Comparison of foot-prints of FFRPs on promoters designed for autoregulation: FL10 (pot0377090, LrpA), FL11 (pot0434017), and Ss/Sa-Lrp

The DNA-binding specificity of archaeal transcription factors, FL10 (pot0377090, LrpA) and Ss/Sa-Lrp, was studied by re-analyzing foot-printing experiments carried out by other groups: Brinkman, A. B., et al., (2000) J Biol. Chem. 275, 38160-38169, Enoru-Eta, J. et al., (2002) Mol. Microbiol. 45, 1541-1555, and Enoru-Eta, J. et al. (2000) J Bacteriol. 182, 3661-3672. The two proteins are closely related, classified into the same group of FFRPs, feast/famine regulatory proteins. Many FFRPs, by forming dimers, bind DNAs in the 5-3-(5) under bar arrangement: NANBNCNDNE[TTT/AAA]N (E) under barN (D) under barN (C) under barN (B) under barN (A) under bar, where, e.g. N (A) under bar is the base complementary to N-A. In the light of this new observation, the ideal binding site of FL10 was identified as TTCGA[TCT/AGA]TCGAA or GTCGA[TCT/AGA]TCGAC. The ideal site recognized by Ss/Sa-Lrp was identified as ATTTT[TTT/AAA]AAAAT. By comparing these analyses with our experiments using another archaeal FFRP, FL11 (pot0434017), characteristics of the foot-prints shared by FFRPs were discussed.