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Zhang H. Regulation of DNA Replication Licensing and Re-Replication by Cdt1. Int J Mol Sci 2021; 22:ijms22105195. [PMID: 34068957 PMCID: PMC8155957 DOI: 10.3390/ijms22105195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022] Open
Abstract
In eukaryotic cells, DNA replication licensing is precisely regulated to ensure that the initiation of genomic DNA replication in S phase occurs once and only once for each mitotic cell division. A key regulatory mechanism by which DNA re-replication is suppressed is the S phase-dependent proteolysis of Cdt1, an essential replication protein for licensing DNA replication origins by loading the Mcm2-7 replication helicase for DNA duplication in S phase. Cdt1 degradation is mediated by CRL4Cdt2 ubiquitin E3 ligase, which further requires Cdt1 binding to proliferating cell nuclear antigen (PCNA) through a PIP box domain in Cdt1 during DNA synthesis. Recent studies found that Cdt2, the specific subunit of CRL4Cdt2 ubiquitin E3 ligase that targets Cdt1 for degradation, also contains an evolutionarily conserved PIP box-like domain that mediates the interaction with PCNA. These findings suggest that the initiation and elongation of DNA replication or DNA damage-induced repair synthesis provide a novel mechanism by which Cdt1 and CRL4Cdt2 are both recruited onto the trimeric PCNA clamp encircling the replicating DNA strands to promote the interaction between Cdt1 and CRL4Cdt2. The proximity of PCNA-bound Cdt1 to CRL4Cdt2 facilitates the destruction of Cdt1 in response to DNA damage or after DNA replication initiation to prevent DNA re-replication in the cell cycle. CRL4Cdt2 ubiquitin E3 ligase may also regulate the degradation of other PIP box-containing proteins, such as CDK inhibitor p21 and histone methylase Set8, to regulate DNA replication licensing, cell cycle progression, DNA repair, and genome stability by directly interacting with PCNA during DNA replication and repair synthesis.
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Affiliation(s)
- Hui Zhang
- Department of Chemistry and Biochemistry, Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 South Maryland Parkway, Box 454003, Las Vegas, NV 89154, USA
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Fleck O, Fahnøe U, Løvschal KV, Gasasira MU, Marinova IN, Kragelund BB, Carr AM, Hartsuiker E, Holmberg C, Nielsen O. Deoxynucleoside Salvage in Fission Yeast Allows Rescue of Ribonucleotide Reductase Deficiency but Not Spd1-Mediated Inhibition of Replication. Genes (Basel) 2017; 8:E128. [PMID: 28441348 DOI: 10.3390/genes8050128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/10/2017] [Accepted: 04/20/2017] [Indexed: 12/12/2022] Open
Abstract
In fission yeast, the small, intrinsically disordered protein S-phase delaying protein 1 (Spd1) blocks DNA replication and causes checkpoint activation at least in part, by inhibiting the enzyme ribonucleotide reductase, which is responsible for the synthesis of DNA building blocks. The CRL4Cdt2 E3 ubiquitin ligase mediates degradation of Spd1 and the related protein Spd2 at S phase of the cell cycle. We have generated a conditional allele of CRL4Cdt2, by expressing the highly unstable substrate-recruiting protein Cdt2 from a repressible promoter. Unlike Spd1, Spd2 does not regulate deoxynucleotide triphosphate (dNTP) pools; yet we find that Spd1 and Spd2 together inhibit DNA replication upon Cdt2 depletion. To directly test whether this block of replication was solely due to insufficient dNTP levels, we established a deoxy-nucleotide salvage pathway in fission yeast by expressing the human equilibrative nucleoside transporter 1 (hENT1) and the Drosophila deoxynucleoside kinase. We present evidence that this salvage pathway is functional, as 2 µM of deoxynucleosides in the culture medium is able to rescue the growth of two different temperature-sensitive alleles controlling ribonucleotide reductase. However, salvage completely failed to rescue S phase delay, checkpoint activation, and damage sensitivity, which was caused by CRL4Cdt2 inactivation, suggesting that Spd1—in addition to repressing dNTP synthesis—together with Spd2, can inhibit other replication functions. We propose that this inhibition works at the point of the replication clamp proliferating cell nuclear antigen, a co-factor for DNA replication.
