Literature DB >> 15340155

Robustness properties of circadian clock architectures.

Jörg Stelling1, Ernst Dieter Gilles, Francis J Doyle.   

Abstract

Robustness, a relative insensitivity to perturbations, is a key characteristic of living cells. However, the specific structural characteristics that are responsible for robust performance are not clear, even in genetic circuits of moderate complexity. Formal sensitivity analysis allows the investigation of robustness and fragility properties of mathematical models representing regulatory networks, but it yields only local properties with respect to a particular choice of parameter values. Here, we show that by systematically investigating the parameter space, more global properties linked to network structure can be derived. Our analysis focuses on the genetic oscillator responsible for generating circadian rhythms in Drosophila as a prototypic dynamical cellular system. Analysis of two mathematical models of moderate complexity shows that the tradeoff between robustness and fragility is largely determined by the regulatory structure. Rank-ordered sensitivities, for instance, allow the correct identification of protein phosphorylation as an influential process determining the oscillator's period. Furthermore, sensitivity analysis confirms the theoretical insight that hierarchical control might be important for achieving robustness. The complex feedback structures encountered in vivo, however, do not seem to enhance robustness per se but confer robust precision and adjustability of the clock while avoiding catastrophic failure.

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Year:  2004        PMID: 15340155      PMCID: PMC516549          DOI: 10.1073/pnas.0401463101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  39 in total

1.  Cell signaling pathways as control modules: complexity for simplicity?

Authors:  D A Lauffenburger
Journal:  Proc Natl Acad Sci U S A       Date:  2000-05-09       Impact factor: 11.205

Review 2.  Time zones: a comparative genetics of circadian clocks.

Authors:  M W Young; S A Kay
Journal:  Nat Rev Genet       Date:  2001-09       Impact factor: 53.242

3.  Metabolic network structure determines key aspects of functionality and regulation.

Authors:  Jörg Stelling; Steffen Klamt; Katja Bettenbrock; Stefan Schuster; Ernst Dieter Gilles
Journal:  Nature       Date:  2002-11-14       Impact factor: 49.962

4.  Robustness as a measure of plausibility in models of biochemical networks.

Authors:  Mineo Morohashi; Amanda E Winn; Mark T Borisuk; Hamid Bolouri; John Doyle; Hiroaki Kitano
Journal:  J Theor Biol       Date:  2002-05-07       Impact factor: 2.691

5.  Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories.

Authors:  Brian P Ingalls; Herbert M Sauro
Journal:  J Theor Biol       Date:  2003-05-07       Impact factor: 2.691

Review 6.  Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora.

Authors:  J C Leloup; D Gonze; A Goldbeter
Journal:  J Biol Rhythms       Date:  1999-12       Impact factor: 3.182

7.  A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins.

Authors:  J C Leloup; A Goldbeter
Journal:  J Biol Rhythms       Date:  1998-02       Impact factor: 3.182

Review 8.  Engineered gene circuits.

Authors:  Jeff Hasty; David McMillen; J J Collins
Journal:  Nature       Date:  2002-11-14       Impact factor: 49.962

9.  vrille, Pdp1, and dClock form a second feedback loop in the Drosophila circadian clock.

Authors:  Shawn A Cyran; Anna M Buchsbaum; Karen L Reddy; Meng-Chi Lin; Nicholas R J Glossop; Paul E Hardin; Michael W Young; Robert V Storti; Justin Blau
Journal:  Cell       Date:  2003-02-07       Impact factor: 41.582

10.  Posttranslational regulation of Drosophila PERIOD protein by protein phosphatase 2A.

Authors:  Sriram Sathyanarayanan; Xiangzhong Zheng; Rui Xiao; Amita Sehgal
Journal:  Cell       Date:  2004-02-20       Impact factor: 41.582

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  78 in total

1.  A dynamic model for functional mapping of biological rhythms.

Authors:  Guifang Fu; Jiangtao Luo; Arthur Berg; Zhong Wang; Jiahan Li; Kiranmoy Das; Runze Li; Rongling Wu
Journal:  J Biol Dyn       Date:  2011-01       Impact factor: 2.179

2.  Architecture-dependent robustness and bistability in a class of genetic circuits.

Authors:  Jiajun Zhang; Zhanjiang Yuan; Han-Xiong Li; Tianshou Zhou
Journal:  Biophys J       Date:  2010-08-09       Impact factor: 4.033

Review 3.  Clocks not winding down: unravelling circadian networks.

Authors:  Eric E Zhang; Steve A Kay
Journal:  Nat Rev Mol Cell Biol       Date:  2010-11       Impact factor: 94.444

4.  The Steroid Hormone 20-Hydroxyecdysone Up-regulates Ste-20 Family Serine/Threonine Kinase Hippo to Induce Programmed Cell Death.

Authors:  Du-Juan Dong; Yu-Pu Jing; Wen Liu; Jin-Xing Wang; Xiao-Fan Zhao
Journal:  J Biol Chem       Date:  2015-08-13       Impact factor: 5.157

5.  Sensitivity analysis of discrete stochastic systems.

Authors:  Rudiyanto Gunawan; Yang Cao; Linda Petzold; Francis J Doyle
Journal:  Biophys J       Date:  2005-02-04       Impact factor: 4.033

6.  Model-driven designs of an oscillating gene network.

Authors:  Lisa M Tuttle; Howard Salis; Jonathan Tomshine; Yiannis N Kaznessis
Journal:  Biophys J       Date:  2005-09-23       Impact factor: 4.033

7.  Circuit topology and the evolution of robustness in two-gene circadian oscillators.

Authors:  Andreas Wagner
Journal:  Proc Natl Acad Sci U S A       Date:  2005-08-08       Impact factor: 11.205

8.  A model for the circadian rhythm of cyanobacteria that maintains oscillation without gene expression.

Authors:  Gen Kurosawa; Kazuyuki Aihara; Yoh Iwasa
Journal:  Biophys J       Date:  2006-06-23       Impact factor: 4.033

9.  Isochron-based phase response analysis of circadian rhythms.

Authors:  Rudiyanto Gunawan; Francis J Doyle
Journal:  Biophys J       Date:  2006-06-30       Impact factor: 4.033

10.  A method for determining the robustness of bio-molecular oscillator models.

Authors:  Reza Ghaemi; Jing Sun; Pablo A Iglesias; Domitilla Del Vecchio
Journal:  BMC Syst Biol       Date:  2009-09-21
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