New tools for the genetic manipulation of filamentous fungi

Inducible promoters and functional genomic approaches for the genetic engineering of filamentous fungi

In industry, filamentous fungi have a prominent position as producers of economically relevant primary or secondary metabolites. Particularly, the advent of genetic engineering of filamentous fungi has led to a growing number of molecular tools to adopt filamentous fungi for biotechnical applications. Here, we summarize recent developments in fungal biology, where fungal host systems were genetically manipulated for optimal industrial applications. Firstly, available inducible promoter systems depending on carbon sources are mentioned together with various adaptations of the Tet-Off and Tet-On systems for use in different industrial fungal host systems. Subsequently, we summarize representative examples, where diverse expression systems were used for the production of heterologous products, including proteins from mammalian systems. In addition, the progressing usage of genomics and functional genomics data for strain improvement strategies are addressed, for the identification of biosynthesis genes and their related metabolic pathways. Functional genomic data are further used to decipher genomic differences between wild-type and high-production strains, in order to optimize endogenous metabolic pathways that lead to the synthesis of pharmaceutically relevant end products. Lastly, we discuss how molecular data sets can be used to modify products for optimized applications.

A highly efficient genetic system for the identification of a harzianum B biosynthetic gene cluster in Trichoderma hypoxylon

Trichoderma hypoxylon is a fungicolous species which produces rich secondary metabolites. However, no genetic transformation method is available for further studies. Here, we developed a marker-less transformation system based on the complementation of an uridine/uracil biosynthetic gene by protoplast transformation. An uridine/uracil auxotrophic mutant of Δthpyr4 was obtained by using a positive screening protocol with 5'-fluoroorotic acid as a selective reagent. To improve the homologous integration rates, the orthologues of ku70 and lig4 which play critical roles in non-homologous end-joining recombination were disrupted. The resulting thlig4 mutant showed remarkable transformation rates of 89 %, while no change was found in the thku70 deletion mutant compared with the WT strain. This suggests that thlig4 play a key role in the non-homologous recombination in this strain. Using this system, the biosynthetic gene cluster of trichothecene (tri) harzianum B was identified by deletion of the thtri5 in T. hypoxylon. Comparative genome analysis revealed that the trichothecene biosynthetic gene cluster in T. hypoxylon shared similar organizations with T. arundinaceum and T. brevicompactum, even though their encoded products are different in structures. Taken together, the highly efficient genetic system provides a convenient tool for studying the biosynthetic diversity and mining the novel natural product from the fungi.

Improvement in xylooligosaccharides production by knockout of the β-xyl1 gene in Trichoderma orientalis EU7-22

The goal of this study was to enhance the production of xylooligosaccharides (XOs) and reduce the production of xylose. We investigated β-xylosidases, which were key enzymes in the hydrolysis of xylan into xylose, in Trichoderma orientalis EU7-22. The binary vector pUR5750G/bxl::hph was constructed to knock out the β-xyl1 gene (encoding β-xylosidases) in T. orientalis EU7-22 by homologous integration, producing the mutant strain T. orientalis Bxyl-1. Xylanase activity for strain Bxyl-1 was 452.42 IU/mL, which increased by only 0.07% compared to that of parental strain EU7-22, whereas β-xylosidase activity was 0.06 IU/mL, representing a 91.89% decrease. When xylanase (200 IU/g xylan), produced by T. orientalis EU7-22 and T. orientalis Bxyl-1, was used to hydrolyze beechwood xylan, in contrast to the parental strain, the XOs were enhanced by 83.27%, whereas xylose decreased by 45.80% after 36 h in T. orientalis Bxyl-1. Based on these results, T. orientalis Bxyl-1 has great potential for application in the production of XOs from lignocellulosic biomass.

Unique molecular mechanisms for maintenance and alteration of genetic information in the budding yeast Saccharomyces cerevisiae

The high-fidelity transmission of genetic information is crucial for the survival of organisms, the cells of which have the ability to protect DNA against endogenous and environmental agents, including reactive oxygen species (ROS), ionizing radiation, and various chemical compounds. The basis of protection mechanisms has been evolutionarily conserved from yeast to humans; however, each organism often has a specialized mode of regulation that uses different sets of machineries, particularly in lower eukaryotes. The divergence of molecular mechanisms among related organisms has provided insights into the evolution of cellular machineries to a higher architecture. Uncommon characteristics of machineries may also contribute to the development of new applications such as drugs with novel mechanisms of action. In contrast to the cellular properties for maintaining genetic information, living organisms, particularly microbes, inevitably undergo genetic alterations in order to adapt to environmental conditions. The maintenance and alteration of genetic information may be inextricably linked to each other. In this review, we describe recent findings on the unconventional molecular mechanisms of DNA damage response and DNA double-strand break (DSB) repair in the budding yeast Saccharomyces cerevisiae. We also introduce our previous research on genetic and phenotypic instabilities observed in a clonal population of clinically-derived S. cerevisiae. The molecular mechanisms of this case were associated with mutations to generate tyrosine-inserting tRNA-Tyr ochre suppressors and the position effects of mutation frequencies among eight tRNA-Tyr loci dispersed in the genome. Phenotypic variations among different strain backgrounds have also been observed by another type of nonsense suppressor, the aberrant form of the translation termination factor. Nonsense suppressors are considered to be responsible for the genome-wide translational readthrough of termination codons, including natural nonsense codons. The nonsense suppressor-mediated acquisition of phenotypic variations may be advantageous for adaptation to environmental conditions and survival during evolution.

