Robustness of cell cycle control and flexible orders of signaling events

The highly robust control of cell cycles in eukaryotes enables cells to undergo strictly ordered G1/S/G2/M phases and respond adaptively to regulatory signals; however the nature of the robustness remains obscure. Specifically, it is unclear whether events of signaling should be strictly ordered and whether some events are more robust than others. To quantitatively address the two questions, we have developed a novel cell cycle model upon experimental observations. It contains positive and negative E2F proteins and two Cdk inhibitors, and is parameterized, for the first time, to generate not only oscillating protein concentrations but also periodic signaling events. Events and their orders reconstructed under varied conditions indicate that proteolysis of cyclins and Cdk complexes by APC and Skp2 occurs highly robustly in a strict order, but many other events are either dispensable or can occur in flexible orders. These results suggest that strictly ordered proteolytic events are essential for irreversible cell cycle progression and the robustness of cell cycles copes with flexible orders of signaling events, and unveil a new and important dimension to the robustness of cell cycle control in particular and to biological signaling in general.

[1]  Eduardo Sontag,et al.  Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2 , 2003, Nature Cell Biology.

[2]  B. Edgar,et al.  Developmental Control of Cell Cycle Regulators: A Fly's Perspective , 1996, Science.

[3]  J. Ferrell,et al.  Ultrasensitivity in the Regulation of Cdc25C by Cdk1. , 2011, Molecular cell.

[4]  James E. Ferrell,et al.  Substrate Competition as a Source of Ultrasensitivity in the Inactivation of Wee1 , 2007, Cell.

[5]  V. Janssens,et al.  PP1 and PP2A phosphatases – cooperating partners in modulating retinoblastoma protein activation , 2013, The FEBS journal.

[6]  R. Brent,et al.  roughex down-regulates G2 cyclins in G1. , 1997, Genes & development.

[7]  A. Almasan,et al.  Opposing roles of E2Fs in cell proliferation and death , 2004, Cancer biology & therapy.

[8]  M. Barbacid,et al.  Mammalian cyclin-dependent kinases. , 2005, Trends in biochemical sciences.

[9]  J. S. Britton,et al.  Cis-regulatory elements of the mitotic regulator, string/Cdc25. , 1999, Development.

[10]  Katherine C. Chen,et al.  Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions. , 1998, Biophysical chemistry.

[11]  Brian David Dynlacht,et al.  E2F mediates cell cycle-dependent transcriptional repression in vivo by recruitment of an HDAC1/mSin3B corepressor complex. , 2002, Genes & development.

[12]  M. Gossen,et al.  Acceleration of the G1/S phase transition by expression of cyclins D1 and E with an inducible system. , 1994, Molecular and cellular biology.

[13]  D. Morgan,et al.  Finishing mitosis, one step at a time , 2007, Nature Reviews Molecular Cell Biology.

[14]  Yuh Nung Jan,et al.  Dacapo, a Cyclin-Dependent Kinase Inhibitor, Stops Cell Proliferation during Drosophila Development , 1996, Cell.

[15]  T. P. Neufeld,et al.  Coordination of Growth and Cell Division in the Drosophila Wing , 1998, Cell.

[16]  J. Tyson,et al.  The dynamics of cell cycle regulation. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[17]  Daniel A. Haber,et al.  Archipelago regulates Cyclin E levels in Drosophila and is mutated in human cancer cell lines , 2001, Nature.

[18]  T. Orr-Weaver,et al.  Regulation of cell cycles in Drosophila development: intrinsic and extrinsic cues. , 2003, Annual review of genetics.

[19]  Paul Russell,et al.  cdc25 + functions as an inducer in the mitotic control of fission yeast , 1986, Cell.

[20]  D. Morgan The Hidden Rhythms of the Dividing Cell , 2010, Cell.

[21]  M. Pagano,et al.  Regulation of the CRL4(Cdt2) ubiquitin ligase and cell-cycle exit by the SCF(Fbxo11) ubiquitin ligase. , 2013, Molecular cell.

[22]  J. R. Daum,et al.  The reversibility of mitotic exit in vertebrate cells , 2006, Nature.

[23]  B. Amati,et al.  Kip1 meets SKP2: new links in cell-cycle control , 1999, Nature Cell Biology.

[24]  C. Sherr The Pezcoller lecture: cancer cell cycles revisited. , 2000, Cancer research.

[25]  Attila Csikász-Nagy,et al.  Analysis of a generic model of eukaryotic cell-cycle regulation. , 2006, Biophysical journal.

[26]  Jun Ma,et al.  The Drosophila F-box protein dSkp2 regulates cell proliferation by targeting Dacapo for degradation , 2013, Molecular biology of the cell.

[27]  S. V. Aksenov,et al.  A systems biology dynamical model of mammalian G1 cell cycle progression , 2007, Molecular systems biology.

