Efficient cloning of genes of Neurospora crassa

An electrophoretic karyotype of Neurospora crassa

A molecular karyotype of Neurospora crassa was obtained by using an alternating-field gel electrophoresis system which employs contour-clamped homogeneous electric fields. The migration of all seven N. crassa chromosomal DNAs was defined, and five of the seven molecules were separated from one another. The estimated sizes of these molecules, based on their migration relative to Schizosaccharomyces pombe chromosomal DNA molecules, are 4 to 12.6 megabases. The seven linkage groups were correlated with specific chromosomal DNA bands by hybridizing transfers of contour-clamped homogeneous electric field gels with radioactive probes specific to each linkage group. The mobilities of minichromosomal DNAs generated from translocation strains were also examined. The methods used for preparation of chromosomal DNA molecules and the conditions for their separation should be applicable to other filamentous fungi.

Molecular cloning and analysis of the regulation of cys-14+, a structural gene of the sulfur regulatory circuit of Neurospora crassa

The cys-14+ gene encodes sulfate permease II, which is primarily expressed in mycelia. cys-14+ is one of a set of sulfur-related structural genes under the control of cys-3+ and scon+, the regulatory genes of the sulfur control circuit. We have cloned cys-14+ from a cosmid library of Neurospora crassa DNA. A restriction fragment length polymorphism analysis showed that this clone maps to the region of chromosome IV corresponding to the cys-14+ locus. Northern blot analyses were used to examine the regulated expression of the cys-14+ gene. In the wild type, a 3-kilobase cys-14+ transcript was highly expressed under sulfur-derepressing conditions but completely absent during sulfur repression. A cys-3 mutant, which cannot synthesize any of the sulfur-controlled enzymes, including sulfate permease II, did not possess any cys-14+ transcript under either condition. A cys-3 temperature-sensitive revertant completely lacked any cys-14+ mRNA at the conditional temperature but expressed the cys-14+ transcript upon derepression at the permissive temperature. Mutation of a second sulfur regulatory gene, scon(c), causes the expression of sulfur-related enzymes in a constitutive fashion; the scon(c) mutant showed a corresponding constitutive expression of cys-14+ mRNA, such that it was present even in cells subjected to sulfur repression conditions. These results show that the cys-14+ gene is regulated through the modulation of message content by the cys-3+ and scon(c) control genes in response to the sulfur levels of the cells.

The structural gene for a phosphorus-repressible phosphate permease in Neurospora crassa can complement a mutation in positive regulatory gene nuc-1

van+, a gene encoding a phosphorus-repressible phosphate permease, was isolated by its ability to complement nuc-1, a positive regulatory locus that normally regulates van+ expression. This was unexpected because the nuc-1 host already contained a resident van+ gene. Plasmids carrying van+ complemented a nuc-2 mutation as well. Probing of RNA from untransformed wild-type (nuc-1+) and constitutive (nuc-1c) strains by van+ probes indicated that levels of the van+ transcript were subject to control by nuc-1+. Probing of the same RNAs with a cosmid clone, containing approximately 15 kilobases of upstream and downstream DNA, revealed no other detectable phosphorus-regulated transcripts within this 40-kilobase region of the chromosome.

Transformation of Neurospora crassa with the trp-1 gene and the effect of host strain upon the fate of the transforming DNA

Neurospora trp-1+ transformants, obtained by transforming a trp-1 inl strain with plasmid DNA containing the wild type trp1+ gene, were characterized by genetic and Southern blot analyses. The transforming trp-1 gene integrated at or near the resident site in all of the trp-1+ transformants obtained with circular DNA or DNA cut within the trp-1 coding region. The frequency of homologous integration decreased substantially when the donor DNA was cleaved outside the trp-1 coding region. The transformants were very stable mitotically and, in general, also showed meiotic stability. Analysis of trp-1+ transformants obtained with another recipient strain, trp-1+ ga-2 aro-9 inl, showed that homologous integration of donor DNA occurred in only 20% of the transformants, whether circular or linear DNA was used. Thus, the host strain employed for transformation appears to be a major factor in determining the fate of transforming DNA. Southern blot analysis of transformants showed that integration of the transforming DNA at the homologous site occurred by double crossover or gene conversion events rather than by insertion of the entire plasmid DNA. Multiple and apparently non functional integration events were observed in some transformants.

