The prion hypothesis: from biological anomaly to basic regulatory mechanism

Abstract

Prions are unusual proteinaceous infectious agents that are typically associated with a class of fatal degenerative diseases of the mammalian brain. However, the discovery of fungal prions, which are not associated with disease, suggests that we must now consider the effect of these factors on basic cellular physiology in a different light. Fungal prions are epigenetic determinants that can alter a range of cellular processes, including metabolism and gene expression pathways, and these changes can lead to a range of prion-associated phenotypes. The mechanistic similarities between prion propagation in mammals and fungi suggest that prions are not a biological anomaly but instead could be a newly appreciated and perhaps ubiquitous regulatory mechanism.

Figure 1. Cellular consequences of termination codon readthrough and +1 ribosomal frameshifting mediated by the [PSI⁺] prion

The [PSI⁺] prion compromises the function of the translation termination release factor Sup35, leading to the readthrough of stop codons or translational frameshifting. This epigenetic loss of Sup35 function creates new phenotypes based on the altered translation of specific mRNA transcripts. a. OAZ1 in yeast consists of two overlapping open reading frames (ORF1 and YPL052w), with the latter in the +1 frame with respect to ORF1. During translation the ribosomes can either terminate or shift into the +1 frame at the ORF1 UGA codon, thus by-passing the stop codon and continuing translation into the YPL052w ORF. This +1 frameshift increases as polyamine levels rise. The resulting fused protein, antizyme, regulates the ubiquitin-dependent degradation of ornithine decarboxylase (ODC), which mediates the synthesis of the polyamines spermidine, spermine and putrescine. In [PSI⁺] cells there is a significant reduction in the levels of functional release factor, leading to an increase in the pause time at the UGA codon. This in turn leads to increased levels of +1 frameshifting and hence antizyme synthesis, resulting in a reduction in ODC and polyamine synthesis when compared with a [psi⁻] cell. b. As a component of the cAMP-dependent protein kinase signalling system in yeast, Pde2p controls the basal levels of cAMP by hydrolysing cAMP to AMP. Readthough of the native UGA codon gives rise to a form of Pde2p (Pde2Lp) that has no phosphodiesterase activity. Consequently [PSI⁺] cells have approximately two-fold higher levels of cAMP than [PSI⁺] cells.

Figure 2. Fungal prions and their associated phenotypes

Prion and non-prion conformers confer unique phenotypes by altering the normal activity of the prion protein. Several transcriptional regulators in yeast have been identified as prions. The [URE3] prion alters the capacity of Ure2 to associate with the transcriptional activators Gln3 and Gat1 in the cytoplasm (left), which occurs in the non-prion [ure-o] state, allowing these activators to translocate into the nucleus (centre), where they up-regulate genes that allow [URE3] cells to use the poor nitrogen source ureidosuccinate (USA) in the presence of ammonia (right). Figure kindly provided by C. Cullin (Institut de Biochimie Génétique Cellulaires, Bordeaux). The [OCT⁺] prion compromises the ability of the Cyc8 transcriptional repressor to associate with its co-repressor Tup1 (oval, left), leading to the upregulation of many genes, including CYC7 (centre), which allows the use of lactate in cyc1Δ strains (right). Figure kindly provided by S. Liebman (University of Illinois-Chicago). b. The [Het-s] prion allows the Het-s protein to acquire a new activity to induce cell death (compare left and centre) following mating with a P. anserina strain that expresses the Het-S allele, leading to a block in heterokaryon formation, which leads to a barrier band of cell death (arrow, right). Figure kindly provided by S. Saupe (Institut de Biochimie Génétique Cellulaires, Bordeaux). c. The [PIN⁺] (also known as [RNQ⁺]) prion allows Rnq1p to support the de novo formation of the [PSI⁺] prion especially when the levels of Sup35 protein are artificially elevated (center and right).

Figure 3. How prions are propagated in the cell

Conformationally flexible prion proteins are converted from their normal non-prion form to the self-replicating prion form by associating with existing oligomeric complexes of the same protein in the prion form. These extended polymers may then be dissociated into smaller units (polymer fragmentation) either enzymatically in yeast or mechanically in mammals to produce transmissible oligomers (propagons). This process of conformational self-replication is limited in efficiency by the degradation of normal conformers or of dissociated prion monomers and by the formation of large, non-transmissible aggregates ([Agg⁺]). Changes in the rates of these dynamic transitions create a range of protein-based phenotypes from a single prion protein.

Figure 4. Prion mixtures, strain competition and the species barrier

a. Mixtures of prion strains in the same cell compete for non-prion state protein. Differences in the rate of fragmentation or conversion allow strains to establish phenotypic dominance by increasing their steady-state concentrations. In extreme cases, this competition leads to loss of one strain. b. Sequence variants of prion proteins dominantly inhibit conformational replication of other alleles by incorporating into prion complexes and inhibiting further conformational conversion or fragmentation. Variants interfering with conversion exert their effects at substochiometic levels as they function at the site of conversion, whereas variants interfering with prion aggregate dynamics exert their effects at stochiometric levels since they must incorporate throughout the complex. c. Incompatibility between donor and recipient prion proteins creates a barrier to interspecies transmission. This barrier may reflect an inability of the proteins to associate (not shown) or alternately to adopt compatible conformations. For strains capable of traversing a species barrier, the recipient prion protein may adopt an identical conformation (selection), leading to the conservation of strain identity on transfer, or, alternately, may adopt a partially compatible conformation that leads to a change in strain (adaptation).