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Helleckes LM, Küsters K, Wagner C, Hamel R, Saborowski R, Marienhagen J, Wiechert W, Oldiges M. "High-throughput screening of catalytically active inclusion bodies using laboratory automation and Bayesian optimization". Microb Cell Fact 2024; 23:67. [PMID: 38402403 PMCID: PMC10894497 DOI: 10.1186/s12934-024-02319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/27/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND In recent years, the production of inclusion bodies that retain substantial catalytic activity was demonstrated. These catalytically active inclusion bodies (CatIBs) are formed by genetic fusion of an aggregation-inducing tag to a gene of interest via short linker polypeptides. The resulting CatIBs are known for their easy and cost-efficient production, recyclability as well as their improved stability. Recent studies have outlined the cooperative effects of linker and aggregation-inducing tag on CatIB activities. However, no a priori prediction is possible so far to indicate the best combination thereof. Consequently, extensive screening is required to find the best performing CatIB variant. RESULTS In this work, a semi-automated cloning workflow was implemented and used for fast generation of 63 CatIB variants with glucose dehydrogenase of Bacillus subtilis (BsGDH). Furthermore, the variant BsGDH-PT-CBDCell was used to develop, optimize and validate an automated CatIB screening workflow, enhancing the analysis of many CatIB candidates in parallel. Compared to previous studies with CatIBs, important optimization steps include the exclusion of plate position effects in the BioLector by changing the cultivation temperature. For the overall workflow including strain construction, the manual workload could be reduced from 59 to 7 h for 48 variants (88%). After demonstration of high reproducibility with 1.9% relative standard deviation across 42 biological replicates, the workflow was performed in combination with a Bayesian process model and Thompson sampling. While the process model is crucial to derive key performance indicators of CatIBs, Thompson sampling serves as a strategy to balance exploitation and exploration in screening procedures. Our methodology allowed analysis of 63 BsGDH-CatIB variants within only three batch experiments. Because of the high likelihood of TDoT-PT-BsGDH being the best CatIB performer, it was selected in 50 biological replicates during the three screening rounds, much more than other, low-performing variants. CONCLUSIONS At the current state of knowledge, every new enzyme requires screening for different linker/aggregation-inducing tag combinations. For this purpose, the presented CatIB toolbox facilitates fast and simplified construction and screening procedures. The methodology thus assists in finding the best CatIB producer from large libraries in short time, rendering possible automated Design-Build-Test-Learn cycles to generate structure/function learnings.
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Affiliation(s)
- Laura Marie Helleckes
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Kira Küsters
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Christian Wagner
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Rebecca Hamel
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Ronja Saborowski
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52074, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany.
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2
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Dong S, Wang L, Qin H, Zhan H, Wang D, Cao X. Expression Patterns and Functional Analysis of Three SmTAT Genes Encoding Tyrosine Aminotransferases in Salvia miltiorrhiza. Int J Mol Sci 2023; 24:15575. [PMID: 37958559 PMCID: PMC10649420 DOI: 10.3390/ijms242115575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Tyrosine aminotransferase (TAT, E.C. 2.6.1.5) is a pyridoxal phosphate-dependent aminotransferase that is widely found in living organisms. It catalyzes the transfer of the amino group on tyrosine to α-ketoglutarate to produce 4-hydroxyphenylpyruvic acid (4-HPP) and is the first enzyme for tyrosine degradation. Three SmTATs have been identified in the genome of Salvia miltiorrhiza (a model medicinal plant), but their information is very limited. Here, the expression profiles of the three SmTAT genes (SmTAT1, SmTAT2, and SmTAT3) were studied. All three genes expressed in different tissues and responded to methyl jasmonate stimuli. SmTAT proteins are localized in the cytoplasm. The recombinant SmTATs were subjected to in vitro biochemical properties. All three recombinant enzymes had TAT activities and SmTAT1 had the highest catalytic activity for tyrosine, followed by SmTAT3. Also, SmTAT1 preferred the direction of tyrosine deamination to 4-HPP, while SmTAT2 preferred transamination of 4-HPP to tyrosine. In parallel, transient overexpression of SmTATs in tobacco leaves revealed that all three SmTAT proteins catalyzed tyrosine to 4-HPP in vivo, with SmTAT1 exhibiting the highest enzymatic activity. Overall, our results lay a foundation for the production of tyrosine-derived secondary metabolites via metabolic engineering or synthetic biology in the future.
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Affiliation(s)
| | | | | | | | | | - Xiaoyan Cao
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Science, Shaanxi Normal University, Xi’an 710062, China; (S.D.); (L.W.); (H.Q.); (H.Z.); (D.W.)
