A COMPREHENSIVE LIBRARY OF DNA-BINDING SITE MATRICES FOR 55 PROTEINS APPLIED TO THE COMPLETE ESCHERICHIA-COLI K-12 GENOME

A major mode of gene regulation occurs via the binding of specific pro teins to specific DNA sequences. The availability of complete bacteria l genome sequences offers an unprecedented opportunity to describe net works of such interactions by correlating existing experimental data w ith computational predictions. Of the 240 candidate Escherichia coli D NA-binding proteins, about 55 have DNA-binding sites identified by DNA footprinting. We used these sites to construct recognition matrices, which we used to search for additional binding sites in the E. coli ge nomic sequence. Many of these matrices show a strong preference for no n-coding DNA. Discrepancies are identified between matrices derived fr om natural sites and those derived from SELEX (Systematic Evolution of Ligands by Exponential enrichment) experiments. We have constructed a database of these proteins and binding sites, called DPInteract (avai lable at http://arep.med.harvard.edu/dpinteract). (C) 1998 Academic Pr ess.