Dataset Information

Genomic, Proteomic, and Biochemical Study of Pleurotus pulmonarius Secretome and Its Role in Biomass Saccharification

ABSTRACT: Pleurotus species include edible mushrooms that can grow on a broad range of lignocellulosic substrates by secreting a coordinated system of hydrolytic and oxidative enzymes. This flexibility offers opportunities to valorize agro-industrial residues for production of food and biomaterials using sustainable processes. In this study, we analyzed the genome of Pleurotus pulmonarius LGAM 28684 and investigated its biocatalytic potential for saccharification of pretreated lignocellulose using LC-MS/MS proteomics and biochemical assays. The fungus was cultivated on two lignocellulosic substrates, beechwood and corn stover, as well as xylose as a control. The fungus was cultivated on beechwood, corn stover, and xylose. Beechwood induced the richest secretome with abundant oxidases. The corn stover secretome had fewer proteins but was focused on carbohydrate-acting enzymes, with abundant polysaccharide-degrading and accessory enzymes. Despite lower enzyme diversity, the corn stover secretome achieved higher lignocellulose saccharification, further improved by oxidoreductase inhibition. Supplementing an industrial cellulase cocktail with P. pulmonarius corn stover secretomes enhanced sugar release by 40%. These findings highlight the dynamic enzymatic response of P. pulmonarius to lignocellulosic substrates and its potential in biomass valorization and the design of enzymatic cocktails.

INSTRUMENT(S):

ORGANISM(S): Pleurotus Pulmonarius

SUBMITTER: Romanos Siaperas

LAB HEAD: Dr Evangelos

PROVIDER: PXD065010 | Pride | 2025-11-03

REPOSITORIES: Pride

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			Action	DRS
	B28543_10ul_IonOpt_PRC6063.raw	Raw
	B28545_10ul_IonOpt_PRC6063.raw	Raw
	B28547_10ul_IonOpt_PRC6063.raw	Raw
	B28549_10ul_IonOpt_PRC6063.raw	Raw
	B28551_10ul_IonOpt_PRC6063.raw	Raw

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Publications

Genomic, Proteomic, and Biochemical Study of Pleurotus pulmonarius Secretome and Its Role in Biomass Saccharification.

Siaperas Romanos R Papadaki Eftychia E Giannikos Panagiotis P Zerva Anastasia A Topakas Evangelos E

Journal of agricultural and food chemistry 20251027 44

Pleurotus species include edible mushrooms that grow on a range of lignocellulosic substrates by secreting hydrolytic and oxidative enzymes. This flexibility offers opportunities to valorize agro-industrial residues for sustainable production of food and biomaterials. In this study, we analyzed the genome of Pleurotus pulmonarius and its biocatalytic potential for lignocellulose saccharification using proteomics and biochemical assays. The fungus was cultivated on beechwood, corn s ...[more]

PMID: 41140144

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Project description:Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5M-bM-^@M-^Qhydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts. E.coli ethanologen strain GLBRCE1 was grown in 3 media, AFEX corn stover hydrolysate (ACSH), synthetic hydrolysate (SynH) and syntetic hydrolysate with added lignotoxins (SynH_LT). Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2. 3 biological replicates (independent cultures) were grown in each medium. RNA samples were obtained at 4 time points, corresponding to exponential (Exp), transitional (Trans), stationary (Stat1) and late stationary (Stat2) growth phases.

Project description:Background: Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers [GSE33852]. Results: In this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study. Conclusions: By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production. Six samples in total consisting of duplicate shake flask Aspergillus niger cultures from three conditions: glucose 48 h, willow 24 h, willow 24 h + glucose 5 h

Dataset Information

Genomic, Proteomic, and Biochemical Study of Pleurotus pulmonarius Secretome and Its Role in Biomass Saccharification

Dataset's files

Publications

Genomic, Proteomic, and Biochemical Study of <i>Pleurotus pulmonarius</i> Secretome and Its Role in Biomass Saccharification.

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Dataset Information

Genomic, Proteomic, and Biochemical Study of Pleurotus pulmonarius Secretome and Its Role in Biomass Saccharification

Dataset's files

Publications

Genomic, Proteomic, and Biochemical Study of &lt;i&gt;Pleurotus pulmonarius&lt;/i&gt; Secretome and Its Role in Biomass Saccharification.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Genomic, Proteomic, and Biochemical Study of <i>Pleurotus pulmonarius</i> Secretome and Its Role in Biomass Saccharification.