Extracellular Matrix Proteins of the Jellyfish Clytia hemisphaerica: Sequence, Structure, and Evolution
Summary of the five ECM protein families I 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.
The Clytia Genome
At the time of this work (2020), the Clytia genome had been fully sequenced, but many of its predicted proteins had not yet been identified or functionally characterized. We therefore identified candidate ECM proteins by searching the available Clytia sequences and comparing them with characterized proteins from humans and other species. In 2024, NCBI released a RefSeq annotation of the Clytia hemisphaerica genome, providing updated gene and protein annotations. I plan to revisit these proteins in a future project, comparing the current annotations with the candidates identified in our original work.
Scientific Questions
The ECM is a network of secreted proteins that provides structural support and participates in cell signaling. Major basement-membrane components include type IV collagen, laminin, nidogen, and perlecan, many of which are conserved across animal lineages.
This project examined whether homologs of major human ECM proteins could be identified in Clytia and how their sequences and domain architectures compared with those of homologs from other cnidarians and vertebrates. Identifying these proteins also provided candidates for future functional studies, including CRISPR knockout experiments examining their roles in wound healing.
My Role
I investigated five ECM and basement-membrane protein families:
- Collagens: Characterized type IV and short-chain collagen candidates and compared their conserved domains and protein families with human collagens.
- Nidogen: Identified a single nidogen-1-like candidate (TCON 6428); no nidogen-2 homolog was identified.
- Perlecan: Identified a candidate (TCON 11086) containing three conserved C-terminal domains involved in basement-membrane interactions, while lacking two N-terminal domains present in vertebrate perlecan.
- Spongins / short-chain collagen C4 proteins: Sequence alignment using Clustal Omega identified two strong candidates (TCON 71482 and TCON 34838).
- Agrin: Identified a candidate (TCON 2898) dominated by Kazal and follistatin repeats. Its domain architecture was similar to the Nematostella homolog but differed substantially from vertebrate agrin.
Outcome
For each protein family, I assembled reference sequences from characterized proteins, searched the Clytia proteome for candidate homologs, and compared sequence similarity and conserved domain architecture. The analysis identified candidate Clytia homologs for several major ECM proteins and documented both conserved domains and lineage-specific differences relative to vertebrate proteins.
These results provided a working characterization of key components of the Clytia extracellular matrix and a set of candidate proteins for subsequent experimental studies of epithelial wound healing.
Tools and Resources
- NCBI - reference protein sequences and literature
- NCBI BLAST - sequence homology searching
- NCBI Conserved Domain Database (CDD) - domain architecture analysis
- UniProt - curated protein sequence and functional data
- SMART (EMBL) - protein domain identification
- Clustal Omega (EMBL-EBI) - multiple sequence alignment
- SnapGene - sequence viewing and signal-peptide analysis
- MARIMBA - the dedicated Clytia hemisphaerica genome and transcriptome database
Recent Malamy Lab Publications
- Characterizing Epithelial Wound Healing In Vivo Using the Cnidarian Model Organism Clytia hemisphaerica - Jove
- Epithelial wound healing in Clytia hemisphaerica provides insights into extracellular ATP signaling mechanisms and P2XR evolution - Nature
- The basement membrane determines the choice of wound healing mechanism across wound scales in the basal eukaryote Clytia hemisphaerica - Molecular Biology of the Cell