Transcriptional regulation of two cellobiohydrolase encoding genes (cel1 and cel2) from the wood-degrading basidiomycete Polyporus arcularius

Transcription factor FfMYB15 regulates the expression of cellulase gene FfCEL6B during mycelial growth of Flammulina filiformis

Background

Cellulose degradation can determine mycelial growth rate and affect yield during the growth of Flammulina filiformis. The degradation of cellulose requires the joint action of a variety of cellulases, and some cellulase-related genes have been detected in mushrooms. However, little is known about the transcriptional regulatory mechanisms of cellulose degradation.

Results

In this study, FfMYB15 that may regulate the expression of cellulase gene FfCEL6B in F. filiformis was identified. RNA interference (RNAi) showed that FfCEL6B positively regulated mycelial growth. Gene expression analyses indicated that the expression patterns of FfCEL6B and FfMYB15 in mycelia cultured on the 0.9% cellulose medium for different times were similar with a correlation coefficient of 0.953. Subcellular localization and transcriptional activity analyses implied that FfMYB15 was located in the nucleus and was a transcriptional activator. Electrophoretic mobility shift assay (EMSA) and dual-luciferase assays demonstrated that FfMYB15 could bind and activate FfCEL6B promoter by recognizing MYB cis-acting element.

Conclusions

This study indicated that FfCEL6B played an active role in mycelial growth of F. filiformis and was regulated by FfMYB15.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01932-z.

How Carbon Source and Degree of Oligosaccharide Polymerization Affect Production of Cellulase-Degrading Enzymes by Fusarium oxysporum f. sp. lycopersici

Cellulases are a group of enzymes responsible for the degradation of cellulose, which is one of the most abundant polymers on Earth. The three main groups of cellulases are endoglucosidases, exoglucosidases, and β-glucosidases; however, the mechanism of induction of these enzymes remains poorly characterized. Cellooligosaccharides are among the main inducers of these enzymes in filamentous fungi, yet it is not clear how their degree of polymerization may affect the strength of induction. In the present study, we investigated the effect of different carbohydrate-based inducers, such as lactose, sophorose, cellooligosaccharides, and xylooligosacharides, characterized by different concentrations and degree of polymerization, on cellulases production by the fungus Fusarium oxysporum f. sp. lycopersici, which is one of the most studied lignocellulose degrading fungi with the ability to consume both cellulose and hemicellulose. Moreover, the effect of carbon source on cellulase induction was assessed by growing the biomass on sucrose or glycerol. Results showed a correlation between induction efficiency and the cellooligosaccharides' concentration and size, as well as the carbon source available. Specifically, cellotetraose was a better inducer when sucrose was the carbon source, while cellobiose yielded a better result on glycerol. These findings can help optimize industrial cellulase production.

Mini review: Advances in understanding regulation of cellulase enzyme in white-rot basidiomycetes

White-rot basidiomycetic fungi have gained a lot of scientific attention in recent years owing to their ability to produce cellulase enzymes that are of great importance in numerous industrial applications. This has seen a rise in number of studies seeking to comprehend both physical and molecular mechanisms that regulate the production of cellulase enzymes in these fungi. Cellulase has several applications in production of food and beverages, biofuel, biological detergents, pharmaceuticals, and deinking in paper and pulp industry. Enhanced understanding of genetic mechanisms that regulate cellulase production would have utility for optimal cellulase production in white-rot basidiomycetes using biotechnology approaches. Carbon catabolite repression and various transcriptional factors such as XlnR, Cre, Clr, Ace, and gna1 control expression of genes encoding cellobiohydrolase (CBH), endoglucanase (EGL) and β-glucosidase (BGL). In this review, we have consolidated and summarised some of recent findings on genetic regulation of cellulase with an aim of highlighting the general regulatory mechanisms that underlie cellulase expressions in white-rot fungi. This review further outlines some of important transcription factors that regulate cellulase genes, and key research gaps that may need to be addressed by future research.

