Dif1 Controls Subcellular Localization of Ribonucleotide Reductase by Mediating Nuclear Import of the R2 Subunit

Wu, Xianghua; Huang, Mingxia

doi:10.1128/mcb.01388-08

Cited by 64 publications

(87 citation statements)

References 56 publications

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“…Regulation of RNR activity by Dun1 occurs by at least three separate mechanisms (50)(51)(52). One of these mechanisms involves Sml1, a small protein that binds to and inhibits RNR (50).…”

Section: Resultsmentioning

confidence: 99%

Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity

Mertz

Sharma²,

Chabes

et al. 2015

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

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Defects in DNA polymerases δ (Polδ) and e (Pole) cause hereditary colorectal cancer and have been implicated in the etiology of some sporadic colorectal and endometrial tumors. We previously reported that the yeast pol3-R696W allele mimicking a human cancer-associated variant, POLD1-R689W, causes a catastrophic increase in spontaneous mutagenesis. Here, we describe the mechanism of this extraordinary mutator effect. We found that the mutation rate increased synergistically when the R696W mutation was combined with defects in Polδ proofreading or mismatch repair, indicating that pathways correcting DNA replication errors are not compromised in pol3-R696W mutants. DNA synthesis by purified Polδ-R696W was error-prone, but not to the extent that could account for the unprecedented mutator phenotype of pol3-R696W strains. In a search for cellular factors that augment the mutagenic potential of Polδ-R696W, we discovered that pol3-R696W causes S-phase checkpoint-dependent elevation of dNTP pools. Abrogating this elevation by strategic mutations in dNTP metabolism genes eliminated the mutator effect of pol3-R696W, whereas restoration of high intracellular dNTP levels restored the mutator phenotype. Further, the use of dNTP concentrations present in pol3-R696W cells for in vitro DNA synthesis greatly decreased the fidelity of Polδ-R696W and produced a mutation spectrum strikingly similar to the spectrum observed in vivo. The results support a model in which (i) faulty synthesis by Polδ-R696W leads to a checkpoint-dependent increase in dNTP levels and (ii) this increase mediates the hypermutator effect of Polδ-R696W by facilitating the extension of mismatched primer termini it creates and by promoting further errors that continue to fuel the mutagenic pathway.DNA polymerase δ | colon cancer | dNTP pools | mutagenesis | DNA replication fidelity W hen functioning properly, DNA replication is phenomenally accurate, making ∼10 −10 mutations per base pair during each replication cycle (1). In respect to human biology, it means that, on average, less than one mutation occurs each time the human genome is replicated. This amazing exactitude is contingent upon the serial action of DNA polymerase selectivity, exonucleolytic proofreading, and DNA mismatch repair (MMR). MMR defects increase spontaneous mutagenesis in numerous model systems (2) and give rise to cancer in mice (3). In humans, inherited mutations in MMR genes predispose to colorectal cancer (CRC) in Lynch syndrome (4, 5). Additionally, MMR genes are inactivated via hypermethylation in ∼15% of sporadic CRC, endometrial cancer (EC), and gastric cancer (6).Like defects in MMR, mutations that decrease the base selectivity or proofreading activity of replicative DNA polymerases elevate spontaneous mutagenesis in eukaryotic cells (7-14) and cancer incidence in mice (15)(16)(17)(18). Germline mutations affecting the exonuclease domains of DNA polymerases δ (Polδ) and e (Pole) cause hereditary CRC (19), and somatic changes in the exonuclease domain of Pole were found in sporad...

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“…Regulation of RNR activity by Dun1 occurs by at least three separate mechanisms (50)(51)(52). One of these mechanisms involves Sml1, a small protein that binds to and inhibits RNR (50).…”

Section: Resultsmentioning

confidence: 99%

Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity

Mertz

Sharma²,

Chabes

et al. 2015

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

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“…S. cerevisiae Dif1 or Schizosaccharomyces pombe Spd1 retain Rnr2 in the nucleus, preventing its interaction with cytoplasmic Rnr1. Like Crt1 or Sml1, deletion of spd1 or dif1 increases RNR activity and suppresses the lethality of checkpoint mutants (Liu et al 2003;Lee et al 2008;Wu and Huang 2008). Even though no clear orthologs for yeast RNR inhibitory proteins have been found in mammals, evidence suggests that the connection between ATR and RNR is conserved to some extent.…”

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confidence: 99%

“…S. cerevisiae Dif1 or Schizosaccharomyces pombe Spd1 retain Rnr2 in the nucleus, preventing its interaction with cytoplasmic Rnr1. Like Crt1 or Sml1, deletion of spd1 or dif1 increases RNR activity and suppresses the lethality of checkpoint mutants (Liu et al 2003;Lee et al 2008;Wu and Huang 2008 (Bester et al 2011;Danilova et al 2014). Furthermore, CHK1 activation by topoisomerase inhibitors induces the expression of RRM2 through E2F-dependent transcription (Zhang et al 2009).…”

