Mesoscale Structure-Function Relationships in Mitochondrial Transcriptional Condensates

In live cells, phase separation is thought to organize macromolecules into membraneless structures known as biomolecular condensates. Here, we reconstituted transcription in condensates from purified mitochondrial components using optimized in vitro reaction conditions to probe the structure-function relationships of biomolecular condensates. We find that the core components of the mt-transcription machinery form multiphasic, viscoelastic condensates in vitro. Strikingly, the rates of condensate-mediated transcription are substantially lower than in solution. The condensate-mediated decrease in transcriptional rates is associated with the formation of vesicle-like structures that are driven by the production and accumulation of RNA during transcription. The generation of RNA alters the global phase behavior and organization of transcription components within condensates. Coarse-grained simulations of mesoscale structures at equilibrium show that the components stably assemble into multiphasic condensates and that the vesicles formed in vitro are the result of dynamical arrest. Overall, our findings illustrate the complex phase behavior of transcribing, multicomponent condensates, and they highlight the intimate, bidirectional interplay of structure and function in transcriptional condensates

Mechanics of Cell Growth

Organisms vary in size by orders of magnitude spanning 1 μm to hundreds of meters, yet their cells remain on the micron length scale. The physical mechanisms that control the size of cells remain unclear. Here, I study the extraordinarily large oocytes (immature eggs) from the frog Xenopus laevis to understand how cell organization and mechanics change as these cells grow to reach sizes of 1 mm. I discover that these oocytes have evolved to contain a unique nuclear actin meshwork that supports the liquid-like nuclear bodies from gravitational sedimentation and mass fusion events. I find that gravitational forces on organelles dominate random thermal forces for cell sizes greater than ~100 μm, suggesting that large cells require novel mechanisms to maintain proper spatial organization. Directly probing the material properties with active microrheology, I find that nuclear actin forms a soft viscoelastic network that is capable of undergoing gravitational creep on the time scale of growth. This suggests that the material properties of nuclear actin are matched to its mechanical role in kinetically stabilizing an emulsion of nuclear bodies during growth. For forces higher than 1 g and for longer times, these nuclear bodies will undergo significant displacements in the nucleus due to gravitational creep, thereby disrupting proper cellular organization. Although these nuclear bodies are known to behave as liquids, it still remains unknown how they maintain three distinct compartments. Visualizing nuclear actin shows protrusion of filaments inside these nuclear bodies in between different compartments, and by disrupting nuclear actin, I find that these compartments are able to rearrange and undergo homotypic fusion events. In combination with in vitro approaches, I determine that each nucleolar compartment represents a distinct liquid-like phase, and these nuclear bodies are thus behaving as multiphase droplets. Principles from liquid-liquid phase transitions provide a physical framework for organization even within organelles. Overall, X. laevis oocytes are an example of how cells can evolve to reach large sizes. Simple biophysical mechanisms can allow cells to maintain structural organization, even on length scales ~1,000 times their typical size

Soft viscoelastic properties of nuclear actin age oocytes due to gravitational creep

The actin cytoskeleton helps maintain structural organization within living cells. In large X. laevis oocytes, gravity becomes a dominant force and is countered by a nuclear actin network that prevents liquid-like nuclear bodies from immediate sedimentation and coalescence. However, nuclear actin's mechanical properties, and how they facilitate the stabilization of nuclear bodies, remain unknown. Using active microrheology, we find that nuclear actin forms a weak viscoelastic network, with a modulus of roughly 0.1 Pa. Embedded probe particles subjected to a constant force exhibit continuous displacement, due to viscoelastic creep. Gravitational forces also cause creep displacement of nuclear bodies, resulting in their asymmetric nuclear distribution. Thus, nuclear actin does not indefinitely support the emulsion of nuclear bodies, but only kinetically stabilizes them by slowing down gravitational creep to ∼2 months. This is similar to the viability time of large oocytes, suggesting gravitational creep ages oocytes, with fatal consequences on long timescales

Large-scale phosphoproteomic analysis of membrane proteins in renal proximal and distal tubule

