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LC-MS/MS secretome analysis of Pleurotus ostreatus PC9 (wild type) and two transformants

ABSTRACT: The white rot fungi Pleurotus ostreatus was studied for its potential as a biological pretreatment agent, i.e- its potential for decomposing lignocellulosic biomass. P. ostreatus PC9 was manipulate to either overexpress or eliminate (by gene replacement) the transcriptional regulator CRE1, known to act as a repressor in the process of carbon catabolite repression. The parental PC9 and the two transformants were grown on microcrystalline cellulose and wheat straw (3 replicates each) and the content of the resulted secretomes was analyzed by LC-MS/MS. An extensive range of carbohydrate active enzymes (CAZymes) were affected by the modification of cre1 expression levels. The three fungi revealed also differentiation towards the carbon source used in the growth media.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Pleurotus Ostreatus Pc9

SUBMITTER: Shahar Yoav

LAB HEAD: Prof. Yitzhak Hadar

PROVIDER: PXD010100 | Pride | 2018-08-06

REPOSITORIES: Pride

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Project description:Investigation of whole genome gene expression level changes in response to different light conditions of the T. reesei QM9414 deletion strains delta-blr1, delta-blr2 and delta env1 cultivated on 1% microcrystalline cellulose. Perception and proper interpretation of environmental signals is crucial for survival in any natural habitat. Although the biotechnological workhorse Trichoderma reesei (Hypocrea jecorina) is predominantly known for its capability of efficient plant cell wall degradation, recent studies show that it has not lost its evolutionary heritage. Transmission of nutrient signals via the heterotrimeric G protein pathway has been shown to be influenced by light. We show that this interconnection is mainly established by the light regulatory protein ENV1 and the phosducin-like protein PhLP1 via mutual transcriptional regulation and influence on GNB1 (G protein beta subunit) function. ENV1 thereby exerts a more severe effect on gene transcription than BLR1 or BLR2. Lack of either one of the photoreceptors or PhLP1, GNB1 or GNG1 leads to a partial shutdown of processes upregulated in light, indicating that heterotrimeric G protein signalling exerts its major function in light and is a target of the light response machinery. Consequently, signals transmitted via the G protein pathway are of different relevance in light and darkness. Investigation of regulation of glycoside hydrolases as one of the major output pathways of this mechanism revealed that 79% of all genes belonging to this group, representing all GH-families available in T. reesei, are potentially responsive to light. We conclude that ENV1 is a key factor in connecting nutrient signalling with light response and establishes a signalling output pathway independent of BLR1 and BLR2. We used two biological replicates of three T. reesei strains (delta-blr1, delta-blr2 and delta-env1), cultivated in constant light (LL, 1800 lux) or constant darkness (DD) on microcrystalline cellulose. The strains used in this study were cultivated, hybridized and analyzed together with strains and samples from GSE27581; the corresponding wild-type strain QM9414 samples have accession numbers GSM683732, GSM683733, GSM683734 and GSM683735.

Project description:Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling. Transcriptomes were collected for diatom cultures harvested at the onset of stationary phase in low nitrate media (55 M-NM-<M NaNO3, 212 M-NM-<M Na2SiO3, 72.4 M-NM-<M NaH2PO4) or during mid-exponential growth in nutrient-replete media (882 M-NM-<M NaNO3, 106 M-NM-<M Na2SiO3, 36.2 M-NM-<M NaH2PO4) in artificial seawater, maintaining three biological replicates per condition and per diatom (N=18). The SOLiD sequencer (version 4) was used to generate the transcriptomes and the SEAStAR software package was used to process the SOLiD reads and to calculate gene counts. Pooled counts for the nitrate-limited treatment were normalized to pooled counts for the nutrient-replete M-bM-^@M-^\controlM-bM-^@M-^] treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor.

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	Seq53899_QE2.raw	Raw
	Seq53900_QE2.raw	Raw
	Seq53901_QE2.raw	Raw
	Seq53903_QE2.raw	Raw
	Seq53904_QE2.raw	Raw

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LC-MS/MS secretome analysis of Pleurotus ostreatus PC9 (wild type) and two transformants

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