1
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Radde N, Mortensen GA, Bhat D, Shah S, Clements JJ, Leonard SP, McGuffie MJ, Mishler DM, Barrick JE. Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology. Nat Commun 2024; 15:6242. [PMID: 39048554 PMCID: PMC11269670 DOI: 10.1038/s41467-024-50639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
Engineered DNA will slow the growth of a host cell if it redirects limiting resources or otherwise interferes with homeostasis. Escape mutants that alleviate this burden can rapidly evolve and take over cell populations, making genetic engineering less reliable and predictable. Synthetic biologists often use genetic parts encoded on plasmids, but their burden is rarely characterized. We measured how 301 BioBrick plasmids affected Escherichia coli growth and found that 59 (19.6%) were burdensome, primarily because they depleted the limited gene expression resources of host cells. Overall, no BioBricks reduced the growth rate of E. coli by >45%, which agreed with a population genetic model that predicts such plasmids should be unclonable. We made this model available online for education ( https://barricklab.org/burden-model ) and added our burden measurements to the iGEM Registry. Our results establish a fundamental limit on what DNA constructs and genetic modifications can be successfully engineered into cells.
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Affiliation(s)
- Noor Radde
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Genevieve A Mortensen
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Diya Bhat
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Shireen Shah
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Joseph J Clements
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Sean P Leonard
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Matthew J McGuffie
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Dennis M Mishler
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
- The Freshman Research Initiative, College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
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2
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Durmusoglu D, Haller DJ, Al'Abri IS, Day K, Sands C, Clark A, San-Miguel A, Vazquez-Uribe R, Sommer MOA, Crook NC. Programming Probiotics: Diet-Responsive Gene Expression and Colonization Control in Engineered S. boulardii. ACS Synth Biol 2024; 13:1851-1865. [PMID: 38787439 DOI: 10.1021/acssynbio.4c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Saccharomyces boulardii (Sb) is an emerging probiotic chassis for delivering biomolecules to the mammalian gut, offering unique advantages as the only eukaryotic probiotic. However, precise control over gene expression and gut residence time in Sb have remained challenging. To address this, we developed five ligand-responsive gene expression systems and repaired galactose metabolism in Sb, enabling inducible gene expression in this strain. Engineering these systems allowed us to construct AND logic gates, control the surface display of proteins, and turn on protein production in the mouse gut in response to dietary sugar. Additionally, repairing galactose metabolism expanded Sb's habitat within the intestines and resulted in galactose-responsive control over gut residence time. This work opens new avenues for precise dosing of therapeutics by Sb via control over its in vivo gene expression levels and localization within the gastrointestinal tract.
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Affiliation(s)
- Deniz Durmusoglu
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Daniel J Haller
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Ibrahim S Al'Abri
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Katie Day
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Carmen Sands
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Andrew Clark
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Adriana San-Miguel
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nathan C Crook
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
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3
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Radde N, Mortensen GA, Bhat D, Shah S, Clements JJ, Leonard SP, McGuffie MJ, Mishler DM, Barrick JE. Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588465. [PMID: 38645188 PMCID: PMC11030366 DOI: 10.1101/2024.04.08.588465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Engineered DNA will slow the growth of a host cell if it redirects limiting resources or otherwise interferes with homeostasis. Populations of engineered cells can rapidly become dominated by "escape mutants" that evolve to alleviate this burden by inactivating the intended function. Synthetic biologists working with bacteria rely on genetic parts and devices encoded on plasmids, but the burden of different engineered DNA sequences is rarely characterized. We measured how 301 BioBricks on high-copy plasmids affected the growth rate of Escherichia coli. Of these, 59 (19.6%) negatively impacted growth. The burden imposed by engineered DNA is commonly associated with diverting ribosomes or other gene expression factors away from producing endogenous genes that are essential for cellular replication. In line with this expectation, BioBricks exhibiting burden were more likely to contain highly active constitutive promoters and strong ribosome binding sites. By monitoring how much each BioBrick reduced expression of a chromosomal GFP reporter, we found that the burden of most, but not all, BioBricks could be wholly explained by diversion of gene expression resources. Overall, no BioBricks reduced the growth rate of E. coli by >45%, which agreed with a population genetic model that predicts such plasmids should be "unclonable" because escape mutants will take over during growth of a bacterial colony or small laboratory culture from a transformed cell. We made this model available as an interactive web tool for synthetic biology education and added our burden measurements to the iGEM Registry descriptions of each BioBrick.
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Affiliation(s)
- Noor Radde
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Genevieve A. Mortensen
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Diya Bhat
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Shireen Shah
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Joseph J. Clements
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sean P. Leonard
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Matthew J. McGuffie
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Dennis M. Mishler
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
- The Freshman Research Initiative, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
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4
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Glass DS, Bren A, Vaisbourd E, Mayo A, Alon U. A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover. Cell 2024; 187:931-944.e12. [PMID: 38320549 PMCID: PMC10882425 DOI: 10.1016/j.cell.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/27/2023] [Accepted: 01/16/2024] [Indexed: 02/08/2024]
Abstract
Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.
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Affiliation(s)
- David S Glass
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elizabeth Vaisbourd
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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5
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Ma Y, Ye JW, Lin Y, Yi X, Wang X, Wang H, Huang R, Wu F, Wu Q, Liu X, Chen GQ. Flux optimization using multiple promoters in Halomonas bluephagenesis as a model chassis of the next generation industrial biotechnology. Metab Eng 2024; 81:249-261. [PMID: 38159902 DOI: 10.1016/j.ymben.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/16/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
Predictability and robustness are challenges for bioproduction because of the unstable intracellular synthetic activities. With the deeper understanding of the gene expression process, fine-tuning has become a meaningful tool for biosynthesis optimization. This study characterized several gene expression elements and constructed a multiple inducible system that responds to ten different small chemical inducers in halophile bacterium Halomonas bluephagenesis. Genome insertion of regulators was conducted for the purpose of gene cluster stabilization and regulatory plasmid simplification. Additionally, dynamic ranges of the multiple inducible systems were tuned by promoter sequence mutations to achieve diverse scopes for high-resolution gene expression control. The multiple inducible system was successfully employed to precisely control chromoprotein expression, lycopene and poly-3-hydroxybutyrate (PHB) biosynthesis, resulting in colorful bacterial pictures, optimized cell growth, lycopene and PHB accumulation. This study demonstrates a desirable approach for fine-tuning of rational and efficient gene expressions, displaying the significance for metabolic pathway optimization.
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Affiliation(s)
- Yueyuan Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yina Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xueqing Yi
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ruiyan Huang
- Garrison Forest School, Owings Mills, MD, 21117, USA
| | - Fuqing Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Beijing, 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; MOE Key Laboratory for Industrial Biocatalysts, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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6
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Arbel-Groissman M, Menuhin-Gruman I, Yehezkeli H, Naki D, Bergman S, Udi Y, Tuller T. The Causes for Genomic Instability and How to Try and Reduce Them Through Rational Design of Synthetic DNA. Methods Mol Biol 2024; 2760:371-392. [PMID: 38468099 DOI: 10.1007/978-1-0716-3658-9_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Genetic engineering has revolutionized our ability to manipulate DNA and engineer organisms for various applications. However, this approach can lead to genomic instability, which can result in unwanted effects such as toxicity, mutagenesis, and reduced productivity. To overcome these challenges, smart design of synthetic DNA has emerged as a promising solution. By taking into consideration the intricate relationships between gene expression and cellular metabolism, researchers can design synthetic constructs that minimize metabolic stress on the host cell, reduce mutagenesis, and increase protein yield. In this chapter, we summarize the main challenges of genomic instability in genetic engineering and address the dangers of unknowingly incorporating genomically unstable sequences in synthetic DNA. We also demonstrate the instability of those sequences by the fact that they are selected against conserved sequences in nature. We highlight the benefits of using ESO, a tool for the rational design of DNA for avoiding genetically unstable sequences, and also summarize the main principles and working parameters of the software that allow maximizing its benefits and impact.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hader Yehezkeli
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Yarin Udi
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel.
