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Mitochondrial DNA. Part B, Resources 2024The complete mitochondrial genome of I. Saar, is unveiled in this research for the first time. It covers 76,643 base pairs (bp) and exhibits a guanine-cytosine (GC)...
The complete mitochondrial genome of I. Saar, is unveiled in this research for the first time. It covers 76,643 base pairs (bp) and exhibits a guanine-cytosine (GC) content of 23%. The genome includes 14 conserved protein-coding genes, 1 DNA polymerase gene, 2 ribosomal RNA gene (RNS and RNL), 25 transfer RNA (tRNA) genes and 18 open reading frames (ORFs). Phylogenetic analysis, utilizing a mitochondrial gene dataset from 15 taxa across seven families within the Agaricales order, was conducted employing the maximum-likelihood (ML) approach. This analysis identified a close phylogenetic relationship between and (Alb. & Schwein.) Pouzar 1957, positioning both within the Squamanitaceae family.
PubMed: 38868489
DOI: 10.1080/23802359.2024.2356131 -
Scientific Reports Jun 2024Present study concerns the transformation of the agro-industrial by-products olive mill stone waste (OMSW) and walnut shell (WS) to a protein-enriched animal feedstuff...
Present study concerns the transformation of the agro-industrial by-products olive mill stone waste (OMSW) and walnut shell (WS) to a protein-enriched animal feedstuff utilizing the solid state fermentation (SSF) technique. For this purpose, various mixtures of these by-products were exploited as substrates of the SSF process which was initiated by the P. ostreatus fungus. The respective results indicated that the substrate consisted of 80% WS and 20% OMSW afforded the product with the highest increase in protein content, which accounted the 7.57% of its mass (69.35% increase). In addition, a 26.13% reduction of lignin content was observed, while the most profound effect was observed for their 1,3-1,6 β-glucans profile, which was increased by 3-folds reaching the 6.94% of substrate's mass. These results are indicative of the OMSW and WS mixtures potential to act as efficient substrate for the development of novel proteinaceous animal feed supplements using the SSF procedure. Study herein contributes to the reintegration of the agro-industrial by-products aiming to confront the problem of proteinaceous animal feed scarcity and reduce in parallel the environmental footprint of the agro-industrial processes within the context of circular economy.
Topics: Pleurotus; Juglans; Olea; Fermentation; Animal Feed; Industrial Waste; Lignin; Animals
PubMed: 38862766
DOI: 10.1038/s41598-024-64470-1 -
BMC Microbiology Jun 2024The Gastrodia elata Bl. is an orchid, and its growth demands the presence of Armillaria species. The strong competitiveness of Armillaria species has always been a...
BACKGROUND
The Gastrodia elata Bl. is an orchid, and its growth demands the presence of Armillaria species. The strong competitiveness of Armillaria species has always been a concern of major threat to other soil organisms, thus disrupting the equilibrium of soil biodiversity. Introducing other species to where G. elata was cultivated, could possibly alleviate the problems associated with the disequilibrium of soil microenvironment; however, their impacts on the soil microbial communities and the underlying mechanisms remain unclear. To reveal the changes of microbial groups associated with soil chemical properties responding to different cultivation species, the chemical property measurements coupled with the next-generation pyrosequencing analyses were applied with soil samples collected from fallow land, cultivation of G. elata and Phallus impudicus, respectively.
RESULTS
The cultivation of G. elata induced significant increases (p < 0.05) in soil pH and NO-N content compared with fallow land, whereas subsequent cultivation of P. impudicus reversed these G. elata-induced increases and was also found to significantly increase (p < 0.05) the content of soil NH-N and AP. The alpha diversities of soil microbial communities were significantly increased (p < 0.01) by cultivation of G. elata and P. impudicus as indicated with Chao1 estimator and Shannon index. The structure and composition of soil microbial communities differed responding to different cultivation species. In particular, the relative abundances of Bacillus, norank_o_Gaiellales, Mortierella and unclassified_k_Fungi were significantly increased (p < 0.05), while the abundances of potentially beneficial genera such as Acidibacter, Acidothermus, Cryptococcus, and Penicillium etc., were significantly decreased (p < 0.05) by cultivation of G. elata. It's interesting to find that cultivation of P. impudicus increased the abundances of these genera that G. elata decreased before, which contributed to the difference of composition and structure. The results of CCA and heatmap indicated that the changes of soil microbial communities had strong correlations with soil nutrients. Specifically, among 28 genera presented, 50% and 42.9% demonstrated significant correlations with soil pH and NO-N in response to cultivation of G. elata and P. impudicus.
