Serine- and Threonine/Valine-Dependent Activation of PDK and Tor Orthologs Converge on Sch9 to Promote Aging
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{"title"=>"Serine- and Threonine/Valine-Dependent Activation of PDK and Tor Orthologs Converge on Sch9 to Promote Aging", "type"=>"journal", "authors"=>[{"first_name"=>"Mario G.", "last_name"=>"Mirisola", "scopus_author_id"=>"6603471426"}, {"first_name"=>"Giusi", "last_name"=>"Taormina", "scopus_author_id"=>"56191592300"}, {"first_name"=>"Paola", "last_name"=>"Fabrizio", "scopus_author_id"=>"35615904900"}, {"first_name"=>"Min", "last_name"=>"Wei", "scopus_author_id"=>"35363140800"}, {"first_name"=>"Jia", "last_name"=>"Hu", "scopus_author_id"=>"55499379500"}, {"first_name"=>"Valter D.", "last_name"=>"Longo", "scopus_author_id"=>"7005786660"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"pui"=>"372548512", "issn"=>"15537390", "pmid"=>"24516402", "sgr"=>"84901743802", "scopus"=>"2-s2.0-84901743802", "isbn"=>"1553-7404 (Electronic)\r1553-7390 (Linking)", "doi"=>"10.1371/journal.pgen.1004113"}, "id"=>"911e47d3-9712-37ef-bcae-a21b65a8d327", "abstract"=>"Dietary restriction extends longevity in organisms ranging from bacteria to mice and protects primates from a variety of diseases, but the contribution of each dietary component to aging is poorly understood. Here we demonstrate that glucose and specific amino acids promote stress sensitization and aging through the differential activation of the Ras/cAMP/PKA, PKH1/2 and Tor/S6K pathways. Whereas glucose sensitized cells through a Ras-dependent mechanism, threonine and valine promoted cellular sensitization and aging primarily by activating the Tor/S6K pathway and serine promoted sensitization via PDK1 orthologs Pkh1/2. Serine, threonine and valine activated a signaling network in which Sch9 integrates TORC1 and Pkh signaling via phosphorylation of threonines 570 and 737 and promoted intracellular relocalization and transcriptional inhibition of the stress resistance protein kinase Rim15. Because of the conserved pro-aging role of nutrient and growth signaling pathways in higher eukaryotes, these results raise the possibility that similar mechanisms contribute to aging in mammals.", "link"=>"http://www.mendeley.com/research/serine-threoninevalinedependent-activation-pdk-tor-orthologs-converge-sch9-promote-aging", "reader_count"=>51, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>15, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>5, "Student > Master"=>9, "Student > Bachelor"=>9}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>15, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>5, "Student > Master"=>9, "Student > Bachelor"=>9}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>35, "Medicine and Dentistry"=>4, "Business, Management and Accounting"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>35}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>1, "Chile"=>1, "Switzerland"=>1, "Spain"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1554908"], "description"=>"<p>(A) Wild type DBY746, was transformed with a plasmid coding for the Rim15-GFP fusion protein, after two days of growth the exhausted medium was replaced (upper panel) with fresh synthetic medium lacking all the amino acids (dextrose) or with the complete medium (SDC), pictures were taken after the indicated time. In the lower panel the fresh medium contained also compounds necessary to compensate the auxothrophies (the amino acids L, H, W and the nucleotide Uracil) plus the indicated amino acid (pictures were taken after two hours of incubation). (B) Wild type (Wt) and <i>sch9Δ</i> mutants (<i>sch9Δ</i>) were transformed with a plasmid coding for the Rim15-GFP fusion protein. After two days of growth wild type cells were transferred onto fresh medium while sch9Δ cells were left in the exhausted medium. GFP fluorescence or DAPI staining were observed after 2 additional hours in the aforementioned medium. (C) Wild type DBY746 strain, transformed with Rim15-GFP and Pab1-RFP expressing plasmids was grown to the post-diauxic phase (two days of growth) and then transferred onto fresh complete SDC medium, fluorescence was observed after two hours of incubation. (D) Rim15 mRNA level fluctuation in response to nutrients addition. mRNA obtained from stationary phase DBY746 cell culture (T = 0) or from the same culture but collected after 1, 2 or 4 hours after the switch to fresh SDC was subjected to Real Time PCR with Rim15 specific oligonucleotides. The amount of mRNA used for each PCR was normalized using the actin (ACT1) transcript levels as an internal control. The expression level of Rim15 before the medium switch (T = 0), which was the highest, was used as a reference point (100% of expression). The expression at the others time points was calculated using the formula [expr level(T = 1, 2, 4)/expr level (T = 0)] * 100.