Newly identified prion linked to the chromatin-remodeling factor Swi1 in Saccharomyces cerevisiae

Abstract

SWI/SNF, an evolutionarily conserved ATP-dependent chromatin-remodeling complex, has an important role in transcriptional regulation 1 . In Saccharomyces cerevisiae, SWI/SNF regulates the expression of ~6% of total genes through activation or repression 2 . Swi1, a subunit of SWI/SNF, contains an N-terminal region rich in glutamine and asparagine, a notable feature shared by all characterized yeast prions-a group of unique proteins capable of self-perpetuating changes in conformation and function 3 . Here we provide evidence that Swi1 can become a prion, [ [PIN + ] are three reported prions in S. cerevisiae 6-9 , and their protein determinants are Sup35, Ure2 and Rnq1, respectively. They all contain an intrinsic domain with high glutamine and asparagine content essential for prion formation and propagation (Fig. 1a). Yeast prions can be formed and lost at a low spontaneous rate 10 . Overproduction of a prion protein considerably increases de novo formation of the corresponding prion 8,11,12 . [PSI + ] induction by Sup35 overproduction requires a [PSI + ] inducible factor (Pin + ), which can be an event such as overproduction of particular glutamine-, asparagine-or glutamine and asparagine-rich proteins, or another prion 13-15 . Notably, several members of the yeast SWI/SNF complex, including Swi1 and Snf5, also contain glutamine and asparagine-rich regions 16 (Fig. 1a), and Swi1 overproduction has been implicated as a Pin + factor 9 . SWI/SNF is an evolutionarily conserved, ATP-dependent chromatin-remodeling complex that has a regulatory role in gene expression 17 . In S. cerevisiae, the SWI/SNF complex is composed of at least 11 subunits, for a total molecular weight of ~1 MDa 18 . Null mutants of SWI/SNF are viable, but show phenotypes of slow growth, reduced mating-type switching, and inability to utilize nonfermentable carbon sources, such as raffinose, galactose, glycerol and sucrose 19 . In mammals, Ini1, a Snf5 homolog, is essential for embryo viability and tumor suppression 20 . Various mutations affecting the human Ini1 or Snf2 homologs, BRM and BRG-1, are (Fig. 1b-d). Although the Nterminal region of Snf5 is also rich in glutamine (Fig. 1a), overexpression of SNF5 did not function as a Pin + (Fig. 1b) Only two were able to grow on raffinose after 5 mM guanidine hydrochloride treatment (Fig. 2a). This guanidine hydrochloride treatment eliminates all known yeast prions, but does not usually cause nucleic acid mutations 23 . Like SWI/SNF mutants, both candidates grew poorly in galactose (Gal -) and glycerol (Gly -) (Fig. 2b). However, they showed only a mild defect in using sucrose (Fig. 2b). Unlike SWI/SNF mutants, they did not show any detectable sensitivity to 0.3 M LiCl or 1 M NaCl ( Fig. 2b and data not shown). These results suggest that the two [SWI + ] candidates show an epigenetically conferred, partial loss-of-function SWI/SNF phenotype.To further investigate whether the observed effect is SWI/SNF specific, we developed a bluewhite visual assay using a previously described lacZ repor...

The sensitive [SWI+] prion

“…In sum, since [SWI + ] was previously shown to rely upon the activity of the disaggregating ATPase Hsp104 for propagation, 11 it was not surprising to find that the other core components of …”

“…The uninduced rate of [PSI + ] formation, that is, the rate uninfluenced by protein overexpression or environmental stresses, was recently reported to be 5.7 x 10 -7 /cell/generation. 25 In contrast, some, if not all, of the N-rich prions discussed above form at much higher rates ( Table 2 11 While they note that they tried the experiment several times before succeeding, the ability to detect spontaneous [SWI + ] formation from a relatively small yeast cell population strongly suggests that [SWI + ] appears significantly more often than [PSI + ], which would only be expected to appear at a rate of 5 out of 10,000,000 ©2 0 1 1 L a n d e s B i o s c i e n c e .…”

Conversion of a yeast prion protein to an infectious form in bacteria

“…However, unlike mammalian prions, yeast prions do not result in cell death, but instead act as heritable, protein-based genetic elements, conferring on the cell new phenotypic traits that are propagated epigenetically (6,7). Although work over the last 15 years has uncovered a growing number of prions and prospective prion proteins in evolutionarily divergent members of the fungal kingdom (8)(9)(10)(11)(12)(13)(14), it is not yet known how pervasive prions are in nature; more specifically, it is not known whether bacteria contain prions or whether the bacterial cytoplasm can support the formation of prions. The study of yeast prions has revealed an essential interplay between prion proteins and cellular chaperone proteins (15,16); thus, it is of particular interest to learn whether the bacterial chaperone environment is permissive for the formation of prion-like aggregates.…”

Prions, amyloids, and RNA: Pieces of a puzzle

“…88 Also, [SWI C ] manifests not only beneficial, but also harmful phenotypes: it inhibits vegetative growth on media containing non-fermentable carbon sources. 40 This might mean that these prions are egoistic elements or even that they are harmful. However, we cannot exclude the possibility that these prions provide a survival advantage under certain conditions that occur rarely and which we do not yet know, and thus act as bet hedging prions.…”

“…While opinions still differ on whether the majority of yeast prions are functional epigenetic modifiers, egoistic elements or diseases, most of them do not have a significant negative effect on fitness and can be maintained in yeast populations for a long time, or even indefinitely. 33,34 To date there are nine known amyloid-based yeast prions, [PSI C ] 35 (for which structural protein is Sup35), 36 [URE3] 37 (Ure2), 36 [PIN C ] (Rnq1), 38,39 [SWI C ] (Swi1), 40 [OCT C ] (Cyc8), 41 [MOT3 C ] (Mot3), 14 [ISP C ] (Sfp1), 42 [NUP100 C ] (Nup100), 43 [MOD C ] (Mod5), 44 as well as two functional prion-like amyloids:…”