Recent advances in mass spectrometry (MS) have provided means for large-scale phosphoproteomic profiling of specific tissues. Here, we report results from large-scale tandem MS [liquid chromatography (LC)-MS/MS]-based phosphoproteomic profiling of biochemically isolated membranes from the renal cortex, with focus on transporters and regulatory proteins. Data sets were filtered (by target-decoy analysis) to limit false-positive identifications to <2%. A total of 7,125 unique nonphosphorylated and 743 unique phosphorylated peptides were identified. Among the phosphopeptides identified were sites on transporter proteins, i.e., solute carrier (Slc, n = 63), ATP-binding cassette (Abc, n = 4), and aquaporin (Aqp, n = 3) family proteins. Database searches reveal that a majority of the phosphorylation sites identified in transporter proteins were previously unreported. Most of the Slc family proteins are apical or basolateral transporters expressed in proximal tubule cells, including proteins known to mediate transport of glucose, amino acids, organic ions, and inorganic ions. In addition, we identified potentially important phosphorylation sites for transport proteins from distal nephron segments, including the bumetanide-sensitive Na-K-2Cl cotransporter (Slc12a1 or NKCC2) at Ser87, Thr101, and Ser126 and the thiazide-sensitive Na-Cl cotransporter (Slc12a3 or NCC) at Ser71 and Ser124. A subset of phosphorylation sites in regulatory proteins coincided with known functional motifs, suggesting specific regulatory roles. An online database from this study (http://dir.nhlbi.nih.gov/papers/lkem/rcmpd/) provides a resource for future studies of transporter regulation

Controlling the material properties and rRNA processing function of the nucleolus using light

The nucleolus is a prominent nuclear condensate that plays a central role in ribosome biogenesis by facilitating the transcription and processing of nascent ribosomal RNA (rRNA). A number of studies have highlighted the active viscoelastic nature of the nucleolus, whose material properties and phase behavior are a consequence of underlying molecular interactions. However, the ways in which the material properties of the nucleolus impact its function in rRNA biogenesis are not understood. Here we utilize the Cry2olig optogenetic system to modulate the viscoelastic properties of the nucleolus. We show that above a threshold concentration of Cry2olig protein, the nucleolus can be gelled into a tightly linked, low mobility meshwork. Gelled nucleoli no longer coalesce and relax into spheres but nonetheless permit continued internal molecular mobility of small proteins. These changes in nucleolar material properties manifest in specific alterations in rRNA processing steps, including a buildup of larger rRNA precursors and a depletion of smaller rRNA precursors. We propose that the flux of processed rRNA may be actively tuned by the cell through modulating nucleolar material properties, which suggests the potential of materials-based approaches for therapeutic intervention in ribosomopathies.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

The nucleolus and other ribonucleoprotein (RNP) bodies are membrane-less organelles that appear to assemble through phase separation of their molecular components. However, many such RNP bodies contain internal subcompartments, and the mechanism of their formation remains unclear. Here, we combine in vivo and in vitro studies, together with computational modeling, to show that subcompartments within the nucleolus represent distinct, coexisting liquid phases. Consistent with their in vivo immiscibility, purified nucleolar proteins phase separate into droplets containing distinct non-coalescing phases that are remarkably similar to nucleoli in vivo. This layered droplet organization is caused by differences in the biophysical properties of the phases - particularly droplet surface tension - which arises from sequence-encoded features of their macromolecular components. These results suggest that phase separation can give rise to multilayered liquids that may facilitate sequential RNA processing reactions in a variety of RNP bodies

Remodeling nuclear architecture allows efficient transport of herpesvirus capsids by diffusion

The nuclear chromatin structure confines the movement of large macromolecular complexes to interchromatin corrals. Herpesvirus capsids of approximately 125 nm assemble in the nucleoplasm and must reach the nuclear membranes for egress. Previous studies concluded that nuclear herpesvirus capsid motility is active, directed, and based on nuclear filamentous actin, suggesting that large nuclear complexes need metabolic energy to escape nuclear entrapment. However, this hypothesis has recently been challenged. Commonly used microscopy techniques do not allow the imaging of rapid nuclear particle motility with sufficient spatiotemporal resolution. Here, we use a rotating, oblique light sheet, which we dubbed a ring-sheet, to image and track viral capsids with high temporal and spatial resolution. We do not find any evidence for directed transport. Instead, infection with different herpesviruses induced an enlargement of interchromatin domains and allowed particles to diffuse unrestricted over longer distances, thereby facilitating nuclear egress for a larger fraction of capsids