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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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Halvorsen TM, Ricci DP, Park DM, Jiao Y, Yung MC. Comparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and Escape. ACS Synth Biol 2022; 11:3785-3796. [PMID: 36346907 DOI: 10.1021/acssynbio.2c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Kill switches provide a biocontainment strategy in which unwanted growth of an engineered microorganism is prevented by expression of a toxin gene. A major challenge in kill switch engineering is balancing evolutionary stability with robust cell killing activity in application relevant host strains. Understanding host-specific containment dynamics and modes of failure helps to develop potent yet stable kill switches. To guide the design of robust kill switches in the agriculturally relevant strain Pseudomonas fluorescens SBW25, we present a comparison of lethality, stability, and genetic escape of eight different toxic effectors in the presence of their cognate inactivators (i.e., toxin-antitoxin modules, polymorphic exotoxin-immunity systems, restriction endonuclease-methyltransferase pair). We find that cell killing capacity and evolutionary stability are inversely correlated and dependent on the level of protection provided by the inactivator gene. Decreasing the proteolytic stability of the inactivator protein can increase cell killing capacity, but at the cost of long-term circuit stability. By comparing toxins within the same genetic context, we determine that modes of genetic escape increase with circuit complexity and are driven by toxin activity, the protective capacity of the inactivator, and the presence of mutation-prone sequences within the circuit. Collectively, the results of our study reveal that circuit complexity, toxin choice, inactivator stability, and DNA sequence design are powerful drivers of kill switch stability and valuable targets for optimization of biocontainment systems.
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Affiliation(s)
- Tiffany M Halvorsen
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Dante P Ricci
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Dan M Park
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Yongqin Jiao
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Mimi C Yung
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
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3
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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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4
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Davey JA, Wilson CJ. Engineered signal-coupled inducible promoters: measuring the apparent RNA-polymerase resource budget. Nucleic Acids Res 2020; 48:9995-10012. [PMID: 32890400 PMCID: PMC7515704 DOI: 10.1093/nar/gkaa734] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023] Open
Abstract
Inducible promoters are a central regulatory component in synthetic biology, metabolic engineering, and protein production for laboratory and commercial uses. Many of these applications utilize two or more exogenous promoters, imposing a currently unquantifiable metabolic burden on the living system. Here, we engineered a collection of inducible promoters (regulated by LacI-based transcription factors) that maximize the free-state of endogenous RNA polymerase (RNAP). We leveraged this collection of inducible promotors to construct simple two-channel logical controls that enabled us to measure metabolic burden – as it relates to RNAP resource partitioning. The two-channel genetic circuits utilized sets of signal-coupled transcription factors that regulate cognate inducible promoters in a coordinated logical fashion. With this fundamental genetic architecture, we evaluated the performance of each inducible promoter as discrete operations, and as coupled systems to evaluate and quantify the effects of resource partitioning. Obtaining the ability to systematically and accurately measure the apparent RNA-polymerase resource budget will enable researchers to design more robust genetic circuits, with significantly higher fidelity. Moreover, this study presents a workflow that can be used to better understand how living systems adapt RNAP resources, via the complementary pairing of constitutive and regulated promoters that vary in strength.
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Affiliation(s)
- James A Davey
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA 30332-0100, USA
| | - Corey J Wilson
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA 30332-0100, USA
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5
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Suárez GA, Dugan KR, Renda BA, Leonard SP, Gangavarapu LS, Barrick JE. Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining. Nucleic Acids Res 2020; 48:4585-4600. [PMID: 32232367 PMCID: PMC7192602 DOI: 10.1093/nar/gkaa204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 03/15/2020] [Accepted: 03/18/2020] [Indexed: 01/10/2023] Open
Abstract
One goal of synthetic biology is to improve the efficiency and predictability of living cells by removing extraneous genes from their genomes. We demonstrate improved methods for engineering the genome of the metabolically versatile and naturally transformable bacterium Acinetobacter baylyi ADP1 and apply them to a genome streamlining project. In Golden Transformation, linear DNA fragments constructed by Golden Gate Assembly are directly added to cells to create targeted deletions, edits, or additions to the chromosome. We tested the dispensability of 55 regions of the ADP1 chromosome using Golden Transformation. The 18 successful multiple-gene deletions ranged in size from 21 to 183 kb and collectively accounted for 23.4% of its genome. The success of each multiple-gene deletion attempt could only be partially predicted on the basis of an existing collection of viable ADP1 single-gene deletion strains and a new transposon insertion sequencing (Tn-Seq) dataset that we generated. We further show that ADP1’s native CRISPR/Cas locus is active and can be retargeted using Golden Transformation. We reprogrammed it to create a CRISPR-Lock, which validates that a gene has been successfully removed from the chromosome and prevents it from being reacquired. These methods can be used together to implement combinatorial routes to further genome streamlining and for more rapid and assured metabolic engineering of this versatile chassis organism.
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Affiliation(s)
- Gabriel A Suárez
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kyle R Dugan
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brian A Renda
- 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
| | - Lakshmi Suryateja Gangavarapu
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, 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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6
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Gulli J, Kroll E, Rosenzweig F. Encapsulation enhances protoplast fusant stability. Biotechnol Bioeng 2020; 117:1696-1709. [PMID: 32100874 PMCID: PMC7318116 DOI: 10.1002/bit.27318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 01/13/2023]
Abstract
A barrier to cost‐efficient biomanufacturing is the instability of engineered genetic elements, such as plasmids. Instability can also manifest at the whole‐genome level, when fungal dikaryons revert to parental species due to nuclear segregation during cell division. Here, we show that by encapsulating Saccharomyces cerevisiae‐Pichia stipitis dikaryons in an alginate matrix, we can limit cell division and preserve their expanded metabolic capabilities. As a proxy to cellulosic ethanol production, we tested the capacity of such cells to carry out ethanologenic fermentation of glucose and xylose, examining substrate use, ploidy, and cell viability in relation to planktonic fusants, as well as in relation to planktonic and encapsulated cell cultures consisting of mixtures of these species. Glucose and xylose consumption and ethanol production by encapsulated dikaryons were greater than planktonic controls. Simultaneous co‐fermentation did not occur; rather the order and kinetics of glucose and xylose catabolism by encapsulated dikaryons were similar to cultures where the two species were encapsulated together. Over repeated cycles of fed‐batch culture, encapsulated S. cerevisiae‐P. stipitis fusants exhibited a dramatic increase in genomic stability, relative to planktonic fusants. Encapsulation also increased the stability of antibiotic‐resistance plasmids used to mark each species and preserved a fixed ratio of S. cerevisiae to P. stipitis cells in mixed cultures. Our data demonstrate how encapsulating cells in an extracellular matrix restricts cell division and, thereby, preserves the stability and biological activity of entities ranging from genomes to plasmids to mixed populations, each of which can be essential to cost‐efficient biomanufacturing.
