Cohesin Irr1/Scc3 is likely to influence transcription in Saccharomyces cerevisiae via interaction with Mediator complex.

The evolutionarily conserved proteins forming sister chromatid cohesion complex are also involved in the regulation of gene transcription. The participation of SA2p (mammalian ortholog of yeast Irr1p, associated with the core of the complex) in the regulation of transcription is already described. Here we analyzed microarray profiles of gene expression of a Saccharomyces cerevisiae irr1-1/IRR1 heterozygous diploid strain. We report that expression of 33 genes is affected by the presence of the mutated Irr1-1p and identify those genes. This supports the suggested role of Irr1p in the regulation of transcription. We also indicate that Irr1p may interact with elements of transcriptional coactivator Mediator.

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A Role for Mediator Core in Limiting Coactivator Recruitment in Saccharomyces cerevisiae

Genetics ◽

10.1534/genetics.120.303254 ◽

2020 ◽

Vol 215 (2) ◽

pp. 407-420 ◽

Cited By ~ 1

Author(s):

Robert M. Yarrington ◽

Yaxin Yu ◽

Chao Yan ◽

Lu Bai ◽

David J. Stillman

Keyword(s):

Saccharomyces Cerevisiae ◽

Gene Regulation ◽

Transcription Factors ◽

Gene Activation ◽

Mediator Complex ◽

Transcriptional Coactivator ◽

The Core ◽

Link Type ◽

Upstream Activating Sequence ◽

Eukaryotic Organisms

Mediator is an essential, multisubunit complex that functions as a transcriptional coactivator in yeast and other eukaryotic organisms. Mediator has four conserved modules, Head, Middle, Tail, and Kinase, and has been implicated in nearly all aspects of gene regulation. The Tail module has been shown to recruit the Mediator complex to the enhancer or upstream activating sequence (UAS) regions of genes via interactions with transcription factors, and the Kinase module facilitates the transition of Mediator from the UAS/enhancer to the preinitiation complex via protein phosphorylation. Here, we analyze expression of the Saccharomyces cerevisiae HO gene using a sin4 Mediator Tail mutation that separates the Tail module from the rest of the complex; the sin4 mutation permits independent recruitment of the Tail module to promoters without the rest of Mediator. Significant increases in recruitment of the SWI/SNF and SAGA coactivators to the HO promoter UAS were observed in a sin4 mutant, along with increased gene activation. These results are consistent with recent studies that have suggested that the Kinase module functions negatively to inhibit activation by the Tail. However, we found that Kinase module mutations did not mimic the effect of a sin4 mutation on HO expression. This suggests that at HO the core Mediator complex (Middle and Head modules) must play a role in limiting Tail binding to the promoter UAS and gene activation. We propose that the core Mediator complex helps modulate Mediator binding to the UAS regions of genes to limit coactivator recruitment and ensure proper regulation of gene transcription.

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Independent Recruitment of the Mediator Tail Module to the HO Promoter Suggests Mediator Core Limits Coactivator Recruitment in Saccharomyces cerevisiae

10.1101/766006 ◽

2019 ◽

Author(s):

Robert M. Yarrington ◽

Yaxin Yu ◽

Chao Yan ◽

Lu Bai ◽

David J. Stillman

Keyword(s):

Saccharomyces Cerevisiae ◽

Gene Regulation ◽

Transcription Factors ◽

Gene Transcription ◽

Gene Activation ◽

Kinase Domain ◽

Mediator Complex ◽

Transcriptional Coactivator ◽

The Core ◽

Eukaryotic Organisms

ABSTRACTMediator is an essential, multisubunit complex that functions as a transcriptional coactivator in yeast and other eukaryotic organisms. Mediator has four conserved modules, Head, Middle, Tail, and Kinase, and has been implicated in nearly all aspects of gene regulation. The Tail module has been shown to recruit the Mediator complex to the enhancer or UAS regions of genes via interactions with transcription factors, and the Kinase domain facilitates the transition of Mediator from the UAS/enhancer to the preinitiation complex via protein phosphorylation. Here we analyze expression of the Saccharomyces cerevisiae HO gene using a sin4 Mediator Tail mutation that separates the Tail module from the rest of the complex; the sin4 mutation permits independent recruitment of the Tail module to promoters without the rest of Mediator. Significant increases in recruitment of the SWI/SNF and SAGA coactivators to the HO promoter UAS were observed in a sin4 mutant, along with increased gene activation. These results are consistent with recent studies that have suggested the Kinase module functions negatively to inhibit activation by the Tail. However, we found that Kinase module mutations did not mimic the effect of a sin4 mutation on HO expression. This suggests that at HO the core Mediator complex (Middle and Head modules) must play a role in limiting Tail binding to the promoter UAS and gene activation. We propose that the core Mediator complex helps modulate Mediator binding to the UAS regions of genes to limit coactivator recruitment and ensure proper regulation of gene transcription.

