Spatial biology of Ising-like synthetic genetic networks

BMC Biology

Research Article

Kevin Simpson¹  Fernán Federici²  Juan Keymer³  Alfredo L’Homme⁴ 

[1] ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile;ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile;Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile;FONDAP Center for Genome Regulation - Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile;Institute for Advanced Studies, Shenzhen X-Institute, Shenzhen, China;Schools of Physics and Biology, Pontificia Universidad Católica de Chile, Santiago, Chile;Department of Natural Sciences and Technology, Universidad de Aysén, Coyhaique, Chile;Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile;

关键词: Ising model;    Bi-stable;    Synthetic gene networks;    Spatial correlation;    Criticality;   

DOI  :  10.1186/s12915-023-01681-4

 received in 2022-12-20, accepted in 2023-08-11,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundUnderstanding how spatial patterns of gene expression emerge from the interaction of individual gene networks is a fundamental challenge in biology. Developing a synthetic experimental system with a common theoretical framework that captures the emergence of short- and long-range spatial correlations (and anti-correlations) from interacting gene networks could serve to uncover generic scaling properties of these ubiquitous phenomena.ResultsHere, we combine synthetic biology, statistical mechanics models, and computational simulations to study the spatial behavior of synthetic gene networks (SGNs) in Escherichia coli quasi-2D colonies growing on hard agar surfaces. Guided by the combined mechanisms of the contact process lattice simulation and two-dimensional Ising model (CPIM), we describe the spatial behavior of bi-stable and chemically coupled SGNs that self-organize into patterns of long-range correlations with power-law scaling or short-range anti-correlations. These patterns, resembling ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points, maintain their scaling properties upon changes in growth rate and cell shape.ConclusionsOur findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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