Proteomic analysis reveals the direct recruitment of intrinsically disordered regions to stress granules in S. cerevisiae.

Stress granules (SGs) are stress-induced membraneless condensates that store non-translating mRNA and stalled translation initiation complexes. Although metazoan SGs are dynamic compartments where proteins can rapidly exchange with their surroundings, yeast SGs seem largely static. To gain a better understanding of yeast SGs, we identified proteins that sediment after heat shock using mass spectrometry. Proteins that sediment upon heat shock are biased toward a subset of abundant proteins that are significantly enriched in intrinsically disordered regions (IDRs). Heat-induced SG localization of over 80 proteins were confirmed using microscopy, including 32 proteins not previously known to localize to SGs. We found that several IDRs were sufficient to mediate SG recruitment. Moreover, the dynamic exchange of IDRs can be observed using fluorescence recovery after photobleaching, whereas other components remain immobile. Lastly, we showed that the IDR of the Ubp3 deubiquitinase was critical for yeast SG formation. This work shows that IDRs can be sufficient for SG incorporation, can remain dynamic in vitrified SGs, and can play an important role in cellular compartmentalization upon stress.This article has an associated First Person interview with the first author of the paper.

Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions.

In eukaryotes, disordered regions cover up to 50% of proteomes and mediate fundamental cellular processes. In contrast to globular domains, where about half of the amino acids are buried in the protein interior, disordered regions show higher solvent accessibility, which makes them prone to engage in non-functional interactions. Such interactions are exacerbated by the law of mass action, prompting the question of how they are minimized in abundant proteins. We find that interaction propensity or "stickiness" of disordered regions negatively correlates with their cellular abundance, both in yeast and human. Strikingly, considering yeast proteins where a large fraction of the sequence is disordered, the correlation between stickiness and abundance reaches R=-0.55. Beyond this global amino-acid composition bias, we identify three rules by which amino-acid composition of disordered regions adjusts with high abundance. First, lysines are preferred over arginines, consistent with the latter amino acid being stickier than the former. Second, compensatory effects exist, whereby a sticky region can be tolerated if it is compensated by a distal non-sticky region. Third, such compensation requires a lower average stickiness at the same abundance when compared to a scenario where stickiness is homogeneous throughout the sequence. We validate these rules experimentally, employing them as different strategies to rescue an otherwise sticky protein fragment from aggregation. Our results highlight that non-functional interactions represent a significant constraint in cellular systems and reveal simple rules by which protein sequences adapt to that constraint. Data from this work are deposited in Figshare, at https://doi.org/10.6084/m9.figshare.8068937.v3.

Different subunits belonging to the same protein complex often exhibit discordant expression levels and evolutionary properties.

Hetero-oligomeric protein complexes are involved in many of the key processes in cells. Given that the subunits of a complex function together, it has often been expected to find that (i) they are expressed at similar levels in cells; (ii) they are simultaneously present or absent in genomes; and that (iii) the effects on fitness of deleting their genes should be similar. Such a coherence is, however, often found to be weak or absent. Multi-functionality of subunits and mechanisms of complex assembly are discussed as possible sources for the lack of coherence.