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3
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Kopp J, Spadiut O. Inclusion Bodies: Status Quo and Perspectives. Methods Mol Biol 2023; 2617:1-13. [PMID: 36656513 DOI: 10.1007/978-1-0716-2930-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Multiple E. coli cultivations, producing recombinant proteins, lead to the formation of inclusion bodies (IBs). IBs historically were considered as nondesired by-products, due to their time- and cost-intensive purification. Nowadays, many obstacles in IB processing can be overcome. As a consequence, several industrial processes with E. coli favor IB formation over soluble production options due to the high space time yields obtained. Within this chapter, we discuss the state-of-the art biopharmaceutical IB process, review its challenges, highlight the recent developments and perspectives, and also propose alternative solutions, compared to the state-of-the art processing.
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Affiliation(s)
- Julian Kopp
- Research Division Integrated Bioprocess Development, TU Wien Institute of Chemical, Environmental, and Bioscience Engineering, Vienna, Austria.
| | - Oliver Spadiut
- Research Division Integrated Bioprocess Development, TU Wien Institute of Chemical, Environmental, and Bioscience Engineering, Vienna, Austria.
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4
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Gabryelczyk B, Sammalisto FE, Gandier JA, Feng J, Beaune G, Timonen JV, Linder MB. Recombinant protein condensation inside E. coli enables the development of building blocks for bioinspired materials engineering – Biomimetic spider silk protein as a case study. Mater Today Bio 2022; 17:100492. [DOI: 10.1016/j.mtbio.2022.100492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
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5
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Tarasca MV, Naser D, Schaefer A, Soule TG, Meiering EM. Quenched hydrogen-deuterium amide exchange optimization for high-resolution structural analysis of cellular protein aggregates. Anal Biochem 2022; 652:114675. [PMID: 35390328 DOI: 10.1016/j.ab.2022.114675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/17/2022]
Abstract
Inclusion bodies (IBs) are large, insoluble aggregates that often form during the overexpression of proteins in bacteria. These aggregates are of broad fundamental and practical significance, for recombinant protein preparation and due to their relevance to aggregation-related medical conditions and their recent emergence as promising functional nanomaterials. Despite their significance, high resolution knowledge of IB structure remains very limited. Such knowledge will advance understanding and control of IB formation and properties in myriad practical applications. Here, we report a detailed quenched hydrogen-deuterium amide exchange (qHDX) method with NMR readout to define the structure of IBs at the level of individual residues throughout the protein. Applying proper control of experimental conditions, such as sample pH, water content, temperature, and intrinsic rate of amide exchange, yields in depth results for these cellular protein aggregates. qHDX results illustrated for Cu, Zn superoxide dismutase 1 (SOD1) and Adnectins show their IBs include native-like structure and some but not all mutations alter IB structure.
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Affiliation(s)
| | - Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Tyler Gb Soule
- Department of Chemistry, University of Waterloo, Waterloo, Canada
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6
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Küsters K, Saborowski R, Wagner C, Hamel R, Spöring JD, Wiechert W, Oldiges M. Construction and characterization of BsGDH-CatIB variants and application as robust and highly active redox cofactor regeneration module for biocatalysis. Microb Cell Fact 2022; 21:108. [PMID: 35655182 PMCID: PMC9161568 DOI: 10.1186/s12934-022-01816-2] [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: 04/04/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Catalytically active inclusion bodies (CatIBs) are known for their easy and cost efficient production, recyclability as well as high stability and provide an alternative purely biological technology for enzyme immobilization. Due to their ability to self-aggregate in a carrier-free, biodegradable form, no further laborious immobilization steps or additional reagents are needed. These advantages put CatIBs in a beneficial position in comparison to traditional immobilization techniques. Recent studies outlined the impact of cooperative effects of the linker and aggregation inducing tag on the activity level of CatIBs, requiring to test many combinations to find the best performing CatIB variant. RESULTS Here, we present the formation of 14 glucose dehydrogenase CatIB variants of Bacillus subtilis, a well-known enzyme in biocatalysis due to its capability for substrate coupled regeneration of reduced cofactors with cheap substrate glucose. Nine variants revealed activity, with highest productivity levels for the more rigid PT-Linker combinations. The best performing CatIB, BsGDH-PT-CBDCell, was characterized in more detail including long-term storage at -20 °C as well as NADH cofactor regeneration performance in repetitive batch experiments with CatIB recycling. After freezing, BsGDH-PT-CBDCell CatIB only lost approx. 10% activity after 8 weeks of storage. Moreover, after 11 CatIB recycling cycles in repetitive batch operation 80% of the activity was still present. CONCLUSIONS This work presents a method for the effective formation of a highly active and long-term stable BsGDH-CatIB as an immobilized enzyme for robust and convenient NADH regeneration.
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Affiliation(s)
- Kira Küsters
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Ronja Saborowski
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Christian Wagner
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Rebecca Hamel
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jan-Dirk Spöring
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52074, Aachen, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52074, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany.
