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1.
Nucleic Acids Res ; 49(4): 1914-1934, 2021 02 26.
Article in English | MEDLINE | ID: mdl-33511417

ABSTRACT

During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δ transcriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δ are closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway.


Subject(s)
Cell Cycle Proteins/metabolism , Gene Expression Regulation, Fungal , Gene Silencing , Homologous Recombination , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces pombe Proteins/physiology , Transcription Factors/metabolism , Cell Cycle Proteins/antagonists & inhibitors , Centromere , Histone Code , Nucleosomes/metabolism , Repressor Proteins/physiology , Schizosaccharomyces/genetics , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Transcription Factors/antagonists & inhibitors
2.
Mol Genet Genomics ; 295(3): 695-703, 2020 May.
Article in English | MEDLINE | ID: mdl-32124033

ABSTRACT

Fission yeast Cds1 is responsible for the replication checkpoint activation and helps to protect replication fork collapse in response to hydroxyurea (HU). Here, we investigated the role of histone deacetylase in response to replication fork arrest and observed that in the presence of HU, the survival of cds1Δ cells was improved when the cells were simultaneously treated with histone deacetylase inhibitors. Furthermore, a mutation in the histone deacetylase gene, clr6, also suppresses the growth defect of cds1Δ cells in response to HU indicating a suppressive role of clr6-1 mutation in cds1 deletion background upon HU treatment. Interestingly, in response to HU, phosphorylation of Chk1 kinase and the number of Rad52YFP foci was reduced in cds1Δ clr6-1 double mutant as compared to cds1Δ single mutant indicating a decrease in the level of DNA damage in response to HU. Accordingly, the single-cell gel electrophoresis assay revealed a drastic reduction in the tail length of cds1Δ clr6-1 double mutant as compared to cds1Δ cells in the presence of HU suggesting the suppression of chromosomal defects in the double mutant. Taken together, we proposed that there could be transient suppression of fork collapse in cds1Δ clr6-1 double mutant upon HU treatment due to the delay in mitotic progression that leads to the facilitation of cell growth.


Subject(s)
Cell Cycle Proteins/metabolism , Checkpoint Kinase 2/genetics , Checkpoint Kinase 2/metabolism , Hydroxyurea/pharmacology , Mutation , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/growth & development , Cell Cycle Proteins/antagonists & inhibitors , Cell Cycle Proteins/genetics , Enzyme Inhibitors/pharmacology , Histone Deacetylase Inhibitors/pharmacology , Hydroxamic Acids/pharmacology , Phosphorylation , Schizosaccharomyces/drug effects , Schizosaccharomyces/genetics , Schizosaccharomyces pombe Proteins/antagonists & inhibitors
3.
Mol Cell Biol ; 40(7)2020 03 16.
Article in English | MEDLINE | ID: mdl-31932483

ABSTRACT

Oxidation of a highly conserved cysteine (Cys) residue located in the kinase activation loop of mitogen-activated protein kinase kinases (MAPKK) inactivates mammalian MKK6. This residue is conserved in the fission yeast Schizosaccharomyces pombe MAPKK Wis1, which belongs to the H2O2-responsive MAPK Sty1 pathway. Here, we show that H2O2 reversibly inactivates Wis1 through this residue (C458) in vitro We found that C458 is oxidized in vivo and that serine replacement of this residue significantly enhances Wis1 activation upon addition of H2O2 The allosteric MAPKK inhibitor INR119, which binds in a pocket next to the activation loop and C458, prevented the inhibition of Wis1 by H2O2in vitro and significantly increased Wis1 activation by low levels of H2O2in vivo We propose that oxidation of C458 inhibits Wis1 and that INR119 cancels out this inhibitory effect by binding close to this residue. Kinase inhibition through the oxidation of a conserved Cys residue in MKK6 (C196) is thus conserved in the S. pombe MAPKK Wis1.


Subject(s)
Hydrogen Peroxide/pharmacology , Mitogen-Activated Protein Kinase Kinases/metabolism , Mitogen-Activated Protein Kinases/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , Cysteine/chemistry , Gene Expression Regulation, Fungal/physiology , Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors , Mitogen-Activated Protein Kinase Kinases/genetics , Oxidation-Reduction , Protein Kinase Inhibitors/pharmacology , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/genetics , Sequence Alignment
4.
RNA Biol ; 16(6): 742-753, 2019 06.
Article in English | MEDLINE | ID: mdl-30794054

ABSTRACT

In the fission yeast Schizosaccharomyces pombe (S.pombe), heterochromatin domains are established and maintained by protein complexes that contain numerous RNA binding domains among their components. The fission yeast HP1 protein Swi6 is one such component and contains an unstructured RNA-binding hinge, which is important for the integrity and silencing of heterochromatin. In this study, we have used an RNA aptamer that likely binds to the Swi6 hinge with high affinity, as a tool to perturb the natural interactions mediated by this domain. When the hinge is blocked by the aptamer RNA, Swi6 appears to become less restricted to the pericentromeres and is enriched at specific euchromatic loci. This suggests a role for the Swi6 hinge, along with the chromoshadow domain (previously shown) in controlling the spread of heterochromatin in S.pombe. The study also highlights the potential of using a synthetic aptamer RNA as a tool to perturb nucleic acid - protein interaction in vivo with the objective of understanding the functional relevance of such an interaction.


