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Huang SJ, Lai MJ, Chen AY, Lan EI. De novo biosynthesis of 3-hydroxy-3-methylbutyrate as anti-catabolic supplement by metabolically engineered Escherichia coli. Metab Eng 2024; 84:48-58. [PMID: 38810867 DOI: 10.1016/j.ymben.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/27/2024] [Accepted: 05/27/2024] [Indexed: 05/31/2024]
Abstract
3-Hydroxy-3-methylbutyrate (HMB) is a five-carbon branch-chain hydroxy acid currently used as a dietary supplement to treat sarcopenia and exercise training. However, its current production relies on conventional chemical processes which require toxic substances and are generally non-sustainable. While bio-based syntheses of HMB have been developed, they are dependent on biotransformation of its direct precursors which are generally costly. Therefore, in this work, we developed a synthetic de novo HMB biosynthetic pathway that enables HMB production from renewable resources. This novel HMB biosynthesis employs heterologous enzymes from mevalonate pathway and myxobacterial iso-fatty acid pathway for converting acetyl-CoA to HMB-CoA. Subsequently, HMB-CoA is hydrolyzed by a thioesterase to yield HMB. Upon expression of this pathway, our initial Escherichia coli strain produced 660 mg/L of HMB from glucose in 48 hours. Through optimization of coenzyme A removal from HMB-CoA and genetic operon structure, our final strain achieved HMB production titer of 17.7 g/L in glucose minimal media using a bench-top bioreactor. This engineered strain was further demonstrated to produce HMB from other renewable carbon sources such as xylose, glycerol, and acetate. The results from this work provided a flexible and environmentally benign method for producing HMB.
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Affiliation(s)
- Sally J Huang
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu City, 300, Taiwan.
| | - Martin J Lai
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu City, 300, Taiwan.
| | - Arvin Y Chen
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu City, 300, Taiwan.
| | - Ethan I Lan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu City, 300, Taiwan.
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Ferreira S, Balola A, Sveshnikova A, Hatzimanikatis V, Vilaça P, Maia P, Carreira R, Stoney R, Carbonell P, Souza CS, Correia J, Lousa D, Soares CM, Rocha I. Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli. Front Bioeng Biotechnol 2024; 12:1360740. [PMID: 38978715 PMCID: PMC11228882 DOI: 10.3389/fbioe.2024.1360740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
Developing efficient bioprocesses requires selecting the best biosynthetic pathways, which can be challenging and time-consuming due to the vast amount of data available in databases and literature. The extension of the shikimate pathway for the biosynthesis of commercially attractive molecules often involves promiscuous enzymes or lacks well-established routes. To address these challenges, we developed a computational workflow integrating enumeration/retrosynthesis algorithms, a toolbox for pathway analysis, enzyme selection tools, and a gene discovery pipeline, supported by manual curation and literature review. Our focus has been on implementing biosynthetic pathways for tyrosine-derived compounds, specifically L-3,4-dihydroxyphenylalanine (L-DOPA) and dopamine, with significant applications in health and nutrition. We selected one pathway to produce L-DOPA and two different pathways for dopamine-one already described in the literature and a novel pathway. Our goal was either to identify the most suitable gene candidates for expression in Escherichia coli for the known pathways or to discover innovative pathways. Although not all implemented pathways resulted in the accumulation of target compounds, in our shake-flask experiments we achieved a maximum L-DOPA titer of 0.71 g/L and dopamine titers of 0.29 and 0.21 g/L for known and novel pathways, respectively. In the case of L-DOPA, we utilized, for the first time, a mutant version of tyrosinase from Ralstonia solanacearum. Production of dopamine via the known biosynthesis route was accomplished by coupling the L-DOPA pathway with the expression of DOPA decarboxylase from Pseudomonas putida, resulting in a unique biosynthetic pathway never reported in literature before. In the context of the novel pathway, dopamine was produced using tyramine as the intermediate compound. To achieve this, tyrosine was initially converted into tyramine by expressing TDC from Levilactobacillus brevis, which, in turn, was converted into dopamine through the action of the enzyme encoded by ppoMP from Mucuna pruriens. This marks the first time that an alternative biosynthetic pathway for dopamine has been validated in microbes. These findings underscore the effectiveness of our computational workflow in facilitating pathway enumeration and selection, offering the potential to uncover novel biosynthetic routes, thus paving the way for other target compounds of biotechnological interest.
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Affiliation(s)
- Sofia Ferreira
- Systems and Synthetic Biology Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Alexandra Balola
- Systems and Synthetic Biology Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Anastasia Sveshnikova
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paulo Vilaça
- SilicoLife-Computational Biology Solutions for the Life Sciences, Braga, Portugal
| | - Paulo Maia
- SilicoLife-Computational Biology Solutions for the Life Sciences, Braga, Portugal
| | - Rafael Carreira
- SilicoLife-Computational Biology Solutions for the Life Sciences, Braga, Portugal
| | - Ruth Stoney
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
- Institute for Integrative Systems Biology I2SysBio, Universitat de València-CSIC: Consejo Superior de Investigaciones Científicas, Paterna, Spain
| | - Caio Silva Souza
- Protein Modelling Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - João Correia
- Protein Modelling Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Diana Lousa
- Protein Modelling Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Cláudio M Soares
- Protein Modelling Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Isabel Rocha
- Systems and Synthetic Biology Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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Gibisch M, Müller M, Tauer C, Albrecht B, Hahn R, Cserjan-Puschmann M, Striedner G. A production platform for disulfide-bonded peptides in the periplasm of Escherichia coli. Microb Cell Fact 2024; 23:166. [PMID: 38840157 PMCID: PMC11155123 DOI: 10.1186/s12934-024-02446-6] [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: 04/03/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Recombinant peptide production in Escherichia coli provides a sustainable alternative to environmentally harmful and size-limited chemical synthesis. However, in-vivo production of disulfide-bonded peptides at high yields remains challenging, due to degradation by host proteases/peptidases and the necessity of translocation into the periplasmic space for disulfide bond formation. RESULTS In this study, we established an expression system for efficient and soluble production of disulfide-bonded peptides in the periplasm of E. coli. We chose model peptides with varying complexity (size, structure, number of disulfide bonds), namely parathyroid hormone 1-84, somatostatin 1-28, plectasin, and bovine pancreatic trypsin inhibitor (aprotinin). All peptides were expressed without and with the N-terminal, low molecular weight CASPON™ tag (4.1 kDa), with the expression cassette being integrated into the host genome. During BioLector™ cultivations at microliter scale, we found that most of our model peptides can only be sufficiently expressed in combination with the CASPON™ tag, otherwise expression was only weak or undetectable on SDS-PAGE. Undesired degradation by host proteases/peptidases was evident even with the CASPON™ tag. Therefore, we investigated whether degradation happened before or after translocation by expressing the peptides in combination with either a co- or post-translational signal sequence. Our results suggest that degradation predominantly happened after the translocation, as degradation fragments appeared to be identical independent of the signal sequence, and expression was not enhanced with the co-translational signal sequence. Lastly, we expressed all CASPON™-tagged peptides in two industry-relevant host strains during C-limited fed-batch cultivations in bioreactors. We found that the process performance was highly dependent on the peptide-host-combination. The titers that were reached varied between 0.6-2.6 g L-1, and exceeded previously published data in E. coli. Moreover, all peptides were shown by mass spectrometry to be expressed to completion, including full formation of disulfide bonds. CONCLUSION In this work, we demonstrated the potential of the CASPON™ technology as a highly efficient platform for the production of soluble peptides in the periplasm of E. coli. The titers we show here are unprecedented whenever parathyroid hormone, somatostatin, plectasin or bovine pancreatic trypsin inhibitor were produced in E. coli, thus making our proposed upstream platform favorable over previously published approaches and chemical synthesis.
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Affiliation(s)
- Martin Gibisch
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Matthias Müller
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Bernd Albrecht
- Boehringer-Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
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Free TJ, Talley JP, Hyer CD, Miller CJ, Griffitts JS, Bundy BC. Engineering the Signal Resolution of a Paper-Based Cell-Free Glutamine Biosensor with Genetic Engineering, Metabolic Engineering, and Process Optimization. SENSORS (BASEL, SWITZERLAND) 2024; 24:3073. [PMID: 38793927 PMCID: PMC11124800 DOI: 10.3390/s24103073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Specialized cancer treatments have the potential to exploit glutamine dependence to increase patient survival rates. Glutamine diagnostics capable of tracking a patient's response to treatment would enable a personalized treatment dosage to optimize the tradeoff between treatment success and dangerous side effects. Current clinical glutamine testing requires sophisticated and expensive lab-based tests, which are not broadly available on a frequent, individualized basis. To address the need for a low-cost, portable glutamine diagnostic, this work engineers a cell-free glutamine biosensor to overcome assay background and signal-to-noise limitations evident in previously reported studies. The findings from this work culminate in the development of a shelf-stable, paper-based, colorimetric glutamine test with a high signal strength and a high signal-to-background ratio for dramatically improved signal resolution. While the engineered glutamine test is important progress towards improving the management of cancer and other health conditions, this work also expands the assay development field of the promising cell-free biosensing platform, which can facilitate the low-cost detection of a broad variety of target molecules with high clinical value.
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Affiliation(s)
- Tyler J. Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Joseph P. Talley
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Chad D. Hyer
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Catherine J. Miller
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
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Matsuyama C, Seike T, Okahashi N, Niide T, Hara KY, Hirono-Hara Y, Ishii J, Shimizu H, Toya Y, Matsuda F. Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin. J Biosci Bioeng 2024; 137:187-194. [PMID: 38281859 DOI: 10.1016/j.jbiosc.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/18/2023] [Accepted: 12/04/2023] [Indexed: 01/30/2024]
Abstract
Overexpression of proteins by introducing a DNA vector is among the most important tools for the metabolic engineering of microorganisms such as Escherichia coli. Protein overexpression imposes a burden on metabolism because metabolic pathways must supply building blocks for protein and DNA synthesis. Different E. coli strains have distinct metabolic capacities. In this study, two proteins were overexpressed in four E. coli strains (MG1655(DE3), W3110(DE3), BL21star(DE3), and Rosetta(DE3)), and their effects on metabolic burden were investigated. Metabolomic analysis showed that E. coli strains overexpressing green fluorescent protein had decreased levels of several metabolites, with a positive correlation between the number of reduced metabolites and green fluorescent protein expression levels. Moreover, nucleic acid-related metabolites decreased, indicating a metabolic burden in the E. coli strains, and the growth rate and protein expression levels were improved by supplementation with the five nucleosides. In contrast, two strains overexpressing delta rhodopsin, a microbial membrane rhodopsin from Haloterrigena turkmenica, led to a metabolic burden and decrease in the amino acids Ala, Val, Leu, Ile, Thr, Phe, Asp, and Trp, which are the most frequent amino acids in the delta rhodopsin protein sequence. The metabolic burden caused by protein overexpression was influenced by the metabolic capacity of the host strains and the sequences of the overexpressed proteins. Detailed characterization of the effects of protein expression on the metabolic state of engineered cells using metabolomics will provide insights into improving the production of target compounds.
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Affiliation(s)
- Chinatsu Matsuyama
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Taisuke Seike
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Nobuyuki Okahashi
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan
| | - Teppei Niide
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | | | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Shimizu
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Yoshihiro Toya
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Fumio Matsuda
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan.
