Literature DB >> 22304295

Competition for catalytic resources alters biological network dynamics.

Yannick Rondelez1.   

Abstract

Genetic regulation networks orchestrate many complex cellular behaviors. Dynamic operations that take place within cells are thus dependent on the gene expression machinery, enabled by powerful enzymes such as polymerases, ribosomes, or nucleases. These generalist enzymes typically process many different substrates, potentially leading to competitive situations: by saturating the common enzyme, one substrate may down-regulate its competitors. However, most theoretical or experimental models simply omit these effects, focusing on the pattern of genetic regulatory interactions as the main determinant of network function. We show here that competition effects have important outcomes, which can be spotted within the global dynamics of experimental systems. Further we demonstrate that enzyme saturation creates a layer of cross couplings that may foster, but also hamper, the expected behavior of synthetic biology constructs.

Mesh:

Year:  2012        PMID: 22304295     DOI: 10.1103/PhysRevLett.108.018102

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  24 in total

1.  Scaling down DNA circuits with competitive neural networks.

Authors:  Anthony J Genot; Teruo Fujii; Yannick Rondelez
Journal:  J R Soc Interface       Date:  2013-06-12       Impact factor: 4.118

2.  Translational cross talk in gene networks.

Authors:  William H Mather; Jeff Hasty; Lev S Tsimring; Ruth J Williams
Journal:  Biophys J       Date:  2013-06-04       Impact factor: 4.033

3.  A little cooperation helps murine cytomegalovirus (MCMV) go a long way: MCMV co-infection rescues a chemokine salivary gland defect.

Authors:  Pranay Dogra; Mindy Miller-Kittrell; Elisabeth Pitt; Joseph W Jackson; Tom Masi; Courtney Copeland; Shuen Wu; William E Miller; Tim Sparer
Journal:  J Gen Virol       Date:  2016-09-13       Impact factor: 3.891

4.  Prediction of Cellular Burden with Host-Circuit Models.

Authors:  Evangelos-Marios Nikolados; Andrea Y Weiße; Diego A Oyarzún
Journal:  Methods Mol Biol       Date:  2021

5.  Microscopic agents programmed by DNA circuits.

Authors:  G Gines; A S Zadorin; J-C Galas; T Fujii; A Estevez-Torres; Y Rondelez
Journal:  Nat Nanotechnol       Date:  2017-01-30       Impact factor: 39.213

6.  Bottom-up construction of in vitro switchable memories.

Authors:  Adrien Padirac; Teruo Fujii; Yannick Rondelez
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-29       Impact factor: 11.205

7.  Computer-assisted design for scaling up systems based on DNA reaction networks.

Authors:  Nathanaël Aubert; Clément Mosca; Teruo Fujii; Masami Hagiya; Yannick Rondelez
Journal:  J R Soc Interface       Date:  2014-01-22       Impact factor: 4.118

Review 8.  Noise in biology.

Authors:  Lev S Tsimring
Journal:  Rep Prog Phys       Date:  2014-01-20

9.  Diverse role of decoys on emergence and precision of oscillations in a biomolecular clock.

Authors:  Supravat Dey; Abhyudai Singh
Journal:  Biophys J       Date:  2021-11-11       Impact factor: 4.033

10.  Invariance and optimality in the regulation of an enzyme.

Authors:  Ed Reznik; Stefan Yohe; Daniel Segrè
Journal:  Biol Direct       Date:  2013-03-22       Impact factor: 4.540

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