Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast

Balazs Papp, Balázs Papp, Csaba Pál, Laurence D. Hurst

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Under laboratory conditions 80% of yeast genes seem not to be essential for viability. This raises the question of what the mechanistic basis for dispensability is, and whether it is the result of selection for buffering or an incidental side product. Here we analyse these issues using an in silico flux model of the yeast metabolic network. The model correctly predicts the knockout fitness effects in 88% of the genes studied and in vivo fluxes. Dispensable genes might be important, but under conditions not yet examined in the laboratory. Our model indicates that this is the dominant explanation for apparent dispensability, accounting for 37-68% of dispensable genes, whereas 15-28% of them are compensated by a duplicate, and only 4-17% are buffered by metabolic network flux reorganization. For over one-half of those not important under nutrient-rich conditions, we can predict conditions when they will be important. As expected, such condition-specific genes have a more restricted phylogenetic distribution. Gene duplicates catalysing the same reaction are not more common for indispensable reactions, suggesting that the reason for their retention is not to provide compensation. Instead their presence is better explained by selection for high enzymatic flux.
    Original languageEnglish
    Pages (from-to)661-664
    Number of pages3
    JournalNature
    Volume429
    Issue number6992
    DOIs
    Publication statusPublished - 10 Jun 2004

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