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Sun T, Jin Y, Rao Z, Liyan W, Tang R, Zaryab KM, Li M, Li Z, Wang Y, Xu J, Han R, Cao L. Knockdown of Thitarodes host genes influences dimorphic transition of Ophiocordyceps sinensis in the host hemolymph. Front Cell Infect Microbiol 2024; 14:1451628. [PMID: 39397862 PMCID: PMC11466941 DOI: 10.3389/fcimb.2024.1451628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/22/2024] [Indexed: 10/15/2024] Open
Abstract
The Chinese cordyceps, a unique parasitic complex of Thitarodes/Hepialus ghost moths and Ophiocordyceps sinensis fungus in the Tibetan Plateau, is a highly valuable biological resource for medicine and health foods in Asian countries. Efficient system for artificial cultivation of Chinese cordyceps relies on understanding the gene functions involved in the induction of growing blastospores into hyphae in the larval hemolymph of insect host, during O. sinensis infection. Transcriptome analysis and ribonucleic acid interference (RNA interference) method were employed to identify the key differentially expressed genes and to demonstrate their functions in Thitarodes xiaojinensis. Key larval genes critical for O. sinensis blastospore development or filamentation were identified. Nine of the 20 top upregulated genes encoded cuticles proteins, indicating that these proteins highly activated when the larval hemolymph was full of blastospores. Small interfering RNA (siRNA) knockdown of five larval genes such as Flightin, larval cuticle protein LCP-30, 26-hydroxylase (CYP18A1), cuticle protein 18.6, isoform B, and probable chitinase 3 significantly stimulated the dimorphic transition from blastospores to prehyphae in O. sinensis in the larval hemolymph after 120 h after injection. The expressions of these genes determined by quantitative real-time PCR were suppressed in various levels from 38.64% to 91.54%, compared to the controls. These results demonstrated that injection of the siRNAs of key upregulated genes into the larval hemolymph containing high load of blastospores caused the gene silence in T. xiaojinensis larvae and induced the fungal transition from blastospores to prehyphae, providing novel knowledge on the regulation of O. sinensis fungal dimorphism by Thitarodes host and cues for further study of Thitarodes biology and commercial cultivation of Chinese cordyceps.
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Affiliation(s)
- Tanqi Sun
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yongling Jin
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhongchen Rao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Wang Liyan
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Rui Tang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Khalid Muhammad Zaryab
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Mingyan Li
- Research Centre, Zhejiang Shouxiangu Pharmaceutical Co. Ltd, Zhejiang, Jinhua, China
| | - Zhenhao Li
- Research Centre, Zhejiang Shouxiangu Pharmaceutical Co. Ltd, Zhejiang, Jinhua, China
| | - Ying Wang
- Research Centre, Zhejiang Shouxiangu Pharmaceutical Co. Ltd, Zhejiang, Jinhua, China
| | - Jing Xu
- Research Centre, Zhejiang Shouxiangu Pharmaceutical Co. Ltd, Zhejiang, Jinhua, China
| | - Richou Han
- Research Centre, Zhejiang Yuewangshengcao Biotechnological Company Limited, Zhejiang, Jinhua, China
| | - Li Cao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
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Wu H, Rao ZC, Cao L, De Clercq P, Han RC. Infection of Ophiocordyceps sinensis Fungus Causes Dramatic Changes in the Microbiota of Its Thitarodes Host. Front Microbiol 2020; 11:577268. [PMID: 33343519 PMCID: PMC7744566 DOI: 10.3389/fmicb.2020.577268] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/13/2020] [Indexed: 12/31/2022] Open
Abstract
The Chinese cordyceps is a unique and valuable parasitic complex of Thitarodes/Hepialus ghost moths and the Ophiocordyceps sinensis fungus for medicine and health foods from the Tibetan Plateau. During artificial cultivation of Chinese cordyceps, the induction of blastospores into hyphae is a prerequisite for mummification of the infected Thitarodes larvae. To explore the microbial involvement in the induction of mycelia-blastospore transition, the microbiota of the hemolymph and gut from Thitarodes xiaojinensis larvae with or without injected O. sinensis blastospores were investigated by culture-dependent and -independent methods. Twenty-five culturable bacterial species and 14 fungal species, together with 537 bacterial operational taxonomic units (OTUs) and 218 fungal OTUs, were identified from the hemolymph and gut of samples from five stages including living larvae without injected fungi (A) or with high blastospore load (B), mummifying larvae without mycelia coating (C), freshly mummifying larvae coated with mycelia (D), and completely mummified larvae with mycelia (E). Two culturable bacterial species (Serratia plymuthica, Serratia proteamaculans), and 47 bacterial and 15 fungal OTUs were considered as shared species. The uninfected larval hemolymph contained 13 culturable bacterial species but no fungal species, together with 164 bacterial and 73 fungal OTUs. To our knowledge, this is the first study to detect large bacterial communities from the hemolymph of healthy insect larvae. When the living larvae contained high blastospore load, the culturable bacterial community was sharply inhibited in the hemolymph but the bacterial and fungal community greatly increased in the gut. In general, high blastospore load increased bacterial diversity but sharply decreased fungal diversity in the hemolymph and gut by OTUs. The bacterial loads of four culturable species (Chryseobacterium sp., Pseudomonas fragi, S. plymuthica, S. proteamaculans) increased significantly and O. sinensis and Pseudomonas spp. became dominant microbes, when the infected larvae became mummified, indicating their possible involvement in the larval mummification process. The discovery of many opportunistic pathogenic bacteria in the hemolymph of the healthy larvae, the larval microbial diversity influenced by O. sinensis challenge and the involvement of dominant bacteria during larval mummification process provide new insight into the infection and mummification mechanisms of O. sinensis in its Thitarodes hosts.
