Isolation and genetic analysis of nuclease halo (nuh) mutants of Neurospora crassa

Protein interactors of Spindle Pole Body (SPB) components and septal proteins in fungus Neurospora crassa: A mass spectrometry-based dataset

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 Centrosomes in animal cells) is the principal MTOC. Other MTOCs have been identified in filamentous fungi, such as the Spitzenkörper in the hyphal tips of Schizosaccharomyces pombe or the septal pore of Aspergillus nidulans. However, in the fungal-model organism Neurospora crassa, these alternative MTOCs have not been recognized. Here, we present a Mass spectrometry-based dataset of proteins interacting with four MTOC components of N. crassa tagged with fluorescent proteins: γ-Tubulin-sGFP (main nucleator at the SPB), MZT-1-sGFP (structural SPB microprotein), APS-2-dRFP (septal protein and recognized SPB component), and SPA-10-sGFP (septal MTOC protein). A WT and a cytosolic GFP expressing strain were included as controls. The protein interactors were pulled down by Co-IP1, using GFP-Magnetic agarose that captures recombinant GFP proteins (including GFP-derivatives) in their native state. Bounded proteins were separated by SDS-PAGE and identified by nano LC-MS/MS2. The protein annotation was done using the N. crassa protein database.

A DNase from a Fungal Phytopathogen Is a Virulence Factor Likely Deployed as Counter Defense against Host-Secreted Extracellular DNA

We document that the absence of a single gene encoding a DNase in a fungal plant pathogen results in significantly reduced virulence to a plant host. We compared a wild-type strain of the maize pathogen Cochliobolus heterostrophus and an isogenic mutant lacking a candidate secreted DNase-encoding gene and demonstrated that the mutant is reduced in virulence on leaves and on roots. There are no previous reports of deletion of such a gene from either an animal or plant fungal pathogen accompanied by comparative assays of mutants and wild type for alterations in virulence. We observed DNase activity, in fungal culture filtrates, that is Mg²⁺ dependent and induced when plant host leaf material is present. Our findings demonstrate not only that fungi use extracellular DNases (exDNases) for virulence, but also that the relevant molecules are deployed in above-ground leaves as well as below-ground plant tissues. Overall, these data provide support for a common defense/counter defense virulence mechanism used by animals, plants, and their fungal and bacterial pathogens and suggest that components of the mechanism might be novel targets for the control of plant disease.

Histone-linked extracellular DNA (exDNA) is a component of neutrophil extracellular traps (NETs). NETs have been shown to play a role in immune response to bacteria, fungi, viruses, and protozoan parasites. Mutation of genes encoding group A Streptococcus extracellular DNases (exDNases) results in reduced virulence in animals, a finding that implies that exDNases are deployed as counter defense against host DNA-containing NETs. Is the exDNA/exDNase mechanism also relevant to plants and their pathogens? It has been demonstrated previously that exDNA is a component of a matrix secreted from plant root caps and that plants also carry out an extracellular trapping process. Treatment with DNase I destroys root tip resistance to infection by fungi, the most abundant plant pathogens. We show that the absence of a single gene encoding a candidate exDNase results in significantly reduced virulence of a fungal plant pathogen to its host on leaves, the known infection site, and on roots. Mg²⁺-dependent exDNase activity was demonstrated in fungal culture filtrates and induced when host leaf material was present. It is speculated that the enzyme functions to degrade plant-secreted DNA, a component of a complex matrix akin to neutrophil extracellular traps of animals.

Ferrochelatase is a conserved downstream target of the blue light-sensing White collar complex in fungi

