The Whole Set of Constitutive Promoters Recognized by RNA Polymerase RpoD Holoenzyme of Escherichia coli
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{"title"=>"The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli", "type"=>"journal", "authors"=>[{"first_name"=>"Tomohiro", "last_name"=>"Shimada", "scopus_author_id"=>"15760805100"}, {"first_name"=>"Yukiko", "last_name"=>"Yamazaki", "scopus_author_id"=>"55605034900"}, {"first_name"=>"Kan", "last_name"=>"Tanaka", "scopus_author_id"=>"7406936682"}, {"first_name"=>"Akira", "last_name"=>"Ishihama", "scopus_author_id"=>"55811394100"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84897383324", "doi"=>"10.1371/journal.pone.0090447", "pui"=>"372731526", "issn"=>"19326203", "pmid"=>"24603758", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84897383324"}, "id"=>"e3ecbed6-aaaf-371d-903d-c20904782298", "abstract"=>"The promoter selectivity of Escherichia coli RNA polymerase is determined by the sigma subunit with promoter recognition activity. The model prokaryote Escherichia coli contains seven species of the sigma subunit, each recognizing a specific set of promoters. The major sigma subunit, sigma-70 encoded by rpoD, plays a major role in transcription of growth-related genes. Concomitant with the increase in detection of promoters functioning in vivo under various stressful conditions, the variation is expanding in the consensus sequence of RpoD promoters. In order to identify the canonical sequence of \"constitutive promoters\" that are recognized by the RNA polymerase holoenzyme containing RpoD sigma in the absence of supporting transcription factors, an in vitro mixed transcription assay was carried out using a whole set of variant promoters, each harboring one base replacement, within the model promoter with the conserved -35 and -10 sequences of RpoD promoters. The consensus sequences, TTGACA(-35) and TATAAT(-10), were identified to be ideal for the maximum level of open complex formation and the highest rate of promoter opening, respectively. For identification of the full range of constitutive promoters on the E. coli genome, a total of 2,701 RpoD holoenzyme-binding sites were identified by Genomic SELEX screening, and using the reconfirmed consensus promoter sequence, a total of maximum 669 constitutive promoters were identified, implying that the majority of hitherto identified promoters represents the TF-dependent \"inducible promoters\". One unique feature of the constitutive promoters is the high level of promoter sequence conservation, about 85% carrying five-out-of-six agreements with -35 or -10 consensus sequence. The list of constitutive promoters provides the community resource toward estimation of the inducible promoters that operate under various stressful conditions in nature.", "link"=>"http://www.mendeley.com/research/whole-set-constitutive-promoters-recognized-rna-polymerase-rpod-holoenzyme-escherichia-coli", "reader_count"=>119, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>22, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>47, "Student > Postgraduate"=>7, "Student > Master"=>17, "Other"=>3, "Student > Bachelor"=>11}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>22, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>47, "Student > Postgraduate"=>7, "Student > Master"=>17, "Other"=>3, "Student > Bachelor"=>11}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Agricultural and Biological Sciences"=>65, "Philosophy"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Chemical Engineering"=>1, "Chemistry"=>1, "Engineering"=>6, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>33, "Medicine and Dentistry"=>2, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Engineering"=>{"Engineering"=>6}, "Chemistry"=>{"Chemistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>65}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>33}, "Philosophy"=>{"Philosophy"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>2, "China"=>1, "Mexico"=>1, "Peru"=>1, "Indonesia"=>1, "Russia"=>1, "India"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1410589"], "description"=>"<p>RpoD holoenzyme-binding peaks were identified within a total of 315 type-B spacers. Some representative patterns of RpoD holoenzyme-peaks are shown, which are located, which include the constitutive promoters for <i>cydA</i> (a), <i>yfcV</i> (b), <i>yobF</i> (c), <i>ompT</i> (d), <i>yjeJ</i> (e), <i>yhcN</i> (f), <i>yfjL</i> (g) and <i>phoH</i> (h) operons. Distribution of promoter -35 and -10 is shown below each panel.