An engineered eukaryotic clock

Natalie Ostroff, University of California, San Diego

One of the defining characteristics of life is the ability to keep time, which organisms often achieve by using internal genetic clocks to govern fundamental cellular behavior. While the gene networks that produce oscillatory expression signals are typically quite elaborate, certain recurring network motifs are
often found at the core of these biological clocks. Here, we design and construct a one-gene oscillatory network based on a motif of delayed negative feedback, which is common to many eukaryotic clock and signaling networks. Computational modeling is used to develop design criteria necessary for sustained oscillations, and upon integration into the yeast genome the clock maintains oscillatory behavior throughout many cellular generations. The clock exhibits large variability in frequency and amplitude, and a generalized computational model incorporating biochemical noise and cellular growth dynamics is used to explain the observed behavior. Finally, we demonstrate tunability of the period of the clock through the addition of a chemical inducer to the growth media and compare the results with predictions from the computational modeling. Our results demonstrate that negative feedback can serve as a core module for generating regulatory oscillations.

Abstract Author(s): Natalie A. Ostroff, Ting Lu, William J. Blake, Chung S. Luke, Lev S. Tsimring, Jeff Hasty