Fungal strain improvement for efficient cellulase production and lignocellulosic biorefinery: Current status and future prospects

Enhancing cellulase production in Neurospora crassa through combined deletion of the phospholipase D-encoding gene pla-7 and modulation of transcription factor CLR-2 expression

Neurospora crassa, a saprophytic fungus, naturally secretes plant cell wall-degrading enzymes, demonstrating strong cellulases production. Despite its century-long use as a model organism, its industrial applications are underexplored. We compared N. crassa with Trichoderma reesei, an industrial workhorse, for cellulases production and lignocellulose degradation. The extracellular protein secretion level of N. crassa WT is significantly higher than that of T. reesei QM6a, indicating industrial potential. However, its mycelial morphology and dependence on insoluble substrates like lignocellulose pose bioreactor challenges. Deleting the phospholipase D gene pla-7 in N. crassa resulted in shorter aerial hyphae, increased branching, and improved biomass on sucrose. Although pla-7 deletion hindered cellulase induction on cellulose in shake flasks, mis-expressing clr-2 restored cellulase production in Δpla-7 strains. Additionally, protein secretion levels in Δpla-7::Mclr-2 strains were approximately doubled on both sucrose and cellulose carbon sources compared to WT::Mclr-2 strains in shake flasks. Furthermore, Δpla-7::Mclr-2 strains demonstrated enhanced fermentation properties in bioreactors using sucrose. These results highlight N. crassa' s industrial promise and provide insights for enhancing production of cellulases in other fungi.

Cutting-edge advances in strain and process engineering for boosting cellulase production in Trichoderma reesei

Low-cost production of cellulases is a key factor in advancing the commercialization of lignocellulosic biorefinery. Thus far, Trichoderma reesei is the leading cellulase producer for biorefinery applications. Over 70 years of research, considerable advancements have been made in comprehending the mechanisms underlying cellulases biosynthesis and secretion in T. reesei, as well as enzymatic cellulose hydrolysis. However, many unknowns still hinder the rational design of strains for robust cellulase production, with an optimized ratio of cellulolytic enzymes to reduce the required dosage for cellulose hydrolysis. Moreover, large-scale cellulase production relies on submerged fermentation, which suffers from several mass transfer limitations. As the mycelia grow, the fermentation broth rapidly develops non-Newtonian properties, necessitating energy-intensive mixing and aeration to facilitate oxygen transfer essential for strain growth. Herein, this paper critically reviews updated progress in these regards, highlights challenges, and outlines potential solutions.

Discovery of a novel translation-machinery-associated protein that positively correlates with cellulase production

BACKGROUND

The production of cellulases by filamentous fungi is a crucial aspect of sustainable bioproduction from renewable lignocellulosic biomass. Following the transcription of cellulase genes in the nucleus, a complex pathway involving translation, folding, and secretion is required to produce extracellular cellulases. Most studies about cellulase production have focused on examining transcriptional regulatory mechanisms and enhancement of enzyme gene levels; comparatively, little is known about protein translation and secretion for cellulase production.

RESULTS

A translation-machinery-associated (TMA) protein PoTma15 was identified in cellulosic Penicillium oxalicum. The PoTma15 is conserved in various filamentous fungi, but not in yeast, plants, or animals. All homologous proteins of PoTma15 have previously been uncharacterized. PoTma15 was initially thought to be one of the putative interactors of transcription factor PoXlnR, as it was preyed by tandem affinity purification (TAP) coupled with the mass spectrometry (TAP-MS) technique using PoXlnR as the bait. Subsequent research revealed that PoTma15 is associated with the translation machinery. The top three proteins associated with PoTma15 are orthologs of Saccharomyces cerevisiae translation-machinery-associated protein (Tma19), translation elongation factor eIF5A, and ribosomal protein S28, respectively. PoTma15 is widely distributed in fungal hyphae and positively correlates with the production of cellulases and extracellular proteins. Deleting the Potma15 gene (Δtma15) decreased cellulase production, while overexpressing the Potma15 gene (OEtma15) increased cellulase production. However, the Δtma15 mutant was not observed to have downregulated transcript levels of major (hemi)cellulase and amylase genes, compared to the P. oxalicum wild type (WT). The production of extracellular cellulases and extracellular proteins of the Δtma15 mutant was less affected by cycloheximide, an inhibitor of eukaryotic translation elongation, compared to the WT strain and OEtma15 mutant, suggesting a stronger resistance to the translation-inhibiting effects of cycloheximide in the Δtma15 mutant. The results demonstrate that PoTma15 is a translation-machinery-associated protein that affects translation elongation and, consequently, the production of enzyme proteins.