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "RNA synthesis", "proteins", "DNA-binding proteins", "biophysics", "dna", "genetics", "gene expression", "DNA transcription", "Molecular genetics", "Gene regulation", "Gene networks", "Genome-wide association studies", "microbiology", "bacteriology", "Bacterial biochemistry", "Model organisms", "Prokaryotic models", "Escherichia coli", "systems biology", "holoenzyme-binding", "peaks", "type-b"], "article_id"=>954316, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Shimada", "Yukiko Yamazaki", "Kan Tanaka", "Akira Ishihama"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090447.g003", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RpoD_holoenzyme_binding_peaks_within_type_B_spacers_/954316", "title"=>"RpoD holoenzyme-binding peaks within type-B spacers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-06 04:09:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1410584"], "description"=>"<p>Genomic SELEX search of RpoD holoenzyme-binding sequences was performed using the standard procedure <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone.0090447-Shimada1\" target=\"_blank\">[21]</a>. RpoD holoenzyme-bound DNA fragments were recovered by immunoprecipitation using anti-RpoC antibody. SELEX fragments were isolated from the immuno-precipitates and subjected to mapping on the <i>E. coli</i> genome by using tilling DNA microarray as described previously <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone.0090447-Teramoto1\" target=\"_blank\">[32]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone.0090447-Ogasawara1\" target=\"_blank\">[33]</a>. <b>[A] Location of the constitutive promoters.</b> A total of 2,701 RpoD holoenzyme-binding sites were identified (see Fig. 1), of which 1,075 (40%) are located within intergenic spacers. On the basis of transcription direction of flanking genes, the spacers were classified into three types: type-A between bidirectional transcription units; type-B upstream of one transcription unit but downstream of another transcription unit; and type-C, downstream of both transcription units. <b>[B] Classification of the constitutive promoters.</b> A total of 2,082 promoters have been identified and listed in the current versions of RegulonDB and EcoCyc databases, whereas the total number of constitutive promoters identified by Genomix SELEX screening ranges between minimum 492 and maximum 669, indicating that the majority of <i>E. coli</i> promoters listed in promoter database are TF-dependent inducible promoters.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "RNA synthesis", "proteins", "DNA-binding proteins", "biophysics", "dna", "genetics", "gene expression", "DNA transcription", "Molecular genetics", "Gene regulation", "Gene networks", "Genome-wide association studies", "microbiology", "bacteriology", "Bacterial biochemistry", "Model organisms", "Prokaryotic models", "Escherichia coli", "systems biology", "classification", "constitutive"], "article_id"=>954311, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Shimada", "Yukiko Yamazaki", "Kan Tanaka", "Akira Ishihama"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090447.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_and_classification_of_the_constitutive_promoters_/954311", "title"=>"Distribution and classification of the constitutive promoters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-06 04:09:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1410597", "https://ndownloader.figshare.com/files/1410598"], "description"=>"<div><p>The promoter selectivity of <i>Escherichia coli</i> RNA polymerase is determined by the sigma subunit with promoter recognition activity. The model prokaryote <i>Escherichia coli</i> contains seven species of the sigma subunit, each recognizing a specific set of promoters. The major sigma subunit, sigma-70 encoded by <i>rpoD</i>, plays a major role in transcription of growth-related genes. Concomitant with the increase in detection of promoters functioning <i>in vivo</i> under various stressful conditions, the variation is expanding in the consensus sequence of RpoD promoters. In order to identify the canonical sequence of “constitutive promoters” that are recognized by the RNA polymerase holoenzyme containing RpoD sigma in the absence of supporting transcription factors, an <i>in vitro</i> mixed transcription assay was carried out using a whole set of variant promoters, each harboring one base replacement, within the model promoter with the conserved -35 and -10 sequences of RpoD promoters. The consensus sequences, TTGACA(-35) and TATAAT(-10), were identified to be ideal for the maximum level of open complex formation and the highest rate of promoter opening, respectively. For identification of the full range of constitutive promoters on the <i>E. coli</i> genome, a total of 2,701 RpoD holoenzyme-binding sites were identified by Genomic SELEX screening, and using the reconfirmed consensus promoter sequence, a total of maximum 669 constitutive promoters were identified, implying that the majority of hitherto identified promoters represents the TF-dependent “inducible promoters”. One unique feature of the constitutive promoters is the high level of promoter sequence conservation, about 85% carrying five-out-of-six agreements with -35 or -10 consensus sequence. The list of constitutive promoters provides the community resource toward estimation of the inducible promoters that operate under various stressful conditions in nature.