Domain-wide, locus-specific suppression of nitrogen metabolite repressed mutations in Aspergillus nidulans

The role of the GATA transcription factor AreB in regulation of nitrogen and carbon metabolism in Aspergillus nidulans

In Aspergillus nidulans, nitrogen and carbon metabolism are under the control of wide-domain regulatory systems, including nitrogen metabolite repression, carbon catabolite repression and the nutrient starvation response. Transcriptomic analysis of the wild type strain grown under different combinations of carbon and nitrogen regimes was performed, to identify differentially regulated genes. Carbon metabolism predominates as the most important regulatory signal but for many genes, both carbon and nitrogen metabolisms coordinate regulation. To identify mechanisms coordinating nitrogen and carbon metabolism, we tested the role of AreB, previously identified as a regulator of genes involved in nitrogen metabolism. Deletion of areB has significant phenotypic effects on the utilization of specific carbon sources, confirming its role in the regulation of carbon metabolism. AreB was shown to regulate the expression of areA, tamA, creA, xprG and cpcA regulatory genes suggesting areB has a range of indirect, regulatory effects. Different isoforms of AreB are produced as a result of differential splicing and use of two promoters which are differentially regulated by carbon and nitrogen conditions. These isoforms are likely to be functionally distinct and thus contributing to the modulation of AreB activity.

Deletion and overexpression of the Aspergillus nidulans GATA factor AreB reveals unexpected pleiotropy

The Aspergillus nidulans transcription factor AreA is a key regulator of nitrogen metabolic gene expression. AreA contains a C-terminal GATA zinc finger DNA-binding domain and activates expression of genes necessary for nitrogen acquisition. Previous studies identified AreB as a potential negative regulator of nitrogen catabolism showing similarity with Penicillium chrysogenum NreB and Neurospora crassa ASD4. The areB gene encodes multiple products containing an N-terminal GATA zinc finger and a leucine zipper motif. We deleted the areB gene and now show that AreB negatively regulates AreA-dependent nitrogen catabolic gene expression under nitrogen-limiting or nitrogen-starvation conditions. AreB also acts pleiotropically, with functions in growth, conidial germination and asexual development, though not in sexual development. AreB overexpression results in severe growth inhibition, aberrant cell morphology and reduced AreA-dependent gene expression. Deletion of either the DNA-binding domain or the leucine zipper domain results in loss of both nitrogen and developmental phenotypes.

Specific induction and carbon/nitrogen repression of arginine catabolism gene of Aspergillus nidulans--functional in vivo analysis of the otaA promoter

The arginine catabolism gene otaA encoding ornithine transaminase (OTAse) is specifically induced by arginine and is under the control of the broad-domain carbon and nitrogen repression systems. Arginine induction is mediated by a product of arcA gene coding for Zn(2)C(6) activator. We have identified a region responsible for arginine induction in the otaA promoter (AnUAS(arg)). Deletions within this region result in non-inducibility of OTAse by arginine, whether in an arcA(+) strain or in the presence of the arcA(d)47 gain of function allele. AnUAS(arg) is very similar to the Saccharomyces cerevisiae UAS(arg), a sequence bound by the Zn(2)C(6) activator (ArgRIIp), acting in a complex with two MADS-box proteins (McmIp and ArgRIp). We demonstrate here that two CREA in vitro binding sites in the otaA promoter are functional in vivo. CREA is directly involved in carbon repression of the otaA gene and it also reduces its basal level of expression. Although AREA binds to the otaA promoter in vitro, it probably does not participate in nitrogen metabolite repression of the gene in vivo. We show here that another putative negatively acting GATA factor AREB participates directly or indirectly in otaA nitrogen repression. We also demonstrate that the high levels of OTAse activity are an important factor in the suppression of proline auxotrophic mutations. This suppression can be achieved neither by growing of the proline auxotroph under carbon/nitrogen derepressing conditions nor by introducing of a creA(d) mutation.

