Literature DB >> 25456048

Ultrasensitivity part III: cascades, bistable switches, and oscillators.

James E Ferrell1, Sang Hoon Ha2.   

Abstract

Switch-like, ultrasensitive responses - responses that resemble those of cooperative enzymes but are not necessarily generated by cooperativity - are widespread in signal transduction. In the previous installments in this series, we reviewed several mechanisms for generating ultrasensitivity: zero-order ultrasensitivity; multistep ultrasensitivity; inhibitor ultrasensitivity; and positive feedback (or double negative feedback) loops. In this review, we focus on how ultrasensitive components can be important for the functioning of more complex signaling circuits. Ultrasensitivity can allow the effective transmission of signals down a signaling cascade, can contribute to the generation of bistability by positive feedback, and can promote the production of biochemical oscillations in negative feedback loops. This makes ultrasensitivity a key building block in systems biology and synthetic biology.
Copyright © 2014 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  bistability; limit cycle oscillations; negative feedback; positive feedback; signaling cascades; ultrasensitivity

Mesh:

Year:  2014        PMID: 25456048      PMCID: PMC4254632          DOI: 10.1016/j.tibs.2014.10.002

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  23 in total

1.  A synthetic oscillatory network of transcriptional regulators.

Authors:  M B Elowitz; S Leibler
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

2.  Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2.

Authors:  Joseph R Pomerening; Eduardo D Sontag; James E Ferrell
Journal:  Nat Cell Biol       Date:  2003-04       Impact factor: 28.824

3.  Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible.

Authors:  James E. Ferrell; Wen Xiong
Journal:  Chaos       Date:  2001-03       Impact factor: 3.642

4.  Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.

Authors:  Sara Hooshangi; Stephan Thiberge; Ron Weiss
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-28       Impact factor: 11.205

5.  Substrate competition as a source of ultrasensitivity in the inactivation of Wee1.

Authors:  Sun Young Kim; James E Ferrell
Journal:  Cell       Date:  2007-03-23       Impact factor: 41.582

6.  The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch.

Authors:  Qiong Yang; James E Ferrell
Journal:  Nat Cell Biol       Date:  2013-04-28       Impact factor: 28.824

Review 7.  Ultrasensitivity part II: multisite phosphorylation, stoichiometric inhibitors, and positive feedback.

Authors:  James E Ferrell; Sang Hoon Ha
Journal:  Trends Biochem Sci       Date:  2014-10-23       Impact factor: 13.807

8.  Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos.

Authors:  B Novak; J J Tyson
Journal:  J Cell Sci       Date:  1993-12       Impact factor: 5.285

9.  Changes in oscillatory dynamics in the cell cycle of early Xenopus laevis embryos.

Authors:  Tony Y-C Tsai; Julie A Theriot; James E Ferrell
Journal:  PLoS Biol       Date:  2014-02-11       Impact factor: 8.029

10.  A fast, robust and tunable synthetic gene oscillator.

Authors:  Jesse Stricker; Scott Cookson; Matthew R Bennett; William H Mather; Lev S Tsimring; Jeff Hasty
Journal:  Nature       Date:  2008-10-29       Impact factor: 49.962

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  51 in total

Review 1.  Illuminating the Cell's Biochemical Activity Architecture.

Authors:  Sohum Mehta; Jin Zhang
Journal:  Biochemistry       Date:  2017-08-01       Impact factor: 3.162

2.  Single-Molecule Threshold of HIV Fate Decision.

Authors:  Roy Wollman
Journal:  Biophys J       Date:  2017-06-06       Impact factor: 4.033

Review 3.  Bistable switches as integrators and actuators during cell cycle progression.

Authors:  Wayne Stallaert; Katarzyna M Kedziora; Hui Xiao Chao; Jeremy E Purvis
Journal:  FEBS Lett       Date:  2019-10-16       Impact factor: 4.124

4.  Feedforward Control of Plant Nitrate Transporter NRT1.1 Biphasic Adaptive Activity.

Authors:  Mubasher Rashid; Soumen Bera; Malay Banerjee; Alexander B Medvinsky; Gui-Quan Sun; Bai-Lian Li; Adnan Sljoka; Amit Chakraborty
Journal:  Biophys J       Date:  2019-10-22       Impact factor: 4.033

5.  Switches induced by quorum sensing in a model of enzyme-loaded microparticles.

Authors:  Tamás Bánsági; Annette F Taylor
Journal:  J R Soc Interface       Date:  2017-03       Impact factor: 4.118

6.  Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch.

Authors:  Kotaro Fujimaki; Ruoyan Li; Hengyu Chen; Kimiko Della Croce; Hao Helen Zhang; Jianhua Xing; Fan Bai; Guang Yao
Journal:  Proc Natl Acad Sci U S A       Date:  2019-10-21       Impact factor: 11.205

7.  Thresholds and ultrasensitivity from negative cooperativity.

Authors:  S H Ha; J E Ferrell
Journal:  Science       Date:  2016-05-12       Impact factor: 47.728

8.  Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design.

Authors:  Shuyi Zhang; Christopher A Voigt
Journal:  Nucleic Acids Res       Date:  2018-11-16       Impact factor: 16.971

9.  Interlinked GTPase cascades provide a motif for both robust switches and oscillators.

Authors:  Andreas Ehrmann; Basile Nguyen; Udo Seifert
Journal:  J R Soc Interface       Date:  2019-08-07       Impact factor: 4.118

10.  Ubiquitin Receptor Protein UBASH3B Drives Aurora B Recruitment to Mitotic Microtubules.

Authors:  Ksenia Krupina; Charlotte Kleiss; Thibaud Metzger; Sadek Fournane; Stephane Schmucker; Kay Hofmann; Benoit Fischer; Nicodeme Paul; Iain Malcolm Porter; Wolfgang Raffelsberger; Olivier Poch; Jason Reese Swedlow; Laurent Brino; Izabela Sumara
Journal:  Dev Cell       Date:  2016-01-11       Impact factor: 12.270

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