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      A cell-free biosynthesis platform for modular construction of protein glycosylation pathways

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          Abstract

          Glycosylation plays important roles in cellular function and endows protein therapeutics with beneficial properties. However, constructing biosynthetic pathways to study and engineer precise glycan structures on proteins remains a bottleneck. Here, we report a modular, versatile cell-free platform for glycosylation pathway assembly by rapid in vitro mixing and expression (GlycoPRIME). In GlycoPRIME, glycosylation pathways are assembled by mixing-and-matching cell-free synthesized glycosyltransferases that can elaborate a glucose primer installed onto protein targets by an N-glycosyltransferase. We demonstrate GlycoPRIME by constructing 37 putative protein glycosylation pathways, creating 23 unique glycan motifs, 18 of which have not yet been synthesized on proteins. We use selected pathways to synthesize a protein vaccine candidate with an α-galactose adjuvant motif in a one-pot cell-free system and human antibody constant regions with minimal sialic acid motifs in glycoengineered Escherichia coli. We anticipate that these methods and pathways will facilitate glycoscience and make possible new glycoengineering applications.

          Abstract

          Constructing biosynthetic pathways to study and engineer glycoprotein structures is difficult. Here, the authors use GlycoPRIME, a cell-free workflow for mixing-and-matching glycosylation enzymes, to evaluate 37 putative glycosylation pathways and discover routes to 18 new glycoprotein structures

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          Most cited references66

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          Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

          We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants—the ‘Keio collection'—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).
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            Intracellular functions of N-linked glycans.

            N-linked oligosaccharides arise when blocks of 14 sugars are added cotranslationally to newly synthesized polypeptides in the endoplasmic reticulum (ER). These glycans are then subjected to extensive modification as the glycoproteins mature and move through the ER via the Golgi complex to their final destinations inside and outside the cell. In the ER and in the early secretory pathway, where the repertoire of oligosaccharide structures is still rather small, the glycans play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport. They are used as universal "tags" that allow specific lectins and modifying enzymes to establish order among the diversity of maturing glycoproteins. In the Golgi complex, the glycans acquire more complex structures and a new set of functions. The division of synthesis and processing between the ER and the Golgi complex represents an evolutionary adaptation that allows efficient exploitation of the potential of oligosaccharides.
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              Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

              Post-translational modifications (PTMs) broadly contribute to the recent explosion of proteomic data and possess a complexity surpassing that of protein design. PTMs are the chemical modification of a protein after its translation, and have wide effects broadening its range of functionality. Based on previous estimates, it is widely believed that more than half of proteins are glycoproteins. Whereas mutations can only occur once per position, different forms of post-translational modifications may occur in tandem. With the number and abundances of modifications constantly being discovered, there is no method to readily assess their relative levels. Here we report the relative abundances of each PTM found experimentally and putatively, from high-quality, manually curated, proteome-wide data, and show that at best, less than one-fifth of proteins are glycosylated. We make available to the academic community a continuously updated resource (http://selene.princeton.edu/PTMCuration) containing the statistics so scientists can assess “how many” of each PTM exists.
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                Author and article information

                Contributors
                (+1) 847 467 5007 , m-jewett@northwestern.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                27 November 2019
                27 November 2019
                2019
                : 10
                : 5404
                Affiliations
                [1 ]ISNI 0000 0001 2299 3507, GRID grid.16753.36, Department of Chemical and Biological Engineering, , Northwestern University, ; 2145 Sheridan Road, Tech E136, Evanston, IL 60208 USA
                [2 ]ISNI 0000 0001 2299 3507, GRID grid.16753.36, Center for Synthetic Biology, , Northwestern University, ; 2145 Sheridan Road, Tech B486, Evanston, IL 60208 USA
                [3 ]ISNI 0000 0001 2299 3507, GRID grid.16753.36, Department of Biomedical Engineering, , Northwestern University, ; 2145 Sheridan Road, Evanston, IL 60208 USA
                [4 ]ISNI 0000 0001 2299 3507, GRID grid.16753.36, Medical Scientist Training Program, Feinberg School of Medicine, , Northwestern University, ; Morton Building 1-670, 303 E. Chicago Avenue, Chicago, IL 60611 USA
                [5 ]ISNI 000000041936877X, GRID grid.5386.8, Department of Microbiology, , Cornell University, ; 123 Wing Drive, Ithaca, NY 14853 USA
                [6 ]ISNI 0000 0001 2299 3507, GRID grid.16753.36, Department of Chemistry, , Northwestern University, ; Evanston, IL 60208 USA
                [7 ]ISNI 000000041936877X, GRID grid.5386.8, Robert Frederick Smith School of Chemical and Biomolecular Engineering, , Cornell University, ; 120 Olin Hall, Ithaca, NY 14853 USA
                [8 ]ISNI 000000041936877X, GRID grid.5386.8, Nancy E. and Peter C. Meinig School of Biomedical Engineering, , Cornell University, Weill Hall, ; Ithaca, NY 14853 USA
                Author information
                http://orcid.org/0000-0002-5264-4866
                http://orcid.org/0000-0003-4585-5507
                http://orcid.org/0000-0002-6468-0709
                http://orcid.org/0000-0001-5418-6048
                http://orcid.org/0000-0003-2180-7842
                http://orcid.org/0000-0003-3828-5438
                http://orcid.org/0000-0001-6517-769X
                http://orcid.org/0000-0002-4964-796X
                http://orcid.org/0000-0003-3226-1566
                http://orcid.org/0000-0003-2948-6211
                Article
                12024
                10.1038/s41467-019-12024-9
                6881289
                31776339
                cdb05aae-e390-4e1f-a295-45b59ba7d09f
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 13 January 2019
                : 15 August 2019
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000001, National Science Foundation (NSF);
                Award ID: DGE-1324585
                Award ID: MCB-1413563
                Award ID: MCB-1413563
                Award ID: NSF ECCS-1542205
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000774, United States Department of Defense | Defense Threat Reduction Agency (DTRA);
                Award ID: HDTRA1-15-10052/P00001
                Award ID: HDTRA1-15-10052/P00001
                Award ID: HDTRA1-15-10052/P00001
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000008, David and Lucile Packard Foundation (David & Lucile Packard Foundation);
                Funded by: FundRef https://doi.org/10.13039/100001082, Camille and Henry Dreyfus Foundation (Camille and Henry Dreyfus Foundation, Inc.);
                Categories
                Article
                Custom metadata
                © The Author(s) 2019

                Uncategorized
                biological techniques,biotechnology,synthetic biology,chemical biology,glycobiology
                Uncategorized
                biological techniques, biotechnology, synthetic biology, chemical biology, glycobiology

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