TitleAbstractYear(sorted descending)
the trichoderma atroviride photolyase-encoding gene is transcriptionally regulated by non-canonical light response elements.the blr-1 and blr-2 proteins of trichoderma atroviride are the neurospora crassa homologs of white collar-1 and -2, two transcription factors involved in the regulation of genes by blue light. blr-1 and blr-2 are essential for photoinduction of phr-1, a photolyase-encoding gene whose promoter exhibits sequences similar to well-characterized light regulatory elements of neurospora, including the albino proximal element and the light response element (lre). however, despite the fact that this gene ...201323721733
septins are important for cell polarity, septation and asexual spore formation in neurospora crassa and show different patterns of localisation at germ tube tips.septins are gtp-binding cytoskeletal proteins that contribute to cell polarity, vesicle trafficking, cytokinesis and cell morphogenesis. here we have characterised the six septins encoded by the genome of the model filamentous fungus neurospora crassa. analysis of septin null mutants demonstrated that septins limit the sites of emergence of germ tubes and are important for septation and conidiation in n. crassa. septins constituted a range of different higher-order structures in n. crassa - ring ...201323691103
an apparent increase in meiotic silencing strength in crosses involving inbred neurospora crassa strains.meiotic silencing by unpaired dna is a presumed rnai-mediated elimination of the transcripts of any gene that is not properly paired with a homolog in meiosis. wild-isolated strains of neurospora crassa can be classified into three types based on the apparent strength of meiotic silencing of the bml (β-tubulin) and mei-3 genes in crosses of the wild strains with the tester strains ::bml(r) and ::mei-3. crosses with "or" and "sad" type wild-isolates, respectively, did or did not silence both the ...201323685173
reduced glutathione export during programmed cell death of neurospora a previous study, we demonstrated that staurosporine (sts) induces programmed cell death (pcd) in the fungus neurospora crassa and that glutathione has the capability of inhibiting both sts-induced reactive oxygen species (ros) formation and cell death. here, we further investigated the role of glutathione in sts-induced pcd in n. crassa and observed an efflux of reduced glutathione (gsh) together with a change in the cell internal redox state to a more oxidative environment. this event was a ...201323666236
novel insights into the role of neurospora crassa ndufaf2, an evolutionarily conserved mitochondrial complex i assembly factor.complex i deficiency is commonly associated with mitochondrial oxidative phosphorylation diseases. mutations in nuclear genes encoding structural subunits or assembly factors of complex i have been increasingly identified as the cause of the diseases. one such factor, ndufaf2, is a paralog of the ndufa12 structural subunit of the enzyme, but the mechanism by which it exerts its function remains unknown. herein, we demonstrate that the neurospora crassa ndufaf2 homologue, the 13.4 l protein, is a ...201323648483
the bacterial secondary metabolite 2,4-diacetylphloroglucinol impairs mitochondrial function and affects calcium homeostasis in neurospora crassa.the bacterial secondary metabolite 2,4-diacetylphloroglucinol (dapg) is of interest as an active ingredient of biological control strains of pseudomonas fluorescens and as a potential lead pharmaceutical molecule because of its capacity to inhibit growth of diverse microbial and non-microbial cells. the mechanism by which this occurs is unknown and in this study the filamentous fungus neurospora crassa was used as a model to investigate the effects of dapg on a eukaryotic cell. colony growth, co ...201323624246
the type of mutations induced by carbon-ion-beam irradiation of the filamentous fungus neurospora crassa.heavy-ion beams are known to cause great damage to cellular components and are particularly renowned for their ability to generate dna double-strand breaks (dsbs). to gain insight into the mutagenic effect of carbon-ion beams and how such damage is repaired by the cell, neurospora crassa mutants deficient in one of three components involved in the repair of dsbs, nonhomologous end-joining (nhej), homologous recombination repair (hr), and the mre11-rad50-xrs2 (mrx) complex, were irradiated with a ...201323622717
production of xylitol by recombinant microalgae.microalgae have received significant attention recently as a potential low-cost host for the production of next-generation biofuels and natural products. here we show that the chloroplast genome of the eukaryotic green microalga chlamydomonas reinhardtii can be genetically engineered to produce xylitol through the introduction of a gene encoding a xylose reductase (xr) from the fungi neurospora crassa. increased levels of heterologous protein accumulation and xylitol production were achieved by ...201323597921
the transcriptional response to nonself in the fungus podospora fungi, heterokaryon incompatibility is a nonself recognition process occurring when filaments of different isolates of the same species fuse. compatibility is controlled by so-called het loci and fusion of strains of unlike het genotype triggers a complex incompatibility reaction that leads to the death of the fusion cell. herein, we analyze the transcriptional changes during the incompatibility reaction in podospora anserina. the incompatibility response was found to be associated with a mas ...201323589521
computational discovery of transcriptional regulatory modules in fungal ribosome biogenesis genes reveals novel sequence and function patterns.genes involved in ribosome biogenesis and assembly (rba) are responsible for ribosome formation. in saccharomyces cerevisiae, their transcription is regulated by two dissimilar dna motifs. we were interested in analyzing conservation and divergence of rba transcription regulation machinery throughout fungal evolution. we have identified orthologs of s. cerevisiae rba genes in 39 species across fungal phylogeny and searched upstream regions of these gene sets for dna sequences significantly simil ...201323555806
biochemical characterization of molybdenum cofactor-free nitrate reductase from neurospora crassa.nitrate reductase (nr) is a complex molybdenum cofactor (moco)-dependent homodimeric metalloenzyme that is vitally important for autotrophic organism as it catalyzes the first and rate-limiting step of nitrate assimilation. beside moco, eukaryotic nr also binds fad and heme as additional redox active cofactors, and these are involved in electron transfer from nad(p)h to the enzyme molybdenum center where reduction of nitrate to nitrite takes place. we report the first biochemical characterizatio ...201323539622
regional control of histone h3 lysine 27 methylation in neurospora.trimethylated lysine 27 on histone h3 (h3k27me3) is present in drosophila, arabidopsis, worms, and mammals, but is absent from yeasts that have been examined. we identified and analyzed h3k27me3 in the filamentous fungus neurospora crassa and in other neurospora species. h3k27me3 covers 6.8% of the n. crassa genome, encompassing 223 domains, including 774 genes, all of which are transcriptionally silent. n. crassa h3k27me3-marked genes are less conserved than unmarked genes and only ∼35% of gene ...201323530226
