Critical slowing down and attractive manifold: A mechanism for dynamic robustness in the yeast cell-cycle process.

Biological processes that execute complex multiple functions, such as the cell cycle, must ensure the order of sequential events and maintain dynamic robustness against various fluctuations. Here, we examine the mechanisms and fundamental structure that achieve these properties in the cell cycle of the budding yeast Saccharomyces cerevisiae. We show that this process behaves like an excitable system containing three well-decoupled saddle-node bifurcations to execute DNA replication and mitosis events. The yeast cell-cycle regulatory network can be divided into three modules-the G1/S phase, early M phase, and late M phase-wherein both positive feedback loops in each module and interactions among modules play important roles. Specifically, when the cell-cycle process operates near the critical points of the saddle-node bifurcations, a critical slowing down effect takes place. Such interregnum then allows for an attractive manifold and sufficient duration for cell-cycle events, within which to assess the completion of DNA replication and mitosis, e.g., spindle assembly. Moreover, such arrangement ensures that any fluctuation in an early module or event will not transmit to a later module or event. Thus, our results suggest a possible dynamical mechanism of the cell-cycle process to ensure event order and dynamic robustness and give insight into the evolution of eukaryotic cell-cycle processes.

[1]  Mike Tyers,et al.  G1/S Transcription Factor Copy Number Is a Growth-Dependent Determinant of Cell Cycle Commitment in Yeast. , 2018, Cell systems.

[2]  Albert Goldbeter,et al.  A skeleton model for the network of cyclin-dependent kinases driving the mammalian cell cycle , 2011, Interface Focus.

[3]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[4]  U. Alon,et al.  Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria , 2001, Science.

[5]  T. Weinert,et al.  RAD53, DUN1 and PDS1 define two parallel G2/M checkpoint pathways in budding yeast , 1999, The EMBO journal.

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

[7]  F. M. Yeong,et al.  Exit from mitosis in budding yeast: biphasic inactivation of the Cdc28-Clb2 mitotic kinase and the role of Cdc20. , 2000, Molecular cell.

[8]  W. Seufert,et al.  Yeast Hct1 recognizes the mitotic cyclin Clb2 and other substrates of the ubiquitin ligase APC , 2001, The EMBO journal.

[9]  M. Gerstein,et al.  Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. , 2002, Genes & development.

[10]  G Blomqvist,et al.  Kinetic analysis. , 1991, Wiener klinische Wochenschrift.

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

[12]  K Nasmyth,et al.  SWI5 instability may be necessary but is not sufficient for asymmetric HO expression in yeast. , 1993, Genes & development.

[13]  Tamás Turányi,et al.  Time scale and dimension analysis of a budding yeast cell cycle model , 2006, BMC Bioinformatics.

[14]  Tony Pawson,et al.  Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication , 2001, Nature.

[15]  Costanzo Manes,et al.  Whi5 phosphorylation embedded in the G1/S network dynamically controls critical cell size and cell fate , 2016, Nature Communications.

[16]  Andrew W. Murray,et al.  Phosphorylation by Cdc28 Activates the Cdc20-Dependent Activity of the Anaphase-Promoting Complex , 2000, The Journal of cell biology.

[17]  Mike Tyers,et al.  Cell cycle goes global. , 2004, Current opinion in cell biology.

[18]  Frederick R. Cross,et al.  APC-dependent proteolysis of the mitotic cyclin Clb2 is essential for mitotic exit , 2002, Nature.

[19]  Frederick R. Cross,et al.  Distinct Subcellular Localization Patterns Contribute to Functional Specificity of the Cln2 and Cln3 Cyclins of Saccharomyces cerevisiae , 2000, Molecular and Cellular Biology.

[20]  A. Murray,et al.  Recycling the Cell Cycle Cyclins Revisited , 2004, Cell.

[21]  E. Schiebel,et al.  The role of the yeast spindle pole body and the mammalian centrosome in regulating late mitotic events. , 2001, Current opinion in cell biology.

[22]  Kim Nasmyth,et al.  Genes involved in sister chromatid separation are needed for b-type cyclin proteolysis in budding yeast , 1995, Cell.

