Synergistic and Dose-Controlled Regulation of Cellulase Gene Expression in Penicillium oxalicum
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{"title"=>"Synergistic and Dose-Controlled Regulation of Cellulase Gene Expression in Penicillium oxalicum", "type"=>"journal", "authors"=>[{"first_name"=>"Zhonghai", "last_name"=>"Li", "scopus_author_id"=>"55631192000"}, {"first_name"=>"Guangshan", "last_name"=>"Yao", "scopus_author_id"=>"56612779400"}, {"first_name"=>"Ruimei", "last_name"=>"Wu", "scopus_author_id"=>"56612639700"}, {"first_name"=>"Liwei", "last_name"=>"Gao", "scopus_author_id"=>"56072697000"}, {"first_name"=>"Qinbiao", "last_name"=>"Kan", "scopus_author_id"=>"56612995000"}, {"first_name"=>"Meng", "last_name"=>"Liu", "scopus_author_id"=>"56895346900"}, {"first_name"=>"Piao", "last_name"=>"Yang", "scopus_author_id"=>"56895426300"}, {"first_name"=>"Guodong", "last_name"=>"Liu", "scopus_author_id"=>"56895328900"}, {"first_name"=>"Yuqi", "last_name"=>"Qin", "scopus_author_id"=>"23470550400"}, {"first_name"=>"Xin", "last_name"=>"Song", "scopus_author_id"=>"55119474500"}, {"first_name"=>"Yaohua", "last_name"=>"Zhong", "scopus_author_id"=>"55004036500"}, {"first_name"=>"Xu", "last_name"=>"Fang", "scopus_author_id"=>"35760191000"}, {"first_name"=>"Yinbo", "last_name"=>"Qu", "scopus_author_id"=>"7201791440"}], "year"=>2015, "source"=>"PLoS Genetics", "identifiers"=>{"doi"=>"10.1371/journal.pgen.1005509", "sgr"=>"84943560881", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pmid"=>"26360497", "issn"=>"15537404", "scopus"=>"2-s2.0-84943560881", "pui"=>"606367676"}, "id"=>"02b9de2b-ec1d-3520-b3de-62f67c4311a4", "abstract"=>"Filamentous fungus Penicillium oxalicum produces diverse lignocellulolytic enzymes, which are regulated by the combinations of many transcription factors. Here, a single-gene disruptant library for 470 transcription factors was constructed and systematically screened for cellulase production. Twenty transcription factors (including ClrB, CreA, XlnR, Ace1, AmyR, and 15 unknown proteins) were identified to play putative roles in the activation or repression of cellulase synthesis. Most of these regulators have not been characterized in any fungi before. We identified the ClrB, CreA, XlnR, and AmyR transcription factors as critical dose-dependent regulators of cellulase expression, the core regulons of which were identified by analyzing several transcriptomes and/or secretomes. Synergistic and additive modes of combinatorial control of each cellulase gene by these regulatory factors were achieved, and cellulase expression was fine-tuned in a proper and controlled manner. With one of these targets, the expression of the major intracellular β-glucosidase Bgl2 was found to be dependent on ClrB. The Bgl2-deficient background resulted in a substantial gene activation by ClrB and proved to be closely correlated with the relief of repression mediated by CreA and AmyR during cellulase induction. Our results also signify that probing the synergistic and dose-controlled regulation mechanisms of cellulolytic regulators and using it for reconstruction of expression regulation network (RERN) may be a promising strategy for cellulolytic fungi to develop enzyme hyper-producers. Based on our data, ClrB was identified as focal point for the synergistic activation regulation of cellulase expression by integrating cellulolytic regulators and their target genes, which refined our understanding of transcriptional-regulatory network as a \"seesaw model\" in which the coordinated regulation of cellulolytic genes is established by counteracting activators and repressors.", "link"=>"http://www.mendeley.com/research/synergistic-dosecontrolled-regulation-cellulase-gene-expression-penicillium-oxalicum", "reader_count"=>28, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>6, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>4, "Other"=>1, "Lecturer"=>1, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>6, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>4, "Other"=>1, "Lecturer"=>1, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>16}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>16}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>4}}, "reader_count_by_country"=>{"Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2258804", "https://ndownloader