trans-species activity of a nonself recognition domain.the ability to distinguish nonself from self is a fundamental characteristic of biological systems. in the filamentous fungus neurospora crassa, multiple incompatibility genes mediate nonself recognition during vegetative growth. one of these genes, un-24, encodes both nonself recognition function and the large subunit of a type i ribonucleotide reductase, an evolutionarily conserved enzyme that is essential for the conversion of ndp precursors into dndps for use in dna synthesis. previous studi ...201323517247
alternative splicing in ascomycetes.alternative splicing is a complex and regulated process, which results in mrna with different coding capacities from a single gene. extend and types of alternative splicing vary greatly among eukaryotes. in this review, i focus on alternative splicing in ascomycetes, which in general have significant lower extend of alternative splicing than mammals. yeast-like species have low numbers of introns and consequently alternative splicing is lower compared to filamentous fungi. several examples from ...201323515838
novel proteins required for meiotic silencing by unpaired dna and sirna generation in neurospora crassa.during meiosis in the filamentous fungus neurospora crassa, unpaired genes are identified and silenced by a process known as meiotic silencing by unpaired dna (msud). previous work has uncovered six proteins required for msud, all of which are also essential for meiotic progression. additionally, they all localize in the perinuclear region, suggesting that it is a center of msud activity. nevertheless, at least a subset of msud proteins must be present inside the nucleus, as unpaired dna recogni ...201323502675
identification of small rnas associated with meiotic silencing by unpaired neurospora crassa, unpaired genes are silenced by a mechanism called meiotic silencing by unpaired dna (msud). although some rna interference proteins are necessary for this process, its requirement of small rnas has yet to be formally established. here we report the characterization of small rnas targeting an unpaired region, using illumina sequencing.201323502674
coordination of k+ transporters in neurospora: trk1 is scarce and constitutive, while hak1 is abundant and highly regulated.fungi, plants, and bacteria accumulate potassium via two distinct molecular machines not directly coupled to atp hydrolysis. the first, designated trk, hkt, or ktr, has eight transmembrane helices and is folded like known potassium channels, while the second, designated hak, kt, or kup, has 12 transmembrane helices and resembles mfs class proteins. one of each type functions in the model organism neurospora crassa, where both are readily accessible for biochemical, genetic, and electrophysiologi ...201323475706
biotransformation of 14-deoxy-14-methylenetriptolide into a novel hydroxylation product by neurospora crassa.the biotransformation of 14-deoxy-14-methylenetriptolide by neurospora crassa cgmcc as 3.1604 to produce a new hydroxylation derivative was studied. the structure of this novel compound was determined using spectral data. this biotransformation using whole cells conditioned for 4 days transformed approximately 65% (mol ratio) of the substrate into the compound (5r)-5-hydroxy-14-deoxy-14-methylenetriptolide.201323465510
genetics of cordyceps and related fungi.ascomycete cordyceps sensu lato consists of hundreds of species of fungi capable of infecting different insects. species of these fungi are either valued traditional chinese medicines or used for biocontrol of insect pests. phylogenomic analysis indicated that fungal entomopathogenicity has evolved for multiple times, and the species of cordyceps were diverged from the mycoparasite or plant endophyte. relative to plant pathogens and saprophytes, cordyceps species demonstrate characteristic genom ...201323435902
direct cellobiose production from cellulose using sextuple beta-glucosidase gene deletion neurospora crassa cellobiose production from cellulose by a genetically modified fungus-neurospora crassa, was explored in this study. a library of n. crassa sextuple beta-glucosidase (bgl) gene deletion strains was constructed. various concentrations of cellobiose were detected in the culture broth of the n. crassa sextuple beta-glucosidase (bgl) gene deletion strains when grown on avicel without exogenous cellulase addition. the sextuple bgl deletion strains expressing one of the three basally transcribe ...201323410930
the stringency of start codon selection in the filamentous fungus neurospora eukaryotic cells initiation may occur from near-cognate codons that differ from aug by a single nucleotide. the stringency of start codon selection impacts the efficiency of initiation at near-cognate codons and the efficiency of initiation at aug codons in different contexts. we used a codon-optimized firefly luciferase reporter initiated with aug or each of the nine near-cognate codons in preferred context to examine the stringency of start codon selection in the model filamentous fungus ne ...201323396971
global analyses of ceratocystis cacaofunesta mitochondria: from genome to proteome.the ascomycete fungus ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. despite the economic importance of the ceratocystis complex of species, no genomic data are available for any of its members. given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in ceratocystis us ...201323394930
both osrecq1 and osrdr1 are required for the production of small rna in response to dna-damage in rice.small rna-mediated gene silencing pathways play important roles in the regulation of development, genome stability and various stress responses in many eukaryotes. recently, a new type of small interfering rnas (qirnas) approximately 20-21 nucleotides long in neurospora crassa have been shown to mediate gene silencing in the dna damage response (ddr) pathway. however, the mechanism for rna silencing in the ddr pathway is largely unknown in plants. here, we report that a class of small rnas (qirn ...201323383126
eukaryotic tpp riboswitch regulation of alternative splicing involving long-distance base pairing.thiamin pyrophosphate (tpp) riboswitches are found in organisms from all three domains of life. examples in bacteria commonly repress gene expression by terminating transcription or by blocking ribosome binding, whereas most eukaryotic tpp riboswitches are predicted to regulate gene expression by modulating rna splicing. given the widespread distribution of eukaryotic tpp riboswitches and the diversity of their locations in precursor messenger rnas (pre-mrnas), we sought to examine the mechanism ...201323376932
glucoamylase is a potential allergen in products expressed in neurospora crassa. 201323352537
