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Bello MN, Sabri S, Mohd Yahaya N, Mohd Shariff F, Mohamad Ali MS. Catalytically active inclusion bodies as a potential tool for biotechnology. Biotechnol Appl Biochem 2024. [PMID: 38863240 DOI: 10.1002/bab.2624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]
Abstract
The initial assumption that viewed inclusion bodies as a hindrance to the efficient production of protein is no longer held due to the emergence of catalytically active inclusion bodies (CatIBs). Recent studies revealed their potential to be used in free form or immobilized as biocatalysts. The curiosity to acquire suitable catalysts has remained the measure of concern for researchers and industrialists. Numerous processes and production in various sectors of food industries, petroleum, pharmaceutical, cosmetics, and many others are still searching for a robust catalyst with outstanding features such as recyclability, resistance to pH, as well as temperature. CatIBs are forms of inclusion bodies that possess catalytic activity, which can improve catalysis efficiency, stability, and recyclability. One of the advantages of CatIBs is their potential to be used as catalysts for numerous bioprocesses when generated by an enzyme. These aggregates can efficiently be used as a replacement for traditional enzyme immobilization. This review tends to focus on the possibility of its application in various processes. The novelty of this review is that it considered the production of CatIBs both from artificial and natural perspectives, as well as how to improve it. Inclusion bodies' immobilization may provide an efficient alternative in the area of biocatalysis, and hence it will improve industrial sectors and substantially provide a means of achieving excellent performance in the near future.
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Affiliation(s)
- Muhammad Nura Bello
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Biochemistry, Faculty of Science, Sokoto State University, Sokoto, Nigeria
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Normi Mohd Yahaya
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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Design, Production, and Characterization of Catalytically Active Inclusion Bodies. Methods Mol Biol 2023; 2617:49-74. [PMID: 36656516 DOI: 10.1007/978-1-0716-2930-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Catalytically active inclusion bodies (CatIBs) are promising biologically produced enzyme/protein immobilizates for application in biocatalysis, synthetic chemistry, and biomedicine. CatIB formation is commonly induced by fusion of suitable aggregation-inducing tags to a given target protein. Heterologous production of the fusion protein in turn yields CatIBs. This chapter presents the methodology needed to design, produce, and characterize CatIBs.
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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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Kachhawaha K, Singh S, Joshi K, Nain P, Singh SK. Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications. Prep Biochem Biotechnol 2022; 53:728-752. [PMID: 36534636 DOI: 10.1080/10826068.2022.2155835] [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: 12/23/2022]
Abstract
The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.
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Affiliation(s)
- Kajal Kachhawaha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Santanu Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Khyati Joshi
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Priyanka Nain
- Department of Chemical and Bimolecular Engineering, University of Delaware, Newark, DE, USA
| | - Sumit K Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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5
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Ruzaeva K, Kusters K, Wiechert W, Berkels B, Oldiges M, Noh K. Automated Characterization of Catalytically Active Inclusion Body Production in Biotechnological Screening Systems. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022; 2022:3874-3877. [PMID: 36086505 DOI: 10.1109/embc48229.2022.9871325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We here propose an automated pipeline for the microscopy image-based characterization of catalytically active inclusion bodies (CatIBs), which includes a fully automatic experimental high-throughput workflow combined with a hybrid approach for multi-object microbial cell segmentation. For automated microscopy, a CatIB producer strain was cultivated in a microbioreactor from which samples were injected into a flow chamber. The flow chamber was fixed under a microscope and an integrated camera took a series of images per sample. To explore heterogeneity of CatIB development during the cultivation and track the size and quantity of CatIBs over time, a hybrid image processing pipeline approach was developed, which combines an ML-based detection of in-focus cells with model-based segmentation. The experimental setup in combination with an automated image analysis unlocks high-throughput screening of CatIB production, saving time and resources. Biotechnological relevance- CatIBs have wide application in synthetic chemistry and biocatalysis, but also could have future biomedical applications such as therapeutics. The proposed hybrid automatic image processing pipeline can be adjusted to treat comparable biological microorganisms, where fully data-driven ML-based segmentation approaches are not feasible due to the lack of training data. Our work is the first step towards image- based bioprocess control.
