A homologous gene-reporter system for the basidiomycete Schizophyllum commune based on internally deleted homologous genes

Abundant Small Protein ICARUS Inside the Cell Wall of Stress-Resistant Ascospores of Talaromyces macrosporus Suggests a Novel Mechanism of Constitutive Dormancy

Ascospores of Talaromyces.macrosporus belong to the most stress resistant eukaryotic cells and show a constitutive dormancy, i.e., no germination occurs in the presence of rich growth medium. Only an extreme trigger as very high temperature or pressure is able to evoke synchronized germination. In this study, several changes within the thick cell wall of these cells are observed after a heat treatment: (i.) a change in its structure as shown with EPR and X-ray diffraction; (ii.) a release of an abundant protein into the supernatant, which is proportional to the extent of heat activation; (iii.) a change in the permeability of the cell wall as judged by fluorescence studies in which staining of the interior of the cell wall correlates with germination of individual ascospores. The gene encoding the protein, dubbed ICARUS, was studied in detail and was expressed under growth conditions that showed intense ascomata (fruit body) and ascospore formation. It encodes a small 7–14 kD protein. Blast search exhibits that different Talaromyces species show a similar sequence, indicating that the protein also occurs in other species of the genus. Deletion strains show delayed ascomata formation, release of pigments into the growth medium, higher permeability of the cell wall and a markedly shorter heat activation needed for activation. Further, wild type ascospores are more heat-resistant. All these observations suggest that the protein plays a role in dormancy and is related to the structure and permeability of the ascospore cell wall. However, more research on this topic is needed to study constitutive dormancy in other fungal species that form stress-resistant ascospores.

The septal pore cap is an organelle that functions in vegetative growth and mushroom formation of the wood-rot fungus Schizophyllum commune

Mushroom-forming basidiomycetes colonize large areas in nature. Their hyphae are compartmentalized by perforated septa, which are usually covered by a septal pore cap (SPC). Here, we describe, for the first time, the composition and function of SPCs using the model system Schizophyllum commune. The SPC of S. commune was shown to consist of a proteinaceous matrix covered by a lipid membrane. The matrix was demonstrated to define the ultrastructure of the SPC and to consist of two main proteins, Spc14 and Spc33. Gene spc14 encodes a protein of 86 amino acids, which lacks known domain, signal or localization sequences. Gene spc33 encodes a 239 and a 340 amino acid variant. Both forms contain a predicted signal anchor that targets them to the ER. Immuno-localization showed the presence of Spc33 in the SPC but not in ER. From this and previous reports it is concluded that the SPC is derived from this organelle. Inactivation of spc33 resulted in loss of SPCs and the inability to close septa. The latter may well explain why vegetative growth and mushroom formation were severely reduced in strains in which spc33 was inactivated.

Karyotype analysis, genome organization, and stable genetic transformation of the root colonizing fungus Piriformospora indica

Piriformospora indica (Basidiomycota, Sebacinales) is a root colonizing fungus which is able to increase biomass and yield of crop plants and to induce local and systemic resistance to fungal diseases and tolerance to abiotic stress. A prerequisite for the elucidation of the mode of action of this novel kind of symbiosis is knowledge of the genome organization as well as the development of tools to study and modify gene functions. Here we provide data on the karyotype and genetic transformation strategies. The fungus was shown to possess at least six chromosomes and a genome size of about 15.4-24Mb. Sequences of the genes encoding the elongation factor 1-alpha (TEF) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were used for genome size estimation through real-time PCR analysis. Chromosomal location investigated by Southern blot and expression analysis suggested that TEF and GAPDH are single-copy genes with strong and constitutive promoters. A genetic transformation system was established using a fragment of the TEF promoter region for construction of vectors carrying the selectable marker hygromycin B phosphotransferase. Results demonstrate that P. indica can be stably transformed by random genomic integration of foreign DNA and that it posses a relative small genome as compared to other members of the Basidiomycota.

Phleomycin increases transformation efficiency and promotes single integrations in Schizophyllum commune

Phleomycin is mutagenic by introducing double-strand breaks in DNA. The ble gene of Streptoalloteychus hindustanus, which confers resistance to this substance, is widely used as a selection marker for transformation. Schizophyllum commune grows on 25 microg of phleomycin ml(-1) after introduction of a resistance cassette based on the ble gene. However, we here report that growth of resistant colonies on this concentration of phleomycin resulted in aberrant colony morphologies. Apparently, phleomycin was mutagenic despite acquired resistance. Therefore, a new selection system was developed based on resistance to the antibiotic nourseothricin. However, the transformation efficiency was tenfold lower than that obtained with phleomycin as a selection agent. This low transformation efficiency could be rescued by addition of a nonselective concentration of phleomycin during protoplast regeneration. This was accompanied by a higher incidence of single-copy integrations and with an increase of expression of key genes involved in double-strand break repair. Taken together, we conclude that the effect of a nonselective concentration of phleomycin strongly resembles the effect of restriction enzyme-mediated integration (REMI) but, unlike REMI, it does not depend on the presence of a target restriction site.

