Cellulase secretion from a hyper-cellulolytic mutant of Trichoderma reesei Rut-C30

A bird's-eye view of the endoplasmic reticulum in filamentous fungi

SUMMARYThe endoplasmic reticulum (ER) is one of the most extensive organelles in eukaryotic cells. It performs crucial roles in protein and lipid synthesis and Ca2+ homeostasis. Most information on ER types, functions, organization, and domains comes from studies in uninucleate animal, plant, and yeast cells. In contrast, there is limited information on the multinucleate cells of filamentous fungi, i.e., hyphae. We provide an analytical review of existing literature to categorize different types of ER described in filamentous fungi while emphasizing the research techniques and markers used. Additionally, we identify the knowledge gaps that need to be resolved better to understand the structure-function correlation of ER in filamentous fungi. Finally, advanced technologies that can provide breakthroughs in understanding the ER in filamentous fungi are discussed.

Effect of the res2 transcription factor gene deletion on protein secretion and stress response in the hyperproducer strain Trichoderma reesei Rut-C30

BACKGROUND

The fungus Trichoderma reesei is one of the most used industrial cellulase producers due to its high capacity of protein secretion. Strains of T. reesei with enhanced protein secretion capacity, such as Rut-C30, have been obtained after several rounds of random mutagenesis. The strain was shown to possess an expanded endoplasmic reticulum, but the genetic factors responsible for this phenotype remain still unidentified. Recently, three new transcription factors were described in Neurospora crassa which were demonstrated to be involved in protein secretion. One of them, RES2, was involved in upregulation of secretion-related genes. The aim of our present study was therefore to analyze the role of RES2, on protein secretion in the T. reesei Rut-C30 strain.

RESULT

Deletion of the res2 gene in Rut-C30 resulted in slightly slower growth on all substrates tested, and lower germination rate as well as lower protein secretion compared to the parental strain Rut-C30. Transcriptomic analysis of the Rut-C30 and the Δres2 mutant strain in secretion stress conditions showed remarkably few differences : 971 genes were differentially expressed (DE) in both strains while 192 genes out of 1163 (~ 16.5%) were DE in Rut-C30 only and 693 out of 1664 genes (~ 41.6%) displayed differential expression solely in Δres2. Notably, induction of protein secretion by cultivating on lactose and addition of secretion stress inducer DTT induced many genes of the secretion pathway similarly in both strains. Among the differentially expressed genes, those coding for amino acid biosynthesis genes, transporters and genes involved in lipid metabolism were found to be enriched specifically in the Δres2 strain upon exposure to lactose or DTT. Besides, redox homeostasis and DNA repair genes were specifically upregulated in the Δres2 strain, indicating an altered stress response.

CONCLUSION

These results indicate that in the T. reesei Rut-C30 strain, RES2 does not act as a master regulator of the secretion pathway, but it contributes to a higher protein secretion by adjusting the expression of genes involved in different steps of protein synthesis and the secretion pathway.

A Combined Study on Optimization, In Silico Modeling, and Genetic Modification of Large Scale Microbial Cellulase Production

Cellulase is a biocatalyst that hydrolyzes cellulosic biomass and is considered a major group of industrial enzymes for its applications. Extensive work has been done on microbial cellulase but fungi are considered a novel strain for their maximum cellulase production. Production cost and novel microbial strains are major challenges for its improvement where cheap agro wastes can be essential sources of cellulose as substrates. The researcher searches for more cellulolytic microbes from natural sources but the production level of isolated strains is comparatively low. So genetic modification or mutation can be employed for large-scale cellulase production before optimization. After genetic modification than in silico molecular modeling can be evaluated for substrate molecule's binding affinity. In this review, we focus not only on the conventional methods of cellulase production but also on modern biotechnological approaches applied to cellulase production by a sequential study on common cellulase-producing microbes, modified microbes, culture media, carbon sources, substrate pretreatment process, and the importance of optimum pH and temperature on fermentation. In this review, we also compare different cellulase activity determination methods. As a result, this review provides insights into the interrelationship between the characteristics of optimizing different culture conditions, genetic modification, and in silico enzyme modeling for the production of cellulase enzymes, which may aid in the advancement of large-scale integrated enzyme manufacturing of substrate-specific enzymes.