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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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Peng M, Siebert DL, Engqvist MKM, Niemeyer CM, Rabe KS. Modeling-Assisted Design of Thermostable Benzaldehyde Lyases from Rhodococcus erythropolis for Continuous Production of α-Hydroxy Ketones. Chembiochem 2021; 23:e202100468. [PMID: 34558792 PMCID: PMC9293332 DOI: 10.1002/cbic.202100468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Indexed: 12/18/2022]
Abstract
Enantiopure α-hydroxy ketones are important building blocks of active pharmaceutical ingredients (APIs), which can be produced by thiamine-diphosphate-dependent lyases, such as benzaldehyde lyase. Here we report the discovery of a novel thermostable benzaldehyde lyase from Rhodococcus erythropolis R138 (ReBAL). While the overall sequence identity to the only experimentally confirmed benzaldehyde lyase from Pseudomonas fluorescens Biovar I (PfBAL) was only 65 %, comparison of a structural model of ReBAL with the crystal structure of PfBAL revealed only four divergent amino acids in the substrate binding cavity. Based on rational design, we generated two ReBAL variants, which were characterized along with the wild-type enzyme in terms of their substrate spectrum, thermostability and biocatalytic performance in the presence of different co-solvents. We found that the new enzyme variants have a significantly higher thermostability (up to 22 °C increase in T50 ) and a different co-solvent-dependent activity. Using the most stable variant immobilized in packed-bed reactors via the SpyCatcher/SpyTag system, (R)-benzoin was synthesized from benzaldehyde over a period of seven days with a stable space-time-yield of 9.3 mmol ⋅ L-1 ⋅ d-1 . Our work expands the important class of benzaldehyde lyases and therefore contributes to the development of continuous biocatalytic processes for the production of α-hydroxy ketones and APIs.
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Affiliation(s)
- Martin Peng
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Dominik L Siebert
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin K M Engqvist
- Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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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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Han Y, Zhang X, Zheng L. Engineering actively magnetic crosslinked inclusion bodies of Candida antarctica lipase B: An efficient and stable biocatalyst for enzyme-catalyzed reactions. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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Mikl M, Dennig A, Nidetzky B. Efficient enzyme formulation promotes Leloir glycosyltransferases for glycoside synthesis. J Biotechnol 2020; 322:74-78. [PMID: 32687957 DOI: 10.1016/j.jbiotec.2020.06.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/26/2020] [Accepted: 06/14/2020] [Indexed: 01/17/2023]
Abstract
Sugar nucleotide-dependent (Leloir) glycosyltransferases are powerful catalysts for glycoside synthesis. Their applicability can be limited due to elaborate production of enzyme preparations deployable in biocatalytic processes. Here, we show that efficient enzyme formulation promotes glycosyltransferases for the synthesis of the natural C-glycoside nothofagin. Adding Brij-35 detergent (1 %, w/v) during sonication of the E. coli BL21-Gold (DE3) expression strain, recovery of Oryza sativa C-glycosyltransferase was enhanced by ∼3-fold, partly due to the release of enzyme activity trapped in insoluble pellet. Freeze drying of the resulting cell-free extract (∼17 U ml-1) reduced the volume ∼20-fold and gave ∼55 mg solids ml-1 liquid processed, with 83 % retention of the original activity and a specific activity of 0.20 U mg-1 solids. The Glycine max sucrose synthase was processed analogously, giving a solid enzyme preparation of 0.28 U mg-1 in 63 % yield. Both enzyme formulations were stable for several weeks. The glycosyltransferase cascade reaction for 3'-β-C-glucosylation of phloretin (60 mM; as inclusion complex with hydroxypropyl-β-cyclodextrin) from UDP-glucose (generated in situ by sucrose synthase from 500 mM sucrose and 0.5 mM UDP) showed excellent performance metrics (≥ 98 % yield; 3.2 g l-1 h-1 space-time yield; ∼90 regeneration cycles for UDP). Collectively, our study demonstrates a facile procedure for solid glycosyltransferase formulations practically usable in glycoside synthesis.