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7
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Ölçücü G, Baumer B, Küsters K, Möllenhoff K, Oldiges M, Pietruszka J, Jaeger KE, Krauss U. Catalytically Active Inclusion Bodies─Benchmarking and Application in Flow Chemistry. ACS Synth Biol 2022; 11:1881-1896. [PMID: 35500299 DOI: 10.1021/acssynbio.2c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In industries, enzymes are often immobilized to obtain stable preparations that can be utilized in batch and flow processes. In contrast to traditional immobilization methods that rely on carrier binding, various immobilization strategies have been recently presented that enable the simultaneous production and in vivo immobilization of enzymes. Catalytically active inclusion bodies (CatIBs) are a promising example for such in vivo enzyme immobilizates. CatIB formation is commonly induced by fusion of aggregation-inducing tags, and numerous tags, ranging from small synthetic peptides to protein domains or whole proteins, have been successfully used. However, since these systems have been characterized by different groups employing different methods, a direct comparison remains difficult, which prompted us to benchmark different CatIB-formation-inducing tags and fusion strategies. Our study highlights that important CatIB properties like yield, activity, and stability are strongly influenced by tag selection and fusion strategy. Optimization enabled us to obtain alcohol dehydrogenase CatIBs with superior activity and stability, which were subsequently applied for the first time in a flow synthesis approach. Our study highlights the potential of CatIB-based immobilizates, while at the same time demonstrating the robust use of CatIBs in flow chemistry.
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Affiliation(s)
- Gizem Ölçücü
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Benedikt Baumer
- Institute of Biorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Kira Küsters
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Kathrin Möllenhoff
- Mathematical Institute, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
| | - Jörg Pietruszka
- Institute of Biorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
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8
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Dong W, Sun H, Chen Q, Hou L, Chang Y, Luo H. SpyTag/Catcher chemistry induces the formation of active inclusion bodies in E. coli. Int J Biol Macromol 2022; 199:358-371. [PMID: 35031313 DOI: 10.1016/j.ijbiomac.2022.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 02/09/2023]
Abstract
SpyTag/Catcher chemistry is usually applied to engineer robust enzymes via head-to-tail cyclization using spontaneous intramolecular isopeptide bond formation. However, the SpyTag/Catcher induced intercellular protein assembly in vivo cannot be ignored. It was found that some active inclusion bodies had generated to different proportions in the expression of six SpyTag/Catcher labeled proteins (CatIBs-STCProtein). Some factors that may affect the formation of CatIBs-STCProtein were discussed, and the subunit quantities were found to be strongly positively related to the formation of protein aggregates. Approximately 85.44% of the activity of the octameric protein leucine dehydrogenase (LDH) was expressed in aggregates, while the activity of the monomeric protein green fluorescence protein (GFP) in aggregates was 12.51%. The results indicated that SpyTag/Catcher can be used to form protein aggregates in E. coli. To facilitate the advantages of CatIBs-STCProtein, we took the CatIBs-STCLDH as an example and further chemically cross-linked with glutaraldehyde to obtain novel cross-linked enzyme aggregates (CLEAs-CatIBs-STCLDH). CLEAs-CatIBs-STCLDH had good thermal stability and organic solvents stability, and its activity remained 51.03% after incubation at 60 °C for 100 mins. Moreover, the crosslinked CatIBs-STCLDH also showed superior stability over traditional CLEAs, and its activity remained 98.70% after 10 cycles of catalysis.
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Affiliation(s)
- Wenge Dong
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hongxu Sun
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Qiwei Chen
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Liangyu Hou
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yanhong Chang
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China.
| | - Hui Luo
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
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9
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Gil-Garcia M, Ventura S. Coiled-Coil Based Inclusion Bodies and Their Potential Applications. Front Bioeng Biotechnol 2021; 9:734068. [PMID: 34485264 PMCID: PMC8415879 DOI: 10.3389/fbioe.2021.734068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 02/01/2023] Open
Abstract
The production of recombinant proteins using microbial cell factories is frequently associated with the formation of inclusion bodies (IBs). These proteinaceous entities can be sometimes a reservoir of stable and active protein, might display good biocompatibility, and are produced efficiently and cost-effectively. Thus, these submicrometric particles are increasingly exploited as functional biomaterials for biotechnological and biomedical purposes. The fusion of aggregation-prone sequences to the target protein is a successful strategy to sequester soluble recombinant polypeptides into IBs. Traditionally, the use of these IB-tags results in the formation of amyloid-like scaffolds where the protein of interest is trapped. This amyloid conformation might compromise the protein's activity and be potentially cytotoxic. One promising alternative to overcome these limitations exploits the coiled-coil fold, composed of two or more α-helices and widely used by nature to create supramolecular assemblies. In this review, we summarize the state-of-the-art of functional IBs technology, focusing on the coiled-coil-assembly strategy, describing its advantages and applications, delving into future developments and necessary improvements in the field.