</p></div>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "RNA synthesis", "proteins", "DNA-binding proteins", "biophysics", "dna", "genetics", "gene expression", "DNA transcription", "Molecular genetics", "Gene regulation", "Gene networks", "Genome-wide association studies", "microbiology", "bacteriology", "Bacterial biochemistry", "Model organisms", "Prokaryotic models", "Escherichia coli", "systems biology", "constitutive", "promoters", "recognized", "polymerase", "rpod", "holoenzyme"], "article_id"=>954324, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Shimada", "Yukiko Yamazaki", "Kan Tanaka", "Akira Ishihama"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0090447.s001", "https://dx.doi.org/10.1371/journal.pone.0090447.s002"], "stats"=>{"downloads"=>9, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Whole_Set_of_Constitutive_Promoters_Recognized_by_RNA_Polymerase_RpoD_Holoenzyme_of_Escherichia_coli_/954324", "title"=>"The Whole Set of Constitutive Promoters Recognized by RNA Polymerase RpoD Holoenzyme of <i>Escherichia coli</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-06 04:09:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1410594"], "description"=>"<p>Among the total of 1,075 RpoD holoenzyme-binding sites, 154 are located within type-B spacers upstream of right-side genes and downstream of lest-side genes, indicating that these promoters direct rightward transcription. The genes and operons under the control of these 154 promoters were estimated, of which 18 represent putative internal promoters. A total of 9 genes encoding transcription factors are indicated by star symbols (*). The essential genes listed in the PEC database are underlined within the operons. The promoter sequence with complete match with the canonical promoter (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone-0090447-g004\" target=\"_blank\">Fig. 4</a>) is shown in bold and italic while the promoter sequence with 5-out of-6 match is shown in bold. The spacers including H-NS binding sites are marked as HNS in the spacer column. Total number of genes under the control of 154 promoters were 271 (1.76 gene per promoter). Among the total of 154 RpoD holoenyme-binding sites, 38 (25%) overlap with the H-NS-binding sites.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "RNA synthesis", "proteins", "DNA-binding proteins", "biophysics", "dna", "genetics", "gene expression", "DNA transcription", "Molecular genetics", "Gene regulation", "Gene networks", "Genome-wide association studies", "microbiology", "bacteriology", "Bacterial biochemistry", "Model organisms", "Prokaryotic models", "Escherichia coli", "systems biology", "promoters"], "article_id"=>954321, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Shimada", "Yukiko Yamazaki", "Kan Tanaka", "Akira Ishihama"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090447.t003", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Constitutive_Promoters_Type_B_Spacers_Rightward_transcription_/954321", "title"=>"Constitutive Promoters (Type-B Spacers) (Rightward transcription).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-06 04:09:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1410592"], "description"=>"<p>[A] The known consensus sequences of RpoD-dependent promoter, TTGAAC (-35) and TATAAT (-10) separated by 17 plus/minus 2 bp, were searched for all type-A (177) and type-B (315) spacers (see Experimental Procedure for the analysis method). Most of the constitutive promoters carry high-levels of the consensus sequence as listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone-0090447-t001\" target=\"_blank\">Table 1</a>. The composition of promoter -35 and -10 sequence was classified into 8 groups based on the conservation level of consensus sequences. About 89% of type-A promoters and 82% of type-B promoters (or 86% of A- plus B-type promoters) contain the sequence higher than 4/6 agreement with the consensus sequence at both -35 or -10 positions (A1), while only 39% of a total of 582 known promoters carries this level of consensus sequences (B1). [B] The whole set of constitutive promoter sequences were subjected to Logo analysis <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone.0090447-Crooks1\" target=\"_blank\">[73]</a>. The Logo patterns of -35 and -10 sequences are essentially the same among the constitutive promoters within type-A and type-B spacers. The Logo pattern of the whole set of constitutive promoters was compared with the Logo pattern generated using the total of 582 experimentally identified promoters <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone.0090447-Salgado1\" target=\"_blank\">[19]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone.0090447-Keseler1\" target=\"_blank\">[20]</a>. The contribution of each base of the consensus -35 and -10 sequences is significantly different between the constitutive promoters and the set of known promoters.