A Markov model of glycosylation elucidates isozyme specificity and glycosyltransferase interactions for glycoengineering

Current Research in Biotechnology - Tập 2 - Trang 22-36 - 2020
Chenguang Liang1,2, Austin W.T. Chiang3,4, Anders H. Hansen5, Johnny Arnsdorf5, Sanne Schoffelen5, James T. Sorrentino1,4,6, Benjamin P. Kellman1,6, Bokan Bao1,4,6, Bjørn G. Voldborg5, Nathan E. Lewis3,2,4
1Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
2Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
3Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
4The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA
5The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
6Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA

Tài liệu tham khảo

Amann, 2019, Glyco-engineered CHO cell lines producing alpha-1-antitrypsin and C1 esterase inhibitor with fully humanized N-glycosylation profiles, Metab. Eng., 52, 143, 10.1016/j.ymben.2018.11.014 Amann, 2019, Genetic engineering approaches to improve posttranslational modification of biopharmaceuticals in different production platforms, Biotechnol. Bioeng., 116, 2778, 10.1002/bit.27101 Ardèvol, 2015, Reaction mechanisms in carbohydrate-active enzymes: glycoside hydrolases and glycosyltransferases. Insights from ab initio quantum mechanics/molecular mechanics dynamic simulations, J. Am. Chem. Soc., 137, 7528, 10.1021/jacs.5b01156 Bankaitis, 2012, Golgi membrane dynamics and lipid metabolism, Curr. Biol., 22, R414, 10.1016/j.cub.2012.03.004 Beerli, 2006, Comparison of Bayesian and maximum-likelihood inference of population genetic parameters, Bioinformatics., 22, 341, 10.1093/bioinformatics/bti803 Blanchard, 2011, N-glycosylation and biological activity of recombinant human alpha1-antitrypsin expressed in a novel human neuronal cell line, Biotechnol. Bioeng., 108, 2118, 10.1002/bit.23158 Bydlinski, 2018, The contributions of individual galactosyltransferases to protein specific N-glycan processing in Chinese Hamster Ovary cells, J Biotechnol., 282, 101, 10.1016/j.jbiotec.2018.07.015 Castilho, 2015, Processing of complex N-glycans in IgG Fc-region is affected by core fucosylation, mAbs., 7, 863, 10.1080/19420862.2015.1053683 Čaval, 2018, Direct quality control of glycoengineered erythropoietin variants, Nat. Commun., 9, 10.1038/s41467-018-05536-3 Chiang, 2016, Modulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiology, Curr. Opin. Struct. Biol., 40, 104, 10.1016/j.sbi.2016.08.008 Chuang, 2012, Computational prediction of N-linked glycosylation incorporating structural properties and patterns, Bioinformatics., 28, 2249, 10.1093/bioinformatics/bts426 Chung, 2015, Assessment of the coordinated role of ST3GAL3, ST3GAL4 and ST3GAL6 on the α2,3 sialylation linkage of mammalian glycoproteins, Biochem. Biophys. Res. Commun., 463, 211, 10.1016/j.bbrc.2015.05.023 Conn, 1991, A globally convergent augmented Lagrangian algorithm for optimization with general constraints and simple bounds, SIAM J. Numer. Anal., 28, 545, 10.1137/0728030 Darling, 2002, Glycosylation of erythropoietin affects receptor binding kinetics: role of electrostatic interactions, Biochemistry, 41, 14524, 10.1021/bi0265022 Deb, 2012, A genetic algorithm based augmented Lagrangian method for constrained optimization, Comput. Optim. Appl., 53, 869, 10.1007/s10589-012-9468-9 El-Battari, 2003, Different glycosyltransferases are differentially processed for secretion, dimerization, and autoglycosylation, Glycobiology., 13, 941, 10.1093/glycob/cwg117 García-Ródenas, 2019, A memetic chaotic gravitational search algorithm for unconstrained global optimization problems, Appl. Soft Comput., 79, 14, 10.1016/j.asoc.2019.03.011 Goh, 2014, Producing recombinant therapeutic glycoproteins with enhanced sialylation using CHO-gmt4 glycosylation mutant cells, Bioengineered., 