.figshare.com/files/2258805", "https://ndownloader.figshare.com/files/2258806", "https://ndownloader.figshare.com/files/2258807", "https://ndownloader.figshare.com/files/2258808", "https://ndownloader.figshare.com/files/2258809", "https://ndownloader.figshare.com/files/2258810", "https://ndownloader.figshare.com/files/2258811", "https://ndownloader.figshare.com/files/2258812", "https://ndownloader.figshare.com/files/2258813", "https://ndownloader.figshare.com/files/2258814", "https://ndownloader.figshare.com/files/2258815", "https://ndownloader.figshare.com/files/2258816", "https://ndownloader.figshare.com/files/2258817", "https://ndownloader.figshare.com/files/2258819", "https://ndownloader.figshare.com/files/2258820", "https://ndownloader.figshare.com/files/2258821", "https://ndownloader.figshare.com/files/2258822", "https://ndownloader.figshare.com/files/2258823", "https://ndownloader.figshare.com/files/2258824"], "description"=>"<div><p>Filamentous fungus <i>Penicillium oxalicum</i> produces diverse lignocellulolytic enzymes, which are regulated by the combinations of many transcription factors. Here, a single-gene disruptant library for 470 transcription factors was constructed and systematically screened for cellulase production. Twenty transcription factors (including ClrB, CreA, XlnR, Ace1, AmyR, and 15 unknown proteins) were identified to play putative roles in the activation or repression of cellulase synthesis. Most of these regulators have not been characterized in any fungi before. We identified the ClrB, CreA, XlnR, and AmyR transcription factors as critical dose-dependent regulators of cellulase expression, the core regulons of which were identified by analyzing several transcriptomes and/or secretomes. Synergistic and additive modes of combinatorial control of each cellulase gene by these regulatory factors were achieved, and cellulase expression was fine-tuned in a proper and controlled manner. With one of these targets, the expression of the major intracellular β-glucosidase Bgl2 was found to be dependent on ClrB. The Bgl2-deficient background resulted in a substantial gene activation by ClrB and proved to be closely correlated with the relief of repression mediated by CreA and AmyR during cellulase induction. Our results also signify that probing the synergistic and dose-controlled regulation mechanisms of cellulolytic regulators and using it for reconstruction of expression regulation network (RERN) may be a promising strategy for cellulolytic fungi to develop enzyme hyper-producers. Based on our data, ClrB was identified as focal point for the synergistic activation regulation of cellulase expression by integrating cellulolytic regulators and their target genes, which refined our understanding of transcriptional-regulatory network as a “seesaw model” in which the coordinated regulation of cellulolytic genes is established by counteracting activators and repressors.</p></div>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540123, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1005509.s001", "https://dx.doi.org/10.1371/journal.pgen.1005509.s002", "https://dx.doi.org/10.1371/journal.pgen.1005509.s003", "https://dx.doi.org/10.1371/journal.pgen.1005509.s004", "https://dx.doi.org/10.1371/journal.pgen.1005509.s005", "https://dx.doi.org/10.1371/journal.pgen.1005509.s006", "https://dx.doi.org/10.1371/journal.pgen.1005509.s007", "https://dx.doi.org/10.1371/journal.pgen.1005509.s008", "https://dx.doi.org/10.1371/journal.pgen.1005509.s009", "https://dx.doi.org/10.1371/journal.pgen.1005509.s010", "https://dx.doi.org/10.1371/journal.pgen.1005509.s011", "https://dx.doi.org/10.1371/journal.pgen.1005509.s012", "https://dx.doi.org/10.1371/journal.pgen.1005509.s013", "https://dx.doi.org/10.1371/journal.pgen.1005509.s014", "https://dx.doi.org/10.1371/journal.pgen.1005509.s015", "https://dx.doi.org/10.1371/journal.pgen.1005509.s016", "https://dx.doi.org/10.1371/journal.pgen.1005509.s017", "https://dx.doi.org/10.1371/journal.pgen.1005509.s018", "https://dx.doi.org/10.1371/journal.pgen.1005509.s019", "https://dx.doi.org/10.1371/journal.pgen.1005509.s020"], "stats"=>{"downloads"=>37, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Synergistic_and_Dose_Controlled_Regulation_of_Cellulase_Gene_Expression_in_Penicillium_oxalicum_/1540123", "title"=>"Synergistic