Multifunctionality and robustness trade-offs in model genetic circuits.

Most cellular systems, from macromolecules to genetic networks, have more than one function. Examples involving networks include the transcriptional regulation circuits formed by Hox genes and the Drosophila segmentation genes, which function in both early and later developmental events. Does the need to carry out more than one function severely constrain network architecture? Does it imply robustness trade-offs among functions? That is, if one function is highly robust to mutations, are other functions highly sensitive, and vice versa? Little available evidence speaks to these questions. We address them with a general model of transcriptional regulation networks. We show that requiring a regulatory network to carry out additional functions constrains the number of permissible network architectures exponentially. However, robustness of one function to regulatory mutations is uncorrelated or weakly positively correlated to robustness of other functions. This means that robustness trade-offs generally do not arise in the systems we study. As long as there are many alternative network structures, each of which can fulfill all required functions, multiple functions may acquire high robustness through gradual Darwinian evolution.

[1]  Gerard Toulouse,et al.  Theory of the frustration effect in spin glasses: I , 1986 .

[2]  Daniel J. Amit,et al.  Modeling brain function: the world of attractor neural networks, 1st Edition , 1989 .

[3]  David H. Sharp,et al.  A connectionist model of development. , 1991, Journal of theoretical biology.

[4]  P. Schuster,et al.  From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[5]  David H. Sharp,et al.  Mechanism of eve stripe formation , 1995, Mechanisms of Development.

[6]  A. Wagner DOES EVOLUTIONARY PLASTICITY EVOLVE? , 1996, Evolution; international journal of organic evolution.

[7]  David H. Sharp,et al.  Prediction of mutant expression patterns using gene circuits. , 1998, Bio Systems.

[8]  U. Alon,et al.  Robustness in bacterial chemotaxis , 2022 .

[9]  M. Freeman Feedback control of intercellular signalling in development , 2000, Nature.

[10]  S. Carroll,et al.  From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design , 2000 .

[11]  G. Odell,et al.  The segment polarity network is a robust developmental module , 2000, Nature.

[12]  J. Edwards,et al.  Robustness Analysis of the Escherichiacoli Metabolic Network , 2000, Biotechnology progress.

[13]  A. Bergman,et al.  Waddington's canalization revisited: Developmental stability and evolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[14]  A. Goldbeter,et al.  Robustness of circadian rhythms with respect to molecular noise , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[15]  J. Doyle,et al.  Robustness as a measure of plausibility in models of biochemical networks. , 2002, Journal of theoretical biology.

[16]  N. Barkai,et al.  Robustness of the BMP morphogen gradient in Drosophila embryonic patterning , 2022 .

[17]  M. Laubichler Review of: Carroll, Sean B., Jennifer K. Grenier and Scott D. Weatherbee: From DNA to diversity : molecular genetics and the evolution of animal design. Malden, Mass [u.a.]: Blackwell Science 2001 , 2003 .

[18]  A. Bergman,et al.  Evolutionary capacitance as a general feature of complex gene networks , 2003, Nature.

[19]  H. Othmer,et al.  The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. , 2003, Journal of theoretical biology.

[20]  J. Doyle,et al.  Metabolic syndrome and robustness tradeoffs. , 2004, Diabetes.

[21]  Q. Ouyang,et al.  The yeast cell-cycle network is robustly designed. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[22]  J. Stelling,et al.  Robustness properties of circadian clock architectures. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Nicholas T Ingolia,et al.  Topology and Robustness in the Drosophila Segment Polarity Network , 2004, PLoS biology.

[24]  C. Espinosa-Soto,et al.  A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is Robust and Recovers Experimental Gene Expression Profilesw⃞ , 2004, The Plant Cell Online.

[25]  David H. Sharp,et al.  Dynamic control of positional information in the early Drosophila embryo , 2004, Nature.

[26]  Massimo Marchiori,et al.  Error and attacktolerance of complex network s , 2004 .

[27]  A. Wagner Circuit topology and the evolution of robustness in two-gene circadian oscillators. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Kristen K. Dang,et al.  Sexual reproduction selects for robustness and negative epistasis in artificial gene networks , 2006, Nature.

[29]  Luhua Lai,et al.  Robustness and modular design of the Drosophila segment polarity network , 2006, Molecular systems biology.

[30]  Andreas Wagner,et al.  Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology , 2007, PLoS Comput. Biol..