known as antibody-dependent cellular cytotoxicity (ADCC). Eliminating core-fucose from the N-glycans of a mAb enhances its capacity to induce ADCC. As such, inhibitors of fucosylation are highly desirable for the production of mAbs for research and therapeutic use. Herein, we describe a simple synthesis of 6,6,6-trifluoro-l-fucose (F3Fuc), a metabolic inhibitor of fucosylation, and demonstrate the utility of this molecule in the production of low-fucose mAbs from murine hybridoma cell lines.
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23
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Jinnelov A, Ali L, Tinti M, Güther MLS, Ferguson MAJ. Single-subunit oligosaccharyltransferases of Trypanosoma brucei display different and predictable peptide acceptor specificities. J Biol Chem 2017; 292:20328-20341. [PMID: 28928222 PMCID: PMC5724017 DOI: 10.1074/jbc.m117.810945] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/13/2017] [Indexed: 11/10/2022] Open
Abstract
Trypanosoma brucei causes African trypanosomiasis and contains three full-length oligosaccharyltransferase (OST) genes; two of which, TbSTT3A and TbSTT3B, are expressed in the bloodstream form of the parasite. These OSTs have different peptide acceptor and lipid-linked oligosaccharide donor specificities, and trypanosomes do not follow many of the canonical rules developed for other eukaryotic N-glycosylation pathways, raising questions as to the basic architecture and detailed function of trypanosome OSTs. Here, we show by blue-native gel electrophoresis and stable isotope labeling in cell culture proteomics that the TbSTT3A and TbSTT3B proteins associate with each other in large complexes that contain no other detectable protein subunits. We probed the peptide acceptor specificities of the OSTs in vivo using a transgenic glycoprotein reporter system and performed glycoproteomics on endogenous parasite glycoproteins using sequential endoglycosidase H and peptide:N-glycosidase-F digestions. This allowed us to assess the relative occupancies of numerous N-glycosylation sites by endoglycosidase H-resistant N-glycans originating from Man5GlcNAc2-PP-dolichol transferred by TbSTT3A, and endoglycosidase H-sensitive N-glycans originating from Man9GlcNAc2-PP-dolichol transferred by TbSTT3B. Using machine learning, we assessed the features that best define TbSTT3A and TbSTT3B substrates in vivo and built an algorithm to predict the types of N-glycan most likely to predominate at all the putative N-glycosylation sites in the parasite proteome. Finally, molecular modeling was used to suggest why TbSTT3A has a distinct preference for sequons containing and/or flanked by acidic amino acid residues. Together, these studies provide insights into how a highly divergent eukaryote has re-wired protein N-glycosylation to provide protein sequence-specific N-glycan modifications. Data are available via ProteomeXchange with identifiers PXD007236, PXD007267, and PXD007268.
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Affiliation(s)
- Anders Jinnelov
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Liaqat Ali
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Michele Tinti
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Maria Lucia S Güther
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Michael A J Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom.
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24
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Poljak K, Breitling J, Gauss R, Rugarabamu G, Pellanda M, Aebi M. Analysis of substrate specificity of Trypanosoma brucei oligosaccharyltransferases (OSTs) by functional expression of domain-swapped chimeras in yeast. J Biol Chem 2017; 292:20342-20352. [PMID: 29042445 DOI: 10.1074/jbc.m117.811133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/11/2017] [Indexed: 11/06/2022] Open
Abstract
N-Linked protein glycosylation is an essential and highly conserved post-translational modification in eukaryotes. The transfer of a glycan from a lipid-linked oligosaccharide (LLO) donor to the asparagine residue of a nascent polypeptide chain is catalyzed by an oligosaccharyltransferase (OST) in the lumen of the endoplasmic reticulum (ER). Trypanosoma brucei encodes three paralogue single-protein OSTs called TbSTT3A, TbSTT3B, and TbSTT3C that can functionally complement the Saccharomyces cerevisiae OST, making it an ideal experimental system to study the fundamental properties of OST activity. We characterized the LLO and polypeptide specificity of all three TbOST isoforms and their chimeric forms in the heterologous expression host S. cerevisiae where we were able to apply yeast genetic tools and newly developed glycoproteomics methods. We demonstrated that TbSTT3A accepted LLO substrates ranging from Man5GlcNAc2 to Man7GlcNAc2 In contrast, TbSTT3B required more complex precursors ranging from Man6GlcNAc2 to Glc3Man9GlcNAc2 structures, and TbSTT3C did not display any LLO preference. Sequence differences between the isoforms cluster in three distinct regions. We have swapped the individual regions between different OST proteins and identified region 2 to influence the specificity toward the LLO and region 1 to influence polypeptide substrate specificity. These results provide a basis to further investigate the molecular mechanisms and contribution of single amino acids in OST interaction with its substrates.
