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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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Ma J, Liu P, Cai S, Wu T, Chen D, Zhu C, Li S. Discovery and Identification of a Novel Tag of HlyA60 for Protein Active Aggregate Formation in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:493-503. [PMID: 38109329 DOI: 10.1021/acs.jafc.3c05860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The strategy of active aggregation tag fusion expression with target proteins can solve the problems of restricted expression, inefficient purification, and laborious immobilization faced in the production of recombinant proteins in Escherichia coli. We localized a novel active aggregation peptide HlyA60 from the hemolysin A secretion system, which can effectively induce aggregate formation with satisfactory protein activities in E. coli after fusion expression with the protein of interest. Based on structural prediction and surface properties, the process of active aggregation of HlyA60 through electrostatic interactions and hydrophobic interactions was analyzed. To investigate the potential application of HlyA60 as an efficient aggregation tag, it was fused with acetyl xylan esterase and lipase A, separately. The resulting fusion proteins demonstrated active aggregation rates of 97.6 and 66.7%, respectively, leading to 1.9-fold and 1.7-fold increases in bacterial density at the end of fermentation. The AXE-HlyA60 fusion protein, which exhibited superior performance, was subjected to purification and immobilization. It was able to achieve column-free purification with an impressive 98.8% recovery and in situ immobilization; the immobilization enabled 30 cycles of reactions to take place with 85% residual activity maintained. Our findings provide a novel tool for efficiently producing recombinant proteins in E. coli.
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Affiliation(s)
- Jiayuan Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Peiling Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shengliang Cai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Tao Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Dongying Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Chaoyi Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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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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Kamel S, Schollmeyer J, Kurreck A, Neubauer P. Optimization of Inclusion Body Formation and Purification in Multi-well Plates. Methods Mol Biol 2023; 2617:121-138. [PMID: 36656520 DOI: 10.1007/978-1-0716-2930-7_8] [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
Heterologous expression has long been used for the efficient production of proteins and enzymes as it offers significant advantages over purification of proteins from their native organisms. When first established, great efforts have been made to heterologously express proteins with high yields in the soluble fraction, hence, avoiding protein aggregation. In recent decades, however, it has been shown that the formation of aggregates (inclusion bodies; IBs) can be beneficial. To recover active protein, however, proteins should have been refolded from IBs after purification. The discovery that IBs themselves can also be active has revolutionized the entire protein production field. Therefore, several approaches have been described to generate catalytically active IBs during heterologous expression. Since several extrinsic and intrinsic factors such as protein structure and toxicity, pH and temperature of expression, and the used media might influence the formation of IBs, it is time and material consuming to use shake flask to examine and optimize different expression conditions. However, by using multi-well plates, it is possible to rapidly develop an efficient protocol for the expression of catalytically active IBs in a rational approach. The presented protocol was used for the heterologous expression of a 5'-adenosine monophosphate phosphorylase which forms catalytically active aggregates during expression in E. coli.
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Affiliation(s)
- Sarah Kamel
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Berlin, Germany
| | - Julia Schollmeyer
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Berlin, Germany
- BioNukleo GmbH, Berlin, Germany
| | | | - Peter Neubauer
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Berlin, Germany.
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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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Evaluating Enzymatic Productivity—The Missing Link to Enzyme Utility. Int J Mol Sci 2022; 23:ijms23136908. [PMID: 35805910 PMCID: PMC9266678 DOI: 10.3390/ijms23136908] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 01/07/2023] Open
Abstract
Kinetic productivity analysis is critical to the characterization of enzyme catalytic performance and capacity. However, productivity analysis has been largely overlooked in the published literature. Less than 0.01% of studies which report on enzyme characterization present productivity analysis, despite the fact that this is the only measurement method that provides a reliable indicator of potential commercial utility. Here, we argue that reporting productivity data involving native, modified, and immobilized enzymes under different reaction conditions will be of immense value in optimizing enzymatic processes, with a view to accelerating biotechnological applications. With the use of examples from wide-ranging studies, we demonstrate that productivity is a measure of critical importance to the translational and commercial use of enzymes and processes that employ them. We conclude the review by suggesting steps to maximize the productivity of enzyme catalyzed reactions.
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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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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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Exploring the Strategy of Fusing Sucrose Synthase to Glycosyltransferase UGT76G1 in Enzymatic Biotransformation. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Uridine diphosphate glycosyltransferases (UGTs) as fine catalysts of glycosylation are increasingly used in the synthesis of natural products. Sucrose synthase (SuSy) is recognized as a powerful tool for in situ regenerating sugar donors for the UGT-catalyzed reaction. It is crucial to select the appropriate SuSy for cooperation with UGT in a suitable way. In the present study, eukaryotic SuSy from Arabidopsisthaliana (AtSUS1) helped stevia glycosyltransferase UGT76G1 achieve the complete conversion of stevioside (30 g/L) into rebaudioside A (RebA). Position of the individual transcription units containing the genes encoding AtSUS1 and UGT76G1 in the expression plasmid has an effect, but less than that of the fusion order of these genes on RebA yield. Fusion of the C-terminal of AtSUS1 and the N-terminal of UGT76G1 with rigid linkers are conducive to maintaining enzyme activities. When the same fusion strategy was applied to a L637M-T640V double mutant of prokaryotic SuSy from Acidithiobacillus caldus (AcSuSym), 18.8 ± 0.6 g/L RebA (a yield of 78.2%) was accumulated in the reaction mixture catalyzed by the fusion protein Acm-R3-76G1 (the C-terminal of AcSuSym and the N-terminal of UGT76G1 were linked with (EAAAK)3). This work would hopefully reveal the potential of UGT-SuSy fusion in improving the cascade enzymatic glycosylation.
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