Cole John A, Kohler Lars, Hedhli Jamila, Luthey-Schulten Zaida
Department of Physics, University of Illinois, 1110 W. Green St., Urbana, 61801, IL, USA.
Department of Chemistry, University of Illinois, 600 S. Matthews Ave., Urbana, 61801, IL, USA.
BMC Syst Biol. 2015 Mar 18;9:15. doi: 10.1186/s12918-015-0155-1.
The exchange of metabolites and the reprogramming of metabolism in response to shifting microenvironmental conditions can drive subpopulations of cells within colonies toward divergent behaviors. Understanding the interactions of these subpopulations-their potential for competition as well as cooperation-requires both a metabolic model capable of accounting for a wide range of environmental conditions, and a detailed dynamic description of the cells' shared extracellular space.
Here we show that a cell's position within an in silico Escherichia coli colony grown on glucose minimal agar can drastically affect its metabolism: "pioneer" cells at the outer edge engage in rapid growth that expands the colony, while dormant cells in the interior separate two spatially distinct subpopulations linked by a cooperative form of acetate crossfeeding that has so far gone unnoticed. Our hybrid simulation technique integrates 3D reaction-diffusion modeling with genome-scale flux balance analysis (FBA) to describe the position-dependent metabolism and growth of cells within a colony. Our results are supported by imaging experiments involving strains of fluorescently-labeled E. coli. The spatial patterns of fluorescence within these experimental colonies identify cells with upregulated genes associated with acetate crossfeeding and are in excellent agreement with the predictions. Furthermore, the height-to-width ratios of both the experimental and simulated colonies are in good agreement over a growth period of 48 hours.
Our modeling paradigm can accurately reproduce a number of known features of E. coli colony growth, as well as predict a novel one that had until now gone unrecognized. The acetate crossfeeding we see has a direct analogue in a form of lactate crossfeeding observed in certain forms of cancer, and we anticipate future application of our methodology to models of tissues and tumors.
代谢物的交换以及代谢重编程以响应不断变化的微环境条件，可驱使菌落中的细胞亚群表现出不同行为。要理解这些亚群之间的相互作用——它们竞争与合作的潜力——既需要一个能够考虑广泛环境条件的代谢模型，也需要对细胞共享的细胞外空间进行详细的动态描述。
我们在此表明，在以葡萄糖为唯一碳源的最小琼脂平板上生长的计算机模拟大肠杆菌菌落中，细胞的位置可极大地影响其代谢：边缘的“先锋”细胞快速生长以扩张菌落，而内部的休眠细胞将两个空间上不同的亚群分隔开来，这两个亚群通过一种迄今未被注意到的乙酸盐互养的合作形式相联系。我们的混合模拟技术将三维反应扩散建模与基因组尺度通量平衡分析（FBA）相结合，以描述菌落中细胞位置依赖性的代谢和生长。我们的结果得到了涉及荧光标记大肠杆菌菌株的成像实验的支持。这些实验菌落内的荧光空间模式识别出与乙酸盐互养相关基因上调的细胞，并且与预测结果高度吻合。此外，在48小时的生长周期内，实验菌落和模拟菌落的高宽比也高度一致。
我们的建模范式能够准确再现大肠杆菌菌落生长的许多已知特征，并预测一个迄今未被识别的新特征。我们所观察到的乙酸盐互养在某些形式的癌症中观察到的乳酸盐互养形式中有直接类似物，我们预计我们的方法未来将应用于组织和肿瘤模型。
