Alternative titles; symbols
HGNC Approved Gene Symbol: PEX5
Cytogenetic location: 12p13.31 Genomic coordinates (GRCh38): 12:7,188,653-7,218,574 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 12p13.31 | Peroxisome biogenesis disorder 2A (Zellweger) | 214110 | Autosomal recessive | 3 |
| Peroxisome biogenesis disorder 2B | 202370 | Autosomal recessive | 3 | |
| Rhizomelic chondrodysplasia punctata, type 5 | 616716 | Autosomal recessive | 3 |
Peroxisomal matrix enzymes are synthesized on free polyribosomes and imported into the peroxisome posttranslationally. Import of the matrix proteins requires cis-acting peroxisomal targeting signals (PTSs), the 2 best-characterized being PTS1 and PTS2 (Subramani, 1993). The C-terminal PTS1 motif is present on most peroxisomal matrix proteins and is found in mammals, insects, plants, yeast, and protozoans. In mammals, the consensus PTS1 is ser-lys-leu-COOH, but some variability is allowed, with ala or cys also possible at the -3 position; arg or his at the -2 position; and met at the -1 position. PTS1-mediated peroxisomal protein import requires ATP and one or more cytosolic factors, and is stimulated by HSP70 heat-shock proteins. PTS2, which has been identified in only a few proteins (peroxisomal thiolase from numerous species, a glyoxysomal malate dehydrogenase from watermelon, and human phytanic acid oxidase), is located within 40 amino acids of the N terminus and has a consensus of arg/lys-leu-X5-gln/his-leu. Mutants deficient in peroxisome assembly, previously called pas mutants and now known as pex mutants, have been identified in several yeast species. Among the 10 or more complementation groups of pas mutants in the yeast Pichia pastoris, the phenotype of the pas8 mutant is unique in that it displays a selective defect in the import of PTS1 proteins. PAS8 encodes a 68-kD protein with multiple tetratricopeptide repeat motifs. Because of the phenotype of the pas8 mutant and the fact that the protein that is missing in that mutant has PTS1-binding activity in vitro, it was proposed that PAS8 encodes the PTS1 receptor of P. pastoris. Dodt et al. (1995) identified and characterized the human gene PXR1, a homolog of P. pastoris PAS8, and demonstrated that it is indeed the human PTS1 receptor. PXR1, like PAS8, encodes a receptor for proteins with the type 1 peroxisomal targeting signal (PTS1). Mutations in PXR1 define complementation group 2 of the peroxisome biogenesis disorders (PBDs), and expression of PXR1 rescues the PTS1 import defect of fibroblasts from these patients. Based on the observation that PXR1 exists both in the cytosol and in association with peroxisomes, Dodt et al. (1995) proposed that PXR1 protein recognizes PTS1-containing proteins in the cytosol and directs them to the peroxisome. In the revised nomenclature (vide infra) both PAS8 and PXR1 are designated PEX5.
Wiemer et al. (1995) cloned a human liver cDNA encoding PEX5, which they called PTS1R. The predicted 602-amino acid protein has a calculated molecular mass of 67 kD but an 80-kD mass by immunoblot analysis; the authors indicated that the discrepancy is due to aberrant migration on SDS-polyacrylamide gels. Northern blot analysis detected an approximately 3.4-kb transcript in all human tissues examined.
Shepard et al. (2007) identified long and short isoforms of PTS1R by yeast 2-hybrid analysis of human trabecular meshwork and heart cell cDNA libraries using C-terminal MYOC (601652) as bait. The long splice variant contains 639 amino acids, and the short splice variant contains 602 amino acids.
By somatic cell hybrid and fluorescence in situ hybridization analyses, Wiemer et al. (1995) mapped the human PEX5 gene to chromosome 12p13.3. Marynen et al. (1995) mapped the PEX5 gene to chromosome 12p13 by in situ hybridization using a cosmid containing the gene as a probe. A radiation hybrid DNA panel was used to map the gene between TPI1 (190450) and the marker D12S1089.
Crystal Structure
Stanley et al. (2006) solved the crystal structure of PXR1 at 2.3-angstrom resolution in the presence and absence of a cargo protein, SCP2 (184755). PXR1 showed major structural changes from an open, snail-like conformation in the absence of cargo into a closed, circular conformation when bound by SCP2. These changes occurred within a long loop C-terminal to the 7-fold tetratricopeptide repeat segments. Stanley et al. (2006) identified residues within this loop that were critical for in vivo cargo import, and their mutation led to defective cargo import into peroxisomes.