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Affiliation(s)
- Markus Mikl
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010, Graz, Austria
| | - Alexander Dennig
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010, Graz, Austria; Austrian Centre of Industrial Biotechnology (acib), 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010, Graz, Austria; Austrian Centre of Industrial Biotechnology (acib), 8010, Graz, Austria.
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14
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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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15
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Mikl M, Dennig A, Nidetzky B. WITHDRAWN: Efficient enzyme formulation promotes Leloir glycosyltransferases for glycoside synthesis. J Biotechnol 2020; 324S:100023. [PMID: 34154728 DOI: 10.1016/j.btecx.2020.100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/26/2020] [Accepted: 06/14/2020] [Indexed: 11/28/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published in BIOTEC, 322C (2020) 74-78, https://doi.org/10.1016/j.jbiotec.2020.06.023. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Markus Mikl
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010 Graz, Austria
| | - Alexander Dennig
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010 Graz, Austria; Austrian Centre of Industrial Biotechnology (acib), 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010 Graz, Austria; Austrian Centre of Industrial Biotechnology (acib), 8010 Graz, Austria.
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16
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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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17
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Mestrom L, Marsden SR, McMillan DGG, Schoevaart R, Hagedoorn P, Hanefeld U. Comparison of Enzymes Immobilised on Immobeads and Inclusion Bodies: A Case Study of a Trehalose Transferase. ChemCatChem 2020. [DOI: 10.1002/cctc.202000241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Luuk Mestrom
- Biokatalyse, Afdeling BiotechnologieTechnische Universiteit Delft Van Der Maasweg 9 2629 HZ Delft The Netherlands
| | - Stefan R. Marsden
- Biokatalyse, Afdeling BiotechnologieTechnische Universiteit Delft Van Der Maasweg 9 2629 HZ Delft The Netherlands
| | - Duncan G. G. McMillan
- Biokatalyse, Afdeling BiotechnologieTechnische Universiteit Delft Van Der Maasweg 9 2629 HZ Delft The Netherlands
| | - Rob Schoevaart
- ChiralVisionHoog-Harnasch 44 2635 DL Den Hoorn The Netherlands
| | - Peter‐Leon Hagedoorn
- Biokatalyse, Afdeling BiotechnologieTechnische Universiteit Delft Van Der Maasweg 9 2629 HZ Delft The Netherlands
| | - Ulf Hanefeld
- Biokatalyse, Afdeling BiotechnologieTechnische Universiteit Delft Van Der Maasweg 9 2629 HZ Delft The Netherlands
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18
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Lv X, Cui S, Gu Y, Li J, Du G, Liu L. Enzyme Assembly for Compartmentalized Metabolic Flux Control. Metabolites 2020; 10:E125. [PMID: 32224973 PMCID: PMC7241084 DOI: 10.3390/metabo10040125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022] Open
Abstract
Enzyme assembly by ligand binding or physically sequestrating enzymes, substrates, or metabolites into isolated compartments can bring key molecules closer to enhance the flux of a metabolic pathway. The emergence of enzyme assembly has provided both opportunities and challenges for metabolic engineering. At present, with the development of synthetic biology and systems biology, a variety of enzyme assembly strategies have been proposed, from the initial direct enzyme fusion to scaffold-free assembly, as well as artificial scaffolds, such as nucleic acid/protein scaffolds, and even some more complex physical compartments. These assembly strategies have been explored and applied to the synthesis of various important bio-based products, and have achieved different degrees of success. Despite some achievements, enzyme assembly, especially in vivo, still has many problems that have attracted significant attention from researchers. Here, we focus on some selected examples to review recent research on scaffold-free strategies, synthetic artificial scaffolds, and physical compartments for enzyme assembly or pathway sequestration, and we discuss their notable advances. In addition, the potential applications and challenges in the applications are highlighted.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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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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Lv X, Jin K, Wu Y, Zhang C, Cui S, Zhu X, Li J, Du G, Liu L. Enzyme assembly guided by SPFH-induced functional inclusion bodies for enhanced cascade biocatalysis. Biotechnol Bioeng 2020; 117:1446-1457. [PMID: 32043560 DOI: 10.1002/bit.27304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/05/2020] [Accepted: 02/09/2020] [Indexed: 01/01/2023]
Abstract
