Comparison of modes of DNA-binding and bending by archaeal transcription factors, Phr, TrmB, GvpE, GvpD, NrpR, Lrs14 and MDR1
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In earlier publications, I have discussed that transcription of the majority of archaeal genes could be regulated by a single type of factors, i.e. homologues of E. coli Lrp and AsnC, now referred to as feast/famine regulatory proteins (FFRPs). Also I have noted that the 13 bp nucleotide sequences recognized by dimers of various FFRPs are in the same arrangement, here referred to as 5-3-5. In the present study it is shown that the above descriptions also apply to the archaeal transcription factors that have been experimentally identified by other groups since then. In promoters regulated by transcription factors, Phr and TrmB, 13 bp elements in the 5-3-5 arrangement are identified. The amino acid sequences of the two proteins resemble those of known FFRPs at positions important for forming 3D structures of a standard (i.e. full length) FFRP. The same is observed with the amino acid sequences of a transcription factor, GvpE, and its modulator GvpD at its N-terminus. Regulation of promoters by Gvps E and D is explained well by assuming that two types of 13 bp elements in the 5-3-5 arrangement are recognized, respectively, by homo-dimers of GvpE and hetero-dimers of Gvps E and D. Another transcription factor, MDR1, like Lrs14, has a DBD of the FFRP type, but lacks the standard assembly domain: an N-demi FFRP. Including another transcription factor, NrpR, characteristics common with known FFRPs are found for all the transcription factors analyzed, consistently with my earlier arguments. (Communicated by Masanori OTSUKA, M.J.A.)