scholarly journals Ddi1 is a ubiquitin-dependent protease

2020 ◽  
Vol 117 (14) ◽  
pp. 7776-7781 ◽  
Author(s):  
Matthew C. J. Yip ◽  
Nicholas O. Bodnar ◽  
Tom A. Rapoport
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Enzymatic Activity ◽  
Yeast Cells ◽  
Polyubiquitin Chain ◽  
High Affinity ◽  
Helical Domain ◽  
Higher Eukaryotes ◽  
Affinity Interaction ◽  
Substrate Proteins

TheSaccharomyces cerevisiaeprotein Ddi1 and its homologs in higher eukaryotes have been proposed to serve as shuttling factors that deliver ubiquitinated substrates to the proteasome. Although Ddi1 contains both ubiquitin-interacting UBA and proteasome-interacting UBL domains, the UBL domain is atypical, as it binds ubiquitin. Furthermore, unlike other shuttling factors, Ddi1 and its homologs contain a conserved helical domain (helical domain of Ddi1, HDD) and a retroviral-like protease (RVP) domain. The RVP domain is probably responsible for cleavage of the precursor of the transcription factor Nrf1 in higher eukaryotes, which results in the up-regulation of proteasomal subunit genes. However, enzymatic activity of the RVP domain has not yet been demonstrated, and the function of Ddi1 remains poorly understood. Here, we show that Ddi1 is a ubiquitin-dependent protease, which cleaves substrate proteins only when they are tagged with long ubiquitin chains (longer than about eight ubiquitins). The RVP domain is inactive in isolation, in contrast to its retroviral counterpart. Proteolytic activity of Ddi1 requires the HDD domain and is stimulated by the UBL domain, which mediates high-affinity interaction with the polyubiquitin chain. Compromising the activity of Ddi1 in yeast cells results in the accumulation of polyubiquitinated proteins. Aside from the proteasome, Ddi1 is the only known endoprotease that acts on polyubiquitinated substrates. Ddi1 and its homologs likely cleave polyubiquitinated substrates under conditions where proteasome function is compromised.

Cloning and characterization of the low-affinity cyclic AMP phosphodiesterase gene of Saccharomyces cerevisiae

1987 ◽  
Vol 7 (10) ◽  
pp. 3629-3636
Author(s):  
J Nikawa ◽  
P Sass ◽  
M Wigler
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cyclic Amp ◽  
Copy Number ◽  
Growth Arrest ◽  
Yeast Cells ◽  
Phosphodiesterase Activity ◽  
Camp Phosphodiesterase ◽  
High Affinity ◽  
Cyclic Amp Phosphodiesterase

Saccharomyces cerevisiae contains two genes which encode cyclic AMP (cAMP) phosphodiesterase. We previously isolated and characterized PDE2, which encodes a high-affinity cAMP phosphodiesterase. We have now isolated the PDE1 gene of S. cerevisiae, which encodes a low-affinity cAMP phosphodiesterase. These two genes represent highly divergent branches in the evolution of phosphodiesterases. High-copy-number plasmids containing either PDE1 or PDE2 can reverse the growth arrest defects of yeast cells carrying the RAS2(Val-19) mutation. PDE1 and PDE2 appear to account for the aggregate cAMP phosphodiesterase activity of S. cerevisiae. Disruption of both PDE genes results in a phenotype which resembles that induced by the RAS2(Val-19) mutation. pde1- pde2- ras1- ras2- cells are viable.

scholarly journals The mitochondrial iron exporter genes MMT1 and MMT2 in yeast are transcriptionally regulated by Aft1 and Yap1

2020 ◽  
Vol 295 (6) ◽  
pp. 1716-1726 ◽  
Author(s):  
Liangtao Li ◽  
Sophie Bertram ◽  
Jerry Kaplan ◽  
Xuan Jia ◽  
Diane M. Ward
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Promoter Region ◽  
Iron Transport ◽  
Mitochondrial Proteins ◽  
Upstream Region ◽  
Iron Sulfur Cluster ◽  
High Affinity ◽  
Iron Sulfur ◽  
Mitochondrial Iron