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Affiliation(s)
- Jordan Gulli
- School of Biological Sciences, College of Science, Georgia Institute of Technology, Atlanta, Georgia
| | - Eugene Kroll
- School of Biological Sciences, College of Science, Georgia Institute of Technology, Atlanta, Georgia
| | - Frank Rosenzweig
- School of Biological Sciences, College of Science, Georgia Institute of Technology, Atlanta, Georgia.,Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia
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7
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Calles J, Justice I, Brinkley D, Garcia A, Endy D. Fail-safe genetic codes designed to intrinsically contain engineered organisms. Nucleic Acids Res 2019; 47:10439-10451. [PMID: 31511890 PMCID: PMC6821295 DOI: 10.1093/nar/gkz745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 11/24/2022] Open
Abstract
One challenge in engineering organisms is taking responsibility for their behavior over many generations. Spontaneous mutations arising before or during use can impact heterologous genetic functions, disrupt system integration, or change organism phenotype. Here, we propose restructuring the genetic code itself such that point mutations in protein-coding sequences are selected against. Synthetic genetic systems so-encoded should fail more safely in response to most spontaneous mutations. We designed fail-safe codes and simulated their expected effects on the evolution of so-encoded proteins. We predict fail-safe codes supporting expression of 20 or 15 amino acids could slow protein evolution to ∼30% or 0% the rate of standard-encoded proteins, respectively. We also designed quadruplet-codon codes that should ensure all single point mutations in protein-coding sequences are selected against while maintaining expression of 20 or more amino acids. We demonstrate experimentally that a reduced set of 21 tRNAs is capable of expressing a protein encoded by only 20 sense codons, whereas a standard 64-codon encoding is not expressed. Our work suggests that biological systems using rationally depleted but otherwise natural translation systems should evolve more slowly and that such hypoevolvable organisms may be less likely to invade new niches or outcompete native populations.
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Affiliation(s)
- Jonathan Calles
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Isaac Justice
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Detravious Brinkley
- Department of Mathematics and Computer Science, Claflin University, Orangeburg, SC 29115, USA
| | - Alexa Garcia
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Drew Endy
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
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8
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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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9
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Design Methodologies and the Limits of the Engineering-Dominated Conception of Synthetic Biology. Acta Biotheor 2019; 67:1-18. [PMID: 30121875 DOI: 10.1007/s10441-018-9338-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 08/14/2018] [Indexed: 10/28/2022]
Abstract
Synthetic biology is described as a new field of biotechnology that models itself on engineering sciences. However, this view of synthetic biology as an engineering field has received criticism, and both biologists and philosophers have argued for a more nuanced and heterogeneous understanding of the field. This paper elaborates the heterogeneity of synthetic biology by clarifying the role of design and the variability of design methodologies in synthetic biology. I focus on two prominent design methodologies: rational design and directed evolution. Rational design resembles the design methodology of traditional engineering sciences. However, it is often replaced and complemented by the more biologically-inspired method of directed evolution, which models itself on natural evolution. These two approaches take philosophically different stances to the design of biological systems. Rational design aims to make biological systems more machine-like, whereas directed evolution utilizes variation and emergent features of living systems. I provide an analysis of the methodological basis of these design approaches, and highlight important methodological differences between them. By analyzing the respective benefits and limitations of these approaches, I argue against the engineering-dominated conception of synthetic biology and its "methodological monism", where the rational design approach is taken as the default design methodology. Alternative design methodologies, like directed evolution, should be considered as complementary, not competitive, to rational design.
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10
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Dzhavakhiya VV, Glagoleva EV, Savelyeva VV, Statsyuk NV, Kartashov MI, Voinova TM, Sergeeva AV. New bacitracin-resistant nisin-producing strain of Lactococcus lactis and its physiological characterization. AIMS Microbiol 2018; 4:608-621. [PMID: 31294237 PMCID: PMC6613330 DOI: 10.3934/microbiol.2018.4.608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/25/2018] [Indexed: 11/18/2022] Open
Abstract
Nisin A belonging to the class I bacteriocins and produced by Lactococcus lactis subsp. lactis is widely used in many countries as highly efficient and safe preservative preventing growth of undesirable bacteria in food products. Though this compound is efficient at very low concentrations, reduction of its manufacturing cost is still relevant problem. An increased nisin A production requires improved resistance of its producer to nisin. According to some studies, mechanisms of microbial resistance to nisin A and bacitracin have a similar basis, and the same transporters are used to export these antibiotics from cells. To obtain strains with improved growth rate and nisin A productivity, selection of spontaneous bacitracin-resistant L. lactis mutants followed by examination of their stability as well as physiological and fermentation characteristics was carried out. Spontaneous mutants were obtained by culturing of L. lactis VKPM B-2092 strain on selective bacitracin-containing agar medium. The obtained bacitracin-resistant strain FL-75 was characterized by accelerated growth rate, doubled biomass accumulation, and improved nisin A resistance. The nisin A productivity of FL-75 exceeded that of the parental strain by 25% reaching 8902 U/mL after 14-h cultivation. In addition, FL-75 was characterized by the improved resistance to oxidative stress that has never been reported earlier for bacitracin-resistant microorganisms. Based on the performed characterization of FL-75, we can consider it as a new independent strain promising for the industrial production of food and feed biopreservatives. Comparison of published data and the obtained results allowed us to suppose that the bacitracin resistance mutation in FL-75 is determined rather by an increased expression of a gene homologous to the bcrC gene of Bacillus sp. than by the activation of multidrug resistance mechanisms. The revealed resistance of FL-75 to bacitracin and oxidative stress can be regulated by a common transcription factor activating in response to various environmental stresses.