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "RNA synthesis", "proteins", "DNA-binding proteins", "biophysics", "dna", "genetics", "gene expression", "DNA transcription", "Molecular genetics", "Gene regulation", "Gene networks", "Genome-wide association studies", "microbiology", "bacteriology", "Bacterial biochemistry", "Model organisms", "Prokaryotic models", "Escherichia coli", "systems biology", "constitutive"], "article_id"=>954319, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Shimada", "Yukiko Yamazaki", "Kan Tanaka", "Akira Ishihama"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090447.g005", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_composition_of_constitutive_promoters_/954319", "title"=>"The composition of constitutive promoters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-06 04:09:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1410593"], "description"=>"<p>Among the total of 1,075 RpoD holoenzyme-binding sites, 181 are located within type-B spacers upstream of left-side genes and downstream of right-side genes, indicating that these promoters direct leftward transcription. The genes and operons under the control of these 181 promoters were estimated, of which 16 represent putative internal promoters. Descriptions and symbols are as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone-0090447-t001\" target=\"_blank\">Table 1</a>. A total of 15 genes encoding transcription factors are indicated by star symbols (*). The essential genes listed in the PEC database are underlined within the operons. The promoter sequence with complete match with the canonical promoter (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone-0090447-g004\" target=\"_blank\">Fig. 4</a>) is shown in bold and italic while the promoter sequence with 5-out of-6 match is shown in bold. The spacers including H-NS binding sites are marked as HNS in the spacer column. Total number of genes under the control of these 181 promoters were 290 (1.80 gene per promoter). Among the total of 181 RpoD holoenyme-binding sites, 39 (24%) overlap with the H-NS-binding sites.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "RNA synthesis", "proteins", "DNA-binding proteins", "biophysics", "dna", "genetics", "gene expression", "DNA transcription", "Molecular genetics", "Gene regulation", "Gene networks", "Genome-wide association studies", "microbiology", "bacteriology", "Bacterial biochemistry", "Model organisms", "Prokaryotic models", "Escherichia coli", "systems biology", "promoters"], "article_id"=>954320, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Shimada", "Yukiko Yamazaki", "Kan Tanaka", "Akira Ishihama"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090447.t002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Constitutive_Promoters_Type_B_Spacers_Leftward_transcription_/954320", "title"=>"Constitutive Promoters (Type-B Spacers) (Leftward transcription).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-06 04:09:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1410591"], "description"=>"<p>Mixtures of equal amounts of 195 bp-long template containing the ideal promoter of complete consensus sequence and 175 bp-long mutant template, each carrying one base substitution, were subjected to the <i>in vitro</i> mixed transcription <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone.0090447-Kajitani1\" target=\"_blank\">[24]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone.0090447-Kajitani2\" target=\"_blank\">[25]</a>. After preincubation for 0.5, 1.0, 2.5, 5.0, 7.5, 10 and 15 min, a mixture of substrates and heparin was added and RNA synthesis was allowed for 10 min. The final level of RNA synthesis represents the level of RpoD holoenzyme binding (parameter I) while the rate of open complex formation (parameter II) was determined as a reciprocal of the time required to reach the plateau level. For each set of four promoters with mutations at the same position, the promoter activities are shown as the values relative to the promoter with the highest activity.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "RNA synthesis", "proteins", "DNA-binding proteins", "biophysics", "dna", "genetics", "gene expression", "DNA transcription", "Molecular genetics", "Gene regulation", "Gene networks", "Genome-wide association studies", "microbiology", "bacteriology", "Bacterial biochemistry", "Model organisms", "Prokaryotic models", "Escherichia coli", "systems biology", "constitutive", "promoters", "transcription"], "article_id"=>954318, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Shimada", "Yukiko Yamazaki", "Kan Tanaka", "Akira Ishihama"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090447.g004", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Determination_of_the_consensus_sequence_of_constitutive_promoters_using_the_in_vitro_mixed_transcription_system_/954318", "title"=>"Determination of the consensus sequence of constitutive promoters using the <i>in vitro</i> mixed transcription system.