transcription of the major neurospora crassa microrna-like small rnas relies on rna polymerase iii.most plant and animal micrornas (mirnas) are transcribed by rna polymerase ii. we previously discovered mirna-like small rnas (milrnas) in the filamentous fungus neurospora crassa and uncovered at least four different pathways for milrna production. to understand the evolutionary origin of milrnas, we determined the roles of polymerases ii and iii (pol ii and pol iii) in milrna transcription. our results show that pol iii is responsible for the transcription of the major milrnas produced in this ...201323349642
using a model filamentous fungus to unravel mechanisms of lignocellulose deconstruction.filamentous fungi are the main source of enzymes used to degrade lignocellulose to fermentable sugars for the production of biofuels. while the most commonly used organism for the production of cellulases in an industrial setting is trichoderma reesei (hypocrea jecorina), recent work in the model filamentous fungus neurospora crassa has shown that the variety of molecular, genetic and biochemical techniques developed for this organism can expedite analyses of the complexities involved in the uti ...201323339486
nonself recognition through intermolecular disulfide bond formation of ribonucleotide reductase in neurospora.type i ribonucleotide reductases (rnrs) are conserved across diverse taxa and are essential for the conversion of rna into dna precursors. in neurospora crassa, the large subunit of rnr (un-24) is unusual in that it also has a nonself recognition function, whereby coexpression of oak ridge (or) and panama (pa) alleles of un-24 in the same cell leads to growth inhibition and cell death. we show that coexpressing these incompatible alleles of un-24 in n. crassa results in a high molecular weight u ...201323335337
biotechnological production of ethanol from renewable resources by neurospora crassa: an alternative to conventional yeast fermentations?microbial production of ethanol might be a potential route to replace oil and chemical feedstocks. bioethanol is by far the most common biofuel in use worldwide. lignocellulosic biomass is the most promising renewable resource for fuel bioethanol production. bioconversion of lignocellulosics to ethanol consists of four major unit operations: pretreatment, hydrolysis, fermentation, and product separation/distillation. conventional bioethanol processes for lignocellulosics apply commercial fungal ...201323318834
reactive oxygen species can modulate circadian phase and period in neurospora crassa.reactive oxygen species (ros) may serve as signals coupling metabolism to other cell functions. in addition to being by-products of normal metabolism, they are generated at elevated levels under environmental stress situations. we analyzed how reactive oxygen species affect the circadian clock in the model organism neurospora crassa. in light/dark cycles, an increase in the levels of reactive oxygen species advanced the phase of both the conidiation rhythm and the expression of the clock gene fr ...201323277144
deletion and expression analysis of beta-(1,3)-glucanosyltransferase genes in neurospora crassa.gpi(glycosylphosphatidylinositol)-anchored beta-(1,3)-glucanosyltransferases play an active role in cell wall biosynthesis in fungi. neurospora crassa has 5 putative beta-(1,3)-glucanosyltransferase genes, namely, gel-1, gel-2, gel-3, gel-4, and gel-5, in its genome. among them, the gel-3 gene is constitutively expressed at the highest level in growing hyphae, whereas gel-1 is expressed at the lowest level. the gel-3 deletion mutant displayed slow growth, while other gel gene disruptants exhibit ...201323274249
[organization of mitochondria in the growing hyphae of neurospora crassa].in vivo fluorescent labeling of mitochondria in neurospora crassa showed the concentration of filamentous mitochondria within 30 μm of apex in growing hyphae. these mitochondrial assemblies propagated forward with the elongation of hyphae, split and segregated as the growing tip bifurcated and formed de novo when new branches formed farther away from the apex. the efficiency of the mitochondria concentration in the apical 30 μm zone is related to the growth rate and identical in hyphae cultivate ...201325509139
the n-terminal region of the neurospora ndr kinase cot1 regulates morphology via its interactions with mob2a/b.nuclear dbf2p-related (ndr) protein kinases are important for cell differentiation and polar morphogenesis in various organisms, yet some of their functions are still elusive. dysfunction of the neurospora crassa ndr kinase cot1 leads to cessation of tip extension and hyperbranching. ndr kinases require the physical interaction between the kinase's n-terminal region (ntr) and the mps1-binding (mob) proteins for their activity and functions. to study the interactions between cot1 and mob2 protein ...201323962317
investigation of the functional role of aldose 1-epimerase in engineered cellobiose utilization.functional expression of a cellodextrin transporter and an intracellular β-glucosidase from neurospora crassa in saccharomyces cerevisiae enables simultaneous co-fermentation of cellobiose and non-glucose sugars such as xylose. here we investigate the functional role of aldose 1-epimerase (aep) in engineered cellobiose utilization. one aep (gal10) and two putative aeps (yhr210c and ynr071c sharing 50.6% and 51.0% amino acid identity with gal10, respectively) were selected. deletion of gal10 led ...201323954547
mtb-3, a microtubule plus-end tracking protein (+tip) of neurospora crassa.the microtubule (mt) "plus end" constitutes the platform for the accumulation of a structurally and functionally diverse group of proteins, collectively called "mt plus-end tracking proteins" (+tips). +tips control mt dynamics and link mts to diverse sub-cellular structures. neurospora crassamicrotubule binding protein-3 (mtb-3) is the homolog of yeast eb1, a highly conserved +tip. to address the function of mtb-3, we examined strains with mtb-3 deletions, and we tagged mtb-3 with gfp to assess ...201323950979
analysis of mutations in neurospora crassa ermes components reveals specific functions related to β-barrel protein assembly and maintenance of mitochondrial morphology.the endoplasmic reticulum mitochondria encounter structure (ermes) tethers the er to mitochondria and contains four structural components: mmm1, mdm12, mdm10, and mmm2 (mdm34). the gem1 protein may play a role in regulating ermes function. saccharomyces cerevisiae and neurospora crassa strains lacking any of mmm1, mdm12, or mdm10 are known to show a variety of phenotypic defects including altered mitochondrial morphology and defects in the assembly of β-barrel proteins into the mitochondrial out ...201323940790
genome wide association identifies novel loci involved in fungal communication.understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics. unlike classical screening methods, analysis of genetic variation that occurs naturally in wild populations can enable rapid, genome-scale mapping of genotype to phenotype with a medium-throughput experimental design. here we describe the results of the first genome-wide association study (gwas) used to identify novel loci underlying trait variation in a microbial e ...201323935534