Budding yeast (Saccharomyces cerevisiae) responds to low cytosolic iron by up-regulating the expression of iron import genes; iron import can reflect iron transport into the cytosol or mitochondria. Mmt1 and Mmt2 are nuclearly encoded mitochondrial proteins that export iron from the mitochondria into the cytosol. Here we report that MMT1 and MMT2 expression is transcriptionally regulated by two pathways: the low-iron-sensing transcription factor Aft1 and the oxidant-sensing transcription factor Yap1. We determined that MMT1 and MMT2 expression is increased under low-iron conditions and decreased when mitochondrial iron import is increased through overexpression of the high-affinity mitochondrial iron importer Mrs3. Moreover, loss of iron-sulfur cluster synthesis induced expression of MMT1 and MMT2. We show that exposure to the oxidant H2O2 induced MMT1 expression but not MMT2 expression and identified the transcription factor Yap1 as being involved in oxidant-mediated MMT1 expression. We defined Aft1- and Yap1-dependent transcriptional sites in the MMT1 promoter that are necessary for low-iron- or oxidant-mediated MMT1 expression. We also found that the MMT2 promoter contains domains that are important for regulating its expression under low-iron conditions, including an upstream region that appears to partially repress expression under low-iron conditions. Our findings reveal that MMT1 and MMT2 are induced under low-iron conditions and that the low-iron regulator Aft1 is required for this induction. We further uncover an Aft1-binding site in the MMT1 promoter sufficient for inducing MMT1 transcription and identify an MMT2 promoter region required for low iron induction.

scholarly journals High-Affinity Copper Transport and Snq2 Export Permease of Saccharomyces cerevisiae Modulate Cytotoxicity of PR-10 from Theobroma cacao

2009 ◽  
Vol 22 (1) ◽  
pp. 39-51 ◽  
Author(s):  
Cristina Pungartnik ◽  
Aline Clara da Silva ◽  
Sarah Alves de Melo ◽  
Karina Peres Gramacho ◽  
Júlio Cézar de Mattos Cascardo ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Theobroma Cacao ◽  
Single Gene ◽  
Copper Transport ◽  
Amino Acid Sequences ◽  
Yeast Cells ◽  
Antioxidant Defenses ◽  
Copper Transporter ◽  
High Affinity ◽  
Yeast Mutants

A pathogenesis-related (PR) protein from Theobroma cacao (TcPR-10) was identified from a cacao–Moniliophthora perniciosa interaction cDNA library. Nucleotide and amino acid sequences showed homology with other PR-10 proteins having P loop motif and Betv1 domain. Recombinant TcPR-10 showed in vitro and in vivo ribonuclease activity, and antifungal activity against the basidiomycete cacao pathogen M. perniciosa and the yeast Saccharomyces cerevisiae. Fluorescein isothiocyanate-labeled TcPR-10 was internalized by M. perniciosa hyphae and S. cerevisiae cells and inhibited growth of both fungi. Energy and temperature-dependent internalization of the TcPR-10 suggested an active importation into the fungal cells. Chronical exposure to TcPR-10 of 29 yeast mutants with single gene defects in DNA repair, general membrane transport, metal transport, and antioxidant defenses was tested. Two yeast mutants were hyperresistant compared with their respective isogenic wild type: ctr3Δ mutant, lacking the high-affinity plasma membrane copper transporter and mac1Δ, the copper-sensing transcription factor involved in regulation of high-affinity copper transport. Acute exposure of exponentially growing yeast cells revealed that TcPR-10 resistance is also enhanced in the Snq2 export permease-lacking mutant which has reduced intracellular presence of TcPR-10.

Adenovirus transcriptional regulatory regions are conserved in mammalian cells and Saccharomyces cerevisiae

1988 ◽  
Vol 8 (9) ◽  
pp. 3717-3725
Author(s):  
M Kornuc ◽  
R Altman ◽  
D Harrich ◽  
J Garcia ◽  
J Chao ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Binding Sites ◽  
Mammalian Cells ◽  
Yeast Cells ◽  
Binding Domains ◽  
Cell Extracts ◽  
Dnase I Footprinting ◽  
Transactivator Protein

