Scientists discovered a protein secreted by a deep-sea extremophile — an organism adapted to extreme environmental conditions — that self-assembles into a biofilm and is highly stable, boosting its potential for biomedical applications.
The journal PNAS published the discovery and characterization of the protein. Dubbed AbpX, it represents a new clade, or evolutionary branch, of a larger family of previously known biomatrix-forming proteins.
“What makes AbpX unique is it doesn’t require complex processing methods in order to form a biofilm,” says Vincent Conticello, a senior author of the PNAS paper and professor of chemistry at Emory University. “All you have to do is add calcium and it self-assembles.”
This quality makes the protein an attractive base for the creation of synthetic biomaterials. Since no harsh chemicals are required for its assembly, that potentially minimizes damage to cells and sensitive therapeutics.
AbpX is also remarkably stable and durable, found in the extremophile Pyrodictium abyssi , which grows at the temperature of boiling water.
The research team was studying another protein produced by P. abyssi when they noticed a faint mesh of fibers in the background of an electron microscope image. These miniscule fibers, 10,000 times smaller than a human hair in diameter, turned out to be AbpX.
“It was an accidental discovery,” Conticello says. “Advances in microscopy made it possible to gain this new insight into the natural world that could also be of real therapeutic use.”
Han Remaut, a structural and molecular microbiologist at Vrije Universiteit Brussel and VIB-VUB Center for Structural Biology, in Brussels, Belgium, is co-senior author of the paper.
Emory PhD candidate Andres Gonzalez Socorro is co-first author of the paper, along with Mike Sleutel and Adrià Sogues, who spearheaded efforts at Vrije Universiteit Brussel and VIB-VUB Center for Structural Biology.
The search for living treasure
Pyrodictium abyssi , which takes its name from the Greek root word for “fire,” “network” and “abyss,” was isolated from deep-sea vents in 1991. It belongs to the domain of Archaea, a branch of single-celled organisms which have a separate evolutionary lineage from the domains of bacteria and of Eukarya, which includes all multicellular organisms.
While some “bioprospectors” venture deep into ocean to look for “living” treasure, others stick to the lab where they can explore valuable mysteries hidden within these newfound life forms.
The Conticello lab began studying P. abyssi as part of an international collaboration to characterize one of the organism’s previously known proteins, which forms a biomatrix of tiny, stiff tubes, or cannulae.
That investigation yielded a 2025 paper in Nature Communications, characterizing the structure of the cannulae and the mechanism by which it self-assembles.
A new clade of proteins
The researchers next turned to investigating the mesh of filaments secreted by P. abyssi cells. Bioinformatic analysis showed that the filaments represent a distinct clade of proteins in the TasA superfamily of biomatrix proteins, and that members of this newly discovered clade are widely distributed in bacteria and archaea.
“Microbes secrete these filaments and they bundle together to form a biofilm,” Conticello explains. “The biofilm allows the cells to attach to things and also forms a protective shell over them.”
The researchers named their biofilm-forming protein AbpX: “A” for archaea, “b” for bundling, “p” for protein and “X” for unknown.
To learn more about the structure of AbpX and how it forms into a biofilm, Gonzalez Socorro cloned the DNA sequence of the protein. He then implanted this genetic material into laboratory specimens of E. coli bacteria, which read the information coded by the gene and produced the protein.
He demonstrated in experiments how AbpX fibers rapidly bundle into a biofilm when he added calcium ions to a liquid sample of the fibers.
“I used a rheometer, an instrument that studies the flow of materials under tension,” Gonzalez Socorro explains. “You can see how a substance changes from a liquid into a gel. If I push on water, for example, it’s going to keep flowing. But if I push on Jell-O, it’s going to bounce back.”
“It’s interesting that the same organism, P. abyssi , produces two proteins that form a biomatrix with the simple addition of calcium,” he adds.
But while the stiff cannulae tubes resemble a straight, raw pasta, AbpX fibers are more like “wavy, cooked noodles,” Conticello says.
An atomic-level view
Transmission electron microscopy at Emory’s Robert P. Apkarian Integrated Electron Microscopy Core documented the crystalline structure of the AbpX matrix.
The VIB-VUB Facility for Bio Electron Cryogenic Microscopy zoomed in further to reveal the AbpX matrix at the atomic scale. The images show how the top of one wave of an undulating AbpX fiber interacts with the bottom of another wave to join individual fibers into a crisscross lattice.
Studying AbpX may help uncover secrets about biofilms of pathogenic microbes, including harmful bacteria that use these slimy shields to block antibiotics. AbpX also holds potential for biomedical applications such as wound dressing, coatings for medical devices and tissue engineering.
“We’re going to continue to characterize AbpX to better understand it’s different mechanical properties and behaviors,” Conticello says. “It’s opened up a new area for us to explore.”
The international project was funded by the U.S. National Science Foundation, the Human Frontier Science Program, the European Molecular Biology Organization, Marie Sklodowska-Curie Actions and the Max Planck Society.
Additional authors include Vita Cooman and Marcus Fislage (Vrije Universiteit Brussel); Adam Nijhawan and Xiaobing Zuo (Argonne National Laboratory); and Vikram Alva (Max Planck Institute, Tübingen, Germany).
Proceedings of the National Academy of Sciences
Imaging analysis
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Pyrodictium abyssi AbpX reveals a calcium-responsive family of microbial biomatrix proteins that form thermostable hydrogels
17-Jun-2026