Dammai and Subramani (2001) showed that human PEX5 does not just bind cargo and deliver it to the peroxisome membrane, but instead participates in multiple rounds of entry into the peroxisome matrix and export to the cytosol independent of the PTS2 import pathway. The authors noted that this unusual shuttling mechanism for the PTS1 receptor distinguishes protein import into peroxisomes from that into most other organelles, with the exception of the nucleus.
Shepard et al. (2007) identified PTS1R as a binding partner for misfolded mutant MYOC and demonstrated that glaucoma (137750)-causing mutations in human MYOC induce exposure of a cryptic peroxisomal targeting sequence, which must interact with PTS1R to elevate intraocular pressure.
Peroxisome Biogenesis Disorders
Dodt et al. (1995) found that of the 2 reported patients in complementation group 2 showing mutations in PEX5, cells from the patient homozygous for N489K (600414.0001) were defective in the import of PTS1 proteins into peroxisomes, as expected. However, cells from the patient homozygous for the nonsense mutation R390X (600414.0002) were defective in the import of both PTS1 and PTS2 proteins, suggesting that the PTS1 receptor also mediates PTS2-targeted protein import. To investigate this possibility, Braverman et al. (1998) characterized PEX5 expression and found that it undergoes alternative splicing, producing 2 transcripts, 1 containing and 1 lacking a 111-bp internal exon. Fibroblasts from the patient with the nonsense mutation had greatly reduced levels of PEX5 transcript and protein as compared with the patient with the missense mutation N489K. Transfection of the R390X cells with PEX5 cDNA lacking the 1 exon restored PTS1 but not PTS2 import; transfection with the long form of PEX5 cDNA restored both PTS1 and PTS2 protein import. Furthermore, transfection of the R390X cells with PEX5 cDNAs containing the mutations, which are located downstream of the additional exon, restored PTS2 but not PTS1 import. Taken together, these data provided an explanation for the different protein import defects in CG2 patients and showed that the long isoform of the PEX5 protein is required for peroxisomal import of PTS2 proteins.
Rhizomelic Chondrodysplasia Punctata, Type 5
In 3 sibs, born to consanguineous Pakistani parents, with rhizomelic chondrodysplasia punctate type 5 (RCDP5; 616716), Baroy et al. (2015) identified a homozygous frameshift mutation in exon 9 (coding exon 7) of the long isoform of PEX5 (c.722dupA; 600414.0003). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. The same mutation was identified in an unrelated Pakistani girl, born to consanguineous Pakistani parents, with RCDP. Studies of peroxisomal parameters in cultured fibroblasts of this patient had indicated a PTS2 protein import defect; no mutation was identified in PEX7 (601757). Baroy et al. (2015) showed that, similar to mutations in PEX7, loss of the PEX5-long isoform results in a peroxisomal dysfunction due to selective defect in the import of PTS2-tagged proteins only, causing RCDP instead of a peroxisome biogenesis disorder.
Patients with Zellweger syndrome have an inability to assemble functional peroxisomes, resulting in a multiorgan defect during fetal development and death, usually within the first year of life. Patients suffer from extreme hypotonia, neonatal seizures, and severe mental retardation and accumulate very-long-chain fatty acids (VLCFAs), pristanic acid, phytanic acid, and bile acid intermediates. At the time of death, liver fibrosis, renal cysts, and severe brain malformations are among the most prominent organ abnormalities. The thin cortical plates and subcortical heterotopias are attributed to a partial impediment to gliophilic neuronal migration. To investigate the pleiotropic role of peroxisomes in vivo, Baes et al. (1997) generated an animal model of peroxisome deficiency through inactivation of the Pxr1 gene in mice. Homozygous Pxr1 knockout mice lacked morphologically identifiable peroxisomes and exhibited the typical biochemical abnormalities of Zellweger patients. They displayed intrauterine growth retardation, were severely hypotonic at birth, and died within 72 hours. Analysis of the neocortex revealed impaired neuronal migration and maturation and extensive apoptotic death of neurons.
Baumgart et al. (2001) generated homozygous Pex5-knockout mice. Histochemical staining showed that Pex5-knockout hepatocytes lacked peroxisomes and contained large aggregates of pleomorphic mitochondria. Mitochondrial aggregates were randomly distributed in liver and were often found under the sinusoidal and basolateral surface of hepatocytes. Electron microscopy revealed that mitochondrial alterations had different types and involved all subcompartments of mitochondria. The alterations were heterogeneous in different liver cells, and within the same cell severely altered mitochondria were observed adjacent to normal mitochondria. Mitochondrial alterations were also present in other tissues and in blood cells of Pex5-knockout mice. Damaged mitochondria were removed from cytoplasm in large autophagic vacuoles, likely to reduce the cellular toxicity and further damage to mitochondria. Ultrastructural alterations of liver mitochondria were accompanied by altered activity and distribution of mitochondrial respiratory chain complexes, leading to a heterogeneous mitochondrial population with an overall decrease of complex I and complex V activities in livers of newborn Pex5-knockout mice. However, changes in the overall activities of complex I and complex V did not affect ATP levels in Pex5-knockout liver cells. In situ hybridization and immunocytochemical analyses revealed that the changes of mitochondrial respiratory chain enzymes resulted in signs of oxidative stress in liver mitochondria of Pex5-knockout mice.