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7
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Arbel-Groissman M, Menuhin-Gruman I, Naki D, Bergman S, Tuller T. Fighting the battle against evolution: designing genetically modified organisms for evolutionary stability. Trends Biotechnol 2023; 41:1518-1531. [PMID: 37442714 DOI: 10.1016/j.tibtech.2023.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Synthetic biology has made significant progress in many areas, but a major challenge that has received limited attention is the evolutionary stability of synthetic constructs made of heterologous genes. The expression of these constructs in microorganisms, that is, production of proteins that are not necessary for the organism, is a metabolic burden, leading to a decrease in relative fitness and make the synthetic constructs unstable over time. This is a significant concern for the synthetic biology community, particularly when it comes to bringing this technology out of the laboratory. In this review, we discuss the issue of evolutionary stability in synthetic biology and review the available tools to address this challenge.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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8
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Arboleda-García A, Alarcon-Ruiz I, Boada-Acosta L, Boada Y, Vignoni A, Jantus-Lewintre E. Advancements in synthetic biology-based bacterial cancer therapy: A modular design approach. Crit Rev Oncol Hematol 2023; 190:104088. [PMID: 37541537 DOI: 10.1016/j.critrevonc.2023.104088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/18/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023] Open
Abstract
Synthetic biology aims to program living bacteria cells with artificial genetic circuits for user-defined functions, transforming them into powerful tools with numerous applications in various fields, including oncology. Cancer treatments have serious side effects on patients due to the systemic action of the drugs involved. To address this, new systems that provide localized antitumoral action while minimizing damage to healthy tissues are required. Bacteria, often considered pathogenic agents, have been used as cancer treatments since the early 20th century. Advances in genetic engineering, synthetic biology, microbiology, and oncology have improved bacterial therapies, making them safer and more effective. Here we propose six modules for a successful synthetic biology-based bacterial cancer therapy, the modules include Payload, Release, Tumor-targeting, Biocontainment, Memory, and Genetic Circuit Stability Module. These will ensure antitumor activity, safety for the environment and patient, prevent bacterial colonization, maintain cell stability, and prevent loss or defunctionalization of the genetic circuit.
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Affiliation(s)
- Andrés Arboleda-García
- Systems Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, Spain
| | - Ivan Alarcon-Ruiz
- Gene Regulation in Cardiovascular Remodeling and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Lissette Boada-Acosta
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, Madrid, Spain; TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Molecular Oncology Laboratory, Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain
| | - Yadira Boada
- Systems Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, Spain
| | - Alejandro Vignoni
- Systems Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, Spain.
| | - Eloisa Jantus-Lewintre
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, Madrid, Spain; TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Molecular Oncology Laboratory, Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Department of Biotechnology, Universitat Politècnica de València, Valencia, Spain
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9
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Arcidiacono S, Spangler JR, Litteral V, Doherty LA, Stamps B, Walper S, Goodson M, Soares JW. In Vitro Fermentation Evaluation of Engineered Sense and Respond Probiotics in Polymicrobial Communities. ACS Biomater Sci Eng 2023; 9:5176-5185. [PMID: 37642529 DOI: 10.1021/acsbiomaterials.3c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Synthetic biology provides a means of engineering tailored functions into probiotic bacteria. Of particular interest is introducing microbial sense and response functions; however, techniques for testing in physiologically relevant environments, such as those for the intended use, are still lacking. Typically, engineered probiotics are developed and tested in monoculture or in simplified cocultures still within ideal environments. In vitro fermentation models using simplified microbial communities now allow us to simulate engineered organism behavior, specifically organism persistence and intended functionality, within more physiologically relevant, tailored microbial communities. Here, probiotic bacteria Escherichia coli Nissle and Lactobacillus plantarum engineered with sense and response functionalities were evaluated for the ability to persist and function without adverse impact on commensal bacteria within simplified polymicrobial communities with increasing metabolic competition that simulate gut microbe community dynamics. Probiotic abundance and plasmid stability, measured by viability qPCR, decreased for engineered E. coli Nissle relative to monocultures as metabolic competition increased; functional output was not affected. For engineered L. plantarum, abundance and plasmid stability were not adversely impacted; however, functional output was decreased universally as metabolic competition was introduced. For both organisms, adverse effects on select commensals were not evident. Testing engineered probiotics in more physiologically relevant in vitro test beds can provide critical knowledge for circuit design feedback and functional validation prior to the transition to more costly and time-consuming higher-fidelity testing in animal or human studies.
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Affiliation(s)
- Steven Arcidiacono
- Soldier Effectiveness Directorate, US Army DEVCOM Soldier Center, Natick, Massachusetts 01760, United States
| | - Joseph R Spangler
- Center for Bio/Molecular Science & Engineering, US Naval Research Laboratory, Washington, D.C.20375, United States
| | - Vaughn Litteral
- UES Inc, US Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Laurel A Doherty
- Soldier Effectiveness Directorate, US Army DEVCOM Soldier Center, Natick, Massachusetts 01760, United States
| | - Blake Stamps
- 711th Human Performance Wing, US Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Scott Walper
- Center for Bio/Molecular Science & Engineering, US Naval Research Laboratory, Washington, D.C.20375, United States
| | - Michael Goodson
- 711th Human Performance Wing, US Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Jason W Soares
- Soldier Effectiveness Directorate, US Army DEVCOM Soldier Center, Natick, Massachusetts 01760, United States
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10
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Chlebek JL, Leonard SP, Kang-Yun C, Yung MC, Ricci DP, Jiao Y, Park DM. Prolonging genetic circuit stability through adaptive evolution of overlapping genes. Nucleic Acids Res 2023; 51:7094-7108. [PMID: 37260076 PMCID: PMC10359631 DOI: 10.1093/nar/gkad484] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023] Open
Abstract
The development of synthetic biological circuits that maintain functionality over application-relevant time scales remains a significant challenge. Here, we employed synthetic overlapping sequences in which one gene is encoded or 'entangled' entirely within an alternative reading frame of another gene. In this design, the toxin-encoding relE was entangled within ilvA, which encodes threonine deaminase, an enzyme essential for isoleucine biosynthesis. A functional entanglement construct was obtained upon modification of the ribosome-binding site of the internal relE gene. Using this optimized design, we found that the selection pressure to maintain functional IlvA stabilized the production of burdensome RelE for >130 generations, which compares favorably with the most stable kill-switch circuits developed to date. This stabilizing effect was achieved through a complete alteration of the allowable landscape of mutations such that mutations inactivating the entangled genes were disfavored. Instead, the majority of lineages accumulated mutations within the regulatory region of ilvA. By reducing baseline relE expression, these more 'benign' mutations lowered circuit burden, which suppressed the accumulation of relE-inactivating mutations, thereby prolonging kill-switch function. Overall, this work demonstrates the utility of sequence entanglement paired with an adaptive laboratory evolution campaign to increase the evolutionary stability of burdensome synthetic circuits.