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Affiliation(s)
- Vakhtang V Dzhavakhiya
- Laboratory of Biotechnology of Physiologically Active Compounds, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 117312, Russia
| | - Elena V Glagoleva
- Laboratory of Biotechnology of Physiologically Active Compounds, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 117312, Russia
| | - Veronika V Savelyeva
- Laboratory of Biotechnology of Physiologically Active Compounds, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 117312, Russia
| | - Natalia V Statsyuk
- Department of Molecular Biology, All-Russian Research Institute of Phytopathology, Bolshie Vyazemy, Moscow region 143050, Russia
| | - Maksim I Kartashov
- Department of Molecular Biology, All-Russian Research Institute of Phytopathology, Bolshie Vyazemy, Moscow region 143050, Russia
| | - Tatiana M Voinova
- Department of Molecular Biology, All-Russian Research Institute of Phytopathology, Bolshie Vyazemy, Moscow region 143050, Russia
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11
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Deatherage DE, Leon D, Rodriguez ÁE, Omar SK, Barrick JE. Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates. Nucleic Acids Res 2018; 46:9236-9250. [PMID: 30137492 PMCID: PMC6158703 DOI: 10.1093/nar/gky751] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/03/2018] [Accepted: 08/08/2018] [Indexed: 12/24/2022] Open
Abstract
Unwanted evolution of designed DNA sequences limits metabolic and genome engineering efforts. Engineered functions that are burdensome to host cells and slow their replication are rapidly inactivated by mutations, and unplanned mutations with unpredictable effects often accumulate alongside designed changes in large-scale genome editing projects. We developed a directed evolution strategy, Periodic Reselection for Evolutionarily Reliable Variants (PResERV), to discover mutations that prolong the function of a burdensome DNA sequence in an engineered organism. Here, we used PResERV to isolate Escherichia coli cells that replicate ColE1-type plasmids with higher fidelity. We found mutations in DNA polymerase I and in RNase E that reduce plasmid mutation rates by 6- to 30-fold. The PResERV method implicitly selects to maintain the growth rate of host cells, and high plasmid copy numbers and gene expression levels are maintained in some of the evolved E. coli strains, indicating that it is possible to improve the genetic stability of cellular chassis without encountering trade-offs in other desirable performance characteristics. Utilizing these new antimutator E. coli and applying PResERV to other organisms in the future promises to prevent evolutionary failures and unpredictability to provide a more stable genetic foundation for synthetic biology.
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Affiliation(s)
- Daniel E Deatherage
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Dacia Leon
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Álvaro E Rodriguez
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Salma K Omar
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, 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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12
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Abstract
Metabolic pathways are often engineered in single microbial populations. However, the introduction of heterologous circuits into the host can create a substantial metabolic burden that limits the overall productivity of the system. This limitation could be overcome by metabolic division of labor (DOL), whereby distinct populations perform different steps in a metabolic pathway, reducing the burden each population will experience. While conceptually appealing, the conditions when DOL is advantageous have not been rigorously established. Here, we have analyzed 24 common architectures of metabolic pathways in which DOL can be implemented. Our analysis reveals general criteria defining the conditions that favor DOL, accounting for the burden or benefit of the pathway activity on the host populations as well as the transport and turnover of enzymes and intermediate metabolites. These criteria can help guide engineering of metabolic pathways and have implications for understanding evolution of natural microbial communities.
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13
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Morris SE, Feldman AW, Romesberg FE. Synthetic Biology Parts for the Storage of Increased Genetic Information in Cells. ACS Synth Biol 2017; 6:1834-1840. [PMID: 28654252 DOI: 10.1021/acssynbio.7b00115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To bestow cells with novel forms and functions, the goal of synthetic biology, we have developed the unnatural nucleoside triphosphates dNaMTP and dTPT3TP, which form an unnatural base pair (UBP) and expand the genetic alphabet. While the UBP may be retained in the DNA of a living cell, its retention is sequence-dependent. We now report a steady-state kinetic characterization of the rate with which the Klenow fragment of E. coli DNA polymerase I synthesizes the UBP and its mispairs in a variety of sequence contexts. Correct UBP synthesis is as efficient as for a natural base pair, except in one sequence context, and in vitro performance is correlated with in vivo performance. The data elucidate the determinants of efficient UBP synthesis, show that the dNaM-dTPT3 UBP is the first generally recognized natural-like base pair, and importantly, demonstrate that dNaMTP and dTPT3TP are well optimized and standardized parts for the expansion of the genetic alphabet.
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Affiliation(s)
- Sydney E. Morris
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Aaron W. Feldman
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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14
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Obst U, Lu TK, Sieber V. A Modular Toolkit for Generating Pichia pastoris Secretion Libraries. ACS Synth Biol 2017; 6:1016-1025. [PMID: 28252957 DOI: 10.1021/acssynbio.6b00337] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Yeasts are powerful eukaryotic hosts for the production of recombinant proteins due to their rapid growth to high cell densities and ease of genetic modification. For large-scale industrial production, secretion of a protein offers the advantage of simple and efficient downstream purification that avoids costly cell rupture, denaturation and refolding. The methylotrophic yeast Pichia pastoris (Komagataella phaffi) is a well-established expression host that has the ability to perform post-translational modifications and is generally regarded as safe (GRAS). Nevertheless, optimization of protein secretion in this host remains a challenge due to the multiple steps involved during secretion and a lack of genetic tools to tune this process. Here, we developed a toolkit of standardized regulatory elements specific for Pichia pastoris allowing the tuning of gene expression and choice of protein secretion tag. As protein secretion is a complex process, these parts are compatible with a hierarchical assembly method to enable the generation of large and diverse secretion libraries in order to explore a wide range of secretion constructs, achieve successful secretion, and better understand the regulatory factors of importance to specific proteins of interest. To assess the performance of these parts, we built and characterized the expression and secretion efficiency of 124 constructs that combined different regulatory elements with two fluorescent reporter proteins (RFP, yEGFP). Intracellular expression from our promoters was comparatively independent of whether RFP or yEGFP, and whether plasmid-based expression or genomically integrated expression, was used. In contrast, secretion efficiency significantly varied for different genes expressed using identical regulatory elements, with differences in secretion efficiency of >10-fold observed. These results highlight the importance of generating diverse secretion libraries when searching for optimal expression conditions, and demonstrate that our toolkit is a valuable asset for the creation of efficient microbial cell factories.
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Affiliation(s)
- Ulrike Obst
- Straubing Centre of Science, 94315 Straubing, Germany
| | - Timothy K. Lu
- Biophysics
Program, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Volker Sieber
- Catalysis
Research Center, Technical University of Munich, 85748 Garching, Germany
- Fraunhofer IGB, Straubing Branch Bio, Electro, and
Chemocatalysis BioCat, 94315 Straubing, Germany
- Straubing Centre of Science, 94315 Straubing, Germany
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15
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Nielsen AAK, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA. Genetic circuit design automation. Science 2016; 352:aac7341. [PMID: 27034378 DOI: 10.1126/science.aac7341] [Citation(s) in RCA: 576] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 01/21/2016] [Indexed: 12/12/2022]
Abstract
Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transformed into a DNA sequence. Algorithms build a circuit diagram, assign and connect gates, and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design 60 circuits forEscherichia coli(880,000 base pairs of DNA), for which each DNA sequence was built as predicted by the software with no additional tuning. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts), and across all circuits 92% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decision-making, control, sensing, or spatial organization.
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Affiliation(s)
- Alec A K Nielsen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bryan S Der
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Biological Design Center, Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Jonghyeon Shin
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Prashant Vaidyanathan
- Biological Design Center, Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Vanya Paralanov
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20817, USA
| | - Elizabeth A Strychalski
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20817, USA
| | - David Ross
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20817, USA
| | - Douglas Densmore
- Biological Design Center, Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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16
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Lee ME, DeLoache WC, Cervantes B, Dueber JE. A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. ACS Synth Biol 2015; 4:975-86. [PMID: 25871405 DOI: 10.1021/sb500366v] [Citation(s) in RCA: 525] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Saccharomyces cerevisiae is an increasingly attractive host for synthetic biology because of its long history in industrial fermentations. However, until recently, most synthetic biology systems have focused on bacteria. While there is a wealth of resources and literature about the biology of yeast, it can be daunting to navigate and extract the tools needed for engineering applications. Here we present a versatile engineering platform for yeast, which contains both a rapid, modular assembly method and a basic set of characterized parts. This platform provides a framework in which to create new designs, as well as data on promoters, terminators, degradation tags, and copy number to inform those designs. Additionally, we describe genome-editing tools for making modifications directly to the yeast chromosomes, which we find preferable to plasmids due to reduced variability in expression. With this toolkit, we strive to simplify the process of engineering yeast by standardizing the physical manipulations and suggesting best practices that together will enable more straightforward translation of materials and data from one group to another. Additionally, by relieving researchers of the burden of technical details, they can focus on higher-level aspects of experimental design.
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Affiliation(s)
- Michael E. Lee
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
- The UC Berkeley & UCSF Graduate Program in Bioengineering, Berkeley, California 94720, United States
| | - William C. DeLoache
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
- The UC Berkeley & UCSF Graduate Program in Bioengineering, Berkeley, California 94720, United States
| | - Bernardo Cervantes
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
| | - John E. Dueber
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
- QB3: California Institute for Quantitative Biological Research, Berkeley, California 94720, United States
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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17
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Jack BR, Leonard SP, Mishler DM, Renda BA, Leon D, Suárez GA, Barrick JE. Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator. ACS Synth Biol 2015; 4:939-43. [PMID: 26096262 DOI: 10.1021/acssynbio.5b00068] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Unwanted evolution can rapidly degrade the performance of genetically engineered circuits and metabolic pathways installed in living organisms. We created the Evolutionary Failure Mode (EFM) Calculator to computationally detect common sources of genetic instability in an input DNA sequence. It predicts two types of mutational hotspots: deletions mediated by homologous recombination and indels caused by replication slippage on simple sequence repeats. We tested the performance of our algorithm on genetic circuits that were previously redesigned for greater evolutionary reliability and analyzed the stability of sequences in the iGEM Registry of Standard Biological Parts. More than half of the parts in the Registry are predicted to experience >100-fold elevated mutation rates due to the inclusion of unstable sequence configurations. We anticipate that the EFM Calculator will be a useful negative design tool for avoiding volatile DNA encodings, thereby increasing the evolutionary lifetimes of synthetic biology devices.
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Affiliation(s)
- Benjamin R. Jack
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sean P. Leonard
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dennis M. Mishler
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian A. Renda
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dacia Leon
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Gabriel A. Suárez
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jeffrey E. Barrick
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
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18
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DeLoache WC, Russ ZN, Narcross L, Gonzales AM, Martin VJJ, Dueber JE. An enzyme-coupled biosensor enables (S)-reticuline production in yeast from glucose. Nat Chem Biol 2015; 11:465-71. [DOI: 10.1038/nchembio.1816] [Citation(s) in RCA: 261] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/09/2015] [Indexed: 12/31/2022]
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19
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20
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Otero-Muras I, Banga JR. Multicriteria global optimization for biocircuit design. BMC SYSTEMS BIOLOGY 2014; 8:113. [PMID: 25248337 PMCID: PMC4180256 DOI: 10.1186/s12918-014-0113-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 09/16/2014] [Indexed: 11/10/2022]
Abstract
Background One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of regulatory regions, and have been designed to meet a single design criterion. Results In this contribution we introduce a multiobjective formulation for the design of biocircuits. We set up the basis for an advanced optimization tool for the modular and systematic design of biocircuits capable of handling high levels of complexity and multiple design criteria. Our methodology combines the efficiency of global Mixed Integer Nonlinear Programming solvers with multiobjective optimization techniques. Through a number of examples we show the capability of the method to generate non intuitive designs with a desired functionality setting up a priori the desired level of complexity. Conclusions The methodology presented here can be used for biocircuit design and also to explore and identify different design principles for synthetic gene circuits. The presence of more than one competing objective provides a realistic design setting where every solution represents an optimal trade-off between different criteria. Electronic supplementary material The online version of this article (doi:10.1186/s12918-014-0113-3) contains supplementary material, which is available to authorized users.
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21
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Scott M, Klumpp S, Mateescu EM, Hwa T. Emergence of robust growth laws from optimal regulation of ribosome synthesis. Mol Syst Biol 2014; 10:747. [PMID: 25149558 PMCID: PMC4299513 DOI: 10.15252/msb.20145379] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Bacteria must constantly adapt their growth to changes in nutrient availability; yet despite
large-scale changes in protein expression associated with sensing, adaptation, and processing
different environmental nutrients, simple growth laws connect the ribosome abundance and the growth
rate. Here, we investigate the origin of these growth laws by analyzing the features of ribosomal
regulation that coordinate proteome-wide expression changes with cell growth in a variety of
nutrient conditions in the model organism Escherichia coli. We identify
supply-driven feedforward activation of ribosomal protein synthesis as the key regulatory motif
maximizing amino acid flux, and autonomously guiding a cell to achieve optimal growth in different
environments. The growth laws emerge naturally from the robust regulatory strategy underlying growth
rate control, irrespective of the details of the molecular implementation. The study highlights the
interplay between phenomenological modeling and molecular mechanisms in uncovering fundamental
operating constraints, with implications for endogenous and synthetic design of microorganisms.
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Affiliation(s)
- Matthew Scott
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Eduard M Mateescu
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego La Jolla, CA, USA
| | - Terence Hwa
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego La Jolla, CA, USA Institute for Theoretical Studies, ETH Zurich, Zurich, Switzerland
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22
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Segall-Shapiro TH, Meyer AJ, Ellington AD, Sontag ED, Voigt CA. A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase. Mol Syst Biol 2014; 10:742. [PMID: 25080493 PMCID: PMC4299498 DOI: 10.15252/msb.20145299] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic genetic systems share resources with the host, including machinery for transcription
and translation. Phage RNA polymerases (RNAPs) decouple transcription from the host and generate
high expression. However, they can exhibit toxicity and lack accessory proteins (σ factors
and activators) that enable switching between different promoters and modulation of activity. Here,
we show that T7 RNAP (883 amino acids) can be divided into four fragments that have to be
co-expressed to function. The DNA-binding loop is encoded in a C-terminal 285-aa ‘σ
fragment’, and fragments with different specificity can direct the remaining 601-aa
‘core fragment’ to different promoters. Using these parts, we have built a resource
allocator that sets the core fragment concentration, which is then shared by multiple σ
fragments. Adjusting the concentration of the core fragment sets the maximum transcriptional
capacity available to a synthetic system. Further, positive and negative regulation is implemented
using a 67-aa N-terminal ‘α fragment’ and a null (inactivated) σ
fragment, respectively. The α fragment can be fused to recombinant proteins to make promoters
responsive to their levels. These parts provide a toolbox to allocate transcriptional resources via
different schemes, which we demonstrate by building a system which adjusts promoter activity to
compensate for the difference in copy number of two plasmids.
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Affiliation(s)
- Thomas H Segall-Shapiro
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam J Meyer
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Eduardo D Sontag
- Department of Mathematics, Rutgers University, Piscataway, NJ, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
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23
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Brophy JAN, Voigt CA. Principles of genetic circuit design. Nat Methods 2014; 11:508-20. [PMID: 24781324 DOI: 10.1038/nmeth.2926] [Citation(s) in RCA: 573] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/18/2014] [Indexed: 12/17/2022]
Abstract
Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.
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Affiliation(s)
- Jennifer A N Brophy
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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24
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Renda BA, Hammerling MJ, Barrick JE. Engineering reduced evolutionary potential for synthetic biology. MOLECULAR BIOSYSTEMS 2014; 10:1668-78. [PMID: 24556867 DOI: 10.1039/c3mb70606k] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The field of synthetic biology seeks to engineer reliable and predictable behaviors in organisms from collections of standardized genetic parts. However, unlike other types of machines, genetically encoded biological systems are prone to changes in their designed sequences due to mutations in their DNA sequences after these devices are constructed and deployed. Thus, biological engineering efforts can be confounded by undesired evolution that rapidly breaks the functions of parts and systems, particularly when they are costly to the host cell to maintain. Here, we explain the fundamental properties that determine the evolvability of biological systems. Then, we use this framework to review current efforts to engineer the DNA sequences that encode synthetic biology devices and the genomes of their microbial hosts to reduce their ability to evolve and therefore increase their genetic reliability so that they maintain their intended functions over longer timescales.
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Affiliation(s)
- Brian A Renda
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
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25
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Deibel E. Open Genetic Code: on open source in the life sciences. LIFE SCIENCES, SOCIETY AND POLICY 2014; 10:2. [PMID: 26573980 PMCID: PMC4513027 DOI: 10.1186/2195-7819-10-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/15/2013] [Indexed: 06/04/2023]
Abstract
The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first section discusses the greater flexibly in regard of patenting and the relationship to the introduction of open source in the life sciences. The main argument is that the ownership of knowledge in the life sciences should be reconsidered in the context of the centrality of DNA in informatic formats. This is illustrated by discussing a range of examples of open source models. The second part focuses on open source in synthetic biology as exemplary for the re-materialization of information into food, energy, medicine and so forth. The paper ends by raising the question whether another kind of alternative might be possible: one that looks at open source as a model for an alternative to the commodification of life that is understood as an attempt to comprehensively remove the restrictions from the usage of DNA in any of its formats.
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Affiliation(s)
- Eric Deibel
- Department of Biotechnology, Delft University of Technology, Kragujevac, The Netherlands.
- Institute Francilien Recherche, Innovation Société (IFRIS), Paris, France.
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26
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Innate immunity in disease: insights from mathematical modeling and analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 844:227-43. [PMID: 25480644 DOI: 10.1007/978-1-4939-2095-2_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The acute inflammatory response is a complex defense mechanism that has evolved to respond rapidly to injury, infection, and other disruptions in homeostasis. This robust responsiveness to biological stress likely endows the host with increased fitness, but over-robust or inadequate inflammation predisposes the host to various diseases. Importantly, well-compartmentalized inflammation is generally beneficial, but spillover of inflammation into the blood is a hallmark-and likely also a driver-of self-maintaining inflammation. The blood is also a key entry point and immunological interface for vectors of parasitic diseases, diseases that themselves incite systemic inflammation. The complex role of inflammation in health and disease has made this biological system difficult to understand comprehensively and modulate rationally for therapeutic purposes. Consequently, systems approaches have been applied in order to characterize dynamical properties and identify key control points in inflammation. This process begins with the collection of high-dimensional, experimental, and clinical data, followed by data reduction and data-driven modeling that finally informs mechanistic computational models for analysis, prediction, and rational modulation. These studies have suggested that the overall architecture of the inflammatory response includes a multiscale positive feedback from inflammation → tissue damage → inflammation, which is often inadequately controlled by negative feedback from anti-inflammatory mediators. Given the importance of the blood interface for the inflammatory response, and the accessibility of this compartment both as an immunological sampling reservoir for vectors as well as for diagnosis and therapy, we suggest that any rational efforts at modulating inflammation via the blood compartment must involve computational modeling.
