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1.
Genes Dev ; 32(11-12): 806-821, 2018 06 01.
Article in English | MEDLINE | ID: mdl-29899141

ABSTRACT

Post-replicative correction of replication errors by the mismatch repair (MMR) system is critical for suppression of mutations. Although the MMR system may need to handle nucleosomes at the site of chromatin replication, how MMR occurs in the chromatin environment remains unclear. Here, we show that nucleosomes are excluded from a >1-kb region surrounding a mismatched base pair in Xenopus egg extracts. The exclusion was dependent on the Msh2-Msh6 mismatch recognition complex but not the Mlh1-containing MutL homologs and counteracts both the HIRA- and CAF-1 (chromatin assembly factor 1)-mediated chromatin assembly pathways. We further found that the Smarcad1 chromatin remodeling ATPase is recruited to mismatch-carrying DNA in an Msh2-dependent but Mlh1-independent manner to assist nucleosome exclusion and that Smarcad1 facilitates the repair of mismatches when nucleosomes are preassembled on DNA. In budding yeast, deletion of FUN30, the homolog of Smarcad1, showed a synergistic increase of spontaneous mutations in combination with MSH6 or MSH3 deletion but no significant increase with MSH2 deletion. Genetic analyses also suggested that the function of Fun30 in MMR is to counteract CAF-1. Our study uncovers that the eukaryotic MMR system has an ability to exclude local nucleosomes and identifies Smarcad1/Fun30 as an accessory factor for the MMR reaction.


Subject(s)
Base Pair Mismatch/physiology , DNA Helicases/metabolism , DNA Mismatch Repair/genetics , MutS Homolog 2 Protein/metabolism , Nucleosomes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Animals , Base Pair Mismatch/genetics , Chromatin Assembly and Disassembly/genetics , DNA/genetics , DNA/metabolism , DNA Helicases/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Transcription Factors/genetics , Transcription Factors/metabolism , Xenopus laevis
2.
Development ; 149(15)2022 08 01.
Article in English | MEDLINE | ID: mdl-35831949

ABSTRACT

Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher-order chromatin structure of the Xi, the underlying mechanism is largely unknown. Here, we explore the epigenetic state of the Xi in SmcHD1-deficient epiblast stem cells and mouse embryonic fibroblasts in comparison with their wild-type counterparts. The results suggest that SmcHD1 underlies the formation of H3K9me3-enriched blocks on the Xi, which, although the importance of H3K9me3 has been largely overlooked in mice, play a crucial role in the establishment of the stably silenced state. We propose that the H3K9me3 blocks formed on the Xi facilitate robust heterochromatin formation in combination with H3K27me3, and that the substantial loss of H3K9me3 caused by SmcHD1 deficiency leads to aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes.


Subject(s)
Histones , X Chromosome Inactivation , Animals , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , Female , Fibroblasts/metabolism , Germ Layers/metabolism , Histones/metabolism , Mammals/genetics , Mice , X Chromosome/genetics , X Chromosome/metabolism , X Chromosome Inactivation/genetics
3.
Genet Med ; 25(7): 100861, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37087635

ABSTRACT

PURPOSE: This study aimed to establish variants in CBX1, encoding heterochromatin protein 1ß (HP1ß), as a cause of a novel syndromic neurodevelopmental disorder. METHODS: Patients with CBX1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. To investigate the pathogenicity of identified variants, we performed in vitro cellular assays and neurobehavioral and cytological analyses of neuronal cells obtained from newly generated Cbx1 mutant mouse lines. RESULTS: In 3 unrelated individuals with developmental delay, hypotonia, and autistic features, we identified heterozygous de novo variants in CBX1. The identified variants were in the chromodomain, the functional domain of HP1ß, which mediates interactions with chromatin. Cbx1 chromodomain mutant mice displayed increased latency-to-peak response, suggesting the possibility of synaptic delay or myelination deficits. Cytological and chromatin immunoprecipitation experiments confirmed the reduction of mutant HP1ß binding to heterochromatin, whereas HP1ß interactome analysis demonstrated that the majority of HP1ß-interacting proteins remained unchanged between the wild-type and mutant HP1ß. CONCLUSION: These collective findings confirm the role of CBX1 in developmental disabilities through the disruption of HP1ß chromatin binding during neurocognitive development. Because HP1ß forms homodimers and heterodimers, mutant HP1ß likely sequesters wild-type HP1ß and other HP1 proteins, exerting dominant-negative effects.


