Replication Origins and Timing of Temporal Replication in Budding Yeast: How to Solve the Conundrum?

2013 ◽  
pp. 15-44
Keyword(s):  
Budding Yeast ◽  
Replication Origins

scholarly journals Activation of Silent Replication Origins at Autonomously Replicating Sequence Elements near the HML Locus in Budding Yeast

1999 ◽  
Vol 19 (9) ◽  
pp. 6098-6109 ◽  
Author(s):  
Marija Vujcic ◽  
Charles A. Miller ◽  
David Kowalski
Keyword(s):  
Replication Origin ◽  
Budding Yeast ◽  
Transcriptional Silencing ◽  
Growth Conditions ◽  
Replication Origins ◽  
Additional Time ◽  
Autonomously Replicating Sequence ◽  
Ars Elements ◽  
Active Replication ◽  
Chromosome Iii

ABSTRACT In the budding yeast, Saccharomyces cerevisiae, replicators can function outside the chromosome as autonomously replicating sequence (ARS) elements; however, within chromosome III, certain ARSs near the transcriptionally silent HML locus show no replication origin activity. Two of these ARSs comprise the transcriptional silencers E (ARS301) and I (ARS302). Another, ARS303, resides betweenHML and the CHA1 gene, and its function is not known. Here we further localized and characterized ARS303and in the process discovered a new ARS, ARS320. BothARS303 and ARS320 are competent as chromosomal replication origins since origin activity was seen when they were inserted at a different position in chromosome III. However, at their native locations, where the two ARSs are in a cluster withARS302, the I silencer, no replication origin activity was detected regardless of yeast mating type, special growth conditions that induce the transcriptionally repressed CHA1 gene,trans-acting mutations that abrogate transcriptional silencing at HML (sir3, orc5), orcis-acting mutations that delete the E and I silencers containing ARS elements. These results suggest that, for theHML ARS cluster (ARS303, ARS320, and ARS302), inactivity of origins is independent of local transcriptional silencing, even though origins and silencers share keycis- and trans-acting components. Surprisingly, deletion of active replication origins located 25 kb (ORI305) and 59 kb (ORI306) away led to detection of replication origin function at theHML ARS cluster, as well as at ARS301, the E silencer. Thus, replication origin silencing at HML ARSs is mediated by active replication origins residing at long distances fromHML in the chromosome. The distal active origins are known to fire early in S phase, and we propose that their inactivation delays replication fork arrival at HML, providing additional time for HML ARSs to fire as origins.

scholarly journals Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks

EMBO Reports ◽  
2019 ◽  
Vol 20 (7) ◽  
Author(s):  
Shin‐ichiro Hiraga ◽  
Chandre Monerawela ◽  
Yuki Katou ◽  
Sophie Shaw ◽  
Kate RM Clark ◽  
...  
Keyword(s):  
Budding Yeast ◽  
Replication Forks ◽  
Replication Origins

scholarly journals Relicensing of Transcriptionally Inactivated Replication Origins in Budding Yeast

2010 ◽  
Vol 285 (51) ◽  
pp. 40004-40011 ◽  
Author(s):  
Marko Lõoke ◽  
Jüri Reimand ◽  
Tiina Sedman ◽  
Juhan Sedman ◽  
Lari Järvinen ◽  
...  
Keyword(s):  
Budding Yeast ◽  
Replication Origins

scholarly journals Replication Origins and Timing of Temporal Replication in Budding Yeast: How to Solve the Conundrum?

2010 ◽  
Vol 11 (3) ◽  
pp. 199-211 ◽  
Author(s):  
Matteo Barberis ◽  
Thomas W. Spiesser ◽  
Edda Klipp
Keyword(s):  
Budding Yeast ◽  
Replication Origins

Stepwise assembly of initiation complexes at budding yeast replication origins during the cell cycle

1995 ◽  
Vol 1995 (Supplement 19) ◽  
pp. 67-72 ◽  
Author(s):  
J. F. X. Diffley ◽  
J. H. Cocker ◽  
S. J. Dowell ◽  
J. Harwood ◽  
A. Rowley
Keyword(s):  
Cell Cycle ◽  
Budding Yeast ◽  
Replication Origins ◽  
Stepwise Assembly

scholarly journals CDK promotes interactions of Sld3 and Drc1 with Cut5 for initiation of DNA replication in fission yeast

