1
|
Lam C. Mathematical and In Silico Analysis of Synthetic Inhibitory Circuits That Program Self-Organizing Multicellular Structures. ACS Synth Biol 2024; 13:1925-1940. [PMID: 38781040 DOI: 10.1021/acssynbio.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Bottom-up approaches are becoming increasingly popular for studying multicellular self-organization and development. In contrast to the classic top-down approach, where parts of the organization/developmental process are broken to understand the process, the goal is to build the process to understand it. For example, synthetic circuits have been built to understand how cell-cell communication and differential adhesion can drive multicellular development. The majority of current bottom-up efforts focus on using activatory circuits to engineer and understand development, but efforts with inhibitory circuits have been minimal. Yet, inhibitory circuits are ubiquitous and vital to native developmental processes. Thus, inhibitory circuits are a crucial yet poorly studied facet of bottom-up multicellular development. To demonstrate the potential of inhibitory circuits for building and developing multicellular structures, several synthetic inhibitory circuits that combine engineered cell-cell communication and differential adhesion were designed, and then examined for synthetic development capability using a previously validated in silico framework. These designed inhibitory circuits can build a variety of patterned, self-organized structures and even morphological oscillations. These results support that inhibitory circuits can be powerful tools for building, studying, and understanding developmental processes.
Collapse
Affiliation(s)
- Calvin Lam
- Independent Investigator, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| |
Collapse
|
2
|
Kim J, de Lorenzo V, Goñi‐Moreno Á. Pressure-dependent growth controls 3D architecture of Pseudomonas putida microcolonies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:708-715. [PMID: 37231623 PMCID: PMC10667634 DOI: 10.1111/1758-2229.13182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
Colony formation is key to many ecological and biotechnological processes. In its early stages, colony formation involves the concourse of a number of physical and biological parameters for generation of a distinct 3D structure-the specific influence of which remains unclear. We focused on a thus far neglected aspect of the process, specifically the consequences of the differential pressure experienced by cells in the middle of a colony versus that endured by bacteria located in the growing periphery. This feature was characterized experimentally in the soil bacterium Pseudomonas putida. Using an agent-based model we recreated the growth of microcolonies in a scenario in which pressure was the only parameter affecting proliferation of cells. Simulations exposed that, due to constant collisions with other growing bacteria, cells have virtually no free space to move sideways, thereby delaying growth and boosting chances of overlapping on top of each other. This scenario was tested experimentally on agar surfaces. Comparison between experiments and simulations suggested that the inside/outside differential pressure determines growth, both timewise and in terms of spatial directions, eventually moulding colony shape. We thus argue that-at least in the case studied-mere physical pressure of growing cells suffices to explain key dynamics of colony formation.
Collapse
Affiliation(s)
- Juhyun Kim
- School of Life ScienceBK21 FOUR KNU Creative BioResearch Group Kyungpook National UniversityDaeguRepublic of Korea
| | - Víctor de Lorenzo
- Systems Biology DepartmentCentro Nacional de Biotecnología (CNB‐CSIC)Cantoblanco‐MadridSpain
| | - Ángel Goñi‐Moreno
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)‐Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC)MadridSpain
| |
Collapse
|
3
|
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
|
4
|
Roy U, Singh D, Vincent N, Haritas CK, Jolly MK. Spatiotemporal Patterning Enabled by Gene Regulatory Networks. ACS OMEGA 2023; 8:3713-3725. [PMID: 36743018 PMCID: PMC9893257 DOI: 10.1021/acsomega.2c04581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/24/2022] [Indexed: 06/18/2023]
Abstract
Spatiotemporal pattern formation plays a key role in various biological phenomena including embryogenesis and neural network formation. Though the reaction-diffusion systems enabling pattern formation have been studied phenomenologically, the biomolecular mechanisms behind these processes have not been modeled in detail. Here, we study the emergence of spatiotemporal patterns due to simple, synthetic and commonly observed two- and three-node gene regulatory network motifs coupled with their molecular diffusion in one- and two-dimensional space. We investigate the patterns formed due to the coupling of inherent multistable and oscillatory behavior of the toggle switch, toggle switch with double self-activation, toggle triad, and repressilator with the effect of spatial diffusion of these molecules. We probe multiple parameter regimes corresponding to different regions of stability (monostable, multistable, oscillatory) and assess the impact of varying diffusion coefficients. This analysis offers valuable insights into the design principles of pattern formation facilitated by these network motifs, and it suggests the mechanistic underpinnings of biological pattern formation.
