Literature DB >> 25504722

Systems biology. Accurate information transmission through dynamic biochemical signaling networks.

Jangir Selimkhanov1, Brooks Taylor1, Jason Yao2, Anna Pilko2, John Albeck3, Alexander Hoffmann4, Lev Tsimring5, Roy Wollman6.   

Abstract

Stochasticity inherent to biochemical reactions (intrinsic noise) and variability in cellular states (extrinsic noise) degrade information transmitted through signaling networks. We analyzed the ability of temporal signal modulation--that is, dynamics--to reduce noise-induced information loss. In the extracellular signal-regulated kinase (ERK), calcium (Ca(2+)), and nuclear factor kappa-B (NF-κB) pathways, response dynamics resulted in significantly greater information transmission capacities compared to nondynamic responses. Theoretical analysis demonstrated that signaling dynamics has a key role in overcoming extrinsic noise. Experimental measurements of information transmission in the ERK network under varying signal-to-noise levels confirmed our predictions and showed that signaling dynamics mitigate, and can potentially eliminate, extrinsic noise-induced information loss. By curbing the information-degrading effects of cell-to-cell variability, dynamic responses substantially increase the accuracy of biochemical signaling networks.
Copyright © 2014, American Association for the Advancement of Science.

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Year:  2014        PMID: 25504722      PMCID: PMC4813785          DOI: 10.1126/science.1254933

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  24 in total

1.  Optimizing information flow in small genetic networks. II. Feed-forward interactions.

Authors:  Aleksandra M Walczak; Gasper Tkacik; William Bialek
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-04-06

2.  The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier.

Authors:  Oliver E Sturm; Richard Orton; Joan Grindlay; Marc Birtwistle; Vladislav Vyshemirsky; David Gilbert; Muffy Calder; Andrew Pitt; Boris Kholodenko; Walter Kolch
Journal:  Sci Signal       Date:  2010-12-21       Impact factor: 8.192

3.  Information flow and optimization in transcriptional regulation.

Authors:  Gasper Tkacik; Curtis G Callan; William Bialek
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-21       Impact factor: 11.205

4.  Mutual information between input and output trajectories of biochemical networks.

Authors:  Filipe Tostevin; Pieter Rein ten Wolde
Journal:  Phys Rev Lett       Date:  2009-05-27       Impact factor: 9.161

5.  Effect of feedback on the fidelity of information transmission of time-varying signals.

Authors:  Wiet Hendrik de Ronde; Filipe Tostevin; Pieter Rein ten Wolde
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-09-24

6.  Robustness in simple biochemical networks.

Authors:  N Barkai; S Leibler
Journal:  Nature       Date:  1997-06-26       Impact factor: 49.962

7.  Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate.

Authors:  Silvia D M Santos; Peter J Verveer; Philippe I H Bastiaens
Journal:  Nat Cell Biol       Date:  2007-02-18       Impact factor: 28.824

8.  Dynamics and variability of ERK2 response to EGF in individual living cells.

Authors:  Cellina Cohen-Saidon; Ariel A Cohen; Alex Sigal; Yuvalal Liron; Uri Alon
Journal:  Mol Cell       Date:  2009-12-11       Impact factor: 17.970

9.  Information processing and signal integration in bacterial quorum sensing.

Authors:  Pankaj Mehta; Sidhartha Goyal; Tao Long; Bonnie L Bassler; Ned S Wingreen
Journal:  Mol Syst Biol       Date:  2009-11-17       Impact factor: 11.429

10.  Negative feedback that improves information transmission in yeast signalling.

Authors:  Richard C Yu; C Gustavo Pesce; Alejandro Colman-Lerner; Larry Lok; David Pincus; Eduard Serra; Mark Holl; Kirsten Benjamin; Andrew Gordon; Roger Brent
Journal:  Nature       Date:  2008-12-11       Impact factor: 49.962

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  130 in total

Review 1.  Signal Transduction at the Single-Cell Level: Approaches to Study the Dynamic Nature of Signaling Networks.

Authors:  L Naomi Handly; Jason Yao; Roy Wollman
Journal:  J Mol Biol       Date:  2016-07-16       Impact factor: 5.469

2.  Identifying Noise Sources governing cell-to-cell variability.

Authors:  Simon Mitchell; Alexander Hoffmann
Journal:  Curr Opin Syst Biol       Date:  2017-12-06

3.  High-throughput microfluidics to control and measure signaling dynamics in single yeast cells.

Authors:  Anders S Hansen; Nan Hao; Erin K O'Shea
Journal:  Nat Protoc       Date:  2015-07-09       Impact factor: 13.491

4.  Robustness, Accuracy, and Cell State Heterogeneity in Biological Systems.

Authors:  Roy Wollman
Journal:  Curr Opin Syst Biol       Date:  2017-12-15

Review 5.  Information processing in bacteria: memory, computation, and statistical physics: a key issues review.

Authors:  Ganhui Lan; Yuhai Tu
Journal:  Rep Prog Phys       Date:  2016-04-08

6.  Distinct single-cell signaling characteristics are conferred by the MyD88 and TRIF pathways during TLR4 activation.

Authors:  Zhang Cheng; Brooks Taylor; Diana R Ourthiague; Alexander Hoffmann
Journal:  Sci Signal       Date:  2015-07-14       Impact factor: 8.192

7.  NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop.

Authors:  Mialy M DeFelice; Helen R Clark; Jacob J Hughey; Inbal Maayan; Takamasa Kudo; Miriam V Gutschow; Markus W Covert; Sergi Regot
Journal:  Sci Signal       Date:  2019-04-30       Impact factor: 8.192

8.  Dynamic Sampling and Information Encoding in Biochemical Networks.

Authors:  Garrett D Potter; Tommy A Byrd; Andrew Mugler; Bo Sun
Journal:  Biophys J       Date:  2017-02-28       Impact factor: 4.033

9.  Sensing relative signal in the Tgf-β/Smad pathway.

Authors:  Christopher L Frick; Clare Yarka; Harry Nunns; Lea Goentoro
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-20       Impact factor: 11.205

10.  Fundamental trade-offs between information flow in single cells and cellular populations.

Authors:  Ryan Suderman; John A Bachman; Adam Smith; Peter K Sorger; Eric J Deeds
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-12       Impact factor: 11.205

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