Drift and Behavior of E. coli Cells

Abstract

Chemotaxis of the bacterium Escherichia coli is well understood in shallow chemical gradients, but its swimming behavior remains difficult to interpret in steep gradients. By focusing on single-cell trajectories from simulations, we investigated the dependence of the chemotactic drift velocity on attractant concentration in an exponential gradient. While maxima of the average drift velocity can be interpreted within analytical linearresponse theory of chemotaxis in shallow gradients, limits in drift due to steep gradients and finite number of receptor-methylation sites for adaptation go beyond perturbation theory. For instance, we found a surprising pinning of the cells to the concentration in the gradient at which cells run out of methylation sites. To validate the positions of maximal drift, we recorded single-cell trajectories in carefully designed chemical gradients using microfluidics.Cell behavior is notoriously difficult to interpret due to short observation times, variability, and dependence on experimental conditions. Take for instance the bacterium E. coli, which is able to swim up gradients of nutrients in a process called chemotaxis. Its swimming behavior is a result of sensing by cooperative mixed-receptor clusters, signaling by phosphorylation of a response regulator, adaptation by covalent receptor methylation, and motility by flagellated rotary motors [1], operating on wide-ranging time scales. This bacterium's chemotaxis pathway has been extremely well characterized experimentally, but when conducting single-cell experiments using microfluidics in a simple linear chemical gradient of chemoattractant α-D,L-methylaspartic acid (MeAsp), the obtained trajectories depict a complex structure in space and time (Fig. 1, see Figure 1: Schematic of the experimental setup. A chemical gradient of α-D,L-methylaspartic acid (MeAsp, a non-metabolizable analogue of the amino acid Asp) is created in a microfluidic device by maintaining a fixed concentration on one side of the channel and zero on the other. E. coli cells (strain MG1655) are injected on both sides and free to move in aerobic conditions. The gradient is stable after about 1h 30min and the data were acquired after 2h, 3h and 4h with each experiment repeated 3 times [3]. The gradient was measured after the final acquisition using fluorescein. (Middle) Fluorescence picture of the microfluidic chamber with the white bar representing 500 µm. (Left and right) Exemplar of single-E. coli trajectories from a typical movie, acquired in the middle of the channel with trajectory starting points marked with black dots (dashed box, for details see [3]). Some of them are relatively straight (left) while others are curled (right). The MeAsp gradient is oriented to the right in this image (lighter shading corresponds to higher ligand concentration). The average concentration in the channel was 1mM.One primary way to quantify the effectiveness of chemotaxis up a gradient is the determination of the drift velocity, defined as the cell's velocity component in the dire...

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“…Nevertheless, our model is valid for information transmission by initial transient chemotactic responses, and as this applies anywhere in the gradient, our model describes chemotaxis even including adaptation 15 . We expect that our model even works in relatively steep gradients, where, in addition to adaptation, long-history effects are important, such as caused by receptor saturation and rotational diffusion 24 . The main assumption in 15 is that gradients can be linearized over the range of input distributions.…”

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“…The experimental setup is a microfluidics device consisting of an open-ended channel attached on one side to a reservoir with a high concentration of chemoattractant and on the other side to one with zero concentration, creating a linear concentration gradient along the channel (see Micali et al 2017 for further details). The bacteria follow a so-called run and tumble trajectory, in which they move in a straight line for some distance (a run) and then re-orient randomly (a tumble) every so often.…”

“…is low, longer when the concentration increases. The trajectories of the bacteria are captured on camera, and their positions in a linear coordinate system are digitized (Micali et al 2017). Figure 3 shows the setup schematically.…”

“…The statistics of good and bad moves obtained from each band were entered into equation 1. No physical structure or force constrained the E. coli's direction of movement in the x direction, Figure 3: The experimental setting for E. coli chemotaxis developed by Micali et al (2017). E. coli are released into the microfluidics device-essentially a narrow channel-with a fixed, linear gradient of MeAsp, a non-metabolizable chemoattractant.…”

“…The camera captured only the area within the channel of the microfluidics device, so contrary to the figure, E. coli's movements are not actually constrained by the apparent boundaries in the coordinate system. After the gradient becomes stable, bacterial motion data are collected 3 times with 1-hour interval for each of 3 repeats (see Micali et al [2017] for further detail). Figure 4: Persistence of E. coli along a linear MeAsp gradient.…”