1
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Wang X, Zhou X, Kang L, Lai Y, Ye H. Engineering natural molecule-triggered genetic control systems for tunable gene- and cell-based therapies. Synth Syst Biotechnol 2023; 8:416-426. [PMID: 37384125 PMCID: PMC10293594 DOI: 10.1016/j.synbio.2023.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023] Open
Abstract
The ability to precisely control activities of engineered designer cells provides a novel strategy for modern precision medicine. Dynamically adjustable gene- and cell-based precision therapies are recognized as next generation medicines. However, the translation of these controllable therapeutics into clinical practice is severely hampered by the lack of safe and highly specific genetic switches controlled by triggers that are nontoxic and side-effect free. Recently, natural products derived from plants have been extensively explored as trigger molecules to control genetic switches and synthetic gene networks for multiple applications. These controlled genetic switches could be further introduced into mammalian cells to obtain synthetic designer cells for adjustable and fine tunable cell-based precision therapy. In this review, we introduce various available natural molecules that were engineered to control genetic switches for controllable transgene expression, complex logic computation, and therapeutic drug delivery to achieve precision therapy. We also discuss current challenges and prospects in translating these natural molecule-controlled genetic switches developed for biomedical applications from the laboratory to the clinic.
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2
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Donaldson J, Kleinjan DJ, Rosser S. Synthetic biology approaches for dynamic CHO cell engineering. Curr Opin Biotechnol 2022; 78:102806. [PMID: 36194920 DOI: 10.1016/j.copbio.2022.102806] [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: 05/31/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022]
Abstract
Fed-batch culture of Chinese hamster ovary (CHO) cells remains the most commonly used method for producing biopharmaceuticals. Static CHO cell-line engineering approaches have incrementally improved productivity, growth and product quality through permanent knockout of genes with a negative impact on production, or constitutive overexpression of genes with a positive impact. However, during fed-batch culture, conditions (such as nutrient availability) are continually changing. Therefore, traits that are most beneficial during early-phase culture (such as high growth rate) may be less desirable in late phase. Unlike with static approaches, dynamic cell line engineering strategies can optimise such traits by implementing synthetic sense-and-respond programmes. Here, we review emerging synthetic biology tools that can be used to build dynamic, self-regulating CHO cells, capable of detecting intra-/extracellular cues and generating user-defined responses tailored to the stage-specific needs of the production process.
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Affiliation(s)
- James Donaldson
- UK Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Dirk-Jan Kleinjan
- UK Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan Rosser
- UK Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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3
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Yang J, Wang C, Lu Y. A Temperature-Controlled Cell-Free Expression System by Dynamic Repressor. ACS Synth Biol 2022; 11:1408-1416. [PMID: 35319196 DOI: 10.1021/acssynbio.1c00641] [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: 11/30/2022]
Abstract
The cell-free protein synthesis (CFPS) system is a typical protein production platform in the field of synthetic biology. However, there are limitations in controlling protein synthesis in the CFPS system. Compared with the traditional method of adding chemicals, temperature is an ideal control switch to achieve precise spatiotemporal control with few side effects. Hence, the design of a temperature-controlled cell-free protein synthesis (tcCFPS) system based on E. coli was carried out with the repressor cI protein in this study. The corresponding tcCFPS achieved a 143-fold dynamic protein expression level at 37 °C than that at 30 °C. Besides, the artificial cell controlled by temperature was constructed to expand the applications of tcCFPS. This study provides a new effective method for active protein synthesis in a cell-free system and a potential means of drug synthesis and delivery.
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Affiliation(s)
- Junzhu Yang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Chen Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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4
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Donaldson JS, Dale MP, Rosser SJ. Decoupling Growth and Protein Production in CHO Cells: A Targeted Approach. Front Bioeng Biotechnol 2021; 9:658325. [PMID: 34150726 PMCID: PMC8207133 DOI: 10.3389/fbioe.2021.658325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/09/2021] [Indexed: 11/28/2022] Open
Abstract
Fed-batch cultures of Chinese Hamster Ovary cells have been used to produce high quantities of biotherapeutics, particularly monoclonal antibodies. However, a growing number of next-generation biotherapeutics, such as bi-specific antibodies and fusion proteins, are difficult to express using standard fed-batch processes. Decoupling cell growth and biotherapeutic production is becoming an increasingly desired strategy for the biomanufacturing industry, especially for difficult-to-express products. Cells are grown to a high cell density in the absence of recombinant protein production (the growth phase), then expression of the recombinant protein is induced and cell proliferation halted (the production phase), usually by combining an inducible gene expression system with a proliferation control strategy. Separating the growth and production phases allows cell resources to be more efficiently directed toward either growth or production, improving growth characteristics and enhancing the production of difficult to express proteins. However, current mammalian cell proliferation control methods rely on temperature shifts and chemical agents, which interact with many non-proliferation pathways, leading to variable impacts on product quality and culture viability. Synthetic biology offers an alternative approach by strategically targeting proliferation pathways to arrest cell growth but have largely remained unused in industrial bioproduction. Due to recent developments in microbial decoupling systems and advances in available mammalian cell engineering tools, we propose that the synthetic biology approach to decoupling growth and production needs revisiting.