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Affiliation(s)
- Jennifer L Chlebek
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean P Leonard
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Christina Kang-Yun
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Mimi C Yung
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Dante P Ricci
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Yongqin Jiao
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Dan M Park
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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11
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Triassi AJ, Fields BD, Monahan CE, Means JM, Park Y, Doosthosseini H, Padmakumar JP, Isabella VM, Voigt CA. Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden. Cell Syst 2023; 14:512-524.e12. [PMID: 37348465 DOI: 10.1016/j.cels.2023.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 01/18/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
To build therapeutic strains, Escherichia coli Nissle (EcN) have been engineered to express antibiotics, toxin-degrading enzymes, immunoregulators, and anti-cancer chemotherapies. For efficacy, the recombinant genes need to be highly expressed, but this imposes a burden on the cell, and plasmids are difficult to maintain in the body. To address these problems, we have developed landing pads in the EcN genome and genetic circuits to control therapeutic gene expression. These tools were applied to EcN SYNB1618, undergoing clinical trials as a phenylketonuria treatment. The pathway for converting phenylalanine to trans-cinnamic acid was moved to a landing pad under the control of a circuit that keeps the pathway off during storage. The resulting strain (EcN SYN8784) achieved higher activity than EcN SYNB1618, reaching levels near when the pathway is carried on a plasmid. This work demonstrates a simple system for engineering EcN that aids quantitative strain design for therapeutics.
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Affiliation(s)
- Alexander J Triassi
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brandon D Fields
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Yongjin Park
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hamid Doosthosseini
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jai P Padmakumar
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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12
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Assessing and reducing phenotypic instability in cyanobacteria. Curr Opin Biotechnol 2023; 80:102899. [PMID: 36724584 DOI: 10.1016/j.copbio.2023.102899] [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: 10/12/2022] [Revised: 12/23/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023]
Abstract
Cyanobacteria have promising potential as sustainable cell factories. However, one challenge that is still largely unreported in scaling-up cyanobacteria bioproduction is phenotypic instability, where the emergence and selection of nonproducing cells leading to loss in production has longer evolutionary timescales to take place in industrial-scale bioreactors. Quantifying phenotypic instability early on in strain development allows researchers to make informed decisions on whether to proceed with scalable designs, or if present, devise countermeasures to reduce instability. One particularly effective strategy to mitigate instability is the use of genome-scale metabolic models to design growth-coupled production strains. In silico studies have predicted that creating certain cofactor imbalances or removing recycling reactions in cyanobacteria can be exploited to stably produce a wide variety of metabolites.
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13
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Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria. Nat Biotechnol 2023:10.1038/s41587-022-01581-y. [PMID: 36593411 DOI: 10.1038/s41587-022-01581-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/20/2022] [Indexed: 01/03/2023]
Abstract
Ultrasound allows imaging at a much greater depth than optical methods, but existing genetically encoded acoustic reporters for in vivo cellular imaging have been limited by poor sensitivity, specificity and in vivo expression. Here we describe two acoustic reporter genes (ARGs)-one for use in bacteria and one for use in mammalian cells-identified through a phylogenetic screen of candidate gas vesicle gene clusters from diverse bacteria and archaea that provide stronger ultrasound contrast, produce non-linear signals distinguishable from background tissue and have stable long-term expression. Compared to their first-generation counterparts, these improved bacterial and mammalian ARGs produce 9-fold and 38-fold stronger non-linear contrast, respectively. Using these new ARGs, we non-invasively imaged in situ tumor colonization and gene expression in tumor-homing therapeutic bacteria, tracked the progression of tumor gene expression and growth in a mouse model of breast cancer, and performed gene-expression-guided needle biopsies of a genetically mosaic tumor, demonstrating non-invasive access to dynamic biological processes at centimeter depth.
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14
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Williams RL, Murray RM. Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli. Nat Commun 2022; 13:6822. [PMID: 36357387 PMCID: PMC9649629 DOI: 10.1038/s41467-022-34361-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/22/2022] [Indexed: 11/12/2022] Open
Abstract
Advances in synthetic biology, bioengineering, and computation allow us to rapidly and reliably program cells with increasingly complex and useful functions. However, because the functions we engineer cells to perform are typically burdensome to cell growth, they can be rapidly lost due to the processes of mutation and natural selection. Here, we show that a strategy of terminal differentiation improves the evolutionary stability of burdensome functions in a general manner by realizing a reproductive and metabolic division of labor. To implement this strategy, we develop a genetic differentiation circuit in Escherichia coli using unidirectional integrase-recombination. With terminal differentiation, differentiated cells uniquely express burdensome functions driven by the orthogonal T7 RNA polymerase, but their capacity to proliferate is limited to prevent the propagation of advantageous loss-of-function mutations that inevitably occur. We demonstrate computationally and experimentally that terminal differentiation increases duration and yield of high-burden expression and that its evolutionary stability can be improved with strategic redundancy. Further, we show this strategy can even be applied to toxic functions. Overall, this study provides an effective, generalizable approach for protecting burdensome engineered functions from evolutionary degradation.
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Affiliation(s)
- Rory L. Williams
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 US ,grid.266093.80000 0001 0668 7243Present Address: Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 US
| | - Richard M. Murray
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 US
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15
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Davenport BI, Tica J, Isalan M. Reducing metabolic burden in the PACEmid evolver system by remastering high-copy phagemid vectors. ENGINEERING BIOLOGY 2022; 6:50-61. [PMID: 36969104 PMCID: PMC9996709 DOI: 10.1049/enb2.12021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/07/2022] [Accepted: 04/20/2022] [Indexed: 01/12/2023] Open
Abstract
Orthogonal or non-cross-reacting transcription factors are used in synthetic biology as components of genetic circuits. Brödel et al. (2016) engineered 12 such cIλ transcription factor variants using a directed evolution 'PACEmid' system. The variants operate as dual activator/repressors and expand gene circuit construction possibilities. However, the high-copy phagemid vectors carrying the cIλ variants imposed high metabolic burden upon cells. Here, the authors 'remaster' the phagemid backbones to relieve their burden substantially, exhibited by a recovery in Escherichia coli growth. The remastered phagemids' ability to function within the PACEmid evolver system is maintained, as is the cIλ transcription factors' activity within these vectors. The low-burden phagemid versions are more suitable for use in PACEmid experiments and synthetic gene circuits; the authors have, therefore, replaced the original high-burden phagemids on the Addgene repository. The authors' work emphasises the importance of understanding metabolic burden and incorporating it into design steps in future synthetic biology ventures.
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Affiliation(s)
- Beth India Davenport
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
| | - Jure Tica
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
| | - Mark Isalan
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
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16
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Kydd L, Alalhareth F, Mendez A, Hohn M, Radunskaya A, Kojouharov H, Jaworski J. Introduction of Plasmid to the Murine Gut via Consumption of an Escherichia coli Carrier and Examining the Impact of Bacterial Dosing and Antibiotics on Persistence. REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE 2022; 8:489-497. [PMID: 36274752 PMCID: PMC9576642 DOI: 10.1007/s40883-022-00248-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 12/20/2021] [Accepted: 12/27/2021] [Indexed: 11/29/2022]
Abstract
Purpose We examine the impacts of dosing strategies of plasmids on bacterial communities in the murine gut by measuring the quantity of plasmids in mouse feces. Methods We fed mice carrier bacteria, E. coli, that contain plasmids with both a reporter gene and an antibiotic resistant gene. We varied the quantity of the plasmid-carrying bacteria and the length of time the mice consumed the bacteria. We also pretreated the gut with broad-spectrum antibiotics and used continuous antibiotic treatment to investigate selection pressure. We collected bacteria from fecal pellets to quantify the number of plasmid-carrying bacteria via plate assay. Results Dosing regimens with plasmid-carrying bacteria resulted in a significantly increased duration of persistence of the plasmid within the gut when supplemented continuously with kanamycin during as well as after completion of bacterial dosing. The carrier bacteria concentration influenced the short-term abundance of carrier bacteria. Conclusion We evaluated the persistence of plasmid-carrying bacteria in the murine gut over time using varying dosage strategies. In future work, we will study how bacterial diversity in the gut impacts the degree of plasmid transfer and the prevalence of plasmid-carrying bacteria over time. Lay Summary Observing how plasmids persist within the gut can help us understand how newly introduced genes, including antibiotic resistance, are transmitted within the gut microbiome. In our experiments, mice were given bacteria containing a genetically engineered plasmid and were examined for the persistence of the plasmid in the gut. We found long-term persistence of the plasmid in the gut when administering antibiotics during and following dosing of the mice with bacteria carrying the plasmid. The use of higher concentrations of carrier bacteria influenced the short-term abundance of the plasmid-carrying bacteria in the gut. Description of Future Works
Building on evidence from these initial studies that persistence of plasmids within the gut can be regulated by the dosage strategy, we will explore future studies and models of gene uptake in the context of spatial and taxonomic control and further determine if dosing strategies alter the compositional diversity of the gut microbiome. Graphical abstract ![]()
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Affiliation(s)
- LeNaiya Kydd
- Department of Bioengineering, The University of Texas at Arlington, Arlington, TX 76010 USA
| | - Fawaz Alalhareth
- Department of Mathematics, The University of Texas at Arlington, Arlington, TX 76010 USA
| | - Ana Mendez
- Department of Mathematics, The University of Texas at Arlington, Arlington, TX 76010 USA
| | - Maryann Hohn
- Department of Mathematics, Pomona College, Claremont, CA 91711 USA
| | - Ami Radunskaya
- Department of Mathematics, Pomona College, Claremont, CA 91711 USA
| | - Hristo Kojouharov
- Department of Mathematics, The University of Texas at Arlington, Arlington, TX 76010 USA
| | - Justyn Jaworski
- Department of Bioengineering, The University of Texas at Arlington, Arlington, TX 76010 USA
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17
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Abedi MH, Yao MS, Mittelstein DR, Bar-Zion A, Swift MB, Lee-Gosselin A, Barturen-Larrea P, Buss MT, Shapiro MG. Ultrasound-controllable engineered bacteria for cancer immunotherapy. Nat Commun 2022; 13:1585. [PMID: 35332124 PMCID: PMC8948203 DOI: 10.1038/s41467-022-29065-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 02/16/2022] [Indexed: 12/25/2022] Open
Abstract
Rapid advances in synthetic biology are driving the development of genetically engineered microbes as therapeutic agents for a multitude of human diseases, including cancer. The immunosuppressive microenvironment of solid tumors, in particular, creates a favorable niche for systemically administered bacteria to engraft and release therapeutic payloads. However, such payloads can be harmful if released outside the tumor in healthy tissues where the bacteria also engraft in smaller numbers. To address this limitation, we engineer therapeutic bacteria to be controlled by focused ultrasound, a form of energy that can be applied noninvasively to specific anatomical sites such as solid tumors. This control is provided by a temperature-actuated genetic state switch that produces lasting therapeutic output in response to briefly applied focused ultrasound hyperthermia. Using a combination of rational design and high-throughput screening we optimize the switching circuits of engineered cells and connect their activity to the release of immune checkpoint inhibitors. In a clinically relevant cancer model, ultrasound-activated therapeutic microbes successfully turn on in situ and induce a marked suppression of tumor growth. This technology provides a critical tool for the spatiotemporal targeting of potent bacterial therapeutics in a variety of biological and clinical scenarios.
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Affiliation(s)
- Mohamad H Abedi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Michael S Yao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - David R Mittelstein
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Avinoam Bar-Zion
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Margaret B Swift
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Audrey Lee-Gosselin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Pierina Barturen-Larrea
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Marjorie T Buss
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
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18
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Lim B, Yin Y, Ye H, Cui Z, Papachristodoulou A, Huang WE. Reprogramming Synthetic Cells for Targeted Cancer Therapy. ACS Synth Biol 2022; 11:1349-1360. [PMID: 35255684 PMCID: PMC9084601 DOI: 10.1021/acssynbio.1c00631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Advances
in synthetic biology enable the reprogramming of bacteria
as smart agents to specifically target tumors and locally release
anticancer drugs in a highly controlled manner. However, the bench-to-bedside
translation of engineered bacteria is often impeded by genetic instability
and the potential risk of uncontrollable replication of engineered
bacteria inside the patient. SimCells (simple cells) are chromosome-free
bacteria controlled by designed gene circuits, which can bypass the
interference of the native gene network in bacteria and eliminate
the risk of bacterial uncontrolled growth. Here, we describe the reprogramming
of SimCells and mini-SimCells to serve as “safe and live drugs”
for targeted cancer therapy. We engineer SimCells to display nanobodies
on the surface for the binding of carcinoembryonic antigen (CEA),
which is an important biomarker found commonly in colorectal cancer
cells. We show that SimCells and mini-SimCells with surface display
of anti-CEA nanobody can specifically bind CEA-expressing Caco2 cancer
cells in vitro while leaving the non-CEA-expressing
SW80 cancer cells untouched. These cancer-targeting SimCells and mini-SimCells
induced cancer cell death in vitro by compromising
the plasma membrane of cancer cells. The cancer-killing effect can
be further enhanced by an aspirin/salicylate inducible gene circuit
that converts salicylate into catechol, a potent anticancer. This
work highlights the potential of SimCells and mini-SimCells for targeted
cancer therapy and lays the foundation for the application of synthetic
biology to medicine.
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Affiliation(s)
- Boon Lim
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, U.K
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, OX3 7DQ Oxford, U.K
| | - Yutong Yin
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, U.K
| | - Hua Ye
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, U.K
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, OX3 7DQ Oxford, U.K
| | - Zhanfeng Cui
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, U.K
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, OX3 7DQ Oxford, U.K
| | | | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, U.K
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19
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Menuhin-Gruman I, Arbel M, Amitay N, Sionov K, Naki D, Katzir I, Edgar O, Bergman S, Tuller T. Evolutionary Stability Optimizer (ESO): A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High Expression Levels. ACS Synth Biol 2022; 11:1142-1151. [PMID: 34928133 PMCID: PMC8938948 DOI: 10.1021/acssynbio.1c00426] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Modern
synthetic biology procedures rely on the ability to generate
stable genetic constructs that keep their functionality over long
periods of time. However, maintenance of these constructs requires
energy from the cell and thus reduces the host’s fitness. Natural
selection results in loss-of-functionality mutations that negate the
expression of the construct in the population. Current approaches
for the prevention of this phenomenon focus on either small-scale,
manual design of evolutionary stable constructs or the detection of
mutational sites with unstable tendencies. We designed the Evolutionary
Stability Optimizer (ESO), a software tool that enables the large-scale
automatic design of evolutionarily stable constructs with respect
to both mutational and epigenetic hotspots and allows users to define
custom hotspots to avoid. Furthermore, our tool takes the expression
of the input constructs into account by considering the guanine-cytosine
(GC) content and codon usage of the host organism, balancing the trade-off
between stability and gene expression, allowing to increase evolutionary
stability while maintaining the high expression. In this study, we
present the many features of the ESO and show that it accurately predicts
the evolutionary stability of endogenous genes. The ESO was created
as an easy-to-use, flexible platform based on the notion that directed
genetic stability research will continue to evolve and revolutionize
current applications of synthetic biology. The ESO is available at
the following link: https://www.cs.tau.ac.il/~tamirtul/ESO/.
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Affiliation(s)
- Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Matan Arbel
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Niv Amitay
- School of Electrical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Karin Sionov
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Itai Katzir
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Omer Edgar
- School of Medicine, The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel 6997801
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20
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Robustness: linking strain design to viable bioprocesses. Trends Biotechnol 2022; 40:918-931. [PMID: 35120750 DOI: 10.1016/j.tibtech.2022.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/18/2022]
Abstract
Microbial cell factories are becoming increasingly popular for the sustainable production of various chemicals. Metabolic engineering has led to the design of advanced cell factories; however, their long-term yield, titer, and productivity falter when scaled up and subjected to industrial conditions. This limitation arises from a lack of robustness - the ability to maintain a constant phenotype despite the perturbations of such processes. This review describes predictable and stochastic industrial perturbations as well as state-of-the-art technologies to counter process variability. Moreover, we distinguish robustness from tolerance and discuss the potential of single-cell studies for improving system robustness. Finally, we highlight ways of achieving consistent and comparable quantification of robustness that can guide the selection of strains for industrial bioprocesses.
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21
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Son HI, Weiss A, You L. Design patterns for engineering genetic stability. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 19. [PMID: 34308010 DOI: 10.1016/j.cobme.2021.100297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The past 20 years have witnessed enormous progress in synthetic biology in the development of engineered cells for diverse applications, including biomanufacturing, materials fabrication, and potential therapeutics and diagnostics. However, it still remains a major challenge to maintain long-term performance of synthetic gene circuits, due to the emergence of mutants that lose circuit function. Here, we highlight major vulnerabilities of synthetic gene circuits resulting in circuit failure and mutant escape. We also discuss engineering strategies to enhance long-term circuit stability and performance. These approaches can be divided into two strategies: the suppression of the emergence of mutants and the suppression of their relative fitness if mutants do emerge. We anticipate that mechanistic understanding of the modes of circuit failure will facilitate future efforts to design evolutionarily robust synthetic biology-inspired applications.
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Affiliation(s)
- Hye-In Son
- Department of Biomedical Engineering, Duke University
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University
| | - Lingchong You
- Department of Biomedical Engineering, Duke University.,Center for Genomic and Computational Biology, Duke University.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine
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22
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Castle SD, Grierson CS, Gorochowski TE. Towards an engineering theory of evolution. Nat Commun 2021; 12:3326. [PMID: 34099656 PMCID: PMC8185075 DOI: 10.1038/s41467-021-23573-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Biological technologies are fundamentally unlike any other because biology evolves. Bioengineering therefore requires novel design methodologies with evolution at their core. Knowledge about evolution is currently applied to the design of biosystems ad hoc. Unless we have an engineering theory of evolution, we will neither be able to meet evolution's potential as an engineering tool, nor understand or limit its unintended consequences for our biological designs. Here, we propose the evotype as a helpful concept for engineering the evolutionary potential of biosystems, or other self-adaptive technologies, potentially beyond the realm of biology.
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Affiliation(s)
- Simeon D Castle
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Claire S Grierson
- School of Biological Sciences, University of Bristol, Bristol, UK
- BrisSynBio, University of Bristol, Bristol, UK
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Bristol, UK.
- BrisSynBio, University of Bristol, Bristol, UK.
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23
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Manrubia S, Cuesta JA, Aguirre J, Ahnert SE, Altenberg L, Cano AV, Catalán P, Diaz-Uriarte R, Elena SF, García-Martín JA, Hogeweg P, Khatri BS, Krug J, Louis AA, Martin NS, Payne JL, Tarnowski MJ, Weiß M. From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics. Phys Life Rev 2021; 38:55-106. [PMID: 34088608 DOI: 10.1016/j.plrev.2021.03.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.
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Affiliation(s)
- Susanna Manrubia
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - José A Cuesta
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BiFi), Universidad de Zaragoza, Spain; UC3M-Santander Big Data Institute (IBiDat), Getafe, Madrid, Spain
| | - Jacobo Aguirre
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Centro de Astrobiología, CSIC-INTA, ctra. de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Sebastian E Ahnert
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | | | - Alejandro V Cano
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pablo Catalán
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain
| | - Ramon Diaz-Uriarte
- Department of Biochemistry, Universidad Autónoma de Madrid, Madrid, Spain; Instituto de Investigaciones Biomédicas "Alberto Sols" (UAM-CSIC), Madrid, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, I(2)SysBio (CSIC-UV), València, Spain; The Santa Fe Institute, Santa Fe, NM, USA
| | | | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics Group, Utrecht University, the Netherlands
| | - Bhavin S Khatri
- The Francis Crick Institute, London, UK; Department of Life Sciences, Imperial College London, London, UK
| | - Joachim Krug
- Institute for Biological Physics, University of Cologne, Köln, Germany
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK
| | - Nora S Martin
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Marcel Weiß
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
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24
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Wang T, Tague N, Whelan SA, Dunlop MJ. Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites. Nucleic Acids Res 2021; 49:1163-1172. [PMID: 33367820 PMCID: PMC7826281 DOI: 10.1093/nar/gkaa1234] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/12/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.
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Affiliation(s)
- Tiebin Wang
- Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA 02215, USA.,Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Nathan Tague
- Biological Design Center, Boston University, Boston, MA 02215, USA.,Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Mary J Dunlop
- Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA 02215, USA.,Biological Design Center, Boston University, Boston, MA 02215, USA.,Biomedical Engineering, Boston University, Boston, MA 02215, USA
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25
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Costello A, Badran AH. Synthetic Biological Circuits within an Orthogonal Central Dogma. Trends Biotechnol 2021; 39:59-71. [PMID: 32586633 PMCID: PMC7746572 DOI: 10.1016/j.tibtech.2020.05.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022]
Abstract
Synthetic biology strives to reliably control cellular behavior, typically in the form of user-designed interactions of biological components to produce a predetermined output. Engineered circuit components are frequently derived from natural sources and are therefore often hampered by inadvertent interactions with host machinery, most notably within the host central dogma. Reliable and predictable gene circuits require the targeted reduction or elimination of these undesirable interactions to mitigate negative consequences on host fitness and develop context-independent bioactivities. Here, we review recent advances in biological orthogonalization, namely the insulation of researcher-dictated bioactivities from host processes, with a focus on systematic developments that may culminate in the creation of an orthogonal central dogma and novel cellular functions.
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Affiliation(s)
- Alan Costello
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ahmed H Badran
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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26
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Rugbjerg P, Olsson L. The future of self-selecting and stable fermentations. J Ind Microbiol Biotechnol 2020; 47:993-1004. [PMID: 33136197 PMCID: PMC7695646 DOI: 10.1007/s10295-020-02325-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/17/2020] [Indexed: 02/08/2023]
Abstract
Unfavorable cell heterogeneity is a frequent risk during bioprocess scale-up and characterized by rising frequencies of low-producing cells. Low-producing cells emerge by both non-genetic and genetic variation and will enrich due to their higher specific growth rate during the extended number of cell divisions of large-scale bioproduction. Here, we discuss recent strategies for synthetic stabilization of fermentation populations and argue for their application to make cell factory designs that better suit industrial needs. Genotype-directed strategies leverage DNA-sequencing data to inform strain design. Self-selecting phenotype-directed strategies couple high production with cell proliferation, either by redirected metabolic pathways or synthetic product biosensing to enrich for high-performing cell variants. Evaluating production stability early in new cell factory projects will guide heterogeneity-reducing design choices. As good initial metrics, we propose production half-life from standardized serial-passage stability screens and production load, quantified as production-associated percent-wise growth rate reduction. Incorporating more stable genetic designs will greatly increase scalability of future cell factories through sustaining a high-production phenotype and enabling stable long-term production.
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Affiliation(s)
- Peter Rugbjerg
- Enduro Genetics ApS, Copenhagen, Denmark. .,Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden.
