Efficient association of in vitro translation products with purified stable Candida tropicalis peroxisomes

The Craft of Peroxisome Purification-A Technical Survey Through the Decades

Purification technologies are one of the working horses in organelle proteomics studies as they guarantee the separation of organelle-specific proteins from the background contamination by other subcellular compartments. The development of methods for the separation of organelles was a major prerequisite for the initial detection and characterization of peroxisome as a discrete entity of the cell. Since then, isolated peroxisomes fractions have been used in numerous studies in order to characterize organelle-specific enzyme functions, to allocate the peroxisome-specific proteome or to unravel the organellar membrane composition. This review will give an overview of the fractionation methods used for the isolation of peroxisomes from animals, plants and fungi. In addition to "classic" centrifugation-based isolation methods, relying on the different densities of individual organelles, the review will also summarize work on alternative technologies like free-flow-electrophoresis or flow field fractionation which are based on distinct physicochemical parameters. A final chapter will further describe how different separation methods and quantitative mass spectrometry have been used in proteomics studies to assign the proteome of PO.

Peroxisomal Membrane and Matrix Protein Import Using a Semi-Intact Mammalian Cell System

Peroxisomes are essential intracellular organelles that catalyze a number of essential metabolic pathways including β-oxidation of very long chain fatty acids, synthesis of plasmalogen, bile acids, and generation and degradation of hydrogen peroxide. These peroxisomal functions are accomplished by strictly and spatiotemporally regulated compartmentalization of the enzymes catalyzing these reactions. Defects in peroxisomal protein import result in inherited peroxisome biogenesis disorders in humans. Peroxisomal matrix and membrane proteins are synthesized on free ribosomes and transported to peroxisomes in a manner dependent on their specific targeting signals and their receptors. Peroxisomal protein import can be analyzed using a semi-intact assay system, in which targeting efficiency is readily monitored by immunofluorescence microscopy. Furthermore, cytosolic factors required for peroxisomal protein import can be manipulated, suggesting that the semi-intact system is a useful and convenient system to uncover the molecular mechanisms of peroxisomal protein import.

A cell-free organelle-based in vitro system for studying the peroxisomal protein import machinery

Here we describe a protocol to dissect the peroxisomal matrix protein import pathway using a cell-free in vitro system. The system relies on a postnuclear supernatant (PNS), which is prepared from rat/mouse liver, to act as a source of peroxisomes and cytosolic components. A typical in vitro assay comprises the following steps: (i) incubation of the PNS with an in vitro-synthesized ³⁵S-labeled reporter protein; (ii) treatment of the organelle suspension with a protease that degrades reporter proteins that have not associated with peroxisomes; and (iii) SDS-PAGE/autoradiography analysis. To study transport of proteins into peroxisomes, it is possible to use organelle-resident proteins that contain a peroxisomal targeting signal (PTS) as reporters in the assay. In addition, a receptor (PEX5L/S or PEX5L.PEX7) can be used to report the dynamics of shuttling proteins that mediate the import process. Thus, different but complementary perspectives on the mechanism of this pathway can be obtained. We also describe strategies to fortify the system with recombinant proteins to increase import yields and block specific parts of the machinery at a number of steps. The system recapitulates all the steps of the pathway, including mono-ubiquitination of PEX5L/S at the peroxisome membrane and its ATP-dependent export back into the cytosol by PEX1/PEX6. An in vitro import(/export) experiment can be completed in 24 h.

Transport of proteins in eukaryotic cells: more questions ahead

Some newly synthesized proteins contain signals that direct their transport to their final location within or outside of the cell. Targeting signals are recognized by specific protein receptors located either in the cytoplasm or in the membrane of the target organelle. Specific membrane protein complexes are involved in insertion and translocation of polypeptides across the membranes. Often, additional targeting signals are required for a polypeptide to be further transported to its site of function. In this review, we will describe the trafficking of proteins to various cellular organelles (nucleus, chloroplasts, mitochondria, peroxisomes) with emphasis on transport to and through the secretory pathway.