2011 ◽  
Vol 22 (14) ◽  
pp. 2620-2633 ◽  
Author(s):  
Masayoshi Fukuura ◽  
Koji Nagao ◽  
Chikashi Obuse ◽  
Tatsuro S. Takahashi ◽  
Takuro Nakagawa ◽  
...  
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Ternary Complex ◽  
Budding Yeast ◽  
S Phase ◽  
Replication Proteins ◽  
Cyclin Dependent Kinase ◽  
Replication Origins ◽  
Initiation Of Dna Replication

Cyclin-dependent kinase (CDK) plays essential roles in the initiation of DNA replication in eukaryotes. Although interactions of CDK-phosphorylated Sld2/Drc1 and Sld3 with Dpb11 have been shown to be essential in budding yeast, it is not known whether the mechanism is conserved. In this study, we investigated how CDK promotes the assembly of replication proteins onto replication origins in fission yeast. Phosphorylation of Sld3 was found to be dependent on CDK in S phase. Alanine substitutions at CDK sites decreased the interaction with Cut5/Dpb11 at the N-terminal BRCT motifs and decreased the loading of Cut5 onto replication origins. This defect was suppressed by overexpression of drc1+. Phosphorylation of a conserved CDK site, Thr-111, in Drc1 was critical for interaction with Cut5 at the C-terminal BRCT motifs and was required for loading of Cut5. In a yeast three-hybrid assay, Sld3, Cut5, and Drc1 were found to form a ternary complex dependent on the CDK sites of Sld3 and Drc1, and Drc1–Cut5 binding enhanced the Sld3–Cut5 interaction. These results show that the mechanism of CDK-dependent loading of Cut5 is conserved in fission yeast in a manner similar to that elucidated in budding yeast.

scholarly journals DNA Replication Forks Pause at Silent Origins near the HML Locus in Budding Yeast

2001 ◽  
Vol 21 (15) ◽  
pp. 4938-4948 ◽  
Author(s):  
Yangzhou Wang ◽  
Marija Vujcic ◽  
David Kowalski
Keyword(s):  
Dna Replication ◽  
Mating Type ◽  
Replication Fork ◽  
Budding Yeast ◽  
Transcriptional Silencing ◽  
Replication Initiation ◽  
Replication Origins ◽  
Autonomously Replicating Sequence ◽  
Type Locus ◽  
Pause Site

ABSTRACT Chromosomal replicators in budding yeast contain an autonomously replicating sequence (ARS) that functions in a plasmid, but certain ARSs are silent as replication origins in their natural chromosomal context. In chromosome III, the HML ARS cluster (ARS302-ARS303-ARS320) and ARS301 flank the transcriptionally silent mating-type locus HML, and all of these ARSs are silent as replication origins. ARS301 andARS302 function in transcriptional silencing mediated by the origin recognition complex (ORC) and a heterochromatin structure, while the functions of ARS303 and ARS320 are not known. In this work, we discovered replication fork pause sites at the HML ARS cluster and ARS301 by analyzing DNA replication intermediates from the chromosome via two-dimensional gel electrophoresis. The replication fork pause at the HML ARS cluster was independent of cis- andtrans-acting mutations that abrogate transcriptional silencing at HML. Deletion of the HML ARS cluster led to loss of the pause site. Insertion of a single, heterologous ARS (ARS305) in place of the HMLARS cluster reconstituted the pause site, as did multiple copies of DNA elements (A and B1) that bind ORC. The orc2-1 mutation, known to alter replication timing at origins, did not detectably affect the pause but activated the silent origin at the HML ARS cluster in a minority of cells. Delaying the time of fork arrival atHML led to the elimination of the pause sites at theHML ARS cluster and at the copy of ARS305inserted in place of the cluster. Loss of the pause sites was accompanied by activation of the silent origins in the majority of cells. Thus, replication fork movement near HML pauses at a silent origin which is competent for replication initiation but kept silent through Orc2p, a component of the replication initiator. Possible functions for replication fork pause sites in checkpoints, S-phase regulation, mating-type switching, and transcriptionally silent heterochromatin are discussed.

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