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Affiliation(s)
- Marcos Gil-Garcia
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
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10
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Gil-Garcia M, Ventura S. Multifunctional antibody-conjugated coiled-coil protein nanoparticles for selective cell targeting. Acta Biomater 2021; 131:472-482. [PMID: 34192568 DOI: 10.1016/j.actbio.2021.06.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022]
Abstract
Nanostructures decorated with antibodies (Abs) are applied in bioimaging and therapeutics. However, most covalent conjugation strategies affect Abs functionality. In this study, we aimed to create protein-based nanoparticles to which intact Abs can be attached through tight, specific, and noncovalent interactions. Initially considered waste products, bacterial inclusion bodies (IBs) have been used in biotechnology and biomedicine. However, the amyloid-like nature of IBs limits their functionality and raises safety concerns. To bypass these obstacles, we have recently developed highly functional α-helix-rich IBs exploiting the natural self-assembly capacity of coiled-coil domains. We used this approach to create spherical, submicrometric, biocompatible and fluorescent protein nanoparticles capable of capturing Abs with high affinity. We showed that these IBs can be exploited for Ab-directed cell targeting. Simultaneous decoration of the nanoparticles with two different Abs in a controllable ratio enabled the construction of a bispecific antibody mimic that redirected T lymphocytes specifically to cancer cells. Overall, we describe an easy and cost-effective strategy to produce multivalent, traceable protein nanostructures with the potential to be used for biomedical applications. STATEMENT OF SIGNIFICANCE: Functional inclusion bodies (IBs) are promising platforms for biomedical and biotechnological applications. These nanoparticles are usually sustained by amyloid-like interactions, which imposes some limitations on their use. In this work, we exploit the natural coiled-coil self-assembly properties to create highly functional, nonamyloid, and fluorescent IBs capable of capturing antibodies. These protein-based nanoparticles are successfully used to specifically and simultaneously target two unrelated cell types and bring them close together, becoming a technology with potential application in bioimaging and immunotherapy.
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11
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Kamel S, Walczak MC, Kaspar F, Westarp S, Neubauer P, Kurreck A. Thermostable adenosine 5'-monophosphate phosphorylase from Thermococcus kodakarensis forms catalytically active inclusion bodies. Sci Rep 2021; 11:16880. [PMID: 34413335 PMCID: PMC8376864 DOI: 10.1038/s41598-021-96073-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/04/2021] [Indexed: 11/24/2022] Open
Abstract
Catalytically active inclusion bodies (CatIBs) produced in Escherichia coli are an interesting but currently underexplored strategy for enzyme immobilization. They can be purified easily and used directly as stable and reusable heterogenous catalysts. However, very few examples of CatIBs that are naturally formed during heterologous expression have been reported so far. Previous studies have revealed that the adenosine 5′-monophosphate phosphorylase of Thermococcus kodakarensis (TkAMPpase) forms large soluble multimers with high thermal stability. Herein, we show that heat treatment of soluble protein from crude extract induces aggregation of active protein which phosphorolyse all natural 5′-mononucleotides. Additionally, inclusion bodies formed during the expression in E. coli were found to be similarly active with 2–6 folds higher specific activity compared to these heat-induced aggregates. Interestingly, differences in the substrate preference were observed. These results show that the recombinant thermostable TkAMPpase is one of rare examples of naturally formed CatIBs.
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Affiliation(s)
- Sarah Kamel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Miriam C Walczak
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Felix Kaspar
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany. .,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany.
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12
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Küsters K, Pohl M, Krauss U, Ölçücü G, Albert S, Jaeger KE, Wiechert W, Oldiges M. Construction and comprehensive characterization of an EcLDCc-CatIB set-varying linkers and aggregation inducing tags. Microb Cell Fact 2021; 20:49. [PMID: 33596923 PMCID: PMC7891155 DOI: 10.1186/s12934-021-01539-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/05/2021] [Indexed: 12/03/2022] Open
Abstract
Background
In recent years, the production of inclusion bodies that retained substantial catalytic activity was demonstrated. These catalytically active inclusion bodies (CatIBs) were formed by genetic fusion of an aggregation inducing tag to a gene of interest via short linker polypeptides and overproduction of the resulting gene fusion in Escherichia coli. The resulting CatIBs are known for their high stability, easy and cost efficient production, and recyclability and thus provide an interesting alternative to conventionally immobilized enzymes. Results Here, we present the construction and characterization of a CatIB set of the lysine decarboxylase from Escherichia coli (EcLDCc), constructed via Golden Gate Assembly. A total of ten EcLDCc variants consisting of combinations of two linker and five aggregation inducing tag sequences were generated. A flexible Serine/Glycine (SG)- as well as a rigid Proline/Threonine (PT)-Linker were tested in combination with the artificial peptides (18AWT, L6KD and GFIL8) or the coiled-coil domains (TDoT and 3HAMP) as aggregation inducing tags. The linkers were fused to the C-terminus of the EcLDCc to form a linkage between the enzyme and the aggregation inducing tags. Comprehensive morphology and enzymatic activity analyses were performed for the ten EcLDCc-CatIB variants and a wild type EcLDCc control to identify the CatIB variant with the highest activity for the decarboxylation of l-lysine to 1,5-diaminopentane. Interestingly, all of the CatIB variants possessed at least some activity, whilst most of the combinations with the rigid PT-Linker showed the highest conversion rates. EcLDCc-PT-L6KD was identified as the best of all variants allowing a volumetric productivity of 457 g L− 1 d− 1 and a specific volumetric productivity of 256 g L− 1 d− 1 gCatIB−1. Noteworthy, wild type EcLDCc, without specific aggregation inducing tags, also partially formed CatIBs, which, however showed lower activity compared to most of the newly constructed CatIB variants (volumetric productivity: 219 g L− 1 d− 1, specific volumetric activity: 106 g L− 1 d− 1 gCatIB− 1). Furthermore, we demonstrate that microscopic analysis can serve as a tool to find CatIB producing strains and thus allow for prescreening at an early stage to save time and resources. Conclusions Our results clearly show that the choice of linker and aggregation inducing tag has a strong influence on the morphology and the enzymatic activity of the CatIBs. Strikingly, the linker had the most pronounced influence on these characteristics.