[23]  F. Cross,et al.  Coherence and timing of cell cycle start examined at single-cell resolution. , 2006, Molecular cell.

[24]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[25]  G. Braus,et al.  A Process Independent of the Anaphase-promoting Complex Contributes to Instability of the Yeast S Phase Cyclin Clb5* , 2007, Journal of Biological Chemistry.

[26]  Kathy Chen,et al.  Network dynamics and cell physiology , 2001, Nature Reviews Molecular Cell Biology.

[27]  Angelika Amon,et al.  The regulation of Cdc20 proteolysis reveals a role for the APC components Cdc23 and Cdc27 during S phase and early mitosis , 1998, Current Biology.

[28]  Kim Nasmyth,et al.  An ESP1/PDS1 Complex Regulates Loss of Sister Chromatid Cohesion at the Metaphase to Anaphase Transition in Yeast , 1998, Cell.

[29]  Curt Wittenberg,et al.  Cln3 Activates G1-Specific Transcription via Phosphorylation of the SBF Bound Repressor Whi5 , 2004, Cell.

[30]  S. Dorland,et al.  Parallel pathways of gene regulation: homologous regulators SWI5 and ACE2 differentially control transcription of HO and chitinase. , 1992, Genes & development.

[31]  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.

[32]  Pablo A. Iglesias,et al.  Quantifying robustness of biochemical network models , 2002, BMC Bioinformatics.

[33]  Bruce Futcher,et al.  Role of a ubiquitin-conjugating enzyme in degradation of S- and M-phase cyclins , 1995, Nature.

[34]  K. Hughes,et al.  Regulation of flagellar assembly. , 2002, Current opinion in microbiology.

[35]  A. Arkin,et al.  It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.

[36]  M. Mendenhall,et al.  An inhibitor of yeast cyclin-dependent protein kinase plays an important role in ensuring the genomic integrity of daughter cells. , 1994, Molecular and cellular biology.

[37]  Michael Schwab,et al.  Yeast Hct1 Is a Regulator of Clb2 Cyclin Proteolysis , 1997, Cell.

[38]  E. D. Gilles,et al.  Robustness vs. identifiability of regulatory modules? The case of mitotic control in budding yeast cell cycle regulation , 2001 .

[39]  P. Nurse A Long Twentieth Century of the Cell Cycle and Beyond , 2000, Cell.

[40]  C. Wittenberg,et al.  Rapid Degradation of the G1 Cyclin Cln2 Induced by CDK-Dependent Phosphorylation , 1996, Science.

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

[42]  D. Koshland,et al.  An amplified sensitivity arising from covalent modification in biological systems. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[43]  F. Cross,et al.  Testing a mathematical model of the yeast cell cycle. , 2002, Molecular biology of the cell.

[44]  Kim Nasmyth,et al.  The Polo‐like kinase Cdc5p and the WD‐repeat protein Cdc20p/fizzy are regulators and substrates of the anaphase promoting complex in Saccharomyces cerevisiae , 1998, The EMBO journal.

[45]  F. Cross,et al.  Two redundant oscillatory mechanisms in the yeast cell cycle. , 2003, Developmental cell.

[46]  L. Breeden,et al.  Periodic Transcription: A Cycle within a Cycle , 2003, Current Biology.

[47]  Katherine C. Chen,et al.  Kinetic analysis of a molecular model of the budding yeast cell cycle. , 2000, Molecular biology of the cell.

[48]  Bin Wu,et al.  A globally attractive cycle driven by sequential bifurcations containing ghost effects in a 3-node yeast cell cycle model , 2013, 1312.5204.

[49]  Volkan Sevim,et al.  Design Principles of the Yeast G1/S Switch , 2013, PLoS biology.

[50]  Kim Nasmyth,et al.  Closing the cell cycle circle in yeast: G2 cyclin proteolysis initiated at mitosis persists until the activation of G1 cyclins in the next cycle , 1994, Cell.

[51]  Jiri Bartek,et al.  Checking on DNA damage in S phase , 2004, Nature Reviews Molecular Cell Biology.

[52]  Curt Wittenberg,et al.  An essential G1 function for cyclin-like proteins in yeast , 1989, Cell.

