Every year, the production of traditional Chinese medicine generates millions of tons of herbal residue—and Glycyrrhiza uralensis is one of the biggest contributors. More than 6 million tons of Glycyrrhiza uralensis residue are produced annually in China alone. This residue is rich in cellulose, hemicellulose, and flavonoids, making it a promising resource for bioconversion. But there is a catch: the same flavonoids that give Glycyrrhiza uralensis its health benefits also inhibit the growth of the very microbes needed to ferment it.
Now, a team of researchers from Nanjing University of Chinese Medicine has identified a fungal strain that overcomes this obstacle—and does so in a remarkably sophisticated way.
The researchers studied Penicillium oxalicum Z2, a strain originally isolated from Glycyrrhiza uralensis rhizosphere soil. When exposed to increasing concentrations of Glycyrrhiza uralensis flavonoids—from 0.25 mg/mL up to 2.00 mg/mL—the fungus did not simply shut down. Instead, it mounted what the team describes as a "tiered response": one set of survival strategies at low concentrations, and a completely different set at high concentrations.
At low flavonoid levels (up to 1.00 mg/mL), the fungus reprogrammed its carbohydrate metabolism and activated ABC transporter pathways—essentially adjusting how it consumes carbon sources and manages what enters and leaves its cells. This metabolic fine‑tuning allowed it to maintain normal growth and enzyme production.
But at the highest concentration tested (2.00 mg/mL)—a level that would cripple most other Penicillium strains—the fungus switched to an emergency mode. It ramped up ribosome biosynthesis and oxidative phosphorylation, with 65 genes in the ribosome pathway alone turning on. Key protective genes including EF‑Tu, SecY, and FtsY—which are involved in protein translation, transport, and folding—were all significantly upregulated.
"Think of it like a plant responding to drought," explains Professor Sen Zhang, corresponding author of the study and a researcher at Nanjing University of Chinese Medicine. "At first, it adjusts its water use. But if the drought worsens, it activates a completely different set of emergency responses to survive. That is what we are seeing here—a fungus with a two‑layer defense system."
"Previous studies have shown that flavonoids from various medicinal plants can significantly inhibit fungal growth and enzyme production," says Professor Siyuan Chang. "Most research has focused on strain screening or process optimization. But we wanted to understand how a tolerant strain actually works at the molecular level—and that understanding is what will allow us to engineer even better strains in the future."
The results were striking. Even under the highest flavonoid stress, Penicillium oxalicum Z2 maintained a biomass of 4.84 g/L and produced cellulase and xylanase activities more than ten times higher than those of conventional Penicillium oxalicum strains. Its endoglucanase, β‑glucosidase, filter paper enzyme, and xylanase activities reached 74.78, 3.24, 6.99, and 562.5 U/mL, respectively.
The findings, published in Acta Microbiologica Sinica, are based on transcriptomic analysis that identified 3,945 differentially expressed genes under the highest flavonoid concentration—compared to just 818 at the lowest dose. The number of genes affected increased in a concentration‑dependent manner, revealing that the fungus's response is finely calibrated to the level of threat.
The research team is now exploring ways to apply these findings at an industrial scale. One direction involves using strong constitutive or inducible promoters to drive overexpression of the key protective genes identified in this study, creating a more robust "chassis" strain for Glycyrrhiza uralensis residue fermentation. Another avenue is to develop a staged fermentation strategy that mirrors the fungus's natural response pattern—starting with lower flavonoid concentrations to activate metabolic adjustments, then gradually increasing the stress to trigger the full protective response.
The findings, published in Acta Microbiologica Sinica , are based on transcriptomic analysis that identified 3,945 differentially expressed genes under the highest flavonoid concentration—compared to just 818 at the lowest dose. The number of genes affected increased in a concentration‑dependent manner, revealing that the fungus's response is finely calibrated to the level of threat.
ACTA MICROBIOLOGICA SINICA
Investigating the tiered responses and tolerance mechanisms of Penicillium oxalicum Z2 to licorice flavonoids based on transcriptomics
4-Jul-2026