5, 269, 10.4161/bioe.29490 Gupta, 2016, A systematic analysis of acceptor specificity and reaction kinetics of five human α(2,3)sialyltransferases: product inhibition studies illustrates reaction mechanism for ST3Gal-I, Biochem. Biophys. Res. Commun., 469, 606, 10.1016/j.bbrc.2015.11.130 Hassinen, 2019, A Golgi-associated redox switch regulates catalytic activation and cooperative functioning of ST6Gal-I with B4GalT-I, Redox Biol., 101182, 24 Heirendt, 2019, Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0, Nat Protoc., 14, 639, 10.1038/s41596-018-0098-2 Hossler, 2012, Protein glycosylation control in mammalian cell culture: past precedents and contemporary prospects, 187 Hou, 2016, Aoki-Kinoshita KF. A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks, BMC Bioinformatics., 17, 240, 10.1186/s12859-016-1094-6 Ito, 2007, Strategy for the fine characterization of glycosyltransferase specificity using isotopomer assembly, Nat. Methods, 4, 577, 10.1038/nmeth1050 Jeong, 2008, Enhanced sialylation of recombinant erythropoietin in CHO cells by human glycosyltransferase expression, J. Microbiol. Biotechnol., 18, 1945 Kawano, 2005, Prediction of glycan structures from gene expression data based on glycosyltransferase reactions, Bioinforma Oxf Engl., 21, 3976, 10.1093/bioinformatics/bti666 Kolda, 2006 Krambeck, 2005, A mathematical model of N-linked glycosylation, Biotechnol. Bioeng., 92, 711, 10.1002/bit.20645 Krambeck, 2009, A mathematical model to derive N-glycan structures and cellular enzyme activities from mass spectrometric data, Glycobiology., 19, 1163, 10.1093/glycob/cwp081 Krambeck, 2017, Model-based analysis of N-glycosylation in Chinese hamster ovary cells, PLoS One, 12, 10.1371/journal.pone.0175376 Kremkow, 2018, Glyco-mapper: a Chinese hamster ovary (CHO) genome-specific glycosylation prediction tool, Metab. Eng., 47, 134, 10.1016/j.ymben.2018.03.002 Kruschke, 2013, Bayesian estimation supersedes the t test, J Exp Psychol Gen., 142, 573, 10.1037/a0029146 Kruschke, 2018, The Bayesian new statistics: hypothesis testing, estimation, meta-analysis, and power analysis from a Bayesian perspective, Psychon. Bull. Rev., 25, 178, 10.3758/s13423-016-1221-4 Lageveen-Kammeijer, 2019, Highly sensitive CE-ESI-MS analysis of N -glycans from complex biological samples, Nat. Commun., 10, 1, 10.1038/s41467-019-09910-7 Lee, 2001, Chinese hamster ovary (CHO) cells may express six β4-galactosyltransferases (β4GalTs) consequences of the loss of functional β4GalT-1, β4GalT-6, or both in Cho glycosylation mutants, J. Biol. Chem., 276, 13924, 10.1074/jbc.M010046200 Lee, 2009, Association of β-1,3-N-acetylglucosaminyltransferase 1 and β-1,4-galactosyltransferase 1, trans-Golgi enzymes involved in coupled poly-N-acetyllactosamine synthesis, Glycobiology., 19, 655, 10.1093/glycob/cwp035 Lewis, 2007, Implementing generating set search methods for linearly constrained minimization, SIAM J. Sci. Comput., 29, 2507, 10.1137/050635432 Liu, 2014, Computational framework for the automated construction of glycosylation reaction networks, PLoS One, 9 Liu, 2008, Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands, Bioinformatics., 24, 2740, 10.1093/bioinformatics/btn515 Luo, 2017, Glycoengineering of pertuzumab and its impact on the pharmacokinetic/pharmacodynamic properties, Sci. Rep., 7 McDonald, 2016, A knowledge-based system for display and prediction of O-glycosylation network behaviour in response to enzyme knockouts, PLoS Comput. Biol., 12, 10.1371/journal.pcbi.1004844 Megchelenbrink, 2014, An improved tool for uniformly sampling the solution-space of genome-scale metabolic networks, PLoS One, 9, 10.1371/journal.pone.0086587 Mkhikian, 2016, Golgi self-correction generates bioequivalent glycans to preserve cellular homeostasis, eLife., 5, 10.7554/eLife.14814 