Biology subjects

Biedzinski, S.

Publications and source records attributed to Biedzinski, S..

3 recordsLinked to original sources

bioRxiv2026

Omega stabilizes RNA polymerase condensates andcontributes to cellular fitness during acid stress

In eukaryotes, organization of the nucleolus is tightly linked to ribosomal RNA (rRNA) synthesis. External stresses, such as heat shock and acidosis, induce a transition of the nucleolus from a liquid- to solid-like state. Bacterial RNA polymerase (RNAP) condensates share similarities with the nucleolus as they colocalize with pre-rRNA synthesis and their assembly correlates with high rRNA synthesis. In addition, their organization is growth dependent, highlighted by dissolution upon nutritional stress. However, their behavior and biophysical properties during other stresses remain unknown. Here, we find that RNAP condensates persist during acid stress despite an arrest in cell growth. In contrast to fast-growth RNAP condensates, acid-stabilized RNAP condensates become insensitive to drug treatments, suggesting a change in their dynamics. We identify both passive and active mechanisms that contribute to the maintenance of RNAP condensates during acid stress: a drop in intracellular pH and the stringent response. Specifically, the omega subunit of RNAP, which contributes to (p)ppGpp binding site 1, is critical for condensate maintenance during acid stress. In contrast, we show that DksA, a major stress regulator that binds to RNAP, does not contribute to RNAP condensate stabilization. Interestingly, we find that maintenance of RNAP condensates correlates with survival during recovery from acid stress. Our work sheds light on a new aspect of bacterial stress tolerance through regulation of RNAP codensates and a new role for the omega subunit. Our data bring RNAP condensates conceptually one step closer to nucleoli.

microbiology↗

bioRxiv2020

Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation

Once described as mere "bags of enzymes", bacterial cells are in fact highly organized, with many macromolecules exhibiting non-uniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid-liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in E. coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and suggests that this process serves as a universal mechanism for intracellular organization across the tree of life. SignificanceBacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid-liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid-liquid phase separation is a universal mechanism for intracellular organization that extends across the tree of life.

cell biology↗

bioRxiv2019

Microtubules deform the nucleus and force chromatin reorganization during early differentiation of human hematopoietic stem cells.

Hematopoietic stem cells (HSC) can differentiate into all hematopoietic lineages to support hematopoiesis. Cells from the myeloid and lymphoid lineages fulfill distinct functions with specific shapes and intra-cellular architectures. The role of cytokines in the regulation of HSC differentiation has been intensively studied but our understanding of the potential contribution of inner cell architecture is relatively poor. Here we show that large invaginations are generated by microtubule constraints on the swelling nucleus of human HSCs during early commitment toward the myeloid lineage. These invaginations are associated with chromatin reorganization, local loss of H3K9 trimethylation and changes in expression of specific hematopoietic genes. This establishes the role of microtubules in defining the unique lobulated nuclear shape observed in myeloid progenitor cells and suggests that this shape is important to establish the gene expression profile specific to this hematopoietic lineage. It opens new perspectives on the implications of microtubule-generated forces, in the early specification of the myeloid lineage.

cell biology↗