Subject(s)
Aptamers, Nucleotide/metabolism , Chromosomal Proteins, Non-Histone/antagonists & inhibitors , Heterochromatin , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Aptamers, Nucleotide/chemistry , Chromosomal Proteins, Non-Histone/chemistry , Chromosomal Proteins, Non-Histone/metabolism , Nucleotide Motifs , Protein Domains , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/chemistry , Schizosaccharomyces pombe Proteins/metabolism
5.
Sci Rep ; 8(1): 6880, 2018 05 02.
Article in English | MEDLINE | ID: mdl-29720710

ABSTRACT

Checkpoint kinases are important in cellular surveillance pathways that help cells to cope with DNA damage and protect their genomes. In cycling cells, DNA replication is one of the most sensitive processes and therefore all organisms carefully regulate replication initiation and progression. The checkpoint kinase ATR plays important roles both in response to DNA damage and replication stress, and ATR inhibitors are currently in clinical trials for cancer treatment. Therefore, it is important to understand the roles of ATR in detail. Here we show that the fission yeast homologue Rad3 and the human ATR regulate events also in G1 phase in an unperturbed cell cycle. Rad3Δ mutants or human cells exposed to ATR inhibitor in G1 enter S phase prematurely, which results in increased DNA damage. Furthermore, ATR inhibition in a single G1 reduces clonogenic survival, demonstrating that long-term effects of ATR inhibition during G1 are deleterious for the cell. Interestingly, ATR inhibition through G1 and S phase reduces survival in an additive manner, strongly arguing that different functions of ATR are targeted in the different cell-cycle phases. We propose that potential effects of ATR inhibitors in G1 should be considered when designing future treatment protocols with such inhibitors.


Subject(s)
Ataxia Telangiectasia Mutated Proteins/metabolism , Checkpoint Kinase 2/metabolism , G1 Phase , Schizosaccharomyces pombe Proteins/metabolism , Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors , Ataxia Telangiectasia Mutated Proteins/genetics , Cell Line , Cell Line, Tumor , Cell Survival/drug effects , Checkpoint Kinase 2/antagonists & inhibitors , Checkpoint Kinase 2/genetics , Humans , Protein Kinase Inhibitors/pharmacology , S Phase , Schizosaccharomyces , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/genetics
6.
J Biol Chem ; 292(37): 15240-15253, 2017 09 15.
Article in English | MEDLINE | ID: mdl-28765280

ABSTRACT

Exocytosis involves fusion of secretory vesicles with the plasma membrane, thereby delivering membrane proteins to the cell surface and releasing material into the extracellular space. The tethering of the secretory vesicles before membrane fusion is mediated by the exocyst, an essential phylogenetically conserved octameric protein complex. Exocyst biogenesis is regulated by several processes, but the mechanisms by which the exocyst is degraded are unknown. Here, to unravel the components of the exocyst degradation pathway, we screened for extragenic suppressors of a temperature-sensitive fission yeast strain mutated in the exocyst subunit Sec3 (sec3-913). One of the suppressing DNAs encoded a truncated dominant-negative variant of the 26S proteasome subunit, Rpt2, indicating that exocyst degradation is controlled by the ubiquitin-proteasome system. The temperature-dependent growth defect of the sec3-913 strain was gene dosage-dependent and suppressed by blocking the proteasome, Hsp70-type molecular chaperones, the Pib1 E3 ubiquitin-protein ligase, and the deubiquitylating enzyme Ubp3. Moreover, defects in cell septation, exocytosis, and endocytosis in sec3 mutant strains were similarly alleviated by mutation of components in this pathway. We also found that, particularly under stress conditions, wild-type Sec3 degradation is regulated by Pib1 and the 26S proteasome. In conclusion, our results suggest that a cytosolic protein quality control pathway monitors folding and proteasome-dependent turnover of an exocyst subunit and, thereby, controls exocytosis in fission yeast.


