Table 2 Models addressing the viral protein Tat-circuit architecture

Tat feedback-loop & Proviral Fate

L. Weinberger et al.²⁰

Understand the factors and mechanisms regulating HIV developmental fate.

GFP expression sampled from Jurkat T-cells, infected with a single LTR-GFP-IRES-Tat (LGIT) HIV model vector.

(i) Proviral developmental fate (active replication vs latency) is regulated by Tat. (ii) Proviruses showing a relatively high basal gene-expression rate (high Tat), experience active replication; (iii) Provirus clones showing relatively low basal gene-expression rate (low Tat) face a stochastic decision between high and negligible activity (PheB);

B. S. Razooky et al.¹⁸

Understand the relationship between proviral fate (active vs latent) and host-cell state (active vs resting)

GFP expression sampled from Jurkat and CEM T-cells infected with HIV-d2GFP virus env-mutated (avoid expansion).

(i) The LTR is intrinsically capable of generating bimodal ON/OFF expression, even in the absence of Tat; (ii) Tat slows LTR toggling, shifting, and expanding the regime of LTR bimodality ultimately characterizing a stabler active replication regime;

L. Weinberger et al.²⁵

Understand the mechanisms by which Tat-positive feedback is counteracted, allowing the existence of a stable transcriptionally-off state (latency).

GFP expression sampled from Jurkat cells, infected with LTR-GFP and LTR-GFP-IRES-Tat (LGIT) HIV model vector.

(i) The Tat-feedback circuit lacks bi-stability and self-cooperativity; however, it exhibits pulsatile activity patterns triggered by stochastic basal activity; (ii) An enzymatic Tat-resistor reduces the Tat-amplification susceptibility to transcriptional noise, explaining the HIV off (latent) state and the pulsatile HIV gene-expression activity.

K. H. Aull et al.⁵⁸

Understand the mechanisms by which the Tat-positive feedback is counteracted, allowing the existence of a stable transcriptionally-off state (latency).

flow cytometry and single-cell imaging

(i) The Tat-feedback circuit exhibits a transient threshold lasting ~40 h before disappearing (ii) whose lifetime is shortened by promoter activation;

L. Weinberger et al.²⁶

Understand how Tat-feedback strength modulates the pulsatile HIV gene-expression dynamics.

GFP expression sampled from TNF-α-stimulated^76,77 (10 ng/ml) Jurkat T-cells (J-Lat full-length clone 10.6 ⁷⁴) infected with a single LTR-GFP or LTR-GFP-IRES-Tat (LGIT) HIV model vector.

(i) Tat positive-feedback extends viral gene-expression lifetime 2-6 fold. (ii) weak Tat-amplifications provide a shortened gene-expression pulse, favoring the latent phenotype.

B. S. Razooky et. al. ¹⁷

Understand the relationship between proviral fate (active vs latent) and host-cell state (active vs resting)

GFP expression sampled from activated (CD25⁺ CD69⁺) and resting (CD25⁻ CD69^-) Jurkat and CEM T-cells infected with HIV-d2GFP virus env-mutated (avoid expansion).

(i) HIV gene-expression persists in acutely-infected cells after transitioning to their resting state (ii) Tat circuit is autonomous and regulates proviral fate (iii) Host factors stochastically ignite Tat amplification.