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control of alternative rna splicing and gene expression by eukaryotic riboswitches.bacteria make extensive use of riboswitches to sense metabolites and control gene expression, and typically do so by modulating premature transcription termination or translation initiation. the most widespread riboswitch class known in bacteria responds to the coenzyme thiamine pyrophosphate (tpp), which is a derivative of vitamin b1. representatives of this class have also been identified in fungi and plants, where they are predicted to control messenger rna splicing or processing. we examined ...200717468745
fkbp22 is part of chaperone/folding catalyst complexes in the endoplasmic reticulum of neurospora crassa.fkbp22 is a dimeric protein in the lumen of the endoplasmic reticulum, which exhibits a chaperone as well as a ppiase activity. it binds via its fk506 binding protein (fkbp) domain directly to the hsp70 chaperone bip that stimulates the chaperone activity of fkbp22. here we demonstrate additionally the association of fkbp22 with the molecular chaperones and folding catalysts grp170, alpha-subunit of glucosidase ii, pdi, erp38, and cyp23. these proteins are associated with fkbp22 in at least two ...200717470367
mutation of msh-2 in neurospora crassa does not reduce the incidence of recombinants with multiple patches of donor chromosome sequence.the neurospora homologue msh-2 of the escherichia coli mismatch repair gene muts was mutated by repeat-induced point mutation (rip) of a 1.9-kb duplication covering 1661bp of the coding sequence and 302 bp 5' of the gene. msh-2(rip-lk1) exhibited a mutator phenotype conferring a 17-fold increase in the frequency of spontaneous mitotic reversion of his-3 allele k458. in msh-2(rip-lk1) homozygotes, recombination frequency at the his-3 locus increased up to 2.9-fold over that in msh-2(+) diploids. ...200717475521
localization of rho-4 indicates differential regulation of conidial versus vegetative septation in the filamentous fungus neurospora crassa.rho-4 mutants of the filamentous fungus neurospora crassa lack septa and asexual spores (conidia) and grow slowly. in this report, localization of green fluorescent protein-tagged rho-4 is used to elucidate the differences in factors controlling rho-4 localization during vegetative growth versus asexual development. rho-4 forms a ring at incipient vegetative septation sites that constricts with the formation of the septum toward the septal pore; rho-4 persists around the septal pore after septum ...200717496127
model of hyphal tip growth involving microtubule-based transport.we propose a simple model for mass transport within a fungal hypha and its subsequent growth. inspired by the role of microtubule-transported vesicles, we embody the internal dynamics of mass inside a hypha with mutually excluding particles progressing stochastically along a growing one-dimensional lattice. the connection between long-range transport of materials for growth and the resulting extension of the hyphal tip has not previously been addressed in the modeling literature to our knowledge ...200717500728
conformational switching in the fungal light sensor vivid.the neurospora crassa photoreceptor vivid tunes blue-light responses and modulates gating of the circadian clock. crystal structures of dark-state and light-state vivid reveal a light, oxygen, or voltage per-arnt-sim domain with an unusual n-terminal cap region and a loop insertion that accommodates the flavin cofactor. photoinduced formation of a cystein-flavin adduct drives flavin protonation to induce an n-terminal conformational change. a cysteine-to-serine substitution remote from the flavi ...200717510367
characterization of alcohol dehydrogenase 1 and 3 from neurospora crassa fgsc2489.alcohol dehydrogenase (adh) is a key enzyme in the production and utilization of alcohols. some also catalyze the formation of carboxylate esters from alcohols and aldehydes. the adh1 and adh3 genes of neurospora crassa fgsc2489 were cloned and expressed in recombinant escherichia coli to investigate their alcohol dehydrogenation and carboxylate ester formation abilities. homology analysis and sequence alignment of amino acid sequence indicated that adh1 and adh3 of n. crassa contained a zinc-bi ...200717516063
the band mutation in neurospora crassa is a dominant allele of ras-1 implicating ras signaling in circadian output.band, an allele enabling clear visualization of circadianly regulated spore formation (conidial banding), has remained an integral tool in the study of circadian rhythms for 40 years. bd was mapped using single-nucleotide polymorphisms (snps), cloned, and determined to be a t79i point mutation in ras-1. alterations in light-regulated gene expression in the ras-1(bd) mutant suggests that the neurospora photoreceptor white collar-1 is a target of ras signaling, and increases in transcription of bo ...200717575051
design and analysis of an efficient recursive linking algorithm for constructing likelihood based genetic maps for a large number of markers.a multi-locus likelihood of a genetic map is computed based on a mathematical model of chromatid exchange in meiosis that accounts for any type of bivalent configuration in a genetic interval in any specified order of genetic markers. the computational problem is to calculate the likelihood (l) and maximize l by choosing an ordering of genetic markers on the map and the recombination distances between markers. this maximum likelihood estimate (mle) could be found either with a straightforward al ...200717589960
genome-wide expression analysis of genetic networks in neurospora crassa.the products of five structural genes and two regulatory genes of the qa gene cluster of neurospora crassa control the metabolism of quinic acid (qa) as a carbon source. a detailed genetic network model of this metabolic process has been reported. this investigation is designed to expand the current model of the qa reaction network. the ensemble method of network identification was used to model rna profiling data on the qa gene cluster. through microarray and cluster analysis, genome-wide ident ...200717597928
fungal multienzyme production on industrial by-products of the citrus-processing industry.orange peels is the principal solid by-product of the citrus processing industry and the disposal of the fresh peels is becoming a major problem to many factories. dry citrus peels are rich in pectin, cellulose and hemicellulose and may be used as a fermentation substrate. production of multienzyme preparations containing pectinolytic, cellulolytic and xylanolytic enzymes by the mesophilic fungi aspergillus niger btl, fusarium oxysporum f3, neurospora crassa dsm 1129 and penicillium decumbens un ...200817604624
fungal photoreceptors: sensory molecules for fungal development and behaviour.light regulates fungal development and behaviour and activates metabolic pathways. in addition, light is one of the many signals that fungi use to perceive and interact with the environment. in the ascomycete neurospora crassa blue light is perceived by the white collar (wc) complex, a protein complex formed by wc-1 and wc-2. wc-1 is a protein with a flavin-binding domain and a zinc-finger domain, and interacts with wc-2, another zinc-finger domain protein. the wc complex operates as a photorece ...200717609765
