Heterologous insertion of transforming DNA and generation of new deletions associated with transformation in Aspergillus nidulans

Current progress in the biology of members of the Sporothrix schenckii complex following the genomic era

Sporotrichosis has been attributed for more than a century to one single etiological agent, Sporothrix schencki. Only eight years ago, it was described that, in fact, the disease is caused by several pathogenic cryptic species. The present review will focus on recent advances to understand the biology and virulence of epidemiologically relevant pathogenic species of the S. schenckii complex. The main subjects covered are the new clinical and epidemiological aspects including diagnostic and therapeutic challenges, the development of molecular tools, the genome database and the perspectives for study of virulence of emerging Sporothrix species.

Genetic manipulation of Aspergillus nidulans: meiotic progeny for genetic analysis and strain construction

The multicellular microbial eukaryote Aspergillus nidulans is an excellent model for the study of a wide array of biological processes. Studies in this system contribute significantly to understanding fundamental biological principles and are relevant for biotechnology and industrial applications, as well as human, animal and plant fungal pathogenesis. A. nidulans is easily manipulated using classical and molecular genetics. Here, we describe the storage and handling of A. nidulans and procedures for genetic crossing, progeny analysis and growth testing. These procedures are used for Mendelian analysis of segregation of alleles to show whether a mutant phenotype segregates as a single gene and independent assortment of genes to determine the linkage relationship between genes. Meiotic crossing is used for construction of multiple mutant strains for genetic analysis. Genetic crossing and analysis of progeny can be undertaken in 2-3 weeks and growth testing takes 2-3 days.

Suppression of tandem-multimer formation during genetic transformation of the mycotoxin-producing fungus Penicillium paxilli by disrupting an orthologue of Aspergillus nidulans uvsC

An orthologue of Aspergillus nidulans uvsC and Saccharomyces cerevisiae RAD51 was cloned from the filamentous fungus, Penicillium paxilli. A mutation in uvsC causes UV sensitivity during germination. The product of RAD51 is involved in meiotic recombination and DNA damage repair. The deduced amino acid sequence of the product of this gene (Pprad51) shared 92% identity with UVSC. Site-specific disruption of pprad51 showed a significant effect for extra-cellular DNA integration. Transformation of the null mutant with pII99, which confers geneticin resistance, resulted in a shift from a predominance of direct repeats at a single site to single copies when compared with a control strain. A copy-number effect of integrated pII99 for geneticin selection was suggested as the frequency of direct repeat formation was less when selected at a lower concentration in the control strain. However, such an effect was not observed in the null mutant, further supporting an involvement of Pprad51 in direct repeat formation.

Regulation of the acuF gene, encoding phosphoenolpyruvate carboxykinase in the filamentous fungus Aspergillus nidulans

Phosphoenolpyruvate carboxykinase (PEPCK) is a key enzyme required for gluconeogenesis when microorganisms grow on carbon sources metabolized via the tricarboxylic acid (TCA) cycle. Aspergillus nidulans acuF mutants isolated by their inability to use acetate as a carbon source specifically lack PEPCK. The acuF gene has been cloned and shown to encode a protein with high similarity to PEPCK from bacteria, plants, and fungi. The regulation of acuF expression has been studied by Northern blotting and by the construction of lacZ fusion reporters. Induction by acetate is abolished in mutants unable to metabolize acetate via the TCA cycle, and induction by amino acids metabolized via 2-oxoglutarate is lost in mutants unable to form 2-oxoglutarate. Induction by acetate and proline is not additive, consistent with a single mechanism of induction. Malate and succinate result in induction, and it is proposed that PEPCK is controlled by a novel mechanism of induction by a TCA cycle intermediate or derivative, thereby allowing gluconeogenesis to occur during growth on any carbon source metabolized via the TCA cycle. It has been shown that the facB gene, which mediates acetate induction of enzymes specifically required for acetate utilization, is not directly involved in PEPCK induction. This is in contrast to Saccharomyces cerevisiae, where Cat8p and Sip4p, homologs of FacB, regulate PEPCK as well as the expression of other genes necessary for growth on nonfermentable carbon sources in response to the carbon source present. This difference in the control of gluconeogenesis reflects the ability of A. nidulans and other filamentous fungi to use a wide variety of carbon sources in comparison with S. cerevisiae. The acuF gene was also found to be subject to activation by the CCAAT binding protein AnCF, a protein homologous to the S. cerevisiae Hap complex and the mammalian NFY complex.

Sequence, exon-intron organization, transcription and mutational analysis of prnA, the gene encoding the transcriptional activator of the prn gene cluster in Aspergillus nidulans

The prnA gene codes for a transcriptional activator that mediates proline induction of four other genes involved in proline utilization as a nitrogen and/or carbon source in Aspergillus nidulans. In this paper, we present the genomic and cDNA sequence and the transcript map of prnA. The PrnA protein belongs to the Zn binuclear cluster family of transcriptional activators. The gene shows a striking intron-exon organization, with the putative nuclear localization sequence and the Zn cluster domain in discrete exons. Although the protein sequence presents some interesting similarities with the isofunctional protein of Saccharomyces cerevisiae Put3p, a higher degree of similarity is found with a functionally unrelated protein Thi1 of Schizosaccharomyces pombe. A number of mutations mapping in the prnA gene were sequenced. This comprises a deletion that results in an almost complete loss of the prnA-specific mRNA, a mutation in the putative nuclear localization signal, a proline to leucine mutation in the second loop of the zinc cluster and a cold-sensitive mutation in the so-called 'central region'. Other complete or partial loss of function mutations map in regions of unknown function. We establish that the transcription of the gene is neither self-regulated nor significantly affected by carbon and/or nitrogen metabolite repression.

