A novel transcriptional repressor specifically regulates xylanase gene 1 in Trichoderma reesei

BACKGROUND

The well-known industrial fungus Trichoderma reesei has an excellent capability of secreting a large amount of cellulases and xylanases. The induced expression of cellulase and xylanase genes is tightly controlled at the transcriptional level. However, compared to the intensive studies on the intricate regulatory mechanism of cellulase genes, efforts to understand how xylanase genes are regulated are relatively limited, which impedes the further improvement of xylanase production by T. reesei via rational strain engineering.

RESULTS

To identify transcription factors involved in regulating xylanase gene expression in T. reesei, yeast one-hybrid screen was performed based on the promoters of two major extracellular xylanase genes xyn1 and xyn2. A putative transcription factor named XTR1 showing significant binding capability to the xyn1 promoter but not that of xyn2, was successfully isolated. Deletion of xtr1 significantly increased the transcriptional level of xyn1, but only exerted a minor promoting effect on that of xyn2. The xylanase activity was increased by ~ 50% with XTR1 elimination but the cellulase activity was hardly affected. Subcellular localization analysis of XTR1 fused to a green fluorescence protein demonstrated that XTR1 is a nuclear protein. Further analyses revealed the precise binding site of XTR1 and nucleotides critical for the binding within the xyn1 promoter. Moreover, competitive EMSAs indicated that XTR1 competes with the essential transactivator XYR1 for binding to the xyn1 promoter.

CONCLUSIONS

XTR1 represents a new transcriptional repressor specific for controlling xylanase gene expression. Isolation and functional characterization of this new factor not only contribute to further understanding the stringent regulatory network of xylanase genes, but also provide important clues for boosting xylanase biosynthesis in T. reesei.

Endogenous production of 2-phenylethanol by Cunninghamella echinulata inhibits biofilm growth of the fungus

The filamentous fungus Cunninghamella echinulata is a model of mammalian xenobiotic metabolism. Under certain conditions it grows as a biofilm, which is a natural form of immobilisation and enables the fungus to catalyse repeated biotransformations. Putative signalling molecules produced by other Cunninghamella spp., such as 3-hydroxytyrosol and tyrosol, do not affect the biofilm growth of C. echinulata, suggesting that it employs a different molecule to regulate biofilm growth. In this paper we report that 2-phenylethanol is produced in higher concentrations in planktonic cultures of C. echinulata than when the fungus is grown as a biofilm. We demonstrate that exogenously added 2-phenylethanol inhibits biofilm growth of C. echinulata but has no effect on planktonic growth. Furthermore, we show that addition of 2-phenylethanol to established C. echinulata biofilm causes detachment. Therefore, we conclude that this molecule is produced by the fungus to regulate biofilm growth.

A secondary function of trehalose-6-phosphate synthase is required for resistance to oxidative and desiccation stress in Fusarium verticillioides

The disaccharide trehalose has long been recognized for its role as a stress solute, but in recent years some of the protective effects previously ascribed to trehalose have been suggested to arise from a function of the trehalose biosynthesis enzyme trehalose-6-phosphate (T6P) synthase that is distinct from its catalytic activity. In this study, we use the maize pathogenic fungus Fusarium verticillioides as a model to explore the relative contributions of trehalose itself and a putative secondary function of T6P synthase in protection against stress as well as to understand why, as shown in a previous study, deletion of the TPS1 gene coding for T6P synthase reduces pathogenicity against maize. We report that a TPS1-deletion mutant of F. verticillioides is compromised in its ability to withstand exposure to oxidative stress meant to simulate the oxidative burst phase of maize defense and experiences more ROS-induced lipid damage than the wild-type strain. Eliminating T6P synthase expression also reduces resistance to desiccation, but not resistance to phenolic acids. Expression of catalytically-inactive T6P synthase in the TPS1-deletion mutant leads to a partial rescue of the oxidative and desiccation stress-sensitive phenotypes, suggesting the importance of a T6P synthase function that is independent of its role in trehalose synthesis.

Engineered living materials grown from programmable Aspergillus niger mycelial pellets

The development of engineered living materials (ELMs) has recently attracted significant attention from researchers across multiple disciplines. Fungi-derived ELMs represent a new type of macroscale, cost-effective, environmentally sustainable materials. However, current fungi-based ELMs either have to undergo a final process to heat-kill the living cells or rely on the co-culture with a model organism for functional modification, which hinders the engineerability and versatility of these materials. In this study, we report a new type of ELMs - grown from programmable Aspergillus niger mycelial pellets - by a simple filtration step under ambient conditions. We demonstrate that A. Niger pellets can provide sufficient cohesion to maintain large-area self-supporting structures even under low pH conditions. Subsequently, by tuning the inducible expression of genes involved in melanin biosynthesis, we verified the fabrication of self-supporting living membrane materials with tunable colors in response to xylose concentration in the surroundings, which can be further explored as a potential biosensor for detecting xylose level in industrial wastewater. Notably, the living materials remain alive, self-regenerative, and functional even after 3-month storage. Thus, beyond reporting a new engineerable fungi chassis for constructing ELMs, our study provides new opportunities for developing bulk living materials for real-world applications such as the production of fabrics, packaging materials, and biosensors.

