Common features and differences in the expression of the three genes forming the UGA regulon in Saccharomyces cerevisiae

The biological relevance of the FspTF transcription factor, homologous of Bqt4, in Fusarium sp. associated with the ambrosia beetle Xylosandrus morigerus

Transcription factors in phytopathogenic fungi are key players due to their gene expression regulation leading to fungal growth and pathogenicity. The KilA-N family encompasses transcription factors unique to fungi, and the Bqt4 subfamily is included in it and is poorly understood in filamentous fungi. In this study, we evaluated the role in growth and pathogenesis of the homologous of Bqt4, FspTF, in Fusarium sp. isolated from the ambrosia beetle Xylosandrus morigerus through the characterization of a CRISPR/Cas9 edited strain in Fsptf. The phenotypic analysis revealed that TF65-6, the edited strain, modified its mycelia growth and conidia production, exhibited affectation in mycelia and culture pigmentation, and in the response to certain stress conditions. In addition, the plant infection process was compromised. Untargeted metabolomic and transcriptomic analysis, clearly showed that FspTF may regulate secondary metabolism, transmembrane transport, virulence, and diverse metabolic pathways such as lipid metabolism, and signal transduction. These data highlight for the first time the biological relevance of an orthologue of Bqt4 in Fusarium sp. associated with an ambrosia beetle.

Novel function of transcription factor Uga3 as an activator of branched-chain amino acid permease BAP2 gene expression

Gene regulation in yeast occurs at the transcription level, i.e. the basal level of expression is very low and increased transcription requires gene-specific transcription factors allowing the recruitment of basal transcriptional machinery. Saccharomyces cerevisiae BAP2 gene encodes the permease responsible for most uptake of leucine, valine and isoleucine, amino acids that this yeast can use as nitrogen sources. Moreover, BAP2 expression is known to be induced by the presence of amino acids such as leucine. In this context, the results presented in this paper show that BAP2 is an inducible gene in the presence of nitrogen-non-preferred source proline but exhibits high constitutive non-inducible expression in nitrogen-preferred source ammonium. BAP2 expression is regulated by the SPS sensor system and transcription factors Leu3, Gcn4 and Dal81. This can be achieved or not through a direct binding to the promoter depending on the quality of the nitrogen source. We further demonstrate here that an interaction occurs in vivo between Uga3 ‒ the transcriptional activator responsible for γ-aminobutyric acid (GABA)-dependent induction of the GABA genes ‒ and the regulatory region of the BAP2 gene, which leads to an increase in BAP2 transcription.

Regulation of Amino Acid Transport in Saccharomyces cerevisiae

We review the mechanisms responsible for amino acid homeostasis in Saccharomyces cerevisiae and other fungi. Amino acid homeostasis is essential for cell growth and survival. Hence, the de novo synthesis reactions, metabolic conversions, and transport of amino acids are tightly regulated. Regulation varies from nitrogen pool sensing to control by individual amino acids and takes place at the gene (transcription), protein (posttranslational modification and allostery), and vesicle (trafficking and endocytosis) levels. The pools of amino acids are controlled via import, export, and compartmentalization. In yeast, the majority of the amino acid transporters belong to the APC (amino acid-polyamine-organocation) superfamily, and the proteins couple the uphill transport of amino acids to the electrochemical proton gradient. Although high-resolution structures of yeast amino acid transporters are not available, homology models have been successfully exploited to determine and engineer the catalytic and regulatory functions of the proteins. This has led to a further understanding of the underlying mechanisms of amino acid sensing and subsequent downregulation of transport. Advances in optical microscopy have revealed a new level of regulation of yeast amino acid transporters, which involves membrane domain partitioning. The significance and the interrelationships of the latest discoveries on amino acid homeostasis are put in context.

Unravelling the transcriptional regulation of Saccharomyces cerevisiae UGA genes: the dual role of transcription factor Leu3

Yeast cells can use γ-aminobutyric acid (GABA), a non-protein amino acid, as a nitrogen source that is mainly imported by the permease Uga4 and catabolized by the enzymes GABA transaminase and succinate-semialdehyde dehydrogenase, encoded by the UGA1 and UGA2 genes, respectively. The three UGA genes are inducible by GABA and subject to nitrogen catabolite repression. Hence, their regulation occurs through two mechanisms, one dependent on the inducer and the other on nitrogen source quality. The aim of this work was to better understand the molecular mechanisms of transcription factors acting on different regulatory elements present in UGA promoters, such as Uga3, Dal81, Leu3 and the GATA factors, and to establish the mechanism of the concerted action between them. We found that Gat1 plays an important role in the induction of UGA4 transcription by GABA and that Gzf3 has an effect in cells grown in a poor nitrogen source such as proline and that this effect is positive on UGA4 expression. We also found that Gln3 and Dal80 affect the interaction of Uga3 and Dal81 on UGA promoters. Moreover, our results indicated that the repressing activity of Leu3 on UGA4 and UGA1 occurs through Dal80 since we demonstrated that Leu3 facilitates Dal80 interaction with DNA. However, when the expression of GATA factors is null or negligible, Leu3 functions as an activator.

