Engineering stability in gene networks by autoregulation

Abstract

The genetic and biochemical networks which underlie such things as homeostasis in metabolism and the developmental programs of living cells, must withstand considerable variations and random perturbations of biochemical parameters1,2,3. These occur as transient changes in, for example, transcription, translation, and RNA and protein degradation. The intensity and duration of these perturbations differ between cells in a population4. The unique state of cells, and thus the diversity in a population, is owing to the different environmental stimuli the individual cells experience and the inherent stochastic nature of biochemical processes (for example, refs 5 and 6). It has been proposed, but not demonstrated, that autoregulatory, negative feedback loops in gene circuits provide stability7, thereby limiting the range over which the concentrations of network components fluctuate. Here we have designed and constructed simple gene circuits consisting of a regulator and transcriptional repressor modules in Escherichia coli and we show the gain of stability produced by negative feedback.

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Figure 1: Stability properties of gene circuits.
Figure 2: Gene circuits and corresponding typical distributions of fluorescence intensities.
Figure 3: Variability in classical and autoregulatory systems.

References

  1. 1

    Little, J. W., Shepley, D. P. & Wert, D. W. Robustness of a gene regulatory circuit. EMBO J. 18, 4299–4307 ( 1999).

    CAS  Article  Google Scholar 

  2. 2

    Barkai, N. & Leibler, S. Robustness in simple biochemical networks. Nature 387, 913– 917 (1997).

    ADS  CAS  Article  Google Scholar 

  3. 3

    Alon, U., Surette, M. G., Barkai, N. & Leibler, S. Robustness in bacterial chemotaxis. Nature 397, 168–171 (1999).

    ADS  CAS  Article  Google Scholar 

  4. 4

    Ko, M. S., Nakauchi, H. & Takahashi, N. The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO J. 9, 2835– 2842 (1990).

    CAS  Article  Google Scholar 

  5. 5

    Nutt, S. L. et al. Independent regulation of the two Pax5 alleles during B-cell development. Nat. Genet 21, 390– 395 (1999).

    CAS  Article  Google Scholar 

  6. 6

    Novick, A. & Weiner, M. Enzyme induction as an all-or-none phenomenon. Proc. Natl Acad. Sci. USA 43, 553–566 (1957).

    ADS  CAS  Article  Google Scholar 

  7. 7

    Savageau, M. A. Comparison of classical and autogenous systems of regulation in inducible operons. Nature 252, 546– 549 (1974).

    ADS  CAS  Article  Google Scholar 

  8. 8

    Baumeister, R., Helbl, V. & Hillen, W. Contacts between Tet repressor and tet operator revealed by new recognition specificities of single amino acid replacement mutants. J. Mol. Biol. 226, 1257– 1270 (1992).

    CAS  Article  Google Scholar 

  9. 9

    Lederer, T. et al. Tetracycline analogs affecting binding to Tn10-Encoded Tet repressor trigger the same mechanism of induction. Biochemistry 35, 7439–7446 ( 1996).

    CAS  Article  Google Scholar 

  10. 10

    Siegele, D. A. & Hu, J. C. Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations. Proc. Natl Acad. Sci. USA 94, 8168–8172 (1997).

    ADS  CAS  Article  Google Scholar 

  11. 11

    Blau, H. M. & Rossi, F. M. Tet B or not tet B: advances in tetracycline-inducible gene expression. Proc. Natl Acad. Sci. USA 96, 797–799 ( 1999).

    ADS  CAS  Article  Google Scholar 

  12. 12

    Moran, L., Norris, D. & Osley, M. A. A yeast H2A-H2B promoter can be regulated by changes in histone gene copy number. Genes Dev. 4, 752–763 (1990).

    CAS  Article  Google Scholar 

  13. 13

    Osley, M. A. & Hereford, L. M. Yeast histone genes show dosage compensation. Cell 24, 377– 384 (1981).

    CAS  Article  Google Scholar 

  14. 14

    Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339– 342 (2000).

    ADS  CAS  Article  Google Scholar 

  15. 15

    Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000).

    ADS  CAS  Article  Google Scholar 

  16. 16

    Thieffry, D., Huerta, A. M., Perez-Rueda, E. & Collado-Vides, J. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 20 , 433–440 (1998).

    CAS  Article  Google Scholar 

  17. 17

    Schedl, A. et al. Influence of PAX6 gene dosage on development: overexpression causes severe eye abnormalities. Cell 86, 71–82 (1996).

    CAS  Article  Google Scholar 

  18. 18

    Rutherford, S. L. & Lindquist, S. Hsp90 as a capacitor for morphological evolution. Nature 396, 336–342 (1998).

    ADS  CAS  Article  Google Scholar 

  19. 19

    Wolf, D. M. & Eeckman, F. H. On the relationship between genomic regulatory element organization and gene regulatory dynamics. J. Theor. Biol. 195, 167–186 (1998).

    CAS  Article  Google Scholar 

  20. 20

    Backes, H. et al. Combinations of the alpha-helix-turn-alpha-helix motif of TetR with respective residues from LacI or 434Cro: DNA recognition, inducer binding, and urea-dependent denaturation. Biochemistry 36, 5311–5322 (1997).

    CAS  Article  Google Scholar 

  21. 21

    Lanzer, M. & Bujard, H. Promoters largely determine the efficiency of repressor action. Proc. Natl Acad. Sci. USA 85, 8973–8977 (1988).

    ADS  CAS  Article  Google Scholar 

  22. 22

    Strogatz, S. H. Nonlinear Dynamics and Chaos: With Applications in Physics, Biology, Chemistry, and Engineering (Perseus, Boulder, CO, 1994).

    Google Scholar 

  23. 23

    Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1–I2 regulatory elements. Nucleic Acids Res. 25, 1203–1210 (1997).

    CAS  Article  Google Scholar 

  24. 24

    Record JR., M. T., Reznikoff, W. S., Craig, M. L., McQuade, K. L. & Schlax, P. J. E. coli and S. typhimurium: Cellular and Molecular Biology (ed. Neidhardt, F. C.) 792–821 (American Society of Microbiology, Washington DC, 1996).

    Google Scholar 

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Acknowledgements

We thank H. Bujard for the plasmids; J. Rietdorf and R. Pepperkok for help with fluorescence microscopy; M. Diehl and D. Thieffry for discussions; and H. Domingues and R. Guerois for reading the manuscript. A.B. is supported by the Louis-Jeantet foundation.

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Correspondence to Attila Becskei.

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Becskei, A., Serrano, L. Engineering stability in gene networks by autoregulation. Nature 405, 590–593 (2000). https://doi.org/10.1038/35014651

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