PMID: 25792768Mar 1, 2006Paper

A SELEX study of the DNA-binding specificity of archaeal FFRPs: 2. FL4 (pot1613368)

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
Katsushi YokoyamaMasashi Suzuki

Abstract

The DNA-binding specificity of a transcription factor, the FFRP FL4 (pot1613368) from Pyrococcus sp. OT3, was studied. Using SELEX (systematic evolution of ligands by exponential environment) experiments, from a set of fragments, ∼150 bps, of the genomic DNA of P. OT3, seven were selected as containing binding sites. Thirteen bases identified as shared by the seven selected fragments with the least mismatches, 2.71 on average, was ATGAA AAAGTCAT. This sequence was closely related with another sequence, ATGAA[AAA/TTT]TTCAT, in the 5-3-5 arrangement, i.e. NANBNCNDNE [AAA/TTT]NENDNCNBNA , where, e.g. NA was the base complementary to NA. The average number of mismatches found between this sequence and the seven fragments was 3.14. A sequence, TTGAA ATT TACAA, resembling the sequence ATGAA[AAA/TTT]TTCAT and also another 5-3-5 sequence, TTGAA[AAA/TTT]TTCAA, was found upstream of the fl4 gene, which is potentially recognized by FL4 for auto-regulation. Thus it is likely that an ideal binding-site of FL4 is ATGAA[AAA/TTT]TTCAT or TTGAA[AAA/TTT]TTCAA. In this abstract, the sequences were highlighted in Italic at 3, and with bold characters at 5 and 5. When two sequences compared were the same at some positions, there they were underlined.

References

Oct 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·D StetlerH A Erlich
Jul 29, 1998·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Y KawarabayasiH Kikuchi
Feb 27, 2001·Acta Crystallographica. Section D, Biological Crystallography·N KudoM Suzuki
Feb 21, 2004·Proceedings of the National Academy of Sciences of the United States of America·Hideaki KoikeMasashi Suzuki

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Citations

Dec 15, 2010·Archaea : an International Microbiological Journal·Eveline Peeters, Daniel Charlier
Feb 2, 2008·Biological & Pharmaceutical Bulletin·Tsuyoshi KawashimaMasashi Suzuki

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