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Published online
doi:10.1083/jcb.200710009
The Journal of Cell Biology, Vol. 181, No. 2, 281-292
The Rockefeller University Press, 0021-9525 $30.00
© Saleem et al.
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Article

Genome-wide analysis of signaling networks regulating fatty acid–induced gene expression and organelle biogenesis



Ramsey A. Saleem1, Barbara Knoblach2, Fred D. Mast2, Jennifer J. Smith1, John Boyle1, C. Melissa Dobson2, Rose Long-O'Donnell1, Richard A. Rachubinski2, and John D. Aitchison1,2

1 Institute for Systems Biology, Seattle, WA 98103
2 Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada

Correspondence to John D. Aitchison: jaitchison{at}systemsbiology.org; or Richard A. Rachubinski: rick.rachubinski{at}ualberta.ca

Reversible phosphorylation is the most common posttranslational modification used in the regulation of cellular processes. This study of phosphatases and kinases required for peroxisome biogenesis is the first genome-wide analysis of phosphorylation events controlling organelle biogenesis. We evaluate signaling molecule deletion strains of the yeast Saccharomyces cerevisiae for presence of a green fluorescent protein chimera of peroxisomal thiolase, formation of peroxisomes, and peroxisome functionality. We find that distinct signaling networks involving glucose-mediated gene repression, derepression, oleate-mediated induction, and peroxisome formation promote stages of the biogenesis pathway. Additionally, separate classes of signaling proteins are responsible for the regulation of peroxisome number and size. These signaling networks specify the requirements of early and late events of peroxisome biogenesis. Among the numerous signaling proteins involved, Pho85p is exceptional, with functional involvements in both gene expression and peroxisome formation. Our study represents the first global study of signaling networks regulating the biogenesis of an organelle.

R.A. Saleem and B. Knoblach contributed equally to this paper.

Abbreviations used in this paper: GO, gene ontology; ORE, oleate-responsive elements.


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