CONCLUSIONS

PoTma15 is the first TMA protein characterized in cellulosic filamentous fungi and the first TMA protein used in fungi to increase cellulase production. PoTma15's role in the production of cellulases and total extracellular proteins suggests that not only can it be used to widen the cellulase production pathway, but can even be engineered as a target to improve the production of other heterologous protein or bioproducts using filamentous fungi as cell factories in the future.

Advances in fungal sugar transporters: unlocking the potential of second-generation bioethanol production

Second-generation (2G) bioethanol production, derived from lignocellulosic biomass, has emerged as a sustainable alternative to fossil fuels by addressing growing energy demands and environmental concerns. Fungal sugar transporters (STs) play a critical role in this process, enabling the uptake of monosaccharides such as glucose and xylose, which are released during the enzymatic hydrolysis of biomass. This mini-review explores recent advances in the structural and functional characterization of STs in filamentous fungi and yeasts, highlighting their roles in processes such as cellulase induction, carbon catabolite repression, and sugar signaling pathways. The review also emphasizes the potential of genetic engineering to enhance the specificity and efficiency of these transporters, overcoming challenges such as substrate competition and limited pentose metabolism in industrial strains. By integrating the latest research findings, this work underscores the pivotal role of fungal STs in optimizing lignocellulosic bioethanol production and advancing the bioeconomy. Future prospects for engineering transport systems and their implications for industrial biotechnology are also discussed. KEY POINTS: STs present a conserved structure with different sugar affinities STs are involved in the signaling and transport of sugars derived from plant biomass Genetic engineering of STs can improve 2G bioethanol production.

Genomic Characterization and Establishment of a Genetic Manipulation System for Trichoderma sp. (Harzianum Clade) LZ117

Trichoderma species have been reported as masters in producing cellulolytic enzymes for the biodegradation of lignocellulolytic biomass and biocontrol agents against plant pathogens and pests. In our previous study, a novel Trichoderma strain LZ117, which shows potent capability in cellulase production, was isolated. Herein, we conducted multilocus phylogenetic analyses based on DNA barcodes and performed time-scaled phylogenomic analyses using the whole genome sequences of the strain, annotated by integrating transcriptome data. Our results suggest that this strain represents a new species closely related to T. atrobrunneum (Harzianum clade). Genes encoding carbohydrate-active enzymes (CAZymes), transporters, and secondary metabolites were annotated and predicted secretome in Trichoderma sp. LZ117 was also presented. Furthermore, genetic manipulation of this strain was successfully achieved using PEG-mediated protoplast transformation. A putative transporter gene encoding maltose permease (Mal1) was overexpressed, which proved that this transporter does not affect cellulase production. Moreover, overexpressing the native Cre1 homolog in LZ117 demonstrated a more pronounced impact of glucose-caused carbon catabolite repression (CCR), suggesting the importance of Cre1-mediated CCR in cellulase production of Trichoderma sp. LZ117. The results of this study will benefit further exploration of the strain LZ117 and related species for their applications in bioproduction.

