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Mesdaghi S, Price R, Li M, Migrino RQ, Madine J, Rigden DJ. Investigating Medin Cleavage Accessibility in MfgE8: Conformational Insights Derived from Molecular Dynamics Simulations and AlphaFold2 Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.27.605412. [PMID: 39131300 PMCID: PMC11312466 DOI: 10.1101/2024.07.27.605412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Recent studies have indicated that the human amyloidogenic protein medin is associated with a range of vascular diseases, including aortic aneurysms, vascular dementia, and Alzheimer's disease. Medin accumulates in the vasculature with age, leading to endothelial dysfunction through oxidative and nitrative stress and inducing pro-inflammatory activation. Medin is a cleavage product from the C2 domain of MfgE8. The exact mechanism of medin production from MfgE8 is unknown, with crystal structures of homologous C2 domains suggesting that the cleavage sites are buried, requiring a conformational transition for medin production. Molecular dynamics simulations can explore a wide range of conformations, from small-scale bond rotations to large-scale changes like protein folding or ligand binding. This study employed a combination of full-atom and coarse-grained molecular dynamics simulations, along with CONCOORD- and AlphaFold2-generated models, to investigate MfgE8 conformations and their implications for medin cleavage site accessibility. The simulations revealed that MfgE8 tends to adopt a compact conformation with the RGD motif, important for cell attachment within the N-terminal domain, and the medin region in the C-terminal domain close in proximity. Formation of this compact structure is facilitated by interdomain electrostatic interactions that promote stability and in turn decrease the solvent-accessible surface area of the medin region and particularly the C-terminal medin cleavage site. This data enhances current knowledge on medin generation to propose that alterations in local environmental conditions, possibly through changes in glycosylation or other post-translational modifications are required to induce MfgE8 to unfold partially or fully: this would result in enhanced accessibility of the cleavage sites and therefore enable medin generation.
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Affiliation(s)
- Shahram Mesdaghi
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Rebecca Price
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Ming Li
- Phoenix Veterans Affairs, Phoenix, Arizona, USA
- University of Arizona College of Medicine-Phoenix, Arizona, USA
| | - Raymond Q Migrino
- Phoenix Veterans Affairs, Phoenix, Arizona, USA
- University of Arizona College of Medicine-Phoenix, Arizona, USA
| | - Jillian Madine
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Daniel J Rigden
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
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2
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Gazi I, Reiding KR, Groeneveld A, Bastiaans J, Huppertz T, Heck AJR. LacdiNAc to LacNAc: remodelling of bovine α-lactalbumin N-glycosylation during the transition from colostrum to mature milk. Glycobiology 2024; 34:cwae062. [PMID: 39115362 PMCID: PMC11319639 DOI: 10.1093/glycob/cwae062] [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: 03/05/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
α -Lactalbumin, an abundant protein present in the milk of most mammals, is associated with biological, nutritional and technological functionality. Its sequence presents N-glycosylation motifs, the occupancy of which is species-specific, ranging from no to full occupancy. Here, we investigated the N-glycosylation of bovine α-lactalbumin in colostrum and milk sampled from four individual cows, each at 9 time points starting from the day of calving up to 28.0 d post-partum. Using a glycopeptide-centric mass spectrometry-based glycoproteomics approach, we identified N-glycosylation at both Asn residues found in the canonical Asn-Xxx-Ser/Thr motif, i.e. Asn45 and Asn74 of the secreted protein. We found similar glycan profiles in all four cows, with partial site occupancies, averaging at 35% and 4% for Asn45 and Asn74, respectively. No substantial changes in occupancy occurred over lactation at either site. Fucosylation, sialylation, primarily with N-acetylneuraminic acid (Neu5Ac), and a high ratio of N,N'-diacetyllactosamine (LacdiNAc)/N-acetyllactosamine (LacNAc) motifs were characteristic features of the identified N-glycans. While no substantial changes occurred in site occupancy at either site during lactation, the glycoproteoform (i.e. glycosylated form of the protein) profile revealed dynamic changes; the maturation of the α-lactalbumin glycoproteoform repertoire from colostrum to mature milk was marked by substantial increases in neutral glycans and the number of LacNAc motifs per glycan, at the expense of LacdiNAc motifs. While the implications of α-lactalbumin N-glycosylation on functionality are still unclear, we speculate that N-glycosylation at Asn74 results in a structurally and functionally different protein, due to competition with the formation of its two intra-molecular disulphide bridges.
