Energy landscape reveals that the budding yeast cell cycle is a robust and adaptive multi-stage process

PLoS Computational Biology
Cheng LvTiejun Li

Abstract

Quantitatively understanding the robustness, adaptivity and efficiency of cell cycle dynamics under the influence of noise is a fundamental but difficult question to answer for most eukaryotic organisms. Using a simplified budding yeast cell cycle model perturbed by intrinsic noise, we systematically explore these issues from an energy landscape point of view by constructing an energy landscape for the considered system based on large deviation theory. Analysis shows that the cell cycle trajectory is sharply confined by the ambient energy barrier, and the landscape along this trajectory exhibits a generally flat shape. We explain the evolution of the system on this flat path by incorporating its non-gradient nature. Furthermore, we illustrate how this global landscape changes in response to external signals, observing a nice transformation of the landscapes as the excitable system approaches a limit cycle system when nutrients are sufficient, as well as the formation of additional energy wells when the DNA replication checkpoint is activated. By taking into account the finite volume effect, we find additional pits along the flat cycle path in the landscape associated with the checkpoint mechanism of the cell cycle. The differen...Continue Reading

References

Nov 3, 1989·Science·L H Hartwell, T A Weinert
Jan 19, 2000·Molecular Biology of the Cell·K C ChenJ J Tyson
Feb 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·J A Sethian
Dec 6, 2001·Nature Reviews. Molecular Cell Biology·J J TysonB Novak
Aug 17, 2002·Science·Michael B ElowitzPeter S Swain
Sep 19, 2002·Proceedings of the National Academy of Sciences of the United States of America·Peter S SwainEric D Siggia
Nov 1, 2002·Cell·Wayne A Wilson, Peter J Roach
Mar 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Fangting LiChao Tang
May 29, 2004·Science·Jonathan M Raser, Erin K O'Shea
Sep 24, 2005·Science·Jonathan M Raser, Erin K O'Shea
Oct 11, 2005·Annual Review of Cell and Developmental Biology·Christopher M Waters, Bonnie L Bassler
Jun 2, 2006·Molecular Systems Biology·Jeffrey A Ubersax, James E Ferrell
Apr 20, 2007·Journal of Cellular Physiology·Qi LuDavid Jourd'Heuil
Jul 3, 2007·Nature Cell Biology·Bela NovakAttila Csikasz-Nagy
Jul 18, 2008·Nature·Jan M SkotheimFrederick R Cross
Aug 23, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jin WangErkang Wang
Feb 24, 2009·Current Opinion in Cell Biology·Anna M FriedelSusan M Gasser
Apr 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·G CharvinE D Siggia
Dec 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Claude Gérard, Albert Goldbeter
Apr 16, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jin WangErkang Wang
Sep 11, 2010·Nature·Avigdor Eldar, Michael B Elowitz
Mar 19, 2011·Cell·James E FerrellQiong Yang
Mar 19, 2011·Cell·Gábor BalázsiJames J Collins
Jul 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Andreas Hilfinger, Johan Paulsson
Apr 14, 2012·Science·Brian MunskyAlexander van Oudenaarden
Aug 18, 2012·The Journal of Chemical Physics·Feng ZhangJin Wang
Nov 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Weihua ZhengPeter G Wolynes
Apr 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Lei Shi, Benjamin P Tu
Nov 29, 2013·Proceedings of the National Academy of Sciences of the United States of America·Weihua ZhengPeter G Wolynes
Dec 7, 2013·Science·Joe H LevineMichael B Elowitz
Sep 18, 2014·Proceedings of the National Academy of Sciences of the United States of America·Chunhe Li, Jin Wang

❮ Previous
Next ❯

Citations

Jan 18, 2018·Integrative Biology : Quantitative Biosciences From Nano to Macro·Chunhe Li
Jun 19, 2015·BMC Systems Biology·Ye ChenTiejun Li
Aug 30, 2018·NPJ Systems Biology and Applications·Chunhe Li, Gabor Balazsi
Aug 14, 2020·Journal of Clinical Medicine·Zihao Chen, Chunhe Li
Mar 5, 2020·Computational and Structural Biotechnology Journal·Xin Kang, Chunhe Li
Oct 10, 2021·Cell Systems·Megan A CoomerMichael P H Stumpf
Nov 16, 2021·Frontiers in Computational Neuroscience·Leijun Ye, Chunhe Li

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cell Cycle Pathways

Cell cycle is a complex process regulated by several signal transduction pathways and enzymes. Here is the latest research on regulation of cell cycle and cell cycle pathways.

Cell Checkpoints & Regulators

Cell cycle checkpoints are a series of complex checkpoint mechanisms that detect DNA abnormalities and ensure that DNA replication and repair are complete before cell division. They are primarily regulated by cyclins, cyclin-dependent kinases, and the anaphase-promoting complex/cyclosome. Here is the latest research.