STK-12 acts as a transcriptional brake to control the expression of cellulase-encoding genes in Neurospora crassa

Cellulolytic fungi have evolved a complex regulatory network to maintain the precise balance of nutrients required for growth and hydrolytic enzyme production. When fungi are exposed to cellulose, the transcript levels of cellulase genes rapidly increase and then decline. However, the mechanisms underlying this bell-shaped expression pattern are unclear. We systematically screened a protein kinase deletion set in the filamentous fungus Neurospora crassa to search for mutants exhibiting aberrant expression patterns of cellulase genes. We observed that the loss of stk-12 (NCU07378) caused a dramatic increase in cellulase production and an extended period of high transcript abundance of major cellulase genes. These results suggested that stk-12 plays a critical role as a brake to turn down the transcription of cellulase genes to repress the overexpression of hydrolytic enzymes and prevent energy wastage. Transcriptional profiling analyses revealed that cellulase gene expression levels were maintained at high levels for 56 h in the Δstk-12 mutant, compared to only 8 h in the wild-type (WT) strain. After growth on cellulose for 3 days, the transcript levels of cellulase genes in the Δstk-12 mutant were 3.3-fold over WT, and clr-2 (encoding a transcriptional activator) was up-regulated in Δstk-12 while res-1 and rca-1 (encoding two cellulase repressors) were down-regulated. Consequently, total cellulase production in the Δstk-12 mutant was 7-fold higher than in the WT. These results strongly suggest that stk-12 deletion results in dysregulation of the cellulase expression machinery. Further analyses showed that STK-12 directly targets IGO-1 to regulate cellulase production. The TORC1 pathway promoted cellulase production, at least partly, by inhibiting STK-12 function, and STK-12 and CRE-1 functioned in parallel pathways to repress cellulase gene expression. Our results clarify how cellulase genes are repressed at the transcriptional level during cellulose induction, and highlight a new strategy to improve industrial fungal strains.

Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei, the hyper-cellulolytic filamentous fungus

The filamentous fungus Trichoderma reesei is a potent cellulase producer and the best-studied cellulolytic fungus. A lot of investigations not only on glycoside hydrolases produced by T. reesei, but also on the machinery controlling gene expression of these enzyme have made this fungus a model organism for cellulolytic fungi. We have investigated the T. reesei strain including mutants developed in Japan in detail to understand the molecular mechanisms that control the cellulase gene expression, the biochemical and morphological aspects that could favor this phenotype, and have attempted to generate novel strains that may be appropriate for industrial use. Subsequently, we developed recombinant strains by combination of these insights and the heterologous-efficient saccharifing enzymes. Resulting enzyme preparations were highly effective for saccharification of various biomass. In this review, we present some of the salient findings from the recent biochemical, morphological, and molecular analyses of this remarkable cellulase hyper-producing fungus.

Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes

The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.

Ultrastructural features of the early secretory pathway in Trichoderma reesei

We have systematically analysed the ultrastructure of the early secretory pathway in the Trichoderma reesei hyphae in the wild-type QM6a, cellulase-overexpressing Rut-C30 strain and a Rut-C30 transformant BV47 overexpressing a recombinant BiP1-VenusYFP fusion protein with an endoplasmic reticulum (ER) retention signal. The hyphae were studied after 24 h of growth using transmission electron microscopy, confocal microscopy and quantitative stereological techniques. All three strains exhibited different spatial organisation of the ER at 24 h in both a cellulase-inducing medium and a minimal medium containing glycerol as a carbon source (non-cellulase-inducing medium). The wild-type displayed a number of ER subdomains including parallel tubular/cisternal ER, ER whorls, ER-isolation membrane complexes with abundant autophagy vacuoles and dense bodies. Rut-C30 and its transformant BV47 overexpressing the BiP1-VenusYFP fusion protein also contained parallel tubular/cisternal ER, but no ER whorls; also, there were very few autophagy vacuoles and an increasing amount of punctate bodies where particularly the recombinant BiP1-VenusYFP fusion protein was localised. The early presence of distinct strain-specific features such as the dominance of ER whorls in the wild type and tub/cis ER in Rut-C30 suggests that these are inherent traits and not solely a result of cellular response mechanisms by the high secreting mutant to protein overload.

Genome-wide analysis of the endoplasmic reticulum stress response during lignocellulase production in Neurospora crassa

BACKGROUND

Lignocellulolytic fungal cells suffer endoplasmic reticulum (ER) stress during lignocellulase synthesis; however, an understanding of this integrated process on a genome-wide scale remains poor. Here, we undertook a systematic investigation of this process in Neurospora crassa (N. crassa) using transcriptomic analysis coupled with genetic screens.

RESULTS

A set of 766 genes was identified as the ER stress response targets (ESRTs) in N. crassa under cellulose utilization conditions. Among these, the expression of 223 and 186 genes showed dependence on IRE-1 and HAC-1, respectively. A total of 527 available mutants for ESRT genes were screened, 249 of which exhibited ER stress susceptibility, including 100 genes with unknown function. Disruption of ire-1 or hac-1 in N. crassa did not affect transcriptional induction of lignocellulase genes by cellulose but severely affected secretion of the corresponding enzymes. A global investigation of transcription factors (TFs) discovered three novel regulators (RES-1, RES-2, RRG-2) involved in lignocellulase secretion. Production of lignocellulases in Δres-1 increased by more than 30% in comparison to wild type (WT), while secretion decreased by nearly 30% in strains Δres-2 and Δrrg-2. Transcriptional profiling of the three TF mutants suggests they are deeply involved in lignocellulase secretion and ER stress response.

