Functional mapping of Bas2. Identification of activation and Bas1-interaction domains

Chromatin regulator Eaf3p regulates nitrogen metabolism in Saccharomyces cerevisiae as a trans-acting factor

IMPORTANCE

In this study, the mechanism of chromatin regulator Eaf3p regulating nitrogen metabolism in S. cerevisiae was investigated. It provides theoretical support for epigenetic modifications of cells to alter the level of histone modifications, coordinate the expression of multiple genes, and make it more conducive to the co-metabolism of multiple nitrogen sources. Moreover, it provides new ideas for industrial brewing yeast strains to achieve nitrogen source metabolism balance, reduce the accumulation of harmful nitrogen metabolites, and improve fermentation efficiency. This study provides a reference for changing the performance of microbial strains and improving the quality of traditional fermentation products and provides a theoretical basis for studying epigenetic modification and nitrogen metabolism regulation. It has an important theoretical explanation and practical application value. In addition, this study also provides useful clues for the study.

Functional Mapping of Transcription Factor Grf10 That Regulates Adenine-Responsive and Filamentation Genes in Candida albicans

Grf10, a homeodomain-containing transcription factor, regulates adenylate and one-carbon metabolism and morphogenesis in the human fungal pathogen Candida albicans Here, we identified functional domains and key residues involved in transcription factor activity using one-hybrid and mutational analyses. We localized activation domains to the C-terminal half of the Grf10 protein by one-hybrid analysis and identified motifs using bioinformatic analyses; one of the characterized activation domains (AD1) responded to temperature. The LexA-Grf10 fusion protein activated the lexAop-HIS1 reporter in an adenine-dependent fashion, and this activation was independent of Bas1, showing that the adenine limitation signal is transmitted directly to Grf10. Overexpression of LexA-Grf10 led to filamentation, and this required a functioning homeodomain, consistent with Grf10 controlling the expression of key filamentation genes; filamentation induced by LexA-Grf10 overexpression was independent of adenine levels and Bas1. Alanine substitutions were made within the conserved interaction regions (IR) of LexA-Grf10 and Grf10 to investigate roles in transcription. In LexA-Grf10, the D302A mutation activated transcription constitutively, and the E305A mutation was regulated by adenine. When these mutations were introduced into the native gene locus, the D302A mutation was unable to complement the ADE phenotype and did not promote filamentation under hypha-inducing conditions; the E305A mutant behaved as the native gene with respect to the ADE phenotype and was partially defective in inducing hyphae. These results demonstrate allele-specific responses with respect to the different phenotypes, consistent with perturbations in the ability of Grf10 to interact with multiple partner proteins.IMPORTANCE Metabolic adaptation and morphogenesis are essential for Candida albicans, a major human fungal pathogen, to survive and infect diverse body sites in the mammalian host. C. albicans utilizes transcription factors to tightly control the transcription of metabolic genes and morphogenesis genes. Grf10, a critical homeodomain transcription factor, controls purine and one-carbon metabolism in response to adenine limitation, and Grf10 is necessary for the yeast-to-hypha morphological switching, a known virulence factor. Here, we carried out one-hybrid and mutational analyses to identify functional domains of Grf10. Our results show that Grf10 separately regulates metabolic and morphogenesis genes, and it contains a conserved protein domain for protein partner interaction, allowing Grf10 to control the transcription of multiple distinct pathways. Our findings contribute significantly to understanding the role and mechanism of transcription factors that control multiple pathogenic traits in C. albicans.

A homeobox protein Phx1 regulates long-term survival and meiotic sporulation in Schizosaccharomyces pombe

BACKGROUND

In the fission yeast Schizosaccharomyces pombe, the phx1+ (pombe homeobox) gene was initially isolated as a multi-copy suppressor of lysine auxotrophy caused by depletion of copper/zinc-containing superoxide dismutase (CuZn-SOD). Overproduction of Phx1 increased the synthesis of homocitrate synthase, the first enzyme in lysine biosynthetic pathway, which is labile to oxidative stress. Phx1 has a well conserved DNA-binding domain called homeodomain at the N-terminal region and is predicted to be a transcription factor in S. pombe. However, its role has not been revealed in further detail. Here we examined its expression pattern and the phenotype of its null mutant to get clues on its function.

