Functional Study of the Hap4-Like Genes Suggests That the Key Regulators of Carbon Metabolism HAP4 and Oxidative Stress Response YAP1 in Yeast Diverged from a Common Ancestor
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{"title"=>"Functional study of the HAP4-like genes suggests that the key regulators of carbon metabolism HAP4 and oxidative stress response YAP1 in yeast diverged from a common ancestor", "type"=>"journal", "authors"=>[{"first_name"=>"Nataliya", "last_name"=>"Petryk", "scopus_author_id"=>"37034767000"}, {"first_name"=>"You Fang", "last_name"=>"Zhou", "scopus_author_id"=>"35338373000"}, {"first_name"=>"Kateryna", "last_name"=>"Sybirna", "scopus_author_id"=>"6505879997"}, {"first_name"=>"Marie Hélène", "last_name"=>"Mucchielli", "scopus_author_id"=>"22954373900"}, {"first_name"=>"Bernard", "last_name"=>"Guiard", "scopus_author_id"=>"7006646853"}, {"first_name"=>"Wei Guo", "last_name"=>"Bao", "scopus_author_id"=>"7101934123"}, {"first_name"=>"Oleh V.", "last_name"=>"Stasyk", "scopus_author_id"=>"6603272093"}, {"first_name"=>"Olena G.", "last_name"=>"Stasyk", "scopus_author_id"=>"6603272092"}, {"first_name"=>"Olena S.", "last_name"=>"Krasovska", "scopus_author_id"=>"6602442107"}, {"first_name"=>"Karine", "last_name"=>"Budin", "scopus_author_id"=>"6506433957"}, {"first_name"=>"Nancie", "last_name"=>"Reymond", "scopus_author_id"=>"23052513700"}, {"first_name"=>"Sandrine", "last_name"=>"Imbeaud", "scopus_author_id"=>"6701661451"}, {"first_name"=>"Sophie", "last_name"=>"Coudouel", "scopus_author_id"=>"6507926152"}, {"first_name"=>"Hervé", "last_name"=>"Delacroix", "scopus_author_id"=>"6701772701"}, {"first_name"=>"Andriy", "last_name"=>"Sibirny", "scopus_author_id"=>"16310463400"}, {"first_name"=>"Monique", "last_name"=>"Bolotin-Fukuhara", "scopus_author_id"=>"56207615600"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84916227256", "pui"=>"600696663", "doi"=>"10.1371/journal.pone.0112263", "sgr"=>"84916227256", "pmid"=>"25479159"}, "id"=>"e1367d86-5bd2-3754-8c29-c3181ac10b11", "abstract"=>"The transcriptional regulator HAP4, induced by respiratory substrates, is involved in the balance between fermentation and respiration in S. cerevisiae. We identified putative orthologues of the Hap4 protein in all ascomycetes, based only on a conserved sixteen amino acid-long motif. In addition to this motif, some of these proteins contain a DNA-binding motif of the bZIP type, while being nonetheless globally highly divergent. The genome of the yeast Hansenula polymorpha contains two HAP4-like genes encoding the protein HpHap4-A which, like ScHap4, is devoid of a bZIP motif, and HpHap4-B which contains it. This species has been chosen for a detailed examination of their respective properties. Based mostly on global gene expression studies performed in the S. cerevisiae HAP4 disruption mutant (ScΔhap4), we show here that HpHap4-A is functionally equivalent to ScHap4, whereas HpHap4-B is not. Moreover HpHAP4-B is able to complement the H2O2 hypersensitivity of the ScYap1 deletant, YAP1 being, in S. cerevisiae, the main regulator of oxidative stress. Finally, a transcriptomic analysis performed in the ScΔyap1 strain overexpressing HpHAP4-B shows that HpHap4-B acts both on oxidative stress response and carbohydrate metabolism in a manner different from both ScYap1 and ScHap4. Deletion of these two genes in their natural host, H. polymorpha, confirms that HpHAP4-A participates in the control of the fermentation/respiration balance, while HpHAP4-B is involved in oxidative stress since its deletion leads to hypersensitivity to H2O2. These data, placed in an evolutionary context, raise new questions concerning the evolution of the HAP4 transcriptional regulation function and suggest that Yap1 and Hap4 have diverged from a unique regulatory protein in the fungal ancestor.", "link"=>"http://www.mendeley.com/research/functional-study-hap4like-genes-suggests-key-regulators-carbon-metabolism-hap4-oxidative-stress-resp", "reader_count"=>9, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>3, "Student > Ph. D. Student"=>1, "Student > Master"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>3, "Student > Ph. D. Student"=>1, "Student > Master"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"France"=>2}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1826615", "https://ndownloader.figshare.com/files/1826616", "https://ndownloader.figshare.com/files/1826617", "https://ndownloader.figshare.com/files/1826618"], "description"=>"<div><p>The