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Hussnaetter KP, Palm P, Pich A, Franzreb M, Rapp E, Elling L. Strategies for Automated Enzymatic Glycan Synthesis (AEGS). Biotechnol Adv 2023; 67:108208. [PMID: 37437855 DOI: 10.1016/j.biotechadv.2023.108208] [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: 12/22/2022] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Glycans are the most abundant biopolymers on earth and are constituents of glycoproteins, glycolipids, and proteoglycans with multiple biological functions. The availability of different complex glycan structures is of major interest in biotechnology and basic research of biological systems. High complexity, establishment of general and ubiquitous synthesis techniques, as well as sophisticated analytics, are major challenges in the development of glycan synthesis strategies. Enzymatic glycan synthesis with Leloir-glycosyltransferases is an attractive alternative to chemical synthesis as it can achieve quantitative regio- and stereoselective glycosylation in a single step. Various strategies for synthesis of a wide variety of different glycan structures has already be established and will exemplarily be discussed in the scope of this review. However, the application of enzymatic glycan synthesis in an automated system has high demands on the equipment, techniques, and methods. Different automation approaches have already been shown. However, while these techniques have been applied for several glycans, only a few strategies are able to conserve the full potential of enzymatic glycan synthesis during the process - economical and enzyme technological recycling of enzymes is still rare. In this review, we show the major challenges towards Automated Enzymatic Glycan Synthesis (AEGS). First, we discuss examples for immobilization of glycans or glycosyltransferases as an important prerequisite for the embedment and implementation in an enzyme reactor. Next, improvement of bioreactors towards automation will be described. Finally, analysis and monitoring of the synthesis process are discussed. Furthermore, automation processes and cycle design are highlighted. Accordingly, the transition of recent approaches towards a universal automated glycan synthesis platform will be projected. To this end, this review aims to describe essential key features for AEGS, evaluate the current state-of-the-art and give thought- encouraging impulses towards future full automated enzymatic glycan synthesis.
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Affiliation(s)
- Kai Philip Hussnaetter
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany
| | - Philip Palm
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany
| | - Andrij Pich
- Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry and DWI Leibniz-Institute for Interactive Materials e.V., RWTH Aachen University, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Matthias Franzreb
- Karlsruher Institute of Technology (KIT), Institute of Functional Interfaces, Hermann v. Helmholtz, Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Erdmann Rapp
- glyXera GmbH, Brenneckestrasse 20 * ZENIT, 39120 Magdeburg, Germany; Max Planck Institute for Dynamics of Complex Technical System, Bioprocess Engineering, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Lothar Elling
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany.
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2
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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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3
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Unione L, Ardá A, Jiménez-Barbero J, Millet O. NMR of glycoproteins: profiling, structure, conformation and interactions. Curr Opin Struct Biol 2020; 68:9-17. [PMID: 33129067 DOI: 10.1016/j.sbi.2020.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
In glycoproteins, carbohydrates are responsible for the selective interaction and tight regulation of cellular processes, constituting the main information transducer interface in protein-glycoprotein interactions. Increasing experimental and computational evidence suggest that such interactions often induce allosteric changes in the host protein, underlining the importance of studying intact glycoproteins. Technical issues have precluded such studies for years but, nowadays, a promising era is emerging where NMR spectroscopy, among other techniques, allows the characterization of the composition, structure and segmental dynamics of glycoproteins. In this review, we discuss such advances and highlight some selected examples. This novel technology unravels multiple new functional mechanisms, subtly hidden within the sugar code.
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Affiliation(s)
- Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Oscar Millet
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain.
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4
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Jaroentomeechai T, Taw MN, Li M, Aquino A, Agashe N, Chung S, Jewett MC, DeLisa MP. Cell-Free Synthetic Glycobiology: Designing and Engineering Glycomolecules Outside of Living Cells. Front Chem 2020; 8:645. [PMID: 32850660 PMCID: PMC7403607 DOI: 10.3389/fchem.2020.00645] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Glycans and glycosylated biomolecules are directly involved in almost every biological process as well as the etiology of most major diseases. Hence, glycoscience knowledge is essential to efforts aimed at addressing fundamental challenges in understanding and improving human health, protecting the environment and enhancing energy security, and developing renewable and sustainable resources that can serve as the source of next-generation materials. While much progress has been made, there remains an urgent need for new tools that can overexpress structurally uniform glycans and glycoconjugates in the quantities needed for characterization and that can be used to mechanistically dissect the enzymatic reactions and multi-enzyme assembly lines that promote their construction. To address this technology gap, cell-free synthetic glycobiology has emerged as a simplified and highly modular framework to investigate, prototype, and engineer pathways for glycan biosynthesis and biomolecule glycosylation outside the confines of living cells. From nucleotide sugars to complex glycoproteins, we summarize here recent efforts that harness the power of cell-free approaches to design, build, test, and utilize glyco-enzyme reaction networks that produce desired glycomolecules in a predictable and controllable manner. We also highlight novel cell-free methods for shedding light on poorly understood aspects of diverse glycosylation processes and engineering these processes toward desired outcomes. Taken together, cell-free synthetic glycobiology represents a promising set of tools and techniques for accelerating basic glycoscience research (e.g., deciphering the "glycan code") and its application (e.g., biomanufacturing high-value glycomolecules on demand).
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - May N. Taw
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Mingji Li
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Alicia Aquino
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Ninad Agashe
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Sean Chung
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
- Center for Synthetic Biology, Northwestern University, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
| | - Matthew P. DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
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5
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Synthesis of lipid-linked oligosaccharides by a compartmentalized multi-enzyme cascade for the in vitro N-glycosylation of peptides. J Biotechnol 2020; 322:54-65. [PMID: 32653637 DOI: 10.1016/j.jbiotec.2020.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/18/2020] [Accepted: 07/08/2020] [Indexed: 01/21/2023]
Abstract
A wide range of glycoproteins can be recombinantly expressed in aglycosylated forms in bacterial and cell-free production systems. To investigate the effect of glycosylation of these proteins on receptor binding, stability, efficacy as drugs, pharmacodynamics and pharmacokinetics, an efficient glycosylation platform is required. Here, we present a cell-free synthetic platform for the in vitro N-glycosylation of peptides mimicking the endoplasmic reticulum (ER) glycosylation machinery of eukaryotes. The one-pot, two compartment multi-enzyme cascade consisting of eight recombinant enzymes including the three Leloir glycosyltransferases, Alg1, Alg2 and Alg11, expressed in E. coli and S. cerevisiae, respectively, has been engineered to produce the core lipid-linked (LL) oligosaccharide mannopentaose-di-(N-acetylglucosamine) (LL-Man5). Pythanol (C20H42O), a readily available alcohol consisting of regular isoprenoid units, was utilized as the lipid anchor. As part of the cascade, GDP-mannose was de novo produced from the inexpensive substrates ADP, polyphosphate and mannose. To prevent enzyme inhibition, the nucleotide sugar cascade and the glycosyltransferase were segregated into two compartments by a cellulose ester membrane with 3.5 kDa cut-off allowing for the effective diffusion of GDP-mannose across compartments. Finally, as a proof-of-principle, pythanyl-linked Man5 and the single-subunit oligosaccharyltransferase Trypanosoma brucei STT3A expressed in Sf9 insect cells were used to in vitro N-glycosylate a synthetic peptide of ten amino acids bearing the eukaryotic consensus motif N-X-S/T.
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6
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Dow JM, Mauri M, Scott TA, Wren BW. Improving protein glycan coupling technology (PGCT) for glycoconjugate vaccine production. Expert Rev Vaccines 2020; 19:507-527. [DOI: 10.1080/14760584.2020.1775077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jennifer Mhairi Dow
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Marta Mauri
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Brendan William Wren
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
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Bokhari H, Maryam A, Shahid R, Siddiqi AR. Oligosaccharyltransferase PglB of Campylobacter jejuni is a glycoprotein. World J Microbiol Biotechnol 2019; 36:9. [PMID: 31858269 DOI: 10.1007/s11274-019-2784-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/10/2019] [Indexed: 11/29/2022]
Abstract
Campylobacter jejuni is the one of the leading cause of bacterial food borne gastroenteritis. PglB, a glycosyltransferase, plays a crucial role of mediating glycosylation of numerous periplasmic proteins. It catalyzes N-glycosylation at the sequon D/E-X1-N-X2-S/T in its substrate proteins. Here we report that the PglB itself is a glycoprotein which self-glycosylates at N534 site in its DYNQS sequon by its own catalytic WWDYG motif. Site-directed mutagenesis, lectin Immunoblot, and mobility shift assays confirmed that the DYNQS is an N-glycosylation motif. PglB's N-glycosylation motif is structurally and functionally similar to its widely studied glycosylation substrate, the OMPH1. Its DYNQS motif forms a solvent-exposed crest. This motif is close to a cluster of polar and hydrophilic residues, which form a loop flanked by two α helices. This arrangement extremely apposite for auto-glycosylation at N534. This self-glycosylation ability of PglB could mediate C. jejuni's ability to colonize the intestinal epithelium. Further this capability may also bear significance for the development of novel conjugated vaccines and diagnostic tests.