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27
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Lewens T. From bricolage to BioBricks™: Synthetic biology and rational design. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:641-648. [PMID: 23838473 DOI: 10.1016/j.shpsc.2013.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Synthetic biology is often described as a project that applies rational design methods to the organic world. Although humans have influenced organic lineages in many ways, it is nonetheless reasonable to place synthetic biology towards one end of a continuum between purely 'blind' processes of organic modification at one extreme, and wholly rational, design-led processes at the other. An example from evolutionary electronics illustrates some of the constraints imposed by the rational design methodology itself. These constraints reinforce the limitations of the synthetic biology ideal, limitations that are often freely acknowledged by synthetic biology's own practitioners. The synthetic biology methodology reflects a series of constraints imposed on finite human designers who wish, as far as is practicable, to communicate with each other and to intervene in nature in reasonably targeted and well-understood ways. This is better understood as indicative of an underlying awareness of human limitations, rather than as expressive of an objectionable impulse to mastery over nature.
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Affiliation(s)
- Tim Lewens
- University of Cambridge, Department of History and Philosophy of Science, Free School Lane, Cambridge CB2 3RH, UK.
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28
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Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc Natl Acad Sci U S A 2013; 110:14592-7. [PMID: 23959872 DOI: 10.1073/pnas.1218447110] [Citation(s) in RCA: 264] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Synergistic microbial communities are ubiquitous in nature and exhibit appealing features, such as sophisticated metabolic capabilities and robustness. This has inspired fast-growing interest in engineering synthetic microbial consortia for biotechnology development. However, there are relatively few reports of their use in real-world applications, and achieving population stability and regulation has proven to be challenging. In this work, we bridge ecology theory with engineering principles to develop robust synthetic fungal-bacterial consortia for efficient biosynthesis of valuable products from lignocellulosic feedstocks. The required biological functions are divided between two specialists: the fungus Trichoderma reesei, which secretes cellulase enzymes to hydrolyze lignocellulosic biomass into soluble saccharides, and the bacterium Escherichia coli, which metabolizes soluble saccharides into desired products. We developed and experimentally validated a comprehensive mathematical model for T. reesei/E. coli consortia, providing insights on key determinants of the system's performance. To illustrate the bioprocessing potential of this consortium, we demonstrate direct conversion of microcrystalline cellulose and pretreated corn stover to isobutanol. Without costly nutrient supplementation, we achieved titers up to 1.88 g/L and yields up to 62% of theoretical maximum. In addition, we show that cooperator-cheater dynamics within T. reesei/E. coli consortia lead to stable population equilibria and provide a mechanism for tuning composition. Although we offer isobutanol production as a proof-of-concept application, our modular system could be readily adapted for production of many other valuable biochemicals.
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29
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Giese B, Koenigstein S, Wigger H, Schmidt JC, von Gleich A. Rational Engineering Principles in Synthetic Biology: A Framework for Quantitative Analysis and an Initial Assessment. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s13752-013-0130-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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30
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Designing de novo: interdisciplinary debates in synthetic biology. SYSTEMS AND SYNTHETIC BIOLOGY 2013; 7:41-50. [PMID: 24432141 DOI: 10.1007/s11693-013-9106-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/27/2013] [Accepted: 03/30/2013] [Indexed: 12/11/2022]
Abstract
Synthetic biology is often presented as a promissory field that ambitions to produce novelty by design. The ultimate promise is the production of living systems that will perform new and desired functions in predictable ways. Nevertheless, realizing promises of novelty has not proven to be a straightforward endeavour. This paper provides an overview of, and explores the existing debates on, the possibility of designing living systems de novo as they appear in interdisciplinary talks between engineering and biological views within the field of synthetic biology. To broaden such interdisciplinary debates, we include the views from the social sciences and the humanities and we point to some fundamental sources of disagreement within the field. Different views co-exist, sometimes as controversial tensions, but sometimes also pointing to integration in the form of intermediate positions. As the field is emerging, multiple choices are possible. They will inform alternative trajectories in synthetic biology and will certainly shape its future. What direction is best is to be decided in reflexive and socially robust ways.
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31
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Woodruff LB, May BL, Warner JR, Gill RT. Towards a metabolic engineering strain “commons”: AnEscherichia coliplatform strain for ethanol production. Biotechnol Bioeng 2013; 110:1520-6. [DOI: 10.1002/bit.24840] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/28/2012] [Accepted: 12/28/2012] [Indexed: 11/09/2022]
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32
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Yang S, Sleight SC, Sauro HM. Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits. Nucleic Acids Res 2012; 41:e33. [PMID: 23093602 PMCID: PMC3592475 DOI: 10.1093/nar/gks972] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
One problem with synthetic genes in genetically engineered organisms is that these foreign DNAs will eventually lose their functions over evolutionary time in absence of selective pressures. This general limitation can restrain the long-term study and industrial application of synthetic genetic circuits. Previous studies have shown that because of their crucial regulatory functions, prokaryotic promoters in synthetic genetic circuits are especially vulnerable to mutations. In this study, we rationally designed robust bidirectional promoters (BDPs), which are self-protected through the complementarity of their overlapping forward and backward promoter sequences on DNA duplex. When the transcription of a target non-essential gene (e.g. green fluorescent protein) was coupled to the transcription of an essential gene (e.g. antibiotic resistance gene) through the BDP, the evolutionary half-time of the gene of interest increases 4–10 times, depending on the strain and experimental conditions used. This design of using BDPs to increase the mutational stability of genetic circuits can be potentially applied to synthetic biology applications in general.
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Affiliation(s)
- Song Yang
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-363, Berkeley, CA 94720, USA.
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33
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Abstract
The parameters in a complex synthetic gene network must be extensively tuned before the network functions as designed. Here, we introduce a simple and general approach to rapidly tune gene networks in Escherichia coli using hypermutable simple sequence repeats embedded in the spacer region of the ribosome binding site. By varying repeat length, we generated expression libraries that incrementally and predictably sample gene expression levels over a 1,000-fold range. We demonstrate the utility of the approach by creating a bistable switch library that programmatically samples the expression space to balance the two states of the switch, and we illustrate the need for tuning by showing that the switch's behavior is sensitive to host context. Further, we show that mutation rates of the repeats are controllable in vivo for stability or for targeted mutagenesis--suggesting a new approach to optimizing gene networks via directed evolution. This tuning methodology should accelerate the process of engineering functionally complex gene networks.
