Ds-like restless deletion derivatives occur in Tolypocladium inflatum and two foreign hosts, Neurospora crassa and Penicillium chrysogenum

Minos and Restless transposon insertion mutagenesis of psychrotrophic fungus for red pigment synthesis adaptive to normal temperature

The polar psychrotrophic fungus Geomyces sp. WNF-15A can produce high-quality natural red pigment for the potential use as edible pigment. However, it shows low-temperature-dependent synthesis of red pigment, which limits its large-scale industrial applications due to the difficult and high-cost bioprocess control. This study aims to develop transposon-mediated mutagenesis methods to generate mutants that are able to synthesize red pigment at normal temperature. Four transposable systems, including single and dual transposable systems, were established in this fungus based on the Minos from Drosophila hydei and the Restless from Tolypocladium inflatum. A total of 23 production-dominant mutants and 12 growth-dominant mutants were thus obtained by constructed transposable systems. At 14 °C and 20 °C, the MPS1 mutant strain achieved the highest level of red pigment (OD520 of 43.3 and 29.7, respectively), which was increased by 78.4% and 128.7% compared to the wild-type, respectively. Of note, 4 mutants (MPS1, MPS3, MPS4 and MPD1) successfully synthesized red pigment (OD520 of 5.0, 5.3, 4.7 and 4.9, respectively) at 25 °C, which broke the limit of the wild-type production under normal temperature. Generally, the dual transposable systems of Minos and Restless were more efficient than their single transposable systems for mutagenesis in this fungus. However, the positive mutation ratios were similar between the dual and single transposable systems for either Minos or Restless. This study provides alternative tools for genetic mutagenesis breeding of fungi from extreme environments.

An inducible tool for random mutagenesis in Aspergillus niger based on the transposon Vader

The ascomycete Aspergillus niger is widely used in the biotechnology, for instance in producing most of the world's citric acid. It is also known as a major food and feed contaminant. While generation of gene knockouts for functional genomics has become feasible in ku70 mutants, analyzing gene functions or metabolic pathways remains a laborious task. An unbiased transposon-based mutagenesis approach may aid this process of analyzing gene functions by providing mutant libraries in a short time. The Vader transposon is a non-autonomous DNA-transposon, which is activated by the homologous tan1-transposase. However, in the most commonly used lab strain of A. niger (N400 strain and derivatives), we found that the transposase, encoded by the tan1 gene, is mutated and inactive. To establish a Vader transposon-based mutagenesis system in the N400 background, we expressed the functional transposase of A. niger strain CBS 513.88 under the control of an inducible promoter based on the Tet-on system, which is activated in the presence of the antibiotic doxycycline (DOX). Increasing amounts of doxycycline lead to higher Vader excision frequencies, whereas little to none activity of Vader was observed without addition of doxycycline. Hence, this system appears to be suitable for producing stable mutants in the A. niger N400 background.

Dicer-Dependent Biogenesis of Small RNAs and Evidence for MicroRNA-Like RNAs in the Penicillin Producing Fungus Penicillium chrysogenum

MicroRNAs (miRNAs) are non-coding small RNAs (sRNAs) that regulate gene expression in a wide range of eukaryotes. In this study, we analyzed regulatory sRNAs in Penicillium chrysogenum, the industrial producer of the β-lactam antibiotic penicillin. To identify sRNAs and microRNA-like RNAs (milRNAs) on a global approach, two sRNA sequencing libraries were constructed. One library was created with pooled total RNA, obtained from twelve differently grown cultures (RNA Mix), and the other with total RNA from a single submerged cultivation (∆ku70FRT2). Illumina sequencing of both RNA libraries produced 84,322,825 mapped reads. To distinguish between Dicer-dependent and independent sRNA formation, we further constructed two single dicer gene mutants (∆dcl2 and ∆dcl1) and a dicer double mutant (∆dcl2∆dcl1) and analyzed an sRNA library from the Dicer-deficient double-mutant. We identified 661 Dicer-dependent loci and in silico prediction revealed 34 milRNAs. Northern blot hybridization of two milRNAs provided evidence for mature milRNAs that are processed either in a complete or partial Dicer-dependent manner from an RNA precursor. Identified milRNAs share typical characteristics of previously discovered fungal milRNAs, like a strong preference for a 5' uracil and the typical length distribution. The detection of potential milRNA target sites in the genome suggests that milRNAs might play a role in posttranscriptional gene regulation. Our data will further increase our knowledge of sRNA dependent gene regulation processes, which is an important prerequisite to develop more effective strategies for improving industrial fermentations with P. chrysogenum.

The genome of tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster

The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of cyclosporin and other secondary metabolites in T. inflatum and related taxa. Phylogenomic analyses reveal previously undetected and complex patterns of homology between the nonribosomal peptide synthetase (NRPS) that encodes for cyclosporin synthetase (simA) and those of other secondary metabolites with activities against insects (e.g., beauvericin, destruxins, etc.), and demonstrate the roles of module duplication and gene fusion in diversification of NRPSs. The secondary metabolite gene cluster responsible for cyclosporin biosynthesis is described. In addition to genes necessary for cyclosporin biosynthesis, it harbors a gene for a cyclophilin, which is a member of a family of immunophilins known to bind cyclosporin. Comparative analyses support a lineage specific origin of the cyclosporin gene cluster rather than horizontal gene transfer from bacteria or other fungi. RNA-Seq transcriptome analyses in a cyclosporin-inducing medium delineate the boundaries of the cyclosporin cluster and reveal high levels of expression of the gene cluster cyclophilin. In medium containing insect hemolymph, weaker but significant upregulation of several genes within the cyclosporin cluster, including the highly expressed cyclophilin gene, was observed. T. inflatum also represents the first reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal order Hypocreales, and supports parallel and qualitatively distinct radiations of insect pathogens. The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role of secondary metabolite gene clusters and their metabolites in fungal biology.

Impact of the Penicillium chrysogenum genome on industrial production of metabolites

The genome sequence of Penicillium chrysogenum has initiated a range of fundamental studies, deciphering the genetic secrets of the industrial penicillin producer. More than 60 years of classical strain improvement has resulted in major but delicate rebalancing of the intracellular metabolism leading to the impressive penicillin titres of the current production strains. Several leads for further improvement are being followed up, including the use of P. chrysogenum as a cell factory for other products than β-lactam antibiotics.

Suitability of Vader for transposon-mediated mutagenesis in Aspergillus niger

The filamentous fungus Aspergillus niger is widely used in biotechnological applications. Strain CBS513.88 is known to harbor 21 copies of the nonautonomous transposon Vader. Upon selection of chlorate-resistant A. niger colonies, one Vader copy was found integrated in the nirA gene. This copy was used for vector construction and development of a transposon-tagging method. Vader showed an excision frequency of about 1 in 2.2 × 10(5) conidiospores. A total of 95 of 97 colonies analyzed exhibited an excision event at the DNA level, and Vader footprints were found. By employing thermal asymmetric interlaced (TAIL)-PCR, the reintegration sites of 21 independent excision events were determined. All reintegration events occurred within or very close to genes. Therefore, this method can be used for transposon mutagenesis in A. niger.

Among developmental regulators, StuA but not BrlA is essential for penicillin V production in Penicillium chrysogenum

In filamentous fungi, secondary metabolism is often linked with developmental processes such as conidiation. In this study we analyzed the link between secondary metabolism and conidiation in the main industrial producer of the β-lactam antibiotic penicillin, the ascomycete Penicillium chrysogenum. Therefore, we generated mutants defective in two central regulators of conidiation, the transcription factors BrlA and StuA. Inactivation of either brlA or stuA blocked conidiation and altered hyphal morphology during growth on solid media, as shown by light and scanning electron microscopy, but did not affect biomass production during liquid-submerged growth. Genome-wide transcriptional profiling identified a complex StuA- and BrlA-dependent regulatory network, including genes previously shown to be involved in development and secondary metabolism. Remarkably, inactivation of stuA, but not brlA, drastically downregulated expression of the penicillin biosynthetic gene cluster during solid and liquid-submerged growth. In agreement, penicillin V production was wild-type-like in brlA-deficient strains but 99% decreased in stuA-deficient strains during liquid-submerged growth, as shown by high-performance liquid chromatography (HPLC) analysis. Thus, among identified regulators of penicillin V production StuA has the most severe influence. Overexpression of stuA increased the transcript levels of brlA and abaA (another developmental regulator) and derepressed conidiation during liquid-submerged growth but did not affect penicillin V productivity. Taken together, these data demonstrate an intimate but not exclusive link between regulation of development and secondary metabolism in P. chrysogenum.

