RuvAB: Another Elegant Molecular Motor Visualized
David Coppedge
Admirers of molecular machines will love RuvAB. This machine looks like something out of a CAD/CAM project, but it’s found in bacteria. And it plays an essential role in maintaining this “primitive” microbe’s genomic integrity.
A picture is worth a thousand words. Before we talk about it, look at the 30-second animation of RuvAB modeled by scientists at Deutsches Elektronen-Synchrotron (DESY), a research center of the Helmholtz Association in Hamburg, Germany.
That’s an eye-popping example of irreducible complexity if there ever was one. Are those gears, rotors, and clutches operating in a detailed sequence of moving parts? The scientists must have thought so; a graphic in the press release portrays the operation as a set of twenty gears operating on DNA strands, with the caption, “Artistic representation of the Holliday junction and the RuvB motors.”
A Minor Correction
One little correction to the animation should be noted. They show it in slow motion. The actual movements are “very fast and highly dynamic,” they say — so much so that they “provided the … motor with a slower burning fuel which allowed us to capture the biochemical reactions as they occur.” They took “over ten million images” of the motor in action.
Using the high-performance computing facility at DESY, the scientists were then able to put all the puzzle pieces together to generate a high-resolution movie detailing how the RuvAB complex functions on the molecular scale.
Is this molecular machine important?
DNA recombination is one of the most fundamental biological processes in living organisms. It is the process by which chromosomes “swap” DNA either to generate genetic diversity, by creating new offspring, or to maintain genetic integrity, by repairing breaks in existing chromosomes. During DNA recombination, four DNA arms separate from their double-helix formations and join together at an intersection known as a Holliday junction. Here the DNA arms exchange strands in a process called active branch migration.
RuvA is the stator and RuvB is the motor. The two form the “RuvAB branch migration complex” that handles DNA recombination and repair.
The essential energy needed for this branch migration to occur comes from a molecular machinery that scientists have tagged as the RuvAB branch migration complex. This complex assembles around the Holliday junction and is made of two motors labelled RuvB AAA+ ATPases, that fuel the reaction, and a RuvA stator. The research team has now provided an intricate blueprint that explains how the RuvB AAA+ motors work under the regulation of the RuvA protein to perform synchronized DNA movement.
The AAA+ family of molecular machines deserves attention from ID researchers, because they move things in elaborate ways and take part in diverse cellular activities (see another example reported here in 2019).
AAA+ motors are often used in other biological systems, such as protein transport, therefore this detailed model of the RuvB AAA+ motor can be used as a blueprint for similar molecular motors. “We understand how the motor works and now we can put this motor into another system with some minor adaptations,” explains Marlovits. “We are essentially presenting core principles for AAA+ motors.”
More detail is given in an open-access paper in Nature by Wald et al. , “Mechanism of AAA+ ATPase-mediated RuvAB–Holliday junction branch migration.”
Coordinated motions in a converter formed by DNA-disengaged RuvB subunits stimulate hydrolysis and nucleotide exchange. Immobilization of the converter enables RuvB to convert the ATP-contained energy into a lever motion, which generates the pulling force driving the branch migration. We show that RuvB motors rotate together with the DNA substrate, which, together with a progressing nucleotide cycle, forms the mechanistic basis for DNA recombination by continuous branch migration.
A Feast for the Eyes
The figures in the paper are worth feasting your eyes on. Hmmm; I wonder why they didn’t say anything about how it evolved? Look for the word “mutation” and you will find that “mutational studies markedly compromised branch migration activity, and mutation of trans-Glu128 resulted in a bacterial growth defect.”
Here is another biological wonder that needs little verbiage to convince readers of intelligent design. It certainly spoke to the researchers:
“We were able to visualize seven distinct states of the motor and demonstrate how the interconnected elements work together in a cyclical manner,” explains Wald. “We also demonstrated that the RuvB motor converts energy into a lever motion which generates the force that drives branch migration. We were amazed by the discovery that the motors use a basic lever mechanism to move the DNA substrate. Overall, the sequential mechanism, coordination and force generation manner of the RuvAB motor share conceptual similarities with combustion engines.”
I would love to see this motor star in an expanded animation documentary with dramatic music.
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