A SELEX study of the DNA-binding specificity of archaeal FFRPs: FL10 (pot0377090, LrpA)

Abstract

Using SELEX (systematic evolution of ligands by exponential environment) experiments, from a set of DNA fragments, ∼150 bps, most of them originated in the genome of an archaeon, Pyrococcus furiosus, five fragments were selected as containing binding-sites of a transcription factor, FL10 (pot0377090, LrpA). The nucleotide sequences of these fragments were analyzed in the light of our previous finding that FFRPs in general recognize DNA sequences in the 5-3-5 arrangement: N AN BN CN DN E[TTT/AAA]N EN DN CN BN A, where, e.g. N A is the base complementary to N A. One of the seven 5-3-5 sequences, shared by the five fragments with the smallest numbers of mismatches, was TTCGA[TTT/AAA]TCGAA. In three of the five fragments selected, signal sequences were found immediately upstream of TATA boxes, suggesting possible activation of transcription by FL10 by recruiting the TATA-binding protein (TBP). In another fragment the signal sequence was positioned upstream of a TATA box, and at the same time downstream of another TATA box, thereby repressing transcription of another gene coded in the other direction. Some of the genes coded in these fragments are involved in active oxygen detoxification, suggesting the nature of regulation by FL10.