[28]  Vuong Tran,et al.  Control of Drosophila endocycles by E2F and CRL4Cdt2 , 2011, Nature.

[29]  Eric Karsenti,et al.  Triggering of cyclin degradation in interphase extracts of amphibian eggs by cdc2 kinase , 1990, Nature.

[30]  J. Nevins,et al.  E2Fs link the control of G1/S and G2/M transcription , 2004, The EMBO journal.

[31]  Guo-Jun Zhang,et al.  Degradation of the SCF component Skp2 in cell-cycle phase G1 by the anaphase-promoting complex , 2004, Nature.

[32]  Katherine C. Chen,et al.  Integrative analysis of cell cycle control in budding yeast. , 2004, Molecular biology of the cell.

[33]  Marc W. Kirschner,et al.  How Proteolysis Drives the Cell Cycle , 1996, Science.

[34]  Denis Thieffry,et al.  Dynamical modeling of syncytial mitotic cycles in Drosophila embryos , 2007, Molecular systems biology.

[35]  John J Tyson,et al.  A model for restriction point control of the mammalian cell cycle. , 2004, Journal of theoretical biology.

[36]  P. O’Farrell,et al.  Rux is a cyclin-dependent kinase inhibitor (CKI) specific for mitotic cyclin–Cdk complexes , 1999, Current Biology.

[37]  N. Baker,et al.  Patterning signals and proliferation in Drosophila imaginal discs. , 2007, Current opinion in genetics & development.

[38]  John J Tyson,et al.  A model of yeast cell-cycle regulation based on multisite phosphorylation , 2010, Molecular systems biology.

[39]  Frank Uhlmann,et al.  A Quantitative Model for Ordered Cdk Substrate Dephosphorylation during Mitotic Exit , 2011, Cell.

[40]  B. Edgar,et al.  Negative Regulation of dE2F1 by Cyclin-Dependent Kinases Controls Cell Cycle Timing , 2004, Cell.

[41]  C. Peng,et al.  Cyclin A/CDK2 binds directly to E2F-1 and inhibits the DNA-binding activity of E2F-1/DP-1 by phosphorylation , 1994, Molecular and cellular biology.

[42]  R. Wolthuis,et al.  Cdc20 and Cks direct the spindle checkpoint-independent destruction of cyclin A. , 2008, Molecular cell.

[43]  N. López-Bigas,et al.  p27Kip1 represses transcription by direct interaction with p130/E2F4 at the promoters of target genes , 2012, Oncogene.

[44]  J. Ferrell,et al.  Modeling the Cell Cycle: Why Do Certain Circuits Oscillate? , 2011, Cell.

[45]  Qiong Yang,et al.  The Cdk1–APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch , 2013, Nature Cell Biology.

[46]  R. Macklis,et al.  E2F4 regulates a stable G2 arrest response to genotoxic stress in prostate carcinoma , 2007, Oncogene.

[47]  John J. Tyson,et al.  A Stochastic Model Correctly Predicts Changes in Budding Yeast Cell Cycle Dynamics upon Periodic Expression of CLN2 , 2014, PloS one.

[48]  Jesper Tegnér,et al.  Decoding complex biological networks - tracing essential and modulatory parameters in complex and simplified models of the cell cycle , 2011, BMC Systems Biology.

[49]  I. Hariharan,et al.  A Cyclin-Dependent Kinase Inhibitor, Dacapo, Is Necessary for Timely Exit from the Cell Cycle during Drosophila Embryogenesis , 1996, Cell.

[50]  B. Novák,et al.  Protein phosphatase 2A controls the order and dynamics of cell-cycle transitions. , 2011, Molecular cell.

[51]  Mode locking the cell cycle. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[52]  M. Pagano,et al.  Stabilizers and destabilizers controlling cell cycle oscillators. , 2006, Molecular cell.

[53]  A. Almasan,et al.  E2F4 Function in G2 Maintaining G2-arrest to Prevent Mitotic Entry with Damaged DNA , 2007, Cell cycle.

[54]  C. Lehner,et al.  The anaphase-promoting complex/cyclosome (APC/C) is required for rereplication control in endoreplication cycles. , 2008, Genes & development.

[55]  John J. Tyson,et al.  Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Tae J. Lee,et al.  A bistable Rb–E2F switch underlies the restriction point , 2008, Nature Cell Biology.

[57]  James E. Ferrell,et al.  Systems-Level Dissection of the Cell-Cycle Oscillator: Bypassing Positive Feedback Produces Damped Oscillations , 2005, Cell.

[58]  R. Poon,et al.  Specialized roles of the two mitotic cyclins in somatic cells: cyclin A as an activator of M phase-promoting factor. , 2007, Molecular biology of the cell.