Evidence for Dicer-dependent RNA interference in the industrial penicillin producer Penicillium chrysogenum

RNA interference (RNAi) is a sequence-specific post-transcriptional gene silencing system that downregulates target gene expression. Here, we provide several lines of evidence for RNA silencing in the industrial beta-lactam antibiotic producer Penicillium chrysogenum using the DsRed reporter gene under the control of the constitutive trpC promoter or the inducible xylP promoter. The functional RNAi system was verified by detection of siRNAs that hybridized exclusively with gene-specific (32)P-labelled RNA probes. Moreover, when RNAi was used to silence the endogenous PcbrlA morphogene that controls conidiophore development, a dramatic reduction in the formation of conidiospores was observed in 47 % of the corresponding transformants. Evidence that RNAi in P. chrysogenum is dependent on a Dicer peptide was provided with a strain lacking Pcdcl2. In the DeltaPcdcl2 background, silencing of the PcbrlA gene was tested. None of the transformants analysed showed a developmental defect. The applicability of the RNAi system in P. chrysogenum was finally demonstrated by silencing the Pcku70 gene to increase homologous recombination frequency. This led to the generation of single and double knockout mutants.

Repeat induced point mutation in two asexual fungi, Aspergillus niger and Penicillium chrysogenum

Repeat induced point mutation (RIP) is a gene silencing mechanism present in fungal genomes. During RIP, duplicated sequences are efficiently and irreversibly mutated by transitions from C:G to T:A. For the first time, we have identified traces of RIP in transposable elements of Aspergillus niger and Penicillium chrysogenum, two biotechnologically relevant fungi. We found that RIP in P. chrysogenum has affected a large set of sequences, which also contain other mutations. On the other hand, RIP in A. niger is limited to only few sequences, but literally all mutations are RIP-like. Surprisingly, RIP occurred only in transposon sequences that have disrupted open reading frames in A. niger, a phenomenon not yet reported for other fungi. In both fungal species, we identified two sequences with strong sequence similarity to Neurospora crassa RID. RID is a putative DNA methyltransferase and the only known enzyme involved in the RIP process. Our findings suggest that both A. niger and P. chrysogenum either had a sexual past or have a sexual potential. These findings have important implications for future strain development of these fungi.

Drifter, a novel, low copy hAT-like transposon in Fusarium oxysporum is activated during starvation

The facultative pathogenic fungus Fusarium oxysporum is known to harbour many different transposable and/or repetitive elements. We have identified Drifter, a novel DNA transposon of the hAT family in F. oxysporum. It was found adjoining SIX1-H, a truncated homolog of the SIX1 avirulence gene in F. oxysporum f. sp. lycopersici. Absence of a target site duplication as well as the 5' part of SIX1-H suggests that transposition of Drifter into the ancestor of SIX1-H was followed by loss of a chromosomal segment through recombination between Drifters. F. oxysporum isolates belonging to various formae speciales harbour between 0 and 5 full-length copies of Drifter and/or one or more copies with an internal deletion. Transcription of Drifter is activated during starvation for carbon or nitrogen.

