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Davis AR, Roberts ET, Amster IJ, Barb AW. Uniform [ 13C, 15N]-labeled and glycosylated IgG1 Fc expressed in Saccharomyces cerevisiae. J Biomol NMR 2024; 78:9-18. [PMID: 37989910 PMCID: PMC11025670 DOI: 10.1007/s10858-023-00428-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Despite the prevalence and importance of glycoproteins in human biology, methods for isotope labeling suffer significant limitations. Common prokaryotic platforms do not produce mammalian post-translation modifications that are essential to the function of many human glycoproteins, including immunoglobulin G1 (IgG1). Mammalian expression systems require complex media and thus introduce significant costs to achieve uniform labeling. Expression with Pichia is available, though expertise and equipment requirements surpass E. coli culture. We developed a system utilizing Saccharomyces cerevisiae, [13C]-glucose, and [15N]-ammonium chloride with complexity comparable to E. coli. Here we report two vectors for expressing the crystallizable fragment (Fc) of IgG1 for secretion into the culture medium, utilizing the ADH2 or DDI2 promoters. We also report a strategy to optimize the expression yield using orthogonal Taguchi arrays. Lastly, we developed two different media formulations, a standard medium which provides 86-92% 15N and 30% 13C incorporation into the polypeptide, or a rich medium which provides 98% 15N and 95% 13C incorporation as determined by mass spectrometry. This advance represents an expression and optimization strategy accessible to experimenters with the capability to grow and produce proteins for NMR-based experiments using E. coli.
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Affiliation(s)
- Alexander R Davis
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St, Davison Life Science Complex, Athens, GA, 30602, USA
| | | | | | - Adam W Barb
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St, Davison Life Science Complex, Athens, GA, 30602, USA.
- Department of Chemistry, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
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Subedi GP, Roberts ET, Davis AR, Kremer PG, Amster IJ, Barb AW. A comprehensive assessment of selective amino acid 15N-labeling in human embryonic kidney 293 cells for NMR spectroscopy. J Biomol NMR 2024:10.1007/s10858-023-00434-3. [PMID: 38407675 DOI: 10.1007/s10858-023-00434-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/31/2023] [Indexed: 02/27/2024]
Abstract
A large proportion of human proteins contain post-translational modifications that cannot be synthesized by prokaryotes. Thus, mammalian expression systems are often employed to characterize structure/function relationships using NMR spectroscopy. Here we define the selective isotope labeling of secreted, post-translationally modified proteins using human embryonic kidney (HEK)293 cells. We determined that alpha-[15N]- atoms from 10 amino acids experience minimal metabolic scrambling (C, F, H, K, M, N, R, T, W, Y). Two more interconvert to each other (G, S). Six others experience significant scrambling (A, D, E, I, L, V). We also demonstrate that tuning culture conditions suppressed V and I scrambling. These results define expectations for 15N-labeling in HEK293 cells.
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Affiliation(s)
- Ganesh P Subedi
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Elijah T Roberts
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA
| | - Alexander R Davis
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA
| | - Paul G Kremer
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA.
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
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Prestegard JH. A consensus structural motif for the capsular polysaccharide of Cryptococcus Neoformans by NMR/MD. Proc Natl Acad Sci U S A 2024; 121:e2322413121. [PMID: 38335259 PMCID: PMC10873558 DOI: 10.1073/pnas.2322413121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024] Open
Affiliation(s)
- James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA30601
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Wu FJ, Kronenberg D, Hertel I, Grzesiek S. The key role of glutamine for protein expression and isotopic labeling in insect cells. J Biol Chem 2023; 299:105142. [PMID: 37553040 PMCID: PMC10556780 DOI: 10.1016/j.jbc.2023.105142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/10/2023] Open
Abstract
Nuclear magnetic resonance studies of many physiologically important proteins have long been impeded by the necessity to express such proteins in isotope-labeled form in higher eukaryotic cells and the concomitant high costs of providing isotope-labeled amino acids in the growth medium. Economical routes use isotope-labeled yeast or algae extracts but still require expensive isotope-labeled glutamine. Here, we have systematically quantified the effect of 15N2-glutamine on the expression and isotope labeling of different proteins in insect cells. Sufficient levels of glutamine in the medium increase the protein expression by four to five times relative to deprived conditions. 1H-15N nuclear magnetic resonance spectroscopy shows that the 15N atoms from 15N2-glutamine are scrambled with surprisingly high (60-70%) efficiency into the three amino acids alanine, aspartate, and glutamate. This phenomenon gives direct evidence that the high energy demand of insect cells during baculovirus infection and concomitant heterologous protein expression is predominantly satisfied by glutamine feeding the tricarboxylic acid cycle. To overcome the high costs of supplementing isotope-labeled glutamine, we have developed a robust method for the large-scale synthesis of 15N2-glutamine and partially deuterated 15N2-glutamine-α,β,β-d3 from inexpensive precursors. An application is shown for the effective large-scale expression of the isotope-labeled β1-adrenergic receptor using the synthesized 15N2-glutamine-α,β,β-d3.