Molecular tools for gene manipulation in filamentous fungi

Functional genomics of filamentous fungi has gradually uncovered gene information for constructing 'cell factories' and controlling pathogens. Available gene manipulation methods of filamentous fungi include random integration methods, gene targeting technology, gene editing with artificial nucleases and RNA technology. This review describes random gene integration constructed by restriction enzyme-mediated integration (REMI); Agrobacterium-mediated transformation (AMT); transposon-arrayed gene knockout (TAGKO); gene targeting technology, mainly about homologous recombination; and modern gene editing strategies containing transcription activator-like effector nucleases (TALENs) and a clustered regularly interspaced short palindromic repeat/associated protein system (CRISPR/Cas) developed in filamentous fungi and RNA technology including RNA interference (RNAi) and ribozymes. This review describes historical and modern gene manipulation methods in filamentous fungi and presents the molecular tools available to researchers investigating filamentous fungi. The biggest difference of this review from the previous ones is the addition of successful application and details of the promising gene editing tool CRISPR/Cas9 system in filamentous fungi.

CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art

In recent years, a variety of genetic tools have been developed and applied to various filamentous fungi, which are widely applied in agriculture and the food industry. However, the low efficiency of gene targeting has for many years hampered studies on functional genomics in this important group of microorganisms. The emergence of CRISPR/Cas9 genome-editing technology has sparked a revolution in genetic research due to its high efficiency, versatility, and easy operation and opened the door for the discovery and exploitation of many new natural products. Although the application of the CRISPR/Cas9 system in filamentous fungi is still in its infancy compared to its common use in E. coli, yeasts, and mammals, the deep development of this system will certainly drive the exploitation of fungal diversity. In this review, we summarize the research progress on CRISPR/Cas9 systems in filamentous fungi and finally highlight further prospects in this area.

Deletion of TpKu70 facilitates gene targeting in Talaromyces pinophilus and identification of TpAmyR involvement in amylase production

Talaromyces pinophilus is a promising filamentous fungus for industrial production of biomass-degrading enzymes used in biorefining, and its genome was recently sequenced and reported. However, functional analysis of genes in T. pinophilus is rather limited owing to lack of genetic tools. In this study, a putative TpKu70 encoding the Ku70 homolog involved in the classic non-homologous end-joining pathway was deleted in T. pinophilus 1-95. ΔTpKu70 displayed no apparent defect in vegetative growth and enzyme production, and presented similar sensitivity to benomyl, bleomycin, and UV, when compared with the wild-type T. pinophilus strain 1-95. Seven genes that encode putative transcription factors, including TpAmyR, were successfully knocked out in ΔTpKu70 at 61.5-100% of homologous recombination frequency, which is significantly higher than that noted in the wild-type. Interestingly, ΔTpAmyR produced approximately 20% of amylase secreted by the parent strain ΔTpKu70 in medium containing soluble starch from corn as the sole carbon source. Real-time quantitative reverse transcription PCR showed that TpAmyR positively regulated the expression of genes encoding α-amylase and glucoamylase. Thus, this study provides a useful tool for genetic analysis of T. pinophilus, and identification of a key role for the transcription factor TpAmyR in amylase production in T. pinophilus.

Accumulation of sugar from pulp and xylitol from xylose by pyruvate decarboxylase-negative white-rot fungus Phlebia sp. MG-60

Phlebia sp. MG-60 is a white-rot fungus that produces ethanol with high efficiency from lignocellulosic biomass without additional enzymes. Through engineering of this powerful metabolic pathway for fermentation in Phlebia sp. MG-60, chemical compounds other than ethanol could be produced. Here, we demonstrate sugar accumulation from unbleached hardwood kraft pulp and conversion of xylose to xylitol by pyruvate decarboxylase (pdc)-negative Phlebia sp. MG-60. We isolated Phlebia sp. strain MG-60-P2 from protoplasts to unify the protoplast phenotypes of the regenerated strains. Homologous recombination achieved a stable pdc-knockout line, designated KO77. The KO77 line produced traces of ethanol, but accumulated xylitol from xylose or glucose from unbleached hardwood kraft pulp. These metabolic changes in the pdc-knockout strain reflect the potential of metabolic engineering in Phlebia sp. MG-60 for direct production of chemical compounds from lignocellulosic biomass.

