Masters of Acclimation: Octopuses Adjust to Cold by Editing their RNA

[This is really interesting and the full paper is open access –cr]

Octopuses use RNA editing to rapidly respond to environmental temperature changes by altering protein function

Peer-Reviewed Publication



WOODS HOLE, Mass. — Each cell comes with a finite set of instructions encoded in its DNA. Life, however, is unpredictable, and when circumstances change, animals need flexibility to acclimate. New research led by Joshua Rosenthal of the Marine Biological Laboratory (MBL) and Eli Eisenberg at Tel Aviv University indicates that octopuses and their close relatives elegantly adjust to environmental challenges by tinkering with their RNA — an intermediary molecule that conveys DNA’s directions.
In a new study appearing in Cell on June 8, Rosenthal and colleagues document an enormous uptick in RNA editing when octopus, squid and cuttlefish, known as coleoid cephalopods, acclimate to cold water. After cooling the octopuses’ tanks, the team saw increases in protein-altering activity at more than 13,000 RNA sites in the animals’ nervous systems. In two of these cases, they investigated how swapping out a single letter of the RNA molecule’s code alters the function of proteins the neurons produce. 
Through RNA editing, the cephalopods appear to have found a unique way of tweaking their own physiology, according to Rosenthal, a senior scientist at MBL. 
“We’re used to thinking all living things are preprogrammed from birth with a certain set of instructions,” he says. “The idea the environment can influence that genetic information, as we’ve shown in cephalopods, is a new concept.” 

The mystery of massive RNA editing in cephalopods
A cell’s molecular machinery transcribes the instructions encoded in DNA into RNA, some of which goes on to make protein. Researchers have learned that cells have the capacity to swap one member of the four-letter genetic code, Adenosine, for a substitute molecule, Inosine, which behaves like Guanosine, one of the original four. While the same process occurs in humans and most other animals, it only rarely affects RNA that’s bound to produce protein.
In 2015, Rosenthal and his colleagues showed that squid employ this kind of protein-altering RNA editing (called A-to-I)  on a massive scale, and later showed the same in octopus. 
“A big question for us was, ‘What are they using it for?’” Rosenthal says. 
Because editing changes RNA only temporarily, the researchers suspected these animals use it to acclimate to their environment. For the current study, they focused on the effects of one such factor, temperature, within the nervous system. Temperature matters because it governs the activity of enzymes, which in turn drive chemical reactions crucial to all physiological processes.
Like other cephalopods, the California two-spot octopus (Octopus bimaculoides) they studied cannot generate its own body heat to counteract the temperature drops that accompany tides, changes in water depth, and seasons. 
After acclimating octopuses to temperatures at the warm end of their natural range (22 degrees C/ 72 degrees F) and the cool end (about 13 degrees C / 55 degrees F), the researchers examined their RNA. Within its molecular code, they tracked activity at locations where they already knew editing occurs. In the octopuses in the cold tanks, they found significant increases at 13,285 sites where the one-letter change alters protein. For those in the warm tanks, they found upticks at 550 such places.
Follow-up experiments suggested RNA editing may help the animals adapt to gradual changes, but not to rapid ones associated with, for example, traveling from warmer surface water down to cooler depths. 
To corroborate the lab work, Matthew Birk, now an assistant professor at Saint Francis University in Pennsylvania, recorded temperature near octopus dens in winter and late summer, then collected the animals. 
With help from collaborators at the University of Michigan and Texas Tech University, the team investigated how RNA editing tweaked the function of two proteins that are vital for neural function in the octopuses. The first protein, kinesin-1, ferries cargo along the long branches of neurons. RNA editing, they found, changes the rate at which this molecule travels. Likewise, it alters the responsiveness of a protein called synaptotagmin that enables communication between neurons. 
One secret to cephalopods’ sophistication?
Cephalopods likely use this form of genetic tinkering to adjust to change in many ways, well beyond acclimating to cold water, Rosenthal suspects. “I think it’s the tip of the iceberg,” he says of this study’s findings.
It may explain, in part, how these organisms have achieved sophisticated behavior. Octopuses, for example, can solve mechanical puzzles, and mimic colors and textures to camouflage themselves. Capabilities like these require nervous systems composed of a complex set of proteins.  
“What mechanisms do they use to create this complexity? I believe that RNA editing is one of them,” Rosenthal says. 

