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Grant PK, Szep G, Patange O, Halatek J, Coppard V, Csikász-Nagy A, Haseloff J, Locke JCW, Dalchau N, Phillips A. Interpretation of morphogen gradients by a synthetic bistable circuit. Nat Commun 2020; 11:5545. [PMID: 33139718 PMCID: PMC7608687 DOI: 10.1038/s41467-020-19098-w] [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: 07/15/2020] [Accepted: 09/23/2020] [Indexed: 12/02/2022] Open
Abstract
During development, cells gain positional information through the interpretation of dynamic morphogen gradients. A proposed mechanism for interpreting opposing morphogen gradients is mutual inhibition of downstream transcription factors, but isolating the role of this specific motif within a natural network remains a challenge. Here, we engineer a synthetic morphogen-induced mutual inhibition circuit in E. coli populations and show that mutual inhibition alone is sufficient to produce stable domains of gene expression in response to dynamic morphogen gradients, provided the spatial average of the morphogens falls within the region of bistability at the single cell level. When we add sender devices, the resulting patterning circuit produces theoretically predicted self-organised gene expression domains in response to a single gradient. We develop computational models of our synthetic circuits parameterised to timecourse fluorescence data, providing both a theoretical and experimental framework for engineering morphogen-induced spatial patterning in cell populations. Morphogen gradients can be dynamic and transient yet give rise to stable cellular patterns. Here the authors show that a synthetic morphogen-induced mutual inhibition circuit produces stable boundaries when the spatial average of morphogens falls within the region of bistability.
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Affiliation(s)
- Paul K Grant
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.
| | - Gregory Szep
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.,Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Om Patange
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jacob Halatek
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | | | - Attila Csikász-Nagy
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK.,Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, 1083, Hungary
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - James C W Locke
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.,Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.,Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Neil Dalchau
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Andrew Phillips
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.
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Vollmer J, Casares F, Iber D. Growth and size control during development. Open Biol 2018; 7:rsob.170190. [PMID: 29142108 PMCID: PMC5717347 DOI: 10.1098/rsob.170190] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/17/2017] [Indexed: 11/30/2022] Open
Abstract
The size and shape of organs are characteristic for each species. Even when organisms develop to different sizes due to varying environmental conditions, such as nutrition, organ size follows species-specific rules of proportionality to the rest of the body, a phenomenon referred to as allometry. Therefore, for a given environment, organs stop growth at a predictable size set by the species's genotype. How do organs stop growth? How can related species give rise to organs of strikingly different size? No definitive answer has been given to date. One of the major models for the studies of growth termination is the vinegar fly Drosophila melanogaster. Therefore, this review will focus mostly on work carried out in Drosophila to try to tease apart potential mechanisms and identify routes for further investigation. One general rule, found across the animal kingdom, is that the rate of growth declines with developmental time. Therefore, answers to the problem of growth termination should explain this seemingly universal fact. In addition, growth termination is intimately related to the problems of robustness (i.e. precision) and plasticity in organ size, symmetric and asymmetric organ development, and of how the ‘target’ size depends on extrinsic, environmental factors.
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Affiliation(s)
- Jannik Vollmer
- D-BSSE, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics (SIB), Mattenstrasse 26, 4058 Basel, Switzerland
| | - Fernando Casares
- CABD, CSIC-Universidad Pablo de Olavide-JA, 41013 Seville, Spain
| | - Dagmar Iber
- D-BSSE, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland .,Swiss Institute of Bioinformatics (SIB), Mattenstrasse 26, 4058 Basel, Switzerland
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Multerer MD, Wittwer LD, Stopka A, Barac D, Lang C, Iber D. Simulation of Morphogen and Tissue Dynamics. Methods Mol Biol 2018; 1863:223-250. [PMID: 30324601 DOI: 10.1007/978-1-4939-8772-6_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Morphogenesis, the process by which an adult organism emerges from a single cell, has fascinated humans for a long time. Modeling this process can provide novel insights into development and the principles that orchestrate the developmental processes. This chapter focuses on the mathematical description and numerical simulation of developmental processes. In particular, we discuss the mathematical representation of morphogen and tissue dynamics on static and growing domains, as well as the corresponding tissue mechanics. In addition, we give an overview of numerical methods that are routinely used to solve the resulting systems of partial differential equations. These include the finite element method and the Lattice Boltzmann method for the discretization as well as the arbitrary Lagrangian-Eulerian method and the Diffuse-Domain method to numerically treat deforming domains.
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Affiliation(s)
- Michael D Multerer
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Lucas D Wittwer
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Anna Stopka
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Diana Barac
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christine Lang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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