Comparative transcriptome and WGCNA reveal key genes involved in lignocellulose degradation in Sarcomyxa edulis.

The developmental transcriptomes of Sarcomyxa edulis were assessed to explore the molecular mechanisms underlying lignocellulose degradation. Six stages were analyzed, spanning the entire developmental process: growth of mycelium until occupying half the bag (B1), mycelium under low-temperature stimulation after occupying the entire bag (B2), appearance of mycelium in primordia (B3), primordia (B4), mycelium at the harvest stage (B5), and mature fruiting body (B6). Samples from all six developmental stages were used for transcriptome sequencing, with three biological replicates for all experiments. A co-expression network of weighted genes associated with extracellular enzyme physiological traits was constructed using weighted gene co-expression network analysis (WGCNA). We obtained 19 gene co-expression modules significantly associated with lignocellulose degradation. In addition, 12 key genes and 8 kinds of TF families involved in lignocellulose degradation pathways were discovered from the four modules that exhibited the highest correlation with the target traits. These results provide new insights that advance our understanding of the molecular genetic mechanisms of lignocellulose degradation in S. edulis to facilitate its utilization by the edible mushroom industry.

Systematic analysis of changes across different developmental stages of the mushroom Sarcomyxa edulis.

Sarcomyxa edulis is a widely harvested mushroom of Northeastern Asia. Its development can be divided into six stages: growth of mycelium until occupying half the bag (B1), mycelium under low-temperature stimulation after occupying the entire bag (B2), appearance of mycelium in primordia (B3), primordia (B4), mycelium at the harvest stage (B5), and mature fruiting body (B6). Differentially expressed gene (DEG) analysis and weighted gene coexpression network analysis (WGCNA) are important bioinformatic methods for screening key genes. To explore the growth and development mechanisms of the mushroom S. edulis and clarify its genetic background, DEG and WGCNA analyses were combined to screen key genes at different developmental stages. From A1 to A6, respectively, 459, 97, 885, 169, 277, and 712 key genes were identified. Then the Gene Ontology (GO) terms and KEGG pathways of key genes were analyzed, and GO and KEGG analyses were performed on all genes across different periods using GSEA. In summary, the genes in A1 were mainly involved in amino sugar and nucleotide sugar metabolism, structural molecule activity, and oxidative phosphorylation. At the A2 stage, genes were mainly involved in peptidase activity, peroxidase activity, oxidoreductase activity, antioxidant activity, biosynthesis of secondary metabolites, and glycolysis and gluconeogenesis. A3 genes were involved in gene expression, RNA metabolism, spliceosome, RNA transport, and ribosome biogenesis. A4 genes were mainly involved in the biosynthesis of secondary metabolites, proteasome complex, cellular protein complex assembly, actin filament-based processes, oxidative phosphorylation, and carbon metabolism. The A5 stage genes were involved in the carbohydrate metabolic process, polysaccharide metabolic process, and the biosynthesis of secondary metabolites, leucine, isoleucine, and ABC transporters. Finally, A6 genes were mainly involved in the cell cycle, meiosis of yeast, MAPK signaling pathway, cellular response to DNA damage stimulus, DNA metabolic process, DNA replication, and DNA repair. The combination of multiple analyses provides us with an in-depth understanding of the network that regulates mushroom development.

Novel hypoglycemic compounds from wild mushroom Paxillus involutus.

Wild mushrooms are an important source of secondary metabolites possessing a broad range of biological activities. In this study, eight new compounds, named furanopaxin A-F (1-6), deoxybisinvolutone (7), and coumarinvol (8) along with two known compounds were isolated from fruiting bodies of the wild mushroom Paxillus involutus (Batsch) Fr. Their structures were established based on HR-ESI-MS and 1D and 2D NMR spectroscopic data. The results of hypoglycemic assays indicated that compounds 5-8 possessed significant α-glucosidase inhibitory activities, with IC50 values ranging from 14.65 ± 1.68 to 47.55 ± 1.47 µM, and each compound could enhance glucose consumption in insulin-resistance HepG2 cells. Further analysis by molecular docking implied that compounds 5-8 could interact with the amino acid residues of α-glucosidase, supporting the hypoglycemic activity of the compounds.

Transcriptomic profiling sheds light on the blue-light and red-light response of oyster mushroom (Pleurotus ostreatus).

Blue light is an important environmental factor that induces mushroom primordium differentiation and fruiting body development. Although blue-light treatment has been applied for the production of oyster mushroom (Pleurotus ostreatus), the blue-light response mechanisms of P. ostreatus still remain unclear. In the present study, we exposed the primordium of P. ostreatus to blue-light, red-light, and dark conditions for 7 days. Subsequently, comparative transcriptomics analysis of the stipe, pileus, and gill under the three light conditions was performed to reveal the gene expression response mechanism of P. ostreatus to blue light and red light. The results showed that blue light enhanced the growth and development of all the three organs of P. ostreatus, especially the pileus. In contrast, red light slightly (non-significantly) inhibited pileus growth. When compared with red-light and dark treatments, blue-light treatment significantly upregulated gene expression involved in glycolysis/gluconeogenesis, the pentose phosphate pathway and the peroxisome in the pileus, but not in the gill or stipe. Most of the glycolysis and pentose phosphate pathway genes were upregulated in the pileus by blue light. When compared with dark treatment, red-light treatment downregulated the expression of many respiration metabolism genes in the pileus. These results revealed that blue light enhanced the activation of glycolysis and the pentose phosphate pathway, whereas red light weakened glycolysis and pentose phosphate pathway activation. The conclusion can be drawn that blue light improved P. ostreatus fruiting body (particularly, the pileus) growth rate via enhancement of glycolysis and the pentose phosphate pathway.