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Affiliation(s)
- Kristina Poljak
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Jörg Breitling
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Robert Gauss
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - George Rugarabamu
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Mauro Pellanda
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland.
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25
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Poljak K, Selevsek N, Ngwa E, Grossmann J, Losfeld ME, Aebi M. Quantitative Profiling of N-linked Glycosylation Machinery in Yeast Saccharomyces cerevisiae. Mol Cell Proteomics 2017; 17:18-30. [PMID: 28993419 DOI: 10.1074/mcp.ra117.000096] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Indexed: 11/06/2022] Open
Abstract
Asparagine-linked glycosylation is a common posttranslational protein modification regulating the structure, stability and function of many proteins. The N-linked glycosylation machinery involves enzymes responsible for the assembly of the lipid-linked oligosaccharide (LLO), which is then transferred to the asparagine residues on the polypeptides by the enzyme oligosaccharyltransferase (OST). A major goal in the study of protein glycosylation is to establish quantitative methods for the analysis of site-specific extent of glycosylation. We developed a sensitive approach to examine glycosylation site occupancy in Saccharomyces cerevisiae by coupling stable isotope labeling (SILAC) approach to parallel reaction monitoring (PRM) mass spectrometry (MS). We combined the method with genetic tools and validated the approach with the identification of novel glycosylation sites dependent on the Ost3p and Ost6p regulatory subunits of OST. Based on the observations that alternations in LLO substrate structure and OST subunits activity differentially alter the systemic output of OST, we conclude that sequon recognition is a direct property of the catalytic subunit Stt3p, auxiliary subunits such as Ost3p and Ost6p extend the OST substrate range by modulating interfering pathways such as protein folding. In addition, our proteomics approach revealed a novel regulatory network that connects isoprenoid lipid biosynthesis and LLO substrate assembly.
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Affiliation(s)
- Kristina Poljak
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Nathalie Selevsek
- §Functional Genomics Center Zurich, UZH/ETH Zurich, CH-8057 Zurich, Switzerland
| | - Elsy Ngwa
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Jonas Grossmann
- §Functional Genomics Center Zurich, UZH/ETH Zurich, CH-8057 Zurich, Switzerland
| | - Marie Estelle Losfeld
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Markus Aebi
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland;
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26
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N-glycosylation Triggers a Dual Selection Pressure in Eukaryotic Secretory Proteins. Sci Rep 2017; 7:8788. [PMID: 28821844 PMCID: PMC5562741 DOI: 10.1038/s41598-017-09173-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/07/2017] [Indexed: 01/08/2023] Open
Abstract
Nearly one third of the eukaryotic proteome traverses the secretory pathway and most of these proteins are N-glycosylated in the lumen of the endoplasmic reticulum. N-glycans fulfill multiple structural and biological functions, and are crucial for productive folding of many glycoproteins. N-glycosylation involves the attachment of an oligosaccharide to selected asparagine residues in the sequence N-X-S/T (X ≠ P), a motif known as an N-glycosylation’sequon’. Mutations that create novel sequons can cause disease due to the destabilizing effect of a bulky N-glycan. Thus, an analogous process must have occurred during evolution, whenever ancestrally cytosolic proteins were recruited to the secretory pathway. Here, we show that during evolution N-glycosylation triggered a dual selection pressure on secretory pathway proteins: while sequons were positively selected in solvent exposed regions, they were almost completely eliminated from buried sites. This process is one of the sharpest evolutionary signatures of secretory pathway proteins, and was therefore critical for the evolution of an efficient secretory pathway.