The adenovirus early region 3 (E3) promoter is an early viral promoter which is strongly induced by the adenovirus transactivator protein E1A. DNase I footprinting with HeLa cell extracts has identified four factor-binding domains which appear to be involved in basal and E1A-induced transcriptional regulation. These binding domains may bind TATA region-binding factors (site I), the CREB/ATF protein (site II), the AP-1 protein (site III), and nuclear factor I/CTF (site IV). Recently, it has been shown that the DNA-binding domain of transcription factor AP-1 has homology with the yeast transcription factor GCN4 and that the yeast transactivator protein GAL4 is able to stimulate transcription in HeLa cells from promoters containing GAL4-binding sites. These results suggest an evolutionary conservation of both transcription factors and the mechanisms responsible for transcriptional activation in Saccharomyces cerevisiae and higher eucaryotic organisms. To determine whether similar patterns of transcriptional regulation were seen with the E3 promoter in HeLa and yeast cells, the E3 promoter fused to the chloramphenicol acetyltransferase (cat) gene was cloned into a high-copy-number plasmid and stably introduced into yeast cells. S1 analysis revealed that similar E3 promoter mRNA start sites were found in yeast and HeLa cells. DNase I footprinting with partially purified yeast extracts revealed that four regions of the E3 promoter were protected. Several of these regions were similar to binding sites determined by using HeLa cell extracts. Oligonucleotide mutagenesis of these binding domains indicated their importance in the transcriptional regulation of the E3 promoter in yeast cells. These results suggest that similar cellular transcription factor-binding sites may be involved in the regulation of promoters in both yeast and mammalian cells.

scholarly journals Pho85 Kinase, a Cyclin-Dependent Kinase, Regulates Nuclear Accumulation of the Rim101 Transcription Factor in the Stress Response of Saccharomyces cerevisiae

2010 ◽  
Vol 9 (6) ◽  
pp. 943-951 ◽  
Author(s):  
Masafumi Nishizawa ◽  
Mirai Tanigawa ◽  
Michio Hayashi ◽  
Tatsuya Maeda ◽  
Yoshiaki Yazaki ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Cellular Response ◽  
Proteolytic Processing ◽  
Yeast Cells ◽  
Nuclear Accumulation ◽  
Alkaline Stress ◽  
Content Type ◽  
Its Gene ◽  
Alkaline Conditions

ABSTRACT The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to changing environmental conditions. The Pho85 kinase, one of the yeast cyclin-dependent kinases (CDK), is known to play an important role in the cellular response to alterations in parameters such as nutrient levels and salinity. Several genes whose expression is regulated, either directly or indirectly, by the Rim101 transcription factor become constitutively activated when Pho85 function is absent,. Because Rim101 is responsible for adaptation to alkaline conditions, this observation suggests an interaction between Pho85 and Rim101 in the response to alkaline stress. We have found that Pho85 affects neither RIM101 transcription, the proteolytic processing that is required for Rim101 activation, nor Rim101 stability. Rather, Pho85 regulates the nuclear accumulation of active Rim101, possibly via phosphorylation. Additionally, we report that Pho85 and the transcription factor Pho4 are necessary for adaptation to alkaline conditions and that PTK2 activation by Pho4 is involved in this process. These findings illustrate novel roles for the regulators of the PHO system when yeast cells cope with various environmental stresses potentially threatening their survival.

scholarly journals Adenovirus transcriptional regulatory regions are conserved in mammalian cells and Saccharomyces cerevisiae.

1988 ◽  
Vol 8 (9) ◽  
pp. 3717-3725 ◽  
Author(s):  
M Kornuc ◽  
R Altman ◽  
D Harrich ◽  
J Garcia ◽  
J Chao ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Binding Sites ◽  
Mammalian Cells ◽  
Yeast Cells ◽  
Binding Domains ◽  
Cell Extracts ◽  
Dnase I Footprinting ◽  
Transactivator Protein

