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Zutz A, Hamborg L, Pedersen LE, Kassem MM, Papaleo E, Koza A, Herrgård MJ, Jensen SI, Teilum K, Lindorff-Larsen K, Nielsen AT. A dual-reporter system for investigating and optimizing protein translation and folding in E. coli. Nat Commun 2021; 12:6093. [PMID: 34667164 PMCID: PMC8526717 DOI: 10.1038/s41467-021-26337-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 10/01/2021] [Indexed: 01/29/2023] Open
Abstract
Strategies for investigating and optimizing the expression and folding of proteins for biotechnological and pharmaceutical purposes are in high demand. Here, we describe a dual-reporter biosensor system that simultaneously assesses in vivo protein translation and protein folding, thereby enabling rapid screening of mutant libraries. We have validated the dual-reporter system on five different proteins and find an excellent correlation between reporter signals and the levels of protein expression and solubility of the proteins. We further demonstrate the applicability of the dual-reporter system as a screening assay for deep mutational scanning experiments. The system enables high throughput selection of protein variants with high expression levels and altered protein stability. Next generation sequencing analysis of the resulting libraries of protein variants show a good correlation between computationally predicted and experimentally determined protein stabilities. We furthermore show that the mutational experimental data obtained using this system may be useful for protein structure calculations.
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Affiliation(s)
- Ariane Zutz
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Louise Hamborg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Maher M Kassem
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Elena Papaleo
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark.
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2
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Soleymani B, Barzegari E, Mansouri K, Karami K, Mohammadi P, Kiani S, Moasefi N, Tabar MS, Mostafaie A. Heterologous expression, purification, and refolding of SRY protein: role of L-arginine as analyzed by simulation and practical study. Mol Biol Rep 2020; 47:5943-5951. [PMID: 32696344 DOI: 10.1007/s11033-020-05667-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/13/2020] [Indexed: 11/24/2022]
Abstract
Escherichia coli is a widely-used cell factory for recombinant protein production, nevertheless, high amount of produced protein is seen in aggregated form. The purpose of this study was to improve the solubility of recombinant bovine sex-determining region Y protein (rbSRY) by exploring the effect of temperature, inducer, and water-arginine mixed solvent. Codon-optimized rbSRY expressed in Rosetta-gami B (DE3) pLysS and purified by NI-NTA His-select affinity chromatography in the native and denaturing conditions. A three-dimensional model of SRY was built and studied through molecular dynamics simulations in water and in the presence of L-arginine as co-solvent. Results indicated the significant effects of temperature and IPTG concentration (P < 0.001) on the solubility of rbSRY. The binding activity of native, inclusion bodies and refolded fractions to anti-rbSRY monoclonal antibody were concentration-dependent (P < 0.001). Based on molecular modeling results, the propensity of fragments in the N-terminal domain to form β-sheet and the relative instability of α-helices in terminal domains are the probable reasons for the high aggregation potential of SRY, which are mitigated in the presence of L-arginine. Altogether, our rbSRY protein was properly produced and applying appropriate culture conditions could help enhance its solubility, refold inclusion bodies, and improve its activity upon refolding.
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Affiliation(s)
- Bijan Soleymani
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Kamran Mansouri
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Keyvan Karami
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Pantea Mohammadi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sarah Kiani
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Narges Moasefi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mehdi Sharifi Tabar
- School of Life and Environmental Science, University of Sydney, Camperdown, Australia
| | - Ali Mostafaie
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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3
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Simpson LW, Good TA, Leach JB. Protein folding and assembly in confined environments: Implications for protein aggregation in hydrogels and tissues. Biotechnol Adv 2020; 42:107573. [PMID: 32512220 DOI: 10.1016/j.biotechadv.2020.107573] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 05/03/2020] [Accepted: 05/30/2020] [Indexed: 12/20/2022]
Abstract
In the biological milieu of a cell, soluble crowding molecules and rigid confined environments strongly influence whether the protein is properly folded, intrinsically disordered proteins assemble into distinct phases, or a denatured or aggregated protein species is favored. Such crowding and confinement factors act to exclude solvent volume from the protein molecules, resulting in an increased local protein concentration and decreased protein entropy. A protein's structure is inherently tied to its function. Examples of processes where crowding and confinement may strongly influence protein function include transmembrane protein dimerization, enzymatic activity, assembly of supramolecular structures (e.g., microtubules), nuclear condensates containing transcriptional machinery, protein aggregation in the contexts of disease and protein therapeutics. Historically, most protein structures have been determined from pure, dilute protein solutions or pure crystals. However, these are not the environments in which these proteins function. Thus, there has been an increased emphasis on analyzing protein structure and dynamics in more "in vivo-like" environments. Complex in vitro models using hydrogel scaffolds to study proteins may better mimic features of the in vivo environment. Therefore, analytical techniques need to be optimized for real-time analysis of proteins within hydrogel scaffolds.
