Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes

ABSTRACT: Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Lentinula Edodes

TISSUE(S): Whole Body

SUBMITTER: xiaonan fu

LAB HEAD: WeiMing Cai

PROVIDER: PXD016536 | Pride | 2020-10-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Gene expression induced by blue light stimulation to oyster mushroom mycelia

Project description:Photoresponse mechanism of oyster muchroom mycelia was studied using a custom microarray prepared on the basis of the genome information (Pleurotus ostreatus PC15 v2.0) in JGI Genome Portal. Blue light stimulation to the mycelia caused the up-regulation and down-regulation of genes expression. Particulary, the genes coding rate-controlling enzymes in glycolysis, pentose phosphate, and sikimic acid pathways were up-regulated to accumulate shikimic acid dramatically.

2017-02-09 | GSE58522 | GEO

Potential role of lysine acetylation in brown film formation and post-ripening of Lentinula edodes mycelium

Project description:Lentinula edodes is one of the most widely cultivated edible mushrooms in the world. When cultivated in sawdust, the surface mycelium of L. edodes needs a long post-ripening stage wherein it forms a brown film (BF) by secreting and accumulating pigments. BF formation is critical for the high quality and yield of fruiting bodies. Protein lysine acetylation (KAC) is an important post-translational modification that regulates growth and development. Previous studies have shown that deacetylase levels are significantly increased during BF formation in the post-ripening stage of L. edodes. The aim of this study was to assess the role of protein acetylation during BF formation. To this end, we compared the proteomes and acetylomes of L. edodes mycelia before and after BF formation using label-free quantitative proteomics, acetylation enrichment techniques and high-resolution liquid chromatography-mass spectrometry-based quantitative proteomics. We identified 5613 acetylation sites in 1991 proteins, and quantitative information was available for 4848 of these sites in 1815 proteins. Comparative acetylome analysis showed that the modification of 699 sites increased and that of 562 sites decreased during BF formation. Bioinformatics analysis of the differentially acetylated proteins showed significant enrichment in the tricarboxylic acid (TCA) cycle and proteasome pathways. Furthermore, functional assays showed that BF formation is associated with significant changes in the activities of proteasome, citrate synthase and isocitrate dehydrogenase, indicating that the acetylation of proteasomal and TCA cycle proteins are critical for BF formation and post-ripening. Consistent with this hypothesis, the lysine deacetylase inhibitor trichostatin (TSA) delayed autophagy and BF formation in L. edodes. Taken together, KAC and autophagy play important roles in the mycelial BF formation and post-ripening stage of L. edodes.

2023-06-08 | PXD042811 | iProX

The Blue-Light Photoreceptor Sfwc-1 Gene Regulates the Phototropic Response and Fruiting-Body Development in the Homothallic Ascomycete Sordaria fimicola

Project description:Purpose: The goal of this stufy is to elucidate the transcriptional regulatory network in response to light in S. fimicola. We analyzed blue-light-induced genome-wide transcriptional responses by high-throughput RNA-seq to determine the transcriptional profiles between the wild type and Sfwc-1(∆lov) mutant. Untreated mycelia (constant darkness sample) and mycelia treated with blue light for 15 and 45 min were used to explore. Method: the S. fimiocla wild type and Sfwc-1(∆lov) mutant were grown on malt extract agar I in constant dark for 2 days. The drak grown samples were exposed to blue light for 15 and 45 min. The cDNA was synthesized from mRNA by using the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA)and then sequencing involved using Illumina NextSeq 500. The clean RNA-seq reads were then de novo assembled into a transcript sequence by using the Trinity platform and the jaccard_clip option. The quantified gene and isoform abundances (transcript abundance estimation) were obtained by using RNA-seq by expectation-maximization (RSEM) software with the default setting of Bowtie. Then differentially expressed genes (DEGs) were identified by using the EdgeR Bioconductor package in Trinity platform. The normalized RSEM-estimated abundances weighted by Trimmed Mean of M values (TMM) method counted by EdgeR was used for pairwise comparison of each of the sample pairs. Conclusion: Our study represents the transcription regulatory nextwork existing in S. fmicola, generated by RNA-seq technology. The data analysis has been providing a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and contribute the understanding of biologic functions in S. fimicola.

2019-05-06 | GSE123811 | GEO

Analyses of the brown stain on the Parthenon Centaur head

Project description:Marbles of Greek origin have been reported to form a brown stain layer, also known as patina or film. Early investigations discovered that this layer is formed by the two calcium oxalate minerals whewellite and weddellite. The origin of this oxalate film is, however, not clear, while one of the hypotheses is that it is a result of bacteria, fungi, or lichen growing on the surface of the marble. The present study characterizes the brown stain from one of the Parthenon marbles in Danish custody using LC-MS-based proteomics aiming to shed light on the possible biological origin of the staining layer. The marbles curated in Copenhagen are particularly interesting because the pieces have been kept indoors since before the onset of the industrial revolution, therefore they have experienced air pollution to a much lesser degree than the marbles still residing at the Acropolis.