Septal pore cap protein SPC18, isolated from the basidiomycetous fungus Rhizoctonia solani, also resides in pore plugs

The hyphae of filamentous fungi are compartmentalized by septa that have a central pore. The fungal septa and septum-associated structures play an important role in maintaining cellular and intrahyphal homeostasis. The dolipore septa in the higher Basidiomycota (i.e., Agaricomycotina) are associated with septal pore caps. Although the ultrastructure of the septal pore caps has been studied extensively, neither the biochemical composition nor the function of these organelles is known. Here, we report the identification of the glycoprotein SPC18 that was found in the septal pore cap-enriched fraction of the basidiomycetous fungus Rhizoctonia solani. Based on its N-terminal sequence, the SPC18 gene was isolated. SPC18 encodes a protein of 158 amino acid residues, which contains a hydrophobic signal peptide for targeting to the endoplasmic reticulum and has an N-glycosylation motif. Immunolocalization showed that SPC18 is present in the septal pore caps. Surprisingly, we also observed SPC18 being localized in some plugs. The data reported here strongly support the hypothesis that septal pore caps are derived from endoplasmic reticulum and are involved in dolipore plugging and, thus, contribute to hyphal homeostasis in basidiomycetous fungi.

Transformation by complementation of a uracil auxotroph of the hyper lignin-degrading basidiomycete Phanerochaete sordida YK-624

Phanerochaete sordida YK-624 is a hyper lignin-degrading basidiomycete possessing greater ligninolytic selectivity than either P. chrysosporium or Trametes versicolor. To construct a gene transformation system for P. sordida YK-624, uracil auxotrophic mutants were generated using a combination of ultraviolet (UV) radiation and 5-fluoroorotate resistance as a selection scheme. An uracil auxotrophic strain (UV-64) was transformed into a uracil prototroph using the marker plasmid pPsURA5 containing the orotate phosphoribosyltransferase gene from P. sordida YK-624. This system generated approximately 50 stable transformants using 2 x 10(7) protoplasts. Southern blot analysis demonstrated that the transformed pPsURA5 was ectopically integrated into the chromosomal DNA of all transformants. The enhanced green fluorescent protein (EGFP) gene was also introduced into UV-64. The transformed EGFP was expressed in the co-transformants driven by P. sordida glyceraldehyde-3-phosphate dehydrogenase gene promoter and terminator regions.

The SC15 protein of Schizophyllum commune mediates formation of aerial hyphae and attachment in the absence of the SC3 hydrophobin

Disruption of the SC3 gene in the basidiomycete Schizophyllum commune affected not only formation of aerial hyphae but also attachment to hydrophobic surfaces. However, these processes were not completely abolished, indicating involvement of other molecules. We here show that the SC15 protein mediates formation of aerial hyphae and attachment in the absence of SC3. SC15 is a secreted protein of 191 aa with a hydrophilic N-terminal half and a highly hydrophobic C-terminal half. It is not a hydrophobin as it lacks the eight conserved cysteine residues found in these proteins. Besides being secreted into the medium, SC15 was localized in the cell wall and the mucilage that binds aerial hyphae together. In a strain in which the SC15 gene was deleted (DeltaSC15) formation of aerial hyphae and attachment were not affected. However, these processes were almost completely abolished when the SC15 gene was deleted in the DeltaSC3 background. The absence of aerial hyphae in the DeltaSC3DeltaSC15 strain can be explained by the inability of the strain to lower the water surface tension and to make aerial hyphae hydrophobic.