Subject(s)
Deubiquitinating Enzymes/metabolism , Endopeptidases/metabolism , Models, Biological , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/physiology , Secretory Vesicles/physiology , Ubiquitin-Protein Ligases/metabolism , Vesicular Transport Proteins/metabolism , Deubiquitinating Enzymes/antagonists & inhibitors , Deubiquitinating Enzymes/genetics , Endocytosis/drug effects , Endopeptidases/genetics , Enzyme Inhibitors/pharmacology , Exocytosis/drug effects , Gene Deletion , HSP70 Heat-Shock Proteins/antagonists & inhibitors , HSP70 Heat-Shock Proteins/genetics , HSP70 Heat-Shock Proteins/metabolism , Microscopy, Electron, Transmission , Mutation , Proteasome Endopeptidase Complex/drug effects , Proteasome Endopeptidase Complex/genetics , Proteasome Endopeptidase Complex/metabolism , Proteasome Endopeptidase Complex/ultrastructure , Protein Stability/drug effects , Proteolysis/drug effects , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/metabolism , Schizosaccharomyces/drug effects , Schizosaccharomyces/growth & development , Schizosaccharomyces/ultrastructure , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/genetics , Secretory Vesicles/drug effects , Secretory Vesicles/ultrastructure , Stress, Physiological/drug effects , Temperature , Ubiquitin-Protein Ligases/antagonists & inhibitors , Ubiquitin-Protein Ligases/genetics , Ubiquitination/drug effects , Vesicular Transport Proteins/antagonists & inhibitors , Vesicular Transport Proteins/genetics
7.
J Biol Chem ; 292(29): 12089-12099, 2017 07 21.
Article in English | MEDLINE | ID: mdl-28572513

ABSTRACT

E1 enzymes for ubiquitin (Ub) and Ub-like modifiers (Ubls) harbor two catalytic activities that are required for Ub/Ubl activation: adenylation and thioester bond formation. Structural studies of the E1 for the Ubl small ubiquitin-like modifier (SUMO) revealed a single active site that is transformed by a conformational switch that toggles its competency for catalysis of these two distinct chemical reactions. Although the mechanisms of adenylation and thioester bond formation revealed by SUMO E1 structures are thought to be conserved in Ub E1, there is currently a lack of structural data supporting this hypothesis. Here, we present a structure of Schizosaccharomyces pombe Uba1 in which the second catalytic cysteine half-domain (SCCH domain) harboring the catalytic cysteine has undergone a 106° rotation that results in a completely different network of intramolecular interactions between the SCCH and adenylation domains and translocation of the catalytic cysteine 12 Å closer to the Ub C terminus compared with previous Uba1 structures. SCCH domain alternation is accompanied by conformational changes within the Uba1 adenylation domains that effectively disassemble the adenylation active site. Importantly, the structural and biochemical data suggest that domain alternation and remodeling of the adenylation active site are interconnected and are intrinsic structural features of Uba1 and that the overall structural basis for adenylation and thioester bond formation exhibited by SUMO E1 is indeed conserved in Ub E1. Finally, the mechanistic insights provided by the novel conformational snapshot of Uba1 presented in this study may guide efforts to develop small molecule inhibitors of this critically important enzyme that is an active target for anticancer therapeutics.


Subject(s)
Models, Molecular , Protein Processing, Post-Translational , SUMO-1 Protein/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Ubiquitin-Activating Enzymes/metabolism , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitin/metabolism , Amino Acid Substitution , Catalytic Domain , Crystallography, X-Ray , Cysteine/metabolism , Databases, Protein , Disulfides/chemistry , Disulfides/metabolism , Disulfides/pharmacology , Enzyme Activation , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacology , Ligands , Mutation , Protein Conformation , Protein Interaction Domains and Motifs , Protein Multimerization/drug effects , Protein Processing, Post-Translational/drug effects , Protein Refolding , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , SUMO-1 Protein/chemistry , SUMO-1 Protein/genetics , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/chemistry , Schizosaccharomyces pombe Proteins/genetics , Structural Homology, Protein , Ubiquitin/chemistry , Ubiquitin/genetics , Ubiquitin-Activating Enzymes/antagonists & inhibitors , Ubiquitin-Activating Enzymes/chemistry , Ubiquitin-Activating Enzymes/genetics , Ubiquitin-Conjugating Enzymes/chemistry , Ubiquitin-Conjugating Enzymes/genetics
8.
Cell ; 167(2): 512-524.e14, 2016 Oct 06.
Article in English | MEDLINE | ID: mdl-27667686

ABSTRACT

All cellular proteins are synthesized by ribosomes, whose biogenesis in eukaryotes is a complex multi-step process completed within minutes. Several chemical inhibitors of ribosome function are available and used as tools or drugs. By contrast, we lack potent validated chemical probes to analyze the dynamics of eukaryotic ribosome assembly. Here, we combine chemical and genetic approaches to discover ribozinoindoles (or Rbins), potent and reversible triazinoindole-based inhibitors of eukaryotic ribosome biogenesis. Analyses of Rbin sensitivity and resistance conferring mutations in fission yeast, along with biochemical assays with recombinant proteins, provide evidence that Rbins' physiological target is Midasin, an essential ∼540-kDa AAA+ (ATPases associated with diverse cellular activities) protein. Using Rbins to acutely inhibit or activate Midasin function, in parallel experiments with inhibitor-sensitive or inhibitor-resistant cells, we uncover Midasin's role in assembling Nsa1 particles, nucleolar precursors of the 60S subunit. Together, our findings demonstrate that Rbins are powerful probes for eukaryotic ribosome assembly.