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27
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Zatorska E, Gal L, Schmitt J, Bausewein D, Schuldiner M, Strahl S. Cellular Consequences of Diminished Protein O-Mannosyltransferase Activity in Baker's Yeast. Int J Mol Sci 2017; 18:ijms18061226. [PMID: 28598353 PMCID: PMC5486049 DOI: 10.3390/ijms18061226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023] Open
Abstract
O-Mannosylation is a type of protein glycosylation initiated in the endoplasmic reticulum (ER) by the protein O-mannosyltransferase (PMT) family. Despite the vital role of O-mannosylation, its molecular functions and regulation are not fully characterized. To further explore the cellular impact of protein O-mannosylation, we performed a genome-wide screen to identify Saccharomyces cerevisiae mutants with increased sensitivity towards the PMT-specific inhibitor compound R3A-5a. We identified the cell wall and the ER as the cell compartments affected most upon PMT inhibition. Especially mutants with defects in N-glycosylation, biosynthesis of glycosylphosphatidylinositol-anchored proteins and cell wall β-1,6-glucan showed impaired growth when O-mannosylation became limiting. Signaling pathways that counteract cell wall defects and unbalanced ER homeostasis, namely the cell wall integrity pathway and the unfolded protein response, were highly crucial for the cell growth. Moreover, among the most affected mutants, we identified Ost3, one of two homologous subunits of the oligosaccharyltransferase complexes involved in N-glycosylation, suggesting a functional link between the two pathways. Indeed, we identified Pmt2 as a substrate for Ost3 suggesting that the reduced function of Pmt2 in the absence of N-glycosylation promoted sensitivity to the drug. Interestingly, even though S. cerevisiae Pmt1 and Pmt2 proteins are highly similar on the sequence, as well as the structural level and act as a complex, we identified only Pmt2, but not Pmt1, as an Ost3-specific substrate protein.
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Affiliation(s)
- Ewa Zatorska
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| | - Jaro Schmitt
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Daniela Bausewein
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
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Quantification of N-glycosylation site occupancy status based on labeling/label-free strategies with LC-MS/MS. Talanta 2017; 170:509-513. [PMID: 28501204 DOI: 10.1016/j.talanta.2017.04.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 12/30/2022]
Abstract
Protein N-glycosylation plays important roles in physiological and pathological processes. Characterizing the site-specific N-glycosylation including N-glycan macroheterogeneity (glycosylation site occupancy) and microheterogeneity (site-specific glycan structure) is important for understanding of glycoprotein biosynthesis and function. N-Glycan macroheterogeneity is a physiological property of glycoprotein and the technical obstacles have restricted research into the regulation and functions of this heterogeneity. Quantification of N-glycosylation site occupancy would uncover the critical role of macroheterogeneity in a variety of biological properties. Liquid chromatography (LC)- mass spectrometry (MS)-based quantification is emerging as a powerful tool for glycosylation characterization. This review summarizes the labeling and label-free quantitative MS approaches for quantifying N-glycosylation site occupancy, including its quantification for target glycoproteins in recent years.
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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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30
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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: 67] [Impact Index Per Article: 8.4] [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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31
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Cherepanova N, Shrimal S, Gilmore R. N-linked glycosylation and homeostasis of the endoplasmic reticulum. Curr Opin Cell Biol 2016; 41:57-65. [PMID: 27085638 DOI: 10.1016/j.ceb.2016.03.021] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/24/2016] [Accepted: 03/30/2016] [Indexed: 01/17/2023]
Abstract
As a major site of protein biosynthesis, homeostasis of the endoplasmic reticulum is critical for cell viability. Asparagine linked glycosylation of newly synthesized proteins by the oligosaccharyltransferase plays a central role in ER homeostasis due to the use of protein-linked oligosaccharides as recognition and timing markers for glycoprotein quality control pathways that discriminate between correctly folded proteins and terminally malfolded proteins destined for ER associated degradation. Recent findings indicate how the oligosaccharyltransferase achieves efficient and accurate glycosylation of the diverse proteins that enter the endoplasmic reticulum. In metazoan organisms two distinct OST complexes cooperate to maximize the glycosylation of nascent proteins. The STT3B complex glycosylates acceptor sites that have been skipped by the translocation channel associated STT3A complex.
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Affiliation(s)
- Natalia Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States
| | - Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States.
