Molecular Networks of Postia placenta Involved in Degradation of Lignocellulosic Biomass Revealed from Metadata Analysis of Open Access Gene Expression Data

Parascedosporium putredinis NO1 tailors its secretome for different lignocellulosic substrates

Parascedosporium putredinis NO1 is a plant biomass-degrading ascomycete with a propensity to target the most recalcitrant components of lignocellulose. Here we applied proteomics and activity-based protein profiling (ABPP) to investigate the ability of P. putredinis NO1 to tailor its secretome for growth on different lignocellulosic substrates. Proteomic analysis of soluble and insoluble culture fractions following the growth of P. putredinis NO1 on six lignocellulosic substrates highlights the adaptability of the response of the P. putredinis NO1 secretome to different substrates. Differences in protein abundance profiles were maintained and observed across substrates after bioinformatic filtering of the data to remove intracellular protein contamination to identify the components of the secretome more accurately. These differences across substrates extended to carbohydrate-active enzymes (CAZymes) at both class and family levels. Investigation of abundant activities in the secretomes for each substrate revealed similar variation but also a high abundance of "unknown" proteins in all conditions investigated. Fluorescence-based and chemical proteomic ABPP of secreted cellulases, xylanases, and β-glucosidases applied to secretomes from multiple growth substrates for the first time confirmed highly adaptive time- and substrate-dependent glycoside hydrolase production by this fungus. P. putredinis NO1 is a promising new candidate for the identification of enzymes suited to the degradation of recalcitrant lignocellulosic feedstocks. The investigation of proteomes from the biomass bound and culture supernatant fractions provides a more complete picture of a fungal lignocellulose-degrading response. An in-depth understanding of this varied response will enhance efforts toward the development of tailored enzyme systems for use in biorefining.IMPORTANCEThe ability of the lignocellulose-degrading fungus Parascedosporium putredinis NO1 to tailor its secreted enzymes to different sources of plant biomass was revealed here. Through a combination of proteomic, bioinformatic, and fluorescent labeling techniques, remarkable variation was demonstrated in the secreted enzyme response for this ascomycete when grown on multiple lignocellulosic substrates. The maintenance of this variation over time when exploring hydrolytic polysaccharide-active enzymes through fluorescent labeling, suggests that this variation results from an actively tailored secretome response based on substrate. Understanding the tailored secretomes of wood-degrading fungi, especially from underexplored and poorly represented families, will be important for the development of effective substrate-tailored treatments for the conversion and valorization of lignocellulose.

Whole genome structural predictions reveal hidden diversity in putative oxidative enzymes of the lignocellulose-degrading ascomycete Parascedosporium putredinis NO1

IMPORTANCE

An annotated reference genome has revealed P. putredinis NO1 as a useful resource for the identification of new lignocellulose-degrading enzymes for biorefining of woody plant biomass. Utilizing a "structure-omics"-based searching strategy, we identified new potentially lignocellulose-active sequences that would have been missed by traditional sequence searching methods. These new identifications, alongside the discovery of novel enzymatic functions from this underexplored lineage with the recent discovery of a new phenol oxidase that cleaves the main structural β-O-4 linkage in lignin from P. putredinis NO1, highlight the underexplored and poorly represented family Microascaceae as a particularly interesting candidate worthy of further exploration toward the valorization of high value biorenewable products.

Oxidative stress facilitates infection of the unicellular alga Haematococcus pluvialis by the fungus Paraphysoderma sedebokerense

Background

The green microalga Haematococcus pluvialis is used as a cell factory for producing astaxanthin, the high-value carotenoid with multiple biological functions. However, H. pluvialis is prone to the infection by a parasitic fungus Paraphysoderma sedebokerense, which is the most devastating threat to the mass culture of H. pluvialis all over the world. Through dissecting the mechanisms underlying the infection process, effective measures could be developed to mitigate the pathogen threatening for the natural astaxanthin industry. By far, understanding about the interaction between the algal host and fungal pathogen remains very limited.