reconstruction and validation of a genome-scale metabolic model for the filamentous fungus neurospora crassa using farm.the filamentous fungus neurospora crassa played a central role in the development of twentieth-century genetics, biochemistry and molecular biology, and continues to serve as a model organism for eukaryotic biology. here, we have reconstructed a genome-scale model of its metabolism. this model consists of 836 metabolic genes, 257 pathways, 6 cellular compartments, and is supported by extensive manual curation of 491 literature citations. to aid our reconstruction, we developed three optimization ...201323935467
characterization of bud emergence 46 (bem46) protein: sequence, structural, phylogenetic and subcellular localization analyses.the bud emergence 46 (bem46) protein from neurospora crassa belongs to the α/β-hydrolase superfamily. recently, we have reported that the bem46 protein is localized in the perinuclear er and also forms spots close by the plasma membrane. the protein appears to be required for cell type-specific polarity formation in n. crassa. furthermore, initial studies suggested that the bem46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved "known unknown ...201323916612
recent advances in septum biogenesis in neurospora crassa.hyphae of the ascomycota are tubular cells compartmentalized by perforated septa, whose central pore allows the flow of organelles and cytoplasm. while in plants and yeast septation leads to cell separation, in filamentous fungi the formation of crosswalls appears to have an architectural role, limits the extent of mechanical damage thus maintaining hyphal integrity, and also is of fundamental importance as part of cell differentiation. the increasing number of available fungal genome sequences, ...201323890213
synchronous activation of cell division by light or temperature stimuli in the dimorphic yeast schizosaccharomyces japonicus.many fungi respond to light and regulate fungal development and behavior. a blue light-activated complex has been identified in neurospora crassa as the product of the wc-1 and wc-2 genes. orthologs of wc-1 and wc-2 have hitherto been found only in filamentous fungi and not in yeast, with the exception of the basidiomycete pathogenic yeast cryptococcus. here, we report that the fission yeast schizosaccharomyces japonicus responds to blue light depending on wcs1 and wcs2, orthologs of components ...201323873862
nuclear dynamics in a fungal chimera.a fungal colony is a syncytium composed of a branched and interconnected network of cells. chimerism endows colonies with increased virulence and ability to exploit nutritionally complex substrates. moreover, chimera formation may be a driver for diversification at the species level by allowing lateral gene transfer between strains that are too distantly related to hybridize sexually. however, the processes by which genomic diversity develops and is maintained within a single colony are little u ...201323861490
optimization of cdt-1 and xyl1 expression for balanced co-production of ethanol and xylitol from cellobiose and xylose by engineered saccharomyces cerevisiae.production of ethanol and xylitol from lignocellulosic hydrolysates is an alternative to the traditional production of ethanol in utilizing biomass. however, the conversion efficiency of xylose to xylitol is restricted by glucose repression, causing a low xylitol titer. to this end, we cloned genes cdt-1 (encoding a cellodextrin transporter) and gh1-1 (encoding an intracellular β-glucosidase) from neurospora crassa and xyl1 (encoding a xylose reductase that converts xylose into xylitol) from sch ...201323844185
simultaneous saccharification and fermentation by engineered saccharomyces cerevisiae without supplementing extracellular β-glucosidase.simultaneous saccharification and fermentation (ssf) has been considered a promising and economical process for cellulosic ethanol production. further cost savings could be gained by reducing enzyme loading and engineering host strain for ethanol production. in this study, we demonstrate efficient ethanol production by ssf without supplementation of β-glucosidase using an engineered saccharomyces cerevisiae strain expressing a cellodextrin transporter and an intracellular β-glucosidase from neur ...201323835155
sulfur-regulated control of the met-2⁺ gene of neurospora crassa encoding cystathionine β-lyase.cystathionine β-lyase performs an essential role in the transsulfuration pathway by its primary reaction of forming homocysteine from cystathionine. understanding how the neurospora crassa met-2⁺ gene, which encodes cystathionine β-lyase, is regulated is important in determining the basis of the cellular control of transsulfuration. the aim of this study was to determine the nature of a potential regulatory connection of met-2⁺ to the neurospora sulfur regulatory network.201323835025
conformational stability and crystal packing: polymorphism in neurospora crassa cat-3.polymorphism is frequently observed from different crystallization conditions. in proteins, the effect on conformational variability is poorly documented, with only a few reported examples. here, three polymorphic crystal structures determined for a large-subunit catalase, cat-3 from neurospora crassa, are reported. two of them belonged to new space groups, p1 and p43212, and a third structure belonged to the same space group, p212121, as the previously deposited 2.3 å resolution structure (pdb ...201323832201
transcriptomic profiling-based mutant screen reveals three new transcription factors mediating menadione resistance in neurospora gain insight into the regulatory mechanisms of oxidative stress responses in filamentous fungi, the genome-wide transcriptional response of neurospora crassa to menadione was analysed by digital gene expression (dge) profiling, which identified 779 upregulated genes and 576 downregulated genes. knockout mutants affecting 130 highly-upregulated genes were tested for menadione sensitivity, which revealed that loss of the transcription factor siderophore regulation (sre) (a transcriptional repre ...201323809652
residual recombination in neurospora crassa spo11 deletion homozygotes occurs during meiosis.spo11 is considered responsible for initiation of meiotic recombination in higher organisms, but previous analysis using spo11 (rip) mutants suggests that the his-3 region of neurospora crassa experiences spo11-independent recombination. however, despite possessing several stop codons, it is conceivable that the mutants are not completely null. also, since lack of spo11 interferes with chromosomal pairing and proper segregation at meiosis i, spores can be partially diploid for a period after mei ...201323801409
phospho-regulation of the neurospora crassa septation initiation network.proper cell division is essential for growth and development of uni- and multicellular organisms. the fungal septation initiation network (sin) functions as kinase cascade that connects cell cycle progression with the initiation of cytokinesis. miss-regulation of the homologous hippo pathway in animals results in excessive cell proliferation and formation of tumors, underscoring the conservation of both pathways. how sin proteins interact and transmit signals through the cascade is only beginnin ...201324205386
