Research highlights

Lorenzo Gotor N., Armaos A., Calloni G., Torrent Burgas M., Vabulas R.M., de Groot N.S.*, Tartaglia G.G. RNA-binding and prion domains: the Yin and Yang of phase separation. Nucleic Acids Research, 48, 9491-9504 (2020) (*Corresponding author) (top-decile, IF 11.5)

Proteins and RNAs assemble in membrane-less organelles that organize intracellular spaces and regulate biochemical reactions. The ability of proteins and RNAs to form condensates is encoded in their sequences, yet it is unknown which domains drive the phase separation (PS) process and what are their specific roles. Here, we systematically investigated the human and yeast proteomes to find regions promoting condensation. Using advanced computational methods to predict the PS propensity of proteins, we designed a set of experiments to investigate the contributions of Prion-Like Domains (PrLDs) and RNA-binding domains (RBDs). We found that one PrLD is sufficient to drive PS, whereas multiple RBDs are needed to modulate the dynamics of the assemblies. In the case of stress granule protein Pub1 we show that the PrLD promotes sequestration of protein partners and the RBD confers liquid-like behaviour to the condensate. Our work sheds light on the fine interplay between RBDs and PrLD to regulate formation of membrane-less organelles, opening up the avenue for their manipulation.

Natalia Sanchez de Groot*; Marc Torrent Burgas; Charles Ravarani; Ala Trusina; Salvador Ventura; Madam M. Babu*. The fitness cost and benefit of phase-separated protein deposits. Molecular System Biology. 15:e8075. 2019. (*Corresponding author) (top-decile, IF 8.99)

Phase separation affects cell fitness and population variability. Up, different outcomes due to the phase separation of a protein. Middle, we mathematically distinguish and quantify different fitness effects associated with protein phase separation. Down, we show that selectable phenotypic variability is a general property of proteins that can form phase-separated assemblies.

Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane-less compartments for many cellular processes. Consequently, there is controversy about the fitness costs and benefits of forming such deposits. In this work, we combined a protein model that phase-separates into deposits and a mathematical equation, to distinguish, isolate and quantify the fitness contribution due to (i) the loss or (ii) gain of protein function and (iii) deposit formation. We used this approach to measure these contributions in different conditions. We observed that the environmental condition and the cellular demand for the protein function were key determinants of fitness. In addition, we showed that protein deposit formation can influence cell-to-cell variation in free protein abundance between individuals of a cell population (i.e., gene expression noise). Overall, this property results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favouring survival of some individuals in certain environments. Thus, this data suggests that protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. Moreover, we have demonstrated that the selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase-separated assemblies and may influence cell fitness.

Natalia Sanchez de Groot*; Ricardo A. Gomes; Anna Villar-Pique; Madan M Babu; Ana Varela Coelho; Salvador Ventura. Proteome response at the edge of protein aggregation. Open Biology. 5 – 2, pp 140221. 2015. (*Corresponding author) (First quartile, IF 5.78)

Proteins adopt defined structures and are crucial to most cellular functions. Their misfolding and aggregation is associated with numerous degenerative human disorders such as type II diabetes, Huntington’s or Alzheimer’s diseases. Here, I aim to understand why cells promote the formation of protein foci. Comparison of two amyloid-b-peptide variants, mostly insoluble but differently recruited by the cell (deposited versus diffused), reveals small differences in cell fitness and proteome response. A deeper analysis revealed that the levels of oxidative stress might act as a sensor to trigger protein recruitment into foci. These data support that protein aggregation can be a beneficial cellular mechanism that is activated specifically against certain polypeptides.