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Affiliation(s)
- Habib Bokhari
- Department of Biosciences, COMSATS University, Islamabad, Chak Shazad Campus, Islamabad, Pakistan.
| | - Arooma Maryam
- Department of Biosciences, COMSATS University, Islamabad, Chak Shazad Campus, Islamabad, Pakistan
| | - Ramla Shahid
- Department of Biosciences, COMSATS University, Islamabad, Chak Shazad Campus, Islamabad, Pakistan
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University, Islamabad, Chak Shazad Campus, Islamabad, Pakistan
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8
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Jervis AJ, Wood AG, Cain JA, Butler JA, Frost H, Lord E, Langdon R, Cordwell SJ, Wren BW, Linton D. Functional analysis of the Helicobacter pullorum N-linked protein glycosylation system. Glycobiology 2018; 28:233-244. [PMID: 29340583 PMCID: PMC6025236 DOI: 10.1093/glycob/cwx110] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/10/2018] [Indexed: 11/23/2022] Open
Abstract
N-linked protein glycosylation systems operate in species from all three domains of life. The model bacterial N-linked glycosylation system from Campylobacter jejuni is encoded by pgl genes present at a single chromosomal locus. This gene cluster includes the pglB oligosaccharyltransferase responsible for transfer of glycan from lipid carrier to protein. Although all genomes from species of the Campylobacter genus contain a pgl locus, among the related Helicobacter genus only three evolutionarily related species (H. pullorum, H. canadensis and H. winghamensis) potentially encode N-linked protein glycosylation systems. Helicobacter putative pgl genes are scattered in five chromosomal loci and include two putative oligosaccharyltransferase-encoding pglB genes per genome. We have previously demonstrated the in vitro N-linked glycosylation activity of H. pullorum resulting in transfer of a pentasaccharide to a peptide at asparagine within the sequon (D/E)XNXS/T. In this study, we identified the first H. pullorum N-linked glycoprotein, termed HgpA. Production of histidine-tagged HgpA in the background of insertional knockout mutants of H. pullorum pgl/wbp genes followed by analysis of HgpA glycan structures demonstrated the role of individual gene products in the PglB1-dependent N-linked protein glycosylation pathway. Glycopeptide purification by zwitterionic-hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry identified six glycosites from five H. pullorum proteins, which was consistent with proteins reactive with a polyclonal antiserum generated against glycosylated HgpA. This study demonstrates functioning of a H. pullorum N-linked general protein glycosylation system.
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Affiliation(s)
- Adrian J Jervis
- Manchester Institute of Biotechnology, SYNBIOCHEM, University of Manchester, Manchester, UK
| | - Alison G Wood
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Joel A Cain
- School of Molecular Bioscience and Charles Perkins Centre, The University of Sydney, 2006Australia
| | - Jonathan A Butler
- School of Healthcare Science, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - Helen Frost
- Faculty of Biology, Medicine and Health, Michael Smith Building, University of Manchester, Manchester M13 9PT, UK
| | - Elizabeth Lord
- Faculty of Biology, Medicine and Health, Michael Smith Building, University of Manchester, Manchester M13 9PT, UK
| | - Rebecca Langdon
- Pathogen Molecular Biology Unit, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Stuart J Cordwell
- School of Molecular Bioscience and Charles Perkins Centre, The University of Sydney, 2006Australia
| | - Brendan W Wren
- Pathogen Molecular Biology Unit, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Dennis Linton
- Faculty of Biology, Medicine and Health, Michael Smith Building, University of Manchester, Manchester M13 9PT, UK
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9
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Abstract
Glycosylation is one of the most prevalent posttranslational modifications that profoundly affects the structure and functions of proteins in a wide variety of biological recognition events. However, the structural complexity and heterogeneity of glycoproteins, usually resulting from the variations of glycan components and/or the sites of glycosylation, often complicates detailed structure-function relationship studies and hampers the therapeutic applications of glycoproteins. To address these challenges, various chemical and biological strategies have been developed for producing glycan-defined homogeneous glycoproteins. This review highlights recent advances in the development of chemoenzymatic methods for synthesizing homogeneous glycoproteins, including the generation of various glycosynthases for synthetic purposes, endoglycosidase-catalyzed glycoprotein synthesis and glycan remodeling, and direct enzymatic glycosylation of polypeptides and proteins. The scope, limitation, and future directions of each method are discussed.
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Affiliation(s)
- Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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10
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Metabolic engineering of glycoprotein biosynthesis in bacteria. Emerg Top Life Sci 2018; 2:419-432. [PMID: 33525794 DOI: 10.1042/etls20180004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/12/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023]
Abstract
The demonstration more than a decade ago that glycoproteins could be produced in Escherichia coli cells equipped with the N-linked protein glycosylation machinery from Campylobacter jejuni opened the door to using simple bacteria for the expression and engineering of complex glycoproteins. Since that time, metabolic engineering has played an increasingly important role in developing and optimizing microbial cell glyco-factories for the production of diverse glycoproteins and other glycoconjugates. It is becoming clear that future progress in creating efficient glycoprotein expression platforms in bacteria will depend on the adoption of advanced strain engineering strategies such as rational design and assembly of orthogonal glycosylation pathways, genome-wide identification of metabolic engineering targets, and evolutionary engineering of pathway performance. Here, we highlight recent advances in the deployment of metabolic engineering tools and strategies to develop microbial cell glyco-factories for the production of high-value glycoprotein targets with applications in research and medicine.
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11
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Behera A, Kulkarni SS. Chemical Synthesis of Rare, Deoxy-Amino Sugars Containing Bacterial Glycoconjugates as Potential Vaccine Candidates. Molecules 2018; 23:molecules23081997. [PMID: 30103434 PMCID: PMC6222762 DOI: 10.3390/molecules23081997] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/04/2018] [Accepted: 08/08/2018] [Indexed: 12/30/2022] Open
Abstract
Bacteria often contain rare deoxy amino sugars which are absent in the host cells. This structural difference can be harnessed for the development of vaccines. Over the last fifteen years, remarkable progress has been made toward the development of novel and efficient protocols for obtaining the rare sugar building blocks and their stereoselective assembly to construct conjugation ready bacterial glycans. In this review, we discuss the total synthesis of a variety of rare sugar containing bacterial glycoconjugates which are potential vaccine candidates.
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Affiliation(s)
- Archanamayee Behera
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Suvarn S Kulkarni
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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12
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Jaroentomeechai T, Stark JC, Natarajan A, Glasscock CJ, Yates LE, Hsu KJ, Mrksich M, Jewett MC, DeLisa MP. Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery. Nat Commun 2018; 9:2686. [PMID: 30002445 PMCID: PMC6043479 DOI: 10.1038/s41467-018-05110-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/06/2018] [Indexed: 12/13/2022] Open
Abstract
The emerging discipline of bacterial glycoengineering has made it possible to produce designer glycans and glycoconjugates for use as vaccines and therapeutics. Unfortunately, cell-based production of homogeneous glycoproteins remains a significant challenge due to cell viability constraints and the inability to control glycosylation components at precise ratios in vivo. To address these challenges, we describe a novel cell-free glycoprotein synthesis (CFGpS) technology that seamlessly integrates protein biosynthesis with asparagine-linked protein glycosylation. This technology leverages a glyco-optimized Escherichia coli strain to source cell extracts that are selectively enriched with glycosylation components, including oligosaccharyltransferases (OSTs) and lipid-linked oligosaccharides (LLOs). The resulting extracts enable a one-pot reaction scheme for efficient and site-specific glycosylation of target proteins. The CFGpS platform is highly modular, allowing the use of multiple distinct OSTs and structurally diverse LLOs. As such, we anticipate CFGpS will facilitate fundamental understanding in glycoscience and make possible applications in on demand biomanufacturing of glycoproteins. The ability to produce homogeneous glycoproteins is expected to advance fundamental understanding in glycoscience, but current in vivo-based production systems have several limitations. Here, the authors develop an E. coli extract-based one-pot system for customized production of N-linked glycoproteins.
