SUMMARY Biological circuits can be controlled by two general schemes: environmental sensing or autonomous programs. For viruses such as HIV, the prevailing hypothesis is that latent infection is controlled by cellular state (i.e. environment) with latency simply an epiphenomenon of infected cells transitioning from an activated to resting state. However, we find HIV expression persists despite the activated-to-resting cellular transition. Mathematical modeling indicates that HIV’s Tat positive-feedback circuitry enables this persistence and strongly controls latency. To overcome the inherent crosstalk between viral circuitry and cellular activation, and directly test this hypothesis, we synthetically decouple viral dependence on cellular environment from viral transcription. These circuits enable control of viral transcription without cellular activation and show that Tat feedback is sufficient to regulate latency independent of cellular activation. Overall, synthetic reconstruction demonstrates that a largely autonomous, viral-encoded program underlies HIV latency—potentially explaining why cell-targeted latency-reversing agents exhibit incomplete penetrance.

During bacterial growth, a cell approximately doubles in size prior to division, upon which it splits into two daughter cells. This process is subjected to the inherent perturbations of cellular noise 1,2 and thus requires regulation for cell-size homeostasis. The mechanisms underlying cell-size control and their dynamics consequences remain poorly understood due to the difficulty in sizing individual bacteria over long periods of time in a high-throughput manner. Here, we measured and analyzed long-term, single-cell growth and division across different Escherichia coli strains and growth conditions 3 . We found that a subset of cells in a population exhibited transient oscillations in cell size with periods that stretch across multiple (>10) generations. Our analysis revealed that a simple law governing cell size control -a noisy linear map -explains the origins of these cell-size oscillations across all strains. This noisy linear map implements a negative feedback on cell-size control: a cell with a larger initial size tends to divide earlier, whereas one with a smaller initial size tends to divide later. Combining simulations of cell growth and division with experimental data, we demonstrate that this noisy linear map generates transient oscillations, not just in cell size, but also in constitutive gene expression. Our work provides new insights into the dynamics of bacterial cell-size regulation with implications for the physiological processes involved.We used a "mother machine" microfluidic device 3 and time-lapse microscopy to monitor long-term cell-size dynamics in E. coli at the single-cell level. The device enables the measurement of cell size and gene expression for hundreds of E. coli mother lineages over †

Through production and sensing of small signal molecules, quorum sensing (QS) enables bacteria to detect changes in their density and regulate their functions accordingly. QS systems are tremendously diverse in terms of their specific sensory components, the biochemical and transport properties of signaling molecules, their target functions and the context in which QS-mediated functions are activated. Cutting across this diversity, however, the central architecture of QS systems is universal; it comprises signal synthesis, secretion, degradation and detection. We are thus able to derive a general metric for QS 'sensing potential' based on this 'core' module. The sensing potential quantifies the ability of a single bacterium to sense the dimensions of its microenvironment. This simple metric captures the dominant activation properties of diverse QS systems, giving a concise description of the sensing characteristics. As such, it provides a convenient quantitative framework to study the phenotypic effects of QS characteristics. As an example, we show how QS characteristics uniquely determine the scenarios in which regulation of a typical QS-controlled function, such as exoenzyme secretion, becomes advantageous.