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A framework for understanding the functions of biomolecular condensates across scales

Nature Reviews Molecular Cell Biology volume 22, pages 215–235 (2021)Cite this article

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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.

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Fig. 1: Overview of biomolecular condensate functions across scales.
Fig. 2: Molecular-scale functions of biomolecular condensates.
Fig. 3: Mesoscale functions of biomolecular condensates.
Fig. 4: Cellular-scale functions of biomolecular condensates.

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Acknowledgements

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.).

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Authors and Affiliations

  1. 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

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  1. Andrew S. Lyon
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The authors contributed equally to all aspects of the article.

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Correspondence to Michael K. Rosen.

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M.K.R. is a co-founder of the biotechnology company Faze Medicines. A.S.L and W.B.P. declare no competing interests.

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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 KM 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.

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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

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