1
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Kay EJ, Dooda MK, Bryant JC, Reid AJ, Wren BW, Troutman JM, Jorgenson MA. Engineering Escherichia coli for increased Und-P availability leads to material improvements in glycan expression technology. Microb Cell Fact 2024; 23:72. [PMID: 38429691 PMCID: PMC10908060 DOI: 10.1186/s12934-024-02339-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Bacterial surface glycans are assembled by glycosyltransferases (GTs) that transfer sugar monomers to long-chained lipid carriers. Most bacteria employ the 55-carbon chain undecaprenyl phosphate (Und-P) to scaffold glycan assembly. The amount of Und-P available for glycan synthesis is thought to be limited by the rate of Und-P synthesis and by competition for Und-P between phosphoglycosyl transferases (PGTs) and GTs that prime glycan assembly (which we collectively refer to as PGT/GTs). While decreasing Und-P availability disrupts glycan synthesis and promotes cell death, less is known about the effects of increased Und-P availability. RESULTS To determine if cells can maintain higher Und-P levels, we first reduced intracellular competition for Und-P by deleting all known non-essential PGT/GTs in the Gram-negative bacterium Escherichia coli (hereafter called ΔPGT/GT cells). We then increased the rate of Und-P synthesis in ΔPGT/GT cells by overexpressing the Und-P(P) synthase uppS from a plasmid (puppS). Und-P quantitation revealed that ΔPGT/GT/puppS cells can be induced to maintain 3-fold more Und-P than wild type cells. Next, we determined how increasing Und-P availability affects glycan expression. Interestingly, increasing Und-P availability increased endogenous and recombinant glycan expression. In particular, ΔPGT/GT/puppS cells could be induced to express 7-fold more capsule from Streptococcus pneumoniae serotype 4 than traditional E. coli cells used to express recombinant glycans. CONCLUSIONS We demonstrate that the biotechnology standard bacterium E. coli can be engineered to maintain higher levels of Und-P. The results also strongly suggest that Und-P pathways can be engineered to increase the expression of potentially any Und-P-dependent polymer. Given that many bacterial glycans are central to the production of vaccines, diagnostics, and therapeutics, increasing Und-P availability should be a foremost consideration when designing bacterial glycan expression systems.
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Affiliation(s)
- Emily J Kay
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Manoj K Dooda
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Joseph C Bryant
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, 4301 West Markham St. / Biomed I, Room 511 / Little Rock, Little Rock, AR, 72205, USA
| | - Amanda J Reid
- Nanoscale Science Program, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jerry M Troutman
- Nanoscale Science Program, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Matthew A Jorgenson
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, 4301 West Markham St. / Biomed I, Room 511 / Little Rock, Little Rock, AR, 72205, USA.
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2
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Paliya BS, Sharma VK, Tuohy MG, Singh HB, Koffas M, Benhida R, Tiwari BK, Kalaskar DM, Singh BN, Gupta VK. Bacterial glycobiotechnology: A biosynthetic route for the production of biopharmaceutical glycans. Biotechnol Adv 2023; 67:108180. [PMID: 37236328 DOI: 10.1016/j.biotechadv.2023.108180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023]
Abstract
The recent advancement in the human glycome and progress in the development of an inclusive network of glycosylation pathways allow the incorporation of suitable machinery for protein modification in non-natural hosts and explore novel opportunities for constructing next-generation tailored glycans and glycoconjugates. Fortunately, the emerging field of bacterial metabolic engineering has enabled the production of tailored biopolymers by harnessing living microbial factories (prokaryotes) as whole-cell biocatalysts. Microbial catalysts offer sophisticated means to develop a variety of valuable polysaccharides in bulk quantities for practical clinical applications. Glycans production through this technique is highly efficient and cost-effective, as it does not involve expensive initial materials. Metabolic glycoengineering primarily focuses on utilizing small metabolite molecules to alter biosynthetic pathways, optimization of cellular processes for glycan and glycoconjugate production, characteristic to a specific organism to produce interest tailored glycans in microbes, using preferably cheap and simple substrate. However, metabolic engineering faces one of the unique challenges, such as the need for an enzyme to catalyze desired substrate conversion when natural native substrates are already present. So, in metabolic engineering, such challenges are evaluated, and different strategies have been developed to overcome them. The generation of glycans and glycoconjugates via metabolic intermediate pathways can still be supported by glycol modeling achieved through metabolic engineering. It is evident that modern glycans engineering requires adoption of improved strain engineering strategies for creating competent glycoprotein expression platforms in bacterial hosts, in the future. These strategies include logically designing and introducing orthogonal glycosylation pathways, identifying metabolic engineering targets at the genome level, and strategically improving pathway performance (for example, through genetic modification of pathway enzymes). Here, we highlight current strategies, applications, and recent progress in metabolic engineering for producing high-value tailored glycans and their applications in biotherapeutics and diagnostics.
