How Biomolecular Condensates Control Gene Expressions

Intrinsically disordered proteins (IDPs) undergo spontaneous phase separation (PS) in living cells to form biomolecular condensates. As a result, cytoplasm will de-mix into two phases: one enriched with the IDP and another depleted with IDP. By fusing enzymes and transcriptional factors with IDPs, we can create synthetic biomolecular condensates. As a result, corresponding biochemical reaction rates are modulated. It has been hypothesized that biomolecular condensates accelerate gene expression since many transcriptional activator (TA) proteins are enriched with IDPs. However, previous experimental measurements reported contradictory results. Motivated by this, this study investigates roles of PS in modulating gene expression through measurements in E. coli and mathematical modeling. First, synthetic TA proteins are created by fusing E. coli's native TA with a variety of IDPs and red fluorescent protein (RFP) so that 1) the TA will undergo PS, and 2) the TAs concentration can be approximated by RFPs fluorescent intensity. At the same time, green fluorescent protein (GFP) gene is placed under the control of TA so that we can quantify the TA-IDPs strength by measuring the GFP fluorescent intensity. In parallel, a coarse-grained gene expression model is developed to describe dynamics of gene expression in the presence of PS. To estimate unknown parameters of the model, single-cell fluorescent microscopy is employed to measure both RFP and GFP. Based on the model, we will discuss implications of PS in kinetics of gene expression.