Dynamic protein interaction networks to map molecular origins of envronmental and genomic variations.

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Problem and Hypotheses: The fate of an organisms is governed by its genome and the environment and the interactions of both with the biochemical networks that make up living cells. A surrogate measurement for the contributions of all biomolecules to cell fate can be found in the spatiotemporal dynamics of protein-protein interaction networks (PINS). We have developed methods to address the dynamics of PINS on a whole proteome scale in the budding yeast Saccharomyces cerevisiae by means of a Protein-fragment Complementation Assay (PCA) using a methotrexate-resistant the enzyme Dihydrofolate Reductase (DHFR) as reporter (Tarassov, et al. Science, 2008; Stynen, Abd Rabbo, et al., Cell, 2018). Surprisingly, we also observed a remarkable overlap between the proteins that respond to drug treatments and human homologues that have been found in genome-wide association studies (GWAS) associated with human disease, suggesting that PCA can link environmental and genomic variation effects to mechanistic consequences. Our central hypothesis is that the dynamics of PINS will accurately capture the biochemical-mechanistic effects of environmental stimuli and genetic variation. At what scale i.e. how many PCA reporters are needed to make accurate predictions of environmental or single nucleotide polymorphisms (SNP) on biochemical mechanisms? To address this question, we will perform two studies: in the short term we will cross PCA containing strains with existing outbred laboratory strains (Sen & Jarosz, Cell, 2018) to establish a benchmark for SNP resolution at which we can predict mechanistic effects from PINs. Second, in the medium term we will implement a new strategy to perform whole protein interactomes in a single test. This massive simplification of DHFR PCA screening will permit us to perform interactomes on large numbers of outbred strains and under a variety of different environmental conditions and to address a variety of fundamental questions in molecular genetics. Objectives: We will ask the following questions: 1 - How is genetic variation reflected in changes in PINs? 2 - How do genetic variation and environmental stress synergize on the structure of the PIN? 3 - At what SNP resolution do PINs resolve genomic effects on biochemical processes? 4-How much are variations in genes or environment reflected in the organization of the PINs, including among orthologs, at hubs and clusters within the network? 5-Can we predict genomic variation associated with human diseases from yeast PIN variation caused by gene and environment effects? These studies will contribute to advancement of knowledge by: 1- Providing a new strategy to directly probe the dynamics of an entire protein interactome. 2 - Revealing principles and mechanisms of dynamic biochemical network organization. 3 - Providing new insight into the principles of evolution of the cellular machinery. 4 - Providing insight into genome-environment interactions with molecular networks.