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32
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Piirainen MA, Boer H, de Ruijter JC, Frey AD. A dual approach for improving homogeneity of a human-type N-glycan structure in Saccharomyces cerevisiae. Glycoconj J 2016; 33:189-99. [PMID: 26983412 DOI: 10.1007/s10719-016-9656-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 01/26/2016] [Accepted: 02/04/2016] [Indexed: 11/30/2022]
Abstract
N-glycosylation is an important feature of therapeutic and other industrially relevant proteins, and engineering of the N-glycosylation pathway provides opportunities for developing alternative, non-mammalian glycoprotein expression systems. Among yeasts, Saccharomyces cerevisiae is the most established host organism used in therapeutic protein production and therefore an interesting host for glycoengineering. In this work, we present further improvements in the humanization of the N-glycans in a recently developed S. cerevisiae strain. In this strain, a tailored trimannosyl lipid-linked oligosaccharide is formed and transferred to the protein, followed by complex-type glycan formation by Golgi apparatus-targeted human N-acetylglucosamine transferases. We improved the glycan pattern of the glycoengineered strain both in terms of glycoform homogeneity and the efficiency of complex-type glycosylation. Most of the interfering structures present in the glycoengineered strain were eliminated by deletion of the MNN1 gene. The relative abundance of the complex-type target glycan was increased by the expression of a UDP-N-acetylglucosamine transporter from Kluyveromyces lactis, indicating that the import of UDP-N-acetylglucosamine into the Golgi apparatus is a limiting factor for efficient complex-type N-glycosylation in S. cerevisiae. By a combination of the MNN1 deletion and the expression of a UDP-N-acetylglucosamine transporter, a strain forming complex-type glycans with a significantly improved homogeneity was obtained. Our results represent a further step towards obtaining humanized glycoproteins with a high homogeneity in S. cerevisiae.
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Affiliation(s)
- Mari A Piirainen
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Harry Boer
- VTT Technical research centre of Finland, Espoo, Finland
| | - Jorg C de Ruijter
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Alexander D Frey
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
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33
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A subunit of the oligosaccharyltransferase complex is required for interspecific gametophyte recognition in Arabidopsis. Nat Commun 2016; 7:10826. [PMID: 26964640 PMCID: PMC4792959 DOI: 10.1038/ncomms10826] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/21/2016] [Indexed: 12/11/2022] Open
Abstract
Species-specific gamete recognition is a key premise to ensure reproductive success and the maintenance of species boundaries. During plant pollen tube (PT) reception, gametophyte interactions likely allow the species-specific recognition of signals from the PT (male gametophyte) by the embryo sac (female gametophyte), resulting in PT rupture, sperm release, and double fertilization. This process is impaired in interspecific crosses between Arabidopsis thaliana and related species, leading to PT overgrowth and a failure to deliver the sperm cells. Here we show that ARTUMES (ARU) specifically regulates the recognition of interspecific PTs in A. thaliana. ARU, identified in a genome-wide association study (GWAS), exclusively influences interspecific--but not intraspecific--gametophyte interactions. ARU encodes the OST3/6 subunit of the oligosaccharyltransferase complex conferring protein N-glycosylation. Our results suggest that glycosylation patterns of cell surface proteins may represent an important mechanism of gametophyte recognition and thus speciation.
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Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen ISB, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S. Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae. Mol Cell Proteomics 2016; 15:1323-37. [PMID: 26764011 PMCID: PMC4824858 DOI: 10.1074/mcp.m115.057505] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 11/17/2022] Open
Abstract
O-Mannosylation is a vital protein modification conserved from fungi to humans. Yeast is a perfect model to study this post-translational modification, because in contrast to mammals O-mannosylation is the only type of O-glycosylation. In an essential step toward the full understanding of protein O-mannosylation we mapped the O-mannose glycoproteome in baker's yeast. Taking advantage of an O-glycan elongation deficient yeast strain to simplify sample complexity, we identified over 500 O-glycoproteins from all subcellular compartments for which over 2300 O-mannosylation sites were mapped by electron-transfer dissociation (ETD)-based MS/MS. In this study, we focus on the 293 O-glycoproteins (over 1900 glycosylation sites identified by ETD-MS/MS) that enter the secretory pathway and are targets of ER-localized protein O-mannosyltransferases. We find that O-mannosylation is not only a prominent modification of cell wall and plasma membrane proteins, but also of a large number of proteins from the secretory pathway with crucial functions in protein glycosylation, folding, quality control, and trafficking. The analysis of glycosylation sites revealed that O-mannosylation is favored in unstructured regions and β-strands. Furthermore, O-mannosylation is impeded in the proximity of N-glycosylation sites suggesting the interplay of these types of post-translational modifications. The detailed knowledge of the target proteins and their O-mannosylation sites opens for discovery of new roles of this essential modification in eukaryotes, and for a first glance on the evolution of different types of O-glycosylation from yeast to mammals.