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Affiliation(s)
- Kira Küsters
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Martina Pohl
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Ulrich Krauss
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Gizem Ölçücü
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Sandor Albert
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Faculty of Biotechnology, University of Applied Sciences Mannheim, 68163, Mannheim, Germany
| | - Karl-Erich Jaeger
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52074, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany.
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13
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Dubey NC, Tripathi BP. Nature Inspired Multienzyme Immobilization: Strategies and Concepts. ACS APPLIED BIO MATERIALS 2021; 4:1077-1114. [PMID: 35014469 DOI: 10.1021/acsabm.0c01293] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In a biological system, the spatiotemporal arrangement of enzymes in a dense cellular milieu, subcellular compartments, membrane-associated enzyme complexes on cell surfaces, scaffold-organized proteins, protein clusters, and modular enzymes have presented many paradigms for possible multienzyme immobilization designs that were adapted artificially. In metabolic channeling, the catalytic sites of participating enzymes are close enough to channelize the transient compound, creating a high local concentration of the metabolite and minimizing the interference of a competing pathway for the same precursor. Over the years, these phenomena had motivated researchers to make their immobilization approach naturally realistic by generating multienzyme fusion, cluster formation via affinity domain-ligand binding, cross-linking, conjugation on/in the biomolecular scaffold of the protein and nucleic acids, and self-assembly of amphiphilic molecules. This review begins with the discussion of substrate channeling strategies and recent empirical efforts to build it synthetically. After that, an elaborate discussion covering prevalent concepts related to the enhancement of immobilized enzymes' catalytic performance is presented. Further, the central part of the review summarizes the progress in nature motivated multienzyme assembly over the past decade. In this section, special attention has been rendered by classifying the nature-inspired strategies into three main categories: (i) multienzyme/domain complex mimic (scaffold-free), (ii) immobilization on the biomolecular scaffold, and (iii) compartmentalization. In particular, a detailed overview is correlated to the natural counterpart with advances made in the field. We have then discussed the beneficial account of coassembly of multienzymes and provided a synopsis of the essential parameters in the rational coimmobilization design.
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Affiliation(s)
- Nidhi C Dubey
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science and Engineering, Indian institute of Technology Delhi, New Delhi 110016, India
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14
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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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15
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Račková L, Csekes E. Proteasome Biology: Chemistry and Bioengineering Insights. Polymers (Basel) 2020; 12:E2909. [PMID: 33291646 PMCID: PMC7761984 DOI: 10.3390/polym12122909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Proteasomal degradation provides the crucial machinery for maintaining cellular proteostasis. The biological origins of modulation or impairment of the function of proteasomal complexes may include changes in gene expression of their subunits, ubiquitin mutation, or indirect mechanisms arising from the overall impairment of proteostasis. However, changes in the physico-chemical characteristics of the cellular environment might also meaningfully contribute to altered performance. This review summarizes the effects of physicochemical factors in the cell, such as pH, temperature fluctuations, and reactions with the products of oxidative metabolism, on the function of the proteasome. Furthermore, evidence of the direct interaction of proteasomal complexes with protein aggregates is compared against the knowledge obtained from immobilization biotechnologies. In this regard, factors such as the structures of the natural polymeric scaffolds in the cells, their content of reactive groups or the sequestration of metal ions, and processes at the interface, are discussed here with regard to their influences on proteasomal function.
