A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors

The low rate of homologous recombination exhibited by wild-type strains of filamentous fungi has hindered development of high-throughput gene knockout procedures for this group of organisms. In this study, we describe a method for rapidly creating knockout mutants in which we make use of yeast recombinational cloning, Neurospora mutant strains deficient in nonhomologous end-joining DNA repair, custom-written software tools, and robotics. To illustrate our approach, we have created strains bearing deletions of 103 Neurospora genes encoding transcription factors. Characterization of strains during growth and both asexual and sexual development revealed phenotypes for 43% of the deletion mutants, with more than half of these strains possessing multiple defects. Overall, the methodology, which achieves high-throughput gene disruption at an efficiency >90% in this filamentous fungus, promises to be applicable to other eukaryotic organisms that have a low frequency of homologous recombination.

Spin-labeled Neurospora mitochondria

Spin-label studies were carried out on Neurospora mitochondria under in vivo and in vitro labeling conditions. A long-chained spin-labeled fatty acid was incorporated by Neurospora and was found in mitochondrial phospholipids. The molecular motion at various temperatures was different from that for the same spin label under in vitro labeling conditions. The results for spin-labeled mitochondria were compared with those from isolated lipids and with those from aggregates of spin-labeled fatty acid and isolated bovine serum albumin. These comparisons suggest that the hydrocarbon portions of membranes are relatively fluid and are not extensively restricted in motion by association with proteins.

A study of the kinetics of hyphal extension and branch initiation of fungal mycelia

Growth of Mucor hiemalis, Geotrichum candidum, Aspergillus nidulans, Neurospora crassa and Penicillium chrysogenum was studied by time lapse photography. The total hyphal length of the mycelium of each species increased at an exponential rate; in M. hiemalis exponential growth continued until the mycelium had a total hyphal length in excess of 10 mm. After spore germination there was an initial phase of discontinuous tip production followed by a phase of ‘continuous’ tip production. The hyphal length and number of tips possessed by a mycelium increased exponentially at approximately the same specific growth rate. The amplitude of the oscillations in the length of the hyphal growth unit of a mycelium decreased progressively during mycelial growth and eventually the growth unit attained a more or less constant value. The results support the hypothesis that mycelial growth involves the duplication of a ‘growth unit’ which consists of a tip and a certain mean length of hypha.

Circadian nature of a rhythm expressed by an invertaseless strain of Neurospora crassa

A new strain of Neurospora crassa which exhibits a rhythm of conidiation when growing along an agar surface in a growth tube is described. The rhythm has been shown to be circadian for it meets the following criteria: A) the period under constant environmental conditions in the dark is about 24 hours (22.7 hours at 25 degrees ); B) the period is relatively temperature-independent (Q(10) is between 0.95 and 1.21 for temperature range of 18 to 35 degrees ); C) the rhythm persists in continuous darkness at constant temperature for a minimum of 14 days without damping out; and D) the phase of the rhythm can be shifted by a single brief exposure to light. The sensitivity of this strain to light has been demonstrated further by the entrainment of the rhythm to a period of 24.0 hours using a suitable light-dark regime, and by the inhibition by light of the appearance of a rhythm; i.e., continuous conidiation occurs when the strain is subjected to continuous light. The new strain is compared to 2 other strains of Neurospora which also express a rhythm, patch and clock.

Feedback inhibition of key glycolytic enzymes in liver: action of free fatty acids

Increasing concentrations of sodium octanoate were progressively inhibitory to the activities of glucokinase, hexokinase, phosphofructokinase, and pyruvate kinase. Glucose-6-phosphate and 6-phosphogluconate dehydrogenases were also markedly inhibited. Other enzymes of carbohydrate metabolism such as lactate dehydrogenase, phosphohexose isomerase, and fructose-1,6-diphosphatase were not decreased. Among the key glycolytic enzymes, the inhibition of pyruvate kinase by the fatty acid was most marked. The biological significance of the inhibition of the key glycolytic enzymes is interpreted as a feedback inhibitory mechanism in regulation of fatty acid biosynthesis. The mechanism may function for rapid adaptation by which the organism can use the fatty acid level as a metabolic directional switch in decreasing glycolysis and turning on gluconeogenesis.

