Topogenesis of peroxisomal proteins

Immunoelectron microscopy of peroxisomes employing the antibody for the SKL sequence PTS1 C-terminus common to peroxisomal enzymes

Immunohistochemistry employing a new hapten antibody that detects the SKL sequence and its variants of the PTS1 C-terminus of peroxisomal enzymes was attempted to visualize peroxisomes across species. Rabbits were immunized with the SKL sequence coupled with KLH, between which an arm molecule was interposed. IgG fractions of antisera were affinity-purified against the hapten and employed for immunochemical analyses and immunoelectron microscopy. The specificity of the antibody was examined by immunoblot analyses for various purified enzymes of rat liver peroxisomes and by dot-blot analyses inhibited by SKL peptide and its variants. Various animal and plant tissues were subjected to immunoelectron microscopy with the protein A-gold technique. The antibody reacted with various enzymes in the peroxisome with the SKL motif. The affinity of the antibody for tripeptides, which varied depending on their structures, was higher for SKL than for its variants. Hepatic and renal peroxisomes of vertebrates, peroxisomes in the fat body of an insect, and the cotyledon of a plant were visualized by immunoelectron microscopy. Immunohistochemistry employing this SKL antibody may provide specific staining that can detect peroxisomes across different species.

Biochemistry of peroxisomes in health and disease

The ubiquitous distribution of peroxisomes and the identification of a number of inherited diseases associated with peroxisomal dysfunction indicate that peroxisomes play an essential part in cellular metabolism. Some of the most important metabolic functions of peroxisomes include the synthesis of plasmalogens, bile acids, cholesterol and dolichol, and the oxidation of fatty acids (very long chain fatty acids > C22, branched chain fatty acids (e.g. phytanic acid), dicarboxylic acids, unsaturated fatty acids, prostaglandins, pipecolic acid and glutaric acid). Peroxisomes are also responsible for the metabolism of purines, polyamines, amino acids, glyoxylate and reactive oxygen species (e.g. O-2 and H2O2). Peroxisomal diseases result from the dysfunction of one or more peroxisomal metabolic functions, the majority of which manifest as neurological abnormalities. The quantitation of peroxisomal metabolic functions (e.g. levels of specific metabolites and/or enzyme activity) has become the basis of clinical diagnosis of diseases associated with the organelle. The study of peroxisomal diseases has also contributed towards the further elucidation of a number of metabolic functions of peroxisomes.

Effect of ischemia-reperfusion injury on the morphology of peroxisomes

We have previously demonstrated that ischemic injury changed the density of peroxisomes into two distinct peaks, one with a normal density (1.21 g/cm3; Peak I) and a second peak with a lighter density (1.14 g/cm3; Peak II). We studied the peroxisomes from both peaks under the Electron microscope. Examination of peak I following ischemia showed loss of matrix proteins and damaged limiting membranes with leakage of DAB positive material in direct proportion to the duration of ischemia. Upon reperfusion of the ischemic liver Peak I showed more severe damage to the organelle. These observations clearly demonstrated that ischemia reperfusion injury causes structural damage to peroxisomes. Interestingly ultrastructural examination of Peak II following ischemia showed evidence of perisomal proliferation with budding of existing peroxisomes and the presence of micro peroxisomes (changes similar to those noted under conditions leading to perisomal proliferation). However, peak II following reperfusion showed only damaged organelle. These observations underline the importance of peroxisomes in the response of the cell to ischemia-reperfusion injury.

Molecular organization of hepatocyte peroxisomes

The matrix of peroxisomes has been considered to be homogeneous. However, a fine network of tubules is visible in electron micrographs at very high magnification. This substructure becomes more positive in a high-contrast photocopy and with an imaging-plate method. Clofibrate, bezafibrate, and aspirin increase peroxisomes. In proliferated peroxisomes, the density of matrix is low and the fine network is more visible. The effect of proliferators is more significant in males than in females. This sex difference may involve the action of estrogen, growth hormone, cytochrome P-450 and thyroxine. Mg-ATPase is localized on the limiting membrane of peroxisomes. Even on the membrane of irregular projections of proliferated peroxisomes, Mg-ATPase is evident cytochemically. Carnitine acetyltransferase is detectable in the matrix of proliferated peroxisomes. Withdrawal of proliferators results in a rapid decrease of peroxisomes. This may indicate the existence of peroxisome suppressors. Alternatively, dynamic transformation of vesicular to tubular types in peroxisome reticulum may occur. Such transformation has been described in lysosomes and mitochondria.