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Affiliation(s)
- Lucia Račková
- Centre of Experimental Medicine, Institute of Experimental Pharmacology and Toxicology, Slovak Academy of Sciences, Dúbravská cesta 9, 841 04 Bratislava, Slovakia;
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16
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Jäger VD, Lamm R, Küsters K, Ölçücü G, Oldiges M, Jaeger KE, Büchs J, Krauss U. Catalytically-active inclusion bodies for biotechnology-general concepts, optimization, and application. Appl Microbiol Biotechnol 2020; 104:7313-7329. [PMID: 32651598 PMCID: PMC7413871 DOI: 10.1007/s00253-020-10760-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022]
Abstract
Bacterial inclusion bodies (IBs) have long been considered as inactive, unfolded waste material produced by heterologous overexpression of recombinant genes. In industrial applications, they are occasionally used as an alternative in cases where a protein cannot be expressed in soluble form and in high enough amounts. Then, however, refolding approaches are needed to transform inactive IBs into active soluble protein. While anecdotal reports about IBs themselves showing catalytic functionality/activity (CatIB) are found throughout literature, only recently, the use of protein engineering methods has facilitated the on-demand production of CatIBs. CatIB formation is induced usually by fusing short peptide tags or aggregation-inducing protein domains to a target protein. The resulting proteinaceous particles formed by heterologous expression of the respective genes can be regarded as a biologically produced bionanomaterial or, if enzymes are used as target protein, carrier-free enzyme immobilizates. In the present contribution, we review general concepts important for CatIB production, processing, and application. KEY POINTS: • Catalytically active inclusion bodies (CatIBs) are promising bionanomaterials. • Potential applications in biocatalysis, synthetic chemistry, and biotechnology. • CatIB formation represents a generic approach for enzyme immobilization. • CatIB formation efficiency depends on construct design and expression conditions.
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Affiliation(s)
- Vera D Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, Espoo, 02150, Finland
| | - Robin Lamm
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Kira Küsters
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Gizem Ölçücü
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Jochen Büchs
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany.
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
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17
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Formation and functionalization of membraneless compartments in Escherichia coli. Nat Chem Biol 2020; 16:1143-1148. [DOI: 10.1038/s41589-020-0579-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 06/01/2020] [Indexed: 01/09/2023]
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18
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Gil-Garcia M, Navarro S, Ventura S. Coiled-coil inspired functional inclusion bodies. Microb Cell Fact 2020; 19:117. [PMID: 32487230 PMCID: PMC7268670 DOI: 10.1186/s12934-020-01375-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Recombinant protein expression in bacteria often leads to the formation of intracellular insoluble protein deposits, a major bottleneck for the production of soluble and active products. However, in recent years, these bacterial protein aggregates, commonly known as inclusion bodies (IBs), have been shown to be a source of stable and active protein for biotechnological and biomedical applications. The formation of these functional IBs is usually facilitated by the fusion of aggregation-prone peptides or proteins to the protein of interest, leading to the formation of amyloid-like nanostructures, where the functional protein is embedded. RESULTS In order to offer an alternative to the classical amyloid-like IBs, here we develop functional IBs exploiting the coiled-coil fold. An in silico analysis of coiled-coil and aggregation propensities, net charge, and hydropathicity of different potential tags identified the natural homo-dimeric and anti-parallel coiled-coil ZapB bacterial protein as an optimal candidate to form assemblies in which the native state of the fused protein is preserved. The protein itself forms supramolecular fibrillar networks exhibiting only α-helix secondary structure. This non-amyloid self-assembly propensity allows generating innocuous IBs in which the recombinant protein of interest remains folded and functional, as demonstrated using two different fluorescent proteins. CONCLUSIONS Here, we present a proof of concept for the use of a natural coiled-coil domain as a versatile tool for the production of functional IBs in bacteria. This α-helix-based strategy excludes any potential toxicity drawback that might arise from the amyloid nature of β-sheet-based IBs and renders highly active and homogeneous submicrometric particles.
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Affiliation(s)
- Marcos Gil-Garcia
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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19
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Detailed small-scale characterization and scale-up of active YFP inclusion body production with Escherichia coli induced by a tetrameric coiled coil domain. J Biosci Bioeng 2020; 129:730-740. [PMID: 32143998 DOI: 10.1016/j.jbiosc.2020.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/13/2020] [Accepted: 02/03/2020] [Indexed: 12/16/2022]
Abstract
During heterologous protein production with Escherichia coli, the formation of inclusion bodies (IBs) is often a major drawback as these aggregated proteins are usually inactive. However, different strategies for the generation of IBs consisting of catalytically active proteins have recently been described. In this study, the archaeal tetrameric coiled-coil domain of the cell-surface protein tetrabrachion was fused to a target reporter protein to produce fluorescent IBs (FIBs). As the cultivation conditions severely influence IB formation, the entire cultivation process resulting in the production of FIBs were thoroughly studied. First, the cultivation process was scaled down based on the maximum oxygen transfer capacity, combining online monitoring technologies for shake flasks and microtiter plates with offline sampling. The evaluation of culture conditions in complex terrific broth autoinduction medium showed strong oxygen limitation and leaky expression. Furthermore, strong acetate formation and pH changes from 6.5 to 8.8 led to sub-optimal cultivation conditions. However, in minimal Wilms-MOPS autoinduction medium, defined culture conditions and a tightly controlled expression were achieved. The production of FIBs is strongly influenced by the induction strength. Increasing induction strengths result in lower total amounts of functional protein. However, the amount of functional FIBs increases. Furthermore, to prevent the formation of conventional inactive IBs, a temperature shift from 37 °C to 15 °C is crucial to generate FIBs. Finally, the gained insights were transferred to a stirred tank reactor batch fermentation. Hereby, 12 g/L FIBs were produced, making up 43 % (w/w) of the total generated biomass.