A cytoplasmic character in Neurospora crassa. The role of nuclei and mitochondria

Nuclear fractions isolated from mutants of Neurospora produced no effect when microinjected into mutants with complementary biochemical requirements. DNA isolated from the nuclear fractions similarly injected also had no effect. Mitochondrial fractions isolated from an abnormal inositolless strain (abn-1) produced drastic changes in the rate of growth, morphology, reproductive characteristics, and cytochrome spectra of normal inositolless strains when single hyphal compartments were microinjected and isolated, whereas the mitochondrial fractions of the wild type produced no effect. These results provide evidence for the transmission of biochemical and biological characters when mitochondria are transferred to new nucleocytoplasmic environments.

Use of external, biosynthetic, and organellar arginine by Neurospora

The fate of very low amounts of (14)C-arginine derived from the medium or from biosynthesis was studied in Neurospora cells grown in minimal medium. In both cases, the label enters the cytoplasm, where it is very briefly used with high efficiency for protein synthesis without mixing with the bulk of the large, endogenous pool of (12)C-arginine. The soluble (14)C-arginine which is not used for protein synthesis is sequestered in a vesicle with the bulk of the endogenous arginine pool. After this time, it is selectively excluded from use in protein synthesis except by exchange with cytoplasmic arginine. The data suggest that in vivo, the non-organellar cytoplasm contains less than 5% of the soluble, cellular arginine. The cellular organization of Neurospora described here also prevents the catabolism of arginine. Our results are discussed in relation to previous work on amino acid pools of other eukaryotic systems.

Net uptake of potassium in Neurospora. Exchange for sodium and hydrogen ions

Net uptake of potassium by low K, high Na cells of Neurospora at pH 5.8 is accompanied by net extrusion of sodium and hydrogen ions. The amount of potassium taken up by the cells is matched by the sum of sodium and hydrogen ions lost, under a variety of conditions: prolonged preincubation, partial respiratory inhibition (DNP), and lowered [K](o). All three fluxes are exponential with time and obey Michaelis kinetics as functions of [K](o). The V(max) for net potassium uptake, 22.7 mmoles/kg cell water/min, is very close to that for K/K exchange reported previously (20 mmoles/kg cell water/min). However, the apparent K(m) for net potassium uptake, 11.8 mM [K](o), is an order of magnitude larger than the value (1 mM) for K/K exchange. It is suggested that a single transport system handles both net K uptake and K/K exchange, but that the affinity of the external site for potassium is influenced by the species of ion being extruded.

Kinetic characteristics of the two glucose transport systems in Neurospora crassa

Glucose is transported across the cell membrane of Neurospora crassa by two physiologically and kinetically distinct transport systems. System II is repressed by growth of the cells in 0.1 m glucose. System I is synthesized constitutively. The apparent K(m) for glucose uptake by system I and system II are 25 and 0.04 mm, respectively. Both uptake systems are temperature dependent, and are inhibited by NaN(3) and 2,4-dinitrophenol. Glucose uptake by system II was not inhibited by fructose, galactose, or lactose. However, glucose was shown to be a noncompetitive inhibitor of fructose and galactose uptake. The transport rate of [(14)C]3-0-methyl-d-glucose (3-0-MG) was higher in cells preloaded with unlabeled 3-0-MG than in control cells. The rate of entry of labeled 3-0-MG was only slightly inhibited by the presence of NaN(3) in the medium. Further, NaN(3) caused a rapid efflux of accumulated [(14)C]3-0-MG. These data imply that the energetic step in the transport process prevents efflux.

