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Foroutan Kalourazi A, Nazemi SA, Unniram Parambil AR, Muñoz-Tafalla R, Vidal P, Shahangian SS, Guallar V, Ferrer M, Shahgaldian P. Exploiting cyclodextrins as artificial chaperones to enhance enzyme protection through supramolecular engineering. NANOSCALE 2024; 16:5123-5129. [PMID: 38349359 DOI: 10.1039/d3nr06044f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
We report a method of enzyme stabilisation exploiting the artificial protein chaperone properties of β-cyclodextrin (β-CD) covalently embedded in an ultrathin organosilica layer. Putative interaction points of this artificial chaperone system with the surface of the selected enzyme were studied in silico using a protein energy landscape exploration simulation algorithm. We show that this enzyme shielding method allows for drastic enhancement of enzyme stability under thermal and chemical stress conditions, along with broadening the optimal temperature range of the biocatalyst. The presence of the β-CD macrocycle within the protective layer supports protein refolding after treatment with a surfactant.
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Affiliation(s)
- Ali Foroutan Kalourazi
- School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, Muttenz CH-4132, Switzerland.
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran.
| | - Seyed Amirabbas Nazemi
- School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, Muttenz CH-4132, Switzerland.
| | - Ajmal Roshan Unniram Parambil
- School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, Muttenz CH-4132, Switzerland.
- Swiss Nanoscience Institute, Klingelbergstrasse 82, Basel CH-4056, Switzerland
| | - Ruben Muñoz-Tafalla
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Faculty of Pharmacy and Food Science, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - Paula Vidal
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain
| | - S Shirin Shahangian
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran.
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain
| | - Patrick Shahgaldian
- School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, Muttenz CH-4132, Switzerland.
- Swiss Nanoscience Institute, Klingelbergstrasse 82, Basel CH-4056, Switzerland
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2
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Carratalá JV, Cisneros A, Hellman E, Villaverde A, Ferrer-Miralles N. Title: insoluble proteins catch heterologous soluble proteins into inclusion bodies by intermolecular interaction of aggregating peptides. Microb Cell Fact 2021; 20:30. [PMID: 33531005 PMCID: PMC7852131 DOI: 10.1186/s12934-021-01524-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
Background Protein aggregation is a biological event observed in expression systems in which the recombinant protein is produced under stressful conditions surpassing the homeostasis of the protein quality control system. In addition, protein aggregation is also related to conformational diseases in animals as transmissible prion diseases or non-transmissible neurodegenerative diseases including Alzheimer, Parkinson’s disease, amyloidosis and multiple system atrophy among others. At the molecular level, the presence of aggregation-prone domains in protein molecules act as seeding igniters to induce the accumulation of protein molecules in protease-resistant clusters by intermolecular interactions. Results
In this work we have studied the aggregating-prone performance of a small peptide (L6K2) with additional antimicrobial activity and we have elucidated the relevance of the accompanying scaffold protein to enhance the aggregating profile of the fusion protein. Furthermore, we demonstrated that the fusion of L6K2 to highly soluble recombinant proteins directs the protein to inclusion bodies (IBs) in E. coli through stereospecific interactions in the presence of an insoluble protein displaying the same aggregating-prone peptide (APP). Conclusions These data suggest that the molecular bases of protein aggregation are related to the net balance of protein aggregation potential and not only to the presence of APPs. This is then presented as a generic platform to generate hybrid protein aggregates in microbial cell factories for biopharmaceutical and biotechnological applications.
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Affiliation(s)
- Jose Vicente Carratalá
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain.,Department of Genetics and Microbiology, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain.,Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), 08193, Bellaterra, Barcelona, Spain
| | - Andrés Cisneros
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain.,Department of Genetics and Microbiology, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Elijah Hellman
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain.,Department of Genetics and Microbiology, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Antonio Villaverde
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain.,Department of Genetics and Microbiology, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain.,Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), 08193, Bellaterra, Barcelona, Spain
| | - Neus Ferrer-Miralles
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain. .,Department of Genetics and Microbiology, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain. .,Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), 08193, Bellaterra, Barcelona, Spain.
