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Abstract
Cells have developed diverse mechanisms to monitor changes in their surroundings. This allows them to establish effective responses to cope with adverse environments. Some of these mechanisms have been well characterized in the budding yeast Saccharomyces cerevisiae, an excellent experimental model to explore and elucidate some of the strategies selected in eukaryotic organisms to adjust their growth and development in stressful conditions. The relevance of structural disorder in proteins and the impact on their functions has been uncovered for proteins participating in different processes. This is the case of some transcription factors (TFs) and other signaling hub proteins, where intrinsically disordered regions (IDRs) play a critical role in their function. In this work, we present a comprehensive bioinformatic analysis to evaluate the significance of structural disorder in those TFs (170) recognized in S. cerevisiae. Our findings show that 85.2% of these TFs contain at least one IDR, whereas ~30% exhibit a higher disorder level and thus were considered as intrinsically disordered proteins (IDPs). We also found that TFs contain a higher number of IDRs compared to the rest of the yeast proteins, and that intrinsically disordered TFs (IDTFs) have a higher number of protein-protein interactions than those with low structural disorder. The analysis of different stress response pathways showed a high content of structural disorder not only in TFs but also in other signaling proteins. The propensity of yeast proteome to undergo a liquid-liquid phase separation (LLPS) was also analyzed, showing that a significant proportion of IDTFs may undergo this phenomenon. Our analysis is a starting point for future research on the importance of structural disorder in yeast stress responses.
Highlights
Stressful environments alter cellular homeostasis, leading to a diversity of adjustment mechanisms in metabolic and developmental programs
This report highlights the fact that intrinsically disordered regions (IDRs) are more frequent in transcription factors (TFs) than in all yeast proteins, among which stand out those involved in the stress response signaling pathways over TFs participating in other routes
intrinsically disordered TFs (IDTFs) are highly represented in the osmotic and nutrient stress response pathways, and in lower level in the oxidative and heat stress signaling cascades. It is noteworthy the presence of structural disorder in many of the signaling proteins involved in this communication networks, where various IDRs are in protein regions critical for their perception function
Summary
Stressful environments alter cellular homeostasis, leading to a diversity of adjustment mechanisms in metabolic and developmental programs. Different mechanisms involved in yeast stress acclimation have been described, including adjustments in RNA and protein synthesis [5], chromatin remodeling by changes in histone modifications and its dynamics [6], and other epigenomic tunings, as mechanisms underlying cellular stress memory [7]. A number of reports have shown that diverse stress conditions trigger the formation of a variety of cellular granules or bodies, through the recruitment of proteins and RNAs involving liquid-liquid phase separation for their ensemble [8, 9]
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