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Postrecruitment Function of Yeast Med6 Protein during the Transcriptional Activation by Mediator Complex

Biochemistry Research International ◽

10.1155/2018/6406372 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9

Author(s):

Gwang Sik Kim ◽

Young Chul Lee

Keyword(s):

Gene Expression ◽

Reporter Gene ◽

Transcriptional Activation ◽

Reporter Gene Expression ◽

Temperature Sensitive ◽

Internal Deletion ◽

Cell Extracts ◽

Evolutionarily Conserved

Med6 protein (Med6p) is a hallmark component of evolutionarily conserved Mediator complexes, and the genuine role of Med6p in Mediator functions remains elusive. For the functional analysis ofSaccharomyces cerevisiaeMed6p (scMed6p), we generated a series of scMed6p mutants harboring a small internal deletion. Genetic analysis of these mutants revealed that three regions (amino acids 33–42 (Δ2), 125–134 (Δ5), and 157–166 (Δ6)) of scMed6p are required for cell viability and are located at highly conserved regions of Med6 homologs. Notably, the Med6p-Δ2 mutant was barely detectable in whole-cell extracts and purified Mediator, suggesting a loss of Mediator association and concurrent rapid degradation. Consistent with this, the recombinant forms of Med6p having these mutations partially (Δ2) restore or fail (Δ5 and Δ6) to restore in vitro transcriptional defects caused by temperature-sensitivemed6mutation. In an artificial recruitment assay, Mediator containing a LexA-fused wild-type Med6p or Med6p-Δ5 was recruited to thelexAoperator region with TBP and activated reporter gene expression. However, the recruitment of Mediator containing LexA-Med6p-Δ6 tolexAoperator region resulted in neither TBP recruitment nor reporter gene expression. This result demonstrates a pivotal role of Med6p in the postrecruitment function of Mediator, which is essential for transcriptional activation by Mediator.

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A UPF1 variant drives conditional remodeling of nonsense-mediated mRNA decay

10.1101/2021.01.27.428318 ◽

2021 ◽

Author(s):

Sarah E. Fritz ◽

Soumya Ranganathan ◽

J. Robert Hogg

Keyword(s):

Gene Expression ◽

Mrna Decay ◽

Gene Expression Regulation ◽

Translation Termination ◽

Translational Repression ◽

The Core ◽

Human Genes ◽

Rna Quality Control ◽

Nonsense Mediated Mrna Decay

AbstractThe nonsense-mediated mRNA decay (NMD) pathway monitors translation termination to degrade transcripts with premature stop codons and regulate thousands of human genes. Due to the major role of NMD in RNA quality control and gene expression regulation, it is important to understand how the pathway responds to changing cellular conditions. Here we show that an alternative mammalian-specific isoform of the core NMD factor UPF1, termed UPF1LL, enables condition-dependent remodeling of NMD specificity. UPF1LL associates more stably with potential NMD target mRNAs than the major UPF1SL isoform, expanding the scope of NMD to include many transcripts normally immune to the pathway. Unexpectedly, the enhanced persistence of UPF1LL on mRNAs supports induction of NMD in response to rare translation termination events. Thus, while canonical NMD is abolished by translational repression, UPF1LL activity is enhanced, providing a mechanism to rapidly rewire NMD specificity in response to cellular stress.

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Hrr25 triggers selective autophagy–related pathways by phosphorylating receptor proteins

The Journal of Cell Biology ◽

10.1083/jcb.201402128 ◽

2014 ◽

Vol 207 (1) ◽

pp. 91-105 ◽

Cited By ~ 69

Author(s):

Chikara Tanaka ◽

Li-Jing Tan ◽

Keisuke Mochida ◽

Hiromi Kirisako ◽

Michiko Koizumi ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Molecular Basis ◽

Receptor Proteins ◽

Selective Autophagy ◽

The Core ◽

The Common ◽

Related Proteins

In selective autophagy, degradation targets are specifically recognized, sequestered by the autophagosome, and transported into the lysosome or vacuole. Previous studies delineated the molecular basis by which the autophagy machinery recognizes those targets, but the regulation of this process is still poorly understood. In this paper, we find that the highly conserved multifunctional kinase Hrr25 regulates two distinct selective autophagy–related pathways in Saccharomyces cerevisiae. Hrr25 is responsible for the phosphorylation of two receptor proteins: Atg19, which recognizes the assembly of vacuolar enzymes in the cytoplasm-to-vacuole targeting pathway, and Atg36, which recognizes superfluous peroxisomes in pexophagy. Hrr25-mediated phosphorylation enhances the interactions of these receptors with the common adaptor Atg11, which recruits the core autophagy-related proteins that mediate the formation of the autophagosomal membrane. Thus, this study introduces regulation of selective autophagy as a new role of Hrr25 and, together with other recent studies, reveals that different selective autophagy–related pathways are regulated by a uniform mechanism: phosphoregulation of the receptor–adaptor interaction.

