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Nucleic Acids Research Advance Access published online on May 25, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp378
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Gene Regulation, Chromatin and Epigenetics

The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB

Katsushi Yokoyama1,2, Hideki Nogami1,2, Mamiko Kabasawa1,2, Sonomi Ebihara1,2, Ai Shimowasa1,2, Keiko Hashimoto1,2, Tsuyoshi Kawashima1,2, Sanae A. Ishijima1,2 and Masashi Suzuki1,*

1National Institute of Advanced Industrial Science and Technology, Tsukuba Center 6-10, Higashi 1-1-1, Tsukuba 305-8566 and 2Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan

*To whom correspondence should be addressed. Tel: +81 29 861 6583; Fax: +81 29 861 6041; Email: masashi.suzuki{at}aist.go.jp

Received February 2, 2009. Revised April 26, 2009. Accepted April 27, 2009.

The DNA-binding mode of archaeal feast/famine-regulatory proteins (FFRPs), i.e. paralogs of the Esherichia coli leucine-responsive regulatory protein (Lrp), was studied. Using the method of systematic evolution of ligands by exponential enrichment (SELEX), optimal DNA duplexes for interacting with TvFL3, FL10, FL11 and Ss-LrpB were identified as TACGA[AAT/ATT]TCGTA, GTTCGA[AAT/ATT]TCGAAC, CCGAAA[AAT/ATT]TTTCGG and TTGCAA[AAT/ATT]TTGCAA, respectively, all fitting into the form abcdeWWWedcba. Here W is A or T, and e.g. a and a are bases complementary to each other. Apparent equilibrium binding constants of the FFRPs and various DNA duplexes were determined, thereby confirming the DNA-binding specificities of the FFRPs. It is likely that these FFRPs recognize DNA in essentially the same way, since their DNA-binding specificities were all explained by the same pattern of relationship between amino-acid positions and base positions to form chemical interactions. As predicted from this relationship, when Gly36 of TvFL3 was replaced by Thr, the b base in the optimal DNA duplex changed from A to T, and, when Thr36 of FL10 was replaced by Ser, the b base changed from T to G/A. DNA-binding characteristics of other archaeal FFRPs, Ptr1, Ptr2, Ss-Lrp and LysM, are also consistent with the relationship.

Present address: Tsuyoshi Kawashima, Yokohama College of Pharmacy, Laboratory of Molecular Biology, Matano 601, Totsuka-ku, Yokohama 245-0066, Japan.


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