Recombinational stability of replicating plasmids in Aspergillus nidulans during transformation, vegetative growth and sexual reproduction

Plasmids containing the AMA1 replicon are capable of autonomous maintenance in Aspergillus nidulans. It has been reported previously that these plasmids can form concatenates by recombination in a transformed mycelium, and up to 10% of molecules are involved in such events. The present study demonstrates that plasmid recombination, although frequent during transformation, rarely occurs during vegetative growth. As a result, the structure and phenotypic stability of AMA1 plasmids generally remains unaltered for many asexual (conidial) generations. It is also evident that plasmid replication does not require specific recombination events in the AMA1 palindrome. However, during sexual reproduction, autonomous plasmids exhibit increased recombination, which results in both plasmid concatenation and integration into the chromosome.

The Thom Award address. Industrial mycology and the new genetics

The genetic investigation of fungi has been extended substantially by DNA-mediated transformation, providing a supplement to more conventional genetic approaches based upon sexual and parasexual processes. Initial transformation studies with the yeast Saccharomyces cerevisiae provided the model for transformation systems in other fungi with regard to methodology, vector construction and selection strategies. There are, however, certain differences between S. cerevisiae and filamentous fungi with regard to type of genomic insertion and the availability of shuttle vectors. Single-site linked insertions are common in yeast due to the high level of homology required for recombination between vectored and genomic sequences, whereas mycelial fungi often show a high frequency of heterologous and unlinked insertions, often in the form of random and multiple-site integrations. While extrachromosomally-maintained or replicative vectors are readily available for use with yeasts, such vectors have been difficult to construct for use with filamentous fungi. The development of vectors for replicative transformation with these fungi awaits further study. It is proposed that replicative vectors may be inherently less efficient for use with mycelial fungi relative to yeasts, since the mycelium, as an extended and semicontinuous network of cells, may delimit an adequate diffusion of the vector carrying the selectable gene, thus leading to a high frequency of abortive or unstable transformants.

Heterologous and homologous plasmid integration at a spore-pigment locus in Penicillium paxilli generates large deletions

Mutations in a spore pigmentation locus (brs; brown spore) in Penicillium paxilli were isolated at a relatively-high frequency (0.17%) following integrative transformation of the hygromycin-resistance plasmid pAN7-1. A molecular analysis of four independently-isolated Brs- mutants showed that all contained pAN7-1 integrated at a single-site that was unique for each mutant. A previously-described Brs- mutant, YI-34 (Itoh et al. 1994), was a two-site integration. Three of the mutants had multiple copies of pAN7-1 arranged in head-to-tail tandem arrays. A 9.6-kb BamHI junction fragment was cloned from one of these, YI-33, by plasmid rescue and used to isolate two overlapping lambda clones, lambda WB33-1 and lambda WB33-2, that span about 30 kb in the region of the wild-type locus. When genomic digests of the five Brs- mutants were probed with these lambda clones all of them were found to contain an extensive deletion through a common region of the P. paxilli genome. Subsequent attempts to generate one-step gene replacements within a 4.5-kb EcoRI fragment at the wild-type locus resulted in the isolation of Brs- mutants at a frequency of 1.6%, but all mutants with this phenotype were also found to contain an extensive genomic deletion. Therefore, a common outcome of both heterologous and homologous plasmid integration at this locus is deletion formation.

Characterisation, cloning and integrative properties of the gene encoding urate oxidase in Aspergillus nidulans

A number of mutations have been obtained which define the structural gene (uaZ) coding for urate oxidase in linkage group I of Aspergillus nidulans. This gene has been cloned by transformation of a uaZ- null mutant. A chromosome I/VIII translocation which splits the gene has been defined both genetically and physically. All known mutations are contained in a 1-kb fragment, itself contained in the probe which recognizes a 1.2-kb inducible message. Plasmids carrying uaZ show a strict bias towards homologous recombination in transformation experiments.

Characterization of the amdA-regulated aciA gene of Aspergillus nidulans

The structure, function and regulation of the acetate inducible aciA gene of Aspergillus nidulans was analysed. The aciA locus was mapped to chromosome 1 at a position where no acetate inducible gene has been previously located. The nucleotide sequence of aciA was determined, the structures of two transcripts were determined and the sequences of the polypeptide products of the gene were deduced. Construction of an aciA loss-of-function mutant was achieved via insertional inactivation, but it did not reveal a phenotype for an aciA- strain. The larger polypeptide, AciA, was found to have a putative dinucleotide cofactor binding site. Acetate inducibility of aciA was found to be dependent on the amdA regulatory gene. Use of a 5' deletion series of an aciA--lacZ fusion and an in vivo regulatory protein binding (titration) assay allowed the region required for amdA activity to be localized to a 124 bp segment 5' to aciA. A 13 bp region of sequence similarity was observed between aciA and the coregulated amdS gene in the regions required for amdA-mediated regulation of these genes. This sequence may have a role in amdA regulation of the two genes.