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Affiliation(s)
- Laura W Simpson
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Eng 314, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Theresa A Good
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Ave, Alexandria, VA 22314, USA
| | - Jennie B Leach
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Eng 314, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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4
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de Marco A, Ferrer-Miralles N, Garcia-Fruitós E, Mitraki A, Peternel S, Rinas U, Trujillo-Roldán MA, Valdez-Cruz NA, Vázquez E, Villaverde A. Bacterial inclusion bodies are industrially exploitable amyloids. FEMS Microbiol Rev 2019; 43:53-72. [PMID: 30357330 DOI: 10.1093/femsre/fuy038] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
Understanding the structure, functionalities and biology of functional amyloids is an issue of emerging interest. Inclusion bodies, namely protein clusters formed in recombinant bacteria during protein production processes, have emerged as unanticipated, highly tunable models for the scrutiny of the physiology and architecture of functional amyloids. Based on an amyloidal skeleton combined with varying amounts of native or native-like protein forms, bacterial inclusion bodies exhibit an unusual arrangement that confers mechanical stability, biological activity and conditional protein release, being thus exploitable as versatile biomaterials. The applicability of inclusion bodies in biotechnology as enriched sources of protein and reusable catalysts, and in biomedicine as biocompatible topographies, nanopills or mimetics of endocrine secretory granules has been largely validated. Beyond these uses, the dissection of how recombinant bacteria manage the aggregation of functional protein species into structures of highly variable complexity offers insights about unsuspected connections between protein quality (conformational status compatible with functionality) and cell physiology.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Vassilika Vouton, 70013 Heraklion, Crete, Greece.,Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology Hellas (FORTH), N. Plastira 100, Vassilika Vouton, 70013 Heraklion, Crete, Greece
| | | | - Ursula Rinas
- Leibniz University of Hannover, Technical Chemistry and Life Science, 30167 Hannover, Germany.,Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
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5
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Ami D, Natalello A, Lotti M, Doglia SM. Why and how protein aggregation has to be studied in vivo. Microb Cell Fact 2013; 12:17. [PMID: 23410248 PMCID: PMC3583745 DOI: 10.1186/1475-2859-12-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/07/2013] [Indexed: 11/10/2022] Open
Abstract
The understanding of protein aggregation is a central issue in different fields of protein science, from the heterologous protein production in biotechnology to amyloid aggregation in several neurodegenerative and systemic diseases. To this goal, it became more and more evident the crucial relevance of studying protein aggregation in the complex cellular environment, since it allows to take into account the cellular components affecting protein aggregation, such as chaperones, proteases, and molecular crowding. Here, we discuss the use of several biochemical and biophysical approaches that can be employed to monitor protein aggregation within intact cells, focusing in particular on bacteria that are widely employed as microbial cell factories.
