Theory in Biosciences

, Volume 135, Issue 4, pp 231–240 | Cite as

Design specifications for cellular regulation

  • David C. Krakauer
  • Lydia Müller
  • Sonja J. Prohaska
  • Peter F. Stadler
Original Paper

Abstract

A critical feature of all cellular processes is the ability to control the rate of gene or protein expression and metabolic flux in changing environments through regulatory feedback. We review the many ways that regulation is represented through causal, logical, and dynamical components. Formalizing the nature of these components promotes effective comparison among distinct regulatory networks and provides a common framework for the potential design and control of regulatory systems in synthetic biology.

Keywords

Typed I/O maps Feedback Memory Codes 

Notes

Acknowledgements

The authors thank the John Templeton Foundation for funding this research with the Grant “Origins and Evolution of Regulation in Biological Systems”—ID: 24332. The opinions expressed in this publication are those of the author(s) and do not necessarily reflect the views of the John Templeton Foundation. This work was partially funded by the the German Federal Ministry of Science (0316165C) as part of the e:Bio initiative.

References

  1. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8:450–461CrossRefPubMedGoogle Scholar
  2. Armstrong M, Sappington DEM (2007) Recent developments in the theory of regulation. In: Armstrong M, Sappington DEM (eds) Handbook of Industrial Organization, vol III, North Holland, chap 27, pp 1557–1700Google Scholar
  3. Arnold C, Stadler PF, Prohaska SJ (2013) Chromatin computation: epigenetic inheritance as a pattern reconstruction problem. J Theor Biol 336:61–74CrossRefPubMedGoogle Scholar
  4. Ay N, Polani D (2008) Information flows in causal networks. Adv Complex Syst 11(01):17–41CrossRefGoogle Scholar
  5. Badeaux AI, Shi Y (2013) Emerging roles for chromatin as a signal integration and storage platform. Nat Rev Mol Cell Biol 14(4):211–224CrossRefPubMedCentralGoogle Scholar
  6. Barbieri M (2015) Code biology. Springer, HeidelbergCrossRefGoogle Scholar
  7. Bergman A, Siegal ML (2003) Evolutionary capacitance as a general feature of complex gene networks. Nature 424:549–552CrossRefPubMedGoogle Scholar
  8. Bolouri H, Davidson EH et al. (2002) Modeling transcriptional regulatory networks. BioEssays 24(12):1118–1129CrossRefPubMedGoogle Scholar
  9. Buchler NE, Gerland U, Hwa T (2003) On schemes of combinatorial transcription logic. Proc Natl Acad Sci 100(9):5136–5141CrossRefPubMedPubMedCentralGoogle Scholar
  10. Chen T, Dent SY (2014) Chromatin modifiers and remodellers: regulators of cellular differentiation. Nat Rev Genet 15(2):93–106CrossRefPubMedGoogle Scholar
  11. Chin JW (2012) Reprogramming the genetic code. Science 336:428–429CrossRefPubMedGoogle Scholar
  12. Churaev RI, Prokudina EI (1989) Modelling of the regulatory system of tryptophan biosynthesis using generalized threshold models. Genetika 25(3):535–44PubMedGoogle Scholar
  13. Darwiche A (2009) Modeling and Reasoning with Bayesian Networks. Cambridge Univ. Press, CambridgeCrossRefGoogle Scholar
  14. Davidson EH (2006) The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. Academic PressGoogle Scholar
  15. Davidson EH, Erwin DH (2006) Gene regulatory networks and the evolution of animal body plans. Science 311:796–800CrossRefPubMedGoogle Scholar
  16. Dion MF, Altschuler SJ, Wu LF, Rando OJ (2005) Genomic characterization reveals a simple histone h4 acetylation code. Proc Natl Acad Sci USA 102(15):5501–5506CrossRefPubMedPubMedCentralGoogle Scholar
  17. Djuranovic S, Nahvi A, Green R (2011) A parsimonious model for gene regulation by miRNAs. Science 331:550–553CrossRefPubMedPubMedCentralGoogle Scholar
  18. Hoffmann GW (1975) A theory of regulation and self-nonself discrimination in an immune network. Eur J Immunol 5:638–647CrossRefPubMedGoogle Scholar
  19. Inada T, Kimata K, Aiba H (1996) Mechanism responsible for glucose-lactose diauxie in Escherichia coli: challenge to the cAMP model. Genes Cells 1:293–301CrossRefPubMedGoogle Scholar
  20. Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3(3):318–356CrossRefPubMedGoogle Scholar
  21. Krebs J, Lewin B, Goldstein E, Kilpatrick S (2014) Lewin’s GENES XI. Jones & Bartlett Learning, BurlingtonGoogle Scholar
  22. Krishna R, Ramachandran P (1975) Analysis of diffusional effects in immobilized two-enzyme systems. J Appl Chem Biotechnol 25:623–640CrossRefGoogle Scholar
  23. MacDonald CT, Gibbs JH, Pipkin AC (1968) Kinetics of biopolymerization on nucleic acid templates. Biopolymers 6(1):1–5. doi: 10.1002/bip.1968.360060102 CrossRefPubMedGoogle Scholar
  24. Materna SC, Davidson EH (2007) Logic of gene regulatory networks. Curr Opin Biotechnol 18(4):351–354CrossRefPubMedPubMedCentralGoogle Scholar
  25. Mattick JS (2004) The hidden genetic program of complex organisms. Sci Am 291:60–67CrossRefPubMedGoogle Scholar
  26. Neumann H (2012) Rewiring translation—genetic code expansion and its applications. FEBS Lett 586:2057–2064CrossRefPubMedGoogle Scholar
  27. Prohaska SJ, Stadler PF, Krakauer DC (2010) Innovation in gene regulation: the case of chromatin computation. J Theor Biol 265:27–44CrossRefPubMedGoogle Scholar
  28. Silva-Rocha R, de Lorenzo V (2008) Mining logic gates in prokaryotic transcriptional regulation networks. FEBS Letters 582(8):1237–1244CrossRefPubMedGoogle Scholar
  29. Smith E, Krishnamurthy S, Fontana W, Krakauer D (2011) Nonequilibrium phase transitions in biomolecular signal transduction. Phys Rev E 84(051):917Google Scholar
  30. Spivak DI (2014) Category theory for the sciences. MIT Press, CambridgeGoogle Scholar
  31. Wagner A (1996) Does evolutionary plasticity evolve? Evolution 50:1008–1023CrossRefGoogle Scholar
  32. West M, Harrison J (2006) Bayesian forecasting and dynamic models. Springer Series in Statistics. Springer New York, New YorkGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Santa Fe InstituteSanta FeUSA
  2. 2.Natural Language Processing Group, Department of Computer Science, and Interdisciplinary Center for BioinformaticsUniversity LeipzigLeipzigGermany
  3. 3.Computational EvoDevo Group, Department of Computer Science and Interdisciplinary Center for BioinformaticsUniversity LeipzigLeipzigGermany
  4. 4.Bioinformatics Group at the Department of Computer Science, Interdisciplinary Center for Bioinformatics, ScaDS, Competence Center for Scalable Data services and Solutions, and German Center for Integrative Biodiversity ResearchUniversity LeipzigLeipzigGermany
  5. 5.Max-Planck Institute for Mathematics in the SciencesLeipzigGermany
  6. 6.Fraunhofer Institut für Zelltherapie und Immunologie–IZILeipzigGermany
  7. 7.Department of Theoretical ChemistryUniversity of ViennaWienAustria
  8. 8.Center for Non-Coding RNA in Technology and HealthUniversity of CopenhagenFrederiksberg CDenmark

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