conserved rna helicase frh acts nonenzymatically to support the intrinsically disordered neurospora clock protein frq.protein conformation dictates a great deal of protein function. a class of naturally unstructured proteins, termed intrinsically disordered proteins (idps), demonstrates that flexibility in structure can be as important mechanistically as rigid structure. at the core of the circadian transcription/translation feedback loop in neurospora crassa is the protein frequency (frq), shown here shown to share many characteristics of idps. frq in turn binds to frequency-interacting rna helicase (frh), who ...201324316221
neurospora crassa protein arginine methyl transferases are involved in growth and development and interact with the ndr kinase cot1.the protein arginine methyltransferaseas (prmts) family is conserved from yeast to human, and regulates stability, localization and activity of proteins. we have characterized deletion strains corresponding to genes encoding for prmt1/3/5 (designated amt-1, amt-3 and skb-1, respectively) in neurospora crassa. deletion of prmt-encoding genes conferred altered arg-methylated protein profiles, as determined immunologically. δamt-1 exhibited reduced hyphal elongation rates (70% of wild type) and inc ...201324260473
human-like eukaryotic translation initiation factor 3 from neurospora crassa.eukaryotic translation initiation factor 3 (eif3) is a key regulator of translation initiation, but its in vivo assembly and molecular functions remain unclear. here we show that eif3 from neurospora crassa is structurally and compositionally similar to human eif3. n. crassa eif3 forms a stable 12-subunit complex linked genetically and biochemically to the 13(th) subunit, eif3j, which in humans modulates mrna start codon selection. based on n. crassa genetic analysis, most subunits in eif3 are e ...201324250809
fungal gene expression levels do not display a common mode of distribution.rna-seq studies in metazoa have revealed a distinct, double-peaked (bimodal) distribution of gene expression independent of species and cell type. however, two studies in filamentous fungi yielded conflicting results, with a bimodal distribution in pyronema confluens and varying distributions in sordaria macrospora. to obtain a broader overview of global gene expression distributions in fungi, an additional 60 publicly available rna-seq data sets from six ascomycetes and one basidiomycete were a ...201324373411
neurospora crassa ncs-1, mid-1 and nca-2 double-mutant phenotypes suggest diverse interaction among three ca(2+)-regulating gene products. 201324371176
molecular analysis of intragenic recombination at the tryptophan synthetase locus in neurospora crassa.fifteen different classically generated and mapped mutations at the tryptophan synthetase locus in neurospora crassa have been characterized to the level of the primary sequence of the gene. this sequence analysis has demonstrated that intragenic recombination is accurate to order mutations within one open reading frame. while classic genetic analysis correctly ordered the mutations, the position of mutations characterized by gene sequence analysis was more accurate. a leaky mutation was found t ...201324371173
phylogenetics and gene structure dynamics of polygalacturonase genes in aspergillus and neurospora crassa.polygalacturonase (pg) gene is a typical gene family present in eukaryotes. forty-nine pgs were mined from the genomes of neurospora crassa and five aspergillus species. the pgs were classified into 3 clades such as clade 1 for rhamno-pgs, clade 2 for exo-pgs and clade 3 for exo- and endo-pgs, which were further grouped into 13 sub-clades based on the polypeptide sequence similarity. in gene structure analysis, a total of 124 introns were present in 44 genes and five genes lacked introns to give ...201325288950
[on the localization of inorganic polyphosphates and nucleotides in neurospora crassa mycelium]. 20135999969
mutagenicity of methylhydroxylamines in neurospora crassa. 20136054956
correlation between base-pair transition and complementation pattern in nitrous acid-induced ad-3b mutants of neurospora crassa. 20135727269
the essential phosphoinositide kinase mss-4 is required for polar hyphal morphogenesis, localizing to sites of growth and cell fusion in neurospora crassa.fungal hyphae and plant pollen tubes are among the most highly polarized cells known and pose extraordinary requirements on their cell polarity machinery. cellular morphogenesis is driven through the phospholipid-dependent organization at the apical plasma membrane. we characterized the contribution of phosphoinositides (pis) in hyphal growth of the filamentous ascomycete neurospora crassa. mss-4 is an essential gene and its deletion resulted in spherically growing cells that ultimately lyse. tw ...201223272106
the translin-trax complex (c3po) is a ribonuclease in trna processing.conserved translin-trax complexes, also known as c3pos, have been implicated in many biological processes, but how they function remains unclear. recently, c3po was shown to be an endornase that promotes rna interference (rnai) in animal cells. here, we show that c3po does not play a significant role in rnai in the filamentous fungus neurospora crassa. instead, the neurospora c3po functions as an rnase that removes the 5' pre-trna fragments after the processing of pre-trnas by rnase p. in additi ...201222773104
cdr4 is the major contributor to azole resistance among four pdr5p-like abc transporters in neurospora crassa.pdr5p-like abc transporters play a significant role in azole resistance in saccharomyces cerevisiae and candida spp. most of filamentous fungal species have multiple pdr5p homologues. in this study, phylogenic analysis identified that filamentous fungi have at least two phylogenically distant groups of pdr5p homologues. one contains pmr1-like pdr5p homologues while the other contains both atrf-like and atrb-like pdr5p homologues. neurospora crassa has a total of four genes encoding pdr5p homolog ...201222749171
analysis of the sulfur-regulated control of the cystathionine γ-lyase gene of neurospora crassa.cystathionine γ-lyase plays a key role in the transsulfuration pathway through its primary reaction of catalyzing the formation of cysteine from cystathionine. the neurospora crassa cystathionine γ-lyase gene (cys-16(+)) is of particular interest in dissecting the regulation and dynamics of transsulfuration. the aim of this study was to determine the regulatory connection of cys-16(+) to the neurospora sulfur regulatory network. in addition, the cys-16(+) promoter was characterized with the goal ...201222748183
rna interference pathways in fungi: mechanisms and functions.rna interference (rnai) is a conserved eukaryotic gene regulatory mechanism that uses small noncoding rnas to mediate posttranscriptional/transcriptional gene silencing. the fission yeast schizosaccharomyces pombe and the filamentous fungus neurospora crassa have served as important model systems for rnai research. studies on these two organisms and other fungi have contributed significantly to our understanding of the mechanisms and functions of rnai in eukaryotes. in addition, surprisingly div ...201222746336