Subject(s)
Chromobox Protein Homolog 5 , Heterochromatin , Animals , Mice , Chromatin/genetics , Chromosomal Proteins, Non-Histone/genetics , Histones/genetics , Histones/metabolism
4.
PLoS Genet ; 15(6): e1008061, 2019 06.
Article in English | MEDLINE | ID: mdl-31170156

ABSTRACT

The nuclear pore complex (NPC) forms a gateway for nucleocytoplasmic transport. The outer ring protein complex of the NPC (the Nup107-160 subcomplex in humans) is a key component for building the NPC. Nup107-160 subcomplexes are believed to be symmetrically localized on the nuclear and cytoplasmic sides of the NPC. However, in S. pombe immunoelectron and fluorescence microscopic analyses revealed that the homologous components of the human Nup107-160 subcomplex had an asymmetrical localization: constituent proteins spNup132 and spNup107 were present only on the nuclear side (designated the spNup132 subcomplex), while spNup131, spNup120, spNup85, spNup96, spNup37, spEly5 and spSeh1 were localized only on the cytoplasmic side (designated the spNup120 subcomplex), suggesting the complex was split into two pieces at the interface between spNup96 and spNup107. This contrasts with the symmetrical localization reported in other organisms. Fusion of spNup96 (cytoplasmic localization) with spNup107 (nuclear localization) caused cytoplasmic relocalization of spNup107. In this strain, half of the spNup132 proteins, which interact with spNup107, changed their localization to the cytoplasmic side of the NPC, leading to defects in mitotic and meiotic progression similar to an spNup132 deletion strain. These observations suggest the asymmetrical localization of the outer ring spNup132 and spNup120 subcomplexes of the NPC is necessary for normal cell cycle progression in fission yeast.


Subject(s)
Nuclear Pore Complex Proteins/genetics , Nuclear Pore/genetics , Schizosaccharomyces pombe Proteins/genetics , Active Transport, Cell Nucleus/genetics , Cell Cycle/genetics , Cell Division/genetics , Cell Nucleus/genetics , Cell Nucleus/ultrastructure , Cytoplasm/genetics , Cytoplasm/ultrastructure , Humans , Meiosis/genetics , Microscopy, Fluorescence , Nuclear Envelope/genetics , Nuclear Pore/ultrastructure , Protein Binding/genetics , Saccharomyces cerevisiae/genetics , Schizosaccharomyces/genetics
5.
Molecules ; 27(9)2022 Apr 20.
Article in English | MEDLINE | ID: mdl-35565990

ABSTRACT

Edible algae Neopyropia yezoensis is used as "Nori", its dried sheet product, in Japanese cuisine. Its lipid components reportedly improve hepatic steatosis in obese db/db mice. In this study, we prepared "Nori powder (NP)" and "fermented Nori powder (FNP)" to utilize the functional lipids contained in "Nori" and examined their nutraceutical effects in vivo. Male db/db mice were fed a basal AIN-76 diet, a 10% NP-supplemented diet, or a 10% FNP-supplemented diet for 4 weeks. We detected eicosapentaenoic acid (EPA) present in both NP and FNP in the serum and liver of db/db mice in a dose-dependent manner. The NP diet reduced hepatic triglyceride accumulation (by 58%) in db/db mice by modulating gene expression, which resulted in the inhibition of lipogenic enzyme activity. Additionally, NP intake significantly suppressed the expression of inflammatory genes in the liver and hepatic injury marker levels in the sera (by 26%) of db/db mice. The FNP diet also led to a marked reduction in hepatic triglyceride accumulation (by 50%) and hepatic injury (by 28%) in db/db mice, and the mechanism of these alleviative actions was similar to that of the NP diet. Although the EPA content of FNP was one-third that of NP, metabolomic analysis revealed that bioactive betaine analogs, such as stachydrine, betaine, and carnitine, were detected only in FNP. In conclusion, we suggest that (1) mechanical processing of "Nori" makes its lipid components readily absorbable by the body to exert their lipid-lowering effects, and (2) fermentation of "Nori" produces anti-inflammatory molecules and lipid-lowering molecules, which together with the lipid components, can exert hepatic steatosis-alleviating effects.