Distel et al. (1996) provided a unified nomenclature for peroxisome biogenesis. By the use of genetic approaches in a wide variety of experimental organisms, 13 proteins required for peroxisome biogenesis had been identified in the previous 10 years. Three of these had been shown to be defective in lethal peroxisome biogenesis disorders (PBDs). However, the diverse experimental systems had led to a profusion of names for peroxisome assembly genes and proteins. Distel et al. (1996) suggested that proteins involved in peroxisome biogenesis should be designated 'peroxins,' with PEX representing the gene acronym. Even though defects in peroxisomal metabolic enzymes or transcription factors may affect peroxisome proliferation and/or morphology, such proteins should not, they recommended, be included in this group. The proteins and genes were to be numbered by date of published characterization, both for known factors and those identified in the future. When necessary, species of origin could be specified by 1-letter abbreviations for genus and species (e.g., hsPEX2).
In a cell line from a patient with neonatal adrenoleukodystrophy (see PBD2B, 202370), Dodt et al. (1995) identified a specific defect in PTS1-mediated uptake of peroxisomal proteins and examined the PXR1 gene in this patient by RT-PCR amplification of fibroblast RNA followed by SSCP analysis. Sequencing of an abnormally migrating fragment demonstrated a PXR1 allele with a T-to-G transversion at basepair 1467, producing an asn489-to-lys (N489K) substitution. The patient appeared to be homozygous for the mutant allele, but family studies were not performed. The N489K substitution was not found in 130 unrelated control individuals. Transfection of the normal gene into the patient's cells restored normal import of PTS1-containing proteins into peroxisomes, as well as normal peroxisome morphology. In contrast, normal cells transfected with PXR1 carrying the N489K mutation were unable to import PTS1-containing proteins into peroxisomes. (The cells of the patient showed normal import of the PTS2 marker protein, thiolase, into peroxisomal structures.)
In a cell line from a patient with Zellweger syndrome (PBD2A; 214110), Dodt et al. (1995) identified a C-to-T transition at nucleotide 1168 resulting in an arg390-to-ter substitution. The patient was homozygous for the mutation.
In 3 sibs, born to consanguineous Pakistani parents, with rhizomelic chondrodysplasia punctata type 5 (RCDP5; 616716), Baroy et al. (2015) identified a homozygous 1-bp deletion (c.722dupA, NM_001131023.1) in exon 9 (coding exon 7) of the long isoform of PEX5, resulting in a frameshift (Val242GlyfsTer33). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. The same mutation was identified in an unrelated Pakistani girl, born to consanguineous Pakistani parents, with RCDP. Studies of peroxisomal parameters in cultured fibroblasts of this patient had indicated a PTS2 protein import defect; no mutation was identified in PEX7 (601757). Baroy et al. (2015) showed that, similar to mutations in PEX7, loss of the PEX5-long isoform results in peroxisomal dysfunction due to selective defect in the import of PTS2-tagged proteins, causing RCDP instead of a peroxisome biogenesis disorder. Baroy et al. (2015) demonstrated that expression of the PEX5-long isoform restored the import of PTS2-tagged proteins in patient fibroblasts.
