ABOVE: A female sexual polyp of the cnidarian Hydractinia symbiolongicarpus, with oocytes in yellow and cell nuclei in blue © FLICKR, TIMOTHY DUBUC, PH.D., SWARTHMORE COLLEGE

The marine invertebrate Hydractinia symbiolongicarpus, a colonial cnidarian that lives on rocks and shells in coastal oceans, must be able to defend its territory from other individuals without attacking itself in the process. A study published on September 26 in PNAS probed the underlying genetics of the animal’s allorecognition—the animal’s ability to distinguish itself from other members of the same species—and to the researchers’ surprise, the proteins involved in such recognition bear a striking resemblance to immunoglobulin proteins. The findings suggest that immunoglobulin genes evolved much earlier than previously thought.

“It is another milestone in our understanding of allorecognition in a cnidarian”, Ulrich Technau, a developmental biologist at the University of Vienna in Austria, who was not involved in the study, tells The Scientist over email. “[The study] is great, because it opens a completely new view on the subject, by combining genomics with novel structural biological methods.”

Hydractinia symbiolongicarpus is a member of the phylum Cnidaria, making it a close relative of jellyfish and corals. The animal’s tendency to form large colonies comes with problems, says study coauthor Matthew Nicotra, an ecologist at the University of Pittsburgh. As members of the same species inhabit the same space, they frequently bump into each other. And when one grows, for example, around the side of a rock and encounters itself on the other side, it needs to know whether it’s encountering itself or another. “If it’s encountering itself, it will just fuse together,” says Nicotra. “But if it’s an unrelated animal, they will start fighting with each other for that space.”

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Nicola and his team previously identified that allorecognition in Hydractinia symbiolognicarpus involves the genes Alr1 and Alr2. The researchers also knew that Alr1 and Alr2 were located close together in the genome, in a region called the allorecognition complex. Nicotra says that this suggested that the region resembles a histocompatibility complex, a genetic locus found in vertebrates at which genes coding for cell surface proteins in the immune system cluster.

     Microscopy image of the cnidarian <em>Hydractinia symbiolongicarpus</em> with cell nuclei stained turquoise, spermatogonia stained yellow, and spermatocytes stained purple
A male Hydractinia symbiolongicarpus polyp with spermatogonia in yellow; spermatocytes in purple, and cell nuclei in turquoise

In the new study, Nicotra and his team sequenced the whole genome of Hydractinia symbiolongicarpus and assembled the allorecognition complex to see if other genes similar to Alr1 and Alr2 were present in the region. They found not just the two genes, but 40 similar loci. Of these, 18 genes seem to code for proteins, which contain areas—or domains—that are highly similar in all these 18 genes.

The amino acid sequences resembled Ig-domains, a domain contained by immunoglobulin proteins, which include the antibodies and receptors on B- and T-cells of our immune system. However, the researchers weren’t sure of the sequences’ true identities, as “they didn’t match a lot of the traditional sequences,” Nicotra recalls. But when they used AlphaFold, an algorithm that predicts the 3D structure of proteins based on their amino acid sequence, “it becomes very clear that these are in fact immunoglobulin domains in these proteins.” Immunoglobulin proteins share some characteristic regions.

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One of these regions is the so-called V-set (for variable) domain, which allows specialized immune cells to recognize pathogens or cells. Looking at the protein structure, the Hydractinia proteins possess a V-set domain at the very tip of each protein. “That domain hadn’t been identified in organisms outside of the group called Bilateria—organisms with a bilateral symmetry. Cnidarians are the sister taxa to all those animals.”

These results suggest that V-set domains evolved earlier than expected, says Nicotra, “back in the last common ancestor of Cnidarians and all the Bilatarians.” However, Technau cautions that it is not easy to tell whether the domain evolved in a shared ancestor or whether it evolved separately in both cnidarians and bilaterians. To determine which of the two scenarios likely led to the new results, Technau suggests adding an outgroup to the analysis, i.e. looking at an even more distantly related group of organisms as a reference.

“Selection pressure for certain protein structures might facilitate and favor the presence of specific amino acids at specific positions,” writes Technau. Although he says he’s unsure which scenario is more likely, “[B]oth are equally exciting and fascinating, because either they uncovered the origin of self-nonself recognition based on the same kind of Immunoglobin-like molecules in the common ancestor of vertebrates and cnidarians, or different animal lineages have evolved very similar solutions to the same problem.”

Nicotra counters that convergent evolution—in which bilaterians and cnidarians would have independently developed the trait—is a less likely scenario, as some sequence-level homology was detected. While the extracellular domains of the newly identified proteins are highly similar, the intracellular domains look different. Some proteins might also play a role in allorecognition, like Alr1 and Alr2, but looking at those that don’t “might give a clue as to how the allorecognition system evolved” and what other function they derive from.

Having identified this group of genes, Nicotra will now turn his attention toward what these genes are doing. There might be a link to our immune system: Some newly discovered proteins contain an intracellular motif that, in vertebrate proteins, acts as an on-switch for immune cells. “Maybe they are involved in the other half of this response, where instead of fusing together, they start fighting [the nonself].”

Correction (October 11): The language used in the headline and first paragraph of this article has been updated to reflect that Hydractinia symbiolongicarpus would attack, not cannibalize, a hostile neighbor. The Scientist regrets the error.