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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
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
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
is the fungus magnaporthe losing dna methylation?the long terminal repeat retrotransposon, magnaporthe gypsy-like element (maggy), has been shown to be targeted for cytosine methylation in a subset of magnaporthe oryzae field isolates. analysis of the f1 progeny from a genetic cross between methylation-proficient (br48) and methylation-deficient (gfsi1-7-2) isolates revealed that methylation of the maggy element was governed by a single dominant gene. positional cloning followed by gene disruption and complementation experiments revealed that ...201323979580
the transcriptional response to nonself in the fungus podospora anserina.in 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
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
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
transcriptomic profiling-based mutant screen reveals three new transcription factors mediating menadione resistance in neurospora crassa.to 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
the plasma membrane proton pump pma-1 is incorporated into distal parts of the hyphae independently of the spitzenkörper in neurospora crassa.most models for fungal growth have proposed a directional traffic of secretory vesicles to the hyphal apex, where they temporarily aggregate at the spitzenkörper before they fuse with the plasma membrane (pm). the pm h(+)-translocating atpase (pma-1) is delivered via the classical secretory pathway (endoplasmic reticulum [er] to golgi) to the cell surface, where it pumps h(+) out of the cell, generating a large electrochemical gradient that supplies energy to h(+)-coupled nutrient uptake systems ...201323729384
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
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 dna.in 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
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 crassa.in 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
homology modeling, ligand docking and in silico mutagenesis of neurospora hsp80 (90): insight into intrinsic atpase activity.the hsp90 family of proteins is an important component of the cellular response to elevated temperatures, environmental or physiological stress and nuclear receptor signalling. the primary object of this work is the 80-kda heat shock protein, a member of the hsp90 family, from the model filamentous fungus neurospora crassa, (henceforth referred to as hsp80nc). in contrast to more extensively characterized members of the same family, (e.g. hsp82sc of saccharomyces cerevisiae) it exhibits a higher ...201323735900
transcriptional profiling of neurospora crassa δmak-2 reveals that mitogen-activated protein kinase mak-2 participates in the phosphate signaling pathway.the filamentous fungus neurospora crassa is an excellent model system for examining molecular responses to ambient signals in eukaryotic microorganisms. inorganic phosphate (pi) is an essential growth-limiting nutrient in nature and is crucial for the synthesis of nucleic acids and the flow of genetic information. the genetic and molecular mechanisms controlling the response to pi starvation in n. crassa include at least four genes (nuc-2, preg, pogv, and nuc-1), which are involved in a hierarch ...201323733042
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 mutants.direct 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 crassa.in 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
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
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
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
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
biological activity of secondary metabolites isolated from mangrove fungi neurospora crassa.the screening of antimicrobial compounds from mangrove-associated fungi is a promising way to meet the increasing threat of drug-resistant strains of human pathogens. in the present study, a novel foliar fungus was isolated from the leaves of rhizophora mucronata. crude fungal extracts were obtained through solvent extraction. the fungal extracts exhibited an effective antimicrobial activity against bacterial strains. this study reports the cytotoxic activity of the secondary metabolite produced ...201324640249
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
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
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
neurospora crassa ncs-1, mid-1 and nca-2 double-mutant phenotypes suggest diverse interaction among three ca(2+)-regulating gene products. 201324371176
circadian rhythms in neurospora crassa on a polydimethylsiloxane microfluidic device for real-time gas perturbations.racetubes, a conventional system employing hollow glass tubes, are typically used for monitoring circadian rhythms from the model filamentous fungus, neurospora crassa. however, a major technical limitation in using a conventional system is that racetubes are not amenable for real-time gas perturbations. in this work, we demonstrate a simple microfluidic device combined with real-time gas perturbations for monitoring circadian rhythms in neurospora crassa using bioluminescence assays. the develo ...201324404062