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

[54]  J. Tyson,et al.  Mathematical model for early development of the sea urchin embryo , 2000, Bulletin of mathematical biology.

[55]  G S Taylor,et al.  The Activity of Cdc14p, an Oligomeric Dual Specificity Protein Phosphatase from Saccharomyces cerevisiae, Is Required for Cell Cycle Progression* , 1997, The Journal of Biological Chemistry.

[56]  Xiaoguang Li,et al.  Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process , 2015, PLoS Comput. Biol..

[57]  Frederick R. Cross,et al.  Periodic Cyclin-Cdk Activity Entrains an Autonomous Cdc14 Release Oscillator , 2010, Cell.

[58]  R. Deshaies,et al.  SIC1 is ubiquitinated in vitro by a pathway that requires CDC4, CDC34, and cyclin/CDK activities. , 1997, Molecular biology of the cell.

[59]  K Nasmyth,et al.  CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae. , 1993, Genes & development.

[60]  Attila Tóth,et al.  APCCdc20 promotes exit from mitosis by destroying the anaphase inhibitor Pds1 and cyclin Clb5 , 1999, Nature.

[61]  John J. Tyson,et al.  Molecular mechanisms creating bistable switches at cell cycle transitions , 2013, Open Biology.

[62]  S. Prinz,et al.  CDC20 and CDH1: a family of substrate-specific activators of APC-dependent proteolysis. , 1997, Science.

[63]  B. Futcher,et al.  The Cln3‐Cdc28 kinase complex of S. cerevisiae is regulated by proteolysis and phosphorylation. , 1992, The EMBO journal.

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

[65]  Mike Tyers,et al.  Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins , 1993, Cell.

[66]  F. Cross,et al.  Saccharomyces cerevisiae G1 cyclins differ in their intrinsic functional specificities , 1996, Molecular and cellular biology.

[67]  B. Futcher Transcriptional regulatory networks and the yeast cell cycle. , 2002, Current opinion in cell biology.

[68]  D. Burke,et al.  The spindle assembly and spindle position checkpoints. , 2003, Annual review of genetics.

[69]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[70]  David O. Morgan,et al.  Cyclin specificity in the phosphorylation of cyclin-dependent kinase substrates , 2005, Nature.

[71]  Mike Tyers,et al.  CDK Activity Antagonizes Whi5, an Inhibitor of G1/S Transcription in Yeast , 2004, Cell.

[72]  G. Braus,et al.  Two different modes of cyclin Clb2 proteolysis during mitosis in Saccharomyces cerevisiae , 2000, FEBS letters.

[73]  Chao Tang,et al.  Reliable cell cycle commitment in budding yeast is ensured by signal integration , 2014, eLife.

[74]  D. Koshland,et al.  The CDC20 gene product of Saccharomyces cerevisiae, a beta-transducin homolog, is required for a subset of microtubule-dependent cellular processes , 1991, Molecular and cellular biology.

[75]  F. Cross,et al.  Cyclin specificity: how many wheels do you need on a unicycle? , 2001, Journal of cell science.

[76]  J. Skotheim,et al.  Dilution of the cell cycle inhibitor Whi5 controls budding yeast cell size , 2015, Nature.

[77]  Nicola J. Rinaldi,et al.  Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle , 2001, Cell.

[78]  S. Reed,et al.  Ratchets and clocks: the cell cycle, ubiquitylation and protein turnover , 2003, Nature Reviews Molecular Cell Biology.

[79]  Hongtao Yu,et al.  Regulation of APC-Cdc20 by the spindle checkpoint. , 2002, Current opinion in cell biology.

[80]  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.

[81]  Claude Gérard,et al.  Minimal models for cell-cycle control based on competitive inhibition and multisite phosphorylations of Cdk substrates. , 2013, Biophysical journal.

[82]  F. Cross,et al.  Testing Cyclin Specificity in the Exit from Mitosis , 2000, Molecular and Cellular Biology.

[83]  Uttam Surana,et al.  The role of CDC28 and cyclins during mitosis in the budding yeast S. cerevisiae , 1991, Cell.

[84]  David O. Morgan,et al.  Positive feedback sharpens the anaphase switch , 2008, Nature.