Peroxisome assembly factor 1: nonsense mutation in a peroxisome-deficient Chinese hamster ovary cell mutant and deletion analysis

A cDNA encoding 35-kDa peroxisome assembly factor 1 (PAF-1), a peroxisomal integral membrane protein, was cloned from Chinese hamster ovary (CHO) cells and sequenced. The CHO PAF-1 comprised 304 amino acids, one residue shorter than rat or human PAF-1, and showed high homology to rat and human PAF-1: 90 and 86% at the nucleotide sequence level and 92 and 90% in amino acid sequence, respectively. PAF-1 from these three species contains a conserved cysteine-rich sequence at the C-terminal region which is exactly the same as that of a novel cysteine-rich RING finger motif family. PAF-1 cDNA from a peroxisome-deficient CHO cell mutant, Z65 (T. Tsukamoto, S. Yokota, and Y. Fujiki, J. Cell Biol. 110:651-660, 1990), contained a nonsense mutation at the codon for Trp-114, resulting in premature termination. Truncation in PAF-1 of either 19 amino acids from the N terminus or 92 residues from the C terminus maintained the peroxisome assembly-restoring activity when tested in both the Z65 mutant and the fibroblasts from a Zellweger patient. In contrast, deletion of 27 or 102 residues from the N or C terminus eliminated the activity. PAF-1 is encoded by free polysomal RNA, consistent with a general rule for biogenesis of peroxisomal proteins, including membrane polypeptides, implying the posttranslational transport and integration of PAF-1 into peroxisomal membrane.

Peroxisome assembly factor 1: nonsense mutation in a peroxisome-deficient Chinese hamster ovary cell mutant and deletion analysis

A cDNA encoding 35-kDa peroxisome assembly factor 1 (PAF-1), a peroxisomal integral membrane protein, was cloned from Chinese hamster ovary (CHO) cells and sequenced. The CHO PAF-1 comprised 304 amino acids, one residue shorter than rat or human PAF-1, and showed high homology to rat and human PAF-1: 90 and 86% at the nucleotide sequence level and 92 and 90% in amino acid sequence, respectively. PAF-1 from these three species contains a conserved cysteine-rich sequence at the C-terminal region which is exactly the same as that of a novel cysteine-rich RING finger motif family. PAF-1 cDNA from a peroxisome-deficient CHO cell mutant, Z65 (T. Tsukamoto, S. Yokota, and Y. Fujiki, J. Cell Biol. 110:651-660, 1990), contained a nonsense mutation at the codon for Trp-114, resulting in premature termination. Truncation in PAF-1 of either 19 amino acids from the N terminus or 92 residues from the C terminus maintained the peroxisome assembly-restoring activity when tested in both the Z65 mutant and the fibroblasts from a Zellweger patient. In contrast, deletion of 27 or 102 residues from the N or C terminus eliminated the activity. PAF-1 is encoded by free polysomal RNA, consistent with a general rule for biogenesis of peroxisomal proteins, including membrane polypeptides, implying the posttranslational transport and integration of PAF-1 into peroxisomal membrane.

A protein histidine kinase induced in rat liver by peroxisome proliferators. In vitro activation by Ras protein and guanine nucleotides

A novel protein kinase is induced in rat liver plasma membrane by the administration of peroxisome proliferators. A 36 kDa protein (P36) on the membrane was rapidly phosphorylated in vitro by the kinase and the phosphorylated amino acid was identified as phosphohistidine. Histidine phosphorylation of P36 was activated in vitro by recombinant Ras protein and GTP; both decreased Michaelis constant (Km) for ATP from 1.25 to 0.25 microM. The novel histidine kinase, products of which have been overlooked due to their acid lability, may participate in cellular signaling and peroxisome proliferators may perturb the pathway.