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Affiliation(s)
- Inge Gazi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - André Groeneveld
- Research and Development, FrieslandCampina, Stationsplein 4, Amersfoort 3818 LE, The Netherlands
| | - Jan Bastiaans
- Research and Development, FrieslandCampina, Stationsplein 4, Amersfoort 3818 LE, The Netherlands
| | - Thom Huppertz
- Research and Development, FrieslandCampina, Stationsplein 4, Amersfoort 3818 LE, The Netherlands
- Department of Agrotechnology and Food Sciences, Wageningen University, Bornse Weilanden 9, Wageningen 6708 WG, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
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Adolf-Bryfogle J, Labonte JW, Kraft JC, Shapovalov M, Raemisch S, Lütteke T, DiMaio F, Bahl CD, Pallesen J, King NP, Gray JJ, Kulp DW, Schief WR. Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design. PLoS Comput Biol 2024; 20:e1011895. [PMID: 38913746 PMCID: PMC11288642 DOI: 10.1371/journal.pcbi.1011895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/30/2024] [Accepted: 02/06/2024] [Indexed: 06/26/2024] Open
Abstract
Carbohydrates and glycoproteins modulate key biological functions. However, experimental structure determination of sugar polymers is notoriously difficult. Computational approaches can aid in carbohydrate structure prediction, structure determination, and design. In this work, we developed a glycan-modeling algorithm, GlycanTreeModeler, that computationally builds glycans layer-by-layer, using adaptive kernel density estimates (KDE) of common glycan conformations derived from data in the Protein Data Bank (PDB) and from quantum mechanics (QM) calculations. GlycanTreeModeler was benchmarked on a test set of glycan structures of varying lengths, or "trees". Structures predicted by GlycanTreeModeler agreed with native structures at high accuracy for both de novo modeling and experimental density-guided building. We employed these tools to design de novo glycan trees into a protein nanoparticle vaccine to shield regions of the scaffold from antibody recognition, and experimentally verified shielding. This work will inform glycoprotein model prediction, glycan masking, and further aid computational methods in experimental structure determination and refinement.
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Affiliation(s)
- Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, United States of America
- Institute for Protein Innovation, Boston, Massachusetts, United States of America
- Division of Hematology-Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jason W. Labonte
- Department of Chemistry & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - John C. Kraft
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Maxim Shapovalov
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Sebastian Raemisch
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, United States of America
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Christopher D. Bahl
- Institute for Protein Innovation, Boston, Massachusetts, United States of America
- Division of Hematology-Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jesper Pallesen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Jeffrey J. Gray
- Department of Chemistry & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Daniel W. Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - William R. Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, United States of America
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Hiono T, Sakaue H, Tomioka A, Kaji H, Sasaki M, Orba Y, Sawa H, Kuno A. Combinatorial Approach with Mass Spectrometry and Lectin Microarray Dissected Site-Specific Glycostem and Glycoleaf Features of the Virion-Derived Spike Protein of Ancestral and γ Variant SARS-CoV-2 Strains. J Proteome Res 2024; 23:1408-1419. [PMID: 38536229 DOI: 10.1021/acs.jproteome.3c00874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
The coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has impacted public health globally. As the glycosylation of viral envelope glycoproteins is strongly associated with their immunogenicity, intensive studies have been conducted on the glycans of the glycoprotein of SARS-CoV-2, the spike (S) protein. Here, we conducted intensive glycoproteomic analyses of the SARS-CoV-2 S protein of ancestral and γ-variant strains using a combinatorial approach with two different technologies: mass spectrometry (MS) and lectin microarrays (LMA). Our unique MS1-based glycoproteomic technique, Glyco-RIDGE, in addition to MS2-based Byonic search, identified 1448 (ancestral strain) and 1785 (γ-variant strain) site-specific glycan compositions, respectively. Asparagine at amino acid position 20 (N20) is mainly glycosylated within two successive potential glycosylation sites, N17 and N20, of the γ-variant S protein; however, we found low-frequency glycosylation at N17. Our novel approaches, glycostem mapping and glycoleaf scoring, also illustrate the moderately branched/extended, highly fucosylated, and less sialylated natures of the glycoforms of S proteins. Subsequent LMA analysis emphasized the intensive end-capping of glycans by Lewis fucoses, which complemented the glycoproteomic features. These results illustrate the high-resolution glycoproteomic features of the SARS-CoV-2 S protein, contributing to vaccine design and understanding of viral protein synthesis.