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Affiliation(s)
- James S Donaldson
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Matthew P Dale
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Susan J Rosser
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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5
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Glasscock CJ, Biggs BW, Lazar JT, Arnold JH, Burdette LA, Valdes A, Kang MK, Tullman-Ercek D, Tyo KEJ, Lucks JB. Dynamic Control of Gene Expression with Riboregulated Switchable Feedback Promoters. ACS Synth Biol 2021; 10:1199-1213. [PMID: 33834762 DOI: 10.1021/acssynbio.1c00015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One major challenge in synthetic biology is the deleterious impacts of cellular stress caused by expression of heterologous pathways, sensors, and circuits. Feedback control and dynamic regulation are broadly proposed strategies to mitigate this cellular stress by optimizing gene expression levels temporally and in response to biological cues. While a variety of approaches for feedback implementation exist, they are often complex and cannot be easily manipulated. Here, we report a strategy that uses RNA transcriptional regulators to integrate additional layers of control over the output of natural and engineered feedback responsive circuits. Called riboregulated switchable feedback promoters (rSFPs), these gene expression cassettes can be modularly activated using multiple mechanisms, from manual induction to autonomous quorum sensing, allowing control over the timing, magnitude, and autonomy of expression. We develop rSFPs in Escherichia coli to regulate multiple feedback networks and apply them to control the output of two metabolic pathways. We envision that rSFPs will become a valuable tool for flexible and dynamic control of gene expression in metabolic engineering, biological therapeutic production, and many other applications.
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Affiliation(s)
- Cameron J. Glasscock
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 113 Ho Plaza, Ithaca, New York 14853, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Bradley W. Biggs
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - John T. Lazar
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Jack H. Arnold
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lisa A. Burdette
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Aliki Valdes
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Min-Kyoung Kang
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Danielle Tullman-Ercek
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Keith E. J. Tyo
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Julius B. Lucks
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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6
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Fang Y, Wang J, Ma W, Yang J, Zhang H, Zhao L, Chen S, Zhang S, Hu X, Li Y, Wang X. Rebalancing microbial carbon distribution for L-threonine maximization using a thermal switch system. Metab Eng 2020; 61:33-46. [PMID: 32371091 DOI: 10.1016/j.ymben.2020.01.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/16/2020] [Accepted: 01/29/2020] [Indexed: 12/14/2022]
Abstract
In metabolic engineering, unbalanced microbial carbon distribution has long blocked the further improvement in yield and productivity of high-volume natural metabolites. Current studies mostly focus on regulating desired biosynthetic pathways, whereas few strategies are available to maximize L-threonine efficiently. Here, we present a strategy to guarantee the supply of reduced cofactors and actualize L-threonine maximization by regulating cellular carbon distribution in central metabolic pathways. A thermal switch system was designed and applied to divide the whole fermentation process into two stages: growth and production. This system could rebalance carbon substrates between pyruvate and oxaloacetate by controlling the heterogenous expression of pyruvate carboxylase and oxaloacetate decarboxylation that responds to temperature. The system was tested in an L-threonine producer Escherichia coli TWF001, and the resulting strain TWF106/pFT24rp overproduced L-threonine from glucose with 111.78% molar yield. The thermal switch system was then employed to switch off the L-alanine synthesis pathway, resulting in the highest L-threonine yield of 124.03%, which exceeds the best reported yield (87.88%) and the maximum available theoretical value of L-threonine production (122.47%). This inducer-free genetic circuit design can be also developed for other biosynthetic pathways to increase product conversion rates and shorten production cycles.
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Affiliation(s)
- Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jun Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Hailing Zhang
- Department of Biological Engineering, College of Life Science, Yantai University, Shandong, 264005, China
| | - Lei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Shanshan Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Shuyan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, 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; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
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7
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Liu Y, Charpin-El Hamri G, Ye H, Fussenegger M. A synthetic free fatty acid-regulated transgene switch in mammalian cells and mice. Nucleic Acids Res 2019; 46:9864-9874. [PMID: 30219861 PMCID: PMC6182168 DOI: 10.1093/nar/gky805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023] Open
Abstract
Trigger-inducible transgene expression systems are utilized in biopharmaceutical manufacturing and also to enable controlled release of therapeutic agents in vivo. We considered that free fatty acids (FFAs), which are dietary components, signaling molecules and important biomarkers, would be attractive candidates as triggers for novel transgene switches with many potential applications, e.g. in future gene- and cell-based therapies. To develop such a switch, we rewired the signal pathway of human G-protein coupled receptor 40 to a chimeric promoter triggering gene expression through an increase of intracellular calcium concentration. This synthetic gene switch is responsive to physiologically relevant FFA concentrations in different mammalian cell types grown in culture or in a bioreactor, or implanted into mice. Animal recipients of microencapsulated sensor cells containing this switch exhibited significant transgene induction following consumption of dietary fat (such as Swiss cheese) or under hyperlipidaemic conditions, including obesity, diabetes and lipodystrophy.
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Affiliation(s)
- Ying Liu
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Ghislaine Charpin-El Hamri
- Département Génie Biologique, Université Claude Bernard 1, 43 Boulevard du 11 Novembre 1918, F-69100 Villeurbanne, France
| | - Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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8
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Gupta A, Reizman IMB, Reisch CR, Prather KLJ. Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit. Nat Biotechnol 2017; 35:273-279. [PMID: 28191902 PMCID: PMC5340623 DOI: 10.1038/nbt.3796] [Citation(s) in RCA: 309] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/13/2017] [Indexed: 01/20/2023]
Abstract
Metabolic engineering of microorganisms to produce desirable products on an industrial scale can result in unbalanced cellular metabolic networks that reduce productivity and yield. Metabolic fluxes can be rebalanced using dynamic pathway regulation, but few broadly applicable tools are available to achieve this. We present a pathway-independent genetic control module that can be used to dynamically regulate the expression of target genes. We applied our module to identify the optimal point to redirect glycolytic flux into heterologous engineered pathways in Escherichia coli, resulting in 5.5-fold increased titres of myo-inositol and titers of glucaric acid that improved from unmeasurable quantities to >0.8 g/L. Scaled-up production in benchtop bioreactors resulted in almost 10-fold and 5-fold increases in titers of myo-inositol and glucaric acid. We also used our module to control flux into aromatic amino acid biosynthesis to increase titers of shikimate in E. coli from unmeasurable quantities to >100 mg/L.
