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Tricks of the Cell Trade

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Photo: Clifton Suspension Bridge, by Nic Trott, CC BY 2.0 , via Wikimedia Commons.

Both cables on a suspension bridge snap. It’s going to collapse. If repairmen cannot mend the cables extremely rapidly, the bridge is doomed, and all the cars on it will dump into the water. Time is of the essence. The task looks hopeless. What to do?

Homologous Recombination

Cells face that kind of challenge every day, but they are well equipped to handle it. When both DNA strands break (the “double-stranded break” crisis, or DSB), a cell can die. Molecular machines fly into action as the strands flail about, threatening genomic catastrophe. The repair crew has an additional problem: unlike the bridge cable, the DNA strand is made up of a sequence of code that needs to match what was there before the DSB. In a process called homologous recombination, the machinery searches for a template to rebuild the broken sequence. Researchers at Uppsala University know that this process is mostly “well described in the literature.”

However, the description usually disregards the daunting task of finding the matching template among all the other genome sequences. The chromosome is a complex structure with several million base pairs of genetic code and it is quite clear that simple diffusion in 3D would not be sufficiently fast by a long shot. But then, how is it done? This has been the mystery of homologous recombination for 50 years. From previous studies, it is clear that the molecule RecA is involved and important in the search process, but, up until now, this has been the limit of our understanding of this process. [Emphasis added.]

Even a simple bacterium knows a trick to make the search easier. It reduces the search from a 3D problem to a 2D problem. With that shortcut, the cell reduces the time to repair down to 15 minutes on average. The Uppsala group, using CRISPR and fluorescent tags, watched the RecA proteins in real time. They published their findings in Nature.

“We can see the formation of a thin, flexible structure that protrudes from the break site just after the DNA damage. Since the DNA ends are incorporated into this fiber, it is sufficient that any part of the filament findsthe precious template and thus the search is theoretically reduced from three to two dimensions. Our model suggests that this is the key to fast and successful homology repair,” says Arvid Gynnå, who has worked on the project throughout his PhD studies.

Earth’s Electrical Grid

The world beneath our feet is electrically wired. That’s the surprising announcement from Yale University about bacteria that live in soil and under the seafloor. 

A hair-like protein hidden inside bacteria serves as a sort of on-off switch for nature’s “electric grid,” a global web of bacteria-generated nanowires that permeates all oxygen-less soil and deep ocean beds, Yale researchers report in the journal Nature.

“The ground beneath our feet, the entire globe, is electrically wired,” said Nikhil Malvankar, assistant professor of molecular biophysics and biochemistry at the Microbial Science Institute at Yale’s West Campus and senior author of the paper. “These previously hidden bacterial hairs are the molecular switch controlling the release of nanowires that make up nature’s electrical grid.”

The Yale team found more about the “pili” which were thought to be made of a surface proteins by that name. Their findings, also published in Naturewe learn, call into question “thousands of publications about pili.” Pili are not the nanowires; they are machines that pump the nanowires out of the cell. Bacteria use these electrical conduits for respiration. Lacking access to oxygen (the primary electron receptor of oxygen-breathing organisms like humans), the bacteria use nanowires like snorkels to “breathe minerals” below the surface. The nanowires push excess electrons up and out of sediments.

A short animation shows how the pili work. They extend and retract repeatedly, pushing the nanowires out a bit at a time. Engineers might watch this trick to solve the problem of how to push a rope! The nanowires from bacteria link up and can extend a considerable distance on a bacterial scale. Because they conduct electrons, are ubiquitous around the earth, and provide global recycling services (see here), the nanowires justify the description of “nature’s electrical grid” under our feet. For fun, consider a new kind of silicon-impregnated wood flooring that generates electricity. Just walking on the floor, invented in Switzerland, can generate enough electricity to power a light bulb, reports Science Daily.

Tunnel Experts

A robot spacecraft, resembling an old Apollo lunar lander, touches down secretly on an enemy cargo ship. Underneath, a powerful drill breaks through the steel exterior. Material flows into the breach, melting the metal casing and building a tunnel through which the craft sends code to infect the enemy ship’s computers. Moments later, the enemy ship explodes, releasing hundreds of copies of the robot to go fight other enemy ships.

Viruses do things like that. A good one, the T7 bacteriophage, protects us from E. coli infections. Scientists in Spain, publishing in PNAS, learned more about how T7 builds its export tunnel through which it sends DNA into the harmful bacterial cell. 

Bacteriophage T7 infects Escherichia coli bacteria, and its genomic DNA traverses the bacterial cell envelope,but the precise mechanism used by the virus remains unknown. Previous studies suggested that proteins found inside the viral capsid (core proteins) disassemble and reassemble in the bacterial periplasm to form a DNA translocation channel. In this article, we have solved the structure of two different assemblies of the core proteins gp15 and gp16. These findings confirm the ability of core proteins to form tubes compatible with the periplasmic space and show the location of the transglycosylase enzyme involved in peptidoglycan degradation. Our results reveal key structural details of the assembly of the core translocation complex involved in the DNA transport through the bacterial wall.

The paper mentions an interesting fact: “Bacteriophages (phages) are viruses that infect bacteria and are considered to be the most abundant entities on Earth.” 

Windows on the Unseen

In each of these discoveries, cryo-electron microscopy opened windows to unseen realities. This revolutionary tool and other methods of super-resolution microscopy are enabling scientists to see biological wonders that have existed as far back as the first bacterial cells, but have been hidden from our eyes till now. Step by step, molecule by molecule, the evidence for intelligent design at the tiniest levels of life is coming into focus. With more academicians taking leave of Darwin, how can the scientific community deny a seat at the table to design proponents who have the necessary and sufficient causes to explain these things? 

Neil Thomas, calling the materialist paradigm a “flawed hypothesis” that is “squandering public trust,” concludes that it’s time to open the doors to alternatives:

Faced with the sheer unfeasibility of a purely natural explanation, logic leaves us with little other choice. Extending the old adage that nothing comes of nothing, it might be contended that real life, in contradistinction to the magician’s claim of a rabbit magically emerging from the hat, nothing can “magically emerge” or “naturally evolve” without a supporting agency — little though we may know of that originating agency. In default of a better explanation than that offered by the Darwinian paradigm and its various materialistic descendants and kissing cousins, however, this hypothesis surely cannot be discounted out of hand. 

Neil Thomas, Taking Leave of Darwin, p. 143