Results

We observed that there were heat-stable substances with small molecular weight produced during the infection process and enhanced the susceptibility of H. pluvialis cells to the pathogen. The infection ratio increased from 10.2% (for the algal cells treated with the BG11 medium as the control) to 52.9% (for the algal cells treated with supernatant contained such substances) on the second day post-infection, indicating the yet unknown substances in the supernatant stimulated the parasitism process. Systematic approaches including multi-omics, biochemical and imaging analysis were deployed to uncover the identity of the metabolites and the underlying mechanisms. Two metabolites, 3-hydroxyanthranilic acid and hordenine were identified and proved to stimulate the infection via driving oxidative stress to the algal cells. These metabolites generated hydroxyl radicals to disrupt the subcellular components of the algal cells and to make the algal cells more susceptible to the infection. Based on these findings, a biosafe and environment-friendly antioxidant butylated hydroxyanisole (BHA) was selected to inhibit the fungal infection, which completely abolished the infection at 12 ppm. By applying 7 ppm BHA every 2 days to the algal cell culture infected with P. sedebokerense in the 100 L open raceway ponds, the biomass of H. pluvialis reached 0.448 g/L, which was comparable to that of the control (0.473 g/L).

Conclusions

This study provides for the first time, a framework to dissect the functions of secondary metabolites in the interaction between the unicellular alga H. pluvialis and its fungal parasite, indicating that oxidative degradation is a strategy used for the fungal infest. Eliminating the oxidative burst through adding antioxidant BHA could be an effective measure to reduce parasitic infection in H. pluvialis mass culture.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02140-y.

Insights into enhanced biodegradation of sulfadimethoxine by catalyst: Transcriptomic responses and free radical interactions

The occurrence of sulfonamides in the environment is a severe global threat to public health due to the increasing prevalence of antibiotic selection pressure that may lead to the development of antibiotic resistance. We report an enhanced biodegradation of sulfadimethoxine (SDM) by Phanerochaete chrysosporium (Pc) with lignocellulosic biomass (Lb) using Fe₃O₄-ZSM-5 as a catalyst (Pc/Fe₃O₄-ZSM-5/Lb). SDM was completely degraded within 4 days at pH 7.0 in the Pc/Fe₃O₄-ZSM-5/Lb system. Transcriptomic, metabolites and free radical analyses were performed to explore the detailed molecular mechanisms of SDM degradation. A total of 246 genes of Pc in the Pc/Fe₃O₄-ZSM-5/Lb system exhibited significant upregulation compared to that in Pc alone. Upregulated genes encoding cellulases, cytochrome P450, cellobiose quinone oxidoreductase, and cellobiose dehydrogenase were involved in SDM degradation in the Pc/Fe₃O₄-ZSM-5/Lb system. In addition, genes encoding glutathione S-transferase and cytochrome P450 genes related to oxidative stress and detoxification were all significantly upregulated (P < 0.01). Electron paramagnetic resonance revealed the generation of OH suggesting a free radical pathway could be catalyzed by Fe₃O₄-ZSM-5 and the enzymes. These findings of catalyst-assisted SDM biodegradation will be valuable for remediation of antibiotics from contaminated wastewater.

Systematic metadata analysis of brown rot fungi gene expression data reveals the genes involved in Fenton's reaction and wood decay process