CONCLUSIONS

Here, we determined the transcriptional scope of the ER stress response during lignocellulase synthesis in the model cellulolytic fungus N. crassa. Through genome-wide mutant screening and analysis, dozens of novel genes were discovered to be involved in the process. The findings of this work will be useful for strain improvement to facilitate lignocellulase and biomass-based chemical production.

Hyphal surface architecture and cell morphology of Trichoderma reesei

The filamentous fungus Trichoderma reesei which is known to secrete high amounts of cellulolytic enzymes was found to produce a massive amount of fibrous material at the outer surface of the cell wall as observed by ultrahigh-resolution low-voltage scanning electron microscopy. Using transmission electron microscopy, the cell wall ornamentation of the hyper-cellulosic mutant PC-3-7 was found to be less massive and much thinner than for QM9414. A significant amount of fibrous material was produced in Avicel-grown cultures that were less abundant in glucose-grown cultures and Avicel was occasionally found entangled within the cell wall-associated fibrous layer.

Trichoderma reesei RUT-C30--thirty years of strain improvement

The hypersecreting mutant Trichoderma reesei RUT-C30 (ATCC 56765) is one of the most widely used strains of filamentous fungi for the production of cellulolytic enzymes and recombinant proteins, and for academic research. The strain was obtained after three rounds of random mutagenesis of the wild-type QM6a in a screening program focused on high cellulase production and catabolite derepression. Whereas RUT-C30 achieves outstanding levels of protein secretion and high cellulolytic activity in comparison to the wild-type QM6a, recombinant protein production has been less successful. Here, we bring together and discuss the results from biochemical-, microscopic-, genomic-, transcriptomic-, glycomic- and proteomic-based research on the RUT-C30 strain published over the last 30 years.

Arsenal of plant cell wall degrading enzymes reflects host preference among plant pathogenic fungi

BACKGROUND

The discovery and development of novel plant cell wall degrading enzymes is a key step towards more efficient depolymerization of polysaccharides to fermentable sugars for the production of liquid transportation biofuels and other bioproducts. The industrial fungus Trichoderma reesei is known to be highly cellulolytic and is a major industrial microbial source for commercial cellulases, xylanases and other cell wall degrading enzymes. However, enzyme-prospecting research continues to identify opportunities to enhance the activity of T. reesei enzyme preparations by supplementing with enzymatic diversity from other microbes. The goal of this study was to evaluate the enzymatic potential of a broad range of plant pathogenic and non-pathogenic fungi for their ability to degrade plant biomass and isolated polysaccharides.

RESULTS

Large-scale screening identified a range of hydrolytic activities among 348 unique isolates representing 156 species of plant pathogenic and non-pathogenic fungi. Hierarchical clustering was used to identify groups of species with similar hydrolytic profiles. Among moderately and highly active species, plant pathogenic species were found to be more active than non-pathogens on six of eight substrates tested, with no significant difference seen on the other two substrates. Among the pathogenic fungi, greater hydrolysis was seen when they were tested on biomass and hemicellulose derived from their host plants (commelinoid monocot or dicot). Although T. reesei has a hydrolytic profile that is highly active on cellulose and pretreated biomass, it was less active than some natural isolates of fungi when tested on xylans and untreated biomass.

CONCLUSIONS

Several highly active isolates of plant pathogenic fungi were identified, particularly when tested on xylans and untreated biomass. There were statistically significant preferences for biomass type reflecting the monocot or dicot host preference of the pathogen tested. These highly active fungi are promising targets for identification and characterization of novel cell wall degrading enzymes for industrial applications.

Three microbial strategies for plant cell wall degradation

Cellulolytic bacteria and fungi have been shown to use two different approaches to degrade cellulose. Most aerobic microbes secrete sets of individual cellulases, many of which contain a carbohydrate binding molecule (CBM), which act synergistically on native cellulose. Most anaerobic microorganisms produce large multienzyme complexes called cellulosomes, which are usually attached to the outer surface of the microorganism. Most of the cellulosomal enzymes lack a CBM, but the cohesin subunit, to which they are bound, does contain a CBM. The cellulases present in each class show considerable overlap in their catalytic domains, and processive cellulases (exocellulases and processive endocellulases) are the most abundant components of both the sets of free enzymes and of the cellulosomal cellulases. Analysis of the genomic sequences of two cellulolytic bacteria, Cytophaga hutchinsonii, an aerobe, and Fibrobacter succinogenes, an anaerobe, suggest that these organisms must use a third mechanism. This is because neither of these organisms, encodes processive cellulases and most of their many endocellulase genes do not encode CBMs. Furthermore, neither organism appears to encode the dockerin and cohesin domains that are key components of cellulosomes.