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20
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Céspedes MV, Cano-Garrido O, Álamo P, Sala R, Gallardo A, Serna N, Falgàs A, Voltà-Durán E, Casanova I, Sánchez-Chardi A, López-Laguna H, Sánchez-García L, Sánchez JM, Unzueta U, Vázquez E, Mangues R, Villaverde A. Engineering Secretory Amyloids for Remote and Highly Selective Destruction of Metastatic Foci. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1907348. [PMID: 31879981 DOI: 10.1002/adma.201907348] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/28/2019] [Indexed: 05/05/2023]
Abstract
Functional amyloids produced in bacteria as nanoscale inclusion bodies are intriguing but poorly explored protein materials with wide therapeutic potential. Since they release functional polypeptides under physiological conditions, these materials can be potentially tailored as mimetic of secretory granules for slow systemic delivery of smart protein drugs. To explore this possibility, bacterial inclusion bodies formed by a self-assembled, tumor-targeted Pseudomonas exotoxin (PE24) are administered subcutaneously in mouse models of human metastatic colorectal cancer, for sustained secretion of tumor-targeted therapeutic nanoparticles. These proteins are functionalized with a peptidic ligand of CXCR4, a chemokine receptor overexpressed in metastatic cancer stem cells that confers high selective cytotoxicity in vitro and in vivo. In the mouse models of human colorectal cancer, time-deferred anticancer activity is detected after the subcutaneous deposition of 500 µg of PE24-based amyloids, which promotes a dramatic arrest of tumor growth in the absence of side toxicity. In addition, long-term prevention of lymphatic, hematogenous, and peritoneal metastases is achieved. These results reveal the biomedical potential and versatility of bacterial inclusion bodies as novel tunable secretory materials usable in delivery, and they also instruct how therapeutic proteins, even with high functional and structural complexity, can be packaged in this convenient format.
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Affiliation(s)
- María Virtudes Céspedes
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
| | - Olivia Cano-Garrido
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Nanoligent SL, Edifici EUREKA, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Patricia Álamo
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
| | - Rita Sala
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
| | - Alberto Gallardo
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
| | - Naroa Serna
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Aïda Falgàs
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
| | - Eric Voltà-Durán
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Isolda Casanova
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
| | | | - Hèctor López-Laguna
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Laura Sánchez-García
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Julieta M Sánchez
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT) (CONICET-Universidad Nacional de Córdoba), ICTA & Cátedra de Química Biológica, Departamento de Química, FCEFyN, UNC, Av. Velez Sarsfield 1611, X 5016GCA, Córdoba, Argentina
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
| | - Esther Vázquez
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
| | - Antonio Villaverde
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, 08041, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
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21
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High pressure homogenization is a key unit operation in inclusion body processing. J Biotechnol 2020; 324S:100022. [PMID: 34154734 DOI: 10.1016/j.btecx.2020.100022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/24/2020] [Accepted: 06/10/2020] [Indexed: 11/23/2022]
Abstract
Recombinant protein production in E. coli often leads to the formation of inclusion bodies (IBs). Although downstream processing of IBs has the reputation of being a great hurdle, advantages of IBs can be substantial. Highly pure recombinant protein with the possibility of correctly folded structures and an easy separation from cell matter are decisive factors that make IB processes so interesting. Product yield, purity and biological activity of the refolded protein are the responses to evaluate an IB process. The objective of this case study was to develop a refolding process in an integrated manner. The effects of the unit operations 1) homogenization, 2) IB wash and 3) IB solubilisation as well as their interdependencies were analyzed. We revealed interesting factor interactions between homogenization and IB wash, as well as homogenization and solubilisation, which would be overlooked if the single unit operations were investigated individually. Furthermore, we found that homogenization was a key unit operation for IB processing. By changing the conditions during homogenization only, the product yield, purity and biological activity of the refolded product was affected 2-fold, 1.2-fold and 2.5-fold, respectively.
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22
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Pesarrodona M, Jauset T, Díaz‐Riascos ZV, Sánchez‐Chardi A, Beaulieu M, Seras‐Franzoso J, Sánchez‐García L, Baltà‐Foix R, Mancilla S, Fernández Y, Rinas U, Schwartz S, Soucek L, Villaverde A, Abasolo I, Vázquez E. Targeting Antitumoral Proteins to Breast Cancer by Local Administration of Functional Inclusion Bodies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900849. [PMID: 31559131 PMCID: PMC6755514 DOI: 10.1002/advs.201900849] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/11/2019] [Indexed: 05/07/2023]
Abstract
Two structurally and functionally unrelated proteins, namely Omomyc and p31, are engineered as CD44-targeted inclusion bodies produced in recombinant bacteria. In this unusual particulate form, both types of protein materials selectively penetrate and kill CD44+ tumor cells in culture, and upon local administration, promote destruction of tumoral tissue in orthotropic mouse models of human breast cancer. These findings support the concept of bacterial inclusion bodies as versatile protein materials suitable for application in chronic diseases that, like cancer, can benefit from a local slow release of therapeutic proteins.
