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How coleoid cephalopods use RNA editing to defy conventional genomic DNA evolution

Coleoid cephalopods use RNA editing to defy conventional genomic DNA evolution they do this by...

By, James Linacre | Date: 10/07/2017

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Fun Fact:

In UK law it is considered too cruel to operate on octopi without some form of pain relief or anesthetic. They are the only invertebrate given this special protection due to their intelligence.

baby octopus

How coleoid cephalopods use RNA editing to defy conventional genomic DNA evolution

Coleoid Cephalopods – the class of animals that octopus and squids belong to – are some of the most interesting creatures on this planet. They’ve exhibited surprising levels of intelligence and possess some of the most incredible and versatile anatomies known to nature, being able to manipulate their own bodies to fit into tight gaps, camouflage themselves and even mimic the movements of other creatures to set elaborate traps.

But scientists have recently discovered another fascinating feat these aquatic creatures are capable of, and one that’s completely unparalleled in the worlds of biology and genetics.

Cephalopods have took an entirely different path of evolution from almost all other life forms, forgoing traditional evolution through slow changes to their DNA in favour of rapid changes in their RNA in a process known as RNA Editing.

The link between DNA and RNA

DNA strand RNA editing

Conventional Genomic DNA evolution occurs through changes to the DNA (Deoxyribonucleic Acid) of creatures over generations, primarily through two natural processes: mutation and recombination.

Mutation occurs when DNA is being copied – sometimes a copying error occurs and the information stored within the copy of the DNA is slightly different to that of the original.

Recombination – male sperm and female eggs each contain a randomly selected 50% of DNA from their parent. When a sperm inseminates an egg, the offspring created through mating possesses 50% of each of its parents DNA. Keep in mind that each 50% of the DNA from the parents may have slight differences to the original due to mutation, so the result is offspring which resemble a mixture of both parents, which some entirely unique traits.

Natural selection means the creatures with the most desirable traits to survive in their environment –for example, animals with colourations that allow them to blend into their environments and escape the notice of predators – are the ones to pass their genes on, resulting in more of these beneficial traits in the gene pool.

This is evolution in a nutshell; slow gradual changes to DNA over generations of creatures, which become more dominant in a species due to natural selection. 

However, DNA is just the blueprint for a living being; a collection of information and instructions to build a creature from. The actual builder in this process is the less known RNA - Ribonucleic Acid.

Two processes are involved in RNA taking the data contained in DNA and turning it into protein: transcription and translation.

Transcription – this is when the RNA enters the nucleus to retrieve information from the DNA inside. This means the DNA does not have to leave the nucleus and doesn’t risk being damaged, whilst also allowing multiple copies of RNA to come from the same DNA, allowing faster, safer and much more efficient means of producing proteins in the long run.

Translation – after the RNA has retrieved the necessary information from the DNA, it is translated into amino acids to form various proteins which perform a wide array of functions within our body from repairing damaged portions of the body to growing others over time; all that so they resemble the designs kept within the DNA.

However, things do get more complicated at this stage and this is where cephalopods differ from most beings on the planet.

There is one more step involved in RNA creating proteins, splicing. DNA contains a lot of redundant or useless information for a number of reasons. During the translation process, this information is cut out of the RNA and the RNA is put back together in what is called the Spliceosome Complex.

This is essentially a safety procedure to ensure the exact same information is processed each time; by including information that isn’t necessary, this is basically forcing the body to “double-check” each RNA it translates and make sure no unwanted information slips through (Such as through the copy-error mutations mentioned earlier) and our body does not produce proteins incompatible with itself.

All life undergoes this procedure; from Daffodils to Rhinoceros and yes, from Octopuses to us Humans, we all use our RNA to build our bodies based on the information contained in our DNA and must splice this RNA to ensure it is suitable to be put to work and turned into cells.

But unlike most creatures which evolve by passing down their DNA through generations, Cephalopods use this RNA translation and splicing process to make direct changes to their own biology in a process known as RNA Editing.

RNA Editing – Where cephalopods defy conventional evolution

cephalopod, RNA editing

During splicing, cephalopods are able to directly change the information contained within the RNA, deviating from the template contained within the DNA and allowing them to change the genetic instructions to produce different proteins. This allows them to adapt to their environment and challenges by simply telling their bodies to produce the necessary proteins for the situation, bypassing the slow process of natural selection and evolution entirely.