A knowledge base for predicting protein localization sites in eukaryotic cells

To automate examination of massive amounts of sequence data for biological function, it is important to computerize interpretation based on empirical knowledge of sequence-function relationships. For this purpose, we have been constructing a knowledge base by organizing various experimental and computational observations as a collection of if-then rules. Here we report an expert system, which utilizes this knowledge base, for predicting localization sites of proteins only from the information on the amino acid sequence and the source origin. We collected data for 401 eukaryotic proteins with known localization sites (subcellular and extracellular) and divided them into training data and testing data. Fourteen localization sites were distinguished for animal cells and 17 for plant cells. When sorting signals were not well characterized experimentally, various sequence features were computationally derived from the training data. It was found that 66% of the training data and 59% of the testing data were correctly predicted by our expert system. This artificial intelligence approach is powerful and flexible enough to be used in genome analyses.

Rat liver BiP/GRP78 is down-regulated by a peroxisome-proliferator, clofibrate

Administration of clofibrate in rat results in down-regulation of several liver proteins and a vast induction of peroxisomal proteins. One protein was identified as BiP/GRP78 using antibodies and cDNA cloning. The level of mRNA was reduced by the drug.

Signal peptide for peroxisomal targeting: replacement of an essential histidine residue by certain amino acids converts the amino-terminal presequence of peroxisomal 3-ketoacyl-CoA thiolase to a mitochondrial signal peptide

The role of the histidine residue at position -17 of the amino-terminal signal peptide of rat peroxisomal 3-ketoacyl-CoA thiolase was studied in vivo, employing site-directed mutagenesis. Among the nine amino acids tested, only glutamine could partially substitute for the histidine. Mutants carrying basic amino acids, arginine and lysine, and hydrophobic residues, leucine and valine, in place of histidine were all translocated to mitochondria, but not to peroxisomes. These results indicate that the signal peptide of the thiolase is recognized by a mechanism totally different from that for the SKL motif, a known peroxisomal targeting signal. Relationship of the thiolase signal peptide to those of mitochondrial proteins is discussed.

Targeting proteins to mitochondria: a current overview

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cDNA cloning of mitochondrial delta 3, delta 2-enoyl-CoA isomerase of rat liver

A 1.08 kbp cDNA encoding rat liver mitochondrial delta 3, delta 2-enoyl-CoA isomerase (ECI) of 298 amino acid residues (Mr 32,895) was isolated from rat liver lambda gt11, lambda gt10 cDNA libraries by the combination of an immunochemical method with a rabbit-antibody against rat liver ECI and a plaque hybridization method. The deduced amino acid sequence from the cDNA indicates that ECI is synthesized with an amino-terminal extrasequence of 35 amino acid residues and processed to the mature enzyme (Mr 29,256).

Amino-terminal presequence of the precursor of peroxisomal 3-ketoacyl-CoA thiolase is a cleavable signal peptide for peroxisomal targeting

To examine the function of the amino-terminal presequence of rat peroxisomal 3-ketoacyl-CoA thiolase precursor, fusion proteins of various amino-terminal regions of the precursor with non-peroxisomal enzymes were expressed in cultured mammalian cells. On immunofluorescence microscopy, all constructs carrying the presequence part exhibited punctate patterns of distribution, identical with that of catalase, a peroxisomal marker. Proteins lacking all or a part of the prepiece were found in the cytosol. These results indicate that the presequence of the thiolase has sufficient information for peroxisomal targeting.

Structure-function relationships in the peroxisome: implications for human disease

Progress relevant to human peroxisomal disorders over the past 3 years includes improved biochemical delineation of disease phenotypes and new insights into peroxisomal structure and biogenesis. Immunoblotting studies using antibodies to peroxisomal beta-oxidation enzymes have defined mutations affecting each step of the pathway, some with clinical phenotypes as severe as disorders with global peroxisome deficiency. The latter disorders, typified by Zellweger syndrome, often lack matrix proteins but retain major membrane species of 150, 70, 35, and 22 kDa in empty peroxisomal "ghost" structures. The hypothesis that peroxisomal deficiency disorders result from altered targeting or import of peroxisomal matrix proteins has been strengthened by the demonstration of a carboxy terminal peroxisome-targeting signal which is distinct from amino terminal signals directing proteins to mitochondria. A mutation which mistargets alanine/glyoxylate aminotransferase from peroxisomes to mitochondria in primary hyperoxaluria provides a graphic example of these signals. The structural significance of membrane function is supported by the primacy of membrane assembly in normal ontogeny or regenerating liver. The coordinate control, targeting, and striking inducibility of peroxisomal proteins suggests a potential vehicle for gene and enzyme therapy.

Molecular organisation of the malate synthase genes of Aspergillus nidulans and Neurospora crassa

The sequencing and comparison of the genes encoding the glyoxylate bypass enzyme malate synthase of Aspergillus nidulans (acuE) and Neurospora crassa (acu-9) are presented. The predicted amino acid sequences of the A. nidulans and N. crassa enzymes are 538 and 542 residues respectively and the proteins are 87% homologous. In fungi, the malate synthase proteins are located in glyoxysomes and the deduced acuE and acu-9 proteins both contain a C-terminal S-K-L sequence, which has been implicated in transport into peroxisomes. The acuE coding region is interrupted by four introns and the acu-9 coding region is interrupted by one intron which occurs at the same position as the C-terminal acuE intron. The 5' non-coding regions of the two genes were examined for short homologous sequences that may represent the binding sites for regulatory proteins. Pyrimidine-rich sequences with weak homology to the amdI9 sequence, which has been implicated in facB-mediated acetate regulation of the amdS gene, were found but their functional significance remains to be determined.

Peroxisomal disorders

Peroxisomal disorders occur more frequently and have a wider range of clinical manifestations than has been realized in the past. Precise diagnosis can be achieved with non-invasive biochemical assays and all can be diagnosed prenatally, thus providing the option of genetic counseling. Specific therapy is being evaluated for one of these disorders (adrenoleukodystrophy). In addition to these clinical advances, a great deal of information has been gained recently about the biogenesis and normal function of peroxisomes. These latter advances have been stimulated, and in part created, by the study of human disease states. It is for these reasons that a review of these human disease states is relevant for the clinical biochemist.

Molecular cloning and deduced amino acid sequence of nonspecific lipid transfer protein (sterol carrier protein 2) of rat liver: a higher molecular mass (60 kDa) protein contains the primary sequence of nonspecific lipid transfer protein as its C-terminal part

Two types of cDNA for nonspecific lipid transfer protein (nsLTP), identical to sterol carrier protein 2, of rat liver were cloned; one was 787 base pairs (bp) long containing a 429-bp open reading frame of 143 amino acids, with a mass of 15,303 Da (15-kDa protein). The cDNA from the other type was 1966 bp long, including a 1641-bp open reading frame of 547 amino acids, giving a mass of 59,002 Da (60-kDa protein). The deduced primary sequence for the 15-kDa protein was exactly the same as the published sequence of purified nsLTP, except for an extra N-terminal sequence of 20 amino acids, consistent with the finding that nsLTP is synthesized as a larger precursor and processed to a mature form. The sequence for the 60-kDa protein contained, at the 3' end, the full sequence of the 15-kDa protein, a larger precursor to nsLTP. The 15- and 60-kDa proteins, synthesized in vitro from the respective cDNAs, were both immunoprecipitated by rabbit anti-rat liver nsLTP antibody and comigrated in SDS/PAGE with the proteins made in vitro from total liver RNA. These results shed new light on the dispute among several groups of investigators about the crossreactivity of anti-nsLTP antibody with a higher molecular mass, 60-kDa protein. In Northern blot analysis, two major RNA bands, 0.85 and 2.2 kilobases (kb) long, were detected together with two minor bands of 1.6 and 2.9 kb. The 0.85- and 2.2-kb RNAs most likely encode the 15-and 60-kDa proteins, respectively.