Subject(s)
Adenosine Triphosphatases/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Indoles/pharmacology , Ribosome Subunits, Large, Eukaryotic/drug effects , Ribosome Subunits, Large, Eukaryotic/metabolism , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Triazines/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/isolation & purification , Indoles/chemistry , Indoles/isolation & purification , Schizosaccharomyces/drug effects , Schizosaccharomyces/metabolism , Structure-Activity Relationship , Triazines/chemistry , Triazines/isolation & purification
9.
PLoS One ; 11(5): e0156239, 2016.
Article in English | MEDLINE | ID: mdl-27227887

ABSTRACT

In mammalian cells, mTORC1 activity is regulated by Rag GTPases. It is thought that the Ragulator complex and the GATOR (GAP activity towards Rags) complex regulate RagA/B as its GDP/GTP exchange factor (GEF) and GTPase-activating protein (GAP), respectively. However, the functions of components in these complexes remain elusive. Using fission yeast as a model organism, here we found that the loss of Lam2 (SPBC1778.05c), a homolog of a Ragulator component LAMTOR2, as well as the loss of Gtr1 or Gtr2 phenocopies the loss of Npr2 or Npr3, homologs of GATOR components Nprl2 or Nprl3, respectively. These phenotypes were rescued by TORC1 inhibition using pharmacological or genetic means, and the loss of Lam2, Gtr1, Gtr2, Npr2 or Npr3 disinhibited TORC1 activity under nitrogen depletion, as measured by Rps6 phosphorylation. Consistently, overexpression of GDP-locked Gtr1S20L or GTP-locked Gtr2Q60L, which suppress TORC1 activity in budding yeast, rescued the growth defect of Δgtr1 cells or Δgtr2 cells, respectively, and the loss of Lam2, Npr2 or Npr3 similarly diminished the vacuolar localization and the protein levels of Gtr1 and Gtr2. Furthermore, Lam2 physically interacted with Npr2 and Gtr1. These findings suggest that Lam2 and Npr2-Npr3 function together as a tether for GDP-bound Gtr1 to the vacuolar membrane, thereby suppressing TORC1 activity for multiple cellular functions.


Subject(s)
Endosomes/metabolism , Gene Expression Regulation, Fungal , Intracellular Membranes/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , Vacuoles/metabolism , Protein Binding , Schizosaccharomyces/genetics , Schizosaccharomyces/growth & development , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/genetics , Signal Transduction
10.
RNA ; 22(4): 518-29, 2016 Apr.
Article in English | MEDLINE | ID: mdl-26826132

ABSTRACT

Dcp1/2 is the major eukaryotic RNA decapping complex, comprised of the enzyme Dcp2 and activator Dcp1, which removes the 5' m(7)G cap from mRNA, committing the transcript to degradation. Dcp1/2 activity is crucial for RNA quality control and turnover, and deregulation of these processes may lead to disease development. The molecular details of Dcp1/2 catalysis remain elusive, in part because both cap substrate (m(7)GpppN) and m(7)GDP product are bound by Dcp1/2 with weak (mM) affinity. In order to find inhibitors to use in elucidating the catalytic mechanism of Dcp2, we screened a small library of synthetic m(7)G nucleotides (cap analogs) bearing modifications in the oligophosphate chain. One of the most potent cap analogs, m(7)GpSpppSm(7)G, inhibited Dcp1/2 20 times more efficiently than m(7)GpppN or m(7)GDP. NMR experiments revealed that the compound interacts with specific surfaces of both regulatory and catalytic domains of Dcp2 with submillimolar affinities. Kinetics analysis revealed that m(7)GpSpppSm(7)G is a mixed inhibitor that competes for the Dcp2 active site with micromolar affinity. m(7)GpSpppSm(7)G-capped RNA undergoes rapid decapping, suggesting that the compound may act as a tightly bound cap mimic. Our identification of the first small molecule inhibitor of Dcp2 should be instrumental in future studies aimed at understanding the structural basis of RNA decapping and may provide insight toward the development of novel therapeutically relevant decapping inhibitors.