Subject(s)
Fatty Liver , Porphyra , Animals , Betaine/pharmacology , Eicosapentaenoic Acid/pharmacology , Fatty Liver/drug therapy , Fatty Liver/metabolism , Liver , Male , Mice , Mice, Inbred C57BL , Mice, Obese , Powders/metabolism , Triglycerides/metabolism
6.
Development ; 145(18)2018 09 25.
Article in English | MEDLINE | ID: mdl-30126901

ABSTRACT

X inactivation in mammals is regulated by epigenetic modifications. Functional deficiency of SmcHD1 has been shown to cause de-repression of X-inactivated genes in post-implantation female mouse embryos, suggesting a role of SmcHD1 in the maintenance of X inactivation. Here, we show that de-repression of X-inactivated genes accompanied a local reduction in the enrichment of H3K27me3 in mouse embryonic fibroblasts deficient for SmcHD1. Furthermore, many of these genes overlapped with those having a significantly lower enrichment of H3K27me3 at the blastocyst stage in wild type. Intriguingly, however, depletion of SmcHD1 did not compromise the X-inactivated state in immortalized female mouse embryonic fibroblasts, in which X inactivation had been established and maintained. Taking all these findings together, we suggest that SmcHD1 facilitates the incorporation of H3K27me3 and perhaps other epigenetic modifications at gene loci that are silenced even with the lower enrichment of H3K27me3 at the early stage of X inactivation. The epigenetic state at these loci would, however, remain as it is at the blastocyst stage in the absence of SmcHD1 after implantation, which would eventually compromise the maintenance of the X-inactivated state at later stages.


Subject(s)
Chromosomal Proteins, Non-Histone/metabolism , Epigenesis, Genetic/genetics , Genes, X-Linked/genetics , X Chromosome Inactivation/genetics , Animals , Cells, Cultured , Chromosomal Proteins, Non-Histone/genetics , Embryo, Mammalian/embryology , Female , Fibroblasts/cytology , Histones/genetics , Histones/metabolism , Mice , Mice, Inbred C57BL , Mice, Transgenic
7.
Development ; 144(15): 2784-2797, 2017 08 01.
Article in English | MEDLINE | ID: mdl-28684628

ABSTRACT

Xist RNA, which is responsible for X inactivation, is a key epigenetic player in the embryogenesis of female mammals. Of the several repeats conserved in Xist RNA, the A-repeat has been shown to be essential for its silencing function in differentiating embryonic stem cells. Here, we introduced a new Xist allele into mouse that produces mutated Xist RNA lacking the A-repeat (XistCAGΔ5' ). XistCAGΔ5' RNA expressed in the embryo coated the X chromosome but failed to silence it. Although imprinted X inactivation was substantially compromised upon paternal transmission, allele-specific RNA-seq in the trophoblast revealed that XistCAGΔ5' RNA still retained some silencing ability. Furthermore, the failure of imprinted X inactivation had more significant impacts than expected on genome-wide gene expression. It is likely that dosage compensation is required not only for equalizing X-linked gene expression between the sexes but also for proper global gene regulation in differentiated female somatic cells.


Subject(s)
Dosage Compensation, Genetic/physiology , Gene Expression Regulation, Developmental/genetics , Trophoblasts/metabolism , Alleles , Animals , Cells, Cultured , Dosage Compensation, Genetic/genetics , Embryonic Stem Cells/metabolism , Female , Fluorescent Antibody Technique , Mice , X Chromosome/genetics , X Chromosome Inactivation/genetics
8.
Arch Biochem Biophys ; 691: 108486, 2020 09 30.
Article in English | MEDLINE | ID: mdl-32710880

ABSTRACT

Nonalcoholic fatty liver disease (NAFLD) is emerging as the most common liver disease in industrialized countries. Because hepatic steatosis is an early pathogenesis of NAFLD, the discovery of food components that could ameliorate hepatic steatosis is of interest. Susabinori (Pyropia yezoensis) is recognized as one of the most delicious edible brown algae, and we prepared lipid component of susabinori (SNL), which is rich in eicosapentaenoic acid (EPA)-containing polar lipids. In this study, we tested whether feeding SNL to db/db mice protects them from developing obesity-induced hepatic steatosis. After four weeks of feeding, hepatomegaly, hepatic steatosis, and hepatic injury were markedly alleviated in SNL-fed db/db mice. These effects were partly attributable to the suppression of activities and mRNA expressions of lipogenic enzymes and enhanced levels of adiponectin due to the SNL diet. Additionally, mRNA expression of monocyte chemoattractant protein-1, an inflammatory chemokine, was markedly suppressed, and the mRNA levels of PPARδ, the anti-inflammatory transcription factor, were strongly enhanced in the livers of db/db mice by the SNL diet. We speculate that the development and progression of obesity-induced hepatic steatosis was prevented by the suppression of chronic inflammation due to the combination of bioactivities of EPA, phospholipids, and glycolipids in the SNL diet.


