PEX12 Interacts with PEX5 and PEX10 and Acts Downstream of Receptor Docking in Peroxisomal Matrix Import Chia-Che Chang, Daniel S. Warren, Katherine A. Sacksteder, and Stephen J. Gould The Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205

Abstract. Peroxisomal matrix protein import requires PEX5 or PEX10 can suppress this PEX12 mutation, PEX12, an integral peroxisomal membrane protein providing genetic evidence that these interactions are with a zinc ring domain at its carboxy terminus. Muta- biologically relevant. PEX5 is a predominantly cyto- tions in human PEX12 result in , a plasmic protein and previous PEX5-binding lethal neurological disorder, and implicate the zinc ring have been implicated in docking PEX5 to the peroxi- domain in PEX12 function. Using two-hybrid studies, some surface. However, we find that loss of PEX12 or blot overlay assays, and coimmunoprecipitation experi- PEX10 does not reduce the association of PEX5 with Downloaded from ments, we observed that the zinc-binding domain of , demonstrating that these peroxins are not PEX12 binds both PEX5, the PTS1 receptor, and required for receptor docking. These and other results PEX10, another integral peroxisomal membrane pro- lead us to propose that PEX12 and PEX10 play direct tein required for peroxisomal matrix protein import. roles in peroxisomal matrix protein import downstream Furthermore, we identified a patient with a missense of the receptor docking event. mutation in the PEX12 zinc-binding domain, S320F, jcb.rupress.org and observed that this mutation reduces the binding of Key words: PTS1 receptor • PEX5 • PEX10 • Zell- PEX12 to PEX5 and PEX10. Overexpression of either weger syndrome • biogenesis disorder on November 7, 2017

UBCELLULAR organelles are a defining feature of eu- port completely folded proteins, internally cross-linked karyotes and make essential contributions to virtu- isopeptide complexes, and even gold particles, whereas S ally all aspects of cellular metabolism. Although the ER and mitochondria can only accommodate unfolded each organelle is physically and chemically unique, there precursors; and peroxisomes lack detectable pores, whereas are several common aspects to the biogenesis of all mem- the nucleus utilizes large gated pores to allow entry of brane-limited compartments. One is that all or most of their folded import substrates. Thus, the elucidation of peroxi- protein content must be imported. The protein uptake somal protein import mechanisms will undoubtedly reveal mechanisms used in the biogenesis of each organelle must new concepts in organelle biogenesis. account for the recognition of newly synthesized proteins Peroxisomal proteins are encoded by nuclear , syn- that are destined for each organelle, the transport of these thesized in the cytoplasm, and imported posttranslation- proteins to the surface of the appropriate compartment, ally into peroxisomes (Lazarow and Fujiki, 1985). Peroxi- and the vectorial translocation of these proteins across one somal matrix proteins contain either of two peroxisomal or more lipid bilayers (Schatz and Dobberstein, 1996). targeting signals, the PTS1 (Gould et al., 1989) and PTS2 Several paradigms for protein import into organelles (Swinkels et al., 1991). Although either of these signals is have emerged from studies of the ER (Matlack et al., sufficient to direct proteins into the peroxisome matrix, 1998), the mitochondrion (Pfanner et al., 1997), and the the vast majority of peroxisomal matrix proteins utilize the nucleus (Mattaj and Englmeier, 1998). However, the pro- COOH-terminal PTS1 rather than the NH2-terminal PTS2 cess of peroxisomal protein import does not conform to (Subramani, 1993). These signals are recognized by PEX5 any of these paradigms (Subramani, 1993): proteins are and PEX7, the physical receptors for the PTS1 and PTS2, posttranslationally imported into the peroxisome but co- respectively (McCollum et al., 1993; Marzioch et al., 1994; translationally inserted into the ER; peroxisomes can im- Distel et al., 1996). In contrast, integral peroxisomal mem- brane proteins (PMPs)1 do not use either PTS1 or PTS2

Address correspondence to Dr. Stephen J. Gould, Department of Biologi- cal Chemistry, The Johns Hopkins University School of Medicine, 725 1. Abbreviations used in this paper: MBP, maltose-binding protein; ORF, North Wolfe Street, Baltimore, MD 21205. Tel.: (410) 955-3424/3085. Fax: open reading frame; PBD, peroxisome biogenesis disorder; PMP, peroxi- (410) 955-0215. E-mail: [email protected] somal membrane protein.

 The Rockefeller University Press, 0021-9525/99/11/761/13 $5.00 The Journal of Cell Biology, Volume 147, Number 4, November 15, 1999 761Ð773 http://www.jcb.org 761

