The DNA-binding specificity of eubacterial and archaeal FFRPs

In the light of crystal 3D structures of feast/famine regulatory proteins (FFRPs), biochemical and biological experiments characterizing DNA-binding by FFRPs, carried out by other groups, have been reanalyzed. An important conclusion is that the consensus sequences of DNA sites recognized by dimers of types of FFRPs are in the same form of NANBNCNDNETTTNENDNCNBNA, where, e.g., N-A is the base complementary to N-A (e.g., when G is N-A, C is N-A), and N-E is either A or T. The NANBNCND and NDNCNBNA parts are different among FFRPs, and are important for discrimination between DNA promoters. The cluster of four T bases (i.e. the three Ts plus N-E or N-E) in the center appears to be important for bending of the DNA sites, and possibly used as the unit for formation of superstructures. Either 7-8 or similar to18 (i.e. 7-8 plus a helical turn of DNA, similar to10.5) basepairs are inserted between dimer-binding sites in many promoters, e.g. [NANBNCNDNETTTNENDNCNBNA]N1N2N3N4N5N6N7[NANBNCNDNETTTNENDNCNBNA], when dimer-binding sites repeat, most frequently, four times.