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J. Biol. Chem., Vol. 279, Issue 29, 30236-30243, July 16, 2004

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Binding of SeqA Protein to Hemi-methylated GATC Sequences Enhances Their Interaction and Aggregation Properties^*

Joo Seok Han, Sukhyun Kang, Sung Ho Kim, Min Ji Ko, and Deog Su Hwang

From the School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Korea

The SeqA protein regulates chromosome initiation and is involved in segregation in Escherichia coli. One SeqA protein binds to two hemi-methylated GATC sequences to form a stable SeqA-DNA complex. We found that binding induced DNA bending, which was pronounced when the two sequences were on the same face of the DNA. Two SeqA molecules bound cooperatively to each pair of hemi-methylated sites when the spacing between the sites was <30 bp. This cooperative binding was able to stabilize the binding of a wild type to a single hemi-methylated site, or mutant form of SeqA protein to hemi-methylated sites, although such binding did not occur without cooperative interaction. Two cooperatively bound SeqA molecules interacted with another SeqA bound up to 185 bp away from the two bound SeqA proteins, and this was followed by aggregation of free SeqA proteins onto the bound proteins. These results suggest that the stepwise interaction of SeqA proteins with hemi-methylated GATC sites enhances their interaction and leads to the formation of SeqA aggregates. Cooperative interaction followed by aggregation may be the driving force for formation of the SeqA foci that appear to be located behind replication forks.

Received for publication, March 8, 2004 , and in revised form, May 14, 2004.

^* This work was supported by Grant M102KK010001-02K1101-00820 from the 21C Frontier Microbial Genomics and Applications Center Program and from Systems Biology, Ministry of Science and Technology, Republic of Korea. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Supported by a BK21 Research Fellowship from the Ministry of Education, Republic of Korea.

To whom correspondence should be addressed. E-mail: dshwang{at}plaza.snu.ac.kr.

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