Reinhard Fischer

• Professor
• Professor (Full) at Karlsruhe Institute of Technology

Filamentous fungi grow by apical extension where secretory vesicles are transported long distances by microtubules and by actin prior to fusion with the cell membrane. Apical, membrane-bound cell-end marker proteins (CEMPs) organise the cytoskeletons and thereby the growth machinery. CEMPs have been characterised mainly in Schizosaccharomyces pombe...

Introduction Translation is a fundamental process of life. In eukaryotes, the elongation step of translation is highly conserved and is driven by eukaryotic translation elongation factors (eEF)1A and eEF2. A significant variation of the elongation is the activity of eukaryotic elongation factor (eEF) 3 in Saccharomyces cerevisiae encoded by the gen...

Depending on their phosphorylation status, derivatives of phosphatidylinositol play important roles in vesicle identity, recognition and intracellular trafficking processes. In eukaryotic cells, phosphatidylinositol-4 phosphate pools generated by specific kinases are key determinants of the conventional secretion pathways. Earlier work in yeast has...

Animals protect themself from microbial attacks by robust skins or a cuticle as in Caenorhabditis elegans. Nematode-trapping fungi, like Arthrobotrys flagrans, overcome the cuticle barrier and colonize the nematode body. While lytic enzymes are important for infection, small-secreted proteins (SSPs) without enzymatic activity, emerge as crucial vir...

Initiation of development requires differential gene expression and metabolic adaptations. Here we show in the nematode-trapping fungus, Arthrobotrys flagrans, that both are achieved through a dual-function G-protein-coupled receptor (GPCR). A. flagrans develops adhesive traps and recognizes its prey, Caenorhabditis elegans, through nematode-specif...

Light as a source of information regulates morphological and physiological processes of fungi, including development, primary and secondary metabolism, or the circadian rhythm. Light signaling in fungi depends on photoreceptors and downstream components that amplify the signal to govern the expression of an array of genes. Here, we investigated the...

The nervous system of metazoans is involved in host-pathogen interactions to control immune activation. In Caenorhabditis elegans, this includes sleep induction, mediated by neuropeptide-like proteins (NLPs), which increases the chance of survival after wounding. Here we analyzed the role of NLP-27 in the infection of C. elegans with the nematode-t...

Light and temperature sensing are important features of many organisms. Light may provide energy but may also be used by non-photosynthetic organisms for orientation in the environment. Recent evidence suggests that plant and fungal phytochrome and plant phototropin serve dual functions as light and temperature sensors. Here we characterized the fu...

Microtubule Organizing Centers (MTOC) are subcellular structures in eukaryotic cells where nucleation of microtubules (MTs) takes place and represents the filament's minus end. Their localization depends on the species, cell type, and cell cycle stage. Along the fungal kingdom, the Spindle Pole Body (SPB) in the nucleus (an equivalent to Centrosome...

Where does one draw the line between primary and secondary metabolism? The answer depends on the perspective. Microbial secondary metabolites (SMs) were at first believed not to be very important for the producers because they are dispensable for growth under laboratory conditions. However, such compounds become important in natural niches of the o...

Communication is crucial for organismic interactions, from bacteria, to fungi, to humans. Humans may use the visual sense to monitor the environment before starting acoustic interactions. In comparison, fungi, lacking a visual system, rely on a cell-to-cell dialogue based on secreted signaling molecules to coordinate cell fusion and establish hypha...

Plant‐parasitic nematodes cause devastating agricultural damage worldwide. Only a few synthetic nematicides can be used and their application is limited in fields. Therefore, there is a need for sustainable and environment‐friendly alternatives. Nematode‐trapping fungi (NTF) are natural predators of nematodes. They capture and digest them with thei...

Communication is crucial for organismic interactions, from bacteria, to fungi, to humans. Humans may use the visual sense to monitor the environment before starting acoustic interactions. In comparison, fungi lack a visual system, instead, hyphae use a cell-to-cell dialogue based on secreted signaling molecules to orchestrate cell fusion and establ...

γ-Tubulin ring complexes (γ-TuRC) mediate nucleation and anchorage of microtubules (MTs) to microtubule organizing centers (MTOCs). In fungi, the spindle pole body (SPB) is the functional equivalent of the centrosome, which is the main MTOC. In addition, non-centrosomal MTOCs (ncMTOCs) contribute to MT formation in some fungi like Schizosaccharomyc...

Contamination of food and feed with toxin-producing fungi is a major threat in agriculture and for human health. The filamentous fungus Alternaria alternata is one of the most widespread postharvest contaminants and a weak plant pathogen. It produces a large variety of secondary metabolites with alternariol and its derivatives as characteristic myc...

Significance This study reveals that a dialogue-like communication mechanism, which mediates cell–cell fusion in filamentous fungi, is a conserved complex trait. It allows the communication and behavioral coordination of cells of distantly related species and mediates their mutual attraction and subsequent physical contact, although interspecies fu...

Nematode-trapping fungi (NTF), such as Arthrobotrys flagrans (Duddingtonia flagrans), are soil-borne fungi able to form adhesive trapping networks to attract and catch nematodes. In this forum piece we highlight some of their most fascinating features with a special focus on the role of small-secreted proteins in the predatory interaction.

Light is perceived by photoreceptors in fungi and further integrated into the stress-activated MAPK HOG pathway, and thereby potentially activates the expression of genes for stress responses. This indicates that the precise control of light conditions can likely improve the conidial yield and stress resistance to guarantee the low cost and long sh...

Nematode-trapping fungi (NTF) are a diverse and intriguing group of fungi that live saprotrophically but can switch to a predatory lifestyle when starving and in the presence of nematodes. NTF like Arthrobotrys oligospora or Duddingtonia flagrans produce adhesive trapping networks to catch and immobilize nematodes. After penetration of the cuticle,...

Nematode-trapping fungi, such as Duddingtonia flagrans , are fascinating carnivorous microorganisms. In a nutrient-rich environment they live as saprotrophs, but if nutrients are scarce and in the presence of nematodes, they can switch to a predatory lifestyle. The switch is characterized by the formation of complex, adhesive trap structures. The i...

Fungi sense light of different wavelengths using blue-, green-, and red-light photoreceptors. Blue light sensing requires the “white-collar” proteins with flavin as chromophore, and red light is sensed through phytochrome. Here we analyzed genome-wide gene expression changes caused by short-term, low-light intensity illumination with blue-, red- or...

The striatin-interacting phosphatase and kinase complex (STRIPAK) is a highly conserved eukaryotic signaling hub involved in the regulation of many cellular processes. In filamentous fungi, STRIPAK controls multicellular development, hyphal fusion, septation and pathogenicity. In this study we analyzed the role of the STRIPAK complex in the nematod...

Salicylic acid is a phenolic phytohormone which controls plant growth and development. A methyl ester (MSA) derivative thereof is volatile and involved in plant-insect or plant-plant communication. Here we show that the nematode-trapping fungus Duddingtonia flagrans uses a methyl-salicylic acid isomer, 6-MSA as morphogen for spatiotemporal control...

Conidia of Trichoderma guizhouense (Hypocreales, Ascomycota) are frequently applied to the production of biofertilizers and biocontrol agents. Conidiation of some Trichoderma species depends on blue light and the action of different blue light receptors. However, the interplay between different blue‐light receptors in light signaling remained elusi...

Centrosomes are important microtubule-organizing centers (MTOC) in animal cells. In addition, non-centrosomal MTOCs (ncMTOCs) were described in many cell types. Functional analogs of centrosomes in fungi are the spindle pole bodies (SPBs). In Aspergillus nidulans additional MTOCs were discovered at septa (sMTOC). Although the core components are co...

Mitochondria are essential organelles because of their function in energy conservation. Here, we show an involvement of mitochondria in phytochrome-dependent light sensing in fungi. Phytochrome photoreceptors are found in plants, bacteria, and fungi and contain a linear, heme-derived tetrapyrrole as chromophore. Linearization of heme requires heme...

Fungi grow by apical extension of their hyphae. The continuous growth requires constant delivery of vesicles, which fuse with the membrane and secrete cell wall biosynthesis enzymes. The growth mechanism requires the fungal cytoskeleton and turgor pressure. In a recent study by Fukuda et al. (mBio 12:e03196-20, 2021, https://doi.org/10.1128/mBio.03...

Photoactivated localization microscopy (PALM), one of the super resolution microscopy methods improving the resolution limit to 20 nm, allows the detection of single molecules in complex protein structures in living cells. Microtubule-organizing centres (MTOCs) are large, multisubunit protein complexes, required for microtubule polymerization. The...

Conidiophore of A. fumigatus carrying asexual spores that are coated with GFP as expressed from the defensin‐like peptide‐encoding defX gene. For further details, readers are referred to the article by Dümig et al. on p. e13301 of this issue.

Hydrophobins are relatively small proteins produced naturally by filamentous fungi with interesting biotechnological and biomedical applications given their self-assembly capacity, efficient adherence to natural and artificial surfaces, and to introduce modifications on the hydrophobicity/hydrophilicity of surfaces. In this work we demonstrate the...

Fungal spores are unique cells that mediate dispersal and survival in the environment. For pathogenic fungi encountering a susceptible host, these specialized structures may serve as infectious particles. The main causative agent of the opportunistic disease aspergillosis, Aspergillus fumigatus, produces asexual spores, the conidia, that become dis...

Phytochrome-dependent light signaling has been studied in several fungi. In Aspergillus nidulans light-stimulated phytochrome activates the high-osmolarity glycerol (HOG) signaling pathway and thereby controls the expression of a large number of genes, many of which are related to stress responses. In a genome-wide expression analysis in A. nidulan...

The black mold Alternaria alternata causes dramatic losses in agriculture due to postharvest colonization and mycotoxin formation and is a weak pathogen on living plants. Fungal signaling processes are crucial for successful colonization of a host plant. Because the mitogen-activated protein kinase HogA is important for the expression of stress-ass...

Stress is a normal part of life for fungi, which can survive in environments considered inhospitable or hostile for other organisms. Due to the ability of fungi to respond to, survive in, and transform the environment, even under severe stresses, many researchers are exploring the mechanisms that enable fungi to adapt to stress. The International S...

Zygosaccharomyces seidelii, a new species in the genus Zygosaccharomyces is described. The description of the species is based on a single strain that was isolated from flowers collected on the Maldives. On this occasion, the description of yeast species from single strains was revisited. Sequence analysis of the D1/D2 domain of the nuclear large s...

Iron is one of the most abundant elements on earth and essential for life. However, Fe3+ ions are rather insoluble and microorganisms such as fungi may use siderophores as strong chelators for uptake. In addition, free cytoplasmic iron is rather toxic and intracellular siderophores are used to control the toxicity. Siderophores are also important f...

A large proportion of fungal genomes are under the control of light. Most fungi employ complex light sensing systems, consisting of red-, blue-, and in some cases green-light photoreceptors. Here we studied the light response in Aspergillus nidulans. In a genetic screen, followed by whole-genome sequencing we identified a global regulator, which ap...

Centrosomes are important microtubule-organizing centers (MTOCs) in animal cells. In addition, non-centrosomal MTOCs (ncMTOCs) are found in many cell types. Their composition and structure are only poorly understood. Here, we analyzed nuclear MTOCs (spindle-pole bodies, SPBs) and septal MTOCs in Aspergillus nidulans. They both contain γ-tubulin alo...

The adaptation of microorganisms to different temperatures is an advantage in habitats with steadily changing conditions and raises the question about temperature sensing. Here we show that in the filamentous fungus Aspergillus nidulans the hybrid histidine kinase TcsB and phytochrome are involved in temperature‐induced gene transcription. Temperat...

Eight yeast strains which asexually reproduce by cell fission were isolated from bee bread of different solitary bees in Germany. DNA sequence analysis revealed that the strains shared the same sequence in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene with a strain that was previously isolated from a fig snack from Spain. The closes...

During bacterial conjugation, plasmid DNA is transferred from cell to cell. In Agrobacterium fabrum, conjugation is regulated by the phytochrome photoreceptors Agp1 and Agp2. Both contribute equally to this regulation. Agp1 and Agp2 are histidine kinases, but, for Agp2, we found no autophosphorylation activity. A clear autophosphorylation signal, h...

The filamentous fungus Alternaria alternata is a potent producer of many toxic secondary metabolites, which contaminate food and feed. The most prominent one is the polyketide‐derived alternariol (AOH) and its derivative alternariol monomethyl ether (AME). Here we identified the gene cluster for the biosynthesis of AOH and AME by CRISPR/Cas9‐mediat...

The conservation of architectural heritage is a big challenge in times with increasing air pollution with aggressive gases. A second major threat to buildings is the combination of water and air contaminants which may be used by microorganisms for their metabolism. Hence, myriads of different bacteria and fungi populate stone surfaces and penetrate...

Light controls many processes in filamentous fungi. The study of light regulation in a number of model organisms revealed an unexpected complexity. Although the molecular components for light sensing appear to be widely conserved in fungal genomes, the regulatory circuits and the sensitivity of certain species toward specific wavelengths seem diffe...

Nematode-trapping fungi (NTF) are a large and diverse group of fungi, which may switch from a saprotrophic to a predatory lifestyle if nematodes are present. Different fungi have developed different trapping devices, ranging from adhesive cells to constricting rings. After trapping, fungal hyphae penetrate the worm, secrete lytic enzymes and form a...

Genome-based phylogenomic tree of NTF and other fungi. Bootstrap values are indicated beside the nodes. Orange color indicates the clade grouping of nematode trapping fungi. The proteomes of Arthrobotrys oligospora (ADOT00000000.1), Drechmeria coniospora (LAYC00000000.1), Dactylellina haptotyla (AQGS00000000.1), Fusarium graminearum (AACM00000000.2...

Germling and hyphal fusion pathway in D. flagrans. The pathway was reconstructed using the N. crassa model [52]. A so far unknown signaling molecule is released by the signal-emitting cell, probably by exocytosis, in a SO-dependent manner. The signal is perceived by a so far unknown receptor of the signal-receiving cell. The binding leads to the as...

Graphical representation of the GO term association data for 6,878 proteins and pathways identified in D. flagrans (https://chirimoyo.ac.uma.es/bitlab/portfolio/sma3s/). The slices represent the percentage of unigenes identified in the particular category. (A) Biological process. (B) Molecular function. (C) Uniprot pathways. (PPTX)

Comparison of the proteomes and secretomes of several fungi. 21 fungal secretomes and effectors were predicted and were compared to those of D. flagrans. All secretomes were generated on the same way as for D. flagrans (See Materials and methods). The proteomes of A. oligospora (ADOT00000000.1), Fusarium graminearium (AACM00000000.2), Aspergillus n...

Length and mean coverage of D. flagrans contigs. The length of the contigs is given in bp. The mean coverage is calculated for each contig and the last row is the sum of length and mean coverage of all contigs. (XLS)

BlastP result of D. flagrans proteins compared with A. oligospora proteins with e-values below 10 E-5. The columns are the same as in S4 Table. (XLS)

Comparison of the Pfam domains in 4 NTF. Pfam domains and the corresponding numbers found in D. flagrans, A. oligospora, Da. haptotyla and Dre. coniospora. (XLS)

PHI base and the corresponding number of genes in D. flagrans. D. flagrans proteins blasted against the Pathogen–Host Interaction database (PHI). Columns: PHI accession number, number of proteins found in D. flagrans and virulence effect level. (XLS)

Pathogenesis-related genes in several fungal genomes. Comparison between proteins (transporter, signaling, oxidation, transcription regulation, metabolism and some others) from the PHI database between D. flagrans, A. oligospora, Da. haptotyla, Dre. coniospora and Pochonia chlamydospora. Columns: PHI accession number, description of the protein wit...