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Affiliation(s)
- Takahiro Hiono
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Hiroaki Sakaue
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Azusa Tomioka
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Hiroyuki Kaji
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Michihito Sasaki
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Yasuko Orba
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Hirofumi Sawa
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
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5
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Rao RSP, Ahsan N, Xu C, Su L, Verburgt J, Fornelli L, Kihara D, Xu D. Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein. Evol Bioinform Online 2021; 17:11769343211064616. [PMID: 34898980 PMCID: PMC8655444 DOI: 10.1177/11769343211064616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/12/2021] [Indexed: 01/28/2023] Open
Abstract
SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 5.0 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants have emerged in SARS-CoV-2, posing a serious challenge to the global vaccination effort and COVID-19 management. The evolutionary dynamics of this virus are only beginning to be explored. In this work, we have analysed 1.79 million spike glycoprotein sequences of SARS-CoV-2 and found that the virus is fine-tuning the spike with numerous amino acid insertions and deletions (indels). Indels seem to have a selective advantage as the proportions of sequences with indels steadily increased over time, currently at over 89%, with similar trends across countries/variants. There were as many as 420 unique indel positions and 447 unique combinations of indels. Despite their high frequency, indels resulted in only minimal alteration of N-glycosylation sites, including both gain and loss. As indels and point mutations are positively correlated and sequences with indels have significantly more point mutations, they have implications in the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein.
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Affiliation(s)
- R Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangaluru, Karnataka, India
| | - Nagib Ahsan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, USA
| | - Chunhui Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Lingtao Su
- Department of Electrical Engineering and Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Luca Fornelli
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
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Turnšek J, Brunson JK, Viedma MDPM, Deerinck TJ, Horák A, Oborník M, Bielinski VA, Allen AE. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 2021; 10:e52770. [PMID: 33591270 PMCID: PMC7972479 DOI: 10.7554/elife.52770] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
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Affiliation(s)
- Jernej Turnšek
- Biological and Biomedical Sciences, The Graduate School of Arts and Sciences, Harvard UniversityCambridgeUnited States
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Wyss Institute for Biologically Inspired Engineering, Harvard UniversityBostonUnited States
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Center for Research in Biological Systems, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
| | - John K Brunson
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California San DiegoLa JollaUnited States
| | - Aleš Horák
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Miroslav Oborník
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy, J. Craig Venter InstituteLa JollaUnited States
| | - Andrew Ellis Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
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Lim B, Kydd L, Jaworski J. Engineering a reporter cell line to mimic the high oligomannose presenting surface immunoglobulin of follicular lymphoma B cells. Sci Rep 2021; 11:87. [PMID: 33420165 PMCID: PMC7794505 DOI: 10.1038/s41598-020-79862-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/10/2020] [Indexed: 11/28/2022] Open
Abstract
Subtypes of B cell non-Hodgkin’s lymphomas, including follicular lymphomas, have shown a unique high oligomannose presentation on their immunoglobulins that will interact with natural receptors of the innate immunity, reportedly causing stimulation and proliferation. From deep sequencing of the variable heavy and light chain sequences of follicular lymphoma involved tissue sections, we identified the consensus variable sequences possessing glycosylation sites at the complementarity determining region. Using this information, we developed a cell line, referred to here as BZ, which displays the consensus variable segments as part of a surface antibody (IgM) and confirmed its presentation of high oligomannose on the heavy chain both in vitro and in vivo. An mCherry expressing variant provided a reporter cell line displaying the high oligomannose surface biomarker while affording clear fluorescent signals for FACS screening as well as for fluorescent in vivo imaging of ectopic xenograft tumors. In developing this reporter cell line that displays the biomarker glycan of follicular lymphoma, we provide a tool that may be used for future screening and validation of receptive moieties for selectively binding high oligomannose for development of targeted diagnostics or therapeutics to such B cell malignancies that display this unique glycan.
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Affiliation(s)
- Butaek Lim
- Department of Bioengineering, University of Texas at Arlington, 500 UTA Blvd., Arlington, TX, 76019, USA
| | - LeNaiya Kydd
- Department of Bioengineering, University of Texas at Arlington, 500 UTA Blvd., Arlington, TX, 76019, USA
| | - Justyn Jaworski
- Department of Bioengineering, University of Texas at Arlington, 500 UTA Blvd., Arlington, TX, 76019, USA.