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Affiliation(s)
- Feng-Jie Wu
- Biozentrum, University of Basel, Basel, Switzerland.
| | | | - Ines Hertel
- Biozentrum, University of Basel, Basel, Switzerland
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Yanaka S, Yogo R, Yagi H, Onitsuka M, Wakaizumi N, Yamaguchi Y, Uchiyama S, Kato K. Negative interference with antibody-dependent cellular cytotoxicity mediated by rituximab from its interactions with human serum proteins. Front Immunol 2023; 14:1090898. [PMID: 36761774 PMCID: PMC9905677 DOI: 10.3389/fimmu.2023.1090898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
Although interactions of small molecular drugs with serum proteins have been widely studied from pharmacokinetic and pharmacodynamic perspectives, there have been few reports on the effects of serum components on therapeutic antibody functions. This study reports the effect of abundant serum proteins on antibody-dependent cellular cytotoxicity (ADCC) mediated by rituximab and Fcγ receptor III (FcγRIII). Human serum albumin (HSA) and the Fab fragment from the pooled serum polyclonal IgG were found to compromise ADCC as non-competitive inhibitors. Our nuclear magnetic resonance data provided direct evidence for the interactions of HSA with both the Fab and Fc regions of rituximab and also with the extracellular region of FcγRIII (sFcγRIII). The degree of involvement in the interaction decreased in the order of rituximab-Fab > rituximab-Fc > sFcγRIII, suggesting preferential binding of HSA to net positively charged proteins. Although much less pronounced than the effect of HSA, polyclonal IgG-Fab specifically interacted with rituximab-Fc. The NMR data also showed that the serum protein interactions cover the Fc surface extensively, suggesting that they can act as pan-inhibitors against various Fc receptor-mediated functions and pharmacokinetics. Our findings highlight the importance of considering serum-protein interactions in the design and application of antibody-based drugs with increased efficacy and safety.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Hirokazu Yagi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | | | - Yuki Yamaguchi
- Graduate School of Engineering, University of Osaka, Osaka, Japan
| | - Susumu Uchiyama
- Graduate School of Engineering, University of Osaka, Osaka, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
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Shenoy A, Davis AR, Roberts ET, Amster IJ, Barb AW. Metabolic 15N labeling of the N-glycosylated immunoglobulin G1 Fc with an engineered Saccharomyces cerevisiae strain. J Biomol NMR 2022; 76:95-105. [PMID: 35802275 DOI: 10.1007/s10858-022-00397-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The predominant protein expression host for NMR spectroscopy is Escherichia coli, however, it does not synthesize appropriate post-translation modifications required for mammalian protein function and is not ideal for expressing naturally secreted proteins that occupy an oxidative environment. Mammalian expression platforms can address these limitations; however, these are not amenable to cost-effective uniform 15 N labeling resulting from highly complex growth media requirements. Yeast expression platforms combine the simplicity of bacterial expression with the capabilities of mammalian platforms, however yeasts require optimization prior to isotope labeling. Yeast expression will benefit from methods to boost protein expression levels and developing labeling conditions to facilitate growth and high isotope incorporation within the target protein. In this work, we describe a novel platform based on the yeast Saccharomyces cerevisiae that simultaneously expresses the Kar2p chaperone and protein disulfide isomerase in the ER to facilitate the expression of secreted proteins. Furthermore, we developed a growth medium for uniform 15 N labeling. We recovered 2.2 mg/L of uniformly 15 N-labeled human immunoglobulin (Ig)G1 Fc domain with 90.6% 15 N labeling. NMR spectroscopy revealed a high degree of similarity between the yeast and mammalian-expressed IgG1 Fc domains. Furthermore, we were able to map the binding interaction between IgG1 Fc and the Z domain through chemical shift perturbations. This platform represents a novel cost-effective strategy for 15 N-labeled immunoglobulin fragments.
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Affiliation(s)
- Anjali Shenoy
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Alexander R Davis
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | | | | | - Adam W Barb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
- Department of Chemistry, University of Georgia, Athens, GA, USA.
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