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
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
[on the biosynthesis of inorganic polyphosphates in neurospora crassa]. 20134300424
[study of phosphorus compounds of mitochrndria from neurospora crassa]. 20134302491
[considerations on the specificity of the microbiological determination of adenine using neurospora crassa]. 20135728610
[the uptake of orthophosphate by adenine-deficient mutant of neurospora crassa 286-10 hsa]. 20135599898
[on the localization of inorganic polyphosphates and nucleotides in neurospora crassa mycelium]. 20135999969
a poly u directed phenylalanine polymerizing system from neurospora crassa: general characterization and ionic effects. 20135515872
correlation between base-pair transition and complementation pattern in nitrous acid-induced ad-3b mutants of neurospora crassa. 20135727269
mutagenicity of methylhydroxylamines in neurospora crassa. 20136054956
improved cellulase production via disruption of pde01641 in cellulolytic fungus penicillium decumbens.to investigate the function of pde01641, the homologue of neurospora crassa ncu05137, during cellulase production in penicillium decumbens, the pde01641 encoding gene was knocked out in the present work. the pde01641 deletion mutant showed enhanced cellobiohydrolase activity and β-glucosidase activity compared to the parental strain 114-2. increased transcription of the main cellulase and hemicellulase genes in δpde01641 gave evidence that pde01641 might affect the process associated with the re ...201222981621
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 pmr gene, encoding a ca2+-atpase, is required for calcium and manganese homeostasis and normal development of hyphae and conidia in neurospora crassa.the pmr gene is predicted to encode a ca(2+)-atpase in the secretory pathway. we examined two strains of neurospora crassa that lacked pmr: the δpmr strain, in which pmr was completely deleted, and pmr(rip), in which the gene was extensively mutated. both strains had identical, complex phenotypes. compared to the wild type, these strains required high concentrations of calcium or manganese for optimal growth and had highly branched, slow-growing hyphae. they conidiated poorly, and the shape and ...201222983986
evidence for tryptophan being a signal molecule that inhibits conidial anastomosis tube fusion during colony initiation in neurospora crassa.mycelial interconnectedness achieved by hyphal fusion has been hypothesized to facilitate the distribution and sharing of nutrients between different parts of a mycelium, especially when nutrients are heterogeneously distributed in the environment. however, the link between environmental nutrient availability and hyphal fusion is little understood. here, we report that amino acids and extracellular ph regulate conidial anastomosis tube (cat) fusion during colony initiation in neurospora crassa. ...201222939838
[effect of oxylipins on neurospora crassa growth and differentiation ion]. 201223234069
small rna isolation and library construction for expression profiling of small rnas from neurospora and fusarium using illumina high-throughput deep sequencing.due to crucial roles in gene regulation, noncoding small rnas (smrnas) of 20-30 nucleotides (nt) have been intensively studied in mammals and plants, and are known to be implicated in significant diseases and metabolic disorders. elucidation of biogenesis mechanisms and functional characterization of smrnas are often achieved using tools, such as separation of small-sized rna and high-throughput sequencing. although rna interference pathways such as quelling and meiotic silencing have been well ...201222589132
a novel biochemical route for fuels and chemicals production from cellulosic biomass.the conventional biochemical platform featuring enzymatic hydrolysis involves five key steps: pretreatment, cellulase production, enzymatic hydrolysis, fermentation, and product recovery. sugars are produced as reactive intermediates for subsequent fermentation to fuels and chemicals. herein, an alternative biochemical route is proposed. pretreatment, enzymatic hydrolysis and cellulase production is consolidated into one single step, referred to as consolidated aerobic processing, and sugar aldo ...201222384058
fungal catalases: function, phylogenetic origin and structure.most fungi have several monofunctional heme-catalases. filamentous ascomycetes (pezizomycotina) have two types of large-size subunit catalases (l1 and l2). l2-type are usually induced by different stressors and are extracellular enzymes; those from the l1-type are not inducible and accumulate in asexual spores. l2 catalases are important for growth and the start of cell differentiation, while l1 are required for spore germination. in addition, pezizomycetes have one to four small-size subunit ca ...201222698962
a novel activity for fungal nitronate monooxygenase: detoxification of the metabolic inhibitor propionate-3-nitronate.nitronate monooxygenase (nmo; e.c. 1.13.12.16) oxidizes alkyl nitronates to aldehydes and nitrite. although the biochemistry of the enzyme from fungal sources has been studied extensively, the physiological role is unknown. the ability of nmo to detoxify propionate-3-nitronate was tested by measuring growth of recombinant escherichia coli containing the gene encoding for the enzyme in either the absence or presence of the nitronate and its conjugate acid 3-nitropropionate. the mixture propionate ...201222464989
