Circuit Motifs

  • Mario Andrea Marchisio
Part of the Learning Materials in Biosciences book series (LMB)


Gene circuit motifs are structural patterns associated with specific functions. In genetic networks, motifs are made of a small number of transcription units. A single transcription unit that contains a regulated promoter is sufficient to have either a negative or a positive feedback loop. Although very simple, they carry out important tasks such as speed up or slow down the circuit response time, achieve homeostatis (see Chap.  10 ) or obtain bistability (see Chap.  6). The latter is an essential feature to build genetic memory devices. Like these feedback loops, most of the motifs presented in this chapter are based on transcription regulation. Logic operations (Boolean gates) can be carried out by controlling translation as well, either with structures such as riboswitches and ribozymes or via RNA interference (see Chap.  8). We considered as motifs also cell consortia. They are populations of cells where a given function emerges from the interactions of sets of cells devoted to different tasks. As we will see, digital circuits have been engineered as S. cerevisiae cell consortia, where some cells sense the inputs and other perform the logic operation and express a fluorescent output. Finally, we included among circuit motifs re-engineered pathways too. We will show that natural signaling pathways have been modified, both in eukaryotic and bacterial cells, to either respond to an input or express an output different from the original one. Complex circuits can potentially arise by the composition of all these basic motifs.


  1. 1.
    C.M. Ajo-Franklin, D.A. Drubin, J.A. Eskin, E.P.S. Gee, D. Landgraf, I. Phillips, P.A. Silver, Rational design of memory in eukaryotic cells. Genes. Dev. 21(18), 2271–2276 (2007)CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    U. Alon, An Introduction to Systems Biology (Chapman & Hall/CRC Press, Boca Raton, 2006)Google Scholar
  3. 5.
    M.R. Atkinson, M.A. Savageau, J.T. Myers, A.J. Ninfa, Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113(5), 597–607 (2003)CrossRefPubMedPubMedCentralGoogle Scholar
  4. 7.
    C.J. Bashor, N.C. Helman, S. Yan, W.A. Lim, Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319(5869), 1543 (2008)CrossRefGoogle Scholar
  5. 8.
    S. Basu, R. Mehreja, S. Thiberge, M.T. Chen, R. Weiss, Spatiotemporal control of gene expression with pulse-generating networks. Proc. Nat. Acad. Sci. 101(17), 6355–6360 (2004)CrossRefPubMedGoogle Scholar
  6. 10.
    L. Bintu, N.E. Buchler, H.G. Garcia, U. Gerland, T. Hwa, J. Kondev, T. Kuhlman, R. Phillips, Transcriptional regulation by the numbers: applications. Curr. Opin. Genet. Dev. 15(2), 125–135 (2005)CrossRefPubMedPubMedCentralGoogle Scholar
  7. 25.
    S. Hooshangi, S. Thiberge, R. Weiss, Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl. Acad. Sci. USA 102(10), 3581–3586 (2005)CrossRefPubMedGoogle Scholar
  8. 30.
    A. Levskaya, A.A. Chevalier, J.J. Tabor, Z.B. Simpson, L.A. Lavery, M. Levy, E.A. Davidson, A. Scouras, A.D. Ellington, E.M. Marcotte, C.A. Voigt, Synthetic biology: engineering Escherichia coli to see light. Nature 438(7067), 441–442 (2005)CrossRefPubMedPubMedCentralGoogle Scholar
  9. 42.
    S. Regot, J. Macia, N. Conde, K. Furukawa, J. Kjellén, T. Peeters, S. Hohmann, E. de Nadal, F. Posas, R. Solé, Distributed biological computation with multicellular engineered networks. Nature 469(7329), 207–211 (2011)CrossRefPubMedPubMedCentralGoogle Scholar
  10. 43.
    K. Rinaudo, L. Bleris, R. Maddamsetti, S. Subramanian, R. Weiss, Y. Benenson, A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol. 25(7), 795–801 (2007)CrossRefGoogle Scholar
  11. 45.
    B. Wang, R.I. Kitney, N. Joly, M. Buck, Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat. Commun. 2, 508 (2011)CrossRefPubMedPubMedCentralGoogle Scholar
  12. 46.
    M.N. Win, C.D. Smolke, A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc. Natl. Acad. Sci. USA 104(36), 14283–14288 (2007)CrossRefGoogle Scholar
  13. 47.
    M.N. Win, C.D. Smolke, Higher-order cellular information processing with synthetic RNA devices. Science 322(5900), 456–460 (2008)CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Mario Andrea Marchisio
    • 1
  1. 1.School of Life Science and TechnologyHarbin Institute of TechnologyHarbinChina

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