Subject(s)
RNA Cap Analogs/chemistry , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Drug Evaluation, Preclinical , RNA Cleavage , RNA, Messenger/chemistry , Schizosaccharomyces/enzymology
11.
J Cell Sci ; 128(15): 2842-53, 2015 Aug 01.
Article in English | MEDLINE | ID: mdl-26071525

ABSTRACT

Cell growth and division are tightly coordinated to maintain cell size constant during successive cell cycles. In Schizosaccharomyces pombe, the SAD kinase Cdr2 regulates the cell size at division and the positioning of the division plane. Cdr2 forms nodes on the medial cortex containing factors that constitute an inhibitory pathway for Wee1. This pathway is regulated by polar gradients of the DYRK kinase Pom1, and involves a direct inhibitor of Wee1, the SAD kinase Cdr1. Cdr2 also interacts with the anillin Mid1, which defines the division plane, and with additional components of the medial cortical nodes, including Blt1, which participate in the mitotic-promoting and cytokinetic functions of nodes. Here, we show that the interaction of Cdr2 with Wee1 and Mid1 requires the UBA domain of Cdr2, which is necessary for its kinase activity. In contrast, Cdr1 associates with the C-terminus of Cdr2, which is composed of basic and KA-1 lipid-binding domains. Mid1 also interacts with the C-terminus of Cdr2 and might bridge the N- and C-terminal domains, whereas Blt1 associates with the central spacer region. We propose that the association of Cdr2 effectors with different domains might constrain Cdr1 and Wee1 spatially to promote Wee1 inhibition upon Cdr2 kinase activation.


Subject(s)
Cell Cycle Proteins/antagonists & inhibitors , Nuclear Proteins/antagonists & inhibitors , Protein Serine-Threonine Kinases/metabolism , Protein-Tyrosine Kinases/antagonists & inhibitors , Protein-Tyrosine Kinases/metabolism , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/genetics , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Size , DNA, Fungal/genetics , Mitosis/genetics , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Phosphorylation/genetics , Protein Binding , Protein Kinases/metabolism , Protein Structure, Tertiary , Protein-Tyrosine Kinases/genetics , Schizosaccharomyces pombe Proteins/genetics
12.
Mol Cell Biol ; 35(4): 662-74, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25487573

ABSTRACT

Heterochromatin underpins gene repression, genome integrity, and chromosome segregation. In the fission yeast Schizosaccharomyces pombe, conserved protein complexes effect heterochromatin formation via RNA interference-mediated recruitment of a histone H3 lysine 9 methyltransferase to cognate chromatin regions. To identify small molecules that inhibit heterochromatin formation, we performed an in vivo screen for loss of silencing of a dominant selectable kanMX reporter gene embedded within fission yeast centromeric heterochromatin. Two structurally unrelated compounds, HMS-I1 and HMS-I2, alleviated kanMX silencing and decreased repressive H3K9 methylation levels at the transgene. The decrease in methylation caused by HMS-I1 and HMS-I2 was observed at all loci regulated by histone methylation, including centromeric repeats, telomeric regions, and the mating-type locus, consistent with inhibition of the histone deacetylases (HDACs) Clr3 and/or Sir2. Chemical-genetic epistasis and expression profiles revealed that both compounds affect the activity of the Clr3-containing Snf2/HDAC repressor complex (SHREC). In vitro HDAC assays revealed that HMS-I1 and HMS-I2 inhibit Clr3 HDAC activity. HMS-I1 also alleviated transgene reporter silencing by heterochromatin in Arabidopsis and a mouse cell line, suggesting a conserved mechanism of action. HMS-I1 and HMS-I2 bear no resemblance to known inhibitors of chromatin-based activities and thus represent novel chemical probes for heterochromatin formation and function.


Subject(s)
Dioxanes/pharmacology , Gene Expression Regulation, Fungal/drug effects , Gene Silencing/drug effects , Heterochromatin/drug effects , Heterocyclic Compounds, 2-Ring/pharmacology , Piperazines/pharmacology , Pyridines/pharmacology , Schizosaccharomyces/drug effects , Thiophenes/pharmacology , Animals , Arabidopsis/drug effects , Arabidopsis/genetics , Arabidopsis/metabolism , Cell Cycle Proteins/antagonists & inhibitors , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Line, Tumor , Chromatin Assembly and Disassembly , DNA Methylation , Dioxanes/chemical synthesis , Dioxanes/chemistry , Heterochromatin/chemistry , Heterocyclic Compounds, 2-Ring/chemical synthesis , Heterocyclic Compounds, 2-Ring/chemistry , Histone Methyltransferases , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Histones/genetics , Histones/metabolism , Mice , Piperazines/chemical synthesis , Piperazines/chemistry , Pyridines/chemical synthesis , Pyridines/chemistry , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism , Thiophenes/chemical synthesis , Thiophenes/chemistry
13.
PLoS Biol ; 12(9): e1001946, 2014 Sep.
Article in English | MEDLINE | ID: mdl-25203555

ABSTRACT

Structure-specific nucleases play crucial roles in many DNA repair pathways. They must be precisely controlled to ensure optimal repair outcomes; however, mechanisms of their regulation are not fully understood. Here, we report a fission yeast protein, Pxd1, that binds to and regulates two structure-specific nucleases: Rad16XPF-Swi10ERCC1 and Dna2-Cdc24. Strikingly, Pxd1 influences the activities of these two nucleases in opposite ways: It activates the 3' endonuclease activity of Rad16-Swi10 but inhibits the RPA-mediated activation of the 5' endonuclease activity of Dna2. Pxd1 is required for Rad16-Swi10 to function in single-strand annealing, mating-type switching, and the removal of Top1-DNA adducts. Meanwhile, Pxd1 attenuates DNA end resection mediated by the Rqh1-Dna2 pathway. Disabling the Dna2-inhibitory activity of Pxd1 results in enhanced use of a break-distal repeat sequence in single-strand annealing and a greater loss of genetic information. We propose that Pxd1 promotes proper DNA repair by differentially regulating two structure-specific nucleases.