Written by Wynne Parry


The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.






Experimental study




Temperature-dependent RNA editing in octopus extensively recodes the neural proteome



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Rud Istvan
June 11, 2023 2:28 pm

This is really interesting. Like coral blanching to then adopt new zooxanthellae symbiotic photosynthetic algae better adapted to different sea conditions.
to quote Jurassic World, ‘Life finds a way’.

A more off topic but related note. Functioning eyes evolved three different ways during/after the Cambrian explosion. All three disproving the ‘intelligent design’ God argument used by creationists.

  1. Multi compartmented, aka ‘segmented’, all insects and most crustaceans.
  2. Monocompartmented, but with blood vessels in front of rather than behind the retina. All vertebrates. Results in some light insensitivity and human macular degeneration disease.
  3. Monocompartmented, but with blood vessels behind the retina. All cephalopods. Octopus and squid have ‘perfect’ eyes with optimal light sensativity.
Reply to  Charles Rotter
June 11, 2023 3:21 pm

They’re already scarily smart, but only live three years. If they decide to live longer, then we’re in trouble.

I for one would not welcome our new cephalopod masters.

Reply to  Milo
June 11, 2023 8:26 pm

Cephalopod masters are not likely to consider people anything less or more than food.

Reply to  Charles Rotter
June 11, 2023 3:26 pm

Edit the genes and then pass them on?
Maybe Fauci knows something about this?

Reply to  Charles Rotter
June 12, 2023 8:19 pm

Octopuses are quick learners but have very poor memory. Tricks taught to them have to be retaught from scratch the next day and every day after that.

Reply to  Rud Istvan
June 11, 2023 3:32 pm

There are more than three kinds of eyes. Even among arthropods, compound and simple eyes evolved more than once, but annelids and bivalves also have eyes.

Excluding simple eye spots, capable of distinguishing only light and dark, more complex eyes have evolved around 1500 times.

Reply to  Milo
June 11, 2023 9:01 pm

“Monocompartmented, but with blood vessels behind the retina. All cephalopods. Octopus and squid have ‘perfect’ eyes with optimal light sensativity {sic}.”

a) One of the very rare errors I’ve seen in any of Rud’s work.

b) All cephalopods have very short lifecycles allowing for a much more rapid evolution of their needs.
1) color is very important to cephalopods, so reflecting eyes to maximize light is not to their benefit.
2) Cephalopods hunt down deep during the day and shallower at night. They must be accurate when gauging distance and depth perception for their hunting. Improved vision provides huge benefits during their short life cycles.

Just a little further south and the above researchers could have investigated Humboldt squid.
Maybe they should have?

Rud Istvan
June 11, 2023 3:33 pm

Thought I would lob in a definitely OT but still related interesting topic.
I oversaw the MOT gene chip effort in the 1990’s. Close association with Mayo on ‘individualized’ medicine. Had no idea then how much we still do NOT know about the evolutionary DNA/mRNA/protein life complex.

Turns out that all the pulse dry bean landraces—black, white, navy. red, pinto, kidney…are all the same plant DNA, P. Vulgaris. 25 years ago, we did NOT know that this evidence for epigenetics even existed. It does, in any grocery store.

Reply to  Rud Istvan
June 11, 2023 9:30 pm

Biology still has ‘splitters’ in key decision positions. As long as they have influence, they’ll obstruct any definitive DNA results that might affect any species name with which they have been involved.

Mankind is another example of same genetics different appearances and response to where they originated and physically grew up.