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Affiliation(s)
- Hua Wu
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhong-Chen Rao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Li Cao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Patrick De Clercq
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Ri-Chou Han
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
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Saltepe B, Bozkurt EU, Hacıosmanoğlu N, Şeker UÖŞ. Genetic Circuits To Detect Nanomaterial Triggered Toxicity through Engineered Heat Shock Response Mechanism. ACS Synth Biol 2019; 8:2404-2417. [PMID: 31536326 DOI: 10.1021/acssynbio.9b00291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biocompatibility assessment of nanomaterials has been of great interest due to their potential toxicity. However, conventional biocompatibility tests fall short of providing a fast toxicity report. We developed a whole cell based biosensor to track biocompatibility of nanomaterials with the aim of providing fast feedback to engineer them with lower toxicity levels. We engineered promoters of four heat shock response (HSR) proteins utilizing synthetic biology approaches. As an initial design, a reporter coding gene was cloned downstream of the selected promoter regions. Initial results indicated that native heat shock protein (HSP) promoter regions were not very promising to generate signals with low background signals. Introducing riboregulators to native promoters eliminated unwanted background signals almost entirely. Yet, this approach also led to a decrease in expected sensor signal upon stress treatment. Thus, a repression based genetic circuit, inspired by the HSR mechanism of Mycobacterium tuberculosis, was constructed. These genetic circuits could report the toxicity of quantum dot nanoparticles in 1 h. Our designed nanoparticle toxicity sensors can provide quick reports, which can lower the demand for additional experiments with more complex organisms.
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Affiliation(s)
- Behide Saltepe
- UNAM−Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Eray Ulaş Bozkurt
- UNAM−Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Nedim Hacıosmanoğlu
- UNAM−Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM−Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
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Huo YX, Ren H, Yu H, Zhao L, Yu S, Yan Y, Chen Z. CipA-mediating enzyme self-assembly to enhance the biosynthesis of pyrogallol in Escherichia coli. Appl Microbiol Biotechnol 2018; 102:10005-10015. [DOI: 10.1007/s00253-018-9365-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/20/2018] [Accepted: 09/03/2018] [Indexed: 11/28/2022]
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Potential Applications of the Escherichia coli Heat Shock Response in Synthetic Biology. Trends Biotechnol 2018; 36:186-198. [DOI: 10.1016/j.tibtech.2017.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/20/2017] [Accepted: 10/20/2017] [Indexed: 01/06/2023]
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Ude C, Ben-Dov N, Jochums A, Li Z, Segal E, Scheper T, Beutel S. Online analysis of protein inclusion bodies produced in E. coli by monitoring alterations in scattered and reflected light. Appl Microbiol Biotechnol 2016; 100:4147-59. [PMID: 26940052 DOI: 10.1007/s00253-016-7403-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/29/2022]
Abstract
The online monitoring of recombinant protein aggregate inclusion bodies during microbial cultivation is an immense challenge. Measurement of scattered and reflected light offers a versatile and non-invasive measurement technique. Therefore, we investigated two methods to detect the formation of inclusion bodies and monitor their production: (1) online 180° scattered light measurement (λ = 625 nm) using a sensor platform during cultivation in shake flask and (2) online measurement of the light reflective interference using a porous Si-based optical biosensor (SiPA). It could be shown that 180° scattered light measurement allows monitoring of alterations in the optical properties of Escherichia coli BL21 cells, associated with the formation of inclusion bodies during cultivation. A reproducible linear correlation between the inclusion body concentration of the non-fluorescent protein human leukemia inhibitory factor (hLIF) carrying a thioredoxin tag and the shift ("Δamp") in scattered light signal intensity was observed. This was also observed for the glutathione-S-transferase-tagged green fluorescent protein (GFP-GST). Continuous online monitoring of reflective interference spectra reveals a significant increase in the bacterium refractive index during hLIF production in comparison to a non-induced reference that coincide with the formation of inclusion bodies. These online monitoring techniques could be applied for fast and cost-effective screening of different protein expression systems.
