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Mayer F, Cserjan-Puschmann M, Haslinger B, Shpylovyi A, Dalik T, Sam C, Hahn R, Striedner G. Strain specific properties of Escherichia coli can prevent non-canonical amino acid misincorporation caused by scale-related process heterogeneities. Microb Cell Fact 2022; 21:170. [PMID: 35999607 PMCID: PMC9396823 DOI: 10.1186/s12934-022-01895-1] [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: 06/10/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Escherichia coli is one of the most important hosts for production of recombinant proteins in biopharmaceutical industry. However, when selecting a suitable production strain, it is often not considered that a lot of different sub-species exist, which can differ in their genotypes and phenotypes. Another important development step is the scale-up of bioprocesses with the particular challenge that heterogeneities and gradients occur at production scale. These in turn can affect the production organism and can have negative impact on the process and the product quality. Therefore, researchers developed scale-down reactors, which are used to mimic manufacturing conditions in laboratory scale. The main objectives of this study were to determine the extent to which scale-related process inhomogeneities affect the misincorporation of non-canonical amino acids into the recombinant target protein, which is an important quality attribute, and whether strain specific properties may have an impact. Results We investigated two industrially relevant E. coli strains, BL21(DE3) and HMS174(DE3), which produced an antigen binding fragment (Fab). The cells were cultivated in high cell density fed-batch mode at laboratory scale and under scale-down conditions. We demonstrated that the two host strains differ significantly with respect to norleucine misincorporation into the target protein, especially under heterogeneous cultivation conditions in the scale-down reactor. No norleucine misincorporation was observed in E. coli BL21(DE3) for either cultivation condition. In contrast, norleucine incorporation into HMS174(DE3) was already detectable in the reference process and increased dramatically in scale-down experiments. Norleucine incorporation was not random and certain positions were preferred over others, even though only a single codon exists. Differences in biomass and Fab production between the strains during scale-down cultivations could be observed as well. Conclusions This study has shown that E. coli BL21(DE3) is much more robust to scale-up effects in terms of norleucine misincorporation than the K12 strain tested. In this respect, BL21(DE3) enables better transferability of results at different scales, simplifies process implementation at production scale, and helps to meet regulatory quality guidelines defined for biopharmaceutical manufacturing. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01895-1.
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Affiliation(s)
- Florian Mayer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Benedikt Haslinger
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Anton Shpylovyi
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Thomas Dalik
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Christian Sam
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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Durmaz YT, Shatadal A, Friend K. Geneticin reduces mRNA stability. PLoS One 2022; 17:e0272058. [PMID: 35901009 PMCID: PMC9333311 DOI: 10.1371/journal.pone.0272058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
Messenger RNA (mRNA) translation can lead to higher rates of mRNA decay, suggesting the ribosome plays a role in mRNA destruction. Furthermore, mRNA features, such as codon identities, which are directly probed by the ribosome, correlate with mRNA decay rates. Many amino acids are encoded by synonymous codons, some of which are decoded by more abundant tRNAs leading to more optimal translation and increased mRNA stability. Variable translation rates for synonymous codons can lead to ribosomal collisions as ribosomes transit regions with suboptimal codons, and ribosomal collisions can promote mRNA decay. In addition to different translation rates, the presence of certain codons can also lead to higher or lower rates of amino acid misincorporation which could potentially lead to protein misfolding if a substituted amino acid fails to make critical contacts in a structure. Here, we test whether Geneticin—G418, an aminoglycoside antibiotic known to promote amino acid misincorporation—affects mRNA stability. We observe that G418 decreases firefly luciferase mRNA stability in an in vitro translation system and also reduces mRNA stability in mouse embryonic stem cells (mESCs). G418-sensitive mRNAs are enriched for certain optimal codons that contain G or C in the wobble position, arguing that G418 blunts the stabilizing effects of codon optimality.