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
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27
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Park Y, Espah Borujeni A, Gorochowski TE, Shin J, Voigt CA. Precision design of stable genetic circuits carried in highly-insulated E. coli genomic landing pads. Mol Syst Biol 2020; 16:e9584. [PMID: 32812710 PMCID: PMC7436927 DOI: 10.15252/msb.20209584] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 01/02/2023] Open
Abstract
Genetic circuits have many applications, from guiding living therapeutics to ordering process in a bioreactor, but to be useful they have to be genetically stable and not hinder the host. Encoding circuits in the genome reduces burden, but this decreases performance and can interfere with native transcription. We have designed genomic landing pads in Escherichia coli at high-expression sites, flanked by ultrastrong double terminators. DNA payloads >8 kb are targeted to the landing pads using phage integrases. One landing pad is dedicated to carrying a sensor array, and two are used to carry genetic circuits. NOT/NOR gates based on repressors are optimized for the genome and characterized in the landing pads. These data are used, in conjunction with design automation software (Cello 2.0), to design circuits that perform quantitatively as predicted. These circuits require fourfold less RNA polymerase than when carried on a plasmid and are stable for weeks in a recA+ strain without selection. This approach enables the design of synthetic regulatory networks to guide cells in environments or for applications where plasmid use is infeasible.
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Affiliation(s)
- Yongjin Park
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Amin Espah Borujeni
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Thomas E Gorochowski
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Jonghyeon Shin
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Christopher A Voigt
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
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28
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Toward a systematic design of smart probiotics. Curr Opin Biotechnol 2020; 64:199-209. [DOI: 10.1016/j.copbio.2020.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/24/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
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29
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Shin J, Zhang S, Der BS, Nielsen AAK, Voigt CA. Programming Escherichia coli to function as a digital display. Mol Syst Biol 2020; 16:e9401. [PMID: 32141239 PMCID: PMC7058928 DOI: 10.15252/msb.20199401] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 01/18/2023] Open
Abstract
Synthetic genetic circuits offer the potential to wield computational control over biology, but their complexity is limited by the accuracy of mathematical models. Here, we present advances that enable the complete encoding of an electronic chip in the DNA carried by Escherichia coli (E. coli). The chip is a binary-coded digit (BCD) to 7-segment decoder, associated with clocks and calculators, to turn on segments to visualize 0-9. Design automation is used to build seven strains, each of which contains a circuit with up to 12 repressors and two activators (totaling 63 regulators and 76,000 bp DNA). The inputs to each circuit represent the digit to be displayed (encoded in binary by four molecules), and output is the segment state, reported as fluorescence. Implementation requires an advanced gate model that captures dynamics, promoter interference, and a measure of total power usage (RNAP flux). This project is an exemplar of design automation pushing engineering beyond that achievable "by hand", essential for realizing the potential of biology.
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Affiliation(s)
- Jonghyeon Shin
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Shuyi Zhang
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Bryan S Der
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Alec AK Nielsen
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Christopher A Voigt
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
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30
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Pollak B, Matute T, Nuñez I, Cerda A, Lopez C, Vargas V, Kan A, Bielinski V, von Dassow P, Dupont CL, Federici F. Universal loop assembly: open, efficient and cross-kingdom DNA fabrication. Synth Biol (Oxf) 2020; 5:ysaa001. [PMID: 32161816 PMCID: PMC7052795 DOI: 10.1093/synbio/ysaa001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/04/2019] [Accepted: 12/23/2019] [Indexed: 01/22/2023] Open
Abstract
Standardized type IIS DNA assembly methods are becoming essential for biological engineering and research. These methods are becoming widespread and more accessible due to the proposition of a 'common syntax' that enables higher interoperability between DNA libraries. Currently, Golden Gate (GG)-based assembly systems, originally implemented in host-specific vectors, are being made compatible with multiple organisms. We have recently developed the GG-based Loop assembly system for plants, which uses a small library and an intuitive strategy for hierarchical fabrication of large DNA constructs (>30 kb). Here, we describe 'universal Loop' (uLoop) assembly, a system based on Loop assembly for use in potentially any organism of choice. This design permits the use of a compact number of plasmids (two sets of four odd and even vectors), which are utilized repeatedly in alternating steps. The elements required for transformation/maintenance in target organisms are also assembled as standardized parts, enabling customization of host-specific plasmids. Decoupling of the Loop assembly logic from the host-specific propagation elements enables universal DNA assembly that retains high efficiency regardless of the final host. As a proof-of-concept, we show the engineering of multigene expression vectors in diatoms, yeast, plants and bacteria. These resources are available through the OpenMTA for unrestricted sharing and open access.
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Affiliation(s)
- Bernardo Pollak
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Fundación Ciencia y Vida, Santiago, Chile
| | - Tamara Matute
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ariel Cerda
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Lopez
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Valentina Vargas
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Vincent Bielinski
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Peter von Dassow
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto Milenio de Oceanografía de Chile, Concepción, Chile
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Chris L Dupont
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Fernán Federici
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Santiago, Chile
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31
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Fan C, Wu YH, Decker CM, Rohani R, Gesell Salazar M, Ye H, Cui Z, Schmidt F, Huang WE. Defensive Function of Transposable Elements in Bacteria. ACS Synth Biol 2019; 8:2141-2151. [PMID: 31375026 DOI: 10.1021/acssynbio.9b00218] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It has been widely debated whether transposable elements have a positive or a negative effect on their host cells. This study demonstrated that transposable elements, specifically insertion sequences (ISs), can adopt a defensive role in Escherichia coli. In three different E. coli strains (S17, DH5α, and Nissle 1917), IS1 and IS10 rapidly disrupted the I-CeuI gene (encoding I-CeuI endonuclease) on the plasmid pLO11-ICeuI as early as the first generation, despite the gene-circuit being under control of an arabinose promoter. Proteomics analysis showed that the protein abundance profile of E. coli DH5α with pLO11-ICeuI in the fifth generation was nearly opposite to that of control strain (E. coli with pLO11, no I-CeuI). The DNA damage caused by the leaky expression of I-CeuI was enough to trigger a SOS response and alter lipid synthesis, ribosomal activity, RNA/DNA metabolism, central dogma and cell cycle processes in E. coli DH5α. After the ISs disrupted the expression of I-CeuI, cells fully recovered by the 31st generation had a protein abundance profile similar to that of the control strain. This study showed that ISs readily mutated a harmful gene which subsequently restored host fitness. These observations have implications for the stability of designed gene circuits in synthetic biology.
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Affiliation(s)
- Catherine Fan
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Yin-Hu Wu
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Christoph M. Decker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Reza Rohani
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Hua Ye
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Zhanfeng Cui
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
- Proteomics Core, Weill Cornel Medicine-Qatar, Education City, PO 24144 Doha, Qatar
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
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32
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Nikolados EM, Weiße AY, Ceroni F, Oyarzún DA. Growth Defects and Loss-of-Function in Synthetic Gene Circuits. ACS Synth Biol 2019; 8:1231-1240. [PMID: 31181895 DOI: 10.1021/acssynbio.8b00531] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic gene circuits perturb the physiology of their cellular host. The extra load on endogenous processes shifts the equilibrium of resource allocation in the host, leading to slow growth and reduced biosynthesis. Here we built integrated host-circuit models to quantify growth defects caused by synthetic gene circuits. Simulations reveal a complex relation between circuit output and cellular capacity for gene expression. For weak induction of heterologous genes, protein output can be increased at the expense of growth defects. Yet for stronger induction, cellular capacity reaches a tipping point, beyond which both gene expression and growth rate drop sharply. Extensive simulations across various growth conditions and large regions of the design space suggest that the critical capacity is a result of ribosomal scarcity. We studied the impact of growth defects on various gene circuits and transcriptional logic gates, which highlights the extent to which cellular burden can limit, shape, and even break down circuit function. Our approach offers a comprehensive framework to assess the impact of host-circuit interactions in silico, with wide-ranging implications for the design and optimization of bacterial gene circuits.