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.,Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL, 60208-3120, USA.,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA
| | - Aravind Natarajan
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Cameron J Glasscock
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Laura E Yates
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Karen J Hsu
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute B224, Evanston, IL, 60208-3120, USA
| | - Milan Mrksich
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.,Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.,Department of Cell and Molecular Biology, Northwestern University, Chicago, IL, 60611, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL, 60208-3120, USA. .,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA. .,Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.
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13
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Interplay of Carbohydrate and Carrier in Antibacterial Glycoconjugate Vaccines. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 175:355-378. [PMID: 30143807 DOI: 10.1007/10_2018_71] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacterial infections are a serious health concern and are responsible for millions of illnesses and deaths each year in communities around the world. Vaccination is an important public health measure for reducing and eliminating this burden, and regions with comprehensive vaccination programs have achieved significant reductions in infection and mortality. This is often accomplished by immunization with bacteria-derived carbohydrates, typically in conjunction with other biomolecules, which induce immunological memory and durable protection against bacterial human pathogens. For many species, however, vaccines are currently unavailable or have suboptimal efficacy characterized by short-lived memory and incomplete protection, especially among at-risk populations. To address this challenge, new tools and techniques have emerged for engineering carbohydrates and conjugating them to carrier molecules in a tractable and scalable manner. Collectively, these approaches are yielding carbohydrate-based vaccine designs with increased immunogenicity and protective efficacy, thereby opening up new opportunities for this important class of antigens. In this chapter we detail the current understanding of how carbohydrates interact with the immune system to provide immunity; how glycoengineering, especially in the context of glycoconjugate vaccines, can be used to modify and enhance immune responses; and current trends and strategies being pursued for the rational design of next-generation glycosylated antibacterial vaccines. Graphical Abstract.
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14
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Silverman JM, Imperiali B. Bacterial N-Glycosylation Efficiency Is Dependent on the Structural Context of Target Sequons. J Biol Chem 2016; 291:22001-22010. [PMID: 27573243 DOI: 10.1074/jbc.m116.747121] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Indexed: 01/08/2023] Open
Abstract
Site selectivity of protein N-linked glycosylation is dependent on many factors, including accessibility of the modification site, amino acid composition of the glycosylation consensus sequence, and cellular localization of target proteins. Previous studies have shown that the bacterial oligosaccharyltransferase, PglB, of Campylobacter jejuni favors acceptor proteins with consensus sequences ((D/E)X1NX2(S/T), where X1,2 ≠ proline) in flexible, solvent-exposed motifs; however, several native glycoproteins are known to harbor consensus sequences within structured regions of the acceptor protein, suggesting that unfolding or partial unfolding is required for efficient N-linked glycosylation in the native environment. To derive insight into these observations, we generated structural homology models of the N-linked glycoproteome of C. jejuni This evaluation highlights the potential diversity of secondary structural conformations of previously identified N-linked glycosylation sequons. Detailed assessment of PglB activity with a structurally characterized acceptor protein, PEB3, demonstrated that this natively folded substrate protein is not efficiently glycosylated in vitro, whereas structural destabilization increases glycosylation efficiency. Furthermore, in vivo glycosylation studies in both glyco-competent Escherichia coli and the native system, C. jejuni, revealed that efficient glycosylation of glycoproteins, AcrA and PEB3, depends on translocation to the periplasmic space via the general secretory pathway. Our studies provide quantitative evidence that many acceptor proteins are likely to be N-linked-glycosylated before complete folding and suggest that PglB activity is coupled to general secretion-mediated translocation to the periplasm. This work extends our understanding of the molecular mechanisms underlying N-linked glycosylation in bacteria.
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Affiliation(s)
- Julie Michelle Silverman
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Barbara Imperiali
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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15
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Li L, Woodward RL, Han W, Qu J, Song J, Ma C, Wang PG. Chemoenzymatic synthesis of the bacterial polysaccharide repeating unit undecaprenyl pyrophosphate and its analogs. Nat Protoc 2016; 11:1280-98. [PMID: 27336706 DOI: 10.1038/nprot.2016.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polysaccharides are essential and immunologically relevant components of bacterial cell walls. These biomolecules can be found covalently attached to lipids (e.g., O-polysaccharide (PS) contains undecaprenyl and lipopolysaccharide (LPS) contains lipid A) or noncovalently associated with cell wells (e.g., capsular PS (CPS)). Although extensive genetic studies have indicated that the Wzy-dependent biosynthetic pathway is primarily responsible for producing such polysaccharides, in vitro biochemical studies are needed to determine, for example, which gene product is responsible for catalyzing each step in the pathway, and to reveal molecular details about the Wzx translocase, Wzy polymerase and O-PS chain-length determinant. Many of these biochemical studies require access to a structurally well-defined PS repeating unit undecaprenyl pyrophosphate (RU-PP-Und), the key building block in this pathway. We describe herein the chemoenzymatic synthesis of Escherichia coli (serotype O157) RU-PP-Und. This involves (i) chemical synthesis of precursor N-acetyl-D-galactosamine (GalNAc)-PP-Und (2 weeks) and (ii) enzymatic extension of the precursor to produce RU-PP-Und (2 weeks). Undecaprenyl phosphate and peracetylated GalNAc-1-phosphate are prepared from commercially available undecaprenol and peracetylated GalNAc. The chemical coupling of these two products, followed by structural confirmation (mass spectrometry and NMR) and deprotection, generates GalNAc-PP-Und. This compound is then sequentially modified by enzymes in the E. coli serotype O157 (E. coli O157) O-PS biosynthetic pathway. Three glycosyltransferases (GTs) are involved (WbdN, WbdO and WbdP) and they transfer glucose (Glc), L-fucose (L-Fuc) and N-acetylperosamine (PerNAc) onto GalNAc-PP-Und to form the intact RU-PP-Und in a stepwise manner. Final compounds and intermediates are confirmed by mass spectrometry. The procedure can be adapted to the synthesis of analogs with different PS or lipid moieties.
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Affiliation(s)
- Lei Li
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Robert L Woodward
- Department of Chemistry and Biochemistry, University of Mount Union, Alliance, Ohio, USA
| | - Weiqing Han
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Jingyao Qu
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Jing Song
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Cheng Ma
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Peng G Wang
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
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16
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Moradi SV, Hussein WM, Varamini P, Simerska P, Toth I. Glycosylation, an effective synthetic strategy to improve the bioavailability of therapeutic peptides. Chem Sci 2016; 7:2492-2500. [PMID: 28660018 PMCID: PMC5477030 DOI: 10.1039/c5sc04392a] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/26/2016] [Indexed: 01/22/2023] Open
Abstract
Glycosylation of peptides is a promising strategy for modulating the physicochemical properties of peptide drugs and for improving their absorption through biological membranes. This review highlights various methods for the synthesis of glycoconjugates and recent progress in the development of glycosylated peptide therapeutics. Furthermore, the impacts of glycosylation in overcoming the existing barriers that restrict oral and brain delivery of peptides are described herein.
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Affiliation(s)
- Shayli Varasteh Moradi
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia .
| | - Waleed M Hussein
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia .
| | - Pegah Varamini
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia .
| | - Pavla Simerska
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia .
| | - Istvan Toth
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia .
- Institute for Molecular Bioscience , The University of Queensland , St. Lucia , QLD 4072 , Australia
- The University of Queensland , School of Pharmacy , Brisbane , QLD 4072 , Australia
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17
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Zemella A, Thoring L, Hoffmeister C, Kubick S. Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems. Chembiochem 2015; 16:2420-31. [PMID: 26478227 PMCID: PMC4676933 DOI: 10.1002/cbic.201500340] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/07/2023]
Abstract
From its start as a small-scale in vitro system to study fundamental translation processes, cell-free protein synthesis quickly rose to become a potent platform for the high-yield production of proteins. In contrast to classical in vivo protein expression, cell-free systems do not need time-consuming cloning steps, and the open nature provides easy manipulation of reaction conditions as well as high-throughput potential. Especially for the synthesis of difficult to express proteins, such as toxic and transmembrane proteins, cell-free systems are of enormous interest. The modification of the genetic code to incorporate non-canonical amino acids into the target protein in particular provides enormous potential in biotechnology and pharmaceutical research and is in the focus of many cell-free projects. Many sophisticated cell-free systems for manifold applications have been established. This review describes the recent advances in cell-free protein synthesis and details the expanding applications in this field.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
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18
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The sweet tooth of bacteria: common themes in bacterial glycoconjugates. Microbiol Mol Biol Rev 2015; 78:372-417. [PMID: 25184559 DOI: 10.1128/mmbr.00007-14] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Humans have been increasingly recognized as being superorganisms, living in close contact with a microbiota on all their mucosal surfaces. However, most studies on the human microbiota have focused on gaining comprehensive insights into the composition of the microbiota under different health conditions (e.g., enterotypes), while there is also a need for detailed knowledge of the different molecules that mediate interactions with the host. Glycoconjugates are an interesting class of molecules for detailed studies, as they form a strain-specific barcode on the surface of bacteria, mediating specific interactions with the host. Strikingly, most glycoconjugates are synthesized by similar biosynthesis mechanisms. Bacteria can produce their major glycoconjugates by using a sequential or an en bloc mechanism, with both mechanistic options coexisting in many species for different macromolecules. In this review, these common themes are conceptualized and illustrated for all major classes of known bacterial glycoconjugates, with a special focus on the rather recently emergent field of glycosylated proteins. We describe the biosynthesis and importance of glycoconjugates in both pathogenic and beneficial bacteria and in both Gram-positive and -negative organisms. The focus lies on microorganisms important for human physiology. In addition, the potential for a better knowledge of bacterial glycoconjugates in the emerging field of glycoengineering and other perspectives is discussed.
