A gene product needed for induction of allantoin system genes in Saccharomyces cerevisiae but not for their transcriptional activation

Dal81 Regulates Expression of Arginine Metabolism Genes in Candida parapsilosis

Fungi can use a wide variety of nitrogen sources. In the absence of preferred sources such as ammonium, glutamate, and glutamine, secondary sources, including most other amino acids, are used. Expression of the nitrogen utilization pathways is very strongly controlled at the transcriptional level. Here, we investigated the regulation of nitrogen utilization in the pathogenic yeast Candida parapsilosis. We found that the functions of many regulators are conserved with respect to Saccharomyces cerevisiae and other fungi. For example, the core GATA activators GAT1 and GLN3 have a conserved role in nitrogen catabolite repression (NCR). There is one ortholog of GZF3 and DAL80, which represses expression of genes in preferred nitrogen sources. The regulators PUT3 and UGA3 are required for metabolism of proline and γ-aminobutyric acid (GABA), respectively. However, the role of the Dal81 transcription factor is distinctly different. In S. cerevisiae, Dal81 is a positive regulator of acquisition of nitrogen from GABA, allantoin, urea, and leucine, and it is required for maximal induction of expression of the relevant pathway genes. In C. parapsilosis, induction of GABA genes is independent of Dal81, and deleting DAL81 has no effect on acquisition of nitrogen from GABA or allantoin. Instead, Dal81 represses arginine synthesis during growth under preferred nitrogen conditions. IMPORTANCE Utilization of nitrogen by fungi is controlled by nitrogen catabolite repression (NCR). Expression of many genes is switched off during growth on nonpreferred nitrogen sources. Gene expression is regulated through a combination of activation and repression. Nitrogen regulation has been studied best in the model yeast Saccharomyces cerevisiae. We found that although many nitrogen regulators have a conserved function in Saccharomyces species, some do not. The Dal81 transcriptional regulator has distinctly different functions in S. cerevisiae and C. parapsilosis. In the former, it regulates utilization of nitrogen from GABA and allantoin, whereas in the latter, it regulates expression of arginine synthesis genes. Our findings make an important contribution to our understanding of nitrogen regulation in a human-pathogenic fungus.

Functional domain mapping and subcellular distribution of Dal82p in Saccharomyces cerevisiae

Previous studies have shown that (i) Dal81p and Dal82p are required for allophanate-induced gene expression in Saccharomyces cerevisiae; (ii) the cis-acting element mediating the induced transcriptional response to allophanate is a dodecanucleotide, UIS(ALL); and (iii) Dal82p binds specifically to UIS(ALL). Here we show that Dal82p is localized to the nucleus and parallels movement of the DNA through the cell cycle. Deletion analysis of DAL82 identified and localized three functional domains. Electrophoretic mobility shift assays identified a peptide (consisting of Dal82p amino acids 1-85) that is sufficient to bind a DNA fragment containing UIS(ALL). LexA-tethering experiments demonstrated that Dal82p is capable of mediating transcriptional activation. The activation domain consists of two parts: (i) an absolutely required core region (amino acids 66-99) and (ii) less well defined regions flanking residues 66-99 that are required for full wild-type levels of activation. The Dal82p C terminus contains a predicted coiled-coil motif that down-regulates Dal82p-mediated transcriptional activation.

The S1, S2 and SGA1 ancestral genes for the STA glucoamylase genes all map to chromosome IX in Saccharomyces cerevisiae

The polymorphic extracellular glucoamylase-encoding genes STA1 (chr. IV), STA2 (chr. II) and STA3 (chr. XIV), from Saccharomyces cerevisiae var. diastaticus probably evolved by genomic rearrangement of DNA regions (S1, S2 and SGA1) present in S. cerevisiae, and subsequent translocation to unlinked regions of chromosomal regions. S1, encoding a homologue to the threonine/serine-rich domain of STA glucoamylases (GAI-III), mapped to the right arm of chromosome IX. S2, encoding the hydrophobic leader peptide of GAI-III), was also mapped on the right arm of chromosome IX, next to S1, close to DAL81. The SGA1 sporulation-specific, intracellular glucoamylase-encoding gene is located on the left arm of chromosome IX, 32 kb proximal of HIS5.