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Kaplan NA, Islam KN, Kanis FC, Verderber JR, Wang X, Jones JA, Koffas MAG. Simultaneous glucose and xylose utilization by an Escherichia coli catabolite repression mutant. Appl Environ Microbiol 2024; 90:e0216923. [PMID: 38289128 PMCID: PMC10880614 DOI: 10.1128/aem.02169-23] [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: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 02/22/2024] Open
Abstract
As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including Escherichia coli, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation of the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutant of the gene encoding the cyclic AMP receptor protein, crp*, has been shown to disable CCR and improve the co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site-specific crp* chromosomal mutant in E. coli BL21 star (DE3). The crp* mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomics further showed that glucose was routed to the C5 carbon utilization pathways to support both de novo nucleotide synthesis and energy production in the crp* mutant strain. Metabolite analyses further show that overflow metabolism contributes to the slower growth in the crp* mutant. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.IMPORTANCEAs the need for renewable biofuel and biochemical production processes continues to grow, there is an associated need for microbial technology capable of utilizing cheap, widely available, and renewable carbon substrates. This work details the construction and characterization of the first B-lineage Escherichia coli strain with mutated cyclic AMP receptor protein, Crp*, which deregulates the carbon catabolite repression (CCR) system and enables the co-utilization of multiple sugar sources in the growth medium. In this study, we focus our analysis on glucose and xylose utilization as these two sugars are the primary components in lignocellulosic biomass hydrolysate, a promising renewable carbon feedstock for industrial bioprocesses. This strain is valuable to the field as it enables the use of mixed sugar sources in traditional fed-batch based approaches, whereas the wild-type carbon catabolite repression system leads to biphasic growth and possible buildup of non-preferential sugars, reducing process efficiency at scale.
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Affiliation(s)
- Nicholas A. Kaplan
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Khondokar Nowshin Islam
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Fiona C. Kanis
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Jack R. Verderber
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Xin Wang
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - J. Andrew Jones
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Mattheos A. G. Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
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Vazulka S, Schiavinato M, Tauer C, Wagenknecht M, Cserjan-Puschmann M, Striedner G. RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling. Microb Cell Fact 2024; 23:14. [PMID: 38183013 PMCID: PMC10768439 DOI: 10.1186/s12934-023-02278-w] [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: 10/12/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Escherichia coli is a cost-effective expression system for production of antibody fragments like Fabs. Various yield improvement strategies have been applied, however, Fabs remain challenging to produce. This study aimed to characterize the gene expression response of commonly used E. coli strains BL21(DE3) and HMS174(DE3) to periplasmic Fab expression using RNA sequencing (RNA-seq). Two Fabs, Fabx and FTN2, fused to a post-translational translocation signal sequence, were produced in carbon-limited fed-batch cultivations. RESULTS Production of Fabx impeded cell growth substantially stronger than FTN2 and yields of both Fabs differed considerably. The most noticeable, common changes in Fab-producing cells suggested by our RNA-seq data concern the cell envelope. The Cpx and Psp stress responses, both connected to inner membrane integrity, were activated, presumably by recombinant protein aggregation and impairment of the Sec translocon. The data additionally suggest changes in lipopolysaccharide synthesis, adjustment of membrane permeability, and peptidoglycan maturation and remodeling. Moreover, all Fab-producing strains showed depletion of Mg2+, indicated by activation of the PhoQP two-component signal transduction system during the early stage and sulfur and phosphate starvation during the later stage of the process. Furthermore, our data revealed ribosome stalling, caused by the Fabx amino acid sequence, as a contributor to low Fabx yields. Increased Fabx yields were obtained by a site-specific amino acid exchange replacing the stalling sequence. Contrary to expectations, cell growth was not impacted by presence or removal of the stalling sequence. Considering ribosome rescue is a conserved mechanism, the substantial differences observed in gene expression between BL21(DE3) and HMS174(DE3) in response to ribosome stalling on the recombinant mRNA were surprising. CONCLUSIONS Through characterization of the gene expression response to Fab production under industrially relevant cultivation conditions, we identified potential cell engineering targets. Thereby, we hope to enable rational approaches to improve cell fitness and Fab yields. Furthermore, we highlight ribosome stalling caused by the amino acid sequence of the recombinant protein as a possible challenge during recombinant protein production.
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Affiliation(s)
- Sophie Vazulka
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Matteo Schiavinato
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Martin Wagenknecht
- Boehringer Ingelheim RCV, GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1120, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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Xu L, Liaqat F, Sun J, Khazi MI, Xie R, Zhu D. Advances in the vanillin synthesis and biotransformation: A review. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2024; 189:113905. [DOI: 10.1016/j.rser.2023.113905] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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9
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Voinova VV, Zhuikov VA, Zhuikova YV, Sorokina AA, Makhina TK, Bonartseva GA, Parshina EY, Hossain MA, Shaitan KV, Pryadko AS, Chernozem RV, Mukhortova YR, Shlapakova LE, Surmenev RA, Surmeneva MA, Bonartsev AP. Adhesion of Escherichia coli and Lactobacillus fermentum to Films and Electrospun Fibrous Scaffolds from Composites of Poly(3-hydroxybutyrate) with Magnetic Nanoparticles in a Low-Frequency Magnetic Field. Int J Mol Sci 2023; 25:208. [PMID: 38203380 PMCID: PMC10778586 DOI: 10.3390/ijms25010208] [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: 11/01/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The ability of materials to adhere bacteria on their surface is one of the most important aspects of their development and application in bioengineering. In this work, the effect of the properties of films and electrospun scaffolds made of composite materials based on biosynthetic poly(3-hydroxybutyrate) (PHB) with the addition of magnetite nanoparticles (MNP) and their complex with graphene oxide (MNP/GO) on the adhesion of E. coli and L. fermentum under the influence of a low-frequency magnetic field and without it was investigated. The physicochemical properties (crystallinity; surface hydrophilicity) of the materials were investigated by X-ray structural analysis, differential scanning calorimetry and "drop deposition" methods, and their surface topography was studied by scanning electron and atomic force microscopy. Crystal violet staining made it possible to reveal differences in the surface charge value and to study the adhesion of bacteria to it. It was shown that the differences in physicochemical properties of materials and the manifestation of magnetoactive properties of materials have a multidirectional effect on the adhesion of model microorganisms. Compared to pure PHB, the adhesion of E. coli to PHB-MNP/GO, and for L. fermentum to both composite materials, was higher. In the magnetic field, the adhesion of E. coli increased markedly compared to PHB-MNP/GO, whereas the effect on the adhesion of L. fermentum was reversed and was only evident in samples with PHB-MNP. Thus, the resultant factors enhancing and impairing the substrate binding of Gram-negative E. coli and Gram-positive L. fermentum turned out to be multidirectional, as they probably have different sensitivity to them. The results obtained will allow for the development of materials with externally controlled adhesion of bacteria to them for biotechnology and medicine.
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Affiliation(s)
- Vera V. Voinova
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Vsevolod A. Zhuikov
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (V.A.Z.); (Y.V.Z.); (T.K.M.); (G.A.B.)
| | - Yulia V. Zhuikova
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (V.A.Z.); (Y.V.Z.); (T.K.M.); (G.A.B.)
| | - Anastasia A. Sorokina
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Tatiana K. Makhina
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (V.A.Z.); (Y.V.Z.); (T.K.M.); (G.A.B.)
| | - Garina A. Bonartseva
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (V.A.Z.); (Y.V.Z.); (T.K.M.); (G.A.B.)
| | - Evgeniia Yu. Parshina
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Muhammad Asif Hossain
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Artyom S. Pryadko
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
| | - Roman V. Chernozem
- International Research and Development Center “Piezo- and Magnetoelectric Materials”, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia;
| | - Yulia R. Mukhortova
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
- International Research and Development Center “Piezo- and Magnetoelectric Materials”, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia;
| | - Lada E. Shlapakova
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
| | - Roman A. Surmenev
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
- International Research and Development Center “Piezo- and Magnetoelectric Materials”, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia;
| | - Maria A. Surmeneva
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
- International Research and Development Center “Piezo- and Magnetoelectric Materials”, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia;
| | - Anton P. Bonartsev
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
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10
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Li J, Li P, Liu Q, Li J, Qi H. Translation initiation consistency between in vivo and in vitro bacterial protein expression systems. Front Bioeng Biotechnol 2023; 11:1201580. [PMID: 37304134 PMCID: PMC10248181 DOI: 10.3389/fbioe.2023.1201580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/17/2023] [Indexed: 06/13/2023] Open
Abstract
Strict on-demand control of protein synthesis is a crucial aspect of synthetic biology. The 5'-terminal untranslated region (5'-UTR) is an essential bacterial genetic element that can be designed for the regulation of translation initiation. However, there is insufficient systematical data on the consistency of 5'-UTR function among various bacterial cells and in vitro protein synthesis systems, which is crucial for the standardization and modularization of genetic elements in synthetic biology. Here, more than 400 expression cassettes comprising the GFP gene under the regulation of various 5'-UTRs were systematically characterized to evaluate the protein translation consistency in the two popular Escherichia coli strains of JM109 and BL21, as well as an in vitro protein expression system based on cell lysate. In contrast to the very strong correlation between the two cellular systems, the consistency between in vivo and in vitro protein translation was lost, whereby both in vivo and in vitro translation evidently deviated from the estimation of the standard statistical thermodynamic model. Finally, we found that the absence of nucleotide C and complex secondary structure in the 5'-UTR significantly improve the efficiency of protein translation, both in vitro and in vivo.
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Affiliation(s)
- Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Peixian Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Qian Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jinjin Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing, China
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11
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Arauzo-Aguilera K, Buscajoni L, Koch K, Thompson G, Robinson C, Berkemeyer M. Yields and product comparison between Escherichia coli BL21 and W3110 in industrially relevant conditions: anti-c-Met scFv as a case study. Microb Cell Fact 2023; 22:104. [PMID: 37208750 PMCID: PMC10197847 DOI: 10.1186/s12934-023-02111-4] [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: 01/17/2023] [Accepted: 05/01/2023] [Indexed: 05/21/2023] Open
Abstract
INTRODUCTION In the biopharmaceutical industry, Escherichia coli is one of the preferred expression hosts for large-scale production of therapeutic proteins. Although increasing the product yield is important, product quality is a major factor in this industry because greatest productivity does not always correspond with the highest quality of the produced protein. While some post-translational modifications, such as disulphide bonds, are required to achieve the biologically active conformation, others may have a negative impact on the product's activity, effectiveness, and/or safety. Therefore, they are classified as product associated impurities, and they represent a crucial quality parameter for regulatory authorities. RESULTS In this study, fermentation conditions of two widely employed industrial E. coli strains, BL21 and W3110 are compared for recombinant protein production of a single-chain variable fragment (scFv) in an industrial setting. We found that the BL21 strain produces more soluble scFv than the W3110 strain, even though W3110 produces more recombinant protein in total. A quality assessment on the scFv recovered from the supernatant was then performed. Unexpectedly, even when our scFv is correctly disulphide bonded and cleaved from its signal peptide in both strains, the protein shows charge heterogeneity with up to seven distinguishable variants on cation exchange chromatography. Biophysical characterization confirmed the presence of altered conformations of the two main charged variants. CONCLUSIONS The findings indicated that BL21 is more productive for this specific scFv than W3110. When assessing product quality, a distinctive profile of the protein was found which was independent of the E. coli strain. This suggests that alterations are present in the recovered product although the exact nature of them could not be determined. This similarity between the two strains' generated products also serves as a sign of their interchangeability. This study encourages the development of innovative, fast, and inexpensive techniques for the detection of heterogeneity while also provoking a debate about whether intact mass spectrometry-based analysis of the protein of interest is sufficient to detect heterogeneity in a product.
