The relation between xyr1 overexpression in Trichoderma harzianum and sugarcane bagasse saccharification performance

Growth, Enzymatic, and Transcriptomic Analysis of xyr1 Deletion Reveals a Major Regulator of Plant Biomass-Degrading Enzymes in Trichoderma harzianum

The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in this species. The T. harzianum ortholog of the transcriptional activator XYR1/XlnR/XLR-1 was deleted, and the mutant strains were analyzed through growth profiling, enzymatic activities, and transcriptomics on cellulose. From plate cultures, the Δxyr1 mutant had reduced growth on D-xylose, xylan, and cellulose, and from shake-flask cultures with cellulose, the Δxyr1 mutant had ~90% lower β-glucosidase activity, and no detectable β-xylosidase or cellulase activity. The comparison of the transcriptomes from 18 h shake-flask cultures on D-fructose, without a carbon source, and cellulose, showed major effects of XYR1 deletion whereby the Δxyr1 mutant on cellulose was transcriptionally most similar to the cultures without a carbon source. The cellulose induced 43 plant biomass-degrading CAZymes including xylanases as well as cellulases, and most of these had massively lower expression in the Δxyr1 mutant. The expression of a subset of carbon catabolic enzymes, other transcription factors, and sugar transporters was also lower in the Δxyr1 mutant on cellulose. In summary, T. harzianum XYR1 is the master regulator of cellulases and xylanases, as well as regulating carbon catabolic enzymes.

Strain improvement of Trichoderma harzianum for enhanced biocontrol capacity: Strategies and prospects

In the control of plant diseases, biocontrol has the advantages of being efficient and safe for human health and the environment. The filamentous fungus Trichoderma harzianum and its closely related species can inhibit the growth of many phytopathogenic fungi, and have been developed as commercial biocontrol agents for decades. In this review, we summarize studies on T. harzianum species complex from the perspective of strain improvement. To elevate the biocontrol ability, the production of extracellular proteins and compounds with antimicrobial or plant immunity-eliciting activities need to be enhanced. In addition, resistance to various environmental stressors should be strengthened. Engineering the gene regulatory system has the potential to modulate a variety of biological processes related to biocontrol. With the rapidly developing technologies for fungal genetic engineering, T. harzianum strains with increased biocontrol activities are expected to be constructed to promote the sustainable development of agriculture.

Factors regulating cellulolytic gene expression in filamentous fungi: an overview

The growing demand for biofuels such as bioethanol has led to the need for identifying alternative feedstock instead of conventional substrates like molasses, etc. Lignocellulosic biomass is a relatively inexpensive feedstock that is available in abundance, however, its conversion to bioethanol involves a multistep process with different unit operations such as size reduction, pretreatment, saccharification, fermentation, distillation, etc. The saccharification or enzymatic hydrolysis of cellulose to glucose involves a complex family of enzymes called cellulases that are usually fungal in origin. Cellulose hydrolysis requires the synergistic action of several classes of enzymes, and achieving the optimum secretion of these simultaneously remains a challenge. The expression of fungal cellulases is controlled by an intricate network of transcription factors and sugar transporters. Several genetic engineering efforts have been undertaken to modulate the expression of cellulolytic genes, as well as their regulators. This review, therefore, focuses on the molecular mechanism of action of these transcription factors and their effect on the expression of cellulases and hemicellulases.

Network Analysis Reveals Different Cellulose Degradation Strategies Across Trichoderma harzianum Strains Associated With XYR1 and CRE1

Trichoderma harzianum, whose gene expression is tightly controlled by the transcription factors (TFs) XYR1 and CRE1, is a potential candidate for hydrolytic enzyme production. Here, we performed a network analysis of T. harzianum IOC-3844 and T. harzianum CBMAI-0179 to explore how the regulation of these TFs varies between these strains. In addition, we explored the evolutionary relationships of XYR1 and CRE1 protein sequences among Trichoderma spp. The results of the T. harzianum strains were compared with those of Trichoderma atroviride CBMAI-0020, a mycoparasitic species. Although transcripts encoding carbohydrate-active enzymes (CAZymes), TFs, transporters, and proteins with unknown functions were coexpressed with cre1 or xyr1, other proteins indirectly related to cellulose degradation were identified. The enriched GO terms describing the transcripts of these groups differed across all strains, and several metabolic pathways with high similarity between both regulators but strain-specific differences were identified. In addition, the CRE1 and XYR1 subnetworks presented different topology profiles in each strain, likely indicating differences in the influences of these regulators according to the fungi. The hubs of the cre1 and xyr1 groups included transcripts not yet characterized or described as being related to cellulose degradation. The first-neighbor analyses confirmed the results of the profile of the coexpressed transcripts in cre1 and xyr1. The analyses of the shortest paths revealed that CAZymes upregulated under cellulose degradation conditions are most closely related to both regulators, and new targets between such signaling pathways were discovered. Although the evaluated T. harzianum strains are phylogenetically close and their amino acid sequences related to XYR1 and CRE1 are very similar, the set of transcripts related to xyr1 and cre1 differed, suggesting that each T. harzianum strain used a specific regulation strategy for cellulose degradation. More interestingly, our findings may suggest that XYR1 and CRE1 indirectly regulate genes encoding proteins related to cellulose degradation in the evaluated T. harzianum strains. An improved understanding of the basic biology of fungi during the cellulose degradation process can contribute to the use of their enzymes in several biotechnological applications and pave the way for further studies on the differences across strains of the same species.

