1
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Couto PM, Guardia CMA, Couto FL, Labriola CA, Labanda MS, Caramelo JJ. Acceptors stability modulates the efficiency of post-translational protein N-glycosylation. FASEB J 2024; 38:e23782. [PMID: 38934375 DOI: 10.1096/fj.202302267r] [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: 11/03/2023] [Revised: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
N-glycosylation is the most common protein modification in the eukaryotic secretory pathway. It involves the attachment a high mannose glycan to Asn residues in the context of Asn-X-Ser/Thr/Cys, a motif known as N-glycosylation sequon. This process is mediated by STT3A and STT3B, the catalytic subunits of the oligosaccharyltransferase complexes. STT3A forms part of complexes associated with the SEC61 translocon and functions co-translationally. Vacant sequons have another opportunity for glycosylation by complexes carrying STT3B. Local sequence information plays an important role in determining N-glycosylation efficiency, but non-local factors can also have a significant impact. For instance, certain proteins associated with human genetic diseases exhibit abnormal N-glycosylation levels despite having wild-type acceptor sites. Here, we investigated the effect of protein stability on this process. To this end, we generated a family of 40 N-glycan acceptors based on superfolder GFP, and we measured their efficiency in HEK293 cells and in two derived cell lines lacking STT3B or STT3A. Sequon occupancy was highly dependent on protein stability, improving as the thermodynamic stability of the acceptor proteins decreases. This effect is mainly due to the activity of the STT3B-based OST complex. These findings can be integrated into a simple kinetic model that distinguishes local information within sequons from global information of the acceptor proteins.
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Affiliation(s)
- Paula M Couto
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina
| | - Carlos M A Guardia
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Facundo L Couto
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina
| | - Carlos A Labriola
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina
| | - María S Labanda
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina
| | - Julio J Caramelo
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina
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2
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Ochiai H, Elouali S, Yamamoto T, Asai H, Noguchi M, Nishiuchi Y. Chemical and Chemoenzymatic Synthesis of Peptide and Protein Therapeutics Conjugated with Human N-Glycans. ChemMedChem 2024; 19:e202300692. [PMID: 38572578 DOI: 10.1002/cmdc.202300692] [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: 12/08/2023] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Glycosylation is one of the most ubiquitous post-translational modifications. It affects the structure and function of peptides/proteins and consequently has a significant impact on various biological events. However, the structural complexity and heterogeneity of glycopeptides/proteins caused by the diversity of glycan structures and glycosylation sites complicates the detailed elucidation of glycan function and hampers their clinical applications. To address these challenges, chemical and/or enzyme-assisted synthesis methods have been developed to realize glycopeptides/proteins with well-defined glycan morphologies. In particular, N-glycans are expected to be useful for improving the solubility, in vivo half-life and aggregation of bioactive peptides/proteins that have had limited clinical applications so far due to their short duration of action in the blood and unsuitable physicochemical properties. Chemical glycosylation performed in a post-synthetic procedure can be used to facilitate the development of glycopeptide/protein analogues or mimetics that are superior to the original molecules in terms of physicochemical and pharmacokinetic properties. N-glycans are used to modify targets because they are highly biodegradable and biocompatible and have structures that already exist in the human body. On the practical side, from a quality control perspective, close attention should be paid to their structural homogeneity when they are to be applied to pharmaceuticals.
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Affiliation(s)
- Hirofumi Ochiai
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Sofia Elouali
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Takahiro Yamamoto
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Hiroaki Asai
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Masato Noguchi
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Yuji Nishiuchi
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
- Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
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3
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Chaudhary BP, Struppe J, Moktan H, Zoetewey D, Zhou DH, Mohanty S. Reconstitution and resonance assignments of yeast OST subunit Ost4 and its critical mutant Ost4V23D in liposomes by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2024; 78:109-117. [PMID: 38421550 DOI: 10.1007/s10858-024-00437-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
N-linked glycosylation is an essential and highly conserved co- and post-translational protein modification in all domains of life. In humans, genetic defects in N-linked glycosylation pathways result in metabolic diseases collectively called Congenital Disorders of Glycosylation. In this modification reaction, a mannose rich oligosaccharide is transferred from a lipid-linked donor substrate to a specific asparagine side-chain within the -N-X-T/S- sequence (where X ≠ Proline) of the nascent protein. Oligosaccharyltransferase (OST), a multi-subunit membrane embedded enzyme catalyzes this glycosylation reaction in eukaryotes. In yeast, Ost4 is the smallest of nine subunits and bridges the interaction of the catalytic subunit, Stt3, with Ost3 (or its homolog, Ost6). Mutations of any C-terminal hydrophobic residues in Ost4 to a charged residue destabilizes the enzyme and negatively impacts its function. Specifically, the V23D mutation results in a temperature-sensitive phenotype in yeast. Here, we report the reconstitution of both purified recombinant Ost4 and Ost4V23D each in a POPC/POPE lipid bilayer and their resonance assignments using heteronuclear 2D and 3D solid-state NMR with magic-angle spinning. The chemical shifts of Ost4 changed significantly upon the V23D mutation, suggesting a dramatic change in its chemical environment.
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Affiliation(s)
- Bharat P Chaudhary
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | | | - Hem Moktan
- Department of Physics, Oklahoma State University, Stillwater, OK, 74078, USA
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David Zoetewey
- Department of Chemistry, Physics and Astronomy, Georgia College and State University, Milledgeville, GA, 31061, USA
| | - Donghua H Zhou
- Department of Physics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Smita Mohanty
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
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4
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Ahmed MZ, Alqahtani AS. Cell surface expression of Ribophorin I, an endoplasmic reticulum protein, over different cell types. Int J Biol Macromol 2024; 264:130278. [PMID: 38373565 DOI: 10.1016/j.ijbiomac.2024.130278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Ribophorin-1 serves as one of the subunits of the oligosaccharyltransferase (OST) complex located in the endoplasmic reticulum (ER). Until now, RPN-1 was considered an ER protein. However, our findings reveal that a minor fraction of RPN-1 escapes from the lumen of the ER and is ectopically expressed on the surface of different cell lines. The precise mechanism of protein translocation is unknown. The expression of RPN-1 was demonstrated through the isolation of membrane proteins using surface biotinylation and sucrose density gradient techniques. The confirmation of RPN-1 was obtained through surface staining using a specific antibody, revealing its expression on various cell lines. Additionally, we examined the expression of RPN-1 in different populations of PBMCs and observed a differential regulation of RPN-1 within PBMC subpopulations. Notably, there was a significant expression of RPN-1 on monocytes and B cells, but there was little to no population of T cells expressing RPN-1. We confirmed the expression of RPN-1 on THP-1, U937, and Jurkat cells. We also confirmed their surface expression through si-RNA knockdown. Our study shows RPN-1 expression on various cell surfaces, suggesting varied regulation among cell types. In the future, we may uncover its roles in immune function, signaling, and differentiation/proliferation.
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Affiliation(s)
- Mohammad Z Ahmed
- King Saud University College of Pharmacy, Department of Pharmacognosy, Riyadh 11451, Saudi Arabia.
| | - Ali S Alqahtani
- King Saud University College of Pharmacy, Department of Pharmacognosy, Riyadh 11451, Saudi Arabia
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5
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Schoberer J, Shin YJ, Vavra U, Veit C, Strasser R. Analysis of Protein Glycosylation in the ER. Methods Mol Biol 2024; 2772:221-238. [PMID: 38411817 DOI: 10.1007/978-1-0716-3710-4_16] [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: 02/28/2024]
Abstract
Protein N-glycosylation is an essential posttranslational modification which is initiated in the endoplasmic reticulum (ER). In plants, the N-glycans play a pivotal role in protein folding and quality control. Through the interaction of glycan processing and binding reactions mediated by ER-resident glycosidases and specific carbohydrate-binding proteins, the N-glycans contribute to the adoption of a native protein conformation. Properly folded glycoproteins are released from these processes and allowed to continue their transit to the Golgi where further processing and maturation of N-glycans leads to the formation of more complex structures with different functions. Incompletely folded glycoproteins are removed from the ER by a highly conserved degradation process to prevent the accumulation or secretion of misfolded proteins and maintain ER homeostasis. Here, we describe methods to analyze the N-glycosylation status and the glycan-dependent ER-associated degradation process in plants.
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Affiliation(s)
- Jennifer Schoberer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Yun-Ji Shin
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ulrike Vavra
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christiane Veit
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
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6
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Ramírez AS, Locher KP. Structural and mechanistic studies of the N-glycosylation machinery: from lipid-linked oligosaccharide biosynthesis to glycan transfer. Glycobiology 2023; 33:861-872. [PMID: 37399117 PMCID: PMC10859629 DOI: 10.1093/glycob/cwad053] [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: 05/29/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023] Open
Abstract
N-linked protein glycosylation is a post-translational modification that exists in all domains of life. It involves two consecutive steps: (i) biosynthesis of a lipid-linked oligosaccharide (LLO), and (ii) glycan transfer from the LLO to asparagine residues in secretory proteins, which is catalyzed by the integral membrane enzyme oligosaccharyltransferase (OST). In the last decade, structural and functional studies of the N-glycosylation machinery have increased our mechanistic understanding of the pathway. The structures of bacterial and eukaryotic glycosyltransferases involved in LLO elongation provided an insight into the mechanism of LLO biosynthesis, whereas structures of OST enzymes revealed the molecular basis of sequon recognition and catalysis. In this review, we will discuss approaches used and insight obtained from these studies with a special emphasis on the design and preparation of substrate analogs.
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Affiliation(s)
- Ana S Ramírez
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), Zürich 8093, Switzerland
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), Zürich 8093, Switzerland
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7
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Liu J, Nagy N, Ayala-Torres C, Aguilar-Alonso F, Morais-Esteves F, Xu S, Masucci MG. Remodeling of the ribosomal quality control and integrated stress response by viral ubiquitin deconjugases. Nat Commun 2023; 14:8315. [PMID: 38097648 PMCID: PMC10721647 DOI: 10.1038/s41467-023-43946-0] [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: 03/02/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
The strategies adopted by viruses to reprogram the translation and protein quality control machinery and promote infection are poorly understood. Here, we report that the viral ubiquitin deconjugase (vDUB)-encoded in the large tegument protein of Epstein-Barr virus (EBV BPLF1)-regulates the ribosomal quality control (RQC) and integrated stress responses (ISR). The vDUB participates in protein complexes that include the RQC ubiquitin ligases ZNF598 and LTN1. Upon ribosomal stalling, the vDUB counteracts the ubiquitination of the 40 S particle and inhibits the degradation of translation-stalled polypeptides by the proteasome. Impairment of the RQC correlates with the readthrough of stall-inducing mRNAs and with activation of a GCN2-dependent ISR that redirects translation towards upstream open reading frames (uORFs)- and internal ribosome entry sites (IRES)-containing transcripts. Physiological levels of active BPLF1 promote the translation of the EBV Nuclear Antigen (EBNA)1 mRNA in productively infected cells and enhance the release of progeny virus, pointing to a pivotal role of the vDUB in the translation reprogramming that enables efficient virus production.