motifs for targeting and are efficiently imported into per- PBD patients and nine of the eleven known PBD comple- oxisomes independently of PEX5 and PEX7 (Subramani, mentation groups. These include PEX1 (Portsteffen et al., 1993; Dyer et al., 1996; Chang et al., 1999). 1997; Reuber et al., 1997), PEX2 (Shimozawa et al., 1992), Current models of peroxisomal matrix protein import PEX5 (Dodt et al., 1995), PEX6 (Fukuda et al., 1996; are heavily influenced by the fact that PEX5 is a predomi- Yahraus et al., 1996), PEX10 (Okumoto et al., 1998a; nantly cytoplasmic protein in several species (Dodt et al., Warren et al., 1998), PEX12 (Chang et al., 1997; Okumoto 1995; Wiemer et al., 1995; Elgersma et al., 1996; Gould et al., 1998b), PEX13 (Liu et al., 1999; Shimozawa et al., et al., 1996) and appears to cycle between the cytoplasm 1999), PEX16 (Honsho et al., 1998; South and Gould, and peroxisomes in mammalian cells (Dodt and Gould, 1999), and PEX19 (Matsuzono et al., 1999). Variations in 1996). The dynamic distribution of the PTS1 receptor the clinical and cellular phenotypes within the Zellweger implies that peroxisomal matrix protein import involves spectrum are related primarily to the severity of the af- overlapping cytoplasmic and peroxisomal events in addi- fected alleles, with mild phenotypes arising from PEX tion to the actual translocation process (Braverman et al., mutations that only partially reduce PEX gene func- 1995; Rachubinski and Subramani, 1995). Before translo- tion (Reuber et al., 1997; Chang and Gould, 1998; Col- cation, import of PTS1-containing proteins (ligands) is lins and Gould, 1999). In contrast to the Zellweger spec- likely to involve recognition by PEX5 in the cytoplasm, trum of diseases, rhizomelic chondrodysplasia punctata is followed by transport of the receptor–ligand complex to caused by mutations in PEX7, which encodes the PTS2 re- the peroxisome surface and binding of the receptor–ligand ceptor (Braverman et al., 1997; Motley et al., 1997; Purdue complex to docking factors on the peroxisome membrane. et al., 1997). After ligand translocation, additional factors are thought We initially identified PEX12 in the yeast Pichia pas- to mediate the recycling of PEX5 back to the cytoplasm. toris as a gene that is required for normal peroxisome bio- PEX14, PEX13, and PEX17 have been implicated in re- genesis (Kalish et al., 1996). More recent studies have de- ceptor docking (Elgersma et al., 1996; Erdmann and Blo- scribed the human homologue of this gene and reported Downloaded from bel, 1996; Gould et al., 1996; Albertini et al., 1997; Huhse that mutations in PEX12 are responsible for complemen- et al., 1998; Girzalsky et al., 1999), and PEX4 has been re- tation group 3 of the PBDs (Chang et al., 1997; Okumoto ported to act in the recycling of PEX5 from the peroxi- and Fujiki, 1997; Chang and Gould, 1998; Okumoto et al., some to the cytoplasm (van der Klei et al., 1998). Other 1998b). Both yeast and human PEX12 encode an integral PEX genes such as PEX1 (Portsteffen et al., 1997; Reuber peroxisomal membrane protein with a zinc ring motif at its

et al., 1997; Chang et al., 1999), PEX2 (Shimozawa et al., COOH terminus (Kalish et al., 1996; Okumoto and Fujiki, jcb.rupress.org 1992; Chang et al., 1999), PEX6 (Yahraus et al., 1996; 1997). These studies also established that PEX12 spans the Chang et al., 1999), PEX10 (Kalish et al., 1995; Warren et al., peroxisome membrane twice and extends its NH2 and 1998; Chang et al., 1999), and PEX12 (Kalish et al., 1996; COOH termini into the cytoplasm. In this report, we in- Chang et al., 1997; Chang and Gould, 1998; Chang et al., vestigate the function of human PEX12 in peroxisome bio- 1999) have also been implicated in peroxisomal matrix genesis. We find that PEX12 interacts with PEX5 and protein import. However, their roles in matrix protein im- PEX10 via its COOH-terminal zinc-binding domain, that on November 7, 2017 port are only poorly understood and other reports have these interactions are biologically significant, and that suggested that PEX1 and PEX6 may instead participate in PEX12 and PEX10 participate in an aspect of peroxisomal the biogenesis of peroxisome membranes (Erdmann et al., matrix protein import that occurs downstream of receptor 1991; Spong and Subramani, 1993; Heyman et al., 1994; docking. Titorenko et al., 1997; Faber et al., 1998; Titorenko and Rachubinski, 1998a,b). Although most PEX genes were originally identified in Materials and Methods yeast, our understanding of peroxisome biogenesis has also been advanced by the analysis of this process in hu- Cell Lines, Transfections, and mans and how it is disrupted in the peroxisome biogenesis Indirect Immunofluorescence disorders (PBDs) (Lazarow and Moser, 1995). Zellweger Skin fibroblast cell lines from patients with peroxisome biogenesis disor- syndrome, neonatal , and infantile ders are referred to by their PBD numbers and were cultured in complete Refsum disease represent a phenotypic continuum of dis- medium (DME supplemented with 10% FBS and penicillin/streptomy- eases within the PBDs that we refer to as the Zellweger cin). Transfections were performed by electroporation using the protocol spectrum. Their clinical phenotypes include developmen- outlined by Chang et al. (1997) and were processed 2 d later for immuno- fluorescence. Immunofluorescence experiments were performed essen- tal delay, multiple neural, hepatic, and renal defects, and tially as described (Slawecki et al., 1995). In brief, cells were grown on pronounced mental retardation. These clinical phenotypes cover glasses, fixed, permeabilized, washed, incubated with the primary are most severe in Zellweger syndrome patients, who antibodies, washed extensively, incubated with the secondary antibodies, rarely survive their first year, are milder in neonatal adre- washed extensively, and then mounted on glass slides. Standard permeabi- noleukodystrophy, and even less pronounced in infantile lization was for 5 min with 1% Triton X-100, which permeabilizes both plasma and peroxisome membranes. Differential permeabilization was for Refsum disease. At the cellular level, virtually all Zell- 2–4 min with 25 ␮g/ml digitonin, which permeabilizes the plasma mem- weger spectrum patients display defects in the import of brane but does not permeabilize the peroxisome membrane. Hence, only both PTS1 and PTS2 proteins, though there are rare pa- cytoplasmically exposed antigens can be detected under these conditions. tients who are defective only in PTS1 protein import Differential permeabilization experiments were generally performed with additional controls to ensure that the incubation in digitonin had not per- (Slawecki et al., 1995). There is significant genetic hetero- meabilized any intracellular membranes. Rabbit polyclonal antibodies geneity within the Zellweger spectrum and recent studies against the PTS1 tripeptide ser-lys-leu-COOH have been described have identified the genes that are mutated in Ͼ95% of (Gould et al., 1990) and the anti-human PEX5 antibodies were generated