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Affiliation(s)
- Apoorv Gupta
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Irene M Brockman Reizman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher R Reisch
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kristala L J Prather
- Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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9
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Müller M, Ausländer S, Spinnler A, Ausländer D, Sikorski J, Folcher M, Fussenegger M. Designed cell consortia as fragrance-programmable analog-to-digital converters. Nat Chem Biol 2017; 13:309-316. [DOI: 10.1038/nchembio.2281] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/22/2016] [Indexed: 01/09/2023]
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10
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Marchand N, Collins CH. Synthetic Quorum Sensing and Cell-Cell Communication in Gram-Positive Bacillus megaterium. ACS Synth Biol 2016. [PMID: 26203497 DOI: 10.1021/acssynbio.5b00099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The components of natural quorum-sensing (QS) systems can be used to engineer synthetic communication systems that regulate gene expression in response to chemical signals. We have used the machinery from the peptide-based agr QS system from Staphylococcus aureus to engineer a synthetic QS system in Bacillus megaterium to enable autoinduction of a target gene at high cell densities. Growth and gene expression from these synthetic QS cells were characterized in both complex and minimal media. We also split the signal production and sensing components between two strains of B. megaterium to produce sender and receiver cells and characterized the resulting communication in liquid media and on semisolid agar. The system described in this work represents the first synthetic QS and cell-cell communication system that has been engineered to function in a Gram-positive host, and it has the potential to enable the generation of dynamic gene regulatory networks in B. megaterium and other Gram-positive organisms.
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Affiliation(s)
- Nicholas Marchand
- Department of Chemical and Biological Engineering, ‡Center for Biotechnology
and Interdisciplinary
Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Cynthia H. Collins
- Department of Chemical and Biological Engineering, ‡Center for Biotechnology
and Interdisciplinary
Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
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11
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Saarenpää T, Jaakola VP, Goldman A. Baculovirus-mediated expression of GPCRs in insect cells. Methods Enzymol 2015; 556:185-218. [PMID: 25857783 DOI: 10.1016/bs.mie.2014.12.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
G-protein-coupled receptors (GPCRs) are a large family of seven transmembrane proteins that influence a considerable number of cellular events. For this reason, they are one of the most studied receptor types for their pharmacological and structural properties. Solving the structure of several GPCR receptor types has been possible using almost all expression systems, including Escherichia coli, yeast, mammalian, and insect cells. So far, however, most of the GPCR structures solved have been done using the baculovirus insect cell expression system. The reason for this is mainly due to cost-effectiveness, posttranslational modification efficiency, and overall effortless maintenance. The system has evolved so much that variables starting from vector type, purification tags, cell line, and growth conditions can be varied and optimized countless ways to suit the needs of new constructs. Here, we present the array of techniques that enable the rapid and efficient optimization of expression steps for maximal protein quality and quantity, including our emendations.
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Affiliation(s)
- Tuulia Saarenpää
- Department of Biochemistry, Helsinki University, Helsinki, Finland
| | | | - Adrian Goldman
- Department of Biochemistry, Helsinki University, Helsinki, Finland; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
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12
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Ochab-Marcinek A, Tabaka M. Transcriptional leakage versus noise: a simple mechanism of conversion between binary and graded response in autoregulated genes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:012704. [PMID: 25679640 DOI: 10.1103/physreve.91.012704] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 06/04/2023]
Abstract
We study the response of an autoregulated gene to a range of concentrations of signal molecules. We show that transcriptional leakage and noise due to translational bursting have the opposite effects. In a positively autoregulated gene, increasing the noise converts the response from graded to binary, while increasing the leakage converts the response from binary to graded. Our findings support the hypothesis that, being a common phenomenon, leaky expression may be a relatively easy way for evolutionary tuning of the type of gene response without changing the type of regulation from positive to negative.
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Affiliation(s)
- Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
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13
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Stanton BC, Siciliano V, Ghodasara A, Wroblewska L, Clancy K, Trefzer AC, Chesnut JD, Weiss R, Voigt CA. Systematic transfer of prokaryotic sensors and circuits to mammalian cells. ACS Synth Biol 2014; 3:880-91. [PMID: 25360681 PMCID: PMC4277766 DOI: 10.1021/sb5002856] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prokaryotic regulatory proteins respond to diverse signals and represent a rich resource for building synthetic sensors and circuits. The TetR family contains >10(5) members that use a simple mechanism to respond to stimuli and bind distinct DNA operators. We present a platform that enables the transfer of these regulators to mammalian cells, which is demonstrated using human embryonic kidney (HEK293) and Chinese hamster ovary (CHO) cells. The repressors are modified to include nuclear localization signals (NLS) and responsive promoters are built by incorporating multiple operators. Activators are also constructed by modifying the protein to include a VP16 domain. Together, this approach yields 15 new regulators that demonstrate 19- to 551-fold induction and retain both the low levels of crosstalk in DNA binding specificity observed between the parent regulators in Escherichia coli, as well as their dynamic range of activity. By taking advantage of the DAPG small molecule sensing mediated by the PhlF repressor, we introduce a new inducible system with 50-fold induction and a threshold of 0.9 μM DAPG, which is comparable to the classic Dox-induced TetR system. A set of NOT gates is constructed from the new repressors and their response function quantified. Finally, the Dox- and DAPG- inducible systems and two new activators are used to build a synthetic enhancer (fuzzy AND gate), requiring the coordination of 5 transcription factors organized into two layers. This work introduces a generic approach for the development of mammalian genetic sensors and circuits to populate a toolbox that can be applied to diverse applications from biomanufacturing to living therapeutics.