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Affiliation(s)
- Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
- Department of Physics “G. Occhialini”, University of Milano-Bicocca, Piazza della Scienza 3, 20126, Milano, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Silvia Maria Doglia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
- Department of Physics “G. Occhialini”, University of Milano-Bicocca, Piazza della Scienza 3, 20126, Milano, Italy
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6
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Cytoplasmic expression, antibody production, and characterization of the novel zinc finger protein 637. Appl Microbiol Biotechnol 2012; 97:741-9. [PMID: 22733115 DOI: 10.1007/s00253-012-4235-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 06/07/2012] [Accepted: 06/08/2012] [Indexed: 02/05/2023]
Abstract
Zinc finger protein 637 (zfp637), belonging to the Kruppel-like protein family, comprises one atypical C(2)H(2) and six consecutive typical zinc finger motifs. Based on the structural characterization of zfp637 and its location in the cell nucleus, we predict that zfp637 might function as a DNA-binding protein to regulate gene transcription. However, the absence of both a purified zfp637 protein and any commercial antibody for detecting it in cells and tissues has limited functional studies of zfp637 to date. Here, we developed and optimized an expression system by fusing zfp637 with glutathione S-transferase (GST) to achieve a maximal yield of soluble GST-zfp637 fusion protein in Escherichia coli BL21(DE3) cells. The yield was about 10 mg/l of the original bacterial culture. The recombinant GST-zfp637 fusion protein was purified and used for polyclonal antibody production in rabbits. In addition, we developed a method to remove the anti-GST antibody component and obtained a highly purified anti-zfp637 antibody, as demonstrated by an enzyme-linked immunosorbent assay. Western blotting showed that the anti-zfp637 antibody recognized not only the recombinant zfp637 protein but also endogenous zfp637 in several cell lines. The protein was localized mainly in the cell nucleus by immunofluorescence and immunohistochemistry. The expression levels of zfp637 mRNA and protein were significantly increased in NIH3T3 cells treated with 200 μM of H(2)O(2) in a time-dependent manner. The recombinant GST-zfp637 fusion protein and our purified anti-zfp637 antibody will help in elucidating the function of zfp637.
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7
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de Marco A. Molecular and chemical chaperones for improving the yields of soluble recombinant proteins. Methods Mol Biol 2011; 705:31-51. [PMID: 21125379 DOI: 10.1007/978-1-61737-967-3_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Molecular chaperones and chemical compounds like amino acids and osmolytes share the capability to prevent protein aggregation and can contribute to rescue in vivo aggregated proteins. Therefore, both overexpression of the molecular folding machinery and induced accumulation of chemical chaperones are options to improve the correct folding of recombinantly expressed proteins. These two parameters may show synergistic effects, although success remains protein specific and, therefore, several combinations of molecular and chemical chaperones should be compared. However, proteins can fail to fold correctly even in optimized culture conditions. In this case, protein aggregates can be recovered and their refolding assisted by an osmolyte/chaperone-dependent system. The selection of aggregates with different degrees of complexity can be exploited to maximize the yields of native proteins at the end of the refolding process.
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Affiliation(s)
- Ario de Marco
- Biochemistry Unit, IFOM-IEO Campus for Oncogenomics, Cogentech, Milano, Italy.
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8
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Hartinger D, Heinl S, Schwartz HE, Grabherr R, Schatzmayr G, Haltrich D, Moll WD. Enhancement of solubility in Escherichia coli and purification of an aminotransferase from Sphingopyxis sp. MTA144 for deamination of hydrolyzed fumonisin B(1). Microb Cell Fact 2010; 9:62. [PMID: 20718948 PMCID: PMC2933618 DOI: 10.1186/1475-2859-9-62] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 08/18/2010] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Fumonisin B(1) is a cancerogenic mycotoxin produced by Fusarium verticillioides and other fungi. Sphingopyxis sp. MTA144 can degrade fumonisin B(1), and a key enzyme in the catabolic pathway is an aminotransferase which removes the C2-amino group from hydrolyzed fumonisin B(1). In order to study this aminotransferase with respect to a possible future application in enzymatic fumonisin detoxification, we attempted expression of the corresponding fumI gene in E. coli and purification of the enzyme. Since the aminotransferase initially accumulated in inclusion