The Aspergillus nidulans GATA transcription factor gene areB encodes at least three proteins and features three classes of mutation

In Aspergillus nidulans, the principal transcription factor regulating nitrogen metabolism, AREA, belongs to the GATA family of DNA-binding proteins. In seeking additional GATA factors, we have cloned areB, which was originally identified via a genetic screen for suppressors of areA loss-of-function mutations. Based on our analysis, areB is predicted to encode at least three distinct protein products. These arise from the use of two promoters, differential splicing and translation initiating at AUG and non-AUG start codons. All the putative products include a GATA domain and a putative Leu zipper. These regions show strong sequence similarity to regulatory proteins from Saccharomyces cerevisiae (Dal80p and Gzf3p), Penicillium chrysogenum (NREB) and Neurospora crassa (ASD4). We have characterized three classes of mutation in areB; the first are loss-of-function mutations that terminate the polypeptides within or before the GATA domain. The second class truncates the GATA factor either within or upstream of the putative Leu zipper but retains the GATA domain. The third class fuses novel gene sequences to areB with the potential to produce putative chimeric polypeptides. These novel gene fusions transform the putative negative-acting transcription factor into an activator that can partially replace areA.

The fungal GATA factors

The DNA-binding domains of eucaryotic GATA factors comprise a four-cysteine Zn finger and an adjacent basic region. Fungal GATA factors regulate nitrogen metabolism, light induction, siderophore biosynthesis and mating-type switching. Hydrophobic interactions determine binding-site specificity. Interactions with other factors may determine promoter specificity. One GATA factor has recently been shown to determine a drastic chromatin rearrangement.

Chromosome rearrangements in Neurospora and other filamentous fungi

Knowledge of fungal chromosome rearrangements comes primarily from N. crassa, but important information has also been obtained from A. nidulans and S. macrospora. Rearrangements have been identified in other Sordaria species and in Cochliobolus, Coprinus, Magnaporthe, Podospora, and Ustilago. In Neurospora, heterozygosity for most chromosome rearrangements is signaled by the appearance of unpigmented deficiency ascospores, with frequencies and ascus types that are characteristic of the type of rearrangement. Summary information is provided on each of 355 rearrangements analyzed in N. crassa. These include 262 reciprocal translocations, 31 insertional translocations, 27 quasiterminal translocations, 6 pericentric inversions, 1 intrachromosomal transposition, and numerous complex or cryptic rearrangements. Breakpoints are distributed more or less randomly among the seven chromosomes. Sixty of the rearrangements have readily detected mutant phenotypes, of which half are allelic with known genes. Constitutive mutations at certain positively regulated loci involve rearrangements having one breakpoint in an upstream regulatory region. Of 11 rearrangements that have one breakpoint in or near the NOR, most appear genetically to be terminal but are in fact physically reciprocal. Partial diploid strains can be obtained as recombinant progeny from crosses heterozygous for insertional or quasiterminal rearrangements. Duplications produced in this way precisely define segments that cover more than two thirds of the genome. Duplication-producing rearrangements have many uses, including precise genetic mapping by duplication coverage and alignment of physical and genetic maps. Typically, fertility is greatly reduced in crosses parented by a duplication strain. The finding that genes within the duplicated segment have undergone RIP mutation in some of the surviving progeny suggests that RIP may be responsible for the infertility. Meiotically generated recessive-lethal segmental deficiencies can be rescued in heterokaryons. New rearrangements are found in 10% or more of strains in which transforming DNA has been stably integrated. Electrophoretic separation of rearranged chromosomal DNAs has found useful applications. Synaptic adjustment occurs in inversion heterozygotes, leading progressively to nonhomologous association of synaptonemal complex lateral elements, transforming loop pairing into linear pairing. Transvection has been demonstrated in Neurospora. Beginnings have been made in constructing effective balancers. Experience has increased our understanding of several phenomena that may complicate analysis. With some rearrangements, nondisjunction of centromeres from reciprocal translocation quadrivalents results in 3:1 segregation and produces asci with four deficiency ascospores that occupy diagnostic positions in linear asci. Three-to-one segregation is most frequent when breakpoints are near centromeres. With some rearrangements, inviable deficiency ascospores become pigmented. Diagnosis must then depend on ascospore viability. In crosses between highly inbred strains, analysis may be handicapped by random ascospore abortion. This is minimized by using noninbred strains as testers.

