A framework for understanding the functions of biomolecular condensates across scales

ABSTRACT Biomolecular condensates are found throughout eukaryotic cells, including in the nucleus, in the cytoplasm and on membranes. They are also implicated in a wide range of cellular

functions, organizing molecules that act in processes ranging from RNA metabolism to signalling to gene regulation. Early work in the field focused on identifying condensates and

understanding how their physical properties and regulation arise from molecular constituents. Recent years have brought a focus on understanding condensate functions. Studies have revealed

functions that span different length scales: from molecular (modulating the rates of chemical reactions) to mesoscale (organizing large structures within cells) to cellular (facilitating

localization of cellular materials and homeostatic responses). In this Roadmap, we discuss representative examples of biochemical and cellular functions of biomolecular condensates from the

recent literature and organize these functions into a series of non-exclusive classes across the different length scales. We conclude with a discussion of areas of current interest and

challenges in the field, and thoughts about how progress may be made to further our understanding of the widespread roles of condensates in cell biology. Access through your institution Buy

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BIOMOLECULAR CONDENSATES REVEALED BY GENETIC COMPLEMENTATION Article 21 October 2024 BIOMOLECULAR CONDENSATES – EXTANT RELICS OR EVOLVING MICROCOMPARTMENTS? Article Open access 21 June 2023

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Research on biomolecular condensates is supported in the Rosen laboratory by the Howard Hughes Medical Institute, a Paul G. Allen Frontiers Distinguished Investigator Award to M.K.R. and

grants from the Welch Foundation (I-1544 to M.K.R.) and the National Institutes of Health (NIH) (F32 GM136058 to A.S.L.). AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of

Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA Andrew S. Lyon, William B. Peeples & Michael K. Rosen Authors * Andrew S.

Lyon View author publications You can also search for this author inPubMed Google Scholar * William B. Peeples View author publications You can also search for this author inPubMed Google

Scholar * Michael K. Rosen View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS The authors contributed equally to all aspects of the article.

CORRESPONDING AUTHOR Correspondence to Michael K. Rosen. ETHICS DECLARATIONS COMPETING INTERESTS M.K.R. is a co-founder of the biotechnology company Faze Medicines. A.S.L and W.B.P. declare

no competing interests. ADDITIONAL INFORMATION PEER REVIEW INFORMATION _Nature Reviews Molecular Cell Biology_ thanks M. Babu, S. Michnick and the other, anonymous, reviewer(s) for their

contribution to the peer review of this work. PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. GLOSSARY

* Material properties In the context of biomolecular condensates, physical properties of the assembly of constituent macromolecules including viscosity, surface tension and porosity. *

Interfacial tension (Also known as surface tension). For separate liquid phases in contact with each other, the work required to increase the surface area of contact between the two phases.

In the absence of external forces, interfacial/surface tension causes phase-separated liquids to form spherical droplets as spheres have minimal surface area for a given volume. *

Multivalent interactions Interactions occurring between macromolecules with multiple sites of interaction, such that each molecule can interact with multiple binding partners. *

Intrinsically disordered regions Protein regions that do not adopt any stable ordered three-dimensional structure. * Law of mass action In the context of enzymology, the principle that the

chemical reaction rate is proportional to the concentration of enzymes and substrates. * Ribulose bisphosphate carboxylase/oxygenase (Rubisco). An enzyme acting in carbon fixation in

photosynthetic organisms, catalysing the reaction between ribulose bisphosphate and atmospheric carbon dioxide. * Cyclic guanosine monophosphate–adenosine monophosphate (cGAMP) synthase

(cGAS). An innate immune signalling enzyme that senses cytosolic DNA, a pathogen-associated molecular pattern, and produces cGAMP, which activates the stimulator of interferon genes (STING)

protein to induce pro-inflammatory transcriptional responses. * Allostery Regulation of enzyme activity via binding by a second molecule at a site other than the enzyme’s active site, often

by inducing a conformational change. * Scaffold In simple molecular systems, a macromolecule that is required for condensate formation. The other, general group of condensate components are

client molecules, which bind to and selectively partition into condensates without affecting condensate formation. In many natural condensates, this distinction is not absolute, and whereas

some macromolecules act as pure scaffolds and some as pure clients, others can have varying impacts on the formation (threshold concentration) and composition of the compartment. * _K_ M A

parameter of the Michaelis–Menten model of enzyme kinetics, describing the concentration of a substrate molecule at which the rate of product formation reaches half of the maximum possible

rate under a given set of conditions. If the rate of enzyme–substrate binding is rapid relative to catalysis, the _K_M value approximates the dissociation constant for the enzyme–substrate

complex. * Paraspeckles Nuclear condensates implicated in RNA base editing as well as transcriptional regulation. Paraspeckles are formed from the long non-coding RNA NEAT1 and the DBHS

family of proteins (NONO, SFPQ and PSPC1). * Kinetic proofreading A biochemical error-correction mechanism favouring reaction pathways that lead to correct over incorrect products, wherein

an irreversible step that leads to exit of reaction intermediates from the pathway is more likely to occur for incorrect intermediates. * Processing bodies Cytoplasmic condensates found in

yeast and humans that contains mRNA, RNA decapping and RNA degradation machinery. P bodies are thought to either store or degrade mRNA during stress. * Argonaute A protein component of the