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8
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Nguyen TTD, Le NQK, Tran TA, Pham DM, Ou YY. Incorporating a transfer learning technique with amino acid embeddings to efficiently predict N-linked glycosylation sites in ion channels. Comput Biol Med 2021; 130:104212. [PMID: 33454535 DOI: 10.1016/j.compbiomed.2021.104212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 11/27/2022]
Abstract
Glycosylation is a dynamic enzymatic process that attaches glycan to proteins or other organic molecules such as lipoproteins. Research has shown that such a process in ion channel proteins plays a fundamental role in modulating ion channel functions. This study used a computational method to predict N-linked glycosylation sites, the most common type, in ion channel proteins. From segments of ion channel proteins centered around N-linked glycosylation sites, the amino acid embedding vectors of each residue were concatenated to create features for prediction. We experimented with two different models for converting amino acids to their corresponding embeddings: one was fed with ion channel sequences and the other with a large dataset composed of more than one million protein sequences. The latter model stemmed from the idea of transfer learning technique and emerged as a more efficient feature extractor. Our best model was obtained from this transfer learning approach and a hyperparameter tuning process with a random search on 5-fold cross-validation data. It achieved an accuracy, specificity, sensitivity, and Matthews correlation coefficient of 93.4%, 92.8%, 98.6%, and 0.726, respectively. Corresponding scores on an independent test were 92.9%, 92.2%, 99%, and 0.717. These results outperform the position-specific scoring matrix features that are predominantly employed in post-translational modification site predictions. Furthermore, compared to N-GlyDE, GlycoEP, SPRINT-Gly, the most recent N-linked glycosylation site predictors, our model yields higher scores on the above 4 metrics, thus further demonstrating the efficiency of our approach.
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Affiliation(s)
| | - Nguyen-Quoc-Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, 106, Taiwan; Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei, 106, Taiwan
| | | | - Dinh-Minh Pham
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Yu-Yen Ou
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, 32003, Taiwan.
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Viinikangas T, Khosrowabadi E, Kellokumpu S. N-Glycan Biosynthesis: Basic Principles and Factors Affecting Its Outcome. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:237-257. [PMID: 34687012 DOI: 10.1007/978-3-030-76912-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Carbohydrate chains are the most abundant and diverse of nature's biopolymers and represent one of the four fundamental macromolecular building blocks of life together with proteins, nucleic acids, and lipids. Indicative of their essential roles in cells and in multicellular organisms, genes encoding proteins associated with glycosylation account for approximately 2% of the human genome. It has been estimated that 50-80% of all human proteins carry carbohydrate chains-glycans-as part of their structure. Despite cells utilize only nine different monosaccharides for making their glycans, their order and conformational variation in glycan chains together with chain branching differences and frequent post-synthetic modifications can give rise to an enormous repertoire of different glycan structures of which few thousand is estimated to carry important structural or functional information for a cell. Thus, glycans are immensely versatile encoders of multicellular life. Yet, glycans do not represent a random collection of unpredictable structures but rather, a collection of predetermined but still dynamic entities that are present at defined quantities in each glycosylation site of a given protein in a cell, tissue, or organism.In this chapter, we will give an overview of what is currently known about N-glycan synthesis in higher eukaryotes, focusing not only on the processes themselves but also on factors that will affect or can affect the final outcome-the dynamicity and heterogeneity of the N-glycome. We hope that this review will help understand the molecular details underneath this diversity, and in addition, be helpful for those who plan to produce optimally glycosylated antibody-based therapeutics.
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Affiliation(s)
- Teemu Viinikangas
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Elham Khosrowabadi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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Plant lectins and their usage in preparing targeted nanovaccines for cancer immunotherapy. Semin Cancer Biol 2020; 80:87-106. [PMID: 32068087 DOI: 10.1016/j.semcancer.2020.02.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/30/2020] [Accepted: 02/06/2020] [Indexed: 01/06/2023]
Abstract
Plant lectins, a natural source of glycans with a therapeutic potential may lead to the discovery of new targeted therapies. Glycans extracted from plant lectins are known to act as ligands for C-type lectin receptors (CLRs) that are primarily present on immune cells. Plant-derived glycosylated lectins offer diversity in their N-linked oligosaccharide structures that can serve as a unique source of homogenous and heterogenous glycans. Among the plant lectins-derived glycan motifs, Man9GlcNAc2Asn exhibits high-affinity interactions with CLRs that may resemble glycan motifs of pathogens. Thus, such glycan domains when presented along with antigens complexed with a nanocarrier of choice may bewilder the immune cells and direct antigen cross-presentation - a cytotoxic T lymphocyte immune response mediated by CD8+ T cells. Glycan structure analysis has attracted considerable interest as glycans are looked upon as better therapeutic alternatives than monoclonal antibodies due to their cost-effectiveness, reduced toxicity and side effects, and high specificity. Furthermore, this approach will be useful to understand whether the multivalent glycan presentation on the surface of nanocarriers can overcome the low-affinity lectin-ligand interaction and thereby modulation of CLR-dependent immune response. Besides this, understanding how the heterogeneity of glycan structure impacts the antigen cross-presentation is pivotal to develop alternative targeted therapies. In the present review, we discuss the findings on structural analysis of glycans from natural lectins performed using GlycanBuilder2 - a software tool based on a thorough literature review of natural lectins. Additionally, we discuss how multiple parameters like the orientation of glycan ligands, ligand density, simultaneous targeting of multiple CLRs and design of antigen delivery nanocarriers may influence the CLR targeting efficacy. Integrating this information will eventually set the ground for new generation immunotherapeutic vaccine design for the treatment of various human malignancies.