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Affiliation(s)
| | - Luisa Buscajoni
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Karin Koch
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Gary Thompson
- Wellcome Trust Biological NMR Facility, School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Colin Robinson
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Matthias Berkemeyer
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
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12
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Saif NA, Hashem YA, Amin HM, Aziz RK. In Silico and In Vitro Investigation of the Distribution and Expression of Key Genes in the Fucose Operon of Escherichia coli. Microorganisms 2023; 11:1265. [PMID: 37317239 DOI: 10.3390/microorganisms11051265] [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: 02/22/2023] [Revised: 04/02/2023] [Accepted: 04/22/2023] [Indexed: 06/16/2023] Open
Abstract
Many gut bacteria degrade polysaccharides, providing nutritional advantages to their hosts. Fucose, a mucin degradation product, was suggested as a communication molecule between the resident microbiota and external pathogens. However, the precise role and variants of the fucose utilization pathway remain to be elucidated. Here, we computationally and experimentally investigated the fucose utilization operon of E. coli. While the operon is conserved among E. coli genomes, a variant pathway, in which an ABC transporter system replaces the fucose permease gene (fucP), was computationally identified in 50 out of 1058 genomes. Comparative genomics and subsystems analysis results were confirmed by polymerase chain reaction-based screening of 40 human E. coli isolates, which indicated the conservation of fucP in 92.5% of the isolates (vs. 7.5% of its suggested alternative, yjfF). The in silico predictions were confirmed by in vitro experiments comparing the growth of E. coli strains K12, BL21, and isogenic fucose-utilization K12 mutants. Additionally, fucP and fucI transcripts were quantified in E. coli K12 and BL21, after in silico analysis of their expression in 483 public transcriptomes. In conclusion, E. coli utilizes fucose by two pathway variants, with measurable transcriptional differences. Future studies will explore this variation's impact on signaling and virulence.
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Affiliation(s)
- Nehal A Saif
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt
| | - Yomna A Hashem
- Department of Microbiology, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt
| | - Heba M Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Center for Genome and Microbiome Research, Cairo University, Cairo 11562, Egypt
- Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt 57357, Cairo 11617, Egypt
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13
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Sri Wahyu Effendi S, Lin JY, Ng IS. Simultaneous carbon dioxide sequestration and utilization for cadaverine production using dual promoters in engineered Escherichia coli strains. BIORESOURCE TECHNOLOGY 2022; 363:127980. [PMID: 36137445 DOI: 10.1016/j.biortech.2022.127980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Human carbonic anhydrase II (hCAII) is a rapid-acting zinc-metalloenzyme that catalyzes CO2 hydration reversibly, with encouraging applications in carbon capture, sequestration, and utilization (CCSU). However, biocatalyst durability is a major challenge. Herein, hCAII is emphasized in 4 different Escherichia coli strains and designated under dual promoters from sigma factor 70 (σ70) and heat shock protein (HSP70A) to suppress the usage of inducer and stimulate activity in heat environments. As a result, hCAII under high-efficient dual promoters regulation retained high residual activity in CO2 biomineralization of 68.8 % after 4 cycles at 40 °C. Moreover, co-expression of CAC9 with lysine decarboxylase (CadA) simultaneously sequestered CO2 release up to 95.7 % and increased cadaverine titer from 18.0 to 36.7 g/L by using E. coli MG1655. The remnant biomass from cadaverine synthesis sustained converting CO2 to 57.9 mg-CaCO3. Thus, the dual promoters design demonstrated the promising potential for CCSU through simultaneous CO2 utilization and cadaverine synthesis.
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Affiliation(s)
| | - Jia-Yi Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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14
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Chaos in synthetic microbial communities. PLoS Comput Biol 2022; 18:e1010548. [PMID: 36215322 PMCID: PMC9584520 DOI: 10.1371/journal.pcbi.1010548] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/20/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022] Open
Abstract
Predictability is a fundamental requirement in biological engineering. As we move to building coordinated multicellular systems, the potential for such systems to display chaotic behaviour becomes a concern. Therefore understanding which systems show chaos is an important design consideration. We developed a methodology to explore the potential for chaotic dynamics in small microbial communities governed by resource competition, intercellular communication and competitive bacteriocin interactions. Our model selection pipeline uses Approximate Bayesian Computation to first identify oscillatory behaviours as a route to finding chaotic behaviour. We have shown that we can expect to find chaotic states in relatively small synthetic microbial systems, understand the governing dynamics and provide insights into how to control such systems. This work is the first to query the existence of chaotic behaviour in synthetic microbial communities and has important ramifications for the fields of biotechnology, bioprocessing and synthetic biology.
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15
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Mayer F, Cserjan-Puschmann M, Haslinger B, Shpylovyi A, Dalik T, Sam C, Hahn R, Striedner G. Strain specific properties of Escherichia coli can prevent non-canonical amino acid misincorporation caused by scale-related process heterogeneities. Microb Cell Fact 2022; 21:170. [PMID: 35999607 PMCID: PMC9396823 DOI: 10.1186/s12934-022-01895-1] [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: 06/10/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Escherichia coli is one of the most important hosts for production of recombinant proteins in biopharmaceutical industry. However, when selecting a suitable production strain, it is often not considered that a lot of different sub-species exist, which can differ in their genotypes and phenotypes. Another important development step is the scale-up of bioprocesses with the particular challenge that heterogeneities and gradients occur at production scale. These in turn can affect the production organism and can have negative impact on the process and the product quality. Therefore, researchers developed scale-down reactors, which are used to mimic manufacturing conditions in laboratory scale. The main objectives of this study were to determine the extent to which scale-related process inhomogeneities affect the misincorporation of non-canonical amino acids into the recombinant target protein, which is an important quality attribute, and whether strain specific properties may have an impact. Results We investigated two industrially relevant E. coli strains, BL21(DE3) and HMS174(DE3), which produced an antigen binding fragment (Fab). The cells were cultivated in high cell density fed-batch mode at laboratory scale and under scale-down conditions. We demonstrated that the two host strains differ significantly with respect to norleucine misincorporation into the target protein, especially under heterogeneous cultivation conditions in the scale-down reactor. No norleucine misincorporation was observed in E. coli BL21(DE3) for either cultivation condition. In contrast, norleucine incorporation into HMS174(DE3) was already detectable in the reference process and increased dramatically in scale-down experiments. Norleucine incorporation was not random and certain positions were preferred over others, even though only a single codon exists. Differences in biomass and Fab production between the strains during scale-down cultivations could be observed as well. Conclusions This study has shown that E. coli BL21(DE3) is much more robust to scale-up effects in terms of norleucine misincorporation than the K12 strain tested. In this respect, BL21(DE3) enables better transferability of results at different scales, simplifies process implementation at production scale, and helps to meet regulatory quality guidelines defined for biopharmaceutical manufacturing. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01895-1.
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Affiliation(s)
- Florian Mayer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Benedikt Haslinger
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Anton Shpylovyi
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Thomas Dalik
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Christian Sam
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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16
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Rajagopal S, Hmar RV, Mookherjee D, Ghatak A, Shanbhag AP, Katagihallimath N, Venkatraman J, Ks R, Datta S. Validated In Silico Population Model of Escherichia coli. ACS Synth Biol 2022; 11:2672-2684. [PMID: 35801944 DOI: 10.1021/acssynbio.2c00097] [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: 11/28/2022]
Abstract
Flux balance analysis (FBA) and ordinary differential equation models have been instrumental in depicting the metabolic functioning of a cell. Nevertheless, they demonstrate a population's average behavior (summation of individuals), thereby portraying homogeneity. However, living organisms such as Escherichia coli contain more biochemical reactions than engaging metabolites, making them an underdetermined and degenerate system. This results in a heterogeneous population with varying metabolic patterns. We have formulated a population systems biology model that predicts this degeneracy by emulating a diverse metabolic makeup with unique biochemical signatures. The model mimics the universally accepted experimental view that a subpopulation of bacteria, even under normal growth conditions, renders a unique biochemical state, leading to the synthesis of metabolites and persister progenitors of antibiotic resistance and biofilms. We validate the platform's predictions by producing commercially important heterologous (isobutanol) and homologous (shikimate) metabolites. The predicted fluxes are tested in vitro resulting in 32- and 42-fold increased product of isobutanol and shikimate, respectively. Moreover, we authenticate the platform by mimicking a bacterial population in the presence of glyphosate, a metabolic pathway inhibitor. Here, we observe a fraction of subsisting persisters despite inhibition, thus affirming the signature of a heterogeneous populace. The platform has multiple uses based on the disposition of the user.
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Affiliation(s)
- Sreenath Rajagopal
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India
| | - Rothangmawi Victoria Hmar
- Biomoneta Research Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560092, India
| | - Debdatto Mookherjee
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India
| | - Arindam Ghatak
- Biomoneta Research Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560092, India.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700073, India
| | - Anirudh P Shanbhag
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700073, India
| | - Nainesh Katagihallimath
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India
| | - Janani Venkatraman
- Biomoneta Research Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560092, India
| | - Ramanujan Ks
- Biomoneta Research Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560092, India
| | - Santanu Datta
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India
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17
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Al-Janabi SS, Shawky H, El-Waseif AA, Farrag AA, Abdelghany TM, El-Ghwas DE. Stable, efficient, and cost-effective system for the biosynthesis of recombinant bacterial cellulose in Escherichia coli DH5α platform. J Genet Eng Biotechnol 2022; 20:90. [PMID: 35737166 PMCID: PMC9226222 DOI: 10.1186/s43141-022-00384-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 06/14/2022] [Indexed: 11/23/2022]
Abstract
Background Owing to its remarkable mechanical properties that surpass the plant-based cellulose, bacterial cellulose production has been targeted for commercialization during the last few years. However, the large-scale production of cellulose is generally limited by the slow growth of producing strains and low productivity which ultimately makes the commercial production of cellulose using the conventional strains non cost-effective. In this study, we developed a novel plasmid-based expression system for the biosynthesis of cellulose in E.coli DH5α and assessed the cellulose productivity relative to the typically used E.coli BL21 (DE) expression strain. Results No production was detected in BL21 (DE3) cultures upon expression induction; however, cellulose was detected in E.coli DH5α as early as 1 h post-induction. The total yield in induced DH5α cultures was estimated as 200 ± 5.42 mg/L (dry weight) after 18 h induction, which surpassed the yield reported in previous studies and even the wild-type Gluconacetobacterxylinum BRC5 under the same conditions. As confirmed with electron microscope micrograph, E.coli DH5α produced dense cellulose fibers with ~ 10 μm diameter and 1000–3000 μm length, which were remarkably larger and more crystalline than that typically produced by G.hansenii. Conclusions This is the first report on the successful cellulose production in E.coli DH5α which is typically used for plasmid multiplication rather than protein expression, without the need to co-express cmcax and ccpAx regulator genes present in the wild-type genome upstream the bcs-operon, and reportedly essential for the biosynthesis.
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Affiliation(s)
- Saif S Al-Janabi
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Cairo, Egypt.,Department of Medical Laboratory Techniques, Al-Maarif University College, Al-anbbar, Iraq
| | - Heba Shawky
- Therapeutic Chemistry Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki 12622, Cairo, Egypt.
| | - Amr A El-Waseif
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Cairo, Egypt
| | - Ayman A Farrag
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Cairo, Egypt
| | - Tarek M Abdelghany
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Cairo, Egypt
| | - Dina E El-Ghwas
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
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18
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Richter R, Kamal MAM, Koch M, Niebuur B, Huber A, Goes A, Volz C, Vergalli J, Kraus T, Müller R, Schneider‐Daum N, Fuhrmann G, Pagès J, Lehr C. An Outer Membrane Vesicle-Based Permeation Assay (OMPA) for Assessing Bacterial Bioavailability. Adv Healthc Mater 2022; 11:e2101180. [PMID: 34614289 DOI: 10.1002/adhm.202101180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/14/2021] [Indexed: 11/11/2022]
Abstract
When searching for new antibiotics against Gram-negative bacterial infections, a better understanding of the permeability across the cell envelope and tools to discriminate high from low bacterial bioavailability compounds are urgently needed. Inspired by the phospholipid vesicle-based permeation assay (PVPA), which is designed to predict non-facilitated permeation across phospholipid membranes, outer membrane vesicles (OMVs) of Escherichia coli either enriched or deficient of porins are employed to coat filter supports for predicting drug uptake across the complex cell envelope. OMVs and the obtained in vitro model are structurally and functionally characterized using cryo-TEM, SEM, CLSM, SAXS, and light scattering techniques. In vitro permeability, obtained from the membrane model for a set of nine antibiotics, correlates with reported in bacterio accumulation data and allows to discriminate high from low accumulating antibiotics. In contrast, the correlation of the same data set generated by liposome-based comparator membranes is poor. This better correlation of the OMV-derived membranes points to the importance of hydrophilic membrane components, such as lipopolysaccharides and porins, since those features are lacking in liposomal comparator membranes. This approach can offer in the future a high throughput screening tool with high predictive capacity or can help to identify compound- and bacteria-specific passive uptake pathways.