</p>", "links"=>[], "tags"=>["genetics", "Gene networks", "microbiology", "Model organisms", "Molecular cell biology", "Signal transduction", "Signaling in cellular processes", "Ras signaling", "Tor signaling", "Signaling pathways", "Adenylyl cyclase signaling pathway", "Mechanisms of signal transduction", "Cellular stress responses", "acids", "rim15"], "article_id"=>1074686, "categories"=>["Biological Sciences"], "users"=>["Mario G. Mirisola", "Giusi Taormina", "Paola Fabrizio", "Min Wei", "Jia Hu", "Valter D. Longo"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004113.g005", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amino_acids_affect_Rim15_activity_/1074686", "title"=>"Amino acids affect Rim15 activity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-06 10:24:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1555011", "https://ndownloader.figshare.com/files/1555013", "https://ndownloader.figshare.com/files/1555014", "https://ndownloader.figshare.com/files/1555016", "https://ndownloader.figshare.com/files/1555018", "https://ndownloader.figshare.com/files/1555019", "https://ndownloader.figshare.com/files/1555022", "https://ndownloader.figshare.com/files/1555023"], "description"=>"<div><p>Dietary restriction extends longevity in organisms ranging from bacteria to mice and protects primates from a variety of diseases, but the contribution of each dietary component to aging is poorly understood. Here we demonstrate that glucose and specific amino acids promote stress sensitization and aging through the differential activation of the Ras/cAMP/PKA, PKH1/2 and Tor/S6K pathways. Whereas glucose sensitized cells through a Ras-dependent mechanism, threonine and valine promoted cellular sensitization and aging primarily by activating the Tor/S6K pathway and serine promoted sensitization via PDK1 orthologs Pkh1/2. Serine, threonine and valine activated a signaling network in which Sch9 integrates TORC1 and Pkh signaling via phosphorylation of threonines 570 and 737 and promoted intracellular relocalization and transcriptional inhibition of the stress resistance protein kinase Rim15. Because of the conserved pro-aging role of nutrient and growth signaling pathways in higher eukaryotes, these results raise the possibility that similar mechanisms contribute to aging in mammals.</p></div>", "links"=>[], "tags"=>["genetics", "Gene networks", "microbiology", "Model organisms", "Molecular cell biology", "Signal transduction", "Signaling in cellular processes", "Ras signaling", "Tor signaling", "Signaling pathways", "Adenylyl cyclase signaling pathway", "Mechanisms of signal transduction", "Cellular stress responses", "activation", "pdk", "tor", "orthologs", "converge", "sch9"], "article_id"=>1074778, "categories"=>["Biological Sciences"], "users"=>["Mario G. Mirisola", "Giusi Taormina", "Paola Fabrizio", "Min Wei", "Jia Hu", "Valter D. Longo"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004113.s001", "https://dx.doi.org/10.1371/journal.pgen.1004113.s002", "https://dx.doi.org/10.1371/journal.pgen.1004113.s003", "https://dx.doi.org/10.1371/journal.pgen.1004113.s004", "https://dx.doi.org/10.1371/journal.pgen.1004113.s005", "https://dx.doi.org/10.1371/journal.pgen.1004113.s006", "https://dx.doi.org/10.1371/journal.pgen.1004113.s007", "https://dx.doi.org/10.1371/journal.pgen.1004113.s008"], "stats"=>{"downloads"=>19, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Serine_and_Threonine_Valine_Dependent_Activation_of_PDK_and_Tor_Orthologs_Converge_on_Sch9_to_Promote_Aging_/1074778", "title"=>"Serine- and Threonine/Valine-Dependent Activation of PDK and Tor Orthologs Converge on Sch9 to Promote Aging", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-02-06 10:24:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1554880"], "description"=>"<p>(A) Activation scheme of Sch9 kinase. (B) Western blot of whole protein extract from the indicated W303 