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Affiliation(s)
- Balwant S Paliya
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India
| | - Vivek K Sharma
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India
| | - Maria G Tuohy
- Biochemistry, School of Biological and Chemical Sciences, College of Science & Engineering, University of Galway (Ollscoil na Gaillimhe), University Road, Galway City, Ireland
| | - Harikesh B Singh
- Department of Biotechnology, GLA University, Mathura 281406, Uttar Pradesh, India
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Rachid Benhida
- Institut de Chimie de Nice, UMR7272, Université Côte d'Azur, Nice, France; Mohamed VI Polytechnic University, Lot 660, Hay Moulay Rachid 43150, Benguerir, Morocco
| | | | - Deepak M Kalaskar
- UCL Division of Surgery and Interventional Science, Royal Free Hospital Campus, University College London, Rowland Hill Street, NW3 2PF, UK
| | - Brahma N Singh
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India.
| | - Vijai K Gupta
- Biorefining and Advanced Materials Research Centre, SRUC, Barony Campus, Parkgate, Dumfries DG1 3NE, United Kingdom.
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Kay EJ, Mauri M, Willcocks SJ, Scott TA, Cuccui J, Wren BW. Engineering a suite of E. coli strains for enhanced expression of bacterial polysaccharides and glycoconjugate vaccines. Microb Cell Fact 2022; 21:66. [PMID: 35449016 PMCID: PMC9026721 DOI: 10.1186/s12934-022-01792-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycoengineering, in the biotechnology workhorse bacterium, Escherichia coli, is a rapidly evolving field, particularly for the production of glycoconjugate vaccine candidates (bioconjugation). Efficient production of glycoconjugates requires the coordinated expression within the bacterial cell of three components: a carrier protein, a glycan antigen and a coupling enzyme, in a timely fashion. Thus, the choice of a suitable E. coli host cell is of paramount importance. Microbial chassis engineering has long been used to improve yields of chemicals and biopolymers, but its application to vaccine production is sparse. RESULTS In this study we have engineered a family of 11 E. coli strains by the removal and/or addition of components rationally selected for enhanced expression of Streptococcus pneumoniae capsular polysaccharides with the scope of increasing yield of pneumococcal conjugate vaccines. Importantly, all strains express a detoxified version of endotoxin, a concerning contaminant of therapeutics produced in bacterial cells. The genomic background of each strain was altered using CRISPR in an iterative fashion to generate strains without antibiotic markers or scar sequences. CONCLUSIONS Amongst the 11 modified strains generated in this study, E. coli Falcon, Peregrine and Sparrowhawk all showed increased production of S. pneumoniae serotype 4 capsule. Eagle (a strain without enterobacterial common antigen, containing a GalNAc epimerase and PglB expressed from the chromosome) and Sparrowhawk (a strain without enterobacterial common antigen, O-antigen ligase and chain length determinant, containing a GalNAc epimerase and chain length regulators from Streptococcus pneumoniae) respectively produced an AcrA-SP4 conjugate with 4 × and 14 × more glycan than that produced in the base strain, W3110. Beyond their application to the production of pneumococcal vaccine candidates, the bank of 11 new strains will be an invaluable resource for the glycoengineering community.
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Affiliation(s)
- Emily J Kay
- 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
| | - Sam J Willcocks
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Timothy A Scott
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jon Cuccui
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
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4
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Pratama F, Linton D, Dixon N. Genetic and process engineering strategies for enhanced recombinant N-glycoprotein production in bacteria. Microb Cell Fact 2021; 20:198. [PMID: 34649588 PMCID: PMC8518210 DOI: 10.1186/s12934-021-01689-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/25/2021] [Indexed: 11/28/2022] Open
Abstract
Background The production of N-linked glycoproteins in genetically amenable bacterial hosts offers great potential for reduced cost, faster/simpler bioprocesses, greater customisation, and utility for distributed manufacturing of glycoconjugate vaccines and glycoprotein therapeutics. Efforts to optimize production hosts have included heterologous expression of glycosylation enzymes, metabolic engineering, use of alternative secretion pathways, and attenuation of gene expression. However, a major bottleneck to enhance glycosylation efficiency, which limits the utility of the other improvements, is the impact of target protein sequon accessibility during glycosylation. Results Here, we explore a series of genetic and process engineering strategies to increase recombinant N-linked glycosylation, mediated by the Campylobacter-derived PglB oligosaccharyltransferase in Escherichia coli. Strategies include increasing membrane residency time of the target protein by modifying the cleavage site of its secretion signal, and modulating protein folding in the periplasm by use of oxygen limitation or strains with compromised oxidoreductase or disulphide-bond isomerase activity. These approaches achieve up to twofold improvement in glycosylation efficiency. Furthermore, we also demonstrate that supplementation with the chemical oxidant cystine enhances the titre of glycoprotein in an oxidoreductase knockout strain by improving total protein production and cell fitness, while at the same time maintaining higher levels of glycosylation efficiency. Conclusions In this study, we demonstrate that improved protein glycosylation in the heterologous host could be achieved by mimicking the coordination between protein translocation, folding and glycosylation observed in native host such as Campylobacter jejuni and mammalian cells. Furthermore, it provides insight into strain engineering and bioprocess strategies, to improve glycoprotein yield and titre, and to avoid physiological burden of unfolded protein stress upon cell growth. The process and genetic strategies identified herein will inform further optimisation and scale-up of heterologous recombinant N-glycoprotein production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01689-x.
