The <i>UGA3‐GLT1</i> intergenic region constitutes a promoter whose bidirectional nature is determined by chromatin organization in <i>Saccharomyces cerevisiae</i>

Ishida, Cecilia; Aranda, Cristina; Valenzuela, Lourdes; Riego, Lina; DeLuna, Alexander; Recillas‐Targa, Félix; Filetici, Patrizia; López‐Revilla, Rubén; González, Alicia

doi:10.1111/j.1365-2958.2006.05055.x

Cited by 21 publications

(8 citation statements)

References 53 publications

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“…Gcn4p was suggested to contribute to the transcription of Gln3p-targeted genes, DAL1 and DAL5, which are important for uptake and degradation of the nitrogen source allantoin and for UGA3, a focus of their study (50,73). Those findings further support the idea that the transcription of genes involved in nitrogen assimilation can be coordinately regulated by Gcn4p and Gln3p, as illustrated in Fig.…”

Section: Discussionsupporting

confidence: 73%

Integration of General Amino Acid Control and Target of Rapamycin (TOR) Regulatory Pathways in Nitrogen Assimilation in Yeast

Staschke

Dey

Zaborske

et al. 2010

Journal of Biological Chemistry

114

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Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), participate in the control of yeast growth and metabolism during changes in nutrient availability. Amino acid starvation activates the GAAC through Gcn2p phosphorylation of translation factor eIF2 and preferential translation of GCN4, a transcription activator. TOR senses nitrogen availability and regulates transcription factors such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome during amino acid starvation and rapamycin treatment. We found that GAAC is a major effector of the TOR pathway, with Gcn4p and Gln3p each inducing a similar number of genes during rapamycin treatment. Although Gcn4p activates a common core of 57 genes, the GAAC directs significant variations in the transcriptome during different stresses. In addition to inducing amino acid biosynthetic genes, Gcn4p in conjunction with Gln3p activates genes required for the assimilation of secondary nitrogen sources such as ␥-aminobutyric acid (GABA). Gcn2p activation upon shifting to secondary nitrogen sources is suggested to occur by means of a dual mechanism. First, Gcn2p is induced by the release of TOR repression through a mechanism involving Sit4p protein phosphatase. Second, this eIF2 kinase is activated by select uncharged tRNAs, which were shown to accumulate during the shift to the GABA medium. This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation.

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Section: Discussionsupporting

confidence: 73%

Integration of General Amino Acid Control and Target of Rapamycin (TOR) Regulatory Pathways in Nitrogen Assimilation in Yeast

Staschke

Dey

Zaborske

et al. 2010

Journal of Biological Chemistry

114

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“…1) (85, 136). Among them, GLN1 and GDH2 were previously established as being sensitive to NCR (84), but GDH1 and GLT1 were not, although observations consistent with this view have been reported (65,129). It thus seems that the complete set of enzymes forming the heart of nitrogen metabolism in yeast is subject to NCR.…”

Section: Discussionmentioning

confidence: 56%

“…While these observations indicate that the transcription of GCN4 is subject to NCR, two other studies have highlighted a positive contribution of Gcn4 in NCR (118,128), thus suggesting some cross-regulation between NCR and GAAC (see Discussion). Yet another transcription factor gene classified as an NCR target is UGA3, in keeping with a recent report (65). This factor is responsible for induction by GABA of the transcription of genes involved in GABA catabolism (2,121).…”

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confidence: 56%

Effect of 21 Different Nitrogen Sources on Global Gene Expression in the YeastSaccharomyces cerevisiae

