Noise propagation and signaling sensitivity in biological networks: a role for positive feedback

PLoS Computational Biology
Gil Hornung, Naama Barkai

Abstract

Interactions between genes and proteins are crucial for efficient processing of internal or external signals, but this connectivity also amplifies stochastic fluctuations by propagating noise between components. Linear (unbranched) cascades were shown to exhibit an interplay between the sensitivity to changes in input signals and the ability to buffer noise. We searched for biological circuits that can maintain signaling sensitivity while minimizing noise propagation, focusing on cases where the noise is characterized by rapid fluctuations. Negative feedback can buffer this type of noise, but this buffering comes at the expense of an even greater reduction in signaling sensitivity. By systematically analyzing three-component circuits, we identify positive feedback as a central motif allowing for the buffering of propagated noise while maintaining sensitivity to long-term changes in input signals. We show analytically that noise reduction in the presence of positive feedback results from improved averaging of rapid fluctuations over time, and discuss in detail a particular implementation in the control of nutrient homeostasis in yeast. As the design of biological networks optimizes for multiple constraints, positive feedback can...Continue Reading

References

Jun 13, 2000·Nature·A Becskei, L Serrano
Jun 14, 2002·Gene·Boris Magasanik, Chris A Kaiser
Sep 19, 2002·Proceedings of the National Academy of Sciences of the United States of America·Peter S SwainEric D Siggia
Nov 6, 2002·Journal of Molecular Biology·Nitzan RosenfeldUri Alon
Nov 15, 2002·Nature·Christopher V RaoAdam P Arkin
Apr 3, 2003·Proceedings of the National Academy of Sciences of the United States of America·Michael L SimpsonGary S Sayler
Oct 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·S Mangan, U Alon
Jan 30, 2004·Nature·Johan Paulsson
Dec 31, 2004·Proceedings of the National Academy of Sciences of the United States of America·Tatsuo Shibata, Koichi Fujimoto
Mar 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Sara HooshangiRon Weiss
Mar 26, 2005·Science·Juan M Pedraza, Alexander van Oudenaarden
Apr 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Erik M BoczkoK Sam Wells
Apr 27, 2005·Journal of Bioinformatics and Computational Biology·Stephen RamseyHamid Bolouri
Jul 12, 2005·Proceedings of the National Academy of Sciences of the United States of America·William Bialek, Sima Setayeshgar
Sep 24, 2005·Science·Jonathan M Raser, Erin K O'Shea
Sep 29, 2005·PLoS Biology·Robert J PrillAndre Levchenko
Feb 3, 2006·Nature·D W AustinM L Simpson
Jun 2, 2006·Molecular Systems Biology·Andreas DoncicNaama Barkai
Aug 3, 2006·Molecular Systems Biology·Yann DublancheLuis Serrano
Dec 26, 2006·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Dongsan KimKwang-Hyun Cho
May 5, 2007·Annual Review of Biophysics and Biomolecular Structure·Narendra Maheshri, Erin K O'Shea
Aug 21, 2007·Biophysical Journal·Cheemeng TanLingchong You

❮ Previous
Next ❯

Citations

Mar 8, 2013·The Journal of Chemical Physics·Jiajun ZhangTianshou Zhou
May 12, 2009·Journal of Bacteriology·Szabolcs SemseySankar Adhya
Sep 19, 2009·PLoS Computational Biology·Frank J BruggemanHans V Westerhoff
May 6, 2010·PLoS Computational Biology·Liming WangQing Nie
Sep 25, 2010·PloS One·Raúl GuantesJuan F Poyatos
Jun 1, 2011·PLoS Computational Biology·Volker PerniceStefan Rotter
Jun 3, 2011·Proceedings of the National Academy of Sciences of the United States of America·Malte PaulsenChristof Niehrs
Aug 13, 2011·Physical Biology·Shangying Wang, Sridhar Raghavachari
Sep 29, 2011·BMC Systems Biology·Diana Clausznitzer, Robert G Endres
Jun 7, 2013·Interdisciplinary Sciences, Computational Life Sciences·David G Míguez
Dec 17, 2009·IET Systems Biology·E D Sontag
Dec 15, 2011·BMC Systems Biology·Ching-Shan ChouTau-Mu Yi
Feb 26, 2016·Frontiers in Genetics·Smadar Ben-Tabou de-Leon
Feb 10, 2016·Developmental Cell·Yevgeniy PlavskinMarja C P Timmermans
Mar 1, 2012·Trends in Genetics : TIG·Guilhem ChalanconM Madan Babu
Jul 5, 2011·Journal of Theoretical Biology·Nicolae Radu Zabet
Mar 23, 2011·Mathematical Biosciences·Pau Rué, Jordi Garcia-Ojalvo
Jun 19, 2013·ACS Synthetic Biology·Meng ChenQing Nie
Jun 9, 2009·Journal of Theoretical Biology·Mukhtar Ullah, Olaf Wolkenhauer
Apr 24, 2014·Bulletin of Mathematical Biology·Arnaud Tonnelier
Jul 31, 2013·Scientific Reports·Hiroyuki Kuwahara, Xin Gao
May 27, 2011·Molecular Systems Biology·Raphaela Fritsche-GuentherNils Blüthgen
May 16, 2012·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Kumar Selvarajoo
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Mukhtar Ullah, Olaf Wolkenhauer
Nov 27, 2015·Journal of the Royal Society, Interface·Andreas Milias-ArgeitisMustafa Khammash
Apr 1, 2016·Scientific Reports·Surendhar Reddy ChepyalaChao-Ping Hsu
Dec 6, 2012·Journal of Mathematical Physics·Likun ZhengQing Nie
Dec 7, 2013·Biochemical and Biophysical Research Communications·Eunyeong Shim, Sang-Hyun Park
Feb 13, 2015·SpringerPlus·Pushkar MalakarKareenhalli V Venkatesh
Sep 27, 2012·Biophysical Journal·Zhanghan Wu, Jianhua Xing
Dec 12, 2012·Molecular BioSystems·Javier Estrada, Raúl Guantes

❮ Previous
Next ❯

Software Mentioned

Maple Maple

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.