Light is a universal signal perceived by organisms, including fungi, in which light regulates common and unique biological processes depending on the species. Previous research has established that conserved proteins, originally called White collar 1 and 2 from the ascomycete Neurospora crassa, regulate UV/blue light sensing. Homologous proteins function in distant relatives of N. crassa, including the basidiomycetes and zygomycetes, which diverged as long as a billion years ago. Here we conducted microarray experiments on the basidiomycete fungus Cryptococcus neoformans to identify light-regulated genes. Surprisingly, only a single gene was induced by light above the commonly used twofold threshold. This gene, HEM15, is predicted to encode a ferrochelatase that catalyses the final step in haem biosynthesis from highly photoreactive porphyrins. The C. neoformans gene complements a Saccharomyces cerevisiae hem15Δ strain and is essential for viability, and the Hem15 protein localizes to mitochondria, three lines of evidence that the gene encodes ferrochelatase. Regulation of HEM15 by light suggests a mechanism by which bwc1/bwc2 mutants are photosensitive and exhibit reduced virulence. We show that ferrochelatase is also light-regulated in a white collar-dependent fashion in N. crassa and the zygomycete Phycomyces blakesleeanus, indicating that ferrochelatase is an ancient target of photoregulation in the fungal kingdom.

UV-induced recessive lethals in uvs strains of Neurospora which are deficient in UV mutagenesis

The frequencies of spontaneous and UV-induced recessive lethal mutations were compared for UV-sensitive and wild-type heterokaryons of Neurospora crassa. These heterokaryons were homokaryotic either for one of two alleles of uvs-3, or for uvs-6 or uvs+. For uvs-3, which is known to have mutator effects, spontaneous recessive lethals were found to be 4-6 times more frequent than observed in uvs+. After correction for clonal distribution of spontaneous mutants, an observed 2-fold increase for uvs-6 was not statistically significant and may have been due to chance occurrence of a few large clones of mutants. Treatment with low doses of UV (50-200 J/m2) produced very similar overall rates of increase for recessive lethals in uvs and uvs+ heterokaryons. This means, that in contrast to results obtained when mutation to ad-3 was measured, both uvs-3 alleles showed highly significant increases for recessive lethals when treated with UV. It is proposed that certain types of UV damage may be processed into recessive lethal mutations by an alternate mechanism from that responsible for viable mutations.

Effects of Neurospora nuclease halo (nuh) mutants on secretion of two phosphate-repressible alkaline deoxyribonucleases

Various recently isolated nuh mutants of Neurospora crassa (i.e., mutants which show reduced nuclease haloes on DNA-sorbose plates flooded with HCl) were mapped in several new genes or gene clusters and checked for effects on DNA repair and nuclease secretion. Some of them were found to be sensitive to MMS (methylmethane sulfonate) and sterile in meiosis. Release of nuclease activities into filtrates of liquid cultures was analyzed by DEAE-Sepharose chromatography. In the wild type, three alkaline deoxyribonuclease activities (A, B, and C) can be separated after growth in sorbose minimal media [Fraser, M. J. (1979). Nucleic Acids Res. 6: 231]. When strains were grown in phosphate-free DNA sucrose media, high (200-fold derepressed) DNase levels were found, and crude dialyzed filtrates could be chromatographed. Only two peaks were found, namely, those of DNase A, a Ca2+-dependent strand-nonspecific endonuclease, and DNase B, a ss-DNA-specific Mg2+-dependent exonuclease. Of the nuh mutants analyzed by one or both of these methods, many resembled the wild type. A few showed poor derepression, since their sorbose filtrates were normal, while profiles from DNA media lacked all peaks. These grew variably in liquid media with organic phosphates and probably produced suppressors, as was regularly found for nuc-2. Other mutants, which lacked specific peaks, gave the same results with both methods. One of these, nuh-7, produced no peaks at all but secreted unusually high amounts of protein.

Isolation and characterization of MMS-sensitive mutants of Neurospora crassa

Seven different mutants that show high sensitivity to MMS killing were isolated and mapped at different loci. One group, mms-(SA1), mms-(SA2) and mms-(SA6), showed high sensitivity to MMS but not to UV or gamma-rays. Another group, mms-(SA4) and mms-(SA5), showed extremely high sensitivity to UV and MMS. And mms-(SA3) and mms-(SA7) were moderately sensitive to both UV and MMS. Mms-(SA4) and mms-(SA1) were identified as alleles of uvs-2 and mus-7, respectively, which had been previously isolated. The mms-(SA1), mms-(SA6) and mms-(SA7) strains were barren in homozygous crosses, and the mms-(SA5) strain was barren in heterozygous crosses. The mms-(SA1), mms-(SA3) and mms-(SA5) strains showed high sensitivity to histidine. In summary, at least two new loci involved in the repair of MMS damage have been identified. The possibility that some of these new mutants are in new repair pathways is suggested.