The allantoinase (DAL1) gene of Saccharomyces cerevisiae

The allantoinase (DAL1) gene from Saccharomyces cerevisiae has been cloned, sequenced, and found to encode a 472 amino acid protein with a Mr of 52,028. DAL1 is expressed in an inducer-independent manner in strain M970 (sigma 1278b genetic background) and modestly responds to mutation of the dal80 locus. Expression was also sensitive to nitrogen catabolite repression (NCR). Correlated with these expression characteristics, the upstream region of DAL1 contained five copies of a sequence that is homologous to the DAL UASNTR element previously shown to be required for transcriptional activation and NCR sensitivity of the DAL5 and DAL7 genes. Missing from the DAL1 5' flanking region were any sequences with significant homology to the DAL7 UIS element required for response to inducer. These observations further support the roles of UASNTR and DAL7 UIS in the regulation of allantoin pathway gene expression.

The ureidoglycollate hydrolase (DAL3) gene in Saccharomyces cerevisiae

The DAL3 gene has been sequenced and found to encode a 195 amino acid protein with a molecular weight of 21,727. The four carboxy-terminal amino acids of DAL3 product (Cys-Ile-Ile-Ile) are homologous to those (CAAX) previously shown to be the primary structural signal for post-translational farnesylation of yeast RAS protein and mating factor. This modification is reported to be responsible for membrane localization of proteins containing it. The upstream region of DAL3 contains six copies of a sequence that is homologous to the positively acting DAL UASNTR reported to be required for transcriptional activation of the DAL5 and DAL7 genes. Missing from the DAL3 upstream region were any sequences related to those shown to be required for a DAL7 response to inducer, the UIS element. This correlates with the previous report that DAL3 expression is independent of the allantoin pathway inducer.

Sequences of two adjacent genes, one (DAL2) encoding allantoicase and another (DCG1) sensitive to nitrogen-catabolite repression in Saccharomyces cerevisiae

Reported are the nucleotide sequences of the yeast allantoicase-encoding gene (DAL2) and that of an unknown gene adjacent to it. Expression of the unidentified gene is sensitive to nitrogen catabolite repression (NCR) and regulated by the DAL80 product, a previously documented control element regulating allantoin pathway gene expression. Both genes possess multiple upstream activation sequences (UAS) homologous to the UASNTR element shown to be required for sensitivity to NCR. Also present upstream from DAL2 is a mutant form of the upstream induction sequence required for response of DAL7 to induction. Its occurrence in mutant form is consistent with the poor induction of DAL2 expression observed in vivo.

The pleiotropic UGA35(DURL) regulatory gene of Saccharomyces cerevisiae: cloning, sequence and identity with the DAL81 gene

The UGA35 gene of Saccharomyces cerevisiae (also called DURL) encodes a positive regulator of the expression of structural genes involved in 4-aminobutyric acid (GABA) and urea catabolisms. The UGA35 gene has been cloned by complementation of function and identified by chromosomal gene replacement. The sequence of this regulatory gene and its flanking regions has been established. Our data reveal an open reading frame of 2892 nt, corresponding to 964 amino acids (aa). The deduced UGA35 aa sequence shares several similarities with that of other regulatory proteins, suggesting that the UGA35 gene encodes a DNA-binding transcriptional activator. We also show that UGA35 and the DAL81 regulatory gene controlling allantoin and urea catabolisms are one and the same gene. This means that the same factor is required for specific induction of three distinct catabolic pathways, namely those involved in GABA, urea and allantoin utilization as nitrogen sources.