Biomolecular condensate


In biochemistry, biomolecular condensates are a class of membrane-less organelles and organelle subdomains, which carry out specialized functions within the cell.
Unlike many organelles, biomolecular condensate composition is not controlled by a bounding membrane. Instead, condensates can form and maintain organization through a range of different processes. The most well-known process is phase separation of proteins, RNA, and other biopolymers into either colloidal emulsions, gels, liquid crystals, solid crystals, or protein aggregates within cells.

History

Micellar theory

The micellar theory of Carl Nägeli was developed from his detailed study of starch granules in 1858. Amorphous substances such as starch and cellulose were proposed to consist of building blocks, packed in a loosely crystalline array to form what he later termed "micelles". Water could penetrate between the micelles, and new micelles could form in the interstices between old micelles. The swelling of starch grains and their growth was described by a molecular-aggregate model, which he also applied to the cellulose of the plant cell wall. The modern usage of 'micelle' refers strictly to lipids, but its original usage clearly extended to other types of biomolecule, and this legacy is reflected to this day in the description of milk as being composed of 'casein micelles'.

Colloidal phase separation theory

The concept of intracellular colloids as an organizing principle for the compartmentalization of living cells dates back to the end of the 19th century, beginning with William Bate Hardy and Edmund Beecher Wilson who described the cytoplasm as a colloid. Around the same time, Thomas Harrison Montgomery Jr. described the morphology of the nucleolus, an organelle within the nucleus, which has subsequently been shown to form through intracellular phase separation. WB Hardy linked formation of biological colloids with phase separation in his study of globulins, stating that: "The globulin is dispersed in the solvent as particles which are the colloid particles and which are so large as to form an internal phase", and further contributed to the basic physical description of oil-water phase separation.
Colloidal phase separation as a driving force in cellular organisation appealed strongly to Stephane Leduc, who wrote in his influential 1911 book The Mechanism of Life: "Hence the study of life may be best begun by the study of those physico-chemical phenomena which result from the contact of two different liquids. Biology is thus but a branch of the physico-chemistry of liquids; it includes the study of electrolytic and colloidal solutions, and of the molecular forces brought into play by solution, osmosis, diffusion, cohesion, and crystallization."
The primordial soup theory of the origin of life, proposed by Alexander Oparin in Russian in 1924 and by J.B.S. Haldane in 1929, suggested that life was preceded by the formation of what Haldane called a "hot dilute soup" of "colloidal organic substances", and which Oparin referred to as 'coacervates' – particles composed of two or more colloids which might be protein, lipid or nucleic acid. These ideas strongly influenced the subsequent work of Sidney W. Fox on proteinoid microspheres.

Support from other disciplines

When cell biologists largely abandoned colloidal phase separation, it was left to relative outsiders – agricultural scientists and physicists – to make further progress in the study of phase separating biomolecules in cells.
Beginning in the early 1970s, Harold M Farrell Jr. at the US Department of Agriculture developed a colloidal phase separation model for milk casein micelles that form within mammary gland cells before secretion as milk.
Also in the 1970s, physicists Tanaka & Benedek at MIT identified phase-separation behaviour of gamma-crystallin proteins from lens epithelial cells and cataracts in solution, which Benedek called protein condensation.
In the 1980s and 1990s, Athene Donald's polymer physics lab in Cambridge extensively characterised phase transitions / phase separation of starch granules from the cytoplasm of plant cells, which behave as liquid crystals.
In 1991, Pierre-Gilles de Gennes received the Nobel Prize in Physics for developing a generalized theory of phase transitions with particular applications to describing ordering and phase transitions in polymers. Unfortunately, de Gennes wrote in Nature that polymers should be distinguished from other types of colloids, even though they can display similar clustering and phase separation behaviour, a stance that has been reflected in the reduced usage of the term colloid to describe the higher-order association behaviour of biopolymers in modern cell biology and molecular self-assembly.

Phase separation revisited

Advances in confocal microscopy at the end of the 20th century identified proteins, RNA or carbohydrates localising to many non-membrane bound cellular compartments within the cytoplasm or nucleus which were variously referred to as 'puncta/dots', 'signalosomes', 'granules', 'bodies', 'assemblies', 'paraspeckles', 'purinosomes', 'inclusions', 'aggregates' or 'factories'. During this time period the concept of phase separation was re-borrowed from colloidal chemistry & polymer physics and proposed to underlie both cytoplasmic and nuclear compartmentalization.
Since 2009, further evidence for biomacromolecules undergoing intracellular phase transitions has been observed in many different contexts, both within cells and in reconstituted in vitro experiments.
The newly coined term "biomolecular condensate" refers to biological polymers that undergo self assembly via clustering to increase the local concentration of the assembling components, and is analogous to the physical definition of condensation.
In physics, condensation typically refers to a gas–liquid phase transition.
In biology the term 'condensation' is used much more broadly and can also refer to liquid–liquid phase separation to form colloidal emulsions or liquid crystals within cells, and liquid–solid phase separation to form gels, sols, or suspensions within cells as well as liquid-to-solid phase transitions such as DNA condensation during prophase of the cell cycle or protein condensation of crystallins in cataracts. With this in mind, the term 'biomolecular condensates' was deliberately introduced to reflect this breadth. Since biomolecular condensation generally involves oligomeric or polymeric interactions between an indefinite number of components, it is generally considered distinct from formation of smaller stoichiometric protein complexes with defined numbers of subunits, such as viral capsids or the proteasome – although both are examples of spontaneous molecular self-assembly or self-organisation.
Mechanistically, it appears that the conformational landscape and multivalent interactions between intrinsically disordered proteins, and/or protein domains that induce head-to-tail oligomeric or polymeric clustering, might play a role in phase separation of proteins.

Examples

Many examples of biomolecular condensates have been characterized in the cytoplasm and the nucleus that are thought to arise by either liquid–liquid or liquid–solid phase separation.

Cytoplasmic condensates

Other nuclear structures including heterochromatin form by mechanisms similar to phase separation, so can also be classified as biomolecular condensates.
RNAs with triplet expansion that produce neurodegenerative disorders can also independently form RNA foci in vitro or in mammalian nuclear. This phenomenon is further reconsituted in bacteria E. coli, by expressing engineered CAG repeats, providing strong evidence that these RNA repeats phase separate without the need of additional proteins.

Plasma membrane associated condensates

  • Membrane protein, or membrane-associated protein, clustering at neurological synapses, cell-cell tight junctions, or other membrane domains.

    Secreted extracellular condensates

  • Secreted thyroglobulin colloid and colloid nodules of the thyroid gland
  • Secreted casein 'micelles' of the mammary gland
  • Serum albumin and globulins
  • Secreted lysozyme

    Lipid-enclosed organelles and [lipoprotein]s are not considered condensates

Typical organelles or endosomes enclosed by a lipid bilayer are not considered biomolecular condensates. In addition, lipid droplets are surrounded by a lipid monolayer in the cytoplasm, or in milk, or in tears, so appear to fall under the 'membrane bound' category. Finally, secreted LDL and HDL lipoprotein particles are also enclosed by a lipid monolayer. The formation of these structures involves phase separation to from colloidal micelles or liquid crystal bilayers, but they are not classified as biomolecular condensates, as this term is reserved for non-membrane bound organelles.