The difficulty in finding these proteins was not a matter of absence but of detection. Conventional sequence-similarity tools such as BLAST and HMMER rely on recognizable stretches of amino acids, and cytokines evolve exceptionally fast, driven by pathogen-mediated selection pressure. IL-1 family members are also small proteins with complex exon-intron architectures, further muddying homology signals. The research team, led by Francisco Fontenla-Iglesias, Jonathan P. Rast, Katherine M. Buckley and Sebastian D. Fugmann, sidestepped this problem by exploiting what sequence searches miss: structure. Using the protein-structure prediction programs AlphaFold2 and ESMFold, together with the structure-alignment search tool Foldseek, they scanned proteomes for the hallmark three-dimensional signature of IL-1 proteins, the conserved carboxy-terminal beta-trefoil fold.

The beta-trefoil is a compact architecture of twelve beta-strands assembled into three beta-sheet foils, a shape shared with other protein families such as fibroblast growth factors but diagnostic in its details for the IL-1 superfamily. When the team applied this structural lens to the sea lamprey Petromyzon marinus, a jawless vertebrate whose lineage split from ours over 500 million years ago, three candidate proteins emerged. Their sequence similarity to mammalian IL-1 was so low as to be nearly invisible, yet their predicted structures reproduced the canonical twelve-strand trefoil, including the conserved ordering of beta-strands and the (F/L)ES motif in beta-strand 9 found in many vertebrate IL-1 family members. Structure, it turned out, had outlasted sequence.

What the researchers found next gave the discovery its name. Most of these ancient proteins carry not just the trefoil domain but also an amino-terminal PDZ domain, an ancient protein-protein interaction module that typically functions as a signalling scaffold. The team designated this family IL-1anc, for ancestral IL-1. A systematic screen of 39 representative genomes revealed IL-1anc genes across an astonishing breadth of animal life: all cartilaginous and bony fish examined, jawless vertebrates, cephalochordates such as amphioxus, hemichordates, echinoderms including the purple sea urchin, bivalve molluscs, crustacean arthropods and cnidarians such as the starlet sea anemone. No homologues were detected in sponges or ctenophores, bracketing the family’s origin to the base of Eumetazoa. Intriguingly, IL-1anc genes were independently lost in non-caecilian amphibians and in crown-group amniotes, which explains why they are absent from mammals, including humans.

Genomic context provided independent confirmation of deep common ancestry. The IL-1anc genes sit in conserved syntenic chromosomal neighbourhoods, and in cnidarians and ambulacrarians the microsynteny is remarkably tight: IL-1 genes are flanked by homologues of TRAF3, GCC2, ESD and, in many species, putative IL-1 receptor genes. The researchers infer an ancestral locus containing an IL-1 cytokine, an IL-1 receptor and two unrelated marker genes, with that arrangement preserved across phyla whose lineages diverged more than 600 million years ago. Exon-intron structures reinforce the picture: the beta-trefoil domains are encoded by three to five exons with conserved intron phasing across species, and the PDZ domains, where present, show the same pattern. Convergent evolution could not plausibly produce such coordinated conservation of structure, gene order and gene architecture.

But structural and genomic evidence alone does not prove function. The team therefore asked whether these ancient proteins behave like mammalian IL-1 in the context of real immune responses, testing four predictions: expression in immunologically relevant tissues, upregulation upon immune challenge, proteolytic processing and secretion, and interaction with an IL-1 receptor. In sea lamprey larvae, injection of flagellin, a potent bacterial pathogen-associated molecular pattern, significantly upregulated all three PmarIL-1 transcripts in the intestine and typhlosole, a gut-associated lymphopoietic tissue, alongside known inflammatory cytokines such as TNF-alpha and IL-8. Lipopolysaccharide, by contrast, did not induce the IL-1 genes, indicating a stimulus-specific response rather than a generic stress reaction.

