Δg-based prediction and experimental confirmation of SYCRP1-binding sites on the Synechocystis genome

Katsumi Omagari, Hidehisa Yoshimura, Takayuki Suzuki, Mitsunori Takano, Masayuki Ohmori, Akinori Sarai

    Research output: Contribution to journalArticle

    8 Citations (Scopus)

    Abstract

    DNA-binding sites for SYCRP1, which is a regulatory protein of the cyanobacterium Synechocystis sp. PCC6803, were predicted for the whole genome sequence by estimating changes in the binding free energy () for SYCRP1 for those sites. The values were calculated by summing ΔΔG values derived from systematic single base-pair substitution experiments (symmetrical and cooperative binding model). Of the calculated binding sites, 23 sites with a value < 3.9 kcal·mol-1 located upstream or between the ORFs were selected as putative binding sites for SYCRP1. In order to confirm whether SYCRP1 actually binds to these binding sites or not, 11 sites with the lowest values were tested experimentally, and we confirmed that SYCRP1 binds to ten of the 11 sites with a ΔΔGtotal value < 3.9 kcal·mol-1. The best correlation coefficient between and the observed ΔΔGtotal for binding of SYCRP1 to those sites was 0.78. These results suggest that the ΔΔG values derived from systematic single base-pair experiments may be used to screen for potential binding sites of a regulatory protein in the genome sequence.

    Original languageEnglish
    Pages (from-to)4786-4795
    Number of pages10
    JournalFEBS Journal
    Volume275
    Issue number19
    DOIs
    Publication statusPublished - 2008 Oct

    Fingerprint

    Synechocystis
    Genes
    Binding Sites
    Genome
    Base Pairing
    Cyanobacteria
    Open Reading Frames
    Free energy
    Proteins
    Substitution reactions
    Experiments
    DNA

    Keywords

    • Additivity
    • Binding free energy change
    • DNA-binding sites
    • Prediction
    • Regulatory protein

    ASJC Scopus subject areas

    • Biochemistry
    • Cell Biology
    • Molecular Biology

    Cite this

    Δg-based prediction and experimental confirmation of SYCRP1-binding sites on the Synechocystis genome. / Omagari, Katsumi; Yoshimura, Hidehisa; Suzuki, Takayuki; Takano, Mitsunori; Ohmori, Masayuki; Sarai, Akinori.

    In: FEBS Journal, Vol. 275, No. 19, 10.2008, p. 4786-4795.

    Research output: Contribution to journalArticle

    Omagari, Katsumi ; Yoshimura, Hidehisa ; Suzuki, Takayuki ; Takano, Mitsunori ; Ohmori, Masayuki ; Sarai, Akinori. / Δg-based prediction and experimental confirmation of SYCRP1-binding sites on the Synechocystis genome. In: FEBS Journal. 2008 ; Vol. 275, No. 19. pp. 4786-4795.
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