Protein regulation by self-association

Gel with labelled bands
Native agarose gel electrophoresis resolution of oligomeric and polymeric complexes of low-complexity proteins.

We are interested in the contributions of protein aggregation to the functions of regulatory proteins such as transcription factors and signaling proteins. How frequently do these proteins aggregate in a non-pathological context, and what are the consequences? We seek to address these questions systematically and quantitatively with novel approaches to characterize the distribution of aggregated states of individual proteins within large cell populations .

Contributions of protein aggregation to cell individuality and differentiation

A prion-containing yeast colony demonstrating metabolic oscillations (pseudocolored in red and blue).

Despite being genetically identical, individual cells within clonal populations are often phenotypically distinct. These distinctions facilitate cooperative interactions between cells, contribute to the overall fitness of cell populations, and may even accelerate the somatic evolution of tumors. As a stochastic process that can occur in virtually all cells, protein aggregation stands to be a major contributor to non-genetic cell individuality. To overcome the experimental difficulties imposed by the normally chaotic process of protein aggregation, we employ a subset of well-behaved proteins whose aggregated states perpetuate themselves through specific, self-sustaining protein-folding cascades. These proteins, known as prions, form epigenetically stable states that allow for the precise experimental manipulation of aggregate frequencies and therefore the elucidation of fitness interactions between aggregate-free and aggregate-containing cells. Using this system in the genetically tractable model organism, the baker’s yeast Saccharomyces cerevisiae, we seek to understand how the stochastic appearance and self-sustaining nature of protein aggregates influences not only the fitness of individual cells, but of the cell populations and organisms that harbor them.

In 2013, we reported that a yeast transcription factor, Mot3, reversibly acquires a prion form in response to natural environmental changes. The prion causes yeast cells to grow in a multicellular fashion, and thereby acts as an environmentally-responsive determinant of cell fate. We are investigating additional roles of prions in cell differentiation, including metabolic divisions of labor leading to cooperative, self-sustaining partnerships.

Differentiation and self-organization within yeast communities

Labyrinthine growth patterns in a yeast biofilm.

Contrasting with the common perception of yeasts as “unicellular,” they in fact naturally form complex communities that have defining characteristics of multicellular organisms. Our discovery that prions can act as epigenetic determinants of cell differentiation has driven us to consider broader questions involving multicellularity in its own right. Despite yeast being one of the most thoroughly studied organisms in biology, we know very little about the functions of multicellularity and the mechanisms by which cell fate are assigned within yeast communities. These omissions hinder a fuller biomedical realization of yeast as a model organism. We seek to leverage our expertise with prions and cell-to-cell heterogeneity to bridge this knowledge gap.

Heritable remodeling of yeast mutlicellularity by an environmentally responsive prion