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19
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Ishiwata A, Taguchi Y, Lee YJ, Watanabe T, Kohda D, Ito Y. N-Glycosylation with synthetic undecaprenyl pyrophosphate-linked oligosaccharide to oligopeptides by PglB oligosaccharyltransferase from Campylobacter jejuni. Chembiochem 2015; 16:731-7. [PMID: 25688550 DOI: 10.1002/cbic.201402658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 11/11/2022]
Abstract
The oligosaccharyltransferase PglB from Campylobacter jejuni catalyses the N-glycosylation reaction with undecaprenyl-pyrophosphate-linked Glc1 GalNAc5 Bac1 (Und-PP-Glc1 GalNAc5 Bac1 ). Experiments using chemically synthesized donors coupled to fluorescently tagged peptides confirmed that biosynthetic intermediate Und-PP-Bac1 and Und-PP-GalNAc2 Bac1 are transferred efficiently to the Asn residue in the consensus sequence (D/E-X'-N-X-T/S, X',X≠P). The products were analyzed in detail by tandem MS to confirm their chemical structures.
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20
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Wang LX, Amin MN. Chemical and chemoenzymatic synthesis of glycoproteins for deciphering functions. ACTA ACUST UNITED AC 2015; 21:51-66. [PMID: 24439206 DOI: 10.1016/j.chembiol.2014.01.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 12/31/2013] [Accepted: 01/02/2014] [Indexed: 12/11/2022]
Abstract
Glycoproteins are an important class of biomolecules involved in a number of biological recognition processes. However, natural and recombinant glycoproteins are usually produced as mixtures of glycoforms that differ in the structures of the pendent glycans, which are difficult to separate in pure glycoforms. As a result, synthetic homogeneous glycopeptides and glycoproteins have become indispensable probes for detailed structural and functional studies. A number of elegant chemical and biological strategies have been developed for synthetic construction of tailor-made, full-size glycoproteins to address specific biological problems. In this review, we highlight recent advances in chemical and chemoenzymatic synthesis of homogeneous glycoproteins. Selected examples are given to demonstrate the applications of tailor-made, glycan-defined glycoproteins for deciphering glycosylation functions.
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Affiliation(s)
- Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Mohammed N Amin
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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21
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Srichaisupakit A, Ohashi T, Misaki R, Fujiyama K. Production of initial-stage eukaryotic N-glycan and its protein glycosylation in Escherichia coli. J Biosci Bioeng 2014; 119:399-405. [PMID: 25449758 DOI: 10.1016/j.jbiosc.2014.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 09/13/2014] [Accepted: 09/17/2014] [Indexed: 11/20/2022]
Abstract
N-Glycosylation is a ubiquitous protein post-translational modification mechanism in eukaryotes. In this work, a synthetic pathway containing glycosyltransferases from Saccharomyces cerevisiae was introduced to Escherichia coli to synthesize lipid-linked mannosyl-chitobiose (Man-GlcNAc2) and trimannosyl-chitobiose (Man3-GlcNAc2). Transfer of Man3-GlcNAc2 onto a model periplasmic protein occurred in the engineered E. coli cell using oligosaccharyltransferase PglB from Campylobacter jejuni. Mass spectrometric analysis of the fluorescently labeled N-glycan indicated a glycan signal composed of 2 HexNAc and 3 Hex residues. The reversed-phase HPLC analysis suggested that the Hex residues were α1,3-, α1,6- and β1,4-linked mannoses. These results indicated that the constructed system synthesizes a Man3-GlcNAc2, identical to that observed in an early eukaryotic dolichol pathway. Finally, glycopeptide mass spectrometry confirmed the transfer of the assembled glycan moiety onto an engineered glycosylation motif of recombinant maltose binding protein. Surprisingly, the Man3-GlcNAc2 structure but not Man-GlcNAc2 was transferred onto maltose binding protein. This work showed that PglB protein might be able to accommodate the transfer of the further engineered glycan with greater complexity.
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Affiliation(s)
| | - Takao Ohashi
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryo Misaki
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan.
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22
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Srichaisupakit A, Ohashi T, Fujiyama K. Identification of a protein glycosylation operon from Campylobacter jejuni JCM 2013 and its heterologous expression in Escherichia coli. J Biosci Bioeng 2014; 118:256-62. [DOI: 10.1016/j.jbiosc.2014.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 02/01/2014] [Accepted: 02/11/2014] [Indexed: 01/23/2023]
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23
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Meyer BH, Albers SV. AglB, catalyzing the oligosaccharyl transferase step of the archaeal N-glycosylation process, is essential in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. Microbiologyopen 2014; 3:531-43. [PMID: 24916761 PMCID: PMC4287180 DOI: 10.1002/mbo3.185] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/01/2014] [Accepted: 05/15/2014] [Indexed: 11/10/2022] Open
Abstract
Sulfolobus acidocaldarius, a thermo-acidophilic crenarchaeon which grows optimally at 76°C and pH 3, exhibits an astonishing high number of N-glycans linked to the surface (S-) layer proteins. The S-layer proteins as well as other surface-exposed proteins are modified via N-glycosylation, in which the oligosaccharyl transferase AglB catalyzes the final step of the transfer of the glycan tree to the nascent protein. In this study, we demonstrated that AglB is essential for the viability of S. acidocaldarius. Different deletion approaches, that is, markerless in-frame deletion as well as a marker insertion were unsuccessful to create an aglB deletion mutant. Only the integration of a second aglB gene copy allowed the successful deletion of the original aglB.
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Affiliation(s)
| | - Sonja-Verena Albers
- Correspondence S. V. Albers, Molecular Biology of Archaea, Max-Planck Institute for terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg. Tel: +496421178426;, Fax: +496421178429;, E-mail:
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24
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Jarrell KF, Ding Y, Meyer BH, Albers SV, Kaminski L, Eichler J. N-linked glycosylation in Archaea: a structural, functional, and genetic analysis. Microbiol Mol Biol Rev 2014; 78:304-41. [PMID: 24847024 PMCID: PMC4054257 DOI: 10.1128/mmbr.00052-13] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N-glycosylation of proteins is one of the most prevalent posttranslational modifications in nature. Accordingly, a pathway with shared commonalities is found in all three domains of life. While excellent model systems have been developed for studying N-glycosylation in both Eukarya and Bacteria, an understanding of this process in Archaea was hampered until recently by a lack of effective molecular tools. However, within the last decade, impressive advances in the study of the archaeal version of this important pathway have been made for halophiles, methanogens, and thermoacidophiles, combining glycan structural information obtained by mass spectrometry with bioinformatic, genetic, biochemical, and enzymatic data. These studies reveal both features shared with the eukaryal and bacterial domains and novel archaeon-specific aspects. Unique features of N-glycosylation in Archaea include the presence of unusual dolichol lipid carriers, the use of a variety of linking sugars that connect the glycan to proteins, the presence of novel sugars as glycan constituents, the presence of two very different N-linked glycans attached to the same protein, and the ability to vary the N-glycan composition under different growth conditions. These advances are the focus of this review, with an emphasis on N-glycosylation pathways in Haloferax, Methanococcus, and Sulfolobus.
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Affiliation(s)
- Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Yan Ding
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Benjamin H Meyer
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lina Kaminski
- Department of Life Sciences, Ben Gurion University, Beersheva, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University, Beersheva, Israel
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25
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Lizak C, Gerber S, Michaud G, Schubert M, Fan YY, Bucher M, Darbre T, Aebi M, Reymond JL, Locher KP. Unexpected reactivity and mechanism of carboxamide activation in bacterial N-linked protein glycosylation. Nat Commun 2014; 4:2627. [PMID: 24149797 DOI: 10.1038/ncomms3627] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/16/2013] [Indexed: 11/09/2022] Open
Abstract
The initial glycan transfer in asparagine-linked protein glycosylation is catalysed by the integral membrane enzyme oligosaccharyltransferase (OST). Here we study the mechanism of the bacterial PglB protein, a single-subunit OST, using chemically synthesized acceptor peptide analogues. We find that PglB can glycosylate not only asparagine but also glutamine, homoserine and the hydroxamate Asp(NHOH), although at much lower rates. In contrast, N-methylated asparagine or 2,4-diaminobutanoic acid (Dab) are not glycosylated. We find that of the various peptide analogues, only asparagine- or Dab-containing peptides bind tightly to PglB. Glycopeptide products are unable to bind, providing the driving force of product release. We find no suitably positioned residues near the active site of PglB that can activate the acceptor asparagine by deprotonation, making a general base mechanism unlikely and leaving carboxamide twisting as the most likely mechanistic proposal for asparagine activation.
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Affiliation(s)
- Christian Lizak
- 1] Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland [2]
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26
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Genes involved in the endoplasmic reticulum N-glycosylation pathway of the red microalga Porphyridium sp.: a bioinformatic study. Int J Mol Sci 2014; 15:2305-26. [PMID: 24514561 PMCID: PMC3958852 DOI: 10.3390/ijms15022305] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/13/2014] [Accepted: 01/23/2014] [Indexed: 11/17/2022] Open
Abstract
N-glycosylation is one of the most important post-translational modifications that influence protein polymorphism, including protein structures and their functions. Although this important biological process has been extensively studied in mammals, only limited knowledge exists regarding glycosylation in algae. The current research is focused on the red microalga Porphyridium sp., which is a potentially valuable source for various applications, such as skin therapy, food, and pharmaceuticals. The enzymes involved in the biosynthesis and processing of N-glycans remain undefined in this species, and the mechanism(s) of their genetic regulation is completely unknown. In this study, we describe our pioneering attempt to understand the endoplasmic reticulum N-Glycosylation pathway in Porphyridium sp., using a bioinformatic approach. Homology searches, based on sequence similarities with genes encoding proteins involved in the ER N-glycosylation pathway (including their conserved parts) were conducted using the TBLASTN function on the algae DNA scaffold contigs database. This approach led to the identification of 24 encoded-genes implicated with the ER N-glycosylation pathway in Porphyridium sp. Homologs were found for almost all known N-glycosylation protein sequences in the ER pathway of Porphyridium sp.; thus, suggesting that the ER-pathway is conserved; as it is in other organisms (animals, plants, yeasts, etc.).
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27
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Liu F, Vijayakrishnan B, Faridmoayer A, Taylor TA, Parsons TB, Bernardes GJL, Kowarik M, Davis BG. Rationally designed short polyisoprenol-linked PglB substrates for engineered polypeptide and protein N-glycosylation. J Am Chem Soc 2013; 136:566-9. [PMID: 24377322 DOI: 10.1021/ja409409h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The lipid carrier specificity of the protein N-glycosylation enzyme C. jejuni PglB was tested using a logical, synthetic array of natural and unnatural C10, C20, C30, and C40 polyisoprenol sugar pyrophosphates, including those bearing repeating cis-prenyl units. Unusual, short, synthetically accessible C20 prenols (nerylnerol 1d and geranylnerol 1e) were shown to be effective lipid carriers for PglB sugar substrates. Kinetic analyses for PglB revealed clear K(M)-only modulation with lipid chain length, thereby implicating successful in vitro application at appropriate concentrations. This was confirmed by optimized, efficient in vitro synthesis allowing >90% of Asn-linked β-N-GlcNAc-ylated peptide and proteins. This reveals a simple, flexible biocatalytic method for glycoconjugate synthesis using PglB N-glycosylation machinery and varied chemically synthesized glycosylation donor precursors.
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Affiliation(s)
- Feng Liu
- Department of Chemistry, Chemistry Research Laboratory, Oxford University , Oxford OX1 3TA United Kingdom
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28
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Hartley MD, Schneggenburger PE, Imperiali B. Lipid bilayer nanodisc platform for investigating polyprenol-dependent enzyme interactions and activities. Proc Natl Acad Sci U S A 2013; 110:20863-70. [PMID: 24302767 PMCID: PMC3876266 DOI: 10.1073/pnas.1320852110] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Membrane-bound polyprenol-dependent pathways are important for the assembly of essential glycoconjugates in all domains of life. However, despite their prevalence, the functional significance of the extended linear polyprenyl groups in the interactions of the glycan substrates, the biosynthetic enzymes that act upon them, and the membrane bilayer in which they are embedded remains a mystery. These interactions are investigated simultaneously and uniquely through application of the nanodisc membrane technology. The Campylobacter jejuni N-linked glycosylation pathway has been chosen as a model pathway in which all of the enzymes and substrates are biochemically accessible. We present the functional reconstitution of two enzymes responsible for the early membrane-committed steps in glycan assembly. Protein stoichiometry analysis, fluorescence-based approaches, and biochemical activity assays are used to demonstrate the colocalization of the two enzymes in nanodiscs. Isotopic labeling of the substrates reveals that undecaprenyl-phosphate is coincorporated into discs with the two enzymes, and furthermore, that both enzymes are functionally reconstituted and can sequentially convert the coembedded undecaprenyl-phosphate into undecaprenyl-diphosphate-linked disaccharide. These studies provide a proof-of-concept demonstrating that the nanodisc model membrane system represents a promising experimental platform for analyzing the multifaceted interactions among the enzymes involved in polyprenol-dependent glycan assembly pathways, the membrane-associated substrates, and the lipid bilayer. The stage is now set for exploration of the roles of the conserved polyprenols in promoting protein-protein interactions among pathway enzymes and processing of substrates through sequential steps in membrane-associated glycan assembly.
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Affiliation(s)
| | | | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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29
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Cain JA, Solis N, Cordwell SJ. Beyond gene expression: the impact of protein post-translational modifications in bacteria. J Proteomics 2013; 97:265-86. [PMID: 23994099 DOI: 10.1016/j.jprot.2013.08.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/08/2013] [Accepted: 08/10/2013] [Indexed: 12/12/2022]
Abstract
The post-translational modification (PTM) of proteins plays a critical role in the regulation of a broad range of cellular processes in eukaryotes. Yet their role in governing similar systems in the conventionally presumed 'simpler' forms of life has been largely neglected and, until recently, was thought to occur only rarely, with some modifications assumed to be limited to higher organisms alone. Recent developments in mass spectrometry-based proteomics have provided an unparalleled power to enrich, identify and quantify peptides with PTMs. Additional modifications to biological molecules such as lipids and carbohydrates that are essential for bacterial pathophysiology have only recently been detected on proteins. Here we review bacterial protein PTMs, focusing on phosphorylation, acetylation, proteolytic degradation, methylation and lipidation and the roles they play in bacterial adaptation - thus highlighting the importance of proteomic techniques in a field that is only just in its infancy. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Joel A Cain
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Nestor Solis
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Stuart J Cordwell
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006, Australia.
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Biochemical evidence for an alternate pathway in N-linked glycoprotein biosynthesis. Nat Chem Biol 2013; 9:367-73. [PMID: 23624439 PMCID: PMC3661703 DOI: 10.1038/nchembio.1249] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 04/01/2013] [Indexed: 11/09/2022]
Abstract
Asparagine-linked glycosylation is a complex protein modification conserved among all three domains of life. Herein we report the in vitro analysis of N-linked glycosylation from the methanogenic archaeon Methanococcus voltae. Using a suite of synthetic and semisynthetic substrates, we show that AglK initiates N-linked glycosylation in M. voltae through the formation of α-linked dolichyl monophosphate N-acetylglucosamine (Dol-P-GlcNAc), which contrasts with the polyprenyl-diphosphate intermediates that feature in both eukaryotes and bacteria. Intriguingly, AglK exhibits high sequence homology to dolichyl-phosphate β-glucosyltransferases, including Alg5 in eukaryotes, suggesting a common evolutionary origin. The combined action of the first two enzymes, AglK and AglC, afforded an α-linked Dol-P-glycan that serves as a competent substrate for the archaeal oligosaccharyl transferase AglB. These studies provide the first biochemical evidence revealing that despite the apparent similarity of the overall pathways, there are actually two general strategies to achieve N-linked glycoproteins across the domains of life.