bodies, we compared the effects of induction level, host strain, expression temperature, solubility enhancers and a fusion partner on enzyme solubility and activity. RESULTS When expressed from a T7 promoter at 30 degrees C, the aminotransferase accumulated invariably in inclusion bodies in DE3 lysogens of the E. coli strains BL21, HMS174, Rosetta 2, Origami 2, or Rosetta-gami. Omission of the isopropyl-beta-D-thiogalactopyranoside (IPTG) used for induction caused a reduction of expression level, but no enhancement of solubility. Likewise, protein production but not solubility correlated with the IPTG concentration in E. coli Tuner(DE3). Addition of the solubility enhancers betaine and sorbitol or the co-enzyme pyridoxal phosphate showed no effect. Maltose-binding protein, used as an N-terminal fusion partner, promoted solubility at 30 degrees C or less, but not at 37 degrees C. Low enzyme activity and subsequent aggregation in the course of purification and cleavage indicated that the soluble fusion protein contained incorrectly folded aminotransferase. Expression in E. coli ArcticExpress(DE3), which co-expresses two cold-adapted chaperonins, at 11 degrees C finally resulted in production of appreciable amounts of active enzyme. Since His tag-mediated affinity purification from this strain was hindered by co-elution of chaperonin, two steps of chromatography with optimized imidazole concentration in the binding buffer were performed to obtain 1.45 mg of apparently homogeneous aminotransferase per liter of expression culture. CONCLUSIONS We found that only reduction of temperature, but not reduction of expression level or fusion to maltose-binding protein helped to produce correctly folded, active aminotransferase FumI in E. coli. Our results may provide a starting point for soluble expression of related aminotransferases or other aggregation-prone proteins in E. coli.
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9
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Effects of recombinant protein misfolding and aggregation on bacterial membranes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:263-9. [DOI: 10.1016/j.bbapap.2008.10.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 10/09/2008] [Accepted: 10/23/2008] [Indexed: 11/23/2022]
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10
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Martínez-Alonso M, García-Fruitós E, Villaverde A. Yield, solubility and conformational quality of soluble proteins are not simultaneously favored in recombinant Escherichia coli. Biotechnol Bioeng 2008; 101:1353-8. [PMID: 18980180 DOI: 10.1002/bit.21996] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Many enzymes or fluorescent proteins produced in Escherichia coli are enzymatically active or fluorescent respectively when deposited as inclusion bodies. The occurrence of insoluble but functional protein species with native-like secondary structure indicates that solubility and conformational quality of recombinant proteins are not coincident parameters, and suggests that both properties can be engineered independently. We have here proven this principle by producing elevated yields of a highly fluorescent but insoluble green fluorescent protein (GFP) in a DnaK- background, and further enhancing its solubility through adjusting the growth temperature and GFP gene expression rate. The success of such a two-step approach confirms the independent control of solubility and conformational quality, advocates for new routes towards high quality protein production and intriguingly, proves that high protein yields dramatically compromise the conformational quality of soluble versions.
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Affiliation(s)
- Mónica Martínez-Alonso
- Department of Genetics and Microbiology, Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
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11
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de Groot NS, Espargaró A, Morell M, Ventura S. Studies on bacterial inclusion bodies. Future Microbiol 2008; 3:423-35. [DOI: 10.2217/17460913.3.4.423] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The field of protein misfolding and aggregation has become an extremely active area of research in recent years. Of particular interest is the deposition of polypeptides into inclusion bodies inside bacterial cells. One reason for this interest is that protein aggregation constitutes a major bottleneck in protein production and restricts the spectrum of protein-based drugs available for commercialization. Additionally, prokaryotic cells could provide a simple yet powerful system for studying the formation and prevention of toxic aggregates, such as those responsible for a number of degenerative diseases. Here, we review recent work that has challenged our understanding of the structure and physiology of inclusion bodies and provided us with a new view of intracellular protein deposition, which has important implications in microbiology, biomedicine and biotechnology.
