Phase Separation in Biology
Total Page:16
File Type:pdf, Size:1020Kb
Current Biology Magazine has not yet been applied to all Primer cytoplasm and the distribution of breeding programs, and there are these macromolecules is subject to still some major crop species (e.g., constant change. Early concepts to Phase separation soybean, tomato, sunfl ower) that are explain these density fl uctuations recalcitrant to the currently available in biology proposed a role for local synthesis, procedures, or for which present anchoring or active transport. Yet these protocols are not effi cient enough. Simon Alberti concepts are insuffi cient to explain The understanding of the maize in the complex organization of cells. situ system should help to extend Cells have to organize their complex We now realize that cells can only be the DH technology to more species biochemistry to regulate their properly understood if we also consider or breeding programs by either metabolism and respond to changes the collective properties of biological directly knocking out the functional in the environment. Traditionally, macromolecules. ortholog of the maize gene, or if intracellular organization has been Chemists have known for a long needed by transferring the cellular associated with compartments that time that macromolecules can have and molecular knowledge acquired are surrounded by lipid membranes. collective properties. The science of on maize. In addition to these However, in recent years, phase macromolecular collectives is called applications, the identifi cation of transitions have emerged as a novel colloidal chemistry. One example of a the NLD/MTL/ZmPLA1 gene offers form of cellular organization. Phase colloid is Jell-O, which is composed a unique opportunity to explore the transition is a physical process of colored water and gelatin, a large, many mysteries of double fertilization whereby a substance changes string-like protein. Gelatin dissolves in plants. from one physical state to another. well in hot water; however, when the Examples are provided by the freezing water is cooled, the gelatin molecules Where can I fi nd out more? of water into ice (liquid to solid) or the become insoluble and sticky and then Britt, A.B., and Kuppu, S. (2016). Cenh3: heating of water to generate water form a cross-linked network. The result an emerging player in haploid induction vapor (liquid to gas). of this process is a hydrogel. Technology. Front. Plant Sci. 7, 357. Dunwell, J.M. (2010). Haploids in fl owering plants: Liquid–liquid phase separation is The concept of viewing cells as origins and exploitation. Plant Biotechnol. J. a special form of a phase transition colloidal systems was fi rst proposed 8, 377–424. Dwivedi, S.L., Britt, A.B., Tripathi, L., Sharma, that is particularly relevant for living in the late 19th century by Edmund S., Upadhyaya, H.D., and Ortiz, R. (2015). organisms. Here, a homogenous Wilson. Wilson pointed out that cells Haploids: Constraints and opportunities in solution of molecules spontaneously appear as if they are densely packed plant breeding. Biotechnol. Adv. 33, 812–829. Forster, B.P., Heberle-Bors, E., Kasha, K.J., separates (‘demixes’) into two with macromolecular phases or liquid and Touraev, A. (2007). The resurgence of coexisting liquid phases, a dense phase ‘coacervates’. Alexander Oparin haploids in higher plants. Trends Plant Sci. 12, that is enriched for these molecules and later considered these coacervates 368–375. Gilles, L.M., Khaled, A., Laffaire, J.-B., a phase that is depleted (Figure 1). The an essential constituent of the Chaignon, S., Gendrot, G., Laplaige, J., interface of these dense droplets forms primordial soup. However, these initial Bergès, H., Beydon, G., Bayle, V., Barret, P., et al. (2017). Loss of pollen-specifi c a boundary that allows the selective concepts of cellular organization were phospholipase NOT LIKE DAD triggers passage of some molecules but not eclipsed by the enormous success of gynogenesis in maize. EMBO J. 36, 707–717. others. The presence of this interface reductionist molecular biology. Very Ishii, T., Karimi-Ashtiyani, R., and Houben, A. (2016). Haploidization via chromosome makes it possible that liquid droplets recently, however, we have seen a elimination: Means and mechanisms. Annu. can function as compartments. Once revival of colloidal biochemistry. Key Rev. Plant Biol. 67, 421–438. formed, liquid droplet compartments was the realization that cells contain Jackson, D. (2017). No sex please, we’re (in) breeding. EMBO J. 36, 703–704. can also adopt different physical states; compartments that lack membranes. Kelliher, T., Starr, D., Richbourg, L., Chintamanani, they can, for example, harden into gel- S., Delzer, B., Nuccio, M.L., Green, J., Chen, Z., McCuiston, J., Wang, W., et al. or glass-like