Synchronous long-term oscillations in a synthetic gene circuit

Nature

Volumn 538, Issue 7626, 2016, Pages 514-517

  Potvin Trottier, Laurent ^a,b   Lord, Nathan D ^a,b   Vinnicombe, Glenn ^c   Paulsson, Johan ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b HARVARD UNIVERSITY   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

SYNTHETIC DNA;

CELLS AND CELL COMPONENTS; CHEMISTRY; DESIGN METHOD; GENE EXPRESSION; GENETIC ANALYSIS; STOCHASTICITY;

ARTICLE; BACTERIOPHAGE; CELL DIVISION; CIRCADIAN RHYTHM; CLONING VECTOR; COMPARATIVE STUDY; ENZYME DEGRADATION; ESCHERICHIA COLI; GENETIC ENGINEERING; NONHUMAN; OSCILLATION; PRIORITY JOURNAL; REPRESSOR GENE; SYNTHETIC BIOLOGY; BIOLOGICAL MODEL; BIOLOGICAL RHYTHM; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METHODOLOGY; PROCEDURES;

BIOLOGICAL CLOCKS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; GENES, SYNTHETIC; GENETIC ENGINEERING; MODELS, GENETIC; RESEARCH DESIGN; SYNTHETIC BIOLOGY;

EID: 84994013710     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature19841     Document Type: Article

References (36)

1. Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338 (2000).
2. Nakajima, M. et al. Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 308, 414-415 (2005).
3. Teng, S.-W., Mukherji, S., Moffitt, J. R., de Buyl, S. & O'Shea, E. K. Robust circadian oscillations in growing cyanobacteria require transcriptional feedback. Science 340, 737-740 (2013).
4. Mihalcescu, I., Hsing, W. & Leibler, S. Resilient circadian oscillator revealed in individual cyanobacteria. Nature 430, 81-85 (2004).
5. Chabot, J. R., Pedraza, J. M., Luitel, P. & van Oudenaarden, A. Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock. Nature 450, 1249-1252 (2007).
6. Friedland, A. E. et al. Synthetic gene networks that count. Science 324, 1199-1202 (2009).
7. Daniel, R., Rubens, J. R., Sarpeshkar, R. & Lu, T. K. Synthetic analog computation in living cells. Nature 497, 619-623 (2013).
8. Fung, E. et al. A synthetic gene-metabolic oscillator. Nature 435, 118-122 (2005).
9. Stricker, J. et al. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516-519 (2008).
10. Tigges, M., Marquez-Lago, T. T., Stelling, J. & Fussenegger, M. A tunable synthetic mammalian oscillator. Nature 457, 309-312 (2009).
11. Danino, T., Mondragón-Palomino, O., Tsimring, L. & Hasty, J. A synchronized quorum of genetic clocks. Nature 463, 326-330 (2010).
12. Mondragón-Palomino, O., Danino, T., Selimkhanov, J., Tsimring, L. & Hasty, J. Entrainment of a population of synthetic genetic oscillators. Science 333, 1315-1319 (2011).
13. Prindle, A. et al. Rapid and tunable post-translational coupling of genetic circuits. Nature 508, 387-391 (2014).
14. Bonnet, J., Yin, P., Ortiz, M. E., Subsoontorn, P. & Endy, D. Amplifying genetic logic gates. Science 340, 599-603 (2013).
15. Tabor, J. J. et al. A synthetic genetic edge detection program. Cell 137, 1272-1281 (2009).
16. Paulsson, J., Berg, O. G. & Ehrenberg, M. Stochastic focusing: fluctuationenhanced sensitivity of intracellular regulation. Proc. Natl Acad. Sci. USA 97, 7148-7153 (2000).
17. Vilar, J. M. G., Kueh, H. Y., Barkai, N. & Leibler, S. Mechanisms of noiseresistance in genetic oscillators. Proc. Natl Acad. Sci. USA 99, 5988-5992 (2002).
18. McKane, A. J. & Newman, T. J. Predator-prey cycles from resonant amplification of demographic stochasticity. Phys. Rev. Lett. 94, 218102 (2005).
19. Lestas, I., Vinnicombe, G. & Paulsson, J. Fundamental limits on the suppression of molecular fluctuations. Nature 467, 174-178 (2010).
20. Keiler, K. C., Waller, P. R. & Sauer, R. T. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990-993 (1996).
21. Andersen, J. B. et al. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64, 2240-2246 (1998).
22. Wang, P. et al. Robust growth of Escherichia coli. Curr. Biol. 20, 1099-1103 (2010).
23. Norman, T. M., Lord, N. D., Paulsson, J. & Losick, R. Memory and modularity in cell-fate decision making. Nature 503, 481-486 (2013).
24. Paulsson, J. & Ehrenberg, M. Noise in a minimal regulatory network: plasmid copy number control. Q. Rev. Biophys. 34, 1-59 (2001).
25. Moriya, T., Yamamura, M. & Kiga, D. Effects of downstream genes on synthetic genetic circuits. BMC Syst. Biol. 8 (suppl. 4), S4 (2014).
26. Berg, O. G., Paulsson, J. & Ehrenberg, M. Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated. Biophys. J. 79, 1228-1236 (2000).
27. Niederholtmeyer, H. et al. Rapid cell-free forward engineering of novel genetic ring oscillators. eLife 4, e09771 (2015).
28. van der Pol, B. On relaxation-oscillations. Phil. Mag. 2, 978-992 (1926).
29. Brewster, R. C. et al. The transcription factor titration effect dictates level of gene expression. Cell 156, 1312-1323 (2014).
30. Verdú, S. Poisson communication theory; invited talk. The International Technion Communication Day in honor of Israel Bar-David, Haifa, Israel (25 March 1999).
31. Edelstein, A., Amodaj, N., Hoover, K., Vale, R. & Stuurman, N. Computer control of microscopes using μManager. Curr. Protoc. Mol. Biol. Chapter 14, Unit14.20 (2010).
32. Tikhonov, A. N. & Arsenin, V. Y. Solutions of Ill-posed problems. Math. Comput. 32, 1320-1322 (1978).
33. Blackman, R. B. & Tukey, J. W. The Measurement of Power Spectra (Dover Publications, 1958).
34. Oppenheim, A. V. & Schafer, R. W. Discrete-Time Signal Processing 3rd edn (Prentice Hall, 1989).
35. Jenkins, G. M. & Watts, D. G. Spectral Analysis and Its Applications (Holden-Day, 1968).
36. Chait, R., Shrestha, S., Shah, A. K., Michel, J.-B. & Kishony, R. A differential drug screen for compounds that select against antibiotic resistance. PLoS One 5, e15179 (2010).