Genome complexity: hibernation and dormancy (Introduction)

by David Turell , Sunday, June 09, 2024, 17:38 (168 days ago) @ David Turell
edited by David Turell, Sunday, June 09, 2024, 18:08

Protein controls found:

https://www.quantamagazine.org/most-life-on-earth-is-dormant-after-pulling-an-emergency...

"Researchers recently reported the discovery of a natural protein, named Balon, that can bring a cell’s production of new proteins to a screeching halt. Balon was found in bacteria that hibernate in Arctic permafrost, but it also seems to be made by many other organisms and may be an overlooked mechanism for dormancy throughout the tree of life.

"For most life forms, the ability to shut oneself off is a vital part of staying alive. Harsh conditions like lack of food or cold weather can appear out of nowhere. In these dire straits, rather than keel over and die, many organisms have mastered the art of dormancy. They slow down their activity and metabolism. Then, when better times roll back around, they reanimate.

"Sitting around in a dormant state is actually the norm for the majority of life on Earth: By some estimates, 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.

“'We live on a dormant planet,” said Sergey Melnikov, an evolutionary molecular biologist at Newcastle University. “Life is mainly about being asleep.”

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"Some hibernation factors dismantle cellular machinery; others prevent genes from being expressed. The most important ones, however, shut down the ribosome — the cell’s machine for building new proteins. Making proteins accounts for more than 50% of energy use in a growing bacterial cell. These hibernation factors throw sand in the gears of the ribosome, preventing it from synthesizing new proteins and thereby saving energy for the needs of basic survival.

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"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.

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"Balon’s ability to halt the ribosome’s activity in its tracks is a critical adaptation for a microbe under stress, said Mee-Ngan Frances Yap, a microbiologist at Northwestern University who wasn’t involved in the work. “When bacteria are actively growing, they produce lots of ribosomes and RNA,” she said. “When they encounter stress, a species might need to shut down translation” of RNA into new proteins to begin conserving energy for a potentially long hibernation period.

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"Balon can do this because it latches on to ribosomes in a unique way. Every ribosomal hibernation factor previously discovered physically blocks the ribosome’s A site, so any protein-making process that’s in progress must be completed before the factor can attach to turn off the ribosome. Balon, on the other hand, binds near but not across the channel, which allows it to come and go regardless of what the ribosome is doing.

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"Despite Balon’s mechanistic novelty, it’s an exceedingly common protein. Once it was identified, Helena-Bueno and Melnikov found genetic relatives of Balon in upward of 20% of all the bacterial genomes cataloged in public databases. With help from Mariia Rybak, a molecular biologist at the University of Texas Medical Branch, they characterized two of these alternate bacterial proteins: one from the human pathogen Mycobacterium tuberculosis, which causes tuberculosis, and another in Thermus thermophilus, which lives in the last place you’d catch P. urativorans — in ultra-hot underwater thermal vents. Both proteins also bind to the ribosome’s A site, suggesting that at least some of these genetic relatives act similarly to Balon in other bacterial species.

"Balon is notably absent from Escherichia coli and Staphylococcus aureus, the two most commonly studied bacteria and the most widely used models for cellular dormancy. By focusing on just a few lab organisms, scientists had missed a widespread hibernation tactic, Helena-Bueno said. “I tried to look into an under-studied corner of nature and happened to find something.'”

Comment: we sleep one-third of our lives, so this approach is not an unusual view. The use of one protein over and over points to design.