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Affiliation(s)
| | - Andrea Y. Weiße
- Department of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Diego A. Oyarzún
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
- SynthSys − Centre for Synthetic & Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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33
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Geng P, Leonard SP, Mishler DM, Barrick JE. Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure. ACS Synth Biol 2019; 8:521-531. [PMID: 30703321 DOI: 10.1021/acssynbio.8b00426] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mobile genetic elements drive evolution by disrupting genes and rearranging genomes. Eukaryotes have evolved epigenetic mechanisms, including DNA methylation and RNA interference, that silence mobile elements and thereby preserve the integrity of their genomes. We created an artificial reprogrammable epigenetic system based on CRISPR interference to give engineered bacteria a similar line of defense against transposons and other selfish elements in their genomes. We demonstrate that this CRISPR interference against mobile elements (CRISPRi-ME) approach can be used to simultaneously repress two different transposon families in Escherichia coli, thereby increasing the evolutionary stability of costly protein expression. We further show that silencing a transposon in Acinetobacter baylyi ADP1 reduces mutation rates by a factor of 5, nearly as much as deleting all copies of this element from its genome. By deploying CRISPRi-ME on a broad-host-range vector, we have created a generalizable platform for stabilizing the genomes of engineered bacterial cells for applications in metabolic engineering and synthetic biology.
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Affiliation(s)
- Peng Geng
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sean P. Leonard
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dennis M. Mishler
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
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34
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Cao X, Hamilton JJ, Venturelli OS. Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities. Biochemistry 2019; 58:94-107. [PMID: 30457843 PMCID: PMC6733022 DOI: 10.1021/acs.biochem.8b01006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microbiomes impact nearly every environment on Earth by modulating the molecular composition of the environment. Temporally changing environmental stimuli and spatial organization are major variables shaping the structure and function of microbiomes. The web of interactions among members of these communities and between the organisms and the environment dictates microbiome functions. Microbial interactions are major drivers of microbiomes and are modulated by spatiotemporal parameters. A mechanistic and quantitative understanding of ecological, molecular, and environmental forces shaping microbiomes could inform strategies to control microbiome dynamics and functions. Major challenges for harnessing the potential of microbiomes for diverse applications include the development of predictive modeling frameworks and tools for precise manipulation of microbiome behaviors.
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Affiliation(s)
| | | | - Ophelia S. Venturelli
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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35
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Abstract
In this Crystal Ball article, we look ahead to the possibility of model and tools that can predict the accumulation of mutations that inactivate engineered plasmids.
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Affiliation(s)
- Tom Ellis
- Department of BioengineeringImperial College LondonLondonSW7 2AZUK
- Centre for Synthetic BiologyImperial College LondonLondonSW7 2AZUK
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36
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Zhang S, Voigt CA. Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design. Nucleic Acids Res 2018; 46:11115-11125. [PMID: 30289463 PMCID: PMC6237744 DOI: 10.1093/nar/gky884] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 12/26/2022] Open
Abstract
Large synthetic genetic circuits require the simultaneous expression of many regulators. Deactivated Cas9 (dCas9) can serve as a repressor by having a small guide RNA (sgRNA) direct it to bind a promoter. The programmability and specificity of RNA:DNA basepairing simplifies the generation of many orthogonal sgRNAs that, in theory, could serve as a large set of regulators in a circuit. However, dCas9 is toxic in many bacteria, thus limiting how high it can be expressed, and low concentrations are quickly sequestered by multiple sgRNAs. Here, we construct a non-toxic version of dCas9 by eliminating PAM (protospacer adjacent motif) binding with a R1335K mutation (dCas9*) and recovering DNA binding by fusing it to the PhlF repressor (dCas9*_PhlF). Both the 30 bp PhlF operator and 20 bp sgRNA binding site are required to repress a promoter. The larger region required for recognition mitigates toxicity in Escherichia coli, allowing up to 9600 ± 800 molecules of dCas9*_PhlF per cell before growth or morphology are impacted, as compared to 530 ± 40 molecules of dCas9. Further, PhlF multimerization leads to an increase in average cooperativity from n = 0.9 (dCas9) to 1.6 (dCas9*_PhlF). A set of 30 orthogonal sgRNA-promoter pairs are characterized as NOT gates; however, the simultaneous use of multiple sgRNAs leads to a monotonic decline in repression and after 15 are co-expressed the dynamic range is <10-fold. This work introduces a non-toxic variant of dCas9, critical for its use in applications in metabolic engineering and synthetic biology, and exposes a limitation in the number of regulators that can be used in one cell when they rely on a shared resource.
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Affiliation(s)
- Shuyi Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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37
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Boeing P, Leon M, Nesbeth DN, Finkelstein A, Barnes CP. Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology. Processes (Basel) 2018; 6:167. [PMID: 30568914 PMCID: PMC6296438 DOI: 10.3390/pr6090167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Work on synthetic biology has largely used a component-based metaphor for system construction. While this paradigm has been successful for the construction of numerous systems, the incorporation of contextual design issues-either compositional, host or environmental-will be key to realising more complex applications. Here, we present a design framework that radically steps away from a purely parts-based paradigm by using aspect-oriented software engineering concepts. We believe that the notion of concerns is a powerful and biologically credible way of thinking about system synthesis. By adopting this approach, we can separate core concerns, which represent modular aims of the design, from cross-cutting concerns, which represent system-wide attributes. The explicit handling of cross-cutting concerns allows for contextual information to enter the design process in a modular way. As a proof-of-principle, we implemented the aspect-oriented approach in the Python tool, SynBioWeaver, which enables the combination, or weaving, of core and cross-cutting concerns. The power and flexibility of this framework is demonstrated through a number of examples covering the inclusion of part context, combining circuit designs in a context dependent manner, and the generation of rule, logic and reaction models from synthetic circuit designs.
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Affiliation(s)
- Philipp Boeing
- Department of Computer Science, UCL, London WC1E 6BT, UK
| | - Miriam Leon
- Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
| | | | | | - Chris P. Barnes
- Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
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38
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Shen R, Yin J, Ye JW, Xiang RJ, Ning ZY, Huang WZ, Chen GQ. Promoter Engineering for Enhanced P(3HB- co-4HB) Production by Halomonas bluephagenesis. ACS Synth Biol 2018; 7:1897-1906. [PMID: 30024739 DOI: 10.1021/acssynbio.8b00102] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Promoters for the expression of heterologous genes in Halomonas bluephagenesis are quite limited, and many heterologous promoters function abnormally in this strain. Pporin, a promoter of the strongest expressed protein porin in H. bluephagenesis, is one of the few promoters available for heterologous expression in H. bluephagenesis, yet it has a fixed transcriptional activity that cannot be tuned. A stable promoter library with a wide range of activities is urgently needed. This study reports an approach to construct a promoter library based on the Pporin core region, namely, from the -35 box to the transcription start site, a spacer and an insulator. Saturation mutagenesis was conducted inside the promoter core region to significantly increase the diversity within the promoter library. The promoter library worked in both E. coli and H. bluephagenesis, covering a wide range of relative transcriptional strengths from 40 to 140 000. The library is therefore suitable for the transcription of many different heterologous genes, serving as a platform for protein expression and fine-tuned metabolic engineering of H. bluephagenesis TD01 and its derivative strains. H. bluephagenesis strains harboring the orfZ gene encoding 4HB-CoA transferase driven by selected promoters from the library were constructed, the best one produced over 100 g/L cell dry weight containing 80% poly(3-hydroxybutyrate- co-11 mol % 4-hydroxybutyrate) with a productivity of 1.59 g/L/h after 50 h growth under nonsterile fed-batch conditions. This strain was found the best for P(3HB- co-4HB) production in the laboratory scale.