transcriptional regulator <i>HAP4</i>, induced by respiratory substrates, is involved in the balance between fermentation and respiration in <i>S. cerevisiae</i>. We identified putative orthologues of the Hap4 protein in all ascomycetes, based only on a conserved sixteen amino acid-long motif. In addition to this motif, some of these proteins contain a DNA-binding motif of the bZIP type, while being nonetheless globally highly divergent. The genome of the yeast <i>Hansenula polymorpha</i> contains two <i>HAP4</i>-like genes encoding the protein HpHap4-A which, like ScHap4, is devoid of a bZIP motif, and HpHap4-B which contains it. This species has been chosen for a detailed examination of their respective properties. Based mostly on global gene expression studies performed in the <i>S. cerevisiae HAP4</i> disruption mutant (<i>ScΔhap4</i>), we show here that HpHap4-A is functionally equivalent to ScHap4, whereas HpHap4-B is not. Moreover <i>HpHAP4-B</i> is able to complement the H<sub>2</sub>O<sub>2</sub> hypersensitivity of the <i>ScYap1</i> deletant, <i>YAP1</i> being, in <i>S. cerevisiae</i>, the main regulator of oxidative stress. Finally, a transcriptomic analysis performed in the <i>ScΔyap1</i> strain overexpressing <i>HpHAP4-B</i> shows that HpHap4-B acts both on oxidative stress response and carbohydrate metabolism in a manner different from both ScYap1 and ScHap4. Deletion of these two genes in their natural host, <i>H. polymorpha</i>, confirms that <i>HpHAP4-A</i> participates in the control of the fermentation/respiration balance, while <i>HpHAP4-B</i> is involved in oxidative stress since its deletion leads to hypersensitivity to H<sub>2</sub>O<sub>2</sub>. These data, placed in an evolutionary context, raise new questions concerning the evolution of the <i>HAP4</i> transcriptional regulation function and suggest that Yap1 and Hap4 have diverged from a unique regulatory protein in the fungal ancestor.</p></div>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263042, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0112263.s001", "https://dx.doi.org/10.1371/journal.pone.0112263.s002", "https://dx.doi.org/10.1371/journal.pone.0112263.s003", "https://dx.doi.org/10.1371/journal.pone.0112263.s004"], "stats"=>{"downloads"=>20, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Functional_Study_of_the_Hap4_Like_Genes_Suggests_That_the_Key_Regulators_of_Carbon_Metabolism_HAP4_and_Oxidative_Stress_Response_YAP1_in_Yeast_Diverged_from_a_Common_Ancestor/1263042", "title"=>"Functional Study of the Hap4-Like Genes Suggests That the Key Regulators of Carbon Metabolism <i>HAP4</i> and Oxidative Stress Response <i>YAP1</i> in Yeast Diverged from a Common Ancestor", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826582"], "description"=>"<p>Probe alone (lane 1), <i>S. cerevisiae</i> Δ<i>yap1</i> strain (lane 2), <i>Sc</i>Δ<i>yap1</i> with empty plasmid pBFG1 (lane 3), <i>Sc</i>Δ<i>yap1</i> with pBFG1 plasmid carrying <i>ScHAP4</i> (lane 4), pBFG1-<i>ScYAP1</i>(lane 5), pBFG1-<i>HpHAP4-A</i> (lane 6), pBFG1-<i>HpHAP4-B</i> (lane 7) pBFG1-<i>HpHAP4-B-bZIP</i> (devoid of Hphap4-B BR region; lane 8).</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263011, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.g005", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gel_shift_experiment_with_a_synthetic_ARE_sequence_/1263011", "title"=>"Gel shift experiment with a synthetic ARE sequence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826551"], "description"=>"<p>The <i>Saccharomyces cerevisiae</i> Hap4 and Yap1 proteins are schematically represented relative to the two <i>Hansenula polymorpha</i> HpHap4-A and HpHap4-B ones. The main motifs are indicated in grey (N-terminal Hap4), black (bZIP of BR motif; the BR motif is the DNA binding part of the bZIP motif) and striped (CRD or cysteine rich domain).