Random mutagenesis analysis and identification of a novel C2H2-type transcription factor from the nematode-trapping fungus Arthrobotrys oligospora

Arthrobotrys oligospora is a typical nematode-trapping fungus. In this study, 37 transformants of A. oligospora were obtained by REMI (restriction enzyme mediated integration) method and phenotypic properties of nine transformants were analyzed. The nine transformants showed differences in growth, conidiation, trap formation, stress tolerance, and/or pathogenicity among each other and with those of the parental wild-type strain (WT). The insertional sites of the hph cassette were identified in transformants X5 and X13. In X5, the cassette was inserted in the non-coding region between AOL_s00076g273 (76g273) and AOL_s00076g274 (76g274) and the transcription of 76g274, but not 76g273, was enhanced in X5. 76g274p had two conserved domains and was predicted as a nucleoprotein, which we confirmed by its nuclear localization in Saccharomyces cerevisiae using the green fluorescent protein-fused 76g274p. The transcription of 76g274 was stimulated or inhibited by several environmental factors. The sporulation yields of 76g274-deficient mutants were decreased by 70%, and transcription of several sporulation-related genes was severely diminished compared to the WT during the conidiation. In summary, a method for screening mutants was established in A. oligospora and using the method, we identified a novel C₂H₂-type transcription factor that positively regulates the conidiation of A. oligospora.

Transient Silencing of DNA Repair Genes Improves Targeted Gene Integration in the Filamentous Fungus Trichoderma reesei

Trichoderma reesei is a filamentous fungus that is used worldwide to produce industrial enzymes. Industrial strains have traditionally been created though systematic strain improvement using mutagenesis and screening approaches. It is also desirable to specifically manipulate the genes of the organism to further improve and to modify the strain. Targeted integration in filamentous fungi is typically hampered by very low frequencies of homologous recombination. To address this limitation, we have developed a simple transient method for silencing genes in T. reesei Using gene-specific small interfering RNAs (siRNAs) targeted to mus53, we could achieve up to 90% knockdown of mus53 mRNA. As a practical example, we demonstrated that transient silencing of DNA repair genes significantly improved homologous integration of DNA at a specific locus in a standard protoplast transformation. The best transient silencing of mus53 with siRNAs in protoplasts could achieve up to 59% marker gene integration.IMPORTANCE The previous solution for improving targeted integration efficiency has been deleting nonhomologous end joining (NHEJ) DNA repair genes. However, deleting these important repair genes may lead to unintended consequences for genomic stability and could lead to the accumulation of spontaneous mutations. Our method of transiently silencing NHEJ repair pathway genes allows recovery of their important repair functions. Here we report a silencing approach for improving targeted DNA integration in filamentous fungi. Furthermore, our transient silencing method is a truly flexible approach that is capable of knocking down the expression of a target gene in growing mycelial cultures, which could facilitate the broad study of gene functions in T. reesei.

The Utilization of RNA Silencing Technology to Mitigate the Voriconazole Resistance of Aspergillus Flavus; Lipofectamine-Based Delivery

Purpose: Introducing the effect of RNAi in fungi to downregulate essential genes has made it a powerful tool to investigate gene function, with potential strategies for novel disease treatments. Thus, this study is an endeavor to delve into the silencing potentials of siRNA on cyp51A and MDR1 in voriconazole-resistant Aspergillus flavus as the target genes.

Methods: In this study, we designed three cyp51A-specific siRNAs and three MDR1-specific siRNAs and after the co-transfection of siRNA into Aspergillus flavus, using lipofectamine, we investigated the effect of different siRNA concentrations (5, 15, 25, 50nM) on cyp51A and MDR1 expressions by qRT-PCR. Finally, the Minimum Inhibitory Concentrations (MICs) of voriconazole for isolates were determined by broth dilution method.

Results: Cyp51A siRNA induced 9, 22, 33, 40-fold reductions in cyp51A mRNA expres­sion in a voriconazole-resistant strain following the treatment of the cells with concentrations of 5, 15, 25, 50nM siRNA, respectively. Identically, the same procedure was applied to MDR1, even though it induced 2, 3, 4, 10-fold reductions. The results demonstrated a MIC for voriconazole in the untreated group (4µg per ml), when compared to the group treated with cyp51A-specific siRNA and MDR1-specific siRNA, both at concentrations of 25 and 50nM, yielding 2µg per ml and 1µg per ml when 25 nM was applied and 2µg per ml and 0.5µg per ml when the concentration doubled to 50 nM.

Conclusion: In this study, we suggested that siRNA-mediated specific inhibition of cyp51A and MDR1 genes play roles in voriconazole-resistant A.flavus strain and these could be apt target genes for inactivation. The current study promises a bright prospect for the treatment of invasive aspergillosis through the effective deployment of RNAi and gene therapy.