SC3 and SC4 hydrophobins have distinct roles in formation of aerial structures in dikaryons of Schizophyllum commune

Two monokaryons of Schizophyllum commune can form a fertile dikaryon when the mating-type genes differ. Monokaryons form sterile aerial hyphae, while dikaryons also form fruiting bodies that function in sexual reproduction. The SC3 hydrophobin gene is expressed both in monokaryons and in dikaryons. The SC4 hydrophobin is dikaryon specific. In the monokaryon, SC3 lowers the water surface tension, coats aerial hyphae with a hydrophobic layer and mediates attachment of hyphae to hydrophobic surfaces. The SC4 protein lines gas channels within fruiting bodies with a hydrophobic membrane. Using gene disruptions, in this study, we show that in dikaryons SC3 fulfils the same roles as in monokaryons. SC4, on the other hand, has a role within fruiting bodies. In contrast to gas channels in fruiting bodies of the wild type, those of a DeltaSC4 strain easily filled with water. Thus, SC4 prevents gas channels filling with water under wet conditions, probably serving uninterrupted gas exchange. Other dikaryon-specific hydrophobin genes, SC1 and SC6, apparently do not substitute for the SC4 gene. In addition, by expressing the SC4 gene behind the SC3 promoter in a DeltaSC3 monokaryon, it was shown that SC4 cannot fully substitute for SC3, indicating that both hydrophobins evolved to fulfil specific functions.

Characterization of the glyceraldehyde-3-phosphate dehydrogenase gene [correction of glyceraldehyde-3-phosphate gene] and the use of its promoter for heterologous expression in Cryptococcus neoformans, a human pathogen

The GPD gene encoding glyceraldehyde-3-phosphate dehydrogenase was isolated from Cryptococcus neoformans, a heterobasidiomycetous yeast that is pathogenic to humans. The gene contains 11 introns, differing from the conserved intron positions found in the GPD genes of Basidiomycetes. The predicted amino-acid sequence of this gene is extremely similar to that reported from GPD proteins of other basidiomycetes. The promoter region of the C. neoformans GPD gene was similar to those of other basidiomycetes. Plasmid constructs containing up to 1600 base pairs upstream of the native GPD open reading frame were used to express either the native URA5 gene in a ura5 mutant or the heterologous hphI gene (a bacterial gene that confers resistance to the aminoglycoside hygromycin) in a wild-type strain of C. neoformans. Transformation frequencies resulting from the plasmid-borne Gpdp::URA5 gene were at levels similar to those of the native URA5, which suggested that all the sequences necessary for proper expression were present. Transformation frequencies using the Gpdp::hphI gene constructs were poor. However, addition of DNA sequences flanking the 3'-end of an native C. neoformans gene significantly improved the transformation frequencies resulting from the expression of the heterologous hphI gene.

Introns are necessary for mRNA accumulation in Schizophyllum commune

The cDNA coding sequence of the Agaricus bisporus hydrophobin gene ABH1 under the regulation sequences of the Schizophyllum commune SC3 hydrophobin gene gave no expression in S. commune. In contrast, the genomic coding sequence (containing three introns) produced high levels of ABH1 mRNA when transformed to S. commune in the same configuration. Apparently, introns were needed for the accumulation of mRNAs from the ABH1 gene. When the effect of intron deletion on expression of the homologous genes SC3 and SC6 was examined, it was observed that only the genomic coding sequences were expressed in S. commune. Run-on analysis with nuclei harbouring intron-containing and intronless SC6 showed that this effect did not occur at the level of transcription initiation: genomic and cDNA sequences were equally active in this respect. When a 50 bp artificial intron containing the consensus splice and branch sites of S. commune introns, in addition to random-generated sequences, was introduced in the right orientation into the intronless SC3 transcriptional unit, accumulation of SC3 mRNA was restored. By polymerase chain reaction amplification, no unspliced SC3 mRNA species could be detected. Furthermore, the addition of an intron into the transcriptional unit of the gene for green fluorescent protein (GFP) effected clear fluorescence of the transgenic hyphae. Apparently, splicing is required for the normal processing of primary transcripts in S. commune.

Identification of three differentially expressed hydrophobins in Pleurotus ostreatus (oyster mushroom)

Three proteins with characteristic features of class I hydrophobins, designated POH1, POH2 and POH3, were isolated from the basidiomycete Pleurotus ostreatus. Based on N-terminal sequence analyses, their cDNAs were isolated using RT-PCR; the cDNAs and corresponding genes were sequenced and their regulation studied. POH1 is expressed in the fruiting bodies but not in vegetative mycelium. The regulation of POH2 and POH3 is tightly correlated. Both genes are switched off in the fruiting bodies but abundantly expressed in the vegetative mycelium of both monokaryon and dikaryon. POH2 and POH3 were isolated from the culture medium and from aerial hyphae. Co-purified POH2 and POH3 assembled in vitro into a protein membrane with a typical rodlet pattern as found previously with other hydrophobins. Similar structures were detected on the surface of aerial hyphae.