Biochemical genetics of Neurospora nuclease I: Isolation and characterization of nuclease (nuc) mutants

Isolation and characterization of five new nuclease (nuc) deficient mutants ofNeurosporahave been described. The new mutants are unable to utilize nucleic acids as the sole phosphorus source and possess growth characteristics similar to thosenuc(nuc-1andnuc-2) mutants described previously. Two new mutants (nuc-4andnuc-5) were able to use RNA or predigested DNA (but not intact DNA) as phosphorus source and showed temperature sensitive growth at 37 °C. Based on the data from complementation and genetic analyses the five new nuc mutants (nuc-3, nuc-4, nuc-5, nuc-6andnuc-7) were found nonallelic to each other and to previously describednuc(nuc-1andnuc-2) mutants; the newnucmutants mapped to the right ofarg-12on linkage group II. On biochemical analyses, thesenucmutants were found to possess a lower level of extracellular nucleases and alkaline phosphatase as compared to the wild type strain. The ds DNase activity of the new mutants was only about 2–12% of that of the wild type strain; thus, the low level of these extracellular enzymes in thenucmutants causes their inability to utilize nucleic acids as the sole phosphorus source. Wild type levels of these enzymes were restored in the complementing heterokaryons capable of full growth on the DNA medium. Data from intercrosses, mutagen sensitivity and spontaneous mutation-frequency studies (as discussed in a subsequent paper) indicated the involvement of thenucgenes in DNA repair and recombination.

Biochemical genetics of Neurospora nuclease II: Mutagen sensitivity and other characteristics of the nuclease mutants

Five newnucmutants ofNeurospora crassawere characterized for their relative sensitivities to different mutagens (UV, MNG, MMS), to mitomycin-C and to histidine; latter has been shown to inhibit the growth of certain UV sensitive mutants. These mutants were also compared for their capabilities for spontaneous mutation as determined by resistance to p-fluoro-phenylalanine. Based on these characterization, the mutants seem to belong to two groups. The first group includednuc-3andnuc-6which showed sensitivity to all mutagen tested and possessed capability for a very high frequency of spontaneous mutation (i.e. mutator effect). The second group includednuc-4, nuc-5andnuc-7; these were as resistant to different mutagens as the wild type strain, but possessed an antimutator effect (i.e. the frequency of spontaneous mutation by these three mutants were at least 0·5–100 × less than the wild type strains). There was some variation in these properties of mutants belonging to the two groups. Among all the fivenucmutants,nuc-3was characterized by extreme sensitivity to all mutagens. None of the fivenucmutants were sensitive to histidine. The properties ofnucmutants are discussed in relation to their possible role in DNA repair and recombination.

Intracellular localization of Neurospora crassa endo-exonuclease and its putative precursor

Endo-exonuclease of rapidly growing mycelia of Neurospora crassa was found to be distributed in a ratio of about 1.6:1 in vacuoles and in mitochondria where it is associated with the inner membrane. Although the activity in vacuoles was readily released by osmotic shock, very little of that in mitochondria was released by this method. The mitochondrial activity was partially (60 to 70%) released by sonication, and the remaining activity was solubilized in the presence of Triton X-100. An inactive form of endo-exonuclease, activated in vitro by treatment with trypsin, is present in mycelia at a level over four times that of active enzyme. It was found to be distributed in a ratio of about 2.5:1 in the cytosol and in the inner membrane of mitochondria. The mitochondrial protein was more tightly bound than the active enzyme. Very little of the inactive enzyme was released by sonication, but it was solubilized in the presence of Triton X-100. The intracellular distribution of active and inactive forms of endo-exonuclease differs in a mutagen-sensitive mutant of Neurospora crassa (uvs-3) which shows many pleiotropic effects. The most striking difference in distribution is in the mitochondria where endo-exonuclease is present almost entirely in the inactive form at a level 30% higher than in wild-type mitochondria.

