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Synonyms
histone deacetylase, hdac1, hdac6, hdac2, hdac3, hdac4, hdac5, hdac8, hdac9, hdac7,
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malfunction
transcript levels of ILV2, ILV3 and ILV5 are elevated in Rpd3L-deficient strains (rpd3DELTA, ume1DELTA, dep1DELTA, and sds3DELTA) but not in Rpd3S-single deficient strain (rco1DELTA and eaf3DELTA) compared to wild-type K701. The transcript levels of ATF2, a minor alcohol acetyltransferase, are higher in the rpd3DELTA and ume1DELTA strains than in the parental strain. K701 rpd3DELTA and K701 hda1DELTA alter the response to oxygen of isoamyl acetate production
physiological function
HDAC genes are non-essential in yeast, functional analysis of genes, RPD3, HDA1, SIR2, and HST1 in the Sake yeast strain Kyokai No. 701 (K701). RPD3 and Hda1 are translation regulatory proteins and histone deacetylases. Rpd3L-dependent regulation of genes ILV2, ILV3 and ILV5. Rpd3 and Hda1 may regulate isoamyl acetate production via oxygen in a Rox1-independent manner. Yeast HDACs, and maybe also HAT and their regulatory subunits, are keys to determine fermentation characteristics, and these genes may be an important target for improvement of yeast strains used for alcoholic beverage production
evolution
the protruded arm regions are conserved among the Hda1 homologies, and residues Ile512, Ile523 and Leu525 that play key role in the domain-domain interaction are relatively conserved. The ARB2 domain of Hda1 shows structural similarity to the alpha/beta fold hydrolases
malfunction
K701 rpd3DELTA and K701 hda1DELTA alter the response to oxygen of isoamyl acetate production
malfunction
perturbation of the dimer interface abolishes the histone binding ability of the ARB2 domain
physiological function
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Sir2 is involved in protection against Hog1-induced cell death and can suppress Hog1-induced reactive oxygen species accumulation. Therefore, cell death seems to be dictated by the balance of reactive oxygen species induced by Hog1 and the protective effect of Sir2. Prolonged activation of stress-activated protein kinase leads to cell death, by causing accumulation of reactive oxygen species. Mutations of the SCF-CDC4 ubiquitin ligase complex suppress cell death by preventing the degradation of Msn2 and Msn4 transcription factors. Accumulation of transcription factors Msn2 and Msn4 leads to the induction of PNC1, which is an activator of the Sir2 histone acetylase
physiological function
Hda1 is the catalytic core component of the H2B- and H3-specific histone deacetylase (HDAC) complex from Saccharomyces cerevisiae, which is involved in the epigenetic repression and plays a crucial role in transcriptional regulation and developmental events
physiological function
HDAC genes are non-essential in yeast, functional analysis of genes, RPD3, HDA1, SIR2, and HST1 in the Sake yeast strain Kyokai No. 701 (K701). RPD3 and Hda1 are translation regulatory proteins and histone deacetylases. Rpd3 and Hda1 may regulate isoamyl acetate production via oxygen in a Rox1-independent manner. Yeast HDACs, and maybe also HAT and their regulatory subunits, are keys to determine fermentation characteristics, and these genes may be an important target for improvement of yeast strains used for alcoholic beverage production
additional information
transcript analysis of genes responsible for the production of flavor components
additional information
transcript analysis of genes responsible for the production of flavor components
additional information
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transcript analysis of genes responsible for the production of flavor components
additional information
the ARB2 domain displays an alpha/beta sandwich architecture with an arm protruding outside. Two ARB2 domain molecules form a compact homodimer via the arm elements, and assemble as an inverse V shape. The pull-down and ITC results reveal that the ARB2 domain possesses the histone binding ability, recognizing both the H2A-H2B dimer and H3-H4 tetramer. the unique dimer architecture of the ARB2 domain coincides with the function for anchoring to histone. Hda1 consists of an N-terminal catalytic domain and a C-terminal non-catalytic domain (ARB2). The catalytic domain of Hda1 shows high sequence homology to the HDACs structures. Role of the C-terminal non-catalytic domain of Hda1 functioning in the deacetylation process, overview
additional information
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the ARB2 domain displays an alpha/beta sandwich architecture with an arm protruding outside. Two ARB2 domain molecules form a compact homodimer via the arm elements, and assemble as an inverse V shape. The pull-down and ITC results reveal that the ARB2 domain possesses the histone binding ability, recognizing both the H2A-H2B dimer and H3-H4 tetramer. the unique dimer architecture of the ARB2 domain coincides with the function for anchoring to histone. Hda1 consists of an N-terminal catalytic domain and a C-terminal non-catalytic domain (ARB2). The catalytic domain of Hda1 shows high sequence homology to the HDACs structures. Role of the C-terminal non-catalytic domain of Hda1 functioning in the deacetylation process, overview
additional information
transcript analysis of genes responsible for the production of flavor components
additional information
transcript analysis of genes responsible for the production of flavor components
additional information
