INFORMATION ANALYSIS OF FIS BINDING-SITES

Originally discovered in the bacteriophage Mu DNA inversion system gin , Fis (Factor for Inversion Stimulation) regulates many genetic system s, To determine the base frequency conservation required for Fis to lo cate its binding sites, we collected a set of 60 experimentally define d wild-type Fis DNA binding sequences, The sequence logo for Fis bindi ng sites showed the significance and likely kinds of base contacts, an d these are consistent with available experimental data, Scanning with an information theory based weight matrix within fis, nrd, tgt/sec an d gin revealed Fis sites not previously identified, but for which ther e are published footprinting and biochemical data, DNA mobility shift experiments showed that a site predicted to be 11 bases from the proxi mal Salmonella typhimurium hin site and a site predicted to be 7 bases from the proximal P1 cin site are bound by Fis in vitro. Two predicte d sites separated by 11 bp found within the nrd promoter region, and o ne in the tgt/sec promoter, were also confirmed by gel shift analysis, A sequence in aldB previously reported to be a Fis site, for which in formation theory predicts no site, did not shift, These results demons trate that information analysis is useful for predicting Fis DNA bindi ng.