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Affiliation(s)
- Robert Richter
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
| | - Mohamed A. M. Kamal
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Marcus Koch
- INM – Leibniz Institute for New Materials Campus D2.2 Saarbrücken 66123 Germany
| | - Bart‐Jan Niebuur
- INM – Leibniz Institute for New Materials Campus D2.2 Saarbrücken 66123 Germany
| | - Anna‐Lena Huber
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Adriely Goes
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Carsten Volz
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
| | - Julia Vergalli
- UMR_MD1 U‐1261 Aix‐Marseille Université INSERM IRBA MCT Faculté de Pharmacie 27 Boulevard Jean Moulin Marseille 13005 France
| | - Tobias Kraus
- INM – Leibniz Institute for New Materials Campus D2.2 Saarbrücken 66123 Germany
- Colloid and Interface Chemistry Saarland University Campus D2.2 Saarbrücken 66123 Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Nicole Schneider‐Daum
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
| | - Gregor Fuhrmann
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Jean‐Marie Pagès
- UMR_MD1 U‐1261 Aix‐Marseille Université INSERM IRBA MCT Faculté de Pharmacie 27 Boulevard Jean Moulin Marseille 13005 France
| | - Claus‐Michael Lehr
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
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Developing efficient vanillin biosynthesis system by regulating feruloyl-CoA synthetase and enoyl-CoA hydratase enzymes. Appl Microbiol Biotechnol 2021; 106:247-259. [PMID: 34893929 DOI: 10.1007/s00253-021-11709-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/05/2021] [Accepted: 11/20/2021] [Indexed: 12/31/2022]
Abstract
Vanillin is one of the most commonly used natural-occurring flavors in the world. This study successfully constructed an efficient whole-cell catalytic system for vanillin biosynthesis from ferulic acid by regulating feruloyl-CoA synthetase (FCS) and enoyl-CoA hydratase (ECH). First, we constructed an efficient cell-free catalytic system with FCS-Str (fcs from Streptomyces sp. V-1) and ECH-Str (ech from Streptomyces sp. V-1) combination at 1:1. The efficient cell-free catalytic system provided necessary strategies for optimizing the whole-cell catalytic system. Then, we constructed the recombinant Escherichia coli by heterologously expressing the fcs-Str and ech-Str combination. Moreover, E. coli JM109 was a better recombinant Escherichia coli than E. coli BL21 with higher vanillin production. Finally, we first adjusted the ratio of FCS and ECH in E. coli JM109 to 1:1 using two copies of fcs-Str. For higher vanillin production, we further optimized the induction conditions of E. coli JM109 to increase the amount of FCS and ECH. The optimized E. coli JM109-FE-F constructed in this study has the highest vanillin synthesis rate of converting 20 mM ferulic acid to 15 mM vanillin in 6 h among all of the E. coli catalytic systems. Our study made a significant contribution to the construction of the vanillin biosynthesis system and provided a valuable strategy for increasing vanillin production. KEY POINTS: • The efficient cell-free vanillin biosynthesis system was constructed by FCS-Str and ECH-Str combination at 1:1. • Escherichia coli JM109 was determined as a better recombinant Escherichia coli than E. coli BL21 with higher vanillin production. • Escherichia coli JM109-FE-F with two copies of fcs-Str and one copy of ech-Str has the highest catalytic efficiency for vanillin production.
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Abdollahi S, Morowvat MH, Savardashtaki A, Irajie C, Najafipour S, Ghasemi Y. Evaluating Five Escherichia coli Derivative Strains as a Platform for Arginine Deiminase Overproduction. Recent Pat Biotechnol 2021; 16:174-183. [PMID: 34809551 DOI: 10.2174/1872208315666211122114625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/03/2021] [Accepted: 10/24/2021] [Indexed: 11/22/2022]
Abstract
AIMS This study attempted to evaluate the five host strains, including BL21 (DE3), Rosetta (DE3), DH5α, XL1-BLUE, and SHuffle, in terms of arginine deiminase (ADI) production and enzyme activity. BACKGROUND Escherichia coli is one of the most preferred host microorganisms for the production of recombinant proteins due to its well-characterized genome, availability of various expression vectors, and host strains. Choosing a proper host strain for the overproduction of a desired recombinant protein is very important because of the diversity of genetically modified expression strains. Various E. coli cells have been examined in different patent applications. METHOD ADI was chosen as a bacterial enzyme that degrades L-arginine. It is effective in the treatment of some types of human cancers like melanoma and hepatocellular carcinoma (HCC), which are arginine-auxotrophic. Five mentioned E. coli strains were cultivated. The pET-3a was used as the expression vector. The competent E. coli cells were obtained through the CaCl2 method. It was then transformed with the construct of pET3a-ADI using the heat shock strategy. The ADI production levels were examined by 10% SDS-PAGE analysis. The ability of host strains for the expression of the requested recombinant protein was compared. The enzymatic activity of the obtained recombinant ADI from each studied strain was assessed by a colorimetric 96-well microtiter plate assay. RESULT All the five strains exhibited a significant band at 46 kDa. BL21 (DE3) produced the highest amount of ADI protein, followed by Rosetta (DE3). The following activity assay showed that ADI from BL21 (DE3) and Rosetta (DE3) had the most activity. CONCLUSION There are some genetic and metabolic differences among the various E. coli strains, leading to differences in the amount of recombinant protein production. The results of this study can be used for the efficacy evaluation of the five studied strains for the production of similar pharmaceutical enzymes. The strains also could be analyzed in terms of proteomics.
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Affiliation(s)
- Sara Abdollahi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz. Iran
| | - Mohammad Hossein Morowvat
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz. Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz. Iran
| | - Cambyz Irajie
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz. Iran
| | - Sohrab Najafipour
- Department of Microbiology, School of Medicine, Fasa University of Medical Sciences, P.O. Box 74616-86688, Fasa. Iran
| | - Younes Ghasemi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz. Iran
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Zhan J, Tan X, Wang X. Null mutation in sspA of Cronobacter sakazakii influences its tolerance to environmental stress. Can J Microbiol 2021; 67:902-918. [PMID: 34379995 DOI: 10.1139/cjm-2021-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cronobacter sakazakii is a known foodborne opportunistic pathogen that can affect the intestinal health of infants. Despite undergoing complex manufacturing processes and low water concentration in the finished product, infant formula has been associated with Cronobacter infections, suggesting that C. sakazakii's pathogenicity may be related to its tolerance to stress. In this study, the effect of the stringent starvation protein A (SspA), which plays an important role in E. coli cellular survival under environmental stresses, on the stress tolerance of C. sakazakii BAA894 was investigated by creating an sspA-knockout mutant. The effects of this mutation on the acid, desiccation and drug tolerance were assessed, and results showed that acid tolerance decreased, while desiccation tolerance increased in LB and decreased in M9. Moreover, the MICs of 10 antibiotics in LB medium and 8 antibiotics in M9 medium were determined and compared of the wild-type and ΔsspA. Transcriptome analysis showed that 27.21% or 37.78% of the genes in ΔsspA were significantly differentially expressed in LB or M9 media, the genes relevant to microbial metabolism in diverse environments and bacterial chemotaxis were detailed analyzed. The current study contributes towards an improved understanding of the role of SspA in C. sakazakii BAA894 stress tolerance.
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Affiliation(s)
- Jie Zhan
- Jiangnan University, 66374, State Key Laboratory of Food Science and Technology, Wuxi, China;
| | - Xin Tan
- Jiangnan University, 66374, Wuxi, China.,Jiangnan University, 66374, Wuxi, China;
| | - Xiaoyuan Wang
- Jiangnan University, 66374, Wuxi, China, 214122.,Jiangnan University, 66374, Wuxi, China, 214122.,Jiangnan University, 66374, Wuxi, China, 214122;
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Method for high-efficiency fed-batch cultures of recombinant Escherichia coli. Methods Enzymol 2021; 659:189-217. [PMID: 34752285 DOI: 10.1016/bs.mie.2021.05.004] [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: 01/04/2023]
Abstract
Fed-batch processes are commonly used in industry to obtain sufficient biomass and associated recombinant protein or plasmids. In research laboratories, it is more common to use batch cultures, as the setup of fed-batch processes can be challenging. This method outlines a robust and reliable means to generate Escherichia coli biomass in a minimum amount of fermentation time using a standardized fed-batch process. Final cell densities can reach over 50g dry cell weight per liter (gdcw/L) depending on the strain. This method uses a predefined exponential feeding strategy and conservative induction protocol to achieve these targets without multiple trial and error studies. If desired, productivity can be optimized by balancing the induction time and feed rates. This method utilizes cost-efficient defined media, minimizes process control complexity, and potentially aids downstream purification.
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Qiao J, Tan X, Ren H, Wu Z, Hu X, Wang X. Construction of an Escherichia coli Strain Lacking Fimbriae by Deleting 64 Genes and Its Application for Efficient Production of Poly(3-Hydroxybutyrate) and l-Threonine. Appl Environ Microbiol 2021; 87:e0038121. [PMID: 33863704 PMCID: PMC8174762 DOI: 10.1128/aem.00381-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/03/2021] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli contains 12 chaperone-usher operons for biosynthesis and assembly of various fimbriae. In this study, each of the 12 operons was deleted in E. coli MG1655, and the resulting 12 deletion mutants all grew better than the wild type, especially in the nutrient-deficient M9 medium. When the plasmid pBHR68 containing the key genes for polyhydroxyalkanoate production was introduced into these 12 mutants, each mutant synthesized more polyhydroxyalkanoate than the wild-type control. These results indicate that the fimbria removal in E. coli benefits cell growth and polyhydroxyalkanoate production. Therefore, all 12 chaperone-usher operons, including 64 genes, were deleted in MG1655, resulting in the fimbria-lacking strain WQM026. WQM026 grew better than MG1655, and no fimbria structures were observed on the surface of WQM026 cells. Transcriptomic analysis showed that in WQM026 cells, the genes related to glucose consumption, glycolysis, flagellar synthesis, and biosynthetic pathways of some key amino acids were upregulated, while the tricarboxylic acid cycle-related genes were downregulated. When pBHR68 was introduced into WQM026, huge amounts of poly-3-hydroxybutyrate were produced; when the plasmid pFW01-thrA*BC-rhtC, containing the key genes for l-threonine biosynthesis and transport, was transferred into WQM026, more l-threonine was synthesized than with the control. These results suggest that this fimbria-lacking E. coli WQM026 is a good host for efficient production of polyhydroxyalkanoate and l-threonine and has the potential to be developed into a valuable chassis microorganism. IMPORTANCE In this study, we investigated the interaction between the biosynthesis and assembly of fimbriae and intracellular metabolic networks in E. coli. We found that eliminating fimbriae could effectively improve the production of polyhydroxyalkanoate and l-threonine in E. coli MG1655. These results contribute to understanding the necessity of fimbriae and the advantages of fimbria removal for industrial microorganisms. The knowledge gathered from this study may be applied to the development of superior chassis microorganisms.
