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Extracellular Matrix Proteins of the Jellyfish Clytia hemisphaerica: Sequence, Structure, and Evolution

Lab Manager — University of Chicago, Department of Molecular Genetics & Cell Biology

Covers all five ECM protein families investigated in this project — collagens, nidogens, perlecan, spongins, and agrin.

Overview

In 2020, as lab manager in the Jocelyn Malamy Lab at the University of Chicago, I supported a comparative proteomics and molecular-evolution project on the extracellular matrix (ECM) of the jellyfish Clytia hemisphaerica. The Malamy Lab studies epithelial wound healing, and Clytia is an unusually powerful model for it: its body wall is a simple, largely transparent monolayer of epithelial cells sitting on a basement membrane, and it heals wounds remarkably fast and without scarring. Because the basement membrane and surrounding ECM are so central to how epithelial tissue repairs itself, the lab needed to know exactly which ECM proteins Clytia actually makes.

Scientific Questions

The ECM is a scaffold of secreted proteins that surrounds cells and gives tissues their structure, elasticity, and signaling environment. Its core components — collagen IV, laminin, nidogen, and perlecan, among others — are ancient and highly conserved, which raises a genuinely interesting evolutionary question: how far back do these proteins go, and how much have they changed? Cnidarians such as Clytia, Nematostella, and Hydra diverged from the lineage leading to vertebrates very early in animal evolution, so comparing their ECM proteins to ours offers a window onto what the earliest animal basement membranes may have looked like.

The project also had a concrete downstream purpose. A confidently identified Clytia ECM protein becomes a candidate for CRISPR knockout, after which the lab can observe how losing that protein changes wound healing — directly linking a specific molecule to a specific function in a living animal.

My Role

I explored five families of ECM and basement-membrane proteins:

Collagens, with particular attention to type IV collagen (the defining collagen of basement membranes) and a set of short-chain collagens, which I sorted and compared by shared domains and superfamilies to see how they grouped relative to human collagens.
Nidogens, where I confirmed that Clytia has a single nidogen-1-like protein (candidate transcript TCON 6428) but lacks nidogen-2 — consistent with the known pattern that nidogen-2 is a later vertebrate innovation.
Perlecan, a large heparan-sulfate proteoglycan. My candidate (TCON 11086) retained the three C-terminal domains most responsible for cross-linking laminin and collagen IV networks, while lacking two N-terminal domains associated with vertebrate-specific roles.
Spongins (short-chain collagen C4 proteins), where alignment analysis in Clustal Omega pointed to two strong Clytia candidates (TCON 71482 and TCON 34838).
Agrin, a basement-membrane proteoglycan best known for its role at the vertebrate neuromuscular junction. The Clytia candidate (TCON 2898) consisted almost entirely of Kazal and follistatin repeats, closely resembling agrin in Nematostella but missing the domains that characterize human agrin — suggesting it may represent a very early form of the protein.

Outcome

For each, I built a reference set of well-characterized sequences from humans and other organisms, searched the Clytia proteome for matches, and then dissected the domain structure of the best candidates to judge whether they were true homologs. A recurring finding was that Clytia proteins often carried the functionally essential core domains of their human counterparts while lacking domains tied to later, vertebrate-specific roles — exactly the pattern you’d expect from an early-diverging animal. Overall, the project gave the lab a clearer picture of what the Clytia extracellular matrix is built from, and where its basement-membrane proteins sit in the deep evolutionary history of animal tissues.

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