Polo-like kinase 1 (Plk1) regulates DNA replication origin firing and interacts with Rif1 in Xenopus

Abstract The activation of eukaryotic DNA replication origins needs to be strictly controlled at multiple steps in order to faithfully duplicate the genome and to maintain its stability. How the checkpoint recovery and adaptation protein Polo-like kinase 1 (Plk1) regulates the firing of replication origins during non-challenged S phase remained an open question. Using DNA fiber analysis, we show that immunodepletion of Plk1 in the Xenopus in vitro system decreases replication fork density and initiation frequency. Numerical analyses suggest that Plk1 reduces the overall probability and synchrony of origin firing. We used quantitative chromatin proteomics and co-immunoprecipitations to demonstrate that Plk1 interacts with firing factors MTBP/Treslin/TopBP1 as well as with Rif1, a known regulator of replication timing. Phosphopeptide analysis by LC/MS/MS shows that the C-terminal domain of Rif1, which is necessary for its repressive action on origins through protein phosphatase 1 (PP1), can be phosphorylated in vitro by Plk1 on S2058 in its PP1 binding site. The phosphomimetic S2058D mutant interrupts the Rif1-PP1 interaction and modulates DNA replication. Collectively, our study provides molecular insights into how Plk1 regulates the spatio-temporal replication program and suggests that Plk1 controls origin activation at the level of large chromatin domains in vertebrates.

[1]  J. Altmüller,et al.  MTBP phosphorylation controls DNA replication origin firing , 2021, Scientific Reports.

[2]  B. Audit,et al.  Organization of DNA Replication Origin Firing in Xenopus Egg Extracts: The Role of Intra-S Checkpoint , 2020, bioRxiv.

[3]  M. Cristina Cardoso,et al.  Nuclear organisation and replication timing are coupled through RIF1–PP1 interaction , 2019, Nature Communications.

[4]  A. Kumagai,et al.  Binding of the Treslin-MTBP Complex to Specific Regions of the Human Genome Promotes the Initiation of DNA Replication , 2020, Cell reports.

[5]  C. Seoighe,et al.  ATR Restrains DNA Synthesis and Mitotic Catastrophe in Response to CDC7 Inhibition. , 2020, Cell reports.

[6]  Diletta Ciardo,et al.  Polo-like kinase 1 (Plk1) is a positive regulator of DNA replication in the Xenopus in vitro system , 2020, Cell cycle.

[7]  V. Costanzo,et al.  SSRP1-mediated histone H1 eviction promotes replication origin assembly and accelerated development , 2020, Nature Communications.

[8]  M. Altmeyer,et al.  Basal CHK1 activity safeguards its stability to maintain intrinsic S-phase checkpoint functions , 2019, The Journal of cell biology.

[9]  Simon C Watkins,et al.  An ATR and CHK1 kinase signaling mechanism that limits origin firing during unperturbed DNA replication , 2019, Proceedings of the National Academy of Sciences.

[10]  M. Méchali,et al.  Metazoan DNA replication origins. , 2019, Current opinion in cell biology.

[11]  Diletta Ciardo,et al.  Genome wide decrease of DNA replication eye density at the midblastula transition of Xenopus laevis , 2019, Cell cycle.

[12]  Diletta Ciardo,et al.  On the Interplay of the DNA Replication Program and the Intra-S Phase Checkpoint Pathway , 2019, Genes.

[13]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[14]  Martin Eisenacher,et al.  The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..

[15]  S. Rusin,et al.  Aurora B opposes PP1 function in mitosis by phosphorylating the conserved PP1-binding RVxF motif in PP1 regulatory proteins , 2018, Science Signaling.

[16]  Ying Wang,et al.  Xenbase: a genomic, epigenomic and transcriptomic model organism database , 2017, Nucleic Acids Res..

[17]  P. O’Farrell,et al.  Rif1 prolongs the embryonic S phase at the Drosophila mid-blastula transition , 2017, bioRxiv.

[18]  A. Kumagai,et al.  MTBP, the partner of Treslin, contains a novel DNA-binding domain that is essential for proper initiation of DNA replication , 2017, Molecular biology of the cell.

[19]  M. Blackledge,et al.  Mouse Rif1 is a regulatory subunit of protein phosphatase 1 (PP1) , 2017, Scientific Reports.

[20]  J. Julian Blow,et al.  Reversal of DDK-Mediated MCM Phosphorylation by Rif1-PP1 Regulates Replication Initiation and Replisome Stability Independently of ATR/Chk1 , 2017, Cell reports.