Subject(s)
DNA Repair , DNA, Fungal/genetics , Flap Endonucleases/genetics , Gene Expression Regulation, Fungal , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces/genetics , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , DNA Damage , DNA Helicases/genetics , DNA Helicases/metabolism , DNA Topoisomerases, Type I/genetics , DNA Topoisomerases, Type I/metabolism , DNA, Fungal/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Flap Endonucleases/antagonists & inhibitors , Flap Endonucleases/metabolism , Protein Binding , Schizosaccharomyces/enzymology , Schizosaccharomyces pombe Proteins/agonists , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/metabolism , Signal Transduction
14.
Open Biol ; 4(6): 140022, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24920274

ABSTRACT

Long non-coding RNAs (lncRNAs) play key roles in the formation of nuclear bodies. In the fission yeast Schizosaccharomyces pombe, a lncRNA species termed meiRNA forms a nuclear dot structure at its own genetic locus, the sme2 locus, with its protein-binding partner Mei2. This dot structure, called Mei2 dot, promotes the progression of meiosis by suppressing Mmi1, a crucial factor involved in the selective elimination of meiosis-specific transcripts. The meiRNA itself is a target of Mmi1-mediated elimination and is supposed to function as a decoy to lure Mmi1. However, detailed mechanisms underlying the formation of Mei2 dot and inactivation of Mmi1 remain ambiguous. Here, we show that the localization of meiRNA, at its genetic locus sme2, depends on its association with Mmi1. We also demonstrate that one of the multiple Mmi1 foci in mitotic cells localizes to the sme2 locus. Furthermore, the overexpression of meiRNA promotes the accumulation of Mmi1 to the sme2 locus even in the absence of Mei2 and reduces the activity of Mmi1. These findings indicate that the retention of meiRNA at its genetic locus is facilitated by Mmi1, which then attracts scattered Mmi1 to inhibit its function.


Subject(s)
Meiosis/genetics , RNA, Long Noncoding/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/genetics , mRNA Cleavage and Polyadenylation Factors/metabolism , RNA, Long Noncoding/genetics , RNA-Binding Proteins/metabolism , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/genetics , mRNA Cleavage and Polyadenylation Factors/antagonists & inhibitors , mRNA Cleavage and Polyadenylation Factors/genetics
15.
PLoS One ; 9(6): e98959, 2014.
Article in English | MEDLINE | ID: mdl-24897379

ABSTRACT

Iron is required for several metabolic functions involved in cellular growth. Although several players involved in iron transport have been identified, the mechanisms by which iron-responsive transcription factors are controlled are still poorly understood. In Schizosaccharomyces pombe, the Fep1 transcription factor represses genes involved in iron acquisition in response to high levels of iron. In contrast, when iron levels are low, Fep1 becomes inactive and loses its ability to associate with chromatin. Although the molecular basis by which Fep1 is inactivated under iron starvation remains unknown, this process requires the monothiol glutaredoxin Grx4. Here, we demonstrate that Fra2 plays a role in the negative regulation of Fep1 activity. Disruption of fra2+ (fra2Δ) led to a constitutive repression of the fio1+ gene transcription. Fep1 was consistently active and constitutively bound to its target gene promoters in cells lacking fra2+. A constitutive activation of Fep1 was also observed in a php4Δ fra2Δ double mutant strain in which the behavior of Fep1 is freed of its transcriptional regulation by Php4. Microscopic analyses of cells expressing a functional Fra2-Myc13 protein revealed that Fra2 localized throughout the cells with a significant proportion of Fra2 being observed within the nuclei. Further analysis by coimmunoprecipitation showed that Fra2, Fep1 and Grx4 are associated in a heteroprotein complex. Bimolecular fluorescence complementation experiments brought further evidence that an interaction between Fep1 and Fra2 occurs in the nucleus. Taken together, results reported here revealed that Fra2 plays a role in the Grx4-mediated pathway that inactivates Fep1 in response to iron deficiency.