Functional Reconstitution of a Fungal Natural Product Gene Cluster by Advanced Genome Editing

Filamentous fungi produce varieties of natural products even in a strain dependent manner. However, the genetic basis of chemical speciation between strains is still widely unknown. One example is trypacidin, a natural product of the opportunistic human pathogen Aspergillus fumigatus, which is not produced among different isolates. Combining computational analysis with targeted gene editing, we could link a single nucleotide insertion in the polyketide synthase of the trypacidin biosynthetic pathway and reconstitute its production in a nonproducing strain. Thus, we present a CRISPR/Cas9-based tool for advanced molecular genetic studies in filamentous fungi, exploiting selectable markers separated from the edited locus.

Study on genetic engineering of Acremonium chrysogenum, the cephalosporin C producer

Acremonium chrysogenum is an important filamentous fungus which produces cephalosporin C in industry. This review summarized the study on genetic engineering of Acremonium chrysogenum, including biosynthesis and regulation for fermentation of cephalosporin C, molecular techniques, molecular breeding and transcriptomics of Acremonium chrysogenum. We believe with all the techniques available and full genomic sequence, the industrial strain of Acremonium chrysogenum can be genetically modified to better serve the pharmaceutical industry.

Identification of a Halogenase Involved in the Biosynthesis of Ochratoxin A in Aspergillus carbonarius

Aspergillus carbonarius is the main responsible fungus of ochratoxin A (OTA) contamination of grapes and derived products. To date, the biosynthetic mechanism of this mycotoxin has been partially elucidated. Availability of genome sequence of A. carbonarius has allowed the identification of a putative gene cluster involved in OTA biosynthesis. This region hosts the previously characterized AcOTAnrps and AcOTApks genes encoding two key enzymes of the biosynthetic pathway. At about 4,400 nucleotides downstream of these loci, a gene encoding a putative flavin dependent-halogenase came out from the annotation data. Its proximity to OTA biosynthetic genes and its sequence analysis have suggested a role in the biosynthesis of OTA, directed to the introduction of the chlorine atom in the C-5 position of the final molecular structure of this mycotoxin. The deduced protein sequence of the halogenase gene, we designated AcOTAhal, shows a high similarity to a halogenase that is located in the OTA cluster of A. niger The deletion of the halogenase gene completely eliminated the production of ochratoxin A in A. carbonarius and determined a significant increase of ochratoxin B, as confirmed by mass spectrometry analysis. Moreover, its expression profile was similar to the two biosynthetic genes previously identified, AcOTApks and AcOTAnrps, indicating a strong correlation of the AcOTAhal gene with the kinetics of OTA accumulation in A. carbonarius. Therefore, experimental evidence confirmed that the chlorination step which converts OTB in OTA represents the final stage of the biosynthetic pathway, supporting our earlier hypothesis on the order of enzymatic steps of OTA biosynthesis in A. carbonarius

IMPORTANCE

Ochratoxin A is a potent mycotoxin classified as a possible carcinogen for humans, and Aspergillus carbonarius is the main agent responsible for OTA accumulation in grapes. We demonstrate here that a flavin-halogenase is implicated in the biosynthesis of OTA in A. carbonarius The encoding gene, AcOTAhal, is contiguous to biosynthetic genes that we have already described (nrps and pks), resulting as part of the biosynthetic cluster. The encoded protein is responsible of the introduction of chlorine atom in the final molecular structure and acts at the last step in the pathway. This study can be considered a continuation of an earlier study wherein we started to clarify the molecular basis of OTA biosynthesis in A. carbonarius, which has not been completely elucidated until now. This research represents an important step forward to a better understanding of the production mechanism, which will contribute to the development of improved control strategies to reduce the risk of OTA contamination in food products.

Variation in Growth, Colonization of Maize, and Metabolic Parameters of GFP- and DsRed-Labeled Fusarium verticillioides Strains

Autofluorescent proteins are frequently applied as visual markers in the labeling of filamentous fungi. Genes gfp and DsRed were transformed into the genome of Fusarium verticillioides via the Agrobacterium tumefaciens-mediated transformation method. The selected transformants displayed a bright green or red fluorescence in all the organelles of the growing fungal mycelia and spores (except for the vacuoles) both in cultures and in the maize (Zea mays) roots they colonized. The results of gene-specific polymerase chain reaction (PCR) analysis and the thermal asymmetrical interlaced (TAIL)-PCR analysis demonstrated that gfp and DsRed were integrated on different chromosomes of the fungus. Reductions in the colony growth on the plates at pH 4.0 and 5.5 was observed for the green fluorescent protein (GFP)-transformant G3 and the DsRed-transformant R4, but transformants G4 and R1 grew as well as the wild-type strain at pH 4.0. The speed of growth of all the transformants was similar to the wild-type strain at pH ≥ 7. The insertion of gfp and DsRed did not alter the production of extracellular enzymes and fumonisin B by F. verticillioides. The transformants expressing GFP and DsRed proteins were able to colonize maize roots. However, the four transformants examined produced fewer CFU in the root samples than the wild-type strain during a sampling period of 7 to 28 days after inoculation.

