Binding of the feast/famine regulatory protein (FFRP) FL11 (pot0434017) to DNA in the "promoter to coding" region of gene fl11

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Feast/famine regulatory proteins (FFRPs), including of E. coli Lrp and AsnC, compose a diverse family of transcription factors. In this paper aspects of DNA recognition by an archaeal FFRP, FL11 (pot0434017), is reported. By analyzing foot-prints of FL11, two regions are identified as bound by the protein: one in the promoter of fl11 gene, overlapping onto the TATA and B boxes, and the other inside fl11 gene. An assembly of FL11, when binding the two regions simultaneously, may well prevent transcription of the gene, by preventing binding by general transcription initiators, TATA-binding protein (TBP) and transcription factor B (TFB), and by closing the transcription initiation site into the DNA loop formed between the two regions attaching to the FL11 assembly. Two sites, each best protected in each region, have a consensus, TGAAAAWTTTTCA. Relative shifting between foot-prints on the two DNA strands suggests that FL11 faces the DNA into the major groove at the two ends, i.e. at TGAAA and TTTCA, and into the minor groove at the center, AWT. Archaeal FFRPs can be classified into two types, one which binds upstream of the TATA box, at least in some cases, jointly with TBP binding TATA, and another type which covers the TATA box, and further downwards to or inside the gene-coding region. These differences may well coincide with activating or repressing functional differences of the FFRP-promoter combinations. (Communicated by Masanori OTSUKA, M.J.A.)
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Binding of the feast/famine regulatory protein (FFRP) FL11 (pot0434017) to DNA in the "promoter to coding" region of gene fl11

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