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Tanaka M, Takahara M, Nukina K, Hayashi A, Sakai W, Sugasawa K, Shiomi Y, Nishitani H. Mismatch repair proteins recruited to ultraviolet light-damaged sites lead to degradation of licensing factor Cdt1 in the G1 phase. Cell Cycle 2017; 16:673-684. [PMID: 28278049 DOI: 10.1080/15384101.2017.1295179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cdt1 is rapidly degraded by CRL4Cdt2 E3 ubiquitin ligase after UV (UV) irradiation. Previous reports revealed that the nucleotide excision repair (NER) pathway is responsible for the rapid Cdt1-proteolysis. Here, we show that mismatch repair (MMR) proteins are also involved in the degradation of Cdt1 after UV irradiation in the G1 phase. First, compared with the rapid (within ∼15 min) degradation of Cdt1 in normal fibroblasts, Cdt1 remained stable for ∼30 min in NER-deficient XP-A cells, but was degraded within ∼60 min. The delayed degradation was also dependent on PCNA and CRL4Cdt2. The MMR proteins Msh2 and Msh6 were recruited to the UV-damaged sites of XP-A cells in the G1 phase. Depletion of these factors with small interfering RNAs prevented Cdt1 degradation in XP-A cells. Similar to the findings in XP-A cells, depletion of XPA delayed Cdt1 degradation in normal fibroblasts and U2OS cells, and co-depletion of Msh6 further prevented Cdt1 degradation. Furthermore, depletion of Msh6 alone delayed Cdt1 degradation in both cell types. When Cdt1 degradation was attenuated by high Cdt1 expression, repair synthesis at the damaged sites was inhibited. Our findings demonstrate that UV irradiation induces multiple repair pathways that activate CRL4Cdt2 to degrade its target proteins in the G1 phase of the cell cycle, leading to efficient repair of DNA damage.
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Affiliation(s)
- Miyuki Tanaka
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Michiyo Takahara
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Kohei Nukina
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Akiyo Hayashi
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Wataru Sakai
- b Biosignal Research Center , Kobe University , Kobe , Hyogo , Japan
| | - Kaoru Sugasawa
- b Biosignal Research Center , Kobe University , Kobe , Hyogo , Japan
| | - Yasushi Shiomi
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Hideo Nishitani
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
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Swanson CI, Meserve JH, McCarter PC, Thieme A, Mathew T, Elston TC, Duronio RJ. Expression of an S phase-stabilized version of the CDK inhibitor Dacapo can alter endoreplication. Development 2015; 142:4288-98. [PMID: 26493402 DOI: 10.1242/dev.115006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/12/2015] [Indexed: 01/01/2023]
Abstract
In developing organisms, divergence from the canonical cell division cycle is often necessary to ensure the proper growth, differentiation, and physiological function of a variety of tissues. An important example is endoreplication, in which endocycling cells alternate between G and S phase without intervening mitosis or cytokinesis, resulting in polyploidy. Although significantly different from the canonical cell cycle, endocycles use regulatory pathways that also function in diploid cells, particularly those involved in S phase entry and progression. A key S phase regulator is the Cyclin E-Cdk2 kinase, which must alternate between periods of high (S phase) and low (G phase) activity in order for endocycling cells to achieve repeated rounds of S phase and polyploidy. The mechanisms that drive these oscillations of Cyclin E-Cdk2 activity are not fully understood. Here, we show that the Drosophila Cyclin E-Cdk2 inhibitor Dacapo (Dap) is targeted for destruction during S phase via a PIP degron, contributing to oscillations of Dap protein accumulation during both mitotic cycles and endocycles. Expression of a PIP degron mutant Dap attenuates endocycle progression but does not obviously affect proliferating diploid cells. A mathematical model of the endocycle predicts that the rate of destruction of Dap during S phase modulates the endocycle by regulating the length of G phase. We propose from this model and our in vivo data that endo S phase-coupled destruction of Dap reduces the threshold of Cyclin E-Cdk2 activity necessary to trigger the subsequent G-S transition, thereby influencing endocycle oscillation frequency and the extent of polyploidy.
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Affiliation(s)
- Christina I Swanson
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joy H Meserve
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Patrick C McCarter
- Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Alexis Thieme
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Tony Mathew
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy C Elston
- Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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Hall JR, Bereman MS, Nepomuceno AI, Thompson EA, Muddiman DC, Smart RC. C/EBPα regulates CRL4(Cdt2)-mediated degradation of p21 in response to UVB-induced DNA damage to control the G1/S checkpoint. Cell Cycle 2015; 13:3602-10. [PMID: 25483090 DOI: 10.4161/15384101.2014.962957] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The bZIP transcription factor, C/EBPα is highly inducible by UVB and other DNA damaging agents in keratinocytes. C/EBPα-deficient keratinocytes fail to undergo cell cycle arrest in G1 in response to UVB-induced DNA damage and mice lacking epidermal C/EBPα are highly susceptible to UVB-induced skin cancer. The mechanism through which C/EBPα regulates the cell cycle checkpoint in response to DNA damage is unknown. Here we report untreated C/EBPα-deficient keratinocytes have normal levels of the cyclin-dependent kinase inhibitor, p21, however, UVB-treated C/EBPα-deficient keratinocytes fail to up-regulate nuclear p21 protein levels despite normal up-regulation of Cdkn1a mRNA levels. UVB-treated C/EBPα-deficient keratinocytes displayed a 4-fold decrease in nuclear p21 protein half-life due to the increased proteasomal degradation of p21 via the E3 ubiquitin ligase CRL4(Cdt2). Cdt2 is the substrate recognition subunit of CRL4(Cdt2) and Cdt2 mRNA and protein levels were up-regulated in UVB-treated C/EBPα-deficient keratinocytes. Knockdown of Cdt2 restored p21 protein levels in UVB-treated C/EBPα-deficient keratinocytes. Lastly, the failure to accumulate p21 in response to UVB in C/EBPα-deficient keratinocytes resulted in decreased p21 interactions with critical cell cycle regulatory proteins, increased CDK2 activity, and inappropriate entry into S-phase. These findings reveal C/EBPα regulates G1/S cell cycle arrest in response to DNA damage via the control of CRL4(Cdt2) mediated degradation of p21.