isogenic derivatives grown to exponential phase. T570A refers to protein extract from the strain carrying the <i>SCH9</i> allele coding for the amino acid substitution T570A. Anti-SCH9 P570 was used as a primary antibody. (C) Stress resistance (hydrogen peroxide treatment) of the indicated DBY746 isogenic derivatives grown for 24 h (Day1) or 72 h (Day3) in complete synthetic medium (SDC, all the amino acids supplied), the asterisks followed by a number refer to two different isolates with the same relevant genotype. (D) Chronological life span of the same group of strains. (E) Peroxide (H<sub>2</sub>O<sub>2</sub>) and heat shock (55°C) resistance of wild type DBY746 and of the isogenic indicated derivatives strains cultured to day 2 (upper panel). Chronological life spans of the same group of strains (lower panel). All the cultures, after two days of growth at 30°C, were transferred at 35°C to inactivate the Pkh1 thermo sensitive allele as previously described <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen.1004113-Voordeckers2\" target=\"_blank\">[86]</a>. Experiments were performed in triplicate. Standard errors bars are shown. P values were evaluated by 2 tailed T-test for groups with unequal variants. *, p<0.02; **, p<0.005. (F) Nutrient response assay (hydrogen peroxide treatment after nutrient addition, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen.1004113.s001\" target=\"_blank\">figure S1</a> for the experimental scheme) of strains (DBY746 derivatives) bearing different <i>SCH9</i> alleles. T570A and T737A refer to the amino acid substitutions coded by the mutated alleles.</p>", "links"=>[], "tags"=>["genetics", "Gene networks", "microbiology", "Model organisms", "Molecular cell biology", "Signal transduction", "Signaling in cellular processes", "Ras signaling", "Tor signaling", "Signaling pathways", "Adenylyl cyclase signaling pathway", "Mechanisms of signal transduction", "Cellular stress responses", "sch9", "activation", "amino", "acids"], "article_id"=>1074659, "categories"=>["Biological Sciences"], "users"=>["Mario G. Mirisola", "Giusi Taormina", "Paola Fabrizio", "Min Wei", "Jia Hu", "Valter D. Longo"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004113.g002", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Role_of_Sch9_activation_state_in_survival_stress_resistance_and_amino_acids_response_/1074659", "title"=>"Role of Sch9 activation state in survival, stress resistance and amino acids response.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-06 10:24:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1554925"], "description"=>"<p>Schematic diagram of how specific nutrient activates the known pro-aging pathways, the central role of Sch9 and Rim15 is shown.</p>", "links"=>[], "tags"=>["genetics", "Gene networks", "microbiology", "Model organisms", "Molecular cell biology", "Signal transduction", "Signaling in cellular processes", "Ras signaling", "Tor signaling", "Signaling pathways", "Adenylyl cyclase signaling pathway", "Mechanisms of signal transduction", "Cellular stress responses"], "article_id"=>1074702, "categories"=>["Biological Sciences"], "users"=>["Mario G. Mirisola", "Giusi Taormina", "Paola Fabrizio", "Min Wei", "Jia Hu", "Valter D. Longo"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004113.g007", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scheme_of_the_nutrient_pathways_/1074702", "title"=>"Scheme of the nutrient pathways.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-06 10:24:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1554891"], "description"=>"<p>(A) Nutrient response assay (hydrogen peroxide treatment after nutrient addition) using the wild type DBY746 strain (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen.1004113.s001\" target=\"_blank\">figure S1</a> for the experimental scheme) combining the addition of the auxo mixture (see the legend to the <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen-1004113-g001\" target=\"_blank\">figure 1A</a> for details) plus the indicated amino acid with the presence/absence of the Tor-inhibiting drug rapamycin or with the Pkhs-inhibiting drug myriocin. (B) Nutrient response assay (hydrogen peroxide treatment after nutrient addition) of the DBY746 yeast strain with/out rapamycin after the addition of the indicated mixture of nutrients (see the legend to the <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen-1004113-g001\" target=\"_blank\">figure 1A</a> for details). The components of the synthetic medium were added to all samples. 