Arginaseless Neurospora: genetics, physiology, and polyamine synthesis

Four arginaseless mutants of Neurospora crassa have been isolated. All carry mutations which lie at a single locus, aga, on linkage group VIIR. A study of aga strains shows the arginase reaction to be the major, perhaps the only, route of arginine consumption in Neurospora other than protein synthesis. Ornithine-delta-transaminase, the second enzyme of the arginine catabolic pathway, is present and normally inducible by arginine in aga strains, and ornithine transcarbamylase, an enzyme of arginine synthesis, also has normal activity. Arginine inhibits the growth of aga strains. The inhibition can be reversed by spermidine, putrescine (1,4-diaminobutane), or ornithine. The results suggest that ornithine is the major source of the putrescine moiety of polyamines in Neurospora, and that putrescine is an essential growth factor for this organism. The inhibition of aga strains by arginine can be attributed to feedback inhibition of ornithine synthesis by arginine, combined with the complete lack of ornithine normally provided by the arginase reaction.

Genetic and metabolic controls for sulfate metabolism in Neurospora crassa: isolation and study of chromate-resistant and sulfate transport-negative mutants

Mutants of Neurospora resistant to chromate were selected and all were found to map at a single genetic locus designated as cys-13. The chromate-resistant mutants grow at a wild-type rate on minimal media but are partially deficient in the transport of inorganic sulfate, especially during the conidial stage. An unlinked mutant, cys-14, is sensitive to chromate but transports sulfate during the mycelial stage at only 25% of the wild-type rate; cys-14 also grows at a fully wild-type rate on minimal media. The double-mutant strain, cys-13;cys-14, cannot utilize inorganic sulfate for growth and completely lacks the capacity to transport this anion. The only biochemical lesion that has been detected for the double-mutant strain is its loss in capacity for sulfate transport. Neurospora appears to possess two distinct sulfate permease species encoded by separate genetic loci. The transport system (permease I) encoded by cys-13 predominates in the conidial stage and is replaced by sulfate permease II, encoded by the cys-14 locus, during outgrowth into the mycelial phase. The relationship of these new mutants to cys-3, a regulatory gene that appears to control their expression, is discussed.

Structure and function of a mating-type gene from the homothallic species Neurospora africana

The homothallic Neurospora species, N. africana, contains sequences that hybridize to the A but not to a mating-type sequences of the heterothallic species N. crassa. In this study, the N. africana mating-type gene, mt A-1, was cloned, sequenced and its function analyzed in N. crassa. Although N. africana does not mate in a heterothallic manner, its mt A-1 gene functions as a mating activator in N. crassa. In addition, the N. africana mt A-1 gene confers mating type-associated vegetative incompatibility in N. crassa. DNA sequence analysis shows that the N. africana mt A-1 open reading frame (ORF) is 93% identical to that of N. crassa mt A-1. The mt A-1 ORF of N. africana contains no stop codons and was detected as a cDNA which is processed in a similar manner to mt A-1 of N. crassa. By DNA blot and orthogonal field agarose gel electrophoretic analysis, it is shown that the composition and location of the mating-type locus and the organization of the mating-type chromosome of N. africana are similar to that of N. crassa.

Tryptophan transport in Neurospora crassa: a tryptophan-binding protein released by cold osmotic shock

Osmotic shock treatment of germinated conidia of Neurospora reduced the capacity for tryptophan transport in these cells approximately 90% without an appreciable loss of cell viability. Tryptophan-binding proteins and alkaline phosphatase were consistently released into the osmotic shock fluid by this treatment. Four lines of evidence suggest that the binding protein may be related to the tryptophan transport system. (i) It appears to be located on or near the cell surface. (ii) a decreased capacity for binding tryptophan was observed in shock fluids from cells repressed for tryptophan uptake; reduced or altered binding capacity was released from a transport-negative mutant. (iii) The specificity of tryptophan binding was similar to that observed in the in vivo transport system. (iv) The dissociation constant for binding, as measured by equilibrium dialysis, was approximately the same as the K(m) for tryptophan transport.