Mutagen sensitivities and mutator effects of MMS-sensitive mutants in Neurospora

7 mus (mutagen-sensitive) mutants of Neurospora crassa, which are more sensitive to the toxic effects of MMS (methyl methanesulfonate) than wild-type, were investigated for cross-sensitivities to other mutagens and inhibitors. These mutants have recently been mapped in 5 new genes, mus-7 to mus-11, and mutant alleles from each gene were checked for their effects on mutation frequencies. It was found that mutants in 3 of these 5 genes showed radiation-induced mutation frequencies similar to wild-type. These included 2 alleles of the gene mus-10, which were cross-sensitive only to UV and were the only mutants that produced some viable ascospores in homozygous crosses. The mutant of the second gene, mus-8, was especially sensitive to UV and mitomycin C and produced slightly reduced frequencies of spontaneous mutation. In contrast, the mutant of the third gene, mus-7, was not UV-sensitive but showed some cross-sensitivity to X-rays; mus-7 was highly sensitive to MMS and also to histidine, which inhibits various repair-defective mutants at concentrations well below those that reduce wild-type growth. None of these mus resemble mutants previously found in Neurospora, nor do they conform clearly to mutant types identified in E. coli or yeast. On the other hand mutants in 2 further genes, mus-11, and especially 2 alleles of mus-9, are very similar to uvs-3 of Neurospora and generally resemble mutants that are considered to be defective in "error-prone" repair. They were UV- as well as X-ray-sensitive, and showed strong spontaneous mutator effects but almost no increase in recessive lethal frequencies in heterokaryons after UV-treatments.

Isolation and genetic analysis of MMS-sensitive mus mutants of neurospora

With the aim of obtaining mutants that affect DNA repair or recombination, mutants sensitive to methylmethane sulfonate (MMS) have been isolated in the ascomycete Neurospora crassa. Seven of these mutants were backcrossed repeatedly to produce isogenic strains for measurements of relative mutagen sensitivities and for analysis of recombination frequencies. The new mus (mutagen sensitives) were compared to four previously known radiation-sensitive mutants which were shown to be cross-sensitive to MMS. Tests for allelism assigned the mus mutants to five new genes, mus-7 to mus-11, each mapping in a different linkage group. In homozygous crosses all mutants were sterile, except the two alleles of gene mus-10 which occasionally produced some viable ascospores. Complementation tests on MMS-media identified double mutant strains from many intercrosses. Such strains can be used for analysis of interactions between mutant alleles from different genes and of possible epistatic groupings for repair-deficient mutants in Neurospora. Four of these double mutant strains, all containing mus-8 and previously known mutants, were checked for survival on MMS media and their sensitivities were compared to those of their parental single mutant strains. Results indicate that mus-8 may be epistatic to uvs-2 which is deficient in excision repair, but not to mutants like uvs-3 that appear to be deficient in error-prone repair.

Nucleases and their control in wild-type and nuh mutants of Neurospora

A review of all of the work on Neurospora nucleases strongly suggests that five nucleases, originally isolated on the basis of markedly different properties, may actually be derived from a single inactive precursor polypeptide via different routes of proteolysis. One of these nucleases may be involved in DNA repair and/or recombination. Two repair-deficient mutants of Neurospora, uvs-3 and nuh-4, may have a lesion in protease(s) which control the level of this nuclease or in some function which regulates the protease(s). Both of these mutants map in the same gene region and they may be defective in recombination, since they are sensitive to various mutagens and to mitomycin C and they show high frequency of spontaneous, but not radiation-induced, recessive lethal mutations and/or deletions.

Mutagen-sensitive mutants in Neurospora

Initial work on the fungus Neurospora crassa has shown that a least two DNA-repair systems exist in this eukaryote: excision repair and a mutation-prone repair. The evidence suggests that there is also a third repair system. Recently, new mutagen-sensitive strains have been isolated in several laboratories, but they are not yet fully characterized. A hunt for cytoplasmically inherited UV sensitivity has failed to turn up any such mutants among 25 new UV-sensitive isolates.