Expression of a bacterial aspartase gene in Aspergillus nidulans: an efficient system for selecting multicopy transformants

The Escherichia coli aspartase gene aspA has been expressed in the fungus Aspergillus nidulans using the powerful constitutive gpdA promoter and trpC terminator, both from A. nidulans. Multiple, but not single, copies of aspA overcome nutritional deficiencies resulting from the loss of catabolic NAD-linked glutamate dehydrogenase. They also circumvent certain nutritional deficiencies resulting from loss of the positive-acting regulatory gene product mediating nitrogen metabolite repression. Both of these cases of physiological suppression involve the aspartase-catalyzed catabolism of aspartate to ammonium plus fumarate. No physiological evidence for the opposite reaction leading to aspartate synthesis was obtained as multiple copies of aspA did not affect the phenotype resulting from the loss of anabolic NADP-linked glutamate dehydrogenase. The use of vectors containing aspA and recipients lacking NAD-linked glutamate dehydrogenase is an efficient means of selecting multicopy transformants in A. nidulans and also offers the possibility to select strains having increased aspartase levels from original transformants.

Analysis of the site of action of the amdR product for regulation of the amdS gene of Aspergillus nidulans

The amdR gene of Aspergillus nidulans regulates a number of structural genes in response to omega amino acid inducers. The site of action of the amdR product on expression of the amdS gene was investigated by studying the effects of changes in the 5' region of amdS, generated in vitro, on the induction, and on responses of an amdS-lacZ fusion gene to an amdRc allele. A sequence was identified that is sufficient for amdR regulation and that shows identity with sequences involved in amdR regulation of the gatA and lam genes. This sequence includes a CCAAT sequence and it was shown that this sequence is an important element in setting the basal level of amdS expression.

Molecular characterization of the lam locus and sequences involved in regulation by the AmdR protein of Aspergillus nidulans

The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. The lamB gene and the region between the two genes have been sequenced, and the start points of transcription have been determined. Within the lam locus are two sequences with homology to elements, required for AmdR regulation, found in the 5' regions of the coregulated genes amdS and gatA. In vitro and in vivo assays were used to investigate the lam and gatA regulatory elements. One of the three gatA elements and one of the two lam elements were shown to bind AmdR protein in vivo and activate transcription. With a gel shift mobility assay, in vitro binding of AmdR protein to the functional gatA element was detected. Both the functional gatA and lam boxes contain within them a CAAT sequence. In vitro binding analysis indicates that a CCAAT-specific factor(s) binds at these sequences, adjacent to or overlapping the AmdR protein-binding site.

Molecular characterization of the lam locus and sequences involved in regulation by the AmdR protein of Aspergillus nidulans

The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. The lamB gene and the region between the two genes have been sequenced, and the start points of transcription have been determined. Within the lam locus are two sequences with homology to elements, required for AmdR regulation, found in the 5' regions of the coregulated genes amdS and gatA. In vitro and in vivo assays were used to investigate the lam and gatA regulatory elements. One of the three gatA elements and one of the two lam elements were shown to bind AmdR protein in vivo and activate transcription. With a gel shift mobility assay, in vitro binding of AmdR protein to the functional gatA element was detected. Both the functional gatA and lam boxes contain within them a CAAT sequence. In vitro binding analysis indicates that a CCAAT-specific factor(s) binds at these sequences, adjacent to or overlapping the AmdR protein-binding site.

Molecular cloning and functional characterization of the pathway-specific regulatory gene nirA, which controls nitrate assimilation in Aspergillus nidulans

We have cloned an 11-kbp segment of the genomic DNA of Aspergillus nidulans which complements mutations in nirA, the pathway-specific regulatory gene of the nitrate assimilation pathway. Gene disruption in the corresponding region of the nuclear DNA leads to a phenotype and a gene complementation pattern indistinguishable from that observed in known noninducible nirA mutants. Transformation studies with subclones of the 11-kbp genomic segment showed that a nonreverting null mutation nirA87, maps to a 1.5-kbp stretch within that segment. These data confirm that the cloned segment contains the nirA gene. The gene is completely encompassed in the 11-kbp genomic segment, as a plasmid carrying the corresponding insert gives rise to multicopy transformants exhibiting better growth than wild type on nitrate or nitrite as the sole nitrogen source. Southern and genetic analyses of transformants obtained with various plasmid subclones established a gene size of at most 5.9 kbp. Northern (RNA) hybridization experiments revealed a 4-kb nirA transcript which is barely visible in the wild type but clearly seen in a transformant carrying about 10 gene copies. In both strains, nirA mRNA is synthesized constitutively. Upstream of nirA, a neighboring transcript about 2.8 kbp in length which is transcribed from the opposite strand with respect to nirA was localized. The transcript levels of niaD and niiA, encoding the nitrate and nitrite reductase core proteins, respectively, were investigated in nirA mutants and a nirA multicopy transformant. The results show that the nirA product regulates the transcript steady-state level of these structural genes and that it is a limiting factor for their expression.