Paradoxical performance of tryptophan synthase gene trp1 (+) in transformations of the basidiomycete Coprinopsis cinerea

Several transformation strains of Coprinopsis cinerea carry the defective tryptophan synthase allele trp1-1,1-6 which can be complemented by introduction of the trp1 (+) wild-type gene. Regularly in C. cinerea, single-trp1 (+)-vector transformations yield about half the numbers of clones than cotransformations with a non-trp1 (+)-plasmid done in parallel. The effect is also observed with the orthologous Schizophyllum commune trpB (+) gene shown here to function as a selection marker in C. cinerea. Parts of single-trp1 (+) - or single-trpB (+) -vector transformants are apparently lost. This paradoxical phenomenon relates to de-regulation of aromatic amino acid biosynthesis pathways. Adding tryptophan precursors to protoplast regeneration agar or feeding with other aromatic amino acids increases loss of single-trp1 (+)-vector transformants and also sets off loss of clones in cotransformation with a non-trp1 (+)-plasmid. Feedback control by tryptophan and cross-pathway control by tyrosine and phenylalanine are both active in the process. We deduce from the observations that more cotransformants than single-vector transformants are obtained by in average less disturbance of the tryptophan biosynthesis pathway. DNA in C. cinerea transformation usually integrates into the genome at multiple ectopic places. Integration events for a single vector per nucleus should statistically be 2-fold higher in single-vector transformations than in cotransformations in which the two different molecules compete for the same potential integration sites. Integration of more trp1 (+) copies into the genome might more likely lead to sudden tryptophan overproduction with subsequent rigid shut-down of the pathway. Blocking ectopic DNA integration in a Δku70 mutant abolished the effect of doubling clone numbers in cotransformations due to preferred single trp1 (+) integration by homologous recombination at its native genomic site.

Low-affinity iron transport protein Uvt3277 is important for pathogenesis in the rice false smut fungus Ustilaginoidea virens

Ustilaginoidea virens is the causal agent of rice false smut disease resulting in quantitative and qualitative losses in rice. To gain insights into the pathogenic mechanisms of U. virens, we established a T-DNA insertion mutant library of U. virens through Agrobacterium tumefaciens-mediated transformation and selected an enhanced pathogenicity mutant (i.e., B3277). We analyzed the biological characteristics of the wild-type P1 and B3277. The growth rate and sporulation of B3277 were decreased compared with those of P1; the ferrous iron could be utilized by B3277, but inhibited the growth of P1. Southern blot analysis was performed to verify the copy number of the foreign gene inserted in the genomic DNA and only one copy of the T-DNA was found. The combined hiTAIL-PCR with RACE-PCR analysis showed the successful cloning of full length of the T-DNA flanking gene associated with pathogenicity, named Uvt3277. Gene expression was analyzed using real-time PCR. Results revealed that Uvt3277 was expressed at lower levels in B3277 than in P1. This gene was then subjected to bioinformatics analysis. The encoded protein of Uvt3277 exhibited high homology with low-affinity iron transporter proteins in some fungi. Transformation of the RNAi vector by constructing the hairpin RNA of the target gene was confirmed as successful. The pathogenicity of the transformant also increased. These results suggested that Uvt3277 may have an important function associated with the pathogenesis of U. virens. This study provides insights into the pathogenic mechanism of U. virens and a molecular target of disease control.

Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories

Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories.

Fungal-mediated consolidated bioprocessing: the potential of Fusarium oxysporum for the lignocellulosic ethanol industry

Microbial bioprocessing of lignocellulose to bioethanol still poses challenges in terms of substrate catabolism. The most important challenge is to overcome substrate recalcitrance and to thus reduce the number of steps needed to biorefine lignocellulose. Conventionally, conversion involves chemical pretreatment of lignocellulose, followed by hydrolysis of biomass to monomer sugars that are subsequently fermented into bioethanol. Consolidated bioprocessing (CBP) has been suggested as an efficient and economical method of manufacturing bioethanol from lignocellulose. CBP integrates the hydrolysis and fermentation steps into a single process, thereby significantly reducing the amount of steps in the biorefining process. Filamentous fungi are remarkable organisms that are naturally specialised in deconstructing plant biomass and thus they have tremendous potential as components of CBP. The fungus Fusarium oxysporum has potential for CBP of lignocellulose to bioethanol. Here we discuss the complexity and potential of CBP, the bottlenecks in the process, and the potential influence of fungal genetic diversity, substrate complexity and new technologies on the efficacy of CPB of lignocellulose, with a focus on F. oxysporum.

