Genome complexity: cephalopods edit RNAs (Introduction)

by David Turell , Friday, May 19, 2023, 19:52 (553 days ago) @ David Turell

Like bacteria edit DNA:

https://www.sciencenews.org/article/octopus-squid-rna-editing-dna-cephalopods

"Octopuses are like aliens living among us — they do a lot of things differently from land animals, or even other sea creatures...Andd to a greater extent than most creatures, octopuses squirt the molecular equivalent of red ink over their genetic instructions with astounding abandon, like a copy editor run amok.

"These edits modify RNA, the molecule used to translate information from the genetic blueprint stored in DNA, while leaving the DNA unaltered.

"Scientists don’t yet know for sure why octopuses, and other shell-less cephalopods including squid and cuttlefish, are such prolific editors. Researchers are debating whether this form of genetic editing gave cephalopods an evolutionary leg (or tentacle) up or whether the editing is just a sometimes useful accident.

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"RNA editing can cause divergences from the DNA instructions, creating some proteins that have different amino acids than specified by the DNA.

"Editing chemically modifies one of RNA’s four building blocks, or bases. Those bases are often referred to by the first letters of their names: A, C, G and U, for adenine, cytosine, guanine and uracil (RNA’s version of the DNA base thymine). In an RNA molecule, the bases are linked to sugars; the adenine-sugar unit, for instance, is referred to as adenosine.

"There are many ways to edit RNA letters. Cephalopods excel at a type of editing known as adenosine to inosine, or A-to-I, editing. This happens when an enzyme called ADAR2 strips a nitrogen and two hydrogen atoms off adenosine (the A). That chemical peel turns adenosine into inosine (I).

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"Cephalopods take RNA recoding to a whole new level, Albertin says. Longfin squid (Doryteuthis pealeii) have 57,108 recoding sites, Rosenthal, Eisenberg and colleagues reported in 2015 in eLife. Since then, the researchers have examined multiple species of octopus, squid and cuttlefish, each time finding tens of thousands of recoding sites.

"Soft-bodied, or coleoid, cephalopods may have more opportunities for editing than other animals because of where at least one of the ADAR enzymes, ADAR2, is located in the cell. Most animals edit RNAs in the nucleus — the compartment where DNA is stored and copied into RNA — before sending the messages out to meet up with ribosomes. But cephalopods also have the enzymes in the cytoplasm, the cells’ jellylike guts, Rosenthal and colleagues discovered.

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"In most of a cephalopod’s body, RNA editing doesn’t often affect the makeup of proteins. But in the nervous system, it’s a different story. In longfin squids’ nervous systems, 70 percent of edits in protein-producing RNAs recode proteins. And RNAs in the nervous system of the California two-spot octopus (Octopus bimaculoides) are recoded three to six times as often as in other organs or tissues.

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"Evidence for and against RNA recoding’s evolutionary value has come mainly from examining the total genetic makeup, or genomes, of various cephalopod species. But scientists would like to directly test whether recoded RNAs have an effect on cephalopod biology. Doing that will require some new tools and creative thinking.

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"Albertin, Rosenthal and colleagues have developed ways to change the genes of squid with the gene editor CRISPR/Cas9. The team created an albino squid by using CRISPR/Cas9 to knock out, or disable, a gene that produces pigment. The researchers may be able to change editing sites in DNA or in RNA and test their function, Albertin says.

"This science is still in its early stages, and the story may lead somewhere unexpected. Still, with cephalopods’ skillful editing, it’s bound to be a good read."

Comment: enormous article I chopped short. Basically, they know what is happening, but as yet do not understand why. If evolution produced it there must be a reason. We'll have to wait for results. As with bacteria who edit DNA these are free-living organisms who must have survival protection. Perhaps this is it.