Conserved rules govern genetic interaction degree across species

Elizabeth N. Koch, Michael Costanzo, Jeremy Bellay, Raamesh Deshpande, Kate Chatfield-Reed, Gordon Chua, Gennaro D'urso, Brenda J. Andrews, Charles Boone, Chad L. Myers

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

Background: Synthetic genetic interactions have recently been mapped on a genome scale in the budding yeast Saccharomyces cerevisiae, providing a functional view of the central processes of eukaryotic life. Currently, comprehensive genetic interaction networks have not been determined for other species, and we therefore sought to model conserved aspects of genetic interaction networks in order to enable the transfer of knowledge between species.Results: Using a combination of physiological and evolutionary properties of genes, we built models that successfully predicted the genetic interaction degree of S. cerevisiae genes. Importantly, a model trained on S. cerevisiae gene features and degree also accurately predicted interaction degree in the fission yeast Schizosaccharomyces pombe, suggesting that many of the predictive relationships discovered in S. cerevisiae also hold in this evolutionarily distant yeast. In both species, high single mutant fitness defect, protein disorder, pleiotropy, protein-protein interaction network degree, and low expression variation were significantly predictive of genetic interaction degree. A comparison of the predicted genetic interaction degrees of S. pombe genes to the degrees of S. cerevisiae orthologs revealed functional rewiring of specific biological processes that distinguish these two species. Finally, predicted differences in genetic interaction degree were independently supported by differences in co-expression relationships of the two species.Conclusions: Our findings show that there are common relationships between gene properties and genetic interaction network topology in two evolutionarily distant species. This conservation allows use of the extensively mapped S. cerevisiae genetic interaction network as an orthology-independent reference to guide the study of more complex species.

Original languageEnglish
Article numberR57
JournalGenome Biology
Volume13
Issue number7
DOIs
StatePublished - Jul 2 2012

Fingerprint

Saccharomyces cerevisiae
Schizosaccharomyces
Schizosaccharomyces pombe
Genes
gene
yeast
Protein Interaction Maps
Biological Phenomena
genes
Saccharomycetales
protein
yeasts
pleiotropy
Proteins
Yeasts
protein-protein interactions
Genome
species complex
biological processes
topology

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Koch, E. N., Costanzo, M., Bellay, J., Deshpande, R., Chatfield-Reed, K., Chua, G., ... Myers, C. L. (2012). Conserved rules govern genetic interaction degree across species. Genome Biology, 13(7), [R57]. https://doi.org/10.1186/gb-2012-13-7-r57

Conserved rules govern genetic interaction degree across species. / Koch, Elizabeth N.; Costanzo, Michael; Bellay, Jeremy; Deshpande, Raamesh; Chatfield-Reed, Kate; Chua, Gordon; D'urso, Gennaro; Andrews, Brenda J.; Boone, Charles; Myers, Chad L.

In: Genome Biology, Vol. 13, No. 7, R57, 02.07.2012.

Research output: Contribution to journalArticle

Koch, EN, Costanzo, M, Bellay, J, Deshpande, R, Chatfield-Reed, K, Chua, G, D'urso, G, Andrews, BJ, Boone, C & Myers, CL 2012, 'Conserved rules govern genetic interaction degree across species', Genome Biology, vol. 13, no. 7, R57. https://doi.org/10.1186/gb-2012-13-7-r57
Koch EN, Costanzo M, Bellay J, Deshpande R, Chatfield-Reed K, Chua G et al. Conserved rules govern genetic interaction degree across species. Genome Biology. 2012 Jul 2;13(7). R57. https://doi.org/10.1186/gb-2012-13-7-r57
Koch, Elizabeth N. ; Costanzo, Michael ; Bellay, Jeremy ; Deshpande, Raamesh ; Chatfield-Reed, Kate ; Chua, Gordon ; D'urso, Gennaro ; Andrews, Brenda J. ; Boone, Charles ; Myers, Chad L. / Conserved rules govern genetic interaction degree across species. In: Genome Biology. 2012 ; Vol. 13, No. 7.
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