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Affiliation(s)
- Christian Ude
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Nadav Ben-Dov
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - André Jochums
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Zhaopeng Li
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Thomas Scheper
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Sascha Beutel
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany.
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Gustavsson R, Lukasser C, Mandenius CF. Control of specific carbon dioxide production in a fed-batch culture producing recombinant protein using a soft sensor. J Biotechnol 2015; 200:44-51. [PMID: 25746902 DOI: 10.1016/j.jbiotec.2015.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 02/15/2015] [Accepted: 02/24/2015] [Indexed: 11/30/2022]
Abstract
The feeding of a fed-batch cultivation producing recombinant protein was controlled by a soft sensor set-up. It was assumed that the control approach could be based on the cell's production of carbon dioxide and that this parameter indicates the metabolic state occurring at induced protein expression. The soft sensor used the on-line signals from a carbon dioxide analyser and a near-infrared (NIR) probe for biomass to estimate the specific production rate qCO2. Control experiments were carried out with various qCO2 set-points where we observe that the feeding of nutrients to the culture could easily be controlled and resulted in a decreased variability compared to uncontrolled cultivations. We therefore suggest that this control approach could serve as an alternative to other commonly applied methods such as controlling the cell's overflow metabolism of acetate or the cell's specific growth rate. However, further studies of the internal metabolic fluxes of CO2 during protein expression would be recommended for a more precise characterization of the relationship between qCO2 and protein expression in order to fully interpret the control behaviour.
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Affiliation(s)
- Robert Gustavsson
- Division of Biotechnology, IFM, Linköping University, 581 83 Linköping, Sweden
| | - Cornelia Lukasser
- Division of Biotechnology, IFM, Linköping University, 581 83 Linköping, Sweden
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Rahmen N, Fulton A, Ihling N, Magni M, Jaeger KE, Büchs J. Exchange of single amino acids at different positions of a recombinant protein affects metabolic burden in Escherichia coli. Microb Cell Fact 2015; 14:10. [PMID: 25612616 PMCID: PMC4307990 DOI: 10.1186/s12934-015-0191-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 01/05/2015] [Indexed: 12/19/2022] Open
Abstract
Background Escherichia coli is commonly used in academia and industry for expressing recombinant proteins because of its well-characterized molecular genetics and the availability of numerous expression vectors and strains. One important issue during recombinant protein production is the so-called ‘metabolic burden’: the material and energy normally reserved for microbial metabolism which is sapped from the bacterium to produce the recombinant protein. This material and energy drain harms biomass formation and modifies respiration. To the best of our knowledge, no research has investigated so far whether a single amino acid exchange in a recombinant protein affects the metabolic burden phenomenon. Thus, in this study, 15 E. coli BL21(DE3) clones expressing either the fusion tags, a recombinant wild type lipase, or 13 different lipase variants are investigated to quantitatively analyze the respective effects of single amino acid exchanges at different positions on respiration, biomass and protein production of each clone. Therefore, two small-scale online monitoring systems, namely a Respiration Activity MOnitoring System (RAMOS) and a microtiter plate based cultivation system (BioLector) are applied. Results Upon expression of all enzyme variants, strong variations were found in the Oxygen Transfer Rate (OTR), biomass and protein (lipase) production of the respective E. coli clones. Two distinct patterns of respiration behavior were observed and, so, the clones could be classified into two groups (Type A and B). Potential factors to explain these patterns were evaluated (e.g. plasmid copy number, inclusion body formation). However, no decisive factor could yet be identified. Five distinct cultivation phases could be determined from OTR curves which give real-time information about carbon source consumption, biomass and protein production. In general, it was found that the quantity of product increased with the duration of active respiration. Conclusions This work demonstrates that single amino acid exchanges in a recombinant protein influence the metabolic burden during protein production. The small-scale online monitoring devices RAMOS and BioLector enable the real-time detection of even smallest differences in respiration behavior, biomass and protein production in the E. coli clones investigated. Hence, this study underscores the importance of parallel online monitoring systems to unveil the relevance of single amino acid exchanges for the recombinant protein production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalie Rahmen
- AVT - Biochemical Engineering, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany.