Rapid isolation of the Trichoderma strain with higher degrading ability of a filter paper and superior proliferation characteristics using avicel plates and the double-layer selection medium

The cost of cellulase is still a problem for bioethanol production. As the cellulase of Trichoderma reesei is applicable for producing ethanol from cellulosic materials, the cellulase productivity of this fungus should be increased. Therefore, we attempted to develop a system to isolate the strain with higher degrading ability of a filter paper and superior proliferation characteristics among the conidia treated with the mitotic arrester, colchicine. When green mature conidia of T. reesei RUT C-30 were swollen, autopolyploidized, and incubated in the double-layer selection medium containing Avicel, colonies appeared on the surface earlier than the original strain. When such colonies and the original colony were incubated on the Avicel plates, strain B5, one of the colonies derived from the colchicine-treated conidia, showed superior proliferation characteristics. Moreover, when strain B5 and the original strain were compared in the filter paper degrading ability and the cellulose hydrolyzing activity, strain B5 was also superior to the original strain. It was suspected that superior proliferation characteristics of strain B5 reflects higher filter paper degrading ability. Thus, we concluded that the Trichoderma strain with higher degrading ability of a filter paper and superior proliferation characteristics can be isolated using Avicel plates and the double-layer selection medium.

A hypercellulolytic mutant of Fusarium oxysporum

Multiple mutagenesis of Fusarium oxysporum DSM 841 resulted in enhanced yields of cellulases. The hypercellulolytic mutant (NTG-19) secretes high levels of extracellular cellulases on different cellulosic substrates. Addition of surfactant, Tween-80, further increased enzyme secretion by about 30%. The results on hydrolysis of wheat straw by parent strain, DSM 841 and mutant NTG-19 cellulases also revealed a significant improvement in the hydrolytic potential of the cellulolytic enzymes from the mutant NTG-19.

The Trichoderma cellulase regulatory puzzle: from the interior life of a secretory fungus

Novel applications for cellulases have reinitiated interest in the regulation of production of these enzymes by the soft rot fungus Trichoderma reesei and related species. This paper reviews the current state of knowledge concerning the question "How can insoluble molecules like cellulose initiate their own breakdown by a microorganism?" The evidence available--based on biochemical as well as molecular biological approaches--favors a model in which conidial bound cellobiohydrolases carry out a first exo-exo-wise attack on the cellulose molecule. The disaccharides so formed (cellobiose, alpha-cellobiono-1,5-lactone) are then taken up by the mycelia and promote further cellulase biosynthesis. Evidence available suggests that they are further metabolized to, rather than being, the "true" inducer. Speculations on the nature of the inducer are presented. The roles of the beta-glucosidases of Trichoderma in this process are discussed. The pathway of cellulase secretion is discussed on the basis of electron microscopical as well as gene sequence information.

Fermentation of cellulose and production of cellulolytic and xylanolytic enzymes by anaerobic fungi from ruminant and non-ruminant herbivores

Four anaerobic fungi were grown on filter paper cellulose and monitored over a 7-8 days period for substrate utilisation, fermentation products, and secretion of cellulolytic and xylanolytic enzymes. Two of the fungi (N1 and N2) were Neocallimastix species isolated from a ruminant (sheep) and the other two fungi were Piromyces species (E2 and R1) isolated from an Indian Elephant and an Indian Rhinoceros, respectively. The tested anaerobic fungi degraded the filter paper cellulose almost completely and estimated cellulose digestion rates were 0.25, 0.13, 0.21 and 0.18 g.l-1.h-1 for strains E2, N1, N2, R1, respectively. All strains secreted cellulolytic and xylanolytic enzymes, including endoglucanase, exoglucanase, beta-glucosidase and xylanase. Strain E2 secreted the highest levels of enzymes in a relatively short time. The product formation on avicel by enzymes secreted by the four fungi was studied. Both in the presence and absence of glucurono-1,5-delta-lactone, a specific inhibitor of beta-glucosidase, mainly glucose was formed but no cellobiose. Therefore the exoglucanase secreted by the four fungi is probably a glucohydrolase.

Glucanase gene diversity in prokaryotic and eukaryotic organisms

A number of bacteria and eukaryotes produce extracellular enzymes that degrade various types of polysaccharides including the glucans starch, cellulose and hemicellulose (xylan). The similarities in the modes of expression and specificity of enzyme classes, such as amylase, cellulose and xylanase, suggest common genetic origins for particular activities. Our determination of the extent of similarity between these glucanases suggests that such data may be of very limited use in describing the early evolution of these proteins. The great diversity of these proteins does allow identification of their most highly conserved (and presumably functionally important) regions.