Hemicatenanes form upon inhibition of DNA replication

Lucas, Isabelle; Hyrien, Olivier

doi:10.1093/nar/28.10.2187

Cited by 43 publications

(39 citation statements)

References 36 publications

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“…The maturation of this replication intermediate can lead to the formation of catenanes with single-strand breaks, which then can be processed by a type IA enzyme to generate hemicatenanes. Similar structures of late replication, presegregation sister chromatids with hemicatenane linkage, have been proposed also to exist in the archaeal chromosomes (41) and in the products from in vitro DNA replication of plasmid DNA using Xenopus egg extracts (42). Finally, as described in the previous section, the convergent branch migration of the double Holliday junction leads to the formation of a hemicatenane before the eventual dissolution of the conjoined DNA helices (17).…”

Section: Discussionsupporting

confidence: 62%

Synthesis and dissolution of hemicatenanes by type IA DNA topoisomerases

Lee

Siaw

Willcox

et al. 2013

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

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Type IA DNA topoisomerases work with a unique mechanism of strand passage through an enzyme-bridged, ssDNA gate, thus enabling them to carry out diverse reactions in processing structures important for replication, recombination, and repair. Here we report a unique reaction mediated by an archaeal type IA topoisomerase, the synthesis and dissolution of hemicatenanes. We cloned, purified, and characterized an unusual type IA enzyme from a hyperthermophilic archaeum, Nanoarchaeum equitans, which is split into two pieces. The recombinant heterodimeric enzyme has the expected activities in its preference of relaxing negatively supercoiled DNA. Its amino acid sequence and cleavage site sequence analysis suggest that it is topoisomerase III, and therefore we named it "NeqTop3." At high enzyme concentrations, NeqTop3 can generate high-molecular-weight DNA networks. Biochemical and electron microscopic data indicate that the DNA networks are connected through hemicatenane linkages. The hemicatenane formation likely is mediated by the singlestrand passage through denatured bubbles in the substrate DNA under high temperature. NeqTop3 at lower concentrations can reverse hemicatenanes. A complex of human topoisomerase 3α, Bloom helicase, and RecQ-mediated genome instability protein 1 and 2 can partially disentangle the hemicatenane network. Both the formation and dissolution of hemicatenanes by type IA topoisomerases demonstrate that these enzymes have an important role in regulating intermediates from replication, recombination, and repair.DNA repair | DNA topology | genetic recombination | double Holliday junction T ype IA DNA topoisomerases are ubiquitous and highly conserved enzymes that have essential functions for life. They can efficiently alleviate DNA topological stress arising from unwinding and rewinding DNA during the processes of replication, transcription, recombination, repair, and chromatin remodeling (1-4). These enzymes accomplish the feat of topological transformation via strand passage through a reversible, enzymebridged, single-strand break. The transient break is generated by a reversible transesterification reaction: The active-site tyrosine serves as a nucleophile to create phosphodiester linkage to the nascent 5′-phosphoryl end; the 3′ end is bound noncovalently to the enzyme, and its reversal can reseal the break. This unique mechanism of strand passage through a tethered DNA gate allows type IA enzymes to carry out reactions other than solely serving as a swivel to relieve topological stress. The coordinated action of type IA enzymes with DNA helicases adds further versatility as a tool in regulating the production and resolution of intermediates generated during recombination and repair (5).Type IA enzymes are present in all three domains of life, and they frequently exist in multiple forms in individual organisms. In eubacteria, there are two closely related isozymes of topoisomerase I (Top1) and III (Top3). Archaea have Top1 and/or Top3, and the hyperthermophiles have an additional type IA enzy...

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Section: Discussionsupporting

confidence: 62%

Synthesis and dissolution of hemicatenanes by type IA DNA topoisomerases

Lee

Siaw

Willcox

et al. 2013

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

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“…The abnormal accumulation of X molecules observed in MMS-treated sgs1 cells, together with the observation that a population of X structure is indeed able to migrate with the same kinetics as in MMS-treated wild-type cells, raises the question as to whether the X structures that keep accumulating at late time points represent SCJs or, rather, different intermediates. It should be noted that at least two types of molecules migrate like an X spike on 2D gels: hemicatenanes and HJs (Collins and Newlon 1994;Lockshon et al 1995;Schwacha and Kleckner 1995;Zou and Rothstein 1997;Lucas and Hyrien 2000;Lopes et al 2003;Wellinger et al 2003). Given that SCJs have been suggested to represent hemicatenanes (Lopes et al 2003), we tested whether the X molecules abnormally accumulating in MMS-treated sgs1 cells were instead recombination-dependent structures.…”

Section: Resultsmentioning

confidence: 99%

“…In general, four-branched molecules migrate on 2D gels in the so-called X spike (Brewer and Fangman 1987). X-shaped structures on 2D gels have been related to HJs (Collins and Newlon 1994;Lockshon et al 1995;Schwacha and Kleckner 1995;Zou and Rothstein 1997) or to hemicatenanes (Lucas and Hyrien 2000;Lopes et al 2003;Wellinger et al 2003). The X-shaped SCJ structure Figure 7.…”

Section: Discussionmentioning

confidence: 99%

Rad51-dependent DNA structures accumulate at damaged replication forks in sgs1 mutants defective in the yeast ortholog of BLM RecQ helicase

Liberi¹,

Maffioletti²,

Lucca³

et al. 2005

Genes Dev.