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3
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Saxena A, Ravutla S, Upadhyay V, Jana S, Murhammer D, Giri L. Statistical modeling of cell-to-cell variability in viral infection during passaging in suspension cell culture: Application in Monte-Carlo simulation. Biotechnol Bioeng 2020; 117:1483-1501. [PMID: 32017023 DOI: 10.1002/bit.27295] [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: 08/02/2019] [Revised: 12/13/2019] [Accepted: 02/03/2020] [Indexed: 11/09/2022]
Abstract
Packaging during the passaging of viruses in cell cultures yields various phenotypes and is regulated by viral protein expression in infected cells. Although such a packaging mechanism has a profound effect in controlling the virus yield, little is known about the underlying statistical models followed by virus packaging and protein expression among cells infected with the virus. A predictive framework combining identification of the probability density function (PDF) based on log-likelihood and using the PDF for Monte-Carlo simulations is developed. The Birnbaum-Saunders distribution was found to be consistent with all three-virus packaging levels, including nucleocapsids/occlusion-derived virus (ODV), ODVs/polyhedra, and polyhedra/cell for both wild-type and genetically modified AcMNPV. Next, it was demonstrated that PDF fitting could be used to compare two viruses having distinctly different genetic configurations. Finally, the identified PDF can be incorporated in RNA synthesis parameters for baculovirus infection to predict the cell-to-cell variability in protein expression using Monte-Carlo simulations. The proposed tool can be used for the estimation of uncertainty in the kinetic parameter and prediction of cell-to-cell variability for other biological systems.
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Affiliation(s)
- Abha Saxena
- Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Suryateja Ravutla
- Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Vikas Upadhyay
- Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Soumya Jana
- Electrical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - David Murhammer
- Department of Chemical and Biochemical Engineering, The University of Iowa, Iowa City, Iowa
| | - Lopamudra Giri
- Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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4
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Ashraf R, Muhammad MA, Rashid N, Akhtar M. Cloning and characterization of thermostable GroEL/GroES homologues from Geobacillus thermopakistaniensis and their applications in protein folding. J Biotechnol 2017; 254:9-16. [PMID: 28583821 DOI: 10.1016/j.jbiotec.2017.05.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 05/25/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023]
Abstract
The chaperonin genes encoding GroELGt (ESU72018) and GroESGt (ESU72017), homologues of bacterial GroEL and GroES, from Geobacillus thermopakistaniensis were cloned and expressed in Escherichia coli. The purified gene products possessed the ATPase activity similar to other bacterial and eukaryal counterparts. Recombinant GroELGt and GroESGt were able to refold the denatured insoluble aggregates of α-amylase from Bacillus licheniformis into soluble and active form. Furthermore, GroELGt and GroESGt successfully enhanced the thermostability of porcine heart malate dehydrogenase. Expression of GroELGt gene in E. coli cells enhanced the thermotolerance of the host. Furthermore, soluble production of recombinant alcohol dehydrogenase from Bacillus subtilis strain R5 in E. coli, initially produced as insoluble aggregates, was achieved by co-expressing the gene with GroELGt. Our results implied that GroELGt could assist folding of nascent protein in E. coli with the help of host co-chaperonin without requiring additional ATP. This system can be used for soluble production of recombinant proteins which otherwise are produced in insoluble form in E. coli. To the best of our knowledge this is the first report on functional characterization and applications of chaperonins from genus Geobacillus.