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11
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Role of glycosylation in nucleating protein folding and stability. Biochem J 2017; 474:2333-2347. [PMID: 28673927 DOI: 10.1042/bcj20170111] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/14/2017] [Accepted: 04/19/2017] [Indexed: 12/17/2022]
Abstract
Glycosylation constitutes one of the most common, ubiquitous and complex forms of post-translational modification. It commences with the synthesis of the protein and plays a significant role in deciding its folded state, oligomerization and thus its function. Recent studies have demonstrated that N-linked glycans help proteins to fold as the stability and folding kinetics are altered with the removal of the glycans from them. Several studies have shown that it alters not only the thermodynamic stability but also the structural features of the folded proteins modulating their interactions and functions. Their inhibition and perturbations have been implicated in diseases from diabetes to degenerative disorders. The intent of this review is to provide insight into the recent advancements in the general understanding on the aspect of glycosylation driven stability of proteins that is imperative to their function and finally their role in health and disease states.
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Lazniewska J, Weiss N. Glycosylation of voltage-gated calcium channels in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:662-668. [PMID: 28109749 DOI: 10.1016/j.bbamem.2017.01.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/10/2017] [Accepted: 01/16/2017] [Indexed: 12/26/2022]
Abstract
Voltage-gated calcium channels (VGCCs) are transmembrane proteins that translate electrical activities into intracellular calcium elevations and downstream signaling pathways. They serve essential physiological functions including communication between nerve cells, muscle contraction, cardiac activity, and release of hormones and neurotransmitters. Asparagine-linked glycosylation has emerged as an essential post-translational modification to control the number of channels embedded in the plasma membrane but also their functional gating properties. This review provides a comprehensive overview about the current state of knowledge on the role of glycosylation in the expression and functioning of VGCCs, and discusses how variations in the glycosylation of the channel proteins can contribute to pathological conditions.
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Affiliation(s)
- Joanna Lazniewska
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Norbert Weiss
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.
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Kurniyati K, Kelly JF, Vinogradov E, Robotham A, Tu Y, Wang J, Liu J, Logan SM, Li C. A novel glycan modifies the flagellar filament proteins of the oral bacterium Treponema denticola. Mol Microbiol 2017; 103:67-85. [PMID: 27696564 PMCID: PMC5182079 DOI: 10.1111/mmi.13544] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2016] [Indexed: 01/12/2023]
Abstract
While protein glycosylation has been reported in several spirochetes including the syphilis bacterium Treponema pallidum and Lyme disease pathogen Borrelia burgdorferi, the pertinent glycan structures and their roles remain uncharacterized. Herein, a novel glycan with an unusual chemical composition and structure in the oral spirochete Treponema denticola, a keystone pathogen of periodontitis was reported. The identified glycan of mass 450.2 Da is composed of a monoacetylated nonulosonic acid (Non) with a novel extended N7 acyl modification, a 2-methoxy-4,5,6-trihydroxy-hexanoyl residue in which the Non has a pseudaminic acid configuration (L-glycero-L-manno) and is β-linked to serine or threonine residues. This novel glycan modifies the flagellin proteins (FlaBs) of T. denticola by O-linkage at multiple sites near the D1 domain, a highly conserved region of bacterial flagellins that interact with Toll-like receptor 5. Furthermore, mutagenesis studies demonstrate that the glycosylation plays an essential role in the flagellar assembly and motility of T. denticola. To our knowledge, this novel glycan and its unique modification sites have not been reported previously in any bacteria.