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Affiliation(s)
- Jun Qiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, China
| | - Xin Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, China
| | - Hongyu Ren
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, China
| | - Zheng Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu Province, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu Province, China
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So you want to express your protein in Escherichia coli? Essays Biochem 2021; 65:247-260. [PMID: 33955451 DOI: 10.1042/ebc20200170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Recombinant proteins have been extensively employed as therapeutics for the treatment of various critical and life-threatening diseases and as industrial enzymes in high-value industrial processes. Advances in genetic engineering and synthetic biology have broadened the horizon of heterologous protein production using multiple expression platforms. Selection of a suitable expression system depends on a variety of factors ranging from the physicochemical properties of the target protein to economic considerations. For more than 40 years, Escherichia coli has been an established organism of choice for protein production. This review aims to provide a stepwise approach for any researcher embarking on the journey of recombinant protein production in E. coli. We present an overview of the challenges associated with heterologous protein expression, fundamental considerations connected to the protein of interest (POI) and designing expression constructs, as well as insights into recently developed technologies that have contributed to this ever-growing field.
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Fink M, Schimek C, Cserjan-Puschmann M, Reinisch D, Brocard C, Hahn R, Striedner G. Integrated process development: The key to improve Fab production in E. coli. Biotechnol J 2021; 16:e2000562. [PMID: 33580620 DOI: 10.1002/biot.202000562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 11/09/2022]
Abstract
Bioprocess development and optimization is a challenging, costly, and time-consuming effort. In this multidisciplinary task, upstream processing (USP) and downstream processing (DSP) are conventionally considered distinct disciplines. This consideration fosters "one-way" optimization disregarding interdependencies between unit operations; thus, the full potential of the process chain cannot be achieved. Therefore, it is necessary to fully integrate USP and DSP process development to provide balanced biotechnological production processes. The aim of the present study was to investigate how different host/secretory signal/antigen binding fragment (Fab) combinations in E. coli expression systems influence USP, primary recovery performance and the final product quality. We ran identical fed-batch cultivations with 16 different expression clones to study growth and product formation kinetics, as well as centrifugation efficiency, viscosity, extracellular DNA, and endotoxin content, important parameters in DSP. We observed a severe influence on cell growth, product titer, extracellular product, and cell lysis, accompanied by a significant impact on the analyzed parameters of DSP performance. Our results provide the basis for future research on integrated process development considering interdependencies between USP and DSP; however, individual products need to be considered specifically. These interdependencies need to be understood for rational decision-making and efficient process development in research and industry.
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Affiliation(s)
- Mathias Fink
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Schimek
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | | | - Rainer Hahn
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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García A, Fox JG. A One Health Perspective for Defining and Deciphering Escherichia coli Pathogenic Potential in Multiple Hosts. Comp Med 2021; 71:3-45. [PMID: 33419487 PMCID: PMC7898170 DOI: 10.30802/aalas-cm-20-000054] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/17/2020] [Accepted: 09/19/2020] [Indexed: 11/05/2022]
Abstract
E. coli is one of the most common species of bacteria colonizing humans and animals. The singularity of E. coli 's genus and species underestimates its multifaceted nature, which is represented by different strains, each with different combinations of distinct virulence factors. In fact, several E. coli pathotypes, or hybrid strains, may be associated with both subclinical infection and a range of clinical conditions, including enteric, urinary, and systemic infections. E. coli may also express DNA-damaging toxins that could impact cancer development. This review summarizes the different E. coli pathotypes in the context of their history, hosts, clinical signs, epidemiology, and control. The pathotypic characterization of E. coli in the context of disease in different animals, including humans, provides comparative and One Health perspectives that will guide future clinical and research investigations of E. coli infections.
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Key Words
- aa, aggregative adherence
- a/e, attaching and effacing
- aepec, atypical epec
- afa, afimbrial adhesin
- aida-i, adhesin involved in diffuse adherence
- aiec, adherent invasive e. coli
- apec, avian pathogenic e. coli
- atcc, american type culture collection
- bfp, bundle-forming pilus
- cd, crohn disease
- cdt, cytolethal distending toxin gene
- clb, colibactin
- cnf, cytotoxic necrotizing factor
- cs, coli surface (antigens)
- daec, diffusely adhering e. coli
- db, dutch belted
- eae, e. coli attaching and effacing gene
- eaec, enteroaggregative e. coli
- eaf, epec adherence factor (plasmid)
- eahec, entero-aggregative-hemorrhagic e. coli
- east-1, enteroaggregative e. coli heat-stable enterotoxin
- e. coli, escherichia coli
- ed, edema disease
- ehec, enterohemorrhagic e. coli
- eiec, enteroinvasive e. coli
- epec, enteropathogenic e. coli
- esbl, extended-spectrum β-lactamase
- esp, e. coli secreted protein
- etec, enterotoxigenic e. coli
- expec, extraintestinal pathogenic e. coli
- fyua, yersiniabactin receptor gene
- gi, gastrointestinal
- hly, hemolysin
- hus, hemolytic uremic syndrome
- ibd, inflammatory bowel disease
- la, localized adherence
- lee, locus of enterocyte effacement
- lpf, long polar fimbriae
- lt, heat-labile (enterotoxin)
- mlst, multilocus sequence typing
- ndm, new delhi metallo-β-lactamase
- nzw, new zealand white
- pap, pyelonephritis-associated pilus
- pks, polyketide synthase
- sfa, s fimbrial adhesin
- slt, shiga-like toxin
- st, heat-stable (enterotoxin)
- stec, stx-producing e. coli
- stx, shiga toxin
- tepec, typical epec
- upec, uropathogenic e. coli
- uti, urinary tract infection
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Affiliation(s)
- Alexis García
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts;,
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
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Karkaria BD, Fedorec AJH, Barnes CP. Automated design of synthetic microbial communities. Nat Commun 2021; 12:672. [PMID: 33510148 PMCID: PMC7844305 DOI: 10.1038/s41467-020-20756-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
Microbial species rarely exist in isolation. In naturally occurring microbial systems there is strong evidence for a positive relationship between species diversity and productivity of communities. The pervasiveness of these communities in nature highlights possible advantages for genetically engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigate issues often found in engineering a monoculture, especially as functional complexity increases. Here, we demonstrate a methodology for designing robust synthetic communities that include competition for nutrients, and use quorum sensing to control amensal bacteriocin interactions in a chemostat environment. We computationally explore all two- and three- strain systems, using Bayesian methods to perform model selection, and identify the most robust candidates for producing stable steady state communities. Our findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and further tuning the community composition.
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Affiliation(s)
- Behzad D Karkaria
- Department of Cell & Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Alex J H Fedorec
- Department of Cell & Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Chris P Barnes
- Department of Cell & Developmental Biology, University College London, London, WC1E 6BT, UK.
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
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28
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Separation of truncated basic fibroblast growth factor from the full-length protein by hydrophobic interaction chromatography. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.117564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abstract
The capacity of microbes to resist and overcome environmental insults, known as resilience, allows them to survive in changing environments but also to resist antibiotic and biocide treatments and immune system responses. Although the role of the stringent response in bacterial resilience to nutritional stresses has been well studied, little is known about its importance in the ability of the bacteria to not just resist but also recover from these disturbances. Bacteria grow in constantly changing environments that can suddenly become completely depleted of essential nutrients. The stringent response, a rewiring of the cellular metabolism mediated by the alarmone (p)ppGpp, plays a crucial role in adjusting bacterial growth to the severity of the nutritional stress. The ability of (p)ppGpp to trigger a slowdown of cell growth or induce bacterial dormancy has been widely investigated. However, little is known about the role of (p)ppGpp in promoting growth recovery after severe growth inhibition. In this study, we performed a time-resolved analysis of (p)ppGpp metabolism in Escherichia coli as it recovered from a sudden slowdown in growth. The results show that E. coli recovers by itself from the growth disruption provoked by the addition of serine hydroxamate, the serine analogue that we used to induce the stringent response. Growth inhibition was accompanied by a severe disturbance of metabolic activity and, more surprisingly, a transient overflow of valine and alanine. Our data also show that ppGpp is crucial for growth recovery since in the absence of ppGpp, E. coli’s growth recovery was slower. In contrast, an increased concentration of pppGpp was found to have no significant effect on growth recovery. Interestingly, the observed decrease in intracellular ppGpp levels in the recovery phase correlated with bacterial growth, and the main effect involved in the return to the basal level was identified by flux calculation as growth dilution. This report thus significantly expands our knowledge of (p)ppGpp metabolism in E. coli physiology. IMPORTANCE The capacity of microbes to resist and overcome environmental insults, known as resilience, allows them to survive in changing environments but also to resist antibiotic and biocide treatments and immune system responses. Although the role of the stringent response in bacterial resilience to nutritional stresses has been well studied, little is known about its importance in the ability of the bacteria to not just resist but also recover from these disturbances. To address this important question, we investigated growth disruption resilience in the model bacterium Escherichia coli and its dependence on the stringent response alarmone (p)ppGpp by quantifying ppGpp and pppGpp levels as growth was disrupted and then recovered. Our findings may thus contribute to understanding how ppGpp improves E. coli’s resilience to nutritional stress and other environmental insults.
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Lara AR, Galindo J, Jaén KE, Juárez M, Sigala JC. Physiological Response of Escherichia coli W3110 and BL21 to the Aerobic Expression of Vitreoscilla Hemoglobin. J Microbiol Biotechnol 2020; 30:1592-1596. [PMID: 32699196 PMCID: PMC9728183 DOI: 10.4014/jmb.2004.04030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
The aerobic growth and metabolic performance of Escherichia coli strains BL21 and W3110 were studied when the Vitreoscilla hemoglobin (VHb) was constitutively expressed in the chromosome. When VHb was expressed, acetate production decreased in both strains and was nearly eliminated in BL21. Transcriptional levels of the glyoxylate shunt genes decreased in both strains when VHb was expressed. However, higher transcription of the α-ketoglutarate dehydrogenase genes were observed for W3110, while for BL21 transcription levels decreased. VHb expression reduced the transcription of the cytochrome bo3 genes only in BL21. These results are useful for better selecting a production host.
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Affiliation(s)
- Alvaro R. Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico,Corresponding author Phone: +52-55-58146500 Fax: +52-55-58146500 E-mail:
| | - Janet Galindo
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico
| | - Karim E. Jaén
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico
| | - Mariana Juárez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico
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Wang J, Huang C, Guo K, Ma L, Meng X, Wang N, Huo YX. Converting Escherichia coli MG1655 into a chemical overproducer through inactivating defense system against exogenous DNA. Synth Syst Biotechnol 2020; 5:333-342. [PMID: 33102829 PMCID: PMC7568196 DOI: 10.1016/j.synbio.2020.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 09/30/2020] [Accepted: 10/09/2020] [Indexed: 01/05/2023] Open
Abstract
Escherichia coli strain K-12 MG1655 has been proposed as an appropriate host strain for industrial production. However, the direct application of this strain suffers from the transformation inefficiency and plasmid instability. Herein, we conducted genetic modifications at a serial of loci of MG1655 genome, generating a robust and universal host strain JW128 with higher transformation efficiency and plasmid stability that can be used to efficiently produce desired chemicals after introducing the corresponding synthetic pathways. Using JW128 as the host, the titer of isobutanol reached 5.76 g/L in shake-flask fermentation, and the titer of lycopene reached 1.91 g/L in test-tube fermentation, 40-fold and 5-fold higher than that of original MG1655, respectively. These results demonstrated JW128 is a promising chassis for high-level production of value-added chemicals.
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Affiliation(s)
- Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
- SIP-UCLA Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China
| | - Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Kai Guo
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, China
| | - Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Xiangyu Meng
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
- Corresponding author.
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
- SIP-UCLA Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China
- Corresponding author. Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China.