Light-inducible genetic engineering and control of non-homologous end-joining in industrial eukaryotic microorganisms: LML 3.0 and OFN 1.0

Filamentous fungi play important roles in the production of plant cell-wall degrading enzymes. In recent years, homologous recombinant technologies have contributed significantly to improved enzymes production and system design of genetically manipulated strains. When introducing multiple gene deletions, we need a robust and convenient way to control selectable marker genes, especially when only a limited number of markers are available in filamentous fungi. Integration after transformation is predominantly nonhomologous in most fungi other than yeast. Fungal strains deficient in the non-homologous end-joining (NHEJ) pathway have limitations associated with gene function analyses despite they are excellent recipient strains for gene targets. We describe strategies and methods to address these challenges above and leverage the power of resilient NHEJ deficiency strains. We have established a foolproof light-inducible platform for one-step unmarked genetic modification in industrial eukaryotic microorganisms designated as 'LML 3.0', and an on-off control protocol of NHEJ pathway called 'OFN 1.0', using a synthetic light-switchable transactivation to control Cre recombinase-based excision and inversion. The methods provide a one-step strategy to sequentially modify genes without introducing selectable markers and NHEJ-deficiency. The strategies can be used to manipulate many biological processes in a wide range of eukaryotic cells.

Rational biosynthetic approaches for the production of new-to-nature compounds in fungi

Filamentous fungi have the ability to produce a wide range of secondary metabolites some of which are potent toxins whereas others are exploited as food additives or drugs. Fungal natural products still play an important role in the discovery of new chemical entities for potential use as pharmaceuticals. However, in most cases they cannot be directly used as drugs due to toxic side effects or suboptimal pharmacokinetics. To improve drug-like properties, including bioactivity and stability or to produce better precursors for semi-synthetic routes, one needs to generate non-natural derivatives from known fungal secondary metabolites. In this minireview, we describe past and recent biosynthetic approaches for the diversification of fungal natural products, covering examples from precursor-directed biosynthesis, mutasynthesis, metabolic engineering and biocombinatorial synthesis. To illustrate the current state-of-the-art, challenges and pitfalls, we lay particular emphasis on the class of fungal cyclodepsipeptides which have been studied longtime for product diversification and which are of pharmaceutical relevance as drugs.

Characterization of RNA silencing components in the plant pathogenic fungus Fusarium graminearum

The RNA interference (RNAi) plays a critical role in gene regulation in a variety of eukaryotic organisms. However, the role of RNAi remains largely unclear in plant pathogenic fungi. In this study, we explored the roles of core components of the RNAi pathway in Fusarium graminearum, the major causal agent of wheat head blight. Our results demonstrated that the hairpin RNA (hpRNA) can efficiently silence the expression level of target gene, and the argonaute protein FgAgo1 and dicer protein FgDicer2 are important in this silencing process. RNAi machinery was not involved in growth, abiotic stress and pathogenesis in F. graminearum under tested conditions. We firstly applied high-throughput sequencing technology to elucidate small RNA (17-40 nucleotides) (sRNA) transcriptome in F. graminearum, and found that a total of forty-nine micro-like-RNA (milRNA) candidates were identified in the wild-type and ∆FgDICER2, and twenty-four of them were FgDicer2-dependent. Fg-milRNA-4 negatively regulated expression of its target gene. Taken together, our results indicated that the hpRNA-induced gene silencing was a valuable genetic tool for exploring gene function in F. graminearum. FgAgo1 and FgDicer2 proteins played a critical role in the hpRNA mediated gene silencing process. In addition, FgDicer2 was involved in sRNA transcription and milRNA generation in this fungus.

Tailor-made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus

CRISPR/Cas-derived RNA-guided nucleases (RGNs) that can generate DNA double-strand breaks (DSBs) at a specific sequence are widely used for targeted genome editing by induction of DSB repair in many organisms. The CRISPR/Cas system consists of two components: a single Cas9 nuclease and a single-guide RNA (sgRNA). Therefore, the system for constructing RGNs is simple and efficient, but the utilization of RGNs in filamentous fungi has not been validated. In this study, we established the CRISPR/Cas system in the model filamentous fungus, Pyricularia oryzae, using Cas9 that was codon-optimized for filamentous fungi, and the endogenous RNA polymerase (RNAP) III U6 promoter and a RNAP II fungal promoter for the expression of the sgRNA. We further demonstrated that RGNs could recognize the desired sequences and edit endogenous genes through homologous recombination-mediated targeted gene replacement with high efficiency. Our system will open the way for the development of various CRISPR/Cas-based applications in filamentous fungi.

