Sequence-Directed DNA Curvature in Replication Origins Segments

Abstract

DNA replication is an essential cellular process for the propagation of life. Prokaryotic cells are examples of organisms that display a fast and precise replication process (Robinson & Bell, 2005; Wang & Sugden, 2005). Although the consensus nucleotide sequence in the bacterial replication origin exhibits variation in number and size between different bacterial species (DoriC, a database of the oriC region in bacterial genomes; Gimenes et al., 2008a), it is capable of directing the association of specific proteins in the initiator chromosomal site and thereby the success of the replicative process in eubacteria (reviewed in Mott & Berger, 2007). However, the identification of hundreds to thousands of replication initiation sites in eukaryotes is more complex than locating clearly defined sites with stretches of consensus sequences, as observed in prokaryotes. While complexity exists, some parallels can be drawn between prokaryotic and eukaryotic systems. Less derived eukaryotes, such as the unicellular yeast Saccharomyces cerevisiae, exhibit similar replicative processes to prokaryotes. Replication initiation sites have approximately 120-200 base pairs (bp), termed ARS (Autonomously Replicating Sequences). Although there is sequence diversity among the ARS sites, these sites present a short consensus sequence of 10-11 bp that is rich in A/T residues and called the ACS (ARS Consensus Sequence) and a more divergent motif known as domain B (review in Bell & Dutta, 2002). Although not all of ARS sites are efficiently used, it has been shown that they can be initiate replication if necessary (Sharma et al., 2001). However, S. cerevisiae and closely related species appear to be the only eukaryotic organisms that present consensus elements in their replication initiation sites. Schizosaccharomyces pombe has initiation replication sequences from 600 to 800 bp, which display numerous A/Trich regions, but these replication initiation sites in S. pombe have a low level of similarity to the ARS of S. cerevisiae, and we have not been able to identify a consensus sequence within this region (Dubey et al., 1996; Zhu et al., 1994). The presence of conserved sequences in S. cerevisiae was important for the isolation of the origin recognition complex (ORC; Bell & Stillman, 1992). The existence of this complex revealed that eukaryotes depend on the binding of specific proteins to identify and activate specific genomic regions to initiate replication. The ORC complex, which is composed of six closely related proteins, Orc1-6, is conserved through evolution and has been identified in all analyzed eukaryotic cells (reviewed in Bell, 2002). Before replication begins, numerous other