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Intracellular Maltose Is Sufficient To Induce MAL Gene Expression in Saccharomyces cerevisiae

Eukaryotic Cell ◽

10.1128/ec.1.5.696-703.2002 ◽

2002 ◽

Vol 1 (5) ◽

pp. 696-703 ◽

Cited By ~ 22

Author(s):

Xin Wang ◽

Mehtap Bali ◽

Igor Medintz ◽

Corinne A. Michels

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Plantago Major ◽

Null Mutant ◽

Transport Activity ◽

Maltose Permease ◽

Maltose Transport ◽

Constitutive Overexpression ◽

Reduced Rate

ABSTRACT The presence of maltose induces MAL gene expression in Saccharomyces cells, but little is known about how maltose is sensed. Strains with all maltose permease genes deleted are unable to induce MAL gene expression. In this study, we examined the role of maltose permease in maltose sensing by substituting a heterologous transporter for the native maltose permease. PmSUC2 encodes a sucrose transporter from the dicot plant Plantago major that exhibits no significant sequence homology to maltose permease. When expressed in Saccharomyces cerevisiae, PmSUC2 is capable of transporting maltose, albeit at a reduced rate. We showed that introduction of PmSUC2 restores maltose-inducible MAL gene expression to a maltose permease-null mutant and that this induction requires the MAL activator. These data indicate that intracellular maltose is sufficient to induce MAL gene expression independently of the mechanism of maltose transport. By using strains expressing defective mal61 mutant alleles, we demonstrated a correlation between the rate of maltose transport and the level of the induction, which is particularly evident in medium containing very limiting concentrations of maltose. Moreover, our results indicate that a rather low concentration of intracellular maltose is needed to trigger MAL gene expression. We also showed that constitutive overexpression of either MAL61 maltose permease or PmSUC2 suppresses the noninducible phenotype of a defective mal13 MAL-activator allele, suggesting that this suppression is solely a function of maltose transport activity and is not specific to the sequence of the permease. Our studies indicate that maltose permease does not function as the maltose sensor in S. cerevisiae.

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Distinct molecular etiologies of male and female hepatocellular carcinoma

BMC Cancer ◽

10.1186/s12885-019-6167-2 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 10

Author(s):

Heini M. Natri ◽

Melissa A. Wilson ◽

Kenneth H. Buetow

Keyword(s):

Gene Expression ◽

Hepatocellular Carcinoma ◽

Sex Differences ◽

Differential Expression ◽

Differential Expression Analysis ◽

Regulation Of Transcription ◽

Male And Female ◽

Differential Effects ◽

Pathway Enrichment

Abstract Background Sex-differences in cancer occurrence and mortality are evident across tumor types; men exhibit higher rates of incidence and often poorer responses to treatment. Targeted approaches to the treatment of tumors that account for these sex-differences require the characterization and understanding of the fundamental biological mechanisms that differentiate them. Hepatocellular Carcinoma (HCC) is the second leading cause of cancer death worldwide, with the incidence rapidly rising. HCC exhibits a male-bias in occurrence and mortality, but previous studies have failed to explore the sex-specific dysregulation of gene expression in HCC. Methods Here, we characterize the sex-shared and sex-specific regulatory changes in HCC tumors in the TCGA LIHC cohort using combined and sex-stratified differential expression and eQTL analyses. Results By using a sex-specific differential expression analysis of tumor and tumor-adjacent samples, we uncovered etiologically relevant genes and pathways differentiating male and female HCC. While both sexes exhibited activation of pathways related to apoptosis and cell cycle, males and females differed in the activation of several signaling pathways, with females showing PPAR pathway enrichment while males showed PI3K, PI3K/AKT, FGFR, EGFR, NGF, GF1R, Rap1, DAP12, and IL-2 signaling pathway enrichment. Using eQTL analyses, we discovered germline variants with differential effects on tumor gene expression between the sexes. 24.3% of the discovered eQTLs exhibit differential effects between the sexes, illustrating the substantial role of sex in modifying the effects of eQTLs in HCC. The genes that showed sex-specific dysregulation in tumors and those that harbored a sex-specific eQTL converge in clinically relevant pathways, suggesting that the molecular etiologies of male and female HCC are partially driven by differential genetic effects on gene expression. Conclusions Sex-stratified analyses detect sex-specific molecular etiologies of HCC. Overall, our results provide new insight into the role of inherited genetic regulation of transcription in modulating sex-differences in HCC etiology and provide a framework for future studies on sex-biased cancers.