Molecular cloning and functional characterization of the pathway-specific regulatory gene nirA, which controls nitrate assimilation in Aspergillus nidulans

We have cloned an 11-kbp segment of the genomic DNA of Aspergillus nidulans which complements mutations in nirA, the pathway-specific regulatory gene of the nitrate assimilation pathway. Gene disruption in the corresponding region of the nuclear DNA leads to a phenotype and a gene complementation pattern indistinguishable from that observed in known noninducible nirA mutants. Transformation studies with subclones of the 11-kbp genomic segment showed that a nonreverting null mutation nirA87, maps to a 1.5-kbp stretch within that segment. These data confirm that the cloned segment contains the nirA gene. The gene is completely encompassed in the 11-kbp genomic segment, as a plasmid carrying the corresponding insert gives rise to multicopy transformants exhibiting better growth than wild type on nitrate or nitrite as the sole nitrogen source. Southern and genetic analyses of transformants obtained with various plasmid subclones established a gene size of at most 5.9 kbp. Northern (RNA) hybridization experiments revealed a 4-kb nirA transcript which is barely visible in the wild type but clearly seen in a transformant carrying about 10 gene copies. In both strains, nirA mRNA is synthesized constitutively. Upstream of nirA, a neighboring transcript about 2.8 kbp in length which is transcribed from the opposite strand with respect to nirA was localized. The transcript levels of niaD and niiA, encoding the nitrate and nitrite reductase core proteins, respectively, were investigated in nirA mutants and a nirA multicopy transformant. The results show that the nirA product regulates the transcript steady-state level of these structural genes and that it is a limiting factor for their expression.

Insertional inactivation and cloning of the wA gene of Aspergillus nidulans

We describe examples of wA gene inactivation (resulting in white conidiospores) obtained during transformation of Aspergillus nidulans. One wA- transformant was obtained by transformation with a prn+ plasmid of a strain with green conidia (wA+) which was unable to catabolize L-proline (prn-). This transformant contains a very large number of plasmid copies integrated at a single site inseparable from the wA locus. Passage of this transformant through the sexual cycle generated a variety of novel phenotypes for L-proline utilization, the number and frequency of which depended upon the cleistothecium from which the progeny were obtained, suggesting that the altered phenotypes were due to premeiotic events. The most extreme phenotype was severe hypersensitivity to L-proline. Hypersensitive progeny had a much reduced number of integrated plasmid copies enabling us to identify and clone putative prn-wA fusion sequences and subsequently retrieve wA sequences from a wild-type gene library. One of the wild-type clones overlapped the different sites of the insertional mutations in two wA- transformants and complemented the wA3 allele. Sequences within this clone hybridized to a transcript that was developmentally regulated in the wild type and absent in a number of mutants defective in conidiospore development. A reiterated sequence was also found in the region of the wA gene.

Expression and secretion in Aspergillus nidulans and Aspergillus niger of a cell surface glycoprotein from the cattle tick, Boophilus microplus, by using the fungal amdS promoter system

A cell surface glycoprotein (Bm86) from cells of the digestive tract of the cattle tick Boophilus microplus, which has been shown to elicit a protective immunological response in vaccinated cattle, was expressed and secreted in the filamentous fungi Aspergillus nidulans and Aspergillus niger by using the fungal amdS promoter system. The cloned gene coded for the Bm86 secretory signal and all of the Bm86 mature polypeptide except for the hydrophobic carboxy-terminal segment. High levels of Bm86 mRNA were detected in the transformed cells. Bm86 polypeptide was secreted from the cells in a soluble form and it was glycosylated, probably to a similar extent to the native glycoprotein. The recombinant product had an apparent molecular mass of 83 to 87 kilodaltons, whereas that predicted from the amino acid sequence was 69 kilodaltons. The Bm86 was expressed at levels of up to 1.8 mg/liter, or approximately 6% of secreted protein under the growth conditions used. No intracellular Bm86 was detected. A general relationship was observed between transformants containing a high number of copies of the expression plasmid and high expression levels.

Sequence and functional analysis of the positively acting regulatory gene amdR from Aspergillus nidulans

The positively acting regulatory gene amdR of Aspergillus nidulans coordinately regulates the expression of five structural genes involved in the catabolism of certain amides (amdS), omega amino acids (gatA and gabA), and lactams (lamA and lamB) in the presence of omega amino acid inducers. Analysis of the amdR gene showed that it contains three small introns, heterogeneous 5' and 3' transcription sites, and multiple AUG codons prior to the major AUG initiator. The predicted amdR protein sequence has a cysteine-rich "zinc finger" DNA-binding motif at the amino-terminal end, four putative acidic transcription activation motifs in the carboxyl-terminal half, and two sequences homologous to the simian virus 40 large T antigen nuclear localization motif. These nuclear localization sequences overlap the cysteine-rich DNA-binding motif. A series of 5', 3', and internal deletions were examined in vivo for transcription activator function and showed that the amdR product contains at least two activation regions in the carboxyl-terminal half. Each of these activator amdR product contains at least two activation regions in the carboxyl-terminal half. Each of these activator regions may function independently, but both are required for wild-type levels of transcription activation. A number of the amdR deletion products were found to compete with the wild-type amdR product in vivo. Development of a rapid method for the localization of amdR mutations is presented, and using this technique, we localized and sequenced the mutation in the semiconstitutive amdR6c allele. The amdR6c missense mutation occurs in the middle of the gene, and it is suggested that it results in an altered protein which activates gene expression efficiently in the absence of an inducer.