2% Dextrose was added were indicated. Auxo refers to the addition of all the organic compounds necessary to compensate the DBY746 auxothrophies (leucine, histidine, tryptophan and uracil) while auxo+MTV also contained the amino acids methionine, threonine and valine. (C) Viability of the wild type DBY746 yeast strain grown in the presence of the auxo mixture (auxo, see the legend to the <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen-1004113-g001\" target=\"_blank\">figure 1A</a> for a complete description of this medium) or in the presence of auxo mixture plus the amino acid threonine or valine (auxo+T, auxo+V respectively). Experiments were done in triplicate and mean values are represented with standard errors. P values were evaluated by 2 tailed T-test for groups with unequal variants. *, p<0.1; **, p<0.005. (D and E) Chronological life span and mutation frequency of DBY746 wild type strain, grown in complete medium (SDC) or in SDC with reduced concentration of serine, threonine or valine (0.1×, 1∶10 of the standard concentration, see table S2 for a definition of the standard concentration used). Experiments were done in triplicate and mean values are represented with standard errors. P values were evaluated by 2 tailed T-test for groups with unequal variants. *, p<0.1; **, p<0.04; ***, p<0.02. (F) Nutrient response assay (hydrogen peroxide treatment after nutrient addition) using cultures of stationary phase (two days of growth) wild type DBY746 strain and of the isogenic derivative carrying the Sch9 allele coding for the amino acid substitution T737A (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen.1004113.s001\" target=\"_blank\">figure S1</a> for the experimental scheme). Synthetic medium with dextrose and only the organic compounds necessary to compensate the auxothrophies (leucine, histidine, tryptophan and uracil) were added to ‘auxo’ sample. The other samples were added with the same mixture plus the single indicated non-essential amino acid. After hydrogen peroxide treatment, a small aliquot from each sample was plated on rich (YPD) medium and colony forming units (CFU) counted after 2 days. The CFU number obtained with the ‘auxo’ medium was used as a reference (100%) for all the other samples. The latters were expressed as (CFU/CFU(auxo))*100. *, p<0.1; **, p<0.02; ***, p<0.001 comparing each value against the corresponding (strain specific) “auxo” value.</p>", "links"=>[], "tags"=>["genetics", "Gene networks", "microbiology", "Model organisms", "Molecular cell biology", "Signal transduction", "Signaling in cellular processes", "Ras signaling", "Tor signaling", "Signaling pathways", "Adenylyl cyclase signaling pathway", "Mechanisms of signal transduction", "Cellular stress responses", "amino"], "article_id"=>1074670, "categories"=>["Biological Sciences"], "users"=>["Mario G. Mirisola", "Giusi Taormina", "Paola Fabrizio", "Min Wei", "Jia Hu", "Valter D. Longo"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004113.g004", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Role_of_Tor_S6K_in_amino_acid_response_/1074670", "title"=>"Role of Tor/S6K in amino acid response.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-06 10:24:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1554888"], "description"=>"<p>(A) Nutrient response assay (hydrogen peroxide treatment after nutrient addition) using cultures of stationary phase (two days of growth) wild type DBY746 strain (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen.1004113.s001\" target=\"_blank\">figure S1</a> for the experimental scheme). Synthetic medium with dextrose and only the organic compounds necessary to compensate the auxothrophies (leucine, histidine, tryptophan and uracil) were added to ‘auxo’ sample. The other samples were added with the same mixture plus the single indicated non-essential amino acid. After hydrogen peroxide treatment, a small aliquot from each sample was plated on rich (YPD) medium and colony forming units (CFU) counted after 2 days. The CFU number obtained with the ‘auxo’ medium was the highest and was used as a reference (100%) for all the other samples. The latters were expressed as (CFU/CFU(auxo))*100. The data represent the mean ± standard errors of five independent