Brown-rot fungi are rapid holocellulose degraders and are the most predominant degraders of coniferous wood products in North America. Brown-rot fungi degrades wood by both enzymatic (plant biomass degrading carbohydrate active enzymes-CAZymes) and non-enzymatic systems (Fenton’s reaction) mechanisms. Identifying the genes and molecular mechanisms involved in Fenton’s reaction would significantly improve our understanding about brown-rot decay. Our present study identifies the common gene expression patterns involved in brown rot decay by performing metadata analysis of fungal transcriptome datasets. We have also analyzed and compared the genome-wide annotations (InterPro and CAZymes) of the selected brown rot fungi. Genes encoding for various oxidoreductases, iron homeostasis, and metabolic enzymes involved in Fenton’s mechanism were found to be significantly expressed among all the brown-rot fungal datasets. Interestingly, a higher number of hemicellulases encoding genes were differentially expressed among all the datasets, while a fewer number of cellulases and peroxidases were expressed (especially haem peroxidase and chloroperoxidase). Apart from these lignocellulose degrading enzymes genes encoding for aldo/keto reductases, 2-nitro dioxygenase, aromatic-ring dioxygenase, dienelactone hydrolase, alcohol dehydrogenase, major facilitator superfamily, cytochrome-P450 monoxygenase, cytochrome b5, and short-chain dehydrogenase were common and differentially up regulated among all the analyzed brown-rot fungal datasets.

Metadata Analysis Approaches for Understanding and Improving the Functional Involvement of Rumen Microbial Consortium in Digestion and Metabolism of Plant Biomass

Rumen is one of the most complex gastro-intestinal system in ruminating animals. With bountiful of microorganisms supporting in breakdown and consumption of minerals and nutrients from the complex plant biomass. It is predicted that a table spoon of ruminal fluid can reside up to 150 billion microorganisms including various species of bacteria, fungi and protozoa. Several studies in the past have extensively explained about the structural and functional physiology of the rumen. Studies based on rumen and its microbiota has increased significantly in the last decade to understand and reveal applications of the rumen microbiota in food processing, pharmaceutical, biofuel and biorefining industries. Recent high-throughput meta-genomic and proteomic studies have revealed humongous information on rumen microbial diversity. In this study, we have extensively reviewed and reported present-day's progress in understanding the rumen microbial diversity. As of today, NCBI resides about 821,870 records based on rumen with approximately 889 genome sequencing studies. We have retrieved all the rumen-based records from NCBI and extensively catalogued the rumen microbial diversity and the corresponding genomic and proteomic studies respectively. Also, we have provided a brief inventory of metadata analysis software packages and reviewed the metadata analysis approaches for understanding the functional involvement of these microorganisms. Knowing and understanding the present progress on rumen microbiota and performing metadata analysis studies will significantly benefit the researchers in identifying the molecular mechanisms involved in plant biomass degradation. These studies are also necessary for developing highly efficient microorganisms and enzyme mixtures for enhancing the benefits of cattle-feedstock and biofuel industries.

Role of the antioxidant defense system during the production of lignocellulolytic enzymes by fungi

Fungi are used for the production of several compounds and the efficiency of biotechnological processes is directly related to the metabolic activity of these microorganisms. The reactions catalyzed by lignocellulolytic enzymes are oxidative and generate reactive oxygen species (ROS). Excess of ROS can cause serious damages to cells, including cell death. Thus, the objective of this work was to evaluate the lignocellulolytic enzymes produced by Pleurotus sajor-caju CCB020, Phanerochaete chrysosporium ATCC 28326, Trichoderma reesei RUT-C30, and Aspergillus niger IZ-9 grown in sugarcane bagasse and two yeast extract (YE) concentrations and characterize the antioxidant defense system of fungal cells by the activities of superoxide dismutase (SOD) and catalase (CAT). Pleurotus sajor-caju exhibited the highest activities of laccase and peroxidase in sugarcane bagasse with 2.6 g of YE and an increased activity of manganese peroxidase in sugarcane bagasse with 1.3 g of YE was observed. However, P. chrysosporium showed the highest activities of exoglucanase and endoglucanase in sugarcane bagasse with 1.3 g of YE. Lipid peroxidation and variations in SOD and CAT activities were observed during the production of lignocellulolytic enzymes and depending on the YE concentrations. The antioxidant defense system was induced in response to the oxidative stress caused by imbalances between the production and the detoxification of ROS.