DNA bendability--a novel feature in E. coli promoter recognition.

The distribution of deformable base-pair steps in the structure of bacterial promoters is analyzed with respect to their possible structural and functional role. A regular positioning of TA and TG stacks is detected with the best fit period 5.6 bp. This value is interpreted as a half of the sequence period 11.2 bp, somewhat higher than the structural helical repeat of B-DNA (10.55 bp). The difference, +0.65 bp, suggests a sequence-dependent helical writhe of the promoter DNA--a right-handed superhelix. Apparently, to favour rotational setting of DNA on the surface of RNA polymerase the flexible steps deformable largely towards the grooves, follow the half-period spacing. Such rotational setting is consistent with the DNase I footprinting data. Periodical distribution of deformable base-pair stacks shows negative correlation with the presence of -35 canonical hexamer, suggesting the functional significance of this novel element for promoter recognition. The RNA polymerase--DNA recognition is discussed as interaction of distributional type that involves many elements of different nature which are in partially compensatory relations.

[1]  C. Bustamante,et al.  Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. , 1993, Science.

[2]  H. Fritz,et al.  Unusual properties of promoter‐up mutations in the Escherichia coli galactose operon and evidence suggesting RNA polymerase‐induced DNA bending. , 1987, The EMBO journal.

[3]  J. Gastwirth.  Non-parametric Statistical Methods , 1990 .

[4]  A A Deev,et al.  Non-canonical sequence elements in the promoter structure. Cluster analysis of promoters recognized by Escherichia coli RNA polymerase. , 1997, Nucleic acids research.

[5]  Hanspeter Herzel,et al.  Interpreting correlations in biosequences , 1998 .

[6]  D. K. Hawley,et al.  Compilation and analysis of Escherichia coli promoter DNA sequences. , 1983, Nucleic acids research.

[7]  N. Fujita,et al.  Location of the C-terminal domain of the RNA polymerase alpha subunit in different open complexes at the Escherichia coli galactose operon regulatory region. , 1996, Nucleic acids research.

[8]  J. D. Helmann,et al.  Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA , 1995, Nucleic Acids Res..

[9]  S. Busby,et al.  Recognition of nucleotide sequences at the Escherichia coli galactose operon P1 promoter by RNA polymerase. , 1989, Gene.

[10]  V. Zhurkin,et al.  Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine—pyrimidine and pyrimidine—purine dimers , 1983, FEBS letters.

[11]  R. Gourse,et al.  A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. , 1993, Science.

[12]  H. Margalit,et al.  Compilation of E. coli mRNA promoter sequences. , 1993, Nucleic acids research.

[13]  E N Trifonov,et al.  Sequence-dependent variations of B-DNA structure and protein-DNA recognition. , 1983, Cold Spring Harbor symposia on quantitative biology.

[14]  M. O'Neill.  Escherichia coli promoters. I. Consensus as it relates to spacing class, specificity, repeat substructure, and three-dimensional organization. , 1989, The Journal of biological chemistry.

[15]  R E Harrington,et al.  Sequence-dependent kinks induced in curved DNA. , 1990, Journal of biomolecular structure & dynamics.

[16]  D. Pribnow.  Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[17]  S. Busby,et al.  The Escherichia coli cysG promoter belongs to the 'extended -10' class of bacterial promoters. , 1993, The Biochemical journal.

[18]  O. Ozoline,et al.  Structure of open promoter complexes with Escherichia coli RNA polymerase as revealed by the DNase I footprinting technique: compilation analysis. , 1995, Nucleic acids research.