The Journal of Cell Biology, Volume 147, 1999 762

Table I. Sequence of Primers Used in this Article SmaI and BglII sites of pGAD424, downstream of and in-frame with the GAL4 transcription activation domain. The resulting plasmid, Chang-10 5Ј-CCCGGATCCGTTCTCAGGGGAGTAGAGTTTA- pGAD424-PEX5S, encodes a fusion between the GAL4 activation do- ATC-3Ј main and full-length PEX5S. The plasmid pGAD424-PEX5L was created Chang-17 5Ј-AAAATCGTTTCCAGCGGG-3Ј by cleaving pPEX5L (Braverman et al., 1998) with NcoI, making the ends Chang-20 5Ј-CCAGGATCCGTGAGGATAAGACATGATTCCC-3Ј blunt with the Klenow fragment of DNA PolI and dNTPs, cleaving this Chang-21 5Ј-CAAGGTACCAAGTGAAAGCCAGTACACGCAG-3Ј DNA with BglII, isolating the resulting 2-kb PEX5L fragment, and insert- Chang-24 5Ј-CACAAGTCTCAGAGATTGGC-3Ј ing it between the SmaI and BglII sites of pGAD424. The plasmid pGAD424-PEX5S/⌬N encodes a fusion protein between the GAL4 tran- Chang-30 5Ј-ATGATGCAGCAACCAGCCAG-3Ј scriptional activation domain and the COOH-terminal 317 amino acids of 10.2HC5Ј 5Ј-CCCGTCGACGAGGCAGCGGCAGCGAGCCAGG-3Ј PEX5. It was created by excising the NH2 terminally truncated PEX5 10.2H3Ј 5Ј-CCAAGCGGCCGCCGTAGAGGTCATCTGTGTCC-3Ј fragment from pGD105 (Dodt et al., 1995) with NcoI (after which the 12.2HC5Ј 5Ј-CCCGTCGACGCAGTTCCTTGACTGGTGGTCC-3Ј ends were made blunt with the Klenow fragment of DNA PolI and 12.2H3Ј 5Ј-CCAAGCGGCCGCTCAGTTCTCAGGGGAGTAGAG-3Ј dNTPs) and BglII and inserting the resulting 1-kb PEX5 fragment be- 14.2H5Ј 5Ј-CCCGTCGACGGCGTCCTCGGAGCAGGCAGAG- tween the SmaI and BglII sites of pGAD424. CAG-3Ј Bacterial expression vectors were based on a derivative of pMAL-c2 14.2H3Ј 5Ј-CCAAGCGGCCGCAGCTCCTCCTCCACTGAG-3Ј (New England Biolabs Inc.), pMBP differs from pMAL-c2 in that it con- tains a SalI site downstream of the EcoRI site (GAATTCAAGTCGAC, EcoRI and SalI sites underlined), and a NotI site upstream of the HindIII site (GCGGCCGCAAGCTT, NotI and HindII sites underlined). pMBP- against bacterially expressed forms of the protein. Mouse mAbs against PEX12C was created by excising the PEX12 SalI-NotI fragment from the c-myc epitope were obtained from the tissue culture supernatant of pJL59-PEX12C and inserting it between the SalI and NotI sites of pMBP. the hybridoma 1-9E10 (Evan et al., 1985). Rabbit polyclonal antibodies pMBP-PEX12C/S320F was created by excising the PEX12 SalI-NotI frag- against c-myc, sheep anti-human antibodies, and fluorescently la- ment from pJL59-PEX12C/S320F and inserting it between the SalI and beled secondary antibodies were obtained from commercial sources. NotI sites of pMBP. All mammalian expression vectors are based on pcDNA3 (Invitrogen Mutation Detection Corp.). We have previously described the expression vectors pcDNA3- PEX5S (pGD100; Dodt et al., 1995), pcDNA3-PEX5L (pPEX5L; Braver- Downloaded from We previously described a mutation detection strategy for human PEX12 man et al., 1998), pcDNA3-PEX10 (Warren et al., 1998), and pcDNA3- (Chang et al., 1997; Chang and Gould, 1998). In brief, the entire 2.3-kb PEX12 (Chang et al., 1997). To create pcDNA3-PEX12/3xmyc, the PEX12 gene was amplified from the total human genomic DNA using the PEX12 ORF was amplified using the oligonucleotides Chang-21 and primers Chang-21 and Chang-20 (Table I). The coding regions and intron/ Chang-10 (Table I) and pcDNA3-PEX12 as a template. These primers ap- exon junctions were sequenced directly from the PCR product using the pend an Asp718 site upstream of the ORF and replace the stop codon primers used for amplification as well as several additional gene specific with a BamHI site. The resulting PCR fragment was cleaved with Asp718 primers (Table I, Chang-17, Chang-24, and Chang-30). Total genomic and BamHI and cloned upstream of the triple c-myc tag in pcDNA3- DNA was isolated from PBD054 cells using the PureGene kit (Gentra 3xmyc (Geisbrecht et al., 1998). To create the plasmid pcDNA3-PEX12/ jcb.rupress.org Systems, Inc.). S320F, we first amplified the PEX12 ORF from PBD054 cDNA. Total RNA was extracted from PBD054 cells using the PureScript kit (Gentra Plasmids Systems, Inc.) and PEX12 cDNA was synthesized as described (Chang and Gould, 1998). The PEX12 ORF was amplified from the first strand Most of the plasmids used for yeast two-hybrid studies were based on PBD054 PEX12 cDNA using the primers Chang-21 and Chang-20 (Table pPC62, a LEU2-based GAL4 DNA–binding domain fusion protein ex-