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Affiliation(s)
- Mireia Pesarrodona
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)C/ Monforte de Lemos 3‐528029MadridSpain
| | - Toni Jauset
- Vall d'Hebron Institute of Oncology (VHIO)Edifici CellexHospital Vall d'Hebron08035BarcelonaSpain
- Peptomyc S.L.Edifici CellexHospital Vall d'Hebron08035BarcelonaSpain
| | - Zamira V. Díaz‐Riascos
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)C/ Monforte de Lemos 3‐528029MadridSpain
- Functional Validation & Preclinical ResearchCIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
- Drug Delivery & Targeting CIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
| | - Alejandro Sánchez‐Chardi
- Departament de Biologia EvolutivaEcologia i Ciències AmbientalsFacultat de BiologiaUniversitat de BarcelonaAv. Diagonal 64308028BarcelonaSpain
| | - Marie‐Eve Beaulieu
- Vall d'Hebron Institute of Oncology (VHIO)Edifici CellexHospital Vall d'Hebron08035BarcelonaSpain
- Peptomyc S.L.Edifici CellexHospital Vall d'Hebron08035BarcelonaSpain
| | - Joaquin Seras‐Franzoso
- Drug Delivery & Targeting CIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
| | - Laura Sánchez‐García
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)C/ Monforte de Lemos 3‐528029MadridSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
| | - Ricardo Baltà‐Foix
- Drug Delivery & Targeting CIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
| | - Sandra Mancilla
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)C/ Monforte de Lemos 3‐528029MadridSpain
- Functional Validation & Preclinical ResearchCIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
- Drug Delivery & Targeting CIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
| | - Yolanda Fernández
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)C/ Monforte de Lemos 3‐528029MadridSpain
- Functional Validation & Preclinical ResearchCIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
- Drug Delivery & Targeting CIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
| | - Ursula Rinas
- Leibniz University of HannoverTechnical Chemistry and Life ScienceCallinstr. 530167HannoverGermany
- Helmholtz Centre for Infection ResearchInhoffenstraße 738124BraunschweigGermany
| | - Simó Schwartz
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)C/ Monforte de Lemos 3‐528029MadridSpain
- Drug Delivery & Targeting CIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
| | - Laura Soucek
- Vall d'Hebron Institute of Oncology (VHIO)Edifici CellexHospital Vall d'Hebron08035BarcelonaSpain
- Peptomyc S.L.Edifici CellexHospital Vall d'Hebron08035BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)08010BarcelonaSpain
- Department of Biochemistry and Molecular BiologyUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
| | - Antonio Villaverde
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)C/ Monforte de Lemos 3‐528029MadridSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
| | - Ibane Abasolo
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)C/ Monforte de Lemos 3‐528029MadridSpain
- Functional Validation & Preclinical ResearchCIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
- Drug Delivery & Targeting CIBBIM‐NanomedicineVall d'Hebron Institut de Recerca (VHIR)Universitat Autònoma de Barcelona08035BarcelonaSpain
| | - Esther Vázquez
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)C/ Monforte de Lemos 3‐528029MadridSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
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23
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Jäger VD, Piqueray M, Seide S, Pohl M, Wiechert W, Jaeger K, Krauss U. An Enzymatic 2‐Step Cofactor and Co‐Product Recycling Cascade towards a Chiral 1,2‐Diol. Part II: Catalytically Active Inclusion Bodies. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vera D. Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität DüsseldorfForschungszentrum Jülich 52425 Jülich Germany
- Bioeconomy Science Center (BioSC), c/oForschungszentrum Jülich 52425 Jülich Germany
| | - Maja Piqueray
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität DüsseldorfForschungszentrum Jülich 52425 Jülich Germany
| | - Selina Seide
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology 52425 Jülich Germany
- Bioeconomy Science Center (BioSC), c/oForschungszentrum Jülich 52425 Jülich Germany
| | - Martina Pohl
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology 52425 Jülich Germany
- Bioeconomy Science Center (BioSC), c/oForschungszentrum Jülich 52425 Jülich Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology 52425 Jülich Germany
- Bioeconomy Science Center (BioSC), c/oForschungszentrum Jülich 52425 Jülich Germany
| | - Karl‐Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität DüsseldorfForschungszentrum Jülich 52425 Jülich Germany
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology 52425 Jülich Germany
- Bioeconomy Science Center (BioSC), c/oForschungszentrum Jülich 52425 Jülich Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität DüsseldorfForschungszentrum Jülich 52425 Jülich Germany
- Bioeconomy Science Center (BioSC), c/oForschungszentrum Jülich 52425 Jülich Germany
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