294

358

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S-phase cells overcome chromosome lesions through replication-coupled recombination processes that seem to be assisted by recombination-dependent DNA structures and/or replication-related sister chromatid junctions. RecQ helicases, including yeast Sgs1 and human BLM, have been implicated in both replication and recombination and protect genome integrity by preventing unscheduled mitotic recombination events. We have studied the RecQ helicase-mediated mechanisms controlling genome stability by analyzing replication forks encountering a damaged template in sgs1 cells. We show that, in sgs1 mutants, recombination-dependent cruciform structures accumulate at damaged forks. Their accumulation requires Rad51 protein, is counteracted by Srs2 DNA helicase, and does not prevent fork movement. Sgs1, but not Srs2, promotes resolution of these recombination intermediates. A functional Rad53 checkpoint kinase that is known to protect the integrity of the sister chromatid junctions is required for the accumulation of recombination intermediates in sgs1 mutants. Finally, top3 and top3 sgs1 mutants accumulate the same structures as sgs1 cells. We suggest that, in sgs1 cells, the unscheduled accumulation of Rad51-dependent cruciform structures at damaged forks result from defective maturation of recombination-dependent intermediates that originate from the replication-related sister chromatid junctions. Our findings might contribute to explaining some of the recombination defects of BLM cells.[Keywords: Sgs1; RecQ helicases; DNA replication; recombination; checkpoint; Srs2] Supplemental material is available at http://www.genesdev.org.

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“…Although factors such as hemicatenes of the nascent sister strands (24,28,42) and full intercatenation of sister chromatids may be involved in promoting sister chromatid…”

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confidence: 99%

Mrc1 Is Required for Sister Chromatid Cohesion To Aid in Recombination Repair of Spontaneous Damage

Boone

Klein

2004

Molecular and Cellular Biology

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The SRS2 gene of Saccharomyces cerevisiae encoding a 335 DNA helicase is part of the postreplication repair pathway and functions to ensure proper repair of DNA damage arising during DNA replication through pathways that do not involve homologous recombination. Through a synthetic gene array analysis, genes that are essential when Srs2 is absent have been identified. Among these are MRC1, TOF1, and CSM3, which mediate the intra-S checkpoint response. srs2⌬ mrc1⌬ synthetic lethality is due to inappropriate recombination, as the lethality can be suppressed by genetic elimination of homologous recombination. srs2⌬ mrc1⌬ synthetic lethality is dependent on the role of Mrc1 in DNA replication but independent of the role of Mrc1 in a DNA damage checkpoint response. mrc1⌬, tof1⌬ and csm3⌬ mutants have sister chromatid cohesion defects, implicating sister chromatid cohesion established at the replication fork as an important factor in promoting repair of stalled replication forks through gap repair.The SRS2 gene of Saccharomyces cerevisiae encodes a DNA helicase with a 3Ј35Ј polarity (36). Genetic studies have placed SRS2 in the postreplication DNA repair pathway (1, 25, 37). SRS2 is not an essential gene but is required for complete meiotic viability (1, 33). Mitotically, srs2⌬ mutants have increased spontaneous gene conversion rates but are only modestly sensitive to DNA-damaging agents (1, 25, 37). These phenotypes suggest that Srs2 is involved in regulating a cellular response to spontaneous DNA damage. Indeed, recent in vitro studies have confirmed a proposed negative regulation of recombination by Srs2 (23, 53). Srs2 can destabilize Rad51 nucleoprotein filaments, thereby destroying homologous recombination strand exchange intermediates and allowing other repair pathways such as translesion synthesis or template switching to repair DNA gaps.Although the Srs2 protein is not essential for wild-type yeast cells, in certain mutant strains the SRS2 gene is very important or essential. The synthetic lethalities known for the srs2⌬ mutant include sgs1⌬ (9, 20), rad54⌬ (1, 37), rad50⌬, mre11⌬, xrs2⌬ (1, 20, 37), top3⌬ (6, 20), rad27⌬ (5), and pol32⌬ (13). In addition, there are haploid srs2⌬ synthetic sickness interactions which are enhanced to lethality in the diploid state. The most notable of these is the interaction with the rdh54⌬ mutation (21, 38). Most of these lethalities are due to inappropriate or aberrant homologous recombination, as they can be suppressed by mutation of genes that encode products required for the early steps of homologous recombination. The exception to the list above is the rad27⌬ srs2⌬ synthetic lethality, but as the rad27⌬ single mutant requires an intact homologous recombination pathway for survival, suppression cannot be tested (5).SRS2 expression begins in late G 1 and peaks during S phase (12). Expression can be induced by DNA-damaging agents but only in the G 2 phase of the cell cycle (12). These observations, along with genetic studies of the srs2⌬ mutant and the biochemical studies of...

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Hemicatenanes form upon inhibition of DNA replication

Cited by 43 publications

References 36 publications

Synthesis and dissolution of hemicatenanes by type IA DNA topoisomerases

Synthesis and dissolution of hemicatenanes by type IA DNA topoisomerases

Rad51-dependent DNA structures accumulate at damaged replication forks in sgs1 mutants defective in the yeast ortholog of BLM RecQ helicase

Mrc1 Is Required for Sister Chromatid Cohesion To Aid in Recombination Repair of Spontaneous Damage

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