Scientists have invested decades in decoding the genomes of animals and crops. Fungi, for the most part, have been left out of the spotlight. The fungal kingdom usually only grabs attention when it spoils bread or colonizes someone’s toes. This is a peculiar blind spot, given everything fungi have already given us.
Penicillin came from mold. Statins, the cholesterol-lowering drugs taken by millions, also trace their origins back to chemical processes derived from fungi.
“This neglect is quite remarkable, considering how fungi have shaped modern medicine,” said Xue Gao from the University of Pennsylvania. “From the accidental discovery of penicillin to statins that reduce cholesterol levels, we owe many recent breakthroughs in lifespan extension to fungal chemistry. Yet, despite this, the vast majority of the fungal kingdom remains a black box.”
Part of the problem lies within the fungus itself. In the wild, mold activates gene pathways that produce chemical weapons to fight off bacteria. Transfer that same mold to a clean lab dish, and those pathways go silent. With nothing attacking it, it stops generating the very compounds researchers hope to find.
To access these hidden pathways, scientists must rewrite the genes that block them. This has been a source of frustration for years.
“To reactivate these concealed signaling pathways, we needed a powerful way to precisely manipulate the fungal genome, such as editing their core regulatory genes, but traditional tools were up to the task,” Gao said.
CRISPR-Cas9 has been a household name in gene editing for over a decade. However, in filamentous fungi, it behaves more like a sledgehammer than a scalpel. It cleanly cuts both strands of DNA, and the cell hastily repairs the damage. This leads to a host of unintended insertions and deletions that can derail a carefully designed experiment.
A new approach, called prime editing, completely bypasses these double-strand breaks. It rewrites the genetic code one letter at a time with much finer control. Until now, no one had managed to make prime editing work in filamentous fungi. Gao and her team from the University of Pennsylvania created a version that does, naming it fPE7max. The findings were published in the journal Nature Biotechnology.
Achieving this required overcoming two tough hurdles. The first was unreliable instructions. Prime editing relies on a guide made of RNA, which tells the tool where to go and what to write. As the editing task grows larger, this guide becomes longer, and long guides tend to degrade before the job is done.
The team’s solution was a protein called fLa. It wraps around the fragile RNA and shields it, allowing the tool to handle large insertions and deletions that would disrupt less efficient systems. In an earlier version, this protein was borrowed from humans and worked poorly inside fungal cells. Switching to a native fungal protein changed everything.
The second hitch was that the fungus resisted the changes. Its natural repair machinery viewed each new edit as a mistake and reversed it. So, the researchers added a second protein that temporarily disabled this repair system.
With both fixes working together, the editing precision of fPE7max neared 90 percent, and the program remained reliable across many genes and several species.
Then came the elegant part of the work. The team directed their tool at a regulatory gene called laeA. This single gene controls sprawling networks of chemical production. Tweak its position, and dozens of downstream metabolic pathways start responding.
Right before the laeA gene lie tiny genetic sequences that act as a brake on it. Instead of tinkering directly with the laeA gene, the researchers used fPE7max to delete that brake with pinpoint accuracy.
Freed from the brake, the laeA gene ramped up. Sleeping gene clusters came to life, and unfamiliar compounds began appearing in fungi that had never produced them in the lab. The same trick worked on molds spread across one fungal family. This versatility suggests the method could reach widely across the fungal kingdom.
The payoff was significant.
“We isolated 18 different complex molecules, eight of which had chemical structures entirely new to science,” said Chunxiao Sun, a researcher in Gao’s lab. “Among these discovered molecules, three showed promising anticancer properties. These molecules could serve as lead compounds for disease treatment, opening an important new avenue for drug development.”
Some of the newly found substances belonged to a chemical family called pyranonigrins. Within these, previously unseen structural elements were found woven into the core framework.
First, the team tested the new compounds on common bacteria and yeast. None showed much effect there. On human cancer cells, the story changed drastically. One molecule displayed selective toxicity toward breast, liver, and leukemia cancer cells, while leaving other cells largely untouched.
It turned out that tiny structural details made a huge difference. Apparently, a single sulfur-containing side chain determined whether a molecule could kill cancer cells or have no impact. Remove that one feature, and the activity vanished. Such clues help chemists understand what makes a compound work and how they might improve it.
The findings point to a much larger reservoir hiding in plain sight. More than 90 percent of fungal gene clusters remain unexplored, meaning a vast store of chemicals is still uninvestigated.
“This is a compelling proof of concept, showing that the next generation of vital therapeutics may already exist in nature,” Gao said.
Now, the team wants to aim fPE7max at many more fungal species. The plan is to move away from the old treasure-hunt method of combing wild fungi in hopes of a lucky find, replacing it with something systematic and reproducible. For a long-ignored field of biology, this is a real turning point. The black box is finally starting to open.
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