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Affiliation(s)
- Raza Ashraf
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Majida Atta Muhammad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
| | - Muhammad Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan; School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK
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5
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Peng S, Chu Z, Lu J, Li D, Wang Y, Yang S, Zhang Y. Co-expression of chaperones from P. furiosus enhanced the soluble expression of the recombinant hyperthermophilic α-amylase in E. coli. Cell Stress Chaperones 2016; 21:477-84. [PMID: 26862080 PMCID: PMC4837189 DOI: 10.1007/s12192-016-0675-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 01/14/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022] Open
Abstract
The extracellular α-amylase from the hyperthermophilic archaeum Pyrococcus furiosus (PFA) is extremely thermostable and of an industrial importance and interest. PFA aggregates and accumulates as insoluble inclusion bodies when expressed as a heterologous protein at a high level in Escherichia coli. In the present study, we investigated the roles of chaperones from P. furiosus in the soluble expression of recombinant PFA in E. coli. The results indicate that co-expression of PFA with the molecular chaperone prefoldin alone significantly increased the soluble expression of PFA. Although, co-expression of other main chaperone components from P. furiosus, such as the small heat shock protein (sHSP) or chaperonin (HSP60), was also able to improve the soluble expression of PFA to a certain extent. Co-expression of chaperonin or sHSP in addition to prefoldin did not further increase the soluble expression of PFA. This finding emphasizes the biotechnological potentials of the molecular chaperone prefoldin from P. furiosus, which may facilitate the production of recombinant PFA.
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Affiliation(s)
- Shuaiying Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhongmei Chu
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jianfeng Lu
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China
| | - Dongxiao Li
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yonghong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
| | - Shengli Yang
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhang
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China.
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6
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Seras-Franzoso J, Sánchez-Chardi A, Garcia-Fruitós E, Vázquez E, Villaverde A. Cellular uptake and intracellular fate of protein releasing bacterial amyloids in mammalian cells. SOFT MATTER 2016; 12:3451-3460. [PMID: 26956912 DOI: 10.1039/c5sm02930a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bacterial Inclusion Bodies (IBs) are amyloidal protein deposits that functionally mimic secretory granules from the endocrine system. When formed by therapeutically relevant proteins, they complement missing intracellular activities in jeopardized cell cultures, offering an intriguing platform for protein drug delivery in substitutive therapies. Despite the therapeutic potential of IBs, their capability to interact with eukaryotic cells, cross the cell membrane and release their functional building blocks into the cytosolic space remains essentially unexplored. We have systematically dissected the process by which bacterial amyloids interact with mammalian cells. An early and tight cell membrane anchorage of IBs is followed by cellular uptake of single or grouped IBs of variable sizes by macropinocytosis. Although an important fraction of the penetrating particles is led to lysosomal degradation, biologically significant amounts of protein are released into the cytosol. In addition, our data suggest the involvement of the bacterial cell folding modulator DnaK in the release of functional proteins from these amyloidal reservoirs. The mechanisms supporting the internalization of disintegrable protein nanoparticles revealed here offer clues to implement novel approaches for protein drug delivery based on controlled protein packaging as bacterial IBs.
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Affiliation(s)
- Joaquin Seras-Franzoso
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
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7
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Villaverde A, Corchero JL, Seras-Franzoso J, Garcia-Fruitós E. Functional protein aggregates: just the tip of the iceberg. Nanomedicine (Lond) 2015; 10:2881-91. [PMID: 26370294 DOI: 10.2217/nnm.15.125] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
An increasing number of both prokaryotic and eukaryotic cell types are being adapted as platforms for recombinant protein production. The overproduction of proteins in such expression systems leads to the formation of insoluble protein-based aggregates. Although these protein clusters have been poorly studied in most of the eukaryotic systems, aggregates formed in E. coli, named inclusion bodies (IBs), have been deeply characterized in the last decades. Contrary to the general belief, an important fraction of the protein embedded in IB is functional, showing promise in biocatalysis, regenerative medicine and cell therapy. Thus, the exploration of all these functional protein clusters would largely expand their potential in both pharma and biotech industry.
