Emergent microenvironments of nucleoli

Abstract

In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions

Direct computations of viscoelastic moduli of biomolecular condensates

“…A total of 1.5×10 10 steps was used at each simulation temperature. Equilibration was typically realized after about 2×10 9 steps, as determined by plateauing of the total system energy. All simulation results were analyzed after the halfway point of 7.5×10 9 steps.…”

“…Equilibration was typically realized after about 2×10 9 steps, as determined by plateauing of the total system energy. All simulation results were analyzed after the halfway point of 7.5×10 9 steps. Two distinct order parameters are typically computed in LaSSI simulations.…”

“…Each pair of coexisting phases is delineated by a phase boundary giving rise to distinct equilibrium and dynamical interphase properties 8 . Equilibrium interphase properties refer to differences in concentrations of macromolecules and solutes that are engendered by equalization of chemical potentials across phase boundaries 8,9 . These concentration gradients also create differences in material properties, which we refer to as dynamical interphase properties.…”

Biomolecular condensates are characterized by interphase electric potentials

“…Condensates form via composite processes that combine phase separation, reversible associations, and continuous phase transitions such as percolation [8][9][10][11] or charge-driven complex coacervation 12 . The latter process 13 comes in different flavors 14 and it can give rise to physiologically relevant 10 or de novo nuclear condensates 15 .…”

Nuclear bodies: a gene expression collection for our time

“…Rohit Pappu and colleagues [ 4 ] provide an insightful and comprehensive treatment of ‘The Nucleolus 2024’. Their article captures important recent developments and addresses the liquid-liquid phase separation dimensions of this intriguing organelle in as lucid a manner as anything published before.…”