Harnessing Natural Diversity to Probe Metabolic Pathways

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Abstract
Analyses of cellular processes in the yeast Saccharomyces cerevisiae rely primarily upon a small number of highly domesticated laboratory strains, leaving the extensive natural genetic diversity of the model organism largely unexplored and unexploited. We asked if this diversity could be used to enrich our understanding of basic biological processes. As a test case, we examined a simple trait: the utilization of di/tripeptides as nitrogen sources. The capacity to import small peptides is likely to be under opposing selective pressures (nutrient utilization versus toxin vulnerability) and may therefore be sculpted by diverse pathways and strategies. Hitherto, dipeptide utilization in S. cerevisiae was solely ascribed to the activity of a single protein, the Ptr2p transporter. Using high-throughput phenotyping and several genetically diverse strains, we identified previously unknown cellular activities that contribute to this trait. We find that the Dal5p allantoate/ureidosuccinate permease is also capable of facilitating di/tripeptide transport. Moreover, even in the absence of Dal5p and Ptr2p, an additional activity—almost certainly the periplasmic asparaginase II Asp3p—facilitates the utilization of dipeptides with C-terminal asparagine residues by a different strategy. Another, as-yet-unidentified activity enables the utilization of dipeptides with C-terminal arginine residues. The relative contributions of these activities to the utilization of di/tripeptides vary among the strains analyzed, as does the vulnerability of these strains to a toxic dipeptide. Only by sampling the genetic diversity of multiple strains were we able to uncover several previously unrecognized layers of complexity in this metabolic pathway. High-throughput phenotyping facilitates the rapid exploration of the molecular basis of biological complexity, allowing for future detailed investigation of the selective pressures that drive microbial evolution. Model organisms have allowed researchers to characterize basic biological processes in exquisite detail. Homann et al. suggest that this knowledge base presents a unique opportunity to exploit the natural genetic variation found in diverse isolates of the same species to gain new insights. Using high-throughput technology to assay growth, Homann et al. found that laboratory strains, vineyard isolates, and clinical isolates of the yeast Saccharomyces cerevisiae exhibit very different capacities to utilize di/tripeptides as nutrient sources. This led to the discovery of new di/tripeptide utilization activities and an elaboration of their specificities. Variations in the strength of these activities determine the spectrum of di/tripeptides that are preferentially utilized in a given strain. In turn, this influenced the vulnerability of these strains to a toxic peptide, which exploits the transport machinery to gain entry into the cell. This raises the intriguing possibility that opposing selective pressures, in which the benefit of utilizing di/tripeptides as a nutrient source is offset by the risk of importing toxic peptides, may have shaped the observed natural diversity. The natural genetic diversity present among isolates of model organisms augurs a rich resource for revealing complexities in molecular pathways and exploring the selective pressures that shaped them.