Isolation of telomere DNA from Neurospora crassa

The most distal known gene on Neurospora crassa linkage group VR, his-6, was cloned. A genomic walk resulted in isolation of the telomere at VR. It was obtained from a library in which the endmost nucleotides of the chromosome had not been removed by nuclease treatment before being cloned, and mapping indicates that the entire chromosome end has probably been cloned. Sequences homologous to the terminal 2.5 kilobases of DNA from VR from these Oak Ridge N. crassa strains are found at other sites in the genome. To characterize these sites, I crossed an Oak Ridge-derived his-6 strain with a wild-type strain of different genetic background (Mauriceville) and characterized the hybridization patterns seen in the progeny. It appears that the sequences homologous to the VR terminus are found at genetically different sites in the two parental strains, and no hybridization to the VR telomere from Mauriceville was detected. The other genomic copies identified in the Oak Ridge parent were not telomeres. I suggest that any repeating sequence blocks found immediately adjacent to the VR terminus in Oak Ridge strains must be small and that the repeating element identified in that background may be an N. crassa transposable element integrated near the the chromosome end at VR.

Molecular cloning and analysis of the regulation of nit-3, the structural gene for nitrate reductase in Neurospora crassa

The nit-3 gene of Neurospora crassa encodes the enzyme nitrate reductase and is regulated by nitrogen catabolite repression and by specific induction with nitrate. The nit-3 gene was isolated from a cosmid-based genomic library by dual selection for benomyl resistance and for the ability to complement a nit-3 mutant strain using the sibling-selection procedure. The nit-3 gene was subcloned as a 3.8-kilobase DNA fragment from a cosmid that carried an approximately 40-kilobase N. crassa DNA insert. A restriction fragment length polymorphism analysis revealed that the cloned segment displayed tight linkage to two linkage-group-4 markers that flank the genomic location of nit-3. RNA gel blot analyses of RNA from wild-type and various mutant strains were carried out to examine the molecular mechanism for regulation of nit-3 gene expression. The nit-3 gene was transcribed to give a large mRNA of approximately 3.4 kilobases, the expected size to encode nitrate reductase. The nit-3 gene was only expressed in wild-type cells subject to simultaneous nitrogen derepression and nitrate induction. A mutant of nit-2, the major nitrogen regulatory gene of Neurospora, did not have detectable levels of nit-3 gene transcripts under the exact conditions in which these transcripts were highly expressed in wild type. Similarly, a mutant of nit-4, which defines a minor positive-acting nitrogen control gene, failed to express detectable levels of the nit-3 transcript. Nitrate reductase gene expression was partially resistant to nitrogen repression in a mutant of the nmr gene, which appears to be a regulatory gene with a direct role in nitrogen catabolite repression. Results are presented that suggest that the enzyme glutamine synthetase does not serve any regulatory role in controlling nitrate reductase gene expression.

Sequence and centromere proximal location of a transformation enhancing fragment ans1 from Aspergillus nidulans

The Aspergillus nidulans sequence ans1, previously known to enhance transformation frequencies of pyr4-based vectors, was shown to enhance the efficiency of argB and trpC-based vectors. Increased efficiencies could be obtained by constructing vectors containing argB and ans1 or by cotransforming selectable plasmids (containing argB, trpC, or pyr4) with the non-selectable ans1 sequence. The preponderance of evidence suggests that the mechanism of ans1 activity does not involve homologous recombination events, in spite of the presence of multiple regions of homology in the A. nidulans genome. Genetic mapping localized ans1 to the vicinity of the centromere of linkage group I. The nucleotide sequence of a 1.8 Kb functional subclone of ans1 was determined and found to be highly A + T rich (81%).

The isolation of specific genes from the basidiomycete Schizophyllum commune

We have developed a routine way to isolate genes directly from the basidiomycete fungus, Schizophyllum commune. Plasmid DNA from a genomic gene library was used to isolate five specific genes by complementation of Schizophyllum mutations via transformation. The mutant strains were deficient in the ability to synthesize either adenine (ade2 and ade5), uracil (ura1, encoding orotidine-5'-phosphate decarboxylase; OMPdecase), tryptophan (trp1, encoding indole-3-glycerol phosphate synthetase; IGPS) or para aminobenzoic acid (pab1). In each case, Southern analysis revealed that transformation to prototrophy was concomitant with the integration of vector sequence into the genome of the S. commune mutant. Total DNA from transformants was restricted, religated, and used to transform E. coli. Ampicillin resistant plasmids were recovered from E. coli and tested for their ability to transform the corresponding mutant of S. commune. Plasmids complementing the ade2, ade5, pab1, trp1, and ura1 mutations were recovered.

Isolation of telomere DNA from Neurospora crassa

The most distal known gene on Neurospora crassa linkage group VR, his-6, was cloned. A genomic walk resulted in isolation of the telomere at VR. It was obtained from a library in which the endmost nucleotides of the chromosome had not been removed by nuclease treatment before being cloned, and mapping indicates that the entire chromosome end has probably been cloned. Sequences homologous to the terminal 2.5 kilobases of DNA from VR from these Oak Ridge N. crassa strains are found at other sites in the genome. To characterize these sites, I crossed an Oak Ridge-derived his-6 strain with a wild-type strain of different genetic background (Mauriceville) and characterized the hybridization patterns seen in the progeny. It appears that the sequences homologous to the VR terminus are found at genetically different sites in the two parental strains, and no hybridization to the VR telomere from Mauriceville was detected. The other genomic copies identified in the Oak Ridge parent were not telomeres. I suggest that any repeating sequence blocks found immediately adjacent to the VR terminus in Oak Ridge strains must be small and that the repeating element identified in that background may be an N. crassa transposable element integrated near the the chromosome end at VR.