Cell Cycle-Dependent Expression Dynamics of G1/S Specific Cyclin, Cellulose Synthase and Cellulase in the Dinoflagellate Prorocentrum donghaiense

Dinoflagellates undergo a typical eukaryotic cell cycle consisting of G1, S, G2, and M phases and some of the typical cell cycle related genes have been computationally identified. However, very few of these genes have been experimentally linked to the cell cycle phases. Besides, although thecate dinoflagellates are known to possess theca composed of cellulose, information on cellulose synthesis and degradation associated with the cell cycle is also limited. In this study, we isolated G1/S cyclin, cellulose synthase and cellulase encoding genes in dinoflagellate Prorocentrum donghaiense. Further, using reverse transcription quantitative PCR (RT-qPCR), we characterized the expression profiles of the three genes throughout the cell cycle. All three showed clear expression dynamics throughout the cell cycle, with fold changes of 26, 2.4 and 9.3 for G1/S cyclin, cellulose synthase and cellulase gene, respectively. The transcript abundance of G1/S cyclin increased in late G1 phase and dropped in early S phase, indicating that this protein is involved in the G1/S transition. Throughout the cell cycle, the average transcript level of cellulose synthase was 4.5-fold higher than that of cellulase. Cellulose synthase and cellulase gene expressions showed peak transcript abundances at middle G1 phase and G2M phase, respectively, indicating the respective roles of these enzymes in the growth of newly divided cells and in cytokinesis. Our results suggest that G1/S cyclin, cellulase, and cellulose synthase genes associated with G1/S transition, G2M, and G1 phases of the cell cycle and are candidates of biomarkers for assessing growth status of P. donghaiense.

Quantification of the Genetic Expression of bgl-A, bgl, and CspA and Enzymatic Characterization of β-Glucosidases from Shewanella sp. G5

Shewanella sp. G5, a psychrotolerant marine bacterium, has a cold-shock protein (CspA) and three β-glucosidases, two of which were classified in the glycosyl hydrolase families 1 and 3 and are encoded by bgl-A and bgl genes, respectively. Shewanella sp. G5 was cultured on Luria-Bertani (LB) and Mineral Medium Brunner (MMB) media with glucose and cellobiose at various temperatures and pH 6 and 8. Relative quantification of the expression levels of all three genes was studied by real-time PCR with the comparative Ct method (2(-ΔΔCt)) using the gyrB housekeeping gene as a normalizer. Results showed that the genes had remarkably different genetic expression levels under the conditions evaluated, with increased expression of all genes obtained on MMB with cellobiose at 30 °C. Specific growth rate and specific β-glucosidase activity were also determined for all the culture conditions. Shewanella sp. G5 was able to grow on both media at 4 °C, showing the maximum specific growth rate on LB with cellobiose at 37 °C. The specific β-glucosidase activity obtained on MMB with cellobiose at 30 °C was 25 to 50 % higher than for all other conditions. At pH 8, relative activity was 34, 60, and 63 % higher at 30 °C than at 10 °C, with three peaks at 10, 25, and 37 °C on both media. Enzyme activity increased by 61 and 47 % in the presence of Ca(2+) and by 24 and 31 % in the presence of Mg(2+) on LB and MMB at 30 °C, respectively, but it was totally inhibited by Hg(2+), Cu(2+), and EDTA. Moreover, this activity was slightly decreased by SDS, Zn(2+), and DTT, all at 5 mM. Ethanol (14 % v/v) and glucose (100 mM) also reduced the activity by 63 and 60 %, respectively.

Plant-polysaccharide-degrading enzymes from Basidiomycetes

SUMMARY

Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.

Expression and regulation of genes encoding lignocellulose-degrading activity in the genus Phanerochaete

As white-rot basidiomycetes, Phanerochaete species are critical to the cycling of carbon sequestered as woody biomass, and are predicted to encode many enzymes that can be harnessed to promote the conversion of lignocellulose to sugars for fermentation to fuels and chemicals. Advances in genomic, transcriptomic, and proteomic technologies have enabled detailed analyses of different Phanerochaete species and have revealed numerous enzyme families required for lignocellulose utilization, as well as insight into the regulation of corresponding genes. Recent studies of Phanerochaete are also exemplified by molecular analyses following cultivation on different wood preparations, and show substrate-dependent responses that were difficult to predict using model compounds or isolated plant polysaccharides. The aim of this mini-review is to synthesize results from studies that have applied recent advances in molecular tools to evaluate the expression and regulation of proteins that contribute to lignocellulose conversion in Phanerochaete species. The identification of proteins with as yet unknown function are also highlighted and noted as important targets for future investigation of white-rot decay.