Sequence and functional analysis of the positively acting regulatory gene amdR from Aspergillus nidulans

The positively acting regulatory gene amdR of Aspergillus nidulans coordinately regulates the expression of five structural genes involved in the catabolism of certain amides (amdS), omega amino acids (gatA and gabA), and lactams (lamA and lamB) in the presence of omega amino acid inducers. Analysis of the amdR gene showed that it contains three small introns, heterogeneous 5' and 3' transcription sites, and multiple AUG codons prior to the major AUG initiator. The predicted amdR protein sequence has a cysteine-rich "zinc finger" DNA-binding motif at the amino-terminal end, four putative acidic transcription activation motifs in the carboxyl-terminal half, and two sequences homologous to the simian virus 40 large T antigen nuclear localization motif. These nuclear localization sequences overlap the cysteine-rich DNA-binding motif. A series of 5', 3', and internal deletions were examined in vivo for transcription activator function and showed that the amdR product contains at least two activation regions in the carboxyl-terminal half. Each of these activator amdR product contains at least two activation regions in the carboxyl-terminal half. Each of these activator regions may function independently, but both are required for wild-type levels of transcription activation. A number of the amdR deletion products were found to compete with the wild-type amdR product in vivo. Development of a rapid method for the localization of amdR mutations is presented, and using this technique, we localized and sequenced the mutation in the semiconstitutive amdR6c allele. The amdR6c missense mutation occurs in the middle of the gene, and it is suggested that it results in an altered protein which activates gene expression efficiently in the absence of an inducer.

Isolation and analysis of the acetate regulatory gene, facB, from Aspergillus nidulans

The facB gene of Aspergillus nidulans is thought to be involved in acetate induction of enzymes required for acetate utilization and of the acetamidase encoded by the multiply regulated amdS gene. In addition, some evidence suggests that the facB gene has a structural as well as a regulatory role in acetate metabolism. The facB gene was cloned from a cosmid library by complementation of the facB101 loss-of-function mutation. Transformants receiving multiple copies of facB displayed stronger growth on acetamide media, indicating increased amdS expression, while growth on acetate was inhibited in these multicopy transformants. A 3.1-kilobase acetate-inducible facB transcript was detected by Northern (RNA) blot analysis. Examination of message levels in wild-type and mutant strains indicated that the facB gene is subject to carbon catabolite repression. Previous work has indicated that the presence of multiple copies of the 5' end of the amdS gene can result in titration of regulatory proteins. Additional copies of the facB gene were shown to specifically overcome the effect of facB product titration.

Isolation and analysis of the acetate regulatory gene, facB, from Aspergillus nidulans

The facB gene of Aspergillus nidulans is thought to be involved in acetate induction of enzymes required for acetate utilization and of the acetamidase encoded by the multiply regulated amdS gene. In addition, some evidence suggests that the facB gene has a structural as well as a regulatory role in acetate metabolism. The facB gene was cloned from a cosmid library by complementation of the facB101 loss-of-function mutation. Transformants receiving multiple copies of facB displayed stronger growth on acetamide media, indicating increased amdS expression, while growth on acetate was inhibited in these multicopy transformants. A 3.1-kilobase acetate-inducible facB transcript was detected by Northern (RNA) blot analysis. Examination of message levels in wild-type and mutant strains indicated that the facB gene is subject to carbon catabolite repression. Previous work has indicated that the presence of multiple copies of the 5' end of the amdS gene can result in titration of regulatory proteins. Additional copies of the facB gene were shown to specifically overcome the effect of facB product titration.

Isolation of the facA (acetyl-coenzyme A synthetase) and acuE (malate synthase) genes of Aspergillus nidulans

Acetate inducible genes of Aspergillus nidulans were cloned via differential hybridization to cDNA probes. Using transformation of mutant strains the genes were identified as facA (acetyl-Coenzyme A synthetase) and acuE (malate synthase). The levels of RNA encoded by these genes were shown to be acetate inducible and subject to carbon catabolite repression. Induction is abolished in a facB mutant and carbon catabolite repression is relieved in a creA mutant.

Characterization of the amdR-controlled lamA and lamB genes of Aspergillus nidulans

Four Aspergillus nidulans genes are known to be under the control of the trans-acting regulatory gene amdR. We describe the isolation and initial characterization of one of these amdR-regulated genes, lamA. The lam locus, however, was found to consist of two divergently transcribed genes, the lamA gene, and a new gene, also under amdR control, which we have designated lamB. Using recombinant DNA techniques we have constructed a strain of A. nidulans lacking a functional lamB gene. Experiments conducted with this strain demonstrate that lamB, like lamA, is involved in utilization of 2-pyrrolidinone in A. nidulans. Metabolism of a related compound, gamma-amino butyric acid (GABA) is not affected. We also provide evidence that the conversion of exogenous 2-pyrrolidinone to endogenous GABA requires a functional lamB gene. The expression of both lamA and lamB is subject to carbon and nitrogen metabolite repression in addition to amdR-mediated induction by omega-amino acids.

The proline transport protein of Aspergillus nidulans is very similar to amino acid transporters of Saccharomyces cerevisiae

In Aspergillus nidulans, the gene prnB encoding the major proline transport system is one of a cluster of four genes necessary and sufficient for the utilization of proline as sole nitrogen and/or carbon source. The prn cluster has been cloned and the sequence and transcript map of the prnB gene are presented in this paper. The predicted translated sequence consists of 570 amino acids, resulting in a molecular weight of 63,028 Daltons. Its hydropathy profile shows 10 hydrophobic segments typical of integral membrane proteins. No N-terminal hydrophobic signal peptide is present, the N-terminal and C-terminal ends of the protein being hydrophilic. Similar results were previously found for the arginine and histidine transporters of Saccharomyces cerevisiae, with which the prnB transporter shares regions of highly conserved amino acid sequences. Using S1 mapping and Northern blot analyses, we confirm the presence of a unique inducible prnB transcript of 1.9 kb.

