Could a mutant fish that was genetically engineered backwards tell us where we came from?

Humans and fish (unless you mean a lungfish) don’t really have much in common, except that they are both vertebrates, and all vertebrates have a common ancestor. But how do you go hundreds of millions of years back in time without a fossil of that ancestor?

Technology from the future has now given us a glimpse into the deep past. Biologists from the University of Colorado Boulder have now used CRISPR to genetically reverse-engineer the embryo of a sea lamprey (those freaky fish that stick to their prey and suck its guts out), making it devolve. The wormlike creature they created proved that removing the set of genes that makes vertebrates what they are rewinds evolution. It can also give us a better understanding of the ancestor we have in common with fish and everything else that has a skeleton.

"There is a single gene vaguely similar, and probably distantly related, to the Endothelin receptors in the genome of the invertebrate chordate amphioxus," biologist Daniel Medeiros, who co-authored a study with David Jandzik and lead author Tyler Square, told SYFY WIRE. "What it does is unknown (we have tried to figure out what it does, but have failed so far). So the endothelin receptor likely evolved from some ancient cell surface receptor, perhaps by gaining some new protein coding sequence, or by exon shuffling (being accidentally combined with some other protein-coding sequence from another part of the genome)."

It’s kind of like that spell of Ursula’s in The Little Mermaid that turned poor unfortunate merpeople into primitive worm-things, just not so grim.

500 million years ago, vertebrates somehow evolved the group of genes that made them vertebrates. These genes make up the Endothelin (Edn) signaling pathway, which switches on specialized cells that develop into parts of the skeleton, the peripheral nervous system and pigment cells to multiply as the embryo develops. These cells are neural crest cells (NCCs). What Square and his team wanted to test was whether taking away the Endothelin signaling pathway would turn a vertebrate into an invertebrate that could be eerily similar to something that existed before skeletons were a thing.

Mutant sea lamprey embryo. Credit: David Jandzik

Sea lampreys were used in the experiment because they evolutionarily diverged from other fish around the same time that vertebrates evolved the Endothelin signaling pathway. These jawless fish are living fossils, with ancient vertebrate features that at least give some idea of an early phase of vertebrate evolution.

"The evolution of what we think are two different endothelin signaling pathways allowed neural crest cells to divide themselves up into different groups capable of doing different things," Medeiros said. "We think, based on the lamprey mutant phenotypes, that this facilitated the evolution of different types of vertebrates with different head skeleton features."

Endothelin signals are zapped to different cells in order to tell them what functions to carry out—this is intercellular signaling. Ligands, or molecules that bind to other (often larger) molecules for a specific biological function, are released by signaling cells in this process. The ligands produce a chemical signal when they bind with a protein they target, which is the receptor of that signal. Ligands typically bind only to one particular receptor. Multiple ligands and receptors dedicated to varying functions are involved in Endothelin signaling.

"The endothelin ligands really appeared out of nowhere; there is nothing remotely like them in any invertebrate," Medeiros said. "They must have been transcribed randomly from some non protein-coding DNA on accident at some point. This has been shown to happen in other animals, like fruit flies. Since they are not very large genes, I think that is a good possibility."

In an earlier study, Medieros and his team had analyzed the Endothelin signals in a frog and compared them to those in the lamprey, which they found has specific ligand and receptor pairs that are almost like similar pairs found in jawed vertebrates. This analysis formed the basis of what would be their work with CRISPR.

Genome duplication was previously thought to be behind the evolution of new traits, since copies of genes that already exist can assume new — and possibly, such as in the emergence of vertebrates, unprecedented — functions.

"You sequence the gene you targeted to make sure that you efficiently “broke” the gene, and can then analyze the defects caused by missing the gene," said Medeiros. "The CRISPR method uses the 'programmable' Cas9 enzyme, which cuts DNA. We can injected a solution with the Cas9 enzyme and a piece of RNA into the cell with a tiny glass syringe. In the cell, the Cas9 grabs the RNA guide, then moves into the nucleus and cuts the DNA where we want it, then you let the mutated embryo develop."

Mutant sea lamprey larvae showed just about none of the traits that distinguish vertebrates. What makes this experiment such a breakthrough is that it has been notoriously difficult to find the exact roles for genes that exist only in vertebrates. The team also realized that while gene duplication is definitely involved in evolution, it was not the holy grail that could give rise to an entirely new group of genes, such as NCCs, on its own. Formation of new genes has to be going on at the same time as duplications in order for that to happen.

Could you devolve a human like this? Probably not, but it’s awesome sci-fi-horror movie fodder. What might eventually be done, if you ask Medeiros, is the cancelling out of detrimental genes that could lead to defects.

"As long was we survive as a technological species, we will eventually understand genomes, how they have changed during evolution to make new organisms, and also how it they are disrupted in genetically based diseases and cancer," he said. "At that point we can rewrite the instructions in an intelligent way to create essentially whatever biological outcome we want."