Prion proteins can serve as genetic elements by adopting distinct physical and functional states that are self-perpetuating and heritable. The critical region of one prion protein, Sup35, is initially unstructured in solution and then forms self-seeded amyloid fibers. We examined in vitro the mechanism by which this state is attained and replicated. Structurally fluid oligomeric complexes appear to be crucial intermediates in de novo amyloid nucleus formation. Rapid assembly ensues when these complexes conformationally convert upon association with nuclei. This model for replicating protein-based genetic information, nucleated conformational conversion, may be applicable to other protein assembly processes.

Inheritance of phenotypic traits depends on two key events: replication of the determinant of that trait and partitioning of these copies between mother and daughter cells. Although these processes are well understood for nucleic acid–based genes, the mechanisms by which protein-only or prion-based genetic elements direct phenotypic inheritance are poorly understood. Here, we report a process crucial for inheritance of the Saccharomyces cerevisiae prion [PSI+], a self-replicating conformer of the Sup35 protein. By tightly controlling expression of a Sup35-GFP fusion, we directly observe remodeling of existing Sup35[PSI+] complexes in vivo. This dynamic change in Sup35[PSI+] is lost when the molecular chaperone Hsp104, a factor essential for propagation of all yeast prions, is functionally impaired. The loss of Sup35[PSI+] remodeling by Hsp104 decreases the mobility of these complexes in the cytosol, creates a segregation bias that limits their transmission to daughter cells, and consequently diminishes the efficiency of conversion of newly made Sup35 to the prion form. Our observations resolve several seemingly conflicting reports on the mechanism of Hsp104 action and point to a single Hsp104-dependent event in prion propagation.

According to the prion hypothesis, atypical phenotypes arise when a prion protein adopts an alternative conformation and persist when that form assembles into self-replicating aggregates. Amyloid formation in vitro provides a model for this protein-misfolding pathway, but the mechanism by which this process interacts with the cellular environment to produce transmissible phenotypes is poorly understood. Using the yeast prion Sup35/[PSI + ], we found that protein conformation determined the size distribution of aggregates through its interactions with a molecular chaperone. Shifts in this range created variations in aggregate abundance among cells due to a size threshold for transmission, and this heterogeneity, along with aggregate growth and fragmentation, induced age-dependent fluctuations in phenotype. Thus, prion conformations may specify phenotypes as population averages in a dynamic system. Prion proteins adopt a spectrum of conformations or strains, which create phenotypes of distinct severity and stability in vivo (1-3). These phenotypes are linked to the assembly of the protein into aggregates that, at unique rates, template the conversion of newly-made prion protein to a similar state and are fragmented (4). But, how do these biochemical events translate into distinct phenotypes? One possibility is an "abundance-based" model, in which phenotypes are linked to an equilibrium between aggregated and soluble prion protein that determines protein activity and the number of heritable prions (propagons) (5,6). However, the conversion and fragmentation reactions also create heterogeneity in aggregate size, raising the possibility of a second, "size-based" model in which a subpopulation of aggregates establishes and propagates phenotypes (7).To distinguish between these models, we focused on the [PSI + ] Weak and [PSI + ] Strong conformations of the yeast prion protein Sup35, which create phenotypes of different stabilities in vivo (8). To sustain these phenotypes in a dividing culture, Sup35 protein in the prion conformation must be inherited (7). To test whether conformational differences impact phenotypic stability by altering protein transmissibility, we monitored Sup35-GFP transfer to daughter cells. Using fluorescence loss in photobleaching (FLIP), a [PSI + ] Weak strain transferred half as much Sup35-GFP (~15% vs. ~30%; Fig. 1A) and contained ~50% fewer ** This manuscript has been accepted for publication in Science. This version has not undergone final editing. Please refer to the complete version of record at http://www.sciencemag.org/. The manuscript may not be reproduced or used in any manner that does not fall within the fair use provisions of the