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Affiliation(s)
- Brynne C. Stanton
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Velia Siciliano
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amar Ghodasara
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Liliana Wroblewska
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kevin Clancy
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Axel C. Trefzer
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Jonathan D. Chesnut
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Ron Weiss
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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14
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Jagmann N, Philipp B. Reprint of Design of synthetic microbial communities for biotechnological production processes. J Biotechnol 2014; 192 Pt B:293-301. [DOI: 10.1016/j.jbiotec.2014.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Schmidl SR, Sheth RU, Wu A, Tabor JJ. Refactoring and optimization of light-switchable Escherichia coli two-component systems. ACS Synth Biol 2014; 3:820-31. [PMID: 25250630 DOI: 10.1021/sb500273n] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Light-switchable proteins enable unparalleled control of molecular biological processes in live organisms. Previously, we have engineered red/far-red and green/red photoreversible two-component signal transduction systems (TCSs) with transcriptional outputs in E. coli and used them to characterize and control synthetic gene circuits with exceptional quantitative, temporal, and spatial precision. However, the broad utility of these light sensors is limited by bulky DNA encoding, incompatibility with commonly used ligand-responsive transcription factors, leaky output in deactivating light, and less than 10-fold dynamic range. Here, we compress the four genes required for each TCS onto two streamlined plasmids and replace all chemically inducible and evolved promoters with constitutive, engineered versions. Additionally, we systematically optimize the expression of each sensor histidine kinase and response regulator, and redesign both pathway output promoters, resulting in low leakiness and 72- and 117-fold dynamic range, respectively. These second-generation light sensors can be used to program the expression of more genes over a wider range and can be more easily combined with additional plasmids or moved to different host strains. This work demonstrates that bacterial TCSs can be optimized to function as high-performance sensors for scientific and engineering applications.
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Affiliation(s)
- Sebastian R. Schmidl
- Department of Bioengineering and ‡Department of
Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ravi U. Sheth
- Department of Bioengineering and ‡Department of
Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Andrew Wu
- Department of Bioengineering and ‡Department of
Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey J. Tabor
- Department of Bioengineering and ‡Department of
Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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16
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A Synthetic Multifunctional Mammalian pH Sensor and CO2 Transgene-Control Device. Mol Cell 2014; 55:397-408. [DOI: 10.1016/j.molcel.2014.06.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/07/2014] [Accepted: 05/15/2014] [Indexed: 11/16/2022]
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17
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Oprea II, Viola JR, Moreno PMD, Simonson OE, Rodin S, Teller N, Tryggvason K, Lundin KE, Girnita L, Smith CIE. Repeatable, Inducible Micro-RNA-Based Technology Tightly Controls Liver Transgene Expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e172. [PMID: 24983837 PMCID: PMC4121515 DOI: 10.1038/mtna.2014.25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 12/29/2022]
Abstract
Inducible systems for gene expression emerge as a new class of artificial vectors offering temporal and spatial exogenous control of gene expression. However, most inducible systems are less efficient in vivo and lack the target-organ specificity. In the present study, we have developed and optimized an oligonucleotide-based inducible system for the in vivo control of transgenes in the liver. We generated a set of simple, inducible plasmid-vectors based on the addition of four units of liver-specific miR-122 target sites to the 3′untranslated region of the gene of interest. Once the vector was delivered into hepatocytes this modification induced a dramatic reduction of gene expression that could be restored by the infusion of an antagomir for miR-122. The efficiency of the system was tested in vivo, and displayed low background and strong increase in gene expression upon induction. Moreover, gene expression was repeatedly induced even several months after the first induction showing no toxic effect in vivo. By combining tissue-specific control elements with antagomir treatment we generated, optimized and validated a robust inducible system that could be used successfully for in vivo experimental models requiring tight and cyclic control of gene expression.
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Affiliation(s)
- Iulian I Oprea
- 1] Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden [2] Department of Pharmaceutical Technology and Biopharmaceutics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania [3] Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Joana R Viola
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Pedro M D Moreno
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Oscar E Simonson
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Sergey Rodin
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Karl Tryggvason
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Leonard Girnita
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Carl Inge Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
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18
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Jagmann N, Philipp B. Design of synthetic microbial communities for biotechnological production processes. J Biotechnol 2014; 184:209-18. [PMID: 24943116 DOI: 10.1016/j.jbiotec.2014.05.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/14/2014] [Accepted: 05/19/2014] [Indexed: 12/24/2022]
Abstract
In their natural habitats microorganisms live in multi-species communities, in which the community members exhibit complex metabolic interactions. In contrast, biotechnological production processes catalyzed by microorganisms are usually carried out with single strains in pure cultures. A number of production processes, however, may be more efficiently catalyzed by the concerted action of microbial communities. This review will give an overview of organismic interactions between microbial cells and of biotechnological applications of microbial communities. It focuses on synthetic microbial communities that consist of microorganisms that have been genetically engineered. Design principles for such synthetic communities will be exemplified based on plausible scenarios for biotechnological production processes. These design principles comprise interspecific metabolic interactions via cross-feeding, regulation by interspecific signaling processes via metabolites and autoinducing signal molecules, and spatial structuring of synthetic microbial communities. In particular, the implementation of metabolic interdependencies, of positive feedback regulation and of inducible cell aggregation and biofilm formation will be outlined. Synthetic microbial communities constitute a viable extension of the biotechnological application of metabolically engineered single strains and enlarge the scope of microbial production processes.
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Affiliation(s)
- Nina Jagmann
- Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstr. 3, D-48149 Münster, Germany
| | - Bodo Philipp
- Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstr. 3, D-48149 Münster, Germany.
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19
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An optogenetic gene expression system with rapid activation and deactivation kinetics. Nat Chem Biol 2014; 10:196-202. [PMID: 24413462 PMCID: PMC3944926 DOI: 10.1038/nchembio.1430] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 11/19/2013] [Indexed: 11/08/2022]
Abstract
Optogenetic gene expression systems can control transcription with spatial and temporal detail unequaled with traditional inducible promoter systems. However, current eukaryotic light-gated transcription systems are limited by toxicity, dynamic range or slow activation and deactivation. Here we present an optogenetic gene expression system that addresses these shortcomings and demonstrate its broad utility. Our approach uses an engineered version of EL222, a bacterial light-oxygen-voltage protein that binds DNA when illuminated with blue light. The system has a large (>100-fold) dynamic range of protein expression, rapid activation (<10 s) and deactivation kinetics (<50 s) and a highly linear response to light. With this system, we achieve light-gated transcription in several mammalian cell lines and intact zebrafish embryos with minimal basal gene activation and toxicity. Our approach provides a powerful new tool for optogenetic control of gene expression in space and time.
