Cellular Trade Stuff

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

The two cables on a suspension bridge snap into place. He’s going to collapse. If the repairmen can’t fix the cables extremely quickly, the bridge is doomed and all the cars on it will go down the drain. Hurry up. The task seems hopeless. What to do?

Homologous recombination

Cells face this kind of challenge every day, but they are well equipped to meet it. When both strands of DNA break apart (“double-strand break” crisis, or DSB), a cell can die. Molecular machines kick in as the strands twitch, threatening a genomic catastrophe. The repair team has an additional problem: unlike the bridge cable, the DNA strand consists of a code sequence that must match what existed before the DSB. In a process called homologous recombination, the machine searches for a pattern to reconstruct the broken sequence. Researchers from Uppsala University note that this process is for the most part “well described in the literature”.

However, the description generally does not take into account the arduous task of finding the corresponding model among all the other sequences of the genome. The chromosome is a complex structure with several million base pairs of genetic code and it is quite clear that a simple 3D broadcast would not be fast enough from afar. But then, how does it go? It was the mystery of homologous recombination for 50 years. From previous studies it is clear that the RecA molecule is involved and important in the research process, but so far this has been the limit of our understanding of this process. [Emphasis added.]

Even a simple bacteria knows a trick to make it easier to find. It reduces the search for a 3D problem to a 2D problem. With this shortcut, the cell reduces the repair time to 15 minutes on average. The Uppsala group, using CRISPR and fluorescent markers, observed 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 rupture site right after DNA damage. Since the ends of the DNA are incorporated into this fiber, it suffices that any part of the filament finds the precious template and thus the research is theoretically reduced from three to two dimensions. Our model suggests that it is the key to fast and successful homology repairExplains Arvid Gynnå, who worked on the project throughout his doctoral studies.

Earth’s power grid

The world under our feet is electrically wired. This is the surprising announcement of Yale University on bacteria that live in the soil and under the seabed.

A hair-like protein hidden inside bacteria serves as a sort of on-off switch for nature’s ‘power grid’, a global network of nanowires generated by bacteria that permeates all oxygen-free soils and deep seabeds, Yale researchers report in the journal Nature.

“The ground under our feet, the entire globe, is electrically wired”, said Nikhil Malvankar, assistant professor of molecular biophysics and biochemistry at the Institute for Microbial Sciences at Yale West Campus and lead author of the article. “Those previously hidden bacterial hairs are the molecular switch controlling the release of nanowires that make up nature’s electrical network.

The Yale team found more about the “pili” which were believed to be made from a surface protein of that name. Their discoveries, also published in Nature, we are learning, question “thousands of publications on the pili”. The Pili are not the nanowires; they are machines that pump nanowires out of the cell. Bacteria use these electrical conduits for respiration. Without access to oxygen (the main electron receptor in organisms that breathe oxygen like humans), bacteria use nanowires like snorkels to “breathe minerals” below the surface. Nanowires push excess electrons up and out of the sediment.

A short animation shows how the pili work.. They extend and retract repeatedly, pushing the nanowires a little at a time. Engineers might look at this trick to solve the rope pushing problem! The nanowires produced by bacteria are linked together and can extend over a considerable distance at the bacterial scale. Because they conduct electrons, are ubiquitous around the earth, and provide global recycling services (see here), nanowires justify the description of “nature’s power grid” beneath our feet. For fun, consider a new type of silicone-impregnated wood flooring that generates electricity. The simple act of walking on the ground, invented in Switzerland, can generate enough electricity to power a light bulb, reports Daily science.

Tunnel experts

A robotic spaceship, resembling an old Apollo lunar lander, secretly lands on an enemy freighter. Below, a powerful drill pierces the steel exterior. The 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 and fight other enemy ships.

Viruses do things like that. A good one, the bacteriophage T7, protects us from E. coli infections. Scientists in Spain, publish 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 crosses the bacterial cell envelope,but the precise mechanism used by the virus remains unknown. Previous studies have 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 solved the structure of two different assemblies of core proteins gp15 and gp16. These discoveries confirm the ability of heart proteins to form tubes compatible with the periplasmic space and show the location of the transglycosylase enzyme involved in the degradation of peptidoglycan. Our results reveal key structural details of the assembly of the central translocation complex involved in DNA transport across the bacterial wall.

The article 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 invisible

In each of these discoveries, electron cryomicroscopy has opened windows to invisible realities. This revolutionary tool and other super-resolution microscopy methods allow scientists to see biological wonders that have existed since the earliest bacterial cells, but have been hidden from our eyes until now. Step by step, molecule by molecule, the evidence for intelligent design at the tiniest levels of life is emerging. With more academics take leave of Darwin, how can the scientific community refuse a seat at the table to design promoters who have the necessary and sufficient causes to explain these things?

Neil Thomas, calling the materialist paradigm a “flawed assumption” that “wastes public trust”, concludes that it is time to open the doors to alternatives:

Faced with the sheer infeasibility of a purely natural explanation, logic leaves us little other choice. Extending the old adage that nothing comes from nothing, one could argue that real life, contrary to the magician’s claim of a rabbit magically emerging from the hat, nothing can “magically arise” or “evolve naturally” without a supporting agency – little although we can know this original agency. For want of a better explanation than that offered by the Darwinian paradigm and its various materialistic descendants and embracing cousins, however, this hypothesis certainly cannot be dismissed out of hand.

Neil Thomas, Take leave of Darwin, p. 143


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