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Affiliation(s)
- Patrick Neubert
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - 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
| | - Martin Zauser
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Andreas Essig
- ¶Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Hiren J Joshi
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Ewa Zatorska
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Ida Signe Bohse Larsen
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Martin Loibl
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Joan Castells-Ballester
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Markus Aebi
- ¶Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Henrik Clausen
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sabine Strahl
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany;
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35
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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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36
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Volkers G, Worrall LJ, Kwan DH, Yu CC, Baumann L, Lameignere E, Wasney GA, Scott NE, Wakarchuk W, Foster LJ, Withers SG, Strynadka NCJ. Structure of human ST8SiaIII sialyltransferase provides insight into cell-surface polysialylation. Nat Struct Mol Biol 2015; 22:627-35. [DOI: 10.1038/nsmb.3060] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 06/19/2015] [Indexed: 11/09/2022]
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37
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Harada Y, Hirayama H, Suzuki T. Generation and degradation of free asparagine-linked glycans. Cell Mol Life Sci 2015; 72:2509-33. [PMID: 25772500 PMCID: PMC11113800 DOI: 10.1007/s00018-015-1881-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/19/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
Asparagine (N)-linked protein glycosylation, which takes place in the eukaryotic endoplasmic reticulum (ER), is important for protein folding, quality control and the intracellular trafficking of secretory and membrane proteins. It is known that, during N-glycosylation, considerable amounts of lipid-linked oligosaccharides (LLOs), the glycan donor substrates for N-glycosylation, are hydrolyzed to form free N-glycans (FNGs) by unidentified mechanisms. FNGs are also generated in the cytosol by the enzymatic deglycosylation of misfolded glycoproteins during ER-associated degradation. FNGs derived from LLOs and misfolded glycoproteins are eventually merged into one pool in the cytosol and the various glycan structures are processed to a near homogenous glycoform. This article summarizes the current state of our knowledge concerning the formation and catabolism of FNGs.
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Affiliation(s)
- Yoichiro Harada
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Hiroto Hirayama
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Tadashi Suzuki
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
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38
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Xu Y, Bailey UM, Schulz BL. Automated measurement of site-specific N
-glycosylation occupancy with SWATH-MS. Proteomics 2015; 15:2177-86. [DOI: 10.1002/pmic.201400465] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/08/2015] [Accepted: 02/27/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Ying Xu
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Ulla-Maja Bailey
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
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39
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Evolutionary Engineering Improves Tolerance for Replacement Jet Fuels in Saccharomyces cerevisiae. Appl Environ Microbiol 2015; 81:3316-25. [PMID: 25746998 DOI: 10.1128/aem.04144-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/26/2015] [Indexed: 12/23/2022] Open
Abstract
Monoterpenes are liquid hydrocarbons with applications ranging from flavor and fragrance to replacement jet fuel. Their toxicity, however, presents a major challenge for microbial synthesis. Here we evolved limonene-tolerant Saccharomyces cerevisiae strains and sequenced six strains across the 200-generation evolutionary time course. Mutations were found in the tricalbin proteins Tcb2p and Tcb3p. Genomic reconstruction in the parent strain showed that truncation of a single protein (tTcb3p(1-989)), but not its complete deletion, was sufficient to recover the evolved phenotype improving limonene fitness 9-fold. tTcb3p(1-989) increased tolerance toward two other monoterpenes (β-pinene and myrcene) 11- and 8-fold, respectively, and tolerance toward the biojet fuel blend AMJ-700t (10% cymene, 50% limonene, 40% farnesene) 4-fold. tTcb3p(1-989) is the first example of successful engineering of phase tolerance and creates opportunities for production of the highly toxic C10 alkenes in yeast.
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40
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Frey AD, Aebi M. An enzyme-based screening system for the rapid assessment of protein N-glycosylation efficiency in yeast. Glycobiology 2014; 25:252-7. [DOI: 10.1093/glycob/cwu134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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41
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Shrimal S, Cherepanova NA, Gilmore R. Cotranslational and posttranslocational N-glycosylation of proteins in the endoplasmic reticulum. Semin Cell Dev Biol 2014; 41:71-8. [PMID: 25460543 DOI: 10.1016/j.semcdb.2014.11.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022]
Abstract
Asparagine linked glycosylation of proteins is an essential protein modification reaction in most eukaryotic organisms. N-linked oligosaccharides are important for protein folding and stability, biosynthetic quality control, intracellular traffic and the physiological function of many N-glycosylated proteins. In metazoan organisms, the oligosaccharyltransferase is composed of a catalytic subunit (STT3A or STT3B) and a set of accessory subunits. Duplication of the catalytic subunit gene allowed cells to evolve OST complexes that act sequentially to maximize the glycosylation efficiency of the large number of proteins that are glycosylated in metazoan organisms. We will summarize recent progress in understanding the mechanism of (a) cotranslational glycosylation by the translocation channel associated STT3A complex, (b) the role of the STT3B complex in mediating cotranslational or posttranslocational glycosylation of acceptor sites that have been skipped by the STT3A complex, and (c) the role of the oxidoreductase MagT1 in STT3B-dependent glycosylation of cysteine-proximal acceptor sites.