characterization of the two neurospora crassa cellobiose dehydrogenases and their connection to oxidative cellulose degradation.the genome of neurospora crassa encodes two different cellobiose dehydrogenases (cdhs) with a sequence identity of only 53%. so far, only cdh iia, which is induced during growth on cellulose and features a c-terminal carbohydrate binding module (cbm), was detected in the secretome of n. crassa and preliminarily characterized. cdh iib is not significantly upregulated during growth on cellulosic material and lacks a cbm. since cdh iib could not be identified in the secretome, both cdhs were recomb ...201222729546
neurosporaxanthin production by neurospora and fusarium.the orange pigmentation of the ascomycete fungi neurospora and fusarium is mainly due to the accumulation of neurosporaxanthin, a carboxylic apocarotenoid whose possible biotechnological applications have not been investigated. from the discovery of the first enzyme of the biosynthetic pathway in 1989, the prenyltransferase al-3, to the recent identification of an aldehyde dehydrogenase responsible for the last biosynthetic step, all the enzymes and biochemical reactions needed for neurosporaxan ...201222711132
rho1 and rho2 share partially overlapping functions in the regulation of cell wall integrity and hyphal polarity in neurospora crassa.rho proteins are key regulators of cellular morphogenesis, but their function in filamentous fungi is poorly understood. by generating conditional rho-1 mutants, we dissected the function of the essential gtpase rho1 in cell polarization and maintenance of cell wall integrity in neurospora crassa. we identified ncu00668/rgf1 as rho1-specific exchange factor, which controls actin organization and the cell wall integrity mak1 map kinase pathway through the direct interaction of active rho1 with th ...201222703449
the neurospora crassa dfg5 and dcw1 genes encode α-1,6-mannanases that function in the incorporation of glycoproteins into the cell wall.the covalent cross-linking of cell wall proteins into the cell wall glucan/chitin matrix is an important step in the biogenesis of the fungal cell wall. we demonstrate that the neurospora crassa dfg5 (ncu03770) and dcw1 (ncu08127) enzymes function in vivo to cross-link glycoproteins into the cell wall. mutants lacking dfg5 or dcw1 release slightly elevated levels of cell wall proteins into their growth medium. mutants lacking both dfg5 and dcw1 have substantially reduced levels of cell wall prot ...201222701726
high-resolution spatiotemporal analysis of gene expression in real time: in vivo analysis of circadian rhythms in neurospora crassa using a frequency-luciferase translational reporter.the pacemaker of the neurospora circadian clock is composed of a transcriptional-translational feedback loop that has been intensively studied during the last two decades. invaluable information has been derived from measuring the expression of the central clock component frequency (frq) under liquid culture conditions. direct analyses of frq mrna and protein levels on solid media - where overt circadian rhythms are normally visualized - have not been trivial due to technical issues. nevertheles ...201222695169
coronin is a component of the endocytic collar of hyphae of neurospora crassa and is necessary for normal growth and morphogenesis.coronin plays a major role in the organization and dynamics of actin in yeast. to investigate the role of coronin in a filamentous fungus (neurospora crassa), we examined its subcellular localization using fluorescent proteins and the phenotypic consequences of coronin gene (crn-1) deletion in hyphal morphogenesis, spitzenkörper behavior and endocytosis. coronin-gfp was localized in patches, forming a subapical collar near the hyphal apex; significantly, it was absent from the apex. the subapica ...201222693603
use of fluorescent protein to analyse recombination at three loci in neurospora crassa.we have inserted a histone h1-gfp fusion gene adjacent to three loci on different chromosomes of neurospora crassa and made mating pairs in which a wild type version of gfp is crossed to one with a mutation in the 5' end of gfp. the loci are his-3, am and his-5, chosen because recombination mechanisms appear to differ between his-3 and am, and because crossing over adjacent to his-5, like his-3, is regulated by rec-2. at his-3, the frequencies of crossing over between gfp and the centromere and ...201222691725
analyses of dynein heavy chain mutations reveal complex interactions between dynein motor domains and cellular dynein functions.cytoplasmic dynein transports cargoes for a variety of crucial cellular functions. however, since dynein is essential in most eukaryotic organisms, the in-depth study of the cellular function of dynein via genetic analysis of dynein mutations has not been practical. here, we identify and characterize 34 different dynein heavy chain mutations using a genetic screen of the ascomycete fungus neurospora crassa, in which dynein is nonessential. interestingly, our studies show that these mutations seg ...201222649085
concentration-dependent mechanisms of cell penetration and killing by the de novo designed antifungal hexapeptide paf26.recent evidence indicates that antimicrobial peptides can kill microbes in more complex ways than just by membrane permeabilization. in this study, the mechanism of internalization of the de novo designed cationic hexapeptide paf26 has been characterized in detail using neurospora crassa. live-cell imaging of fluorescently labelled paf26, organelle probes and mutants indicate that the peptide is endocytically internalized at low fungicidal concentrations (2.0-5 µm). at these concentrations, paf2 ...201222646057
role of fig1, a component of the low-affinity calcium uptake system, in growth and sexual development of filamentous fungi.the function of fig1, a transmembrane protein of the low-affinity calcium uptake system (lacs) in fungi, was examined for its role in the growth and development of the plant pathogen fusarium graminearum. the δfig1 mutants failed to produce mature perithecia, and sexual development was halted prior to the formation of perithecium initials. the loss of fig1 function also resulted in a reduced vegetative growth rate. macroconidium production was reduced 70-fold in the δfig1 mutants compared to the ...201222635922
sex-specific gene expression during asexual development of neurospora crassa.the impact of loci that determine sexual identity upon the asexual, dominant stage of fungal life history has been well studied. to investigate their impact, expression differences between strains of different mating type during asexual development were assayed, with rna sampled from otherwise largely isogenic mat a and mat a strains of neurospora crassa at early, middle, and late clonal stages of development. we observed significant differences in overall gene expression between mating types ac ...201222626843
the functions of grainy head-like proteins in animals and fungi and the evolution of apical extracellular barriers.the grainy head (grh) family of transcription factors are crucial for the development and repair of epidermal barriers in all animals in which they have been studied. this is a high-level functional conservation, as the known structural and enzymatic genes regulated by grh proteins differ between species depending on the type of epidermal barrier being formed. interestingly, members of the cp2 superfamily of transcription factors, which encompasses the grh and lsf families in animals, are also f ...201222590528