Two high-mobility group domains of MHG1 are necessary to maintain mtDNA in Neurospora crassa

The mhg1 (NCU02695/ada-23) gene encodes the mitochondrial high-mobility group box (HMG-box or HMGB) protein in Neurospora crassa. The mhg1 KO strain (mhg1^KO) has mitochondrial DNA (mtDNA) instability and a short lifespan; however, the function of MHG1 remains unclear. To investigate the role of this protein in the maintenance of mtDNA, domain deleted MHG1 proteins were expressed in the mhg1^KO strain, and their effects were analyzed. We identified two putative HMG-domains, HMGBI and HMGBII. Although deletion of the HMG-box did not abolish MHG1's mitochondrial localization, the mhg1^KO phenotype of a severe growth defect and a high sensitivity to mutagens could not be restored by introduction of HMG-box deleted mhg1 gene into the KO strain. It was indicated that recombinant full-length MHG1, i.e., mitochondrial targeting sequence (MTS) containing protein, did not exhibit explicit DNA binding, whereas the MHG1 protein truncated for the MTS sequence did in vitro by an electrophoretic mobility shift assay. Furthermore, recombinant MHG1 protein lacking MTS and HMG-domains, either HMGBI or HMGBII, had DNA affinity and an altered band shift pattern compared with MTS-truncated MHG1 protein. These results suggest that cleavage of MTS and appropriate DNA binding via HMG-domains are indispensable for maintaining mtDNA in N. crassa.

Bio-flocculation of Microcystis aeruginosa by using fungal pellets of Aspergillus oryzae: Performance and mechanism

Algal blooms caused by eutrophication are global phenomena that seriously threaten the sustainable use of freshwater resources. Traditional water treatment chemicals often typically lead to high levels of residue and cause damage to the morphology of algal cells. This study investigated an eco-friendly fungal bio-flocculant, Aspergillus oryzae, to remove the representative microalgae (Microcystis aeruginosa). Furthermore, it explored crucial flocculation parameters, adsorption kinetics, and thermodynamics of microalgae using A. oryzae. Accordingly, a flocculation efficiency of >95% was achieved when the fungus was cultured for six days, flocculant dosage was 11 g/L, rotation speed was 100 rpm, temperature was 25 °C, flocculation time was 5 h, and pH ranged between 4.0 and 9.0. KEGG analysis based on the genomic data, and chemical composition analysis revealed that proteins and polysaccharides were the major components of metabolites. Zeta potential analysis, scanning electron microscopy, three-dimensional fluorescence, X-ray spectroscopy, and infrared spectroscopy, electrostatic attraction revealed that electrostatic attraction promoted the destabilization and aggregation of microalgae. Additionally, hyphal surface adsorption and chemisorption from extracellular proteins and exopolysaccharides aided in the removal of microalgae. Therefore, fungi-based bio-flocculants have the potential to remove microalgae in a simple, effective, and eco-friendly manner without the complex extraction of extracellular metabolites.

Transmembrane transport process and endoplasmic reticulum function facilitate the role of gene cel1b in cellulase production of Trichoderma reesei

Background

A total of 11 β-glucosidases are predicted in the genome of Trichoderma reesei, which are of great importance for regulating cellulase biosynthesis. Nevertheless, the relevant function and regulation mechanism of each β-glucosidase remained unknown.

Results

We evidenced that overexpression of cel1b dramatically decreased cellulase synthesis in T. reesei RUT-C30 both at the protein level and the mRNA level. In contrast, the deletion of cel1b did not noticeably affect cellulase production. Protein CEL1B was identified to be intracellular, being located in vacuole and cell membrane. The overexpression of cel1b reduced the intracellular pNPGase activity and intracellular/extracellular glucose concentration without inducing carbon catabolite repression. On the other hand, RNA-sequencing analysis showed the transmembrane transport process and endoplasmic reticulum function were affected noticeably by overexpressing cel1b. In particular, some important sugar transporters were notably downregulated, leading to a compromised cellular uptake of sugars including glucose and cellobiose.

Conclusions

Our data suggests that the cellulase inhibition by cel1b overexpression was not due to the β-glucosidase activity, but probably the dysfunction of the cellular transport process (particularly sugar transport) and endoplasmic reticulum (ER). These findings advance the knowledge of regulation mechanism of cellulase synthesis in filamentous fungi, which is the basis for rationally engineering T. reesei strains to improve cellulase production in industry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01809-1.

Decalintetracids A and B, two pairs of unusual 3-decalinoyltetramic acid derivatives with phytotoxicity from Fusarium equiseti D39

The filamentous fungi Fusarium sp. are well-known for their ability to produce abundant specialised metabolites with attractive chemical structures and bioactivities. In this study, chemical analyses of the endophyte F. equiseti D39 led to the isolation and identification of two pairs of undescribed 3-decalinoyltetramic acids (3DTAs) E/Z diastereomers, decalintetracids A and B. Their structures were elucidated by comprehensive spectroscopic analysis and quantum-chemical calculations. Although 3DTAs were commonly reported from fungi, decalintetracid A possessed an unprecedented tricyclo [7.2.1.0^2,7] dodecane skeleton, which added the diversity of these fungal metabolites. In addition, decalintetracid B was featured by a unique 6/6/5 ring system core. A plausible biosynthetic pathway for decalintetracids A and B was proposed. Both compounds exhibited phytotoxicity toward Amaranthus retroflexus L. and Amaranthus hybrid, indicating their potential as natural herbicides.

