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Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence
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BEREZHNOY Andrey Y., SHCKORBATOV Yuriy G.. Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence[J]. Journal of Zhejiang University Science B, 2005, 6(11): 1063-1068.
@article{title="Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence",
author="BEREZHNOY Andrey Y., SHCKORBATOV Yuriy G.",
journal="Journal of Zhejiang University Science B",
volume="6",
number="11",
pages="1063-1068",
year="2005",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2005.B1063"
}
%0 Journal Article
%T Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence
%A BEREZHNOY Andrey Y.
%A SHCKORBATOV Yuriy G.
%J Journal of Zhejiang University SCIENCE B
%V 6
%N 11
%P 1063-1068
%@ 1673-1581
%D 2005
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2005.B1063
TY - JOUR
T1 - Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence
A1 - BEREZHNOY Andrey Y.
A1 - SHCKORBATOV Yuriy G.
J0 - Journal of Zhejiang University Science B
VL - 6
IS - 11
SP - 1063
EP - 1068
%@ 1673-1581
Y1 - 2005
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.2005.B1063
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.
[1] Babb, K., McAlister, J.D., Miller, J.C., Stevenson, B., 2004. Molecular characterization of borrelia burgdorferi promoter/operator elements. Journal of Bacteriology, 186(9):2745-2756.
[2] Burr, T., Mitchell, J., Minchin, S., Busby, S., 2000. DNA sequence elements located immediately upstream of the −10 hexamer in Escherichia coli promoters: a systematic study. Nucleic. Acids. Res., 28:1864-1870.
[3] Campbell, E.A., Muzzin, O., Chlenov, M., Sun, J.L., Olson, C.A., Weinman, O., Trester-Zedlitz, M.L., Darst, S.A., 2002. Structure of the bacterial RNA polymerase promoter specificity σ subunit. Mol. Cell, 9:527-539.
[4] Gourse, R.L., Ross, W., Gaal, T., 2000. UPs and downs in bacterial transcription initiation: role of the α subunit of RNA polymerase in promoter recognition. Mol. Microbiol., 37:687-695.
[5] Gralla, J.D., 1996. Activation and repression of E. coli promoters. Curr. Opin. Genet., 6(5):526-530.
[6] Guo, Y., Gralla, J.D., 1998. Promoter opening via a DNA fork junction binding activity. Proc. Natl. Acad. Sci. USA, 95(20):11655-11660.
[7] Jones, C.H., Tatti, K.M., Moran, C.P.Jr., 1992. Effects of amino acid substitutions in the −10 binding region of sigma E from Bacillus subtilis. J. Bacteriol., 174(2):6815-6821.
[8] Juang, Y.L., Helmann, J.D., 1994. A promoter melting region in the primary sigma factor of Bacillus subtilis. Identification of functionally important aromatic amino acids. J. Mol. Biol., 235(5):1470-1488.
[9] Kainz, M., Roberts, J., 1992. Structure of transcription elongation complexes in vivo. Science, 255:838-841.
[10] Kajitani, M., Ishihama, A., 1983. Determination of the promoter strength in the mixed transcription system. II. Promoters of ribosomal RNA, ribosomal protein S1 and recA protein operons from Escherichia coli. Nucleic. Acids. Research, 11(12):3873-3888.
[11] Kanehisa, M., Goto, S., Kawashima, S., Kuno, Y., Hattori, M., 2004. The KEGG resources for deciphering the genome. Nucleic. Acids. Res., 32:D277-D280.
[12] Kudritskaya, Z.G., Danilov, V.I., 1976. Quantum mechanical study of bases interactions in various associates in atomic dipole approximation. J. Theor. Biol., 59:301-318.
[13] Meier, T., Schickor, P., Wedel, A., Cellai, L., Heumann, H., 1995. In vitro transcription close to the melting point of DNA: analysis of Thermotoga maritima RNA polymerase-promoter complexes at 75 degrees C using chemical probes. Nucleic. Acids. Research, 23(6):988-994.
[14] Mori, H., Isono, K., Horiuchi, T., Miki, T., 2000. Functional genomics of Escherichia coli in Japan. Res. Microbiol., 151:121-128.
[15] Murakami, K.S., Masuda, S., Campbell, E.A., Muzzin, O., Darst, S.A., 2002. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science, 296:1285-1290.
[16] Roberts, C.W., Roberts, J.W., 1996. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell, 86(3):495-501.
[17] Ross, W., Ernst, A., Gourse, R.L., 2001. Fine structure of E. coli RNA polymerase-promoter interactions: α subunit binding to the UP element minor groove. Genes and Development, 15(5):491-506.
[18] Spassky, A., Kirkegaard, K., Buc, H., 1985. Changes in the DNA structure of the lac UV5 promoter during formation of an open complex with Escherichia coli RNA polymerase. Biochemistry, 24(11):2723-2731.
[19] Vogel, S.K., Schulz, A., Rippe, K., 2002. Binding affinity of Escherichia coli RNA polymerase σ54 holoenzyme for the glnAp2, nifH and nifL promoters. Nucleic. Acids. Research, 30(18):4094-4101.
Open peer comments: Debate/Discuss/Question/Opinion
<1>
kannadasan@Manonmaniam Sudaranar University<Kannagenes@gmail.com>
2013-04-28 14:13:31
Hi My Name is Kannadasan Working in small biotech company as Scientific Assistant. Im looking for E. coli promoters. I found your page. Hope I will be helped by this Paper.