[59]  Michele Pagano,et al.  Control of the SCFSkp2–Cks1 ubiquitin ligase by the APC/CCdh1 ubiquitin ligase , 2004, Nature.

[60]  Vuong Tran,et al.  Intrinsic negative cell cycle regulation provided by PIP box- and Cul4Cdt2-mediated destruction of E2f1 during S phase. , 2008, Developmental cell.

[61]  Joseph B. Rayman,et al.  E 2 F mediates cell cycle-dependent transcriptional repression in vivo by recruitment of an HDAC 1 / mSin 3 B corepressor complex , 2002 .

[62]  A Goldbeter,et al.  A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[63]  P. Thuriaux,et al.  Regulatory genes controlling mitosis in the fission yeast Schizosaccharomyces pombe. , 1980, Genetics.

[64]  Béla Novák,et al.  Supplementary Fig. 1 , 2021 .

[65]  Hiroyuki Osada,et al.  Cyclin-dependent kinase (CDK) phosphorylation destabilizes somatic Wee1 via multiple pathways. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Frederick R. Cross,et al.  The effects of molecular noise and size control on variability in the budding yeast cell cycle , 2007, Nature.

[67]  C. Wittenberg Cell cycle: A division duet , 2012, Nature.

[68]  Shunichi Takeda,et al.  Cyclin-dependent kinases and cell-cycle transitions: does one fit all? , 2008, Nature Reviews Molecular Cell Biology.

[69]  Q. Ouyang,et al.  The yeast cell-cycle network is robustly designed. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[70]  J. Walter,et al.  Mechanism of CRL4(Cdt2), a PCNA-dependent E3 ubiquitin ligase. , 2011, Genes & development.

[71]  L. Hartwell,et al.  Checkpoints: controls that ensure the order of cell cycle events. , 1989, Science.

[72]  N. Baker Cell proliferation, survival, and death in the Drosophila eye. , 2001, Seminars in cell & developmental biology.

[73]  Benjamin L Turner,et al.  Supporting Online Material Materials and Methods Som Text Figs. S1 to S3 Table S1 References Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops , 2022 .

[74]  A. Giordano,et al.  Rb family proteins as modulators of gene expression and new aspects regarding the interaction with chromatin remodeling enzymes , 2006, Oncogene.

[75]  Luis M. Escudero,et al.  Mechanism of G1 arrest in the Drosophila eye imaginal disc , 2007, BMC Developmental Biology.

[76]  B. Novák,et al.  Interplay of transcriptional and proteolytic regulation in driving robust cell cycle progression. , 2012, Molecular bioSystems.

[77]  J. Walter,et al.  Docking of a specialized PIP Box onto chromatin-bound PCNA creates a degron for the ubiquitin ligase CRL4Cdt2. , 2009, Molecular cell.

[78]  B. Thomas,et al.  Roughex Mediates G1 Arrest through a Physical Association with Cyclin A , 2000, Molecular and Cellular Biology.

[79]  M. Asano,et al.  APC/CFzr/Cdh1 promotes cell cycle progression during the Drosophila endocycle , 2008, Development.

[80]  R. Medema,et al.  Assessing kinetics from fixed cells reveals activation of the mitotic entry network at the S/G2 transition. , 2014, Molecular cell.

[81]  S. Zipursky,et al.  Cell cycle progression in the developing Drosophila eye: roughex encodes a novel protein required for the establishment of G1 , 1994, Cell.

[82]  J. Raff,et al.  The roles of Fzy/Cdc20 and Fzr/Cdh1 in regulating the destruction of cyclin B in space and time , 2002, The Journal of cell biology.

[83]  Hao Zhu,et al.  Cellular automata with object-oriented features for parallel molecular network modeling , 2005, IEEE Transactions on NanoBioscience.

[84]  J. Tyson Modeling the cell division cycle: cdc2 and cyclin interactions. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[85]  M. West,et al.  Origin of bistability underlying mammalian cell cycle entry , 2011, Molecular systems biology.

[86]  John J. Tyson,et al.  Temporal Organization of the Cell Cycle , 2008, Current Biology.

[87]  John J. Tyson,et al.  Irreversible cell-cycle transitions are due to systems-level feedback , 2007, Nature Cell Biology.

[88]  M. Kitagawa,et al.  Phosphorylation of E2F-1 by cyclin A-cdk2. , 1995, Oncogene.

[89]  Zhilin Qu,et al.  Linking cell division to cell growth in a spatiotemporal model of the cell cycle. , 2006, Journal of theoretical biology.

[90]  Albert Goldbeter,et al.  Temporal self-organization of the cyclin/Cdk network driving the mammalian cell cycle , 2009, Proceedings of the National Academy of Sciences.

[91]  J. Tyson,et al.  Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. , 1993, Journal of cell science.