</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1262982, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_schematic_representation_of_the_Hap4_and_Yap1_proteins_/1262982", "title"=>"A schematic representation of the Hap4 and Yap1 proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826586"], "description"=>"<p>The analysed data are the normalized median signals obtained in two mutants and in two different growth conditions (with or without H<sub>2</sub>O<sub>2</sub>), compared to the WT by microarray experiments in a <i>ScΔyap1</i> genetic background. The WT is defined as <i>ScΔyap1</i> plus the empty plasmid pBFG1, and the mutants as <i>ScΔyap1</i> plus pBFG1 carrying either the <i>ScYAP1</i> or the <i>HpHAP4-B</i> gene. For each condition, four independent experiments were performed. The two axes of the figure are the second and the third first principal components and explain 7.2% of the variance.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263015, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.g006", "stats"=>{"downloads"=>3, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principal_Component_Analysis_of_transcriptome_data_of_the_Sc_916_yap1_strains_/1263015", "title"=>"Principal Component Analysis of transcriptome data of the <i>ScΔyap1</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826590"], "description"=>"<p>A: <i>H. polymorpha Hp</i>Δ<i>hap4-A</i> and double knock-out strains, but not <i>Hp</i>Δ<i>hap4-B</i> deletion mutant, are sensitive to antimycin A on glucose. B: Growth on xylose plus SHAM or H<sub>2</sub>0<sub>2</sub>. 1: <i>Hp</i>NCYC495<i>leu1_1</i> strain. 2: <i>Hp</i>NCYC495<i>leu1_1</i> with pYT1 (empty plasmid, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112263#s2\" target=\"_blank\">Material and Methods</a>). 3: <i>Hp</i>Δ<i>hap4-A</i>. 4: <i>Hp</i>Δ<i>hap4-B</i>. 5: <i>Hp</i>Δ<i>hap4-A Hp</i>Δ<i>hap4-B</i> (double knock-out strain).</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263017, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.g007", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Growth_of_different_H_polymorpha_strains_on_media_containing_either_antimycin_A_SHAM_or_hydrogen_peroxide_/1263017", "title"=>"Growth of different <i>H. polymorpha</i> strains on media containing either antimycin A, SHAM or hydrogen peroxide.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826558"], "description"=>"<p>Only a limited number of yeast species are presented which span the complete clade of Hemiascomycete yeasts from <i>S. cerevisiae</i> to <i>Y. lipolytica, S. pombe</i> being the outgroup. <i>H. polymorpha</i> is placed on the tree at the same position as <i>P. angusta</i> which is the anamorphic species. The position of the « Whole Genome Duplication » (WGD) is indicated. The tree is taken from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112263#pone.0112263-Souciet1\" target=\"_blank\">[48]</a>.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1262987, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.g002", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_simple_phylogenetic_tree_of_the_hemiascomycete_yeasts_/1262987", "title"=>"A simple phylogenetic tree of the hemiascomycete yeasts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826595"], "description"=>"<p>The phylogenetic tree was adapted from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112263#pone.0112263-Cornell1\" target=\"_blank\">[49]</a>. Species in which proteins such as HpHap4-B (containing both the N- Hap4 and the BR motifs) could be identified are boxed. Aligned with each species, the presence of proteins of the Yap1 type (Yap1 BR motif), HpHap4-B type (BR plus N-ter motifs) and HAP4-A type (N-ter motif) of protein is indicated next to each species. The position of <i>H. polymorpha</i>, which is not on the tree, is indicated, underlining that this yeast belongs to the clade where <i>C. albicans</i> and <i>D. hansenii</i> are localized. * These species were not correctly annotated; for <i>P. nodorum</i>, the BR and N-ter motif are overlapping and degenerate while for <i>U. maydis</i>, the protein annotated as Yap1 turned out to contain also an N-ter motif and belongs therefore to the HpHap4-B family of proteins.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263023, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.g008", "stats"=>{"downloads"=>2, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_fungi_in_relation_with_the_presence_absence_of_HpHap4_B_type_of_proteins_/1263023", "title"=>"Phylogenetic tree of fungi in relation with the presence/absence of HpHap4-B-type of proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826597"], "description"=>"<p>Upper part (Hap4) is the N-ter Hap4 motif with small extensions (the motif itself spans aminoacids 60 to 76). Bottom part (Yap7) is a small sequence in the Yap7 protein which is 68% similar to the upper sequence. Yap7 is a member of the bZIP family of <i>S. cerevisiae</i> transactivators. Its function is not precisely known <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112263#pone.0112263-RodriguesPousada1\" target=\"_blank\">[50]</a>. Refer to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112263#pone-0112263-g001\" target=\"_blank\">Fig 1</a> for the various motifs of these proteins.