Mondal, 2015, ST3Gal-4 is the primary sialyltransferase regulating the synthesis of E-, P-, and L-selectin ligands on human myeloid leukocytes, Blood., 125, 687, 10.1182/blood-2014-07-588590 Montacir, 2018, Physicochemical characterization, glycosylation pattern and biosimilarity assessment of the fusion protein Etanercept, Protein J., 37, 164, 10.1007/s10930-018-9757-y Moremen, 2012, Vertebrate protein glycosylation: diversity, synthesis and function, Nat Rev Mol Cell Biol., 13, 448, 10.1038/nrm3383 Muller, 2006 Nielsen, 2018, Galectin binding to cells and glycoproteins with genetically modified glycosylation reveals galectin-glycan specificities in a natural context, J. Biol. Chem., 293, 20249, 10.1074/jbc.RA118.004636 Pierpont, 2018, Past, present, and future of rituximab-the World’s first oncology monoclonal antibody therapy, Front. Oncol., 8, 163, 10.3389/fonc.2018.00163 Pinho, 2015, Glycosylation in cancer: mechanisms and clinical implications, Nat. Rev. Cancer, 15, 540, 10.1038/nrc3982 Praissman, 2014, B4GAT1 is the priming enzyme for the LARGE-dependent functional glycosylation of α-dystroglycan, eLife., 3, 10.7554/eLife.03943 Puri, 2012, Understanding glycomechanics using mathematical modeling: a review of current approaches to simulate cellular glycosylation reaction networks, Ann. Biomed. Eng., 40, 816, 10.1007/s10439-011-0464-5 Reily, 2019, Glycosylation in health and disease, Nat Rev Nephrol., 1 Rios, 2013, Derivative-free optimization: a review of algorithms and comparison of software implementations, J. Glob. Optim., 56, 1247, 10.1007/s10898-012-9951-y Rohfritsch, 2006, Probing the substrate specificity of four different sialyltransferases using synthetic β-d-Galp-(1→4)-β-d-GlcpNAc-(1→2)-α-d-Manp-(1→O) (CH2)7CH3 analogues: General activating effect of replacing N-acetylglucosamine by N-propionylglucosamine, Biochim Biophys Acta BBA - Gen Subj., 1760, 685, 10.1016/j.bbagen.2005.12.012 Salciccioli, 2016, MIT critical data, 263 Schwarz, 2016, The endoplasmic reticulum: structure, function and response to cellular signaling, Cell. Mol. Life Sci., 73, 79, 10.1007/s00018-015-2052-6 Solá, 2010, Glycosylation of therapeutic proteins: an effective strategy to optimize efficacy, BioDrugs, 24, 9, 10.2165/11530550-000000000-00000 Spahn, 2016, A Markov chain model for N-linked protein glycosylation – towards a low-parameter tool for model-driven glycoengineering, Metab. Eng., 33, 52, 10.1016/j.ymben.2015.10.007 Spahn, 2017, Predictive glycoengineering of biosimilars using a Markov chain glycosylation model, Biotechnol. J., 12, 10.1002/biot.201600489 Stanley, 2009, N-Glycans Taniguchi, 2017, N-glycosylation affects the stability and barrier function of the MUC16 mucin, J. Biol. Chem., 292, 11079, 10.1074/jbc.M116.770123 Ujita, 2000, Poly-N-acetyllactosamine extension inN-glycans and core 2- and Core 4-branchedO-glycans is differentially controlled by i-extension enzyme and different members of the β1,4-galactosyltransferase gene family, J. Biol. Chem., 275, 15868, 10.1074/jbc.M001034200 Umaña, 1997, A mathematical model of N-linked glycoform biosynthesis, Biotechnol. Bioeng., 55, 890, 10.1002/(SICI)1097-0290(19970920)55:6<890::AID-BIT7>3.0.CO;2-B 2009 Winter, 2019, Matlab Toolbox for Bayesian Estimation Yang, 2015, Engineered CHO cells for production of diverse, homogeneous glycoproteins, Nat Biotechnol., 33, 842, 10.1038/nbt.3280 Yang, 2017, Revisiting the substrate specificity of mammalian α1,6-fucosyltransferase reveals that it catalyzes core fucosylation of N-glycans lacking α1,3-arm GlcNAc, J. Biol. Chem., 292, 14796, 10.1074/jbc.M117.804070 Yang, 2017, Glycan remodeling of human erythropoietin (EPO) through combined mammalian cell engineering and Chemoenzymatic Transglycosylation, ACS Chem. Biol., 12, 1665, 10.1021/acschembio.7b00282