Biological complexity: how bacterial flagella operate (Introduction)

by David Turell , Sunday, March 12, 2023, 17:29 (622 days ago) @ David Turell

At the molecular level:

https://inference-review.com/article/bacterial-swimming

"Negative-stain electron microscopy studies of the flagellar motor revealed that the machine is made up of a long filament, connected through a flexible hook to a basal body embedded in the bacterial cell envelope and comprising several rings. The cell envelope in Escherichia coli (E. coli) consists of an inner membrane and an outer membrane separated by a peptidoglycan layer. The energy for the rotation of the flagellum comes from dispersion of a proton motive force.

"E. coli has several flagella on its cell body. When these spin counterclockwise, they come together to form a bundle; the cell moves forward powered by the bundle’s in-unison rotation. If the cell encounters an unfavorable environment, chemical signals cause some of the flagella to rotate in the opposite direction. The bundle falls apart; the cell moves erratically or tumbles. Once the flagella recover and resume counterclockwise motion, the bundle forms again and the cell once more swims straight, but this time, on average, in a different direction. As tumbling is more likely under unfavorable conditions, E. coli can swim away from molecules it dislikes and toward those it likes.

"the power to drive the rotation of the flagellum is derived from the motility proteins, MotA and MotB. Further studies indicated that MotA and MotB form a stator unit with proton channel activity. It is the passage of protons down an electrochemical proton gradient and through the MotAB complex that acts as an energy source. Freeze-fracture electron microscopy studies showed that stator units surround the basal bodies in the inner membrane.5 A model emerged in which stator units, which remain anchored to the rigid peptidoglycan wall of the cell, engage with the cytoplasmic portion of the basal body, or rotor, to power the rotation of the flagellum.

***

" the C-ring, named for its position in the cytoplasmic portion of the basal body, can change its conformation upon binding the phosphorylated chemotaxis-signaling molecule CheY. One of the components of the C-ring, FliG, was shown to have two conformations involving an approximately 180° flip of a torque helix, which, in turn, was thought to interact with the MotAB complex.

***

"...the stator unit is a complex with a stoichiometry of 5:2 MotA:MotB, and not 4:2 as previously believed.16 This ratio introduces an asymmetry, as 4:2 stoichiometry would most likely have been symmetric. MotA has four helices spanning the inner membrane and a cytoplasmic domain. The part of this domain most distal from the membrane is well conserved and binds the rotor. The five MotA molecules make a nearly symmetric, ringlike structure surrounding the N-terminal helices of two MotB molecules, which contain a universally conserved aspartate residue. Each of the MotB N-terminal helices is followed by a plug helix that lies between two MotA molecules. The two plugs cross over and are thought, based on prior experiments, to block activity of the stator unit. As expected, the channel appears in closed conformation.

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"This puzzling result can be explained if it is the rotation of MotA around MotB that drives the rotation of the motor. We proposed that one of the two MotB aspartates—call it MotB1—is protonated and anchored to MotA. This is a high-energy state for MotB1, which would drive MotA rotation were it not for the aspartate of MotB2. This aspartate is both negatively charged and unprotonated: the neutral surface of MotA cannot rotate across it. But when MotB2 accepts a proton from the periplasm, it is neutralized, and rotation of the hydrophobic MotA surface across the neutralized MotB2 aspartate can now occur. After rotation, MotB2 grabs on to MotA in this new position, and MotB1 releases its proton. MotB1 then waits at the cytoplasmic side to pick up a new proton. After these steps, a 36º rotation of the MotA ring around the MotB dimer has occurred.

***

"How does this miniature MotAB rotary motor power the rotation of a large flagellum? Upon incorporation in the motor, the C-terminal domains of MotB dimerize and bind to the peptidoglycan layer that forms part of the cell envelope. Peptidoglycan binding is accompanied by the unplugging of the MotAB ion channel, which allows ions to flow from the periplasm to the cytoplasm. Upon ion flow, MotA rotates clockwise around MotB. Given normal swimming conditions, the rotor is engaged at the proximal side of the MotA ring, and the clockwise rotation of MotA rotates the rotor counterclockwise. When all flagella spin counterclockwise, they form a bundle and swim in a straight line.

"Upon chemotactic signaling, a whole signaling cascade takes place and results in the phosphorylation of CheY. Phosphorylated CheY binds to the rotor and switches its conformation. The rotor now interacts with the distal side of the MotA ring. The same clockwise rotation of MotA around MotB induces a clockwise rotation in the motor.

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"...bacteria swim using long filaments powered by a bidirectional, rotary proteinaceous motor. They know the molecular makeup of the rotary motor, and that this bidirectional motor is itself driven by unidirectional miniature rotary motors.

Comment: irreducibly complex. Must be designed in one step. Recognize a designer God who works intimately at this biochemical level to produce an automatically operating molecular machine.