1
|
Tica J, Oliver Huidobro M, Zhu T, Wachter GKA, Pazuki RH, Bazzoli DG, Scholes NS, Tonello E, Siebert H, Stumpf MPH, Endres RG, Isalan M. A three-node Turing gene circuit forms periodic spatial patterns in bacteria. Cell Syst 2024; 15:1123-1132.e3. [PMID: 39626670 DOI: 10.1016/j.cels.2024.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 08/23/2024] [Accepted: 11/08/2024] [Indexed: 12/21/2024]
Abstract
Turing patterns are self-organizing systems that can form spots, stripes, or labyrinths. Proposed examples in tissue organization include zebrafish pigmentation, digit spacing, and many others. The theory of Turing patterns in biology has been debated because of their stringent fine-tuning requirements, where patterns only occur within a small subset of parameters. This has complicated the engineering of synthetic Turing gene circuits from first principles, although natural genetic Turing networks have been identified. Here, we engineered a synthetic genetic reaction-diffusion system where three nodes interact according to a non-classical Turing network with improved parametric robustness. The system reproducibly generated stationary, periodic, concentric stripe patterns in growing E. coli colonies. A partial differential equation model reproduced the patterns, with a Turing parameter regime obtained by fitting to experimental data. Our synthetic Turing system can contribute to nanotechnologies, such as patterned biomaterial deposition, and provide insights into developmental patterning programs. A record of this paper's transparent peer review process is included in the supplemental information.
Collapse
Affiliation(s)
- Jure Tica
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | | | - Tong Zhu
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Georg K A Wachter
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Roozbeh H Pazuki
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Dario G Bazzoli
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Natalie S Scholes
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Elisa Tonello
- Department of Mathematics, Kiel University, 24118 Kiel, Germany
| | - Heike Siebert
- Department of Mathematics, Kiel University, 24118 Kiel, Germany
| | - Michael P H Stumpf
- Melbourne Integrated Genomics, University of Melbourne, Melbourne, VIC 3010, Australia; School of BioScience, University of Melbourne, Melbourne, VIC 3010, Australia; School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Robert G Endres
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.
| |
Collapse
|
2
|
de Freitas Magalhães B, Fan G, Sontag E, Josić K, Bennett MR. Pattern Formation and Bistability in a Synthetic Intercellular Genetic Toggle. ACS Synth Biol 2024; 13:2844-2860. [PMID: 39214591 DOI: 10.1021/acssynbio.4c00272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Differentiation within multicellular organisms is a complex process that helps to establish spatial patterning and tissue formation within the body. Often, the differentiation of cells is governed by morphogens and intercellular signaling molecules that guide the fate of each cell, frequently using toggle-like regulatory components. Synthetic biologists have long sought to recapitulate patterned differentiation with engineered cellular communities, and various methods for differentiating bacteria have been invented. Here, we couple a synthetic corepressive toggle switch with intercellular signaling pathways to create a "quorum-sensing toggle". We show that this circuit not only exhibits population-wide bistability in a well-mixed liquid environment but also generates patterns of differentiation in colonies grown on agar containing an externally supplied morphogen. If coupled to other metabolic processes, circuits such as the one described here would allow for the engineering of spatially patterned, differentiated bacteria for use in biomaterials and bioelectronics.
Collapse
Affiliation(s)
| | - Gaoyang Fan
- Department of Mathematics, University of Houston, Houston, Texas 77204, United States
| | - Eduardo Sontag
- Department of Bioengineering and Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, Texas 77204, United States
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
3
|
Gómez-Felipe A, Branchini E, Wang B, Marconi M, Bertrand-Rakusová H, Stan T, Burkiewicz J, de Folter S, Routier-Kierzkowska AL, Wabnik K, Kierzkowski D. Two orthogonal differentiation gradients locally coordinate fruit morphogenesis. Nat Commun 2024; 15:2912. [PMID: 38575617 PMCID: PMC10995178 DOI: 10.1038/s41467-024-47325-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Morphogenesis requires the coordination of cellular behaviors along developmental axes. In plants, gradients of growth and differentiation are typically established along a single longitudinal primordium axis to control global organ shape. Yet, it remains unclear how these gradients are locally adjusted to regulate the formation of complex organs that consist of diverse tissue types. Here we combine quantitative live imaging at cellular resolution with genetics, and chemical treatments to understand the formation of Arabidopsis thaliana female reproductive organ (gynoecium). We show that, contrary to other aerial organs, gynoecium shape is determined by two orthogonal, time-shifted differentiation gradients. An early mediolateral gradient controls valve morphogenesis while a late, longitudinal gradient regulates style differentiation. Local, tissue-dependent action of these gradients serves to fine-tune the common developmental program governing organ morphogenesis to ensure the specialized function of the gynoecium.