Optimization of agro-residues as substrates for Pleurotus pulmonarius production.

The "replacing wood by grass" project can partially resolve the conflict between mushroom production and balancing the ecosystem, while promoting agricultural economic sustainability. Pleurotus pulmonarius is an economically important edible and medicinal mushroom, which is traditionally produced using a substrate consisting of sawdust and cottonseed hulls, supplemented with wheat bran. A simplex lattice design was applied to systemically optimize the cultivation of P. pulmonarius using agro-residues as the main substrate to replace sawdust and cottonseed hulls. The effects of differing amounts of wheat straw, corn straw, and soybean straw on the variables of yield, mycelial growth rate, stipe length, pileus length, pileus width, and time to harvest were demonstrated. Results indicated that a mix of wheat straw, corn straw, and soybean straw may have significantly positive effects on each of these variables. The high yield comprehensive formula was then optimized to include 40.4% wheat straw, 20.3% corn straw, 18.3% soybean straw, combined with 20.0% wheat bran, and 1.0% light CaCO3 (C/N = 42.50). The biological efficiency was 15.2% greater than that of the control. Most encouraging was the indication that the high yield comprehensive formula may shorten the time to reach the reproductive stage by 6 days, compared with the control. Based on the results of this study, agro-residues may be used as a suitable substitution for sawdust and cottonseed hulls as the main cultivation substrates of P. pulmonarius. These results provide a theoretical basis for the "replacing wood by grass" project on edible mushroom cultivation.

Bhargavaea changchunensis sp. nov. isolated from soil in China.

A Gram-staining-positive, aerobic, rod-shaped (201802YP6T) bacteria was isolated from soil, Northeast of China. Growth occurred at 10-40 °C (optimum 25-30 °C), at pH 6.0-8.0 (optimum 7.0) and at 0-2% NaCl. Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbors of strain 201802YP6T were identified as Bhargavaea cecembensis DSE10T (99.52%), Bhargavaea beijingensis ge10T (99.45%), Bhargavaea indica KJW98T (99.45%), Bhargavaea ullalensis ZMA19T (98.81%), and Bhargavaea ginsengi ge14T (98.76%). Levels of similarity among strain 201802YP6T and other Bhargavaea species were lower than 98.76%. GyrB amino acid sequence-based analysis supported the phylogenetic position and also distinguished strain 201802YP6T from the other species of the genus Bhargavaea. DNA-DNA hybridization values between strain 201802YP6T and B. cecembensis, B. beijingensis, B. indica, B. ullalensis, B. ginsengi were 43.5%, 43%, 32.5%, 30.5% and 20.4%, respectively. The DNA G + C content of strain 201802YP6T was 51.23 mol%. The average nucleotide identity (ANI) of the draft genome was 87.04% to B. cecembensis DSE10T. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipids, phosphatidylethanolamine, and phosphatidyllipid. The predominant menaquinone was MK-8. The major fatty acids were iso-C15:0 (39.91%), anteiso-C15:0 (28.86%), anteiso-C17:0 (6.30%) and C16:0 (6.13%). On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain 201802YP6T represents a novel species of the genus Bhargavaea, for which the name Bhargavaea changchunensis sp. nov. is proposed. The type strain is 201802YP6T (= CGMCC 1.13508T = KCTC 33975T).

Corynebacterium defluvii sp. nov., isolated from Sewage.

A Gram-positive, aerobic, non-motile, rod-shapeds, catalase-positive, and oxidase-negative strain, designated Y49T, was isolated from sewage collected from Jilin Agricultural University, China. It grew at 20-40°C (optimum at 30°C), at pH 6.0-8.0 (optimum at 7.0) and at 0-1.0% sodium chloride (optimum at 0%). The major isoprenoid quinone was menaquinone-8 (MK-8) and the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, four unidentified lipids, and two unidentified aminolipids. The peptidoglycan was meso-diaminopimelic acid. The cell-wall sugars were galactose, arabinose, and glucose. The fatty acids were C9:0, C16:0, C16:1 ω9c, C17:1 ω9c, C18:3 ω6c (6,9,12), C18:1 ω9c, and C18:0. The DNA G+C content was 51.4 mol%. Based on the 16S rRNA gene sequence analysis, the nearest phylogenetic neighbors of strain Y49T were Corynebacterium efficiens DSM 44549T (97.5%), Corynebacterium callunae DSM 20147T (97.2%), Corynebacterium deserti GIMN 1.010T (96.8%), Corynebacterium glutamicum ATCC 13032T (96.4%), and other species belonging to this genus (92.3-95.4%). The DNA-DNA relatedness value between strain Y49T and C. efficiens DSM 44549T, C. callunae DSM 20147T, C. deserti GIMN1.010T, and C. glutamicum ATCC 13032T was 25.5±2.0%, 21.1±1.0%, 16.5±0.5%, and 13.5±0.9%, respectively. Based on the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain Y49T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium defluvii sp nov. is proposed. The type strain is Y49T (= KCTC 39731T =CGMCC 1.15506T).