I), cleaved with Asp718 and BamHI, and cloned between the Asp718 and on November 7, 2017 pression vector and pPC86, a TRP1-based GAL4 transcriptional activa- BamHI sites of pcDNA3, generating pcDNA3-PEX12/S320F. The se- tion domain (AD) fusion protein expression vector (Chevray and quence of the final plasmid was confirmed to ensure the presence of the Nathans, 1992). These plasmids contain two PvuI sites in symmetric posi- S320F mutation and the absence of any undesired mutations. The plasmid tions, and the PvuI fragments of these plasmids were switched to create pcDNA3-3xHA has a 114-bp DNA insert between the Asp718 and XbaI pJL59 (Vidal et al., 1996) and pPC86/L2. The plasmid pJL59 is identical to sites of pcDNA3, which contains a BglII site (AGATCT) immediately up- pPC62 except that it contains the TRP1 gene in place of the LEU2 gene, stream of short ORF encoding three repeats of the HA epitope tag and pPC86/L2 is identical to pPC86 except that it contains the LEU2 gene (GRIFYPYDVPDYAGYPYDVPDYAGSYPYDVPDYALSTOP, the HA in place of the TRP1 gene. The plasmid pGAD424 (CLONTECH Labo- epitopes are underlined). To create pcDNA3-PEX10/3xHA, we excised ratories) was also used for expression of some GAL4-AD fusion proteins. the PEX10 ORF (lacking its stop codon) from pcDNA-PEX10myc (War- The plasmid pJL59-PEX12C was created by amplifying a subregion of ren et al., 1998) using the restriction enzymes Asp718 and BamHI, excised PEX12 using the primers 12.2HC5Ј and 12.2H3Ј (Table I) and pcDNA3- the 3xHA tag from pcDNA3-3xHA by cleavage with BglII and XbaI, and PEX12 as the template (Chang et al., 1997), cleaving the resulting 370-bp inserted these fragments in tandem between the Asp718 and XbaI sites of product with SalI and NotI, and inserting this fragment between the SalI pcDNA3. and NotI sites of pJL59. This plasmid is designed to express a fusion be- The regions of all plasmids that were generated by PCR were se- tween the GAL4 DNA–binding domain and amino acids 260–359 of hu- quenced to confirm the absence of any unintended mutations. Any plas- man PEX12. The plasmid pJL59-PEX12C/S320F was created using the mids that did contain undesired mutations were discarded and additional same cloning strategy except that pcDNA3-PEX12/S320F (see below) was clones were characterized until one with the desired sequence was ob- used as the template. The plasmid pPC86/L2-PEX10C was created by am- tained. plifying a subregion of PEX10 using the primers 10.2HC5Ј and 10.2H3Ј (Table I) and pcDNA3-PEX10 (Warren et al., 1998) as the template, cleaving the resulting 327-bp product with SalI and NotI, and inserting Two-Hybrid Analysis this fragment between the SalI and NotI sites of pJL59. This plasmid is de- signed to express a fusion between the COOH-terminal 87 amino acids of The Saccharomyces cerevisiae two-hybrid reporter strain BY3168 was human PEX10 and the GAL4 activation domain. The plasmid pPC86/L2- used for all experiments (Vidal et al., 1996). All strains were grown over- PEX14 encodes a fusion between the GAL4 activation domain and full- night on a nitrocellulose filter membrane (Schleicher & Schuell, Inc.) that length PEX14 and was created by amplifying the entire PEX14 open read- was placed on a plate with minimal medium lacking tryptophan and leu- ing frame (ORF) using the primers 14.2H5Ј and 14.2H3Ј (Table I) and cine (Sc-W-L). The cells were lysed by submersion in liquid nitrogen, and total human cDNA as a template, cleaving the resulting product with SalI activity of the two-hybrid reporter gene ␤-galactosidase was assessed by and NotI, and inserting this fragment between the SalI and NotI sites of placing the filter membrane onto a filter paper saturated with 0.1% pPC86/L2. The PEX5 two-hybrid plasmids were created as follows. The 5-bromo-4-chloro-3-indoyl ␤-D-galactopyranoside (X-gal) in 100 mM po- entire PEX5S ORF was excised from plasmid pGD100 (Dodt et al., 1995) tassium phosphate buffer, pH 7.0. The filters were photographed after by cleavage with NcoI, after which the ends were made blunt with the Kle- color development. now fragment of DNA PolI and dNTPs, and then cleavage with BglII. The Protein extracts from BY3168 carrying either pJL59-PEX12C or resulting 2-kb PEX5S fragment was isolated and inserted between the pJL59-PEX12C/S320F were prepared according to established protocols

