Introduction.We have been studying the structure and function of a group of transcription factors, the feast/famine regulatory proteins (FFRPs), regulating transcription of many genes in archaea and eubacteria. reported by two other groups, are re-analyzed and compared with our foot-printing experiments using FL11 (pot0434017). regions protected in these experiments from DNase I were large, 45-60 bps. And so, no short sequence was identified as that of a binding-site in the original papers.
28)-30)Proteins, FL10 and FL11, are shared by anaerobic archaea, Pyrococcus sp. OT3, Pyrococcus abyssi, and Pyrococcus furiosus, in the same genus. While, Ss/SaLrp is shared by organisms in an aerobic genus, Sulfolobus, e.g. S. solfataricus and S. acidocaldarius. Biological processes regulated by these FFRPs are yet unknown. Thus all the foot-printing experiments were carried out using DNA fragments containing regions upstream of the genes coding these transcription factors, by assuming auto-regulation. In general, such auto-regulation is expected to repress expression of the genes.When 13 bps in the 5-3-5 arrangement are positioned by overlapping onto a TATA box or its downstream, transcription of the gene will be repressed by binding by an FFRP. 1),7) While, when such a sequence is positioned immediately upstream of a TATA box with an insertion of ~4 or ~15 basepairs (i.e. 4 plus 10.5), binding of an FFRP will activate transcription most likely by interacting with the TATA box binding protein (TBP), thereby recruiting it to the TATA box.
1),3),7)Overall characteristics of foot-print of FL10. In experiments carried out by another group, ~45 bps positioned upstream of the fl10 gene were protected by