A sustainable approach on biomining of low-grade bauxite by P. simplicissimum using molasses medium

In order to find a sustainable and low-cost alternative route to the traditional recovery of aluminum, the filamentous fungus Penicillium simplicissimum was evaluated for aluminum recovery from low-grade bauxite ore. The oat-agar medium was carefully chosen as the foremost solid medium for fungal sporulation due to lower cost, ease in preparation, and high spore production in a short incubation time. To examine the acid production capability in submerged fermentation, P. simplicissimum was inoculated in a medium augmented with glucose and molasses as an energy source. High-performance liquid chromatography (HPLC) technique was used for the determination of the produced organic acids. Three different bioleaching approaches were evaluated using 1% bauxite pulp density. The culture containing P. simplicissimum spores grown in a medium supplemented with molasses leached 86.6% Al in the direct two steps on the fifth day, 56.5% in the direct one step on the fourth day, and 71.7% in the indirect bioleaching on the fourth day, while in the controlled sterile flasks, Al leaching was almost negligible. A maximal amount of Al was leached by the fungal strains using low-cost molasses as a substrate.

Construction of a novel filamentous fungal protein expression system based on redesigning of regulatory elements

Filamentous fungi are extensively used as an important expression host for the production of a variety of essential industrial proteins. They have significant promise as an expression system for protein synthesis due to their inherent superior secretory capabilities. The purpose of this study was to develop a novel expression system by utilizing a Penicillium oxalicum strain that possesses a high capacity for protein secretion. The expression of glycoside hydrolases in P. oxalicum was evaluated in a cleaner extracellular background where the formation of two major amylases was inhibited. Four glycoside hydrolases (CBHI, Amy15B, BGL1, and Cel12A) were expressed under the highly constitutive promoter PubiD. It was found that the proteins exhibited high purity in the culture supernatant after cultivation with starch. Two inducible promoters, Pamy15A and PempA, under the activation of the transcription factor AmyR were used as elements in the construction of versatile vectors. When using the cellobiohydrolase CBHI as the extracellular quantitative reporter, the empA promoter screened from the AmyR-overexpressing strain was shown to be superior to the amy15A promoter based on RNA-sequencing data. Therefore, we designed an expression system consisting of a cleaner background host strain and an adjustable promoter. This system enables rapid and high-throughput evaluation of glycoside hydrolases from filamentous fungi.Key points• A new protein expression system derived from Penicillium oxalicum has been developed.• The expression platform is capable of secreting recombinant proteins with high purity.• The adjustable promoter may allow for further optimization of recombinant protein synthesis.

A peroxisomal sterol carrier protein 2 (Scp2) contributes to lipid trafficking in differentiation and virulence of the insect pathogenic fungus Beauveria bassiana

Sterol carrier protein 2 (SCP2) represents a family of proteins binding a variety of lipids and plays essential roles in cellular physiology. However, its physiological roles are largely unknown in filamentous fungi. In this study, we functionally characterized an orthologous Scp2 gene in the filamentous insect pathogenic fungus Beauveria bassiana (BbScp2). BbScp2 was verified to be a peroxisomal protein and displayed different affinities to various lipids, with strong affinity to palmitic acid (PA) and ergosterol (ES). No significant binding activity was detected between protein and oleic acid (OA) or linoleic acid (LA). Ablation of BbScp2 did not cause significant effects on fungal growth on various carbon sources, but resulted in a modest reduction in conidial (49%) and blastospore yield (45%). In addition, exogenous lipids could recover the defectives in conidiation of ΔBbScp2 mutant strain. BbScp2 was required for the cytomembrane functionality in germlings, and its loss resulted in a more significant decrease in virulence indicated by cuticle infection assay than intrahemocoel injection assay. Our findings indicate that Scp2 links the lipid trafficking to the asexual differentiation and virulence of B. bassiana.

Talaromyces cellulolyticus as a promising candidate for biofilm construction and treatment of textile wastewater

Screening of microorganisms with broad-spectrum adaptability to extreme acid-base conditions and highperformance is essential for the construction of high-efficient biochemical wastewater treatment system. Herein, an acid-tolerant fungus isolated from acid medium was successfully identified through micromorphological observation and molecular characterization. The isolated fungus matched well with the filamentous fungus and was eventually identified as Talaromyces cellulolyticus. Considering the wide-range adaptability to pH condition (2.0-9.0), high cellulase activity (11.25 U mL^-1), ideal biofilm-forming property (17.87 mg cm^-3) on the surface of ceramsites, high tolerance to metal ions, and potential adsorption performance for aniline dyes, T. cellulolyticus issuitable for the construction of biofilm treatment system and treatment of textile wastewater based on the investigation of the removal efficiency of chemical oxygen demand and chromaticity of the synthetic textile wastewater. A promising candidate filamentous fungus for the treatment of textile wastewater was provided.