The adenovirus early region 3 (E3) promoter is an early viral promoter which is strongly induced by the adenovirus transactivator protein E1A. DNase I footprinting with HeLa cell extracts has identified four factor-binding domains which appear to be involved in basal and E1A-induced transcriptional regulation. These binding domains may bind TATA region-binding factors (site I), the CREB/ATF protein (site II), the AP-1 protein (site III), and nuclear factor I/CTF (site IV). Recently, it has been shown that the DNA-binding domain of transcription factor AP-1 has homology with the yeast transcription factor GCN4 and that the yeast transactivator protein GAL4 is able to stimulate transcription in HeLa cells from promoters containing GAL4-binding sites. These results suggest an evolutionary conservation of both transcription factors and the mechanisms responsible for transcriptional activation in Saccharomyces cerevisiae and higher eucaryotic organisms. To determine whether similar patterns of transcriptional regulation were seen with the E3 promoter in HeLa and yeast cells, the E3 promoter fused to the chloramphenicol acetyltransferase (cat) gene was cloned into a high-copy-number plasmid and stably introduced into yeast cells. S1 analysis revealed that similar E3 promoter mRNA start sites were found in yeast and HeLa cells. DNase I footprinting with partially purified yeast extracts revealed that four regions of the E3 promoter were protected. Several of these regions were similar to binding sites determined by using HeLa cell extracts. Oligonucleotide mutagenesis of these binding domains indicated their importance in the transcriptional regulation of the E3 promoter in yeast cells. These results suggest that similar cellular transcription factor-binding sites may be involved in the regulation of promoters in both yeast and mammalian cells.

scholarly journals Involvement of the Pleiotropic Drug Resistance Response, Protein Kinase C Signaling, and Altered Zinc Homeostasis in Resistance of Saccharomyces cerevisiae to Diclofenac

2011 ◽  
Vol 77 (17) ◽  
pp. 5973-5980 ◽  
Author(s):  
Jolanda S. van Leeuwen ◽  
Nico P. E. Vermeulen ◽  
J. Chris Vos
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Drug Resistance ◽  
Cell Wall ◽  
Transcription Factor ◽  
Protein Kinase C ◽  
Protein Kinase ◽  
Zinc Homeostasis ◽  
Yeast Cells ◽  
Pleiotropic Drug Resistance ◽  
Kinase C

ABSTRACTDiclofenac is a widely used analgesic drug that can cause serious adverse drug reactions. We usedSaccharomyces cerevisiaeas a model eukaryote with which to elucidate the molecular mechanisms of diclofenac toxicity and resistance. Although most yeast cells died during the initial diclofenac treatment, some survived and started growing again. Microarray analysis of the adapted cells identified three major processes involved in diclofenac detoxification and tolerance. In particular, pleiotropic drug resistance (PDR) genes and genes under the control of Rlm1p, a transcription factor in the protein kinase C (PKC) pathway, were upregulated in diclofenac-adapted cells. We tested if these processes or pathways were directly involved in diclofenac toxicity or resistance. Of the pleiotropic drug resistance gene products, the multidrug transporter Pdr5p was crucially important for diclofenac tolerance. Furthermore, deletion of components of the cell wall stress-responsive PKC pathway increased diclofenac toxicity, whereas incubation of cells with the cell wall stressor calcofluor white before the addition of diclofenac decreased its toxicity. Also, diclofenac induced flocculation, which might trigger the cell wall alterations. Genes involved in ribosome biogenesis and rRNA processing were downregulated, as were zinc-responsive genes. Paradoxically, deletion of the zinc-responsive transcription factor Zap1p or addition of the zinc chelator 1,10-phenanthroline significantly increased diclofenac toxicity, establishing a regulatory role for zinc in diclofenac resistance. In conclusion, we have identified three new pathways involved in diclofenac tolerance in yeast, namely, Pdr5p as the main contributor to the PDR response, cell wall signaling via the PKC pathway, and zinc homeostasis, regulated by Zap1p.

scholarly journals The N-Terminal Domain of the Flo1 Flocculation Protein from Saccharomyces cerevisiae Binds Specifically to Mannose Carbohydrates

2010 ◽  
Vol 10 (1) ◽  
pp. 110-117 ◽  
Author(s):  
Katty V. Y. Goossens ◽  
Catherine Stassen ◽  
Ingeborg Stals ◽  
Dagmara S. Donohue ◽  
Bart Devreese ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Binding Site ◽  
Dissociation Constants ◽  
Yeast Cells ◽  
Carbohydrate Binding ◽  
Specific Cell ◽  
Affinity Binding ◽  
Content Type ◽  
High Affinity ◽  
Terminal Domain

