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Wagner L, Jules M, Borkowski O. What remains from living cells in bacterial lysate-based cell-free systems. Comput Struct Biotechnol J 2023; 21:3173-3182. [PMID: 37333859 PMCID: PMC10275740 DOI: 10.1016/j.csbj.2023.05.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Abstract
Because they mimic cells while offering an accessible and controllable environment, lysate-based cell-free systems (CFS) have emerged as valuable biotechnology tools for synthetic biology. Historically used to uncover fundamental mechanisms of life, CFS are nowadays used for a multitude of purposes, including protein production and prototyping of synthetic circuits. Despite the conservation of fundamental functions in CFS like transcription and translation, RNAs and certain membrane-embedded or membrane-bound proteins of the host cell are lost when preparing the lysate. As a result, CFS largely lack some essential properties of living cells, such as the ability to adapt to changing conditions, to maintain homeostasis and spatial organization. Regardless of the application, shedding light on the black-box of the bacterial lysate is necessary to fully exploit the potential of CFS. Most measurements of the activity of synthetic circuits in CFS and in vivo show significant correlations because these only require processes that are preserved in CFS, like transcription and translation. However, prototyping circuits of higher complexity that require functions that are lost in CFS (cell adaptation, homeostasis, spatial organization) will not show such a good correlation with in vivo conditions. Both for prototyping circuits of higher complexity and for building artificial cells, the cell-free community has developed devices to reconstruct cellular functions. This mini-review compares bacterial CFS to living cells, focusing on functional and cellular process differences and the latest developments in restoring lost functions through complementation of the lysate or device engineering.
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Borkowski O, Koch M, Zettor A, Pandi A, Batista AC, Soudier P, Faulon JL. Large scale active-learning-guided exploration for in vitro protein production optimization. Nat Commun 2020; 11:1872. [PMID: 32312991 PMCID: PMC7170859 DOI: 10.1038/s41467-020-15798-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/24/2020] [Indexed: 12/21/2022] Open
Abstract
Lysate-based cell-free systems have become a major platform to study gene expression but batch-to-batch variation makes protein production difficult to predict. Here we describe an active learning approach to explore a combinatorial space of ~4,000,000 cell-free buffer compositions, maximizing protein production and identifying critical parameters involved in cell-free productivity. We also provide a one-step-method to achieve high quality predictions for protein production using minimal experimental effort regardless of the lysate quality.
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Affiliation(s)
- Olivier Borkowski
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Mathilde Koch
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Agnès Zettor
- Chemogenomic and Biological Screening Core Facility, Institut Pasteur, Department of Structural Biology and Chemistry, Center for Technological Resources and Research (C2RT), 25/28 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Amir Pandi
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Paul Soudier
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Loup Faulon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France. .,Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France. .,SYNBIOCHEM Center, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK.
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Abstract
Cell-free systems are promising platforms for rapid and high-throughput prototyping of biological parts in metabolic engineering and synthetic biology. One main limitation of cell-free system applications is the low fold repression of transcriptional repressors. Hence, prokaryotic biosensor development, which mostly relies on repressors, is limited. In this study, we demonstrate how to improve these biosensors in cell-free systems by applying a transcription factor (TF)-doped extract, a preincubation strategy with the TF plasmid, or reinitiation of the cell-free reaction (two-step cell-free reaction). We use the optimized biosensor to sense the enzymatic production of a rare sugar, D-psicose. This work provides a methodology to optimize repressor-based systems in cell-free to further increase the potential of cell-free systems for bioproduction.
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Affiliation(s)
- Amir Pandi
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas 78352, France
| | - Ioana Grigoras
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
| | - Olivier Borkowski
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas 78352, France
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
- SYNBIOCHEM Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
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Koch M, Faulon JL, Borkowski O. Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster. Front Bioeng Biotechnol 2018; 6:182. [PMID: 30555825 PMCID: PMC6281764 DOI: 10.3389/fbioe.2018.00182] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Abstract
Cell-free TX-TL is an increasingly mature and useful platform for prototyping, testing, and engineering biological parts and systems. However, to fully accomplish the promises of synthetic biology, mathematical models are required to facilitate the design and predict the behavior of biological components in cell-free extracts. We review here the latest models accounting for transcription, translation, competition, and depletion of resources as well as genome scale models for lysate-based cell-free TX-TL systems, including their current limitations. These models will have to find ways to account for batch-to-batch variability before being quantitatively predictive in cell-free lysate-based platforms.
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Affiliation(s)
- Mathilde Koch
- Micalis Institute, INRA, AgroParisTech, University of Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, University of Paris-Saclay, Jouy-en-Josas, France
- Systems and Synthetic Biology Lab, CEA, CNRS, UMR 8030, Genomics Metabolics, University Paris-Saclay, Évry, France
- SYNBIOCHEM Center, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Olivier Borkowski
- Micalis Institute, INRA, AgroParisTech, University of Paris-Saclay, Jouy-en-Josas, France
- Systems and Synthetic Biology Lab, CEA, CNRS, UMR 8030, Genomics Metabolics, University Paris-Saclay, Évry, France
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Borkowski O, Bricio C, Murgiano M, Rothschild-Mancinelli B, Stan GB, Ellis T. Cell-free prediction of protein expression costs for growing cells. Nat Commun 2018; 9:1457. [PMID: 29654285 PMCID: PMC5899134 DOI: 10.1038/s41467-018-03970-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 03/26/2018] [Indexed: 01/12/2023] Open
Abstract
Translating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any given gene is a major challenge, as multiple processes and factors combine to determine translation efficiency. To enable prediction of the cost of gene expression in bacteria, we describe here a standard cell-free lysate assay that provides a relative measure of resource consumption when a protein coding sequence is expressed. These lysate measurements can then be used with a computational model of translation to predict the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway.