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Affiliation(s)
- Fenryco Pratama
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, M1 7DN, UK.,Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.,Microbial Biotechnology Research Group, School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Dennis Linton
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M1 7DN, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, M1 7DN, UK. .,Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
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5
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Zhang L, Cong Y, Li H, Chen L, Li B, Huang JX, Dong J. Construction of a full-length antibody phage display vector. J Immunol Methods 2021; 494:113052. [PMID: 33838171 DOI: 10.1016/j.jim.2021.113052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/25/2021] [Accepted: 04/03/2021] [Indexed: 10/21/2022]
Abstract
Antibody phage display technology plays an important role in the development of monoclonal antibodies, humanization, and affinity evolution of antibodies. Thus far, antibody phage display mainly focuses on the display of antibody variable region or antigen-binding fragments. In this study, we constructed a new phage display system that can display full-length IgG antibodies on M13 phage. The phage display vector contains open reading frames (ORFs) encoding full-length the heavy and light chains of the antibody. NcoI/XhoI restriction enzyme sites were used to clone the variable region of the heavy chain into the heavy chain ORF, and SalI/NotI sites were used to clone the light chain variable region. SnaBI and SbfI restriction enzyme sites were designed between the cloning sites of heavy and light chains, respectively, to increase the cloning efficiency. The full-length antibodies of nivolumab against programmed death factor 1, trastuzumab against human epidermal growth factor 2, diL2K against the cluster of differentiation 3 epsilon, and adalimumab against tumor necrosis factor- alpha were displayed on phage with the vector. Phage-displayed antibodies showed their original antigen-binding activity. An amber codon shifted the vector to express IgG in non-suppressed Escherichia coli. The heavy and light chains of the E. coli-expressed antibodies could be detected through western blotting, and the antigen-binding activity was confirmed using an enzyme-linked immunosorbent assay. Biopanning was carried out with a model phage display antibody library, and the results showed that the novel phage system could be used for antibody library construction and highly efficient antibody screening. The reported system is the first full-length antibody phage display system.
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Affiliation(s)
- Liqian Zhang
- Key Laboratory for Biological Medicine in Shandong Universities, Weifang Key Laboratory for Antibodies Medicine, School of Life Science and Technology, Weifang Medical University, Weifang 261053, China
| | - Yang Cong
- Key Laboratory for Biological Medicine in Shandong Universities, Weifang Key Laboratory for Antibodies Medicine, School of Life Science and Technology, Weifang Medical University, Weifang 261053, China
| | - Haimei Li
- Key Laboratory for Biological Medicine in Shandong Universities, Weifang Key Laboratory for Antibodies Medicine, School of Life Science and Technology, Weifang Medical University, Weifang 261053, China
| | - Limei Chen
- Key Laboratory for Biological Medicine in Shandong Universities, Weifang Key Laboratory for Antibodies Medicine, School of Life Science and Technology, Weifang Medical University, Weifang 261053, China
| | - Baowei Li
- Key Laboratory for Biological Medicine in Shandong Universities, Weifang Key Laboratory for Antibodies Medicine, School of Life Science and Technology, Weifang Medical University, Weifang 261053, China
| | - Johnny X Huang
- Key Laboratory for Biological Medicine in Shandong Universities, Weifang Key Laboratory for Antibodies Medicine, School of Life Science and Technology, Weifang Medical University, Weifang 261053, China
| | - Jinhua Dong
- Key Laboratory for Biological Medicine in Shandong Universities, Weifang Key Laboratory for Antibodies Medicine, School of Life Science and Technology, Weifang Medical University, Weifang 261053, China; World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
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6
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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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7
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Wayman JA, Glasscock C, Mansell TJ, DeLisa MP, Varner JD. Improving designer glycan production in Escherichia coli through model-guided metabolic engineering. Metab Eng Commun 2019; 9:e00088. [PMID: 31008057 PMCID: PMC6454127 DOI: 10.1016/j.mec.2019.e00088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022] Open
Abstract
Asparagine-linked (N-linked) glycosylation is the most common protein modification in eukaryotes, affecting over two-thirds of the proteome. Glycosylation is also critical to the pharmacokinetic activity and immunogenicity of many therapeutic proteins currently produced in complex eukaryotic hosts. The discovery of a protein glycosylation pathway in the pathogen Campylobacter jejuni and its subsequent transfer into laboratory strains of Escherichia coli has spurred great interest in glycoprotein production in prokaryotes. However, prokaryotic glycoprotein production has several drawbacks, including insufficient availability of non-native glycan precursors. To address this limitation, we used a constraint-based model of E. coli metabolism in combination with heuristic optimization to design gene knockout strains that overproduced glycan precursors. First, we incorporated reactions associated with C. jejuni glycan assembly into a genome-scale model of E. coli metabolism. We then identified gene knockout strains that coupled optimal growth to glycan synthesis. Simulations suggested that these growth-coupled glycan overproducing strains had metabolic imbalances that rerouted flux toward glycan precursor synthesis. We then validated the model-identified knockout strains experimentally by measuring glycan expression using a flow cytometric-based assay involving fluorescent labeling of cell surface-displayed glycans. Overall, this study demonstrates the promising role that metabolic modeling can play in optimizing the performance of a next-generation microbial glycosylation platform.
