Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean

摘要

Fundamental to biological decision-making is the ability to generate bimodal expression patterns where 2 alternate expression states simultaneously exist. Here, we use a combination of single-cell analysis and mathematical modeling to examine the sources of bimodality in the transcriptional program controlling HIV’s fate decision between active replication and viral latency. We find that the HIV transactivator of transcription (Tat) protein manipulates the intrinsic toggling of HIV’s promoter, the long terminal repeat (LTR), to generate bimodal ON-OFF expression and that transcriptional positive feedback from Tat shifts and expands the regime of LTR bimodality. This result holds for both minimal synthetic viral circuits and full-length virus. Strikingly, computational analysis indicates that the Tat circuit’s noncooperative “nonlatching” feedback architecture is optimized to slow the promoter’s toggling and generate bimodality by stochastic extinction of Tat. In contrast to the standard Poisson model, theory and experiment show that nonlatching positive feedback substantially dampens the inverse noise-mean relationship to maintain stochastic bimodality despite increasing mean expression levels. Given the rapid evolution of HIV, the presence of a circuit optimized to robustly generate bimodal expression appears consistent with the hypothesis that HIV’s decision between active replication and latency provides a viral fitness advantage. More broadly, the results suggest that positive-feedback circuits may have evolved not only for signal amplification but also for robustly generating bimodality by decoupling expression fluctuations (noise) from mean expression levels. Author summary A central and recurring feature of cell-fate regulating circuits is their ability to generate bimodal expression—2 alternate expression states that exist simultaneously—with each state corresponding to a different cell fate. To understand the mechanisms enabling bimodality in a natural decision-making circuit, we examined HIV’s fate-selection circuit, the Tat circuit. This bimodal circuit is sufficient and necessary to generate a bet-hedging decision between 2 alternate HIV fates: active viral replication and long-lived dormancy (proviral latency). The dormant state, which is resistant to most antiviral drugs, is the primary clinical barrier to curing an HIV infection. While the canonical role of positive feedback is to amplify a signal, surprisingly, we find that the HIV transactivator of transcription (Tat) positive-feedback architecture is instead optimized to expand the regime of HIV expression bimodality. From an evolutionary perspective, the results suggest that positive-feedback circuits may have evolved to robustly generate bimodality in certain contexts, and, given the rapid evolution of HIV, the presence of a circuit optimized to robustly generate bimodal expression patterns appears to support the hypothesis that HIV’s active-versus-latent decision confers viral fitness.