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Kittleson JT, Wu GC, Anderson JC. Successes and failures in modular genetic engineering. Curr Opin Chem Biol 2012; 16:329-36. [PMID: 22818777 DOI: 10.1016/j.cbpa.2012.06.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 05/15/2012] [Accepted: 06/20/2012] [Indexed: 11/19/2022]
Abstract
Synthetic biology relies on engineering concepts such as abstraction, standardization, and decoupling to develop systems that address environmental, clinical, and industrial needs. Recent advances in applying modular design to system development have enabled creation of increasingly complex systems. However, several challenges to module and system development remain, including syntactic errors, semantic errors, parameter mismatches, contextual sensitivity, noise and evolution, and load and stress. To combat these challenges, researchers should develop a framework for describing and reasoning about biological information, design systems with modularity in mind, and investigate how to predictively describe the diverse sources and consequences of metabolic load and stress.
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Ownership and sharing in synthetic biology: A ‘diverse ecology’ of the open and the proprietary? BIOSOCIETIES 2012. [DOI: 10.1057/biosoc.2012.3] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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An G, Nieman G, Vodovotz Y. Toward computational identification of multiscale "tipping points" in acute inflammation and multiple organ failure. Ann Biomed Eng 2012; 40:2414-24. [PMID: 22527009 DOI: 10.1007/s10439-012-0565-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 04/02/2012] [Indexed: 12/25/2022]
Abstract
Sepsis accounts annually for nearly 10% of total U.S. deaths, costing nearly $17 billion/year. Sepsis is a manifestation of disordered systemic inflammation. Properly regulated inflammation allows for timely recognition and effective reaction to injury or infection, but inadequate or overly robust inflammation can lead to Multiple Organ Dysfunction Syndrome (MODS). There is an incongruity between the systemic nature of disordered inflammation (as the target of inflammation-modulating therapies), and the regional manifestation of organ-specific failure (as the subject of organ support), that presents a therapeutic dilemma: systemic interventions can interfere with an individual organ system's appropriate response, yet organ-specific interventions may not help the overall system reorient itself. Based on a decade of systems and computational approaches to deciphering acute inflammation, along with translationally-motivated experimental studies in both small and large animals, we propose that MODS evolves due to the feed-forward cycle of inflammation → damage → inflammation. We hypothesize that inflammation proceeds at a given, "nested" level or scale until positive feedback exceeds a "tipping point." Below this tipping point, inflammation is contained and manageable; when this threshold is crossed, inflammation becomes disordered, and dysfunction propagates to a higher biological scale (e.g., progressing from cellular, to tissue/organ, to multiple organs, to the organism). Finally, we suggest that a combination of computational biology approaches involving data-driven and mechanistic mathematical modeling, in close association with studies in clinically relevant paradigms of sepsis/MODS, are necessary in order to define scale-specific "tipping points" and to suggest novel therapies for sepsis.
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Affiliation(s)
- Gary An
- Department of Surgery, University of Chicago, Chicago, IL 60637, USA
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Namas RA, Mikheev M, Yin J, Over P, Young M, Constantine GM, Zamora R, Gerlach J, Vodovotz Y. A Biohybrid Device for the Systemic Control of Acute Inflammation. ACTA ACUST UNITED AC 2012; 1. [DOI: 10.1089/dst.2012.0001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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Boyle PM, Silver PA. Parts plus pipes: synthetic biology approaches to metabolic engineering. Metab Eng 2011; 14:223-32. [PMID: 22037345 DOI: 10.1016/j.ymben.2011.10.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 10/05/2011] [Accepted: 10/16/2011] [Indexed: 11/24/2022]
Abstract
Synthetic biologists combine modular biological "parts" to create higher-order devices. Metabolic engineers construct biological "pipes" by optimizing the microbial conversion of basic substrates to desired compounds. Many scientists work at the intersection of these two philosophies, employing synthetic devices to enhance metabolic engineering efforts. These integrated approaches promise to do more than simply improve product yields; they can expand the array of products that are tractable to produce biologically. In this review, we explore the application of synthetic biology techniques to next-generation metabolic engineering challenges, as well as the emerging engineering principles for biological design.
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Affiliation(s)
- Patrick M Boyle
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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Calvert J, Fujimura JH. Calculating life? Duelling discourses in interdisciplinary systems biology. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2011; 42:155-163. [PMID: 21486653 DOI: 10.1016/j.shpsc.2010.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences.
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Affiliation(s)
- Jane Calvert
- ESRC Innogen Centre, Institute for the Study of Science, Technology and Innovation (ISSTI), University of Edinburgh, Old Surgeons' Hall, Edinburgh EH1 1LZ, UK.
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40
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Scott M, Hwa T. Bacterial growth laws and their applications. Curr Opin Biotechnol 2011; 22:559-65. [PMID: 21592775 DOI: 10.1016/j.copbio.2011.04.014] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 03/24/2011] [Accepted: 04/20/2011] [Indexed: 11/28/2022]
Abstract
Quantitative empirical relationships between cell composition and growth rate played an important role in the early days of microbiology. Gradually, the focus of the field began to shift from growth physiology to the ever more elaborate molecular mechanisms of regulation employed by the organisms. Advances in systems biology and biotechnology have renewed interest in the physiology of the cell as a whole. Furthermore, gene expression is known to be intimately coupled to the growth state of the cell. Here, we review recent efforts in characterizing such couplings, particularly the quantitative phenomenological approaches exploiting bacterial 'growth laws.' These approaches point toward underlying design principles that can guide the predictive manipulation of cell behavior in the absence of molecular details.
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Affiliation(s)
- Matthew Scott
- Department of Applied Mathematics, University of Waterloo, 200 University Ave. W., Waterloo, Ontario N2L 3G1, Canada.
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Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T. Interdependence of cell growth and gene expression: origins and consequences. Science 2010; 330:1099-102. [PMID: 21097934 DOI: 10.1126/science.1192588] [Citation(s) in RCA: 861] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In bacteria, the rate of cell proliferation and the level of gene expression are intimately intertwined. Elucidating these relations is important both for understanding the physiological functions of endogenous genetic circuits and for designing robust synthetic systems. We describe a phenomenological study that reveals intrinsic constraints governing the allocation of resources toward protein synthesis and other aspects of cell growth. A theory incorporating these constraints can accurately predict how cell proliferation and gene expression affect one another, quantitatively accounting for the effect of translation-inhibiting antibiotics on gene expression and the effect of gratuitous protein expression on cell growth. The use of such empirical relations, analogous to phenomenological laws, may facilitate our understanding and manipulation of complex biological systems before underlying regulatory circuits are elucidated.