Identification of peroxisomal membrane ghosts with an epitope-tagged integral membrane protein in yeast mutants lacking peroxisomes

Many yeast peroxisome biogenesis mutants have been isolated in which peroxisomes appear to be completely absent. Introduction of a wild-type copy of the defective gene causes the reappearance of peroxisomes, despite the fact that new peroxisomes are thought to form only from pre-existing peroxisomes. This apparent paradox has been explained for similar human mutant cell lines (from patients with Zellweger syndrome) by the discovery of peroxisomal membrane ghosts in the mutant cells (Santos, M. J., T. Imanaka, H. Shio, G. M. Small and P. B. Lazarow. 1988. Science 239, 1536-1538). Introduction of a wild-type gene is thought to restore to the ghosts the ability to import matrix proteins, and thus lead to the refilling of the peroxisomes. It is vitally important to our understanding of peroxisome biogenesis to determine whether the yeast mutants contain ghosts. We have solved this problem by introducing an epitope-tagged version of Pas3p, a peroxisome integral membrane protein (that is essential for peroxisome biogenesis). Nucleotides encoding a nine amino acid HA epitope were added to the PAS3 gene immediately before the stop codon. The tagged gene (PAS3HA) was inserted in the genome, replacing the wild-type gene at its normal locus. It was fully functional (the cells assembled peroxisomes normally and grew on oleic acid) but the expression level was too low to detect the protein with monoclonal antibody 12CA5. PAS3HA was expressed in greater quantity from an episomal plasmid with the CUP1 promoter. The gene product, Pas3pHA, was detected by immunogold labelling on the membranes of individual and clustered peroxisomes; the clusters appeared as large spots in immunofluorescence. PAS3HA was similarly expressed in peroxisome biogenesis mutants peb2 and peb4, which lack morphologically recognizable peroxisomes. Gold-labelled membranes were clearly visible in both mutants: in peb2 the labelled membrane vesicles were generally much smaller than those in peb4, which resembled normal peroxisomes in size.

Peroxisome biogenesis in Saccharomyces cerevisiae

The observation that peroxisomes of Saccharomyces cerevisiae can be induced by oleic acid has opened the possibility to investigate the biogenesis of these organelles in a biochemically and genetically well characterized organism. Only few enzymes have been identified as peroxisomal proteins in Saccharomyces cerevisiae so far; the three enzymes involved in beta-oxidation of fatty acids, enzymes of the glyoxylate cycle, catalase A and the PAS3 gene product have been unequivocally assigned to the peroxisomal compartment. However, more proteins are expected to be constituents of the peroxisomes in Saccharomyces cerevisiae. Mutagenesis of Saccharomyces cerevisiae cells gave rise to mutants unable to use oleic acid as sole carbon source. These mutants could be divided in two groups: those with defects in structural genes of beta-oxidation enzymes (fox-mutants) and those with defects in peroxisomal assembly (pas-mutants). All fox-mutants possess morphologically normal peroxisomes and can be assigned to one of three complementation groups (FOX1, 2, 3). All three FOX genes have been cloned and characterized. The pas-mutants isolated are distributed among 13 complementation groups and represent 3 different classes: peroxisomes are either morphologically not detectable (type I) or present but non-proliferating (type II). Mislocalization concerns all peroxisomal proteins in cells of these two classes. The third class of mutants contains peroxisomes normal in size and number, however, distinct peroxisomal matrix proteins are mislocalized (type III). Five additional complementation groups were found in the laboratory of H.F. Tabak. Not all PAS genes have been cloned and characterized so far, and only for few of them the function could be deduced from sequence comparisons. Proliferation of microbodies is repressed by glucose, derepressed by non-fermentable carbon sources and fully induced by oleic acid. The regulation of four genes encoding peroxisomal proteins (PAS1, CTA1, FOX2, FOX3) occurs on the transcriptional level and reflects the morphological observations: repression by glucose and induction by oleic acid. Moreover, trans-acting factors like ADR1, SNF1 and SNF4, all involved in derepression of various cellular processes, have been demonstrated to affect transcriptional regulation of genes encoding peroxisomal proteins. The peroxisomal import machinery seems to be conserved between different organisms as indicated by import of heterologous proteins into microbodies of different host cells. In addition, many peroxisomal proteins contain C-terminal targeting signals. However, more than one import route into peroxisomes does exist.(ABSTRACT TRUNCATED AT 400 WORDS)