A virulence-related lectin traffics into eisosome and contributes to functionality of cytomembrane and cell-wall in the insect-pathogenic fungus Beauveria bassiana

Lectins are characterized of the carbohydrate-binding ability and play comprehensive roles in fungal physiology (e.g., defense response, development and host-pathogen interaction). Beauveria bassiana, a filamentous entomopathogenic fungus, has a lectin-like protein containing a Fruit Body_domain (BbLec1). BbLec1 could bind to chitobiose and chitin in fungal cell wall. BbLec1 proteins interacted with each other to form multimers, and translocated into eisosomes. Further, the interdependence between BbLec1 and the eisosome protein PliA was essential for stabilizing the eisosome architecture. To test the BbLec1 roles in B. bassiana, we constructed the gene disruption and complementation mutants. Notably, the BbLec1 loss resulted in the impaired cell wall in mycelia and conidia as well as conidial formation capacity. In addition, disruption of BbLec1 led to the reduced cytomembrane integrity and the enhanced sensitivity to osmotic stress. Finally, ΔBbLec1 mutant strain displayed the weakened virulence when compared with the wild-type strain. Taken together, BbLec1 traffics into eisosome and links the functionality of eisosome to development and virulence of B. bassiana.

A novel vector-based RNAi method using mouse U6 promoter-driven shRNA expression in the filamentous fungus Blakeslea trispora

PURPOSE

There are several studies on the use of RNA interference (RNAi) for gene function analysis in fungi. However, most studies on filamentous fungi are based on in vitro-transcribed or -synthesized small interfering RNA (siRNA), and only a few have reported the use of vector-based RNAi. Here we want to develop and evaluate a new vector-based RNAi method using the mouse U6 promoter to drive short hairpin RNA (shRNA) expression in the filamentous fungi.

METHODS

Molecular techniques were employed to develop and evaluate a new vector-based RNAi method using the mouse U6 promoter to drive short hairpin RNA (shRNA) expression in the filamentous fungus Blakeslea trispora.

RESULTS

We characterized the mouse U6 promoter and utilized it for the expression of shRNA in B. trispora. Using real-time polymerase chain reaction and western blotting analyses, we confirmed the decrease in the mRNA and protein expression of carRA, respectively, in cells transformed with the mouse U6 promoter-driven shRNA expression vector. This indicated that the shRNA was transcribed from the mouse U6 promoter and correctly processed into siRNA and that the mouse U6 promoter exhibited transcription ability in the filamentous fungi.

CONCLUSIONS

The results suggest that the mouse U6 promoter that drives the expression of shRNA vectors may serve as a novel tool for RNAi induction in filamentous fungi.

Disruption of the Trichoderma reesei gul1 gene stimulates hyphal branching and reduces broth viscosity in cellulase production

Hyphal morphology is considered to have a close relationship with the production level of secreted proteins by filamentous fungi. In this study, the gul1 gene, which encodes a putative mRNA-binding protein, was disrupted in cellulase-producing fungus Trichoderma reesei. The hyphae of Δgul1 strain produced more lateral branches than the parent strain. Under the condition for cellulase production, disruption of gul1 resulted in smaller mycelial clumps and significantly lower viscosity of fermentation broth. In addition, cellulase production was improved by 22% relative to the parent strain. Transcriptome analysis revealed that a set of genes encoding cell wall remodeling enzymes as well as hydrophobins were differentially expressed in the Δgul1 strain. The results suggest that the regulatory role of gul1 in cell morphogenesis is likely conserved in filamentous fungi. To our knowledge, this is the first report on the engineering of gul1 in an industrially important fungus.

Acetate as substrate for L-malic acid production with Aspergillus oryzae DSM 1863

BACKGROUND

Microbial malic acid production is currently not able to compete economically with well-established chemical processes using fossil resources. The utilization of inexpensive biomass-based substrates containing acetate could decrease production costs and promote the development of microbial processes. Acetate is a by-product in lignocellulosic hydrolysates and fast pyrolysis products or can be synthesized by acetogens during syngas fermentation. For the fermentation of these substrates, a robust microorganism with a high tolerance for biomass-derived inhibitors is required. Aspergillus oryzae is a suitable candidate due to its high tolerance and broad substrate spectrum. To pave the path towards microbial malic acid production, the potential of acetate as a carbon source for A. oryzae is evaluated in this study.

RESULTS

A broad acetate concentration range was tested both for growth and malic acid production with A. oryzae. Dry biomass concentration was highest for acetic acid concentrations of 40-55 g/L reaching values of about 1.1 g/L within 48 h. Morphological changes were observed depending on the acetate concentration, yielding a pellet-like morphology with low and a filamentous structure with high substrate concentrations. For malic acid production, 45 g/L acetic acid was ideal, resulting in a product concentration of 8.44 ± 0.42 g/L after 192 h. The addition of 5-15 g/L glucose to acetate medium proved beneficial by lowering the time point of maximum productivity and increasing malic acid yield. The side product spectrum of cultures with acetate, glucose, and cultures containing both substrates was compared, showing differences especially in the amount of oxalic, succinic, and citric acid produced. Furthermore, the presence of CaCO3, a pH regulator used for malate production with glucose, was found to be crucial also for malic acid production with acetate.

CONCLUSIONS

This study evaluates relevant aspects of malic acid production with A. oryzae using acetate as carbon source and demonstrates that it is a suitable substrate for biomass formation and acid synthesis. The insights provided here will be useful to further microbial malic acid production using renewable substrates.