neurospora cop9 signalosome integrity plays major roles for hyphal growth, conidial development, and circadian function.the cop9 signalosome (csn) is a highly conserved multifunctional complex that has two major biochemical roles: cleaving nedd8 from cullin proteins and maintaining the stability of crl components. we used mutation analysis to confirm that the jamm domain of the csn-5 subunit is responsible for nedd8 cleavage from cullin proteins in neurospora crassa. point mutations of key residues in the metal-binding motif (ex(n)hxhx(10)d) of the csn-5 jamm domain disrupted csn deneddylation activity without in ...201222589747
on-target labeling of intracellular metabolites combined with chemical mapping of individual hyphae revealing cytoplasmic relocation of isotopologues.a microscale analytical platform integrating microbial cell culture, isotopic labeling, along with visual and mass spectrometric imaging with single-cell resolution has been developed and applied in the monitoring of cellular metabolism in fungal mycelium. the method implements open chips with a two-dimensional surface pattern composed of hydrophobic and hydrophilic zones. two hydrophilic islands are used as medium reservoirs, while the hydrophobic area constitutes the support for the growing ae ...201222583035
production of platinum nanoparticles and nanoaggregates using neurospora crassa.fungal biomass and fungal extract of the nonpathogenic fungus neurospora crassa were successfully used as reducing agents for the biosynthesis of platinum nanoparticles (ptnps). the experiment was carried out by exposing the fungal biomass or the fungal extract to a 0.001 m precursor solution of hexachloroplatinic(iv) acid (h2ptcl6). a change of color of the biomass from pale yellow to dark brown was the first indication of possible formation of ptnps by the fungus. subsequent analyses confirmed ...201222580320
structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases.the use of cellulases remains a major cost in the production of renewable fuels and chemicals from lignocellulosic biomass. fungi secrete copper-dependent polysaccharide monooxygenases (pmos) that oxidatively cleave crystalline cellulose and improve the effectiveness of cellulases. however, the means by which pmos recognize and cleave their substrates in the plant cell wall remain unclear. here, we present structures of neurospora crassa pmo-2 and pmo-3 at 1.10 and 1.37 å resolution, respectivel ...201222578542
bioconversion of dilute-acid pretreated sorghum bagasse to ethanol by neurospora crassa.bioethanol production from sweet sorghum bagasse (sb), the lignocellulosic solid residue obtained after extraction of sugars from sorghum stalks, can further improve the energy yield of the crop. the aim of the present work was to evaluate a cost-efficient bioconversion of sb to ethanol at high solids loadings (16 % at pretreatment and 8 % at fermentation), low cellulase activities (1-7 fpu/g sb) and co-fermentation of hexoses and pentoses. the fungus neurospora crassa dsm 1129 was used, which e ...201222573272
yeast adaptor protein, nbp2p, is conserved regulator of fungal ptc1p phosphatases and is involved in multiple signaling pathways.nbp2p is an src homology 3 (sh3) domain-containing yeast protein that is involved in a variety of cellular processes. this small adaptor protein binds to a number of different proteins through its sh3 domain, and a region n-terminal to the sh3 domain binds to the protein phosphatase, ptc1p. despite its involvement in a large number of physical and genetic interactions, the only well characterized function of nbp2p is to recruit ptc1p to the high osmolarity glycerol pathway, which results in down ...201222570491
enforcing silencing: dynamic hp1 complexes in neurospora.analysis of the neurospora crassa chromodomain protein cdp-2, a component of a newly characterized hp1-containing complex, reveals a second gene-silencing mechanism and provides insights into the dynamic nature of chromatin domains that possess shared components.201222551706
the arginine attenuator peptide interferes with the ribosome peptidyl transferase center.the fungal arginine attenuator peptide (aap) is encoded by a regulatory upstream open reading frame (uorf). the aap acts as a nascent peptide within the ribosome tunnel to stall translation in response to arginine (arg). the effect of aap and arg on ribosome peptidyl transferase center (ptc) function was analyzed in neurospora crassa and wheat germ translation extracts using the transfer of nascent aap to puromycin as an assay. in the presence of a high concentration of arg, the wild-type aap in ...201222508989
heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and dna methylation.dna methylation, methylation of histone h3 at lys9 (h3k9me3) and hypoacetylated histones are common molecular features of heterochromatin. important details of their functions and inter-relationships remain unclear, however. in neurospora crassa, h3k9me3 directs dna methylation through a complex containing heterochromatin protein 1 (hp1) and the dna methyltransferase dim-2. we identified a distinct hp1 complex, hp1, cdp-2, hda-1 and chap (hchc), and found that it is responsible for silencing ind ...201222504884
comprehensive modelling of the neurospora circadian clock and its temperature compensation.circadian clocks provide an internal measure of external time allowing organisms to anticipate and exploit predictable daily changes in the environment. rhythms driven by circadian clocks have a temperature compensated periodicity of approximately 24 hours that persists in constant conditions and can be reset by environmental time cues. computational modelling has aided our understanding of the molecular mechanisms of circadian clocks, nevertheless it remains a major challenge to integrate the l ...201222496627
organic acid excretion in penicillium ochrochloron increases with ambient ph.despite being of high biotechnological relevance, many aspects of organic acid excretion in filamentous fungi like the influence of ambient ph are still insufficiently understood. while the excretion of an individual organic acid may peak at a certain ph value, the few available studies investigating a broader range of organic acids indicate that total organic acid excretion rises with increasing external ph. we hypothesized that this phenomenon might be a general response of filamentous fungi t ...201222493592
induction of lignocellulose-degrading enzymes in neurospora crassa by cellodextrins.neurospora crassa colonizes burnt grasslands in the wild and metabolizes both cellulose and hemicellulose from plant cell walls. when switched from a favored carbon source such as sucrose to cellulose, n. crassa dramatically upregulates expression and secretion of a wide variety of genes encoding lignocellulolytic enzymes. however, the means by which n. crassa and other filamentous fungi sense the presence of cellulose in the environment remains unclear. here, we show that an n. crassa mutant ca ...201222474347