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Affiliation(s)
- Rui Shen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jin Yin
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jian-Wen Ye
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | | | - Zhi-Yu Ning
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wu-Zhe Huang
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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39
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Li T, Dong Y, Zhang X, Ji X, Luo C, Lou C, Zhang HM, Ouyang Q. Engineering of a genetic circuit with regulatable multistability. Integr Biol (Camb) 2018; 10:474-482. [DOI: 10.1039/c8ib00030a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tingting Li
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
| | - Yiming Dong
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
| | - Xuanqi Zhang
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
| | - Xiangyu Ji
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100871, China
| | - Chunxiong Luo
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Chunbo Lou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100871, China
| | - Haoqian M. Zhang
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
- Bluepha Co., Ltd., Beijing 102206, China
| | - Qi Ouyang
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
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40
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Ozdemir T, Fedorec AJ, Danino T, Barnes CP. Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity. Cell Syst 2018; 7:5-16. [DOI: 10.1016/j.cels.2018.06.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/31/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022]
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41
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Fontana J, Voje WE, Zalatan JG, Carothers JM. Prospects for engineering dynamic CRISPR–Cas transcriptional circuits to improve bioproduction. ACTA ACUST UNITED AC 2018; 45:481-490. [DOI: 10.1007/s10295-018-2039-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/26/2018] [Indexed: 12/26/2022]
Abstract
Abstract
Dynamic control of gene expression is emerging as an important strategy for controlling flux in metabolic pathways and improving bioproduction of valuable compounds. Integrating dynamic genetic control tools with CRISPR–Cas transcriptional regulation could significantly improve our ability to fine-tune the expression of multiple endogenous and heterologous genes according to the state of the cell. In this mini-review, we combine an analysis of recent literature with examples from our own work to discuss the prospects and challenges of developing dynamically regulated CRISPR–Cas transcriptional control systems for applications in synthetic biology and metabolic engineering.
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Affiliation(s)
- Jason Fontana
- 0000000122986657 grid.34477.33 Molecular Engineering and Sciences Institute and Center for Synthetic Biology University of Washington 98195 Seattle WA USA
| | - William E Voje
- 0000000122986657 grid.34477.33 Molecular Engineering and Sciences Institute and Center for Synthetic Biology University of Washington 98195 Seattle WA USA
- 0000000122986657 grid.34477.33 Department of Chemical Engineering University of Washington 98195 Seattle WA USA
| | - Jesse G Zalatan
- 0000000122986657 grid.34477.33 Molecular Engineering and Sciences Institute and Center for Synthetic Biology University of Washington 98195 Seattle WA USA
- 0000000122986657 grid.34477.33 Department of Chemistry University of Washington 98195 Seattle WA USA
| | - James M Carothers
- 0000000122986657 grid.34477.33 Molecular Engineering and Sciences Institute and Center for Synthetic Biology University of Washington 98195 Seattle WA USA
- 0000000122986657 grid.34477.33 Department of Chemical Engineering University of Washington 98195 Seattle WA USA
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42
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Enrico Bena C, Grob A, Isalan M, Bosia C, Ceroni F. Commentary: Synthetic Addiction Extends the Productive Life Time of Engineered Escherichia coli Populations. Front Bioeng Biotechnol 2018; 6:77. [PMID: 29946542 PMCID: PMC6005837 DOI: 10.3389/fbioe.2018.00077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 05/24/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- Chiara Enrico Bena
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy.,Italian Institute for Genomic Medicine, Torino, Italy
| | - Alice Grob
- Department of Life Sciences, Imperial College London, London, United Kingdom.,Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, United Kingdom.,Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Carla Bosia
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy.,Italian Institute for Genomic Medicine, Torino, Italy
| | - Francesca Ceroni
- Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.,Department of Chemical Engineering, Imperial College London, London, United Kingdom
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43
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Nyström A, Papachristodoulou A, Angel A. A Dynamic Model of Resource Allocation in Response to the Presence of a Synthetic Construct. ACS Synth Biol 2018; 7:1201-1210. [PMID: 29745649 DOI: 10.1021/acssynbio.8b00015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introducing synthetic constructs into bacteria often carries a burden that leads to reduced fitness and selective pressure for organisms to mutate their constructs and hence to a reduced functional lifetime. Understanding burden requires suitable methods for accurate measurement and quantification. We develop a dynamic growth model from physiologically relevant first-principles that allows parameters relevant to burden to be extracted from standard growth curves. We test several possibilities for the response of a bacterium to a new environment in terms of resource allocation. We find that burden manifests in the time taken to respond to new conditions as well as the rate of growth in exponential phase. Furthermore, we see that the presence of a synthetic construct hastens the reduction of ribosomes when approaching stationary phase, altering memory effects from previous periods of growth.
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Affiliation(s)
- Axel Nyström
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, U.K
| | | | - Andrew Angel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
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44
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Bourdeau RW, Lee-Gosselin A, Lakshmanan A, Farhadi A, Kumar SR, Nety SP, Shapiro MG. Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts. Nature 2018; 553:86-90. [PMID: 29300010 PMCID: PMC5920530 DOI: 10.1038/nature25021] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 11/09/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Raymond W Bourdeau
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Audrey Lee-Gosselin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Anupama Lakshmanan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Sripriya Ravindra Kumar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Suchita P Nety
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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45
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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: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [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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46
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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: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [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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47
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Abstract
Our ability to generate bacterial strains with unique and increasingly complex functions has rapidly expanded in recent times. The capacity for DNA synthesis is increasing and costing less; new tools are being developed for fast, large-scale genetic manipulation; and more tested genetic parts are available for use, as is the knowledge of how to use them effectively. These advances promise to unlock an exciting array of 'smart' bacteria for clinical use but will also challenge scientists to better optimize preclinical testing regimes for early identification and validation of promising strains and strategies. Here, we review recent advances in the development and testing of engineered bacterial diagnostics and therapeutics. We highlight new technologies that will assist the development of more complex, robust and reliable engineered bacteria for future clinical applications, and we discuss approaches to more efficiently evaluate engineered strains throughout their preclinical development.
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48
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Bartley BA, Kim K, Medley JK, Sauro HM. Synthetic Biology: Engineering Living Systems from Biophysical Principles. Biophys J 2017; 112:1050-1058. [PMID: 28355534 DOI: 10.1016/j.bpj.2017.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 02/06/2017] [Accepted: 02/16/2017] [Indexed: 01/02/2023] Open
Abstract
Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties.
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Affiliation(s)
- Bryan A Bartley
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Kyung Kim
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - J Kyle Medley
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, Washington.
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49
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Riglar DT, Giessen TW, Baym M, Kerns SJ, Niederhuber MJ, Bronson RT, Kotula JW, Gerber GK, Way JC, Silver PA. Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Nat Biotechnol 2017; 35:653-658. [PMID: 28553941 DOI: 10.1038/nbt.3879] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/07/2017] [Indexed: 02/07/2023]
Abstract
Bacteria can be engineered to function as diagnostics or therapeutics in the mammalian gut but commercial translation of technologies to accomplish this has been hindered by the susceptibility of synthetic genetic circuits to mutation and unpredictable function during extended gut colonization. Here, we report stable, engineered bacterial strains that maintain their function for 6 months in the mouse gut. We engineered a commensal murine Escherichia coli strain to detect tetrathionate, which is produced during inflammation. Using our engineered diagnostic strain, which retains memory of exposure in the gut for analysis by fecal testing, we detected tetrathionate in both infection-induced and genetic mouse models of inflammation over 6 months. The synthetic genetic circuits in the engineered strain were genetically stable and functioned as intended over time. The durable performance of these strains confirms the potential of engineered bacteria as living diagnostics.
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Affiliation(s)
- David T Riglar
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Michael Baym
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - S Jordan Kerns
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Matthew J Niederhuber
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Roderick T Bronson
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan W Kotula
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Georg K Gerber
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
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50
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Novel T7-like expression systems used for Halomonas. Metab Eng 2017; 39:128-140. [DOI: 10.1016/j.ymben.2016.11.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/21/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022]
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