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Affiliation(s)
- Joseph A Wayman
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA
| | - Cameron Glasscock
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Thomas J Mansell
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Jeffrey D Varner
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
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8
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Strutton B, Jaffe SR, Evans CA, Fowler GJ, Dobson PD, Pandhal J, Wright PC. Engineering Pathways in Central Carbon Metabolism Help to Increase Glycan Production and Improve N-Type Glycosylation of Recombinant Proteins in E. coli. Bioengineering (Basel) 2019; 6:bioengineering6010027. [PMID: 30901908 PMCID: PMC6466297 DOI: 10.3390/bioengineering6010027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 11/26/2022] Open
Abstract
Escherichia coli strains have been modified in a variety of ways to enhance the production of different recombinant proteins, targeting membrane protein expression, proteins with disulphide bonds, and more recently, proteins which require N-linked glycosylation. The addition of glycans to proteins remains a relatively inefficient process and here we aimed to combine genetic modifications within central carbon metabolic pathways in order to increase glycan precursor pools, prior to transfer onto polypeptide backbones. Using a lectin screen that detects cell surface representation of glycans, together with Western blot analyses using an O-antigen ligase mutant strain, the enhanced uptake and phosphorylation of sugars (ptsA) from the media combined with conservation of carbon through the glyoxylate shunt (icl) improved glycosylation efficiency of a bacterial protein AcrA by 69% and over 100% in an engineered human protein IFN-α2b. Unexpectedly, overexpression of a gene involved in the production of DXP from pyruvate (dxs), which was previously seen to have a positive impact on glycosylation, was detrimental to process efficiency and the possible reasons for this are discussed.
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Affiliation(s)
- Benjamin Strutton
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| | - Stephen Rp Jaffe
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| | - Caroline A Evans
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| | - Gregory Js Fowler
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| | - Paul D Dobson
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
- Scruffy Biotech Ltd. Green Bank, Derbyshire SK13 6XT, UK.
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK.
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9
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Caillava AJ, Ortiz GE, Melli LJ, Ugalde JE, Ciocchini AE, Comerci DJ. Improving bioreactor production of a recombinant glycoprotein in
Escherichia coli
: Effect of specific growth rate on protein glycosylation and specific productivity. Biotechnol Bioeng 2019; 116:1427-1438. [DOI: 10.1002/bit.26953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/30/2018] [Accepted: 02/07/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Ana J. Caillava
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Gastón E. Ortiz
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Luciano J. Melli
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Juan E. Ugalde
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Andrés E. Ciocchini
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
| | - Diego J. Comerci
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús (IIB‐INTECH), Universidad Nacional de San Martín, CONICET, San MartínBuenos Aires Argentina
- Comisión Nacional de Energía Atómica, Grupo Pecuario, Centro Atómico EzeizaBuenos Aires Argentina
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10
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Khan AH, Noordin R. Strategies for humanizing glycosylation pathways and producing recombinant glycoproteins in microbial expression systems. Biotechnol Prog 2018; 35:e2752. [DOI: 10.1002/btpr.2752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/26/2018] [Accepted: 11/16/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Amjad Hayat Khan
- Inst. for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 11800 Penang Malaysia
| | - Rahmah Noordin
- Inst. for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 11800 Penang Malaysia
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11
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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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12