Collapse
Affiliation(s)
- Andrea Gómez-Felipe
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Elvis Branchini
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Binghan Wang
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Marco Marconi
- centro De Biotecnología Y Genómica De Plantas (Universidad Politécnica De Madrid (Upm), Instituto Nacional De Investigación Y Tecnología Agraria Y Alimentaria (Inia, Csic), Campus De Montegancedo, Pozuelo De Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Hana Bertrand-Rakusová
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Teodora Stan
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Jérôme Burkiewicz
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), CP, 36824, Irapuato, Mexico
| | - Anne-Lise Routier-Kierzkowska
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Krzysztof Wabnik
- centro De Biotecnología Y Genómica De Plantas (Universidad Politécnica De Madrid (Upm), Instituto Nacional De Investigación Y Tecnología Agraria Y Alimentaria (Inia, Csic), Campus De Montegancedo, Pozuelo De Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Daniel Kierzkowski
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada.
| |
Collapse
|
4
|
Zeng M, Sarker B, Rondthaler SN, Vu V, Andrews LB. Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence-Function Landscape. ACS Synth Biol 2024; 13:568-589. [PMID: 38206199 DOI: 10.1021/acssynbio.3c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Programmable intercellular signaling using components of naturally occurring quorum sensing can allow for coordinated functions to be engineered in microbial consortia. LuxR-type transcriptional regulators are widely used for this purpose and are activated by homoserine lactone (HSL) signals. However, they often suffer from imperfect molecular discrimination of structurally similar HSLs, causing misregulation within engineered consortia containing multiple HSL signals. Here, we studied one such example, the regulator LasR from Pseudomonas aeruginosa. We elucidated its sequence-function relationship for ligand specificity using targeted protein engineering and multiplexed high-throughput biosensor screening. A pooled combinatorial saturation mutagenesis library (9,486 LasR DNA sequences) was created by mutating six residues in LasR's β5 sheet with single, double, or triple amino acid substitutions. Sort-seq assays were performed in parallel using cognate and noncognate HSLs to quantify each corresponding sensor's response to each HSL signal, which identified hundreds of highly specific variants. Sensor variants identified were individually assayed and exhibited up to 60.6-fold (p = 0.0013) improved relative activation by the cognate signal compared to the wildtype. Interestingly, we uncovered prevalent mutational epistasis and previously unidentified residues contributing to signal specificity. The resulting sensors with negligible signal crosstalk could be broadly applied to engineer bacteria consortia.
Collapse
Affiliation(s)
- Min Zeng
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen N Rondthaler
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Vanessa Vu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| |
Collapse
|
5
|
Wauford N, Patel A, Tordoff J, Enghuus C, Jin A, Toppen J, Kemp ML, Weiss R. Synthetic symmetry breaking and programmable multicellular structure formation. Cell Syst 2023; 14:806-818.e5. [PMID: 37689062 PMCID: PMC10919224 DOI: 10.1016/j.cels.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/14/2023] [Accepted: 08/02/2023] [Indexed: 09/11/2023]
Abstract
During development, cells undergo symmetry breaking into differentiated subpopulations that self-organize into complex structures.1,2,3,4,5 However, few tools exist to recapitulate these behaviors in a controllable and coupled manner.6,7,8,9 Here, we engineer a stochastic recombinase genetic switch tunable by small molecules to induce programmable symmetry breaking, commitment to downstream cell fates, and morphological self-organization. Inducers determine commitment probabilities, generating tunable subpopulations as a function of inducer dosage. We use this switch to control the cell-cell adhesion properties of cells committed to each fate.10,11 We generate a wide variety of 3D morphologies from a monoclonal population and develop a computational model showing high concordance with experimental results, yielding new quantitative insights into the relationship between cell-cell adhesion strengths and downstream morphologies. We expect that programmable symmetry breaking, generating precise and tunable subpopulation ratios and coupled to structure formation, will serve as an integral component of the toolbox for complex tissue and organoid engineering.