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Regulation of mitochondrial gene expression in Saccharomyces cerevisiae: the role of RNA-binding enzymes

BMC News and views ◽

10.1186/2048-4623-1-s1-or009 ◽

2001 ◽

Vol 1 (S1) ◽

Author(s):

H van der Spek ◽

M Siep ◽

L de Jong ◽

SDJ Elzinga ◽

K van Oosterum ◽

...

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Rna Binding ◽

Mitochondrial Gene ◽

Mitochondrial Gene Expression

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Role of HSP90 in Salt Stress Tolerance via Stabilization and Regulation of Calcineurin

Molecular and Cellular Biology ◽

10.1128/mcb.20.24.9262-9270.2000 ◽

2000 ◽

Vol 20 (24) ◽

pp. 9262-9270 ◽

Cited By ~ 85

Author(s):

Jun Imai ◽

Ichiro Yahara

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Salt Stress ◽

Stress Tolerance ◽

Normal Level ◽

Immune Complexes ◽

Salt Stress Tolerance ◽

Stressed Cells ◽

Calcineurin Activity

ABSTRACT The role of HSP90 in stress tolerance was investigated inSaccharomyces cerevisiae. Cells showing 20-fold overexpression of Hsc82, an HSP90 homologue in yeast, were hypersensitive to high-NaCl or H-LiCl stresses. Hsc82-overexpressing cells appeared similar to calcineurin-defective cells in salt sensitivity and showed reduced levels of calcineurin-dependent gene expression. Co-overexpression of Cna2, the catalytic subunit of calcineurin, suppressed the hypersensitivity. Cna2 and Hsc82 coimmunoprecipitated from control cells grown under normal conditions but not from stressed cells. In contrast, coimmunoprecipitation was detected with Hsc82-overexpressing cells even after exposure to stresses. Cna2 immune complexes from stressed control cells showed a significant level of calcineurin activity, whereas those from stressed Hsc82-overexpressing cells did not. Treatment of extracts from Hsc82-overexpressing cells with Ca2+-calmodulin increased the calcineurin activity associated with Cna2 immune complexes. Geldanamycin, an inhibitor of HSP90 abolished the coimmunoprecipitation but did not activate calcineurin. When the expression level of Hsc82 decreased to below 30% of the normal level, cells also became hypersensitive to salt stress. In these cells, the amount of Cna2 was reduced, likely as a result of degradation. The present results showed that Hsc82 binds to and stabilizes Cna2 and that dissociation of Cna2 from Hsc82 is necessary for its activation.

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Interplay of a Ligand Sensor and an Enzyme in Controlling Expression of the Saccharomyces cerevisiae GAL Genes

Eukaryotic Cell ◽

10.1128/ec.05294-11 ◽

2011 ◽

Vol 11 (3) ◽

pp. 334-342 ◽

Cited By ~ 17

Author(s):

Dariusz Abramczyk ◽

Stacey Holden ◽

Christopher J. Page ◽

Richard J. Reece

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Transcriptional Control ◽

Transcriptional Response ◽

Content Type ◽

Considerable Debate ◽

Active Transcription ◽

Gal Genes ◽

The Subject

ABSTRACT The regulation of the Saccharomyces cerevisiae GAL genes in response to galactose as a source of carbon has served as a paradigm for eukaryotic transcriptional control over the last 50 years. Three proteins—a transcriptional activator (Gal4p), an inhibitor (Gal80p), and a ligand sensor (Gal3p)—control the switch between inert and active gene expression. The molecular mechanism by which the recognition of galactose within the cell is converted into a transcriptional response has been the subject of considerable debate. In this study, using a novel and powerful method of localizing active transcription factors within the nuclei of cells, we show that a short-lived complex between Gal4p, Gal80p, and Gal3p occurs soon after the addition of galactose to cells to activate GAL gene expression. Gal3p is subsequently replaced in this complex by Gal1p, and a Gal4p-Gal80p-Gal1p complex is responsible for the continued expression of the GAL genes. The transient role of the ligand sensor indicates that current models for the induction and continued expression of the yeast GAL genes need to be reevaluated.

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