Prions in the bacterial domain of life

Harvard Medical School, Boston MA

Investigators

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Abstract

ABSTRACT Prions are infectious, self-propagating protein aggregates that were first described in the context of the transmissible spongiform encephalopathies (TSEs), fatal neurodegenerative diseases afflicting humans and other mammals. The culprit is an endogenous protein called PrP that has an inherent ability to misfold, resulting in the formation of distinctive cross-β aggregates (termed amyloid) that are both self-templating and infectious. Prions have also been uncovered in budding yeast, where they act as protein-based genetic elements that confer new heritable phenotypes on those cells that harbor them. Like PrP, fungal prion proteins can access alternative conformational states, a soluble form and a self-perpetuating, amyloid form (the prion form) that is infectious. However, fungal prions do not typically cause cell death. Our demonstration that bacterial cells could support the propagation of a model yeast prion led us to search for bacterially encoded prion proteins. The initial identification of two bacterial prion proteins and the development of E. coli-based models for investigating their behaviors provide a foundation for the proposed studies. An overarching hypothesis informing our work is that protein-based heredity serves as an epigenetic source of phenotypic diversity in bacteria. Our research goals are to investigate the physiologic impacts of bacterial prions, the cellular determinants of prion formation and propagation, the sequence and structural determinants of heritable amyloid, and the scope of prion-like phenomena in bacteria. Having uncovered functional prion domains in 17 bacterial single-stranded DNA-binding proteins (SSBs), we are focusing our physiological studies on SSBs, while also using them as models to address mechanistic questions about prion formation and propagation. On the one hand, we are genetically dissecting the prion proteins themselves and subjecting informative mutants to high-resolution structural analysis. On the other hand, we are poised to identify cellular factors that alter the behavior of these proteins, either hindering or facilitating prion formation and propagation. To date, our studies have centered on computationally identified bacterial prion proteins. However, existing algorithms would not have identified PrP and several noncanonical fungal prion proteins, motivating us to use novel genetic strategies to identify candidate prion domains irrespective of their sequence characteristics. Fundamental questions that permeate multiple aspects of our work are (i) what distinguishes heritable amyloid from non- heritable amyloid and (ii) what enables certain prion-like assemblies to nucleate the formation of other prions, questions relevant to the understanding of disease-related prion-like phenomena, including a growing body of evidence that bacterial amyloid can facilitate the aggregation of human proteins involved in neurodegeneration. A separate set of investigations centers on translational fidelity and non-programmed ribosomal frameshifting (NPRF). Building on recent findings, we are investigating the mechanistic basis for an unexpected promiscuity among NPRF events in bacteria, as well as striking organism-specific differences in translational fidelity.