Collapse
Affiliation(s)
- Noreen Wauford
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshay Patel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jesse Tordoff
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Casper Enghuus
- Department of Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Jin
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jack Toppen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Melissa L Kemp
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
6
|
Ricci-Tam C, Kuipa S, Kostman MP, Aronson MS, Sgro AE. Microbial models of development: Inspiration for engineering self-assembled synthetic multicellularity. Semin Cell Dev Biol 2023; 141:50-62. [PMID: 35537929 DOI: 10.1016/j.semcdb.2022.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/13/2022] [Indexed: 10/18/2022]
Abstract
While the field of synthetic developmental biology has traditionally focused on the study of the rich developmental processes seen in metazoan systems, an attractive alternate source of inspiration comes from microbial developmental models. Microbes face unique lifestyle challenges when forming emergent multicellular collectives. As a result, the solutions they employ can inspire the design of novel multicellular systems. In this review, we dissect the strategies employed in multicellular development by two model microbial systems: the cellular slime mold Dictyostelium discoideum and the biofilm-forming bacterium Bacillus subtilis. Both microbes face similar challenges but often have different solutions, both from metazoan systems and from each other, to create emergent multicellularity. These challenges include assembling and sustaining a critical mass of participating individuals to support development, regulating entry into development, and assigning cell fates. The mechanisms these microbial systems exploit to robustly coordinate development under a wide range of conditions offer inspiration for a new toolbox of solutions to the synthetic development community. Additionally, recreating these phenomena synthetically offers a pathway to understanding the key principles underlying how these behaviors are coordinated naturally.
Collapse
Affiliation(s)
- Chiara Ricci-Tam
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Sophia Kuipa
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Maya Peters Kostman
- Biological Design Center, Boston University, Boston, MA 02215, USA; Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA 02215, USA
| | - Mark S Aronson
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Allyson E Sgro
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA; Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA 02215, USA.
| |
Collapse
|
7
|
Shtin M, Polverari L, Svolacchia N, Bertolotti G, Unterholzner SJ, Di Mambro R, Costantino P, Dello Ioio R, Sabatini S. The Mutual Inhibition between PLETHORAs and ARABIDOPSIS RESPONSE REGULATORs Controls Root Zonation. PLANT & CELL PHYSIOLOGY 2023; 64:317-324. [PMID: 36611272 DOI: 10.1093/pcp/pcad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/10/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
During organogenesis, a key step toward the development of a functional organ is the separation of cells into specific domains with different activities. Mutual inhibition of gene expression has been shown to be sufficient to establish and maintain these domains during organogenesis in several multicellular organisms. Here, we show that the mutual inhibition between the PLETHORA transcription factors (PLTs) and the ARABIDOPSIS RESPONSE REGULATORs (ARRs) transcription factors is sufficient to separate cell division and cell differentiation during root organogenesis. In particular, we show that ARR1 suppresses PLT activities and that PLTs suppress ARR1 and ARR12 by targeting their proteins for degradation via the KISS ME DEADLY 2 F-box protein. These findings reveal new important aspects of the complex process of root zonation and development.