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Couto N, Davlyatova L, Evans CA, Wright PC. Application of the broadband collision-induced dissociation (bbCID) mass spectrometry approach for protein glycosylation and phosphorylation analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:75-85. [PMID: 29055059 DOI: 10.1002/rcm.8016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/29/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Analysis of post-translationally modified peptides by mass spectrometry (MS) remains incomplete, in part due to incomplete sampling of all peptides which is inherent to traditional data-dependent acquisition (DDA). An alternative MS approach, data-independent acquisition (DIA), enables comprehensive recording of all detectable precursor and product ions, independent of precursor intensity. The use of broadband collision-induced dissociation (bbCID), a DIA method, was evaluated for the identification of protein glycosylation and phosphorylation. METHODS bbCID was applied to identify glycopeptides and phosphopeptides generated from standard proteins using a high-resolution Bruker maXis 3G mass spectrometer. In bbCID, precursor and product ion spectra were obtained by alternating low and high collision energy. Precursor ions were assigned manually based on the detection of diagnostic ions specific to either glycosylation or phosphorylation. The composition of the glycan modification was resolved in the positive ion mode, while the level of phosphorylation was investigated in the negative ion mode. RESULTS The results demonstrate for the first time that the use of a bbCID approach is suitable for the identification of glycopeptides and phosphopeptides based on the detection of specific diagnostic and associated precursor ions. The novel use of bbCID in negative ion mode allowed the discrimination of singly and multiply phosphorylated peptides based on the detection of phosphate diagnostic ions. The results also demonstrate the ability of this approach to allow the identification of glycan composition in N- and O-linked glycopeptides, in positive ion mode. CONCLUSIONS We contend that bbCID is a valuable addition to the existing toolkit for PTM discovery. Moreover, this technique could be employed to direct targeted proteomics methods, particularly where there is no a priori information on glycosylation or phosphorylation status. This technique is immediately relevant to the characterisation of individual proteins or biological samples of low complexity, as demonstrated for the analysis of the glycosylation status of a therapeutic protein.
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Affiliation(s)
- Narciso Couto
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Liliya Davlyatova
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Caroline A Evans
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Phillip C Wright
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
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Strutton B, Jaffé SR, Pandhal J, Wright PC. Producing a glycosylating Escherichia coli cell factory: The placement of the bacterial oligosaccharyl transferase pglB onto the genome. Biochem Biophys Res Commun 2018; 495:686-692. [DOI: 10.1016/j.bbrc.2017.11.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/03/2017] [Indexed: 10/18/2022]
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14
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Jaroentomeechai T, Zheng X, Hershewe J, Stark JC, Jewett MC, DeLisa MP. A Pipeline for Studying and Engineering Single-Subunit Oligosaccharyltransferases. Methods Enzymol 2017; 597:55-81. [PMID: 28935112 DOI: 10.1016/bs.mie.2017.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Asparagine-linked (N-linked) protein glycosylation is one of the most abundant types of posttranslational modification, occurring in all domains of life. The central enzyme in N-linked glycosylation is the oligosaccharyltransferase (OST), which catalyzes the covalent attachment of preassembled glycans to specific asparagine residues in target proteins. Whereas in higher eukaryotes the OST is comprised of eight different membrane proteins, of which the catalytic subunit is STT3, in kinetoplastids and prokaryotes the OST is a monomeric enzyme bearing homology to STT3. Given their relative simplicity, these single-subunit OSTs (ssOSTs) have emerged as important targets for mechanistic dissection of poorly understood aspects of N-glycosylation and at the same time hold great potential for the biosynthesis of custom glycoproteins. To take advantage of this utility, this chapter describes a multipronged approach for studying and engineering ssOSTs that integrates in vivo screening technology with in vitro characterization methods, thereby creating a versatile and readily adaptable pipeline for virtually any ssOST of interest.
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Xiaolu Zheng
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | | | | | - Michael C Jewett
- Northwestern University, Evanston, IL, United States; Center for Synthetic Biology, Northwestern University, Evanston, IL, United States
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States.