CONCLUSIONS
Our findings suggested that the cultivation of P. impudicus might have potential benefits as result of affecting soil microorganisms coupled with changes in soil nutrient profile.
Topics: Soil Microbiology; Soil; Gastrodia; Bacteria; Microbiota; Biodiversity; Hydrogen-Ion Concentration; Nitrogen; Fungi; Armillaria; RNA, Ribosomal, 16S
PubMed: 38851673
DOI: 10.1186/s12866-024-03330-4 -
Regulation of dye-decolorizing peroxidase gene expression in grown on glycerol as the carbon source.PeerJ 2024Dye-decolorizing peroxidases (DyPs) (E.C. 1.11.1.19) are heme peroxidases that catalyze oxygen transfer reactions similarly to oxygenases. DyPs utilize hydrogen peroxide...
Dye-decolorizing peroxidases (DyPs) (E.C. 1.11.1.19) are heme peroxidases that catalyze oxygen transfer reactions similarly to oxygenases. DyPs utilize hydrogen peroxide (HO) both as an electron acceptor co-substrate and as an electron donor when oxidized to their respective radicals. The production of both DyPs and lignin-modifying enzymes (LMEs) is regulated by the carbon source, although less readily metabolizable carbon sources do improve LME production. The present study analyzed the effect of glycerol on growth, total DyP activity, and the expression of three genes (-- and -), real-time RT-qPCR, monitoring the time course of cultures supplemented with either glycerol or glucose and Acetyl Yellow G (AYG) dye. The results obtained indicate that glycerol negatively affects growth, giving a biomass production of 5.31 and 5.62 g/L with respective growth rates (micra; m) of 0.027 and 0.023 h for fermentations in the absence and presence of AYG dye. In contrast, respective biomass production levels of 7.09 and 7.20 g/L and growth rates (μ) of 0.033 and 0.047 h were observed in equivalent control fermentations conducted with glucose in the absence and presence of AYG dye. Higher DyP activity levels, 4,043 and 4,902 IU/L, were obtained for fermentations conducted on glycerol, equivalent to 2.6-fold and 3.16-fold higher than the activity observed when glucose is used as the carbon source. The differential regulation of the DyP-encoding genes in s were explored, evaluating the carbon source, the growth phase, and the influence of the dye. The global analysis of the expression patterns throughout the fermentation showed the up- and down- regulation of the three - genes evaluated. The highest induction observed for the control media was that found for the - gene, which is equivalent to an 11.1-fold increase in relative expression (log) during the stationary phase of the culture (360 h), and for the glucose/AYG media was with 8.28-fold increase after 168 h. In addition, glycerol preferentially induced the - and - genes, leading to respective 11.61 and 4.28-fold increases after 144 h. After 360 and 504 h of culture, 12.86 and 4.02-fold increases were observed in the induction levels presented by - and -, respectively, in the presence of AYG. When transcription levels were referred to those found in the control media, adding AYG led to up-regulation of the three genes throughout the fermentation. Contrary to the fermentation with glycerol, where up- and down-regulation was observed. The present study is the first report describing the effect of a less-metabolizable carbon source, such as glycerol, on the differential expression of DyP-encoding genes and their corresponding activity.
Topics: Glycerol; Pleurotus; Coloring Agents; Carbon; Gene Expression Regulation, Fungal; Peroxidases; Glucose
PubMed: 38827301
DOI: 10.7717/peerj.17467 -
Biotechnology For Biofuels and... Jun 2024Manganese peroxidases (MnPs) are, together with lignin peroxidases and versatile peroxidases, key elements of the enzymatic machineries secreted by white-rot fungi to...
Structure-function characterization of two enzymes from novel subfamilies of manganese peroxidases secreted by the lignocellulose-degrading Agaricales fungi Agrocybe pediades and Cyathus striatus.
BACKGROUND
Manganese peroxidases (MnPs) are, together with lignin peroxidases and versatile peroxidases, key elements of the enzymatic machineries secreted by white-rot fungi to degrade lignin, thus providing access to cellulose and hemicellulose in plant cell walls. A recent genomic analysis of 52 Agaricomycetes species revealed the existence of novel MnP subfamilies differing in the amino-acid residues that constitute the manganese oxidation site. Following this in silico analysis, a comprehensive structure-function study is needed to understand how these enzymes work and contribute to transform the lignin macromolecule.