Chang et al. PEX12 Participates in Peroxisomal Matrix Protein Import 763 (Adams et al., 1997). In brief, the yeast were grown in 4 ml Sc-W-L me- PEX10/3xHA or pcDNA3-PEX12/3xmyc and pcDNA3-PEX10/3xHA. dium to an OD600 of 2. The cells were transferred to a solution containing After preparation of lysates and immunoprecipitation with anti-myc poly- 50 mM Tris, pH 7.5, and 10 mM sodium azide, and then pelleted by cen- clonal antibodies, levels of PEX10/3xHA were determined by immuno- trifugation (5,000 g) for 10 min. The pellets were resuspended in 30 ␮l of blot using the 12CA5 monoclonal anti–HA antibody (Boehringer Mann- ESB (80 mM Tris, pH 6.8, 1.5% DTT, 2% SDS, 10% glycerol, and 0.1 mg/ml heim Corp.). Equivalent levels of PEX5 and PEX10/3xHA in the crude bromophenol blue), and immediately boiled for 3 min. The tubes were lysates were confirmed by standard immunoblotting techniques. cooled on ice, and then mixed vigorously with 0.1 g of 425–600-micron glass beads (Sigma Chemical Co.) for 2 min to lyse the cells. The resulting Cell Fractionation and Protease Protection Assay lysates were added to an additional 70 ␮l of ESB and boiled for 1 min. Equal amounts of each sample were separated by SDS-PAGE, trans- Skin fibroblast cells were grown to 90% confluency in 100-mm dishes, re- ferred to Immobilon-P membranes (Millipore), and probed with antibod- moved from the plate by trypsinization, washed, resuspended in lysis ies raised against the COOH-terminal 17 amino acids of human PEX12 (a buffer, and lysed in a ball bearing homogenizer as previously described segment that is not present in yeast PEX12). (Dodt and Gould, 1996). Postnuclear supernatants were prepared by suc- cessive 1,500 g spins, and then separated into organelle pellets and cytoso- lic supernatants by centrifugation at 15,000 g for 10 min. To determine the Protein Purification, In Vitro Translation of Proteins relative levels of PEX5 in the cytoplasm and peroxisome of human fibro- and Overlay Assays blasts, organelle pellets and cytosolic supernatants were prepared as above, transferred to membranes, and probed with polyclonal anti–PEX5 A 1-liter culture of DH10B cells (Grant et al., 1990) carrying pMBP- antibodies. For protease protection experiments, organelle preparations PEX12C was grown to an OD of 0.4, induced with 1 mM isopro- 600 were derived from PBD006 and PBD054 cells in the same manner and pyl-␤-D-thiogalactopyranoside, and grown overnight at 18ЊC. These cells were each split into eight equal fractions of 8 ␮g of protein. Triton X-100 were harvested and resuspended in column buffer (20 mM Tris, pH 7.4, was added to four of the eight tubes to a final concentration of 1%. We 200 mM NaCl, 1 mM EDTA, and 10 mM ␤-mercaptoethanol) plus 0.5 mg/ placed the samples on ice and added 0, 15, 30, or 60 ␮g of a trypsin prepa- ml lysozyme. The cells were frozen in liquid nitrogen, thawed, and lysed ration (Calbiochem-Novabiochem) to the four samples lacking detergent by sonication. The lysate was centrifuged for 20 min at 14,000 g, and the and the four samples containing detergent. These mixtures were incu- supernatant was loaded onto a column containing 10 ml of amylose resin. bated on ice for 20 min. Reactions were terminated by adding a twofold The column was washed with 12-bed volumes of column buffer and the excess of bovine trypsin inhibitor (Sigma Chemical Co.). Equal amounts protein was eluted with 10 mM maltose. The eluant was collected in 1.5-ml Downloaded from of each sample were processed for immunoblot with anti–PEX5 anti- fractions and the purity was assessed using SDS-PAGE. MBP-PEX12C/ bodies. S320F and MBP-LacZ␣ fusion proteins were purified following the same protocol. Filter binding experiments were performed as follows. 10 ␮g of purified Results MBP-PEX12C and 10 ␮g of MBP-LacZ␣ were spotted separately onto Immobilon-P membranes (Millipore). Two identical membranes were prepared, one for overlay with HsPEX5S and one for HsPEX5L. The The Zinc-binding Domain Is Required for

