Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft Genome Sequence of the White-Rot Fungus Phanerochaete sordida YK-624.

ABSTRACT: Here, we report the draft genome sequence of the white-rot basidiomycete fungus Phanerochaete sordida YK-624 (ATCC 90872), which was isolated in Yakushima, Kagoshima, Japan. The genome of this strain was found to be 41.2 Mbp, with a G+C content of 58.7%, and to comprise 17,108 predicted protein-coding sequences.

SUBMITTER: Mori T

PROVIDER: S-EPMC8530024 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Draft Genome Sequence of the White-Rot Fungus Phanerochaete sordida YK-624.

Mori Toshio T Dohra Hideo H Suzuki Tomohiro T Kawagishi Hirokazu H Hirai Hirofumi H

Microbiology resource announcements 20211021 42

Here, we report the draft genome sequence of the white-rot basidiomycete fungus Phanerochaete sordida YK-624 (ATCC 90872), which was isolated in Yakushima, Kagoshima, Japan. The genome of this strain was found to be 41.2 Mbp, with a G+C content of 58.7%, and to comprise 17,108 predicted protein-coding sequences. ...[more]

PMID: 34672697

Similar Datasets

The complete mitochondrial genome of the white-rot fungus Phanerochaete sordida YK-624.

Project description:The white-rot fungus Phanerochaete sordida (Karsten) Eriksson and Ryvarden 1978 is known for its excellent ligninolytic activity and capability to degrade various recalcitrant organic pollutants. In this study, we determined the complete mitochondrial genome sequence of P. sordida YK-624. The mitochondrial genome is 129,567 bp in length with a GC content of 28.9%, and contains two ribosomal RNA genes, 26 transfer RNA genes, and 50 open reading frames, including 14 conserved proteins. Phylogenetic analysis based on the mitochondrial genome confirmed that P. sordida belongs to the family Phanerochaetaceae in the order Polyporales, and showed the general phylogenetic relationships.

| S-EPMC9543125 | biostudies-literature

RNA-sequencing analysis of bisphenol A biodegradation by white-rot fungus Phanerochaete sordida YK-624.

Project description:Bisphenol A (BPA) is a representative example of an endocrine-disrupting chemical. It is one of the most produced chemical substances in the world, but it causes harmful effects in organisms, such that the effective degradation of BPA is critical. The white-rot fungus Phanerochaete sordida YK-624 has been shown to effectively degrade BPA under ligninolytic and non-ligninolytic conditions. However, it is still unclear what kinds of enzymes are involved in BPA degradation. To explore the mechanism of BPA degradation, the present study analysed the functional genes of P. sordida YK-624 using RNA-sequencing (RNA-Seq). Oxidation-reduction process and metabolic pathway were enriched under ligninolytic and non-ligninolytic conditions by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. It is suggested that BPA might be used as a carbon source by P. sordida YK-624. Lignin peroxidase and cytochrome P450 were detected in upregulated differentially expressed genes (DEGs). The lignin-degrading enzyme lignin peroxidase and the intracellular cytochrome P450 system were involved in BPA degradation by P. sordida YK-624, respectively. Furthermore, quantitative real-time PCR (qPCR) was used to validate the reliability of the RNA-Seq results.Supplementary informationThe online version contains supplementary material available at 10.1007/s13205-022-03298-w.

| S-EPMC9375798 | biostudies-literature

Ergosterol and Its Metabolites Induce Ligninolytic Activity in the Lignin-Degrading Fungus Phanerochaete sordida YK-624.

Project description:White-rot fungi are the most important group of lignin biodegraders. Phanerochaete sordida YK-624 has higher ligninolytic activity than that of model white-rot fungi. However, the underlying mechanism responsible for lignin degradation by white-rot fungi remains unknown, and the induced compounds isolated from white-rot fungi for lignin degradation have never been studied. In the present study, we tried to screen ligninolytic-inducing compounds produced by P. sordida YK-624. After large-scale incubation of P. sordida YK-624, the culture and mycelium were separated by filtration. After the separation and purification, purified compounds were analyzed by high-resolution electrospray ionization mass spectrometry and nuclear magnetic resonance. The sterilized unbleached hardwood kraft pulp was used for the initial evaluation of ligninolytic activity. Ergosterol was isolated and identified and it induced the lignin-degrading activity of this fungus. Moreover, we investigated ergosterol metabolites from P. sordida YK-624, and the ergosterol metabolites ergosta-4,7,22-triene-3,6-dione and ergosta-4,6,8(14),22-tetraen-3-one were identified and then chemically synthesized. These compounds significantly improved the lignin-degrading activity of the fungus. This is the first report on the ligninolytic-inducing compounds produced by white-rot fungi.

