Saccharomyces cerevisiae as a model organism: a comparative study

Abstract

Background: Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. Such organisms should be representative of the living beings for which they are to serve as proxy. However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking. Methodology/Principal Findings: In this work we propose such a method and apply it in a pilot study of strengths and limitations of Saccharomyces cerevisiae as a model organism. The method relies on the functional classification of proteins into different biological pathways and processes and on full proteome comparisons between the putative model organism and other organisms for which we would like to extrapolate results. Here we compare S. cerevisiae to 704 other organisms from various phyla. For each organism, our results identify the pathways and processes for which S. cerevisiae is predicted to be a good model to extrapolate from. We find that animals in general and Homo sapiens in particular are some of the non-fungal organisms for which S. cerevisiae is likely to be a good model in which to study a significant fraction of common biological processes. We validate our approach by correctly predicting which organisms are phenotypically more distant from S. cerevisiae with respect to several different biological processes. Conclusions/Significance: The method we propose could be used to choose appropriate substitute model organisms for the study of biological processes in other species that are harder to study. For example, one could identify appropriate models to study either pathologies in humans or specific biological processes in species with a long development time, such as plants.

This work was partially financed by fellowships AP2002-2772 and Beatriu dePinós to EV. HK is funded by a Generalitat de Catalunya Ph. D. fellowship. RA was partially supported by the Ministerio de Ciencia e Innovación (MICINN, Spain through the Ramon y Cajal program and grants BFU2007-62772/BMC and BFU2010-17704) and by the FLAD foundation during a short stay. AS acknowledges financial support from grant BFU2008-0196 from MICINN. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.