RESULTS

Fluorescence from the Phx1-GFP expressed from a chromosomal fusion gene demonstrated that it is localized primarily in the nucleus, and is distinctly visible during the stationary phase. When we replaced the N-terminal homeobox domain of Phx1 with the DNA binding domain of Pap1, a well-characterized transcription factor, the chimeric protein caused the elevation of transcripts from Pap1-dependent genes such as ctt1+ and trr1+, suggesting that Phx1 possesses transcriptional activating activity when bound to DNA. The amount of phx1+ transcripts sharply increased as cells entered the stationary phase and was maintained at high level throughout the stationary phase. Nutrient shift down to low nitrogen or carbon sources caused phx1+ induction during the exponential phase, suggesting that cells need Phx1 for maintenance function during nutrient starvation. The Δphx1 null mutant showed decreased viability in long-term culture, whereas overproduction of Phx1 increased viability. Decrease in long-term survival was also observed for Δphx1 under N- or C-starved conditions. In addition, Δphx1 mutant was more sensitive to various oxidants and heat shock. When we examined sporulation of the Δphx1/Δphx1 diploid strain, significant decrease in the formation of meiotic spores was observed.

CONCLUSIONS

Phx1 is a transcriptional regulator whose synthesis is elevated during stationary phase and by nutrient starvation in S. pombe. It supports long-term survival and stress tolerance against oxidation and heat, and plays a key role in the formation of meiotic spores.

Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast

While typically many expression levels change in transcription factor mutants, only few of these changes lead to functional changes. The predictive capability of expression and DNA binding data for such functional changes in metabolism is very limited.

Large-scale ¹³C-flux data reveal the condition specificity of transcriptional control of metabolic function.

Transcription control in yeast focuses on the switch between respiration and fermentation.

Follow-up modeling on the basis of transcriptomics and proteomics data suggest the newly discovered Gcn4 control of respiration to be mediated via PKA and Snf1.

Effective control and modulation of cellular behavior is of paramount importance in medicine (Kreeger and Lauffenburger, 2010) and biotechnology (Haynes and Silver, 2009), and requires profound understanding of control mechanisms. In this study, we aim to elucidate the extent to which transcription factors control the operation of yeast metabolism. As a quantitative readout of metabolic function, we monitored the traffic of small molecules through various pathways of central metabolism by ¹³C-flux analysis (Sauer, 2006). The choosen growth conditions represent two different regulatory states of reduced (galactose) and maximal carbon source repression (glucose), as well as a different nitrogen metabolism and two common, permanent stress conditions.

Depending on the growth condition, between 7 and 13% of the deleted transcription factors altered the determined flux ratios (Figure 3). Of the six quantified flux ratios, only the glycolysis/pentose phosphate pathway split, and the convergent ratio of anaplerosis and TCA cycle were controlled by the deleted transcription factors. Thus, we concluded that 23 transcription factors control flux distributions under at least one of the tested growth conditions, leading to 42 condition-dependent interactions of transcription factors with metabolic pathway activity (Figure 4). With two exceptions, all other identified transcription factors interactions controlled the TCA cycle flux. This condition-specific active control of metabolic function could not have been predicted from DNA binding and expression data; that is, 26.1% false negatives, 48.6% true positives.

Of the 23 transcription factors that controlled TCA cycle flux distributions under the tested conditions, only Bas1, Gcn4, Gcr2 and Pho2 exerted control under more than one condition. We identified Cit1, Mdh1 and Idh1/2 with a proteomics approach as the relevant target enzyme that increase the TCA cycle flux. Next, we asked whether Bas1, Gcr2, Gcn4 and Pho2 act directly on the TCA cycle or mediate their effect indirectly. Based on the transcriptomics data, the pattern of differentially activated transcription factors inferred by the differential expression of their target genes suggested reduced glucose repression in all four mutants as the common mechanism.

Starting from the currently largest set of ¹³C-based flux distributions, we identified networks of individual transcription factors that control metabolic pathway activity. These networks of active metabolic control have the following properties. First, they are highly condition dependent, as at most four transcription factors control the same metabolic flux distribution under more than one growth conditions. Second, they focus almost exclusively on the TCA cycle, thereby controlling the switch between respiratory and fermentative metabolism. Third, with four to 14 active transcription factors, they are small compared with gene regulation networks that were obtained from expression and DNA binding data. For the metabolic network studied here, robustness is also apparent from the fact that upregulated TCA cycle fluxes were not sufficient to achieve full respiratory metabolism; that is, absent or low ethanol formation. Several explanations could potentially explain the observed robustness. The most likely explanation is that environmental signals might be transmitted by different signaling pathways to several transcription factors, whose orchestrated action on multiple target genes is necessary to achieve a functional flux response. This hypothesis would explain why several transcription factors exert flux effects on the same pathway, but each flux effect is relatively small, as further, coordinated manipulations would be necessary to further improve the respiratory flux. Our findings demonstrate the importance of identifying and quantifying the extent to which regulatory effectors alter cellular function.