Recent advances in genetic engineering to enhance plant-polysaccharide-degrading enzyme expression in Penicillium oxalicum: A brief review

With the depletion of non-renewable fossil fuels, there has been an increasing emphasis on renewable biomass. Penicillium oxalicum is notable for its exceptional capacity to secrete a diverse array of enzymes that degrade plant polysaccharides into monosaccharides. These valuable monosaccharides can be harnessed in the production of bioethanol and other sustainable forms of energy. By enhancing the production of plant-polysaccharide-degrading enzymes (PPDEs) in P. oxalicum, we can optimize the utilization of plant biomass. This paper presents recent advances in augmenting PPDE expression in P. oxalicum through genetic engineering strategies involving protoplast preparation, transformation, and factors influencing PPDE gene expression.

Review of research progress on the production of cellulase from filamentous fungi

Cellulases have been widely used in many fields such as animal feed, textile, food, lignocellulose bioconversion, etc. Efficient and low-cost production of cellulases is very important for its industrial application, especially in bioconversion of lignocellulosic biomass. Filamentous fungi are currently widely used in industrial cellulase production due to their ability to secrete large amounts of active free cellulases extracellularly. This review comprehensively summarized the research progress on cellulases from filamentous fungi in recent years, including filamentous fungi used for cellulase production and its modification strategies, enzyme compositions, characterization methods and application of fungal cellulase systems, and the production of fungal cellulase includes production processes, factors affecting cellulase production such as inducers, fermentation medium, process parameters and their control strategies. Also, the future perspectives and research topics in fungal cellulase production are presented in the end of the review. The review helps to deepen the understanding of the current status of fungal cellulases, thereby promoting the production technology progress and industrial application of filamentous fungal cellulase.

CRISPR/Cas9 mediated targeted knock-in of eglA gene to improve endoglucanase activity of Aspergillus fumigatus LMB-35Aa

Bioeconomy goals for using biomass feedstock for biofuels and bio-based production has arisen the demand for fungal strains and enzymes for biomass processing. Despite well-known Trichoderma and Aspergillus commercial strains, continuous bioprospecting has revealed the fungal biodiversity potential for production of biomass degrading enzymes. The strain Aspergillus fumigatus LMB-35Aa has revealed a great potential as source of lignocellulose-degrading enzymes. Nevertheless, genetic improvement should be considered to increase its biotechnological potential. Molecular manipulation based on homologous direct recombination (HDR) in filamentous fungi poses a challenge since its low recombination rate. Currently, CRISPR/Cas9-mediated mutagenesis can enable precise and efficient editing of filamentous fungi genomes. In this study, a CRISPR/Cas9-mediated gene editing strategy for improving endoglucanase activity of A. fumigatus LMB-35Aa strain was successfully used, which constitutes the first report of heterologous cellulase production in filamentous fungi using this technology. For this, eglA gene from A. niger ATCC 10,864 was integrated into conidial melanin pksP gene locus, which facilitated the selection of edited events discerned by the emergence of albino colonies. Heterologous production of the EglA enzyme in a biofilm fermentation system resulted in a 40% improvement in endoglucanase activity of the mutant strain compared to the wild type.

Construction of a Synthetic Microbial Community for Enzymatic Pretreatment of Wheat Straw for Biogas Production via Anaerobic Digestion

Biological pretreatment is a viable method for enhancing biogas production from straw crops, with the improvement in lignocellulose degradation efficiency being a crucial factor in this process. Herein, a metagenomic approach was used to screen core microorganisms (Bacillus subtilis, Acinetobacter johnsonii, Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading abilities among samples from three environments: pile retting wheat straw (WS), WS returned to soil, and forest soil. Subsequently, synthetic microbial communities were constructed for fermentation-enzyme production. The crude enzyme solution obtained was used to pretreat WS and was compared with two commercial enzymes. The synthetic microbial community enzyme-producing pretreatment (SMCEP) yielded the highest enzymatic digestion efficacy for WS, yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99, and 19.21%, respectively. Furthermore, pretreatment of WS with an enzyme solution, followed by anaerobic digestion achieved satisfactory results. SMCEP displayed the highest cumulative biogas production at 801.16 mL/g TS, which was 38.79% higher than that observed for WS, 22.15% higher than that of solid-state commercial enzyme pretreatment and 25.41% higher than that of liquid commercial enzyme pretreatment. These results indicate that enzyme-pretreated WS can significantly enhance biogas production. This study represents a solution to the environmental burden and energy use of crop residues.