Recombinant expression of four oxidoreductases in Phanerochaete chrysosporium improves degradation of phenolic and non-phenolic substrates

Phanerochaete chrysosporium belongs to a group of lignin-degrading fungi that secretes various oxidoreductive enzymes, including lignin peroxidase (LiP) and manganese peroxidase (MnP). Previously, we demonstrated that the heterologous expression of a versatile peroxidase (VP) in P. chrysosporium recombinant strains is possible. However, the production of laccases (Lac) in this fungus has not been completely demonstrated and remains controversial. In order to investigate if the co-expression of Lac and VP in P. chrysosporium would improve the degradation of phenolic and non-phenolic substrates, we tested the constitutive co-expression of the lacIIIb gene from Trametes versicolor and the vpl2 gene from Pleurotus eryngii, and also the endogenous genes mnp1 and lipH8 by shock wave mediated transformation. The co-overexpression of peroxidases and laccases was improved up to five-fold as compared with wild type species. Transformant strains showed a broad spectrum in phenolic/non-phenolic biotransformation and a high percentage in synthetic dye decolorization in comparison with the parental strain. Our results show that the four enzymes can be constitutively expressed in a single transformant of P. chrysosporium in minimal medium. These data offer new possibilities for an easy and efficient co-expression of laccases and peroxidases in suitable basidiomycete species.

Gene Overexpression and RNA Silencing Tools for the Genetic Manipulation of the S-(+)-Abscisic Acid Producing Ascomycete Botrytis cinerea

The phytopathogenic ascomycete Botrytis cinerea produces several secondary metabolites that have biotechnical significance and has been particularly used for S-(+)-abscisic acid production at the industrial scale. To manipulate the expression levels of specific secondary metabolite biosynthetic genes of B. cinerea with Agrobacterium tumefaciens-mediated transformation system, two expression vectors (pCBh1 and pCBg1 with different selection markers) and one RNA silencing vector, pCBSilent1, were developed with the In-Fusion assembly method. Both expression vectors were highly effective in constitutively expressing eGFP, and pCBSilent1 effectively silenced the eGFP gene in B. cinerea. Bcaba4, a gene suggested to participate in ABA biosynthesis in B. cinerea, was then targeted for gene overexpression and RNA silencing with these reverse genetic tools. The overexpression of bcaba4 dramatically induced ABA formation in the B. cinerea wild type strain Bc-6, and the gene silencing of bcaba4 significantly reduced ABA-production in an ABA-producing B. cinerea strain.

The pbrB gene encodes a laccase required for DHN-melanin synthesis in conidia of Talaromyces (Penicillium) marneffei

Talaromyces marneffei (Basionym: Penicillium marneffei) is a significant opportunistic fungal pathogen in patients infected with human immunodeficiency virus in Southeast Asia. T. marneffei cells have been shown to become melanized in vivo. Melanins are pigment biopolymers which act as a non-specific protectant against various stressors and which play an important role during virulence in fungi. The synthesis of the two most commonly found melanins in fungi, the eumelanin DOPA-melanin and the allomelanin DHN-melanin, requires the action of laccase enzymes. The T. marneffei genome encodes a number of laccases and this study describes the characterization of one of these, pbrB, during growth and development. A strain carrying a PbrB-GFP fusion shows that pbrB is expressed at high levels during asexual development (conidiation) but not in cells growing vegetatively. The pbrB gene is required for the synthesis of DHN-melanin in conidia and when deleted results in brown pigmented conidia, in contrast to the green conidia of the wild type.

Identification and characterization of a novel gene encoding the NBS1 protein in Pyricularia oryzae

The ascomycete Pyricularia oryzae (teleomorph: Magnaporthe oryzae) causes one of the most serious diseases known as rice blast. The Nijmegen breakage syndrome protein (NBS1) is essential for DNA repair; thus, we studied the P. oryzae NBS1 homolog (PoNBS1). A PoNBS1 null mutant exhibited high sensitivity to DNA damage-inducing agents. The mutant also exhibited the retarded hyphal growth, and induced abnormal conidial germination and shape, but showed normal appressorium formation. The phenotypes of the null mutant were complemented by introducing the cDNA of PoNBS1 driven by a TrpC promoter of Aspergillus nidulans. In addition, the null mutant similarly complemented with the PoNBS1 cDNA lacking the FHA domain that had a normal phenotype except for hyphal growth. These results suggest that PoNBS1 is involved in DNA repair and normal development in P. oryzae. Moreover, the FHA domain of PoNBS1 participates in normal hyphal growth.

A functional genomics method for assaying gene function in phytopathogenic fungi through host-induced gene silencing mediated by agroinfiltration

With the rapid growth of genomic information, there is an increasing demand for efficient analysis tools to study the function of predicted genes coded in genomes. Agroinfiltration, the delivery of gene constructs into plant cells by Agrobacterium tumefaciens infiltrated into leaves, is one such versatile, simple, and rapid technique that is increasingly used for transient gene expression assay in plants. In this chapter, we focus on the use of agroinfiltration as a functional genomics research tool in molecular plant pathology. Specifically, we describe in detail its use in expressing phytopathogenic fungal gene sequences in a host plant to induce RNA silencing of corresponding genes inside the pathogen, a method which has been termed host-induced gene silencing (HIGS). We target the fungal pathogen Puccinia triticina which causes leaf rust on its wheat host, but the method is applicable to a variety of pathosystems.