Baes, M., Gressens, P., Baumgart, E., Carmeliet, P., Casteels, M., Fransen, M., Evrard, P., Fahimi, D., Declercq, P. E., Collen, D., van Veldhoven, P. P., Mannaerts, G. P. A mouse model for Zellweger syndrome. Nature Genet. 17: 49-57, 1997. [PubMed: 9288097] [Full Text: https://doi.org/10.1038/ng0997-49]
Baroy, T., Koster, J., Stromme, P., Ebberink, M. S., Misceo, D., Ferdinandusse, S., Holmgren, A., Hughes, T., Merckoll, E., Westvik, J., Woldseth, B., Walter, J., Wood, N., Tvedt, B., Stadskleiv, K., Wanders, R. J. A., Waterham, H. R., Frengen, E. A novel type of rhizomelic chondrodysplasia punctata, RCDP5, is caused by loss of the PEX5 long isoform. Hum. Molec. Genet. 24: 5845-5854, 2015. [PubMed: 26220973] [Full Text: https://doi.org/10.1093/hmg/ddv305]
Baumgart, E., Vanhorebeek, I., Grabenbauer, M., Borgers, M., Declercq, P. E., Fahimi, H. D., Baes, M. Mitochondrial alterations caused by defective peroxisomal biogenesis in a mouse model for Zellweger syndrome (PEX5 knockout mouse). Am. J. Pathol. 159: 1477-1494, 2001. [PubMed: 11583975] [Full Text: https://doi.org/10.1016/S0002-9440(10)62534-5]
Braverman, N., Dodt, G., Gould, S. J., Valle, D. An isoform of Pex5p, the human PTS1 receptor, is required for the import of PTS2 proteins into peroxisomes. Hum. Molec. Genet. 7: 1195-1205, 1998. [PubMed: 9668159] [Full Text: https://doi.org/10.1093/hmg/7.8.1195]
Dammai, V., Subramani, S. The human peroxisomal targeting signal receptor, Pex5p, is translocated into the peroxisomal matrix and recycled to the cytosol. Cell 105: 187-196, 2001. Note: Erratum: Cell 105: 695 only, 2001. [PubMed: 11336669] [Full Text: https://doi.org/10.1016/s0092-8674(01)00310-5]
Distel, B., Erdmann, R., Gould, S. J., Blobel, G., Crane, D. I., Cregg, J. M., Dodt, G., Fujiki, Y., Goodman, J. M., Just, W. W., Kiel, J. A. K. W., Kunau, W.-H., Lazarow, P. B., Mannaerts, G. P., Moser, H. W., Osumi, T., Rachubinski, R. A., Roscher, A., Subramani, S., Tabak, H. F., Tsukamoto, T., Valle, D., van der Klei, I., van Veldhoven, P. P., Veenhuis, M. A unified nomenclature for peroxisome biogenesis factors. J. Cell Biol. 135: 1-3, 1996. [PubMed: 8858157] [Full Text: https://doi.org/10.1083/jcb.135.1.1]
Dodt, G., Braverman, N., Wong, C., Moser, A., Moser, H. W., Watkins, P., Valle, D., Gould, S. J. Mutations in the PTS1 receptor gene, PXR1, define complementation group 2 of the peroxisome biogenesis disorders. Nature Genet. 9: 115-125, 1995. [PubMed: 7719337] [Full Text: https://doi.org/10.1038/ng0295-115]
Marynen, P., Fransen, M., Raeymaekers, P., Mannaerts, G. P., Van Veldhoven, P. P. The gene for the peroxisomal targeting signal import receptor (PXR1) is located on human chromosome 12p13, flanked by TPI1 and D12S1089. Genomics 30: 366-368, 1995. [PubMed: 8586442] [Full Text: https://doi.org/10.1006/geno.1995.0032]
Shepard, A. R., Jacobson, N., Millar, J. C., Pang, I.-H., Steely, H. T., Searby, C. C., Sheffield, V. C., Stone, E. M., Clark, A. F. Glaucoma-causing myocilin mutants require the peroxisomal targeting signal-1 receptor (PTS1R) to elevate intraocular pressure. Hum. Molec. Genet. 16: 609-617, 2007. [PubMed: 17317787] [Full Text: https://doi.org/10.1093/hmg/ddm001]
Stanley, W. A., Filipp, F. V., Kursula, P., Schuller, N., Erdmann, R., Schliebs, W., Sattler, M., Wilmanns, M. Recognition of a functional peroxisome type 1 target by the dynamic import receptor Pex5p. Molec. Cell 24: 653-663, 2006. [PubMed: 17157249] [Full Text: https://doi.org/10.1016/j.molcel.2006.10.024]
Subramani, S. Protein import into peroxisomes and biogenesis of the organelle. Annu. Rev. Cell Biol. 9: 445-478, 1993. [PubMed: 8280468] [Full Text: https://doi.org/10.1146/annurev.cb.09.110193.002305]
Wiemer, E. A. C., Nuttley, W. M., Bertolaet, B. L., Li, X., Francke, U., Wheelock, M. J., Anne, U. K., Johnson, K. R., Subramani, S. Human peroxisomal targeting signal-1 receptor restores peroxisomal protein import in cells from patients with fatal peroxisomal disorders. J. Cell Biol. 130: 51-65, 1995. [PubMed: 7790377] [Full Text: https://doi.org/10.1083/jcb.130.1.51]