| S-EPMC10532932 | biostudies-literature

Phanerochaete sordida strain:YK-624

Project description:Phanerochaete sordida YK-624 genome

| PRJDB11801 | ENA

Phanerochaete sordida strain:YK-624

Project description:Phanerochaete sordidad RNAseq with TBBPA

| PRJDB16601 | ENA

Phanerochaete sordida strain:YK-624

Project description:Phanerochaete sordida strain:YK-624 Transcriptome or Gene expression

| PRJNA690204 | ENA

Draft Genome Sequence of the White-Rot Fungus Schizophyllum Commune IUM1114-SS01.

Project description:The monokaryotic strain, Schizophyllum commune strain IUM1114-SS01, was generated from a basidiospore of dikaryotic parental strain IUM1114. It even showed the decolorizing activities for several textile dyes much better than its parental strain. Based on the results of a single-molecule real-time sequencing technology, we present the draft genome of S. commune IUM1114-SS01, comprising 41.1 Mb with GC contents of the genome were 57.44%. Among 13,380 protein-coding genes, 534 genes are carbon hydrate-active enzyme coding genes.

| S-EPMC7832597 | biostudies-literature

Target Of Rapamycin pathway in the white-rot fungus Phanerochaete chrysosporium.

Project description:The Target Of Rapamycin (TOR) signaling pathway is known to regulate growth in response to nutrient availability and stress in eukaryotic cells. In the present study, we have investigated the TOR pathway in the white-rot fungus Phanerochaete chrysosporium. Inhibition of TOR activity by rapamycin affects conidia germination and hyphal growth highlighting the conserved mechanism of susceptibility to rapamycin. Interestingly, the secreted protein content is also affected by the rapamycin treatment. Finally, homologs of the components of TOR pathway can be identified in P. chrysosporium. Altogether, those results indicate that the TOR pathway of P. chrysosporium plays a central role in this fungus.

| S-EPMC7032718 | biostudies-literature

P450 monooxygenases (P450ome) of the model white rot fungus Phanerochaete chrysosporium.

Project description:Phanerochaete chrysosporium, the model white rot fungus, has been the focus of research for the past about four decades for understanding the mechanisms and processes of biodegradation of the natural aromatic polymer lignin and a broad range of environmental toxic chemicals. The ability to degrade this vast array of xenobiotic compounds was originally attributed to its lignin-degrading enzyme system, mainly the extracellular peroxidases. However, subsequent physiological, biochemical, and/or genetic studies by us and others identified the involvement of a peroxidase-independent oxidoreductase system, the cytochrome P450 monooxygenase system. The whole genome sequence revealed an extraordinarily large P450 contingent (P450ome) with an estimated 149 P450s in this organism. This review focuses on the current status of understanding on the P450 monooxygenase system of P. chrysosproium in terms of pre-genomic and post-genomic identification, structural and evolutionary analysis, transcriptional regulation, redox partners, and functional characterization for its biodegradative potential. Future research on this catalytically diverse oxidoreductase enzyme system and its major role as a newly emerged player in xenobiotic metabolism/degradation is discussed.

| S-EPMC3567848 | biostudies-literature

Glutathione S-transferases from the white-rot fungus, Phanerochaete chrysosporium.

Project description:A glutathione S-transferase (GST) was purified to homogeneity from the white-rot fungus, Phanerochaete chrysosporium, by affinity chromatography on glutathione-agarose followed by Mono-Q ion-exchange FPLC. This protein immunoblotted with antisera to rat Theta class GST 5-5 and also showed N-terminal sequence similarity to the Theta class, including the presence of a conserved serine residue that has been specifically implicated in catalysis in this class [Wilce, Board, Feil and Parker (1995) EMBO J. 14, 2133-2143] and other residues conserved in plant sequences. Catalytic activity was found to be highly labile in the purified protein, although preliminary evidence for activity (approx. 120 m-units/mg) with 1,2-epoxy-3-(p-nitrophenoxy)propane was obtained in some preparations. The enzyme seems to be a dimer with a subunit molecular mass of 25 kDa by SDS/PAGE. The native molecular masses estimated by non-denaturing electrophoresis and by Superose-12 gel filtration were 58 and 45 kDa respectively. A second protein purified in this study also gave low level of activity with 1,2-epoxy-3-(p-nitrophenoxy)propane and had a subunit molecular mass of 28 kDa (native size 62-63 kDa), but did not immunoblot with any GST class and seemed to be N-terminally blocked.

| S-EPMC1218423 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data