Collapse
Affiliation(s)
- Ushasi Roy
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore560012, India
| | - Divyoj Singh
- Undergraduate
Programme, Indian Institute of Science, Bangalore560012, India
| | - Navin Vincent
- Undergraduate
Programme, Indian Institute of Science, Bangalore560012, India
| | - Chinmay K. Haritas
- Undergraduate
Programme, Indian Institute of Science, Bangalore560012, India
| | - Mohit Kumar Jolly
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore560012, India
| |
Collapse
|
5
|
Godin R, Karamched BR, Ryan SD. The space between us: Modeling spatial heterogeneity in synthetic microbial consortia dynamics. BIOPHYSICAL REPORTS 2022; 2:100085. [PMID: 36479317 PMCID: PMC9720408 DOI: 10.1016/j.bpr.2022.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
A central endeavor in bioengineering concerns the construction of multistrain microbial consortia with desired properties. Typically, a gene network is partitioned between strains, and strains communicate via quorum sensing, allowing for complex behaviors. Yet a fundamental question of how emergent spatiotemporal patterning in multistrain microbial consortia affects consortial dynamics is not understood well. Here, we propose a computationally tractable and straightforward modeling framework that explicitly allows linking spatiotemporal patterning to consortial dynamics. We validate our model against previously published results and make predictions of how spatial heterogeneity impacts interstrain communication. By enabling the investigation of spatial patterns effects on microbial dynamics, our modeling framework informs experimentalists, helps advance the understanding of complex microbial systems, and supports the development of applications involving them.
Collapse
Affiliation(s)
- Ryan Godin
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa
- Department of Biology, Geology, and Environmental Sciences, Cleveland State University, Cleveland, Ohio
- Department of Mathematics and Statistics, Cleveland State University, Cleveland, Ohio
- Center for Applied Data Analysis and Modeling, Cleveland State University, Cleveland, Ohio
| | - Bhargav R. Karamched
- Department of Mathematics, Florida State University, Tallahassee, Florida
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
- Program in Neuroscience, Florida State University, Tallahassee, Florida
| | - Shawn D. Ryan
- Department of Mathematics and Statistics, Cleveland State University, Cleveland, Ohio
- Center for Applied Data Analysis and Modeling, Cleveland State University, Cleveland, Ohio
| |
Collapse
|
6
|
Ecological firewalls for synthetic biology. iScience 2022; 25:104658. [PMID: 35832885 PMCID: PMC9272386 DOI: 10.1016/j.isci.2022.104658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
It has been recently suggested that engineered microbial strains could be used to protect ecosystems from undesirable tipping points and biodiversity loss. A major concern in this context is the potential unintended consequences, which are usually addressed in terms of designed genetic constructs aimed at controlling overproliferation. Here we present and discuss an alternative view grounded in the nonlinear attractor dynamics of some ecological network motifs. These ecological firewalls are designed to perform novel functionalities (such as plastic removal) while containment is achieved within the resident community. That could help provide a self-regulating biocontainment. In this way, engineered organisms have a limited spread while—when required—preventing their extinction. The basic synthetic designs and their dynamical behavior are presented, each one inspired in a given ecological class of interaction. Their possible applications are discussed and the broader connection with invasion ecology outlined. Population control of synthetic strains can be achieved by engineering ecological links We introduce ecological firewalls, inspired in four types of ecological interactions Our firewalls are shown to maintain diversity while performing designed functions Ecological firewalls will help to tackle future bioremediation strategies
Collapse
|
7
|
Lu J, Şimşek E, Silver A, You L. Advances and challenges in programming pattern formation using living cells. Curr Opin Chem Biol 2022; 68:102147. [DOI: 10.1016/j.cbpa.2022.102147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/29/2022]
|
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: 1.0] [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 2021; 15:1685-1694. [PMID: 34843638 PMCID: PMC9151330 DOI: 10.1111/1751-7915.13979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [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 Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Georg K A Wachter
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|