Recent advances in genome mining of secondary metabolites in Aspergillus terreus

Filamentous fungi are rich resources of secondary metabolites (SMs) with a variety of interesting biological activities. Recent advances in genome sequencing and techniques in genetic manipulation have enabled researchers to study the biosynthetic genes of these SMs. Aspergillus terreus is the well-known producer of lovastatin, a cholesterol-lowering drug. This fungus also produces other SMs, including acetylaranotin, butyrolactones, and territram, with interesting bioactivities. This review will cover recent progress in genome mining of SMs identified in this fungus. The identification and characterization of the gene cluster for these SMs, as well as the proposed biosynthetic pathways, will be discussed in depth.

Heterologous protein expression in Hypocrea jecorina: a historical perspective and new developments

Hypocrea jecorina, the sexual teleomorph of Trichoderma reesei, has long been favored as an industrial cellulase producer, first utilizing its native cellulase system and later augmented by the introduction of heterologous enzymatic activities or improved variants of native enzymes. Expression of heterologous proteins in H. jecorina was once considered difficult when the target was an improved variant of a native cellulase. Developments over the past nearly 30 years have produced strains, vectors, and selection mechanisms that have continued to simplify and streamline heterologous protein expression in this fungus. More recent developments in fungal molecular biology have pointed the way toward a fundamental transformation in the ease and efficiency of heterologous protein expression in this important industrial host. Here, 1) we provide a historical perspective on advances in H. jecorina molecular biology, 2) outline host strain engineering, transformation, selection, and expression strategies, 3) detail potential pitfalls when working with this organism, and 4) provide consolidated examples of successful cellulase expression outcomes from our laboratory.

Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity

Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Reproducible community types formed independent of geographic location of production. Intensive temporal sampling demonstrated that assembly of these communities is highly reproducible. Patterns of community composition and succession observed in situ can be recapitulated in a simple in vitro system. Widespread positive and negative interactions were identified between bacterial and fungal community members. Cheese rind microbial communities represent an experimentally tractable system for defining mechanisms that influence microbial community assembly and function.

Efficiency of different strategies for gene silencing in Botrytis cinerea

The generation of knock-out mutants in fungal pathogens by gene replacement and insertional mutagenesis is the classical method to validate virulence factors. An alternative strategy consists of silencing the candidate virulence gene by making use of the phenomenon of RNA interference (RNAi), adding features such as the possibility of generating knock-down mutants with variable expression levels of the target gene or the ability to simultaneously target multiple genes. Two different approaches have been assayed to generate knock-down mutants by RNAi in the phytopathogenic fungus Botrytis cinerea. In the first one, the single nitrate reductase gene in the B. cinerea genome, niaD, was silenced by transformation with a construct containing a 400-bp niaD fragment between two opposing promoters, so that a dsRNA fragment was generated. As an alternative approach, the mgfp4 gene coding for the green fluorescent protein (GFP) was silenced by transforming two different GFP-expressing strains of B. cinerea with a hairpin RNA (hpRNA)-expressing vector, containing two inverted copies of a 300-bp mgfp4 fragment separated by a spacer DNA. While the opposing dual-promoter strategy produced gene silencing in about half of the transformants assayed, the efficiency of the hpRNA-expressing vector was higher, inducing a decrease in GFP levels in more than 90 % of transformants. The degree of silencing achieved was high with both methods, but the hpRNA strategy resulted in a higher proportion of strongly silenced transformants.

Efficient gene targeting in ligase IV-deficient Monascus ruber M7 by perturbing the non-homologous end joining pathway

Inactivating the non-homologous end joining (NHEJ) pathway is a well established method to increase gene replacement frequency (GRF) in filamentous fungi because NHEJ is predominant for the repair of DNA double strand breaks (DSBs), while gene targeting is based on homologous recombination (HR). DNA ligase IV, a component of the NHEJ system, is strictly required for the NHEJ in Saccharomyces cerevisiae and Neurospora crassa. To enhance the GRF in Monascus ruber M7, we deleted the Mrlig4 gene encoding a homolog of N. crassa DNA ligase IV. The obtained mutant (MrΔlig4) showed no apparent defects in vegetative growth, colony phenotype, microscopic morphology, spore yield, and production of Monascus pigments and citrinin compared with the wild-type strain (M. ruber M7). Gene targeting of ku70 and triA genes revealed that GRF in the MrΔlig4 strain increased four-fold compared with that in the wild-type strain, reached 68 % and 85 %, respectively. Thus, the MrΔlig4 strain is a promising host for efficient genetic manipulation. In addition, the MrΔlig4 strain is more sensitive than M. ruber M7 to a DNA-damaging agent, methyl methanesulfonate.