Cloning and molecular characterisation of the amdR controlled gatA gene of Aspergillus nidulans

The gamma-amino-n-butyrate transaminase gene (gatA) of Aspergillus nidulans is one of several genes under positive control by the regulatory gene amdR (also called intA). The gatA gene has been cloned from a cosmid library by complementation of a gatA mutation. The sequence of a 2.6 kb genomic fragment containing gatA has been determined. An open reading frame of 1497 bp within this sequence is interrupted by three putative introns and predicts a protein of 55 kDa. Northern analysis confirms control of gatA RNA levels by amdR and also indicates that gatA is not strongly regulated by areA-mediated nitrogen metabolite repression. A. nidulans transformants containing multiple copies of a plasmid carrying an 88 bp fragment from the 5' untranscribed region of gatA grew poorly on substrates whose utilisation is dependent on genes controlled by amdR. This indicated titration of limiting amounts of the amdR gene product by this 88 bp fragment. Comparison of this sequence with the 5' region of the coregulated gene, amdS, reveals probable sites of action for the amdR protein.

Premeiotic disruption of duplicated and triplicated copies of the Neurospora crassa am (glutamate dehydrogenase) gene

Premeiotic inactivation of duplicated sequences (the RIP phenomenon of Selker et al.) was studied by tetrad analysis using ectopic copies of am+ (coding for NADP-specific glutamate dehydrogenase) and a missense allele am3, coding for a distinctive form of the enzyme, at the normal locus. In duplication crosses either both gene copies were inactivated or neither. Two inactivated am3 derivatives were shown to have undergone methylation and numerous base-pair changes, reflected in losses and gains of restriction sites, but without sequence rearrangement. Cutting at restriction sites within the disrupted sequences was incomplete but became almost complete following growth in the presence of 5-azacytidine. In a triplication cross in which one parent carried two unlinked ectopic gene copies together with am3 at the normal locus, premeiotic inactivation, when it occurred, tended to affect two of the three copies in any one ascus, but there were a few asci in which all three were inactivated.

Cloning and physical characterization of the L-proline catabolism gene cluster of Aspergillus nidulans

The proline catabolism gene cluster of Aspergillus nidulans was cloned using a 'brute force' technique which detects clones hybridizing to restriction fragments overlapping chromosomal rearrangements. A number of deletion mutations and a translocation mutation in the cluster have been physically mapped, and an excellent correlation between the genetic and physical maps was established. Transcripts have been identified and orientated for each of the four genes of the cluster. All are monocistronic by size. All of the transcripts, including that of the regulatory gene prnA, are inducible. Using deletion endpoints and mRNA sizes, approximate gene positions on the physical map have been determined. Finally, the relationship between genetic and physical distance across the cluster has been estimated at 3-4 kilobases per centiMorgan.

Transformation in fungi

Transformation with exogenous deoxyribonucleic acid (DNA) now appears to be possible with all fungal species, or at least all that can be grown in culture. This field of research is at present dominated by Saccharomyces cerevisiae and two filamentous members of the class Ascomycetes, Aspergillus nidulans and Neurospora crassa, with substantial contributions also from fission yeast (Schizosaccharomyces pombe) and another filamentous member of the class Ascomycetes, Podospora anserina. However, transformation has been demonstrated, and will no doubt be extensively used, in representatives of most of the main fungal classes, including Phycomycetes, Basidiomycetes (the order Agaricales and Ustilago species), and a number of the Fungi Imperfecti. The list includes a number of plant pathogens, and transformation is likely to become important in the analysis of the molecular basis of pathogenicity. Transformation may be maintained either by using an autonomously replicating plasmid as a vehicle for the transforming DNA or through integration of the DNA into the chromosomes. In S. cerevisiae and other yeasts, a variety of autonomously replicating plasmids have been used successfully, some of them designed for use as shuttle vectors for Escherichia coli as well as for yeast transformation. Suitable plasmids are not yet available for use in filamentous fungi, in which stable transformation is dependent on chromosomal integration. In Saccharomyces cerevisiae, integration of transforming DNA is virtually always by homology; in filamentous fungi, in contrast, it occurs just as frequently at nonhomologous (ectopic) chromosomal sites. The main importance of transformation in fungi at present is in connection with gene cloning and the analysis of gene function. The most advanced work is being done with S. cerevisiae, in which the virtual restriction of stable DNA integration to homologous chromosome loci enables gene disruption and gene replacement to be carried out with greater precision and efficiency than is possible in other species that show a high proportion of DNA integration events at nonhomologous (ectopic) sites. With a little more trouble, however, the methodology pioneered for S. cerevisiae can be applied to other fungi too. Transformation of fungi with DNA constructs designed for high gene expression and efficient secretion of gene products appears to have great commercial potential.