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Affiliation(s)
- Jiangnan Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Noemi Nagy
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Carlos Ayala-Torres
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Francisco Aguilar-Alonso
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Francisco Morais-Esteves
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Shanshan Xu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria G Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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8
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Mei J, Li Z, Zhou S, Chen XL, Wilson RA, Liu W. Effector secretion and stability in the maize anthracnose pathogen Colletotrichum graminicola requires N-linked protein glycosylation and the ER chaperone pathway. THE NEW PHYTOLOGIST 2023; 240:1449-1466. [PMID: 37598305 DOI: 10.1111/nph.19213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/01/2023] [Indexed: 08/21/2023]
Abstract
N-linked protein glycosylation is a conserved and essential modification mediating protein processing and quality control in the endoplasmic reticulum (ER), but how this contributes to the infection cycle of phytopathogenic fungi is largely unknown. In this study, we discovered that inhibition of protein N-glycosylation severely affected vegetative growth, hyphal tip development, conidial germination, appressorium formation, and, ultimately, the ability of the maize (Zea mays) anthracnose pathogen Colletotrichum graminicola to infect its host. Quantitative proteomics analysis showed that N-glycosylation can coordinate protein O-glycosylation, glycosylphosphatidylinositol anchor modification, and endoplasmic reticulum quality control (ERQC) by directly targeting the proteins from the corresponding pathway in the ER. We performed a functional study of the N-glycosylation pathway-related protein CgALG3 and of the ERQC pathway-related protein CgCNX1, which demonstrated that N-glycosylation of ER chaperone proteins is essential for effector stability, secretion, and pathogenicity of C. graminicola. Our study provides concrete evidence for the regulation of effector protein stability and secretion by N-glycosylation.
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Affiliation(s)
- Jie Mei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shaoqun Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xiao-Lin Chen
- State Key Laboratory of Agricultural Microbiology and Provincial Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Richard A Wilson
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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9
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Sobala ŁF. Evolution and phylogenetic distribution of endo-α-mannosidase. Glycobiology 2023; 33:687-699. [PMID: 37202179 PMCID: PMC11025385 DOI: 10.1093/glycob/cwad041] [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: 12/23/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/20/2023] Open
Abstract
While glycans underlie many biological processes, such as protein folding, cell adhesion, and cell-cell recognition, deep evolution of glycosylation machinery remains an understudied topic. N-linked glycosylation is a conserved process in which mannosidases are key trimming enzymes. One of them is the glycoprotein endo-α-1,2-mannosidase which participates in the initial trimming of mannose moieties from an N-linked glycan inside the cis-Golgi. It is unique as the only endo-acting mannosidase found in this organelle. Relatively little is known about its origins and evolutionary history; so far it was reported to occur only in vertebrates. In this work, a taxon-rich bioinformatic survey to unravel the evolutionary history of this enzyme, including all major eukaryotic clades and a wide representation of animals, is presented. The endomannosidase was found to be more widely distributed in animals and other eukaryotes. The protein motif changes in context of the canonical animal enzyme were tracked. Additionally, the data show the two canonical vertebrate endomannosidase genes, MANEA and MANEAL, arose at the second round of the two vertebrate genome duplications and one more vertebrate paralog, CMANEAL, is uncovered. Finally, a framework where N-glycosylation co-evolved with complex multicellularity is described. A better understanding of the evolution of core glycosylation pathways is pivotal to understanding biology of eukaryotes in general, and the Golgi apparatus in particular. This systematic analysis of the endomannosidase evolution is one step toward this goal.
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Affiliation(s)
- Łukasz F Sobala
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wroclaw, Poland
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10
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Durairaj J, Waterhouse AM, Mets T, Brodiazhenko T, Abdullah M, Studer G, Tauriello G, Akdel M, Andreeva A, Bateman A, Tenson T, Hauryliuk V, Schwede T, Pereira J. Uncovering new families and folds in the natural protein universe. Nature 2023; 622:646-653. [PMID: 37704037 PMCID: PMC10584680 DOI: 10.1038/s41586-023-06622-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023]
Abstract
We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database1. These models cover nearly all proteins that are known, including those challenging to annotate for function or putative biological role using standard homology-based approaches. In this study, we examine the extent to which the AlphaFold database has structurally illuminated this 'dark matter' of the natural protein universe at high predicted accuracy. We further describe the protein diversity that these models cover as an annotated interactive sequence similarity network, accessible at https://uniprot3d.org/atlas/AFDB90v4 . By searching for novelties from sequence, structure and semantic perspectives, we uncovered the β-flower fold, added several protein families to Pfam database2 and experimentally demonstrated that one of these belongs to a new superfamily of translation-targeting toxin-antitoxin systems, TumE-TumA. This work underscores the value of large-scale efforts in identifying, annotating and prioritizing new protein families. By leveraging the recent deep learning revolution in protein bioinformatics, we can now shed light into uncharted areas of the protein universe at an unprecedented scale, paving the way to innovations in life sciences and biotechnology.
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Affiliation(s)
- Janani Durairaj
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland
| | - Andrew M Waterhouse
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland
| | - Toomas Mets
- Institute of Technology, University of Tartu, Tartu, Estonia
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | | | - Minhal Abdullah
- Institute of Technology, University of Tartu, Tartu, Estonia
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Gabriel Studer
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland
| | - Gerardo Tauriello
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland
| | | | - Antonina Andreeva
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Vasili Hauryliuk
- Institute of Technology, University of Tartu, Tartu, Estonia
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Science for Life Laboratory, Lund, Sweden
- Virus Centre, Lund University, Lund, Sweden
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.
| | - Joana Pereira
- Biozentrum, University of Basel, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.
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11
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Wang T, Wang C, Wang J, Wang B. An Intrabody against B-Cell Receptor-Associated Protein 31 (BAP31) Suppresses the Glycosylation of the Epithelial Cell-Adhesion Molecule (EpCAM) via Affecting the Formation of the Sec61-Translocon-Associated Protein (TRAP) Complex. Int J Mol Sci 2023; 24:14787. [PMID: 37834237 PMCID: PMC10572819 DOI: 10.3390/ijms241914787] [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: 07/31/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The epithelial cell-adhesion molecule (EpCAM) is hyperglycosylated in carcinoma tissue and the oncogenic function of EpCAM primarily depends on the degree of glycosylation. Inhibiting EpCAM glycosylation is expected to have an inhibitory effect on cancer. We analyzed the relationship of BAP31 with 84 kinds of tumor-associated antigens and found that BAP31 is positively correlated with the protein level of EpCAM. Triple mutations of EpCAM N76/111/198A, which are no longer modified by glycosylation, were constructed to determine whether BAP31 has an effect on the glycosylation of EpCAM. Plasmids containing different C-termini of BAP31 were constructed to identify the regions of BAP31 that affects EpCAM glycosylation. Antibodies against BAP31 (165-205) were screened from a human phage single-domain antibody library and the effect of the antibody (VH-F12) on EpCAM glycosylation and anticancer was investigated. BAP31 increases protein levels of EpCAM by promoting its glycosylation. The amino acid region from 165 to 205 in BAP31 plays an important role in regulating the glycosylation of EpCAM. The antibody VH-F12 significantly inhibited glycosylation of EpCAM which, subsequently, reduced the adhesion of gastric cancer cells, inducing cytotoxic autophagy, inhibiting the AKT-PI3K-mTOR signaling pathway, and, finally, resulting in proliferation inhibition both in vitro and in vivo. Finally, we clarified that BAP31 plays a key role in promoting N-glycosylation of EpCAM by affecting the Sec61 translocation channels. Altogether, these data implied that BAP31 regulates the N-glycosylation of EpCAM and may represent a potential therapeutic target for cancer therapy.
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Affiliation(s)
| | | | | | - Bing Wang
- College of Life Science and Health, Northeastern University, 195 Chuangxin Road, Hunnan District, Shenyang 110819, China; (T.W.); (C.W.); (J.W.)
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12
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Wenzel L, Hoffmann M, Rapp E, Rexer TFT, Reichl U. Cell-free N-glycosylation of peptides using synthetic lipid-linked hybrid and complex N-glycans. Front Mol Biosci 2023; 10:1266431. [PMID: 37767159 PMCID: PMC10520871 DOI: 10.3389/fmolb.2023.1266431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023] Open
Abstract
Cell-free, chemoenzymatic platforms are emerging technologies towards generating glycoconjugates with defined and homogeneous glycoforms. Recombinant oligosaccharyltransferases can be applied to glycosylate "empty," i.e., aglycosyalted, peptides and proteins. While bacterial oligosaccharlytransferases have been extensively investigated, only recently a recombinant eukaryotic single-subunit oligosaccharyltransferase has been successfully used to in vitro N-glycosylate peptides. However, its applicability towards synthesizing full-length glycoproteins and utilizing glycans beyond mannose-type glycans for the transfer have not be determined. Here, we show for the first time the synthesis of hybrid- and complex-type glycans using synthetic lipid carriers as substrates for in vitro N-glycosylation reactions. For this purpose, transmembrane-deleted human β-1,2 N-acetylglucosamintransferase I and II (MGAT1ΔTM and MGAT2ΔTM) and β-1,4-galactosyltransferase (GalTΔTM) have been expressed in Escherichia coli and used to extend an existing multi-enzyme cascade. Both hybrid and agalactosylated complex structures were transferred to the N-glycosylation consensus sequence of peptides (10 amino acids: G-S-D-A-N-Y-T-Y-T-Q) by the recombinant oligosaccharyltransferase STT3A from Trypanosoma brucei.
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Affiliation(s)
- Lisa Wenzel
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marcus Hoffmann
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- glyXera GmbH, Magdeburg, Germany
| | - Thomas F. T. Rexer
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Chair of Bioprocess Engineering, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
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13
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Komatsu S, Kimura T, Rehman SU, Yamaguchi H, Hitachi K, Tsuchida K. Proteomic Analysis Reveals Salt-Tolerant Mechanism in Soybean Applied with Plant-Derived Smoke Solution. Int J Mol Sci 2023; 24:13734. [PMID: 37762035 PMCID: PMC10530690 DOI: 10.3390/ijms241813734] [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: 08/05/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Salt stress of soybean is a serious problem because it reduces plant growth and seed yield. To investigate the salt-tolerant mechanism of soybean, a plant-derived smoke (PDS) solution was used. Three-day-old soybeans were subjected to PDS solution under 100 mM NaCl for 2 days, resulting in PDS solution improving soybean root growth, even under salt stress. Under the same condition, proteins were analyzed using the proteomic technique. Differential abundance proteins were associated with transport/formaldehyde catabolic process/sucrose metabolism/glutathione metabolism/cell wall organization in the biological process and membrane/Golgi in the cellular component with or without PDS solution under salt stress. Immuno-blot analysis confirmed that osmotin, alcohol dehydrogenase, and sucrose synthase increased with salt stress and decreased with additional PDS solution; however, H+ATPase showed opposite effects. Cellulose synthase and xyloglucan endotransglucosylase/hydrolase increased with salt and decreased with additional PDS solution. Furthermore, glycoproteins decreased with salt stress and recovered with additional treatment. As mitochondrion-related events, the contents of ATP and gamma-aminobutyric acid increased with salt stress and recovered with additional treatment. These results suggest that PDS solution improves the soybean growth by alleviating salt stress. Additionally, the regulation of energy metabolism, protein glycosylation, and cell wall construction might be an important factor for the acquisition of salt tolerance in soybean.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan;
| | - Taiki Kimura
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan;
| | - Shafiq Ur Rehman
- Department of Biology, University of Haripur, Haripur 22620, Pakistan;
| | - Hisateru Yamaguchi
- Department of Medical Technology, Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan;
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (K.T.)