Facing a drastic change in temperature? The next batch of RNA they process will be edited to produce the proteins and cells needed to survive in the new environment. Within hours of venturing or being forced into an unfamiliar environment, they are ready for all the challenges it faces. This allows the creature to “try out” different combinations of traits in rapid succession until it finds the most desirable solution. It’s no coincidence that squids have been proved capable of producing a much more diverse range of proteins than most animals – all the stuff they could ever need is locked right there in their genes, ready to be brought out when the necessary situation occurs – as easy as flipping a switch.

Downsides of RNA editing

Surely RNA Editing is in many ways a superior choice to genomic DNA evolution, which means it’s a complete illogical mystery as to why cephalopods are one of the few species to take full advantage of it? Surely every species would be much more versatile and fit for survival with RNA editing?

Not quite. Heavy RNA editing doesn’t work so well for most species and has actually been phased out through natural selection for many. Mammals have had a less than perfect relationship with RNA editing, due to the fact that it can result in too much evolution and adaption to the surrounding environment, with the body undergoing large changes per minute and/or temporary changes in the environment that don’t require such drastic alterations.

That isn’t to say mammals don’t do any RNA Editing – it’s a function in all lifeforms, just like splicing. The effects are simply much less drastic as our RNA Editing is mostly restricted to RNAs that don’t directly encode proteins and make overt physical changes in our bodies, and only a fraction of 1% of our RNAs are edited. In cephalopods, over a half of their entire genetic code is rewritable – around 55-60% depending on the exact species. In fact, single RNAs are shown to have gone through multiple rewrites: for these creatures, self-driven genetic modification is the norm.

This has come out of the cost of slowing their genomic DNA evolution. The conditions which allow for RNA editing to occur in cephalopods are incredibly delicate and precise. Small changes in the wrong areas – such as the random DNA mutations mentioned earlier – could completely cut off RNA editing for future generations of the species. As such, the biology of these creatures has gone to some astonishing lengths to avoid changes in these areas.

The editing sites (known as ADAR enzymes) must restrict a large portion of the cephalopods’ genome – anywhere between 23% and 41%. Cephalopods have essentially cordoned off large parts of their genome with red tape and stuck a sign outside saying “No evolution here!”, in a slightly ironic sense, the components that make their amazing adaptability and versatility possible MUST NOT ever change themselves. This restricts the pace of evolution for the creature overall.

Whilst conventional genomic DNA evolution and RNA editing are not mutually exclusive, it's clear one must pay a heavy price in one area to keep the other fully functional. Whilst cephalopods undergo DNA evolution much more slowly than other creatures, the benefits that RNA editing brings makes it hard to argue that for these species at least, the trade-off has been worth it.

Closing Thoughts

One enigma still surrounding RNA editing in cephalopods is the correlation it has to the intelligence of the species. Indeed, heavy RNA editing appears to be limited to coleoid cephalopods and then to only the more intelligent species.

For example, nautilus is creature closely related to octopi and squids, sharing the mollusc cephalopod categorization with them, but display comparatively simple and unremarkable behaviour and do not edit their RNA. Coleoids who do use RNA editing also happen to have evolved complex brains and exhibit highly intelligence behaviour. Coincidence?

The possibility of cephalopods editing their own RNA to make themselves smarter is one that is also discussed, as many of the RNA editing sites are found within the nervous system, affecting the production of proteins that are key players in neuronal excitability.

Is it possible that RNA editing is allowing cephalopods to produce brain cells with a much higher level of understanding and pattern recognition to various stimuli? Perhaps, but the evidence is inconclusive.

Scientists have also considered what exactly triggers RNA editing: is it purely a result of surrounding environmental changes or can it be set off through something as complicated as experience and memory?

With their high levels of intelligence and dexterity, alongside their newly discovered RNA editing capabilities it isn’t surprising that cephalopods are one of the primary species speculated to be the next dominant species after humans.

Through their ability to modify their own genetic information, cephalopods are playing by an entirely different set of rules than Charles Darwin set out when he published his theory of evolution. Although much of what they do flies in the face of what Darwin thought possible, they are still proving him right in one key factor: above all else, it is the ability to adapt that determines the success of a species. In this regard, cephalopods are one of the most successful creatures on the planet, and they don’t look set to give up this success anytime soon.

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