A hydrophobin (ABH3) specifically secreted by vegetatively growing hyphae of Agaricus bisporus (common white button mushroom)

Aerial mycelium and hyphal strands of Agaricus bisporus, strain U1, exhibited a rodlet pattern at their surfaces characteristic for assembled class I hydrophobins. An SDS-insoluble/trifluoroacetic-acid-soluble fraction from strands was found to contain one abundant protein with an apparent molecular mass on gel of 19 kDa. Two sequences for this protein (ABH3), typical of class I hydrophobins, could be deduced by sequencing cDNA clones obtained by RT-PCR. The two forms of the protein could be assigned to different alleles present in the two homokaryons that constitute the heterokaryotic U1 strain. ABH3 displays all the in vitro properties of a typical class I hydrophobin such as SC3 from Schizophyllum commune but is not glycosylated or otherwise post-translationally modified because the molecular mass values deduced from the amino acid sequence (9228 and 9271 Da) and derived from mass spectrometry were in good agreement. The ABH3 transcript was found to be present in the vegetative mycelium of both primary and secondary mycelium but not in the fruiting bodies, whereas the reverse was found for the ABH1 hydrophobin. Using an S. commune mutant with a disrupted SC3 gene it was found that ABH3 can substitute for SC3 in inducing formation of aerial hyphae, suggesting a role of ABH3 in the emergence of aerial hyphae and strands in A. bisporus.

Positioning of nuclei in the secondary Mycelium of Schizophyllum commune in relation to differential gene expression

In this paper we propose a novel type of gene regulation in the MATA|l4 MATB|l4 heterokaryon of Schizophyllum commune by means of differential positioning of the nuclei. It was found that binucleate hyphae with juxtaposed nuclei secrete SC4 hydrophobin (abundant during fruit-body formation), while SC3 (abundant during aerial hyphae formation in both mono- and dikaryons) appeared to be absent. Certain growth conditions disrupted the binucleate state in that the compatible nuclei became separated at a considerable distance. Under these conditions SC4 was not secreted while SC3 was secreted to a high degree. Disruption of the binucleate state was earlier observed in developing aerial hyphae which secrete SC3. Apparently, when the nuclei are in close proximity the dikaryon-expressed genes are switched on by interaction of the products of the MATA and MATB mating-type genes, while SC3 is suppressed by interacting products of the MATB genes, as occurs in the common MATA heterokaryon (MATA= MATB|l4). Growth conditions that lead to disruption of the binucleate state apparently result in abolishment of interaction between the MATB mating-type genes. Under these conditions, dikaryon-specific mRNAs do not accumulate in the MATA|l4 MATB|l4 heterokaryon, while SC3 mRNA becomes highly abundant.

Expression of two closely linked hydrophobin genes of Coprinus cinereus is monokaryon-specific and down-regulated by the oid-1 mutation

A protein with characteristic properties of a fungal hydrophobin (CoH1) was isolated from the monokaryotic stage of the basidiomycete Coprinus cinereus. A cosmid clone containing the corresponding gene (coH1) was identified using a cDNA probe derived by RT-PCR. Hybridization and sequence analysis identified a second gene, coH2, just 4.1 kb downstream of coH1 encoding a hydrophobin (CoH2) with 64% sequence identity. Both coH1 and coH2 are subject to developmental regulation. They are expressed in vegetative monokaryotic cells but not in the asexual oidia produced on the surface of monokaryons. Transcripts of the genes were barely detected in dikaryotic mycelium and were absent from fruit bodies. Loss of aerial growth due to a mutation known as oid-1 was correlated with lack of both hydrophobins.

An abundant hydrophobin (ABH1) forms hydrophobic rodlet layers in Agaricus bisporus fruiting bodies

The SDS-insoluble protein fraction of Agaricus bisporus fruiting bodies was solubilized with trifluoroacetic acid. On SDS-PAGE this fraction was found to contain one abundant protein with an apparent M(r) of 16 kDa. The N-terminal amino acid sequence of this protein was determined and RT-PCR used to isolate a cDNA clone which upon sequencing identified the protein as a typical class I hydrophobin (ABH1). The gene (ABH1) was isolated and sequenced, and a second hydrophobin gene (ABH2) was found about 2.5 kbp downstream of ABH1. Purified ABH1 self-assembled at hydrophobic-hydrophilic interfaces, producing the typical rodlet layer known from other hydrophobins. Similar rodlets were observed on the surface of the fruiting body, while immunological localization showed the hydrophobin to be particularly abundant at the outer surface of fruiting bodies, in the veil and in the core tissue of the stipe. Transcripts of ABH1 were found only in fruiting-body hyphae. The ABH1 hydrophobin is probably solely responsible for the hydrophobicity of the fruiting-body surface but may also line air channels within fruiting bodies.