Engineering the endoplasmic reticulum secretory pathway in Trichoderma reesei for improved cellulase production

The filamentous fungus Trichoderma reesei is an extraordinarily efficient cell factory of industrial cellulase for production of biofuels and other bio-based products because of its excellent potential to secrete cellulolytic enzymes. Engineering the protein secretory pathway may be a powerful means for efficient protein production. However, it is uncertain whether this engineering approach could improve cellulase production in T. reesei. Herein, the endoplasmic reticulum (ER) secretory pathway was engineered for the production of cellulolytic enzymes by multiple strategies, including: (I) overexpression of the key components of protein folding (Pdi1, Ero1 and BiP); (II) overexpression of the glycosylation-related elements (Gpt1 and Gls2); (III) knockout of the ER mannosidase I (Mns1) encoding gene mns1. By utilizing these ER engineering strategies, the secretion of β-glucosidase was remarkably elevated in the engineered strains, ranging from 29.2 % to 112.5 %. Furthermore, it was found that engineering these components also regulated the ER stress resistance. More importantly, the total cellulase production was increased with varying degrees, which reached a maximum of 149.4 %, using the filter paper assay (FPA) as a characterization method. These results demonstrated that engineering the ER secretory pathway can enhance protein secretion, particularly for cellulase production, which shed light for the development of high-efficient cellulolytic enzymes for economically feasible bioethanol production from lignocellulosic biomass.

Tailoring in fungi for next generation cellulase production with special reference to CRISPR/CAS system

Cellulose is the utmost plenteous source of biopolymer in our earth, and fungi are the most efficient and ubiquitous organism in degrading the cellulosic biomass by synthesizing cellulases. Tailoring through genetic manipulation has played a substantial role in constructing novel fungal strains towards improved cellulase production of desired traits. However, the traditional methods of genetic manipulation of fungi are time-consuming and tedious. With the availability of the full-genome sequences of several industrially relevant filamentous fungi, CRISPR-CAS (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) technology has come into the focus for the proficient development of manipulated strains of filamentous fungi. This review summarizes the mode of action of cellulases, transcription level regulation for cellulase expression, various traditional strategies of genetic manipulation with CRISPR-CAS technology to develop modified fungal strains for a preferred level of cellulase production, and the futuristic trend in this arena of research.

"Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)"

BACKGROUND

Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3844 containing CAZyme genes, transcription factors and transporters.

RESULTS

We used bioinformatics tools to mine the T. harzianum genome for potential genomics, transcriptomics, and exoproteomics data and coexpression networks. The DNA was sequenced by PacBio SMRT technology for multiomics data analysis and integration. In total, 1676 genes were annotated in the genomic regions analyzed; 222 were identified as CAZymes in T. harzianum IOC3844. When comparing transcriptome data under cellulose or glucose conditions, 114 genes were differentially expressed in cellulose, with 51 being CAZymes. CLR2, a transcription factor physically and phylogenetically conserved in Trichoderma spp., was differentially expressed under cellulose conditions. The genes induced/repressed under cellulose conditions included those important for plant biomass degradation, including CIP2 of the CE15 family and a copper-dependent LPMO of the AA9 family.

CONCLUSIONS

Our results provide new insights into the relationship between genomic organization and hydrolytic enzyme expression and regulation in T. harzianum IOC3844. Our results can improve plant biomass degradation, which is fundamental for developing more efficient strains and/or enzymatic cocktails to produce hydrolytic enzymes.

