An integrated approach to characterize genetic interaction networks in yeast metabolism

Balázs Szappanos, Károly Kovács, Béla Szamecz, Frantisek Honti, Michael Costanzo, Anastasia Baryshnikova, Gabriel Gelius-Dietrich, Martin J. Lercher, M. Jelasity, Chad L. Myers, Brenda J. Andrews, Charles Boone, Stephen G. Oliver, C. Pál, B. Papp

Research output: Contribution to journalArticle

128 Citations (Scopus)

Abstract

Although experimental and theoretical efforts have been applied to globally map genetic interactions, we still do not understand how gene-gene interactions arise from the operation of biomolecular networks. To bridge the gap between empirical and computational studies, we i, quantitatively measured genetic interactions between ∼185,000 metabolic gene pairs in Saccharomyces cerevisiae, ii, superposed the data on a detailed systems biology model of metabolism and iii, introduced a machine-learning method to reconcile empirical interaction data with model predictions. We systematically investigated the relative impacts of functional modularity and metabolic flux coupling on the distribution of negative and positive genetic interactions. We also provide a mechanistic explanation for the link between the degree of genetic interaction, pleiotropy and gene dispensability. Last, we show the feasibility of automated metabolic model refinement by correcting misannotations in NAD biosynthesis and confirming them by in vivo experiments.

Original languageEnglish
Pages (from-to)656-662
Number of pages7
JournalNature Genetics
Volume43
Issue number7
DOIs
Publication statusPublished - Jul 2011

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Yeasts
Genes
Genetic Pleiotropy
Systems Biology
NAD
Saccharomyces cerevisiae

ASJC Scopus subject areas

  • Genetics

Cite this

Szappanos, B., Kovács, K., Szamecz, B., Honti, F., Costanzo, M., Baryshnikova, A., ... Papp, B. (2011). An integrated approach to characterize genetic interaction networks in yeast metabolism. Nature Genetics, 43(7), 656-662. https://doi.org/10.1038/ng.846

An integrated approach to characterize genetic interaction networks in yeast metabolism. / Szappanos, Balázs; Kovács, Károly; Szamecz, Béla; Honti, Frantisek; Costanzo, Michael; Baryshnikova, Anastasia; Gelius-Dietrich, Gabriel; Lercher, Martin J.; Jelasity, M.; Myers, Chad L.; Andrews, Brenda J.; Boone, Charles; Oliver, Stephen G.; Pál, C.; Papp, B.

In: Nature Genetics, Vol. 43, No. 7, 07.2011, p. 656-662.

Research output: Contribution to journalArticle

Szappanos, B, Kovács, K, Szamecz, B, Honti, F, Costanzo, M, Baryshnikova, A, Gelius-Dietrich, G, Lercher, MJ, Jelasity, M, Myers, CL, Andrews, BJ, Boone, C, Oliver, SG, Pál, C & Papp, B 2011, 'An integrated approach to characterize genetic interaction networks in yeast metabolism', Nature Genetics, vol. 43, no. 7, pp. 656-662. https://doi.org/10.1038/ng.846
Szappanos B, Kovács K, Szamecz B, Honti F, Costanzo M, Baryshnikova A et al. An integrated approach to characterize genetic interaction networks in yeast metabolism. Nature Genetics. 2011 Jul;43(7):656-662. https://doi.org/10.1038/ng.846
Szappanos, Balázs ; Kovács, Károly ; Szamecz, Béla ; Honti, Frantisek ; Costanzo, Michael ; Baryshnikova, Anastasia ; Gelius-Dietrich, Gabriel ; Lercher, Martin J. ; Jelasity, M. ; Myers, Chad L. ; Andrews, Brenda J. ; Boone, Charles ; Oliver, Stephen G. ; Pál, C. ; Papp, B. / An integrated approach to characterize genetic interaction networks in yeast metabolism. In: Nature Genetics. 2011 ; Vol. 43, No. 7. pp. 656-662.
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