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Affiliation(s)
- Jonathan R Hall
- a Department of Biological Sciences ; North Carolina State University ; Raleigh , NC USA
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Zhao H, Zhang S, Xu D, Lee MY, Zhang Z, Lee EY, Darzynkiewicz Z. Expression of the p12 subunit of human DNA polymerase δ (Pol δ), CDK inhibitor p21(WAF1), Cdt1, cyclin A, PCNA and Ki-67 in relation to DNA replication in individual cells. Cell Cycle 2015; 13:3529-40. [PMID: 25483089 DOI: 10.4161/15384101.2014.958910] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We recently reported that the p12 subunit of human DNA polymerase δ (Pol δ4) is degraded by CRL4(Cdt2) which regulates the licensing factor Cdt1 and p21(WAF1) during the G1 to S transition. Presently, we performed multiparameter laser scanning cytometric analyses of changes in levels of p12, Cdt1 and p21(WAF1), detected immunocytochemically in individual cells, vis-à-vis the initiation and completion of DNA replication. The latter was assessed by pulse-labeling A549 cells with the DNA precursor ethynyl-2'-deoxyribose (EdU). The loss of p12 preceded the initiation of DNA replication and essentially all cells incorporating EdU were p12 negative. Completion of DNA replication and transition to G2 phase coincided with the re-appearance and rapid rise of p12 levels. Similar to p12 a decline of p21(WAF1) and Cdt1 was seen at the end of G1 phase and all DNA replicating cells were p21(WAF1) and Cdt1 negative. The loss of p21(WAF1) preceded that of Cdt1 and p12 and the disappearance of the latter coincided with the onset of DNA replication. Loss of p12 leads to conversion of Pol δ4 to its trimeric form, Pol δ3, so that the results provide strong support to the notion that Pol δ3 is engaged in DNA replication during unperturbed progression through the S phase of cell cycle. Also assessed was a correlation between EdU incorporation, likely reflecting the rate of DNA replication in individual cells, and the level of expression of positive biomarkers of replication cyclin A, PCNA and Ki-67 in these cells. Of interest was the observation of stronger correlation between EdU incorporation and expression of PCNA (r = 0.73) than expression of cyclin A (r = 0.47) or Ki-67 (r = 0.47).
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Affiliation(s)
- Hong Zhao
- a Brander Cancer Research Institute; Department of Pathology; New York Medical College ; Valhalla , NY USA
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Lee MYWT, Zhang S, Lin SHS, Wang X, Darzynkiewicz Z, Zhang Z, Lee EYC. The tail that wags the dog: p12, the smallest subunit of DNA polymerase δ, is degraded by ubiquitin ligases in response to DNA damage and during cell cycle progression. Cell Cycle 2013; 13:23-31. [PMID: 24300032 DOI: 10.4161/cc.27407] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA polymerase δ (Pol δ) is a key enzyme in eukaryotic DNA replication. Human Pol δ is a heterotetramer whose p12 subunit is degraded in response to DNA damage, leading to the in vivo conversion of Pol δ4 to Pol δ3. Two E3 ubiquitin ligases, RNF8 and CRL4(Cdt2), participate in the DNA damage-induced degradation of p12. We discuss how these E3 ligases integrate the formation of Pol δ3 and ubiquitinated PCNA for DNA repair processes. CRL4(Cdt2) partially degrades p12 during normal cell cycle progression, thereby generating Pol δ3 during S phase. This novel finding extends the current view of the role of Pol δ3 in DNA repair and leads to the hypothesis that it participates in DNA replication. The coordinated regulation of licensing factors and Pol δ3 by CRL4(Cdt2) now opens new avenues for control of DNA replication. A parallel study of Pol δ4 and Pol δ3 in Okazaki fragment processing provides evidence for a role of Pol δ3 in DNA replication. We discuss several new perspectives of the role of the 2 forms of Pol δ in DNA replication and repair, as well the significance of the integration of p12 regulation in DNA repair and cell cycle progression.
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Affiliation(s)
- Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Szu Hua Sharon Lin
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Xiaoxiao Wang
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Zbigniew Darzynkiewicz
- Department of Pathology; Brander Cancer Research Institute; New York Medical College; Valhalla, NY USA
| | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Ernest Y C Lee
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
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