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (K.T.)
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14
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Beihammer G, König-Beihammer J, Kogelmann B, Ruocco V, Grünwald-Gruber C, D’Aoust MA, Lavoie PO, Saxena P, Gach JS, Steinkellner H, Strasser R. An oligosaccharyltransferase from Leishmania donovani increases the N-glycan occupancy on plant-produced IgG1. FRONTIERS IN PLANT SCIENCE 2023; 14:1233666. [PMID: 37615026 PMCID: PMC10442823 DOI: 10.3389/fpls.2023.1233666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/17/2023] [Indexed: 08/25/2023]
Abstract
N-Glycosylation of immunoglobulin G1 (IgG1) at the heavy chain Fc domain (Asn297) plays an important role for antibody structure and effector functions. While numerous recombinant IgG1 antibodies have been successfully expressed in plants, they frequently display a considerable amount (up to 50%) of unglycosylated Fc domain. To overcome this limitation, we tested a single-subunit oligosaccharyltransferase from the protozoan Leishmania donovani (LdOST) for its ability to improve IgG1 Fc glycosylation. LdOST fused to a fluorescent protein was transiently expressed in Nicotiana benthamiana and confocal microscopy confirmed the subcellular location at the endoplasmic reticulum. Transient co-expression of LdOST with two different IgG1 antibodies resulted in a significant increase (up to 97%) of Fc glycosylation while leaving the overall N-glycan composition unmodified, as determined by different mass spectrometry approaches. While biochemical and functional features of "glycosylation improved" antibodies remained unchanged, a slight increase in FcγRIIIa binding and thermal stability was observed. Collectively, our results reveal that LdOST expression is suitable to reduce the heterogeneity of plant-produced antibodies and can contribute to improving their stability and effector functions.
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Affiliation(s)
- Gernot Beihammer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- acib - Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Julia König-Beihammer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Benjamin Kogelmann
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- acib - Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Valentina Ruocco
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | | | | | - Johannes S. Gach
- Division of Infectious Diseases, University of California, Irvine, Irvine, CA, United States
| | - Herta Steinkellner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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15
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Wu X, Wang H, Li S, Luo H, Liu F. Mining glycosylation-related prognostic lncRNAs and constructing a prognostic model for overall survival prediction in glioma: A study based on bioinformatics analysis. Medicine (Baltimore) 2023; 102:e33569. [PMID: 37145002 PMCID: PMC10158895 DOI: 10.1097/md.0000000000033569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/29/2023] [Indexed: 05/06/2023] Open
Abstract
Dysregulation of protein glycosylation plays a crucial role in the development of glioma. Long noncoding RNA (lncRNAs), functional RNA molecules without protein-coding ability, regulate gene expression and participate in malignant glioma progression. However, it remains unclear how lncRNAs are involved in glycosylation glioma malignancy. Identification of prognostic glycosylation-related lncRNAs in gliomas is necessary. We collected RNA-seq data and clinicopathological information of glioma patients from the cancer genome atlas and Chinese glioma genome atlas. We used the "limma" package to explore glycosylation-related gene and screened related lncRNAs from abnormally glycosylated genes. Using univariate Cox analyses Regression and least absolute shrinkage and selection operator analyses, we constructed a risk signature with 7 glycosylation-related lncRNAs. Based on the median risk score (RS), patients with gliomas were divided into low- and high-risk subgroups with different overall survival rates. Univariate and multivariate Cox analyses regression analyses were performed to assess the independent prognostic ability of the RS. Twenty glycosylation-related lncRNAs were identified by univariate Cox regression analyses. Two glioma subgroups were identified using consistent protein clustering, with the prognosis of the former being better than that of the latter. Least absolute shrinkage and selection operator analysis identified 7 survival RSs for glycosylation-related lncRNAs, which were identified as independent prognostic markers and predictors of glioma clinicopathological features. Glycosylation-related lncRNAs play an important role in the malignant development of gliomas and may help guide treatment options.
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Affiliation(s)
- Xiang Wu
- Department of Neurosurgery, Jiangxi Provincial Children’s Hospital, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Haiyan Wang
- Institute of Neuroscience, Nanchang University, Nanchang, China
- Department of Operation, The Second Affiliated Hospital of Nanchang University
| | - Shiqi Li
- Institute of Neuroscience, Nanchang University, Nanchang, China
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Haitao Luo
- Institute of Neuroscience, Nanchang University, Nanchang, China
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Feng Liu
- Department of Neurosurgery, Jiangxi Provincial Children’s Hospital, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
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16
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Cui T, Ma Q, Zhang F, Chen S, Zhang C, Hao J, Liu X. Characterization of PcSTT3B as a Key Oligosaccharyltransferase Subunit Involved in N-glycosylation and Its Role in Development and Pathogenicity of Phytophthora capsici. Int J Mol Sci 2023; 24:ijms24087500. [PMID: 37108663 PMCID: PMC10141488 DOI: 10.3390/ijms24087500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/08/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Asparagine (Asn, N)-linked glycosylation is a conserved process and an essential post-translational modification that occurs on the NXT/S motif of the nascent polypeptides in endoplasmic reticulum (ER). The mechanism of N-glycosylation and biological functions of key catalytic enzymes involved in this process are rarely documented for oomycetes. In this study, an N-glycosylation inhibitor tunicamycin (TM) hampered the mycelial growth, sporangial release, and zoospore production of Phytophthora capsici, indicating that N-glycosylation was crucial for oomycete growth development. Among the key catalytic enzymes involved in N-glycosylation, the PcSTT3B gene was characterized by its functions in P. capsici. As a core subunit of the oligosaccharyltransferase (OST) complex, the staurosporine and temperature sensive 3B (STT3B) subunit were critical for the catalytic activity of OST. The PcSTT3B gene has catalytic activity and is highly conservative in P. capsici. By using a CRISPR/Cas9-mediated gene replacement system to delete the PcSTT3B gene, the transformants impaired mycelial growth, sporangial release, zoospore production, and virulence. The PcSTT3B-deleted transformants were more sensitive to an ER stress inducer TM and display low glycoprotein content in the mycelia, suggesting that PcSTT3B was associated with ER stress responses and N-glycosylation. Therefore, PcSTT3B was involved in the development, pathogenicity, and N-glycosylation of P. capsici.
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Affiliation(s)
- Tongshan Cui
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Quanhe Ma
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Fan Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shanshan Chen
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Can Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jianjun Hao
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Xili Liu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China
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17
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He Y, Hao F, Fu H, Tian G, Zhang Y, Fu K, Qi B. N-glycosylated intestinal protein BCF-1 shapes microbial colonization by binding bacteria via its fimbrial protein. Cell Rep 2023; 42:111993. [PMID: 36662624 DOI: 10.1016/j.celrep.2023.111993] [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: 08/29/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Microbial colonization plays an instrumental role in the health of the host. However, the host factors that facilitate the establishment of the microbial colonization remain unclear. Here, we establish a screening method to identify host factors regulating E. coli colonization in C. elegans. We find that a BCF-1 possessing N-glycosylation promotes E. coli colonization by directly binding to E. coli via its fimbrial protein, YdeR. BCF-1 is activated by the bacteria and interacts with an oligosaccharyl transferase, OSTB-1, which is critical for regulating E. coli colonization. We also show that the N-glycosylation of BCF-1 is critical for E. coli colonization. In addition, we find that the microbiota composition is shaped by BCF-1. In summary, this study shows a "scaffold model" for bacterial colonization between a host glycoprotein and E. coli, and it also introduces a powerful research approach to identify individual host factors involved in modulating bacterial colonization.
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Affiliation(s)
- Yongjuan He
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Fanrui Hao
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Herui Fu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Guojing Tian
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Yingyang Zhang
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Kai Fu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Bin Qi
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China.
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18
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Bieberich E. Synthesis, Processing, and Function of N-Glycans in N-Glycoproteins. ADVANCES IN NEUROBIOLOGY 2023; 29:65-93. [PMID: 36255672 DOI: 10.1007/978-3-031-12390-0_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Many membrane-resident and secreted proteins, including growth factors and their receptors are N-glycosylated. The initial N-glycan structure is synthesized in the endoplasmic reticulum (ER) as a branched structure on a lipid anchor (dolicholpyrophosphate) and then co-translationally, "en bloc" transferred and linked via N-acetylglucosamine to asparagine within a specific N-glycosylation acceptor sequence of the nascent recipient protein. In the ER and then the Golgi apparatus, the N-linked glycan structure is modified by hydrolytic removal of sugar residues ("trimming") followed by re-glycosylation with additional sugar residues ("processing") such as galactose, fucose or sialic acid to form complex N-glycoproteins. While the sequence of the reactions leading to biosynthesis, "en bloc" transfer and processing of N-glycans is well investigated, it is still not completely understood how N-glycans affect the biological fate and function of N-glycoproteins. This review will discuss the biology of N-glycoprotein synthesis, processing and function with specific reference to the physiology and pathophysiology of the immune and nervous system, as well as infectious diseases such as Covid-19.
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Affiliation(s)
- Erhard Bieberich
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA.
- Veteran Affairs Medical Center, Lexington, KY, USA.
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19
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Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Wang P, Lis JT, Feschotte C, Erzurum SC, Cheng F, Yu H. A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. Nat Biotechnol 2023; 41:128-139. [PMID: 36217030 PMCID: PMC9851973 DOI: 10.1038/s41587-022-01474-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/15/2022] [Indexed: 01/25/2023]
Abstract
Studying viral-host protein-protein interactions can facilitate the discovery of therapies for viral infection. We use high-throughput yeast two-hybrid experiments and mass spectrometry to generate a comprehensive SARS-CoV-2-human protein-protein interactome network consisting of 739 high-confidence binary and co-complex interactions, validating 218 known SARS-CoV-2 host factors and revealing 361 novel ones. Our results show the highest overlap of interaction partners between published datasets and of genes differentially expressed in samples from COVID-19 patients. We identify an interaction between the viral protein ORF3a and the human transcription factor ZNF579, illustrating a direct viral impact on host transcription. We perform network-based screens of >2,900 FDA-approved or investigational drugs and identify 23 with significant network proximity to SARS-CoV-2 host factors. One of these drugs, carvedilol, shows clinical benefits for COVID-19 patients in an electronic health records analysis and antiviral properties in a human lung cell line infected with SARS-CoV-2. Our study demonstrates the value of network systems biology to understand human-virus interactions and provides hits for further research on COVID-19 therapeutics.
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Affiliation(s)
- Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yuan Liu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
| | - Shagun Gupta
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Mauricio I Paramo
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Chengsheng Mao
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Yuan Luo
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Shayne Wierbowski
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Marta Bertolotti
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
| | - Mriganka Nerkar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Lara Jehi
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nir Drayman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Haley Gula
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Glenn Randall
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Peihui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA.
- Department of Computational Biology, Cornell University, Ithaca, NY, USA.