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Affiliation(s)
- Yavuz T. Durmaz
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Alankrit Shatadal
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Kyle Friend
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
- * E-mail:
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Stadnik D, Bierczyńska-Krzysik A, Zielińska J, Antosik J, Borowicz P, Bednarek E, Bocian W, Sitkowski J, Kozerski L. Identification of Lysine Misincorporation at Asparagine Position in Recombinant Insulin Analogs Produced in E. coli. Pharm Res 2019; 36:79. [PMID: 30949841 PMCID: PMC6449291 DOI: 10.1007/s11095-019-2601-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/03/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE Identification of human insulin analogs' impurity with a mass shift +14 Da in comparison to a parent protein. METHODS The protein sequence variant was detected and identified with the application of peptide mapping, liquid chromatography, tandem mass spectrometric analysis, nuclear magnetic resonance spectroscopy (NMR) and Edman sequencing. RESULTS The misincorporated lysine (Lys) at asparagine (Asn) position A21 was detected in recombinant human insulin and its analogs. CONCLUSIONS Although there are three asparagine residues in the insulin derivative, the misincorporation of lysine occurred only at position A21. The process involves G/U or A/U wobble base pairing.
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Affiliation(s)
- Dorota Stadnik
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland.
| | - Anna Bierczyńska-Krzysik
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland
| | - Joanna Zielińska
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland
| | - Jarosław Antosik
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland
| | - Piotr Borowicz
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland
| | - Elżbieta Bednarek
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Wojciech Bocian
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Jerzy Sitkowski
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Lech Kozerski
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
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Wong HE, Huang CJ, Zhang Z. Amino acid misincorporation in recombinant proteins. Biotechnol Adv 2017; 36:168-181. [PMID: 29107148 DOI: 10.1016/j.biotechadv.2017.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/12/2017] [Accepted: 10/24/2017] [Indexed: 11/26/2022]
Abstract
Proteins provide the molecular basis for cellular structure, catalytic activity, signal transduction, and molecular transport in biological systems. Recombinant protein expression is widely used to prepare and manufacture novel proteins that serve as the foundation of many biopharmaceutical products. However, protein translation bioprocesses are inherently prone to low-level errors. These sequence variants caused by amino acid misincorporation have been observed in both native and recombinant proteins. Protein sequence variants impact product quality, and their presence can be exacerbated through cellular stress, overexpression, and nutrient starvation. Therefore, the cell line selection process, which is used in the biopharmaceutical industry, is not only directed towards maximizing productivity, but also focuses on selecting clones which yield low sequence variant levels, thereby proactively avoiding potentially inauspicious patient safety and efficacy outcomes. Here, we summarize a number of hallmark studies aimed at understanding the mechanisms of amino acid misincorporation, as well as exacerbating factors, and mitigation strategies. We also describe key advances in analytical technologies in the identification and quantification of sequence variants, and some practical considerations when using LC-MS/MS for detecting sequence variants.
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Affiliation(s)
- H Edward Wong
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Chung-Jr Huang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Zhongqi Zhang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States.
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Villada JC, Brustolini OJB, Batista da Silveira W. Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design. DNA Res 2017; 24:419-434. [PMID: 28449100 PMCID: PMC5737324 DOI: 10.1093/dnares/dsx014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 01/21/2023] Open
Abstract
Gene codon optimization may be impaired by the misinterpretation of frequency and optimality of codons. Although recent studies have revealed the effects of codon usage bias (CUB) on protein biosynthesis, an integrated perspective of the biological role of individual codons remains unknown. Unlike other previous studies, we show, through an integrated framework that attributes of codons such as frequency, optimality and positional dependency should be combined to unveil individual codon contribution for protein biosynthesis. We designed a codon quantification method for assessing CUB as a function of position within genes with a novel constraint: the relativity of position-dependent codon usage shaped by coding sequence length. Thus, we propose a new way of identifying the enrichment, depletion and non-uniform positional distribution of codons in different regions of yeast genes. We clustered codons that shared attributes of frequency and optimality. The cluster of non-optimal codons with rare occurrence displayed two remarkable characteristics: higher codon decoding time than frequent-non-optimal cluster and enrichment at the 5'-end region, where optimal codons with the highest frequency are depleted. Interestingly, frequent codons with non-optimal adaptation to tRNAs are uniformly distributed in the Saccharomyces cerevisiae genes, suggesting their determinant role as a speed regulator in protein elongation.