Collapse
Affiliation(s)
- Margaryta Shtin
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazzale Università 5, Bolzano 39100, Italy
| | - Laura Polverari
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
| | - Noemi Svolacchia
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
| | - Gaia Bertolotti
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
| | - Simon J Unterholzner
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazzale Università 5, Bolzano 39100, Italy
| | - Riccardo Di Mambro
- Department of Biology, University of Pisa, via L. Ghini, 13, Pisa 56126, Italy
| | - Paolo Costantino
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
| | - Raffaele Dello Ioio
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
- Department of Biology, University of Pisa, via L. Ghini, 13, Pisa 56126, Italy
| | - Sabrina Sabatini
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
| |
Collapse
|
8
|
Barbier I, Kusumawardhani H, Schaerli Y. Engineering synthetic spatial patterns in microbial populations and communities. Curr Opin Microbiol 2022; 67:102149. [DOI: 10.1016/j.mib.2022.102149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 02/03/2023]
|
9
|
Oliver Huidobro M, Tica J, Wachter GKA, Isalan M. Synthetic spatial patterning in bacteria: advances based on novel diffusible signals. Microb Biotechnol 2022; 15:1685-1694. [PMID: 34843638 PMCID: PMC9151330 DOI: 10.1111/1751-7915.13979] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/14/2021] [Accepted: 11/14/2021] [Indexed: 12/22/2022] Open
Abstract
Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi-diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small-molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.
Collapse
Affiliation(s)
| | - Jure Tica
- Department of Life SciencesImperial College LondonLondonSW7 2AZUK
| | | | - Mark Isalan
- Department of Life SciencesImperial College LondonLondonSW7 2AZUK
| |
Collapse
|
10
|
Iber D, Vetter R. Relationship between epithelial organization and morphogen interpretation. Curr Opin Genet Dev 2022; 75:101916. [PMID: 35605527 DOI: 10.1016/j.gde.2022.101916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 04/10/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022]
Abstract
Despite molecular noise and genetic differences between individuals, developmental outcomes are remarkably constant. Decades of research has focused on the underlying mechanisms that ensure this precision and robustness. Recent quantifications of chemical gradients and epithelial cell shapes provide novel insights into the basis of precise development. In this review, we argue that these two aspects may be linked in epithelial morphogenesis.
Collapse
Affiliation(s)
- Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland.
| | - Roman Vetter
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| |
Collapse
|
11
|
Dupin A, Aufinger L, Styazhkin I, Rothfischer F, Kaufmann BK, Schwarz S, Galensowske N, Clausen-Schaumann H, Simmel FC. Synthetic cell-based materials extract positional information from morphogen gradients. SCIENCE ADVANCES 2022; 8:eabl9228. [PMID: 35394842 PMCID: PMC8993112 DOI: 10.1126/sciadv.abl9228] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/17/2022] [Indexed: 05/19/2023]
Abstract
Biomaterials composed of synthetic cells have the potential to adapt and differentiate guided by physicochemical environmental cues. Inspired by biological systems in development, which extract positional information (PI) from morphogen gradients in the presence of uncertainties, we here investigate how well synthetic cells can determine their position within a multicellular structure. To calculate PI, we created and analyzed a large number of synthetic cellular assemblies composed of emulsion droplets connected via lipid bilayer membranes. These droplets contained cell-free feedback gene circuits that responded to gradients of a genetic inducer acting as a morphogen. PI is found to be limited by gene expression noise and affected by the temporal evolution of the morphogen gradient and the cell-free expression system itself. The generation of PI can be rationalized by computational modeling of the system. We scale our approach using three-dimensional printing and demonstrate morphogen-based differentiation in larger tissue-like assemblies.
Collapse
Affiliation(s)
- Aurore Dupin
- Physics Department (E14), TU Munich, 85748 Garching, Germany
| | - Lukas Aufinger
- Physics Department (E14), TU Munich, 85748 Garching, Germany
| | - Igor Styazhkin
- Physics Department (E14), TU Munich, 85748 Garching, Germany
| | | | - Benedikt K. Kaufmann
- Center for NanoScience (CeNS), Schellingstraße 4, 80799 Munich, Germany
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Lothstrasse 34, 80335 Munich, Germany
- Heinz-Nixdorf-Chair of Biomedical Electronics, TranslaTUM, TU Munich, 81675 Munich, Germany
| | - Sascha Schwarz
- Center for NanoScience (CeNS), Schellingstraße 4, 80799 Munich, Germany
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Lothstrasse 34, 80335 Munich, Germany
| | | | - Hauke Clausen-Schaumann
- Center for NanoScience (CeNS), Schellingstraße 4, 80799 Munich, Germany
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Lothstrasse 34, 80335 Munich, Germany
| | - Friedrich C. Simmel
- Physics Department (E14), TU Munich, 85748 Garching, Germany
- Corresponding author.