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Affiliation(s)
- Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain
| | - José Luis Corchero
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain
| | - Joaquin Seras-Franzoso
- CIBBIM-Nanomedicine, Hospital Universitari Vall d'Hebron & Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, CIBER en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08035, Barcelona, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, 08140, Barcelona, Spain
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8
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Ferrer-Miralles N, Saccardo P, Corchero JL, Xu Z, García-Fruitós E. General introduction: recombinant protein production and purification of insoluble proteins. Methods Mol Biol 2015; 1258:1-24. [PMID: 25447856 DOI: 10.1007/978-1-4939-2205-5_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proteins are synthesized in heterologous systems because of the impossibility to obtain satisfactory yields from natural sources. The production of soluble and functional recombinant proteins is among the main goals in the biotechnological field. In this context, it is important to point out that under stress conditions, protein folding machinery is saturated and this promotes protein misfolding and, consequently, protein aggregation. Thus, the selection of the optimal expression organism and the most appropriate growth conditions to minimize the formation of insoluble proteins should be done according to the protein characteristics and downstream requirements. Escherichia coli is the most popular recombinant protein expression system despite the great development achieved so far by eukaryotic expression systems. Besides, other prokaryotic expression systems, such as lactic acid bacteria and psychrophilic bacteria, are gaining interest in this field. However, it is worth mentioning that prokaryotic expression system poses, in many cases, severe restrictions for a successful heterologous protein production. Thus, eukaryotic systems such as mammalian cells, insect cells, yeast, filamentous fungus, and microalgae are an interesting alternative for the production of these difficult-to-express proteins.
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Affiliation(s)
- Neus Ferrer-Miralles
- Departament de Genètica i de Microbiologia, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
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9
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Guadalupe-Medina V, Wisselink HW, Luttik MAH, de Hulster E, Daran JM, Pronk JT, van Maris AJA. Carbon dioxide fixation by Calvin-Cycle enzymes improves ethanol yield in yeast. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:125. [PMID: 23987569 PMCID: PMC3766054 DOI: 10.1186/1754-6834-6-125] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/27/2013] [Indexed: 05/12/2023]
Abstract
BACKGROUND Redox-cofactor balancing constrains product yields in anaerobic fermentation processes. This challenge is exemplified by the formation of glycerol as major by-product in yeast-based bioethanol production, which is a direct consequence of the need to reoxidize excess NADH and causes a loss of conversion efficiency. Enabling the use of CO2 as electron acceptor for NADH oxidation in heterotrophic microorganisms would increase product yields in industrial biotechnology. RESULTS A hitherto unexplored strategy to address this redox challenge is the functional expression in yeast of enzymes from autotrophs, thereby enabling the use of CO2 as electron acceptor for NADH reoxidation. Functional expression of the Calvin cycle enzymes phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase (Rubisco) in Saccharomyces cerevisiae led to a 90% reduction of the by-product glycerol and a 10% increase in ethanol production in sugar-limited chemostat cultures on a mixture of glucose and galactose. Co-expression of the Escherichia coli chaperones GroEL and GroES was key to successful expression of CbbM, a form-II Rubisco from the chemolithoautotrophic bacterium Thiobacillus denitrificans in yeast. CONCLUSIONS Our results demonstrate functional expression of Rubisco in a heterotrophic eukaryote and demonstrate how incorporation of CO2 as a co-substrate in metabolic engineering of heterotrophic industrial microorganisms can be used to improve product yields. Rapid advances in molecular biology should allow for rapid insertion of this 4-gene expression cassette in industrial yeast strains to improve production, not only of 1st and 2nd generation ethanol production, but also of other renewable fuels or chemicals.