Subject(s)
Eicosapentaenoic Acid/analogs & derivatives , Eicosapentaenoic Acid/pharmacology , Non-alcoholic Fatty Liver Disease/prevention & control , Plant Extracts/pharmacology , Seaweed/chemistry , Animals , Chemokine CCL2/metabolism , Glycolipids/pharmacology , Hepatomegaly/metabolism , Hepatomegaly/prevention & control , Lipogenesis/drug effects , Liver/metabolism , Male , Mice, Inbred C57BL , Mice, Obese , Non-alcoholic Fatty Liver Disease/metabolism , PPAR delta/metabolism , Phospholipids/pharmacology , RNA, Messenger/metabolism , Rhodophyta/chemistry
9.
Biosci Biotechnol Biochem ; 84(11): 2385-2389, 2020 Nov.
Article in English | MEDLINE | ID: mdl-32741270

ABSTRACT

We investigated the anti-stress effect of rosemary (Rosmarinus officinalis L.) leaf extract (RLE) on restraint-stressed mice and found that RLE alleviated decreases in the number of intestinal goblet cells and amount of hepatic triglycerides. It also decreased the immobility time in the forced-swimming test and activation of microglia in the brain, suggesting that RLE has beneficial effects on stress-induced dysfunctions.


Subject(s)
Goblet Cells/drug effects , Plant Extracts/pharmacology , Plant Leaves/chemistry , Rosmarinus/chemistry , Stress, Psychological/drug therapy , Animals , Goblet Cells/cytology , Immobility Response, Tonic , Mice , Mice, Inbred BALB C , Plant Extracts/therapeutic use , Swimming
10.
J Cell Sci ; 130(10): 1822-1834, 2017 05 15.
Article in English | MEDLINE | ID: mdl-28386019

ABSTRACT

The nuclear pore complex (NPC), a gateway for nucleocytoplasmic trafficking, is composed of ∼30 different proteins called nucleoporins. It remains unknown whether the NPCs within a species are homogeneous or vary depending on the cell type or physiological condition. Here, we present evidence for compositionally distinct NPCs that form within a single cell in a binucleated ciliate. In Tetrahymena thermophila, each cell contains both a transcriptionally active macronucleus (MAC) and a germline micronucleus (MIC). By combining in silico analysis, mass spectrometry analysis for immuno-isolated proteins and subcellular localization analysis of GFP-fused proteins, we identified numerous novel components of MAC and MIC NPCs. Core members of the Nup107-Nup160 scaffold complex were enriched in MIC NPCs. Strikingly, two paralogs of Nup214 and of Nup153 localized exclusively to either the MAC or MIC NPCs. Furthermore, the transmembrane components Pom121 and Pom82 localize exclusively to MAC and MIC NPCs, respectively. Our results argue that functional nuclear dimorphism in ciliates is likely to depend on the compositional and structural specificity of NPCs.


Subject(s)
Nuclear Pore Complex Proteins/metabolism , Nuclear Pore/metabolism , Tetrahymena thermophila/metabolism , Conserved Sequence , Macronucleus/metabolism , Micronucleus, Germline/metabolism , Models, Biological , Nuclear Pore Complex Proteins/chemistry , Permeability , Protein Domains , Protein Structure, Secondary , Protozoan Proteins/chemistry , Protozoan Proteins/metabolism , Sequence Homology, Amino Acid
11.
Biosci Biotechnol Biochem ; 83(8): 1514-1522, 2019 Aug.
Article in English | MEDLINE | ID: mdl-30595103

ABSTRACT

Koji, which is manufactured by proliferating non-pathogenic fungus Aspergillus oryzae on steamed rice, is the base for Japanese traditional fermented foods. We have revealed that koji and related Japanese fermented foods and drinks such as amazake, shio-koji, unfiltered sake and miso contain abundant glycosylceramide. Here, we report that feeding of koji glycosylceramide to obese mice alters the cholesterol metabolism . Liver cholesterol was significantly decreased in obese mice fed with koji glycosylceramide. We hypothesized that their liver cholesterol was decreased because it was converted to bile acids. Consistent with the hypothesis, many bile acids were increased in the cecum and feces of obese mice fed with koji glycosylceramide. Expressions of CYP7A1 and ABCG8 involved in the metabolism of cholesterol were significantly increased in the liver of mice fed with koji glycosylceramide. Therefore, it was considered that koji glycosylceramide affects the cholesterol metabolism in obese mice.