Oligonucleotides used in this study. (XLS)

Additional genome features. (DOCX)

Genome structure of D. flagrans. Circular map displaying genomic features of the D. flagrans genome. Distinct contigs are depicted using Circos with colored sectors on the outer layer resulting in 36.6 Mb. From outside to inside: (a) CDS position, (b) Intron position, (c) percentage of G+C, (d) percentage of GC skew, (e) effector genes, (f) secreto...

Comparison of nematode-trapping fungi secretome proteins. (A) Venn diagram of D. flagrans, A. oligospora and D. haptotyla secretomes, 157 orthologous proteins are shared. (B) Venn diagram of orthologous gene clusters of D. flagrans, A. oligospora, Da. haptotyla and D. stenobrocha. The four nematode trapping fungi share 139 clusters. (PPTX)

Detailed annotations of the D. flagrans secretome based on the Sma3s tool and InterProScan. Columns: protein accession, protein name (when found in Uniprot 90), description of the protein, enzyme reference, GO ontology, keyword, IPR domain and IPR description. (XLS)

Secretome and effector comparison between several fungi. 21 fungi were compared at the proteome, secretome and effectors level. Columns: name of the fungus, number of proteins, number of proteins in secretome, % of secretome compared to proteome, number of protein effectors, % of effectors in secretome. (XLS)

Clustering of orthologous proteins exclusive to D. flagrans common in five chlamydospore-forming fungi. The OrthoVenn diagram shows the clustering of orthologous proteins exclusive to D. flagrans (not found in A. oligospora) in the five chlamydospore forming fungi Botrytis cinerea, Cryptococcus neoformans, Fusarium oxysporum and Pochonia chlamydosp...

ATGC repartition in each contig. The length of the contigs is given in bp. The rest of the columns show the percentage of nucleotide usage in each contig. (XLS)

Genome size, number of predicted protein-coding genes, G + C content and best Blast top hit homology between D. flagrans and other 8 fungal genomes. The columns show: Genome size in Mb, percentage of GC content, number of proteins, best blast top hit (orthologous proteins), the life style and NCBI project accession number. (XLS)

BlastP result of D. flagrans proteins analyzed using the Swissprot database. Columns show: qseqid: query accession dot version, sseqid: subject accession dot version (database hit), pident: percentage of identical matches, length: alignment length, mismatch: number of mismatches, gapopen: number of gap openings, qstart: start of alignment in query,...

D. flagrans mitochondrial genes and their annotation. Mitochrondrial proteins and their corresponding description in the InterProScan database. (XLS)

Annotated D. flagrans proteome using Pfam. All D. flagrans proteins with Pfam or Interpro domains are depicted. Columns: proteins assigned with locus-tag, Pfam domain, description from Pfam database, E-value, Interpro domain, description from Interpo database. (XLS)

Genes involved in germling/hyphal fusion in N. crassa, Sordaria macrospora and orthologues in D. flagrans. The orthologues and accession numbers of N. crassa and S. macrospora are shown. The D. flagrans orthologues were identified by BLAST search against N. crassa. (XLS)

Filamentous fungi are highly polarized eukaryotic cells, which continuously elongate their hyphae at the tips. The extension of hyphal tips requires the continuous enlargement of the cell membrane and the extension of the cell wall. Both are achieved through massive vesicle fusion at the tip. Vesicle transport as well as all other dynamic processes...

Filamentöse Pilze spielen eine enorm wichtige Rolle in der Natur. Gemeinsam mit Bakterien sind sie maßgeblich am Abbau organischen Materials beteiligt und zeichnen sich insbesondere durch den Abbau von Polymeren wie Cellulose und Lignin aus. Sie sind also unersetzlich, um den Kohlenstofffluss auf der Erde zu garantieren.

Dieses Buch vermittelt ein Verständnis dafür, was Modellorganismen sind, und wofür sie in der Wissenschaft eingesetzt werden. Im Zentrum steht, welche grundsätzlichen Ansätze mit Modellorganismen verfolgt werden und welche Limitierungen man beachten muss. Die wichtigsten Modellorganismen werden anhand von übersichtlichen Steckbriefen vorgestellt un...