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20
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Rössger K, Charpin-El-Hamri G, Fussenegger M. Bile acid-controlled transgene expression in mammalian cells and mice. Metab Eng 2013; 21:81-90. [PMID: 24280297 DOI: 10.1016/j.ymben.2013.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/08/2013] [Accepted: 11/11/2013] [Indexed: 12/27/2022]
Abstract
In recent years, using trigger-inducible mammalian gene switches to design sophisticated transcription-control networks has become standard practice in synthetic biology. These switches provide unprecedented precision, complexity and reliability when programming novel mammalian cell functions. Metabolite-responsive repressors of human-pathogenic bacteria are particularly attractive for use in these orthogonal synthetic mammalian gene switches because the trigger compound sensitivity often matches the human physiological range. We have designed both a bile acid-repressible (BEAROFF) as well as a bile-acid-inducible (BEARON) gene switch by capitalizing on components that have evolved to manage bile acid resistance in Campylobacter jejuni, the leading causative agent of human food-borne enteritis. We have shown that both of these switches enable bile acid-adjustable transgene expression in different mammalian cell lines as well as in mice. For the BEAROFF device, the C. jejuni repressor CmeR was fused to the VP16 transactivation domain to create a synthetic transactivator that activates minimal promoters containing tandem operator modules (Ocme) in a bile acid-repressible manner. Fusion of CmeR to a transsilencing domain resulted in an artificial transsilencer that binds and represses a constitutive Ocme-containing promoter until it is released by addition of bile acid (BEARON). A tailored multi-step tuning program for the inducible gene switch, which included the optimization of individual component performance, control of their relative abundances, the choice of the cell line and trigger compound, resulted in a BEARON device with significantly improved bile acid-responsive control characteristics. Synthetic metabolite-triggered gene switches that are able to interface with host metabolism may foster advances in future gene and cell-based therapies.
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Affiliation(s)
- Katrin Rössger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Ghislaine Charpin-El-Hamri
- Département Génie Biologique, Institut Universitaire de Technologie (IUTA), F-69622 Villeurbanne Cedex, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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21
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Le H, Vishwanathan N, Kantardjieff A, Doo I, Srienc M, Zheng X, Somia N, Hu WS. Dynamic gene expression for metabolic engineering of mammalian cells in culture. Metab Eng 2013; 20:212-20. [DOI: 10.1016/j.ymben.2013.09.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/26/2013] [Accepted: 09/11/2013] [Indexed: 01/12/2023]
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22
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Umeyama T, Okada S, Ito T. Synthetic gene circuit-mediated monitoring of endogenous metabolites: identification of GAL11 as a novel multicopy enhancer of s-adenosylmethionine level in yeast. ACS Synth Biol 2013; 2:425-30. [PMID: 23654281 DOI: 10.1021/sb300115n] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Monitoring levels of key metabolites in living cells comprises a critical step in various investigations. The simplest approach to this goal is a fluorescent reporter gene using an endogenous promoter responsive to the metabolite. However, such a promoter is often not identified or even present in the species of interest. An alternative can be a synthetic gene circuit based on a heterologous pair consisting of a promoter and a transcription factor known to respond to the metabolite. We exploited the met operator and MetJ repressor of Escherichia coli, the interaction between which depends on S-adenosylmethionine (SAM), to construct synthetic gene circuits that report SAM levels in Saccharomyces cerevisiae. Using a dual-input circuit that outputs selection marker genes in a doxycycline-tunable manner, we screened a genomic library to identify GAL11 as a novel multicopy enhancer of SAM levels. These results demonstrate the potential and utility of synthetic gene circuit-mediated metabolite monitoring.
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Affiliation(s)
- Taichi Umeyama
- Department
of Biophysics and Biochemistry, Graduate School of Science,
and ‡Department of Computational
Biology, Graduate School of Frontier Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Satoshi Okada
- Department
of Biophysics and Biochemistry, Graduate School of Science,
and ‡Department of Computational
Biology, Graduate School of Frontier Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Takashi Ito
- Department
of Biophysics and Biochemistry, Graduate School of Science,
and ‡Department of Computational
Biology, Graduate School of Frontier Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
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23
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Almo SC, Garforth SJ, Hillerich BS, Love JD, Seidel RD, Burley SK. Protein production from the structural genomics perspective: achievements and future needs. Curr Opin Struct Biol 2013; 23:335-44. [PMID: 23642905 PMCID: PMC4163025 DOI: 10.1016/j.sbi.2013.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/18/2013] [Accepted: 02/18/2013] [Indexed: 01/31/2023]
Abstract
Despite a multitude of recent technical breakthroughs speeding high-resolution structural analysis of biological macromolecules, production of sufficient quantities of well-behaved, active protein continues to represent the rate-limiting step in many structure determination efforts. These challenges are only amplified when considered in the context of ongoing structural genomics efforts, which are now contending with multi-domain eukaryotic proteins, secreted proteins, and ever-larger macromolecular assemblies. Exciting new developments in eukaryotic expression platforms, including insect and mammalian-based systems, promise enhanced opportunities for structural approaches to some of the most important biological problems. Development and implementation of automated eukaryotic expression techniques promises to significantly improve production of materials for structural, functional, and biomedical research applications.
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Affiliation(s)
- Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States.