improved gene targeting frequency in marine-derived filamentous fungus aspergillus glaucus by disrupting ligd.filamentous fungi from the marine environment have shown great potential as cell factories for the production of pharmacologically active metabolites, but extremely low frequency of homologous recombination brings difficulty to further molecular biology studies. to bypass this problem and develop a highly efficient gene targeting system in marine-derived filamentous fungus aspergillus glaucus, ligd, a homolog of neurospora crassa mus-53 which is considered to play a significant role in nonhomolo ...201222562375
genetic control of asexual sporulation in filamentous fungi.asexual sporulation (conidiation) in the ascomycetous filamentous fungi involves the formation of conidia, formed on specialized structures called conidiophores. conidiation in filamentous fungi involves many common themes including spatial and temporal regulation of gene expression, specialized cellular differentiation, intra-/inter-cellular communications, and response to environmental factors. the commencement, progression and completion of conidiation are regulated by multiple positive and n ...201223092920
ambient ph controls glycogen levels by regulating glycogen synthase gene expression in neurospora crassa. new insights into the ph signaling pathway.glycogen is a polysaccharide widely distributed in microorganisms and animal cells and its metabolism is under intricate regulation. its accumulation in a specific situation results from the balance between glycogen synthase and glycogen phosphorylase activities that control synthesis and degradation, respectively. these enzymes are highly regulated at transcriptional and post-translational levels. the existence of a dna motif for the aspergillus nidulans ph responsive transcription factor pacc ...201222952943
conserved and essential transcription factors for cellulase gene expression in ascomycete fungi.rational engineering of filamentous fungi for improved cellulase production is hampered by our incomplete knowledge of transcriptional regulatory networks. we therefore used the model filamentous fungus neurospora crassa to search for uncharacterized transcription factors associated with cellulose deconstruction. a screen of a n. crassa transcription factor deletion collection identified two uncharacterized zinc binuclear cluster transcription factors (clr-1 and clr-2) that were required for gro ...201222532664
high abundance of serine/threonine-rich regions predicted to be hyper-o-glycosylated in the secretory proteins coded by eight fungal genomes.o-glycosylation of secretory proteins has been found to be an important factor in fungal biology and virulence. it consists in the addition of short glycosidic chains to ser or thr residues in the protein backbone via o-glycosidic bonds. secretory proteins in fungi frequently display ser/thr rich regions that could be sites of extensive o-glycosylation. we have analyzed in silico the complete sets of putatively secretory proteins coded by eight fungal genomes (botrytis cinerea, magnaporthe grise ...201222994653
prp8 inteins in species of the genus botrytis and other ascomycetes.the mobile elements termed inteins have a sporadic distribution in microorganisms. it is unclear how these elements are maintained. inteins are intervening protein sequences that autocatalytically excise themselves from a precursor. excision is a post-translational process referred to as 'protein splicing' in which the sequences flanking the intein are ligated, reforming the mature host protein. some inteins contain a homing endonuclease domain (heg) that is proposed to facilitate propagation of ...201222285471
transgene induced co-suppression during vegetative growth in cryptococcus neoformans.introduction of dna sequences into the genome often results in homology-dependent gene silencing in organisms as diverse as plants, fungi, flies, nematodes, and mammals. we previously showed in cryptococcus neoformans that a repeat transgene array can induce gene silencing at a high frequency during mating (∼50%), but at a much lower frequency during vegetative growth (∼0.2%). here we report a robust asexual co-suppression phenomenon triggered by the introduction of a cpa1::ade2 transgene. multi ...201222916030
biological activities of extracts from chenopodium ambrosioides lineu and kielmeyera neglecta saddi.chenopodium ambrosioides and kielmeyera neglecta are plants traditionally used in brazil to treat various infectious diseases. the study of the biological activities of these plants is of great importance for the detection of biologically active compounds.201222839690
the carnitine biosynthetic pathway in arabidopsis thaliana shares similar features with the pathway of mammals and fungi.carnitine is an essential quaternary ammonium amino acid that occurs in the microbial, plant and animal kingdoms. the role and synthesis of this compound are very well documented in bacteria, fungi and mammals. on the contrary, although the presence of carnitine in plant tissue has been reported four decades ago and information about its biological implication are available, nothing is known about its synthesis in plants. we designed experiments to determine if the carnitine biosynthetic pathway ...201222922110