| | - Alexander Fulton
- Institute for Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52426, Jülich, Germany.
| | - Nina Ihling
- AVT - Biochemical Engineering, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany.
| | - Marzio Magni
- AVT - Biochemical Engineering, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany.
| | - Karl-Erich Jaeger
- Institute for Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52426, Jülich, Germany. .,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52426, Jülich, Germany.
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany.
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Selection of Escherichia coli heat shock promoters toward their application as stress probes. J Biotechnol 2014; 188:61-71. [PMID: 25128614 DOI: 10.1016/j.jbiotec.2014.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 07/24/2014] [Accepted: 08/05/2014] [Indexed: 02/04/2023]
Abstract
The mechanism of heat shock response of Escherichia coli can be explored to program novel biological functions. In this study, the strongest heat shock promoters were identified by microarray experiments conducted at different temperatures (37°C and 45°C, 5min). The promoters of the genes ibpA, dnaK and fxsA were selected and validated by RT-qPCR. These promoters were used to construct and characterize stress probes using green fluorescence protein (GFP). Cellular stress levels were evaluated in experiments conducted at different shock temperatures during several exposure times. It was concluded that the strength of the promoter is not the only relevant factor in the construction of an efficient stress probe. Furthermore, it was found to be crucial to test and optimize the ribosome binding site (RBS) in order to obtain translational efficiency that balances the transcription levels previously verified by microarrays and RT-qPCR. These heat shock promoters can be used to trigger in situ gene expression of newly constructed biosynthetic pathways.
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Improved production of a heterologous amylase in Saccharomyces cerevisiae by inverse metabolic engineering. Appl Environ Microbiol 2014; 80:5542-50. [PMID: 24973076 DOI: 10.1128/aem.00712-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing demand for industrial enzymes and biopharmaceutical proteins relies on robust production hosts with high protein yield and productivity. Being one of the best-studied model organisms and capable of performing posttranslational modifications, the yeast Saccharomyces cerevisiae is widely used as a cell factory for recombinant protein production. However, many recombinant proteins are produced at only 1% (or less) of the theoretical capacity due to the complexity of the secretory pathway, which has not been fully exploited. In this study, we applied the concept of inverse metabolic engineering to identify novel targets for improving protein secretion. Screening that combined UV-random mutagenesis and selection for growth on starch was performed to find mutant strains producing heterologous amylase 5-fold above the level produced by the reference strain. Genomic mutations that could be associated with higher amylase secretion were identified through whole-genome sequencing. Several single-point mutations, including an S196I point mutation in the VTA1 gene coding for a protein involved in vacuolar sorting, were evaluated by introducing these to the starting strain. By applying this modification alone, the amylase secretion could be improved by 35%. As a complement to the identification of genomic variants, transcriptome analysis was also performed in order to understand on a global level the transcriptional changes associated with the improved amylase production caused by UV mutagenesis.