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transcript analysis of genes responsible for the production of flavor components
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H604A/H608A/R609A
site-directed mutagenesis, the mutant ARB2-M4 completely loses the binding ability to histone H3-H4, histone binding kinetics, overview
Q463A/D471A
site-directed mutagenesis, histone binding kinetics, overview
V481A/S482A/M483A/D484A
site-directed mutagenesis, histone binding kinetics, overview
Y468A/E472A
site-directed mutagenesis, histone binding kinetics, overview
additional information
establishment of HDAC RPD3 and accessory protein gene-disrupted strains, sake strain 701 with deleted gened encoding for other transcription regulatory proteins, e.g. RPD3, HDA1, SDS3, DEP1, and UME1, and NAD-dependent protein deacetylases, e.g. HST1, and quantitative real-time PCR of fusel alcohol or acetate ester synthesis related-genes in these strains, overview. Evaluation of sake fermenatation with the mutant strains, small-scale sake production test
additional information
establishment of HDAC RPD3 and accessory protein gene-disrupted strains, sake strain 701 with deleted gened encoding for other transcription regulatory proteins, e.g. RPD3, HDA1, SDS3, DEP1, and UME1, and NAD-dependent protein deacetylases, e.g. HST1, and quantitative real-time PCR of fusel alcohol or acetate ester synthesis related-genes in these strains, overview. Evaluation of sake fermenatation with the mutant strains, small-scale sake production test
additional information
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establishment of HDAC RPD3 and accessory protein gene-disrupted strains, sake strain 701 with deleted gened encoding for other transcription regulatory proteins, e.g. RPD3, HDA1, SDS3, DEP1, and UME1, and NAD-dependent protein deacetylases, e.g. HST1, and quantitative real-time PCR of fusel alcohol or acetate ester synthesis related-genes in these strains, overview. Evaluation of sake fermenatation with the mutant strains, small-scale sake production test
additional information
construction of four mutants, ARB2-M1 (residues Gln463, His467 and Asp471 mutated to Ala), ARB2-M2 (residues Tyr468 and Glu472 mutated to Ala), ARB2-M3 (residues Val481, Ser482, Met483 and Asp484 mutated to Ala) and ARB2-M4 (residues His604, His608 and Arg609 mutated to Ala). The binding affinity of mutants ARB2-M1, ARB2-M2, ARB2-M3 and ARB2-M4 to histone H2A-H2B dimer is 0.0204 mM, 0.0169 mM, 0.0277 mM, and 0.0174 mM, respectively. And the binding affinity of mutants ARB2-M1, ARB2-M2 and ARB2-M3 to histone H3-H4 tetramer is 0.00984 mM, 0.00693 mM, and 0.00819 mM, respectively. Mutant ARB2-M4 completely loses the binding ability to histone H3-H4
additional information
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construction of four mutants, ARB2-M1 (residues Gln463, His467 and Asp471 mutated to Ala), ARB2-M2 (residues Tyr468 and Glu472 mutated to Ala), ARB2-M3 (residues Val481, Ser482, Met483 and Asp484 mutated to Ala) and ARB2-M4 (residues His604, His608 and Arg609 mutated to Ala). The binding affinity of mutants ARB2-M1, ARB2-M2, ARB2-M3 and ARB2-M4 to histone H2A-H2B dimer is 0.0204 mM, 0.0169 mM, 0.0277 mM, and 0.0174 mM, respectively. And the binding affinity of mutants ARB2-M1, ARB2-M2 and ARB2-M3 to histone H3-H4 tetramer is 0.00984 mM, 0.00693 mM, and 0.00819 mM, respectively. Mutant ARB2-M4 completely loses the binding ability to histone H3-H4
additional information
establishment of HDAC RPD3 and accessory protein gene-disrupted strains, sake strain 701 with deleted gened encoding for other transcription regulatory proteins, e.g. RPD3, HDA1, SDS3, DEP1, and UME1, and NAD-dependent protein deacetylases, e.g. HST1, and quantitative real-time PCR of fusel alcohol or acetate ester synthesis related-genes in these strains, overview. Evaluation of sake fermenatation with the mutant strains, small-scale sake production test
additional information
establishment of HDAC RPD3 and accessory protein gene-disrupted strains, sake strain 701 with deleted gened encoding for other transcription regulatory proteins, e.g. RPD3, HDA1, SDS3, DEP1, and UME1, and NAD-dependent protein deacetylases, e.g. HST1, and quantitative real-time PCR of fusel alcohol or acetate ester synthesis related-genes in these strains, overview. Evaluation of sake fermenatation with the mutant strains, small-scale sake production test
additional information
-
establishment of HDAC RPD3 and accessory protein gene-disrupted strains, sake strain 701 with deleted gened encoding for other transcription regulatory proteins, e.g. RPD3, HDA1, SDS3, DEP1, and UME1, and NAD-dependent protein deacetylases, e.g. HST1, and quantitative real-time PCR of fusel alcohol or acetate ester synthesis related-genes in these strains, overview. Evaluation of sake fermenatation with the mutant strains, small-scale sake production test
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Tomimoto, K.; Akao, T.; Fukuda, H.
Histone deacetylases in sake yeast affect fermentation characteristics
Biosci. Biotechnol. Biochem.
83
1498-1505
2019
Saccharomyces cerevisiae (P32561), Saccharomyces cerevisiae (P53973), Saccharomyces cerevisiae, Saccharomyces cerevisiae ATCC 204508 (P32561), Saccharomyces cerevisiae ATCC 204508 (P53973)
brenda
Shen, H.; Zhu, Y.; Wang, C.; Yan, H.; Teng, M.; Li, X.
Structural and histone binding ability characterization of the ARB2 domain of a histone deacetylase Hda1 from Saccharomyces cerevisiae
Sci. Rep.
6
33905
2016
Saccharomyces cerevisiae (P53973), Saccharomyces cerevisiae, Saccharomyces cerevisiae ATCC 204508 (P53973)
brenda