Horizontal gene transfer unexplained (Introduction)

by David Turell , Thursday, October 27, 2022, 16:47 (548 days ago) @ David Turell

A new review:

https://www.quantamagazine.org/how-genes-can-leap-from-snakes-to-frogs-20221027/

"Perched on a leaf in the rainforest, the tiny golden mantella frog harbors a secret. It shares that secret with the fork-tongued frog, the reed frog and myriad other frogs in the hills and forests of the island nation of Madagascar, as well as with the boas and other snakes that prey on them. On this island, many of whose animal species occur nowhere else, geneticists recently made a surprising discovery: Sprinkled through the genomes of the frogs is a gene, BovB, that seemingly came from snakes.

"After poring over genomes from frog and snake species around the world, the scientists reported in April in a paper in Molecular Biology and Evolution that this gene has somehow traveled from snakes to frogs at least 50 times all over the planet. But in Madagascar it has inserted itself into frogs with startling promiscuity: 91% of the frog species sampled there have it. Something seems to make Madagascar an exceptionally conducive place for the gene to get mobile.

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"...this new paper, which shows that the horizontal transfer of genes may be more likely in some places than others, complicates the story even more. It suggests that when seeking explanations for horizontal transfers, researchers may need to look beyond simple genetic mechanisms to the ecological contexts in which species live. Genomicists are still struggling to understand how common or rare horizontal transfers are in complex organisms, but some places, like Madagascar, may be hot spots for them.

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"The cells of eukaryotic organisms like humans, frogs and snakes, however, are different [than bacteria] Their cell nucleus usually seems like a fortress for protecting the genome. The DNA is carefully coiled up and stored in that citadel’s library, with enzymes calling forth only the genes they need to examine at any given time. The cell is loaded with fail-safes to prevent damage to its DNA and to repair wear and tear. If the genome is like a priceless illuminated manuscript, its librarians carry swords.

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"As strange as it might seem for eukaryotes to pick up genes from bacteria, stranger still is the fact that examples of horizontal gene transfer in the other direction are vastly rarer. For some reason, bacteria don’t want our genes. Eukaryotic genes have structural features that make them less than perfect material for bacteria, but there may be other contributing factors as well.

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"Findings like these have persuaded some biologists that at least some horizontal gene transfers may be facilitated by viruses. If viruses can pick up genes from their hosts, and if they can leave behind pieces of their genomes, it seems possible that they could also sometimes ferry over genes from the last host they infected, or even one from generations ago, and give them to a new host.

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"The involvement of viruses could also help to solve another puzzle about horizontal transfers in eukaryotes. For the transfers to occur, the traveling genes need to clear an entire series of hurdles. First they must get from the donor species to the new host species. Then they must get into the nucleus and ensconce themselves in the host genome. But getting into the genome of just any cell won’t do: In multicellular creatures like frogs and herrings, a gene won’t be passed down to the animal’s offspring unless it can sneak into a germline cell — a sperm or an egg.

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"Is there something about the environment of Madagascar that makes it a hot spot for gene transfers?

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"But the abundance of parasites on the island might also be a contributing factor. For example, “in Madagascar, there are lots of leeches,”

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"Unfortunately, it isn’t easy to prove or disprove scenarios describing how such horizontal transfers might have occurred. Without selection to preserve DNA sequences, they tend to mutate and get scrambled over long stretches of time, erasing the molecular evidence of a transfer. And if a virus is involved in the transfer, it may leave very little evidence in the first place, Graham said. Researchers might therefore almost need to catch a genetic jump in the act to know how it is happening."

Comment: lots of evidence but still no answers as to how horizontal transfer occurs in eukaryotes.