Subject(s)
Ceramides/administration & dosage , Cholesterol/metabolism , Fermented Foods , ATP Binding Cassette Transporter, Subfamily G, Member 8/metabolism , Animals , Aspergillus oryzae/metabolism , Bile Acids and Salts/metabolism , Cholesterol 7-alpha-Hydroxylase/metabolism , Japan , Lipoproteins/metabolism , Liver/metabolism , Male , Mice , Mice, Inbred C57BL , Mice, Obese
12.
Genes Cells ; 22(1): 59-70, 2017 Jan.
Article in English | MEDLINE | ID: mdl-27935167

ABSTRACT

An evolutionarily conserved protein Tel2 regulates a variety of stress signals. In mammals, TEL2 associates with TTI1 and TTI2 to form the Triple T (TTT: TEL2-TTI1-TTI2) complex as well as with all the phosphatidylinositol 3-kinase-like kinases (PIKKs) and the R2TP (Ruvbl1-Ruvbl2-Tah1-Pih1 in budding yeast)/prefoldin-like complex that associates with HSP90. The phosphorylation of TEL2 by casein kinase 2 (CK2) enables direct binding of PIHD1 (mammalian Pih1) to TEL2 and is important for the stability and the functions of PIKKs. However, the regulatory mechanisms of Tel2 in fission yeast Schizosaccharomyces pombe remain largely unknown. Here, we report that S. pombe Tel2 is phosphorylated by CK2 at Ser490 and Thr493. Tel2 forms the TTT complex with Tti1 and Tti2 and also associates with PIKKs, Rvb2, and Hsp90 in vivo; however, the phosphorylation of Tel2 affects neither the stability of the Tel2-associated proteins nor their association with Tel2. Thus, Tel2 stably associates with its binding partners irrespective of its phosphorylation. Furthermore, the Tel2 phosphorylation by CK2 is not required for the various stress responses to which PIKKs are pivotal. Our results suggest that the Tel2-containing protein complexes are conserved among eukaryotes, but the molecular regulation of their formation has been altered during evolution.


Subject(s)
Casein Kinase II/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Stress, Physiological/genetics , Telomere-Binding Proteins/metabolism , Casein Kinase II/genetics , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Multiprotein Complexes/genetics , Multiprotein Complexes/metabolism , Phosphorylation , Protein Binding , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/genetics , Telomere-Binding Proteins/genetics
13.
Nucleic Acids Res ; 44(9): 4147-62, 2016 05 19.
Article in English | MEDLINE | ID: mdl-26792892

ABSTRACT

In budding yeast, Set2 catalyzes di- and trimethylation of H3K36 (H3K36me2 and H3K36me3) via an interaction between its Set2-Rpb1 interaction (SRI) domain and C-terminal repeats of RNA polymerase II (Pol2) phosphorylated at Ser2 and Ser5 (CTD-S2,5-P). H3K36me2 is sufficient for recruitment of the Rpd3S histone deacetylase complex to repress cryptic transcription from transcribed regions. In fission yeast, Set2 is also responsible for H3K36 methylation, which represses a subset of RNAs including heterochromatic and subtelomeric RNAs, at least in part via recruitment of Clr6 complex II, a homolog of Rpd3S. Here, we show that CTD-S2P-dependent interaction of fission yeast Set2 with Pol2 via the SRI domain is required for formation of H3K36me3, but not H3K36me2. H3K36me3 silenced heterochromatic and subtelomeric transcripts mainly through post-transcriptional and transcriptional mechanisms, respectively, whereas H3K36me2 was not enough for silencing. Clr6 complex II appeared not to be responsible for heterochromatic silencing by H3K36me3. Our results demonstrate that H3K36 methylation has multiple outputs in fission yeast; these findings provide insights into the distinct roles of H3K36 methylation in metazoans, which have different enzymes for synthesis of H3K36me1/2 and H3K36me3.


