E. coli DNA-Binding Site Matrices Applied to the Complete E. coli K12 Genome


Sequence-specific DNA-binding proteins perform a variety of roles in the cell, including transcriptional regulation. Known binding sites for a DNA-binding protein can be used to identify additional sites for that protein, and thereby identify further genes regulated by that protein. The availability of complete bacterial genome sequences offers new opportunities to describe networks of regulatory interactions. Of the 240-260 candidate E. coli DNA-binding proteins, only around 59 have binding sites identified by DNA footprinting. We used these sites to construct recognition matrices (based on data in the DPInteract database) which we used to search for additional binding sites in the E .coli genomic sequence. We used the matrix scoring method of Berg and von Hippel to score genomic sites because scores from this method have been shown to correlate with in vitro binding constants. Many of our matrices show a strong preference for non-coding DNA. We have used results from these matrix searches to make a set of predictions which we are currently verifying experimentally.

Robison, K., McGuire, A. M., Church, G. M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K12 genome. Journal of Molecular Biology (1998) 284, 241-254.

Matrices and Search Results

View all matrices in one file

ada araC arcA argR carP cpxR crp cspA cynR cysB cytR
deoR dnaA fadR farR fhlA fis flhCD fnr fruR fur galR
gcvA glpR hipB hns hu iclR ihf ilvY lacI lexA lrp
malT marR melR metJ metR modE nagC narL narP ntrC ompR
oxyR pdhR phoB purR rhaS rpoD rpoE rpoH rpoN rpoS soxS
torR trpR tus tyrR

Summary Table (Number of hits in the genome for each matrix)

Download the code for the matrix search program scanACE

Sequence logos (Postscript format)

explanation of file formats

sequencing inconsistencies noted

Last updated 11/4/98

Click here for a ranked list of predictions based on clusters of predicted sites

Abigail Manson McGuire
Genetics Department
Harvard Medical School
200 Longwood Ave.
Boston, MA. 02115.
Telephone: (617) 432-4136