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15
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Slámová K, Bojarová P. Engineered N-acetylhexosamine-active enzymes in glycoscience. Biochim Biophys Acta Gen Subj 2017; 1861:2070-2087. [PMID: 28347843 DOI: 10.1016/j.bbagen.2017.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 01/17/2023]
Abstract
BACKGROUND In recent years, enzymes modifying N-acetylhexosamine substrates have emerged in numerous theoretical studies as well as practical applications from biology, biomedicine, and biotechnology. Advanced enzyme engineering techniques converted them into potent synthetic instruments affording a variety of valuable glycosides. SCOPE OF REVIEW This review presents the diversity of engineered enzymes active with N-acetylhexosamine carbohydrates: from popular glycoside hydrolases and glycosyltransferases to less known oxidases, epimerases, kinases, sulfotransferases, and acetylases. Though hydrolases in natura, engineered chitinases, β-N-acetylhexosaminidases, and endo-β-N-acetylglucosaminidases were successfully employed in the synthesis of defined natural and derivatized chitooligomers and in the remodeling of N-glycosylation patterns of therapeutic antibodies. The genes of various N-acetylhexosaminyltransferases were cloned into metabolically engineered microorganisms for producing human milk oligosaccharides, Lewis X structures, and human-like glycoproteins. Moreover, mutant N-acetylhexosamine-active glycosyltransferases were applied, e.g., in the construction of glycomimetics and complex glycostructures, industrial production of low-lactose milk, and metabolic labeling of glycans. In the synthesis of biotechnologically important compounds, several innovative glycoengineered systems are presented for an efficient bioproduction of GlcNAc, UDP-GlcNAc, N-acetylneuraminic acid, and of defined glycosaminoglycans. MAJOR CONCLUSIONS The above examples demonstrate that engineering of N-acetylhexosamine-active enzymes was able to solve complex issues such as synthesis of tailored human-like glycoproteins or industrial-scale production of desired oligosaccharides. Due to the specific catalytic mechanism, mutagenesis of these catalysts was often realized through rational solutions. GENERAL SIGNIFICANCE Specific N-acetylhexosamine glycosylation is crucial in biological, biomedical and biotechnological applications and a good understanding of its details opens new possibilities in this fast developing area of glycoscience.
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Affiliation(s)
- Kristýna Slámová
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic.
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16
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Increased glycosylation efficiency of recombinant proteins in Escherichia coli by auto-induction. Biochem Biophys Res Commun 2017; 485:138-143. [DOI: 10.1016/j.bbrc.2017.02.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/07/2017] [Indexed: 01/30/2023]
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17
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Strutton B, Jaffé SRP, Pandhal J, Wright PC. Generation of Recombinant N-Linked Glycoproteins in E. coli. Methods Mol Biol 2017; 1586:233-250. [PMID: 28470609 DOI: 10.1007/978-1-4939-6887-9_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The production of N-linked recombinant glycoproteins is possible in a variety of biotechnology host cells, and more recently in the bacterial workhorse, Escherichia coli. This methods chapter will outline the components and procedures needed to produce N-linked glycoproteins in E. coli, utilizing Campylobacter jejuni glycosylation machinery, although other related genes can be used with minimal tweaks to this methodology. To ensure a successful outcome, various methods will be highlighted that can confirm glycoprotein production to a high degree of confidence, including the gold standard of mass spectrometry analysis.
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Affiliation(s)
- Benjamin Strutton
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Stephen R P Jaffé
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK.
| | - Phillip C Wright
- Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, UK
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18
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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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19
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Chen R. The sweet branch of metabolic engineering: cherry-picking the low-hanging sugary fruits. Microb Cell Fact 2015; 14:197. [PMID: 26655367 PMCID: PMC4674990 DOI: 10.1186/s12934-015-0389-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 11/25/2015] [Indexed: 02/08/2023] Open
Abstract
In the first science review on the then nascent Metabolic Engineering field in 1991, Dr. James E. Bailey described how improving erythropoietin (EPO) glycosylation can be achieved via metabolic engineering of Chinese hamster ovary (CHO) cells. In the intervening decades, metabolic engineering has brought sweet successes in glycoprotein engineering, including antibodies, vaccines, and other human therapeutics. Today, not only eukaryotes (CHO, plant, insect, yeast) are being used for manufacturing protein therapeutics with human-like glycosylation, newly elucidated bacterial glycosylation systems are enthusiastically embraced as potential breakthrough to revolutionize the biopharmaceutical industry. Notwithstanding these excitement in glycoprotein, the sweet metabolic engineering reaches far beyond glycoproteins. Many different types of oligo- and poly-saccharides are synthesized with metabolically engineered cells. For example, several recombinant hyaluronan bioprocesses are now in commercial production, and the titer of 2′-fucosyllactose, the most abundant fucosylated trisaccharide in human milk, reaches over 20 g/L with engineered E. coli cells. These successes represent only the first low hanging fruits, which have been appreciated scientifically, medically and fortunately, commercially as well. As one of the four building blocks of life, sugar molecules permeate almost all aspects of life. They are also unique in being intimately associated with all major types of biopolymers (including DNA/RNA, proteins, lipids) meanwhile they stand alone as bioactive polysaccharides, or free soluble oligosaccharides. As such, all sugar moieties in biological components, small or big and free or bound, are important targets for metabolic engineering. Opportunities abound at the interface of glycosciences and metabolic engineering. Continued investment and successes in this branch of metabolic engineering will make vastly diverse sugar-containing molecules (a.k.a. glycoconjugates) available for biomedical applications, sustainable technology development, and as invaluable tools for basic scientific research. This short review focuses on the most recent development in the field, with emphasis on the synthesis technology for glycoprotein, polysaccharide, and oligosaccharide.
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Affiliation(s)
- Rachel Chen
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive, NW, Atlanta, GA, 30332-0100, USA.
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20
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Kämpf MM, Braun M, Sirena D, Ihssen J, Thöny-Meyer L, Ren Q. In vivo production of a novel glycoconjugate vaccine against Shigella flexneri 2a in recombinant Escherichia coli: identification of stimulating factors for in vivo glycosylation. Microb Cell Fact 2015; 14:12. [PMID: 25612741 PMCID: PMC4308876 DOI: 10.1186/s12934-015-0195-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/12/2015] [Indexed: 11/26/2022] Open
Abstract
Background Glycoconjugated vaccines composed of polysaccharide antigens covalently linked to immunogenic carrier proteins have proved to belong to the most effective and safest vaccines for combating bacterial pathogens. The functional transfer of the N-glycosylation machinery from Campylobacter jejuni to the standard prokaryotic host Escherichia coli established a novel bioconjugation methodology termed bacterial glycoengineering. Results In this study, we report on the production of a new recombinant glycoconjugate vaccine against Shigella flexneri 2a representing the major serotype for global outbreaks of shigellosis. We demonstrate that S. flexneri 2a O-polysaccharides can be transferred to a detoxified variant of Pseudomonas aeruginosa carrier protein exotoxin A (EPA) by the C. jejuni oligosaccharyltransferase PglB, resulting in glycosylated EPA-2a. Moreover, we optimized the in vivo production of this novel vaccine by identification and quantitative analysis of critical process parameters for glycoprotein synthesis. It was found that sequential induction of oligosaccharyltransferase PglB and carrier protein EPA increased the specific productivity of EPA-2a by a factor of 1.6. Furthermore, by the addition of 10 g/L of the monosaccharide N-acetylglucosamine during induction, glycoconjugate vaccine yield was boosted up to 3.1-fold. The optimum concentration of Mg2+ ions for N-glycan transfer was determined to be 10 mM. Finally, optimized parameters were transferred to high cell density cultures with a 46-fold increase of overall yield of glycoconjugate compared to the one in initial shake flask production. Conclusion The present study is the first attempt to identify stimulating parameters for improved productivity of S. flexneri 2a bioconjugates. Optimization of glycosylation efficiency will ultimately foster the transfer of lab-scale expression to a cost-effective in vivo production process for a glycoconjugate vaccine against S. flexneri 2a in E. coli. This study is an important step towards this goal and provides a starting point for further optimization studies.
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Affiliation(s)
- Michael M Kämpf
- Laboratory for Biointerfaces, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St. Gallen, Switzerland. .,GlycoVaxyn AG, Grabenstrasse 3, 8952, Schlieren, Switzerland.
| | - Martin Braun
- GlycoVaxyn AG, Grabenstrasse 3, 8952, Schlieren, Switzerland.
| | | | - Julian Ihssen
- Laboratory for Biointerfaces, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St. Gallen, Switzerland.
| | - Linda Thöny-Meyer
- Laboratory for Biointerfaces, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St. Gallen, Switzerland.
| | - Qun Ren
- Laboratory for Biointerfaces, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St. Gallen, Switzerland.
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21
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Klein T, Niklas J, Heinzle E. Engineering the supply chain for protein production/secretion in yeasts and mammalian cells. J Ind Microbiol Biotechnol 2015; 42:453-64. [PMID: 25561318 DOI: 10.1007/s10295-014-1569-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/16/2014] [Indexed: 12/14/2022]
Abstract
Metabolic bottlenecks play an increasing role in yeasts and mammalian cells applied for high-performance production of proteins, particularly of pharmaceutical ones that require complex posttranslational modifications. We review the present status and developments focusing on the rational metabolic engineering of such cells to optimize the supply chain for building blocks and energy. Methods comprise selection of beneficial genetic modifications, rational design of media and feeding strategies. Design of better producer cells based on whole genome-wide metabolic network analysis becomes increasingly possible. High-resolution methods of metabolic flux analysis for the complex networks in these compartmented cells are increasingly available. We discuss phenomena that are common to both types of organisms but also those that are different with respect to the supply chain for the production and secretion of pharmaceutical proteins.
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Affiliation(s)
- Tobias Klein
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
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22
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Jaffé SRP, Strutton B, Pandhal J, Wright PC. Inverse Metabolic Engineering for Enhanced Glycoprotein Production in Escherichia coli. Methods Mol Biol 2015; 1321:17-35. [PMID: 26082212 DOI: 10.1007/978-1-4939-2760-9_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Inverse metabolic engineering (IME) provides a strategy to rapidly identify the genetic elements responsible for the desired phenotype of a chosen target organism. This methodology has been successfully applied towards enhancing the N-linked glycosylation efficiency of Escherichia coli. Here, we describe the generation of differentially sized libraries from the E. coli W3110 genome followed by high-throughput semiquantitative glycan specific screening. DNA sequenced targets demonstrating increased levels of glycan production were selected for forward engineering, protein overexpression, and absolute quantification of glycoproteins.
