Quantitative modeling of Escherichia coli chemotactic motion in environments varying in space and time.
Quantitative modeling of Escherichia coli chemotactic motion in environments varying in space and time.
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DOI：
10.1371/journal.pcbi.1000735
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发表时间：
2010-04-08
影响因子：
4.3
通讯作者：
Tu Y
中科院分区：
文献类型：
--
作者：
Jiang L;Ouyang Q;Tu Y
大肠杆菌的趋化运动在时空变化的环境中进行了研究，通过使用一个计算模型的基础上粗粒度的描述细胞内信号通路的动力学。我们发现，在指数吸引剂浓度梯度[L]<$exp（Gx）中，细胞的趋化漂移速度vd是一个常数。当G大于临界值GC时，vd在其饱和之前线性地依赖于指数梯度G。我们发现，GC是由细胞内的适应率kR与一个简单的标度律：。vd与G = d（ln[L]）/dx的线性关系直接证明了E. 大肠杆菌感受对数引诱剂浓度的导数的能力。限制梯度GC的存在和其缩放与KR的解释由潜在的细胞内适应动力学和鞭毛运动响应特性。对于单个细胞，我们发现在指数梯度中的总体平均运行长度比在均匀环境中的要长，这是由恒定的激酶活性偏移（降低）引起的。正如预期的那样，向前运行（沿梯度向上）比向后运行更长;并且根据确切的梯度，（较短的）向后运行可以与空间均匀环境中的运行相媲美，与先前的实验一致。在也随时间变化的（空间）配体梯度中，当随时间变化的空间梯度的频率ω变得快于临界值ωc时，趋化运动被阻尼，该临界值ω c由细胞的趋化适应速率kR控制。最后，我们的模型，没有可调参数，同意定量与经典的毛细管分析实验中的引诱剂浓度在空间和时间上的变化。我们的模型可以用来研究E.大肠杆菌在任意时空变化环境中的趋化行为。建议进一步的实验来测试一些模型的预测。一个计算模型，基于一个粗粒度的描述细胞的潜在的趋化性信号通路的动力学，是用来研究大肠杆菌趋化运动在现实的环境中，在空间和时间上的变化。我们发现，在指数吸引梯度下，E。大肠杆菌细胞以与指数梯度成正比的恒定趋化漂移速度（CDV）（随机）游向更高的引诱剂浓度。相反，CDV以线性梯度连续减小。这些结果表明，E.大肠杆菌感测并响应配体浓度的相对梯度，而不是梯度本身。细胞内感觉适应率不直接影响趋化运动，但是，它设置了一个最大的相对配体梯度，超过该梯度CDV饱和。在时变环境中，E.当空间梯度的变化（在时间上）快于由适应率确定的临界频率时，大肠杆菌的趋化运动被阻尼。个别细胞的游程长度统计进行了研究，发现与以前的实验测量是一致的。最后，模拟我们的模型，没有可调的参数，同意定量与经典的毛细管分析中的引诱剂浓度在空间和时间上的变化。该模型可用于预测和研究E.大肠杆菌在任意时空变化环境中的趋化行为。
Escherichia coli chemotactic motion in spatiotemporally varying environments is studied by using a computational model based on a coarse-grained description of the intracellular signaling pathway dynamics. We find that the cell's chemotaxis drift velocity vd is a constant in an exponential attractant concentration gradient [L]∝exp(Gx). vd depends linearly on the exponential gradient G before it saturates when G is larger than a critical value GC. We find that GC is determined by the intracellular adaptation rate kR with a simple scaling law: . The linear dependence of vd on G = d(ln[L])/dx directly demonstrates E. coli's ability in sensing the derivative of the logarithmic attractant concentration. The existence of the limiting gradient GC and its scaling with kR are explained by the underlying intracellular adaptation dynamics and the flagellar motor response characteristics. For individual cells, we find that the overall average run length in an exponential gradient is longer than that in a homogeneous environment, which is caused by the constant kinase activity shift (decrease). The forward runs (up the gradient) are longer than the backward runs, as expected; and depending on the exact gradient, the (shorter) backward runs can be comparable to runs in a spatially homogeneous environment, consistent with previous experiments. In (spatial) ligand gradients that also vary in time, the chemotaxis motion is damped as the frequency ω of the time-varying spatial gradient becomes faster than a critical value ωc, which is controlled by the cell's chemotaxis adaptation rate kR. Finally, our model, with no adjustable parameters, agrees quantitatively with the classical capillary assay experiments where the attractant concentration changes both in space and time. Our model can thus be used to study E. coli chemotaxis behavior in arbitrary spatiotemporally varying environments. Further experiments are suggested to test some of the model predictions. A computational model, based on a coarse-grained description of the cell's underlying chemotaxis signaling pathway dynamics, is used to study Escherichia coli chemotactic motion in realistic environments that change in both space and time. We find that in an exponential attractant gradient, E. coli cells swim (randomly) toward higher attractant concentrations with a constant chemotactic drift velocity (CDV) that is proportional to the exponential gradient. In contrast, CDV continuously decreases in a linear gradient. These findings demonstrate that E. coli senses and responds to the relative gradient of the ligand concentration, instead of the gradient itself. The intracellular sensory adaptation rate does not affect the chemotactic motion directly; however, it sets a maximum relative ligand gradient beyond which CDV saturates. In time-varying environments, the E. coli's chemotactic motion is damped when the spatial gradient varies (in time) faster than a critical frequency determined by the adaptation rate. The run-length statistics of individual cells are studied and found to be consistent with previous experimental measurements. Finally, simulations of our model, with no adjustable parameters, agree quantitatively with the classical capillary assay in which the attractant concentration changes both in space and time. Our model can thus be used to predict and study E. coli chemotaxis behavior in arbitrary spatiotemporally varying environment.
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影响因子：
64.8
作者：
Alon, U;Surette, MG;Leibler, S
通讯作者：
Leibler, S
影响因子：
64.8
作者：
Barkai, N;Leibler, S
通讯作者：
Leibler, S
影响因子：
64.8
作者：
FUTRELLE, RP;BERG, HC
通讯作者：
BERG, HC
影响因子：
64.8
作者：
DiLuzio, WR;Turner, L;Whitesides, GM
通讯作者：
Whitesides, GM
DOI：
10.1073/pnas.1330839100
发表时间：
2003-07-08
影响因子：
11.1
作者：
Mello, BA;Tu, YH
通讯作者：
Tu, YH