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24
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Bacchus W, Fussenegger M. Engineering of synthetic intercellular communication systems. Metab Eng 2013; 16:33-41. [DOI: 10.1016/j.ymben.2012.12.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 12/03/2012] [Accepted: 12/05/2012] [Indexed: 10/27/2022]
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25
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Casteleijn MG, Urtti A, Sarkhel S. Expression without boundaries: Cell-free protein synthesis in pharmaceutical research. Int J Pharm 2013; 440:39-47. [DOI: 10.1016/j.ijpharm.2012.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/01/2012] [Accepted: 04/03/2012] [Indexed: 11/15/2022]
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26
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Gleba YY, Tusé D, Giritch A. Plant viral vectors for delivery by Agrobacterium. Curr Top Microbiol Immunol 2013; 375:155-92. [PMID: 23949286 DOI: 10.1007/82_2013_352] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Plant viral vectors delivered by Agrobacterium are the basis of several manufacturing processes that are currently in use for producing a wide range of proteins for multiple applications, including vaccine antigens, antibodies, protein nanoparticles such as virus-like particles (VLPs), and other protein and protein-RNA scaffolds. Viral vectors delivered by agrobacterial T-DNA transfer (magnifection) have also become important tools in research. In recent years, essential advances have been made both in the development of second-generation vectors designed using the 'deconstructed virus' approach, as well as in the development of upstream manufacturing processes that are robust and fully scalable. The strategy relies on Agrobacterium as a vector to deliver DNA copies of one or more viral RNA/DNA replicons; the bacteria are delivered into leaves by vacuum infiltration, and the viral machinery takes over from the point of T-DNA transfer to the plant cell nucleus, driving massive RNA and protein production and, if required, cell-to-cell spread of the replicons. Among the most often used viral backbones are those of the RNA viruses Tobacco mosaic virus (TMV), Potato virus X (PVX) and Cowpea mosaic virus (CPMV), and the DNA geminivirus Bean yellow dwarf virus. Prototypes of industrial processes that provide for high yield, rapid scale up and fast manufacturing cycles have been designed, and several GMP-compliant and GMP-certified manufacturing facilities are in place. These efforts have been successful as evidenced by the fact that several antibodies and vaccine antigens produced by magnifection are currently in clinical development.
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Affiliation(s)
- Yuri Y Gleba
- Nomad Bioscience GmbH, Weinbergweg 22, Halle (Saale), Germany,
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27
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Bacchus W, Weber W, Fussenegger M. Increasing the dynamic control space of mammalian transcription devices by combinatorial assembly of homologous regulatory elements from different bacterial species. Metab Eng 2013. [DOI: 10.1016/j.ymben.2012.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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28
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Gitzinger M, Kemmer C, Fluri DA, El-Baba MD, Weber W, Fussenegger M. The food additive vanillic acid controls transgene expression in mammalian cells and mice. Nucleic Acids Res 2011; 40:e37. [PMID: 22187155 PMCID: PMC3300003 DOI: 10.1093/nar/gkr1251] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Trigger-inducible transcription-control devices that reversibly fine-tune transgene expression in response to molecular cues have significantly advanced the rational reprogramming of mammalian cells. When designed for use in future gene- and cell-based therapies the trigger molecules have to be carefully chosen in order to provide maximum specificity, minimal side-effects and optimal pharmacokinetics in a mammalian organism. Capitalizing on control components that enable Caulobacter crescentus to metabolize vanillic acid originating from lignin degradation that occurs in its oligotrophic freshwater habitat, we have designed synthetic devices that specifically adjust transgene expression in mammalian cells when exposed to vanillic acid. Even in mice transgene expression was robust, precise and tunable in response to vanillic acid. As a licensed food additive that is regularly consumed by humans via flavoured convenience food and specific fresh vegetable and fruits, vanillic acid can be considered as a safe trigger molecule that could be used for diet-controlled transgene expression in future gene- and cell-based therapies.
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Affiliation(s)
- Marc Gitzinger
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
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29
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Werner S, Breus O, Symonenko Y, Marillonnet S, Gleba Y. High-level recombinant protein expression in transgenic plants by using a double-inducible viral vector. Proc Natl Acad Sci U S A 2011; 108:14061-6. [PMID: 21825158 PMCID: PMC3161547 DOI: 10.1073/pnas.1102928108] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We describe here a unique ethanol-inducible process for expression of recombinant proteins in transgenic plants. The process is based on inducible release of viral RNA replicons from stably integrated DNA proreplicons. A simple treatment with ethanol releases the replicon leading to RNA amplification and high-level protein production. To achieve tight control of replicon activation and spread in the uninduced state, the viral vector has been deconstructed, and its two components, the replicon and the cell-to-cell movement protein, have each been placed separately under the control of an inducible promoter. Transgenic Nicotiana benthamiana plants incorporating this double-inducible system demonstrate negligible background expression, high (over 0.5 × 10(4)-fold) induction multiples, and high absolute levels of protein expression upon induction (up to 4.3 mg/g fresh biomass). The process can be easily scaled up, supports expression of practically important recombinant proteins, and thus can be directly used for industrial manufacturing.
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Affiliation(s)
- Stefan Werner
- Icon Genetics GmbH, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Oksana Breus
- Icon Genetics GmbH, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Yuri Symonenko
- Icon Genetics GmbH, Weinbergweg 22, 06120 Halle/Saale, Germany
| | | | - Yuri Gleba
- Icon Genetics GmbH, Weinbergweg 22, 06120 Halle/Saale, Germany
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30
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Ye H, Daoud-El Baba M, Peng RW, Fussenegger M. A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 2011; 332:1565-8. [PMID: 21700876 DOI: 10.1126/science.1203535] [Citation(s) in RCA: 312] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Synthetic biology has advanced the design of genetic devices that can be used to reprogram metabolic activities in mammalian cells. By functionally linking the signal transduction of melanopsin to the control circuit of the nuclear factor of activated T cells, we have designed a synthetic signaling cascade enabling light-inducible transgene expression in different cell lines grown in culture or bioreactors or implanted into mice. In animals harboring intraperitoneal hollow-fiber or subcutaneous implants containing light-inducible transgenic cells, the serum levels of the human glycoprotein secreted alkaline phosphatase could be remote-controlled with fiber optics or transdermally regulated through direct illumination. Light-controlled expression of the glucagon-like peptide 1 was able to attenuate glycemic excursions in type II diabetic mice. Synthetic light-pulse-transcription converters may have applications in therapeutics and protein expression technology.