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Affiliation(s)
- Kurni Kurniyati
- Department of Oral Biology, The State University of New York at Buffalo, New York 14214, USA
| | - John F. Kelly
- Vaccine Program, Human Health Therapeutics, National Research Council, Ottawa, Ontario, Canada K1A 0R6
| | - Evgeny Vinogradov
- Vaccine Program, Human Health Therapeutics, National Research Council, Ottawa, Ontario, Canada K1A 0R6
| | - Anna Robotham
- Vaccine Program, Human Health Therapeutics, National Research Council, Ottawa, Ontario, Canada K1A 0R6
| | - Youbing Tu
- Department of Oral Biology, The State University of New York at Buffalo, New York 14214, USA
| | - Juyu Wang
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UT Health Science Center, Houston, Texas 77030, USA
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UT Health Science Center, Houston, Texas 77030, USA
| | - Susan M. Logan
- Vaccine Program, Human Health Therapeutics, National Research Council, Ottawa, Ontario, Canada K1A 0R6
| | - Chunhao Li
- Department of Oral Biology, The State University of New York at Buffalo, New York 14214, USA
- Department of Microbiology and Immunology, The State University of New York at Buffalo, New York 14214, USA
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14
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Rubio MV, Zubieta MP, Franco Cairo JPL, Calzado F, Paes Leme AF, Squina FM, Prade RA, de Lima Damásio AR. Mapping N-linked glycosylation of carbohydrate-active enzymes in the secretome of Aspergillus nidulans grown on lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:168. [PMID: 27508003 PMCID: PMC4977673 DOI: 10.1186/s13068-016-0580-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/27/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND The genus Aspergillus includes microorganisms that naturally degrade lignocellulosic biomass, secreting large amounts of carbohydrate-active enzymes (CAZymes) that characterize their saprophyte lifestyle. Aspergillus has the capacity to perform post-translational modifications (PTM), which provides an additional advantage for the use of these organisms as a host for the production of heterologous proteins. In this study, the N-linked glycosylation of CAZymes identified in the secretome of Aspergillus nidulans grown on lignocellulose was mapped. RESULTS Aspergillus nidulans was grown in glucose, xylan and pretreated sugarcane bagasse (SCB) for 96 h, after which glycoproteomics and glycomics were carried out on the extracellular proteins (secretome). A total of 265 proteins were identified, with 153, 210 and 182 proteins in the glucose, xylan and SCB substrates, respectively. CAZymes corresponded to more than 50 % of the total secretome in xylan and SCB. A total of 182 N-glycosylation sites were identified, of which 121 were detected in 67 CAZymes. A prevalence of the N-glyc sequon N-X-T (72.2 %) was observed in N-glyc sites compared with N-X-S (27.8 %). The amino acids flanking the validated N-glyc sites were mainly composed of hydrophobic and polar uncharged amino acids. Selected proteins were evaluated for conservation of the N-glyc sites in Aspergilli homologous proteins, but a pattern of conservation was not observed. A global analysis of N-glycans released from the proteins secreted by A. nidulans was also performed. While the proportion of N-glycans with Hex5 to Hex9 was similar in the xylan condition, a prevalence of Hex5 was observed in the SCB and glucose conditions. CONCLUSIONS The most common and frequent N-glycosylated motifs, an overview of the N-glycosylation of the CAZymes and the number of mannoses found in N-glycans were analyzed. There are many bottlenecks in protein production by filamentous fungi, such as folding, transport by vesicles and secretion, but N-glycosylation in the correct context is a fundamental event for defining the high levels of secretion of target proteins. A comprehensive analysis of the protein glycosylation processes in A. nidulans will assist with a better understanding of glycoprotein structures, profiles, activities and functions. This knowledge can help in the optimization of heterologous expression and protein secretion in the fungal host.