ability to grow on lipids accounts for the fully virulent phenotype in neutropenic mice of aspergillus fumigatus null mutants in the key glyoxylate cycle enzymes.incidence and mortality rates of invasive aspergillosis clearly indicate the need of novel antifungals to treat patients suffering from this disease. fungal proteins playing a crucial role in pathogenesis and with no orthologue in human cells are considered as primary therapeutic targets for the development of new antifungals with a high therapeutic index, one of the major drawbacks of the standard antifungal therapy, so far. in this work, we have analyzed the role in pathogenesis of the key enz ...200817616408
[a study of the nitrate and nitrite discharge from the mutant cells of neurospora crassa lacking nitrate and nitrite reductase activities].the neurospora crassa mutants nit-2 (lacking both nitrite and nitrate reductases) and nit-6 (lacking nitrite reductase) grown in the medium with ammonium chloride as a sole source of nitrogen discharged nitrate and nitrite ions into culture medium. for nit-2, the content of nitrate exceeded that of nitrite in both the homogenate of fungal cells and growth medium; moreover, this difference was more pronounced in the culture medium. unlike nit-2, the content of nitrite in the cultivation medium of ...201317619581
carbon source affects pka-dependent polarity of neurospora crassa in a cre-1-dependent and independent manner.a defect in mcb, encoding the camp-dependent protein kinase a (pka) regulatory subunit in neurospora crassa, which confers an apolar growth phenotype, is accompanied by an increase in pka activity levels. both pka and cre-1 [a key carbon catabolite repression (ccr) regulator] mediate the cellular response to carbon-source availability. inactivation of the cre-1 gene resulted in reduced growth rate, abnormal hyphal morphology and altered ccr. both pka and cre-1 affected morphology in a carbon-dep ...200817625933
neurospora crassa ve-1 affects asexual conidiation.the velvet factor of the homothallic fungus aspergillus nidulans promotes sexual fruiting body formation. the encoding vea gene is conserved among fungi, including the ascomycete neurospora crassa. there, the orthologous ve-1 gene encodes a deduced protein with high similarity to a. nidulans vea. cross-complementation experiments suggest that both the promoter and the coding sequence of n. crassa ve-1 are functional to complement the phenotype of an a. nidulans deletion mutant. moreover, ve-1 ex ...200817631397
catalase-1 (cat-1) and nucleoside diphosphate kinase-1 (ndk-1) play an important role in protecting conidial viability under light stress in neurospora crassa.recently we reported that catalase-1 (cat-1) played an important role in protecting conidial viability in neurospora crassa, and interacted with a light signal transducer, nucleoside diphosphate kinase-1 (ndk-1). to disclose the functional interaction between cat-1 and ndk-1 at the genetic level, we created cat-1 and ndk-1 double mutants, cat-1;ndk-1-1 and cat-1;ndk-1-2, by crossing single mutants of cat-1 ( rip ) and ndk-1 ( p72h ) previously isolated in our laboratory. the double mutant strain ...200717636331
spitzenkorper localization and intracellular traffic of green fluorescent protein-labeled chs-3 and chs-6 chitin synthases in living hyphae of neurospora crassa.the subcellular location and traffic of two selected chitin synthases (chs) from neurospora crassa, chs-3 and chs-6, labeled with green fluorescent protein (gfp), were studied by high-resolution confocal laser scanning microscopy. while we found some differences in the overall distribution patterns and appearances of chs-3-gfp and chs-6-gfp, most features were similar and were observed consistently. at the hyphal apex, fluorescence congregated into a conspicuous single body corresponding to the ...200717644657
evidence that rna silencing functions as an antiviral defense mechanism in fungi.the role of rna silencing as an antiviral defense mechanism in fungi was examined by testing the effect of dicer gene disruptions on mycovirus infection of the chestnut blight fungus cryphonectria parasitica. c. parasitica dicer-like genes dcl-1 and dcl-2 were cloned and shown to share a high level of predicted amino acid sequence identity with the corresponding dicer-like genes from neurospora crassa [ncdcl-1 (50.5%); ncdcl-2 (38.0%)] and magnaporthe oryzae [mdl-1 (45.6%); mdl-2 (38.0%)], respe ...200717646660
high-density detection of restriction-site-associated dna markers for rapid mapping of mutated loci in neurospora.the wealth of sequence information available for neurospora crassa and other fungi has greatly facilitated evolutionary and molecular analyses of this group. although "reverse" genetics, in which genes are first identified by their sequence rather than by their mutant phenotypes, serves as a valuable new approach for elucidating biological processes, classical "forward" genetic analysis is still extremely useful. unfortunately, mapping mutations and identifying the corresponding genes has typica ...200717660537
alternative splicing gives rise to different isoforms of the neurospora crassa tob55 protein that vary in their ability to insert beta-barrel proteins into the outer mitochondrial membrane.tob55 is the major component of the tob complex, which is found in the outer membrane of mitochondria. a sheltered knockout of the tob55 gene was developed in neurospora crassa. when grown under conditions that reduce the levels of the tob55 protein, the strain exhibited a reduced growth rate and mitochondria isolated from these cells were deficient in their ability to import beta-barrel proteins. surprisingly, western blots of wild-type mitochondrial proteins revealed two bands for tob55 that d ...200717660559
purification and antimicrobial activity studies of the n-terminal fragment of ubiquitin from human amniotic fluid.a 4.3-kda antimicrobial peptide was isolated from human amniotic fluid by dialysis, ultrafiltration, and c18 reversed-phase high performance liquid chromatography. this peptide, which we named amniotic fluid peptide-1 (afp-1), possessed antimicrobial activity but lacked hemolytic activity. in addition, afp-1 potently inhibited the growth of a variety of bacteria (escherichia coli, salmonella typhimurium, listeria monocytogenes and staphylococcus aureus), filamentous fungi (botrytis cinerea, aspe ...200717669700
the pas/lov protein vivid controls temperature compensation of circadian clock phase and development in neurospora crassa.circadian clocks are cellular timekeepers that regulate aspects of temporal organization on daily and seasonal time scales. to allow accurate time measurement, the period lengths of clocks are conserved in a range of temperatures--a phenomenon known as temperature compensation. temperature compensation of circadian clock period aids in maintaining a stable "target time" or phase of clock-controlled events. here we show that the neurospora protein vivid (vvd) buffers the circadian system against ...200717671094
