A synthetic oscillatory network of transcriptional regulators

Networks of interacting biomolecules carry out many essential functions in living cells, but the ‘design principles’ underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems. Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function. We used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli. The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells. The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation. This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components. Such ‘rational network design’ may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks.

[1]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[2]  A. Winfree The geometry of biological time , 1991 .

[3]  D. Bray Protein molecules as computational elements in living cells , 1995, Nature.

[4]  W. DeGrado,et al.  Protein Design: A Hierarchic Approach , 1995, Science.

[5]  A. Goldbeter,et al.  Biochemical Oscillations And Cellular Rhythms: Contents , 1996 .

[6]  R. Sauer,et al.  Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA , 1996, Science.

[7]  S. Golden,et al.  Circadian Rhythms in Rapidly Dividing Cyanobacteria , 1997, Science.

[8]  H. Bujard,et al.  Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. , 1997, Nucleic acids research.

[9]  D E Koshland,et al.  The Era of Pathway Quantification , 1998, Science.

[10]  M. Weickert,et al.  Using chromosomal lacIQ1 to control expression of genes on high-copy-number plasmids in Escherichia coli. , 1998, Gene.

[11]  R. Tsien,et al.  green fluorescent protein , 2020, Catalysis from A to Z.

[12]  P. Bouloc,et al.  Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH). , 1998, Genes & development.

[13]  R. Sauer,et al.  The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. , 1998, Genes & development.

[14]  L. Poulsen,et al.  New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria , 1998, Applied and Environmental Microbiology.

[15]  A. Arkin,et al.  It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.

[16]  Transport, assembly, and dynamics in systems of interacting proteins , 1999 .

[17]  J. Dunlap Molecular Bases for Circadian Clocks , 1999, Cell.

[18]  S. Leibler,et al.  Biological rhythms: Circadian clocks limited by noise , 2000, Nature.