Image Analysis Method for the Characterization of Trichoderma reesei During Fermentations

This chapter describes the use of a specific image analysis method with the plug im! software for the characterization of filamentous fungus morphology. It details an application of this method with samples obtained from a fermentation process of a Trichoderma reesei strain. This fully automated and accurate image analysis method provides quantitative and representative data for morphological and topological analyses.

Efficient expressions of reporter genes in the industrial filamentous fungus Sclerotium rolfsii mediated by Agrobacterium tumefaciens

Sclerotium rolfsii (teleomorph Athelia rolfsii) is one of the plant pathogenic basidiomycetes, which causes severe stem-rot disease in hundreds of plants and produces important metabolites, such as scleroglucan and TF-specific lectin. However, further molecular biological research on this filamentous fungus is severely plateaued out due to the lack of genetic methods. In this study, the A. tumefaciens strain LBA4404 harboring a binary vector containing the basta resistance gene fused with three reporters (DsRed, tdTomato, and GUSPlus) respectively, driven by the SrGPD promoter, was used for genetic transformation of S. rolfsii. The results showed that the three reporter genes were all effectively expressed in S. rolfsii. This study also showed that the intron of the SrGPD promoter is not necessary for transgene expression in this fungus. Besides, we showed that these reporters' signals could be observed easily but in a short time window. The efficient Agrobacterium-mediated transformation system and the three reporter gene plasmids for S. rolfsii developed in this study are of significance in overcoming current limitations of no available transformation and genetic manipulation techniques in S. rolfsii, facilitating further genetic manipulations and gene function exploration.

A simple approach to mediate genome editing in the filamentous fungus Trichoderma reesei by CRISPR/Cas9-coupled in vivo gRNA transcription

OBJECTIVE

To simplify CRISPR/Cas9 genome editing in the industrial filamentous fungus Trichoderma reesei based on in vivo guide RNA (gRNA) transcription.

RESULTS

Two putative RNA polymerase III U6 snRNA genes were identified in the genome of T. reesei QM6a by BLASTN using Myceliophthora. thermophila U6 snRNA gene as the template. The regions approximately 500 bp upstream of two U6 genes were efficient promoters for the in vivo expression of gRNA. The CRISPR system consisting of Cas9 and in vivo synthesized gRNA under control of the T. reesei U6 snRNA promoters was sufficient to cause a frameshift mutation in the ura5 gene via non-homologous end-joining-mediated events.

CONCLUSIONS

We report a simple gene editing method using a CRISPR/Cas9-coupled in vivo gRNA transcription system in T. reesei.

Subtopic: Advances in water and wastewater treatment harvesting of Chlorella sp. microalgae using Aspergillus niger as bio-flocculant for aquaculture wastewater treatment

Microalgae have been increasingly used to generate biofuel, thus a sustainable technique should be implemented to harvest the biomass to ensure its existence in the environment. Aspergillus niger was used as bio-flocculant to harvest microalgae from aquaculture wastewater via flocculation technique over a range of pH and mixing rate. The bio-flocculant showed ability to adapt at a wide range of pH from 3.0 to 9.0 and at a mixing rate of 100-150 rpm, producing a harvesting efficiency of higher than 90%. The treated water possessed low concentration of chlorophyll-a (0.3-0.6 mg L^-1) and cell density (2 × 10⁶-3 × 10⁶ cell mL^-1). These indicate that Aspergillus niger is a promising bio-flocculant to be used in harvesting microalgae, thus promoting the use of flocculation as a green technology in aquaculture wastewater treatment.

Characterization of gfdB, putatively encoding a glycerol 3-phosphate dehydrogenase in Aspergillus nidulans

The genome of Aspergillus nidulans accommodates two glycerol 3-phosphate dehydrogenase genes, gfdA and gfdB. Previous studies confirmed that GfdA is involved in the osmotic stress defence of the fungus. In this work, the physiological role of GfdB was characterized via the construction and functional characterization of the gene deletion mutant ΔgfdB. Unexpectedly, ΔgfdB strains showed oxidative stress sensitivity in the presence of a series of well-known oxidants including tert-butyl-hydroperoxide (tBOOH), diamide as well as hydrogen peroxide. Moderate sensitivity of the mutant towards the cell wall stress inducing agent CongoRed was also observed. Hence, both Gfd isoenzymes contributed to the environmental stress defence of the fungus but their functions were stress-type-specific. Furthermore, the specific activities of certain antioxidant enzymes, like catalase and glutathione peroxidase, were lower in ΔgfdB hyphae than those recorded in the control strain. As a consequence, mycelia from ΔgfdB cultures accumulated reactive species at higher levels than the control. On the other hand, the specific glutathione reductase activity was higher in the mutant, most likely to compensate for the elevated intracellular oxidative species concentrations. Nevertheless, the efficient control of reactive species failed in ΔgfdB cultures, which resulted in reduced viability and, concomitantly, early onset of programmed cell death in mutant hyphae. Inactivation of gfdB brought about higher mannitol accumulation in mycelia meanwhile the erythritol production was not disturbed in unstressed cultures. After oxidative stress treatment with tBOOH, only mannitol was detected in both mutant and control mycelia and the accumulation of mannitol even intensified in the ΔgfdB strain.