2024-01-17 | PXD043505 | Pride

UV-B regulation of microRNAs in maize

Project description:Differential expression of microRNAs was studied in maize leaves after an 8-h-exposure under UV-B light. As a control, plants were kept in the greenhouse in the absence of UV-B 4-week maize plants were grown in the greenhouse in the absence of UV-B. Then, they were divided in two groups. One group was treated with UV-B lights provided once for 8 h, starting 3 h after the beginning of the light period, using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) at a UV-B intensity of 2 W m-2, UV-A: 0.65 W m-2. The bulbs were covered with cellulose acetate to exclude wavelengths <280 nm. For the second control group, plants were exposed for 8 h under the same lamps covered with polyester film (no UV-B treatment, UV-B: 0.04 W m-2, UV-A: 0.4 W m-2). Lamp output was recorded using a UV-B/UV-A radiometer (UV203 A+B radiometer, Macam Photometrics, Ltd, Livingston, UK) to insure that both the bulbs and filters provided the designated UV dosage in all treatments. Leaf samples were collected immediately after irradiation. RNA was extracted immediately after the treatments, and used for the microRNA microarray experiments.

2013-10-31 | E-GEOD-19768 | biostudies-arrayexpress

Co-condensation with photoexcited Cryptochromes facilitates MOS4-associated complex subunits 3A/3B to antagonize HY5 activities during photomorphogenesis in Arabidopsis

Project description:Cryptochromes (CRYs) is known as the key blue light receptors that promote photomorphogenesis in Arabidopsis, but to date, the underlying mechanisms are still not fully understood. Through interrogating the CRY2 interactome, we identified MOS4-ASSOCIATED COMPLEX subunits 3A and 3B (MAC3A and MAC3B) as blue light-independent CRY2 interacting partners. MAC3A/B proteins could be assembled into liquid nuclear condensates of CRYs in a blue light-dependent manner. Hypocotyl elongation is markedly repressed in mac3ab double knock-out mutants under various light conditions, which uncovers a previously unknown role of MAC3A/B as negative regulators in plant photomorphogenesis. Our results also uncover the noncanonical activities of MAC3A as the DNA-binding proteins that regulate transcription. Genome-wide mapping of MAC3A-binding sites reveals that blue light facilitates the binding of MAC3A to its targets, which is weakened in cry1cry2 mutants, suggesting that CRYs may enhance MAC3A activities in blue light to negatively influence photomorphogenesis. Interestingly, we observe that the genomic binding sites of MAC3A and HY5 are largely overlapped, and physical interactions between MAC3A and HY5 are detected as well. In addition, the in vitro DNA-binding assay shows that both proteins compete for the same DNA probe. These results indicate that MAC3A may antagonize the function of HY5 by competing for the common binding sites across the genome. Taken together, we propose that cryptochromes may fine-tune Arabidopsis photomorphogenesis by balancing the positive and negative effects on HY5 activities.

2023-08-21 | GSE220945 | GEO

Project description:Transcriptomic analysis of brown film formation in Lentinula edodes under sawdust fermentation

| PRJNA705065 | ENA

Transcriptome of ansamitocin P-3 producer Actinosynnema pretiosum ATCC 31280

Project description:In submerged cultivation of filamentous microbes, including actinomycetes, complex morphology is one of the critical process features for secondary metabolites production. Ansamitocin P-3 (AP-3), an antitumor agent, is a secondary metabolite produced by Actinosynnema pretiosum ATCC 31280. An excessive mycelial fragmentation of A. pretiosum ATCC 31280 was observed during the early stage of fermentation. In order to identify genes involved in the early mycelial fragmentation, the total RNAs of mycelia collected at 15, 18, and 24 h were extracted and subjected to transcriptome sequencing using RNA-seq technology.Through comparative transcriptomic analysis, a subtilisin-like serine peptidase encoded gene APASM_4178 was identified to be responsible for the mycelial fragmentation. Mutant WYT-5 with the APASM_4178 deletion showed increased biomass and improved AP-3 yield by 43.65%.

2020-05-25 | GSE151010 | GEO

Using comparative proteomics reveal the blue body color formation of Rhopilema esculenta

Project description:In this study, we collected the inner epidermis of umbrella from blue and brown R. esculenta for comparative metabolomic and proteomic analyses to reveal the blue body color formation. In summary, these results explored our knowledge of the blue body color formation of R. esculenta and provided valuable guidance to future studies of color breeding and blue pigment application in jellyfish.

2022-12-30 | PXD039114 | iProX

Phosphoproteome of Magnaporthe oryzae

Project description:Rice blast caused by Magnaporthe oryzae is the most devastating disease of cultivated rice. Several protein kinase cascades have been known to be essential to pathogenesis or important for response to stress, mycelial growth and conidiation in M. oryzae. However, phosphoproteins and their phosphorylation sites (p-sites) in this important fungal pathogen remain largely to be identified. In this study, 8087 phosphopeptides corresponding to 9825 p-sites from 1147 phosphoproteins were identified in mycelia of M. oryzae under a false discovery rate of < 0.55% at the peptide level. Notably, 33 previously reported pathogenesis-related proteins were included in the phosphoproteins at the mascot delta score 10. Further analyses of 581 motif-containing phosphoproteins that met more stringent criteria revealed that the phosphoproteins shared 19 distinct phosphorylation motifs, including the motif RxxpSP that was newly identified in this study but is widely distributed in diverse organisms. These phosphoproteins were mapped into 81 biological pathways. A total of 82 acidic motif-containing phosphoproteins were identified. Surprisingly, none of them except one were mapped to any of the metabolic pathways. Furthermore, a prediction disclosed a total of 174 kinase-substrate specific interactions in mycelia of M. oryzae. This study also detected phosphorylation of the tyrosine phosphatase Pmp1 and 7 other proteins upstream of Pmk1, but not Pmk1 and its downstream transcription factors. These results prompted a necessary revision of Pmk1 MAPK cascade, in which dephosphorylation of Pmk1 by Pmp1 in mycelia may block the activation of downstream targets.

2017-07-17 | PXD002364 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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