Subject(s)
Gene Expression Regulation, Fungal , Gene Silencing , Histones/metabolism , Protein Processing, Post-Translational , Schizosaccharomyces/genetics , Chromosomes, Fungal/genetics , Chromosomes, Fungal/ultrastructure , Genes, Fungal , Heterochromatin/genetics , Heterochromatin/ultrastructure , Histone-Lysine N-Methyltransferase/chemistry , Histone-Lysine N-Methyltransferase/physiology , Methylation , Protein Interaction Domains and Motifs , RNA Polymerase II/chemistry , RNA Polymerase II/metabolism , RNA Stability , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/chemistry , Schizosaccharomyces pombe Proteins/physiology , Telomere/genetics , Transcription, Genetic
14.
Br J Nutr ; 116(3): 451-8, 2016 08.
Article in English | MEDLINE | ID: mdl-27267802

ABSTRACT

Probiotic Lactobacillus gasseri SBT2055 (LG2055) reduces postprandial TAG absorption and exerts anti-obesity effects in rats and humans; however, the underlying mechanisms are not fully understood. In the present study, we addressed the mechanistic insights of the anti-obesity activity of LG2055 by feeding Sprague-Dawley rats diets containing skimmed milk fermented or not by LG2055 for 4 weeks and by analysing energy expenditure, glucose tolerance, the levels of SCFA in the caecum and serum inflammatory markers. Rats fed the LG2055-containing diet demonstrated significantly higher carbohydrate oxidation in the dark cycle (active phase for rats) compared with the control group, which resulted in a significant increase in energy expenditure. LG2055 significantly reduced cumulative blood glucose levels (AUC) compared with the control diet after 3 weeks and increased the molar ratio of butyrate:total SCFA in the caecum after 4 weeks. Furthermore, the LG2055-supplemented diet significantly reduced the levels of serum amyloid P component - an indicator of the inflammatory process. In conclusion, our results demonstrate that, in addition to the inhibition of dietary TAG absorption reported previously, the intake of probiotic LG2055 enhanced energy expenditure via carbohydrate oxidation, improved glucose tolerance and attenuated inflammation, suggesting multiple additive and/or synergistic actions underlying the anti-obesity effects exerted by LG2055.


Subject(s)
Anti-Obesity Agents/therapeutic use , Blood Glucose/metabolism , Energy Metabolism , Lactobacillus gasseri , Obesity/prevention & control , Probiotics/therapeutic use , Weight Gain , Animals , Area Under Curve , Butyrates/metabolism , Carbohydrate Metabolism , Cecum/metabolism , Cultured Milk Products/microbiology , Diet , Fatty Acids, Volatile/metabolism , Inflammation/blood , Inflammation/prevention & control , Lipid Metabolism , Male , Rats, Sprague-Dawley , Serum Amyloid P-Component/metabolism , Triglycerides/blood
15.
Genes Cells ; 19(7): 541-54, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24774534

ABSTRACT

CENP-A is a centromere-specific variant of histone H3 that is required for accurate chromosome segregation. The fission yeast Schizosaccharomyces pombe and mammalian Mis16 and Mis18 form a complex essential for CENP-A recruitment to centromeres. It is unclear, however, how the Mis16-Mis18 complex achieves this function. Here, we identified, by mass spectrometry, novel fission yeast centromere proteins Mis19 and Mis20 that directly interact with Mis16 and Mis18. Like Mis18, Mis19 and Mis20 are localized at the centromeres during interphase, but not in mitosis. Inactivation of Mis19 in a newly isolated temperature-sensitive mutant resulted in CENP-A delocalization and massive chromosome missegregation, whereas Mis20 was dispensable for proper chromosome segregation. Mis19 might be a bridge component for Mis16 and Mis18. We isolated extragenic suppressor mutants for temperature-sensitive mis18 and mis19 mutants and used whole-genome sequencing to determine the mutated sites. We identified two groups of loss-of-function suppressor mutations in non-sense-mediated mRNA decay factors (upf2 and ebs1), and in SWI/SNF chromatin-remodeling components (snf5, snf22 and sol1). Our results suggest that the Mis16-Mis18-Mis19-Mis20 CENP-A-recruiting complex, which is functional in the G1-S phase, may be counteracted by the SWI/SNF chromatin-remodeling complex and non-sense-mediated mRNA decay, which may prevent CENP-A deposition at the centromere.


Subject(s)
Carrier Proteins/metabolism , Centromere/metabolism , Chromosomal Proteins, Non-Histone/metabolism , Multiprotein Complexes/metabolism , Nonsense Mediated mRNA Decay , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , Amino Acid Sequence , Carrier Proteins/genetics , Centromere/ultrastructure , Chromosomal Proteins, Non-Histone/genetics , Chromosome Segregation , Mass Spectrometry , Molecular Sequence Data , Mutation , Protein Subunits/metabolism , Schizosaccharomyces pombe Proteins/genetics
16.
Appl Environ Microbiol ; 81(11): 3688-98, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25795678