Prospective survey of Aspergillus species isolated from clinical specimens and their antifungal susceptibility: A five-year single-center study in Japan

Aspergillus fumigatus is the most prevalent species that causes aspergillosis. A. fumigatus strains with tandem repeats in the cyp51A promoter have emerged in the environment. Aspergillus species other than A. fumigatus have also been recognized as causative agents of aspergillosis; however, they show lower susceptibility to antifungals compared with A. fumigatus. Therefore, it is important to precisely identify Aspergillus species and determine their antifungal susceptibility. Herein, we collected 119 mold strains isolated from clinical specimens collected at a hospital between November 2013 and December 2018. The collected strains were identified by sequencing several regions, including internal transcribed spacers, and determined their susceptibility to the antifungals itraconazole, voriconazole, and amphotericin B. Of 119 strains, 107 were Aspergillus species, which were identified as A. fumigatus (67), Aspergillus section Nigri (21), A. flavus (7), A. terreus (6), and A. nidulans (6). In Aspergillus section Nigri, the number of A. niger was less than the number of A. welwitschiae and A. tubingensis. Two azole-resistant A. fumigatus samples were included among the isolates. Four of the eight A. tubingensis isolates showed less susceptibility to voriconazole; however, all isolates of A. niger and A. welwitschiae were susceptible to itraconazole and voriconazole. Because of lack of susceptibility data for non-fumigatus Aspergillus and an increasing frequency of antifungal resistance among A. fumigatus, our data along with further surveillance may contribute to determining the frequency and susceptibility of Aspergillus spp. clinical isolates in Japan.

Progress and Challenges: Development and Implementation of CRISPR/Cas9 Technology in Filamentous Fungi

Widely distributed in various environmental niches, filamentous fungi play an important role in industry, drug development, and plant/animal health. Manipulation of the genome and the coding sequences are essential for a better understanding of the function of genes and their regulation, but traditional genetic approaches in some filamentous fungi are either inefficient or nonfunctional. The rapid development and wide implementation of CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats /(CRISPR)-associated protein-9 nuclease) technology for various model and non-model organisms has provided the initial framework to adapt this gene editing technology for filamentous fungi. In this review, an overview of the CRISPR/Cas9 tools and strategies that have been developed for different filamentous fungi is presented, including integration of the CAS9 gene into the genome, transient expression of Cas9/sgRNA, the AMA1-based plasmid approach, and the Cas9 RNP method. The various applications of CRISPR/Cas9 technology in filamentous fungi that have been implemented are explored, with particular emphasis on gene disruption/deletion and precise genome modification through gene tagging and alteration in gene regulation. Potential challenges that are confronted when developing a CRISPR/Cas9 system for filamentous fungi are also discussed such as the nuclear localization sequence for the CAS9 gene, potential off-target effects, and highly efficient transformation methods. Overcoming these obstacles may further facilitate wide application of this technology. As a simple, economical, and powerful tool, CRISPR/Cas9 systems have the potential for future implementation into many molecular aspects of filamentous fungi.

New insights on yeast and filamentous fungus adhesion in a natural co-immobilization system: proposed advances and applications in wine industry

Fungi possess extraordinary strength in attachment to biotic and abiotic surfaces. This review focuses on adhesion mechanisms of yeast and filamentous fungi and the proposed combination of the adhesive forces of both organisms in an immobilization system called yeast biocapsules, whereby Saccharomyces cerevisiae cells are attached to the hyphae of Penicillium chrysogenum. The natural adherent properties of each organism, one multicellular and another unicellular, allow yeast to be fixated securely on the filamentous fungi and complete alcoholic fermentation. Following alcoholic fermentation, the hyphae become an inert support for yeast cells while maintaining shape and integrity. Biocapsules have been used successfully in both wine and bioethanol production. Investigation of the potential genes involved in fungal-yeast fusion suggests that natural hydrophobic interactions of both organisms play a major role. Analysis of the possible mechanisms involved in fungus and yeast adhesion, future perspectives on improving yeast immobilization, and proposed applications of the biocapsules are explored.

Biodegradation of n-hexadecane by Aspergillus sp. RFC-1 and its mechanism

Fungi can use n-hexadecane (HXD) as a sole carbon source. But the mechanism of HXD degradation remains unclear. This work mainly aimed to study the degradation of HXD by Aspergillus sp. RFC-1 obtained from oil-contaminated soil. The HXD content, medium acidification and presence of hexadecanoic acid in the medium were determined by gas chromatography-mass spectrometry, and fungal growth was observed. Enzyme and gene expression assays suggested the involvement of an alkane hydroxylase, an alcohol dehydrogenase, and a P450 enzyme system in HXD degradation. A biosurfactant produced by the strain RFC-1 was also characterized. During 10 days of incubation, 86.3% of HXD was degraded by RFC-1. The highest activities of alkane hydroxylase (125.4 µmol mg^-1 protein) and alcohol dehydrogenase (12.5 µmol mg^-1 proteins) were recorded. The expression level of cytochrome P450 gene associated with oxidation was induced (from 0.94-fold to 5.45-fold) under the HXD condition by Real-time PCR analysis. In addition, HXD accumulated in inclusion bodies of RFC-1with the maximum of 5.1 g L^-1. Results of blood agar plate and thin-layer chromatography analysis showed RFC-1 released high lipid and emulsification activity in the fungal culture. Induced cell surface hydrophobicity and reduced surface tension also indicated the RFC-1-mediated biosurfactant production, which facilitated the HXD degradation and supported the degradation process.