Godard

Urrestarazu

Vissers

et al. 2007

Molecular and Cellular Biology

220

270

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We compared the transcriptomes of Saccharomyces cerevisiae cells growing under steady-state conditions on 21 unique sources of nitrogen. We found 506 genes differentially regulated by nitrogen and estimated the activation degrees of all identified nitrogen-responding transcriptional controls according to the nitrogen source. One main group of nitrogenous compounds supports fast growth and a highly active nitrogen catabolite repression (NCR) control. Catabolism of these compounds typically yields carbon derivatives directly assimilable by a cell's metabolism. Another group of nitrogen compounds supports slower growth, is associated with excretion by cells of nonmetabolizable carbon compounds such as fusel oils, and is characterized by activation of the general control of amino acid biosynthesis (GAAC). Furthermore, NCR and GAAC appear interlinked, since expression of the GCN4 gene encoding the transcription factor that mediates GAAC is subject to NCR. We also observed that several transcriptional-regulation systems are active under a wider range of nitrogen supply conditions than anticipated. Other transcriptional-regulation systems acting on genes not involved in nitrogen metabolism, e.g., the pleiotropic-drug resistance and the unfolded-protein response systems, also respond to nitrogen. We have completed the lists of target genes of several nitrogen-sensitive regulons and have used sequence comparison tools to propose functions for about 20 orphan genes. Similar studies conducted for other nutrients should provide a more complete view of alternative metabolic pathways in yeast and contribute to the attribution of functions to many other orphan genes.

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“…The mode of interaction in divergent promoters can be quite diverse. Coexpression can be explained by bidirectional transcription attributable to various factors, including common cis -regulatory elements (in MAL6T-MAL6S ) (Bell et al 1995) or chromatin organization (in UGA3-GLT1 ) (Ishida et al 2006). In contrast, some studies reported no dependence on gene orientation (Bae et al 2008) and others reported anticorrelated gene expression between divergent genes (Lin et al 2007).…”

Section: Discussionmentioning

confidence: 99%

Suppression of Expression Between Adjacent Genes Within Heterologous Modules in Yeast

Lee

Parikh

Weitz

et al. 2014

G3 Genes|Genomes|Genetics

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Recent studies have shown that proximal arrangement of multiple genes can have complex effects on gene expression. For example, in the case of heterologous gene expression modules, certain arrangements of the selection marker and the gene expression cassette may have unintended consequences that limit the predictability and interpretability of module behaviors. The relationship between arrangement and expression has not been systematically characterized within heterologous modules to date. In this study, we quantitatively measured gene expression patterns of the selection marker (KlURA3 driven by the promoter, pKlURA) and the gene expression cassette (GFP driven by the galactose-inducible GAL1 promoter, pGAL1) in all their possible relative arrangements in Saccharomyces cerevisiae. First, we observed that pKlURA activity depends strongly on the relative arrangement and the activity of pGAL1. Most notably, we observed transcriptional suppression in the case of divergent arrangements: pKlURA activity was reduced when pGAL1 was inactive. Based on our nucleosome occupancy data, we attribute the observed transcriptional reduction to nucleosome repositioning. Second, we observed that pGAL1 activity also depends on the relative arrangement of pKlURA. In particular, strains with divergent promoters showed significantly different pGAL1 activation patterns from other strains, but only when their growth was compromised by lack of uracil. We reasoned that this difference in pGAL1 activation patterns arises from arrangement-dependent pKlURA activity that can affect the overall cell physiology (i.e., cell growth and survival in the uracil-depleted condition). Our results underscore the necessity to consider ramifications of promoter arrangement when using synthetic gene expression modules.

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The UGA3‐GLT1 intergenic region constitutes a promoter whose bidirectional nature is determined by chromatin organization in Saccharomyces cerevisiae

Cited by 21 publications

References 53 publications

Integration of General Amino Acid Control and Target of Rapamycin (TOR) Regulatory Pathways in Nitrogen Assimilation in Yeast

Integration of General Amino Acid Control and Target of Rapamycin (TOR) Regulatory Pathways in Nitrogen Assimilation in Yeast

Effect of 21 Different Nitrogen Sources on Global Gene Expression in the YeastSaccharomyces cerevisiae

Suppression of Expression Between Adjacent Genes Within Heterologous Modules in Yeast

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