gliotoxin effects on fungal growth: mechanisms and exploitation.although initially investigated for its antifungal properties, little is actually known about the effect of gliotoxin on aspergillus fumigatus and other fungi. we have observed that exposure of a. fumigatus to exogenous gliotoxin (14 μg/ml), under gliotoxin-limited growth conditions, results in significant alteration of the expression of 27 proteins (up- and down-regulated >1.9-fold; p<0.05) including de novo expression of cu, zn superoxide dismutase, up-regulated allergen asp f3 expression and ...201222405895
characterization of the insertase for β-barrel proteins of the outer mitochondrial membrane.the tob-sam complex is an essential component of the mitochondrial outer membrane that mediates the insertion of β-barrel precursor proteins into the membrane. we report here its isolation and determine its size, composition, and structural organization. the complex from neurospora crassa was composed of tob55-sam50, tob38-sam35, and tob37-sam37 in a stoichiometry of 1:1:1 and had a molecular mass of 140 kd. a very minor fraction of the purified complex was associated with one mdm10 protein. usi ...201223128244
the transcriptional response to the inactivation of the pampk1 and pampk2 map kinase pathways in podospora anserina.transcription pattern during mycelium growth of podospora anserina was assayed by microarray analysis in wild type and in mutants affected in the map kinase genes pampk1 and pampk2 and in the nadph oxidase gene panox1. 15% of the genes have their expression modified by a factor two or more as growth proceeds in wild type. the genes whose expression is modified during growth in p. anserina are either not conserved or differently regulated in neurospora crassa and aspergillus niger, two fungi for ...201222721649
genomic characteristics comparisons of 12 food-related filamentous fungi in trna gene set, codon usage and amino acid composition.filamentous fungi are widely exploited in food industry due to their abilities to secrete large amounts of enzymes and metabolites. the recent availability of fungal genome sequences has provided an opportunity to explore the genomic characteristics of these food-related filamentous fungi. in this paper, we selected 12 representative filamentous fungi in the areas of food processing and safety, which were aspergillus clavatus, a. flavus, a. fumigatus, a. nidulans, a. niger, a. oryzae, a. terreus ...201222305983
the neurospora crassa os mapk pathway-activated transcription factor asl-1 contributes to circadian rhythms in pathway responsive clock-controlled genes.the os-pathway mitogen-activated protein kinase (mapk) cascade of neurospora crassa is responsible for adaptation to osmotic stress. activation of the mapk, os-2, leads to the transcriptional induction of many genes involved in the osmotic stress response. we previously demonstrated that there is a circadian rhythm in the phosphorylation of os-2 under constant non-stress inducing conditions. additionally, several osmotic stress-induced genes are known to be regulated by the circadian clock. ther ...201222240319
AreA controls nitrogen source utilisation during both growth programs of the dimorphic fungus Penicillium marneffei.The opportunistic pathogen Penicillium marneffei displays a temperature-dependent dimorphic switching program with saprophytic hyphal growth at 25 °C and yeast growth at 37 °C. The areA gene of P. marneffei has been isolated and found to be required for the utilisation of nonpreferred nitrogen sources during both growth programs of P. marneffei, albeit to differing degrees. Based on this functional characterisation and high degree of sequence conservation with other fungal GATA factors, P. marne ...201222208609
the testing of 4cmb, 4hmb and bc for mutagenicity in a new neurospora crassa heterokaryon.this genetic system permits both point mutations and deletion to be detected in the same experimental material. 4cmb and bc are regarded as being mutagenic in this system. 4hmb induced mutations in only 1 of the 3 treatment protocols used, and its mutagenicity is questionable.20126460177
mitochondrial dysfunction resulting from the absence of mitochondrial porin in neurospora crassa.porin, the voltage-dependent anion-selective channel (vdac) in the mitochondrial outer membrane, contributes to metabolism and apoptosis. vdac function was investigated in neurospora, an obligate aerobe with a single porin. porinless strains are viable, with cold-sensitive growth, cytochrome deficiencies and overexpression of alternative oxidase. itraq labeling of mitochondria from a porinless strain and its progenitor revealed a small group of proteins with altered expression levels in the muta ...201221946565
a crossover hotspot near his-3 in neurospora crassa is a preferential recombination termination site.during analysis of 148 unselected neurospora crassa octads, an above average rate of crossing over was detected within a 360-base region near the 3' end of his-3, suggesting a hotspot for crossing over about 1.8 kb away from the recombination initiation site within cog. homozygous deletion of the 360-base region increases exchanges in his-3 and on the far side of his-3 from cog, with the heterozygote showing an intermediate increase. we conclude that recombination events initiated at cog termina ...201222203161