and Dose-Controlled Regulation of Cellulase Gene Expression in <i>Penicillium oxalicum</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258792"], "description"=>"<p>(A) Bandshifts showing GST-fusion ClrB-DNA-binding domain (GST ClrB-BD), GST-fusion CreA-DNA-binding domain (GST CreA-BD) and GST-fusion XlnR-DNA-binding domain (GST XlnR-BD) binding to <i>cbh1</i> promoter, compared to the GST negative control. FD, free DNA; P+D, protein-DNA complexes. (B) Yeast two-hybrid (Y2H) assay to detect interactions of ClrB with CreA, XlnR and AmyR on SD base medium including every essential amino acid. (C) Cells that contained positive direct interactions proteins for ClrB and XlnR (column, B4), CreA and XlnR (column, B6), AmyR and XlnR (column, B8) as well as ClrB and AmyR (column, C4) <i>in vitro</i> on quadruple dropout medium: SD/-Ade/-His/-Leu/-Trp. NC, negative control. PC, positive control.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540117, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g011", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Electrophoretic_mobility_shift_assay_and_protein_interaction_among_ClrB_CreA_AmyR_and_XlnR_/1540117", "title"=>"Electrophoretic mobility shift assay and protein interaction among ClrB, CreA, AmyR and XlnR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258777"], "description"=>"<p>The Δ<i>clrB</i> mutant and wild-type strains were pre-cultured on glucose for 22 hours and then shifted to Vogel’s media with no carbon source for 2 hours, and then transferred to Vogel’s medium containing 2% (w/v) cellulose for 4 hours. These differential expression genes were subjected to gene ontology enrichment analysis and percentages of genes varying significantly for ClrB regulon distributed within each functional category. The x-axis represents the percentage of genes in the corresponding GO class.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540102, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g003", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Defining_the_categories_of_genes_potentially_regulated_by_ClrB_/1540102", "title"=>"Defining the categories of genes potentially regulated by ClrB.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258788"], "description"=>"<p>(A-E) The FPA, pNPCase activity, xylanase activity, amylase activity and total secreted protein concentration of culture supernatants from RE-27 (Δ<i>bgl2</i>-Δ<i>creA</i>-<i>gpdA</i>(p)::<i>clrB</i>-<i>PDE_02864</i>(p)::<i>clrB</i>) and RE-29 (Δ<i>bgl2</i>-Δ<i>creA</i>-<i>gpdA</i>(p)::<i>clrB</i>-<i>PDE_02864</i>(p)::<i>xlnR</i>) mutants versus the wild-type and triple-mutant RE-10 (Δ<i>bgl2</i>-Δ<i>creA</i>-<i>gpdA</i>(p)::<i>clrB</i>) were separately evaluated when grown on wheat bran medium in flasks. (F) q-PCR measurements of <i>clrB</i>, <i>clrB-2</i>, <i>xlnR</i>, <i>amyR</i>, <i>cbh1</i>, <i>bgl1</i> and <i>gluA</i> expression in RE-27 and RE-29 mutants versus the wild-type and RE-10 strains on cellulose. Expression levels were normalized to the wild-type.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540113, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g008", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overexpression_of_clrB_or_xlnR_in_triple_mutant_RE_10_enhanced_hydrolase_expression_under_inducer_inducing_conditions_/1540113", "title"=>"Overexpression of <i>clrB</i> or <i>xlnR</i> in triple-mutant RE-10 enhanced hydrolase expression under inducer-inducing conditions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258773"], "description"=>"<p>(A) The phenotypes for Δ<i>clrB</i>, R<i>clrB</i>, OE<i>clrB</i>, <i>gpdA</i>(p)::<i>clrB</i>, Δ<i>creA</i>, Δ<i>creA-gpdA</i>(p)::<i>clrB</i>, Δ<i>creA</i>-Δ<i>clrB</i>, Δ<i>xlnR</i>, and Δ<i>xlnR</i>-Δ<i>clrB</i> mutants versus wild-type strain grown on glucose, PDA, xylan or cellulose plates for 5 days. OE<i>clrB</i>: overexpression of ClrB by <i>clrB</i> native promoter; <i>gpdA</i>(p)::<i>clrB</i>: overexpression of ClrB by <i>A</i>. <i>nidulans gpdA</i> promoter. (B-E) Comparison of FPA, pNPCase activity, CMCase activity and xylanase activity from 48-h to 96-h old culture supernatants from Δ<i>clrB</i>, R<i>clrB</i>, OE<i>clrB</i>, <i>gpdA</i>(p)::<i>clrB</i>, Δ<i>creA</i>, Δ<i>creA-gpdA</i>(p)::<i>clrB</i>, Δ<i>creA</i>-Δ<i>clrB</i>, Δ<i>xlnR</i>, and Δ<i>xlnR</i>-Δ<i>clrB</i> mutants versus wild-type strain grown in 2% cellulose as a sole carbon source.