Characterization of nit-2, the major nitrogen regulatory gene of Neurospora crassa

The nit-2 gene is the major nitrogen-regulatory gene of Neurospora crassa, and under conditions of nitrogen limitations, it turns on the expression of various unlinked structural genes which specify nitrogen-catabolic enzymes. The nit-2 gene was subcloned as a 6-kilobase (kb) DNA fragment from a cosmid that carried approximately a 40-kb N. crassa DNA insert. The nit-2 gene was localized in a DNA segment of approximately 3.5 kb and was shown to correspond to a unique DNA sequence located on linkage group 1. Several N. crassa nit-2 transformants were characterized and were found to possess significantly different levels of the regulated enzyme nitrate reductase. Northern blot analysis of RNA from various strains was carried out to determine whether the nit-2 gene was expressed constitutively or was itself subject to regulation. The results revealed that the nit-2 gene is transcribed to give a single large mRNA of approximately 3.5 kb. Expression of the nit-2 gene is regulated such that its transcript is present at a substantially higher level in cells which are limited for nitrogen than in cells growing under nitrogen-repressed conditions. However, the nit-2 gene is not controlled by autogenous regulation. The nit-2 gene was transcribed only at a low level in nmr-1 and in gln-1b, under both nitrogen-repressed and derepressed conditions, suggesting that these unlinked loci may exert a positive regulatory effect on nit-2.

Characterization of nit-2, the major nitrogen regulatory gene of Neurospora crassa

The nit-2 gene is the major nitrogen-regulatory gene of Neurospora crassa, and under conditions of nitrogen limitations, it turns on the expression of various unlinked structural genes which specify nitrogen-catabolic enzymes. The nit-2 gene was subcloned as a 6-kilobase (kb) DNA fragment from a cosmid that carried approximately a 40-kb N. crassa DNA insert. The nit-2 gene was localized in a DNA segment of approximately 3.5 kb and was shown to correspond to a unique DNA sequence located on linkage group 1. Several N. crassa nit-2 transformants were characterized and were found to possess significantly different levels of the regulated enzyme nitrate reductase. Northern blot analysis of RNA from various strains was carried out to determine whether the nit-2 gene was expressed constitutively or was itself subject to regulation. The results revealed that the nit-2 gene is transcribed to give a single large mRNA of approximately 3.5 kb. Expression of the nit-2 gene is regulated such that its transcript is present at a substantially higher level in cells which are limited for nitrogen than in cells growing under nitrogen-repressed conditions. However, the nit-2 gene is not controlled by autogenous regulation. The nit-2 gene was transcribed only at a low level in nmr-1 and in gln-1b, under both nitrogen-repressed and derepressed conditions, suggesting that these unlinked loci may exert a positive regulatory effect on nit-2.

Transformation of Aspergillus niger using the homologous orotidine-5'-phosphate-decarboxylase gene

A homologous transformation system for the filamentous fungus Aspergillus niger has been developed, based on the orotidine-5'-phosphate-decarboxylase gene. A. niger Pyr- mutants have been selected from 5-fluoro-orotic acid resistant mutants. These mutants were found to comprise two complementation groups, pyrA and pyrB. The A. niger OMP-decarboxylase gene was isolated from a gene library by heterologous hybridization with the Neurospora crassa pyr4 gene. The cloned gene is capable to transform A. nidulans pyrG mutants at high frequencies. Transformation of A. niger pyrA mutants occurs with moderate frequencies (about 50 transformants/micrograms DNA) whereas the pyrB mutants cannot be complemented with the cloned OMP-decarboxylase gene. Analysis of the DNA of the A. niger PyrA+ transformants showed that transformation resulted in integration of the vector DNA into the genome by homologous recombination. Both gene replacements and integration of one or more copies of the complete vector have been observed.

Recombinant DNA in filamentous fungi: progress and prospects

Recombinant DNA technology enables the creation of well-defined alterations in the genetic material of an organism. Methods to manipulate recombinant DNA in the filamentous fungi (a group of microorganisms that includes species of academic as well as commercial interest) have recently been developed. This has been the result of adaptation of procedures successfully employed in the manipulation of other microorganisms. There are a number of similarities in the behavior of recombinant DNA in different fungi, but a number of differences have also been observed between the filamentous and the nonfilamentous fungi. Such differences include the ability to identify DNA replication origins and the host range of expression of fungal genes.