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Affiliation(s)
- Natalia S de Groot
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Alba Espargaró
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Montserrat Morell
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
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12
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Gasser B, Saloheimo M, Rinas U, Dragosits M, Rodríguez-Carmona E, Baumann K, Giuliani M, Parrilli E, Branduardi P, Lang C, Porro D, Ferrer P, Tutino ML, Mattanovich D, Villaverde A. Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview. Microb Cell Fact 2008; 7:11. [PMID: 18394160 PMCID: PMC2322954 DOI: 10.1186/1475-2859-7-11] [Citation(s) in RCA: 232] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 04/04/2008] [Indexed: 11/17/2022] Open
Abstract
Different species of microorganisms including yeasts, filamentous fungi and bacteria have been used in the past 25 years for the controlled production of foreign proteins of scientific, pharmacological or industrial interest. A major obstacle for protein production processes and a limit to overall success has been the abundance of misfolded polypeptides, which fail to reach their native conformation. The presence of misfolded or folding-reluctant protein species causes considerable stress in host cells. The characterization of such adverse conditions and the elicited cell responses have permitted to better understand the physiology and molecular biology of conformational stress. Therefore, microbial cell factories for recombinant protein production are depicted here as a source of knowledge that has considerably helped to picture the extremely rich landscape of in vivo protein folding, and the main cellular players of this complex process are described for the most important cell factories used for biotechnological purposes.
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Affiliation(s)
- Brigitte Gasser
- University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Vienna, Austria
| | | | - Ursula Rinas
- Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Martin Dragosits
- University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Vienna, Austria
| | - Escarlata Rodríguez-Carmona
- Autonomous University of Barcelona, Institute for Biotechnology and Biomedicine, Department of Genetics and Microbiology, and CIBER-BBN Network in Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
| | - Kristin Baumann
- Autonomous University of Barcelona, Department of Chemical Engineering, Barcelona, Spain
| | - Maria Giuliani
- University of Naples Federico II, School of Biotechnological Sciences, Naples, Italy
| | - Ermenegilda Parrilli
- University of Naples Federico II, School of Biotechnological Sciences, Naples, Italy
| | - Paola Branduardi
- University of Milano-Bicocca, Department of Biotechnology and Bioscience, Milan, Italy
| | - Christine Lang
- Technical University Berlin, Faculty III, Institute for Microbiology and Genetics, Berlin, Germany
| | - Danilo Porro
- University of Milano-Bicocca, Department of Biotechnology and Bioscience, Milan, Italy
| | - Pau Ferrer
- Autonomous University of Barcelona, Department of Chemical Engineering, Barcelona, Spain
| | - Maria Luisa Tutino
- University of Naples Federico II, School of Biotechnological Sciences, Naples, Italy
| | - Diethard Mattanovich
- University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Vienna, Austria
| | - Antonio Villaverde
- Autonomous University of Barcelona, Institute for Biotechnology and Biomedicine, Department of Genetics and Microbiology, and CIBER-BBN Network in Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
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13
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Martínez-Alonso M, Vera A, Villaverde A. Role of the chaperone DnaK in protein solubility and conformational quality in inclusion body-formingEscherichia colicells. FEMS Microbiol Lett 2007; 273:187-95. [PMID: 17561947 DOI: 10.1111/j.1574-6968.2007.00788.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Misfolding-prone proteins produced in bacteria usually fail to adopt their native conformation and aggregate. In cells producing folding-reluctant protein species, folding modulators are supposed to be limiting, a fact that enhances protein deposition. Therefore, coproducing DnaK or other main chaperones along with the target protein has been a common approach to gain solubility, although with very inconsistent and often discouraging results. In an attempt to understand the reason for this inconsistency, the impact of exogenous DnaK (encoded in an accompanying plasmid) on two protein features observed as indicators of protein quality, namely solubility and functionality, has been analysed here through the specific fluorescence emission of a reporter Green Fluorescent Protein (GFP). Intriguingly, GFP solubility is strongly dependent on its own yield but poorly affected by DnaK levels. On the contrary, the specific fluorescence of both soluble and insoluble GFP populations is simultaneously modulated by the availability of DnaK, with a profile that is clearly dissimilar to that shown by protein solubility. Therefore, solubility, not being coincident with the biological activity of the target protein, might not be a robust indicator of protein quality.