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540098, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phenotypes_on_different_carbon_sources_and_enzyme_activities_of_culture_supernatants_from_mutants_containing_clrB_xlnR_and_or_creA_mutations_/1540098", "title"=>"Phenotypes on different carbon sources and enzyme activities of culture supernatants from mutants containing <i>clrB</i>, <i>xlnR</i> and/or <i>creA</i> mutations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258786"], "description"=>"<p>(A) The hierarchical clustering of expression patterns for the 155 increased genes of cellulose regulon in the mutants versus wild-type strain. Hierarchical clustering analysis was performed using software HCE3.5. Heat maps showing log (RPKM) from minimum (bright green) to maximum (red) revealed four gene sets. (B) SDS-PAGE of proteins from unconcentrated culture supernatants of wild-type strain and <i>clrB</i> or/and <i>creA</i> mutants when cultured on glucose for 22 hours then shifted to cellulose for 96 hours. (C) Venn diagram from analysis of secretomes of culture supernatants from <i>P</i>. <i>oxalicum</i> mutants. The loading samples were normalized to same concentration with buffer.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540111, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g006", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatmap_of_cellulose_regulons_and_protein_profiles_of_culture_supernatants_from_P_oxalicum_strains_containing_mutations_of_clrB_or_and_creA_genes_/1540111", "title"=>"Heatmap of cellulose regulons and protein profiles of culture supernatants from <i>P</i>. <i>oxalicum</i> strains containing mutations of <i>clrB</i> or/and <i>creA</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258787"], "description"=>"<p>(A, B) Lack of Bgl2 in <i>gpdA</i>(p)::<i>clrB</i> or Δ<i>creA</i> mutant additively enhanced FPA and pNPCase activity under cellulose growth conditions. (C) q-PCR measurements of three <i>cbh</i> gene expression in mutants versus wild-type and each single mutation strains shifted to media lacking carbon source versus on cellulose for 4 hours. Gene expression levels were normalized to actin gene as a control. (D) The transcription levels for <i>clrB</i>, <i>clrB-2</i>, <i>creA</i>, <i>xlnR</i> and <i>amyR</i> in the mutants versus wild-type strain under no carbon conditions by q-PCR. Expression levels were normalized to the wild-type.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540112, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g007", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lack_of_Bgl2_and_overexpression_of_ClrB_or_lack_of_CreA_additively_induced_cellulase_expression_/1540112", "title"=>"Lack of Bgl2 and overexpression of ClrB or lack of CreA additively induced cellulase expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258785"], "description"=>"<p>(A) Transcription expression determination for the mutants versus wild-type after a shift to 2% glucose for 4 hours or 2% cellulose for 4 and 24 hours by q-PCR. (B) Microscopic phenotypes of wild-type, Δ<i>clrB</i>, Δ<i>creA</i>, and Δ<i>creA-gpdA</i>(p)::<i>clrB</i> strains. The pictures were taken corresponding to hyphae growing onto the cover glass on glucose. Hyphae were stained by lactophenol cotton blue. Scale bar = 50 μm in panel.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540110, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g005", "stats"=>{"downloads"=>6, "page_views"=>47, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CreA_regulated_clrB_clrB_2_xlnR_and_amyR_expression_and_caused_defects_in_microscopic_phenotypes_/1540110", "title"=>"CreA regulated <i>clrB</i>, <i>clrB-2</i>, <i>xlnR</i>, and <i>amyR</i> expression and caused defects in microscopic phenotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258781"], "description"=>"<p>(A-D) FPA, xylanase activity, pNPCase activity, and pNPGase activity in the culture supernatants from wild-type strain. The mutants grown on cellulose as a sole carbon source for 72 and 96 hours, respectively. Error bars represent the standard deviation of 3 biological replicates.