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Temporal encoding of bacterial identity and traits in growth dynamics. Proc Natl Acad Sci U S A 2020; 117:20202-20210. [PMID: 32747578 DOI: 10.1073/pnas.2008807117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In biology, it is often critical to determine the identity of an organism and phenotypic traits of interest. Whole-genome sequencing can be useful for this but has limited power for trait prediction. However, we can take advantage of the inherent information content of phenotypes to bypass these limitations. We demonstrate, in clinical and environmental bacterial isolates, that growth dynamics in standardized conditions can differentiate between genotypes, even among strains from the same species. We find that for pairs of isolates, there is little correlation between genetic distance, according to phylogenetic analysis, and phenotypic distance, as determined by growth dynamics. This absence of correlation underscores the challenge in using genomics to infer phenotypes and vice versa. Bypassing this complexity, we show that growth dynamics alone can robustly predict antibiotic responses. These findings are a foundation for a method to identify traits not easily traced to a genetic mechanism.
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A novel knock out strategy to enhance recombinant protein expression in Escherichia coli. Microb Cell Fact 2020; 19:148. [PMID: 32703203 PMCID: PMC7376861 DOI: 10.1186/s12934-020-01407-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
Background The expression of recombinant proteins triggers a stress response which downregulates key metabolic pathway genes leading to a decline in cellular health and feedback inhibition of both growth and protein expression. Instead of individually upregulating these downregulated genes or improving transcription rates by better vector design, an innovative strategy would be to block this stress response thereby ensuring a sustained level of protein expression. Results We postulated that the genes which are commonly up-regulated post induction may play the role of signalling messengers in mounting the cellular stress response. We identified those genes which have no known downstream regulatees and created knock outs which were then tested for GFP expression. Many of these knock outs showed significantly higher expression levels which was also sustained for longer periods. The highest product yield (Yp/x) was observed in a BW25113ΔcysJ knock out (Yp/x 0.57) and BW25113ΔelaA (Yp/x 0.49), whereas the Yp/x of the control W3110 strain was 0.08 and BW25113 was 0.16. Double knock out combinations were then created from the ten best performing single knock outs leading to a further enhancement in expression levels. Out of 45 double knock outs created, BW25113ΔelaAΔyhbC (Yp/x 0.7) and BW25113ΔcysJΔyhbC (Yp/x 0.64) showed the highest increase in product yield compared to the single gene mutant strains. We confirmed the improved performance of these knock outs by testing and obtaining higher levels of recombinant asparaginase expression, a system better suited for analysing sustained expression since it gets exported to the extracellular medium. Conclusion Creating key knock outs to block the CSR and enhance expression is a radically different strategy that can be synergistically combined with traditional methods of improving protein yields thus helping in the design of superior host platforms for protein expression.
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Colanic acid biosynthesis in Escherichia coli is dependent on lipopolysaccharide structure and glucose availability. Microbiol Res 2020; 239:126527. [PMID: 32590169 DOI: 10.1016/j.micres.2020.126527] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/06/2020] [Accepted: 06/06/2020] [Indexed: 01/31/2023]
Abstract
Lipopolysaccharide and colanic acid are important forms of exopolysaccharides located on the cell surface of Escherichia coli, but their interrelation with the cell stress response is not well understood. In this study, nine mutant strains with different structures of lipopolysaccharide were constructed from E. coli MG1655 by deletion of a single gene or multiple genes. All mutant strains did not produce colanic acid when grown in LB medium, but six of them could produce colanic acid when grown either in M9 medium in which glucose is the sole carbon source or in LB medium supplemented with glucose. The results indicate that colanic acid production in E. coli is dependent on both lipopolysaccharide structure and glucose availability. However, transcriptional analysis showed that 20 genes related to the colanic acid biosynthesis and the key gene rcsA in the Rcs system were all transcriptionally up-regulated in all of the nine mutant strains no matter they were grown in M9 or LB medium. This suggests that the availability of some nucleotide-sugar precursors shared by the biosynthesis of lipopolysaccharide and colanic acid might play a major role in colanic acid production in E. coli. Lipopolysaccharide pathway might have a huge priority to colanic acid pathway to use the common precursors; therefore, the colanic acid is not produced in MG1655 and the nine mutants when grown in LB medium. In the six mutant strains that can produce colanic acid in the glucose rich media, the common precursors might be abundant because they were not needed for synthesizing the mutant lipopolysaccharide.
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35
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Lee HW, Park JH, Kim WK, Lee JG, Lee JS, Ahn JO, Lee EG, Lee HW. Engineered Escherichia coli strains as platforms for biological production of isoprene. FEBS Open Bio 2020; 10:780-788. [PMID: 32135038 PMCID: PMC7193156 DOI: 10.1002/2211-5463.12829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/20/2020] [Accepted: 03/02/2020] [Indexed: 11/12/2022] Open
Abstract
Volatile compounds can be produced by fermentation from genetically engineered microorganisms. Escherichia coli strains are mainly used for isoprene production owing to their higher titers; however, this has thus far been confined to only strains BL21, BL21 (DE3), Rosetta, and BW25113. Here, we tested four groups of E. coli strains for improved isoprene production, including K-12 (DH5α, BW25113, W3110, MG1655, XL1-Blue, and JM109), B [Rosetta (DE3), BL21, and BL21 (DE3)], Crooks C, and Waksman W strains. The isoprene productivity of BL21 and MG1655 was remarkably higher than that of the others in 5-L fermentation, and scale-up fermentation (300 L) of BL21 was successfully performed. This system shows potential for biobased production of fuel and volatile compounds in industrial applications.
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Affiliation(s)
- Hyeok-Won Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Won-Kyo Kim
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Jin-Gyeom Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Ju-Seok Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Jung-Oh Ahn
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea.,Department of Bioprocess Engineering, University of Science and Technology (UST) of Korea, Daejeon, Korea
| | - Eun-Gyo Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea.,Department of Bioprocess Engineering, University of Science and Technology (UST) of Korea, Daejeon, Korea
| | - Hong-Weon Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea.,Department of Bioprocess Engineering, University of Science and Technology (UST) of Korea, Daejeon, Korea
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Metzger KF, Padutsch W, Pekarsky A, Kopp J, Voloshin AM, Kühnel H, Maurer M. IGF1 inclusion bodies: A QbD based process approach for efficient USP as well as early DSP unit operations. J Biotechnol 2020; 312:23-34. [DOI: 10.1016/j.jbiotec.2020.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/04/2020] [Accepted: 02/26/2020] [Indexed: 12/20/2022]
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37
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Zhao L, Zhang H, Wang X, Han G, Ma W, Hu X, Li Y. Transcriptomic analysis of an l-threonine-producing Escherichia coli TWF001. Biotechnol Appl Biochem 2020; 67:414-429. [PMID: 31976571 DOI: 10.1002/bab.1890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/21/2020] [Indexed: 01/10/2023]
Abstract
Wild-type Escherichia coli usually does not accumulate l-threonine, but E. coli strain TWF001 could produce 30.35 g/L l-threonine after 23-H fed-batch fermentation. To understand the mechanism for the high yield of l-threonine production in TWF001, transcriptomic analyses of the TWF001 cell samples collected at the logarithmic and stationary phases were performed, using the wild-type E. coli strain W3110 as the control. Compared with W3110, 1739 and 2361 genes were differentially transcribed in the logarithmic and stationary phases, respectively. Most genes related to the biosynthesis of l-threonine were significantly upregulated. Some key genes related to the NAD(P)H regeneration were upregulated. Many genes relevant to glycolysis and TCA cycle were downregulated. The key genes involved in the l-threonine degradation were downregulated. The gene rhtA encoding the l-threonine exporter was upregulated, whereas the genes sstT and tdcC encoding the l-threonine importer were downregulated. The upregulated genes in the glutamate pathway might form an amino-providing loop, which is beneficial for the high yield of l-threonine production. Many genes encoding the 30S and 50S subunits of ribosomes were also upregulated. The findings are useful for gene engineering to increase l-threonine production in E. coli.
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Affiliation(s)
- Lei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Hailing Zhang
- Department of Biological Engineering, College of Life Science, Yantai University, Shandong, 408100, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guoqiang Han
- College of Modern Agriculture and Biological Engineering, Yangtze Normal University, Chongqing, 264005, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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38
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Tovar M, Mahler L, Buchheim S, Roth M, Rosenbaum MA. Monitoring and external control of pH in microfluidic droplets during microbial culturing. Microb Cell Fact 2020; 19:16. [PMID: 31996234 PMCID: PMC6990587 DOI: 10.1186/s12934-020-1282-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/11/2020] [Indexed: 11/10/2022] Open
Abstract
Background Cell-based experimentation in microfluidic droplets is becoming increasingly popular among biotechnologists and microbiologists, since inherent characteristics of droplets allow high throughput at low cost and space investment. The range of applications for droplet assays is expanding from single cell analysis toward complex cell–cell incubation and interaction studies. As a result of cellular metabolism in these setups, relevant physicochemical alterations frequently occur before functional assays are conducted. However, to use droplets as truly miniaturized bioreactors, parameters like pH and oxygen availability should be controlled similar to large-scale fermentation to ensure reliable research. Results Here, we introduce a comprehensive strategy to monitor and control pH for large droplet populations during long-term incubation. We show the correlation of fluorescence intensity of 6-carboxyfluorescein and pH in single droplets and entire droplet populations. By taking advantage of inter-droplet transport of pH-mediating molecules, the average pH value of several million droplets is simultaneously adjusted in an a priori defined direction. To demonstrate the need of pH control in practice, we compared the fermentation profiles of two E. coli strains, a K12-strain and a B-strain, in unbuffered medium with 5 g/L glucose for standard 1 L bioreactors and 180 pL droplets. In both fermentation formats, the commonly used B-strain E. coli BL21 is able to consume glucose until depletion and prevent a pH drop, while the growth of the K12-strain E. coli MG1655 is soon inhibited by a low pH caused by its own high acetate production. By regulating the pH during fermentation in droplets with our suggested strategy, we were able to prevent the growth arrest of E. coli MG1655 and obtained an equally high biomass yield as with E. coli BL21. Conclusion We demonstrated a comparable success of pH monitoring and regulation for fermentations in 1 L scale and 180 pL scale for two E. coli strains. This strategy has the potential to improve cell-based experiments for various microbial systems in microfluidic droplets and opens the possibility for new functional assay designs.
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Affiliation(s)
- Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany.,Faculty of Biology and Pharmacy, Friedrich Schiller University, 07743, Jena, Germany
| | - Lisa Mahler
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany.,Faculty of Biology and Pharmacy, Friedrich Schiller University, 07743, Jena, Germany
| | - Stefanie Buchheim
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany.,Faculty of Biology and Pharmacy, Friedrich Schiller University, 07743, Jena, Germany
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany. .,Faculty of Biology and Pharmacy, Friedrich Schiller University, 07743, Jena, Germany.
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39
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Heins AL, Reyelt J, Schmidt M, Kranz H, Weuster-Botz D. Development and characterization of Escherichia coli triple reporter strains for investigation of population heterogeneity in bioprocesses. Microb Cell Fact 2020; 19:14. [PMID: 31992282 PMCID: PMC6988206 DOI: 10.1186/s12934-020-1283-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/12/2020] [Indexed: 12/17/2022] Open
Abstract
Background Today there is an increasing demand for high yielding robust and cost efficient biotechnological production processes. Although cells in these processes originate from isogenic cultures, heterogeneity induced by intrinsic and extrinsic influences is omnipresent. To increase understanding of this mechanistically poorly understood phenomenon, advanced tools that provide insights into single cell physiology are needed. Results Two Escherichia coli triple reporter strains have been designed based on the industrially relevant production host E. coli BL21(DE3) and a modified version thereof, E. coli T7E2. The strains carry three different fluorescence proteins chromosomally integrated. Single cell growth is followed with EmeraldGFP (EmGFP)-expression together with the ribosomal promoter rrnB. General stress response of single cells is monitored by expression of sigma factor rpoS with mStrawberry, whereas expression of the nar-operon together with TagRFP657 gives information about oxygen limitation of single cells. First, the strains were characterized in batch operated stirred-tank bioreactors in comparison to wildtype E. coli BL21(DE3). Afterwards, applicability of the triple reporter strains for investigation of population heterogeneity in bioprocesses was demonstrated in continuous processes in stirred-tank bioreactors at different growth rates and in response to glucose and oxygen perturbation simulating gradients on industrial scale. Population and single cell level physiology was monitored evaluating general physiology and flow cytometry analysis of fluorescence distributions of the triple reporter strains. Although both triple reporter strains reflected physiological changes that were expected based on the expression characteristics of the marker proteins, the triple reporter strain based on E. coli T7E2 showed higher sensitivity in response to environmental changes. For both strains, noise in gene expression was observed during transition from phases of non-growth to growth. Apparently, under some process conditions, e.g. the stationary phase in batch cultures, the fluorescence response of EmGFP and mStrawberry is preserved, whereas TagRFP657 showed a distinct response. Conclusions Single cell growth, general stress response and oxygen limitation of single cells could be followed using the two triple reporter strains developed in this study. They represent valuable tools to study population heterogeneity in bioprocesses significantly increasing the level of information compared to the use of single reporter strains.