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Marisch K, Bayer K, Cserjan-Puschmann M, Luchner M, Striedner G. Evaluation of three industrial Escherichia coli strains in fed-batch cultivations during high-level SOD protein production. Microb Cell Fact 2013; 12:58. [PMID: 23758670 PMCID: PMC3698069 DOI: 10.1186/1475-2859-12-58] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the biopharmaceutical industry, Escherichia coli (E. coli) strains are among the most frequently used bacterial hosts for producing recombinant proteins because they allow a simple process set-up and they are Food and Drug Administration (FDA)-approved for human applications. Widespread use of E. coli in biotechnology has led to the development of many different strains, and selecting an ideal host to produce a specific protein of interest is an important step in developing a production process. E. coli B and K-12 strains are frequently employed in large-scale production processes, and therefore are of particular interest. We previously evaluated the individual cultivation characteristics of E. coli BL21 and the K-12 hosts RV308 and HMS174. To our knowledge, there has not yet been a detailed comparison of the individual performances of these production strains in terms of recombinant protein production and system stability. The present study directly compared the T7-based expression hosts E. coli BL21(DE3), RV308(DE3), and HMS174(DE3), focusing on evaluating the specific attributes of these strains in relation to high-level protein production of the model protein recombinant human superoxide dismutase (SOD). The experimental setup was an exponential carbon-limited fed-batch cultivation with minimal media and single-pulse induction. RESULTS The host strain BL21(DE3) produced the highest amounts of specific protein, followed by HMS174(DE3) and RV308(DE3). The expression system HMS174(DE3) exhibited system stability by retaining the expression vector over the entire process time; however, it entirely stopped growing shortly after induction. In contrast, BL21(DE3) and RV308(DE3) encountered plasmid loss but maintained growth. RV308(DE3) exhibited the lowest ppGpp concentration, which is correlated with the metabolic stress level and lowest degradation of soluble protein fraction compared to both other strains. CONCLUSIONS Overall, this study provides novel data regarding the individual strain properties and production capabilities, which will enable targeted strain selection for producing a specific protein of interest. This information can be used to accelerate future process design and implementation.
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Affiliation(s)
- Karoline Marisch
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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Anaerobic α-amylase production and secretion with fumarate as the final electron acceptor in Saccharomyces cerevisiae. Appl Environ Microbiol 2013; 79:2962-7. [PMID: 23435897 DOI: 10.1128/aem.03207-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In this study, we focus on production of heterologous α-amylase in the yeast Saccharomyces cerevisiae under anaerobic conditions. We compare the metabolic fluxes and transcriptional regulation under aerobic and anaerobic conditions, with the objective of identifying the final electron acceptor for protein folding under anaerobic conditions. We find that yeast produces more amylase under anaerobic conditions than under aerobic conditions, and we propose a model for electron transfer under anaerobic conditions. According to our model, during protein folding the electrons from the endoplasmic reticulum are transferred to fumarate as the final electron acceptor. This model is supported by findings that the addition of fumarate under anaerobic (but not aerobic) conditions improves cell growth, specifically in the α-amylase-producing strain, in which it is not used as a carbon source. Our results provide a model for the molecular mechanism of anaerobic protein secretion using fumarate as the final electron acceptor, which may allow for further engineering of yeast for improved protein secretion under anaerobic growth conditions.
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An advanced monitoring platform for rational design of recombinant processes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012. [PMID: 23207722 DOI: 10.1007/10_2012_169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Bioprocess engineering is an application-oriented science in an interdisciplinary environment, and a meaningful combination of different scientific disciplines is the only way to meet the challenges of bioprocess complexity. Setting up a reasoned process monitoring platform is the first step in an iterative procedure aiming at process and systems understanding, being the key to rational and innovative bioprocess design. This chapter describes a comprehensive process monitoring platform and how the resulting knowledge is translated into new strategies in process and/or host cell design.
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Gustavsson R, Mandenius CF. Soft sensor control of metabolic fluxes in a recombinant Escherichia coli fed-batch cultivation producing green fluorescence protein. Bioprocess Biosyst Eng 2012; 36:1375-84. [PMID: 23104303 DOI: 10.1007/s00449-012-0840-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 10/10/2012] [Indexed: 12/21/2022]
Abstract
A soft sensor approach is described for controlling metabolic overflow from mixed-acid fermentation and glucose overflow metabolism in a fed-batch cultivation for production of recombinant green fluorescence protein (GFP) in Escherichia coli. The hardware part of the sensor consisted of a near-infrared in situ probe that monitored the E. coli biomass and an HPLC analyzer equipped with a filtration unit that measured the overflow metabolites. The computational part of the soft sensor used basic kinetic equations and summations for estimation of specific rates and total metabolite concentrations. Two control strategies for media feeding of the fed-batch cultivation were evaluated: (1) controlling the specific rates of overflow metabolism and mixed-acid fermentation metabolites at a fixed pre-set target values, and (2) controlling the concentration of the sum of these metabolites at a set level. The results indicate that the latter strategy was more efficient for maintaining a high titer and low variability of the produced recombinant GFP protein.
