A tug-of-war explains a decades-old question about how bacteria swim

(Press-News.org) Scientists have uncovered a new explanation for how swimming bacteria change direction, providing fresh insight into one of biology’s most intensively studied molecular machines.

Bacteria move through liquids using propellerlike tails called flagella, which alternate between clockwise and counterclockwise rotation. For decades, this switching behavior has been attributed to an equilibrium ‘domino effect’ model, in which proteins lining the bacterium’s tail exert pressure on their neighbors, prompting a change in rotational direction.

New research in Nature Physics from the Flatiron Institute’s Henry Mattingly and Yuhai Tu proposes a different mechanism, informed by experimental measurements of the molecular structure of the flagellar motor and an analysis of how flagella switch their spin. Rather than relying on passive pressure from neighboring proteins, the switch is driven by an active tug-of-war among distant proteins.

“People have known this switching behavior since the 1950s, but now having this simple molecular-level mechanism to explain it is very exciting,” says Tu, a senior research scientist at the Flatiron Institute’s Center for Computational Biology (CCB) and Center for Computational Neuroscience (CCN).

The Problem With the Domino Effect The flagellar motor is a long-studied structure, and as Tu notes, it’s one of nature’s most beautiful molecular machines. It is composed of 34 proteins arranged in a large central ring, powered by smaller structures called stators — channels that allow electrically charged atoms to flow in and drive the rotation.

The ring proteins control whether the tail rotates clockwise or counterclockwise, depending on signals they receive from a molecule called CheY-P. If CheY-P binds to one of the proteins, it affects the protein’s conformation so that it promotes spinning in one direction or the other.

“CheY-P concentration depends on what the cell is experiencing outside, in its environment,” says Mattingly, an associate research scientist at the CCB. “It’s like a relay from what the cell senses to how it responds with changes in behavior.”

Depending on which proteins are bound by CheY-P, the ring proteins can end up in different states: Some bias the motor to move clockwise, while others favor counterclockwise rotation. In the original equilibrium model, scientists proposed that this disagreement among neighboring proteins would eventually be overcome through a domino effect. If a protein’s neighbors promoted a certain rotational direction, then that protein would be more likely to ‘fall in line’ and adopt that same state.

“The proteins cooperate with each other. If I’m in one state, my neighbor has a higher probability of joining me in that same state,” says Tu. “Once enough of them change state, the motor flips.”

However, when researchers examined the actual frequency with which flagella switched rotational direction, the distribution couldn’t be explained by the equilibrium model. Under that framework, motor switching should follow a memoryless statistical pattern, in which the likelihood of a flip doesn’t depend on how long the motor has been rotating in a given direction.

Instead, the experimental data revealed a peak in the distribution of time spent rotating in one direction rather than the other, which is not possible in an equilibrium system. “If you see this pattern, then the effect cannot be a purely equilibrium phenomenon,” says Tu. “There had to be something else going on.”

A Tug-of-War Inside the Tail Mattingly and Tu reasoned that switching the motor’s rotational direction couldn’t be a passive equilibrium process — there must be energy injected into the system that somehow influences how and when the motor switches.

Several recent discoveries about the physical structure of the motor informed Mattingly and Tu’s theory. First, the ring of proteins in the flagellar motor, known as the C-ring, acts as one big central gear, with each protein acting as one tooth of the gear. Second, the stators aren’t just a general power source; they also function as smaller gears. These stators always rotate clockwise and make contact with the teeth of the large gear. How these teeth touch the stators determines which way they try to get the motor to turn.

The teeth of the large gear can change position to touch the small gears — the stators — on the stators’ outer edge or their inner edge. When the teeth touch the outer edge, the stators push the large gear clockwise; when they touch the inner edge, the stators push them counterclockwise. As a result, even though the small gears always rotate clockwise, the flagellum can rotate either way.

However, conflicts can arise when different teeth adopt different conformations. Some may contact their stators on the outside and favor a clockwise direction, while others contact their stators on the inside and try to turn the other way. According to the new model, this is where the tug-of-war emerges.

“Imagine all the teeth are in the same outer conformation. Then one of them flips,” says Mattingly. “As the gear turns, that lone dissenter eventually comes in contact with a stator that now pushes it in the opposite direction from all the others. Because the teeth are mechanically linked, that one tooth is feeling five active gears pushing one way and one pushing the other. Since it’s out of sync with the rest, the torque on it is much larger. It’s like a mechanical tug-of-war. If the mechanical force on it is too strong, it flips to join the majority. But if enough teeth dissent, then the entire motor changes direction.”

The team calls this process “global mechanical coupling.” The name is meant to underscore that the forces driving each tooth to turn one way or the other aren’t determined solely by the teeth’s interactions with their neighbors; rather, all teeth touching stators will impact one another across the motor in a collective process.

Global mechanical coupling can also produce the peak in the distribution seen in the earlier experiments. Since the stators are active players in the direction switching, not just general power sources for rotation, they inject energy into the system and drive it out of equilibrium.

“Global mechanical coupling explains what the earlier, purely equilibrium theory couldn’t, that switching is energy-driven, directional and cooperative,” says Tu.

Unraveling Mysteries in the Flagella and Beyond With a new model in place, the team hopes it will inform our understanding of other nonequilibrium systems in living organisms.

“Our results make sense to me because I believe living systems always operate out of equilibrium,” says Tu. “They dissipate energy, and that energy is essential for biological function. This is a beautiful example of that principle.”

The researchers will continue to refine their model to integrate more experimental data. For example, their model predicts a peak in the distribution of counterclockwise durations, but on a shorter timescale than in experiments.

Understanding the flagella can also influence how scientists understand more complex systems.

“It’s so well studied that it becomes a perfect system to test ideas — and what we learn here often helps us think about more complex biology,” says Mattingly.

Tu adds that the new research is also exciting for the field of bacterial chemotaxis. “Every so often people say, ‘This is a dead field.’ Every time that turns out to be wrong. There’s always another layer.”

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