Bacterial Chemotaxis, Part 1

Published by Omphalos Lifesciences on January 5, 2024January 5, 2024

All around us, there is a world of microorganisms that is as alien in appearance as an extraterrestrial from an old sci-fi movie. E. coli is a rod-shaped bacterium that is a mere 1-2 micrometers long. Just like larger animals such as humans, it is imperative that E. coli move and respond to their environment, as their survival depends on it. This movement is achieved by a process called chemotaxis. 

Figure 1. Flagella enable E. coli orientation and locomotion 

In a typical micro-environment, E. coli cells just tumble around, seemingly randomly. They move with small appendages known as flagella, which move on a rotor-like system. This natural tumbling motion is achieved by having the flagella in a non-uniform distribution about the cell. The flagella rotors move in a clockwise manner to achieve this arrangement or conformation that results in the non-directed tumbling motion with little propulsion. When a chemical attractant such as food or a repulsion such as poison is detected, the cell must change its strategy to more efficiently move towards or away from the chemical signal. The flagella can work together in a bundle by arranging in a counterclockwise motion to achieve more efficient movement. This is known as a run, as the bacteria smoothly swims towards its desired area of the chemical gradient. Using these techniques of movement, the cell can effectively travel and obtain food when it is available, as well as avoid chemical gradients that would pose a threat to the cell’s health. 

For such a small life form as an E. coli cell, even moving a few millimeters away is a very long journey. Desired food such as glucose might be a short distance from the cell by our perception, but to the E. coli cell it is akin to being miles and miles away. It is interesting to consider how the unicellular organism might detect which direction to move to obtain this food given its relative far distance. Similar to how we can see for miles, E. coli has the capacity to detect these chemical signals using a specialized receptor. When the receptors are bound with food molecules, the cells undergo the appropriate conformation of their flagella in order to run towards the higher concentration of food. This enables the cell to determine which direction to swim in, and is crucial for the cell’s ability to get food and survive. 

Video 1. A 2-dimensional visualization of bacterial chemotaxis in E. coli.

Bacterial chemotaxis is a fascinating mechanism to study, as understanding the way microorganisms function gives us insight into the nature of life itself. Using L++, we have modeled this phenomena and have been able to produce accurate videos of this behavior. Seen above is a 2D representation of bacterial chemotaxis. You can observe as the E. coli moves toward its desired food source, glucose. Note that E. coli does not move straight from its original location to its final location. Instead, E. coli often changes direction by tumbling and moves away from where food is highly abundant, which might look like a waste of time. However, considering that E. coli is a tiny life form and can only employ mechanisms available at its microscale, this could be among the most effective means to achieve chemotaxis at this scale. The details behind this bacterial chemotaxis can be glimpsed in the following L++ code.

 petridish P
 {
   ecoli E
   {
     protein R
     {
       reaction R1(A  -> Am,  k=1);
       reaction R2(AL -> AmL, k=1);
     }
     protein Am
     {
       reaction R(B -> BP, k=5e-7, krev=0.005);
     }
     protein BP
     {
       reaction R1(Am  -> A,  kcat=200, KM=1nM);
       reaction R2(AmL -> AL, kcat=1,   KM=1nM);
     }
     reaction R1(Am + L -> AmL, k=1e-9, krev=1);
     reaction R2(A  + L -> AL,  k=1e-9, krev=1);

     A = 500nM, R = 5nM, B = 0.1nM;
   }
   E(100, 70, 0) = 1;
   glucose L;
   L(200, 100, 0) = 100nmol;
 }
 P = 1;

Code 1. A sample of the L++ code written to represent bacterial chemotaxis.

L++ utilizes easily understandable syntax, which can be used to generate high-quality visualizations of the desired biosystem or biological process. A person with a sophisticated understanding of bacterial chemotaxis should have no trouble writing up a simulation similar to our above example. We will go into more detail about the overall process a researcher might take to come up with this code in a future blog post, so please stay tuned.

Video 2. A 3-dimensional visualization of bacterial chemotaxis with E. coli cells moving towards glucose.

This is a 3D video of what bacterial chemotaxis looks like. By simulating this method of cellular motility in a high-quality, 3D format, it is obvious how alien these small lifeforms really are. Microbiology connects us to a different world that is in many ways far more exotic than that of aliens depicted on television. 

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