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Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemistö A, Boyle J, Rachubinski RA, Shmulevich I, Aitchison JD. Genome-wide analysis of effectors of peroxisome biogenesis. PLoS One 2010; 5:e11953. [PMID: 20694151 PMCID: PMC2915925 DOI: 10.1371/journal.pone.0011953] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 07/12/2010] [Indexed: 11/19/2022] Open
Abstract
Peroxisomes are intracellular organelles that house a number of diverse metabolic processes, notably those required for beta-oxidation of fatty acids. Peroxisomes biogenesis can be induced by the presence of peroxisome proliferators, including fatty acids, which activate complex cellular programs that underlie the induction process. Here, we used multi-parameter quantitative phenotype analyses of an arrayed mutant collection of yeast cells induced to proliferate peroxisomes, to establish a comprehensive inventory of genes required for peroxisome induction and function. The assays employed include growth in the presence of fatty acids, and confocal imaging and flow cytometry through the induction process. In addition to the classical phenotypes associated with loss of peroxisomal functions, these studies identified 169 genes required for robust signaling, transcription, normal peroxisomal development and morphologies, and transmission of peroxisomes to daughter cells. These gene products are localized throughout the cell, and many have indirect connections to peroxisome function. By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function.
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Affiliation(s)
- Ramsey A. Saleem
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Rose Long-O'Donnell
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - David J. Dilworth
- Institute for Systems Biology, Seattle, Washington, United States of America
| | | | | | - Yakun Wan
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Theo A. Knijnenburg
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Antti Niemistö
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - John Boyle
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Richard A. Rachubinski
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ilya Shmulevich
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - John D. Aitchison
- Institute for Systems Biology, Seattle, Washington, United States of America
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Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O'Donnell R, Rachubinski RA, Aitchison JD. Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis. ACTA ACUST UNITED AC 2008; 181:281-92. [PMID: 18426976 PMCID: PMC2315675 DOI: 10.1083/jcb.200710009] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
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.
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