Targeted Gene Deletion in Cordyceps militaris Using the Split-Marker Approach

The macrofungus Cordyceps militaris contains many kinds of bioactive ingredients that are regulated by functional genes, but the functions of many genes in C. militaris are still unknown. In this study, to improve the frequency of homologous integration, a genetic transformation system based on a split-marker approach was developed for the first time in C. militaris to knock out a gene encoding a terpenoid synthase (Tns). The linear and split-marker deletion cassettes were constructed and introduced into C. militaris protoplasts by PEG-mediated transformation. The transformation of split-marker fragments resulted in a higher efficiency of targeted gene disruption than the transformation of linear deletion cassettes did. The color phenotype of the Tns gene deletion mutants was different from that of wild-type C. militaris. Moreover, a PEG-mediated protoplast transformation system was established, and stable genetic transformants were obtained. This method of targeted gene deletion represents an important tool for investigating the role of C. militaris genes.

Comparison of gold nanoparticles biosynthesized by cell-free extracts of Labrys, Trichosporon montevideense, and Aspergillus

Biosynthesis of gold nanoparticles (AuNPs) by microbes has received much attention as an efficient and eco-friendly process. However, the characteristics of AuNPs biosynthesized by different microbial cell-free extracts are rarely comparatively studied. In this study, three locally isolated strains, i.e., bacteria Labrys sp. WJW, yeast Trichosporon montevideense WIN, and filamentous fungus Aspergillus sp. WL-Au, were selected for AuNPs biosynthesis. UV-Vis absorption bands at 538, 539, and 543 nm confirmed the formation of AuNPs by these strains. Transmission electron microscopy and selected area electron diffraction analyses revealed that the as-synthesized AuNPs were crystalline with spherical or pseudo-spherical shapes. However, the average sizes of these AuNPs were diverse, which were 18.8, 22.2 and 9.5 nm, respectively. The biomolecules involved in nanoparticles stabilization were demonstrated by Fourier transform infrared spectroscopy analysis. Four common functional groups such as -N-H, -C=C, -N=O, and -S=O groups were detected in these AuNPs, while a distinct -C=O group was involved in WL-Au-AuNPs. The catalytic rate of WL-Au-AuNPs toward 4-nitrophenol reduction (0.37 min^-1) was much higher than those of others (WJW-AuNPs 0.27 min^-1 and WIN-AuNPs 0.23 min^-1). This research would provide useful information for exploring efficient microbial candidates to synthesize AuNPs with excellent performances.

β-(1→6)-D-glucan secreted during the optimised production of exopolysaccharides by Paecilomyces variotii has immunostimulatory activity

Paecilomyces variotii is a filamentous fungus that occurs worldwide in soil and decaying vegetation. Optimization of the fermentation process for exopolysaccharide (EPS) production from the fungus P. variotii, structure determination and immuno-stimulating activity of EPS were performed. Response surface methodology (RSM) coupled with central composite design (CCD) was used to optimize the physical and chemical factors required to produce EPS in submerged fermentation. Preliminary investigations to choose the three factors for the present work were made using a factorial experimental design. Glucose, ammonium nitrate (NH₄NO₃) and pH were used as variables for which, with constant temperature of 28 °C and agitation of 90 rpm, the optimal process parameters were determined as glucose values of 0.96%, NH₄NO₃ 0.26% and pH 8.0. The three parameters presented significant effects. In this condition of culture, the main composition of the isolated EPS was a linear β-(1 → 6)-linked-D-glucan, as determined by Nuclear Magnetic Resonance (NMR) and methylation analysis. This polysaccharide is a very unusual as an EPS from fungi, especially a filamentous fungus such as P. variotii. Murine peritoneal macrophages cultivated with β-glucan for 6 and 48 h showed an increase in TNF-α, IL-6 and nitric oxide release with increased polysaccharide concentrations. Therefore, we conclude that the β-(1 → 6)-linked-D-glucan produced in optimised conditions of P. variotii cultivation has an immune-stimulatory activity on murine macrophages.

Primers and copper responsive promoter design and data of real-time RT-PCR assay in filamentous fungus Trichoderma reesei

This data article contains data related to the research article entitled “Copper-mediated on-off control of gene expression in filamentous fungus Trichoderma reesei” (Wang et al., 2017) [1]. Four kinds of copper responsive promoters were designed. Quantitative PCR (qPCR) was performed to determine relative mRNA levels of red fluorescent protein gene (rfp) extracted from cells grown under different concentrations of CuSO₄. Three deletion vectors were constructed by using a copper-mediated self-excision cassette instead of a xylose-mediated self-excision cassette (Zhang et al., 2016) [2] to knock out xyn1, one of the two major specific endo-β-1,4-xylanases (Rauscher et al., 2006) [3], xyr1, the key transcriptional activator of cellulolytic and xylanolytic genes (Lichius et al., 2015) [4], and ace3, a factor essential for cellulase production (Häkkinen et al., 2014) [5]. This data article reports the primers, vector construction, and qPCR assay.