Subject(s)
GATA Transcription Factors/antagonists & inhibitors , Gene Expression Regulation, Fungal , Iron Deficiencies , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , Cell Nucleus/metabolism , Chromatin Immunoprecipitation , Fluorescent Antibody Technique, Indirect , GATA Transcription Factors/genetics , Immunoprecipitation , Promoter Regions, Genetic/genetics , Protein Binding , RNA, Messenger/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Schizosaccharomyces/genetics , Schizosaccharomyces/growth & development , Schizosaccharomyces pombe Proteins/antagonists & inhibitors
16.
Protein Cell ; 5(6): 411-9, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24691906

ABSTRACT

Genetic information stored in DNA is accurately copied and transferred to subsequent generations through DNA replication. This process is accomplished through the concerted actions of highly conserved DNA replication components. Epigenetic information stored in the form of histone modifications and DNA methylation, constitutes a second layer of regulatory information important for many cellular processes, such as gene expression regulation, chromatin organization, and genome stability. During DNA replication, epigenetic information must also be faithfully transmitted to subsequent generations. How this monumental task is achieved remains poorly understood. In this review, we will discuss recent advances on the role of DNA replication components in the inheritance of epigenetic marks, with a particular focus on epigenetic regulation in fission yeast. Based on these findings, we propose that specific DNA replication components function as key regulators in the replication of epigenetic information across the genome.


Subject(s)
Centromere/metabolism , DNA, Fungal/metabolism , Schizosaccharomyces/metabolism , Cdc20 Proteins/antagonists & inhibitors , Cdc20 Proteins/genetics , Cdc20 Proteins/metabolism , Chromatin/metabolism , Chromosomal Proteins, Non-Histone/metabolism , DNA Replication , Epigenesis, Genetic , Histones/metabolism , Schizosaccharomyces/genetics , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism
17.
Nature ; 496(7445): 377-81, 2013 Apr 18.
Article in English | MEDLINE | ID: mdl-23485968

ABSTRACT

A hallmark of histone H3 lysine 9 (H3K9)-methylated heterochromatin, conserved from the fission yeast Schizosaccharomyces pombe to humans, is its ability to spread to adjacent genomic regions. Central to heterochromatin spread is heterochromatin protein 1 (HP1), which recognizes H3K9-methylated chromatin, oligomerizes and forms a versatile platform that participates in diverse nuclear functions, ranging from gene silencing to chromosome segregation. How HP1 proteins assemble on methylated nucleosomal templates and how the HP1-nucleosome complex achieves functional versatility remain poorly understood. Here we show that binding of the key S. pombe HP1 protein, Swi6, to methylated nucleosomes drives a switch from an auto-inhibited state to a spreading-competent state. In the auto-inhibited state, a histone-mimic sequence in one Swi6 monomer blocks methyl-mark recognition by the chromodomain of another monomer. Auto-inhibition is relieved by recognition of two template features, the H3K9 methyl mark and nucleosomal DNA. Cryo-electron-microscopy-based reconstruction of the Swi6-nucleosome complex provides the overall architecture of the spreading-competent state in which two unbound chromodomain sticky ends appear exposed. Disruption of the switch between the auto-inhibited and spreading-competent states disrupts heterochromatin assembly and gene silencing in vivo. These findings are reminiscent of other conditionally activated polymerization processes, such as actin nucleation, and open up a new class of regulatory mechanisms that operate on chromatin in vivo.


Subject(s)
Chromatin Assembly and Disassembly , Chromosomal Proteins, Non-Histone/antagonists & inhibitors , Chromosomal Proteins, Non-Histone/chemistry , Chromosomal Proteins, Non-Histone/metabolism , Heterochromatin/metabolism , Schizosaccharomyces pombe Proteins/chemistry , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , Amino Acid Sequence , Animals , Chromobox Protein Homolog 5 , Chromosomal Proteins, Non-Histone/ultrastructure , Cryoelectron Microscopy , Gene Silencing , Heterochromatin/chemistry , Heterochromatin/ultrastructure , Histones/chemistry , Histones/metabolism , Methylation , Models, Molecular , Molecular Sequence Data , Nucleosomes/chemistry , Nucleosomes/genetics , Nucleosomes/metabolism , Nucleosomes/ultrastructure , Protein Structure, Tertiary , Schizosaccharomyces/genetics , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/ultrastructure , Xenopus laevis
18.
Cell Cycle ; 12(4): 618-24, 2013 Feb 15.
Article in English | MEDLINE | ID: mdl-23370392

ABSTRACT

The reduction of chromosome number during meiosis is achieved by two successive rounds of chromosome segregation after just single round of DNA replication. To identify novel proteins required for the proper segregation of chromosomes during meiosis, we analyzed the consequences of deleting Schizosaccharomyces pombe genes predicted to encode protein kinases that are not essential for cell viability. We show that Mph1, a member of the Mps1 family of spindle assembly checkpoint kinases, is required to prevent meiosis I homolog non-disjunction. We also provide evidence for a novel function of Spo4, the fission yeast ortholog of Dbf4-dependent Cdc7 kinase, in regulating the length of anaphase II spindles. In the absence of Spo4, abnormally elongated anaphase II spindles frequently overlap and thus destroy the linear order of nuclei in the ascus. Our observation that the spo4Δ mutant phenotype can be partially suppressed by inhibiting Cdc2-as suggests that dysregulation of the activity of this cyclin-dependent kinase may cause abnormal elongation of anaphase II spindles in spo4Δ mutant cells.