Brassica oleracea is another well known same genetics, different appearances and structures.  Broccoli and cauliflower are sort of similar, but kalecollard greens, even Brussels sprouts, cabbage, collard greens and a great many other varieties are all the same DNA.

Reply to  Rud Istvan
June 11, 2023 11:01 pm

Corn is genetically identical to its wild ancestor teosinte in terms of protein-coding genes. All its great differences with teosinte are epigenetic, ie from control sequences.

Reply to  Rud Istvan
June 12, 2023 2:29 am

Hang on, isn’t this all “settled science”. I thought there was an incontrovertible “consensus”.

Smart Rock
June 11, 2023 5:45 pm

Isn’t this the same as (or perhaps a new branch of) epigenetics, where environmental changes cause parts of the DNA to be turned on or off, but the DNA itself is unchanged. As I understand it, epigenetic changes can be inherited.

Studies like this show that the more we know, the more we discover how much we don’t know.

I think I can hear Lysenko’s ghost saying “I told you so”

Reply to  Smart Rock
June 11, 2023 11:04 pm

Lysenko was wrong as wrong can be. Maybe you mean Lamarck. Still wrong, but less so.

Plus, in this case, it’s RNA, not DNA.

June 11, 2023 8:20 pm

Fortunately we are better off than octopi, we can build new fossil fuel and nuclear power plants and use air conditioning to cool us down or just jump in a pool, lake or stream.

June 11, 2023 8:23 pm

Once again, we read about stupendous changes in salt water fish kept in temperature aquariums. Maintaining salt water aquariums, especially for open water species is notoriously difficult. Even tanks that have fresh seawater pumped through are difficult to set up properly.

From the linked paper:

In most animals, recoding through RNA editing is relatively rare; for example, recoding constitutes less than 1% of all reported editing sites in humans. In contrast, RNA recoding occurs extensively in soft-bodied cephalopods: ∼60% of all mRNAs are recoded in squid, octopus, and cuttlefish.”

A) They already knew cephalopods and relatives recoded their RNA.

“We examined the effects of ocean temperature on recoding of the kinesin motor domain of the opalescent inshore squid Doryteuthis opalescens. These animals make seasonal spawning migrations along the coast of San Diego, providing us local access to a squid population.”

B) Access to squids, accompanied by Confirmation Bias.

D. opalescens egg casings were collected from the ocean, and hatchlings (Figure 3A ) were transferred to temperature-controlled seawater tanks for 24 h before extracting RNA from individual whole animals (Figure 3B). We exposed animals to water temperatures ranging from 6°C to 20°C, which encompasses the extreme range of temperatures these animals experience in the wild.”

C) One wonders if the researchers cooled the seawater before pumping it into the tanks or they just cooled the tank? A concern that leaves me suspecting they changed the flow of fresh seawater to aid their maintaining temperature, bringing us back to properly managing a salt water aquarium.

D) One wonders what the preferred birthing water temperatures are?

There are many creatures that not only survived full glaciation, but in many cases thrived for many millions of years with minimal change.

Humans survive by altering their accessories and hiding in closed systems where they burn things for additional heat.

All in all, it sounds amazing, until one goes looking for control groups for each tank or why the researchers didn’t raise their squids to adulthood?

June 12, 2023 1:43 am
Reply to  observa
June 12, 2023 5:16 am

AI has a conflict of interest – they stand to gain.

Reply to  bonbon
June 13, 2023 4:36 am

Especially as dubious researchers keep rerunning their AI models until they get results they like.

Reply to  observa
June 12, 2023 5:56 am

Just as long as that includes Greta!

June 12, 2023 8:17 pm

Firstly, this is just another example of epigenetics. It is not as new or as groundbreaking as they claim.
Secondly, the four bases are adenine, cytosine, guanine, and thymine in DNA. In RNA thymine is replaced by uracil. What is adenosine, inosine, or guanosine?

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