Independent active and thermodynamic processes govern the nucleolus assembly in vivo

Abstract

Membraneless organelles play a central role in the organization of protoplasm by concentrating macromolecules, which allows efficient cellular processes. Recent studies have shown that, in vitro, certain components in such organelles can assemble through phase separation. Inside the cell, however, such organelles are multicomponent, with numerous intermolecular interactions that can potentially affect the demixing properties of individual components. In addition, the organelles themselves are inherently active, and it is not clear how the active, energy-consuming processes that occur constantly within such organelles affect the phase separation behavior of the constituent macromolecules. Here, we examine the phase separation model for the formation of membraneless organelles in vivo by assessing the two features that collectively distinguish it from active assembly, namely temperature dependence and reversibility. We use a microfluidic device that allows accurate and rapid manipulation of temperature and examine the quantitative dynamics by which six different nucleolar proteins assemble into the nucleoli of Drosophila melanogaster embryos. Our results indicate that, although phase separation is the main mode of recruitment for four of the studied proteins, the assembly of the other two is irreversible and enhanced at higher temperatures, behaviors indicative of active recruitment to the nucleolus. These two subsets of components differ in their requirements for ribosomal DNA; the two actively assembling components fail to assemble in the absence of ribosomal DNA, whereas the thermodynamically driven components assemble but lose temporal and spatial precision.liquid-liquid phase separation | intracellular phase transition | membrane-less organelle | RNA granule | Drosophila nucleologenesis M embraneless organelles are highly concentrated assemblies of proteins and RNAs that provide specialized microenvironments for particular cellular functions (1). Recent studies suggest that such organelles may form via a liquid-liquid phase separation (LLPS) process, in which the constituent components spontaneously assemble on reaching a critical concentration at a given temperature (2-5). LLPS provides an attractive energyefficient mechanism for cells to organize different biochemical reactions spatially, whereas the liquid nature of the emerging organelles, such as P granules and nucleoli (2, 6), allows for rapid exchange of molecules. The role of LLPS has been supported by studies in which the purified RNA binding proteins that localize to such subcellular bodies in vivo also self-assemble in vitro (3-11). However, because of the complexity of living cells, our current understanding of the role of LLPS in membraneless organelle assembly is by far limited to in vitro studies. Particularly, membraneless organelles are multicomponent, and the interactions between different components can enhance or diminish the ability of individual proteins to phase separate inside living cells (12). Therefore, the behavior of the individua...

Thermodynamically driven assemblies and liquid–liquid phase separations in biology

“…What is notable about binary-or pseudo-binary-mixtures is that changing the concentration within the dome will not affect the compositions of the coexisting liquids, and will only alter the partition constant, λ. In biological systems, examples of UCST have been observed in vitro for the low-complexity domain of the RNA binding protein FUS [56], a disordered Nauge protein [57], and lipid bilayers [58], and in vivo for the nucleolar proteins Fibrillarin, Nopp140, RNA polymerase I, and Pitchoune [59].…”

Integrating the genomic architecture of human nucleolar organizer regions with the biophysical properties of nucleoli

“…Its recruitment during telophase is accompanied by the resumption of transcription. Work from the Wieschaus Lab using Drosophila and our work in human cells indicate that an active process centered on rDNA, namely transcription, is required for DFC formation . In human cells, mitotic bookmarking by UBF is a prerequisite for nucleolar formation.…”

Analysis of P granules in vivo and ex vivo

“…S1A) and similar dynamics during granule fusion (Wang, Smith et al 2014). Active and passive liquid-like phases have also been described in nucleoli and stress granules, which also solidify when extruded from cells (Brangwynne, Mitchison et al 2011, Jain, Wheeler et al 2016, Falahati and Wieschaus 2017. Active scaffolds may therefore be a common underlying feature of RNA granules.…”