Non-canonical sequence elements in the promoter structure. Cluster
analysis of promoters recognized by Escherichia coli RNA polymerase
O. N. Ozoline, A. A. Deev1
and M. V. Arkhipova2
Institute of Cell Biophysics, Russian Academy of Sciences (RAS) and
1 Institute of Theoretical and Experimental Biophysics, RAS,
Pushchino, 142292 Moscow region, Russia and
2Department of Biology, Moscow State University, Leninskie
gory, 119899 Moscow, Russia
Nucleic Acids Research ,
25(23): 4703-4709 (Dec 1, 1997)
Abstract
Nucleotide sequences of 441 promoters recognized by Escherichia coli
RNA polymerase were subjected to a site-specific cluster analysis based
on the hierarchical method of classification. Five regions permitting
promoter subgrouping were identified. They are located at
-54 ± 4, -44 ± 3, -35 ± 3 (-35 element), -29 ± 2
and -11 ± 4 (-10 element). Promoters were independently
subgrouped on the basis of their sequence homology in each
of these regions and typical sequence elements were determined.
The putative functional significance of the revealed elements is
discussed on the basis of available biochemical data. Those
promoters that have a high degree of homology with the revealed sequence elements
were selected as representatives of corresponding promoter groups and the presence of
other sequence motifs in their structure was examined. Both positive and negative
correlations in the presence of particular sequence motifs were observed;
however, the degree of these interdependencies was not high in all cases,
probably indicating that different combinations of the signal elements
may create a promoter. The list of promoter sequences with the
presence of different sequence elements is available on request by Email:
