Yáñez Feliú Guillermo, Vidal Gonzalo, Muñoz Silva Macarena, Rudge Timothy J
Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.
Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.
Front Bioeng Biotechnol. 2020 Aug 28;8:893. doi: 10.3389/fbioe.2020.00893. eCollection 2020.
Multicellularity, the coordinated collective behavior of cell populations, gives rise to the emergence of self-organized phenomena at many different spatio-temporal scales. At the genetic scale, oscillators are ubiquitous in regulation of multicellular systems, including during their development and regeneration. Synthetic biologists have successfully created simple synthetic genetic circuits that produce oscillations in single cells. Studying and engineering synthetic oscillators in a multicellular chassis can therefore give us valuable insights into how simple genetic circuits can encode complex multicellular behaviors at different scales. Here we develop a study of the coupling between the repressilator synthetic genetic ring oscillator and constraints on cell growth in colonies. We show how mechanical constraints generate characteristic patterns of growth rate inhomogeneity in growing cell colonies. Next, we develop a simple one-dimensional model which predicts that coupling the repressilator to this pattern of growth rate via protein dilution generates traveling waves of gene expression. We show that the dynamics of these spatio-temporal patterns are determined by two parameters; the protein degradation and maximum expression rates of the repressors. We derive simple relations between these parameters and the key characteristics of the traveling wave patterns: firstly, wave speed is determined by protein degradation and secondly, wavelength is determined by maximum gene expression rate. Our analytical predictions and numerical results were in close quantitative agreement with detailed individual based simulations of growing cell colonies. Confirming published experimental results we also found that static ring patterns occur when protein stability is high. Our results show that this pattern can be induced simply by growth rate dilution and does not require transition to stationary phase as previously suggested. Our method generalizes easily to other genetic circuit architectures thus providing a framework for multi-scale rational design of spatio-temporal patterns from genetic circuits. We use this method to generate testable predictions for the synthetic biology design-build-test-learn cycle.
多细胞性，即细胞群体的协调集体行为，在许多不同的时空尺度上引发了自组织现象的出现。在基因尺度上，振荡器在多细胞系统的调控中无处不在，包括在其发育和再生过程中。合成生物学家已经成功创建了在单细胞中产生振荡的简单合成基因电路。因此，在多细胞底盘中研究和设计合成振荡器可以让我们深入了解简单的基因电路如何在不同尺度上编码复杂的多细胞行为。在这里，我们开展了一项关于阻遏物合成基因环振荡器与菌落中细胞生长限制之间耦合的研究。我们展示了机械限制如何在生长的细胞菌落中产生生长速率不均匀性的特征模式。接下来，我们开发了一个简单的一维模型，该模型预测通过蛋白质稀释将阻遏物与这种生长速率模式耦合会产生基因表达的行波。我们表明，这些时空模式的动态由两个参数决定；阻遏物的蛋白质降解和最大表达速率。我们推导了这些参数与行波模式的关键特征之间的简单关系：首先，波速由蛋白质降解决定，其次，波长由最大基因表达速率决定。我们的分析预测和数值结果与生长细胞菌落的基于个体的详细模拟在定量上密切一致。证实已发表的实验结果，我们还发现当蛋白质稳定性高时会出现静态环模式。我们的结果表明，这种模式可以简单地由生长速率稀释诱导产生，并不像之前所认为的那样需要过渡到稳定期。我们的方法很容易推广到其他基因电路架构，从而为从基因电路进行时空模式的多尺度合理设计提供了一个框架。我们使用这种方法为合成生物学的设计 - 构建 - 测试 - 学习循环生成可测试的预测。