| |
Collapse
|
12
|
Carignano A, Chen DH, Mallory C, Wright RC, Seelig G, Klavins E. Modular, robust and extendible multicellular circuit design in yeast. eLife 2022; 11:74540. [PMID: 35312478 PMCID: PMC9000959 DOI: 10.7554/elife.74540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/20/2022] [Indexed: 11/13/2022] Open
Abstract
Division of labor between cells is ubiquitous in biology but the use of multi-cellular consortia for engineering applications is only beginning to be explored. A significant advantage of multi-cellular circuits is their potential to be modular with respect to composition but this claim has not yet been extensively tested using experiments and quantitative modeling. Here, we construct a library of 24 yeast strains capable of sending, receiving or responding to three molecular signals, characterize them experimentally and build quantitative models of their input-output relationships. We then compose these strains into two- and three-strain cascades as well as a four-strain bistable switch and show that experimentally measured consortia dynamics can be predicted from the models of the constituent parts. To further explore the achievable range of behaviors, we perform a fully automated computational search over all two-, three- and four-strain consortia to identify combinations that realize target behaviors including logic gates, band-pass filters and time pulses. Strain combinations that are predicted to map onto a target behavior are further computationally optimized and then experimentally tested. Experiments closely track computational predictions. The high reliability of these model descriptions further strengthens the feasibility and highlights the potential for distributed computing in synthetic biology.
Collapse
Affiliation(s)
- Alberto Carignano
- Department of Electrical and Computer Engineering, University of Washington, Seattle, United States
| | - Dai Hua Chen
- Department of Electrical and Computer Engineering, University of Washington, Seattle, United States
| | - Cannon Mallory
- Department of Electrical and Computer Engineering, University of Washington, Seattle, United States
| | | | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, United States
| | - Eric Klavins
- Department of Electrical and Computer Engineering, University of Washington, Seattle, United States
| |
Collapse
|
13
|
Perkins ML. Implications of diffusion and time-varying morphogen gradients for the dynamic positioning and precision of bistable gene expression boundaries. PLoS Comput Biol 2021; 17:e1008589. [PMID: 34061823 PMCID: PMC8195430 DOI: 10.1371/journal.pcbi.1008589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/11/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
The earliest models for how morphogen gradients guide embryonic patterning failed to account for experimental observations of temporal refinement in gene expression domains. Following theoretical and experimental work in this area, dynamic positional information has emerged as a conceptual framework to discuss how cells process spatiotemporal inputs into downstream patterns. Here, we show that diffusion determines the mathematical means by which bistable gene expression boundaries shift over time, and therefore how cells interpret positional information conferred from morphogen concentration. First, we introduce a metric for assessing reproducibility in boundary placement or precision in systems where gene products do not diffuse, but where morphogen concentrations are permitted to change in time. We show that the dynamics of the gradient affect the sensitivity of the final pattern to variation in initial conditions, with slower gradients reducing the sensitivity. Second, we allow gene products to diffuse and consider gene expression boundaries as propagating wavefronts with velocity modulated by local morphogen concentration. We harness this perspective to approximate a PDE model as an ODE that captures the position of the boundary in time, and demonstrate the approach with a preexisting model for Hunchback patterning in fruit fly embryos. We then propose a design that employs antiparallel morphogen gradients to achieve accurate boundary placement that is robust to scaling. Throughout our work we draw attention to tradeoffs among initial conditions, boundary positioning, and the relative timescales of network and gradient evolution. We conclude by suggesting that mathematical theory should serve to clarify not just our quantitative, but also our intuitive understanding of patterning processes.
Collapse
Affiliation(s)
- Melinda Liu Perkins
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail:
| |
Collapse
|