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263025, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.g009", "stats"=>{"downloads"=>4, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_a_Relic_sequence_in_S_cerevisiae_/1263025", "title"=>"Identification of a “Relic sequence” in <i>S. cerevisiae</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826598"], "description"=>"<p>Strains and plasmids used in this study.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263026, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.t001", "stats"=>{"downloads"=>7, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Strains_and_plasmids_used_in_this_study_/1263026", "title"=>"Strains and plasmids used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826599"], "description"=>"<p>* The <i>H. polymorpha</i> gene names are given according to their homologues in <i>S. cerevisiae.</i></p><p>**In the case of the Aryl-alcohol dehydrogenase genes (<i>AAD</i> genes, seven in Sc) we found only two genes in Hp and tested both. Priming with the AAD1 oligomers did not work and the experiment was not carried further.</p><p>List of <i>H. polymorpha</i> genes and corresponding primers used for qRT-PCR.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263027, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.t002", "stats"=>{"downloads"=>7, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_H_polymorpha_genes_and_corresponding_primers_used_for_qRT_PCR_/1263027", "title"=>"List of <i>H. polymorpha</i> genes and corresponding primers used for qRT-PCR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826567"], "description"=>"<p>The analysed data are the normalized log2 ratios (intensity in WT strain versus intensity in the mutant strains) obtained from the microarray experiments (four biological replicates per condition) in the <i>ScΔhap4</i> genetic background. The WT strain is defined as <i>ScΔhap4</i> plus the empty plasmid pBFG1 and the three mutant strains as <i>ScΔhap4</i>plus pBFG1 containing the <i>ScHap4</i>, the <i>HpHAP4-A</i> or the <i>HpHAP4-B</i> genes. A: Heat map clustergram. This figure reveals the changes in gene expression between experiments. The experiments and the genes are clustered in a tree from their Pearson correlation coefficient values. Gene expression level is represented on a heat map by colour level (green when overexpressed and red when underexpressed compared to the WT strain). B: Presentation of the experiments in the 3D space of the principal components. The two axes of the figure are the three first principal components determined by Principal Component Analysis (PCA). They explain, respectively, 36%, 27% and 16% of the variance.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1262996, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.g003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_transcriptomic_data_of_the_Sc_hap4_strains_/1262996", "title"=>"Analysis of transcriptomic data of the <i>Sc</i>Δ<i>hap4</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826602"], "description"=>"<p>* indicates the presence(y)/absence (n) of a putative Yap1 binding sites in the promoter as obtained from YEASTRACT (<a href=\"http://www.yeastract.com/index.php\" target=\"_blank\">http://www.yeastract.com/index.php</a>) database.</p><p>** r-factor is the ratio between the normalized value in the strain <i>Δhap4</i> carrying the empty BFG1 plasmid and the value obtained in the strain <i>Δhap4</i> carrying BFG1 plus <i>HpHAP4-B</i>.</p><p>Genes up-regulated by <i>HpHAP4-B</i> in the Δ<i>hap4</i> background.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263030, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.t003", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_up_regulated_by_HpHAP4_B_in_the_hap4_background_/1263030", "title"=>"Genes up-regulated by <i>HpHAP4-B</i> in the Δ<i>hap4</i> background.