the fungal opsin gene nop-1 is negatively-regulated by a component of the blue light sensing pathway and influences conidiation-specific gene expression in neurospora crassa.we previously demonstrated that the nop-1 gene encodes a putative green-light opsin photoreceptor that is highly expressed in cultures that support asexual sporulation (conidiation) in neurospora crassa. in this study, we demonstrate that nop-1 is a late-stage conidiation gene, through analysis of nop-1 transcript levels in wild-type strains and mutants blocked at various stages of conidiation. nop-1 message amounts are similar with constant illumination or darkness during conidiation, consisten ...200717676324
molecular cloning and characterization of a putative protein kinase gene from the thermophilic fungus thermomyces lanuginosus.based on the conserved amino acid sequence (dlkpen) of serine-threonine protein kinase from several fungi, a degenerate primer was designed and synthesized. total rna was isolated from the thermophilic fungus thermomyces lanuginosus. using race-pcr, full-length cdna of a putative serine-threonine protein kinase gene was cloned from t. lanuginosus. the full-length cdna of t. lanuginosus protein kinase was 2551 bp and contained an 1806 bp open reading frame encoding a putative protein kinase precu ...200717676472
neurosprora crassa rad5 homologue, mus-41, inactivation results in higher sensitivity to mutagens but has little effect on pcna-ubiquitylation in response to uv-irradiation.the dna replication machinery stalls at damaged sites on dna. postreplicaton repair (prr) is a system to avoid cell death in such circumstances of deadlock. in saccharomyces cerevisiae, the rad6/rad18 heterodimer plays pivotal roles in prr. it promotes translesion synthesis via the monoubiquitylation of the dna sliding clamp, pcna. ubc13/mms2/rad5 can extend the ubiquitin chain from this monoubiquitylated pcna with a non-canonical lysine 63-linked ubiquitin-chain, resulting in an error-free mode ...200717703305
domain architectures of the scm3p protein provide insights into centromere function and evolution.recently, scm3p has been shown to be a nonhistone component of centromeric chromatin that binds stoichiometrically to cenh3-h4 histones, and to be required for the assembly of kinetochores in saccharomyces cerevisiae. scm3p is conserved across fungi, and displays a remarkable variation in protein size, ranging from approximately 200 amino acids in s. cerevisiae to approximately 1300 amino acids in neurospora crassa. this is primarily due a variable c-terminal segment that is linked to a conserve ...200717704645
simple sequence repeats provide a substrate for phenotypic variation in the neurospora crassa circadian clock.white collar-1 (wc-1) mediates interactions between the circadian clock and the environment by acting as both a core clock component and as a blue light photoreceptor in neurospora crassa. loss of the amino-terminal polyglutamine (npolyq) domain in wc-1 results in an arrhythmic circadian clock; this data is consistent with this simple sequence repeat (ssr) being essential for clock function.200717726525
the use of amphipathic polymers for cryo electron microscopy of nadh:ubiquinone oxidoreductase (complex i).in the three-dimensional (3d) structure determination of macromolecules, cryo electron microscopy (cryo-em) is an important method for obtaining micrographs of unstained specimens for the single-particle reconstruction approach. for cryo-em, proteins are fixed in a frozen hydrated state by quick-freezing in a thin water layer on a holey carbon film. cryo-em of detergent-solubilized membrane proteins is hindered by the fact that detergents reduce the surface tension of water, so that it is diffic ...200717760617
fully codon-optimized luciferase uncovers novel temperature characteristics of the neurospora clock.we report the complete reconstruction of the firefly luciferase gene, fully codon optimized for expression in neurospora crassa. this reporter enhances light output by approximately 4 log orders over that with previously available versions, now producing light that is visible to the naked eye and sufficient for monitoring the activities of many poorly expressed genes. time lapse photography of strains growing in race tubes, in which the frq or eas/ccg-2 promoter is used to drive luciferase, show ...200817766461
new biological effect of the gases of the helium group.the mold neurospora crassa atcc 5297a was grown in gaseous environments of helium, neon, argon, krypton, xenon, or nitrogen containing approximately 5 percent oxygen. a close correlation of the growth rate r (in millimeters per hour at 30 degrees c) with the molecular weight mw of the chemically inert gas was observed. this correlation is described by the empirical equation: r = 3.88 - 0.1785 (mw).196217814509
heterokaryon-incompatibility factor interaction in tests between neurospora mutants.studies on presumably isogenic ad-3a and ad-3b mutants of the ascomycete neurospora crassa derived from the same wild-type strain have revealed that the negative heterokaryon tests shown by certain pairwise combinations can be attributed to interaction of incompatibility factor mutations.196217816561
migration cues induce chromatin alterations.directed cell migration is a property central to multiple basic biological processes. here, we show that directed cell migration is associated with global changes in the chromatin fiber. polarized posttranslational changes in histone h1 along with a transient decrease in h1 mobility were detected in cells facing the scratch in a wound healing assay. in parallel to the changes in h1, the levels of the heterochromatin marker histone h3 lysine 9 tri-methylation were elevated. interestingly, reducti ...200717822403
sequence analysis and expression of a blue-light photoreceptor gene, le.phra from the basidiomycetous mushroom lentinula edodes.we cloned and sequenced a photoreceptor gene (le.phra) from the basidiomycete lentinula edodes. the product of le.phra, le.phra (924 aa residues) contained a serine-rich region, an lov domain and two pas domains. it was clearly smaller than other fungal lov domain-containing blue-light photoreceptors such as coprinopsis cinerea dst1 (1,175 aa), neurospora crassa wc-1 (1,167 aa), and cryptococcus neoformans wc-1 (1,141 aa). the le.phra gene was found to be transcribed at all stages of the fruitin ...200717827679
the effect of ph on the availability of p-aminobenzoic acid to neurospora crassa. 194417844552
comparison of protein coding gene contents of the fungal phyla pezizomycotina and saccharomycotina.several dozen fungi encompassing traditional model organisms, industrial production organisms and human and plant pathogens have been sequenced recently and their particular genomic features analysed in detail. in addition comparative genomics has been used to analyse specific sub groups of fungi. notably, analysis of the phylum saccharomycotina has revealed major events of evolution such as the recent genome duplication and subsequent gene loss. however, little has been done to gain a comprehen ...200717868481