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Affiliation(s)
- Marcelo Ventura Rubio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Mariane Paludetti Zubieta
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - João Paulo Lourenço Franco Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Felipe Calzado
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
| | - Fabio Marcio Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK USA
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
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Stelzl T, Baranov T, Geillinger KE, Kottra G, Daniel H. Effect of N-glycosylation on the transport activity of the peptide transporter PEPT1. Am J Physiol Gastrointest Liver Physiol 2016; 310:G128-41. [PMID: 26585416 DOI: 10.1152/ajpgi.00350.2015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/10/2015] [Indexed: 01/31/2023]
Abstract
The intestinal peptide transporter PEPT1 provides bulk quantities of amino acids to epithelial cells. PEPT1 is a high-capacity and low-affinity solute carrier of the SLC15 family found in apical membranes of enterocytes in small intestine and distal colon. Surprisingly, murine PEPT1 (mPEPT1) has an apparent molecular mass of ∼95 kDa in the small intestine but ∼105 kDa in the large intestine. Here we describe studies on mPEPT1 protein glycosylation and how glycans affect transport function. Putative N-glycosylation sites of mPEPT1 were altered by site-directed mutagenesis followed by expression in Xenopus laevis oocytes. Replacement of six asparagine residues (N) at positions N50, N406, N439, N510, N515, and N532 by glutamine (Q) resulted in a decrease of the mPEPT1 mass by around 35 kDa. Electrophysiology revealed all glycosylation-deficient transporters to be functional with comparable expression levels in oocyte membranes. Strikingly, the mutant protein with N50Q exhibited a twofold decreased affinity for Gly-Sar but a 2.5-fold rise in the maximal inward currents compared with the wild-type protein. Elevated maximal transport currents were also recorded for cefadroxil and tri-l-alanine. Tracer flux studies performed with [(14)C]-Gly-Sar confirmed the reduction in substrate affinity and showed twofold increased maximal transport rates for the N50Q transporter. Elimination of individual N-glycosylation sites did not alter membrane expression in oocytes or overall transport characteristics except for the mutant protein N50Q. Because transporter surface density was not altered in N50Q, removal of the glycan at this location appears to accelerate the substrate turnover rate.
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Affiliation(s)
- Tamara Stelzl
- Chair of Nutritional Physiology, Technische Universität München, Freising, Germany; ZIEL, Institute for Food and Health, Freising, Germany
| | - Tatjana Baranov
- Chair of Nutritional Physiology, Technische Universität München, Freising, Germany; ZIEL, Institute for Food and Health, Freising, Germany
| | - Kerstin E Geillinger
- Chair of Nutritional Physiology, Technische Universität München, Freising, Germany; ZIEL, Institute for Food and Health, Freising, Germany
| | - Gabor Kottra
- Chair of Nutritional Physiology, Technische Universität München, Freising, Germany; ZIEL, Institute for Food and Health, Freising, Germany
| | - Hannelore Daniel
- Chair of Nutritional Physiology, Technische Universität München, Freising, Germany; ZIEL, Institute for Food and Health, Freising, Germany
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16
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Lannoo N, Van Damme EJM. Review/N-glycans: The making of a varied toolbox. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 239:67-83. [PMID: 26398792 DOI: 10.1016/j.plantsci.2015.06.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 05/23/2023]
Abstract
Asparagine (N)-linked protein glycosylation is one of the most crucial, prevalent, and complex co- and post-translational protein modifications. It plays a pivotal role in protein folding, quality control, and endoplasmic reticulum (ER)-associated degradation (ERAD) as well as in protein sorting, protein function, and in signal transduction. Furthermore, glycosylation modulates many important biological processes including growth, development, morphogenesis, and stress signaling processes. As a consequence, aberrant or altered N-glycosylation is often associated with reduced fitness, diseases, and disorders. The initial steps of N-glycan synthesis at the cytosolic side of the ER membrane and in the lumen of the ER are highly conserved. In contrast, the final N-glycan processing in the Golgi apparatus is organism-specific giving rise to a wide variety of carbohydrate structures. Despite our vast knowledge on N-glycans in yeast and mammals, the modus operandi of N-glycan signaling in plants is still largely unknown. This review will elaborate on the N-glycosylation biosynthesis pathway in plants but will also critically assess how N-glycans are involved in different signaling cascades, either active during normal development or upon abiotic and biotic stresses.
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Affiliation(s)
- Nausicaä Lannoo
- Lab Biochemistry and Glycobiology, Department Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Els J M Van Damme
- Lab Biochemistry and Glycobiology, Department Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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17
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Li J, Tao S, Orlando R, Murtaugh MP. N-glycosylation profiling of porcine reproductive and respiratory syndrome virus envelope glycoprotein 5. Virology 2015; 478:86-98. [PMID: 25726973 DOI: 10.1016/j.virol.2015.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 02/04/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a positive-sense ssRNA virus whose envelope contains four glycoproteins and three nonglycosylated proteins. Glycans of major envelope glycoprotein 5 (GP5) are proposed as important for virus assembly and entry into permissive cells. Structural characterization of GP5 glycans would facilitate the mechanistic understanding of these processes. Thus, we purified the PRRSV type 2 prototype strain, VR2332, and analyzed the virion-associated glycans by both biochemical and mass spectrometric methods. Endoglycosidase digestion showed that GP5 was the primary protein substrate, and that the carbohydrate moieties were primarily complex-type N-glycans. Mass spectrometric analysis (HPLC-ESI-MS/MS) of GP5 N-glycans revealed an abundance of N-acetylglucosamine (GlcNAc) and N-acetyllactosamine (LacNAc) oligomers in addition to sialic acids. GlcNAc and LacNAc accessibility to ligands was confirmed by lectin co-precipitation. Our findings help to explain PRRSV infection of cells lacking sialoadhesin and provide a glycan database to facilitate molecular structural studies of PRRSV.