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Affiliation(s)
- Stephen R P Jaffé
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, UK
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23
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A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories. Comput Struct Biotechnol J 2014; 11:91-9. [PMID: 25379147 PMCID: PMC4212277 DOI: 10.1016/j.csbj.2014.08.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Microbial cell factories (MCFs) are of considerable interest to convert low value renewable substrates to biofuels and high value chemicals. This review highlights the progress of computational models for the rational design of an MCF to produce a target bio-commodity. In particular, the rational design of an MCF involves: (i) product selection, (ii) de novo biosynthetic pathway identification (i.e., rational, heterologous, or artificial), (iii) MCF chassis selection, (iv) enzyme engineering of promiscuity to enable the formation of new products, and (v) metabolic engineering to ensure optimal use of the pathway by the MCF host. Computational tools such as (i) de novo biosynthetic pathway builders, (ii) docking, (iii) molecular dynamics (MD) and steered MD (SMD), and (iv) genome-scale metabolic flux modeling all play critical roles in the rational design of an MCF. Genome-scale metabolic flux models are of considerable use to the design process since they can reveal metabolic capabilities of MCF hosts. These can be used for host selection as well as optimizing precursors and cofactors of artificial de novo biosynthetic pathways. In addition, recent advances in genome-scale modeling have enabled the derivation of metabolic engineering strategies, which can be implemented using the genomic tools reviewed here as well.
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Jaffé SRP, Strutton B, Levarski Z, Pandhal J, Wright PC. Escherichia coli as a glycoprotein production host: recent developments and challenges. Curr Opin Biotechnol 2014; 30:205-10. [PMID: 25156401 DOI: 10.1016/j.copbio.2014.07.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 11/19/2022]
Abstract
Chinese Hamster Ovary cells are the most popular host expression system for the large-scale production of human therapeutic glycoproteins, but, the race to engineer Escherichia coli to perform glycosylation is gathering pace. The successful functional transfer of an N-glycosylation pathway from Campylobacter jejuni to Escherichia coli in 2002 can be considered as the crucial first engineering step. Here, we discuss the recent advancements in the field of N-glycosylation of recombinant therapeutic proteins in E. coli cells, from the manipulation of glycan composition, to the improvement in glycosylation efficiency, along with the challenges that remain before E. coli can be available as an industry host cell for economically viable glycoprotein production.
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Affiliation(s)
- Stephen R P Jaffé
- ChELSI Institute, Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, UK
| | - Benjamin Strutton
- ChELSI Institute, Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, UK
| | - Zdenko Levarski
- Comenius University in Bratislava, Faculty of Natural Sciences, Department of Molecular Biology, Mlynská dolina, 842 15 Bratislava 4, Slovak Republic
| | - Jagroop Pandhal
- ChELSI Institute, Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, UK
| | - Phillip C Wright
- ChELSI Institute, Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, UK.
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25
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Ollis AA, Zhang S, Fisher AC, DeLisa MP. Engineered oligosaccharyltransferases with greatly relaxed acceptor-site specificity. Nat Chem Biol 2014; 10:816-22. [PMID: 25129029 DOI: 10.1038/nchembio.1609] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/12/2014] [Indexed: 01/23/2023]
Abstract
The Campylobacter jejuni protein glycosylation locus (pgl) encodes machinery for asparagine-linked (N-linked) glycosylation and serves as the archetype for bacterial N-linked glycosylation. This machinery has been functionally transferred into Escherichia coli, enabling convenient mechanistic dissection of the N-linked glycosylation process in this genetically tractable host. Here we sought to identify sequence determinants in the oligosaccharyltransferase PglB that restrict its specificity to only those glycan acceptor sites containing a negatively charged residue at the -2 position relative to asparagine. This involved creation of a genetic assay, glycosylation of secreted N-linked acceptor proteins (glycoSNAP), that facilitates high-throughput screening of glycophenotypes in E. coli. Using this assay, we isolated several C. jejuni PglB variants that could glycosylate an array of noncanonical acceptor sequences, including one in a eukaryotic N-glycoprotein. These results underscore the utility of glycoSNAP for shedding light on poorly understood aspects of N-linked glycosylation and for engineering designer N-linked glycosylation biocatalysts.
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Affiliation(s)
- Anne A Ollis
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Core Facility, Cornell University, Ithaca, New York, USA
| | | | - Matthew P DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
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