supramolecular organization of the respiratory chain in neurospora crassa mitochondria.the existence of specific respiratory supercomplexes in mitochondria of most organisms has gained much momentum. however, its functional significance is still poorly understood. the availability of many deletion mutants in complex i (nadh:ubiquinone oxidoreductase) of neurospora crassa, distinctly affected in the assembly process, offers unique opportunities to analyze the biogenesis of respiratory supercomplexes. herein, we describe the role of complex i in assembly of respiratory complexes and ...200717873079
involvement of os-2 map kinase in regulation of the large-subunit catalases cat-1 and cat-3 in neurospora crassa.neurospora crassa has four catalase genes--cat-1, cat-2, cat-3, and ctt-1/cat-4. cat-1 and cat-3 encode two fungal-specific large-subunit catalases cat-1 and cat-3 normally produced in conidia and growing hyphae, respectively. cat-2 encodes cat-2 catalase-peroxidase normally produced in conidia. ctt-1 (or cat-4), of which expression was controlled by os-2 map kinase (noguchi et al., fungal genet. biol. 44, 208-218), encodes a small-subunit catalase with unknown function. to clarify the contribut ...200717895581
ionic currents and ion fluxes in neurospora crassa hyphae.voltage dependence of ionic currents and ion fluxes in a walled, turgor-regulating cell were measured in neurospora crassa. the hyphal morphology of the model organism neurospora simplifies cable analysis of ionic currents to determine current density for quantitative comparisons with ion fluxes. the ion fluxes were measured directly and non-invasively with self-referencing ion-selective microelectrodes. four ions (h(+), ca(2+), k(+), and cl(-)) were examined. h(+) net uptake and ca(2+) net rele ...200717898420
the transcription of the gene for iso-orotate decarboxylase (idcase), an enzyme of the thymidine salvage pathway, is downregulated in the pregc mutant strain of neurospora crassa grown under phosphate starvation.the preg gene encodes a cyclin-like protein that is implicated in the derepression of nucleases and phosphatases that scavenge phosphate from the environment. to better understand the regulatory role of the preg gene product, the differential display reverse transcriptase - polymerase chain reaction was used to isolate transcripts differentially expressed in the pregc mutant strain of the mold neurospora crassa grown under phosphate starvation, at ph 7.8. two transcripts, whose differential expr ...200717898858
systems biology of the neurospora biological clock.a major challenge of systems biology is explaining complex traits, such as the biological clock, in terms of the kinetics of macromolecules. the clock poses at least four challenges for systems biology: (i) identifying the genetic network to explain the clock mechanism quantitatively; (ii) specifying the clock's functional connection to a thousand or more genes and their products in the genome; (iii) explaining the clock's response to light and other environmental cues; and (iv) explaining how t ...200717907673
the use of fungal in vitro systems for studying translational regulation.the use of cell-free systems enables biochemical determination of factors and mechanisms contributing to translational processes. the preparation and use of cell-free translation systems from the fungi saccharomyces cerevisiae and neurospora crassa are described. examples provided illustrate the use of these systems, in conjunction with luciferase assays, [(35)s]met incorporation, and primer-extension inhibition (toeprint) analyses, to assess the translational effects of upstream open reading fr ...200717913625
identification and characterization of amidase- homologous ami1 genes of bottom-fermenting yeast.it has been proposed that a bottom-fermenting yeast strain of saccharomyces pastorianus is a natural hybrid between s. cerevisiae and s. bayanus and possesses at least two types of genome. in the process of conducting expressed sequence tag (est) analysis, we isolated bottom-fermenting yeast-specific (bfy) genes that have no significant homology with sequences in the s288c database. one of the bfy genes, ami1, encodes a protein with homology to an amidase conserved among plants, bacillus subtili ...200717924455
meiosis and ascospore development in cochliobolus heterostrophus.cochliobolus heterostrophus produces eight filiform ascospores per ascus, following meiosis and a postmeiotic mitosis. early ascus development and nuclear divisions in c. heterostrophus resemble those of the prototypic pyrenomycete neurospora crassa. however, the two fungi differ in several important details owing to differences in ascus and ascospore shape, spindle pole body (spb) behavior during spore delimitation, and ascospore development. in c. heterostrophus, the two spindles at meiosis ii ...200817931917
studies on fungal pumilio gene family through mining multiple genome-scale data sets.the genes belonging to pumilio gene family of the fission yeast schizosaccharomyces pombe (s. pombe) were compared with genome information of the several fungi and their functions have been inferred using public-access databases disclosed on the internet websites. the pumilio-family genes are conserved from yeast to man and have been considered to suppress the expression of other genes by binding their specific target messenger rnas. in s. pombe genome, nine genes belonging to pumilio gene famil ...200717932456
cloning, characterization, and mutational analysis of a highly active and stable l-arabinitol 4-dehydrogenase from neurospora crassa.an nad(+)-dependent l-arabinitol 4-dehydrogenase (lad, ec 1.1.1.12) from neurospora crassa was cloned and expressed in escherichia coli and purified to homogeneity. the enzyme was a homotetramer and contained two zn(2+) ions per subunit, displaying similar characteristics to medium-chain sorbitol dehydrogenases (sdhs). high enzymatic activity was observed for substrates l-arabinitol, adonitol, and xylitol and no activity for d-mannitol, d-arabinitol, or d-sorbitol. the enzyme showed strong prefe ...200717938906
quantitative trait loci for the circadian clock in neurospora crassa.neurospora crassa has been a model organism for the study of circadian clocks for the past four decades. among natural accessions of neurospora crassa, there is significant variation in clock phenotypes. in an attempt to investigate natural allelic variants contributing to quantitative variation, we used a quantitative trait loci mapping approach to analyze three independent mapping populations whose progenitors were collected from geographically isolated locations. two circadian clock phenotype ...200717947430
the mitochondrial machinery for import of precursor proteins.mitochondria contain a small genome that codes for approx 1% of the total number of proteins that reside in the mitochondria. hence, most mitochondrial proteins are encoded for by the nuclear genome. after transcription in the nucleus these proteins are synthesized by cytosolic ribosomes. like proteins destined for other organellar compartments, mitochondrially destined proteins possess targeting signals within their primary or secondary structure that direct them to the organelle with the assis ...200717951683
protein targeting to mitochondria of saccharomyces cerevisiae and neurospora crassa: in vitro and in vivo studies.most studies on the biogenesis of mitochondrial proteins have been carried out using fungal mitochondria as a model system. in particular, baker's yeast, saccharomyces cerevisiae, combines several experimental advantages, allowing both genetic and biochemical approaches and thus a combination of investigations in vivo and in vitro. however, the red bread mold neurospora crassa has also been an important research tool. isolated mitochondria can be used from both organisms for import experiments i ...200717951686
circadian rhythm in the pink-orange bread mould neurospora crassa: for what? 200717954967
simulating dark expressions and interactions of frq and wc-1 in the neurospora circadian clock.circadian rhythms are considered to play an essential part in the adaptation of organisms to their environments. the occurrence of circadian oscillations appears to be based on the presence of transcriptional-translational negative feedback loops. in neurospora crassa, the protein frequency (frq) is part of such a negative feedback loop apparently by a direct interaction with its transcription factor white collar-1 (wc-1). based on the observation that nuclear frq levels are significantly lower ...200817965132
metabolism of androst-4-en-3,17-dione by the filamentous fungus neurospora crassa.microbial transformation of androst-4-en-3,17-dione (ad; i) using neurospora crassa afforded six metabolites; 6beta,14alpha-dihydroxyandrost-4-en-3,17-dione (ii), 6beta,9alpha-dihydroxyandrost-4-en-3,17-dione (iii), 7alpha-hydroxyandrost-4-en-3,17-dione (iv), 9alpha-hydroxyandrost-4-en-3,17-dione (v), 14alpha-hydroxyandrost-4-en-3,17-dione (vi), and androst-4,6-dien-3,17-dione (vii). the steroid products were assigned by interpretation of their spectral data such as (1)h nmr, (13)c nmr, ftir, an ...200817981313
the neurospora crassa uvs-3 epistasis group encodes homologues of the atr/atrip checkpoint control system.the mutagen sensitive uvs-3 and mus-9 mutants of neurospora show mutagen and hydroxyurea sensitivity, mutator effects and duplication instability typical of recombination repair and dna damage checkpoint defective mutants. to determine the nature of these genes we used cosmids from a genomic library to clone the uvs-3 gene by complementation for mms sensitivity. mutation induction by transposon insertion and rip defined the coding sequence. rflp analysis confirmed that this sequence maps in the ...200817983847
circadian rhythmicity mediated by temporal regulation of the activity of p38 mapk.circadian clocks are composed of central oscillators, input pathways that transduce external information to the oscillators, and output pathways that allow the oscillators to temporally regulate cellular processes. little is known about the output pathways. in this study, we show that the neurospora crassa osmosensing mapk pathway, essential for osmotic stress responses, is a circadian output pathway that regulates daily rhythms in the expression of downstream genes. rhythmic activation of the h ...200717984065
os-2 mitogen activated protein kinase regulates the clock-controlled gene ccg-1 in neurospora crassa.os-2 map kinase is involved in osmoadaptation in neurospora crassa. clock-controlled genes ccg-1, bli-3, and con-10 were induced by osmotic stress in an os-2 dependent manner. in contrast, osmotic stress did not affect the expression of clock genes frq, wc-1, and wc-2 or of clock-controlled genes ccg-2 and bli-4. these results suggest that os-2 participates in the regulation of certain circadian-clock output genes.200717986782
crystal structure of human mitochondrial tyrosyl-trna synthetase reveals common and idiosyncratic features.we report the structure of a strictly mitochondrial human synthetase, namely tyrosyl-trna synthetase (mt-tyrrs), in complex with an adenylate analog at 2.2 a resolution. the structure is that of an active enzyme deprived of the c-terminal s4-like domain and resembles eubacterial tyrrss with a canonical tyrosine-binding pocket and adenylate-binding residues typical of class i synthetases. two bulges at the enzyme surface, not seen in eubacterial tyrrss, correspond to conserved sequences in mt-tyr ...200717997975
evidence for the absence of meiotic silencing by unpaired dna in neurospora tetrasperma.meiotic silencing by unpaired dna is a posttranscriptional gene silencing process in neurospora crassa. any gene without a homolog in the same chromosomal position during meiotic prophase generates a sequence-specific signal that prevents expression of all copies of that gene, but only during meiosis. meiotic silencing is epigenetic and involves components of a meiosis-specific rna silencing machinery. although n. tetrasperma is closely related to n. crassa, its sexual biology is significantly d ...200818023372
the evolution of the pheromonal signal system and its potential role for reproductive isolation in heterothallic neurospora.comparative sequencing studies among a wide range of taxonomic groups, including fungi, provide the overall pattern that reproductive genes evolve more rapidly than other genes, and this divergence is believed to be important in the establishment of reproductive barriers between species. in this study, we investigated the molecular evolution of the pheromone receptor genes pre-1 and pre-2 of strains belonging to 12 and 13 heterothallic taxa, respectively, of the model genus neurospora. furthermo ...200818024989
improved protocols for functional analysis in the pathogenic fungus aspergillus flavus.an available whole genome sequence for aspergillus flavus provides the opportunity to characterize factors involved in pathogenicity and to elucidate the regulatory networks involved in aflatoxin biosynthesis. functional analysis of genes within the genome is greatly facilitated by the ability to disrupt or mis-express target genes and then evaluate their result on the phenotype of the fungus. large-scale functional analysis requires an efficient genetic transformation system and the ability to ...200718039373
vegetative hyphal fusion is not essential for plant infection by fusarium oxysporum.vegetative hyphal fusion (vhf) is a ubiquitous phenomenon in filamentous fungi whose biological role is poorly understood. in neurospora crassa, the mitogen-activated protein kinase (mapk) mak-2 and the ww domain protein so are required for efficient vhf. a mapk orthologous to mak-2, fmk1, was previously shown to be essential for root penetration and pathogenicity of the vascular wilt fungus fusarium oxysporum. here we took a genetic approach to test two hypotheses, that (i) vhf and plant infect ...200818039941
titration of repeat-induced point mutation (rip) by chromosome segment duplications in neurospora crassa.repeat-induced point mutation (rip) is a hypermutational process that alters duplicated dna sequences in neurospora crassa. in previous studies, five of six large ( > 100 kb) chromosome segment duplications (dp's) examined were shown to dominantly suppress rip in smaller (< 5 kb) duplications. the suppressor duplications were > 270 kb, whereas the lone non-suppressor duplication was approximately 117 kb. we have now screened another 33 duplications and found 29 more suppressors and four more non ...200818046508