RESULTS
Two MnPs belonging to the subfamilies recently classified as MnP-DGD and MnP-ESD-referred to as Ape-MnP1 and Cst-MnP1, respectively-were identified as the primary peroxidases secreted by the Agaricales species Agrocybe pediades and Cyathus striatus when growing on lignocellulosic substrates. Following heterologous expression and in vitro activation, their biochemical characterization confirmed that these enzymes are active MnPs. However, crystal structure and mutagenesis studies revealed manganese coordination spheres different from those expected after their initial classification. Specifically, a glutamine residue (Gln333) in the C-terminal tail of Ape-MnP1 was found to be involved in manganese binding, along with Asp35 and Asp177, while Cst-MnP1 counts only two amino acids (Glu36 and Asp176), instead of three, to function as a MnP. These findings led to the renaming of these subfamilies as MnP-DDQ and MnP-ED and to re-evaluate their evolutionary origin. Both enzymes were also able to directly oxidize lignin-derived phenolic compounds, as seen for other short MnPs. Importantly, size-exclusion chromatography analyses showed that both enzymes cause changes in polymeric lignin in the presence of manganese, suggesting their relevance in lignocellulose transformation.
CONCLUSIONS
Understanding the mechanisms used by basidiomycetes to degrade lignin is of particular relevance to comprehend carbon cycle in nature and to design biotechnological tools for the industrial use of plant biomass. Here, we provide the first structure-function characterization of two novel MnP subfamilies present in Agaricales mushrooms, elucidating the main residues involved in catalysis and demonstrating their ability to modify the lignin macromolecule.
PubMed: 38824538
DOI: 10.1186/s13068-024-02517-1 -
Journal of Enzyme Inhibition and... Dec 2024Tyrosinase, a pivotal enzyme in melanin synthesis, is a primary target for the development of depigmenting agents. In this work, and techniques were employed to...
Tyrosinase, a pivotal enzyme in melanin synthesis, is a primary target for the development of depigmenting agents. In this work, and techniques were employed to identify novel tyrosinase inhibitors from a set of 12 anilino-1,4-naphthoquinone derivatives. Results from the mushroom tyrosinase activity assay indicated that, among the 12 derivatives, three compounds (, , and ) demonstrated the most significant inhibitory activity against mushroom tyrosinase, surpassing the effectiveness of the kojic acid. Molecular docking revealed that all studied derivatives interacted with copper ions and amino acid residues at the enzyme active site. Molecular dynamics simulations provided insights into the stability of enzyme-inhibitor complexes, in which compounds , , and particularly displayed greater stability, atomic contacts, and structural compactness than kojic acid. Drug likeness prediction further strengthens the potential of anilino-1,4-naphthoquinones as promising candidates for the development of novel tyrosinase inhibitors for the treatment of hyperpigmentation disorders.
Topics: Monophenol Monooxygenase; Naphthoquinones; Enzyme Inhibitors; Agaricales; Structure-Activity Relationship; Molecular Structure; Dose-Response Relationship, Drug; Molecular Docking Simulation; Molecular Dynamics Simulation
PubMed: 38814149
DOI: 10.1080/14756366.2024.2357174 -
Mycology 2024The order was divided into eight suborders. However, the phylogenetic relationships among some suborders are largely unresolved, and the phylogenetic positions and...
The order was divided into eight suborders. However, the phylogenetic relationships among some suborders are largely unresolved, and the phylogenetic positions and delimitations of some taxa, such as and , remain unsettled. In this study, sequence data of 38 genomes were generated through genome skimming on an Illumina sequencing system. To anchor the systematic position of and , a phylogenetic analysis based on 555 single-copy orthologous genes from the aforementioned genomes and 126 publicly accessible genomes was performed. The results fully supported the clustering of with and within Phyllotopsidaceae, which formed a divergent monophyletic major lineage together with , , and in . The analysis also revealed that formed a unique major clade. Therefore, two new suborders, and , are proposed for the two major lineages. Analyses of 450 single-copy orthologous genes and four loci suggested that consisted of at least four clades. is subsequently subdivided into four distinct sections. Seventeen species in China, including six new species, are reported. is established to accommodate . The substrate preference of species and the transitions of the pileate ornamentations among the species within the genus are discussed.
PubMed: 38813470
DOI: 10.1080/21501203.2023.2263031 -
Scientific Reports May 2024Auricularia heimuer, the third most frequently cultivated edible mushroom species worldwide, has high medicinal value. However, a shortage of molecular marker hinders...
