Negative Autoregulation Promotes the Evolution of Strong Environmental Switching

Living systems rely on gene regulatory circuits to respond to environmental change. Such circuits often act as molecular switches: OFF in the absence of a cue, and ON in its presence. We do not know how the regulatory architecture of a circuit affect its ability to evolve such responsiveness. In nature, a very frequent and simple regulatory architecture involves a transcriptional regulator that negatively regulates its own expression. To study how such autoregulation affects adaptive evolution, we engineered E. coli circuits in which a target gene is regulated by the repressor TetR with (A-) or without (A0) negative autoregulation of TetR. We evolved TetR in both architectures toward responsiveness to a novel environment, embodied by a novel inducer of TetR. Early during their evolution, TetR circuits with negative autoregulation evolved stronger environmental switching. A combination of high throughput DNA sequencing, protein engineering, and biophysical modeling showed why. Only A- circuits favored TetR alleles that interact strongly with both the inducer and DNA. Such alleles combine strong repression caused by strong DNA binding with strong derepression caused by strong inducer binding, the defining property of a strong environmental response. Our biophysical model shows that negative autoregulation helps to create this regulatory regime. As a result, only A- circuits favor alleles that create strong molecular switches. Altogether, our work shows that even the simplest form of gene regulation can change the topography of a fitness landscape, and enable new modes of evolutionary change.