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20
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Suzuki M, Tezuka K, Handa T, Sato R, Takeuchi H, Takao M, Tano M, Uchida Y. Upregulation of ribosome complexes at the blood-brain barrier in Alzheimer's disease patients. J Cereb Blood Flow Metab 2022; 42:2134-2150. [PMID: 35766008 PMCID: PMC9580172 DOI: 10.1177/0271678x221111602] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The cerebrovascular-specific molecular mechanism in Alzheimer's disease (AD) was investigated by employing comprehensive and accurate quantitative proteomics. Highly purified brain capillaries were isolated from cerebral gray and white matter of four AD and three control donors, and examined by SWATH (sequential window acquisition of all theoretical fragment ion spectra) proteomics. Of the 29 ribosomal proteins that were quantified, 28 (RPLP0, RPL4, RPL6, RPL7A, RPL8, RPL10A, RPL11, RPL12, RPL14, RPL15, RPL18, RPL23, RPL27, RPL27A, RPL31, RPL35A, RPS2, RPS3, RPS3A, RPS4X, RPS7, RPS8, RPS14, RPS16, RPS20, RPS24, RPS25, and RPSA) were significantly upregulated in AD patients. This upregulation of ribosomal protein expression occurred only in brain capillaries and not in brain parenchyma. The protein expression of protein processing and N-glycosylation-related proteins in the endoplasmic reticulum (DDOST, STT3A, MOGS, GANAB, RPN1, RPN2, SEC61B, UGGT1, LMAN2, and SSR4) were also upregulated in AD brain capillaries and was correlated with the expression of ribosomal proteins. The findings reported herein indicate that the ribosome complex, the subsequent protein processing and N-glycosylation-related processes are significantly and specifically upregulated in the brain capillaries of AD patients.
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Affiliation(s)
- Masayoshi Suzuki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Kenta Tezuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Takumi Handa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Risa Sato
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hina Takeuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Masaki Takao
- Department of Neurology and Brain Bank, Mihara Memorial Hospital, Isesaki, Japan.,Department of Clinical Laboratory, National Center of Neurology and Psychiatry, National Center Hospital, Kodaira, Japan
| | - Mitsutoshi Tano
- Department of Neurology and Brain Bank, Mihara Memorial Hospital, Isesaki, Japan
| | - Yasuo Uchida
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
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21
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Parys JB, Van Coppenolle F. Sec61 complex/translocon: The role of an atypical ER Ca 2+-leak channel in health and disease. Front Physiol 2022; 13:991149. [PMID: 36277220 PMCID: PMC9582130 DOI: 10.3389/fphys.2022.991149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/20/2022] [Indexed: 11/02/2023] Open
Abstract
The heterotrimeric Sec61 protein complex forms the functional core of the so-called translocon that forms an aqueous channel in the endoplasmic reticulum (ER). The primary role of the Sec61 complex is to allow protein import in the ER during translation. Surprisingly, a completely different function in intracellular Ca2+ homeostasis has emerged for the Sec61 complex, and the latter is now accepted as one of the major Ca2+-leak pathways of the ER. In this review, we first discuss the structure of the Sec61 complex and focus on the pharmacology and regulation of the Sec61 complex as a Ca2+-leak channel. Subsequently, we will pay particular attention to pathologies that are linked to Sec61 mutations, such as plasma cell deficiency and congenital neutropenia. Finally, we will explore the relevance of the Sec61 complex as a Ca2+-leak channel in various pathophysiological (ER stress, apoptosis, ischemia-reperfusion) and pathological (type 2 diabetes, cancer) settings.
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Affiliation(s)
- Jan B. Parys
- Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Leuven, Belgium
| | - Fabien Van Coppenolle
- CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Groupement Hospitalier EST, Department of Cardiology, Hospices Civils de Lyon, Lyon, France
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22
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Varone E, Chernorudskiy A, Cherubini A, Cattaneo A, Bachi A, Fumagalli S, Erol G, Gobbi M, Lenardo MJ, Borgese N, Zito E. ERO1 alpha deficiency impairs angiogenesis by increasing N-glycosylation of a proangiogenic VEGFA. Redox Biol 2022; 56:102455. [PMID: 36063727 PMCID: PMC9463388 DOI: 10.1016/j.redox.2022.102455] [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: 07/18/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
N-glycosylation and disulfide bond formation are two essential steps in protein folding that occur in the endoplasmic reticulum (ER) and reciprocally influence each other. Here, to analyze crosstalk between N-glycosylation and oxidation, we investigated how the protein disulfide oxidase ERO1-alpha affects glycosylation of the angiogenic VEGF121, a key regulator of vascular homeostasis. ERO1 deficiency, while retarding disulfide bond formation in VEGF121, increased utilization of its single N-glycosylation sequon, which lies close to an intra-polypeptide disulfide bridge, and concomitantly slowed its secretion. Unbiased mass-spectrometric analysis revealed interactions between VEGF121 and N-glycosylation pathway proteins in ERO1-knockout (KO), but not wild-type cells. Notably, MAGT1, a thioredoxin-containing component of the post-translational oligosaccharyltransferase complex, was a major hit exclusive to ERO1-deficient cells. Thus, both a reduced rate of formation of disulfide bridges, and the increased trapping potential of MAGT1 may increase N-glycosylation of VEGF121. Extending our investigation to tissues, we observed altered lectin staining of ERO1 KO breast tumor xenografts, implicating ERO1 as a physiologic regulator of protein N-glycosylation. Our study, highlighting the effect of ERO1 loss on N-glycosylation of proteins, is particularly relevant not only to angiogenesis but also to other cancer patho-mechanisms in light of recent findings suggesting a close causal link between alterations in protein glycosylation and cancer development.
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23
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Proteome and Glycoproteome Analyses Reveal the Protein N-Linked Glycosylation Specificity of STT3A and STT3B. Cells 2022; 11:cells11182775. [PMID: 36139350 PMCID: PMC9496733 DOI: 10.3390/cells11182775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
STT3A and STT3B are the main catalytic subunits of the oligosaccharyltransferase complex (OST-A and OST-B in mammalian cells), which primarily mediate cotranslational and post-translocational N-linked glycosylation, respectively. To determine the specificity of STT3A and STT3B, we performed proteomic and glycoproteomic analyses in the gene knock-out (KO) and wild-type HEK293 cells. In total, 3961 proteins, 4265 unique N-linked intact glycopeptides and 629 glycosites representing 349 glycoproteins were identified from all these cells. Deletion of the STT3A gene had a greater impact on the protein expression than deletion of STT3B, especially on glycoproteins. In addition, total mannosylated N-glycans were reduced and fucosylated N-glycans were increased in STT3A-KO cells, which were caused by the differential expression of glycan-related enzymes. Interestingly, hyperglycosylated proteins were identified in KO cells, and the hyperglycosylation of ENPL was caused by the endoplasmic reticulum (ER) stress due to the STT3A deletion. Furthermore, the increased expression of the ATF6 and PERK indicated that the unfolded protein response also happened in STT3A-KO cells. Overall, the specificity of STT3A and STT3B revealed that defects in the OST subunit not only broadly affect N-linked glycosylation of the protein but also affect protein expression.
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24
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Liu D, De Schutter K, Chen P, Smagghe G. The N-glycosylation-related genes as potential targets for RNAi-mediated pest control of the Colorado potato beetle (Leptinotarsa decemlineata). PEST MANAGEMENT SCIENCE 2022; 78:3815-3822. [PMID: 34821017 DOI: 10.1002/ps.6732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/09/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND N-glycosylation is one of the most common and important post-translational modifications in the eukaryotic cell. The study of protein N-glycosylation in several model insects confirmed the importance of this process in insect development, immunity, survival and fertility. The Colorado potato beetle (Leptinotarsa decemlineata) (CPB) is a common pest of Solanaceae crops. With the infamous title of champion of insecticide resistance, novel pest control strategies for this insect are needed. Luckily this pest insect is reported as very sensitive for the post-genomic technology of RNA interference (RNAi). RESULTS In this project, we investigated the importance of N-glycosylation in the survival and development of CPB using RNAi-mediated gene silencing of N-glycosylation-related genes (NGRGs) during the different transition steps from the larva, through the pupa to the adult stage. High mortality was observed in the larval stage with the silencing of early NGRGs, as STT3a, DAD1 and GCS1. With dsRNA against middle NGRGs, abnormal phenotypes at the ecdysis process and adult formation were observed, while the silencing of late NGRGs did not cause mortality. CONCLUSION The lethal phenotypes observed on silencing of the genes involved in the early processing steps of the N-glycosylation pathway suggest these genes are good candidates for RNAi-mediated control of CPB. Next to the gene-specific mechanism of RNAi for biosafety and possible implementation in integrated pest management, we believe these early NGRGs provide a possible alternative to the well-known target genes Snf7 and vacuolar ATPases that are now used in the first commercial RNAi-based products and thus they may be useful in the context of proactive resistance management. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Dongdong Liu
- Laboratory of Agrozoology, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kristof De Schutter
- Laboratory of Agrozoology, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Pengyu Chen
- Laboratory of Agrozoology, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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25
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Meyer BH, Adam PS, Wagstaff BA, Kolyfetis GE, Probst AJ, Albers SV, Dorfmueller HC. Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes. eLife 2022; 11:67448. [PMID: 35394422 PMCID: PMC8993221 DOI: 10.7554/elife.67448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/13/2022] [Indexed: 11/13/2022] Open
Abstract
Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.
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Affiliation(s)
- Benjamin H Meyer
- Environmental Microbiology and Biotechnology (EMB), Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany.,Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Panagiotis S Adam
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry University Duisburg-Essen, Essen, Germany
| | - Ben A Wagstaff
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - George E Kolyfetis
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexander J Probst
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Sonja V Albers
- Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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26
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A Review of Alpha-1 Antitrypsin Binding Partners for Immune Regulation and Potential Therapeutic Application. Int J Mol Sci 2022; 23:ijms23052441. [PMID: 35269582 PMCID: PMC8910375 DOI: 10.3390/ijms23052441] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Alpha-1 antitrypsin (AAT) is the canonical serine protease inhibitor of neutrophil-derived proteases and can modulate innate immune mechanisms through its anti-inflammatory activities mediated by a broad spectrum of protein, cytokine, and cell surface interactions. AAT contains a reactive methionine residue that is critical for its protease-specific binding capacity, whereby AAT entraps the protease on cleavage of its reactive centre loop, neutralises its activity by key changes in its tertiary structure, and permits removal of the AAT-protease complex from the circulation. Recently, however, the immunomodulatory role of AAT has come increasingly to the fore with several prominent studies focused on lipid or protein-protein interactions that are predominantly mediated through electrostatic, glycan, or hydrophobic potential binding sites. The aim of this review was to investigate the spectrum of AAT molecular interactions, with newer studies supporting a potential therapeutic paradigm for AAT augmentation therapy in disorders in which a chronic immune response is strongly linked.
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27
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Fenollar À, Ros-Lucas A, Pía Alberione M, Martínez-Peinado N, Ramírez M, Ángel Rosales-Motos M, Y. Lee L, Alonso-Padilla J, Izquierdo L. Compounds targeting GPI biosynthesis or N-glycosylation are active against Plasmodium falciparum. Comput Struct Biotechnol J 2022; 20:850-863. [PMID: 35222844 PMCID: PMC8841962 DOI: 10.1016/j.csbj.2022.01.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 02/07/2023] Open
Abstract
Compounds targeting key steps in GPI biosynthesis abrogate P. falciparum growth. N-glycosylation disruption halts parasite development and induces delayed death. Tunicamycin-induced delayed death is not linked with the synthesis of isoprenoids. In summary, two metabolic pathways are outlined for further drug target exploration.