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Affiliation(s)
- Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States
| | - Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States.
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42
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Jamaluddin MFB, Bailey UM, Schulz BL. Oligosaccharyltransferase subunits bind polypeptide substrate to locally enhance N-glycosylation. Mol Cell Proteomics 2014; 13:3286-93. [PMID: 25118247 DOI: 10.1074/mcp.m114.041178] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Oligosaccharyltransferase is a multiprotein complex that catalyzes asparagine-linked glycosylation of diverse proteins. Using yeast genetics and glycoproteomics, we found that transient interactions between nascent polypeptide and Ost3p/Ost6p, homologous subunits of oligosaccharyltransferase, were able to modulate glycosylation efficiency in a site-specific manner in vivo. These interactions were driven by hydrophobic and electrostatic complementarity between amino acids in the peptide-binding groove of Ost3p/Ost6p and the sequestered stretch of substrate polypeptide. Based on this dependence, we used in vivo scanning mutagenesis and in vitro biochemistry to map the precise interactions that affect site-specific glycosylation efficiency. We conclude that transient binding of substrate polypeptide by Ost3p/Ost6p increases glycosylation efficiency at asparagines proximal and C-terminal to sequestered sequences. We detail a novel mode of interaction between translocating nascent polypeptide and oligosaccharyltransferase in which binding to Ost3p/Ost6p segregates a short flexible loop of glycosylation-competent polypeptide substrate that is delivered to the oligosaccharyltransferase active site for efficient modification.
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Affiliation(s)
- M Fairuz B Jamaluddin
- From the ‡School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ulla-Maja Bailey
- From the ‡School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin L Schulz
- From the ‡School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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43
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Meyer BH, Albers SV. AglB, catalyzing the oligosaccharyl transferase step of the archaeal N-glycosylation process, is essential in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. Microbiologyopen 2014; 3:531-43. [PMID: 24916761 PMCID: PMC4287180 DOI: 10.1002/mbo3.185] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/01/2014] [Accepted: 05/15/2014] [Indexed: 11/10/2022] Open
Abstract
Sulfolobus acidocaldarius, a thermo-acidophilic crenarchaeon which grows optimally at 76°C and pH 3, exhibits an astonishing high number of N-glycans linked to the surface (S-) layer proteins. The S-layer proteins as well as other surface-exposed proteins are modified via N-glycosylation, in which the oligosaccharyl transferase AglB catalyzes the final step of the transfer of the glycan tree to the nascent protein. In this study, we demonstrated that AglB is essential for the viability of S. acidocaldarius. Different deletion approaches, that is, markerless in-frame deletion as well as a marker insertion were unsuccessful to create an aglB deletion mutant. Only the integration of a second aglB gene copy allowed the successful deletion of the original aglB.
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Affiliation(s)
| | - Sonja-Verena Albers
- Correspondence S. V. Albers, Molecular Biology of Archaea, Max-Planck Institute for terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg. Tel: +496421178426;, Fax: +496421178429;, E-mail:
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44
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Structural basis of substrate specificity of human oligosaccharyl transferase subunit N33/Tusc3 and its role in regulating protein N-glycosylation. Structure 2014; 22:590-601. [PMID: 24685145 DOI: 10.1016/j.str.2014.02.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 02/13/2014] [Accepted: 02/16/2014] [Indexed: 01/04/2023]
Abstract
N-linked glycosylation of proteins in the endoplasmic reticulum (ER) is essential in eukaryotes and catalyzed by oligosaccharyl transferase (OST). Human OST is a hetero-oligomer of seven subunits. The subunit N33/Tusc3 is a tumor suppressor candidate, and defects in the subunit N33/Tusc3 are linked with nonsyndromic mental retardation. Here, we show that N33/Tusc3 possesses a membrane-anchored N-terminal thioredoxin domain located in the ER lumen that may form transient mixed disulfide complexes with OST substrates. X-ray structures of complexes between N33/Tusc3 and two different peptides as model substrates reveal a defined peptide-binding groove adjacent to the active site that can accommodate peptides in opposite orientations. Structural and biochemical data show that N33/Tusc3 prefers peptides bearing a hydrophobic residue two residues away from the cysteine forming the mixed disulfide with N33/Tusc3. Our results support a model in which N33/Tusc3 increases glycosylation efficiency for a subset of human glycoproteins by slowing glycoprotein folding.