Use of transcription activator-like effector for efficient gene modification and transcription in the filamentous fungus Trichoderma reesei

Filamentous fungi have wide applications in the field of biotechnology. The use of transcription activator-like effectors (TALEs) is a powerful genome-engineering tool, which can facilitate genome editing and transcriptional modulation, and has been used for genetic modification in a variety of organisms. However, a transcription activator-like effectors nuclease (TALEN) approach has not been used in filamentous fungi so far. Here, we aimed to establish the shortest TALEN and TALE-transcription factor (TALE-TF) proteins for use in gene modification and transcription in the filamentous fungus Trichoderma reesei. The alternative tandem repeat unit of the TALEs was first established by the ligation of two isocaudamers: XbaI and SpeI, instead of the natural unit. In addition, we adopted T. reesei expression assays to monitor the activities of the TALENs and TALE-TF in vivo in T. reesei. Our results showed that TALEs are a powerful genome-manipulating tool for use in T. reesei and other filamentous fungal species and that their use might facilitate studies on functional genomics and strain improvement in these filamentous fungi.

Isolation of Ustilago bromivora Strains from Infected Spikelets through Spore Recovery and Germination

Ustilago bromivora is a biotrophic smut fungus infecting Brachypodium sp. It is closely related to the barley-infecting smut Ustilago hordei, and related to the well-studied, gall-inducing model pathogen Ustilago maydis. Upon flowering, the spikelets of U. bromivora-infected plants are filled with black fungal spores. While it is possible to directly use this spore material to infect Brachypodium seeds, in many cases it is more useful to isolate individual strains of U. bromivora for a genetically homogenous population. This protocol describes how to collect and germinate the spores of U. bromivora on plate in order to obtain strains derived from a single cell.

Fructose affecting morphology and inducing β-fructofuranosidases in Penicillium janczewskii

Fructose, glucose, and an equimolar mixture of both sugars affected differently hyphae thickness, biomass production and secretion of β-fructofuranosidase in Penicillium janczewskii. Reduced growth, thinner hyphae and visible injuries were early observed during fungal cultivation in fructose-containing medium, reaching the maximum between 12 and 15 days of culture. Total sugar content from the cell wall was lower when fructose was supplied and polysaccharides lower than 10 kDa predominated, regardless the culture age. Maximal inulinase and invertase activities were detected in culture filtrates after 12 days, excepting in the glucose-containing medium. Structural changes in cell walls coincided with the increase of extracellular enzyme activity in the fructose-containing medium. The fragility of the hyphae might be related with both low carbohydrate content and predominance of low molecular weight glucans in the walls. Data presented here suggest changes in carbohydrate component of the cell walls are induced by the carbon source.

GY-1

Mechanisms responsible for the sludge dewaterability enhanced by filamentous fungi during fungal treatment of sludge were investigated in the present study. The filamentous fungus Mucor sp. GY-1, isolated from waste activated sludge, enhanced sludge dewaterability by 82.1% to achieve the lowest value of normalized sludge specific resistance to filtration (SRF), 8.18 × 10(10) m · L/kg · g-TSS. During the fungal treatment of sludge, 57.8% of slime extracellular polymeric substances (EPS) and 51.1% of polysaccharide in slime EPS were degraded, respectively, by Mucor sp. GY-1, contributing to the improvement of sludge dewaterability. Slime EPS is much more available for Mucor sp. GY-1 than either LB-EPS or TB-EPS that bound with microbial cells. In addition, filamentous fungus Mucor sp. GY-1 entrapped small sludge particles and inhibited the destruction of sludge flocs larger than 100 μm, thus enhancing sludge dewaterability, during fungal treatment of sludge using Mucor sp. GY-1.

Analysis of the antimicrobial effects of nonthermal plasma on fungal spores in ionic solutions

The antimicrobial efficiency of reactive species-based control strategies is significantly affected by the dynamics of reactive species in the biological environment. Atmospheric-pressure nonthermal plasma is an ionized gas in which various reactive species are produced. The various levels of antimicrobial activity may result from the dynamic interaction of the plasma-generated reactive species with the environment. However, the nature of the interaction between plasma and environments is poorly understood. In this study, we analyzed the influence of the ionic strength of surrounding solutions (environment) on the antimicrobial activity of plasma in relation to the plasma-generated reactive species using a model filamentous fungus, Neurospora crassa. Our data revealed that the presence of sodium chloride (NaCl) in the background solution attenuated the deleterious effects of plasma on germination, internal structure, and genomic DNA of fungal spores. The protective effects of NaCl were not explained exclusively by pH, osmotic stability, or the level of reactive species in the solution. These were strongly associated with the ionic strength of the background solution. The presence of ions reduced plasma toxicity, which might be due to a reduced access of reactive species to fungal spores, and fungal spores were inactivated by plasma in a background fluid of nonionic osmolytes despite the low level of reactive species. Our results suggest that the surrounding environment may affect the behavior of reactive species, which leads to different biological consequences regardless of their quantity. Moreover, the microbicidal effect of plasma can be synergistically regulated through control of the microenvironment.