Tag: biology

Essential gene evolution

Essential genes are often thought to be frozen in evolutionary time — evolving only very slowly if at all, because changing or dying would lead to the death of the organism. 100s of millions of years of evolution separate insects and mammals, but experiments show that the Hox genes guiding the development of the body plans in Drosophila fruit flies and mice can be swapped without a hitch because they are so similar. This remarkable evolutionary conservation is a foundational concept in genome research.

But a new study turns this rationale for genetic conservation on its head. Researchers at the Fred Hutchinson Cancer Research Center in Seattle reported last week in eLife that a large class of genes in fruit flies are both essential for survival and evolving extremely rapidly. In fact, the scientists’ analysis suggests that the genes’ ability to keep changing is the key to their essential nature. “Not only is this questioning the dogma, it is blowing the dogma out of the water

RNA Memory

Eventually, the worms recoiled to the light alone. Then something interesting happened when he cut the worms in half. The head of one half of the worm grew a tail and, understandably, retained the memory of its training. Surprisingly, however, the tail, which grew a head and a brain, also retained the memory of its training. If a headless worm can regrow a memory, then where is the memory stored, McConnell wondered. And, if a memory can regenerate, could he transfer it? They had transferred a memory, vaguely but surely, from one animal to another, and they had strong evidence that RNA was the memory-transferring agent. Glanzman now believes that synapses are necessary for the activation of a memory, but that the memory is encoded in the nucleus of the neuron through epigenetic changes.

Earlier research had shown that these epigenetic changes can be inherited. Perhaps phobias are epigenetic?

Memories can be passed down to later generations through genetic switches that allow offspring to inherit the experience of their ancestors.

TCA cycle origins

Instead of trying to find the precursor to the TCA cycle by swapping in simpler versions of its components, they started by asking what versatile reactants might have been present in the prebiotic world and then looked at how much they could do under various circumstances. Astonishingly, they found that the glyoxylate and pyruvate reacted to make a range of compounds that included chemical analogues to all the intermediary products in the TCA cycle except for citric acid. Comparatively, the chemistry we discovered here was a dream to run: All you really needed to do to get the pathway started was to drop 2 stable reactants into buffered water and stick it on a warm hotplate. The chemistry was extremely robust.

Multi-species community assembly

Early on, Mehta thought Gore was ignoring important details about microbial environments, but Mehta concedes that these details have proved less important than he believed. “What’s interesting and impressive about the work is that they show that many, many different phenomena — pH changes, competition for nutrients — can all be captured using these simple phenomenological models, at least in systems where you have a few species. This is a true and tried reductionism of the sort that’s served well in physics.”

Unintuitive RNA

RNA are much larger than Proteins

But we don’t have to get into such details in order to see how “off” our perceptions are. I, and probably many others, have a mental picture of an mRNA sequence being read out and transcribed into a larger protein, but that can’t be right. And it isn’t! In reality, the mRNAs are ~10x the size of proteins themselves. This feels wrong to us, because we’re used to our own preferences for algorithmic compression: blueprints are smaller than houses, but not inside the cell.

Life’s Energy Limits

For individual cells, this power minimum hovers around a zeptowatt, or 10−21 watts. That is the power required to lift 0.001% of a grain of salt 1 nanometer once a day. (For reference, a human body uses ~100 watts, the power of a reading light.) The new model suggests that cells living in sub-seafloor sediments are drawing only slightly more power than that.

2022-11-02: Inert spores may be close to that energy limit, and use a passive sensing technique.

The spores might be able to sense small cumulative changes in their environment, until enough signals build up to trigger a sort of wake-up alarm. The mechanism that would induce these changes would be the movement of ions out of the cell—specifically, potassium ions.

These movements can be triggered by positive environmental signals, like the presence of nutrients. When the ions travel out of the cell thanks to passive transport, they generate a difference in potassium concentration inside versus outside the cell. This concentration difference allows the spore to store potential energy. Over time, as the spore continues to sense more positive signals, more ions would move out of the cell. This would also create a corresponding drop in potassium levels, as the ions exit. Eventually, the potassium content in the spore would lower to a certain threshold, signaling that it is safe for the cell to wake up. That would trigger reanimation and germination.

2024-07-23: Most life is dormant

60% of all microbial cells are hibernating at any given time. Even in organisms whose entire bodies do not go dormant, like most mammals, some cellular populations within them rest and wait for the best time to activate. esearchers reported the discovery of a new hibernation factor, which they have named Balon. The protein is shockingly common: A search for its gene sequence uncovered its presence in 20% of all cataloged bacterial genomes. And it works in a way that molecular biologists had never seen before.

Previously, all known ribosome-disrupting hibernation factors worked passively: They waited for a ribosome to finish building a protein and then prevented it from starting a new one. Balon, however, pulls the emergency brake. It stuffs itself into every ribosome in the cell, even interrupting active ribosomes in the middle of their work. Before Balon, hibernation factors had only been seen in empty ribosomes.