Alternative splicing of transcripts of the transposon Restless is maintained in the foreign host Neurospora crassa and can be modified by introducing mutations at the 5' and 3' splice sites

The primary transcript of the transposon Restless from Tolypocladium inflatum undergoes an unusual mechanism of alternative splicing by employing either of two 3' "CAG" splice sites. These are separated by only four nucleotides, thus generating two different splice products, which differ in their coding capacity. To analyse whether this alternative splicing occurs in its natural host exclusively, we introduced the transposon into the heterologous host Neurospora crassa. In addition to the wild -type transposon sequence, transposon sequences mutagenised in vitro with modified 5' and 3' intron splice sites were generated. RNA was isolated from transformants and RT-PCR was performed with specific oligonucleotides flanking the intron sequence. Alternative splicing was analysed, employing a simple test procedure based on the convenient presence of a BamHI restriction site between both splice sites. The ratio of alternative splicing seems to be influenced by both the 5' and the 3' splice site, as mutations at either position influence the ratio of alternative splice products. At the 5' splice site, mutating the first "C" has a strong effect on the ratio of alternative splicing, while mutating the second "C" has little or no effect. Similarly, at the 3' splice site, only mutations at the first 3' "CAG" change the ratio of alternative splicing. It appears that alternative splicing of the Restless intron is not host-specific, but is influenced by the intron splice site sequences themselves.

Guest, a transposable element belonging to the Tc1/mariner superfamily is an ancient invader of Neurospora genomes

Guest is a transposable element of the Tc1/mariner superfamily with 30-40bp terminal inverted repeats and a TA dinucleotide target site duplication. Guest was originally discovered in the St. Lawrence 74A laboratory strain of the filamentous fungus Neurospora crassa. In this report, Guest iterations subcloned from a cosmid library of the Oakridge 74A strain were used to design PCR primers that permitted the detection of Guest in wild isolates of N. crassa. Guest is present in N. crassa as multiple copies ranging between 100bp and 2.4kb and is present in the mating type locus of several Neurospora species. Bioinformatic analysis of the entire N. crassa genome (Oakridge 74A strain) detected 48 Guest iterations. All iterations appeared to have been inactivated either by repeat-induced point mutation or sequence deletion, with the majority being remnants less than 400bp in length. The possible involvement of Guest in the evolution of the variable region that flanks the mating type idiomorphs in several Neurospora species is discussed.

Transposable elements in filamentous fungi

The past 10 years have been productive in the characterization of fungal transposable elements (TEs). All eukaryotic TEs described are found including an extraordinary prevalence of active members of the pogo family. The role of TEs in mutation and genome organization is well documented, leading to significant advances in our perception of the mechanisms underlying genetic changes in these organisms. TE-mediated changes, associated with transposition and recombination, provide a broad range of genetic variation, which is useful for natural populations in their adaptation to environmental constraints, especially for those lacking the sexual stage. Interestingly, some fungal species have evolved distinct silencing mechanisms that are regarded as host defense systems against TEs. The examination of forces acting on the evolutionary dynamics of TEs should provide important insights into the interactions between TEs and the fungal genome. Another issue of major significance is the practical applications of TEs in gene tagging and population analysis, which will undoubtedly facilitate research in systematic biology and functional genomics.

Electroporation of isolated higher-plant mitochondria: transcripts of an introduced cox2 gene, but not an atp6 gene, are edited in organello

To facilitate the analysis of RNA processing in plant mitochondria, a method was established for introducing foreign DNA into mitochondria isolated from maize and sorghum. This method permits the uptake of DNA of up to 11 kb into the mitochondrial matrix. In vitro incubation of maize mitochondria in a specific buffer system was found to permit splicing and editing of newly synthesized RNAs for a period of at least 7 h. This was shown both for transcripts of endogenous mitochondrial genes (atp6, cox2) and for transcripts derived from an introduced Arabidopsis thaliana cox2 gene. In contrast, when a Sorghum bicolor atp6 gene was introduced into isolated maize mitochondria, the gene was transcribed, but the RNA was not edited, although all the editing sites in maize and sorghum atp6 RNA are identical. This may indicate the presence of transcript-specific cis -acting regions in the up- or downstream untranslated sequences of the mRNA. The system described here should allow further dissection of the mechanism of RNA editing in plant mitochondria.