Protein phase separation by a yeast prion protein promotes cellular fitness

Prion-like proteins are multi domain proteins that contain long regions of structural disorder that are termed prion-like domains. Prion-like domains are abundant within eukaryotic cells and their aggregation is associated with human pathological diseases. Despite their importance in disease, the physiological role of prion-like domains has remained enigmatic. This raises an important question: why has evolution kept these domains around? Or in other words: what are these regions good for? In this study the authors identified that the prion domain of the canonical yeast prion protein Sup35 senses environmental stress stimuli and regulates the assembly of the protein into protective protein gels rather than irreversible aggregates. Thus, the prion domain protects the essential Sup35 protein from stress-induced damage.

HFSP Program Grant holders Simon Alberti and Rohit Pappu and colleagues
authored on Fri, 23 March 2018

Cells are stressed, for example, when they are starved of nutrients, become exposed to chemicals or experience sudden temperature fluctuations. In response, cell division stops, the metabolism shuts down and cells enter into a stand-by mode. During stressful conditions, the biochemical pathways that ensure a high energy level break down and consequently cells enter a state that impairs cellular functions and facilitates protein misfolding and aggregation. In yeast, this sudden stress is also accompanied by a dramatic decrease of the cytosolic pH value – the cells acidify. When the stress is over, cells must rapidly reprogram their metabolism and restart growth and division. But the mechanism by which cells switch rapidly between growth and protective stand-by mode remained unclear.

Figure: The Sup35 prion domain regulates phase separation of the translation termination factor Sup35 during cellular stress. The translation termination factor Sup35 (depicted in the magnifying glass) consists of a disordered prion domain (green), a disordered stress sensor domain (magenta) and a folded catalytic domain (blue). During growth, Sup35 catalyzes translation termination. During cell stress, the prion domain and the sensor domain act together to promote phase separation into protective and reversible biomolecular condensates.

The formation of dynamic, membraneless compartments using intracellular phase transitions, such as phase separation and gelation, provides an efficient way for cells to respond to environmental changes. Recent work has identified a special class of intrinsically disordered domains as potential drivers of phase separation in cells. However, more traditional work has highlighted the ability of these domains to drive the formation of fibrillar, amyloid-like aggregates. Such domains are also known as prion domains. In yeast, prion-like aggregates propagate between cells and in mammals the aggregation and spreading of prion-like proteins has been associated with neurodegenerative diseases.

The yeast translation termination factor Sup35 is an archetypal prion domain-containing protein. Its prion domain can form irreversible heritable prion aggregates. But despite having been described almost 25 years ago, the physiological functions of the Sup35 prion domain, as well as the evolutionary pressures acting on this and related prion-like domains remained unclear.

In this paper, the authors show that the prion domain of Sup35 drives the reversible phase separation of the translation termination factor into biomolecular condensates. These condensates are distinct and different from fibrillar amyloid-like prion particles. Sup35 condensates form by pH-induced liquid-like phase separation as a response to sudden stress. The condensates form by liquid-like phase separation but subsequently solidify to form protective protein gels. These gel-like condensates consist of cross-linked Sup35 molecules that form a porous meshwork. A cluster of negatively charged amino acids functions as a pH sensor and regulates condensate formation. The ability to form biomolecular condensates is shared among ~400 million years distantly related budding yeast and fission yeast. This suggests that condensate formation is a conserved function of the prion domain of Sup35. In agreement with an important physiological function of the prion domain in stress-sensing and regulating condensate assembly, the catalytic GTPase domain of the translation termination factor Sup35 readily forms irreversible aggregates in the absence of the prion domain. Consequently, cells lacking the prion domain exhibit impaired translational activity and a growth defect when recovering from stress. Thus, the prion domain rescues the essential GTPase domain of Sup35 from irreversible aggregation, thereby ensuring that the translation termination factor remains functional during harsh environmental conditions.

The prion domain of Sup35 is a highly regulated molecular device that has the ability to sense and respond to physio-chemical changes within cells. The N-terminal prion domain provides the interactions that drive liquid phase separation. Phase separation is regulated by the adjacent stress sensor. The synergy of these two modules enables the essential translation termination factor to rapidly form protective condensates during stress. This suggests that prion domains are protein-specific stress sensors and modifiers of protein phase transitions that allow cells to respond to specific environmental conditions.

Text by Simon Alberti and Titus Franzmann

Reference

Phase separation of a yeast prion protein promotes cellular fitness. Franzmann TM, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse AS, Nüske E, Richter D, Baumeister W, Grill SW, Pappu RV, Hyman AA, Alberti S. Science. 2018 Jan 5;359(6371). pii: eaao5654. doi: 10.1126/science.aao5654.

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