[21]  Angus I Lamond,et al.  Human RIF1 and protein phosphatase 1 stimulate DNA replication origin licensing but suppress origin activation , 2017, EMBO reports.

[22]  Marco Y. Hein,et al.  The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.

[23]  B. Drossel,et al.  3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression , 2016, Nature Communications.

[24]  J. Bartek,et al.  TOPBP1 regulates RAD51 phosphorylation and chromatin loading and determines PARP inhibitor sensitivity , 2016, The Journal of cell biology.

[25]  Wolfgang Huber,et al.  Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program , 2016, Molecular cell.

[26]  Allon M. Klein,et al.  On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development. , 2015, Developmental cell.

[27]  A. Goldar,et al.  Tight Chk1 Levels Control Replication Cluster Activation in Xenopus , 2015, PloS one.

[28]  Junjie Chen.  Faculty Opinions recommendation of DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. , 2015 .

[29]  A. Shevchenko,et al.  Interaction of Chk1 with Treslin negatively regulates the initiation of chromosomal DNA replication. , 2015, Molecular cell.

[30]  Jared M. Peace,et al.  Rif1 Regulates Initiation Timing of Late Replication Origins throughout the S. cerevisiae Genome , 2014, PloS one.

[31]  David Shore,et al.  Rif1 controls DNA replication timing in yeast through the PP1 phosphatase Glc7. , 2014, Cell reports.

[32]  Anoushka Davé,et al.  Protein Phosphatase 1 Recruitment by Rif1 Regulates DNA Replication Origin Firing by Counteracting DDK Activity , 2014, Cell reports.

[33]  Martin Blackledge,et al.  Structural and Biophysical Characterization of Murine Rif1 C Terminus Reveals High Specificity for DNA Cruciform Structures* , 2014, The Journal of Biological Chemistry.

[34]  M. Raghuraman,et al.  Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex , 2014, Genes & development.

[35]  J. Blow,et al.  Xenopus Cdc7 executes its essential function early in S phase and is counteracted by checkpoint-regulated protein phosphatase 1 , 2014, Open Biology.

[36]  C. Bradshaw,et al.  Titration of Four Replication Factors Is Essential for the Xenopus laevis Midblastula Transition , 2013, Science.

[37]  N. Rhind,et al.  DNA replication timing. , 2013, Cold Spring Harbor perspectives in biology.

[38]  J. Diffley,et al.  Identification of a Heteromeric Complex That Promotes DNA Replication Origin Firing in Human Cells , 2013, Science.

[39]  J. Diffley,et al.  Controlling DNA replication origins in response to DNA damage – inhibit globally, activate locally , 2013, Journal of Cell Science.

[40]  Vishnu Dileep,et al.  Mouse Rif1 is a key regulator of the replication‐timing programme in mammalian cells , 2012, The EMBO journal.

[41]  Hisao Masai,et al.  Rif1 regulates the replication timing domains on the human genome , 2012, The EMBO journal.

[42]  A. Shevchenko,et al.  Role for Rif1 in the checkpoint response to damaged DNA in Xenopus egg extracts , 2012, Cell cycle.

[43]  Katsuhiko Shirahige,et al.  Rif1 is a global regulator of timing of replication origin firing in fission yeast. , 2012, Genes & development.

[44]  Alain Arneodo,et al.  Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome , 2011, PLoS Comput. Biol..

[45]  A. Donaldson,et al.  Limiting replication initiation factors execute the temporal programme of origin firing in budding yeast , 2011, The EMBO journal.

[46]  Xiaoqi Liu,et al.  Plk1 Phosphorylation of Orc2 Promotes DNA Replication under Conditions of Stress , 2011, Molecular and Cellular Biology.

[47]  Sebastian A. Wagner,et al.  A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1 , 2011, Genome Biology.

[48]  C. Ponting,et al.  Regulation of DNA Replication through Sld3-Dpb11 Interaction Is Conserved from Yeast to Humans , 2011, Current Biology.

[49]  Devin K Schweppe,et al.  Quantitative Phosphoproteomics Identifies Substrates and Functional Modules of Aurora and Polo-Like Kinase Activities in Mitotic Cells , 2011, Science Signaling.

[50]  A. Shevchenko,et al.  Direct regulation of Treslin by cyclin-dependent kinase is essential for the onset of DNA replication , 2011, The Journal of cell biology.

[51]  C. Obuse,et al.  Sld7, an Sld3‐associated protein required for efficient chromosomal DNA replication in budding yeast , 2011, The EMBO journal.

