The first to mine the fungal genome using multiple base editing

Anyone who's ever been to a cocktail party will tell you that releasing inhibition makes you more talkative and may also make it easier to reveal secrets
.
It turns out that fungi are no different
from humans in this regard.

Xue Sherry Gao, a chemical and biomolecular engineer at Rice University, and his collaborators used a method to simultaneously modify multiple sites in the fungal genome, tricking the fungi into revealing their best-kept secrets, speeding up the pace
of new drug discovery.

This is the first time that multiple base editing (MBE) technology has been used to mine fungal genomes and obtain medically useful compounds
.
Compared to single gene editing, the MBE platform shortens the study time by more than 80% in an equivalent experimental environment, from an estimated 3 months to about 2 weeks
.

Fungi and other organisms produce biologically active small molecules, such as penicillin, to protect themselves from pathogens
.
These biologically active natural products (NPs) can be used both as drugs and as molecular blueprints
for designing new drugs.

Using MBE technology, Rice's Brown School's Gao lab induced the fungus to produce more natural compounds, including some previously unknown to the scientific community
.

The study was published in the Journal of the American Chemical Society
.

Base editing refers to the use of CRISPR-based tools to modify one rung, the base pair
, in the DNA spiral ladder.
Previously, gene modifications using base editing had to be done one at a time, making the research process more time-consuming
.
"We created a new mechanism that enables base editing to work on multiple genomic loci, hence the emergence of 'multiplexing'
," Gao said.

Gao and her team first tested the efficacy of their new base-editing platform by targeting genes encoding pigments in a fungal strain called niidulans
.
The validity and accuracy of MBE enabled genome editing is easily demonstrated in A.
Nidulans colonies are seen in the color change shown
.

"For me, the fungal genome is a treasure," Gao said, referring to the enormous medical potential
of fungal-derived compounds.
"In most cases, however, fungi 'pretend to be' themselves in the lab and do not produce the bioactive small molecules
we are looking for.
In other words, most of the genes or biosynthetic gene clusters we are interested in are "mysterious," meaning they do not exhibit their full biosynthetic potential
.

"In fungi, the genetic, epigenetic, and environmental factors that guide organisms in producing these medicinal compounds are extremely complex
.
We can observe the synergistic effect
of eliminating those factors that silence the biosynthetic machine.
”

After de-inhibition, engineered fungal strains produce more bioactive molecules, each with its own unique chemical signature
.
Of the 30 NPs produced in one trial, 5 were new compounds
that had never been reported.

"These compounds could be useful antibiotics or anticancer drugs," Gao said
.
"We are studying the biological function of these compounds, and we are working with the team at Baylor College of Medicine to study pharmacological small molecule drugs
.
"

Professor Gao's research was funded by the National Institutes of Health for five years to explore the fungal genome in search of gene clusters
that synthesize NPs.
"About 50 percent of FDA-approved clinical drugs are NPs or NP derivatives," and fungal-derived NPs "are an essential source of drugs,"
she said.
Penicillin, lovastatin and cyclosporine are some examples of
drugs derived from fungal NPs.

The National Institutes of Health (GM138207) and the Robert A.
Welch Foundation (C-1952) supported the study
.

Journal Reference:

1. Fanglong Zhao, Chunxiao Sun, Zhiwen Liu, Alan Cabrera, Mario Escobar, Shunyu Huang, Qichen Yuan, Qiuyue Nie, Kevin Lee Luo, Angela Lin, Jeffrey A.
   Vanegas, Tong Zhu, Isaac B.
   Hilton, Xue Gao.
   Multiplex Base-Editing Enables Combinatorial Epigenetic Regulation for Genome Mining of Fungal Natural Products.
   Journal of the American Chemical Society, 2022; DOI: 10.
   1021/jacs.
   2c10211