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Affiliation(s)
- Haifeng Ye
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
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31
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Niklas J, Heinzle E. Metabolic flux analysis in systems biology of mammalian cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2011; 127:109-32. [PMID: 21432052 DOI: 10.1007/10_2011_99] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reaction rates or metabolic fluxes reflect the integrated phenotype of genome, transcriptome and proteome interactions, including regulation at all levels of the cellular hierarchy. Different methods have been developed in the past to analyse intracellular fluxes. However, compartmentation of mammalian cells, varying utilisation of multiple substrates, reversibility of metabolite uptake and production, unbalanced growth behaviour and adaptation of cells to changing environment during cultivation are just some reasons that make metabolic flux analysis (MFA) in mammalian cell culture more challenging compared to microorganisms. In this article MFA using the metabolite balancing methodology and the advantages and disadvantages of (13)C MFA in mammalian cell systems are reviewed. Application examples of MFA in the optimisation of cell culture processes for the production of biopharmaceuticals are presented with a focus on the metabolism of the main industrial workhorse. Another area in which mammalian cell culture plays a key role is in medical and toxicological research. It is shown that MFA can be used to understand pathophysiological mechanisms and can assist in understanding effects of drugs or other compounds on cellular metabolism.
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Affiliation(s)
- Jens Niklas
- Biochemical Engineering Institute, Saarland University, Campus A 1.5, 66123, Saarbrücken, Germany
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32
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Tyo KE, Nevoigt E, Stephanopoulos G. Directed Evolution of Promoters and Tandem Gene Arrays for Customizing RNA Synthesis Rates and Regulation. Methods Enzymol 2011; 497:135-55. [DOI: 10.1016/b978-0-12-385075-1.00006-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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33
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Peng RW, Abellan E, Fussenegger M. Differential effect of exocytic SNAREs on the production of recombinant proteins in mammalian cells. Biotechnol Bioeng 2010; 108:611-20. [PMID: 21246508 DOI: 10.1002/bit.22986] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 09/29/2010] [Accepted: 10/18/2010] [Indexed: 01/09/2023]
Abstract
Mammalian cells play a dominant role in the industrial production of biopharmaceutical proteins. However, the productivity of producer cells is often hindered by a bottleneck in the saturated secretory pathway, where a sophisticated mechanism of vesicle trafficking is mediated by numerous proteins and their complexes, among which are the cross-kingdom conserved SNAREs [soluble NSF (N-ethylmaleimide-sensitive factor) receptor]. The SNAREs assemble into complexes by means of four interactive α-helices and, thus, trigger the fusion of transport vesicles with the respective target membranes. We report that the transgenic expression of exocytic SNAREs, which control the fusion of secretory vesicles to the plasma membrane, differentially impacts the secretory capacity of HEK-293, HeLa, and CHO-K1 cells. While other exocytic SNAREs have no effect or a negative effect, SNAP-23 [synaptosome-associated protein of 23 kDa] and VAMP8 [vesicle-associated membrane protein 8] specifically increase the production of recombinant proteins when they are ectopically and stably expressed in mammalian cells. The targeted and effective intervention in the secretory capacity of SNARE proteins is a novel engineering strategy, which could lead to the development of new therapies by increasing the production of biopharmaceutical proteins or by boosting the secretion of cell implants in cell therapy initiatives.
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Affiliation(s)
- Ren-Wang Peng
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland
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34
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35
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Kämpf MM, Weber W. Synthetic biology in the analysis and engineering of signaling processes. Integr Biol (Camb) 2010; 2:12-24. [DOI: 10.1039/b913490e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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36
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Schucht R, Wirth D, May T. Precise regulation of transgene expression level and control of cell physiology. Cell Biol Toxicol 2009; 26:29-42. [DOI: 10.1007/s10565-009-9135-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 08/10/2009] [Indexed: 12/12/2022]
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37
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Christen EH, Karlsson M, Kämpf MM, Weber CC, Fussenegger M, Weber W. A general strategy for the production of difficult-to-express inducer-dependent bacterial repressor proteins in Escherichia coli. Protein Expr Purif 2009; 66:158-64. [DOI: 10.1016/j.pep.2009.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 03/13/2009] [Accepted: 03/14/2009] [Indexed: 01/14/2023]
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38
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Controlling transgene expression in subcutaneous implants using a skin lotion containing the apple metabolite phloretin. Proc Natl Acad Sci U S A 2009; 106:10638-43. [PMID: 19549857 DOI: 10.1073/pnas.0901501106] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Adjustable control of therapeutic transgenes in engineered cell implants after transdermal and topical delivery of nontoxic trigger molecules would increase convenience, patient compliance, and elimination of hepatic first-pass effect in future therapies. Pseudomonas putida DOT-T1E has evolved the flavonoid-triggered TtgR operon, which controls expression of a multisubstrate-specific efflux pump (TtgABC) to resist plant-derived defense metabolites in its rhizosphere habitat. Taking advantage of the TtgR operon, we have engineered a hybrid P. putida-mammalian genetic unit responsive to phloretin. This flavonoid is contained in apples, and, as such, or as dietary supplement, regularly consumed by humans. The engineered mammalian phloretin-adjustable control element (PEACE) enabled adjustable and reversible transgene expression in different mammalian cell lines and primary cells. Due to the short half-life of phloretin in culture, PEACE could also be used to program expression of difficult-to-produce protein therapeutics during standard bioreactor operation. When formulated in skin lotions and applied to the skin of mice harboring transgenic cell implants, phloretin was able to fine-tune target genes and adjust heterologous protein levels in the bloodstream of treated mice. PEACE-controlled target gene expression could foster advances in biopharmaceutical manufacturing as well as gene- and cell-based therapies.