the rna-dependent rna polymerase essential for post-transcriptional gene silencing in neurospora crassa interacts with replication protein a.post-transcriptional gene silencing (ptgs) pathways play a role in genome defence and have been extensively studied, yet how repetitive elements in the genome are identified is still unclear. it has been suggested that they may produce aberrant transcripts (arna) that are converted by an rna-dependent rna polymerase (rdrp) into double-stranded rna (dsrna), the essential intermediate of ptgs. however, how rdrp enzymes recognize aberrant transcripts remains a key question. here we show that in neu ...200818048414
alternative modes of binding by u2af65 at the polypyrimidine tract.during initial recognition of an intron in pre-mrna, the 3' end of the intron is bound by essential splicing factors. notably, the consensus rna sequences bound by these proteins are highly degenerate in humans. this raises the question of 3' splicing factor function in introns lacking canonical binding sites. investigating the introns of the model organism neurospora crassa revealed a different organization at the 3' end of the intron compared to most eukaryotic organisms. the predicted branch ...200818067274
microtubule dynamics and the role of molecular motors in neurospora crassa.live-cell imaging methods were used to study microtubule dynamics in the apical regions of leading hyphae and germ tubes of neurospora crassa expressing beta-tubulin-gfp. microtubule polymerization rates in hyphae of n. crassa were much faster than those previously reported in any other eukaryotic organism. in order to address the roles of motor proteins in microtubule dynamic instability in n. crassa, the microtubule-motor mutant strains, deltankin and ro-1, were examined. polymerization and de ...200818069024
continuous enzymatic assay for histone lysine methyltransferases.we describe a continuous peptide methylation assay using the neurospora crassa dim-5 histone h3 lysine 9 (h3k9) methyltransferase as a model system. the assay uses streptavidin flashplates coated with target peptide. since no washing and pipeting steps were required after the addition of the enzyme/s-adenosyl-l-methionine (adomet) mixture to the microplate, a continuous readout of the reaction progress was possible. we show that this assay is highly reproducible (with errors in the order of +/- ...200718072589
two zinc-cluster transcription factors control induction of alternative oxidase in neurospora crassa.the alternative oxidase transfers electrons from ubiquinol to molecular oxygen, providing a mechanism for bypassing the later steps of the standard cytochrome-mediated electron transport chain. the enzyme is found in an array of organisms and in many cases is known to be produced in response to perturbations of the standard chain. alternative oxidase is encoded in the nucleus but functions in the inner mitochondrial membrane. this implies the existence of a retrograde regulation pathway for comm ...200718073419
conidiation rhythm and light entrainment in superoxide dismutase mutant in neurospora crassa.conidial formation in the filamentous fungus neurospora crassa is regulated by nutritional conditions, light, and the circadian clock. we found that a sod-1 mutant, with a defective superoxide dismutase catalyzing the conversion of superoxide to hydrogen peroxide, had a slightly shorter period length than the wild type and clear conidial banding similar to a mutant of band (bd). however, unlike the bd mutant, the sod-1 mutant could sustain conidial banding with light pulses on a nutrient-rich me ...200818084778
function of the c-terminal domain of the dead-box protein mss116p analyzed in vivo and in vitro.the dead-box proteins cyt-19 in neurospora crassa and mss116p in saccharomyces cerevisiae are general rna chaperones that function in splicing mitochondrial group i and group ii introns and in translational activation. both proteins consist of a conserved atp-dependent rna helicase core region linked to n and c-terminal domains, the latter with a basic tail similar to many other dead-box proteins. in cyt-19, this basic tail was shown to contribute to non-specific rna binding that helps tether th ...200818096186
the genetics of threonine requiring mutants of neurospora crassa. 194818100320
oleic acid interference in the neurospora crassa assay for biotin. 194918119218
the use of neurospora crassa, mutant 9185, for the assay of aneurine. 194818121875
the occurrence of ergosterol in neurospora crassa. 194918135762
large-scale expressed sequence tag analysis for the chestnut blight fungus cryphonectria parasitica.cryphonectria parasitica is the causal fungal agent responsible for the chestnut blight disease. we report the generation of 14,263 expressed sequence tags representing 6318 unisequences for the fungus. functional annotation of these unisequences revealed different gene expression patterns for wild-type and hypovirus-infected cultures at the sporulation stage and allowed the reconstruction of key c. parasitica signal transduction pathways conserved in the sorbidaryomycetes. a list of homologous ...200818166491
structure of a tyrosyl-trna synthetase splicing factor bound to a group i intron rna.the 'rna world' hypothesis holds that during evolution the structural and enzymatic functions initially served by rna were assumed by proteins, leading to the latter's domination of biological catalysis. this progression can still be seen in modern biology, where ribozymes, such as the ribosome and rnase p, have evolved into protein-dependent rna catalysts ('rnpzymes'). similarly, group i introns use rna-catalysed splicing reactions, but many function as rnpzymes bound to proteins that stabilize ...200818172503
cloning and characterization of the blr2, the homologue of the blue-light regulator of neurospora crassa wc-2, in the phytopathogenic fungus bipolaris oryzae.bipolaris oryzae is a filamentous ascomycetous fungus that causes brown leaf spot disease in rice. we isolated and characterized blr2, a gene that encodes a putative blue-light regulator similar to neurospora crassa white collar-2 (wc-2). the deduced amino acid sequence of the blr2 showed significant homology to other fungal blue-light regulator proteins in the per-arnt-sim (pas) protein-protein interaction domain, nuclear localization signal, and gata zinc finger dna-binding domains. the blr2-s ...200818172720
functional characterization of fusarium verticillioides cpp1, a gene encoding a putative protein phosphatase 2a catalytic subunit.fusarium verticillioides produces the mycotoxin fumonisin b(1) (fb(1)) on maize kernels. in this study, we identified a putative protein phosphatase gene cpp1 in f. verticillioides, and investigated its role in fb(1) regulation. previous work has shown that cpp1 expression is elevated in an fb(1)-suppressing genetic background. thus, we hypothesized that cpp1 is negatively associated with fb(1) production. to test this hypothesis, we generated a cpp1 knockout mutant, pp179, and studied the effec ...200818174151
hydrolysis and fermentation of brewer's spent grain by neurospora crassa.in this study, the ethanol production by the mesophilic fungus neurospora crassa from bg was studied and optimized concerning the induction of lignocellulose degrading enzymes and the production phase as well. the production of cellulolytic and hemicellulolytic enzymes was studied under solid-state cultivation (ssc). ssc in a laboratory horizontal bioreactor using the optimized medium, ws and bg in the ratio 1:1 and initial moisture level 61.5%, allowed the large scale production of the multienz ...200818178432
