Biology subjects

Gruebele, M.

Publications and source records attributed to Gruebele, M..

3 recordsLinked to original sources

bioRxiv2018

Phase Separation of YAP Reprograms Cells for Long-term YAP Target Gene Expression

Yes-associated Protein (YAP) is a transcriptional co-activator that regulates cell proliferation and survival by binding to a selective set of enhancers for potent target gene activation, but how YAP coordinates these transcriptional responses is unknown. Here, we demonstrate that YAP forms liquid-like condensates in the nucleus in response to macromolecular crowding. Formed within seconds of hyperosmotic stress, YAP condensates compartmentalized YAPs DNA binding cofactor TEAD1 along with other YAP-related transcription co-activators, including TAZ, and subsequently induced transcription of YAP-specific proliferation genes. Super-resolution imaging using Assay for Transposase Accessible Chromatin with photoactivated localization microscopy (ATAC-PALM) revealed that YAP nuclear condensates were areas enriched in accessible chromatin domains organized as super-enhancers. Initially devoid of RNA Polymerase II (Pol II), the accessible chromatin domains later acquired Pol II, producing newly transcribed RNA. Removal of YAPs intrinsically-disordered transcription activation domain (TAD) prevented YAP condensate formation and diminished downstream YAP signaling. Thus, dynamic changes in genome organization and gene activation during YAP reprogramming is mediated by liquid-liquid phase separation.

cell biology↗

bioRxiv2018

An In-Silico Mammalian Whole-Cell Model Reveals the Influence of Spatial Organization on RNA Splicing Efficiency

Spatial organization is a characteristic of eukaryotic cells, achieved by utilizing both membrane-bound and non-bound organelles. We model the effects of this organization and of organelle heterogeneity on RNA splicing (the process of making translationally-ready messenger RNA) and on splicing particles (the building blocks of splicing machinery) in mammalian cells. We constructed a spatially-resolved whole HeLa cell model from various experimental data and developed reaction networks to describe the RNA splicing processes. We incorporated these networks into our whole-cell model and performed stochastic simulations for up to 15 minutes of biological time. We find that the number of nuclear pore complexes affects the number of assembled splicing particles; that a slight increase of splicing particle localization in nuclear speckles (non-membrane-bound or- ganelles) leads to disproportionate enhancement in the mRNA splicing and reduction in the transcript noise; and that compartmentalization is critical for a correctly-assembled particle yield. Our model also predicts that the distance between genes and speckles has a considerable effect on effective mRNA production rate, further emphasizing the importance of genome organization around speckles. The HeLa cell model, including organelles and subcompartments, provides an adaptable foundation to study other cellular processes which are strongly modulated by spatio-temporal heterogeneity.\n\nSignificance StatementThe spliceosome is one of the most complex cellular machineries that cuts and splices the RNA code in eukaryotic cells. It dynamically assembles, disassembles, and its components are formed in multiple compartments. The efficiency of splicing process depends on localization of its components in nuclear membrane-less organelles. Therefore, a computational model of spliceosomal function must contain a spatial model of the entire cell. However, building such a model is a challenging task, mainly due to the lack of homogeneous experimental data and a suitable computational framework. Here, we overcome these challenges and present a whole HeLa cell model, with nuclear, subnuclear, and extensive cytoplasmic structures. The three-dimensional model is supplemented by reaction-diffusion processes to shed light on the function of the spliceosome.

biophysics↗

bioRxiv2017

Blue light is a universal tactic signal for Escherichia coli

Blue light has been shown to elicit a tumbling response in E. coli, a non-phototrophic bacterium. The exact mechanism of this phototactic response is still unknown, and its biological significance remains unclear. Here, we quantify phototaxis in E. coli by analyzing single-cell trajectories in populations of free-swimming bacteria before and after light exposure. Bacterial strains expressing only one type of chemoreceptor reveal that all five E. coli receptors - Aer, Tar, Tsr, Tap and Trg - are capable of mediating a response to light. In particular, light exposure elicits a running response in Tap-only strain, the opposite of the tumbling response observed for all other strains. Light therefore emerges as a universal stimulus for all E. coli chemoreceptors. We also show that blue light exposure causes a reversible decrease in swimming velocity, a proxy for proton motive force. We hypothesize that rather than sensing light directly, chemoreceptors sense light-induced perturbations in proton motive force.\n\nImportanceOur findings provide new insights on the mechanism of E. coli phototaxis, showing that all five chemoreceptor types respond to light and that their interactions play an important role in cell behavior. Our results also open up new avenues for examining and manipulating E. coli taxis. Since light is a universal stimulus, it may provide a way to quantify interactions between different types of receptors. Since light is easier to control spatially and temporally than chemicals, it may be used to study swimming behavior in complex environments. Since phototaxis can cause migration of E. coli bacteria in light gradients, light may be used to control bacterial density for studying density-dependent processes in bacteria.

biophysics↗