oxidative cleavage of cellulose by fungal copper-dependent polysaccharide monooxygenases.fungal-derived, copper-dependent polysaccharide monooxygenases (pmos), formerly known as gh61 proteins, have recently been shown to catalyze the o(2)-dependent oxidative cleavage of recalcitrant polysaccharides. different pmos isolated from neurospora crassa were found to generate oxidized cellodextrins modified at the reducing or nonreducing ends upon incubation with cellulose and cellobiose dehydrogenase. here we show that the nonreducing end product formed by an n. crassa pmo is a 4-ketoaldos ...201222188218
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
disruption of alternative nad(p)h dehydrogenases leads to decreased mitochondrial ros in neurospora crassa.mitochondria are a main providers of high levels of energy, but also a major source of reactive oxygen species (ros) during normal oxidative metabolism. the involvement of neurospora crassa alternative nad(p)h dehydrogenases in mitochondrial ros production was evaluated. the growth responses of a series of respiratory mutants to several stress conditions revealed that disrupting alternative dehydrogenases leads to an increased tolerance to the redox cycler paraquat, with a mutant devoid of the e ...201222100504
diverse interactions mediate asymmetric incompatibility by the het-6 supergene complex in neurospora crassa.heterokaryon incompatibility (hi) in filamentous fungi is a form of nonself recognition that operates during the vegetative phase of the life cycle. one hi gene complex in neurospora crassa, the het-6 locus, comprises two incompatibility genes, het-6 and un-24, each having two allelic variants, oak ridge (or) and panama (pa). the un-24 gene also encodes the large subunit of ribonucleotide reductase while het-6 appears to be a member of a repetitive gene family with no other known function aside ...201222094057
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
neurospora crassa light signal transduction is affected by ros.in the ascomycete fungus neurospora crassa blue-violet light controls the expression of genes responsible for differentiation of reproductive structures, synthesis of secondary metabolites, and the circadian oscillator activity. a major photoreceptor in neurospora cells is wcc, a heterodimeric complex formed by the pas-domain-containing polypeptides wc-1 and wc-2, the products of genes white collar-1 and white collar-2. the photosignal transduction is started by photochemical activity of an exci ...201222046507
the circadian clock of neurospora crassa.circadian clocks organize our inner physiology with respect to the external world, providing life with the ability to anticipate and thereby better prepare for major fluctuations in its environment. circadian systems are widely represented in nearly all major branches of life, except archaebacteria, and within the eukaryotes, the filamentous fungus neurospora crassa has served for nearly half a century as a durable model organism for uncovering the basic circadian physiology and molecular biolog ...201221707668
illuminating the early signaling pathway of a fungal light-oxygen-voltage photoreceptor.circadian clocks are molecular timekeepers encountered in a wide variety of organisms, which allow to adapt the cell's metabolism and behavior to the daily and seasonal periods. their function is regulated by light-sensing proteins, among which vivid, a light-oxygen-voltage (lov) sensitive domain of the fungus neurospora crassa, constitutes one of the most prominent examples. although the major photochemical and structural changes during the photocycle of this photosensor have been elucidated th ...201222081493
the ndr kinase scaffold hym1/mo25 is essential for mak2 map kinase signaling in neurospora crassa.cell communication is essential for eukaryotic development, but our knowledge of molecules and mechanisms required for intercellular communication is fragmentary. in particular, the connection between signal sensing and regulation of cell polarity is poorly understood. in the filamentous ascomycete neurospora crassa, germinating spores mutually attract each other and subsequently fuse. during these tropic interactions, the two communicating cells rapidly alternate between two different physiolog ...201223028357
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
genetic and physical interactions between gα subunits and components of the gβγ dimer of heterotrimeric g proteins in neurospora crassa.heterotrimeric g proteins are critical regulators of growth and asexual and sexual development in the filamentous fungus neurospora crassa. three gα subunits (gna-1, gna-2, and gna-3), one gβ subunit (gnb-1), and one gγ subunit (gng-1) have been functionally characterized, but genetic epistasis relationships between gβ and gα subunit genes have not been determined. physical association between gnb-1 and flag-tagged gng-1 has been previously demonstrated by coimmunoprecipitation, but knowledge of ...201222903975
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
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