membranes were allowed to dry for 15 min at room temperature, and then PEX12 Function jcb.rupress.org washed in methanol for 30 s followed by Milli-Q H2O for 1 min. The mem- branes were transferred to buffer A (50 mM Tris-HCl, pH 7.5, 100 mM We have identified an array of PEX12 mutations that potassium acetate, 150 mM NaCl, 1 mM DTT, 5 mM MgCl2, 1 mM cause Zellweger syndrome and the milder phenotypic EDTA, 0.3% [vol/vol] Tween 20, 100 ␮M ZnCl2, 5% [wt/vol] nonfat milk, variants of neonatal adrenoleukodystrophy and infantile and 100 mM methionine; Fransen et al., 1998) and incubated with shaking for 1 h at room temperature. Radiolabled HsPEX5S and HsPEX5L were Refsum disease (Chang et al., 1997; Chang and Gould, made using the TNT T7-Quick Coupled in vitro transcription/translation 1998). To better understand the regions of PEX12 that are on November 7, 2017 kit (Promega Corp.) and [35S]methionine (NEN Life Science Products) important for its role in peroxisome biogenesis, we com- according to the manufacturer’s protocols. 20 ␮l of the in vitro transcrip- pared the deduced products of the PEX12 alleles in se- tion/translation reaction was mixed with 5 ml of buffer A plus 10 ␮g/ml verely and mildly affected patients (Fig. 1). Severe defects BSA and incubated with the membrane for 1 h at 37ЊC with shaking. The membranes were washed twice for 5 min at room temperature with buffer in PEX12 activity were associated with mutations that A, dried, and placed on film. truncated PEX12 upstream of the cytoplasmically exposed For assessing the PEX10-PEX12 interaction, 10 ␮g of purified MBP- zinc ring domain. Furthermore, all moderately and mildly PEX12C and 10 ␮g of MBP-LacZ␣ were separated by SDS-PAGE and affected patients expressed at least one PEX12 allele ca- transferred to Immobilon-P membranes. After transfer, the proteins were renatured for 2 h at 4ЊC in buffer A. Radiolabeled PEX10 was synthesized pable of encoding a protein that contained the COOH-ter- using the TNT T7-Quick Coupled system and [35S]methionine as de- minal zinc ring domain. This phenotype–genotype corre- scribed above. The membranes were incubated overnight at 4ЊC with lation suggested that the COOH-terminal zinc-binding shaking in 5 ml of buffer A containing 25 ␮l of the in vitro transcription/ domain is critical for PEX12 function. This hypothesis is translation reaction. After washing twice with buffer A at room tempera- also supported by the results from directed mutagenesis ture, the membranes were dried, and bound [35S]PEX10 was detected by autoradiography. experiments on PEX12 in both yeast (Kalish et al., 1996) and mammalian cells (Okumoto et al., 1998b). Immunoprecipitations PEX12 Binds PEX5, the PTS1 Receptor Normal human skin fibroblasts were transfected with pcDNA3-PEX12 and pcDNA3-PEX12/3xmyc. 2 d after transfection, cell lysates were pre- Previous studies have suggested that zinc ring domains pared from each of the transfected populations by scraping the cells into may mediate protein–protein interactions (Borden, 1998), TBSN buffer (10 mM Tris, pH 7.8, 150 mM NaCl, 1% NP-40, 5 mM benz- and the important role of this domain in PEX12 suggested amidine, 0.2 mg/ml NaF, 25 ␮g/ml aprotinin, and 62.5 ␮g/ml leupeptin). that it may mediate interactions between PEX12 and Each cell lysate was mixed with 1 ␮g of rabbit polyclonal antibodies against c-myc (Santa Cruz Biotechnology) for 1 h at 4ЊC. Protein A aga- other proteins that are involved in peroxisome biogenesis. rose beads were preincubated with 1% BSA, and then incubated with the We employed the yeast two-hybrid system to search for lysate–antibody mixture for 1 h at 4ЊC with gentle agitation. The agarose such proteins. A fusion between the GAL4 DNA–bind- beads were collected by centrifugation (1,000 g), washed four times with ing domain and the COOH-terminal 100 amino acids of 1 ml of TBSN buffer, and resuspended in 30 ␮l SDS-PAGE sample buffer. Equal amounts of each sample were immunoblotted using anti–PEX5 an- PEX12 was used as bait to screen a library of fusions be- tibodies. For assessing the coimmunoprecipitation between PEX10 and tween the GAL4-activating domain and all known human PEX12, cells were cotransfected with pcDNA3-PEX12 and pcDNA3- peroxins. We detected a strong interaction between the

The Journal of Cell Biology, Volume 147, 1999 764 Figure 1. The deduced PEX12 products of seven PBD patients. The diagram shows the predicted protein product of each PEX12 allele. The zinc ring domain is indicated by a black box and each of two transmembrane domains is indicated by the cross-hatched boxes. Straight lines show the length of additional amino acids that are ap- pended as a result of frameshifting mutations. ZS, Zellweger syndrome; NALD, neonatal adre- noleukodystrophy; and IRD, infantile Refsum disease. zinc-binding domain of PEX12 and PEX5, the PTS1 re- Fransen et al., 1998; Schliebs et al., 1999) (Fig. 2 D). The ceptor (Fig. 2 A). Recent studies (Braverman et al., 1998; PTS1 binding site of PEX5 is contained within its COOH- Downloaded from Otera et al., 1998) have established that two isoforms of terminal half, a region that contains seven tetratricopep- PEX5, PEX5S and PEX5L, are synthesized in roughly tide repeats (Dodt et al., 1995; Terlecky et al., 1995). A equivalent levels in human cells, but we did not observe fragment of PEX5 containing little more than the PTS1- any difference in the interaction between PEX12 and binding domain of PEX5 retained full binding to PEX12. PEX5S or PEX5L. However, it was unable to bind PEX14, as expected from