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540106, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g004", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enzyme_activities_of_culture_supernatants_from_mutants_containing_overexpression_of_clrB_and_or_xlnR_on_cellulose_/1540106", "title"=>"Enzyme activities of culture supernatants from mutants containing overexpression of <i>clrB</i> and/or <i>xlnR</i> on cellulose.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258794"], "description"=>"<p>\"ND\" means that no homolog was detected.</p><p>\"+/-\" means the value for cellulase activity up-regulated or downregulated standard deviation in a strain deleting the gene.</p><p>Transcription factor genes affecting cellulase and xylanase production.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540119, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.t001", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcription_factor_genes_affecting_cellulase_and_xylanase_production_/1540119", "title"=>"Transcription factor genes affecting cellulase and xylanase production.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258776"], "description"=>"<p>(A) Northern blot analysis of the transcription of cellulolytic genes in the mutants versus wild-type strain. The strains were pre-cultured on glucose for 22 hours and then were shifted to Vogel’s medium without carbon source for starvation cultivation for 2 hours, and then transferred to the same medium containing 2% (w/v) cellulose. 2 μg of total RNA was electrophoresed and blotted onto Hybond N+ nylon membrane. <i>cbh1</i>, <i>eg2</i> or <i>xyn1</i> mRNA was probed at different time points after shift to cellulose. (B) Under the same culture condition, gene expression levels of 3 cellobiohydrolase and 15 endoglucanase genes were determined in the mutants versus wild-type strain by q-PCR. All values were normalized using the actin gene value/10000. Values reported were means of three biological replicates of each strain. Error bars represent the standard deviation of 3 biological replicates.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540101, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regulation_of_cellulolytic_gene_expression_by_ClrB_XlnR_and_CreA_/1540101", "title"=>"Regulation of cellulolytic gene expression by ClrB, XlnR and CreA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258793"], "description"=>"<p>(A) Under cellulose growth conditions, cellulolytic inducers (cellodextrins) were liberated from cellulose by cellulase. Lack of the major intracellular beta-glucosidase Bgl2 facilitates the accumulation of intracellular cellodextrins, which can trigger signaling cascades that include expression of cellulase genes repressed by CreA and AmyR and activated by ClrB, XlnR and ClrB-2. Cellulase gene expression was synergistically enhanced by simultaneous overexpression of ClrB and lack of CreA, and additively increased in Δ<i>amyR-gpdA</i>(p)::<i>clrB</i>, Δ<i>amyR</i>-Δ<i>creA</i> and <i>gpdA</i>(p)::<i>clrB</i>-<i>gpdA</i>(p)::<i>xlnR</i> mutants. However, transcriptional regulation for cellulolytic regulator genes is also an important and powerful part of the regulatory network of cellulase gene expression. In the early cellulolytic induction, ClrB functions to repress expression of <i>amyR</i>, whose expression level is downregulated in Δ<i>creA</i>-<i>gpdA</i>(p)::<i>clrB</i> mutant and further in Δ<i>bgl2</i>-Δ<i>creA</i>-<i>gpdA</i>(p)::<i>clrB</i> mutant, and thus is activated by CreA (brown arrow) and reduced in Bgl2-deficient background. AmyR may also play a role in repressing <i>clrB</i>, <i>xlnR</i> and <i>clrB-2</i> expression on cellulose (dotted line). In addition, the novel cellulolytic regulator gene <i>clrB-2</i> expression is induced by ClrB and may be enhanced by XlnR. Moreover, transcriptional expression for ClrB, AmyR, XlnR and ClrB-2 genes is also repressed by CCR mediated by CreA in the presence of glucose (gray plunger). For each regulatory step, arrow means positive control, and plunger means negative control. (B) A “seesaw model” understanding the regulation of the cellulolytic system in transcription levels for the cellulase genes in the <i>P</i>. <i>oxalicum</i> wild-type strain. “R” means repressor, and “A” means activator. “←” means promoters for cellulase genes. (C) A “seesaw model” shows the transcription levels for cellulase genes increase