The impact of putative methyltransferase overexpression on the Trichoderma harzianum cellulolytic system for biomass conversion

Trichoderma harzianum has attracting attention for its potential alternative use in biofuel production, due to a recognized competence for high diversity glycoside hydrolases (GH) enzyme complex, including higher β-glucosidases and auxiliary proteins, using low-cost carbon sources. This strain constitutively overexpressed the global regulator putative methyltransferase - LAE1, in order to improve the GHs production. The recombinant strain achieved 79-fold increase in lae1 expression and high GHs productivity. The evaluation of the LAE1 impact to induce the GHs used soluble and lignocellulose inexpensive carbon sources in a stirred-tank bioreactor. Using sugarcane bagasse with sucrose, the overexpression of lae1 resulted in significantly increment of gh61b (31x), cel7a (25x), bgl1(20x) and xyn3 (20x) genes expression. Reducing sugar released from pretreated sugarcane bagasse, which hydrolyzed by recombinant crude enzyme cocktail, achieved 41% improvement. Therefore, lae1 overexpression effectively is a promising improving GHs target for biomass degradation by T. harzianum.

Diversity of Cellulase-Producing Filamentous Fungi From Tibet and Transcriptomic Analysis of a Superior Cellulase Producer Trichoderma harzianum LZ117

Filamentous fungi are widely used for producing cellulolytic enzymes to degrade lignocellulosic biomass. Microbial resources from Tibet have received great attention due to the unique geographic and climatic conditions in the Qinghai-Tibet Plateau. However, studies on cellulase producing fungal strains originated from Tibet remain very limited, and so far no studies have been focused on regulation of cellulase production of the specific strains thereof. Here, filamentous fungal strains were isolated from soil, plant, and other environments in Tibet, and cellulase-producing strains were further investigated. A total of 88 filamentous fungal strains were identified, and screening of cellulase-producing fungi revealed that 16 strains affiliated with the genera Penicillium, Trichoderma, Aspergillus, and Talaromyces exhibited varying cellulolytic activities. Among these strains, T. harzianum isolate LZ117 is the most potent producer. Comparative transcriptome analysis using T. harzianum LZ117 and the control strain T. harzianum K223452 cultured on cellulose indicated an intensive modulation of gene transcription related to protein synthesis and quality control. Furthermore, transcription of xyr1 which encodes the global transcriptional activator for cellulase expression was significantly up-regulated. Transcription of cre1 and other predicted repressors controlling cellulase gene expression was decreased in T. harzianum LZ117, which may contribute to enhancing formation of primary cellulases. To our knowledge, this is the first report that the transcription landscape at the early enzyme production stage of T. harzianum was comprehensively described, and detailed analysis on modulation of transporters, regulatory proteins as well as protein synthesis and processing was presented. Our study contributes to increasing the catalog of publicly available transcriptome data from T. harzianum, and provides useful clues for unraveling the biotechnological potential of this species for lignocellulosic biorefinery.

The Kinase USK1 Regulates Cellulase Gene Expression and Secondary Metabolite Biosynthesis in Trichoderma reesei

The complex environment of fungi requires a delicate balance between the efforts to acquire nutrition, to reproduce, and to fend off competitors. In Trichoderma reesei, an interrelationship between regulation of enzyme gene expression and secondary metabolism was shown. In this study, we investigated the physiological relevance of the unique YPK1-type kinase USK1 of T. reesei. Usk1 is located in the vicinity of the SOR cluster and is involved in regulation of several genes from this secondary metabolite cluster as well as dihydrotrichotetronine and other secondary metabolites. Moreover, USK1 is required for biosynthesis of normal levels of secondary metabolites in liquid culture. USK1 positively influences cellulase gene regulation, secreted cellulase activity, and biomass formation upon growth in constant darkness on cellulose. Positive effects of USK1 on transcript abundance of the regulator of secondary metabolism, vel1, and the carbon catabolite repressor gene cre1 are in agreement with these functions. In summary, we found that with USK1, T. reesei comprises a unique kinase that adds an additional layer of regulation to the connection of secondary metabolism and enzyme production in fungi.

Engineering the cbh1 Promoter of Trichoderma reesei for Enhanced Protein Production by Replacing the Binding Sites of a Transcription Repressor ACE1 to Those of the Activators

The strong and inducible cbh1 promoter is most widely used to express heterologous proteins, useful in food and feed industries, in Trichoderma reesei. Enhancing its ability to direct transcription provides a general strategy to improve protein production in T. reesei. The cbh1 promoter was engineered by replacing eight binding sites of the transcription repressor ACE1 to those of the activators ACE2, Hap2/3/5, and Xyr1. While changing ACE1 to Hap2/3/5-binding sites completely abolished the transcription ability, replacements with ACE2- and Xyr1-binding sites (designated cbh1pA and cbh1pX promoters, respectively) largely improved the promoter transcription efficiency, as reflected by expression of a reporter gene DsRed. The cbh1pA and cbh1pX promoters were applied to improve secretory expression of a codon-optimized mannanase from Aspergillus niger to 3.6- and 5.0-fold higher, respectively, which has high application potential in feed industry.