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31
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Jaffee MB, Imperiali B. Optimized protocol for expression and purification of membrane-bound PglB, a bacterial oligosaccharyl transferase. Protein Expr Purif 2013; 89:241-50. [PMID: 23583934 DOI: 10.1016/j.pep.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/03/2013] [Accepted: 04/04/2013] [Indexed: 11/26/2022]
Abstract
Asparagine-linked glycosylation (NLG) plays a significant role in a diverse range of cellular processes, including protein signaling and trafficking, the immunologic response, and immune system evasion by pathogens. A major impediment to NLG-related research is an incomplete understanding of the central enzyme in the biosynthetic pathway, the oligosaccharyl transferase (OTase). Characterization of the OTase is critical for developing ways to inhibit, engineer, and otherwise manipulate the enzyme for research and therapeutic purposes. The minimal understanding of this enzyme can be attributed to its complex, transmembrane structure, and the resulting instability and resistance to overexpression and purification. The following article describes an optimized procedure for recombinant expression and purification of PglB, a bacterial OTase, in a stably active form. The conditions screened at each step, the order of screening, and the method of comparing conditions are described. Ultimately, the following approach increased expression levels from tens of micrograms to several milligrams of active protein per liter of Escherichia coli culture, and increased stability from several hours to greater than six months post-purification. This represents the first detailed procedure for attaining a pure, active, and stable OTase in milligram quantities. In addition to presenting an optimized protocol for expression and purification of PglB, these results present a general guide for the systematic optimization of the expression, purification, and stability of a large, transmembrane protein.
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Affiliation(s)
- Marcie B Jaffee
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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32
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Musumeci MA, Hug I, Scott NE, Ielmini MV, Foster LJ, Wang PG, Feldman MF. In vitro activity of Neisseria meningitidis PglL O-oligosaccharyltransferase with diverse synthetic lipid donors and a UDP-activated sugar. J Biol Chem 2013; 288:10578-87. [PMID: 23460642 DOI: 10.1074/jbc.m112.432815] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Oligosaccharyltransferases (OTases) are enzymes that catalyze the transfer of an oligosaccharide from a lipid carrier to an acceptor molecule, commonly a protein. OTases are classified as N-OTases and O-OTases, depending on the nature of the glycosylation reaction. The N-OTases catalyze the glycan transfer to amide groups in asparagines in a reaction named N-linked glycosylation. The O-OTases are responsible for protein O-linked glycosylation, which involves the attachment of glycans to hydroxyl groups of serine or threonine residues. These enzymes exhibit a relaxed specificity and are able to transfer a variety of glycan structures to different protein acceptors. This property confers OTases with great biotechnological potential as these enzymes can produce glycoconjugates relevant to the pharmaceutical industry. Furthermore, OTases are thought to be involved in pathogenesis mechanisms. Several aspects of the functionality of OTases are not fully understood. In this work, we developed a novel approach to perform kinetic studies on PglL, the O-OTase from Neisseria meningitidis. We investigated the importance of the acyl moiety of the lipid glycan donor substrate on the functionality of PglL by testing the efficiency of glycosylation reactions using synthetic substrates carrying the same glycan structure but different acyl moieties. We found that PglL can function with many lipids as glycan donors, although the length and the conformation of the lipid moiety significantly influenced the catalytic efficiency. Interestingly, PglL was also able to transfer a monosaccharide employing its nucleotide-activated form, acting as a Leloir glycosyltransferase. These results provide new insights on the function and the evolution of oligosaccharyltransferases.
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Affiliation(s)
- Matias A Musumeci
- Alberta Glycomics Centre, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Huang C, Bhaskaran R, Mohanty S. Eukaryotic N-glycosylation occurs via the membrane-anchored C-terminal domain of the Stt3p subunit of oligosaccharyltransferase. J Biol Chem 2012; 287:32450-8. [PMID: 22865878 DOI: 10.1074/jbc.m112.342253] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
N-glycosylation is an essential and highly conserved protein modification. In eukaryotes, it is catalyzed by a multisubunit membrane-associated enzyme, oligosaccharyltransferase (OT). We report the high resolution structure of the C-terminal domain of eukaryotic Stt3p. Unlike its soluble β-sheet-rich prokaryotic counterparts, our model reveals that the C-terminal domain of yeast Stt3p is highly helical and has an overall oblate spheroid-shaped structure containing a membrane-embedded region. Anchoring of this protein segment to the endoplasmic reticulum membrane is likely to bring the membrane-embedded donor substrate closer, thus facilitating glycosylation efficiency. Structural comparison of the region near the WWDYG signature motif revealed that the acceptor substrate-binding site of yeast OT strikingly resembles its prokaryotic counterparts, suggesting a conserved mechanism of N-glycosylation from prokaryotes to eukaryotes. Furthermore, comparison of the NMR and cryo-EM structures of yeast OT revealed that the molecular architecture of this acceptor substrate-recognizing domain has interesting spatial specificity for interactions with other essential OT subunits.
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Affiliation(s)
- Chengdong Huang
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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34
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Han W, Cai L, Wu B, Li L, Xiao Z, Cheng J, Wang PG. The wciN gene encodes an α-1,3-galactosyltransferase involved in the biosynthesis of the capsule repeating unit of Streptococcus pneumoniae serotype 6B. Biochemistry 2012; 51:5804-10. [PMID: 22742596 DOI: 10.1021/bi300640b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Almost all Streptococcus pneumoniae (pneumococcus) capsule serotypes employ the Wzy-dependent pathway for their capsular polysaccharide (CPS) biosynthesis. The assembly of the CPS repeating unit (RU) is the first committed step in this pathway. The wciN gene was predicted to encode a galactosyltransferase involved in the RU assembly of pneumococcus type 6B CPS. Herein, we provide the unambiguous in vitro biochemical evidence that wciN encodes an α-1,3-galactosyltransferase catalyzing the transfer of galactosyl from UDP-Gal onto the Glcα-pyrophosphate-lipid (Glcα-PP-lipid) acceptor to form Galα(1-3)Glcα-PP-lipid. A chemically synthesized acceptor (Glcα-PP-O(CH(2))(10)CH(3)) was used to characterize the WciN activity. The disaccharide product, i.e., Galα(1-3)Glcα-PP-O(CH(2))(10)CH(3), was characterized by mass and NMR spectroscopy. Substrate specificity study indicated that the acceptor structural region composed of pyrophosphate and lipid moieties may play an important role in the enzyme-acceptor recognition. Furthermore, divalent metal cations were found indispensable to the WciN activity, suggesting that this glycosyltransferase (GT) belongs to the GT-A superfamily. By analyzing the activities of six WciN mutants, a DXD motif involved in the coordination of a divalent metal cation was identified. This work provides a chemical biology approach to characterize the activities of pneumococcal CPS GTs in vitro and will help to better understand the pneumococcal CPS biosynthetic pathway.
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Affiliation(s)
- Weiqing Han
- State Key Laboratory of Medicinal Chemical Biology, Nankai University , Tianjin 300071, China
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35
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Mechanisms and principles of N-linked protein glycosylation. Curr Opin Struct Biol 2012; 21:576-82. [PMID: 21978957 DOI: 10.1016/j.sbi.2011.08.005] [Citation(s) in RCA: 483] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 08/01/2011] [Accepted: 08/04/2011] [Indexed: 11/20/2022]
Abstract
N-linked glycosylation, a protein modification system present in all domains of life, is characterized by a high structural diversity of N-linked glycans found among different species and by a large number of proteins that are glycosylated. Based on structural, functional, and phylogenetic approaches, this review discusses the highly conserved processes that are at the basis of this unique general protein modification system.
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36
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Hartley MD, Imperiali B. At the membrane frontier: a prospectus on the remarkable evolutionary conservation of polyprenols and polyprenyl-phosphates. Arch Biochem Biophys 2012; 517:83-97. [PMID: 22093697 PMCID: PMC3253937 DOI: 10.1016/j.abb.2011.10.018] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 10/28/2011] [Accepted: 10/30/2011] [Indexed: 11/20/2022]
Abstract
Long-chain polyprenols and polyprenyl-phosphates are ubiquitous and essential components of cellular membranes throughout all domains of life. Polyprenyl-phosphates, which include undecaprenyl-phosphate in bacteria and the dolichyl-phosphates in archaea and eukaryotes, serve as specific membrane-bound carriers in glycan biosynthetic pathways responsible for the production of cellular structures such as N-linked protein glycans and bacterial peptidoglycan. Polyprenyl-phosphates are the only form of polyprenols with a biochemically-defined role; however, unmodified or esterified polyprenols often comprise significant percentages of the cellular polyprenol pool. The strong evolutionary conservation of unmodified polyprenols as membrane constituents and polyprenyl-phosphates as preferred glycan carriers in biosynthetic pathways is poorly understood. This review surveys the available research to explore why unmodified polyprenols have been conserved in evolution and why polyprenyl-phosphates are universally and specifically utilized for membrane-bound glycan assembly.