The emergence of resistance to first-line antimalarials, including artemisinin, the last effective malaria therapy in some regions, stresses the urgent need to develop new effective treatments against this disease. The identification and validation of metabolic pathways that could be targeted for drug development may strongly contribute to accelerate this process. In this study, we use fully characterized specific inhibitors targeting glycan biosynthetic pathways as research tools to analyze their effects on the growth of the malaria parasite Plasmodium falciparum and to validate these metabolic routes as feasible chemotherapeutic targets. Through docking simulations using models predicted by AlphaFold, we also shed new light into the modes of action of some of these inhibitors. Molecules inhibiting N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase (GlcNAc-PI de-N-acetylase, PIGL/GPI12) or the inositol acyltransferase (GWT1), central for glycosylphosphatidylinositol (GPI) biosynthesis, halt the growth of intraerythrocytic asexual parasites during the trophozoite stages of the intraerythrocytic developmental cycle (IDC). Remarkably, the nucleoside antibiotic tunicamycin, which targets UDP-N-acetylglucosamine:dolichyl-phosphate N-acetylglucosaminephosphotransferase (ALG7) and N-glycosylation in other organisms, induces a delayed-death effect and inhibits parasite growth during the second IDC after treatment. Our data indicate that tunicamycin induces a specific inhibitory effect, hinting to a more substantial role of the N-glycosylation pathway in P. falciparum intraerythrocytic asexual stages than previously thought. To sum up, our results place GPI biosynthesis and N-glycosylation pathways as metabolic routes with potential to yield much-needed therapeutic targets against the parasite.
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Affiliation(s)
- Àngel Fenollar
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain
| | - Albert Ros-Lucas
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain
| | - María Pía Alberione
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain
| | - Nieves Martínez-Peinado
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain
| | - Miriam Ramírez
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain
| | - Miguel Ángel Rosales-Motos
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain
| | - Ling Y. Lee
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain
| | - Julio Alonso-Padilla
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Luis Izquierdo
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
- Corresponding author at: Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain.
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28
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Sun X, Guo C, Ali K, Zheng Q, Wei Q, Zhu Y, Wang L, Li G, Li W, Zheng B, Bai Q, Wu G. A Non-redundant Function of MNS5: A Class I α-1, 2 Mannosidase, in the Regulation of Endoplasmic Reticulum-Associated Degradation of Misfolded Glycoproteins. FRONTIERS IN PLANT SCIENCE 2022; 13:873688. [PMID: 35519817 PMCID: PMC9062699 DOI: 10.3389/fpls.2022.873688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/14/2022] [Indexed: 05/14/2023]
Abstract
Endoplasmic Reticulum-Associated Degradation (ERAD) is one of the major processes in maintaining protein homeostasis. Class I α-mannosidases MNS4 and MNS5 are involved in the degradation of misfolded variants of the heavily glycosylated proteins, playing an important role for glycan-dependent ERAD in planta. MNS4 and MNS5 reportedly have functional redundancy, meaning that only the loss of both MNS4 and MNS5 shows phenotypes. However, MNS4 is a membrane-associated protein while MNS5 is a soluble protein, and both can localize to the endoplasmic reticulum (ER). Furthermore, MNS4 and MNS5 differentially demannosylate the glycoprotein substrates. Importantly, we found that their gene expression patterns are complemented rather than overlapped. This raises the question of whether they indeed work redundantly, warranting a further investigation. Here, we conducted an exhaustive genetic screen for a suppressor of the bri1-5, a brassinosteroid (BR) receptor mutant with its receptor downregulated by ERAD, and isolated sbi3, a suppressor of bri1-5 mutant named after sbi1 (suppressor of bri1). After genetic mapping together with whole-genome re-sequencing, we identified a point mutation G343E in AT1G27520 (MNS5) in sbi3. Genetic complementation experiments confirmed that sbi3 was a loss-of-function allele of MNS5. In addition, sbi3 suppressed the dwarf phenotype of bri1-235 in the proteasome-independent ERAD pathway and bri1-9 in the proteasome-dependent ERAD pathway. Importantly, sbi3 could only affect BRI1/bri1 with kinase activities such that it restored BR-sensitivities of bri1-5, bri1-9, and bri1-235 but not null bri1. Furthermore, sbi3 was less tolerant to tunicamycin and salt than the wild-type plants. Thus, our study uncovers a non-redundant function of MNS5 in the regulation of ERAD as well as plant growth and ER stress response, highlighting a need of the traditional forward genetic approach to complement the T-DNA or CRISPR-Cas9 systems on gene functional study.
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29
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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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30
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Gallo GL, Valko A, Aguilar NH, Weisz AD, D'Alessio C. A novel fission yeast platform to model N-glycosylation and the bases of congenital disorders of glycosylation Type I. J Cell Sci 2021; 135:274232. [PMID: 34851357 DOI: 10.1242/jcs.259167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/18/2021] [Indexed: 11/20/2022] Open
Abstract
Congenital Disorders of Glycosylation Type I (CDG-I) are inherited human diseases caused by deficiencies in lipid-linked oligosaccharide (LLO) synthesis or the glycan transfer to proteins during N-glycosylation. We constructed a platform of 16 Schizosaccharomyces pombe mutant strains that synthesize all possible theoretical combinations of LLOs containing three to zero Glc and nine to five Man. The occurrence of unexpected LLOs suggested the requirement of specific Man residues for glucosyltransferases activities. We then quantified protein hypoglycosylation in each strain and found that in S. pombe the presence of Glc in the LLO is more relevant to the transfer efficiency than the amount of Man residues. Surprisingly, a decrease in the number of Man in glycans somehow improved the glycan transfer. The most severe hypoglycosylation was produced in cells completely lacking Glc and having a high number of Man. This deficiency could be reverted by expressing a single subunit OST with a broad range of substrate specificity. Our work shows the usefulness of this new S. pombe set of mutants as a platform to model the molecular bases of human CDG-I diseases.
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Affiliation(s)
- Giovanna L Gallo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Buenos Aires C1428EGA, Argentina.,Consejo Nacional de investigaciones Científicas y Técnicas (CONICET), Argentina.,Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina
| | - Ayelen Valko
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Buenos Aires C1428EGA, Argentina.,Consejo Nacional de investigaciones Científicas y Técnicas (CONICET), Argentina.,Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina
| | - Nathalia Herrera Aguilar
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Buenos Aires C1428EGA, Argentina.,Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina
| | - Ariel D Weisz
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Buenos Aires C1428EGA, Argentina
| | - Cecilia D'Alessio
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Buenos Aires C1428EGA, Argentina.,Consejo Nacional de investigaciones Científicas y Técnicas (CONICET), Argentina
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31
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Ding J, Xu J, Deng Q, Ma W, Zhang R, He X, Liu S, Zhang L. Knockdown of Oligosaccharyltransferase Subunit Ribophorin 1 Induces Endoplasmic-Reticulum-Stress-Dependent Cell Apoptosis in Breast Cancer. Front Oncol 2021; 11:722624. [PMID: 34778038 PMCID: PMC8578895 DOI: 10.3389/fonc.2021.722624] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/07/2021] [Indexed: 12/24/2022] Open
Abstract
Ribophorin 1 (RPN1) is a major part of Oligosaccharyltransferase (OST) complex, which is vital for the N-linked glycosylation. Though it has been verified that the abnormal glycosylation is closely related to the development of breast cancer, the detail role of RPN1 in breast cancer remains unknown. In this study, we explored the public databases to investigate the relationship between the expression levels of OST subunits and the prognosis of breast cancer. Then, we focused on the function of RPN1 in breast cancer and its potential mechanisms. Our study showed that the expression of several OST subunits including RPN1, RPN2, STT3A STT3B, and DDOST were upregulated in breast cancer samples. The protein expression level of RPN1 was also upregulated in breast cancer. Higher expression of RPN1 was correlated with worse clinical features and poorer prognosis. Furthermore, knockdown of RPN1 suppressed the proliferation and invasion of breast cancer cells in vitro and induced cell apoptosis triggered by endoplasmic reticulum stress. Our results identified the oncogenic function of RPN1 in breast cancer, implying that RPN1 might be a potential biomarker and therapeutic target for breast cancer.
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Affiliation(s)
- Jiajun Ding
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China.,Breast Surgery, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jiahui Xu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiaodan Deng
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Ma
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rui Zhang
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xueyan He
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China
| | - Suling Liu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lixing Zhang
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China
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32
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Epigenetically-regulated RPN2 gene influences lymphocyte activation and is involved in pathogenesis of rheumatoid arthritis. Gene 2021; 810:146059. [PMID: 34740730 DOI: 10.1016/j.gene.2021.146059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/22/2021] [Accepted: 10/29/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND To identify RA-associated genes and to ascertain epigenetic factors and functional mechanisms underlying RA pathogenesis. METHODS Peripheral blood mononuclear cells (PBMC) transcriptome- and proteome- wide gene expressions were profiled in a case-control study sample. Differentially expressed genes (DEGs) were discovered and validated independently. In-house PBMC genome-wide SNP genotyping data, miRNA expression data and DNA methylation data in the same sample were utilized to identify SNPs [expression quantitative trait locus (eQTLs) and protein quantitative trait locus (pQTLs)], miRNAs, and DNA methylation positions (DMPs) regulating key DEG of interest. Lentivirus transfection was conducted to study the effects of RPN2 on T lymphocyte activation, proliferation, apoptosis, and inflammatory cytokine expression. Rpn2 protein level in plasma was quantitated by ELISA to assess its performance in discriminating RA cases and controls. RESULTS Twenty-two DEGs were discovered in PBMCs. The most significant DEG, i.e., RPN2, was validated to be up-regulated with RA in PBMCs. A complex regulatory network for RPN2 gene expression in PBMCs was constructed, which consists of 38 eQTL and 53 pQTL SNPs, 3 miRNAs and 2 DMPs. Besides, RPN2 expression was significantly up-regulated with RA in primary T lymphocytes, as well as in PHA-activated T lymphocytes. RPN2 over-expression in T lymphocytes significantly inhibited apoptosis and IL-4 expression and promoted proliferation and activation. PBMCs-expressed RPN2 mRNA and plasma Rpn2 protein demonstrated superior and modest performances in discriminating RA cases and controls, respectively. CONCLUSIONS RPN2 gene influences T lymphocyte growth and activation and is involved in the pathogenesis of RA. Rpn2 may serve as a novel protein biomarker for RA diagnosis.
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Srinivasan K, Banerjee A, Baid P, Dhur A, Sengupta J. Ribosome-membrane crosstalk: Co-translational targeting pathways of proteins across membranes in prokaryotes and eukaryotes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:163-198. [PMID: 35034718 DOI: 10.1016/bs.apcsb.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ribosomes are the molecular machine of living cells designed for decoding mRNA-encoded genetic information into protein. Being sophisticated machinery, both in design and function, the ribosome not only carries out protein synthesis, but also coordinates several other ribosome-associated cellular processes. One such process is the translocation of proteins across or into the membrane depending on their secretory or membrane-associated nature. These proteins comprise a large portion of a cell's proteome and act as key factors for cellular survival as well as several crucial functional pathways. Protein transport to extra- and intra-cytosolic compartments (across the eukaryotic endoplasmic reticulum (ER) or across the prokaryotic plasma membrane) or insertion into membranes majorly occurs through an evolutionarily conserved protein-conducting channel called translocon (eukaryotic Sec61 or prokaryotic SecYEG channels). Targeting proteins to the membrane-bound translocon may occur via post-translational or co-translational modes and it is often mediated by recognition of an N-terminal signal sequence in the newly synthesizes polypeptide chain. Co-translational translocation is coupled to protein synthesis where the ribosome-nascent chain complex (RNC) itself is targeted to the translocon. Here, in the light of recent advances in structural and functional studies, we discuss our current understanding of the mechanistic models of co-translational translocation, coordinated by the actively translating ribosomes, in prokaryotes and eukaryotes.