protein kinases fpk1p and fpk2p are novel regulators of phospholipid asymmetry.type 4 p-type atpases (flippases) are implicated in the generation of phospholipid asymmetry in membranes by the inward translocation of phospholipids. in budding yeast, the drs2/dnf family members lem3p-dnf1p/dnf2p and cdc50p-drs2p are putative flippases that are localized, respectively, to the plasma membrane and endosomal/trans-golgi network (tgn) compartments. herein, we identified a protein kinase gene, fpk1, as a mutation that exhibited synthetic lethality with the cdc50delta mutation. the ...200818199685
a genetic selection for neurospora crassa mutants altered in their light regulation of transcription.transcription of the neurospora crassa gene con-10 is induced during conidiation and following exposure of vegetative mycelia to light, but light activation is transient due to photoadaptation. we describe mutational analyses of photoadaptation using a n. crassa strain bearing a translational fusion of con-10, including its regulatory region, to a selectable bacterial gene conferring hygromycin resistance (hph). growth of this strain was sensitive to hygromycin, upon continuous culture in the li ...200818202366
characterization of interactions between and among components of the meiotic silencing by unpaired dna machinery in neurospora crassa using bimolecular fluorescence complementation.bimolecular fluorescence complementation (bifc) is based on the complementation between two nonfluorescent fragments of the yellow fluorescent protein (yfp) when they are united by interactions between proteins covalently linked to them. we have successfully applied bifc in neurospora crassa using two genes involved in meiotic silencing by unpaired dna (msud) and observed macromolecular complex formation involving only sad-1 proteins, only sad-2 proteins, and mixtures of sad-1 and sad-2 proteins ...200818202398
the white collar protein wcoa of fusarium fujikuroi is not essential for photocarotenogenesis, but is involved in the regulation of secondary metabolism and conidiation.the fungal proteins of the white collar photoreceptor family, represented by wc-1 from neurospora crassa, mediate the control by light of different biochemical and developmental processes, such as carotenogenesis or sporulation. carotenoid biosynthesis is induced by light in the gibberellin-producing fungus fusarium fujikuroi. in an attempt to identify the photoreceptor for this response, we cloned the only wc-1-like gene present in the available fusarium genomes, that we called wcoa. the predic ...200818203635
x-ray structure and microtubule interaction of the motor domain of neurospora crassa nckin3, a kinesin with unusual processivity.neurospora crassa kinesin nckin3 belongs to a unique fungal-specific subgroup of small kinesin-3-related motor proteins. one of its functions appears to be the transport of mitochondria along microtubules. here, we present the x-ray structure of a c-terminally truncated monomeric construct of nckin3 comprising the motor domain and the neck linker, and a 3-d image reconstruction of this motor domain bound to microtubules, by cryoelectron microscopy. the protein contains mg.adp bound to the active ...200818205396
simple sequence repeats in neurospora crassa: distribution, polymorphism and evolutionary inference.simple sequence repeats (ssrs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. the eukaryotic model organism neurospora crassa is an excellent system to study evolution and biological function of ssrs.200818215294
making two organelles from one: woronin body biogenesis by peroxisomal protein sorting.woronin bodies (wbs) are dense-core organelles that are found exclusively in filamentous fungi and that seal the septal pore in response to wounding. these organelles consist of a membrane-bound protein matrix comprised of the hex protein and, although they form from peroxisomes, their biogenesis is poorly understood. in neurospora crassa, we identify woronin sorting complex (wsc), a pmp22/mpv17-related membrane protein with dual functions in wb biogenesis. wsc localizes to large peroxisome memb ...200818227279
isolation and transcript analysis of two-component histidine kinase gene le.nik1 in shiitake mushroom, lentinula edodes.le.nik1, a two-component histidine kinase gene of lentinula edodes, the shiitake mushroom, was identified. the relationship between this two-component signal transduction system and mushroom development was studied. we used a modified rna arbitrarily-primed pcr (rap-pcr) method to isolate le.nik1 as a differentially expressed gene during l. edodes development. we determined the 6.29kb full-length cdna sequence of le.nik1. it had high sequence homology to neurospora crassa nik1, which encoded a h ...200818234485
characterization of mutations in alhk1 gene from alternaria longipes: implication of limited function of two-component histidine kinase on conferring dicarboximide resistance.four series (s, m, r, and w) of alternaria longipes isolates were obtained based on consecutive induction with dimethachlon (dim) and ultraviolet irradiation. these isolates were then characterized according to their tolerance to dim, sensitivity to osmotic stress, and phenotypic properties. all the induced dim-resistant isolates showed a higher osmosensitivity than the parental strains, and the last generation was more resistant than the first generation in the m, r, and w series. in addition, ...200818239410
dominant suppression of repeat-induced point mutation in neurospora crassa by a variant catalytic subunit of dna polymerase zeta.crosses involving the adiopodoumé strain of neurospora crassa are defective for repeat-induced point mutation (rip), a genome defense mechanism of fungi. we show here that the adiopodoumé strain possesses an incompletely penetrant and variably expressive dominant suppressor of rip (srp) that maps to an approximately 34-kbp genome segment that is approximately 26 kbp proximal to mat on linkage group il. gene disruption experiments revealed that srp is the upr-1 allele of adiopodoumé (upr-1(ad)) t ...200818245848
genetic and molecular analysis of the temperature-sensitive mutant un-17 carrying a mutation in the gene encoding poly(a)-polymerase in neurospora crassa.the un-17 mutant was originally isolated as an irreparable temperature-sensitive (ts) mutant in neurospora crassa. early experiments showed that cells of this mutant immediately stopped growing and died when the temperature of the culture was shifted from a permissive temperature (25 degrees c) to non-permissive temperature (35 degrees c). this ts phenotype is suppressed by addition of cycloheximide or in some conditions of growth repression. even at the permissive temperature, it shows a female ...200718270435
