RNA editing in cephalopods

From Wired:

But when Stanford University geneticist Jin Billy Li heard about Joshua Rosenthal’s work on RNA editing in squid, his jaw dropped. That’s because the work, published today in the journal Cell, revealed that many cephalopods present a monumental exception to how living things use the information in DNA to make proteins. In nearly every other animal, RNA—the middleman in that process—faithfully transmits the message in the genes. But octopuses, squid, and cuttlefish (but not their dumber relatives, the nautiluses) edit their RNA, changing the message that gets read out to make proteins.

In exchange for this remarkable adaptation, it appears these squishy, mysterious, and possibly conscious creatures might have given up the ability to evolve relatively quickly. Or, as the researchers put it, “positive selection of editing events slows down genome evolution.” More simply, these cephalopods don’t evolve quite like other animals. And that could one day lead to useful tools for humans.

From the paper itself:

SUMMARY

RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function.

23 thoughts on “RNA editing in cephalopods”

  1. Allan Miller

    The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage.

    Or that not having a reliable site-identifying motif is a bit of a bummer.

  2. keithskeiths Post author

    Glen:

    But they still don’t know how to make myelin sheaths.

    Then again, apparently neither did the cephalopods’ designer.

    One designer didn’t tell the other. Don’t listen to the monodesignist heretics.

  3. Alan FoxAlan Fox

    Joe Felsenstein:
    I wonder how a cephalopod changes its pattern of RNA editing without making any change in its DNA. Leprechauns?

    I wondered that, too. But I think this is the fault of the press release perhaps. I emailed Dr Rosenthal asking whether he was suggesting a violation of the central dogma but he replied:

    At first glance, RNA editing might seem a violation of the central dogma. But the enzymes that are doing it are themselves encoded in DNA.
    ADARs are the enzymes that edit RNA. They edit specific adenosine residues. In order to do so, they require complex surrounding structures in the RNA. The enzymes recognize and bind to these structures before they can edit—and the structures are often 100’s of nucleotides long. If an ocotpus and a squid want to edit the same adenosine, then the underlying structure had to be preserved during evolution. This means that I can’t have accumulated mutations. We show that RNA editing sites are conserved across large evolutionary distances and the mutation rates around the RNA editing sites are depressed. In cephalopods, there are lots of conserved RNA editing sites so there is a lot of the coding sequence with depressed mutations rates.

  4. petrushka

    Looks like trap door evolution.

    How about this analogy: If I misspell a few words in a paragraph, most people can still read it. But if I misspell a decryption key, I can lose everything.

    So the sequences that code for the editor are highly conserved.

  5. MungMung

    If an ocotpus and a squid want to edit the same adenosine, then the underlying structure had to be preserved during evolution.
    And if the ocotpus and the squid don’t want to edit the same adenosine?

  6. keithskeiths Post author

    Mung,

    Evolutionarily conserved is an oxymoron.

    If you truly believe that, then you might benefit from some RNA editing in your own brain tissues.

  7. RumraketRumraket

    None of this RNA editing stuff seems to square well with PZ Myers

    http://freethoughtblogs.com/pharyngula/2017/04/07/cephalopods-are-natural-born-editors/

    Cephalopods are natural-born editors

    Did you know cephalopods may have traded evolution gains for extra smarts? I didn’t either. I don’t believe it, anyway. The paper is fine, though, it’s just the weird spin the media has been putting on it.

    The actual title of the paper is Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods, which is a lot more accurate. The authors discovered that there’s a lot of RNA editing going on in coleoids. The process is not a surprise, we’ve known about RNA editing for a long time, but the extent in squid is unusual.

    http://freethoughtblogs.com/pharyngula/2017/04/07/the-worst-take-on-that-cephalopod-rna-editing-story-yet/

    The worst take on that cephalopod RNA editing story yet

    That article I wrote up today? Take a look at the colossal botch phys.org made of it.

    How octopuses, squid, and cuttlefish defy genetics’ ‘central dogma’
    Jesus fuck, how can you write for a science news site and get everything that wrong? The central dogma of molecular biology (not genetics, dinglepoofs) says that the information in proteins can’t be written back into DNA. This study doesn’t even try to address the central dogma, much less “defy” it.

    http://freethoughtblogs.com/pharyngula/2017/04/09/aaargh-its-like-watching-the-spread-of-a-plague/

    Aaargh. It’s like watching the spread of a plague.

    More noise from that perfectly respectable cephalopod RNA editing paper with the bad press release. This time it comes from Quartz.

    “It turns out these impressive abilities may originate at the molecular level. Researchers from Tel Aviv University in Israel and the Marine Biological Laboratory at Woods Hole, Massachusetts, published a paper on April 6 illustrating that octopuses and their relatives, squid and cuttlefish, can readily change the way they use their DNA. Rather than using their genetic code as a blueprint to build the proteins they need to survive, cephalopods use it more like guidelines.

    “This may explain why they’re such good problem solvers,” Clifton Ragsdale, a neurobiologist at the University of Chicago unaffiliated with the paper, told Scientific American.”

    NO IT DOESN’T! If a paper came out that announced that neurons get more of their ATP from glycolysis (which is actually often the case), would you then declare that you’ve figured out how humans got to be so smart? No, you wouldn’t, because the mechanism is so far from the outcome. LeBron James likes Fruity Pebbles, that must be the secret of his basketball skills!

  8. John HarshmanJohn Harshman

    Alan Fox: In cephalopods, there are lots of conserved RNA editing sites so there is a lot of the coding sequence with depressed mutations rates.

    Pet peeve of mine: confusing mutation rates with fixation rates. He really means the latter.

  9. keithskeiths Post author

    Rumraket,

    None of this RNA editing stuff seems to square well with PZ Myers

    It’s the press coverage he has a problem with, not the RNA editing.

  10. RumraketRumraket

    keiths:
    Rumraket,

    It’s the press coverage he has a problem with, not the RNA editing.

    Yeah that’s what I meant, thanks for the correction. An important distinction.

  11. GlenDavidson

    Check out this talking point: “Cephalopods probably chose to take this RNA bargain over genome evolution, and maybe vertebrates made the other choice — they preferred genome evolution over editing.” They chose? That sounds like intelligent design by the spirits of cephalopods, playing their own evolutionary strategy against the rules of the game established by Darwin. A better model would be pre-programmed software for stability in a dynamic environment.

    And some idiot at the DI chose to take metaphor literally in order to score cheap points.

    Sorry, Evolution New and Views, that’s hardly news.

    Glen Davidson

  12. keithskeiths Post author

    John,

    It’s uncredited. Who writes this stuff?

    Apparently some things are too stupid even for a DI flack to take “credit” for.

Leave a Reply