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45
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Xu Y, Bailey UM, Punyadeera C, Schulz BL. Identification of salivary N-glycoproteins and measurement of glycosylation site occupancy by boronate glycoprotein enrichment and liquid chromatography/electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:471-482. [PMID: 24497285 DOI: 10.1002/rcm.6806] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE Diseases including cancer and congenital disorders of glycosylation have been associated with changes in the site-specific extent of protein glycosylation. Saliva can be non-invasively sampled and is rich in glycoproteins, giving it the potential to be a useful biofluid for the discovery and detection of disease biomarkers associated with changes in glycosylation. METHODS Saliva was collected from healthy individuals and glycoproteins were enriched using phenylboronic acid based glycoprotein enrichment resin. Proteins were deglycosylated with peptide-N-glycosidase F and digested with AspN or trypsin. Desalted peptides and deglycosylated peptides were separated by reversed-phase liquid chromatography and detected with on-line electrospray ionization quadrupole-time-of-flight mass spectrometry using a 5600 TripleTof instrument. Site-specific glycosylation occupancy was semi-quantitatively determined from the abundance of deglycosylated and nonglycosylated versions of each given peptide. RESULTS Glycoprotein enrichment identified 67 independent glycosylation sites from 24 unique proteins, a 3.9-fold increase in the number of glycosylation sites identified. Enrichment of glycoproteins rather than glycopeptides allowed detection of both deglycosylated and nonglycosylated versions of each peptide, and thereby robust measurement of site-specific occupancy at 21 asparagines. Healthy individuals showed limited biological variability in occupancy, with partially modified sites having characteristics consistent with inefficient glycosylation by oligosaccharyltransferase. Inclusion of negative controls without enzymatic deglycosylation controlled for spontaneous chemical deamidation, and identified asparagines previously incorrectly annotated as glycosylated. CONCLUSIONS We developed a sample preparation and mass spectrometry detection strategy for rapid and efficient measurement of site-specific glycosylation occupancy on diverse salivary glycoproteins suitable for biomarker discovery and detection of changes in glycosylation occupancy in human disease.
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Affiliation(s)
- Ying Xu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
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Loibl M, Wunderle L, Hutzler J, Schulz BL, Aebi M, Strahl S. Protein O-mannosyltransferases associate with the translocon to modify translocating polypeptide chains. J Biol Chem 2014; 289:8599-611. [PMID: 24519942 DOI: 10.1074/jbc.m113.543116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
O-Mannosylation and N-glycosylation are essential protein modifications that are initiated in the endoplasmic reticulum (ER). Protein translocation across the ER membrane and N-glycosylation are highly coordinated processes that take place at the translocon-oligosaccharyltransferase (OST) complex. In analogy, it was assumed that protein O-mannosyltransferases (PMTs) also act at the translocon, however, in recent years it turned out that prolonged ER residence allows O-mannosylation of un-/misfolded proteins or slow folding intermediates by Pmt1-Pmt2 complexes. Here, we reinvestigate protein O-mannosylation in the context of protein translocation. We demonstrate the association of Pmt1-Pmt2 with the OST, the trimeric Sec61, and the tetrameric Sec63 complex in vivo by co-immunoprecipitation. The coordinated interplay between PMTs and OST in vivo is further shown by a comprehensive mass spectrometry-based analysis of N-glycosylation site occupancy in pmtΔ mutants. In addition, we established a microsomal translation/translocation/O-mannosylation system. Using the serine/threonine-rich cell wall protein Ccw5 as a model, we show that PMTs efficiently mannosylate proteins during their translocation into microsomes. This in vitro system will help to unravel mechanistic differences between co- and post-translocational O-mannosylation.
