Genome-wide analysis of effectors of peroxisome biogenesis.

Ramsey A Saleem,Rose Long-O'Donnell,Arvind P Jamakhandi,Theo A Knijnenburg,Yakun Wan,Abraham M Armstrong,John Boyle,David J Dilworth,Antti Niemistö,Richard A Rachubinski,Ilya Shmulevich,John D Aitchison,Xuewen Pan

doi:10.1371/journal.pone.0011953

Ramsey A Saleem, Rose Long-O'Donnell + Show 11 more

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https://doi.org/10.1371/journal.pone.0011953

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Abstract

Peroxisomes are intracellular organelles that house a number of diverse metabolic processes, notably those required for β-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.

Highlights

Peroxisomes are membrane-bound organelles that function in a variety of processes including the b-oxidation of long chain fatty acids and elimination of reactive oxygen species [1]
Evaluation of Candidates by Flow Cytometry A fully functional GFP-tagged chimera of the protein Pot1p, a thiolase localized to the peroxisomal matrix, was introduced into an arrayed library containing the complete collection of viable yeast deletion mutant strains (,4000 strains after quality control selection - see Materials and Methods)
Of the 175 regulators identified in the fatty acid utilization studies, we identify a subset of regulators (8 genes (5%)), in which peroxisomes appear to be wild type with respect to Pot1p-GFP levels and peroxisomal morphology, that exclusively perturb the ability of S. cerevisiae to utilize fatty acids

Summary

Introduction

Peroxisomes are membrane-bound organelles that function in a variety of processes including the b-oxidation of long chain fatty acids and elimination of reactive oxygen species [1]. In the yeast Saccharomyces cerevisiae, peroxisomes proliferate when cells are incubated with fatty acids as the sole carbon source. Peroxisomal biogenesis results from the convergence of several processes including signaling [2], chromatin modifications [3] reorganization of the transcriptional networks [4,5,6], and the dynamics of the organellar proteome [7,8]. For example in S. cerevisiae exposure to fatty acids dramatically induces the expression of genes encoding many peroxisomal proteins while concomitantly inducing the biogenesis and/or maturation of organelles; when compared to a fitness data set measuring growth of individual deletion strains on fatty acid-containing media, there is remarkably little overlap between the data sets [10]

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Results

Conclusion