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Affiliation(s)
- Mónica Martínez-Alonso
- Institute for Biotechnology and Biomedicine, Department of Genetics and Microbiology and CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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14
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Chou CP. Engineering cell physiology to enhance recombinant protein production in Escherichia coli. Appl Microbiol Biotechnol 2007; 76:521-32. [PMID: 17571257 DOI: 10.1007/s00253-007-1039-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 05/08/2007] [Accepted: 05/21/2007] [Indexed: 11/26/2022]
Abstract
The advent of recombinant DNA technology has revolutionized the strategies for protein production. Due to the well-characterized genome and a variety of mature tools available for genetic manipulation, Escherichia coli is still the most common workhorse for recombinant protein production. However, the culture for industrial applications often presents E. coli cells with a growth condition that is significantly different from their natural inhabiting environment in the gastrointestinal tract, resulting in deterioration in cell physiology and limitation in cell's productivity. It has been recognized that innovative design of genetically engineered strains can highly increase the bioprocess yield with minimum investment on the capital and operating costs. Nevertheless, most of these genetic manipulations, by which traits are implanted into the workhorse through recombinant DNA technology, for enhancing recombinant protein productivity often translate into the challenges that deteriorate cell physiology or even jeopardize cell survival. An in-depth understanding of these challenges and their corresponding cellular response at the molecular level becomes crucial for developing superior strains that are more physiologically adaptive to the production environment to improve culture productivity. With the accumulated knowledge in cell physiology, whose importance to gene overexpression was to some extent undervalued previously, this review is intended to focus on the recent biotechnological advancement in engineering cell physiology to enhance recombinant protein production in E. coli.
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Affiliation(s)
- C Perry Chou
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON, Canada, N2L 3G1.
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15
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Fernández G, Vera A, Villaverde A, Martínez MA. Analysis of recombinant protein toxicity in E. coli through a phage λ-based genetic screening system. Biotechnol Lett 2007; 29:1381-6. [PMID: 17479218 DOI: 10.1007/s10529-007-9390-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 04/02/2007] [Accepted: 04/03/2007] [Indexed: 11/30/2022]
Abstract
The aspartic protease from the human immunodeficiency virus type 1 (HIV-1) is highly toxic to E. coli, thus impairing its yield in production processes. Proteolytic cleavage of essential cellular proteins is probably a major contributor to the bacteriocidal effect but this has not been proven. Through an adapted high-throughput lambda-based screening system, we have analyzed a set of HIV-1 protease mutants with distinguishable catalytic properties and we show that inactive enzymes are as toxic to E. coli cells as the wild-type enzyme. Together with additional data from directed molecular evolution approaches, these results indicate that the toxicity of the viral protease is not linked to its proteolytic activity. Our study also reveals that the lambda-based screening system is a robust new tool for the genetic analysis of highly toxic recombinant products in E. coli.
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Affiliation(s)
- Guerau Fernández
- Fundació irsiCaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, 08916, Badalona, Spain
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16
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Hazebrouck S, Pothelune L, Azevedo V, Corthier G, Wal JM, Langella P. Efficient production and secretion of bovine beta-lactoglobulin by Lactobacillus casei. Microb Cell Fact 2007; 6:12. [PMID: 17417967 PMCID: PMC1853110 DOI: 10.1186/1475-2859-6-12] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 04/06/2007] [Indexed: 11/24/2022] Open
Abstract
Background Lactic acid bacteria (LAB) are attractive tools to deliver therapeutic molecules at the mucosal level. The model LAB Lactococcus lactis has been intensively used to produce and deliver such heterologous proteins. However, compared to recombinant lactococci, lactobacilli offer some advantages such as better survival in the digestive tract and immunomodulatory properties. Here, we compared different strategies to optimize the production of bovine β-lactoglobulin (BLG), a major cow's milk allergen, in the probiotic strain Lactobacillus casei BL23. Results Using a nisin-inducible plasmid system, we first showed that L. casei BL23 strain could efficiently secrete a reporter protein, the staphylococcal nuclease (Nuc), with the lactococcal signal peptide SPUsp45 fused to its N-terminus. The fusion of SPUsp45 failed to drive BLG secretion but led to a 10-fold increase of intracellular BLG production. Secretion was significantly improved when the synthetic propeptide LEISSTCDA (hereafter called LEISS) was added to the N-terminus of the mature moiety of BLG. Secretion rate of LEISS-BLG was 6-fold higher than that of BLG alone while intracellular production reached then about 1 mg/L of culture. The highest yield of secretion was obtained by using Nuc as carrier protein. Insertion of Nuc between LEISS and BLG resulted in a 20-fold increase in BLG secretion, up to 27 μg/L of culture. Furthermore, the lactococcal nisRK regulatory genes were integrated into the BL23 chromosome. The nisRK insertion allowed a decrease of BLG synthesis in uninduced cultures while BLG production increased by 50% after nisin induction. Moreover, modification of the induction protocol led to increase the proportion of soluble BLG to around 74% of the total BLG production. Conclusion BLG production and secretion in L. casei were significantly improved by fusions to a propeptide enhancer and a carrier protein. The resulting recombinant strains will be further tested for their ability to modulate the immune response against BLG via mucosal delivery in a cow's milk allergy model in mice.