Which transcription factors control the distribution of metabolic fluxes under a given condition? We address this question by systematically quantifying metabolic fluxes in 119 transcription factor deletion mutants of Saccharomyces cerevisiae under five growth conditions. While most knockouts did not affect fluxes, we identified 42 condition-dependent interactions that were mediated by a total of 23 transcription factors that control almost exclusively the cellular decision between respiration and fermentation. This relatively sparse, condition-specific network of active metabolic control contrasts with the much larger gene regulation network inferred from expression and DNA binding data. Based on protein and transcript analyses in key mutants, we identified three enzymes in the tricarboxylic acid cycle as the key targets of this transcriptional control. For the transcription factor Gcn4, we demonstrate that this control is mediated through the PKA and Snf1 signaling cascade. The discrepancy between flux response predictions, based on the known regulatory network architecture and our functional ¹³C-data, demonstrates the importance of identifying and quantifying the extent to which regulatory effectors alter cellular functions.

Activation of the ADE genes requires the chromatin remodeling complexes SAGA and SWI/SNF

The activation of the ADE regulon genes requires the pair of transcription factors Bas1 and Pho2. In a genome-wide screen for additional regulators of the pathway, strains with mutations in multiple subunits of the chromatin remodeling complexes SAGA and SWI/SNF were uncovered. These mutants exhibited decreased expression of an ADE5,7-lacZ reporter and native ADE compared to the wild-type strains, but the expression of the BAS1 and PHO2 genes was not substantially decreased. An unregulated Bas1-Pho2 fusion protein depended upon SAGA and SWI/SNF activity to promote transcription of a reporter. A significant but low-level association of Gcn5-myc and Snf2-myc with the ADE5,7 promoter was independent of adenine growth conditions and independent of the presence of the activator proteins Bas1 and Pho2. However, the increase in occupancy of Bas1 and Pho2 at ADE5,7 depended on both SAGA and SWI/SNF. The loss of catalytic activity of both SAGA and SWI/SNF complexes in the gcn5Delta snf2Delta double mutant was severely detrimental to ADE-lacZ reporter expression and native ADE gene expression, indicating complementary roles for these complexes. We conclude that Bas1 and Pho2 do not recruit the SAGA and SWI/SNF complexes to the ADE5,7 promoter but that the remodeling complexes are necessary to increase the binding of Bas1 and Pho2 in response to the adenine regulatory signal. Our data support the model that the SAGA and SWI/SNF complexes engage in global surveillance that is necessary for the specific response by Bas1 and Pho2.

Regulation of purine nucleotide biosynthesis: in yeast and beyond

Purine nucleotides are critically important for the normal functioning of cells due to their myriad of activities. It is important for cells to maintain a balance in the pool sizes of the adenine-containing and guanine-containing nucleotides, which occurs by a combination of de novo synthesis and salvage pathways that interconvert the purine nucleotides. This review describes the mechanism for regulation of the biosynthetic genes in the yeast Saccharomyces cerevisiae and compares this mechanism with that described in several microbial species.

DNA-bound Bas1 recruits Pho2 to activate ADE genes in Saccharomyces cerevisiae

Expression of the genes in the ADE regulon of Saccharomyces cerevisiae is repressed by the presence of purine bases in the extracellular medium and derepressed when cells are grown in the absence of purines. Derepression requires the transcriptional activators Bas1 and Pho2, as well as the biosynthetic intermediates 5'-phosphoribosyl-4-succinocarboxamide-5-aminoimidazole (SAICAR) and 5'-phosphoribosyl-4-carboxamide- 5-aminoimidazole (AICAR). In this study, we investigated if nuclear localization and binding to promoter DNA by the activators are regulated by purines. Using indirect immunofluorescence, we found that Bas1 is localized to the nucleus under both repressing and derepressing conditions. Importantly, we detected Bas1 bound to promoter DNA under both conditions using chromatin immunoprecipitation assays at several ADE promoters (ADE1, ADE2, ADE4, and ADE5,7) and HIS4. We analyzed the binding of Bas1 to wild-type and mutant sequences of the ADE5,7 promoters in vivo, and found that Bas1 binds independently to each of its two binding sites. Pho2 was not required for the association of Bas1 with chromosomal DNA, but it was required for an increase in Bas1-immunoprecipitated DNA. The presence of Pho2 at promoters was dependent on Bas1 and occurred only under derepressing conditions when the ADE genes are transcribed at elevated levels. We propose a model for regulation of the ADE genes in which DNA-bound Bas1 is inactive due to masking of its activation domain and Pho2 binds poorly to promoters when cells have sufficient purine nucleotides. Upon limitation for purines, the SAICAR/AICAR regulatory signal is transmitted to the nucleus to increase Bas1 and Pho2 interaction, recruiting Pho2 to promoters and freeing the activation domains for transactivation.