An essential component of evolution is adaptation of cells to changing environment. Changes in environment constitute stress conditions. Cells survival under stress conditions has entailed development of pathways that maintain and adapt the structure and function of proteins that are essential for survival.
Since environmental stress can be deleterious to protein structure and function and thus affect cell viability, cells have evolved diverse pathways, like chaperones, that restore their structure and function. Conversely, the altered protein structure may impart new traits that help yeast cells to survive environmental stress. Thus, changes in the protein sequences that help adapt the structure to environment may get selected during evolution. Prions exemplify an altered form of protein structure that carries a structural memory and ability to convert the normal form of protein into its own altered shape and loss of function. This epigenetic role is dominant over the function of the normal protein and is inherited in a non-Mendelian manner in yeast.
“The components of heterochromatin assembly and APC/C not only interact with but also regulate each other.”
In the fission yeast, Schizosachharomyces pombe, centromeres, telomeres and mating type regions are assembled into heterochromatin via epigenetic mechanism. This involves di/tri-methylation of Lys9 in histone H3 (H3-K9-me2/me3) by the histone methyltransferase Clr4/Suv39, followed by binding of H3-K9-me2/me3 by the heterochromatin protein Swi6/HP1. This binding spreads into the neighbouring region to generate a transcriptionally inactive, heterochromatin structure. The integrity of the heterochromatin structure is critical for proper chromosome segregation during mitosis and meiosis, since mutations in Swi6 cause chromosome segregation defects.
APC/C, a multiprotein complex, plays a pivotal role in an orderly cell cycle progression in all eukaryotes from yeast to humans. Its functions are mediated through its biochemical activity of ubiquitination of key regulatory proteins and the orderly degradation. One such pathway leads to separation of sister chromatids during mitosis. Mutations in these pathways can perturb orderly cell cycle progression.
Rather surprisingly, APC/C also ensures chromosome integrity and segregation as well as heterochromatin structure. This function is performed through direct interaction between the APC/C subunits like Cut4/Apc1 and Swi6/HP1 and Clr4/Suv39 (Dubey et al J. Biol Chem 284, 7165 (2009)). This property links the two pathways involved in heterochromatin assembly and cell cycle regulation.
Further, the components of heterochromatin assembly and APC/C not only interact with but also regulate each other. This regulation may occur at the level of ubiquitination of specific proteins of heterochromatin and RNAi pathway. Ubiquitination, in turn, may regulate the activity and levels of the heterochromatin proteins. In turn, heterochromatin proteins can possibly regulate the activity of the APC/C subunit/s. This interaction would ensure that heterochromatin assembly and cell cycle progression are closely coordinated. This coordination is likely to be conserved during evolution and its disruption may lead to chromosome segregation defects, aneuploidy and dysregulation of cell cycle, conditions associated with diseased states.
A recent study showed that Cut4/Apc1, the largest subunit of the Anaphase Promoting Complex/Cyclosome (APC/C), adopts a prion form in yeast strains either due to mutations or overexpression of Cut4/Apc1 (Sharma et al, Nucleic Acids Research, 52, 13792 (2024); Reviewed in Sharma and Singh mBio 17, 1 (2026)).
“Thus, the IDR regions allow for better adaptation of function to changing cellular environment in response to stress.”
An observable characteristic of the cells harbouring a prion form of Cut4/Apc1 is the presence of variable level of aggregates. These aggregates not only lack the normal function of the protein but they also block the activity of the normal protein. Thus, in case of an essential protein, prion formation can be deleterious to cell function and survival. Surprisingly, while the prion form of Cut4/Apc1 also forms aggregates and it abrogates several pathways, like cell cycle progression, heterochromatin assembly and chromosomal integrity and segregation, it confers enhanced resistance to stress: such cells exhibit better survival under conditions of stress – like, oxidative stress, osmotic stress, high ethanol concentration, exposure to high temperature, etc. Pertinently, cancer cells also display similar characteristics: aneuploidy, cell cycle defect and enhanced stress survival.
These apparently opposing effects suggest a role of the prion variant of Cut4 in evolution as well as disease. Changes in sequences of proteins help to adapt to changing environment during evolution. One of the significantly regions within proteins that are associated with adaptation are known as Intrinsically Disordered Regions (IDRs). These regions lack the canonical secondary structures like a-helix and b-sheet or tertiary structures, but have an intrinsic flexibility to adopt conformations that facilitate their interaction with different proteins under different environments. Interestingly, the IDRs show greater level of sequence variation among the homologous proteins even in related species as compared to the remaining parts of proteins, indicating reduced evolutionary pressure and allowance for greater sequence variation. These amino acid changes may perform a dual function: exploration of suitable structures in the conformational space and selection of those conformations which have functions better suited for cell survival.
Notably, IDRs have been found in a large number of proteins especially in metazoans. The greater complexity of cells in metazoans combined with limited protein coding capacity of their genome, requires additional functional diversification of proteins. The conformational flexibility of IDRs allows for multiple regulated interactions with diverse sets of proteins to meet the increased cellular requirements of the organism. Thus, the IDR regions allow for better adaptation of function to changing cellular environment in response to stress.
In a seminal study a transient overexpression of about 50 proteins elicited beneficial traits in yeast cells, including enhanced resistance to stresses. Importantly, these traits persisted even after the expression levels of proteins was restored to normal level (Chakrabortee et al, Cell 167, 369 (2016)). The overexpressed proteins shared the presence of IDRs and traits caused by their overexpression exhibited prion-like inheritance pattern. However, these traits were not necessarily associated with formation of amyloids. Indeed, a comparison of sequences of Cut4/Apc1 from different species of the genus Schizosachharomces reveals conserved location of two IDRs. Sequence comparison shows significantly lower level of sequence similarity in the IDR regions as compared to the complete sequence of Cut4 protein of four species.
In this regard, our recent findings about Cut4/Apc1 and its prion variant may carry broader significance. The Darwinian evolution involves variation in DNA sequence and selection of the organisms with proteins that enhance greater fitness. While protein structure and functions may have inherent malleability to adopt altered conformations that allow functional diversification and adaptation in response to changing environment. These changes are facilitated by the conformational flexibility of the IDRs. Mutations in the IDRs may further help proteins to explore different conformations that are more adapted to maintain the protein functions in response to stress (Wickner and Kelly Cell Mol Life Sci 73, 1131 (2016)).