ABSTRACT

In nature, different microorganisms create communities through their physiochemical and metabolic interactions. Many fermenting microbes, such as yeasts, lactic acid bacteria, and acetic acid bacteria, secrete acidic substances and grow faster at acidic pH values. However, on the surface of cereals, the pH is neutral to alkaline. Therefore, in order to grow on cereals, microbes must adapt to the alkaline environment at the initial stage of colonization; such adaptations are also crucial for industrial fermentation. Here, we show that the yeast Saccharomyces cerevisiae, which is incapable of synthesizing glucosylceramide (GlcCer), adapted to alkaline conditions after exposure to GlcCer from koji cereal cultured with Aspergillus kawachii. We also show that various species of GlcCer derived from different plants and fungi similarly conferred alkali tolerance to yeast. Although exogenous ceramide also enhanced the alkali tolerance of yeast, no discernible degradation of GlcCer to ceramide was observed in the yeast culture, suggesting that exogenous GlcCer itself exerted the activity. Exogenous GlcCer also increased ethanol tolerance and modified the flavor profile of the yeast cells by altering the membrane properties. These results indicate that GlcCer from A. kawachii modifies the physiology of the yeast S. cerevisiae and demonstrate a new mechanism for cooperation between microbes in food fermentation.


Subject(s)
Aspergillus/physiology , Edible Grain/microbiology , Flavoring Agents/metabolism , Glucosylceramides/metabolism , Membranes/drug effects , Saccharomyces cerevisiae/physiology , Stress, Physiological/drug effects , Aspergillus/growth & development , Aspergillus/metabolism , Edible Grain/metabolism , Ethanol/metabolism , Fermentation , Hydrogen-Ion Concentration , Saccharomyces cerevisiae/growth & development , Saccharomyces cerevisiae/metabolism
17.
Nucleic Acids Res ; 41(1): 54-62, 2013 Jan 07.
Article in English | MEDLINE | ID: mdl-23125363

ABSTRACT

Deep sequencing approaches, such as chromatin immunoprecipitation by sequencing (ChIP-seq), have been successful in detecting transcription factor-binding sites and histone modification in the whole genome. An approach for comparing two different ChIP-seq data would be beneficial for predicting unknown functions of a factor. We propose a model to represent co-localization of two different ChIP-seq data. We showed that a meaningful overlapping signal and a meaningless background signal can be separated by this model. We applied this model to compare ChIP-seq data of RNA polymerase II C-terminal domain (CTD) serine 2 phosphorylation with a large amount of peak-called data, including ChIP-seq and other deep sequencing data in the Encyclopedia of DNA Elements (ENCODE) project, and then extracted factors that were related to RNA polymerase II CTD serine 2 in HeLa cells. We further analyzed RNA polymerase II CTD serine 7 phosphorylation, of which their function is still unclear in HeLa cells. Our results were characterized by the similarity of localization for transcription factor/histone modification in the ENCODE data set, and this suggests that our model is appropriate for understanding ChIP-seq data for factors where their function is unknown.


Subject(s)
Chromatin Immunoprecipitation , Epigenesis, Genetic , High-Throughput Nucleotide Sequencing , HeLa Cells , Histones/metabolism , Humans , Models, Genetic , Phosphorylation , RNA Polymerase II/metabolism , Serine/metabolism , Software , Transcription Initiation Site
18.
Protein Expr Purif ; 97: 44-9, 2014 May.
Article in English | MEDLINE | ID: mdl-24583182

ABSTRACT

Chromatin-associated proteins are heterogeneously and dynamically composed. To gain a complete understanding of DNA packaging and basic nuclear functions, it is important to generate a comprehensive inventory of these proteins. However, biochemical purification of chromatin-associated proteins is difficult and is accompanied by concerns over complex stability, protein solubility and yield. Here, we describe a new method for optimized purification of the endogenously expressed fission yeast Set2 complex, histone H3K36 methyltransferase. Using the standard centrifugation procedure for purification, approximately half of the Set2 protein separated into the insoluble chromatin pellet fraction, making it impossible to recover the large amounts of soluble Set2. To overcome this poor recovery, we developed a novel protein purification technique termed the filtration/immunoaffinity purification/mass spectrometry (FIM) method, which eliminates the need for centrifugation. Using the FIM method, in which whole cell lysates were filtered consecutively through eight different pore sizes (53-0.8µm), a high yield of soluble FLAG-tagged Set2 was obtained from fission yeast. The technique was suitable for affinity purification and produced a low background. A mass spectrometry analysis of anti-FLAG immunoprecipitated proteins revealed that Rpb1, Rpb2 and Rpb3, which have all been reported previously as components of the budding yeast Set2 complex, were isolated from fission yeast using the FIM method. In addition, other subunits of RNA polymerase II and its phosphatase were also identified. In conclusion, the FIM method is valid for the efficient purification of protein complexes that separate into the insoluble chromatin pellet fraction during centrifugation.


