Researchers Unveil Chromatin Landscape of Apple-Rotting Pathogen

Research conducted by a team from Jiangsu University has mapped the chromatin landscape of Penicillium expansum, a fungus responsible for severe postharvest losses in apple production. This fungus not only causes blue mold, leading to significant economic damage, but also contaminates fruit products with patulin, a mycotoxin that raises food safety concerns. Despite previous genomic studies, the mechanisms regulating gene expression in P. expansum remain largely unclear.

Understanding chromatin accessibility, which refers to the openness of DNA regions that permit transcription factor binding, is vital for comprehending gene regulation. However, research on this aspect in postharvest pathogens has been limited. To address this gap, the team published their findings in the journal Horticulture Research on September 20, 2024 (DOI: 10.1093/hr/uhae264).

Mapping Chromatin Accessibility

Utilizing assay for transposase-accessible chromatin sequencing (ATAC-seq), the researchers generated over 900 million sequence reads from P. expansum during both vegetative growth and apple infection. Their analysis revealed a notable reduction in chromatin accessibility during infection. This change was primarily observed in promoter regions, indicating that promoter-driven regulation plays a critical role in transcriptional activity.

Furthermore, motif analysis uncovered six enriched cis-regulatory elements, many of which resembled known transcription factor binding sites from Saccharomyces cerevisiae. The study identified the transcription factor PeAtf1, a basic leucine zipper (bZIP) protein, and demonstrated its significant role in growth and stress responses.

The team conducted genetic analyses, knocking out PeAtf1 to observe the effects on the fungus. The mutants exhibited severely impaired growth, reduced biomass, and delayed spore germination, although their pathogenicity on apples remained unchanged. Stress response assays highlighted PeAtf1’s dual role: while it positively regulated osmotic stress tolerance, it negatively impacted responses to oxidative, membrane, and cell wall stresses.

Implications for Food Safety and Postharvest Management

The findings suggest a complex trade-off where the absence of PeAtf1 improves the fungus’s resilience to oxidative stress through the upregulation of genes such as PeAP1, PeSOD, and PeCAT. This indicates that while growth and reproduction capabilities are compromised, the pathogen can still maintain its virulence.

“Our study sheds light on how P. expansum orchestrates growth and stress adaptation at the chromatin level,” said lead author Yiran Wang. “By combining ATAC-seq with functional genetics, we discovered that PeAtf1 plays a dual role—promoting growth but suppressing certain stress responses. This paradox helps explain why mutants maintain pathogenicity even with impaired development.”

The research establishes a molecular framework for tackling blue mold in fruit supply chains. By identifying PeAtf1 as a regulatory hub and mapping chromatin accessibility, the team has pinpointed potential genetic or chemical targets for disrupting fungal growth or enhancing fruit resistance. Insights into stress response pathways could also inform the development of biocontrol agents or optimized storage conditions aimed at weakening the pathogen’s survival strategies.

These advancements are expected to significantly improve food safety by reducing economic losses from fruit decay and fostering sustainable postharvest management practices that benefit producers, distributors, and consumers alike.

Funding for this research was provided by the National Natural Science Foundation of China (32072276; 32102030) and the China Postdoctoral Science Foundation (2023 M741440). The authors acknowledge the support of Professor Hui-Shan Guo and Sheng Wang from the State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, for providing essential technical support.

For further details, the full study is available at Horticulture Research [here](https://doi.org/10.1093/hr/uhae264).