Effect of nitrogen retention composite additives Ca(H2PO4)2 and MgSO4 on the degradation of lignocellulose, compost maturation, and fungal communities in compost

This study investigated the effects of the nitrogen retention composite additives Ca(H2PO4)2 and MgSO4 on lignocellulose degradation, maturation, and fungal communities in composts. The study included control (C, without Ca(H2PO4)2 and MgSO4), 1% Ca(H2PO4)2 + 2% MgSO4 (CaPM1), 1.5% Ca(H2PO4)2 + 3% MgSO4 (CaPM2). The results showed that Ca(H2PO4)2 and MgSO4 enhanced the degradation of total organic carbon (TOC) and promoted the degradation of lignocellulose in compost, with CaPM2 showing the highest TOC and lignocellulose degradation. Changes in the three-dimensional excitation-emission matrix fluorescence spectroscopy (3D-EEM) of dissolved organic matter (DOM) components in compost indicated that the treatment group with the addition of Ca(H2PO4)2 and MgSO4 promoted the production of humic acids (HAs) and increased the degree of compost decomposition, with CaPM2 demonstrating the highest degree of decomposition. The addition of Ca(H2PO4)2 and MgSO4 modified the composition of the fungal community. Ca(H2PO4)2 and MgSO4 increased the relative abundance of Ascomycota, decreased unclassified_Fungi, and Glomeromycota, and activated the fungal genera Thermomyces and Aspergillus, which can degrade lignin and cellulose during the thermophilic stage of composting. Ca(H2PO4)2 and MgSO4 also increased the abundance of Saprotroph, particularly undefined Saprotroph. In conclusion, the addition of Ca(H2PO4)2 and MgSO4 in composting activated fungal communities involved in lignocellulose degradation, promoted the degradation of lignocellulose, and enhanced the maturation degree of compost.

Fungal bioprocessing for circular bioeconomy: Exploring lignocellulosic waste valorization

The rising global demand for sustainable and eco-friendly practices has led to a burgeoning interest in circular bioeconomy, wherein waste materials are repurposed into valuable resources. Lignocellulosic waste, abundant in agricultural residues and forestry by-products, represents a significant untapped resource. This article explores the potential of fungal-mediated processes for the valorisation of lignocellulosic waste, highlighting their role in transforming these recalcitrant materials into bio-based products. The articles delve into the diverse enzymatic and metabolic capabilities of fungi, which enable them to efficiently degrade and metabolise lignocellulosic materials. The paper further highlights key fungal species and their mechanisms involved in the breakdown of complex biomass, emphasising the importance of understanding their intricate biochemical pathways for optimising waste conversion processes. The key insights of the article will significantly contribute to advancing the understanding of fungal biotechnology for circular bioeconomy applications, fostering a paradigm shift towards a more resource-efficient and environmentally friendly approach to waste management and bio-based product manufacturing.

An overview on the current status and future prospects in Aspergillus cellulase production

Cellulase is a new research point besides glucoamylase, amylase, and protease in the enzyme industry. Cellulase can decompose lignocellulosic biomass into small-molecule sugars, which facilitates microbial utilization; thus, it has a vast market potential in the field of feed, food, energy, and chemistry. The Aspergillus was the first strain used in cellulase preparation because of its safety and non-toxicity, strong growth ability, and high enzyme yield. This review provides the latest research and advances on preparing cellulase from Aspergillus. The metabolic mechanisms of cellulase secretion by Aspergillus, the selection of fermentation substrates, the comparison of the fermentation modes, and the effect of fermentation conditions have been discussed in this review. Also, the subsequent separation and purification techniques of Aspergillus cellulase, including salting out, organic solvent precipitation, ultrafiltration, and chromatography, have been declared. Further, bottlenecks in Aspergillus cellulase preparation and corresponding feasible approaches, such as genetic engineering, mixed culture, and cellulase immobilization, have also been proposed in this review. This paper provides theoretical support for the efficient production and application of Aspergillus cellulase.