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826604"], "description"=>"<p>Gene ontology categories of the genes regulated by HpHap4-B and ScYap1.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263032, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.t004", "stats"=>{"downloads"=>6, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_categories_of_the_genes_regulated_by_HpHap4_B_and_ScYap1_/1263032", "title"=>"Gene ontology categories of the genes regulated by HpHap4-B and ScYap1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826574"], "description"=>"<p>Part A: Comparison of the new bZIP type motif identified in HpHap4-B with the YAP family motif. Q234, Q239, A241 and F/Y242 are four basic regions (DNA-binding sites) characteristic residues of the YAP protein family which are rarely or never observed in other bZIP proteins <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112263#pone.0112263-Fernandes1\" target=\"_blank\">[34]</a>. Part B: Heterologous complementation of the growth deficiency of <i>S. cerevisiae</i> Δ<i>yap1</i> in the presence of H<sub>2</sub>0<sub>2</sub> by the <i>HpHAP4-B</i> gene. The gene is expressed on a multicopy plasmid (pBFG1, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112263#s2\" target=\"_blank\"><i>Methods</i></a>) and the growth monitored on minimal medium (W0) containing 0.5 mM of H<sub>2</sub>0<sub>2</sub>. 1: <i>S. cerevisiae</i> Δ<i>yap1</i> strain (with or without H<sub>2</sub>0<sub>2</sub>). 2:Δ<i>yap1</i> strain with empty plasmid BFG1. 3: Δ<i>yap1</i> with BFG1 plasmid containing <i>HpHap4-B</i>. 4: Δ<i>yap1</i> with BFG1 plasmid containing <i>HpHap4-B</i> with deleted bZIP domain (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112263#s2\" target=\"_blank\">Methods</a>). Tests 2, 3 and 4 were performed on medium containing H<sub>2</sub>0<sub>2</sub>. Strains were grown on minimal glucose medium supplemented with the necessary aminoacids at 28°C for 5 days.</p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263003, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.g004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_comparison_between_ScYAP1_and_the_HpHAP4_B_genes_/1263003", "title"=>"Functional comparison between <i>ScYAP1</i> and the <i>HpHAP4-B</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1826608"], "description"=>"<p>The P(H1) value indicates the probability that the difference between the sample and control groups is due only by chance and was analysed with the REST software (Qiagen, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112263#s2\" target=\"_blank\">Material and Methods</a> for more details). Statistically significant results are shown in bold. The case of AAD2* is not conclusive since the data were obtained in two different experiments (two qRT-PCRs, regulated and reproducible and a third one, performed later, which was not).</p><p>qRT-PCR of <i>HpHAP4-A</i> and <i>HpHAP4-B</i> regulation of gene expression in <i>H. polymorpha.</i></p>", "links"=>[], "tags"=>["bzip", "ScHap 4. Deletion", "oxidative stress response", "HpHAP", "ScYap 1 deletant", "motif", "H 2O hypersensitivity", "Hap 4 protein", "Oxidative Stress Response YAP 1", "yeast Hansenula polymorpha", "regulator", "oxidative stress", "Carbon Metabolism HAP 4", "HAP 4 transcriptional regulation function", "cerevisiae HAP 4 disruption", "Gene Expression Studies"], "article_id"=>1263036, "categories"=>["Biological Sciences"], "users"=>["Nataliya Petryk", "You-Fang Zhou", "Kateryna Sybirna", "Marie-Hélène Mucchielli", "Bernard Guiard", "Wei-Guo Bao", "Oleh V. Stasyk", "Olena G. Stasyk", "Olena S. Krasovska", "Karine Budin", "Nancie Reymond", "Sandrine Imbeaud", "Sophie Coudouel", "Hervé Delacroix", "Andriy Sibirny", "Monique Bolotin-Fukuhara"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112263.t005", "stats"=>{"downloads"=>4, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_qRT_PCR_of_HpHAP4_A_and_HpHAP4_B_regulation_of_gene_expression_in_H_polymorpha_/1263036", "title"=>"qRT-PCR of <i>HpHAP4-A</i> and <i>HpHAP4-B</i> regulation of gene expression in <i>H. polymorpha.</i>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-05 03:22:32"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}

Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[286]}, {"subject_area"=>"/Biology and life sciences/Mycology", "average_usage"=>[348, 543]}]}
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