Genetic regulation of emergent growth in Schizophyllum commune

After a period of juvenile growth, Schizophyllum commune starts to transcribe genes for a number of abundant cell-wall proteins that are excreted into the medium by submerged hyphae but become part of the cell wall in emergent structures. The dikaryon transcribes the genes SC1, SC3, SC4, and SC6 that encode hydrophobins and SC7 and SC14 that encode hydrophilic wall proteins of unknown function. Of these, only the SC3 gene is highly transcribed in the monokaryon. The SC3p hydrophobin forms an insoluble hydrophobic rodlet layer by interfacial self-assembly at the outer surface of aerial hyphae of both monokaryon and dikaryon. The SC4p hydrophobin forms an insoluble membrane separating the extracellular matrix surrounding dikaryotic hyphae of the plectenchyma from air cavities in the fruit bodies while the product of the SC7 gene is found within the extracellular matrix. However, these plectenchyma hyphae do not express the SC3 gene. Because SC3 activity is suppressed in a MATA = MATB≠ heterokaryon and a MATAx matBCon homokaryon, interaction between different B mating-type gene products appears responsible for suppression of SC3 in the hyphae that form the plectenchyma. On the other hand, in aerial hyphae of the MATA ≠ MATB≠ heterokaryon the binucleate state of the hyphae appears disrupted and this is accompanied by expression of SC3 only, as in the monokaryon. This suggests that regulation of specific genes by the products of different MATB genes only occurs when these genes are present in closely paired nuclei. Thus, spatial differences in gene expression during emergent growth in the MATA ≠ MATB≠ heterokaryon may occur by regulation of the nuclear distribution. Key words: Schizophyllum commune development, hydrophobins in development, mating-type genes in Schizophyllum, fruit-body development, emergent growth.

Differential expression of genes under control of the mating-type genes in the secondary mycelium of Schizophyllum commune

The Schizophyllum commune SC3 gene, which encodes a hydrophobin that coats aerial hyphae, is expressed in both monokaryons and dikaryons. The dikaryons were formed by mating two monokaryons with different MATA and MATB genes, leading to activation of the MATA- and MATB-controlled pathways (MATA-on and MATB-on). In contrast to the monokaryons, the dikaryons also expressed other hydrophobin genes (SC1, SC4) as well as a gene (SC7) encoding a hydrophilic wall protein. None of these four genes was expressed in MATA-off MATB-on mycelia, indicating that MATB-on represses SC3 and that both MATA-on and MATB-on are required for activation of SC1, SC4 and SC7. In fruiting dikaryons, immunolabelling revealed that SC3p was produced by aerial hyphae but not by hyphae that constitute the fruit-body tissue. In contrast to aerial hyphae, the latter produced dikaryon-specific transcripts and secreted SC7p into the extracellular matrix of the tissue. This suggests that in the aerial hyphae of the dikaryon the MATB-on pathway was not effective (MATB-off). We observed that in these aerial hyphae the two nuclei were wider apart than in a typical dikaryon. Although other explanations are not ruled out, we tentatively propose that effective interaction of different MATB genes requires proximity of the two nuclei containing these genes, and that disruption of this binucleate state represents a novel mechanism of gene control for spatial cell differentiation in the secondary mycelium.

Highly-efficient transformation of the homobasidiomycete Schizophyllum commune to phleomycin resistance

Regulatory sequences of the glyceraldehyde-3-phosphate-dehydrogenase (GPD) gene from the homobasidiomycete Schizophyllum commune were fused to the coding sequence of the ble gene from Streptoalloteichus hindustanus, which codes for a phleomycin-binding protein. The resulting construct transformed S. commune to phleomycin resistance at a high frequency (up to 10(4) transformants/microgram DNA per 10(7) protoplasts) when regeneration was done in 0.5 M MgSO4. A similar construct with regulatory sequences from Aspergillus nidulans failed to give transformants, showing the importance of homologous regulatory sequences for the expression of genes in S. commune. The homologous GPD promoter could be deleted up to position -130 without any effect on the number of phleomycin-resistant transformants. This is the first effective stable transformation system in a homobasidiomycete employing antibiotic resistance.