Auricularia heimuer, the third most frequently cultivated edible mushroom species worldwide, has high medicinal value. However, a shortage of molecular marker hinders the efficiency and accuracy of genetic breeding efforts for A. heimuer. High-throughput transcriptome sequencing data are essential for gene discovery and molecular markers development. This study aimed to clarify the distribution of SSR loci across the A. heimuer transcriptome and to develop highly informative EST-SSR markers. These tools can be used for phylogenetic analysis, functional gene mining, and molecular marker-assisted breeding of A. heimuer. This study used Illumina high-throughput sequencing technology to obtain A. heimuer transcriptome data. The results revealed 37,538 unigenes in the A. heimuer transcriptome. Of these unigenes, 24,777 (66.01%) were annotated via comparison with the COG, Pfam, and NR databases. Overall, 2510 SSRs were identified from the unigenes, including 6 types of SSRs. The most abundant type of repeats were trinucleotides (1425, 56.77%), followed by mononucleotides (391, 15.58%) and dinucleotides (456, 18.17%). Primer pairs for 102 SSR loci were randomly designed for validity confirmation and polymorphism identification; this process yielded 53 polymorphic EST-SSR markers. Finally, 13 pairs of highly polymorphic EST-SSR primers were used to analyze the genetic diversity and population structure of 52 wild A. heimuer germplasms, revealing that the 52 germplasms could be divided into three categories. These results indicated that SSR loci were abundant in types, numbers, and frequencies, providing a potential basis for germplasm resource identification, genetic diversity analysis, and molecular marker-assisted breeding of A. heimuer.
Topics: Microsatellite Repeats; Expressed Sequence Tags; Gene Expression Profiling; Transcriptome; Genetic Markers; Agaricales; High-Throughput Nucleotide Sequencing; Basidiomycota; Polymorphism, Genetic; Molecular Sequence Annotation; Phylogeny
PubMed: 38811679
DOI: 10.1038/s41598-024-63080-1 -
BMC Microbiology May 2024Cobweb disease is a fungal disease that commonly affects the cultivation and production of edible mushrooms, leading to serious yield and economic losses. It is...
BACKGROUND
Cobweb disease is a fungal disease that commonly affects the cultivation and production of edible mushrooms, leading to serious yield and economic losses. It is considered a major fungal disease in the realm of edible mushrooms. The symptoms of cobweb disease were found during the cultivation of Lyophyllum decastes. This study aimed to identify the causative pathogen of cobweb disease and evaluate effective fungicides, providing valuable insights for field control and management of L. decastes cobweb disease.
RESULTS
The causal agent of cobweb disease was isolated from samples infected and identified as Cladobotryum mycophilum based on morphological and cultural characteristics, as well as multi-locus phylogeny analysis (ITS, RPB1, RPB2, and TEF1-α). Pathogenicity tests further confirmed C. mycophilum as the responsible pathogen for this condition. Among the selected fungicides, Prochloraz-manganese chloride complex, Trifloxystrobin, tebuconazole, and Difenoconazole exhibited significant inhibitory effects on the pathogen's mycelium, with EC50 values of 0.076 µg/mL, 0.173 µg/mL, and 0.364 µg/mL, respectively. These fungicides can serve as references for future field control of cobweb disease in L. decastes.
CONCLUSION
This study is the first report of C. mycophilum as the causing agent of cobweb disease in L. decastes in China. Notably, Prochloraz-manganese chloride complex demonstrated the strongest inhibitory efficacy against C. mycophilum.
Topics: China; Fungicides, Industrial; Phylogeny; Agaricales; Ascomycota; DNA, Fungal; Triazoles; Microbial Sensitivity Tests; Strobilurins; Acetates; Dioxolanes; Imines
PubMed: 38789974
DOI: 10.1186/s12866-024-03326-0 -
Wellcome Open Research 2023We present a genome assembly from a specimen (the oyster mushroom; Basidiomycota; Agaricomycetes; Agaricales; Pleurotaceae). The genome sequence is 40.6 megabases in...
We present a genome assembly from a specimen (the oyster mushroom; Basidiomycota; Agaricomycetes; Agaricales; Pleurotaceae). The genome sequence is 40.6 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. Two mitochondrial genomes have been assembled, which are 73.1 and 9.3 kilobases in length.
PubMed: 38784713
DOI: 10.12688/wellcomeopenres.19578.1