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Affiliation(s)
- Víctor Guadalupe-Medina
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628, BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, GA Delft, The Netherlands
| | - H Wouter Wisselink
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628, BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, GA Delft, The Netherlands
| | - Marijke AH Luttik
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628, BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, GA Delft, The Netherlands
| | - Erik de Hulster
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628, BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, GA Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628, BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, GA Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628, BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, GA Delft, The Netherlands
| | - Antonius JA van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628, BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600, GA Delft, The Netherlands
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10
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Corchero JL, Gasser B, Resina D, Smith W, Parrilli E, Vázquez F, Abasolo I, Giuliani M, Jäntti J, Ferrer P, Saloheimo M, Mattanovich D, Schwartz S, Tutino ML, Villaverde A. Unconventional microbial systems for the cost-efficient production of high-quality protein therapeutics. Biotechnol Adv 2012; 31:140-53. [PMID: 22985698 DOI: 10.1016/j.biotechadv.2012.09.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 09/04/2012] [Accepted: 09/07/2012] [Indexed: 12/18/2022]
Abstract
Both conventional and innovative biomedical approaches require cost-effective protein drugs with high therapeutic potency, improved bioavailability, biocompatibility, stability and pharmacokinetics. The growing longevity of the human population, the increasing incidence and prevalence of age-related diseases and the better comprehension of genetic-linked disorders prompt to develop natural and engineered drugs addressed to fulfill emerging therapeutic demands. Conventional microbial systems have been for long time exploited to produce biotherapeutics, competing with animal cells due to easier operation and lower process costs. However, both biological platforms exhibit important drawbacks (mainly associated to intracellular retention of the product, lack of post-translational modifications and conformational stresses), that cannot be overcome through further strain optimization merely due to physiological constraints. The metabolic diversity among microorganisms offers a spectrum of unconventional hosts, that, being able to bypass some of these weaknesses, are under progressive incorporation into production pipelines. In this review we describe the main biological traits and potentials of emerging bacterial, yeast, fungal and microalgae systems, by comparing selected leading species with well established conventional organisms with a long run in protein drug production.
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11
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Sokolenko S, George S, Wagner A, Tuladhar A, Andrich JMS, Aucoin MG. Co-expression vs. co-infection using baculovirus expression vectors in insect cell culture: Benefits and drawbacks. Biotechnol Adv 2012; 30:766-81. [PMID: 22297133 PMCID: PMC7132753 DOI: 10.1016/j.biotechadv.2012.01.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 01/13/2012] [Accepted: 01/17/2012] [Indexed: 12/12/2022]
Abstract
The baculovirus expression vector system (BEVS) is a versatile and powerful platform for protein expression in insect cells. With the ability to approach similar post-translational modifications as in mammalian cells, the BEVS offers a number of advantages including high levels of expression as well as an inherent safety during manufacture and of the final product. Many BEVS products include proteins and protein complexes that require expression from more than one gene. This review examines the expression strategies that have been used to this end and focuses on the distinguishing features between those that make use of single polycistronic baculovirus (co-expression) and those that use multiple monocistronic baculoviruses (co-infection). Three major areas in which researchers have been able to take advantage of co-expression/co-infection are addressed, including compound structure-function studies, insect cell functionality augmentation, and VLP production. The core of the review discusses the parameters of interest for co-infection and co-expression with time of infection (TOI) and multiplicity of infection (MOI) highlighted for the former and the choice of promoter for the latter. In addition, an overview of modeling approaches is presented, with a suggested trajectory for future exploration. The review concludes with an examination of the gaps that still remain in co-expression/co-infection knowledge and practice.
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Affiliation(s)
- Stanislav Sokolenko
- Department of Chemical Engineering, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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12
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García-Fruitós E, Vázquez E, Díez-Gil C, Corchero JL, Seras-Franzoso J, Ratera I, Veciana J, Villaverde A. Bacterial inclusion bodies: making gold from waste. Trends Biotechnol 2011; 30:65-70. [PMID: 22037492 DOI: 10.1016/j.tibtech.2011.09.003] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/22/2011] [Accepted: 09/24/2011] [Indexed: 11/28/2022]
Abstract
Many protein species produced in recombinant bacteria aggregate as insoluble protein clusters named inclusion bodies (IBs). IBs are discarded from further processing or are eventually used as a pure protein source for in vitro refolding. Although usually considered as waste byproducts of protein production, recent insights into the physiology of recombinant bacteria and the molecular architecture of IBs have revealed that these protein particles are unexpected functional materials. In this Opinion article, we present the relevant mechanical properties of IBs and discuss the ways in which they can be explored as biocompatible nanostructured materials, mainly, but not exclusively, in biocatalysis and tissue engineering.