RNA-induced silencing complex that binds several classes of small non-coding RNAs, which direct the complex to mRNA targets via sequence complementarity to downregulate expression through

endonucleolytic mRNA cleavage or translational inhibition. * Transgenerational epigenetic inheritance Biological processes that allow transmission of epigenetic regulatory molecules or

modifications, such as RNAi factors or DNA methylation, from parent to offspring without altering DNA sequences. * P granules Biomolecular condensates formed by liquid–liquid phase

separation in _Caenorhabditis elegans_ composed of RNA and proteins involved in the maintenance of germ cell fate via post-transcriptional regulation and small RNA biogenesis. * Z granules

Biomolecular condensates in _Caenorhabditis elegans_ containing the proteins ZNFX1 and WAGO4 required for transgenerational epigenetic inheritance of RNAi. Associates with both P granules

and Mutator foci, forming a bridge between the two condensates. * Mutator foci A type of biomolecular condensate in _Caenorhabditis elegans_ consisting of proteins encoded by _mutator_ class

genes, originally discovered in genetic screens for activation of transposons in the germline. Functions in siRNA amplification and RNA silencing. * Voltage-gated calcium channels Membrane

protein channels that allow ingress of calcium into the cell at presynaptic terminals of neurons when activated by membrane depolarization. Calcium activates exocytosis of neurotransmitter

vesicles. * _N_-Methyl-d-aspartate (NMDA) receptor A postsynaptic membrane protein channel activated by the excitatory neurotransmitter glutamate, allowing ingress of cations to depolarize

the postsynaptic neuron. * Dendritic spines Small protrusions on postsynaptic dendrites that are sites of excitatory signalling by glutamate neurotransmitter receptors. * Balbiani body A

condensate specifically found during oocyte development that includes nuage, mitochondria and rough endoplasmic reticulum. Although the function is not fully understood, it is thought to

preserve eggs in a dormant state prior to ovulation. * Optical trapping The use of highly focused laser beams to apply force to (‘trap’) very small objects. * Chemogenetic approaches A class

of experimental techniques that introduce proteins or protein domain fusion constructs that have engineered small molecule-dependent activities into cells or in vitro biochemical reactions

to achieve control over cellular or biochemical activities. * Optogenetics A class of experimental techniques using light-responsive proteins or engineered protein domain fusions to acutely

modulate cellular or protein activities by illuminating cells or in vitro biochemical reactions. * Partition coefficient The ratio of molecular concentration within a biomolecular condensate

relative to the concentration in the surrounding solution. * Michaelis-like recruitment For the binding of a molecule to some structure, a non-linear, saturable relationship between the

molecular concentration and the fraction bound described by the rectangular hyperbola of the Michaelis–Menten model of enzyme kinetics. * Promyelocytic leukaemia nuclear bodies Nuclear

condensates formed by the promyelocytic leukaemia protein (PML). Fusion of PML to the retinoic acid receptor causes acute promyelocytic leukaemia. PML bodies are implicated in various

processes, including transcription regulation, viral immunity, post-translational modification and apoptosis. * CAR T cells In cancer immunotherapy, T cells that express engineered T cell

receptors (TCRs) where the native extracellular domains have been replaced by a heterologous binding domain targeted to a tumour-specific cell-surface protein in order to direct increased

cytotoxic activity towards tumour cells. * Kinetic trapping A phenomenon in which a thermodynamically less stable state is maintained due to the high energy barrier, and thus long time

period, required to move to the more stable state. * Split enzyme system The use of an enzyme that has been expressed as two separate polypeptide chains and is only active when the fragments

are brought together to reconstitute the full enzyme. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Lyon, A.S., Peeples, W.B. & Rosen, M.K. A

framework for understanding the functions of biomolecular condensates across scales. _Nat Rev Mol Cell Biol_ 22, 215–235 (2021). https://doi.org/10.1038/s41580-020-00303-z Download citation

* Accepted: 01 October 2020 * Published: 09 November 2020 * Issue Date: March 2021 * DOI: https://doi.org/10.1038/s41580-020-00303-z SHARE THIS ARTICLE Anyone you share the following link

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