Subject(s)
Histone-Lysine N-Methyltransferase/isolation & purification , Histone-Lysine N-Methyltransferase/metabolism , Schizosaccharomyces pombe Proteins/isolation & purification , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , Chromatography, Liquid/methods , Filtration/methods , Immunoblotting/methods , Immunoprecipitation/methods , Mass Spectrometry/methods , Schizosaccharomyces/chemistry
19.
Biosci Biotechnol Biochem ; 78(9): 1584-91, 2014.
Article in English | MEDLINE | ID: mdl-25209508

ABSTRACT

Many animal studies on improvement of lipid metabolism, using dietary components, fast the animals on the final day of the feeding. Although fasting has a significant impact on lipid metabolism, its time-dependent influence is not fully understood. We examined the effects of several fasting times on lipid metabolism. Rats fed with a semisynthetic diet for 2 wk were killed after 0 (9:00 am), 6 (7:00 am-1:00 pm), 9 (0:00 am-9:00 am), and 13 h (8:00 pm-9:00 am) of fasting. Compared to the 0 h group, marked reduction of liver weight and hepatic triacylglycerol content was observed in the 9 and 13 h groups. Activities of hepatic enzymes involved in fatty acid synthesis gradually decreased during fasting. In contrast, drastic time-dependent reduction of gene expression, of the enzymes, was observed. Expression of carnitine palmitoyltransferase mRNA was higher in the fasting groups than in the 0 h group. Our study showed that fasting has a significant impact on several parameters related to lipid metabolism in rat liver.


Subject(s)
Carnitine O-Palmitoyltransferase/biosynthesis , Fasting/physiology , Lipid Metabolism/genetics , Liver/metabolism , Animals , Fasting/metabolism , Gene Expression Regulation, Enzymologic , Liver/enzymology , RNA, Messenger/biosynthesis , Rats
20.
Lipids Health Dis ; 13: 19, 2014 Jan 22.
Article in English | MEDLINE | ID: mdl-24450544

ABSTRACT

BACKGROUND: Exogenously hypercholesterolemic (ExHC) rats develop hypercholesterolemia and low hepatic triacylglycerol (TAG) levels when dietary cholesterol is loaded. The responsible gene Smek2 was identified via linkage analysis using the original strain Sprague-Dawley (SD) rats. In this study, we compared SD and ExHC rats to investigate a relationship between hypercholesterolemia and the low hepatic TAG levels observed in ExHC rats. METHODS: Male 4-weeks-old ExHC and SD rats were fed a 1% cholesterol diet for 1 week. Serum and liver parameters were analyzed. Gene expression and enzyme activities related to TAG metabolism were also assessed. RESULTS: We reproducibly observed higher serum cholesterol and lower hepatic TAG levels in ExHC rats than in SD rats. Golgi apparatus in the livers of ExHC rats secreted ß-very-low-density lipoprotein (ß-VLDL) that had higher cholesterol ester (CE) and lower TAG content than those in the ß-VLDL secreted by SD rats. Gene expression related to fatty acid and TAG synthesis in ExHC rats was lower than that in SD rats. Enzymatic activities for fatty acid synthesis were also relatively lower in ExHC rats. Moreover, the fatty acid composition of hepatic and serum CE in ExHC rats showed that these CEs were not modified after secretion from the liver despite the similar activities of serum lecithin-cholesterol acyltransferase (LCAT) in ExHC rats to those in SD rats. CONCLUSIONS: Low production of liver TAG and secretion of CE-rich, TAG-poor ß-VLDL without modification by LCAT in the circulation contributed to hypercholesterolemia induced by dietary cholesterol in ExHC rats.


Subject(s)
Cholesterol Esters/blood , Cholesterol, Dietary/adverse effects , Hypercholesterolemia/blood , Liver/metabolism , Triglycerides/metabolism , Animals , Biosynthetic Pathways , Diet, High-Fat/adverse effects , Fatty Acids/blood , Golgi Apparatus/metabolism , Hypercholesterolemia/etiology , Lipid Metabolism , Male , Phosphatidylcholine-Sterol O-Acyltransferase/blood , RNA, Messenger/genetics , RNA, Messenger/metabolism , Rats , Rats, Sprague-Dawley , Transcriptome
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