by enhancing the positive regulation of activators or/and reducing the negative control of repressors (i.e. Δ<i>creA</i>, Δ<i>amyR</i>, <i>gpdA</i>(p)::<i>clrB</i>, <i>gpdA</i>(p)::<i>clrB</i>-<i>PDE_02864</i>(p)::<i>clrB</i>, <i>gpdA</i>(p)::<i>xlnR</i>, <i>gpdA</i>(p)::<i>xlnR</i>-<i>gpdA</i>(p)::<i>clrB</i>, Δ<i>creA</i>-<i>gpdA</i>(p)::<i>clrB</i>, RE-10, RE-27 and RE-29). A “seesaw model” in (D) shows the transcription levels for cellulase genes reduce by decreasing the positive regulation of activators or/and increasing the negative regulation of repressors (i.e. Δ<i>clrB</i>, Δ<i>xlnR</i>, Δ<i>clrB-</i>Δ<i>xlnR</i> and <i>gpdA</i>(p)::<i>creA</i>).</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540118, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g012", "stats"=>{"downloads"=>1, "page_views"=>52, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_of_regulation_of_cellulase_expression_by_ClrB_CreA_AmyR_XlnR_and_ClrB_2_in_P_oxalicum_/1540118", "title"=>"Model of regulation of cellulase expression by ClrB, CreA, AmyR, XlnR and ClrB-2 in <i>P</i>. <i>oxalicum</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258790"], "description"=>"<p>(A) The transcription levels for <i>amyR</i> in wild-type strain and mutants containing <i>bgl2</i>, <i>creA</i>, <i>clrB</i> or <i>xlnR</i> deletion were determined on cellulose by q-PCR. (B) Comparative analysis of RNA-seq data from Δ<i>amyR</i> and wild-type strains. Hierarchical clustering of RPKM for 131 AmyR-regulon genes was performed in Δ<i>amyR</i> mutant versus that in wild-type, Δ<i>clrB</i>, Δ<i>creA</i> and Δ<i>creA-gpdA</i>(p)::<i>clrB</i> mutants. (C) q-PCR measurements of PDE_05883 (<i>clrB-2</i>) in wild-type and the mutants after shift to cellulose for 4 and 24 hours. Expression levels were normalized to the wild-type.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540115, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g010", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_amyR_was_regulated_by_ClrB_and_CreA_and_hierarchical_clustering_of_RPKM_for_amyR_regulon_genes_on_cellulose_/1540115", "title"=>"Expression of <i>amyR</i> was regulated by ClrB and CreA, and hierarchical clustering of RPKM for <i>amyR</i> regulon genes on cellulose.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2258789"], "description"=>"<p>(A) Deletion of <i>amyR</i> resulted in visible halo on 1% cellulose plate and decreased starch-degrading halo on starch plate, respectively. (B, C) Lack of AmyR and overexpression of ClrB or lack of CreA additively induced cellulase expression and decreased amylase expression on cellulose. (D-G) Northern blot analysis of the transcription of <i>cbh1</i>, <i>eg2</i>, <i>xyn1</i> and <i>gluA</i> genes in Δ<i>amyR</i>-Δ<i>creA</i>, Δ<i>amyR</i>-<i>gpdA</i>(p)::<i>clrB</i> and Δ<i>amyR</i>-Δ<i>xlnR</i> mutants versus each single mutation strains on cellulose. The mutants were pre-cultured on glucose for 22 hours and then shifted to Vogel’s media with no carbon source for 2 hours, and then transferred to Vogel’s medium containing 2% (w/v) cellulose for 4, 8, 22 or 46 hours. 2 μg of total RNA was electrophoresed. <i>cbh1</i>, <i>eg2</i>, <i>xyn1</i> or <i>gluA</i> mRNA was probed at different time points after shift to cellulose.</p>", "links"=>[], "tags"=>["cellulolytic regulators", "cellulase expression", "transcription factors", "470 transcription factors", "activation", "AmyR transcription factors", "crea", "expression regulation network", "ClrB", "Penicillium oxalicum Filamentous fungus Penicillium oxalicum", "cellulase gene expression", "RERN", "gene"], "article_id"=>1540114, "categories"=>["Uncategorised"], "users"=>["Zhonghai Li", "Guangshan Yao", "Ruimei Wu", "Liwei Gao", "Qinbiao Kan", "Meng Liu", "Piao Yang", "Guodong Liu", "Yuqi Qin", "Xin Song", "Yaohua Zhong", "Xu Fang", "Yinbo Qu"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005509.g009", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lack_of_AmyR_decreased_amylase_activity_and_increased_cellulase_expression_on_cellulose_/1540114", "title"=>"Lack of AmyR decreased amylase activity and increased cellulase expression on cellulose.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-11 03:15:08"}

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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