Targeting of proteins into the peroxisomal matrix

During the last few years much has been learned regarding signals that target proteins into peroxisomes. The emphasis in the near future will undoubtedly shift towards the elucidation of the mechanism of import. The use of mammalian and yeast cells deficient in peroxisome assembly and/or import (Zoeller & Raetz, 1986; Erdmann et al., 1989; Cregg et al., 1990; Morand et al., 1990; Tsukamoto, Yokota & Fujiki, 1990) should provide a handle on the genes (Erdmann et al., 1991; Tsukamoto et al., 1991) involved in these processes. This will have to be coupled with further development of in vitro systems which will permit the dissection of the steps in the translocation of proteins into peroxisomes. Though some progress has been made in the development of such assays (Imanaka et al., 1987; Small et al., 1987, 1988; Miyazawa et al., 1989), the fragility of peroxisomes and the absence of biochemical hallmarks of import (such as protein modifications or proteolytic processing) have hindered progress. Since peroxisomes exist in the form of a reticulum in mammalian cells (Gorgas, 1984), all peroxisome purification schemes (from mammalian cells at least) must undoubtedly rupture the peroxisomes, which then reseal to form vesicular structures. Additionally, the reliance on the latency of catalase alone as a major criterion for the integrity of peroxisomes ignores the fact that many other matrix proteins leak out of peroxisomes at vastly different rates during purification of the organelles (Thompson & Krisans, 1990). In view of these problems, the development of peroxisomal transport assays with semi-intact cells would also constitute an important advance.(ABSTRACT TRUNCATED AT 250 WORDS)

The nucleotide sequence of POX18, a gene encoding a small oleate-inducible peroxisomal protein from Candida tropicalis

We report the molecular cloning and nucleotide sequence of the nuclear gene, POX18, encoding an oleate-inducible peroxisomal protein from the yeast Candida tropicalis. POX18 has a single open reading frame of 381 nucleotides (nt), which encodes a protein of 127 amino acids. The predicted Mr of this protein is 13,792. Codon usage in the expression of POX18 is non-random, and shows a pattern similar to that used for other peroxisomal genes from C. tropicalis and highly expressed genes from Saccharomyces cerevisiae. Northern analysis of total RNA from oleate-grown cells determined that POX18 mRNA is approximately 750 nt in length. The POX18 gene was expressed in vitro, which resulted in a single translation product that co-migrated in denaturing polyacrylamide gels with an abundant peroxisomal protein (apparent mass of 16 kDa) and was immunoprecipitated by an antiserum against peroxisomal protein.

Immunoblotting of hydrophobic integral membrane proteins

For diagnosis and research purposes it is frequently desirable to measure by immunoblotting small amounts of proteins in complex mixtures such as tissue biopsy homogenates. Standard immunoblot procedures that give excellent results for soluble proteins unexpectedly gave low and irreproducible signals with some hydrophobic membrane proteins. We found that this was due to inefficient electrophoretic transfer to nitrocellulose, which could be corrected by modification of the transblot buffer. Hydrophobic integral membrane proteins of peroxisomes as well as other rat and human liver proteins were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred to nitrocellulose filters. The nitrocellulose-bound proteins were detected both by staining and by immunoblotting with an antiserum against the 22-kDa integral membrane protein of peroxisomes plus 125I-labeled protein A. A modified transblot buffer with 0.7 M glycine and 25 mM Tris (pH 7.7) but no methanol allowed use of a much shorter transfer time and strikingly improved the electrophoretic transfer of membrane proteins such that a peroxisomal integral membrane protein could be easily detected in human liver biopsy homogenates.