states or they can turn into Membrane-less organelles (2017). MATRILINEAL, a sperm-specifi c solid crystals. Thus, phase separation Membrane-less organelles are micron- phospholipase, triggers maize haploid allows the formation of a wide range of sized cellular structures that consist of induction. Nature 542, 105–109. Liu, C., Li, X., Meng, D., Zhong, Y., Chen, C., compartments with different physical large collections of macromolecules, Dong, X., Xu, X., Chen, B., Li, W., Li, L., et al. properties. such as RNAs and proteins. Modern (2017). A 4-bp insertion at ZmPLA1 encoding a putative phospholipase A generates haploid In this Primer, I introduce the imaging approaches are revealing an induction in maize. Mol. Plant 10, 520–522. emerging topic of biological phase increasing number of these structures Ren, J., Wu, P., Trampe, B., Tian, X., transitions. I further discuss how cells (Figure 2). One prominent example is Lübberstedt, T., and Chen, S. (2017). Novel technologies in doubled haploid line use phase transitions to regulate provided by the centrosome, which development. Plant Biotechnol. J., http:// biological functions and activities in organizes the microtubule network of dx.doi.org/10.1111/pbi.1280. order to increase their fi tness and cells. Another example is provided by chances of survival. processing bodies or P bodies, which 1Laboratoire Reproduction et store and degrade RNA. Then there Dé veloppement des Plantes, Univ Lyon, The colloidal nature of cells is the example of the nucleolus, an ENS de Lyon, UCB Lyon 1, CNRS, INRA, The cellular interior is not a well- assembly line for ribosomes: it has a F-69342, Lyon, France; 2Limagrain, Limagrain Field Seeds, Research Centre, mixed collection of molecules. fi brillar center, where the ribosomal F-63360 Gerzat, France. Macromolecules are enriched or RNA is produced, and two additional *E-mail: [email protected] depleted in certain areas of the intranucleolar compartments, which Current Biology 27, R1089–R1107, October 23, 2017 © 2017 Elsevier Ltd. R1097 Current Biology Magazine In a key paper in 2012, Mike Phase separation Protein Rosen and colleagues provided conc. the fi rst experimental evidence that multivalency — the availability of many different binding sites on a molecule — is the crucial parameter that determines whether or not a protein will undergo phase separation. C Critical Many proteins, especially those functioning in signaling or gene expression, contain tandem arrays of modular domains. Each of these interaction modules binds a particular Time ligand, often with relatively weak affi nity. The number of these different modules determines the valency of Protein Phase separation the molecule. Importantly, multivalent conc. proteins have a critical threshold for phase separation that depends on the number of modules and available ligands. Increasing the number of the modules promotes the formation of increasingly larger complexes that CCritical PTMs, temperature, manifest macroscopically as phase- ionic strength separated droplets. Thus, although the C Critical composition of cellular bodies appears to be complex, their formation may be governed by very simple rules, such as Time protein valency and the availability of Current Biology ligands. Another feature that strongly affects Figure 1. Protein phase separation. the phase behavior of proteins is their Top: A protein forms dense liquid droplets above the critical concentration (Ccritical) for phase separa- solubility. Many phase-separating tion. The liquid droplets are stable as long as the total concentration is above the critical threshold. proteins have poor solubility in water. The droplets form a compartment that allows the diffusion of molecules within the compartment and Burying such insoluble proteins in a promotes the dynamic exchange of molecules with the dilute surrounding phase. Once the total protein concentration drops below the critical concentration again, the compartments dissolve and the system growing phase-separating structure relapses back to a one-phase state where the molecules are evenly distributed. The insets above show is energetically more favorable than original data from a phase separation experiment with purifi ed GFP-tagged FUS (a prion-like RNA- exposing these proteins to water. As binding protein). Bottom: Post-translational modifi cations (PTMs) or changes in temperature or ionic a consequence, solubility changes strength can increase the affi nity of protein–protein interactions, thus lowering the critical threshold for and phase separation are often phase separation and allowing compartment formation at a much lower protein concentration. coupled. This is particularly relevant for multidomain proteins that are assemble ribosomes from molecular protein–nucleic acid interactions connected