Cloning and analysis of the positively acting regulatory gene amdR from Aspergillus nidulans

The positively acting regulatory gene amdR of Aspergillus nidulans coordinately regulates the expression of four unlinked structural genes involved in acetamide (amdS), omega amino acid (gatA and gabA), and lactam (lamA) catabolism. By the use of DNA-mediated transformation of A. nidulans, the amdR regulatory gene was cloned from a genomic cosmid library. Southern blot analysis of DNA from various loss-of-function amdR mutants revealed the presence of four detectable DNA rearrangements, including a deletion, an insertion, and a translocation. No detectable DNA rearrangements were found in several constitutive amdRc mutants. Analysis of the fate of amdR-bearing plasmids in transformants showed that 10 to 20% of the transformation events were homologous integrations or gene conversions, and this phenomenon was exploited in developing a strategy by which amdRc and amdR- alleles can be readily cloned and analyzed. Examination of the transcription of amdR by Northern blot (RNA blot) analysis revealed the presence of two mRNAs (2.7 and 1.8 kilobases) which were constitutively synthesized at a very low level. In addition, amdR transcription did not appear to depend on the presence of a functional amdR product nor was it altered in amdRc mutants. The dosage effects of multiple copies of amdR in transformants were examined, and it was shown that such transformants exhibited stronger growth than did the wild type on acetamide and pyrrolidinone media, indicating increased expression of the amdS and lamA genes, respectively. These results were used to formulate a model for amdR-mediated regulation of gene expression in which the low constitutive level of amdR product sets the upper limits of basal and induced transcription of the structural genes. Multiple copies of 5' sequences from the amdS gene can result in reduced growth on substrates whose utilization is dependent on amdR-controlled genes. This has been attributed to titration of limiting amdR gene product. Strong support for this proposal was obtained by showing that multiple copies of the amdR gene can reverse this phenomenon (antititration).

Transformation by Complementation of an Adenine Auxotroph of the Lignin-Degrading Basidiomycete Phanerochaete chrysosporium

Swollen basidiospores of an adenine auxotroph of Phanerochaete chrysosporium were protoplasted with Novozyme 234 and transformed to prototrophy by using a plasmid containing the gene for an adenine biosynthetic enzyme from Schizophyllum commune. Transformation frequencies of 100 transformants per μg of DNA were obtained. Southern blot analysis of DNA extracted from transformants demonstrated that plasmid DNA was integrated into the chromosomal DNA in multiple tandem copies. Analysis of conidia and basidiospores from transformants demonstrated that the transforming character was mitotically and meiotically stable on both selective and nonselective media. Genetic crosses between double mutants transformed for adenine prototrophy and other auxotrophic strains yielded Ade − progeny, which indicated that integration occurred at a site(s) other than the resident adenine biosynthetic gene.

Regulatory genes in Aspergillus nidulans

A major area for the study of gene regulation in lower eukaryotes has been the coordinated control of catabolic enzyme synthesis. Studies of catabolic gene regulation aim to define how interactions between input signals and regulatory proteins are transmitted to the transcription machinery to bring about changes in gene expression. In the past, mutants altered in the utilization of a wide variety of substrates have been characterized in Aspergillus nidulans. Recently, the development of a transformation system for A. nidulans has meant that molecular techniques can now be combined with the traditional genetic approach.

Non-homologous integration of transforming vectors in the fungus Podospora anserina: sequences of junctions at the integration sites

Transformation of the ura5-6 mutant strain of Podospora anserina with a recombinant vector carrying the ura5+ gene often results in the integration of the transforming plasmid by non-homologous recombination outside of the genomic ura5 locus. To investigate the mechanism of such integration, we rescued the integrated plasmid from three transformants. In two cases, the rescued plasmid was highly altered compared with the original transforming vector. We cloned the junctions between plasmidic DNA and genomic DNA of the transformants and determined their nucleotide sequences. It was found that there was little homology between plasmidic and genomic DNA sequences. Moreover, in all cases deletions of plasmid sequences at the integration site had occurred. These rearrangements can be explained by the formation of multimeric plasmids prior to integration.

Identification of the sites of action for regulatory genes controlling the amdS gene of Aspergillus nidulans

The amdS gene of Aspergillus nidulans, which encodes an acetamidase enzyme, is positively regulated by the trans-acting genes amdR, facB, amdA, and areA. Sequence changes in several cis-acting mutations in the 5' region of the gene which specifically affect amdS regulation were determined. The amdI9 mutation, which results in increased facB-dependent acetate induction, is due to a single-base change at base pair -210 relative to the start point of translation. The amdI93 mutation, which abolishes amdR-dependent omega-amino acid induction, is a deletion of base pairs -181 to -151. The amdI66 mutation, which causes increased gene activation in strains carrying amdA regulatory gene mutations, is a duplication of base pairs -107 to -90. Transformation of A. nidulans can generate transformants containing multiple integrated copies of plasmid sequences. When these plasmids carry a potential binding site for a regulatory gene product, growth on substrates whose catabolism requires genes activated by that regulatory gene can be reduced, apparently because of titration of the regulatory gene product. Introduction of 5' amdS sequences via cotransformation into strains of various genotypes was used to localize sequences apparently involved in binding of the products of the amdR, amdA, and facB genes. The position of these sequences is in agreement with the positions of the specific cis-acting mutations. Consistent with these results, a transformant of A. nidulans derived from a plasmid deleted for sequences upstream from -111 was found to have lost amdR- and facB-mediated control but was still regulated by the amdA gene. In addition, amdS expression in this transformant was still dependent on the areA gene.