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Affiliation(s)
- Meredith D. Hartley
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
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37
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Affiliation(s)
- Ryan M Schmaltz
- The Department of Chemistry and Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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38
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Jaffee MB, Imperiali B. Exploiting topological constraints to reveal buried sequence motifs in the membrane-bound N-linked oligosaccharyl transferases. Biochemistry 2011; 50:7557-67. [PMID: 21812456 DOI: 10.1021/bi201018d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The central enzyme in N-linked glycosylation is the oligosaccharyl transferase (OTase), which catalyzes glycan transfer from a polyprenyldiphosphate-linked carrier to select asparagines within acceptor proteins. PglB from Campylobacter jejuni is a single-subunit OTase with homology to the Stt3 subunit of the complex multimeric yeast OTase. Sequence identity between PglB and Stt3 is low (17.9%); however, both have a similar predicted architecture and contain the conserved WWDxG motif. To investigate the relationship between PglB and other Stt3 proteins, sequence analysis was performed using 28 homologues from evolutionarily distant organisms. Since detection of small conserved motifs within large membrane-associated proteins is complicated by divergent sequences surrounding the motifs, we developed a program to parse sequences according to predicted topology and then analyze topologically related regions. This approach identified three conserved motifs that served as the basis for subsequent mutagenesis and functional studies. This work reveals that several inter-transmembrane loop regions of PglB/Stt3 contain strictly conserved motifs that are essential for PglB function. The recent publication of a 3.4 Å resolution structure of full-length C. lari OTase provides clear structural evidence that these loops play a fundamental role in catalysis [ Lizak , C. ; ( 2011 ) Nature 474 , 350 - 355 ]. The current study provides biochemical support for the role of the inter-transmembrane domain loops in OTase catalysis and demonstrates the utility of combining topology prediction and sequence analysis for exposing buried pockets of homology in large membrane proteins. The described approach allowed detection of the catalytic motifs prior to availability of structural data and reveals additional catalytically relevant residues that are not predicted by structural data alone.
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Affiliation(s)
- Marcie B Jaffee
- Departments of Biology and Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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39
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Tabish S, Raza A, Nasir A, Zafar S, Bokhari H. Analysis of glycosylation motifs and glycosyltransferases in Bacteria and Archaea. Bioinformation 2011; 6:191-5. [PMID: 21738312 PMCID: PMC3124799 DOI: 10.6026/97320630006191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 03/18/2011] [Indexed: 11/23/2022] Open
Abstract
The process of glycosylation has been studied extensively in prokaryotes but many questions still remain unanswered. Glycosyltransferase is the enzyme which mediates glycosylation and has its preference for the target glycosylation sites as well as for the type of glycosylation i.e. N-linked and O-linked glycosylation. In this study we carried out the bioinformatics analysis of one of the key enzymes of pgl locus from Campylobacter jejuni, known as PglB, which is distributed widely in bacteria and AglB from archaea. Relatively little sequence similarity was observed in the archaeal AglB(s) as compared to those of the bacterial PglB(s). In addition we tried to the answer the question of as to why not all the sequins Asp-X-Ser/Thr have an equal opportunity to be glycosylated by looking at the influence of the neighboring amino acids but no significant conserved pattern of the flanking sites could be identified. The software tool was developed to predict the potential glycosylation sites in autotransporter protein, the virulence factors of gram negative bacteria, and our results revealed that the frequency of glycosylation sites was higher in adhesins (a subclass of autotransporters) relative to the other classes of autotransporters.
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Affiliation(s)
- Syed Tabish
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad, Pakistan
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40
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41
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Hartley MD, Morrison MJ, Aas FE, Børud B, Koomey M, Imperiali B. Biochemical characterization of the O-linked glycosylation pathway in Neisseria gonorrhoeae responsible for biosynthesis of protein glycans containing N,N'-diacetylbacillosamine. Biochemistry 2011; 50:4936-48. [PMID: 21542610 DOI: 10.1021/bi2003372] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The O-linked protein glycosylation pathway in Neisseria gonorrhoeae is responsible for the synthesis of a complex oligosaccharide on undecaprenyl diphosphate and subsequent en bloc transfer of the glycan to serine residues of select periplasmic proteins. Protein glycosylation (pgl) genes have been annotated on the basis of bioinformatics and top-down mass spectrometry analysis of protein modifications in pgl-null strains [Aas, F. E., et al. (2007) Mol. Microbiol. 65, 607-624; Vik, A., et al. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 4447-4452], but relatively little biochemical analysis has been performed to date. In this report, we present the expression, purification, and functional characterization of seven Pgl enzymes. Specifically, the enzymes studied are responsible for synthesis of an uncommon uridine diphosphate (UDP)-sugar (PglD, PglC, and PglB-acetyltransferase domain), glycan assembly (PglB-phospho-glycosyltransferase domain, PglA, PglE, and PglH), and final oligosaccharide transfer (PglO). UDP-2,4-diacetamido-2,4,6-trideoxy-α-d-hexose (DATDH), which is the first sugar in glycan biosynthesis, was produced enzymatically, and the stereochemistry was assigned as uridine diphosphate N'-diacetylbacillosamine (UDP-diNAcBac) by nuclear magnetic resonance characterization. In addition, the substrate specificities of the phospho-glycosyltransferase, glycosyltransferases, and oligosaccharyltransferase (OTase) were analyzed in vitro, and in most cases, these enzymes exhibited strong preferences for the native substrates relative to closely related glycans. In particular, PglO, the O-linked OTase, and PglB(Cj), the N-linked OTase from Campylobacter jejuni, preferred the native N. gonorrhoeae and C. jejuni substrates, respectively. This study represents the first comprehensive biochemical characterization of this important O-linked glycosylation pathway and provides the basis for further investigations of these enzymes as antibacterial targets.
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Affiliation(s)
- Meredith D Hartley
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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42
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Larkin A, Imperiali B. The expanding horizons of asparagine-linked glycosylation. Biochemistry 2011; 50:4411-26. [PMID: 21506607 DOI: 10.1021/bi200346n] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Asparagine-linked glycosylation involves the sequential assembly of an oligosaccharide onto a polyisoprenyl donor, followed by the en bloc transfer of the glycan to particular asparagine residues within acceptor proteins. These N-linked glycans play a critical role in a wide variety of biological processes, such as protein folding, cellular targeting and motility, and the immune response. In the past decade, research in the field of N-linked glycosylation has achieved major advances, including the discovery of new carbohydrate modifications, the biochemical characterization of the enzymes involved in glycan assembly, and the determination of the biological impact of these glycans on target proteins. It is now firmly established that this enzyme-catalyzed modification occurs in all three domains of life. However, despite similarities in the overall logic of N-linked glycoprotein biosynthesis among the three kingdoms, the structures of the appended glycans are markedly different and thus influence the functions of elaborated proteins in various ways. Though nearly all eukaryotes produce the same nascent tetradecasaccharide (Glc(3)Man(9)GlcNAc(2)), heterogeneity is introduced into this glycan structure after it is transferred to the protein through a complex series of glycosyl trimming and addition steps. In contrast, bacteria and archaea display diversity within their N-linked glycan structures through the use of unique monosaccharide building blocks during the assembly process. In this review, recent progress toward gaining a deeper biochemical understanding of this modification across all three kingdoms will be summarized. In addition, a brief overview of the role of N-linked glycosylation in viruses will also be presented.