experiments. Statistical significance was evaluated by 2-tailed T-test for groups with unequal variants. *, p<0.05; **, p<0.02; ***, p<0.001. Amino acids are indicated using the single letter code. (B) Nutrient response assay (hydrogen peroxide treatment after nutrient addition) using the wild type strain DBY746 (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen.1004113.s001\" target=\"_blank\">figure S1</a> for the experimental scheme) combining the addition of the auxo mixture (see the legend to the <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen-1004113-g001\" target=\"_blank\">figure 1A</a> for details) plus the indicated amino acid in the presence/absence of the Pkhs inhibitor myriocin. (C) Dose-response nutrient response assay (hydrogen peroxide treatment after nutrient addition) using the wild type DBY746 strain (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen.1004113.s001\" target=\"_blank\">figure S1</a> for the experimental scheme) obtained combining the addition of the auxo mixture (see A for details) plus different serine concentration with increasing amount of the Pkhs inhibitor myriocin. (D) Chronological life span of the DBY746 yeast strain grown with the auxo medium (see legend to <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen-1004113-g003\" target=\"_blank\">figure 3A</a> for a complete description of this medium) in the absence (auxo AA) or in the presence (auxo AA+S) of the standard concentration of the amino acid serine. P values were evaluated by 2 tailed T-test for groups with unequal variants. *, p<0.002. (E) Effect of serine presence on Sch9 threonine 570 phosphorylation. Upper panel: Western blot of whole protein extracts from wild type yeast stained with a specific anti-P570 antibody. Cells (exponential phase) were grown in the presence of the auxo mixture (Auxo AA) (see legend of <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen-1004113-g001\" target=\"_blank\">figure 1A</a> for a complete description), plus the standard concentration of serine (Auxo AA+S), with the complete amino acid mixture (All AA) and with the complete amino acid mixture lacking only the serine amino acid (All AA-S; standard concentration of amino acids are indicated in table S2). Lower panel: wild type (W303) strain, HA tagged on <i>SCH9</i> gene was treated in the same conditions as the upper panel and stained with an anti-HA primary antibody.</p>", "links"=>[], "tags"=>["genetics", "Gene networks", "microbiology", "Model organisms", "Molecular cell biology", "Signal transduction", "Signaling in cellular processes", "Ras signaling", "Tor signaling", "Signaling pathways", "Adenylyl cyclase signaling pathway", "Mechanisms of signal transduction", "Cellular stress responses", "amino", "acids"], "article_id"=>1074667, "categories"=>["Biological Sciences"], "users"=>["Mario G. Mirisola", "Giusi Taormina", "Paola Fabrizio", "Min Wei", "Jia Hu", "Valter D. Longo"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004113.g003", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Role_of_single_amino_acids_in_stress_sensitization_/1074667", "title"=>"Role of single amino acids in stress sensitization.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-06 10:24:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1554873"], "description"=>"<p>(A) Stress resistance (hydrogen peroxide treatment) of stationary phase laboratory and prototrophic wild type DBY746 yeast strain and winemaking yeast after short time nutrient replenishment (nutrient response assay, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen.1004113.s001\" target=\"_blank\">figure S1</a> for a complete experimental scheme and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#s4\" target=\"_blank\">materials and methods</a> section for details). All mixtures added contained the basic SD components (Yeast nitrogen base, ammonium sulfate and phosphate). “Auxo AA” refers to a nutrient mixture containing the organic compounds required to compensate the wild type DBY746 auxothrophies (histidine, leucine and tryptophan and the nucleotide uracil) while all the other amino acids are missing. “all AA” refers to the complete SDC medium therefore containing all the amino acids (for a complete description see table S2). Dextrose concentration was added as specified. (B) <i>In situ</i> chronological life span (58) of wild type DBY746 in the presence of all or only the auxotrophic (auxo) amino acids (see above and table S2). The data represent the mean ± standard error of five different experiments. P values were evaluated by 2-tailed T-test for groups with unequal variants. *, p = 0.2; **, p<0.05; ***, p<0.005. (C) Stress resistance (hydrogen peroxide treatment) after the addition of the indicated different nutrients mixtures (nutrient response assay, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen.1004113.s001\" target=\"_blank\">figure S1</a> for a complete experimental scheme) using the indicated isogenic derivatives of the DBY746 yeast strain.