Curation of characterized glycoside hydrolases of fungal origin

Fungi produce a wide range of extracellular enzymes to break down plant cell walls, which are composed mainly of cellulose, lignin and hemicellulose. Among them are the glycoside hydrolases (GH), the largest and most diverse family of enzymes active on these substrates. To facilitate research and development of enzymes for the conversion of cell-wall polysaccharides into fermentable sugars, we have manually curated a comprehensive set of characterized fungal glycoside hydrolases. Characterized glycoside hydrolases were retrieved from protein and enzyme databases, as well as literature repositories. A total of 453 characterized glycoside hydrolases have been cataloged. They come from 131 different fungal species, most of which belong to the phylum Ascomycota. These enzymes represent 46 different GH activities and cover 44 of the 115 CAZy GH families. In addition to enzyme source and enzyme family, available biochemical properties such as temperature and pH optima, specific activity, kinetic parameters and substrate specificities were recorded. To simplify comparative studies, enzyme and species abbreviations have been standardized, Gene Ontology terms assigned and reference to supporting evidence provided. The annotated genes have been organized in a searchable, online database called mycoCLAP (Characterized Lignocellulose-Active Proteins of fungal origin). It is anticipated that this manually curated collection of biochemically characterized fungal proteins will be used to enhance functional annotation of novel GH genes. Database URL: http://mycoCLAP.fungalgenomics.ca/.

Cellotriose and cellotetraose as inducers of the genes encoding cellobiohydrolases in the basidiomycete Phanerochaete chrysosporium

The wood decay basidiomycete Phanerochaete chrysosporium produces a variety of cellobiohydrolases belonging to glycoside hydrolase (GH) families 6 and 7 in the presence of cellulose. However, no inducer of the production of these enzymes has yet been identified. Here, we quantitatively compared the transcript levels of the genes encoding GH family 6 cellobiohydrolase (cel6A) and GH family 7 cellobiohydrolase isozymes (cel7A to cel7F/G) in cultures containing glucose, cellulose, and cellooligosaccharides by real-time quantitative PCR, in order to evaluate the transcription-inducing effect of soluble sugars. Upregulation of transcript levels in the presence of cellulose compared to glucose was observed for cel7B, cel7C, cel7D, cel7F/G, and cel6A at all time points during cultivation. In particular, the transcription of cel7C and cel7D was strongly induced by cellotriose or cellotetraose. The highest level of cel7C transcripts was observed in the presence of cellotetraose, whereas the highest level of cel7D transcripts was found in the presence of cellotriose, amounting to 2.7 x 10(6) and 1.7 x 10(6) copies per 10(5) actin gene transcripts, respectively. These numbers of cel7C and cel7D transcripts were higher than those in the presence of cellulose. In contrast, cellobiose had a weaker transcription-inducing effect than either cellotriose or cellotetraose for cel7C and had little effect in the case of cel7D. These results indicate that cellotriose and cellotetraose, but not cellobiose, are possible natural cellobiohydrolase gene transcription inducers derived from cellulose.

Production and characterization of cellobiohydrolase from a novel strain of Penicillium purpurogenum KJS506