[52]  I. Bruck,et al.  Origin Single-stranded DNA Releases Sld3 Protein from the Mcm2–7 Complex, Allowing the GINS Tetramer to Bind the Mcm2–7 Complex* , 2011, The Journal of Biological Chemistry.

[53]  Yves Pommier,et al.  Rif1 provides a new DNA‐binding interface for the Bloom syndrome complex to maintain normal replication , 2010, The EMBO journal.

[54]  K. Strebhardt,et al.  Multifaceted polo-like kinases: drug targets and antitargets for cancer therapy , 2010, Nature Reviews Drug Discovery.

[55]  R. Schwab,et al.  ATR activation and replication fork restart are defective in FANCM‐deficient cells , 2010, The EMBO journal.

[56]  A. Shevchenko,et al.  Treslin Collaborates with TopBP1 in Triggering the Initiation of DNA Replication , 2010, Cell.

[57]  C. Sansam,et al.  A vertebrate gene, ticrr, is an essential checkpoint and replication regulator. , 2010, Genes & development.

[58]  Richard C. Jones,et al.  A key role for Ctf4 in coupling the MCM2‐7 helicase to DNA polymerase α within the eukaryotic replisome , 2009, The EMBO journal.

[59]  Jingchuan Sun,et al.  Mechanism of Replication-Coupled DNA Interstrand Crosslink Repair , 2008, Cell.

[60]  A. Goldar,et al.  Use of DNA combing to study DNA replication in Xenopus and human cell-free systems. , 2009, Methods in molecular biology.

[61]  John Bechhoefer,et al.  Reconciling stochastic origin firing with defined replication timing , 2009, Chromosome Research.

[62]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[63]  Vincenzo Costanzo,et al.  Plx1 is required for chromosomal DNA replication under stressful conditions , 2008, The EMBO journal.

[64]  Xiaoqi Liu,et al.  Role for Plk1 phosphorylation of Hbo1 in regulation of replication licensing , 2008, Proceedings of the National Academy of Sciences.

[65]  Y. Pommier,et al.  The Mammalian DNA Replication Elongation Checkpoint: Implication of Chk1 and Relationship with Origin Firing as Determined by Single DNA Molecule and Single Cell Analyses , 2007, Cell cycle.

[66]  D. Gillespie,et al.  Chk1 regulates the density of active replication origins during the vertebrate S phase , 2007, The EMBO journal.

[67]  S. Gammeltoft,et al.  Proteomic screen defines the Polo‐box domain interactome and identifies Rock2 as a Plk1 substrate , 2007, The EMBO journal.

[68]  F. Grummt,et al.  Mouse pre-replicative complex proteins colocalise and interact with the centrosome. , 2007, European journal of cell biology.

[69]  T. Krude,et al.  Functional Requirement of Noncoding Y RNAs for Human Chromosomal DNA Replication , 2006, Molecular and Cellular Biology.

[70]  Masato T. Kanemaki,et al.  Distinct roles for Sld3 and GINS during establishment and progression of eukaryotic DNA replication forks , 2006, The EMBO journal.

[71]  D. Stern,et al.  Interaction of Chromatin-associated Plk1 and Mcm7* , 2005, Journal of Biological Chemistry.

[72]  K. Marheineke,et al.  Control of Replication Origin Density and Firing Time in Xenopus Egg Extracts , 2004, Journal of Biological Chemistry.

[73]  J. Gautier,et al.  ATR and ATM regulate the timing of DNA replication origin firing , 2004, Nature Cell Biology.

[74]  A. Shevchenko,et al.  Adaptation of a DNA Replication Checkpoint Response Depends upon Inactivation of Claspin by the Polo-like Kinase , 2004, Cell.

[75]  Michael B Yaffe,et al.  Proteomic Screen Finds pSer/pThr-Binding Domain Localizing Plk1 to Mitotic Substrates , 2003, Science.

[76]  T. Prokhorova,et al.  MCM 2 – 7 Complexes Bind Chromatin in a Distributed Pattern Surrounding the Origin Recognition Complex in Xenopus Egg Extracts , 2002 .

[77]  O. Hyrien,et al.  Aphidicolin Triggers a Block to Replication Origin Firing inXenopus Egg Extracts* , 2001, The Journal of Biological Chemistry.

[78]  H. Araki,et al.  Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae , 2001, The EMBO journal.

[79]  J. Blow,et al.  Replication Origins in XenopusEgg Extract Are 5–15 Kilobases Apart and Are Activated in Clusters That Fire at Different Times , 2001, The Journal of cell biology.

[80]  J. Blow,et al.  Initiation of DNA replication in nuclei and purified DNA by a cell-free extract of Xenopus eggs , 1986, Cell.