Next, we used a protein binding assay to independently the recent study by Schliebs et al. (1999) in which the jcb.rupress.org assess the interaction between PEX12 and PEX5. We gen- PEX14 binding sites were localized to the NH2-terminal erated a recombinant fusion protein between maltose- half of PEX5. Additional truncation mutants failed to de- binding protein (MBP) and the COOH-terminal 100 fine a smaller PEX12-binding site within PEX5 (data not amino acids of PEX12, which includes its zinc-binding do- shown). main. The resulting protein, MBP-PEX12, was tested for its ability to bind PEX5 using a filter binding assay. Equal on November 7, 2017 amounts of purified MBP-PEX12 and an MBP-LacZ␣ fu- sion protein were spotted onto membranes and subse- The Zinc-binding Domain of PEX12 Binds PEX10 quently probed with 35S-labeled PEX5 that had been syn- In addition to the interaction between PEX12 and PEX5, thesized in vitro in a rabbit reticulocyte lysate. PEX5 was the yeast two-hybrid screen also revealed an interaction bound by MBP-PEX12 but not by MBP-LacZ␣, indicating between PEX12 and PEX10, an integral PMP that is re- that PEX12 was capable of binding PEX5 (Fig. 2 B). quired for peroxisomal matrix protein import (Fig. 3 A). To determine whether the physical interaction between Like PEX12, human PEX10 contains a cytoplasmically ex- PEX5 and the zinc-binding domain of PEX12 reflected an posed zinc ring domain (Warren et al., 1998) and the inter- association between these proteins in vivo, we tested action we detected between these two proteins was medi- whether PEX12 and PEX5 formed a complex of sufficient ated through their COOH-terminal zinc ring domains stability to withstand coimmunoprecipitation from cell ly- (amino acids 240–326 of PEX10 and 260–359 of PEX12). sates. Human fibroblasts were transfected with either Independent biochemical evidence for physical interaction of two plasmids, pcDNA3-PEX12 or pcDNA3-PEX12/ between PEX12 and PEX10 was obtained using blot over- 3xmyc. 2 d after transfection the cells were lysed, the ly- lay experiments. Equal amounts of purified, recombinant sates were subjected to immunoprecipitation with anti- MBP-PEX12 and MBP-LacZ␣ were resolved by SDS- myc polyclonal antibodies, and the immunoprecipitates PAGE, immobilized on membranes, and probed with were separated by SDS-PAGE and probed with anti– 35S-labeled PEX10 that had been synthesized in vitro in PEX5 antibodies. Equal amounts of PEX5 were present rabbit reticulocytes (Fig. 3 B). PEX10 was bound by the in both crude lysates, but PEX5 was immunoprecipitated MBP-PEX12 fusion protein but not by MBP-LacZ␣, sug- only from the lysate of cells expressing PEX12/3xmyc gesting specific binding between PEX12 and PEX10. To (Fig. 2 C). assess whether these proteins were present in a complex We next mapped the PEX12-binding domain of PEX5 in vivo, we transfected normal human fibroblasts with by expressing different regions of PEX5 in the yeast two- plasmids designed to express tagged forms of these pro- hybrid system and assaying their interaction with the teins, PEX12/3xmyc and PEX10/HA, or PEX10/HA and PEX12 zinc-binding domain. These fragments of PEX5 an untagged version of PEX12. 2 d after transfection, ly- were also assayed for their ability to interact with PEX14, sates were prepared from the two sets of transfected a known docking factor for PEX5 (Albertini et al., 1997; cells, subjected to immunoprecipitation using an anti-myc

Chang et al. PEX12 Participates in Peroxisomal Matrix Protein Import 765 Figure 2. PEX12 interacts with PEX5. (A) Re- sults of two-hybrid studies between PEX12 and PEX5. Two-hybrid reporter strains expressing the indicated fusion proteins were transferred to a nitrocellulose filter, submerged in liquid nitro- gen to lyse the cells, and assayed for ␤-galactosi- dase activity. AD, GAL4 activation domain; and BD, GAL4-binding domain. (B) Filter binding experiments with PEX12 and PEX5. Equal amounts of MBP-LacZ␣ and MBP-PEX12C were spotted on membranes and probed with [35S]PEX5S (upper panel) or [35S]PEX5L (lower panel). (C) PEX5 coimmunoprecipitates with PEX12/3xmyc. Lysates were prepared from fi- broblasts that had been transfected with either pcDNA3-PEX12 or pcDNA3-PEX12/3xmyc. After immunoprecipitation with anti–myc anti- bodies, the immunoprecipitates were analyzed by immunoblot with anti-PEX5 antibodies (up- per panel). In addition, equal amounts of the crude lysate before immunoprecipitation were assayed for PEX5 levels by immunoblot (lower panel). (D) PEX12 interacts with the PTS1-bind- ing domain of PEX5. Two-hybrid reporter strains expressing the indicated fusion proteins Downloaded from were transferred to a nitrocellulose filter, sub- merged in liquid nitrogen to lyse the cells, and assayed for ␤-galactosidase activity. polyclonal antibody, and then blotted with a monoclonal ing PEX12/3xmyc. Thus, PEX12 and PEX10 do appear to anti–HA antibody. Equivalent amounts of PEX10/HA be present in a complex in vivo (Fig. 3 C). Control experi- jcb.rupress.org were detected in both crude lysates, but PEX10/HA was ments revealed that these tagged forms of PEX12 and only detected in the immunoprecipitate from cells express- PEX10 have normal activity in vivo. This region of PEX12 failed to interact with any of the remaining 12 human per- oxins in the yeast two-hybrid assay. on November 7, 2017 Genetic Interactions between PEX12, PEX10, and PEX5 The simplest explanation for the physical association of PEX12 with both PEX5 and PEX10 is that these interac- tions contribute to the biogenesis of peroxisomes. In such an instance, we might expect that high dosage, allele-spe- cific extragenic suppression could be observed among the