A high cellobiohydrolase (CBH)-producing strain was isolated and identified as Penicillium purpurogenum KJS506 according to the morphology and comparison of internal transcribed spacer rDNA gene sequence. When rice straw and corn steep powder were used as carbon and nitrogen sources, respectively, a maximum CBH activity of 2.6 U mg-protein(-1), one of the highest among CBH-producing microorganisms, was obtained. The optimum temperature and pH for CBH production were 30 °C and 4.0, respectively. The increased production of CBH in P. purpurogenum culture at 30 °C was confirmed by two-dimensional electrophoresis followed by MS/MS sequencing of the partial peptide. The internal amino acid sequences of P. purpurogenum CBH showed a significant homology with hydrolases from glycoside hydrolase family 7. The extracellular CBH was purified to homogeneity by sequential chromatography of P. purpurogenum culture supernatants on a DEAE-sepharose column, a gel filtration column, and then on a Mono Q column with fast-protein liquid chromatography. The purified CBH was a monomeric protein with a molecular weight of 60 kDa and showed broad substrate specificity with maximum activity towards p-nitrophenyl β-D: -cellobiopyranoside. P. purpurogenum CBH showed t (1/2) value of 4 h at 60 °C and V (max) value of 11.9 μmol min(-1) mg-protein(-1) for p-nitrophenyl-D: -cellobiopyranoside. Although CBHs have been reported, the high specific activity distinguishes P. purpurogenum CBH.

The activity of a wall-bound cellulase is required for and is coupled to cell cycle progression in the dinoflagellate Crypthecodinium cohnii

Cellulose synthesis, but not its degradation, is generally thought to be required for plant cell growth. In this work, we cloned a dinoflagellate cellulase gene, dCel1, whose activities increased significantly in G(2)/M phase, in agreement with the significant drop of cellulose content reported previously. Cellulase inhibitors not only caused a delay in cell cycle progression at both the G(1) and G(2)/M phases in the dinoflagellate Crypthecodinium cohnii, but also induced a higher level of dCel1p expression. Immunostaining results revealed that dCel1p was mainly localized at the cell wall. Accordingly, the possible role of cellulase activity in cell cycle progression was tested by treating synchronized cells with exogenous dCelp and purified antibody, in experiments analogous to overexpression and knockdown analyses, respectively. Cell cycle advancement was observed in cells treated with exogenous dCel1p, whereas the addition of purified antibody resulted in a cell cycle delay. Furthermore, delaying the G(2)/M phase independently with antimicrotubule inhibitors caused an abrupt and reversible drop in cellulase protein level. Our results provide a conceptual framework for the coordination of cell wall degradation and reconstruction with cell cycle progression in organisms with cell walls. Since cellulase activity has a direct bearing on the cell size, the coupling between cellulase expression and cell cycle progression can also be considered as a feedback mechanism that regulates cell size.

Isolation of fungal cellobiohydrolase I genes from sporocarps and forest soils by PCR

Cellulose is the major component of plant biomass, and microbial cellulose utilization is a key step in the decomposition of plant detritus. Despite this, little is known about the diversity of cellulolytic microbial communities in soil. Fungi are well known for their cellulolytic activity and mediate key functions during the decomposition of plant detritus in terrestrial ecosystems. We developed new oligonucleotide primers for fungal exocellulase genes (cellobiohydrolase, cbhI) and used these to isolate distinct cbhI homologues from four species of litter-decomposing basidiomycete fungi (Clitocybe nuda, Clitocybe gibba, Clitopilus prunulus, and Chlorophyllum molybdites) and two species of ascomycete fungi (Xylaria polymorpha and Sarcoscypha occidentalis). Evidence for cbhI gene families was found in three of the four basidiomycete species. Additionally, we isolated and cloned cbhI genes from the forest floor and mineral soil of two upland forests in northern lower Michigan, one dominated by oak (Quercus velutina, Q. alba) and the other dominated by sugar maple (Acer saccharum) and American basswood (Tilia americana). Phylogenetic analysis demonstrated that cellobiohydrolase genes recovered from the floor of both forests tended to cluster with Xylaria or in one of two unidentified groups, whereas cellobiohydrolase genes recovered from soil tended to cluster with Trichoderma, Alternaria, Eurotiales, and basidiomycete sequences. The ability to amplify a key fungal gene involved in plant litter decomposition has the potential to unlock the identity and dynamics of the cellulolytic fungal community in situ.

Rapid species identification of cooked poisonous mushrooms by using real-time PCR

Species-specific identification of the major cooked and fresh poisonous mushrooms in Japan was performed using a real-time PCR system. Specific fluorescence signals were detected, and no nonspecific signals were detected. Therefore, we succeeded in developing a species-specific test for the identification of poisonous mushrooms within 1.5 h.