Functions of bifans in context of multiple regulatory motifs in signaling networks

Biophysical Journal
Azi LipshtatAvi Ma'ayan

Abstract

Representation of intracellular signaling networks as directed graphs allows for the identification of regulatory motifs. Regulatory motifs are groups of nodes with the same connectivity structure, capable of processing information. The bifan motif, made of two source nodes directly crossregulating two target nodes, is an overrepresented motif in a mammalian cell signaling network and in transcriptional networks. One example of a bifan is the two MAP-kinases, p38, and JNK that phosphorylate and activate the two transcription factors ATF2 and Elk-1. We have used a system of coupled ordinary differential equations to analyze the regulatory capability of this bifan motif by itself, and when it interacts with other motifs such as positive and negative feedback loops. Our results indicate that bifans provide temporal regulation of signal propagation and act as signal sorters, filters, and synchronizers. Bifans that have OR gate configurations show rapid responses whereas AND gate bifans can introduce delays and allow prolongation of signal outputs. Bifans that have AND gates can filter noisy signal inputs. The p38/JNK-ATF2/Elk-1bifan synchronizes the output of activated transcription factors. Synchronization is a robust property of ...Continue Reading

References

Jun 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·V AdlerA S Kraft
Nov 24, 1995·Science·Z XiaM E Greenberg
Nov 24, 1995·The Journal of Biological Chemistry·S BagrodiaR A Cerione
Dec 1, 1993·Molecular and Cellular Biology·R Wisdon, I M Verma
Sep 1, 1993·Molecular and Cellular Biology·T K Kerppola, T Curran
Apr 16, 1996·Proceedings of the National Academy of Sciences of the United States of America·A Sitlani, D M Crothers
Nov 12, 1996·Proceedings of the National Academy of Sciences of the United States of America·K G MendelsonK E Paulson
Mar 4, 1997·Proceedings of the National Academy of Sciences of the United States of America·V AdlerZ Ronai
Aug 26, 1997·Biochemistry·P V LoGrassoE A O'Neill
Jan 15, 2000·The Journal of Biological Chemistry·V DrewettP E Shaw
Feb 5, 2000·Nature·M B Elowitz, S Leibler
Jun 24, 2000·Nature·D EisenbergT O Yeates
Feb 22, 2001·Science·J C VenterX Zhu
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
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
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Nov 5, 2002·The Journal of Biological Chemistry·Pankaj Gupta, Ron Prywes
Jun 5, 2003·Chaos·Upinder S. Bhalla, Ravi Iyengar
Oct 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·S Mangan, U Alon
Jan 28, 2004·The Journal of Cell Biology·Nick I MarkevichBoris N Kholodenko
Feb 10, 2004·Proceedings of the National Academy of Sciences of the United States of America·David AngeliEduardo D Sontag
Jul 3, 2004·American Journal of Respiratory Cell and Molecular Biology·Raj WadgaonkarJoe G N Garcia

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Citations

Oct 23, 2008·The Journal of Biological Chemistry·Avi Ma'ayan
Sep 16, 2011·Science Signaling·Avi Ma'ayan
Apr 19, 2012·Science Signaling·Boris KholodenkoWalter Kolch
Aug 13, 2010·Theoretical Biology & Medical Modelling·Paolo TieriClaudio Franceschi
Mar 8, 2011·Mathematical Biosciences·Yun LeeEberhard O Voit
Sep 10, 2014·IEEE Transactions on Biomedical Circuits and Systems·Pei WangZengrong Liu
Jun 27, 2014·Briefings in Bioinformatics·Ngoc Tam L TranChun-Hsi Huang
Apr 8, 2009·Annals of the New York Academy of Sciences·Azi LipshtatRavi Iyengar
Mar 30, 2021·Frontiers in Microbiology·Gonzalo Durante-RodríguezVíctor de Lorenzo

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