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Affiliation(s)
- Stéphane Hazebrouck
- INRA, Unité d'Immuno-Allergie Alimentaire, CEA de Saclay, 91191 Gif-sur-Yvette, France
| | - Laetitia Pothelune
- INRA, Unité d'Immuno-Allergie Alimentaire, CEA de Saclay, 91191 Gif-sur-Yvette, France
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte – MG, Brasil
| | - Gérard Corthier
- INRA, Unité d'Ecologie et Physiologie du Système Digestif, 78352 Jouy-en-Josas cedex, France
| | - Jean-Michel Wal
- INRA, Unité d'Immuno-Allergie Alimentaire, CEA de Saclay, 91191 Gif-sur-Yvette, France
| | - Philippe Langella
- INRA, Unité d'Ecologie et Physiologie du Système Digestif, 78352 Jouy-en-Josas cedex, France
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Schultz T, Liu J, Capasso P, de Marco A. The solubility of recombinant proteins expressed in Escherichia coli is increased by otsA and otsB co-transformation. Biochem Biophys Res Commun 2007; 355:234-9. [PMID: 17292861 DOI: 10.1016/j.bbrc.2007.01.149] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 01/27/2007] [Indexed: 11/23/2022]
Abstract
The osmolyte trehalose strongly limits protein aggregation both in vitro and in vivo. The addition of trehalose to the culture medium reduced the aggregation of recombinant proteins expressed in Escherichia coli in a concentration-dependent manner. Comparable positive effects were obtained when the host bacteria were engineered to overexpress the gene products of otsA and otsB, the two enzymes involved in trehalose synthesis. Apparently, the osmolyte preserves protein monodispersion rather than directly facilitating protein folding. However, the stabilization of the protein folding intermediate(s) resulted in higher yields of native proteins and aggregates of lower complexity. Other osmolytes have been tested in vitro in comparison with trehalose. Di-myo-inositol1,1'-phosphate (DIP) seems to be a good candidate to test in in vivo applications, although the opportunity of using otsA/B overexpressing cells is simpler and less expensive.
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Affiliation(s)
- Tina Schultz
- EMBL Scientific Core Facilities, Meyerhofstr. 1, D-69117 Heidelberg, Germany
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de Groot NS, Ventura S. Effect of temperature on protein quality in bacterial inclusion bodies. FEBS Lett 2006; 580:6471-6. [PMID: 17101131 DOI: 10.1016/j.febslet.2006.10.071] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Revised: 10/17/2006] [Accepted: 10/31/2006] [Indexed: 11/29/2022]
Abstract
Increasing evidence indicates that protein aggregation in bacteria does not necessarily imply loss of biological activity. Here, we have investigated the effect of growth-temperature on both the activity and stability of the inclusion bodies formed by a point-mutant of Abeta42 Alzheimer peptide, using green fluorescent protein as a reporter. The activity in the aggregates inversely correlates with the temperature. In contrast, inclusion bodies become more stable in front of chemical denaturation and proteolysis when temperature increases. Overall, the data herein open new perspectives in protein production, while suggesting a kinetic competition between protein folding and aggregation during recombinant protein expression.
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Affiliation(s)
- Natalia Sánchez de Groot
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
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