Ultrasonic-Assisted Extraction of Dictyophora rubrovolvata Volva Proteins: Process Optimization, Structural Characterization, Intermolecular Forces, and Functional Properties.

Dictyophora rubrovolvata volva, an agricultural by-product, is often directly discarded resulting in environmental pollution and waste of the proteins' resources. In this study, D. rubrovolvata volva proteins (DRVPs) were recovered using the ultrasound-assisted extraction (UAE) method. Based on one-way tests, orthogonal tests were conducted to identify the effects of the material-liquid ratio, pH, extraction time, and ultrasonic power on the extraction rate of DRVPs. Moreover, the impact of UAE on the physicochemical properties, structure characteristics, intermolecular forces, and functional attributes of DRVPs were also examined. The maximum protein extraction rate was achieved at 43.34% under the best extraction conditions of UAE (1:20 g/mL, pH 11, 25 min, and 550 W). UAE significantly altered proteins' morphology and molecular size compared to the conventional alkaline method. Furthermore, while UAE did not affect the primary structure, it dramatically changed the secondary and tertiary structure of DRVPs. Approximately 13.42% of the compact secondary structures (α-helices and ß-sheets) underwent a transition to looser structures (ß-turns and random coils), resulting in the exposure of hydrophobic groups previously concealed within the molecule's core. In addition, the driving forces maintaining and stabilizing the sonicated protein aggregates mainly involved hydrophobic forces, disulfide bonding, and hydrogen bonding interactions. Under specific pH and temperature conditions, the water holding capacity, oil holding capacity, foaming capacity and stability, emulsion activity, and stability of UAE increased significantly from 2.01 g/g to 2.52 g/g, 3.90 g/g to 5.53 g/g, 92.56% to 111.90%, 58.97% to 89.36%, 13.85% to 15.37%, and 100.22% to 136.53%, respectively, compared to conventional alkali extraction. The findings contributed to a new approach for the high-value utilization of agricultural waste from D. rubrovolvata.

Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis.

Dictyophora rubrovolvata, a rare edible mushroom with both nutritional and medicinal values, was regarded as the "queen of the mushroom" for its attractive appearance. Dictyophora rubrovolvata has been widely cultivated in China in recent years, and many researchers were focusing on its nutrition, culture condition, and artificial cultivation. Due to a lack of genomic information, research on bioactive substances, cross breeding, lignocellulose degradation, and molecular biology is limited. In this study, we report a chromosome-level reference genome of D. rubrovolvata using the PacBio single-molecule real-time-sequencing technique and high-throughput chromosome conformation capture (Hi-C) technologies. A total of 1.83 Gb circular consensus sequencing reads representing ∼983.34 coverage of the D. rubrovolvata genome were generated. The final genome was assembled into 136 contigs with a total length of 32.89 Mb. The scaffold and contig N50 length were 2.71 and 2.48 Mb, respectively. After chromosome-level scaffolding, 11 chromosomes with a total length of 28.24 Mb were constructed. Genome annotation further revealed that 9.86% of the genome was composed of repetitive sequences, and a total of 508 noncoding RNA (rRNA: 329, tRNA: 150, ncRNA: 29) were annotated. In addition, 9,725 protein-coding genes were predicted, among which 8,830 (90.79%) genes were predicted using homology or RNA-seq. Benchmarking Universal Single-Copy Orthologs results further revealed that there were 80.34% complete single-copy fungal orthologs. In this study, a total of 360 genes were annotated as belonging to the carbohydrate-active enzymes family. Further analysis also predicted 425 cytochromes P450 genes, which can be classified into 41 families. This highly accurate, chromosome-level reference genome of D. rubrovolvata will provide essential genomic information for understanding the molecular mechanism in its fruiting body formation during morphological development and facilitate the exploitation of medicinal compounds produced by this mushroom.

Ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry based untargeted metabolomics to reveal the characteristics of Dictyophora rubrovolvata from different drying methods.

Dictyophora rubrovolvata is a highly valuable and economically important edible fungus whose nutrition and flavor components may vary based on drying methods. Herein, an untargeted ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) metabolomics method combined with multivariate analysis was first performed to characterize the metabolomics profiles of D. rubrovolvata upon different drying treatments, viz., coal burning drying (CD), electrothermal hot air drying (ED), and freeze drying (FD). The results indicated that 69 differential metabolites were identified, vastly involving lipids, amino acids, nucleotides, organic acids, carbohydrates, and their derivatives, of which 13 compounds were confirmed as biomarkers in response to diverse drying treatments. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis illustrated that differential metabolites were significantly assigned to 59, 55, and 60 pathways of CD vs. ED, CD vs. FD, and FD vs. ED groups, respectively, with 9 of the top 20 KEGG pathways shared. Specifically, most of lipids, such as fatty acyls, glycerophospholipids and sphingolipids, achieved the highest levels in D. rubrovolvata after the CD treatment. ED method substantially enhanced the contents of sterol lipids, nucleotides, organic acids and carbohydrates, while the levels of amino acids, prenol lipids and glycerolipids were elevated dramatically against the FD treatment. Collectively, this study shed light on metabolomic profiles and proposed biomarkers of D. rubrovolvata subjected to multiple drying techniques, which may contribute to quality control and drying efficiency in edible fungi production.