The purple sea urchin Strongylocentrotus purpuratus offered an even richer picture. Five IL-1anc genes were identified, and analysis of RNA-sequencing data showed tissue-specific baseline expression: SpurIL-1.2 in the axial gland, radial nerve, coelomocytes and gut, and SpurIL-1.1 exclusively in the gut. When adults were infected with the bacterium Vibrio diazotrophicus, SpurIL-1.2 transcripts rose sixteenfold and SpurIL-1.5 sixty-twofold within six hours, mirroring the activation of IL-17 factors that mark an active immune response. Fluorescence in situ hybridization localized this induction to phagocytic coelomocytes, with SpurIL-1.5 expressed in a previously undescribed phagocyte population. In sea urchin larvae, SpurIL-1.2 was upregulated sevenfold after infection and localized to a ring of midgut epithelial cells. The parallel with mammalian IL-1beta, induced in macrophages upon pathogen sensing, is difficult to ignore.

Even a cnidarian joined the pattern. In the starlet sea anemone Nematostella vectensis, treatment with 2’3′-cGAMP, a second messenger that mimics viral infection and activates STING-dependent antiviral and antibacterial pathways, upregulated the single NvecIL-1 gene thirty-five-fold, alongside the inflammatory transcription factor NF-kappaB. Taken together, the expression data from lamprey, sea urchin and sea anemone suggest that inducible IL-1 expression in immune-relevant cells is not a vertebrate specialty but a property the family has carried since the emergence of Eumetazoa.

Subcellular behaviour added further parallels. When expressed in cultured mammalian cells, most of the lamprey and sea urchin IL-1anc proteins localized to the cytoplasm, like mammalian pro-IL-1beta, while two sea urchin proteins accumulated in the nucleus, echoing mammalian IL-1alpha. Most IL-1anc proteins lack signal peptides, implying non-classical secretion routes, though one lamprey protein, PmarIL-1.1, carries a conventional signal peptide and was secreted from transfected cells, suggesting that classical secretion evolved independently more than once. Most strikingly, the sea urchin protein SpurIL-1.3 was cleaved by human caspase-1 at a specific aspartate residue, and by a sea urchin caspase homologue at the very same site, releasing the mature trefoil domain. This mirrors the inflammasome-dependent processing that activates mammalian IL-1beta and hints that two-signal regulation, separating cytokine production from cytokine activation, is an ancient safeguard against runaway inflammation.

The study stops short of demonstrating pro-inflammatory activity directly; formal proof will require knockout models and recombinant protein challenge experiments in lamprey and invertebrate systems, and direct ligand-receptor binding remains to be shown. Even so, the convergence of structural, genomic and functional evidence makes a compelling case that the IL-1/IL-1R axis is a foundational module of animal immunity, predating the jawed vertebrates by hundreds of millions of years. The work also carries a methodological lesson for the field: when sequence similarity fails, machine-learning structure prediction can resurrect long-lost relatives of even the most rapidly evolving protein families. For immunologists, the message is that the molecular grammar of inflammation was written long before antibodies, T cells or even myeloid lineages existed, and the sea anemone on the reef may be running a version of the same inflammatory circuit that fires in human tissue today.

Subject of Research: Evolutionary origins and immune function of ancestral IL-1 cytokine family proteins across metazoans

Article Title: An ancient evolutionary origin for IL-1 cytokines

Article References: Fontenla-Iglesias, F., Lin, T.-M., Williams, A. G., Das, S., Lee, C.-Y., Rast, J. P., Cooper, M. D., Buckley, K. M., & Fugmann, S. D. (2026). An ancient evolutionary origin for IL-1 cytokines. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-026-03191-2

Image Credits: AI Generated

DOI: 10.1038/s41559-026-03191-2

Keywords: IL-1 cytokines, innate immunity, evolution, protein structure prediction, inflammation, sea lamprey, purple sea urchin, cnidarians, synteny, caspase processing, Eumetazoa, comparative genomics