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. 2005 Nov;6(11):1063-8.
doi: 10.1631/jzus.2005.B1063.

Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence

Andrey Y Berezhnoy  1 , Yuriy G Shckorbatov
Affiliations

Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence

Andrey Y Berezhnoy et al. J Zhejiang Univ Sci B. 2005 Nov.

Abstract

The energy of interaction between complementary nucleotides in promoter sequences of E. coli was calculated and visualized. The graphic method for presentation of energy properties of promoter sequences was elaborated on. Data obtained indicated that energy distribution through the length of promoter sequence results in picture with minima at -35, -8 and +7 regions corresponding to areas with elevated AT (adenine-thymine) content. The most important difference from the random sequences area is related to -8. Four promoter groups and their energy properties were revealed. The promoters with minimal and maximal energy of interaction between complementary nucleotides have low strengths, the strongest promoters correspond to promoter clusters characterized by intermediate energy values.

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Figures

Fig. 1
Fig. 1
The specific free energy of complementary base pair interaction in different promoters (forward and reverse promoter sequences and random sequences)
Fig. 2
Fig. 2
The mean energy per nucleotide pair depending on pair position in promoter sequence
Fig. 3
Fig. 3
The mean contents of AT-pairs depending on window position in the promoter sequence
Fig. 4
Fig. 4
The difference between random and forward or reverse promoter sequences (t-criterion)
Fig. 5
Fig. 5
The promoter strength
See this image and copyright information in PMC

References

    1. Babb K, McAlister JD, Miller JC, Stevenson B. Molecular characterization of borrelia burgdorferi promoter/operator elements. Journal of Bacteriology. 2004;186(9):2745–2756. doi: 10.1128/JB.186.9.2745-2756.2004. - DOI - PMC - PubMed
    1. Burr T, Mitchell J, Minchin S, Busby S. DNA sequence elements located immediately upstream of the −10 hexamer in Escherichia coli promoters: a systematic study. Nucleic Acids Res. 2000;28:1864–1870. doi: 10.1093/nar/28.9.1864. - DOI - PMC - PubMed
    1. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA. Structure of the bacterial RNA polymerase promoter specificity σ subunit. Mol Cell. 2002;9:527–539. doi: 10.1016/S1097-2765(02)00470-7. - DOI - PubMed
    1. Gourse RL, Ross W, Gaal T. UPs and downs in bacterial transcription initiation: role of the α subunit of RNA polymerase in promoter recognition. Mol Microbiol. 2000;37:687–695. doi: 10.1046/j.1365-2958.2000.01972.x. - DOI - PubMed
    1. Gralla JD. Activation and repression of E. coli promoters. Curr Opin Genet. 1996;6(5):526–530. doi: 10.1016/S0959-437X(96)80079-7. - DOI - PubMed

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