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Affiliation(s)
- Martin Loibl
- From the Centre for Organismal Studies (COS), Cell Chemistry, Heidelberg University, 69120 Heidelberg, Germany and
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Tan NY, Bailey UM, Jamaluddin MF, Mahmud SHB, Raman SC, Schulz BL. Sequence-based protein stabilization in the absence of glycosylation. Nat Commun 2014; 5:3099. [DOI: 10.1038/ncomms4099] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 12/12/2013] [Indexed: 12/12/2022] Open
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Lattová E, Perreault H. The usefulness of hydrazine derivatives for mass spectrometric analysis of carbohydrates. MASS SPECTROMETRY REVIEWS 2013; 32:366-385. [PMID: 23345114 DOI: 10.1002/mas.21367] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 10/12/2012] [Accepted: 10/12/2012] [Indexed: 06/01/2023]
Abstract
Over the last years, extensive studies have evaluated glycans from different biological samples and validated the importance of glycosylation as one of the most important post-translational modifications of proteins. Although a number of new methods for carbohydrate analysis have been published and there has been significant progress in their identification, the development of new approaches to study these biomolecules and understand their role in living systems are still vivid challenges that intrigue glycobiologists. In the last decade, the success in analyses of oligosaccharides has been driven mainly by the development of innovative, highly sensitive mass spectrometry techniques. For enhanced mass spectrometry detection, carbohydrate molecules are often derivatized. Besides, the type of labeling can influence the fragmentation pattern and make the structural analysis less complicated. In this regard, in 2003 we introduced the low scale, simple non-reductive tagging of glycans employing phenylhydrazine (PHN) as the derivatizing reagent. PHN-labeled glycans showed increased detection and as reported previously they can be analyzed by HPLC, ESI, or MALDI immediately after derivatization. Under tandem mass spectrometry conditions, PHN-derivatives produced useful data for the structural elucidation of oligosaccharides. This approach of analysis has helped to reveal new isomeric structures for glycans of known/unknown composition and has been successfully applied for the profiling of N-glycans obtained from serum samples and cancer cells. The efficacy of this labeling has also been evaluated for different substituted hydrazine reagents. This review summarizes all types of reducing-end labeling based on hydrazone-linkage that have been used for mass spectrometric analyses of oligosaccharides. This review is also aimed at correcting some past misconceptions or interpretations reported in the literature.
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Affiliation(s)
- Erika Lattová
- Chemistry Department, University of Manitoba, 144 Dysart Road, Winnipeg, MB, Canada R3T 2N2.
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Breitling J, Aebi M. N-linked protein glycosylation in the endoplasmic reticulum. Cold Spring Harb Perspect Biol 2013; 5:a013359. [PMID: 23751184 DOI: 10.1101/cshperspect.a013359] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The attachment of glycans to asparagine residues of proteins is an abundant and highly conserved essential modification in eukaryotes. The N-glycosylation process includes two principal phases: the assembly of a lipid-linked oligosaccharide (LLO) and the transfer of the oligosaccharide to selected asparagine residues of polypeptide chains. Biosynthesis of the LLO takes place at both sides of the endoplasmic reticulum (ER) membrane and it involves a series of specific glycosyltransferases that catalyze the assembly of the branched oligosaccharide in a highly defined way. Oligosaccharyltransferase (OST) selects the Asn-X-Ser/Thr consensus sequence on polypeptide chains and generates the N-glycosidic linkage between the side-chain amide of asparagine and the oligosaccharide. This ER-localized pathway results in a systemic modification of the proteome, the basis for the Golgi-catalyzed modification of the N-linked glycans, generating the large diversity of N-glycoproteome in eukaryotic cells. This article focuses on the processes in the ER. Based on the highly conserved nature of this pathway we concentrate on the mechanisms in the eukaryotic model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Jörg Breitling
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
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Schulz BL, Jen FEC, Power PM, Jones CE, Fox KL, Ku SC, Blanchfield JT, Jennings MP. Identification of bacterial protein O-oligosaccharyltransferases and their glycoprotein substrates. PLoS One 2013; 8:e62768. [PMID: 23658772 PMCID: PMC3643930 DOI: 10.1371/journal.pone.0062768] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 03/25/2013] [Indexed: 12/16/2022] Open
Abstract
O-glycosylation of proteins in Neisseria meningitidis is catalyzed by PglL, which belongs to a protein family including WaaL O-antigen ligases. We developed two hidden Markov models that identify 31 novel candidate PglL homologs in diverse bacterial species, and describe several conserved sequence and structural features. Most of these genes are adjacent to possible novel target proteins for glycosylation. We show that in the general glycosylation system of N. meningitidis, efficient glycosylation of additional protein substrates requires local structural similarity to the pilin acceptor site. For some Neisserial PglL substrates identified by sensitive analytical approaches, only a small fraction of the total protein pool is modified in the native organism, whereas others are completely glycosylated. Our results show that bacterial protein O-glycosylation is common, and that substrate selection in the general Neisserial system is dominated by recognition of structural homology.
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Affiliation(s)
- Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Freda E. C. Jen
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Peter M. Power
- Department of Paediatrics, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Christopher E. Jones
- School of Science and Health, The University of Western Sydney, Penrith, New South Wales, Australia
| | - Kate L. Fox
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Shan C. Ku
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Joanne T. Blanchfield
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
- * E-mail:
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