investigation of the ph-dependent electron transfer mechanism of ascomycetous class ii cellobiose dehydrogenases on electrodes.cellobiose dehydrogenase (cdh) is capable of direct electron transfer (det) on various carbon and thiol-modified gold electrodes. as a result, these systems have been utilized as biocatalyst in biosensors and biofuel cell anodes. class i cdhs, from basidiomycetous fungi, are highly specific to cellulose or lactose, and det is only observed at ph values below 5.5. to extend the applicability of cdh-based electrodes, the catalytic properties and the behavior on electrode surfaces of ascomycetous c ...201222471986
characterization of apoptosis-related oxidoreductases from neurospora crassa.the genome from neurospora crassa presented three open reading frames homologous to the genes coding for human aif and amid proteins, which are flavoproteins with oxidoreductase activities implicated in caspase-independent apoptosis. to investigate the role of these proteins, namely within the mitochondrial respiratory chain, we studied their cellular localization and characterized the respective null mutant strains. efficiency of the respiratory chain was analyzed by oxygen consumption studies ...201222470547
differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in neurospora crassa.fungal fruiting body size and form are influenced by the ecology of the species, including diverse environmental stimuli. accordingly, nutritional resources available to the fungus during development can be vital to successful production of fruiting bodies. to investigate the effect of nutrition, perithecial development of neurospora crassa was induced on two different media, a chemically sparsely nutritive synthetic crossing medium (scm) and a natural carrot agar (ca). protoperithecia were coll ...201222469835
unravelling the molecular basis for light modulated cellulase gene expression - the role of photoreceptors in neurospora crassa.light represents an important environmental cue, which exerts considerable influence on the metabolism of fungi. studies with the biotechnological fungal workhorse trichoderma reesei (hypocrea jecorina) have revealed an interconnection between transcriptional regulation of cellulolytic enzymes and the light response. neurospora crassa has been used as a model organism to study light and circadian rhythm biology. we therefore investigated whether light also regulates transcriptional regulation of ...201222462823
hydrophobic motif phosphorylation coordinates activity and polar localization of the neurospora crassa nuclear dbf2-related kinase cot1.nuclear dbf2p-related (ndr) kinases and associated proteins are recognized as a conserved network that regulates eukaryotic cell polarity. ndr kinases require association with mob adaptor proteins and phosphorylation of two conserved residues in the activation segment and hydrophobic motif for activity and function. we demonstrate that the neurospora crassa ndr kinase cot1 forms inactive dimers via a conserved n-terminal extension, which is also required for the interaction of the kinase with mo ...201222451488
analysis of the role of transcription factor vad-5 in conidiation of neurospora crassa.conidiation is the major mode of reproduction in many filamentous fungi. the neurospora crassa gene vad-5, which encodes a gal4-like zn2cys6 transcription factor, was suggested to contribute to conidiation in a previous study using a knockout mutant. in this study, we confirmed the positive contribution of vad-5 to conidiation by gene complementation. to understand the role of vad-5 in conidiation, transcriptomic profiles generated by digital gene expression profiling from the vad-5 deletion mut ...201222445960
electrical phenotypes of calcium transport mutant strains of a filamentous fungus, neurospora crassa.we characterized the electrical phenotypes of mutants with mutations in genes encoding calcium transporters-a mechanosensitive channel homolog (mscs), a ca(2+)/h(+) exchange protein (cax), and ca(2+)-atpases (nca-1, nca-2, nca-3)-as well as those of double mutants (the nca-2 cax, nca-2 nca-3, and nca-3 cax mutants). the electrical characterization used dual impalements to obtain cable-corrected current-voltage measurements. only two types of mutants (the mscs mutant; the nca-2 mutant and nca-2-c ...201222408225
controlling gene expression with the q repressible binary expression system in caenorhabditis elegans.we established a transcription-based binary gene expression system in caenorhabditis elegans using the recently developed q system. this system, derived from genes in neurospora crassa, uses the transcriptional activator qf to induce the expression of target genes. activation can be efficiently suppressed by the transcriptional repressor qs, and suppression can be relieved by the nontoxic small molecule quinic acid. we used qf, qs and quinic acid to achieve temporal and spatial control of transg ...201222406855
neurospora mrc1 homologue is involved in replication stability and is required for normal cell growth and chromosome integrity in mus-9 and mus-21 mutants.stalled replication forks easily collapse and such structures can induce dna strand breaks or toxic recombination products. therefore, factors involved in stabilization of replication should be important for genome integrity. in our previous study, loss of both atm and atr homologues was shown to cause growth defects and chromosome instability in neurospora crassa. to elucidate the relationships between these defects and replication instability, we focused on one of the viable replication factor ...201222395065
heterologous gene expression in filamentous fungi.filamentous fungi are critical to production of many commercial enzymes and organic compounds. fungal-based systems have several advantages over bacterial-based systems for protein production because high-level secretion of enzymes is a common trait of their decomposer lifestyle. furthermore, in the large-scale production of recombinant proteins of eukaryotic origin, the filamentous fungi become the vehicle of choice due to critical processes shared in gene expression with other eukaryotic organ ...201222958526
defective valyl-trna synthetase hampers the mitochondrial respiratory chain in neurospora crassa.respiratory chain deficiency can result from alterations in mitochondrial and/or cytosolic protein synthesis due to the dual genetic origin of mitochondrial oxidative phosphorylation. in the present paper we report a point mutation (d750g) in the bifunctional vars (valyl-trna synthetase) of the fungus neurospora crassa, associated with a temperature-sensitive phenotype. analysis of the mutant strain revealed decreased steady-state levels of vars and a clear reduction in the rate of mitochondrial ...201222957697
glycogen synthase kinase is a regulator of the circadian clock of neurospora crassa.timekeeping by circadian clocks relies upon precise adjustment of expression levels of clock proteins. here we identify glycogen synthase kinase (gsk) as a novel and critical component of the circadian clock of neurospora crassa that regulates the abundance of its core transcription factor white collar complex (wcc) on a post-transcriptional level. we show that gsk specifically binds and phosphorylates both subunits of the wcc. reduced expression of gsk promotes an increased accumulation of wc-1 ...201222955278
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