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Affiliation(s)
- Juan C. Villada
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
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Percy AJ, Michaud SA, Jardim A, Sinclair NJ, Zhang S, Mohammed Y, Palmer AL, Hardie DB, Yang J, LeBlanc AM, Borchers CH. Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600097] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/14/2016] [Accepted: 09/28/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Andrew J. Percy
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Sarah A. Michaud
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Armando Jardim
- Institute of Parasitology; McGill University; Montreal QC Canada
| | - Nicholas J. Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Suping Zhang
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Center for Proteomics and Metabolomics; Leiden University Medical Center; ZA Leiden Netherlands
| | - Andrea L. Palmer
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Darryl B. Hardie
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Andre M. LeBlanc
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC Canada
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Corrigendum. FEBS J 2016; 283:395. [PMID: 26907790 DOI: 10.1111/febs.13619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Routledge SJ, Mikaliunaite L, Patel A, Clare M, Cartwright SP, Bawa Z, Wilks MDB, Low F, Hardy D, Rothnie AJ, Bill RM. The synthesis of recombinant membrane proteins in yeast for structural studies. Methods 2015; 95:26-37. [PMID: 26431670 DOI: 10.1016/j.ymeth.2015.09.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 12/22/2022] Open
Abstract
Historically, recombinant membrane protein production has been a major challenge meaning that many fewer membrane protein structures have been published than those of soluble proteins. However, there has been a recent, almost exponential increase in the number of membrane protein structures being deposited in the Protein Data Bank. This suggests that empirical methods are now available that can ensure the required protein supply for these difficult targets. This review focuses on methods that are available for protein production in yeast, which is an important source of recombinant eukaryotic membrane proteins. We provide an overview of approaches to optimize the expression plasmid, host cell and culture conditions, as well as the extraction and purification of functional protein for crystallization trials in preparation for structural studies.
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Affiliation(s)
- Sarah J Routledge
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK; School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Lina Mikaliunaite
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Anjana Patel
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Michelle Clare
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephanie P Cartwright
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Zharain Bawa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Martin D B Wilks
- Smallpeice Enterprises Ltd, 27 Newbold Terrace East, Leamington Spa, Warwickshire CV32 4ES, UK
| | - Floren Low
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - David Hardy
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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Bill RM, von der Haar T. Hijacked then lost in translation: the plight of the recombinant host cell in membrane protein structural biology projects. Curr Opin Struct Biol 2015; 32:147-55. [PMID: 26037971 PMCID: PMC4521084 DOI: 10.1016/j.sbi.2015.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/10/2015] [Accepted: 04/10/2015] [Indexed: 11/13/2022]
Abstract
Membrane protein structural biologists need high-quality protein for crystallisation. Recombinant proteins are central to the structural biology supply chain. Understanding quality control in protein production is an emerging trend. The roles of translation and protein folding in the host cell are examined.
Membrane protein structural biology is critically dependent upon the supply of high-quality protein. Over the last few years, the value of crystallising biochemically characterised, recombinant targets that incorporate stabilising mutations has been established. Nonetheless, obtaining sufficient yields of many recombinant membrane proteins is still a major challenge. Solutions are now emerging based on an improved understanding of recombinant host cells; as a ‘cell factory’ each cell is tasked with managing limited resources to simultaneously balance its own growth demands with those imposed by an expression plasmid. This review examines emerging insights into the role of translation and protein folding in defining high-yielding recombinant membrane protein production in a range of host cells.
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Affiliation(s)
- Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
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