Promoting cellulase and hemicellulase production from Trichoderma orientalis EU7-22 by overexpression of transcription factors Xyr1 and Ace3

The construction of hyper-production strains of cellulase is the prerequisite for the production of biofuels or biochemicals. Trichoderma orientalis EU7-22 with complete cellulase system shows the potential for cellulase production in industrial scale. To improve the cellulase production, two crucial transcription activators Xyr1 and Ace3 were constitutively overexpressed in EU7-22 strain. Cellulase, xylanase and protein secretion were significantly improved in the recombinant strain dxyA-8 under inducing culture, which were 2.34, 0.68 and 1.06 folds higher than those of EU7-22, respectively. Moreover, the FPase and CMCase activities were up to 2.55 IU/mL and 90.38 IU/mL with glucose as carbon source, which were 2.12 and 1.95 folds higher than those of EU7-22 under inducing condition, respectively. Reducing sugar released from pretreated spartina that hydrolyzed by crude enzyme from dxyA-8 had achieved 24% improvement. Therefore, overexpression of these transcription factors effectively promotes the production of cellulase and hemicellulase of Trichoderma orientalis EU7-22.

Rapid production of lignocellulolytic enzymes by Trichoderma harzianum LZ117 isolated from Tibet for biomass degradation

In this study, Trichoderma harzianum LZ117 was obtained during screening of cellulolytic enzyme producers from samples collected in Tibet. T. harzianum LZ117 exhibits dramatically earlier enzyme induction (48 h) and shorter fermentation time (5 days) during cellulase production when compared with the widely studied strain T. reesei QM9414. Strain LZ117 showed 61% of the maximum cellulase activity at 48 h, whereas only 17% of the maximum cellulase activity was detected in QM9414 at the same culture time. Early induction and rapid production of cellulase were also observed in LZ117 when compared with two other T. harzianum strains. Significantly higher glucose yield was obtained using crude enzyme from strain LZ117 from pretreated corn stover and Jerusalem artichoke stalks when compared with that of T. harzianum reference strain K223452. These results indicate that strain LZ117 is a promising cellulase producer for bioconversion of lignocellulosic biomass.

Defective RNA of a Novel Mycovirus with High Transmissibility Detrimental to Biocontrol Properties of Trichoderma spp

Trichoderma species are a group of fungi which is widely distributed in major terrestrial ecosystems; they are also commonly used as biocontrol agents for many plant diseases. A virus, namely Trichoderma harzianum hypovirus 1 (ThHV1), was identified in T. harzianum isolate T-70, and also infected isolate T-70D, together with its defective RNA (ThHV1-S). The ThHV1 genome possessed two Open Reading Frames (ORFs), namely ORF1 and ORF2. The start codon of ORF2 overlapped with the stop codon of ORF1 in a 43 nt long region. The polypeptide encoded by ORF2 of ThHV1 shared sequence similarities with those of betahypoviruses, indicating that ThHV1 is a novel member of Hypoviridea. Isolate T-70D, carrying both ThHV1 and ThHV1-S, showed abnormal biological properties, notably a decreased mycoparasitism ability when compared with isolate T-70. Both ThHV1 and ThHV1-S could be vertically transmitted to conidia and horizontally transmitted to T. harzianum isolate T-68 and T. koningiopsis T-51. The derivative strains carrying both ThHV1 and ThHV1-S showed decreased mycoparasitism ability, whereas strains carrying ThHV1 alone were normal, indicating that ThHV1-S is closely associated with the decreased mycoparasitism ability of T. harzianum isolate T-70D. ThHV1 was widely detected in isolates of T. harzianum, T. koningiopsis and T. atroviride originating from soil of China. Therefore, viruses in fungal biocontrol agents may also be a factor associated with the stability of their application.