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Affiliation(s)
- Elena García-Fruitós
- Institute for Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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13
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Platas G, Rodríguez-Carmona E, García-Fruitós E, Cano-Garrido O, Villaverde A. Co-production of GroELS discriminates between intrinsic and thermally-induced recombinant protein aggregation during substrate quality control. Microb Cell Fact 2011; 10:79. [PMID: 21992454 PMCID: PMC3207889 DOI: 10.1186/1475-2859-10-79] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 10/12/2011] [Indexed: 11/26/2022] Open
Abstract
Background The effects and effectiveness of the chaperone pair GroELS on the yield and quality of recombinant polypeptides produced in Escherichia coli are matter of controversy, as the reported activities of this complex are not always consistent and eventually indicate undesired side effects. The divergence in the reported data could be due, at least partially, to different experimental conditions in independent research approaches. Results We have then selected two structurally different model proteins (namely GFP and E. coli β-galactosidase) and two derived aggregation-prone fusions to explore, in a systematic way, the eventual effects of GroELS co-production on yield, solubility and conformational quality. Host cells were cultured at two alternative temperatures below the threshold at which thermal stress is expected to be triggered, to minimize the involvement of independent stress factors. Conclusions From the analysis of protein yield, solubility and biological activity of the four model proteins produced alone or along the chaperones, we conclude that GroELS impacts on yield and quality of aggregation-prone proteins with intrinsic determinants but not on thermally induced protein aggregation. No effective modifications of protein solubility have been observed, but significant stabilization of small (encapsulable) substrates and moderate chaperone-induced degradation of larger (excluded) polypeptides. These findings indicate that the activities of this chaperone pair in the context of actively producing recombinant bacteria discriminate between intrinsic and thermally-induced protein aggregation, and that the side effects of GroELS overproduction might be determined by substrate size.
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Affiliation(s)
- Gemma Platas
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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Martínez-Alonso M, Villaverde A, Ferrer-Miralles N. Cross-system excision of chaperone-mediated proteolysis in chaperone-assisted recombinant protein production. Bioeng Bugs 2011; 1:148-50. [PMID: 21326941 DOI: 10.4161/bbug.1.2.11048] [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: 12/20/2009] [Accepted: 12/29/2009] [Indexed: 11/19/2022] Open
Abstract
Main Escherichia coli cytosolic chaperones such as DnaK are key components of the control quality network designed to minimize the prevalence of polypeptides with aberrant conformations. This is achieved by both favoring refolding activities but also stimulating proteolytic degradation of folding reluctant species. This last activity is responsible for the decrease of the proteolytic stability of recombinant proteins when co-produced along with DnaK, where an increase in solubility might be associated to a decrease in protein yield. However, when DnaK and its co-chaperone DnaJ are co-produced in cultured insect cells or whole insect larvae (and expectedly, in other heterologous hosts), only positive, folding-related effects of these chaperones are observed, in absence of proteolysis-mediated reduction of recombinant protein yield.
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Affiliation(s)
- Mónica Martínez-Alonso
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, and CIBER de Bioingeniería, Biomateriales y Nanomedicina, Barcelona, Spain
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Side effects of chaperone gene co-expression in recombinant protein production. Microb Cell Fact 2010; 9:64. [PMID: 20813055 PMCID: PMC2944165 DOI: 10.1186/1475-2859-9-64] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 09/02/2010] [Indexed: 12/14/2022] Open
Abstract
Insufficient availability of molecular chaperones is observed as a major bottleneck for proper protein folding in recombinant protein production. Therefore, co-production of selected sets of cell chaperones along with foreign polypeptides is a common approach to increase the yield of properly folded, recombinant proteins in bacterial cell factories. However, unbalanced amounts of folding modulators handling folding-reluctant protein species might instead trigger undesired proteolytic activities, detrimental regarding recombinant protein stability, quality and yield. This minireview summarizes the most recent observations of chaperone-linked negative side effects, mostly focusing on DnaK and GroEL sets, when using these proteins as folding assistant agents. These events are discussed in the context of the complexity of the cell quality network and the consequent intricacy of the physiological responses triggered by protein misfolding.
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