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Affiliation(s)
- Anna-Lena Heins
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Jan Reyelt
- Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Marlen Schmidt
- Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Harald Kranz
- Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Dirk Weuster-Botz
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany
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40
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Metzger KFJ, Voloshin A, Schillinger H, Kühnel H, Maurer M. Adsorptive filtration: A case study for early impurity reduction in an Escherichia coli production process. Biotechnol Prog 2019; 36:e2948. [PMID: 31837191 DOI: 10.1002/btpr.2948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/22/2019] [Accepted: 12/08/2019] [Indexed: 11/10/2022]
Abstract
Primary recovery of intracellular products from Escherichia coli requires cell disruption which leads to a massive release of process-related impurities burdening subsequent downstream process (DSP) unit operations. Especially, DNA and endotoxins challenge purification operations due to their size and concentrations. Consequently, an early reduction in impurities will not only simplify the production process but also increase robustness while alleviating the workload afterward. In the present work, we studied the proof of concept whether a nonwoven anion exchange filter material decreases soluble impurities immediately at the clarification step of E. coli DSP. In a first attempt, endotoxin burden was reduced by 4.6-fold and the DNA concentration by 3.6-fold compared to conventional depth filtration. A design of experiment for the adsorptive filtration approach was carried out to analyze the influence of different critical process parameters (CPPs) on impurity reduction. We showed that depending on the CPPs chosen, a DNA lowering of more than 3 log values, an endotoxin decrease of approximately 7 logs, and a minor HCP clearance of at least 0.3 logs could be achieved. Thus, we further revealed a chromatography column protecting effect when using adsorptive filtration beforehand.
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Affiliation(s)
- Karl F J Metzger
- Life Sciences, University of Applied Sciences Campus Vienna, Wien, AT, Austria.,Bioprocess Engineering, Austrian Centre of Industrial Biotechnology, Wien, AT, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Wien, AT, Austria
| | - Alexei Voloshin
- 3M Company, Separation and Purification Sciences Division, 3M Center, Saint Paul, Minnesota
| | - Harald Schillinger
- Life Sciences, University of Applied Sciences Campus Vienna, Wien, AT, Austria.,3M Österreich, 3M Separation and Purification Sciences Division, Wien, AT, Austria
| | - Harald Kühnel
- Life Sciences, University of Applied Sciences Campus Vienna, Wien, AT, Austria
| | - Michael Maurer
- Life Sciences, University of Applied Sciences Campus Vienna, Wien, AT, Austria.,Bioprocess Engineering, Austrian Centre of Industrial Biotechnology, Wien, AT, Austria
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41
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Luziatelli F, Brunetti L, Ficca AG, Ruzzi M. Maximizing the Efficiency of Vanillin Production by Biocatalyst Enhancement and Process Optimization. Front Bioeng Biotechnol 2019; 7:279. [PMID: 31681753 PMCID: PMC6813415 DOI: 10.3389/fbioe.2019.00279] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/03/2019] [Indexed: 01/20/2023] Open
Abstract
The rising demand of bio-vanillin and the possibility to use microbial biotransformation to produce this compound from agroindustrial byproducts are economically attractive. However, there are still several bottlenecks, including substrate and product toxicity, formation of undesired products and genetic stability of the recombinant strains, that impede an efficient use of recombinant Escherichia coli strains to make the whole process cost effective. To overcome these problems, we developed a new E. coli strain, named FR13, carrying the Pseudomonas genes encoding feruloyl-CoA synthetase and feruloyl-CoA hydratase/aldolase integrated into the chromosome and, using resting cells, we demonstrated that the vanillin yield and selectivity were strongly affected by the physiological state of the cells, the temperature used for the growth and the recovery of the biomass and the composition and pH of the bioconversion buffer. The substrate consumption rate and the vanillin yield increased using a sodium/potassium phosphate buffer at pH 9.0 as bioconversion medium. Optimization of the bioprocess variables, using response surface methodology, together with the use of a two-phase (solid-liquid) system for the controlled release of ferulic acid allowed us to increase the vanillin yield up to 28.10 ± 0.05 mM. These findings showed that recombinant plasmid-free E. coli strains are promising candidates for the production of vanillin at industrial scale and that a reduction of the cost of the bioconversion process requires approaches that minimize the toxicity of both ferulic acid and vanillin.
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Affiliation(s)
| | | | | | - Maurizio Ruzzi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
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42
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Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate. mSystems 2019; 4:4/4/e00187-19. [PMID: 31186337 PMCID: PMC6561320 DOI: 10.1128/msystems.00187-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Citramalate is an attractive biotechnology target because it is a precursor of methylmethacrylate, which is used to manufacture Perspex and other high-value products. Engineered E. coli strains are able to produce high titers of citramalate, despite having to express a foreign enzyme and tolerate the presence of a nonnative biochemical. A systems analysis of the citramalate fermentation was undertaken to uncover the reasons underpinning its productivity. This showed that E. coli readily adjusts to the redirection of metabolic resources toward recombinant protein and citramalate production and suggests that E. coli is an excellent chassis for manufacturing similar small, polar, foreign molecules. Productivity of bacterial cell factories is frequently compromised by stresses imposed by recombinant protein synthesis and carbon-to-product conversion, but little is known about these bioprocesses at a systems level. Production of the unnatural metabolite citramalate in Escherichia coli requires the expression of a single gene coding for citramalate synthase. Multiomic analyses of a fermentation producing 25 g liter−1 citramalate were undertaken to uncover the reasons for its productivity. Metabolite, transcript, protein, and lipid profiles of high-cell-density, fed-batch fermentations of E. coli expressing either citramalate synthase or an inactivated enzyme were similar. Both fermentations showed downregulation of flagellar genes and upregulation of chaperones IbpA and IbpB, indicating that these responses were due to recombinant protein synthesis and not citramalate production. Citramalate production did not perturb metabolite pools, except for an increased intracellular pyruvate pool. Gene expression changes in response to citramalate were limited; none of the general stress response regulons were activated. Modeling of transcription factor activities suggested that citramalate invoked a GadW-mediated acid response, and changes in GadY and RprA regulatory small RNA (sRNA) expression supported this. Although changes in membrane lipid composition were observed, none were unique to citramalate production. This systems analysis of the citramalate fermentation shows that E. coli has capacity to readily adjust to the redirection of resources toward recombinant protein and citramalate production, suggesting that it is an excellent chassis choice for manufacturing organic acids. IMPORTANCE Citramalate is an attractive biotechnology target because it is a precursor of methylmethacrylate, which is used to manufacture Perspex and other high-value products. Engineered E. coli strains are able to produce high titers of citramalate, despite having to express a foreign enzyme and tolerate the presence of a nonnative biochemical. A systems analysis of the citramalate fermentation was undertaken to uncover the reasons underpinning its productivity. This showed that E. coli readily adjusts to the redirection of metabolic resources toward recombinant protein and citramalate production and suggests that E. coli is an excellent chassis for manufacturing similar small, polar, foreign molecules.
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43
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Anh Le TT, Thuptimdang P, McEvoy J, Khan E. Phage shock protein and gene responses of Escherichia coli exposed to carbon nanotubes. CHEMOSPHERE 2019; 224:461-469. [PMID: 30831497 DOI: 10.1016/j.chemosphere.2019.02.159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
Two-dimensional electrophoretic, western blotting, and quantitative polymerase chain reaction analyses of Escherichia coli cells exposed to pristine single walled carbon nanotubes (SWCNTs), and hydroxyl and carboxylic functionalized SWCNTs (SWCNT-OHs and SWCNT-COOHs) were conducted. SWCNT concentration and length were experimental variables. Exposing E. coli cells to SWCNTs led to changes in protein and gene expressions. Several proteins altered their regulations at a low SWCNT concentration (10 μg/ml) and were shut down at a high SWCNT concentration (100 μg/ml). The expressions of the phage shock protein (psp) operon including pspA, pspB, and pspC genes responded to the membrane stressors, SWCNTs, were also examined. While pspA and pspC expressions were influenced by the length, concentration, and functional groups of SWCNTs, pspB expression was not induced by SWCNTs. The alterations in phage shock protein and gene expressions indicated that SWCNTs caused cell membrane perturbation.
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Affiliation(s)
- Tu Thi Anh Le
- Environmental and Conservation Sciences Program, North Dakota State University, Fargo, ND 58108, USA; Biology Department, Dalat University, Dalat, Lamdong, Viet Nam.
| | - Pumis Thuptimdang
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand; Environmental Science Research Center (ESRC), Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - John McEvoy
- Microbiological Sciences Department, North Dakota State University, Fargo, ND 58108, USA.
| | - Eakalak Khan
- Civil and Environmental Engineering and Construction Department, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA.
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44
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Jaén KE, Velazquez D, Delvigne F, Sigala JC, Lara AR. Engineering E. coli for improved microaerobic pDNA production. Bioprocess Biosyst Eng 2019; 42:1457-1466. [PMID: 31079222 DOI: 10.1007/s00449-019-02142-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/20/2019] [Accepted: 05/02/2019] [Indexed: 02/08/2023]
Abstract
Escherichia coli strains W3110 and BL21 were engineered for the production of plasmid DNA (pDNA) under aerobic and transitions to microaerobic conditions. The gene coding for recombinase A (recA) was deleted in both strains. In addition, the Vitreoscilla hemoglobin (VHb) gene (vgb) was chromosomally inserted and constitutively expressed in each E. coli recA mutant and wild type. The recA inactivation increased the supercoiled pDNA fraction (SCF) in both strains, while VHb expression improved the pDNA production in W3110, but not in BL21. Therefore, a codon-optimized version of vgb was inserted in strain BL21recA-, which, together with W3110recA-vgb+, was tested in cultures with shifts from aerobic to oxygen-limited regimes. VHb expression lowered the accumulation of fermentative by-products in both strains. VHb-expressing cells displayed higher oxidative activity as indicated by the Redox Sensor Green fluorescence, which was more intense in BL21 than in W3110. Furthermore, VHb expression did not change pDNA production in W3110, but decreased it in BL21. These results are useful for understanding the physiological effects of VHb expression in two industrially relevant E. coli strains, and for the selection of a host for pDNA production.
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Affiliation(s)
- Karim E Jaén
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, 05348, Mexico City, Mexico
| | - Daniela Velazquez
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, 05348, Mexico City, Mexico
| | - Frank Delvigne
- Gembloux Agro-Bio Tech, TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), University of Liege, Gembloux, Belgium
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, 05348, Mexico City, Mexico
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, 05348, Mexico City, Mexico.
