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Molecular and Cellular Biology, August 2008, p. 5071-5081, Vol. 28, No. 16
0270-7306/08/$08.00+0     doi:10.1128/MCB.00206-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Analysis of Chromosome III Replicators Reveals an Unusual Structure for the ARS318 Silencer Origin and a Conserved WTW Sequence within the Origin Recognition Complex Binding Site{triangledown} ,{dagger}

FuJung Chang,1 James F. Theis,2 Jeremy Miller,3 Conrad A. Nieduszynski,4 Carol S. Newlon,2 and Michael Weinreich1*

Laboratories of Chromosome Replication,1 Tumor Metastasis and Angiogenesis, Van Andel Research Institute, Grand Rapids, Michigan 49503,3 Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103,2 Institute of Genetics, University of Nottingham, Nottingham, United Kingdom4

Received 8 February 2008/ Returned for modification 28 March 2008/ Accepted 2 June 2008

Saccharomyces cerevisiae chromosome III encodes 11 autonomously replicating sequence (ARS) elements that function as chromosomal replicators. The essential 11-bp ARS consensus sequence (ACS) that binds the origin recognition complex (ORC) has been experimentally defined for most of these replicators but not for ARS318 (HMR-I), which is one of the HMR silencers. In this study, we performed a comprehensive linker scan analysis of ARS318. Unexpectedly, this replicator depends on a 9/11-bp match to the ACS that positions the ORC binding site only 6 bp away from an Abf1p binding site. Although a largely inactive replicator on the chromosome, ARS318 becomes active if the nearby HMR-E silencer is deleted. We also performed a multiple sequence alignment of confirmed replicators on chromosomes III, VI, and VII. This analysis revealed a highly conserved WTW motif 17 to 19 bp from the ACS that is functionally important and is apparent in the 228 phylogenetically conserved ARS elements among the six sensu stricto Saccharomyces species.

* Corresponding author. Mailing address: Laboratory of Chromosome Replication, Van Andel Research Institute, Grand Rapids, MI 49503. Phone: (616) 234-5306. Fax: (616) 234-5307. E-mail: michael.weinreich{at}vai.org

{triangledown} Published ahead of print on 23 June 2008.

{dagger} Supplemental material for this article may be found at http://mcb.asm.org/.

Molecular and Cellular Biology, August 2008, p. 5071-5081, Vol. 28, No. 16
0270-7306/08/$08.00+0     doi:10.1128/MCB.00206-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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