Location of Repository

Epistasis for Growth Rate and Total Metabolic Flux in Yeast

By Agata Jakubowska and Ryszard Korona

Abstract

Studies of interactions between gene deletions repeatedly show that the effect of epistasis on the growth of yeast cells is roughly null or barely positive. These observations relate generally to the pace of growth, its costs in terms of required metabolites and energy are unknown. We measured the maximum rate at which yeast cultures grow and amounts of glucose they consume per synthesized biomass for strains with none, single, or double gene deletions. Because all strains were maintained under a fermentative mode of growth and thus shared a common pattern of metabolic processes, we used the rate of glucose uptake as a proxy for the total flux of metabolites and energy. In the tested sample, the double deletions showed null or slightly positive epistasis both for the mean growth and mean flux. This concordance is explained by the fact that average efficiency of converting glucose into biomass was nearly constant, that is, it did not change with the strength of growth effect. Individual changes in the efficiency caused by gene deletions did have a genetic basis as they were consistent over several environments and transmitted between single and double deletion strains indicating that the efficiency of growth, although independent of its rate, was appreciably heritable. Together, our results suggest that data on the rate of growth can be used as a proxy for the rate of total metabolism when the goal is to find strong individual interactions or estimate the mean epistatic effect. However, it may be necessary to assay both growth and flux in order to detect smaller individual effects of epistasis

Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:3295780
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles

    Preview

    Citations

    1. (1995). A general model for the evolution of recombination.
    2. (2008). A quantitative estimation of the global translational activity in logarithmically growing yeast cells.
    3. (2011). An integrated approach to characterize genetic interaction networks in yeast metabolism.
    4. (1999). Classification and sensitivity analysis of a proposed primary metabolic reaction network for Streptomyces lividans.
    5. (2006). Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.
    6. (1988). Deleterious mutations and the evolution of sexual reproduction.
    7. (1979). Efficiency of truncation selection.
    8. (2010). Environmental duress and epistasis: how does stress affect the strength of selection on new mutations?
    9. (2007). Epistasis between deleterious mutations and the evolution of recombination.
    10. (2007). Epistatic buffering of fitness loss in yeast double deletion strains.
    11. (2010). Experimental genomics of fitness in yeast.
    12. (1999). Function and regulation of yeast hexose transporters.
    13. (1993). Functional studies of yeast glucokinase.
    14. (2004). Global mapping of the yeast genetic interaction network.
    15. (2009). Glucose regulates transcription in yeast through a network of signaling pathways.
    16. (2005). High-dimensional and large-scale phenotyping of yeast mutants.
    17. (2003). Highresolution yeast phenomics resolves different physiological features in the saline response.
    18. (2004). How cells coordinate growth and division.
    19. (2008). How Saccharomyces Responds to Nutrients.
    20. (2011). Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency.
    21. (2008). Interactions between stressful environment and gene deletions alleviate the expected average loss of fitness in yeast.
    22. (1986). Misconceptions about the energy metabolism of Saccharomyces cerevisiae.
    23. (2005). Modular epistasis in yeast metabolism.
    24. (2011). Molecular mechanisms of epistasis within and between genes.
    25. (2001). Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression.
    26. (1991). Physiology of yeasts in relation to biomass yields.
    27. (1996). Pyruvate metabolism in Saccharomyces cerevisiae.
    28. (2009). Reconstruction of biochemical networks in microorganisms.
    29. (2002). Resolving the paradox of sex and recombination.
    30. (2009). Shifts in growth strategies reflect tradeoffs in cellular economics.
    31. (2007). Strategy of transcription regulation in the budding yeast.
    32. (2011). The causes of epistasis.
    33. (2007). The evolution of sex: empirical insights into the roles of epistasis and drift.
    34. (2010). The genetic landscape of a cell.
    35. (2005). Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis.
    36. (2008). Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation.
    37. (1997). Unravelling gene interactions.

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.