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Affiliation(s)
- Juan Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN 51108, USA
| | - Shujuan Tao
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Ron Orlando
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Michael P Murtaugh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN 51108, USA.
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19
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An Y, Rininger JA, Jarvis DL, Jing X, Ye Z, Aumiller JJ, Eichelberger M, Cipollo JF. Comparative glycomics analysis of influenza Hemagglutinin (H5N1) produced in vaccine relevant cell platforms. J Proteome Res 2013; 12:3707-20. [PMID: 23848607 DOI: 10.1021/pr400329k] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hemagglutinin (HA) is the major antigen in influenza vaccines, and glycosylation is known to influence its antigenicity. Embryonated hen eggs are traditionally used for influenza vaccine production, but vaccines produced in mammalian and insect cells were recently licensed. This raises the concern that vaccines produced with different cell systems might not be equivalent due to differences in their glycosylation patterns. Thus, we developed an analytical method to monitor vaccine glycosylation through a combination of nanoLC/MS(E) and quantitative MALDI-TOF MS permethylation profiling. We then used this method to examine glycosylation of HAs from two different influenza H5N1 strains produced in five different platforms, including hen eggs, three different insect cell lines (High Five, expresSF+ and glycoengineered expresSF+), and a human cell line (HEK293). Our results demonstrated that (1) sequon utilization is not necessarily equivalent in different cell types, (2) there are quantitative and qualitative differences in the overall N-glycosylation patterns and structures produced by different cell types, (3) ∼20% of the N-glycans on the HAs produced by High Five cells are core α1,3-fucosylated structures, which may be allergenic in humans, and (4) our method can be used to monitor differences in glycosylation during the cellular glycoengineering stages of vaccine development.
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Affiliation(s)
- Yanming An
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA
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Arnott A, Vong S, Rith S, Naughtin M, Ly S, Guillard B, Deubel V, Buchy P. Human bocavirus amongst an all-ages population hospitalised with acute lower respiratory infections in Cambodia. Influenza Other Respir Viruses 2012; 7:201-10. [PMID: 22531100 PMCID: PMC5780762 DOI: 10.1111/j.1750-2659.2012.00369.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human bocavirus (HBoV) is a novel parvovirus that is associated with respiratory and gastrointestinal tract disease. OBJECTIVES To investigate the prevalence and genetic diversity of HBoV amongst hospitalized patients with acute lower respiratory infection (ALRI) in Cambodia. STUDY DESIGN Samples were collected from 2773 patients of all ages hospitalised with symptoms of ALRI between 2007 and 2009. All samples were screened by multiplex RT-PCR/PCR for 18 respiratory viruses. All samples positive for HBoV were sequenced and included in this study. RESULTS Of the samples tested, 43 (1·5%) were positive for HBoV. The incidence of HBoV did not vary between the consecutive seasons investigated, and HBoV infections were detected year-round. The incidence of HBoV infection was highest in patients aged < 2 years, with pneumonia or bronchopneumonia the most common clinical diagnosis, regardless of age. A total of 19 patients (44%) were co-infected with HBoV and an additional respiratory pathogen. All isolates were classified as HBoV type 1 (HBoV-1). High conservation between Cambodian NP1 and V1V2 gene sequences was observed. CONCLUSIONS Human bocavirus infection can result in serious illness, however is frequently detected in the context of viral co-infection. Specific studies are required to further understand the true pathogenesis of HBoV in the context of severe respiratory illness.
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Affiliation(s)
- Alicia Arnott
- Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
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Rao RSP, Møller IM. Large-scale analysis of phosphorylation site occupancy in eukaryotic proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:405-12. [DOI: 10.1016/j.bbapap.2011.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/28/2011] [Accepted: 12/01/2011] [Indexed: 11/28/2022]
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22
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Rao RSP, Møller IM. Pattern of occurrence and occupancy of carbonylation sites in proteins. Proteomics 2011; 11:4166-73. [DOI: 10.1002/pmic.201100223] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 01/25/2023]
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Rao RSP, Buus OT, Wollenweber B. Distribution of N-glycosylation sequons in proteins: How apart are they? Comput Biol Chem 2011; 35:57-61. [DOI: 10.1016/j.compbiolchem.2011.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 01/19/2011] [Indexed: 10/18/2022]
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