Squid Edit RNA in Thousands of Sites, Reshaping Their Proteins

Squid rewrite the instructions for building their proteins on a scale no other animal is known to match, and the edits change what the proteins do. A team led by bioscientists at the University of California, San Francisco, mapped this in the longfin inshore squid (Doryteuthis pealeii); the work appeared in October in Cell.

The mechanism is called ADAR-mediated RNA editing. ADAR stands for adenosine deaminase acting on RNA, a family of enzymes that change single letters in RNA, the temporary copy of a gene that cells read to build a protein. The result is a different protein from the same gene, while the DNA stays unchanged. The authors' co-author describes it, in simplified terms, as printing a recipe and then swapping raisins for chocolate chips just before it reaches the baker.

How the team looked at the edits

Humans and other animals edit RNA too, but coleoid cephalopods, the group that includes squid, octopus and cuttlefish, do it far more than anyone else. Earlier work had linked their editing to communication in the nervous system, possibly in response to conditions such as temperature changes. Until now little was known about what the edits do to the proteins themselves.

The researchers examined the proteome, the full set of about 24,000 proteins, of the longfin inshore squid. They studied nearly 8,000 edited sites across more than 2,000 different proteins in two tissues: the optic lobe, the part of the brain that handles vision and responses to it, and the gills, a plainer respiratory organ. The optic lobe showed more frequent and more complex editing, which fits the idea that cephalopods' strong ADAR activity and their complex nervous systems, the most complex among invertebrates, emerged together. The edits fall in protein-coding sequences rather than in non-coding stretches of the genome.

What the edits change

"We found effects on protein activity, stability, localization, and even how they interact with other proteins. The downstream effects even go so far as to regulate organelle health," first author Jack Moen, a cell and molecular scientist at UCSF, told ScienceAlert. "By editing the RNA instructions used to make proteins, these animals can generate proteins with different properties, all without changing their DNA."

• Some edits fall in the ADAR proteins themselves, which suggests a way for the editors to regulate their own activity.
• The team identified 5,000 short proteins that are absent from the reference squid proteome and from Swiss-Prot, a curated protein database covering 14,000 organisms.
• Edited proteins can end up in a different place in the cell, moving from the outskirts toward the nucleus.
• Recoding may make squid mitochondria, the cell's energy-producing organelles, more like human ones: more stable under changing conditions and better at recycling themselves.
• It also appears to affect creatine systems, which supply bursts of energy for fast escape movements and demanding brain processing.

Why the numbers are so large

Because each edit changes one base and leaves the DNA alone, it does not pass harmful mutations to offspring. Counting every site found in the RNA sequencing data, Moen said, the theoretical number of possible protein variants comes to about 10²⁴⁸, far above the number of atoms in the universe. "They describe an enormous potential diversity," Moen said. How much of that diversity the animals actually produce remains unknown.

Why cephalopods do this and other animals do not is only partly answered: it comes down to the structure of their ADAR enzymes and to other reasons that need more research. For more science coverage, see our Science section.