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Wallbaum S, Grau N, Schmid A, Frick K, Neeb A, Sleeman JP. Cell cycle quiescence can suppress transcription from an ecdysone receptor–based inducible promoter in mammalian cells. Biotechniques 2009; 46:433-40. [DOI: 10.2144/000113121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Inducible gene expression is a powerful tool for basic research, gene therapy and biotechnology, whose utility depends in part on consistent levels of induction regardless of metabolic status or physiological context. Here we examined the inducibility of the ecdysone receptor–based RheoSwitch mammalian inducible expression system in proliferating cells and in cell cycle–arrested cells. We found that both contact inhibition and growth arrest subsequent to serum deprivation dramatically reduced the levels of induction of reporter genes that could be achieved in 3T3 fibroblasts but in not NMuMG mammary epithelial cells. These data have implications for the use of the RheoSwitch system in inducible gene expression applications.
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Affiliation(s)
- Sabine Wallbaum
- Forschungszentrum Karlsruhe, Institut für Toxikologie und Genetik, Karlsruhe, Germany
| | - Nicole Grau
- Forschungszentrum Karlsruhe, Institut für Toxikologie und Genetik, Karlsruhe, Germany
| | - Anja Schmid
- Forschungszentrum Karlsruhe, Institut für Toxikologie und Genetik, Karlsruhe, Germany
| | - Katharina Frick
- Forschungszentrum Karlsruhe, Institut für Toxikologie und Genetik, Karlsruhe, Germany
| | - Antje Neeb
- Forschungszentrum Karlsruhe, Institut für Toxikologie und Genetik, Karlsruhe, Germany
| | - Jonathan P. Sleeman
- Forschungszentrum Karlsruhe, Institut für Toxikologie und Genetik, Karlsruhe, Germany
- Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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Weber W, Fussenegger M. Engineering of Synthetic Mammalian Gene Networks. ACTA ACUST UNITED AC 2009; 16:287-97. [DOI: 10.1016/j.chembiol.2009.02.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/28/2009] [Accepted: 02/03/2009] [Indexed: 12/15/2022]
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Deshpande R, Yang TH, Heinzle E. Towards a metabolic and isotopic steady state in CHO batch cultures for reliable isotope-based metabolic profiling. Biotechnol J 2009; 4:247-63. [DOI: 10.1002/biot.200800143] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Gitzinger M, Parsons J, Reski R, Fussenegger M. Functional cross-kingdom conservation of mammalian and moss (Physcomitrella patens) transcription, translation and secretion machineries. PLANT BIOTECHNOLOGY JOURNAL 2009; 7:73-86. [PMID: 19021876 DOI: 10.1111/j.1467-7652.2008.00376.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Plants and mammals are separated by a huge evolutionary distance. Consequently, biotechnology and genetics have traditionally been divided into 'green' and 'red'. Here, we provide comprehensive evidence that key components of the mammalian transcription, translation and secretion machineries are functional in the model plant Physcomitrella patens. Cross-kingdom compatibility of different expression modalities originally designed for mammalian cells, such as native and synthetic promoters and polyadenylation sites, viral and cellular internal ribosome entry sites, secretion signal peptides and secreted product proteins, and synthetic transactivators and transrepressors, was established. This mammalian expression portfolio enabled constitutive, conditional and autoregulated expression of different product genes in a multicistronic expression format, optionally adjusted by various trigger molecules, such as butyrolactones, macrolide antibiotics and ethanol. Capitalizing on a cross-kingdom-compatible expression platform, we pioneered a prototype biopharmaceutical manufacturing scenario using microencapsulated transgenic P. patens protoplasts cultivated in a Wave Bioreactor. Vascular endothelial growth factor 121 (VEGF(121)) titres matched those typically achieved by standard protonema populations grown in stirred-tank bioreactors. The full compatibility of mammalian expression systems in P. patens further promotes the use of moss as a cost-effective alternative for the manufacture of complex biopharmaceuticals, and as a valuable host system to advance synthetic biology in plants.
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Affiliation(s)
- Marc Gitzinger
- Department for Biosystems Science and Engineering, ETH Zurich, Wolfgang-Pauli-Strasse 10, HCI F115, CH-8093 Zurich, Switzerland
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Müller D, Katinger H, Grillari J. MicroRNAs as targets for engineering of CHO cell factories. Trends Biotechnol 2008; 26:359-65. [DOI: 10.1016/j.tibtech.2008.03.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2008] [Revised: 03/26/2008] [Accepted: 03/26/2008] [Indexed: 01/10/2023]
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Regenerating cochlear hair cells: quo vadis stem cell. Cell Tissue Res 2008; 333:373-9. [PMID: 18575894 DOI: 10.1007/s00441-008-0639-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 05/07/2008] [Accepted: 05/08/2008] [Indexed: 12/30/2022]
Abstract
Many elderly people worldwide lose the neurosensory part of their ear and turn deaf. Cochlear implants to restore some hearing after neurosensory hearing loss are, at present, the only therapy for these people. In contrast to this therapy, replacement of hair cells via stem cell therapies holds the promise for a cure. We review here current insights into embryonic, adult, and inducible stem cells that might provide cells for seeding the cochlea with the hope of new hair cell formation. We propose a two-step approach using a first set of transcription factors to enhance the generation of inducible pluripotent stem (iPS) cells and a second set of factors to initiate the differentiation of hair cells. Recent evidence regarding ear development and stem cell research strongly suggest that microRNAs will be an important new regulatory factor in both iPS cell formation and differentiation to reprogram cells into hair cells. In addition, we highlight currently insurmountable obstacles to the successful transformation of stem cells into hair cell precursors and their injection into the cochlear canal to replace lost hair cells.
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