isoform switching facilitates period control in the neurospora crassa circadian clock.a striking and defining feature of circadian clocks is the small variation in period over a physiological range of temperatures. this is referred to as temperature compensation, although recent work has suggested that the variation observed is a specific, adaptive control of period. moreover, given that many biological rate constants have a q(10) of around 2, it is remarkable that such clocks remain rhythmic under significant temperature changes. we introduce a new mathematical model for the neu ...200818277380
replacement of two invariant serine residues in chorismate synthase provides evidence that a proton relay system is essential for intermediate formation and catalytic activity.chorismate synthase is the last enzyme of the common shikimate pathway, which catalyzes the anti-1,4-elimination of the 3-phosphate group and the c-(6pror) hydrogen from 5-enolpyruvylshikimate 3-phosphate (epsp) to generate chorismate, a precursor for the biosynthesis of aromatic compounds. enzyme activity relies on reduced fmn, which is thought to donate an electron transiently to the substrate, facilitating c(3)-o bond breakage. the crystal structure of the enzyme with bound epsp and the flavi ...200818279385
functional and physical interaction of blue- and red-light sensors in aspergillus nidulans.light sensing is very important for organisms in all biological kingdoms to adapt to changing environmental conditions. it was discovered recently that plant-like phytochrome is involved in light sensing in the filamentous fungus aspergillus nidulans[1]. here, we show that phytochrome (fpha) is part of a protein complex containing lrea (wc-1) and lreb (wc-2) [2, 3], two central components of the neurospora crassa blue-light-sensing system. we found that fpha represses sexual development and myco ...200818291652
phenotype of a mechanosensitive channel mutant, mid-1, in a filamentous fungus, neurospora crassa.in the yeast saccharomyces cerevisiae, the mid1 (mating-induced death) gene encodes a stretch-activated channel which is required for successful mating; the mutant phenotype is rescued by elevated extracellular calcium. homologs of the mid1 gene are found in fungi that are morphologically complex compared to yeast, both basidiomycetes and ascomycetes. we explored the phenotype of a mid-1 knockout mutant in the filamentous ascomycete neurospora crassa. the mutant exhibits lower growth vigor than ...200818296620
interlocked feedback loops of the circadian clock of neurospora crassa.circadian clocks drive daily rhythms in physiology and behaviour, and thus allow organisms to better adapt to rhythmic changes in the environment. circadian oscillators are cell-autonomous systems, which generate via transcriptional, post-transcriptional, translational and post-translational control mechanisms a daily activity-rhythm of a circadian transcription factor complex. according to recent models, this complex of transcription factors controls directly or indirectly expression of a large ...200818312266
neurospora crassa as a model organism for mitochondrial biogenesis.neurospora crassa has proven to be an excellent organism for studying various aspects of the biology of mitochondria by biochemical and genetic approaches. as n. crassa is an obligate aerobe and contains complex i, its mitochondria are more similar to mammalian mitochondria than those of yeast. the recent sequencing of the genome of n. crassa and a gene knockout project that is under way make the organism even more attractive. we describe some of the advantages of n. crassa as a model organism a ...200718314721
[homology-dependent inactivation of ltr retrotransposons in genomes of aspergillus fumigatus and a. nidulans].repeat-induced point mutation (rip) is the most intriguing among the known mechanisms of repeated sequences inactivation because of its ability to produce irreversible mutation of repeated dna. discovered for the first time in neurospora crassa, rip is characterized by c:g to t:a transitions in duplicated sequences. the mechanisms and distribution of rip are still purely investigated. mobile elements are a common target for the processes which lead to homology-dependent silencing because of thei ...200718318114
likelihood of a particular order of genetic markers and the construction of genetic maps.we model the recombination process of fungal systems via chromatid exchange in meiosis, which accounts for any type of bivalent configuration in a genetic interval in any specified order of genetic markers, for both random spore and tetrad data. first, a probability model framework is developed for two genes and then generalized for an arbitrary number of genes. maximum likelihood estimators (mles) for both random and tetrad data are developed. it is shown that the mle of recombination for tetra ...200818324750
repeat induced point mutation in two asexual fungi, aspergillus niger and penicillium chrysogenum.repeat induced point mutation (rip) is a gene silencing mechanism present in fungal genomes. during rip, duplicated sequences are efficiently and irreversibly mutated by transitions from c:g to t:a. for the first time, we have identified traces of rip in transposable elements of aspergillus niger and penicillium chrysogenum, two biotechnologically relevant fungi. we found that rip in p. chrysogenum has affected a large set of sequences, which also contain other mutations. on the other hand, rip ...200818347798
a novel gene, phca from pseudomonas syringae induces programmed cell death in the filamentous fungus neurospora crassa.the phytopathogen pseudomonas syringae competes with other epiphytic organisms, such as filamentous fungi, for resources. here we characterize a gene in p. syringae pv. syringae b728a and p. syringae pv. tomato dc3000, termed phca, that has homology to a filamentous fungal gene called het-c. phca is conserved in many p. syringae strains, but is absent in one of the major clades, which includes the p. syringae pathovar phaseolicola. in the filamentous fungus neurospora crassa, het-c regulates a c ...200818363647
properties of family 79 beta-glucuronidases that hydrolyze beta-glucuronosyl and 4-o-methyl-beta-glucuronosyl residues of arabinogalactan-protein.the carbohydrate moieties of arabinogalactan-proteins (agps), which are mainly composed of gal, l-ara, glca, and 4-me-glca residues, are essential for the physiological functions of these proteoglycans in higher plants. for this study, we have identified two genes encoding family 79 beta-glucuronidases, designated anglcaase and ncglcaase, in aspergillus niger and neurospora crassa, respectively, based on the amino acid sequence of a native beta-glucuronidase purified from a commercial pectolytic ...200818377882
specificity of commercial anti-spectrin antibody in the study of fungal and oomycete spectrin: cross-reaction with proteins other than spectrin.spectrin was first described in erythrocytes where it forms a filamentous network in the cytoplasmic face of the plasma membrane and participates in the membrane's structural integrity in addition to controlling the lateral mobility of integral membrane proteins. in fungi, spectrin-like proteins have been described in the plasma membrane, concentrated mainly in the region of maximum apical expansion. this localization led to the idea of a spectrin based membrane skeleton in fungi participating i ...200818378170
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