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Affiliation(s)
- Krishnamoorthi Srinivasan
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aneek Banerjee
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priya Baid
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Ankit Dhur
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jayati Sengupta
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Pratama F, Linton D, Dixon N. Genetic and process engineering strategies for enhanced recombinant N-glycoprotein production in bacteria. Microb Cell Fact 2021; 20:198. [PMID: 34649588 PMCID: PMC8518210 DOI: 10.1186/s12934-021-01689-x] [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: 07/19/2021] [Accepted: 09/25/2021] [Indexed: 11/28/2022] Open
Abstract
Background The production of N-linked glycoproteins in genetically amenable bacterial hosts offers great potential for reduced cost, faster/simpler bioprocesses, greater customisation, and utility for distributed manufacturing of glycoconjugate vaccines and glycoprotein therapeutics. Efforts to optimize production hosts have included heterologous expression of glycosylation enzymes, metabolic engineering, use of alternative secretion pathways, and attenuation of gene expression. However, a major bottleneck to enhance glycosylation efficiency, which limits the utility of the other improvements, is the impact of target protein sequon accessibility during glycosylation. Results Here, we explore a series of genetic and process engineering strategies to increase recombinant N-linked glycosylation, mediated by the Campylobacter-derived PglB oligosaccharyltransferase in Escherichia coli. Strategies include increasing membrane residency time of the target protein by modifying the cleavage site of its secretion signal, and modulating protein folding in the periplasm by use of oxygen limitation or strains with compromised oxidoreductase or disulphide-bond isomerase activity. These approaches achieve up to twofold improvement in glycosylation efficiency. Furthermore, we also demonstrate that supplementation with the chemical oxidant cystine enhances the titre of glycoprotein in an oxidoreductase knockout strain by improving total protein production and cell fitness, while at the same time maintaining higher levels of glycosylation efficiency. Conclusions In this study, we demonstrate that improved protein glycosylation in the heterologous host could be achieved by mimicking the coordination between protein translocation, folding and glycosylation observed in native host such as Campylobacter jejuni and mammalian cells. Furthermore, it provides insight into strain engineering and bioprocess strategies, to improve glycoprotein yield and titre, and to avoid physiological burden of unfolded protein stress upon cell growth. The process and genetic strategies identified herein will inform further optimisation and scale-up of heterologous recombinant N-glycoprotein production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01689-x.
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Affiliation(s)
- Fenryco Pratama
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, M1 7DN, UK.,Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.,Microbial Biotechnology Research Group, School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Dennis Linton
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M1 7DN, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, M1 7DN, UK. .,Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
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Morgan BR, Massi F. The Role of Substrate Mediated Allostery in the Catalytic Competency of the Bacterial Oligosaccharyltransferase PglB. Front Mol Biosci 2021; 8:740904. [PMID: 34604309 PMCID: PMC8479172 DOI: 10.3389/fmolb.2021.740904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/24/2021] [Indexed: 11/30/2022] Open
Abstract
The oligosaccharyltransferase of Campylobacter lari (PglB) catalyzes the glycosylation of asparagine in the consensus sequence N-X-S/T, where X is any residue except proline. Molecular dynamics simulations of PglB bound to two different substrates were used to characterize the differences in the structure and dynamics of the substrate-enzyme complexes that can explain the higher catalytic efficiency observed for substrates containing threonine at the +2 position rather than serine. We observed that a threonine-containing substrate is more tightly bound than a serine-containing substrate. Because serine lacks a methyl group relative to threonine, the serine-containing peptide cannot stably form simultaneous van der Waals interactions with T316 and I572 as the threonine-containing substrate can. As a result, the peptide-PglB interaction is destabilized and the allosteric communication between the periplasmic domain and external loop EL5 is disrupted. These changes ultimately lead to the reorientation of the periplasmic domain relative to the transmembrane domain such that the two domains are further apart compared to PglB bound to the threonine-containing peptide. The crystal structure of PglB bound to the peptide and a lipid-linked oligosaccharide analog shows a pronounced closing of the periplasmic domain over the transmembrane domain in comparison to structures of PglB with peptide only, indicating that a closed conformation of the domains is needed for catalysis. The results of our studies suggest that lower enzymatic activity observed for serine versus threonine results from a combination of less stable binding and structural changes in PglB that influence the ability to form a catalytically competent state. This study illustrates a mechanism for substrate specificity via modulation of dynamic allosteric pathways.
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Affiliation(s)
- Brittany R Morgan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Francesca Massi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States
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The structure of an archaeal oligosaccharyltransferase provides insight into the strict exclusion of proline from the N-glycosylation sequon. Commun Biol 2021; 4:941. [PMID: 34354228 PMCID: PMC8342417 DOI: 10.1038/s42003-021-02473-8] [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: 04/02/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
Oligosaccharyltransferase (OST) catalyzes oligosaccharide transfer to the Asn residue in the N-glycosylation sequon, Asn-X-Ser/Thr, where Pro is strictly excluded at position X. Considering the unique structural properties of proline, this exclusion may not be surprising, but the structural basis for the rejection of Pro residues should be explained explicitly. Here we determined the crystal structure of an archaeal OST in a complex with a sequon-containing peptide and dolichol-phosphate to a 2.7 Å resolution. The sequon part in the peptide forms two inter-chain hydrogen bonds with a conserved amino acid motif, TIXE. We confirmed the essential role of the TIXE motif and the adjacent regions by extensive alanine-scanning of the external loop 5. A Ramachandran plot revealed that the ring structure of the Pro side chain is incompatible with the ϕ backbone dihedral angle around -150° in the rigid sequon-TIXE structure. The present structure clearly provides the structural basis for the exclusion of Pro residues from the N-glycosylation sequon.
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Liu C, Niu G, Li X, Zhang H, Chen H, Hou D, Lan P, Hong Z. Comparative Label-Free Quantitative Proteomics Analysis Reveals the Essential Roles of N-Glycans in Salt Tolerance by Modulating Protein Abundance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:646425. [PMID: 34276718 PMCID: PMC8283305 DOI: 10.3389/fpls.2021.646425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/02/2021] [Indexed: 06/01/2023]
Abstract
Many pieces of evidence show that the adaptive response of plants to salt stress requires the maturation of N-glycan on associated proteins. However, it is still little known about the salt-responsive glycoproteins that function in this process. In the present study, we identified salt-responsive glycoproteins in wild-type (WT) Arabidopsis and two mutants defective in N-glycan maturation, mns1 mns2 and cgl1. A total of 97 proteins with abundance changes of >1.5- or <0.67-fold were identified against salt stress by label-free liquid chromatography coupled mass spectrometry (LC-MS/MS) quantitative analyses. A comparison of differentially abundant glycoproteins (DAGs) indicated the substrate preferences regulated by MNS1/MNS2 and CGL1. In addition, the DAGs in mns1 mns2 hardly form functional regulatory networks in STRING analysis. Comparably, the regulatory network in cgl1 was visible and shared overlapping with that in WT. Such difference may supply the evidence to partially explain the lower salt sensitivity of mutant cgl1 than mns1 mns2. We further confirmed that two N-glycosylation clients, peroxidases PRX32 and PRX34, were involved in the salt stress response since the double mutants showed enhanced salt sensitivity. Together, our study provided proteomic evidence that N-glycans are crucial for modulating stress-responsive protein levels, and several novel glycoproteins responsible for salt stress tolerance in Arabidopsis were listed. Data are available via ProteomeXchange with identifier PXD006893.
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Affiliation(s)
- Chuanfa Liu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Guanting Niu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaowen Li
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Huchen Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Huawei Chen
- Research Center for Proteome Analysis, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dongxia Hou
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences (CAS), Nanjing, China
| | - Zhi Hong
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
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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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Zhang X. Alterations of Golgi Structural Proteins and Glycosylation Defects in Cancer. Front Cell Dev Biol 2021; 9:665289. [PMID: 34055798 PMCID: PMC8149618 DOI: 10.3389/fcell.2021.665289] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
As the central hub in the secretory and endocytic pathways, the Golgi apparatus continually receives the flow of cargos and serves as a major processing station in the cell. Due to its dynamic nature, a sophisticated and constantly remodeling mechanism needs to be set up to maintain the Golgi architecture and function in the non-stop trafficking of proteins and lipids. Abundant evidence has been accumulated that a well-organized Golgi structure is required for its proper functions, especially protein glycosylation. Remarkably, altered glycosylation has been a hallmark of most cancer cells. To understand the causes of Golgi defects in cancer, efforts have been made to characterize Golgi structural proteins under physiological and pathological conditions. This review summarizes the current knowledge of crucial Golgi structural proteins and their connections with tumor progression. We foresee that understanding the Golgi structural and functional defects may help solve the puzzle of whether glycosylation defect is a cause or effect of oncogenesis.
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Affiliation(s)
- Xiaoyan Zhang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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40
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Ahangama Liyanage L, Harris MS, Cook GA. In Vitro Glycosylation of Membrane Proteins Using N-Glycosyltransferase. ACS OMEGA 2021; 6:12133-12142. [PMID: 34056367 PMCID: PMC8154143 DOI: 10.1021/acsomega.1c00835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Glycoproteins are post-translationally modified proteins that take part in nearly every biological process and make up a large percent of the proteome. N-Linked glycosylation can be performed by N-glycosyltransferase (NGT), which recognizes the consensus amino acid sequence, -Asn-X-Ser/Thr- (NXT), within the protein. The enzyme catalyzes glycosidic bond formation between the oligosaccharide donor, containing nucleoside phosphatase, and the amide nitrogen of the asparagine residue. The attachment of the sugar moiety can influence physiological and biological properties of the protein by affecting their folding, modulating interactions with other biomolecules, and modifying their functions at the cellular level. We are specifically interested in the properties of membrane glycoproteins, which are key components in a number of different disease states. Therefore, the use of in vitro protein glycosylation can help further evaluate the effects of the properties for these important macromolecules. In vitro studies of N-linked glycosylation were done in a stepwise fashion in a membrane-mimetic environment to confirm that the methods for glycosylating soluble proteins could be applicable to membrane proteins. Detergent and lipid systems were used since hydrophobic peptides and membrane proteins are insoluble in aqueous solvents. The stepwise method consisted of the glycosylation of a soluble 7-residue peptide, a hydrophobic WALP-NVT peptide, and a γ-sarcoglycan membrane protein, all of which contained the glycosylation site Asn-Val-Thr (NVT). Glycosylation of the samples was performed using Escherichia coli-expressed NGT from the Actinobacillus pleuropneumoniae genome, and a single sugar moiety of glucose, provided from a nucleotide-linked donor, was added to the glycosylation site. Gel electrophoresis, mass spectrometry, and NMR studies were used for the detection of glycosyltransferase activity and to show the attachment of a single glucose molecule. Our experiments demonstrated that small or large membrane proteins that contain an N-glycosylation consensus sequence can be glycosylated by NGT in membrane-mimetic environments.