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-06 04:09:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1410587"], "description"=>"<p>RpoD holoenzyme-binding peaks were identified within a total of 177 type-A spacers. Some representative patterns of RpoD holoenzyme-peaks are shown, which are located between <i>leuL-leuO</i> (a), <i>csgD-csgB</i> (b), <i>nanC-fimB</i> (c), <i>lrhA-alaA</i> (d), <i>adhE-ychE</i> (e), <i>waaQ-waaA</i> (f), <i>mdoC-mdoG</i> (g) and <i>ulaG-ulaA</i> (h). Distribution of promoter -35 (indicated by orange arrows) and -10 (indicated by green arrows) signals is shown in the panel under each SELEX pattern.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "RNA synthesis", "proteins", "DNA-binding proteins", "biophysics", "dna", "genetics", "gene expression", "DNA transcription", "Molecular genetics", "Gene regulation", "Gene networks", "Genome-wide association studies", "microbiology", "bacteriology", "Bacterial biochemistry", "Model organisms", "Prokaryotic models", "Escherichia coli", "systems biology", "holoenzyme-binding", "peaks", "type-a"], "article_id"=>954314, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Shimada", "Yukiko Yamazaki", "Kan Tanaka", "Akira Ishihama"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090447.g002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RpoD_holoenzyme_binding_peaks_within_type_A_spacers_/954314", "title"=>"RpoD holoenzyme-binding peaks within type-A spacers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-06 04:09:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1410595"], "description"=>"<p>A total of 1,075 RpoD holoenzyme-binding sites were identified within spacers on the entire <i>E. coli</i> K-12 W3110 genome. The constitutive promoters were predicted within type-A and type-B intergenic spacers (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone-0090447-g001\" target=\"_blank\">Fig. 1A</a> for classficiation). A total of 178 RNA polymerase RpoD holoenzyme-binding sites were identified within type-A spacers, which direct bidirectional transcription. Based on the gene orientation around these promoters, the genes and operons under the control of these promoters were estimated, that are located on either left side (left gene column) or right side (right gene column) of the respective spacers. Genes encoding transcription factors are indicated by star symbols (*) and the operons are shown in the operon columns [note that only the first and the last genes are shown for polycitronic operons]. The directions of transcription for these flanking genes are shown by arrows in column D. The map positions of left-side and right-side genes are shown in the map columns. The essential genes listed in the PEC database are underlined. The promoter sequences were predicted according to the analysis procedure described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#s4\" target=\"_blank\">Materials and Methods</a>. For some spacers, multiple promoters were identified, of which the best-match promoters with the highest scores are described. The promoter sequence with complete match with the canonical promoter (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090447#pone-0090447-g004\" target=\"_blank\">Fig. 4</a>) is shown in bold and italic while the promoter sequence with 5-out of-6 match is shown in bold. The spacer including H-NS binding sites are shown as HNS mark in the spacer column. The numbers of hitherto identified promoters are 121 and 133 for left-ward and right-ward transcription, respectively, which correspond to 68 and 75%. Total number of genes under the control of 178 promoters were 300 for left-ward transcription, and 291 for right-ward transcription. The average numbers of genes under one promoter are 1.68 and 1.63 for left-ward and right-ward transcription, respectively. Among the total of 178 RpoD holoenyme-binding sites, 64 (36%) overlap with the H-NS-binding sites.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "RNA synthesis", "proteins", "DNA-binding proteins", "biophysics", "dna", "genetics", "gene expression", "DNA transcription", "Molecular genetics", "Gene regulation", "Gene networks", "Genome-wide association studies", "microbiology", "bacteriology", "Bacterial biochemistry", "Model organisms", "Prokaryotic models", "Escherichia coli", "systems biology", "promoters"], "article_id"=>954322, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Shimada", "Yukiko Yamazaki", "Kan Tanaka", "Akira Ishihama"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090447.t001", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Constitutive_Promoters_Type_A_Spacers_/954322", "title"=>"Constitutive Promoters (Type-A Spacers).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-06 04:09:02"}

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