NmeA, a novel efflux transporter specific for nucleobases and nucleosides, contributes to metal resistance in Aspergillus nidulans

Comparative genomics of fungal mutants provides a systemic view of extreme cadmium tolerance in eukaryotic microbes

Whether eukaryotic organisms can evolve for higher heavy metal resistance in laboratory conditions remains unknown. In this study, we challenged a macrofungi, Pleurotus ostreatus, in a designed microbial evolution and growth arena (MEGA)-plate with an extreme Cd gradient. Within months, the wild-type strain developed 10 mutants, exhibiting a maximum three-fold increase in Cd tolerance and slower growth rates. Genomic sequencing and re-sequencing of the wild-type and ten mutant strains generated about 51 GB data, allowing a comprehensive comparative genomics analysis. As a result, a total of 2512 common single nucleotide polymorphisms, 70 inserts and deletes, 39 copy number variations and 21 structural variations were found in the 10 mutants. The mutant genes were primarily involved in substrate transport. In combination with transcriptome analysis, we discovered that the ten mutants had a distinct Cd-resistant mechanism compared to the wild-type strain. Genes involved in oxidation-reduction, ion transmembrane transport, and metal compartment/efflux are primarily responsible for the extreme Cd tolerance in the P. ostreatus mutants. Our findings contribute to the understanding of eukaryotic Cd resistance at the genome level and establish a foundation for developing bioremediation tools utilizing highly tolerant macrofungi.

Profile of Membrane Cargo Trafficking Proteins and Transporters Expressed under N Source Derepressing Conditions in Aspergillus nidulans

Solute and ion transporters are proteins essential for cell nutrition, detoxification, signaling, homeostasis and drug resistance. Being polytopic transmembrane proteins, they are co-translationally inserted and folded into the endoplasmic reticulum (ER) of eukaryotic cells and subsequently sorted to their final membrane destination via vesicular secretion. During their trafficking and in response to physiological/stress signals or prolonged activity, transporters undergo multiple quality control processes and regulated turnover. Consequently, transporters interact dynamically and transiently with multiple proteins. To further dissect the trafficking and turnover mechanisms underlying transporter subcellular biology, we herein describe a novel mass spectrometry-based proteomic protocol adapted to conditions allowing for maximal identification of proteins related to N source uptake in A. nidulans. Our analysis led to identification of 5690 proteins, which to our knowledge constitutes the largest protein dataset identified by omics-based approaches in Aspergilli. Importantly, we detected possibly all major proteins involved in basic cellular functions, giving particular emphasis to factors essential for membrane cargo trafficking and turnover. Our protocol is easily reproducible and highly efficient for unearthing the full A. nidulans proteome. The protein list delivered herein will form the basis for downstream systematic approaches and identification of protein–protein interactions in living fungal cells.

Mycoextraction: Rapid Cadmium Removal by Macrofungi-Based Technology from Alkaline Soil

Fungi are promising materials for soil metal bioextraction and thus biomining. Here, a macrofungi-based system was designed for rapid cadmium (Cd) removal from alkaline soil. The system realized directed and rapid fruiting body development for subsequent biomass harvest. The Cd removal efficiency of the system was tested through a pot culture experiment. It was found that aging of the added Cd occurred rapidly in the alkaline soil upon application. During mushroom growth, the soil solution remained considerably alkaline, though a significant reduction in soil pH was observed in both Cd treatments. Cd and dissolved organic carbon (DOC) in soil solution generally increased over time and a significant correlation between them was detected in both Cd treatments, suggesting that the mushroom‒substratum system has an outstanding ability to mobilize Cd in an alkaline environment. Meanwhile, the growth of the mushrooms was not affected relative to the control. The estimated Cd removal efficiency of the system was up to 12.3% yearly thanks to the rapid growth of the mushroom and Cd enrichment in the removable substratum. Transcriptomic analysis showed that gene expression of the fruiting body presented considerable differences between the Cd treatments and control. Annotation of the differentially expressed genes (DEGs) indicated that cell wall sorption, intracellular binding, and vacuole storage may account for the cellular Cd accumulation. In conclusion, the macrofungi-based technology designed in this study has the potential to become a standalone biotechnology with practical value in soil heavy metal removal, and continuous optimization may make the system useful for biomining.