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Affiliation(s)
- Angelyn Larkin
- Department of Chemistry Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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43
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Gilbreath JJ, Cody WL, Merrell DS, Hendrixson DR. Change is good: variations in common biological mechanisms in the epsilonproteobacterial genera Campylobacter and Helicobacter. Microbiol Mol Biol Rev 2011; 75:84-132. [PMID: 21372321 PMCID: PMC3063351 DOI: 10.1128/mmbr.00035-10] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Microbial evolution and subsequent species diversification enable bacterial organisms to perform common biological processes by a variety of means. The epsilonproteobacteria are a diverse class of prokaryotes that thrive in diverse habitats. Many of these environmental niches are labeled as extreme, whereas other niches include various sites within human, animal, and insect hosts. Some epsilonproteobacteria, such as Campylobacter jejuni and Helicobacter pylori, are common pathogens of humans that inhabit specific regions of the gastrointestinal tract. As such, the biological processes of pathogenic Campylobacter and Helicobacter spp. are often modeled after those of common enteric pathogens such as Salmonella spp. and Escherichia coli. While many exquisite biological mechanisms involving biochemical processes, genetic regulatory pathways, and pathogenesis of disease have been elucidated from studies of Salmonella spp. and E. coli, these paradigms often do not apply to the same processes in the epsilonproteobacteria. Instead, these bacteria often display extensive variation in common biological mechanisms relative to those of other prototypical bacteria. In this review, five biological processes of commonly studied model bacterial species are compared to those of the epsilonproteobacteria C. jejuni and H. pylori. Distinct differences in the processes of flagellar biosynthesis, DNA uptake and recombination, iron homeostasis, interaction with epithelial cells, and protein glycosylation are highlighted. Collectively, these studies support a broader view of the vast repertoire of biological mechanisms employed by bacteria and suggest that future studies of the epsilonproteobacteria will continue to provide novel and interesting information regarding prokaryotic cellular biology.
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Affiliation(s)
- Jeremy J. Gilbreath
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - William L. Cody
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - D. Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - David R. Hendrixson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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44
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Igura M, Kohda D. Selective control of oligosaccharide transfer efficiency for the N-glycosylation sequon by a point mutation in oligosaccharyltransferase. J Biol Chem 2011; 286:13255-60. [PMID: 21357684 DOI: 10.1074/jbc.m110.213900] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asn-linked glycosylation is the most ubiquitous posttranslational protein modification in eukaryotes and archaea, and in some eubacteria. Oligosaccharyltransferase (OST) catalyzes the transfer of preassembled oligosaccharides on lipid carriers onto asparagine residues in polypeptide chains. Inefficient oligosaccharide transfer results in glycoprotein heterogeneity, which is particularly bothersome in pharmaceutical glycoprotein production. Amino acid variation at the X position of the Asn-X-Ser/Thr sequon is known to modulate the glycosylation efficiency. The best amino acid at X is valine, for an archaeal Pyrococcus furiosus OST. We performed a systematic alanine mutagenesis study of the archaeal OST to identify the essential and dispensable amino acid residues in the three catalytic motifs. We then investigated the effects of the dispensable mutations on the amino acid preference in the N-glycosylation sequon. One residue position was found to selectively affect the amino acid preference at the X position. This residue is located within the recently identified DXXKXXX(M/I) motif, suggesting the involvement of this motif in N-glycosylation sequon recognition. In applications, mutations at this position may facilitate the design of OST variants adapted to particular N-glycosylation sites to reduce the heterogeneity of glycan occupancy. In fact, a mutation at this position led to 9-fold higher activity relative to the wild-type enzyme, toward a peptide containing arginine at X in place of valine. This mutational approach is potentially applicable to eukaryotic and eubacterial OSTs for the production of homogenous glycoproteins in engineered mammalian and Escherichia coli cells.
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Affiliation(s)
- Mayumi Igura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
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45
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006. MASS SPECTROMETRY REVIEWS 2011; 30:1-100. [PMID: 20222147 DOI: 10.1002/mas.20265] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK.
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46
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Igura M, Kohda D. Quantitative assessment of the preferences for the amino acid residues flanking archaeal N-linked glycosylation sites. Glycobiology 2010; 21:575-83. [PMID: 21115605 DOI: 10.1093/glycob/cwq196] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oligosaccharyltransferase (OST) catalyzes the transfer of an oligosaccharide to an asparagine residue in polypeptide chains. Using positional scanning peptide libraries, we assessed the effects of amino acid variations on the in vitro glycosylation efficiency within and adjacent to an N-glycosylation consensus, Asn-X-Ser/Thr, with an archaeal OST from Pyrococcus furiosus. The amino acid variations at the X(-2), X(-1) and X(+1) positions in the sequence X(-2)-X(-1)-Asn-X-Ser/Thr-X(+1) strongly influenced the glycosylation efficiency to a similar extent at position X. The rank orders of the amino acid preferences were unique at each site. We experimentally confirmed that the archaeal OST does not require an acidic residue at the -2 position, unlike the eubacterial OSTs. Pro was disfavored at the -1 and +1 positions, although the exclusion was not as strict as that at X, whereas Pro was the most favored amino acid residue among those studied at the -2 position. The overall amino acid preferences are correlated with a conformational propensity to extend around the sequon. The results of the library experiments revealed that the optimal acceptor sequence was PYNVTK, with a K(m) of 10 µM. The heat-stable, single-subunit OST of P. furiosus is a potential candidate enzyme for the production of recombinant glycoproteins in bacterial cells. Quantitative assessment of the amino acid preferences of the OST enzyme will facilitate the proper design of a production system.
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Affiliation(s)
- Mayumi Igura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
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47
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Ielmini MV, Feldman MF. Desulfovibrio desulfuricans PglB homolog possesses oligosaccharyltransferase activity with relaxed glycan specificity and distinct protein acceptor sequence requirements. Glycobiology 2010; 21:734-42. [PMID: 21098514 DOI: 10.1093/glycob/cwq192] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Oligosaccharyltransferases (OTases) are responsible for the transfer of carbohydrates from lipid carriers to acceptor proteins and are present in all domains of life. In bacteria, the most studied member of this family is PglB from Campylobacter jejuni (PglB(Cj)). This enzyme is functional in Escherichia coli and, contrary to its eukaryotic counterparts, has the ability to transfer a variety of oligo- and polysaccharides to protein carriers in vivo. Phylogenetic analysis revealed that in the delta proteobacteria Desulfovibrio sp., the PglB homolog is more closely related to eukaryotic and archaeal OTases than to its Campylobacter counterparts. Genetic analysis revealed the presence of a putative operon that might encode all enzymes required for N-glycosylation in Desulfovibrio desulfuricans. D. desulfuricans PglB (PglB(Dd)) was cloned and successfully expressed in E. coli, and its activity was confirmed by transferring the C. jejuni heptasaccharide onto the model protein acceptor AcrA. In contrast to PglB(Cj), which adds two glycan chains to AcrA, a single oligosaccharide was attached to the protein by PglB(Dd). Site-directed mutagenesis of the five putative N-X-S/T glycosylation sites in AcrA and mass spectrometry analysis showed that PglB(Dd) does not recognize the "conventional bacterial glycosylation sequon" consisting of the sequence D/E-X(1)-N-X(2)-S/T (where X(1) and X(2) are any amino acid except proline), and instead used a different site for the attachment of the oligosaccharide than PglB(Cj.). Furthermore, PglB(Dd) exhibited relaxed glycan specificity, being able to transfer mono- and polysaccharides to AcrA. Our analysis constitutes the first characterization of an OTase from delta-proteobacteria involved in N-linked protein glycosylation.
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Affiliation(s)
- Maria V Ielmini
- Alberta Ingenuity Centre for Carbohydrate Science, Department of Biological Sciences, University of Alberta, Edmonton, Alta, Canada
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Schwarz F, Lizak C, Fan YY, Fleurkens S, Kowarik M, Aebi M. Relaxed acceptor site specificity of bacterial oligosaccharyltransferase in vivo. Glycobiology 2010; 21:45-54. [DOI: 10.1093/glycob/cwq130] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Yang L, Ye XS. A highly alpha-selective glycosylation for the convenient synthesis of repeating alpha-(1-->4)-linked N-acetyl-galactosamine units. Carbohydr Res 2010; 345:1713-21. [PMID: 20591420 DOI: 10.1016/j.carres.2010.05.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Revised: 05/24/2010] [Accepted: 05/31/2010] [Indexed: 11/24/2022]
Abstract
The repeating GalpNAc-alpha-(1-->4)-GalpNAc unit is part of a series of essential structures that can be found in many important biomolecules such as the glycoproteins and the O-antigenic polysaccharides of clinically important bacterial strains. In this paper, we describe an exclusive alpha-selective glycosylation reaction, using a 4,6-di-O-tert-butyldimethylsilyl-N-acetyloxazolidinone-protected thioglycoside as the glycosyl donor, under pre-activation conditions, with only half amount of the promoter, providing the product GalpNAc-alpha-(1-->4)-GalpNAc in high isolated yield. This reaction can be also applied to increasing the length of the repeating structure, which is of significant use in further synthesis of branched or linear oligosaccharides.
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Affiliation(s)
- Lin Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Xue Yuan Road 38, Beijing 100191, China
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