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Kerselidou D, Dohai BS, Nelson DR, Daakour S, De Cock N, Hassoun ZAO, Kim DK, Olivet J, El Assal DC, Jaiswal A, Alzahmi A, Saha D, Pain C, Matthijssens F, Lemaitre P, Herfs M, Chapuis J, Ghesquiere B, Vertommen D, Kriechbaumer V, Knoops K, Lopez-Iglesias C, van Zandvoort M, Lambert JC, Hanson J, Desmet C, Thiry M, Lauersen KJ, Vidal M, Van Vlierberghe P, Dequiedt F, Salehi-Ashtiani K, Twizere JC. Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. SCIENCE ADVANCES 2021; 7:7/19/eabe8349. [PMID: 33962942 PMCID: PMC8104865 DOI: 10.1126/sciadv.abe8349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/18/2021] [Indexed: 05/28/2023]
Abstract
The endoplasmic reticulum (ER) is a central eukaryotic organelle with a tubular network made of hairpin proteins linked by hydrolysis of guanosine triphosphate nucleotides. Among posttranslational modifications initiated at the ER level, glycosylation is the most common reaction. However, our understanding of the impact of glycosylation on the ER structure remains unclear. Here, we show that exostosin-1 (EXT1) glycosyltransferase, an enzyme involved in N-glycosylation, is a key regulator of ER morphology and dynamics. We have integrated multiomics and superresolution imaging to characterize the broad effect of EXT1 inactivation, including the ER shape-dynamics-function relationships in mammalian cells. We have observed that inactivating EXT1 induces cell enlargement and enhances metabolic switches such as protein secretion. In particular, suppressing EXT1 in mouse thymocytes causes developmental dysfunctions associated with the ER network extension. Last, our data illuminate the physical and functional aspects of the ER proteome-glycome-lipidome structure axis, with implications in biotechnology and medicine.
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Affiliation(s)
- Despoina Kerselidou
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Bushra Saeed Dohai
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - David R Nelson
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Nicolas De Cock
- TERRA Teaching and Research Centre, University of Liege, Liege, Belgium
| | - Zahra Al Oula Hassoun
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Dae-Kyum Kim
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Julien Olivet
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - Diana C El Assal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Ashish Jaiswal
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Deeya Saha
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Charlotte Pain
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Filip Matthijssens
- Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pierre Lemaitre
- GIGA-I3 Unit, GIGA Institute, University of Liege, Liege, Belgium
| | - Michael Herfs
- GIGA-Cancer Unit, GIGA Institute, University of Liege, Liege, Belgium
| | - Julien Chapuis
- Laboratory of Excellence Distalz, INSERM Unit 1167, Pasteur Institute of Lille, Lille, France
| | - Bart Ghesquiere
- Metabolomics Expertise Center, Center for Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Didier Vertommen
- de Duve Institute, Catholic University of Louvain, Brussels, Belgium
| | - Verena Kriechbaumer
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Kèvin Knoops
- Microscopy CORE Lab, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Carmen Lopez-Iglesias
- Microscopy CORE Lab, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Marc van Zandvoort
- Department of Cell Biology, School for Cardiovascular Diseases (CARIM), School for Nutrition and Translational Research in Metabolism (NUTRIM), School for Mental health and Neuroscience (MHeNS), and School for Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, Netherlands
| | - Jean-Charles Lambert
- Laboratory of Excellence Distalz, INSERM Unit 1167, Pasteur Institute of Lille, Lille, France
| | - Julien Hanson
- GIGA-Molecular Pharmacology, University of Liege, Liege, Belgium
| | | | - Marc Thiry
- Laboratory of cell and tissue Biology, GIGA-Neurosciences, University of Liege, Liege, Belgium
| | - Kyle J Lauersen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Franck Dequiedt
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium.
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium.
- TERRA Teaching and Research Centre, University of Liege, Liege, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
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Determination of Isomeric Glycan Structures by Permethylation and Liquid Chromatography-Mass Spectrometry (LC-MS). Methods Mol Biol 2021. [PMID: 33908015 DOI: 10.1007/978-1-0716-1241-5_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The existence of glycans in isomeric forms is responsible for the multifariousness of their properties and biological functions. Their altered expression has been associated with various diseases and cancers. Analysis of native glycans is not very sensitive due to the low ionization efficiency of glycans. These facts necessitate their comprehensive structural studies and establishes a high demand for sensitive and reliable techniques. In this chapter, we discuss the strategies for effective separation and identification of permethylated isomeric glycans. The sample preparation for permethylated glycans derived from model glycoproteins and complex biological samples, analyzed using LC-MS/MS, is delineated. We introduce protein extraction and release of glycans, followed by strategies to purify the released glycans, which are reduced and permethylated to improve ionization efficiency and stabilize sialic acid residues. High-temperature LC-based separation on PGC (porous graphitized carbon) column is conducive to isomeric separation of glycans and allows their sensitive identification and quantification using MS/MS.
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Mathew C, Weiß RG, Giese C, Lin CW, Losfeld ME, Glockshuber R, Riniker S, Aebi M. Glycan-protein interactions determine kinetics of N-glycan remodeling. RSC Chem Biol 2021; 2:917-931. [PMID: 34212152 PMCID: PMC8207518 DOI: 10.1039/d1cb00019e] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A hallmark of N-linked glycosylation in the secretory compartments of eukaryotic cells is the sequential remodeling of an initially uniform oligosaccharide to a site-specific, heterogeneous ensemble of glycostructures on mature proteins. To understand site-specific processing, we used protein disulfide isomerase (PDI), a model protein with five glycosylation sites, for molecular dynamics (MD) simulations and compared the result to a biochemical in vitro analysis with four different glycan processing enzymes. As predicted by an analysis of the accessibility of the N-glycans for their processing enzymes derived from the MD simulations, N-glycans at different glycosylation sites showed different kinetic properties for the processing enzymes. In addition, altering the tertiary structure of the glycoprotein PDI affected its N-glycan remodeling in a site-specific way. We propose that the observed differential N-glycan reactivities depend on the surrounding protein tertiary structure and lead to different glycan structures in the same protein through kinetically controlled processing pathways. Atomistic glycoprotein simulations reveal a site-specific availability of glycan substrates in time-resolved mass spectrometry of maturating enzyme kinetics.![]()
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Affiliation(s)
- Corina Mathew
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - R Gregor Weiß
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Christoph Giese
- Institute of Molecular Biology & Biophysics, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Chia-Wei Lin
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland .,Functional Genomics Center Zürich 8057 Zürich Switzerland
| | - Marie-Estelle Losfeld
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology & Biophysics, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
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44
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Zhang C, Cai M, Chen S, Zhang F, Cui T, Xue Z, Wang W, Zhang B, Liu X. The consensus N glyco -X-S/T motif and a previously unknown N glyco -N-linked glycosylation are necessary for growth and pathogenicity of Phytophthora. Environ Microbiol 2021; 23:5147-5163. [PMID: 33728790 DOI: 10.1111/1462-2920.15468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Asparagine (Asn, N)-linked glycosylation within Nglyco -X-S/T; X ≠ P motif is a ubiquitously distributed post-translational modification that participates in diverse cellular processes. In this work, N-glycosylation inhibitor was shown to prevent Phytophthora sojae growth, suggesting that N-glycosylation is necessary for oomycete development. We conducted a glycoproteomic analysis of P. sojae to identify and map N-glycosylated proteins and to quantify differentially expressed glycoproteins associated with mycelia, asexual cyst, and sexual oospore developmental stages. A total of 355 N-glycosylated proteins was found, containing 496 glycosites, potentially involved in glycan degradation, carbon metabolism, glycolysis, or other metabolic pathways. Through PNGase F deglycosylation assays and site-directed mutagenesis of a GPI transamidase protein (GPI16) upregulated in cysts and a heat shock protein 70 (HSP70) upregulated in oospores, we demonstrated that both proteins were N-glycosylated and that the Nglyco -N motif is a target site for asparagine - oligosaccharide linkage. Glycosite mutations of Asn 94 Nglyco -X-S/T in the GPI16 led to impaired cyst germination and pathogenicity, while mutation of the previously unknown Asn 270 Nglyco -N motif in HSP70 led to decreased oospore production. In addition to providing a map of the oomycete N-glycoproteome, this work confirms that P. sojae has evolved multiple N-glycosylation motifs essential for growth.
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Affiliation(s)
- Can Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Meng Cai
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Shanshan Chen
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Fan Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Tongshan Cui
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Zhaolin Xue
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Weizhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Borui Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
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45
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Verchère A, Cowton A, Jenni A, Rauch M, Häner R, Graumann J, Bütikofer P, Menon AK. Complexity of the eukaryotic dolichol-linked oligosaccharide scramblase suggested by activity correlation profiling mass spectrometry. Sci Rep 2021; 11:1411. [PMID: 33446867 PMCID: PMC7809446 DOI: 10.1038/s41598-020-80956-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/31/2020] [Indexed: 01/22/2023] Open
Abstract
The oligosaccharide required for asparagine (N)-linked glycosylation of proteins in the endoplasmic reticulum (ER) is donated by the glycolipid Glc3Man9GlcNAc2-PP-dolichol. Remarkably, whereas glycosylation occurs in the ER lumen, the initial steps of Glc3Man9GlcNAc2-PP-dolichol synthesis generate the lipid intermediate Man5GlcNAc2-PP-dolichol (M5-DLO) on the cytoplasmic side of the ER. Glycolipid assembly is completed only after M5-DLO is translocated to the luminal side. The membrane protein (M5-DLO scramblase) that mediates M5-DLO translocation across the ER membrane has not been identified, despite its importance for N-glycosylation. Building on our ability to recapitulate scramblase activity in proteoliposomes reconstituted with a crude mixture of ER membrane proteins, we developed a mass spectrometry-based 'activity correlation profiling' approach to identify scramblase candidates in the yeast Saccharomyces cerevisiae. Data curation prioritized six polytopic ER membrane proteins as scramblase candidates, but reconstitution-based assays and gene disruption in the protist Trypanosoma brucei revealed, unexpectedly, that none of these proteins is necessary for M5-DLO scramblase activity. Our results instead strongly suggest that M5-DLO scramblase activity is due to a protein, or protein complex, whose activity is regulated at the level of quaternary structure.
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Affiliation(s)
- Alice Verchère
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, NY, 10065, USA
| | - Andrew Cowton
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstr. 28, 3012, Bern, Switzerland
| | - Aurelio Jenni
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstr. 28, 3012, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstr. 43, 3012, Bern, Switzerland
| | - Monika Rauch
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstr. 28, 3012, Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestr. 3, 3012, Bern, Switzerland
| | - Johannes Graumann
- Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Ludwigstr. 43, 61231, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK), Rhine-Main site, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstr. 28, 3012, Bern, Switzerland.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, NY, 10065, USA.