Nitrogen regulation in fungi

Nitrogen regulation has been extensively studied in fungi revealing a complex array of interacting regulatory genes. The general characterisation of the systems in Aspergillus nidulans and Neurospora crassa shall be briefly described, but much of this paper will concentrate specifically on the recent molecular characterisation of areA, the principle regulatory gene from A. nidulans which mediates nitrogen metabolite repression. Three areas shall be explored in detail, firstly the DNA binding domain, which has been characterised extensively by both molecular and genetic analysis. Secondly we shall report recent analysis which has revealed the presence of related DNA binding activities in A. nidulans. Finally we shall discuss the mechanism by which the nitrogen state of the cell is monitored by the areA product, in particular localisation of the domain within the areA product which mediates the regulatory response within the protein.

A translocation activating the cryptic nitrogen regulation gene areB inactivates a previously unidentified gene involved in glycerol utilisation in Aspergillus nidulans

The chromosome VIII translocation breakpoint of the areB-404 translocation, selected for its ability to activate the cryptic nitrogen metabolism regulatory gene areB, and the mutation glcD-100 both lead to loss of mitochondrial FAD-dependent sn-glycerol-3-phosphate dehydrogenase in Aspergillus nidulans. These two lesions therefore define glcD, a second gene (in addition to glcB) where mutation can result in loss of this enzyme. The glcD gene has been localised to a centromere-proximal region of the right arm of chromosome VIII. Although all six known areB-activating mutations involve chromosomal rearrangements and presumably therefore gene fusions, areB-404 is the first such rearrangement where the gene involved in an areB fusion has been identified.

A translocation associated, loss-of-function mutation in the nitrogen metabolite repression regulatory gene of Aspergillus nidulans can revert intracistronically

The areAr-18 mutation is a loss-of-function mutation in areA, the positive acting regulatory gene mediating nitrogen metabolite repression in Aspergillus nidulans. It results from a reciprocal translocation which splits the coding region into 5' and 3' moieties. Surprisingly, we have selected rare intracistronic revertants of areAr-18. From crosses heterozygous for areAr-18 revertant alleles, duplication-deficiency progeny containing two copies of a substantial portion of chromosome IV but lacking part of chromosome III, including the 5' moiety of areA, have been obtained. For all four revertants analysed genetically, growth properties of these duplication-deficiency strains indicate that the reversion events involve the 3' portion of areA and that the 5' portion of areA is unnecessary for the revertant phenotype. This conclusion was directly confirmed for one revertant using Southern blotting. As all four reversion events involve additional chromosomal rearrangements, they probably fuse functional promoters, ribosome binding sites and 'in frame' initiation codons to the 3' portion of the gene. In the course of characterisation of these mutations, new mapping data for a large region of chromosome IV have been generated, and a new reciprocal translocation activating the cryptic regulatory gene areB, whose product can substitute for that of areA, has been identified.

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.

Localisation of several chromosome I genes of Aspergillus nidulans: implications for mitotic recombination

Another laboratory previously reported that the vast majority of mitotic recombinants in chromosome I disomics of Aspergillus nidulans arise from double exchange events involving the centromeric region and a far distal, possibly telomeric, region. This conclusion was based on the assumption that the camC gene is located in a position far distal to the centromere on the left arm of chromosome I. As a left arm location for camC distal to the centromere was possibly in conflict with mapping data obtained in the context of an unrelated project, camC was partially mapped along with three other previously unlocated chromosome I genes, davA, ornD and uapA. The data presented here indicate that camC is located in a position far distal to the centromere but on the right arm of chromosome I, a conclusion also supported by the previous data. The positioning of uapA and camC in far distal locations on the right arm of chromosome I indicates the existence of a vast, otherwise nearly unmapped region on this chromosome arm.

Regulation of amino acid utilization in Neurospora crassa: effect of nmr-1 and ms-5 mutations

The effect of the nmr-1 and ms-5 mutations, which lead to insensitivity to glutamine-mediated nitrogen metabolite repression, was examined with respect to extracellular deaminase production by Neurospora crassa. Deaminase production normally requires nitrogen limitation, but these mutations eliminated this requirement and allowed production of deaminase activity under nitrogen metabolite repressing conditions. Demonstration of normal glutamine transport by both strains eliminated the possibility that these mutations exerted their effects through repressor exclusion. We have proposed a new working model for nitrogen regulation in Neurospora based on the findings that these mutations affected a nitrogen-regulated activity in addition to those activities originally reported and that the mutations are genetically very closely linked and likely allelic.