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      The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase

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      PLoS ONE
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          Abstract

          The promoter selectivity of Escherichia coli RNA polymerase (RNAP) is determined by the sigma subunit. The model prokaryote Escherichia coli K-12 contains seven species of the sigma subunit, each recognizing a specific set of promoters. For identification of the “constitutive promoters” that are recognized by each RNAP holoenzyme alone in the absence of other supporting factors, we have performed the genomic SELEX screening in vitro for their binding sites along the E. coli K-12 W3110 genome using each of the reconstituted RNAP holoenzymes and a collection of genome DNA segments of E. coli K-12. The whole set of constitutive promoters for each RNAP holoenzyme was then estimated based on the location of RNAP-binding sites. The first successful screening of the constitutive promoters was achieved for RpoD (σ 70), the principal sigma for transcription of growth-related genes. As an extension, we performed in this study the screening of constitutive promoters for four minor sigma subunits, stationary-phase specific RpoS (σ 38), heat-shock specific RpoH (σ 32), flagellar-chemotaxis specific RpoF (σ 28) and extra-cytoplasmic stress-response RpoE (σ 24). The total number of constitutive promoters were: 129~179 for RpoS; 101~142 for RpoH; 34~41 for RpoF; and 77~106 for RpoE. The list of constitutive promoters were compared with that of known promoters identified in vivo under various conditions and using varieties of E. coli strains, altogether allowing the estimation of “inducible promoters” in the presence of additional supporting factors.

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          Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.

          L Gold, C Tuerk (1990)
          High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.
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            Multiple sigma subunits and the partitioning of bacterial transcription space.

            Promoter recognition in eubacteria is carried out by the initiation factor sigma, which binds RNA polymerase and initiates transcription. Cells have one housekeeping factor and a variable number of alternative sigma factors that possess different promoter-recognition properties. The cell can choose from its repertoire of sigmas to alter its transcriptional program in response to stress. Recent structural information illuminates the process of initiation and also shows that the two key sigma domains are structurally conserved, even among diverse family members. We use the sigma repertoire of Escherichia coli, Bacillus subtilis, Streptomyces coelicolor, and cyanobacteria to illustrate the different strategies utilized to organize transcriptional space using multiple sigma factors.
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              RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

              This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Supervision
                Role: ConceptualizationRole: Funding acquisitionRole: Supervision
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                30 June 2017
                2017
                : 12
                : 6
                : e0179181
                Affiliations
                [1 ]Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
                [2 ]Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
                Indian Institute of Science, INDIA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                [¤]

                Current address: School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan

                Author information
                http://orcid.org/0000-0002-6339-9042
                Article
                PONE-D-17-11189
                10.1371/journal.pone.0179181
                5493296
                28666008
                b05b9b59-fa37-4c23-ac18-f0dee4502997
                © 2017 Shimada et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 22 March 2017
                : 6 May 2017
                Page count
                Figures: 5, Tables: 5, Pages: 33
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001700, Ministry of Education, Culture, Sports, Science and Technology;
                Award ID: Grants-in-Aid for Scientific Research (A) 25430173
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001700, Ministry of Education, Culture, Sports, Science and Technology;
                Award ID: Cooperative Research Program of Network Joint Research Center for Materials and Devices
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001700, Ministry of Education, Culture, Sports, Science and Technology;
                Award ID: Grants-in-Aid for Scientific Research (B) 18310133
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001700, Ministry of Education, Culture, Sports, Science and Technology;
                Award ID: Cooperative Research Program of Network Joint Research Center for Materials and Devices
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001700, Ministry of Education, Culture, Sports, Science and Technology;
                Award ID: Program for the Strategic Research Foundation at Private Universities 208-2012 (S0801037) to Hosei University
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001700, Ministry of Education, Culture, Sports, Science and Technology;
                Award ID: Grant-in-Aid for Young Scientists (B) (24710214)
                Award Recipient :
                Funded by: Ministry of Education, Culture, Sports, Science and Technology (JP)
                Award ID: Grants-in-Aid Scientific Research (C) 16K07195
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001700, Ministry of Education, Culture, Sports, Science and Technology;
                Award ID: Cooperative Research Program of Network Joint Research Center for Materials and Devisec
                Award Recipient :
                This work was supported by National Institute of Genetics to YY; MEXT Grants-in-Aid for Scientific Research (A) (21241047), (B) (18310133), and (C) (25430173) to AI; MEXT Grant-in-Aid for Young Scientists (B) (24710214) to TS; Research Fund from IFO (Institute for Fermentation, Osaka) to TS; funding from the MEXT Cooperative Research Program of Network Joint Research Center for Materials and Devices to AI and KT; and funding to AI and TS from the MEXT-Supported Program for the Strategic Research Foundation at Private Universities 208-2012 (S0801037) to Hosei University.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Proteins
                Recombinant Proteins
                Biology and life sciences
                Biochemistry
                Proteins
                DNA-binding proteins
                Biology and life sciences
                Genetics
                Gene expression
                DNA transcription
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                Custom metadata
                The data described in this report has been deposited to TEC (Transcription Profile of Escherchia coli) database ( https://shigen.nig.ac.jp/ecoli/tec/). The data of each minor sigma will be shown by setting the gene symbol, rpoS, rpoH, rpoF or rpoE, respectively [ https://shigen.nig.ac.jp/ecoli/tec/tfmap]; for details, follow the instructions.

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