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Affiliation(s)
- Robert Gustavsson
- Division of Biotechnology/IFM, Linköping University, 581 83, Linköping, Sweden
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Silva F, Queiroz JA, Domingues FC. Evaluating metabolic stress and plasmid stability in plasmid DNA production by Escherichia coli. Biotechnol Adv 2012; 30:691-708. [DOI: 10.1016/j.biotechadv.2011.12.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 12/01/2011] [Accepted: 12/29/2011] [Indexed: 01/26/2023]
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Rodríguez-Carmona E, Cano-Garrido O, Dragosits M, Maurer M, Mader A, Kunert R, Mattanovich D, Villaverde A, Vázquez F. Recombinant Fab expression and secretion in Escherichia coli continuous culture at medium cell densities: Influence of temperature. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.11.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Sense and nonsense from a systems biology approach to microbial recombinant protein production. Biotechnol Appl Biochem 2010; 55:9-28. [PMID: 20044926 DOI: 10.1042/ba20090174] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The 'Holy Grail' of recombinant protein production remains the availability of generic protocols and hosts for the production of even the most difficult target products. The present review provides first an explanation why the shock imposed on bacteria using a standard induction protocol not only arrests growth, but also decreases the number of colony-forming units by several orders of magnitude. Particular emphasis is placed on findings of numerous genome-wide transcriptomic studies that highlight cellular stress, in which the general stress, heat-shock and stringent responses are the underlying basis for the manifestation of the deterioration of cell physiology. We then review common approaches used to solve bottlenecks in protein folding and post-translational modification that result in recombinant protein deposition in cytoplasmic inclusion bodies. Finally, we suggest a generic approach to process design that minimizes stress on the production host and a strategy for isolating improved hosts.
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Huber R, Ritter D, Hering T, Hillmer AK, Kensy F, Müller C, Wang L, Büchs J. Robo-Lector - a novel platform for automated high-throughput cultivations in microtiter plates with high information content. Microb Cell Fact 2009; 8:42. [PMID: 19646274 PMCID: PMC2731075 DOI: 10.1186/1475-2859-8-42] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 08/01/2009] [Indexed: 11/25/2022] Open
Abstract
Background In industry and academic research, there is an increasing demand for flexible automated microfermentation platforms with advanced sensing technology. However, up to now, conventional platforms cannot generate continuous data in high-throughput cultivations, in particular for monitoring biomass and fluorescent proteins. Furthermore, microfermentation platforms are needed that can easily combine cost-effective, disposable microbioreactors with downstream processing and analytical assays. Results To meet this demand, a novel automated microfermentation platform consisting of a BioLector and a liquid-handling robot (Robo-Lector) was sucessfully built and tested. The BioLector provides a cultivation system that is able to permanently monitor microbial growth and the fluorescence of reporter proteins under defined conditions in microtiter plates. Three examplary methods were programed on the Robo-Lector platform to study in detail high-throughput cultivation processes and especially recombinant protein expression. The host/vector system E. coli BL21(DE3) pRhotHi-2-EcFbFP, expressing the fluorescence protein EcFbFP, was hereby investigated. With the method 'induction profiling' it was possible to conduct 96 different induction experiments (varying inducer concentrations from 0 to 1.5 mM IPTG at 8 different induction times) simultaneously in an automated way. The method 'biomass-specific induction' allowed to automatically induce cultures with different growth kinetics in a microtiter plate at the same biomass concentration, which resulted in a relative standard deviation of the EcFbFP production of only ± 7%. The third method 'biomass-specific replication' enabled to generate equal initial biomass concentrations in main cultures from precultures with different growth kinetics. This was realized by automatically transferring an appropiate inoculum volume from the different preculture microtiter wells to respective wells of the main culture plate, where subsequently similar growth kinetics could be obtained. Conclusion The Robo-Lector generates extensive kinetic data in high-throughput cultivations, particularly for biomass and fluorescence protein formation. Based on the non-invasive on-line-monitoring signals, actions of the liquid-handling robot can easily be triggered. This interaction between the robot and the BioLector (Robo-Lector) combines high-content data generation with systematic high-throughput experimentation in an automated fashion, offering new possibilities to study biological production systems. The presented platform uses a standard liquid-handling workstation with widespread automation possibilities. Thus, high-throughput cultivations can now be combined with small-scale downstream processing techniques and analytical assays. Ultimately, this novel versatile platform can accelerate and intensify research and development in the field of systems biology as well as modelling and bioprocess optimization.
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Affiliation(s)
- Robert Huber
- AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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Graf A, Dragosits M, Gasser B, Mattanovich D. Yeast systems biotechnology for the production of heterologous proteins. FEMS Yeast Res 2009; 9:335-48. [DOI: 10.1111/j.1567-1364.2009.00507.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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