The WW domain protein PRO40 is required for fungal fertility and associates with Woronin bodies

Fruiting body formation in ascomycetes is a highly complex process that is under polygenic control and is a fundamental part of the fungal sexual life cycle. However, the molecular determinants regulating this cellular process are largely unknown. Here we show that the sterile pro40 mutant is defective in a 120-kDa WW domain protein that plays a pivotal role in fruiting body maturation of the homothallic ascomycete Sordaria macrospora. Although WW domains occur in many eukaryotic proteins, homologs of PRO40 are present only in filamentous ascomycetes. Complementation analysis with different pro40 mutant strains, using full-sized or truncated versions of the wild-type pro40 gene, revealed that the C terminus of PRO40 is crucial for restoring the fertile phenotype. Using differential centrifugation and protease protection assays, we determined that a PRO40-FLAG fusion protein is located within organelles. Further microscopic investigations of fusion proteins with DsRed or green fluorescent protein polypeptides showed a colocalization of PRO40 with HEX-1, a Woronin body-specific protein. However, the integrity of Woronin bodies is not affected in mutant strains of S. macrospora and Neurospora crassa, as shown by fluorescence microscopy, sedimentation, and immunoblot analyses. We discuss the function of PRO40 in fruiting body formation.

Polysomes, ribonucleic acid, and protein synthesis during germination of Neurospora crassa conidia

The level of polysomes in ungerminated conidia of Neurospora crassa depends on the method used to collect spores. Spores harvested and exposed to hydration contain 30% of their ribosomes as polysomes, whereas those not exposed to hydration contain only 3% of their ribosomes as polysomes. During the germination process, the percentage of the ribosomes which sediment as polysomes increases rapidly to a level of approximately 75% during the first 15 to 30 min of germination. This rapid increase has been shown to require a carbon source. During the first 30 min of germination, spores synthesize ribosomal ribonucleic acid (RNA) and heterogeneously sedimenting RNA, i.e., presumptive messenger RNA.

Morphology and growth kinetics of hyphae of differentiated and undifferentiated mycelia of Neurospora crassa

A comparison was made of the morphology and growth kinetics of hyphae of differentiated and undifferentiated mycelia of Neurospora crassa. Undifferentiated mycelia were formed during exponential growth on solid media or submerged culture. Hyphae at the margin of differentiated mycelia (colonies) differed from undifferentiated mycelia in diameter, extension rate, extension zone length, and intercalary and apical compartment length. The mean hyphal extension rate (E) of an undifferentiated mycelium was a function of the length of the mycelium's hyphal growth unit (G) and the organism's specific growth rate (alpha). Thus, E=Galpha.

Isolation and classification of extranuclear mutants of Neurospora crassa

Four extranuclear mutants, [exn-1], [exn-2],[exn-4], and [stp-C], were obtained from N-methyl-N'-nitro-N-nitrosoguanidine-treated conidia and mycelium of Neurospora crassa. The three exn mutants grow with a pronounced lag from conidia and ascospores and are female fertile, whereas [stp-C] has a stop-start growth phenotype and is female sterile. The mitochondria from all four mutants are deficient in cytochromes a+a(3) and b, but contain an excess of cytochrome c. On the basis of growth and fertility, nuclear suppressors and complementation in heteroplasmons, 16 of the extranuclear mutants now available in Neurospora can be divided into three groups. Group I consists of 8 female-fertile variants with both poky-like growth and cytochrome defects. Their slow growth is suppressed by the nuclear factor, f, but not by a second nuclear suppressor, su-1([mi-3]). They complement with group III mutants in mixed cytoplasmons. Group II is represented by a single variant, [mi-3]. It is phenotypically modified by the su-1([mi-3]) factor, but not by f. Its unique cytochrome spectrum shows a deficiency of cytochrome a, but c and b are present. It complements in heteroplasmons with group I and III mutants. Group III included 7 female-sterile variants with stopper growth phenotypes and the same cytochrome defects as group I. Group III mutants complement both with group I and II isolates, but they are unaffected by either f or su-1.