Light controls important physiological and morphological responses in fungi. Fungi can sense near-ultraviolet, blue, green, red and far-red light using up to 11 photoreceptors and signalling cascades to control a large proportion of the genome and thereby adapt to environmental conditions. The blue-light photoreceptor functions directly as a transc...

Fungal hydrophobins are small amphiphilic proteins that self-assemble into monolayers on hydrophobic:hydrophilic interfaces and can be used for surface coatings. Because e.g. Aspergillus nidulans contains six different hydrophobins, it is likely that they have different properties and are used for different "applications" in the fungus. We establis...

Filamentous fungi constitute a large group of eukaryotic microorganisms that grow by forming simple tube-like hyphae that are capable of differentiating into more-complex morphological structures and distinct cell types. Hyphae form filamentous networks by extending at their tips while branching in subapical regions. Rapid tip elongation requires m...

Polarized growth of filamentous fungi requires continuous transport of biomolecules to the hyphal tip. To this end, construction materials are packaged in vesicles and transported by motor proteins along microtubules and actin filaments. We have studied these processes with quantitative superresolution localization microscopy of live Aspergillus ni...

Microtubule-organizing centers (MTOCs) are large, multi-subunit protein complexes. Schizosaccharomyces pombe harbors MTOCs at spindle pole bodies, transient MTOCs in the division plane (eMTOCs) and nuclear-envelope associated MTOCs in interphase cells (iMTOCs). In the filamentous fungus Aspergillus nidulans SPBs and septum-associated MTOCs were des...

Filamentous fungi are able to differentiate morphologically and adapt the metabolism to internal and external cues. One major regulator is the so-called velvet protein, VeA, best studied in Aspergillus nidulans. The protein interacts with several other proteins to regulate light sensing, the balance between asexual and sexual development, penicilli...

Significance The day–night rhythm in living organisms controls many processes, which then oscillate in a circadian manner. In addition, there are many processes that appear continuous but the underlying mechanisms oscillate with distinct periods. For example, eukaryotic cells grow by extending their cell periphery in pulses rather than by continuou...

The filamentous fungus Alternaria alternata is a potent producer of many secondary metabolites, some of which like alternariol or alternariol-methyl ether are toxic and/or cancerogenic. Many Alternaria species do not only cause post-harvest losses of food and feed, but are aggressive plant pathogens. Despite the great economic importance and the la...

Background The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate...

The Complexity of Fungal Vision, Page 1 of 2 Abstract Life, as we know it, would not be possible without light. Light is not only a primary source of energy, but also an important source of information for many organisms. To sense light, only a few photoreceptor systems have developed during evolution. They are all based on an organic molecule wi...

Importance: Although fusion with small peptides to modify hydrophobin properties has already been performed in several studies, fusion with an enzyme presents a more challenging task. Both protein partners need to remain in active form so that the hydrophobins can interact with one another and form layers, and so the enzyme (e.g., laccase) will re...

Laccases are multicopper oxidoreductases with broad substrate specificity and are applied in biofuel cells at the cathode to improve its oxygen reduction performance. However, the production of laccases by e.g. fungi is often accompanied by the need of synthetic growth supplements for increased enzyme production. In this study we present a strategy...

Biological membranes have been proposed to contain microdomains of a specific lipid composition, in which distinct groups of proteins are clustered. Flotillin-like proteins are conserved between pro-and eukaryotes, play an important function in several eukaryotic and bacterial cells, and define in vertebrates a type of so-called detergent-resistant...

To spatially resolve genetic differences at the cellular level, the laser-capture microdissection technique was developed. With this method cells can be cut from tissues with a laser beam and be analyzed for DNA, RNA or protein composition. Here we adapted the method to isolate septal microtubule-organizing center (MTOC)-associated proteins in Aspe...

Stress-sensing in fungi depends on a signalling cascade comprised of a two-component phosphorylation relay plus a subsequent MAP kinase cascade to trigger gene expression. Besides osmotic or oxidative stress, fungi sense many other environmental factors, one of which is light1,2. Light controls morphogenetic pathways but also the production of seco...