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Affiliation(s)
- Olivier Borkowski
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Carlos Bricio
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Michela Murgiano
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Brooke Rothschild-Mancinelli
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Guy-Bart Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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Ceroni F, Boo A, Furini S, Gorochowski TE, Borkowski O, Ladak YN, Awan AR, Gilbert C, Stan GB, Ellis T. Burden-driven feedback control of gene expression. Nat Methods 2018; 15:387-393. [PMID: 29578536 DOI: 10.1038/nmeth.4635] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 02/01/2018] [Indexed: 12/21/2022]
Abstract
Cells use feedback regulation to ensure robust growth despite fluctuating demands for resources and differing environmental conditions. However, the expression of foreign proteins from engineered constructs is an unnatural burden that cells are not adapted for. Here we combined RNA-seq with an in vivo assay to identify the major transcriptional changes that occur in Escherichia coli when inducible synthetic constructs are expressed. We observed that native promoters related to the heat-shock response activated expression rapidly in response to synthetic expression, regardless of the construct. Using these promoters, we built a dCas9-based feedback-regulation system that automatically adjusts the expression of a synthetic construct in response to burden. Cells equipped with this general-use controller maintained their capacity for native gene expression to ensure robust growth and thus outperformed unregulated cells in terms of protein yield in batch production. This engineered feedback is to our knowledge the first example of a universal, burden-based biomolecular control system and is modular, tunable and portable.
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Affiliation(s)
- Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Alice Boo
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Olivier Borkowski
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Yaseen N Ladak
- ITMAT Data Science Group, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Ali R Awan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Charlie Gilbert
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Guy-Bart Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
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Borkowski O, Ceroni F, Stan GB, Ellis T. Overloaded and stressed: whole-cell considerations for bacterial synthetic biology. Curr Opin Microbiol 2016; 33:123-130. [PMID: 27494248 DOI: 10.1016/j.mib.2016.07.009] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/04/2016] [Accepted: 07/06/2016] [Indexed: 12/27/2022]
Abstract
The predictability and robustness of engineered bacteria depend on the many interactions between synthetic constructs and their host cells. Expression from synthetic constructs is an unnatural load for the host that typically reduces growth, triggers stresses and leads to decrease in performance or failure of engineered cells. Work in systems and synthetic biology has now begun to address this through new tools, methods and strategies that characterise and exploit host-construct interactions in bacteria. Focusing on work in E. coli, we review here a selection of the recent developments in this area, highlighting the emerging issues and describing the new solutions that are now making the synthetic biology community consider the cell just as much as they consider the construct.
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Affiliation(s)
- Olivier Borkowski
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Francesca Ceroni
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Guy-Bart Stan
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK.
| | - Tom Ellis
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK.
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Affiliation(s)
- Olivier Borkowski
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Charlie Gilbert
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Tom Ellis
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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Borkowski O, Goelzer A, Schaffer M, Calabre M, Mäder U, Aymerich S, Jules M, Fromion V. Translation elicits a growth rate-dependent, genome-wide, differential protein production in Bacillus subtilis. Mol Syst Biol 2016; 12:870. [PMID: 27193784 PMCID: PMC5683663 DOI: 10.15252/msb.20156608] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 11/30/2022] Open
Abstract
Complex regulatory programs control cell adaptation to environmental changes by setting condition-specific proteomes. In balanced growth, bacterial protein abundances depend on the dilution rate, transcript abundances and transcript-specific translation efficiencies. We revisited the current theory claiming the invariance of bacterial translation efficiency. By integrating genome-wide transcriptome datasets and datasets from a library of synthetic gfp-reporter fusions, we demonstrated that translation efficiencies in Bacillus subtilis decreased up to fourfold from slow to fast growth. The translation initiation regions elicited a growth rate-dependent, differential production of proteins without regulators, hence revealing a unique, hard-coded, growth rate-dependent mode of regulation. We combined model-based data analyses of transcript and protein abundances genome-wide and revealed that this global regulation is extensively used in B. subtilis We eventually developed a knowledge-based, three-step translation initiation model, experimentally challenged the model predictions and proposed that a growth rate-dependent drop in free ribosome abundance accounted for the differential protein production.
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Affiliation(s)
- Olivier Borkowski
- Micalis Institute, INRA AgroParisTech Université Paris-Saclay, Jouy-en-Josas, 78350, France MaIAGE, INRA Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Anne Goelzer
- MaIAGE, INRA Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Marc Schaffer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Magali Calabre
- Micalis Institute, INRA AgroParisTech Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stéphane Aymerich
- Micalis Institute, INRA AgroParisTech Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Matthieu Jules
- Micalis Institute, INRA AgroParisTech Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Vincent Fromion
- MaIAGE, INRA Université Paris-Saclay, Jouy-en-Josas, 78350, France
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