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45
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Azarian B, Azimi A, Sepehri M, Samimi Fam V, Rezaie F, Talebkhan Y, Khalaj V, Davami F. Proteomics investigation of molecular mechanisms affected by EnBase culture system in anti-VEGF fab fragment producing E. coli BL21 (DE3). Prep Biochem Biotechnol 2019; 49:48-57. [PMID: 30735089 DOI: 10.1080/10826068.2018.1508037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aggregation of recombinant proteins, a major problem in E. coli expression system, is improved by using EnBase culture system based on slow release of glucose. In the present study, to understand the intracellular mechanisms involved in increased solubility of the target recombinant protein through EnBase system, the effect of this system was investigated on E. coli cells proteome profile. The proteome profile of E. coli cells cultured in EnBase and conventional batch mode was analyzed by two-dimensional gel electrophoresis. The proteins with significant expressional changes were identified through MALDI-TOF/TOF mass spectrometry. In EnBase system, the expressions of carbon metabolism-related proteins, sugar transport system-related proteins, and amino acids metabolism-related proteins were significantly altered. Furthermore, the expression of Thioredoxin 1 as the facilitator of protein folding was up-regulated in EnBase system that could be related to the increased solubility of recombinant protein. The proteomics analysis of E. coli cells cultured in EnBase system revealed that Thioredoxin 1 can be a potential candidate for future studies aiming at increased anti-VEGF fab fragment solubility. Studying proteomics is a valuable tool for revealing the target proteins that play the central role in EnBase culture system for increasing the solubility.
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Affiliation(s)
- Bahareh Azarian
- a Protein Chemistry Unit, Biotechnology Research Centre , Pasteur Institute of Iran , Tehran , Iran
| | - Amin Azimi
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran.,c Department of Biotechnology , College of Science, University of Tehran , Tehran , Iran
| | - Mahboubeh Sepehri
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran.,d Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences & Technology , Pharmaceutical sciences Branch, Islamic Azad University , Tehran , Iran
| | - Vahideh Samimi Fam
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran.,e Department of Microbiology , Islamic Azad University Rasht Branch , Rasht , Guilan , Iran
| | - Faegheh Rezaie
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
| | - Yeganeh Talebkhan
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
| | - Vahid Khalaj
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
| | - Fatemeh Davami
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
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Burdette LA, Leach SA, Wong HT, Tullman-Ercek D. Developing Gram-negative bacteria for the secretion of heterologous proteins. Microb Cell Fact 2018; 17:196. [PMID: 30572895 PMCID: PMC6302416 DOI: 10.1186/s12934-018-1041-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/08/2018] [Indexed: 11/10/2022] Open
Abstract
Gram-negative bacteria are attractive hosts for recombinant protein production because they are fast growing, easy to manipulate, and genetically stable in large cultures. However, the utility of these microbes would expand if they also could secrete the product at commercial scales. Secretion of biotechnologically relevant proteins into the extracellular medium increases product purity from cell culture, decreases downstream processing requirements, and reduces overall cost. Thus, researchers are devoting significant attention to engineering Gram-negative bacteria to secrete recombinant proteins to the extracellular medium. Secretion from these bacteria operates through highly specialized systems, which are able to translocate proteins from the cytosol to the extracellular medium in either one or two steps. Building on past successes, researchers continue to increase the secretion efficiency and titer through these systems in an effort to make them viable for industrial production. Efforts include modifying the secretion tags required for recombinant protein secretion, developing methods to screen or select rapidly for clones with higher titer or efficiency, and improving reliability and robustness of high titer secretion through genetic manipulations. An additional focus is the expression of secretion machineries from pathogenic bacteria in the "workhorse" of biotechnology, Escherichia coli, to reduce handling of pathogenic strains. This review will cover recent advances toward the development of high-expressing, high-secreting Gram-negative production strains.
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Affiliation(s)
- Lisa Ann Burdette
- Department of Chemical and Biomolecular Engineering, University of California-Berkeley, Berkeley, USA
- Present Address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Samuel Alexander Leach
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, USA
| | - Han Teng Wong
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, USA
- Present Address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, USA
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Shimizu K, Matsuoka Y. Regulation of glycolytic flux and overflow metabolism depending on the source of energy generation for energy demand. Biotechnol Adv 2018; 37:284-305. [PMID: 30576718 DOI: 10.1016/j.biotechadv.2018.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/06/2018] [Accepted: 12/15/2018] [Indexed: 12/11/2022]
Abstract
Overflow metabolism is a common phenomenon observed at higher glycolytic flux in many bacteria, yeast (known as Crabtree effect), and mammalian cells including cancer cells (known as Warburg effect). This phenomenon has recently been characterized as the trade-offs between protein costs and enzyme efficiencies based on coarse-graining approaches. Moreover, it has been recognized that the glycolytic flux increases as the source of energy generation changes from energetically efficient respiration to inefficient respiro-fermentative or fermentative metabolism causing overflow metabolism. It is highly desired to clarify the metabolic regulation mechanisms behind such phenomena. Metabolic fluxes are located on top of the hierarchical regulation systems, and represent the outcome of the integrated response of all levels of cellular regulation systems. In the present article, we discuss about the different levels of regulation systems for the modulation of fluxes depending on the growth rate, growth condition such as oxygen limitation that alters the metabolism towards fermentation, and genetic perturbation affecting the source of energy generation from respiration to respiro-fermentative metabolism in relation to overflow metabolism. The intracellular metabolite of the upper glycolysis such as fructose 1,6-bisphosphate (FBP) plays an important role not only for flux sensing, but also for the regulation of the respiratory activity either directly or indirectly (via transcription factors) at higher growth rate. The glycolytic flux regulation is backed up (enhanced) by unphosphorylated EIIA and HPr of the phosphotransferase system (PTS) components, together with the sugar-phosphate stress regulation, where the transcriptional regulation is further modulated by post-transcriptional regulation via the degradation of mRNA (stability of mRNA) in Escherichia coli. Moreover, the channeling may also play some role in modulating the glycolytic cascade reactions.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
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Hausjell J, Weissensteiner J, Molitor C, Halbwirth H, Spadiut O. E. coli HMS174(DE3) is a sustainable alternative to BL21(DE3). Microb Cell Fact 2018; 17:169. [PMID: 30376846 PMCID: PMC6206895 DOI: 10.1186/s12934-018-1016-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023] Open
Abstract
Background Escherichia coli is one of the most widely used hosts for recombinant protein production in academia and industry. Strain BL21(DE3) is frequently employed due to its advantageous feature of lacking proteases which avoids degradation of target protein. Usually it is used in combination with the T7-pET system where induction is performed by one point addition of IPTG. We recently published a few studies regarding lactose induction in BL21(DE3) strains. BL21(DE3) can only take up the glucose-part of the disaccharide when fed with lactose. However, initially additional glucose has to be supplied as otherwise the ATP-related lactose uptake barely happens. Yet, as lactose is an inexpensive compound compared to glucose and IPTG, a new induction strategy by a lactose-only feed during induction seems attractive. Thus, we investigated this idea in the galactose metabolizing strain HMS174(DE3). Results We show that strain HMS174(DE3) can be cultivated on lactose as sole carbon source during induction. We demonstrate that strain HMS174(DE3) exhibits higher product and biomass yields compared to BL21(DE3) when cultivated in a lactose fed-batch. More importantly, HMS174(DE3) cultivated on lactose even expresses more product than BL21(DE3) in a standard IPTG induced glucose fed-batch at the same growth rate. Finally, we demonstrate that productivity in HMS174(DE3) lactose-fed batch cultivations can easily be influenced by the specific lactose uptake rate (qs,lac). This is shown for two model proteins, one expressed in soluble form and one as inclusion body. Conclusions As strain HMS174(DE3) expresses even slightly higher amounts of target protein in a lactose fed-batch than BL21(DE3) in a standard cultivation, it seems a striking alternative for recombinant protein production. Especially for large scale production of industrial enzymes cheap substrates are essential. Besides cost factors, the strategy allows straight forward adjustment of specific product titers by variation of the lactose feed rate. Electronic supplementary material The online version of this article (10.1186/s12934-018-1016-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johanna Hausjell
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Julia Weissensteiner
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Molitor
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Heidi Halbwirth
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
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49
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Effect of amino acids on transcription and translation of key genes in E. coli K and B grown at a steady state in minimal medium. N Biotechnol 2018; 49:120-128. [PMID: 30385399 DOI: 10.1016/j.nbt.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 02/01/2023]
Abstract
Growing E. coli to high densities is a common strategy for biologicals production. The process is implemented by using complex or minimal media with different feeding strategies. To understand the effect of amino acids, E. coli B and K were grown at a steady state of 0.35 h-1 in glucose minimal medium with and without amino acids, while their metabolism, protein abundance and gene expression were compared. The results showed that amino acids promoted higher acetate excretion, higher fatty acid biosynthesis (K strain), repressed glucose uptake rate, and decreased expression of proteins associated with the TCA cycle, glyoxylate shunt and amino acid biosynthesis. In presence of amino acids, E. coli K upregulated fatty acid biosynthesis and repressed more genes and proteins involved in amino acid biosynthesis than E. coli B. These findings are correlated with higher yield on glucose (Yx/s) and high specific biomass production rate (qx) in K strain in the presence of amino acids. In contrast, pre-formed precursor molecules such as amino acids did not affect fatty acid biosynthesis in E. coli B or Yx/s and qx, which were higher than those of E. coli K, suggesting that constitutive synthesis of energetically demanding precursors and higher fatty acid β-oxidation activity is key for high biomass-performer E. coli B. Both strains turned off unnecessary pathways and directed their metabolism to proteome efficient overflow metabolism likely to generate energy and provide protein to functions supporting higher growth rate.
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50
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Sauer DG, Mosor M, Frank AC, Weiß F, Christler A, Walch N, Jungbauer A, Dürauer A. A two-step process for capture and purification of human basic fibroblast growth factor from E. coli homogenate: Yield versus endotoxin clearance. Protein Expr Purif 2018; 153:70-82. [PMID: 30130579 DOI: 10.1016/j.pep.2018.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/31/2018] [Accepted: 08/15/2018] [Indexed: 11/25/2022]
Abstract
A two-step purification process for human basic fibroblast growth factor (FGF-2) from clarified E. coli homogenate has been developed in which the impurity level after the second step is below the limit of quantification. Endotoxin content is cleared to 0.02 EU/μg FGF-2 and the overall yield is 67%. The performance of the cation exchanger Carboxymethyl-Sepharose Fast Flow (CM-SFF) was compared to the affinity resin Heparin-SFF regarding the impurity profile and product quality in the elution peak. The CM-SFF eluate was further purified using hydrophobic interaction resin Toyopearl-Hexyl-650C. The relative amounts of target product, host cell proteins (HCPs), dsDNA, endotoxin, monomer content, and high molecular weight impurities differed along the elution peak depending on the applied method. The bioactive monomer (>99%) was obtained with a yield of 48% for CM-SFF and 68% for Heparin-SFF. A half-load reduction in CM-SFF increased the yield up to 67% without deterioration of the impurity content. Assuming a dose of 400 μg FGF-2, endotoxin was reduced to 188 EU/dose, dsDNA <10 ng/dose, and HCP <2 ppm/dose using the cation exchanger. In the pooled eluate fractions, dsDNA was removed 4-fold (291 ng/mL) and endotoxin 14-fold (0.47 EU/μg FGF-2) more efficiently by CM-SFF than by affinity chromatography. In contrast, HCP clearance was 3-fold (13 ppm) more efficient with Heparin-SFF than CM-SFF. In contrast to process monitoring by UV280nm or SDS-PAGE, this characterization is the basis for a Process Analytical Technology attempt when correlated with online monitored signals, as it enables knowledge-based pooling according to defined quality criteria.
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Affiliation(s)
- Dominik Georg Sauer
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190, Vienna, Austria
| | - Magdalena Mosor
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190, Vienna, Austria
| | - Anna-Carina Frank
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190, Vienna, Austria
| | - Florian Weiß
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190, Vienna, Austria
| | - Anna Christler
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190, Vienna, Austria
| | - Nicole Walch
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190, Vienna, Austria
| | - Alois Jungbauer
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Astrid Dürauer
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.
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