Proteomics of the peroxisome

Institute for Systems Biology, Seattle, WA 98103, USA.
Biochimica et Biophysica Acta (Impact Factor: 4.66). 01/2007; 1763(12):1541-51. DOI: 10.1016/j.bbamcr.2006.09.005
Source: PubMed


Genomes provide us with a blue print for the potential of a cell. However, the activity of a cell is expressed in its proteome. Full understanding of the complexity of cells demands a comprehensive view of the proteome; its interactions, activity states and organization. Comprehensive proteomic approaches applied to peroxisomes have yielded new insights into the organelle and its dynamic interplay with other cellular structures. As technologies and methodologies improve, proteomics hold the promise for new discoveries of peroxisome function and a full description of this dynamic organelle.

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    • "By contrast, other recent research using proteome analysis of Arabidopsis leaf peroxisomes suggested that GLYR1 is associated with peroxisomes (Reumann et al. 2009). While this result seems inconsistent with the abovementioned working model for GLYR1 (e.g., GLYR1 in the peroxisome could form a futile cycle with glycolate oxidase) and could simply be due to contamination of the peroxisome fraction by other cellular compartments, a notorious problem with peroxisome isolations (Saleem et al. 2006), other observations appear to support the possibility that GLYR1 is associated with peroxisomes. For instance, several other proteins previously predicted to be non-peroxisomal have recently been shown to be associated with peroxisomes and thereby have revealed several new, previously unknown metabolic functions associated with the organelle (Palma et al. 2009; Reumann 2011). "
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    ABSTRACT: Glyoxylate reductase (GLYR) is a key enzyme in plant metabolism which catalyzes the detoxification of both photorespiratory glyoxylate and succinic semialdehdye, an intermediate of the γ-aminobutyrate (GABA) pathway. Two isoforms of GLYR exist in plants, GLYR1 and GLYR2, and while GLYR2 is known to be localized in plastids, GLYR1 has been reported to be localized in either peroxisomes or the cytosol. Here, we reappraised the intracellular localization of GLYR1 in Arabidopsis thaliana L. Heynh (ecotype Lansberg erecta) using both transiently-transformed suspension cells and stably-transformed plants, in combination with fluorescence microscopy. The results indicate that GLYR1 is localized exclusively to the cytosol regardless of the species, tissue and/or cell type, or exposure of plants to environmental stresses that would increase flux through the GABA pathway. Moreover, the C-terminal tripeptide sequence of GLYR1, -SRE, despite its resemblance to a type 1 peroxisomal targeting signal, is not sufficient for targeting to peroxisomes. Collectively, these results define the cytosol as the intracellular location of GLYR1 and provide not only important insight to the metabolic roles of GLYR1 and the compartmentation of the GABA and photorespiratory pathways in plant cells, but also serve as a useful reference for future studies of proteins proposed to be localized to peroxisomes and/or the cytosol.
    Journal of Integrative Plant Biology 02/2012; 54(3):152-68. DOI:10.1111/j.1744-7909.2012.01103.x · 3.34 Impact Factor
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    • "First, organelles cannot be purified to homogeneity leading to a large background of low abundant co-purified contaminants readily detected when the latest LC/MS technologies are used. Secondly, isolation of low abundant and highly dynamic organelles such as peroxisomes from different tissues remains difficult [7]. And thirdly, identification of new organellar resident proteins requires the development of comprehensive strategies preferably using quantitative MS for reliably identifying candidate proteins followed, for example, by imaging approaches for in vivo co-localization studies to validate the MS data. "
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    ABSTRACT: We present a label-free quantitative proteomic approach for the study of kidney peroxisomes of Pex7 knockout mice which is a bona-fide model for the human disease rhizomelic chondrodysplasia punctata (RCDP). RCDP is an autosomal recessive human disorder caused by mutations in the PEX7 gene encoding for Pex7, the cytosolic receptor protein that is essential for the import of proteins containing a functional peroxisomal targeting signal (PTS)-type 2. In this work, we quantitatively followed hundreds of proteins through high density gradient fractions of wildtype (WT) and Pex7 knockout (Pex7−/−) mice by high resolution mass spectrometry. A set of candidate proteins with altered abundance was defined via statistical and quantitative assessment of protein profiles obtained from WT and Pex7−/− mice. The results obtained demonstrate the feasibility of this approach to identify proteins specifically affected in abundance by the deletion of Pex7. All three known PTS2 proteins, including acetyl-Coenzyme A acyltransferase, alkylglycerone phosphate synthase and phytanoyl-CoA hydroxylase were determined to be virtually absent in these fractions whereas KIAA0564, a so far uncharacterized protein, was barely detectable in peroxisomal fractions of Pex7−/− mice. Furthermore, we report numerous PTS1 proteins with increased abundance levels in Pex7−/− mice that fulfill essential functions in the β-oxidation of very long-chain fatty acids or the biosynthesis of ether-phospholipids in peroxisomes.
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    • "Evidence for dynamic interplay between peroxisomes and the ER, the mitochondria and the vacuole has been accumulating over the last few years. Our initial characterization of the proteome of the peroxisome revealed a number of ER resident, vacuolar and mitochondrial components that specifically enriched with and were localized to the peroxisome during oleate incubation of S. cerevisiae [7], [8]. Through this present study, we characterize the influence of these organelles on the biogenesis of peroxisomes and can begin to infer normal roles for proteins on peroxisome morphology on a genome-wide scale. "
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    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.
    PLoS ONE 08/2010; 5(8):e11953. DOI:10.1371/journal.pone.0011953 · 3.23 Impact Factor
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