Specific initiation at an origin of replication from Schizosaccharomyces pombe.

Caddle, M S; Calos, Michèle P.

doi:10.1128/mcb.14.3.1796

Cited by 53 publications

(54 citation statements)

References 60 publications

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“…The prediction that proteins involved in initiation should bind to origins has been confirmed in prokaryotes (44,47,81,90,99) and mammalian DNA viruses (24,29,88), and recent data obtained for S. cerevisiae demonstrate that ARSs are footprinted by a multiprotein complex referred to as the origin recognition complex (4,6,42,89). Finally, electron microscopy (56,85,107) and two-dimensional gel electrophoresis studies of bacterial (83,84), yeast (10,19,57,74,127), and mammalian viral (45,91,101,105) ARSs reveal structures consistent with bidirectional replication initiating from these origins in vivo.…”

mentioning

confidence: 84%

Identification of an Origin of Bidirectional DNA Replication in the Ubiquitously Expressed Mammalian CAD Gene

Kelly

Rose

Draper

et al. 1995

Molecular and Cellular Biology

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Most DNA replication origins in eukaryotes localize to nontranscribed regions, and there are no reports of origins within constitutively expressed genes. This observation has led to the proposal that there may be an incompatibility between origin function and location within a ubiquitously expressed gene. The biochemical and functional evidence presented here demonstrates that an origin of bidirectional replication (OBR) resides within the constitutively expressed housekeeping gene CAD, which encodes the first three reactions of de novo uridine biosynthesis (carbamoyl-phosphate synthetase, aspartate carbamoyltransferase, and dihydroorotase). The OBR was localized to a 5-kb region near the center of the Syrian hamster CAD transcriptional unit. DNA replication initiates within this region in the single-copy CAD gene in Syrian baby hamster kidney cells and in the large chromosomal amplicons that were generated after selection with N-phosphonacetyl-L-aspartate, a specific inhibitor of CAD. DNA synthesis also initiates within this OBR in autonomously replicating extrachromosomal amplicons (CAD episomes) located in an N-phosphonacetyl-L-aspartate-resistant clone (5P20) of CHOK1 cells. CAD episomes consist entirely of a multimer of Syrian hamster CAD cosmid sequences (cCAD1). These data limit the functional unit of replication initiation and timing control to the 42 kb of Syrian hamster sequences contained in cCAD1. In addition, the data indicate that the origin recognition machinery is conserved across species, since the same OBR region functions in both Syrian and Chinese hamster cells. Importantly, while cCAD1 exhibits characteristics of a complete replicon, we have not detected autonomous replication directly following transfection. Since the CAD episome was generated after excision of chromosomally integrated transfected cCAD1 sequences, we propose that prior localization within a chromosome may be necessary to ''license'' some biochemically defined OBRs to render them functional.The replicon hypothesis proposes that DNA replication initiates within specific cis-acting sequences referred to as origins (8, 62) (Fig. 1). Origins interact with trans-acting factors that enable the DNA duplex to unwind into a suitable template for DNA synthesis. A direct genetic prediction of this elegant model is that the capacity for replication is transferable; replication-incompetent DNA should replicate upon introduction of an origin. Indeed, extrachromosomal replicons that follow the cellular replication program in Escherichia coli and Saccharomyces cerevisiae can be generated by inserting a small DNA fragment into replication-defective plasmids (15, 37). Mutations within sequences that confer autonomous replication (ARS) reduce initiation efficiency or prevent it from occurring (63,80,115). The prediction that proteins involved in initiation should bind to origins has been confirmed in prokaryotes (44,47,81,90,99) and mammalian DNA viruses (24,29,88), and recent data obtained for S. cerevisiae demonstrate that ARSs are footprint...

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confidence: 84%

Identification of an Origin of Bidirectional DNA Replication in the Ubiquitously Expressed Mammalian CAD Gene

Kelly

Rose

Draper

et al. 1995

Molecular and Cellular Biology

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“…Genetic studies have shown that S. pombe origins contain multiple redundant elements, which can be deleted or replaced by other AT-rich sequences without significantly affecting activity (14)(15)(16)18). Most of the chromosomal origins that have been analyzed in S. pombe fire in only a minority of cell cycles, suggesting that the number of potential origins is greater than the number actually used in any given cell cycle (11,13,17,(19)(20)(21). These properties are not easily reconciled with the classical replicon model.…”

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confidence: 88%

“…Origins of DNA replication in Schizosaccharomyces pombe differ in a number of ways from those of S. cerevisiae (10)(11)(12)(13)(14)(15)(16)(17).…”

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confidence: 99%

DNA replication origins in the Schizosaccharomyces pombe genome

Dai

Chuang

Kelly

2004

Proc. Natl. Acad. Sci. U.S.A.