ABSTRACTSaccharomyces cerevisiaecells possess a remarkable capacity to adhere to other yeast cells, which is called flocculation. Flocculation is defined as the phenomenon wherein yeast cells adhere in clumps and sediment rapidly from the medium in which they are suspended. These cell-cell interactions are mediated by a class of specific cell wall proteins, called flocculins, that stick out of the cell walls of flocculent cells. The N-terminal part of the three-domain protein is responsible for carbohydrate binding. We studied the N-terminal domain of the Flo1 protein (N-Flo1p), which is the most important flocculin responsible for flocculation of yeast cells. It was shown that this domain is both O and N glycosylated and is structurally composed mainly of β-sheets. The binding of N-Flo1p tod-mannose, α-methyl-d-mannoside, various dimannoses, and mannan confirmed that the N-terminal domain of Flo1p is indeed responsible for the sugar-binding activity of the protein. Moreover, fluorescence spectroscopy data suggest that N-Flo1p contains two mannose carbohydrate binding sites with different affinities. The carbohydrate dissociation constants show that the affinity of N-Flo1p for mono- and dimannoses is in the millimolar range for the binding site with low affinity and in the micromolar range for the binding site with high affinity. The high-affinity binding site has a higher affinity for low-molecular-weight (low-MW) mannose carbohydrates and no affinity for mannan. However, mannan as well as low-MW mannose carbohydrates can bind to the low-affinity binding site. These results extend the cellular flocculation model on the molecular level.

scholarly journals Cloning and characterization of the low-affinity cyclic AMP phosphodiesterase gene of Saccharomyces cerevisiae.

1987 ◽  
Vol 7 (10) ◽  
pp. 3629-3636 ◽  
Author(s):  
J Nikawa ◽  
P Sass ◽  
M Wigler
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cyclic Amp ◽  
Copy Number ◽  
Growth Arrest ◽  
Yeast Cells ◽  
Phosphodiesterase Activity ◽  
Camp Phosphodiesterase ◽  
High Affinity ◽  
Cyclic Amp Phosphodiesterase

Saccharomyces cerevisiae contains two genes which encode cyclic AMP (cAMP) phosphodiesterase. We previously isolated and characterized PDE2, which encodes a high-affinity cAMP phosphodiesterase. We have now isolated the PDE1 gene of S. cerevisiae, which encodes a low-affinity cAMP phosphodiesterase. These two genes represent highly divergent branches in the evolution of phosphodiesterases. High-copy-number plasmids containing either PDE1 or PDE2 can reverse the growth arrest defects of yeast cells carrying the RAS2(Val-19) mutation. PDE1 and PDE2 appear to account for the aggregate cAMP phosphodiesterase activity of S. cerevisiae. Disruption of both PDE genes results in a phenotype which resembles that induced by the RAS2(Val-19) mutation. pde1- pde2- ras1- ras2- cells are viable.

scholarly journals Nuclear envelope morphology constrains diffusion and promotes asymmetric protein segregation in closed mitosis

2012 ◽  
Vol 197 (7) ◽  
pp. 921-937 ◽  
Author(s):  
Barbara Boettcher ◽  
Tatiana T. Marquez-Lago ◽  
Mathias Bayer ◽  
Eric L. Weiss ◽  
Yves Barral
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Vegetative Growth ◽  
In Silico ◽  
Mother Cell ◽  
Daughter Cell ◽  
Diffusion Barriers ◽  
Yeast Cells ◽  
Nuclear Membranes ◽  
In Silico Modeling

During vegetative growth, Saccharomyces cerevisiae cells divide asymmetrically: the mother cell buds to produce a smaller daughter cell. This daughter asymmetrically inherits the transcription factor Ace2, which activates daughter-specific transcriptional programs. In this paper, we investigate when and how this asymmetry is established and maintained. We show that Ace2 asymmetry is initiated in the elongated, but undivided, anaphase nucleus. At this stage, the nucleoplasm was highly compartmentalized; little exchange was observed for nucleoplasmic proteins between mother and bud. Using photobleaching and in silico modeling, we show that diffusion barriers compartmentalize the nuclear membranes. In contrast, the behavior of proteins in the nucleoplasm is well explained by the dumbbell shape of the anaphase nucleus. This compartmentalization of the nucleoplasm promoted Ace2 asymmetry in anaphase nuclei. Thus, our data indicate that yeast cells use the process of closed mitosis and the morphological constraints associated with it to asymmetrically segregate nucleoplasmic components.

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