Cloning and analysis of the positively acting regulatory gene amdR from Aspergillus nidulans

The positively acting regulatory gene amdR of Aspergillus nidulans coordinately regulates the expression of four unlinked structural genes involved in acetamide (amdS), omega amino acid (gatA and gabA), and lactam (lamA) catabolism. By the use of DNA-mediated transformation of A. nidulans, the amdR regulatory gene was cloned from a genomic cosmid library. Southern blot analysis of DNA from various loss-of-function amdR mutants revealed the presence of four detectable DNA rearrangements, including a deletion, an insertion, and a translocation. No detectable DNA rearrangements were found in several constitutive amdRc mutants. Analysis of the fate of amdR-bearing plasmids in transformants showed that 10 to 20% of the transformation events were homologous integrations or gene conversions, and this phenomenon was exploited in developing a strategy by which amdRc and amdR- alleles can be readily cloned and analyzed. Examination of the transcription of amdR by Northern blot (RNA blot) analysis revealed the presence of two mRNAs (2.7 and 1.8 kilobases) which were constitutively synthesized at a very low level. In addition, amdR transcription did not appear to depend on the presence of a functional amdR product nor was it altered in amdRc mutants. The dosage effects of multiple copies of amdR in transformants were examined, and it was shown that such transformants exhibited stronger growth than did the wild type on acetamide and pyrrolidinone media, indicating increased expression of the amdS and lamA genes, respectively. These results were used to formulate a model for amdR-mediated regulation of gene expression in which the low constitutive level of amdR product sets the upper limits of basal and induced transcription of the structural genes. Multiple copies of 5' sequences from the amdS gene can result in reduced growth on substrates whose utilization is dependent on amdR-controlled genes. This has been attributed to titration of limiting amdR gene product. Strong support for this proposal was obtained by showing that multiple copies of the amdR gene can reverse this phenomenon (antititration).

Identification of the sites of action for regulatory genes controlling the amdS gene of Aspergillus nidulans

The amdS gene of Aspergillus nidulans, which encodes an acetamidase enzyme, is positively regulated by the trans-acting genes amdR, facB, amdA, and areA. Sequence changes in several cis-acting mutations in the 5' region of the gene which specifically affect amdS regulation were determined. The amdI9 mutation, which results in increased facB-dependent acetate induction, is due to a single-base change at base pair -210 relative to the start point of translation. The amdI93 mutation, which abolishes amdR-dependent omega-amino acid induction, is a deletion of base pairs -181 to -151. The amdI66 mutation, which causes increased gene activation in strains carrying amdA regulatory gene mutations, is a duplication of base pairs -107 to -90. Transformation of A. nidulans can generate transformants containing multiple integrated copies of plasmid sequences. When these plasmids carry a potential binding site for a regulatory gene product, growth on substrates whose catabolism requires genes activated by that regulatory gene can be reduced, apparently because of titration of the regulatory gene product. Introduction of 5' amdS sequences via cotransformation into strains of various genotypes was used to localize sequences apparently involved in binding of the products of the amdR, amdA, and facB genes. The position of these sequences is in agreement with the positions of the specific cis-acting mutations. Consistent with these results, a transformant of A. nidulans derived from a plasmid deleted for sequences upstream from -111 was found to have lost amdR- and facB-mediated control but was still regulated by the amdA gene. In addition, amdS expression in this transformant was still dependent on the areA gene.

An amdS-lacZ fusion for studying gene regulation in Aspergillus

A translational fusion has been constructed between the amdS gene of Aspergillus nidulans and the lacZ gene of Escherichia coli. Sequencing across the fusion junction confirmed the generation of an in-frame fusion at amino acid 34 of amdS and a novel protein has been detected in transformants carrying the fusion plasmid. Transformants of A. nidulans and Aspergillus niger carrying the fusion plasmid were obtained by co-transformation with a second selectable plasmid. These transformants were readily identified on media containing XGal. The intensity of the reaction on XGal media was indicative of the number of copies of the fusion plasmid carried by the transformants. The growth of highly expressing strains of A. nidulans was inhibited on XGal media. The fusion plasmid was used to develop a two-step gene replacement strategy in which the resident amdS gene was replaced with the fusion gene free of vector sequences. Plate tests and in vitro assays of the beta-galactosidase enzyme confirmed that expression of the fusion gene was regulated by amdS flanking sequences and trans-acting regulatory genes.

Complementation of areA- regulatory gene mutations of Aspergillus nidulans by the heterologous regulatory gene nit-2 of Neurospora crassa

Loss-of-function mutations in the regulatory gene areA of Aspergillus nidulans prevent the utilization of a wide variety of nitrogen sources. The phenotypes of nit-2 mutants of Neurospora crassa suggest that this gene may be analogous to the areA gene. Transformation has been used to introduce a plasmid containing the nit-2 gene into A. nidulans. The nit-2 gene of Neurospora complemented mutations in the areA gene, restoring the ability to use a variety of nitrogen sources. This indicated that the activator function of nit-2 and areA gene products was retained across these two fungal species. Southern blot analysis revealed both single-copy and multicopy integrations and, in at least one case, integration appeared to generate a nit-2 mutation. Integration of the transforming plasmid appeared to be by nonhomologous events at a number of different sites in the Aspergillus genome. The transformants were less sensitive to nitrogen-metabolite repression of extracellular protease activity and nitrate reductase (EC 1.6.6.3) than were wild-type A. nidulans. This indicated that nitrogen control was not completely normal in the nit-2 transformants.