* The wild type strain was grown for three days, all the other strains were grown for 1 day only.</p>", "links"=>[], "tags"=>["genetics", "Gene networks", "microbiology", "Model organisms", "Molecular cell biology", "Signal transduction", "Signaling in cellular processes", "Ras signaling", "Tor signaling", "Signaling pathways", "Adenylyl cyclase signaling pathway", "Mechanisms of signal transduction", "Cellular stress responses", "amino", "acids"], "article_id"=>1074652, "categories"=>["Biological Sciences"], "users"=>["Mario G. Mirisola", "Giusi Taormina", "Paola Fabrizio", "Min Wei", "Jia Hu", "Valter D. Longo"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004113.g001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dextrose_and_amino_acids_act_on_separate_pathways_/1074652", "title"=>"Dextrose and amino acids act on separate pathways.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-06 10:24:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1554917"], "description"=>"<p>(A) Nutrient response assay of DBY746 (WT) and of the isogenic derivatives involved in stress response gene transcription. Auxo means the addition of the organic compounds necessary to compensate auxotrophies. (B) DBY746 bearing a wild type (WT) or a null (rim15Δ) <i>RIM15</i> allele were grown until day 3, then switched into fresh synthetic medium containing only ‘auxo’ amino acids or ‘all’ amino acids (for a detailed description of auxo mixture see the legend to the <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#pgen-1004113-g001\" target=\"_blank\">figure 1A</a>); after 4 hours RNA was extracted and retro transcribed as reported in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004113#s4\" target=\"_blank\">materials and methods</a> section; quantitative RT-PCR was performed using <i>SOD2</i> specific primers and gene expression levels were normalized using <i>ACT1</i> as an internal control. The bar chart shows <i>SOD2</i> expression level after SDC incubation with respect to <i>SOD2</i> expression after incubation only with L, H, W as amino acids source. The data represent the mean ± standard errors of three different experiments. (C) Beta galactosidase assay of PDS and STRE reporters. Post-diauxic yeast cell (about 10<sup>8</sup> cells at day 2 in liquid culture) were exposed to nutrients (4 hrs with the indicated mixtures). Cells were then disrupted and beta galactosidase activity was measured. The activity obtained with medium containing only the amino acids necessary to compensate strain auxotrophies (auxo) was referred to as 100% activity. Statistical significance was evaluated by 2-tailed T-test for groups with unequal variants. Data shown are mean and standard deviation of three independent samples assayed. * , p<0.5; **, p<0.05; ***, p<0.01.</p>", "links"=>[], "tags"=>["genetics", "Gene networks", "microbiology", "Model organisms", "Molecular cell biology", "Signal transduction", "Signaling in cellular processes", "Ras signaling", "Tor signaling", "Signaling pathways", "Adenylyl cyclase signaling pathway", "Mechanisms of signal transduction", "Cellular stress responses", "acids", "genes", "rim15-dependent"], "article_id"=>1074693, "categories"=>["Biological Sciences"], "users"=>["Mario G. Mirisola", "Giusi Taormina", "Paola Fabrizio", "Min Wei", "Jia Hu", "Valter D. Longo"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004113.g006", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amino_acids_affect_stress_response_genes_in_a_Rim15_dependent_way_/1074693", "title"=>"Amino acids affect stress response genes in a Rim15-dependent way.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-06 10:24:34"}

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Relative Metric

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