Genes of Different Catabolic Pathways Are Coordinately Regulated by Dal81 in Saccharomyces cerevisiae

Yeast can use a wide variety of nitrogen compounds. However, the ability to synthesize enzymes and permeases for catabolism of poor nitrogen sources is limited in the presence of a rich one. This general mechanism of transcriptional control is called nitrogen catabolite repression. Poor nitrogen sources, such as leucine, γ-aminobutyric acid (GABA), and allantoin, enable growth after the synthesis of pathway-specific catabolic enzymes and permeases. This synthesis occurs only under conditions of nitrogen limitation and in the presence of a pathway-specific signal. In this work we studied the temporal order in the induction of AGP1, BAP2, UGA4, and DAL7, genes that are involved in the catabolism and use of leucine, GABA, and allantoin, three poor nitrogen sources. We found that when these amino acids are available, cells will express AGP1 and BAP2 in the first place, then DAL7, and at last UGA4. Dal81, a general positive regulator of genes involved in nitrogen utilization related to the metabolisms of GABA, leucine, and allantoin, plays a central role in this coordinated regulation.

The global regulator FfSge1 is required for expression of secondary metabolite gene clusters but not for pathogenicity in Fusarium fujikuroi

The plant pathogenic fungus Fusarium fujikuroi is the causal agent of bakanae disease on rice due to its ability to produce gibberellins. Besides these phytohormones, F. fujikuroi is able to produce several other secondary metabolites (SMs). Although much progress has been made in the field of secondary metabolism, the transcriptional regulation of SM biosynthesis is complex and still incompletely understood. Environmental conditions, global as well as pathway-specific regulators and chromatin remodelling have been shown to play major roles. Here, the role of FfSge1, a homologue of the morphological switch regulators Wor1 and Ryp1 in Candida albicans and Histoplasma capsulatum, respectively, is explored with emphasis on secondary metabolism. FfSge1 is not required for formation of conidia and pathogenicity but is involved in vegetative growth. Transcriptome analysis of the mutant Δffsge1 compared with the wild type, as well as comparative chemical analysis between the wild type, Δffsge1 and OE:FfSGE1, revealed that FfSge1 functions as a global activator of secondary metabolism in F. fujikuroi. Double mutants of FfSGE1 and other SM regulatory genes brought insights into the hierarchical regulation of secondary metabolism. In addition, FfSge1 is also required for expression of a yet uncharacterized SM gene cluster containing a non-canonical non-ribosomal peptide synthetase.

GABA induction of the Saccharomyces cerevisiae UGA4 gene depends on the quality of the carbon source: role of the key transcription factors acting in this process

Yeast cells are able to adapt their metabolism according to the quality of both carbon and nitrogen sources available in the environment. Saccharomyces cerevisiae UGA4 gene encodes a permease capable of transporting γ-aminobutyric acid (GABA) into the cells. Yeast uses this amino acid as a nitrogen source or as a carbon skeleton that enters the tricarboxylic acid cycle. The quality of the carbon source modulates UGA4 expression through two parallel pathways, each one acting on different regulatory elements, the UAS(GATA) and the UAS(GABA). In the presence of a fermentable carbon source, UGA4 expression is induced by GABA while in the presence of a non-fermentable carbon source this expression is GABA-independent. The aim of this work was to study the mechanisms responsible for the differences in the profiles of UGA4 expression in both growth conditions. We found that although the subcellular localization of Gln3 depends on the carbon source and UGA4 expression depends on Tor1 and Snf1, Gln3 localization does not depend on these kinases. We also found that the phosphorylation of Gln3 is mediated by two systems activated by a non-fermentable carbon source, involving the Snf1 kinase and an unidentified TORC1-regulated kinase. We also found that the activity of the main transcription factors responsible for UGA4 induction by GABA varies depending on the quality of the carbon source. In a fermentable carbon source such as glucose, the negative GATA factor Dal80 binds to UGA4 promoter; only after the addition of the inducer, the positive factors Uga3, Dal81 and Gln3 interact with the promoter removing Dal80 and leading to gene induction. In contrast, in the non-fermentable carbon source acetate the negative GATA factor remains bound to UGA4 promoter in the presence or absence of GABA, the positive factors are not detected bound in any of these conditions and in consequence, UGA4 is not induced.