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Affiliation(s)
- Matthew Scott
- Center for Theoretical Biological Physics, Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
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43
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Sleight SC, Bartley BA, Lieviant JA, Sauro HM. Designing and engineering evolutionary robust genetic circuits. J Biol Eng 2010; 4:12. [PMID: 21040586 PMCID: PMC2991278 DOI: 10.1186/1754-1611-4-12] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 11/01/2010] [Indexed: 12/25/2022] Open
Abstract
Background One problem with engineered genetic circuits in synthetic microbes is their stability over evolutionary time in the absence of selective pressure. Since design of a selective environment for maintaining function of a circuit will be unique to every circuit, general design principles are needed for engineering evolutionary robust circuits that permit the long-term study or applied use of synthetic circuits. Results We first measured the stability of two BioBrick-assembled genetic circuits propagated in Escherichia coli over multiple generations and the mutations that caused their loss-of-function. The first circuit, T9002, loses function in less than 20 generations and the mutation that repeatedly causes its loss-of-function is a deletion between two homologous transcriptional terminators. To measure the effect between transcriptional terminator homology levels and evolutionary stability, we re-engineered six versions of T9002 with a different transcriptional terminator at the end of the circuit. When there is no homology between terminators, the evolutionary half-life of this circuit is significantly improved over 2-fold and is independent of the expression level. Removing homology between terminators and decreasing expression level 4-fold increases the evolutionary half-life over 17-fold. The second circuit, I7101, loses function in less than 50 generations due to a deletion between repeated operator sequences in the promoter. This circuit was re-engineered with different promoters from a promoter library and using a kanamycin resistance gene (kanR) within the circuit to put a selective pressure on the promoter. The evolutionary stability dynamics and loss-of-function mutations in all these circuits are described. We also found that on average, evolutionary half-life exponentially decreases with increasing expression levels. Conclusions A wide variety of loss-of-function mutations are observed in BioBrick-assembled genetic circuits including point mutations, small insertions and deletions, large deletions, and insertion sequence (IS) element insertions that often occur in the scar sequence between parts. Promoter mutations are selected for more than any other biological part. Genetic circuits can be re-engineered to be more evolutionary robust with a few simple design principles: high expression of genetic circuits comes with the cost of low evolutionary stability, avoid repeated sequences, and the use of inducible promoters increases stability. Inclusion of an antibiotic resistance gene within the circuit does not ensure evolutionary stability.
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Affiliation(s)
- Sean C Sleight
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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Marguet P, Tanouchi Y, Spitz E, Smith C, You L. Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology. PLoS One 2010; 5:e11909. [PMID: 20689598 PMCID: PMC2912849 DOI: 10.1371/journal.pone.0011909] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 07/02/2010] [Indexed: 01/03/2023] Open
Abstract
Synthetic biology seeks to enable programmed control of cellular behavior though engineered biological systems. These systems typically consist of synthetic circuits that function inside, and interact with, complex host cells possessing pre-existing metabolic and regulatory networks. Nevertheless, while designing systems, a simple well-defined interface between the synthetic gene circuit and the host is frequently assumed. We describe the generation of robust but unexpected oscillations in the densities of bacterium Escherichia coli populations by simple synthetic suicide circuits containing quorum components and a lysis gene. Contrary to design expectations, oscillations required neither the quorum sensing genes (luxR and luxI) nor known regulatory elements in the PluxI promoter. Instead, oscillations were likely due to density-dependent plasmid amplification that established a population-level negative feedback. A mathematical model based on this mechanism captures the key characteristics of oscillations, and model predictions regarding perturbations to plasmid amplification were experimentally validated. Our results underscore the importance of plasmid copy number and potential impact of “hidden interactions” on the behavior of engineered gene circuits - a major challenge for standardizing biological parts. As synthetic biology grows as a discipline, increasing value may be derived from tools that enable the assessment of parts in their final context.
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Affiliation(s)
- Philippe Marguet
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Yu Tanouchi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Eric Spitz
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Cameron Smith
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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Kuwahara H, Myers CJ, Samoilov MS. Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction. PLoS Comput Biol 2010; 6:e1000723. [PMID: 20361050 PMCID: PMC2845655 DOI: 10.1371/journal.pcbi.1000723] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 02/25/2010] [Indexed: 02/06/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element-the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase) of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies that this down-regulation mechanism could be particularly significant inside the host environment, thus potentially contributing further understanding toward the development of novel therapeutic approaches to UPEC-caused UTIs.
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Affiliation(s)
- Hiroyuki Kuwahara
- Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Chris J. Myers
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael S. Samoilov
- QB3: California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
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46
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Abstract
An understanding of evolution and ecology will be critical to the success of synthetic biology. As the scope and complexity of synthetic biology grows, an understanding of evolution and ecology will be critical to its success.
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49
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Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. A synthetic genetic edge detection program. Cell 2009; 137:1272-81. [PMID: 19563759 DOI: 10.1016/j.cell.2009.04.048] [Citation(s) in RCA: 330] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 03/09/2009] [Accepted: 04/13/2009] [Indexed: 11/17/2022]
Abstract
Edge detection is a signal processing algorithm common in artificial intelligence and image recognition programs. We have constructed a genetically encoded edge detection algorithm that programs an isogenic community of E. coli to sense an image of light, communicate to identify the light-dark edges, and visually present the result of the computation. The algorithm is implemented using multiple genetic circuits. An engineered light sensor enables cells to distinguish between light and dark regions. In the dark, cells produce a diffusible chemical signal that diffuses into light regions. Genetic logic gates are used so that only cells that sense light and the diffusible signal produce a positive output. A mathematical model constructed from first principles and parameterized with experimental measurements of the component circuits predicts the performance of the complete program. Quantitatively accurate models will facilitate the engineering of more complex biological behaviors and inform bottom-up studies of natural genetic regulatory networks.
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Affiliation(s)
- Jeffrey J Tabor
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, CA 94158, USA
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50
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Synthetic gene networks: the next wave in biotechnology? Trends Biotechnol 2009; 27:368-74. [PMID: 19409633 DOI: 10.1016/j.tibtech.2009.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 02/24/2009] [Accepted: 03/02/2009] [Indexed: 11/22/2022]
Abstract
Engineering novel, reusable gene networks to provide greater control over cellular processes is one of the goals of the emerging discipline of synthetic biology. This article reviews the landmark literature pertaining to the development of synthetic gene networks, the engineering framework used to design and characterize them and the technological developments on the horizon that could potentially advance the field in new directions. As gene network engineering enters its second decade, an attempt is also made to outline the challenges in advancing this nascent field, especially with regard to the practical limitations of component reusability and reliability and the opportunities that present themselves in the development of novel gene expression controllers and single-cell biosensors.
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