Enhanced cellulase and reducing sugar production by a new mutant strain Trichoderma harzianum EUA20

Trichoderma harzianum EU2-77 was a mutant strain of the wild-type strain T. harzianum NP13a isolated in Singapore. A multi-mutagenesis one-screening (MMOS) method was developed to further improve strain EU2-77 and a new mutant EUA20 was obtained. It exhibited filter paper cellulase (FPase) activity up to 14.79 IU/mL within 6 days shake flask cultivation. Activities of FPase, endoglucanase, β-glucosidase, and xylanase, and protein content by EUA20 were respectively increased to 5.73, 4.35, 7.34, 1.80 and 2.70 folds. Using pretreated oil palm empty fruit bunch (OPEFB) and corncob powder as the substrates, strain EUA20 presented approximate 6.52 and 8.80 IU/ml FPase activity. Reducing sugar yield of 615.8 and 636.8 mg/g biomass were respectively obtained for OPEFB and corncob powder using cellulolytic enzymes of strain EUA20. Our results demonstrated that mutant strain EUA20 had great potential in on-site cellulase production for effective biomass bioconversion.

Gene expression engineering in fungi

Fungi are a highly diverse group of microbial species that possess a plethora of biotechnologically useful metabolic and physiological properties. Important enablers for fungal biology studies and their biotechnological use are well-performing gene expression tools. Different types of gene expression tools exist; however, typically they are at best only functional in one or a few closely related species. This has hampered research and development of industrially relevant production systems. Here, we review operational principles and concepts of fungal gene expression tools. We present an overview on tools that utilize endogenous fungal promoters and modified hybrid expression systems composed of engineered promoters and transcription factors. Finally, we review synthetic expression tools that are functional across a broad range of fungal species.

Engineered microbial host selection for value-added bioproducts from lignocellulose

Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.

A closed-loop strategy for endoglucanase production using sugarcane bagasse liquefied by a home-made enzymatic cocktail

Use of the same lignocellulosic biomass as feedstock for enzymes and ethanol production has been suggested as a lower cost option in future biorefineries. Here, we propose a closed-loop strategy to produce the cellulolytic enzymes required for biomass hydrolysis using sugarcane bagasse liquefied by a home-made enzymatic cocktail as carbon source and inducer. The fed-batch liquefaction conditions were firstly evaluated using commercial enzymes. Subsequently, the effects of different liquefied materials and solids loadings on endoglucanase production by Aspergillus niger cultivated in submerged fermentation were investigated. The liquefied bagasse produced using the home-made cocktail was more favorable for endoglucanase production, resulting in improvement up to 17%, compared to bagasse liquefied by commercial enzymes. The results indicated that liquefied bagasse produced by home-made enzymatic cocktail could provide a cost-effective carbon source and inducer for cellulolytic enzyme production, and could contribute to closing loops within the biorefinery, thus reducing costs and minimizing waste.

Genetic engineering of Trichoderma reesei cellulases and their production

Lignocellulosic biomass, which mainly consists of cellulose, hemicellulose and lignin, is the most abundant renewable source for production of biofuel and biorefinery products. The industrial use of plant biomass involves mechanical milling or chipping, followed by chemical or physicochemical pretreatment steps to make the material more susceptible to enzymatic hydrolysis. Thereby the cost of enzyme production still presents the major bottleneck, mostly because some of the produced enzymes have low catalytic activity under industrial conditions and/or because the rate of hydrolysis of some enzymes in the secreted enzyme mixture is limiting. Almost all of the lignocellulolytic enzyme cocktails needed for the hydrolysis step are produced by fermentation of the ascomycete Trichoderma reesei (Hypocreales). For this reason, the structure and mechanism of the enzymes involved, the regulation of their expression and the pathways of their formation and secretion have been investigated in T. reesei in considerable details. Several of the findings thereby obtained have been used to improve the formation of the T. reesei cellulases and their properties. In this article, we will review the achievements that have already been made and also show promising fields for further progress.

Raw sugarcane bagasse as carbon source for xylanase production by Paenibacillus species: a potential degrader of agricultural wastes

Paenibacillus species isolated from a variety of natural sources have shown to be important glycoside hydrolases producers. These enzymes play a key role in bio-refining applications, as they are central biocatalysts for the processing of different types of polymers from vegetal biomass. Xylanase production by three native isolates belonging to the genus Paenibacillus was approached by utilizing mineral-based medium and agricultural by-products as a convenient source to produce biocatalysts suitable for their degradation. While varieties of alkali pretreated sugarcane bagasse were useful substrates for the strains from Paenibacillus genus evaluated, raw sugarcane bagasse was the most effective substrate for endoxylanase production by Paenibacillus sp. AR247. This strain was then selected to further improvement of its enzyme production by means of a two-step statistical approach. It was determined that the carbon source, provided as an inexpensive agro-waste, as well as phosphate and magnesium were the culture media components that most influenced the enzyme production, which was improved three times compared to the screening results.