Subject(s)
Chromosomes, Fungal/genetics , Gene Expression Regulation, Fungal , Meiosis/genetics , Nondisjunction, Genetic , Schizosaccharomyces/genetics , CDC2 Protein Kinase/antagonists & inhibitors , CDC2 Protein Kinase/genetics , CDC2 Protein Kinase/metabolism , Cell Cycle Proteins/deficiency , Cell Cycle Proteins/genetics , Cell Nucleus/genetics , Cell Nucleus/metabolism , Chromosomes, Fungal/ultrastructure , DNA Replication , Gene Knockout Techniques , Genotype , Phenotype , Plasmids/genetics , Protein Kinases/genetics , Protein Kinases/metabolism , Protein Serine-Threonine Kinases/deficiency , Protein Serine-Threonine Kinases/genetics , Schizosaccharomyces/metabolism , Schizosaccharomyces/ultrastructure , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism
19.
Chem Biol ; 20(2): 262-71, 2013 Feb 21.
Article in English | MEDLINE | ID: mdl-23438755

ABSTRACT

Protein kinases may function more like variable rheostats rather than two-state switches. However, we lack approaches to properly analyze this aspect of kinase-dependent regulation. To address this, we develop a strategy in which a kinase inhibitor is identified using genetics-based screens, kinase mutations that confer resistance are characterized, and dose-dependent responses of isogenic drug-sensitive and resistant cells to inhibitor treatments are compared. This approach has the advantage that function of wild-type kinase, rather than mutants, is examined. To develop this approach, we focus on Ark1, the fission yeast member of the conserved Aurora kinase family. Applying this approach reveals that proper chromosome compaction in fission yeast needs high Ark1 activity, while other processes depend on significantly lower activity levels. Our strategy is general and can be used to examine the functions of other molecular rheostats.


Subject(s)
Protein Kinase Inhibitors/chemistry , Aurora Kinase A , Aurora Kinases , Drug Resistance, Fungal , Humans , Mitosis/drug effects , Mutation , Protein Binding , Protein Kinase Inhibitors/metabolism , Protein Kinase Inhibitors/pharmacology , Protein Serine-Threonine Kinases/antagonists & inhibitors , Protein Serine-Threonine Kinases/chemistry , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism
20.
Biol Cell ; 105(3): 129-48, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23294323

ABSTRACT

BACKGROUND INFORMATION: The Kin1 protein kinase of fission yeast, which regulates cell surface cohesiveness during interphase cell growth, is also present at the cell division site during mitosis; however, its function in cell division has remained elusive. RESULTS: In FK506-mediated calcineurin deficient cells, mitosis is extended and ring formation is transiently compromised but septation remains normal. Here, we show that Kin1 inhibition in these cells leads to polyseptation and defects in membrane closure. Actomyosin ring disassembly is prevented and ultimately the daughter cells fail to separate. We show that the Pmk1 MAP kinase pathway and the type V myosin Myo4 act downstream of the cytokinetic function of Kin1. Kin1 inhibition also promotes polyseptation in myo3Δ, a type II myosin heavy-chain mutant defective in ring assembly. In contrast, Kin1 inactivation rescues septation in a myosin light-chain cdc4-8 thermosensitive mutant. A structure/function analysis of the Kin1 protein sequence identified a novel motif outside the kinase domain that is important for its polarised localisation and its catalytic activity. This motif is remarkably conserved in all fungal Kin1 homologues but is absent in related kinases of metazoans. CONCLUSIONS: We conclude that calcineurin and Kin1 activities must be tightly coordinated to link actomyosin ring assembly with septum synthesis and membrane closure and to ensure separation of the daughter cells.


Subject(s)
Actins/metabolism , Cytokinesis , Phosphoric Monoester Hydrolases/metabolism , Protein Serine-Threonine Kinases/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/cytology , Schizosaccharomyces/enzymology , Amino Acid Motifs , Amino Acid Sequence , Cell Wall/drug effects , Cytokinesis/drug effects , Molecular Sequence Data , Mutation/genetics , Myosin Heavy Chains/metabolism , Phenotype , Phosphoric Monoester Hydrolases/antagonists & inhibitors , Protein Serine-Threonine Kinases/antagonists & inhibitors , Protein Serine-Threonine Kinases/chemistry , Protein Transport/drug effects , Pyrazoles/pharmacology , Pyrimidines/pharmacology , Schizosaccharomyces/drug effects , Schizosaccharomyces/growth & development , Schizosaccharomyces pombe Proteins/antagonists & inhibitors , Schizosaccharomyces pombe Proteins/chemistry , Tacrolimus/pharmacology
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