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46
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Chaudhary BP, Zoetewey DL, McCullagh MJ, Mohanty S. NMR and MD Simulations Reveal the Impact of the V23D Mutation on the Function of Yeast Oligosaccharyltransferase Subunit Ost4. Glycobiology 2021; 31:838-850. [PMID: 33442744 DOI: 10.1093/glycob/cwab002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 11/14/2022] Open
Abstract
Asparagine-linked glycosylation, also known as N-linked glycosylation, is an essential and highly conserved co- and post-translational protein modification in eukaryotes and some prokaryotes. In the central step of this reaction, a carbohydrate moiety is transferred from a lipid-linked donor to the side-chain of a consensus asparagine in a nascent protein as it is synthesized at the ribosome. Complete loss of oligosaccharyltransferase (OST) function is lethal in eukaryotes. This reaction is carried out by a membrane-associated multi-subunit enzyme, OST, localized in the endoplasmic reticulum (ER). The smallest subunit, Ost4, contains a single membrane-spanning helix that is critical for maintaining stability and activity of OST. Mutation of any residue from Met18 to Ile24 of Ost4 destabilizes the enzyme complex, affecting its activity. Here, we report solution NMR structures and molecular dynamics simulations of Ost4 and Ost4V23D in micelles. Our studies revealed that while the point mutation did not impact the structure of the protein, it affected its position and solvent exposure in the membrane mimetic environment. Furthermore, our molecular dynamics simulations of the membrane-bound OST complex containing either WT or V23D mutant demonstrated disruption of most hydrophobic helix-helix interactions between Ost4V23D and transmembrane (TM)12 and TM13 of Stt3. This disengagement of Ost4V23D from the OST complex led to solvent exposure of the D23 residue in the hydrophobic pocket created by these interactions. Our study not only solves the structures of yeast Ost4 subunit and its mutant but also provides a basis for the destabilization of the OST complex and reduced OST activity.
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Affiliation(s)
- Bharat P Chaudhary
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
| | - David L Zoetewey
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
| | - Martin J McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
| | - Smita Mohanty
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
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47
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Florin-Christensen M, Rodriguez AE, Suárez CE, Ueti MW, Delgado FO, Echaide I, Schnittger L. N-Glycosylation in Piroplasmids: Diversity within Simplicity. Pathogens 2021; 10:50. [PMID: 33429911 PMCID: PMC7826898 DOI: 10.3390/pathogens10010050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/03/2023] Open
Abstract
N-glycosylation has remained mostly unexplored in Piroplasmida, an order of tick-transmitted pathogens of veterinary and medical relevance. Analysis of 11 piroplasmid genomes revealed three distinct scenarios regarding N-glycosylation: Babesia sensu stricto (s.s.) species add one or two N-acetylglucosamine (NAcGlc) molecules to proteins; Theileria equi and Cytauxzoon felis add (NAcGlc)2-mannose, while B. microti and Theileria s.s. synthesize dolichol-P-P-NAcGlc and dolichol-P-P-(NAcGlc)2 without subsequent transfer to proteins. All piroplasmids possess the gene complement needed for the synthesis of the N-glycosylation substrates, dolichol-P and sugar nucleotides. The oligosaccharyl transferase of Babesia species, T. equi and C. felis, is predicted to be composed of only two subunits, STT3 and Ost1. Occurrence of short N-glycans in B. bovis merozoites was experimentally demonstrated by fluorescence microscopy using a NAcGlc-specific lectin. In vitro growth of B. bovis was significantly impaired by tunicamycin, an inhibitor of N-glycosylation, indicating a relevant role for N-glycosylation in this pathogen. Finally, genes coding for N-glycosylation enzymes and substrate biosynthesis are transcribed in B. bovis blood and tick stages, suggesting that this pathway is biologically relevant throughout the parasite life cycle. Elucidation of the role/s exerted by N-glycans will increase our understanding of these successful parasites, for which improved control measures are needed.
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Affiliation(s)
- Monica Florin-Christensen
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - Anabel E. Rodriguez
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
| | - Carlos E. Suárez
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA; (C.E.S.); (M.W.U.)
- Animal Disease Research Unit, United States Department of Agricultural-Agricultural Research Service, Pullman, WA 99163, USA
| | - Massaro W. Ueti
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA; (C.E.S.); (M.W.U.)
- Animal Disease Research Unit, United States Department of Agricultural-Agricultural Research Service, Pullman, WA 99163, USA
| | - Fernando O. Delgado
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
| | - Ignacio Echaide
- Estación Experimental Agrícola INTA-Rafaela, Santa Fe, Provincia de Buenos Aires S2300, Argentina;
| | - Leonhard Schnittger
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
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48
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Kim T, Croce CM. MicroRNA and ER stress in cancer. Semin Cancer Biol 2021; 75:3-14. [PMID: 33422566 DOI: 10.1016/j.semcancer.2020.12.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/24/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022]
Abstract
The development of biological technologies in genomics, proteomics, and bioinformatics has led to the identification and characterization of the complete set of coding genes and their roles in various cellular pathways in cancer. Nevertheless, the cellular pathways have not been fully figured out like a jigsaw puzzle with missing pieces. The discovery of noncoding RNAs including microRNAs (miRNAs) has provided the missing pieces of the cellular pathways. Likewise, miRNAs have settled many questions of inexplicable patches in the endoplasmic reticulum (ER) stress pathways. The ER stress-caused pathways typified by the unfolded protein response (UPR) are pivotal processes for cellular homeostasis and survival, rectifying uncontrolled proteostasis and determining the cell fate. Although various factors and pathways have been studied and characterized, the understanding of the ER stress requires more wedges to fill the cracks of knowledge about the ER stress pathways. Moreover, the roles of the ER stress and UPR are still controversial in cancer despite their strong potential to promote cancer. The noncoding RNAs, in particular, miRNAs aid in a better understanding of the ER stress and its role in cancer. In this review, miRNAs that are the more-investigated subtype of noncoding RNAs are focused on the interpretation of the ER stress in cancer, following the introduction of miRNA and ER stress.
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Affiliation(s)
- Taewan Kim
- Department of Anatomy, Histology & Developmental Biology, Base for International Science and Technology Cooperation, Carson Cancer Stem Cell Vaccines R&D Center, International Cancer Center, Shenzhen University Health Science Center, Shenzhen 518055, China; The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA.
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49
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Yoo JY, Ko KS, Vu BN, Lee YE, Yoon SH, Pham TT, Kim JY, Lim JM, Kang YJ, Hong JC, Lee KO. N-acetylglucosaminyltransferase II Is Involved in Plant Growth and Development Under Stress Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:761064. [PMID: 34804097 PMCID: PMC8596550 DOI: 10.3389/fpls.2021.761064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/12/2021] [Indexed: 05/04/2023]
Abstract
Alpha-1,6-mannosyl-glycoprotein 2-β-N-acetylglucosaminyltransferase [EC 2.4.1.143, N-acetylglucosaminyltransferase II (GnTII)] catalyzes the transfer of N-acetylglucosamine (GlcNAc) residue from the nucleotide sugar donor UDP-GlcNAc to the α1,6-mannose residue of the di-antennary N-glycan acceptor GlcNAc(Xyl)Man3(Fuc)GlcNAc2 in the Golgi apparatus. Although the formation of the GlcNAc2(Xyl)Man3(Fuc)GlcNAc2 N-glycan is known to be associated with GnTII activity in Arabidopsis thaliana, its physiological significance is still not fully understood in plants. To address the physiological importance of the GlcNAc2(Xyl)Man3(Fuc)GlcNAc2 N-glycan, we examined the phenotypic effects of loss-of-function mutations in GnTII in the presence and absence of stress, and responsiveness to phytohormones. Prolonged stress induced by tunicamycin (TM) or sodium chloride (NaCl) treatment increased GnTII expression in wild-type Arabidopsis (ecotype Col-0) but caused severe developmental damage in GnTII loss-of-function mutants (gnt2-1 and gnt2-2). The absence of the 6-arm GlcNAc residue in the N-glycans in gnt2-1 facilitated the TM-induced unfolded protein response, accelerated dark-induced leaf senescence, and reduced cytokinin signaling, as well as susceptibility to cytokinin-induced root growth inhibition. Furthermore, gnt2-1 and gnt2-2 seedlings exhibited enhanced N-1-naphthylphthalamic acid-induced inhibition of tropic growth and development. Thus, GnTII's promotion of the 6-arm GlcNAc addition to N-glycans is important for plant growth and development under stress conditions, possibly via affecting glycoprotein folding and/or distribution.
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Affiliation(s)
- Jae Yong Yoo
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Jinju, South Korea
| | - Ki Seong Ko
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Jinju, South Korea
| | - Bich Ngoc Vu
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Jinju, South Korea
- Division of Applied Life Sciences (BK4 Program), Jinju, South Korea
| | - Young Eun Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Jinju, South Korea
- Division of Applied Life Sciences (BK4 Program), Jinju, South Korea
| | - Seok Han Yoon
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Jinju, South Korea
- Division of Applied Life Sciences (BK4 Program), Jinju, South Korea
| | - Thao Thi Pham
- Department of Chemistry, Changwon National University, Changwon, South Korea
| | - Ji-Yeon Kim
- Department of Chemistry, Changwon National University, Changwon, South Korea
| | - Jae-Min Lim
- Department of Chemistry, Changwon National University, Changwon, South Korea
| | - Yang Jae Kang
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Jinju, South Korea
- Division of Life Science, Jinju, South Korea
- Division of Bio & Medical Bigdata (BK4 Program), Gyeongsang National University, Jinju, South Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Jinju, South Korea
- Division of Applied Life Sciences (BK4 Program), Jinju, South Korea
- Division of Life Science, Jinju, South Korea
| | - Kyun Oh Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Jinju, South Korea
- Division of Applied Life Sciences (BK4 Program), Jinju, South Korea
- Division of Life Science, Jinju, South Korea
- *Correspondence: Kyun Oh Lee,
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50
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Yakovlieva L, Wood TM, Kemmink J, Kotsogianni I, Koller F, Lassak J, Martin NI, Walvoort MTC. A β-hairpin epitope as novel structural requirement for protein arginine rhamnosylation. Chem Sci 2020; 12:1560-1567. [PMID: 34163919 PMCID: PMC8179230 DOI: 10.1039/d0sc05823h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
For canonical asparagine glycosylation, the primary amino acid sequence that directs glycosylation at specific asparagine residues is well-established. Here we reveal that a recently discovered bacterial enzyme EarP, that transfers rhamnose to a specific arginine residue in its acceptor protein EF-P, specifically recognizes a β-hairpin loop. Notably, while the in vitro rhamnosyltransferase activity of EarP is abolished when presented with linear substrate peptide sequences derived from EF-P, the enzyme readily glycosylates the same sequence in a cyclized β-hairpin mimic. Additional studies with other substrate-mimicking cyclic peptides revealed that EarP activity is sensitive to the method used to induce cyclization and in some cases is tolerant to amino acid sequence variation. Using detailed NMR approaches, we established that the active peptide substrates all share some degree of β-hairpin formation, and therefore conclude that the β-hairpin epitope is the major determinant of arginine-rhamnosylation by EarP. Our findings add a novel recognition motif to the existing knowledge on substrate specificity of protein glycosylation, and are expected to guide future identifications of rhamnosylation sites in other protein substrates.
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Affiliation(s)
- Liubov Yakovlieva
- Chemical Biology Group, Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
| | - Thomas M Wood
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Leiden The Netherlands .,Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University Utrecht The Netherlands
| | - Johan Kemmink
- Chemical Biology Group, Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Leiden The Netherlands
| | - Franziska Koller
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München Planegg/Martinsried Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München Planegg/Martinsried Germany
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Leiden The Netherlands
| | - Marthe T C Walvoort
- Chemical Biology Group, Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
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