121

135

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Origins of DNA replication in Schizosaccharomyces pombe lack a specific consensus sequence analogous to the Saccharomyces cerevisiae autonomously replicating sequence (ARS) consensus, raising the question of how they are recognized by the replication machinery. Because all well characterized S. pombe origins are located in intergenic regions, we analyzed the sequence properties and biological activity of such regions. The AT content of intergenes is very high (Ϸ70%), and runs of A's or T's occur with a significantly greater frequency than expected. Additionally, the two DNA strands in intergenes display compositional asymmetry that strongly correlates with the direction of transcription of flanking genes. Importantly, the sequence properties of known S. pombe origins of DNA replication are similar to those of intergenes in general. In functional studies, we assayed the in vivo origin activity of 26 intergenes in a 68-kb region of S. pombe chromosome 2. We also assayed the origin activity of sets of randomly chosen intergenes with the same length or AT content. Our data demonstrate that at least half of intergenes have potential origin activity and that the relative ability of an intergene to function as an origin is governed primarily by AT content and length. We propose a stochastic model for initiation of DNA replication in the fission yeast. In this model, the number of AT tracts in a given sequence is the major determinant of its probability of binding SpORC and serving as a replication origin. A similar model may explain some features of origins of DNA replication in metazoans. T he replicon model postulates that initiation of DNA replication takes place at specific chromosomal sequence elements (replicators) that are recognized by regulatory proteins (initiators) (1). This model was originally proposed to explain features of the replication of prokaryotic cells and viruses and has been validated in such systems by a large body of evidence (2). In eukaryotic cells, DNA replication is initiated from hundreds to thousands of different chromosomal sites in each cell cycle, raising the question of whether the replicon model provides a valid description of the initiation process. Although early genetic studies indicated that DNA replication in the budding yeast Saccharomyces cerevisiae conforms to the main features of the model, it is not yet clear that this is the case for most other eukaryotic species.Origins of DNA replication in S. cerevisiae were identified as sequence elements that conferred the property of autonomous replication on extrachromosomal plasmids (3). Genetic analysis demonstrated that such autonomously replicating sequences (ARS) were Ϸ100 bp in length and contained a common 11-bp consensus sequence essential for origin activity, as well as other sequences that augmented origin activity (3-7). The characterization of S. cerevisiae ARS elements led to the identification of the yeast origin recognition complex (ScORC), the initiator protein that recognizes the ARS-consensus sequence (8). The spe...

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“…In this organism, as in S. cerevisiae, initiation takes place at discrete sites in the chromosome and each of these sites corresponds to an ARS element (13,22,73,77). S. pombe ARS elements are more than fourfold larger than those of S. cerevisiae, and they are characterized by an abundance of asymmetric AT-rich sequence motifs (14,21,80).…”

Section: Although the Nature Of Higher Eukaryotic Replication Originsmentioning

confidence: 99%

An Origin of Replication and a Centromere Are Both Needed To Establish a Replicative Plasmid in the YeastYarrowia lipolytica

Vernis

Abbas

Chasles

et al. 1997

Molecular and Cellular Biology

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. We have used the integration properties of centromeric sequences to show that all Y. lipolytica ARS elements so far isolated are composed of both a replication origin and a centromere. The sequence and the distance between the origin and centromere do not seem to play a critical role, and many origins can function in association with one given centromere. A centromeric plasmid can therefore be used to clone putative chromosomal origins coming from several genomic locations, which confer the replicative property on the plasmid. The DNA sequences responsible for initiation in plasmids are short (several hundred base pairs) stretches which map close to or at replication initiation sites in the chromosome. Their chromosomal deletion abolishes initiation, but changing their chromosomal environment does not. Although the nature of higher eukaryotic replication originsis not yet clear (12), that of origins in the yeast Saccharomyces cerevisiae is relatively well understood. It has been possible to clone S. cerevisiae genomic sequences that confer on a plasmid the ability to replicate extrachromosomally in this yeast. These sequences are called ARS (autonomously replicating sequence) elements. Most ARS elements are active as origins in their chromosomal context, as shown by two-dimensional (2D) gel replicon mapping studies (8,44,62). ARS elements are usually smaller than 150 bp, and they contain an essential motif that matches the 11-bp ARS consensus sequence (ACS; WTT TAYRTTTW) in at least 9 of 11 positions (61, 72). The ACS is essential for initiation of replication, both on plasmids and in the chromosome (17). Also essential is domain B, located at the 3Ј end of the ACS (54,55,76). Depending on the ARS element, domain B can be subdivided into two or three subdomains with variable sequences but conserved roles (42, 66). Finally, a DNA unwinding element is frequently present in ARS elements and is important for replication of plasmids (60) and chromosomes (41). Initiation at ARS elements is under strict cell cycle control (reviewed in reference 18).In contrast to the defined origin sequences of S. cerevisiae, the degree to which specific sequences are employed as origins in the differentiated cells of higher organisms is not yet clear. Most studies employing labeling techniques suggest that initiation takes place at specific sites or in very small (a few kilobases or less) initiation zones (15,19,35). In contrast, all studies employing 2D gel replicon mapping techniques-and some studies using labeling techniques (31, 71)-suggest that initiation can take place at any of numerous locations within large initiation zones of 50 kb or more (reviewed in reference 36). Furthermore, in contrast to the discrete ARS elements of S. cerevisiae, most human DNA pieces larger than ϳ10 kb permit extrachromosomal plasmid replication (38,51). In this case, initiation does not start at a preferred locus, a result which is also observed in plasmid transformation in Xenopus eggs (46,53). Demonstrations that the choice of initiation sites ...

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Specific initiation at an origin of replication from Schizosaccharomyces pombe.

Cited by 53 publications

References 60 publications

Identification of an Origin of Bidirectional DNA Replication in the Ubiquitously Expressed Mammalian CAD Gene

Identification of an Origin of Bidirectional DNA Replication in the Ubiquitously Expressed Mammalian CAD Gene

DNA replication origins in the Schizosaccharomyces pombe genome

An Origin of Replication and a Centromere Are Both Needed To Establish a Replicative Plasmid in the YeastYarrowia lipolytica

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