Search for: All records

In recent years, it has been experimentally established that transcription, a fundamental biological process that involves the synthesis of messenger RNA molecules from DNA templates, does not proceed continuously as was expected. Rather, it exhibits a distinct dynamic behavior of alternating between productive phases when RNA molecules are actively synthesized and inactive phases when there is no RNA production at all. The bimodal transcriptional dynamics is now confirmed to be present in most living systems. This phenomenon is known as transcriptional bursting and it attracts significant amounts of attention from researchers in different fields. However, despite multiple experimental and theoretical investigations, the microscopic origin and biological functions of the transcriptional bursting remain unclear. Here we discuss the recent developments in uncovering the underlying molecular mechanisms of transcriptional bursting and our current understanding of them. Our analysis presents a physicochemical view of the processes that govern transcriptional bursting in living cells. 

Variability in gene expression causes genetically identical cells to exhibit different phenotypes. One probable cause of this variability is transcriptional bursting, where the synthesis of RNA molecules randomly alternates with periods of silence in the transfer of genetic information. Yet, the molecular mechanisms behind this variability remain unclear. Experiments indicate that multiple biochemical states might be involved in the production of RNA molecules. Stimulated by these observations, we developed a theoretical framework to investigate the mechanisms of transcriptional bursting. It is based on a multi-state stochastic approach that provides a full quantitative description of the dynamic properties in the system. We found that the degree of stochastic fluctuations during transcription directly correlates with the number of biochemical states. This explains experimentally observed variability and fluctuations in the quantities of the produced RNA molecules. The procedure to estimate the number of relevant biochemical states participating in the transcription is outlined and applied for analysis of experimental results. We also developed a general dynamic phase diagram for the transcription process. The presented theoretical method clarifies physical−chemical aspects of the transcriptional bursting and presents a minimal chemical-kinetic description of the process. 

The protein p53 is a crucial tumor suppressor, often called “the guardian of the genome”; however, mutations transform p53 into a powerful cancer promoter. The oncogenic capacity of mutant p53 has been ascribed to enhanced propensity to fibrillize and recruit other cancer fighting proteins in the fibrils, yet the pathways of fibril nucleation and growth remain obscure. Here, we combine immunofluorescence three-dimensional confocal microscopy of human breast cancer cells with light scattering and transmission electron microscopy of solutions of the purified protein and molecular simulations to illuminate the mechanisms of phase transformations across multiple length scales, from cellular to molecular. We report that the p53 mutant R248Q (R, arginine; Q, glutamine) forms, both in cancer cells and in solutions, a condensate with unique properties, mesoscopic protein-rich clusters. The clusters dramatically diverge from other protein condensates. The cluster sizes are decoupled from the total cluster population volume and independent of the p53 concentration and the solution concentration at equilibrium with the clusters varies. We demonstrate that the clusters carry out a crucial biological function: they host and facilitate the nucleation of amyloid fibrils. We demonstrate that the p53 clusters are driven by structural destabilization of the core domain and not by interactions of its extensive unstructured region, in contradistinction to the dense liquids typical of disordered and partially disordered proteins. Two-step nucleation of mutant p53 amyloids suggests means to control fibrillization and the associated pathologies through modifying the cluster characteristics. Our findings exemplify interactions between distinct protein phases that activate complex physicochemical mechanisms operating in biological systems.