Calcium signaling positively regulates cellulase translation and secretion in a Clr-2-overexpressing, catabolically derepressed strain of Penicillium funiculosum

BACKGROUND

Low-cost cellulase production is vital to sustainable second-generation biorefineries. The catabolically derepressed strain of Penicillium funiculosum NCIM1228 (PfMig188 or ∆Mig1) secretes a superior set of cellulolytic enzymes, that are most suitable for 2G biorefineries. At a 3% (w/w) load, the ∆Mig1 secretome can release > 80% of fermentable sugars from lignocellulose at a 15% (w/v) biomass load, irrespective of the type of biomass and pretreatment. The robustness of the secretome can be further increased by improving the cellulase production capacity of the fungal strain.

RESULTS

We began by identifying the transcription factor responsible for cellulase production in NCIM1228. An advanced RNA-seq screen identified three genes, clr-2, ctf1a and ctf1b; the genes were cloned under their native promoters and transformed into NCIM1228. Of the three, clr-2 overexpression led to twofold higher cellulase production than the parent strain and was thus identified as the transcriptional activator of cellulase in NCIM1228. Next, we overexpressed clr-2 in ∆Mig1 and expected an exponential increase in cellulolytic attributes accredited to the reinforced activation mechanisms, conjoint with diminished negative regulation. Although clr-2 overexpression increased the transcript levels of cellulase genes in ∆Mig1, there was no increase in cellulase yield. Even a further increase in the transcript levels of clr-2 via a stronger promoter was ineffective. However, when the CaCO3 concentration was increased to 5 g/l in the growth medium, we achieved a 1.5-fold higher activity of 6.4 FPU/ml in the ∆Mig1 strain with clr-2 overexpression. Enthused by the calcium effect, a transcriptomic screen for genes encoding Ca2+-activated kinase identified ssp1, whose overexpression could further increase cellulase yield to ~ 7.5 FPU/ml. Investigation of the mechanism revealed that calcium signaling exclusively enhances the translation and secretion of cellulase in Penicillium funiculosum.

CONCLUSIONS

Our study identifies for the first time that cellulose activates two discrete signaling events to govern cellulase transcription and posttranscriptional processes (translation, processing and secretion) in P. funiculosum NCIM1228. Whereas Clr-2, the transcriptional activator of cellulase, governs transcription, calcium signaling specifically activates cellulase translation and secretion.

Secretome Analysis of Thermothelomyces thermophilus LMBC 162 Cultivated with Tamarindus indica Seeds Reveals CAZymes for Degradation of Lignocellulosic Biomass

The analysis of the secretome allows us to identify the proteins, especially carbohydrate-active enzymes (CAZymes), secreted by different microorganisms cultivated under different conditions. The CAZymes are divided into five classes containing different protein families. Thermothelomyces thermophilus is a thermophilic ascomycete, a source of many glycoside hydrolases and oxidative enzymes that aid in the breakdown of lignocellulosic materials. The secretome analysis of T. thermophilus LMBC 162 cultivated with submerged fermentation using tamarind seeds as a carbon source revealed 79 proteins distributed between the five diverse classes of CAZymes: 5.55% auxiliary activity (AAs); 2.58% carbohydrate esterases (CEs); 20.58% polysaccharide lyases (PLs); and 71.29% glycoside hydrolases (GHs). In the identified GH families, 54.97% are cellulolytic, 16.27% are hemicellulolytic, and 0.05 are classified as other. Furthermore, 48.74% of CAZymes have carbohydrate-binding modules (CBMs). Observing the relative abundance, it is possible to state that only thirteen proteins comprise 92.19% of the identified proteins secreted and are probably the main proteins responsible for the efficient degradation of the bulk of the biomass: cellulose, hemicellulose, and pectin.