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confidence: 99%

IncreasedRrm2gene dosage reduces fragile site breakage and prolongs survival of ATR mutant mice

et al. 2015

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In Saccharomyces cerevisiae, absence of the checkpoint kinase Mec1 (ATR) is viable upon mutations that increase the activity of the ribonucleotide reductase (RNR) complex. Whether this pathway is conserved in mammals remains unknown. Here we show that cells from mice carrying extra alleles of the RNR regulatory subunit RRM2 (Rrm2 TG ) present supraphysiological RNR activity and reduced chromosomal breakage at fragile sites. Moreover, increased Rrm2 gene dosage significantly extends the life span of ATR mutant mice. Our study reveals the first genetic condition in mammals that reduces fragile site expression and alleviates the severity of a progeroid disease by increasing RNR activity.Supplemental material is available for this article.Received December 5, 2014; revised version accepted March 2, 2015.Replication stress (RS) has emerged as a source of genome instability in human diseases, including cancer and premature aging (Lecona and Fernandez-Capetillo 2014;Zeman and Cimprich 2014). In brief, RS is defined by the accumulation of abnormal amounts of ssDNA at stalled replication forks that, due to its recombinogenic nature, can initiate genomic rearrangements. In mammals, RS is sensed and suppressed by a signaling cascade initiated by the ATR kinase, which, together with its target kinase, CHK1, suppresses RS through the phosphorylation of multiple targets (Cimprich and Cortez 2008;Lopez-Contreras and Fernandez-Capetillo 2010). ATR and CHK1 are essential for embryonic development in mice (Brown and Baltimore 2000;de Klein et al. 2000;Liu et al. 2000), which is due to the role of the RS response (RSR) in preventing replication-born chromosome breakage. Whether the RSR protects all forks or a subset of them during replication is unclear. On the one hand, proteomic studies of the human replisome in unchallenged conditions have failed to detect ATR or CHK1 in the vicinity of replication forks Sirbu et al. 2013), suggesting that their activity might be particularly necessary for only a subset of forks, such as damaged ones. Accordingly, chromosomal breaks that arise upon ATR inactivation locate preferentially at specific loci named common fragile sites (CFSs) (Casper et al. 2002) and early replicating fragile sites (ERFSs) (Barlow et al. 2013). Regardless of whether ATR works at all forks or only some of them, how it suppresses RS and why it is essential are still not fully understood.Ribonucleotide reductase (RNR) is a tetrameric enzyme composed of two catalytic (RRM1, Rnr1 in yeast) and two regulatory (RRM2, Rnr2 in yeast) subunits (Jordan and Reichard 1998). It reduces NDPs into dNDPs, which is a rate-limiting step for the production of dNTPs. In yeast, the lethality of mec1Δ strains can be bypassed by mutations that increase RNR activity. The first evidence of a connection between ATR and RNR came from the discovery of Crt1 (a transcriptional repressor of RNR subunits) as a suppressor of Mec1 lethality in Saccharomyces cerevisiae (Huang et al. 1998). Furthermore, overproduction of Rnr1 was shown to be sufficient ...

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“…Dun1 targets three proteins that repress expression, assembly, or activity of RNR: constitutive RNR transcription (Crt)1 represses transcription of RNR2, RNR3, and RNR4 (28,30,31); damage-regulated import facilitator (Dif)1 prevents RNR assembly by mediating import of Rnr2-Rnr4 into the nucleus, where it is sequestered from Rnr1 (32-34); and suppressor of Mec1 lethality (Sml)1 binds and inhibits RNR activity (35,36). Phosphorylation of Sml1 and Dif1 by Dun1 results in their proteolysis, releasing the negative regulation of RNR catalysis and allowing cytoplasmic localization of Rnr2 and Rnr4, followed by RNR holoenzyme assembly (32)(33)(34). At the same time, phosphorylation of Crt1 increases transcription of RNR2, RNR3, and RNR4.…”

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confidence: 99%

dNTP pool levels modulate mutator phenotypes of error-prone DNA polymerase ε variants

Williams

Marjavaara

Knowels

et al. 2015

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

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Mutator phenotypes create genetic diversity that fuels tumor evolution. DNA polymerase (Pol) e mediates leading strand DNA replication. Proofreading defects in this enzyme drive a number of human malignancies. Here, using budding yeast, we show that mutator variants of Pol e depend on damage uninducible (Dun)1, an S-phase checkpoint kinase that maintains dNTP levels during a normal cell cycle and up-regulates dNTP synthesis upon checkpoint activation. Deletion of DUN1 (dun1Δ) suppresses the mutator phenotype of pol2-4 (encoding Pol e proofreading deficiency) and is synthetically lethal with pol2-M644G (encoding altered Pol e base selectivity). Although pol2-4 cells cycle normally, pol2-M644G cells progress slowly through S-phase. The pol2-M644G cells tolerate deletions of mediator of the replication checkpoint (MRC) 1 (mrc1Δ) and radiation sensitive (Rad) 9 (rad9Δ), which encode mediators of checkpoint responses to replication stress and DNA damage, respectively. The pol2-M644G mutator phenotype is partially suppressed by mrc1Δ but not rad9Δ; neither deletion suppresses the pol2-4 mutator phenotype. Thus, checkpoint activation augments the Dun1 effect on replication fidelity but is not required for it. Deletions of genes encoding key Dun1 targets that negatively regulate dNTP synthesis, suppress the dun1Δ pol2-M644G synthetic lethality and restore the mutator phenotype of pol2-4 in dun1Δ cells. DUN1 pol2-M644G cells have constitutively high dNTP levels, consistent with checkpoint activation. In contrast, pol2-4 and POL2 cells have similar dNTP levels, which decline in the absence of Dun1 and rise in the absence of the negative regulators of dNTP synthesis. Thus, dNTP pool levels correlate with Pol e mutator severity, suggesting that treatments targeting dNTP pools could modulate mutator phenotypes for therapy.DNA replication and repair | polymerase fidelity | cancer | lethal mutagenesis

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Dif1 Controls Subcellular Localization of Ribonucleotide Reductase by Mediating Nuclear Import of the R2 Subunit

Cited by 64 publications

References 56 publications

Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity

Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity

IncreasedRrm2gene dosage reduces fragile site breakage and prolongs survival of ATR mutant mice

dNTP pool levels modulate mutator phenotypes of error-prone DNA polymerase ε variants

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