Enzyme clustering into compact agglomerates could accelerate the processing of intermediates to enhance metabolic pathway flux. However, enzyme clustering is still a challenging task due to the lack of universal assembly strategy applicable to all enzymes. Therefore, we proposed an alternative enzyme assembly strategy based on functional inclusion bodies. First, functional inclusion bodies in cells were formed by the fusion expression of stomatin/prohibitin/flotillin/HflK/C (SPFH) domain and enhanced green fluorescent protein, as observed visually and by transmission electron microscopy. The formation of SPFH-induced functional inclusion bodies enhanced intermolecular polymerization as revealed by further analysis combined with Förster resonance energy transfer and bimolecular fluorescent complimentary. Finally, the functional inclusion bodies significantly improved the enzymatic catalysis in living cells, as proven by the examples with whole-cell biocatalysis of phenyllactic acid by Escherichia coli, and the production of N-acetylglucosamine by Bacillus subtilis. Our findings suggest that SPFH-induced functional inclusion bodies can enhance the cascade reaction of enzymes, to serve as a potential universal strategy for the construction of efficient microbial cell factories.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Cheng Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiaonan Zhu
- School of Bioengineering, Jiangnan University, Wuxi, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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21
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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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22
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Jäger VD, Kloss R, Grünberger A, Seide S, Hahn D, Karmainski T, Piqueray M, Embruch J, Longerich S, Mackfeld U, Jaeger KE, Wiechert W, Pohl M, Krauss U. Tailoring the properties of (catalytically)-active inclusion bodies. Microb Cell Fact 2019; 18:33. [PMID: 30732596 PMCID: PMC6367779 DOI: 10.1186/s12934-019-1081-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/30/2019] [Indexed: 01/02/2023] Open
Abstract
Background Immobilization is an appropriate tool to ease the handling and recycling of enzymes in biocatalytic processes and to increase their stability. Most of the established immobilization methods require case-to-case optimization, which is laborious and time-consuming. Often, (chromatographic) enzyme purification is required and stable immobilization usually includes additional cross-linking or adsorption steps. We have previously shown in a few case studies that the molecular biological fusion of an aggregation-inducing tag to a target protein induces the intracellular formation of protein aggregates, so called inclusion bodies (IBs), which to a certain degree retain their (catalytic) function. This enables the combination of protein production and immobilization in one step. Hence, those biologically-produced immobilizates were named catalytically-active inclusion bodies (CatIBs) or, in case of proteins without catalytic activity, functional IBs (FIBs). While this strategy has been proven successful, the efficiency, the potential for optimization and important CatIB/FIB properties like yield, activity and morphology have not been investigated systematically. Results We here evaluated a CatIB/FIB toolbox of different enzymes and proteins. Different optimization strategies, like linker deletion, C- versus N-terminal fusion and the fusion of alternative aggregation-inducing tags were evaluated. The obtained CatIBs/FIBs varied with respect to formation efficiency, yield, composition and residual activity, which could be correlated to differences in their morphology; as revealed by (electron) microscopy. Last but not least, we demonstrate that the CatIB/FIB formation efficiency appears to be correlated to the solvent-accessible hydrophobic surface area of the target protein, providing a structure-based rationale for our strategy and opening up the possibility to predict its efficiency for any given target protein. Conclusion We here provide evidence for the general applicability, predictability and flexibility of the CatIB/FIB immobilization strategy, highlighting the application potential of CatIB-based enzyme immobilizates for synthetic chemistry, biocatalysis and industry. Electronic supplementary material The online version of this article (10.1186/s12934-019-1081-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V D Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - R Kloss
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - A Grünberger
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Multiscale Bioengineering, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - S Seide
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - D Hahn
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - T Karmainski
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - M Piqueray
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - J Embruch
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - S Longerich
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - U Mackfeld
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - K-E Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany.,IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - W Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - M Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - U Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany. .,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany.
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