Figure 3. The COOH-terminal domain of PEX12 interacts with the COOH-terminal domain of PEX10 in the yeast two-hybrid system. Two-hybrid reporter strains expressing the indicated fu- sion proteins were transferred to a nitrocellulose filter, sub- merged in liquid nitrogen to lyse the cells, and assayed for ␤-galactosidase activity. AD, GAL4 activation domain; and BD, GAL4-binding domain. (B) PEX10 binds immobilized PEX12C in vitro. 10 ␮g of purified MBP-LacZ␣ and purified MBP- PEX12C were resolved by SDS-PAGE, transferred to mem- branes, and probed with 35S-labeled PEX10 (upper panel). A du- plicate gel was stained before transfer with Coomassie blue (lower panel). (C) Coimmunoprecipitation of PEX10 with PEX12. Lysates from cells cotransfected with either pcDNA3- PEX12 and pcDNA3-PEX10/3xHA (left lane) or pcDNA3- PEX12/3xmyc and pcDNA3-PEX10/3xHA (right lane) were immunoprecipitated with anti–myc antibodies and analyzed by immunoblot with anti–HA antibodies. Aliquots of the crude ly- sates before immunoprecipitation were also assayed for PEX10/ 3xHA levels by immunoblot.

The Journal of Cell Biology, Volume 147, 1999 766 corresponding three genes. Therefore, we tested whether Table II. Suppression of Catalase Import Defect in PBD054 overexpression of any one of these genes could suppress Cells by Overexpression of PEX5 and PEX10 mutations in either of the other two genes. In brief, fibro- Percent relative activity to restore blast cell lines with mild or severe mutations in PEX12, PEX gene catalase import in PBD054 cells* PEX10, or PEX5 were transfected separately with expres- HsPEX12 100 sion vectors designed to express these genes, as well as a HsPEX10 40 Ϯ 7 vector control. 2 d later, each cell population was pro- HsPEX5S 19 Ϯ 9 cessed for indirect immunofluorescence using antibodies HsPEX5L 13 Ϯ 3 specific for a peroxisomal matrix protein marker, catalase. The relative rescue activity of each gene in each cell line *n ϭ 3. was calculated by comparing the frequency of cells import- ing catalase in each set of transfected cells. All three patients from complementation group 2 of all six available CG7 patients for our studies. Expression the PBDs have mutations in PEX5 (Dodt et al., 1995; of PEX10 rescued peroxisomal matrix protein import in Slawecki et al., 1995). Two of these patients (PBD018 and all six CG7 cell lines, whereas PEX12 and PEX5 failed to PBD093) are homozygous for a PEX5-N489K/N526K mu- have any effect on the cytosolic catalase distribution in tation (N489/N586 refers to the position of this asparagine five of these cell lines. However, expression of PEX12 in PEX5S and PEX5L, respectively). The other PEX5- clearly led to the restoration of catalase import in PBD054 deficient patient, PBD005, is homozygous for a PEX5 non- cells (Fig. 4, A–F). Expression of PEX5 also rescued per- sense mutation, R390ter/R427ter, which inactivates PEX5. oxisomal matrix protein import in this cell line, though to a PBD018 and PBD005 cells were transfected with the plas- lesser extent (Table II). mids pcDNA3, pcDNA3-PEX5, pcDNA3-PEX12, and To better understand the molecular basis of the appar- pcDNA3-PEX10, incubated for 2 d, and then processed ent suppression of PEX10 allele(s) by overexpression of Downloaded from for immunofluorescence using antibodies specific for per- PEX12 or PEX5, we sequenced the PEX10 gene from oxisomal catalase. Although expression of PEX5 effi- PBD054 cells. Surprisingly, we failed to detect any alter- ciently rescued catalase import in both cell lines, PEX12 ation to the gene in this patient. This result, combined with and PEX10 were unable to restore catalase import in the fact that PEX12 was more effective than PEX10 at these lines (data not shown). rescuing peroxisomal protein import in PBD054 cells (Ta-

We have also characterized eight complementation ble II), led us to consider whether PEX12, rather than jcb.rupress.org group 3 PBD patients, all of whom are mutated in PEX12 PEX10, might be mutated in PBD054. The PEX12 gene (Chang et al., 1997; Chang and Gould, 1998). Fibroblast was amplified from PBD054 genomic DNA and all coding cell lines from each of these patients were transfected with portions of the gene were sequenced directly from the the above vectors, and the import of peroxisomal matrix PCR products. We detected a missense mutation, S320F, proteins was determined in each population of transfected in the PEX12 gene from this patient and no evidence of cells. As expected, pcDNA3-PEX12 efficiently rescued the wild-type sequence, suggesting that this patient was on November 7, 2017 the peroxisomal protein import defects in all of these cell homozygous for this mutation in PEX12 (Fig. 5 A). Al- lines. However, we failed to observe any evidence for ex- though S320 is a conserved residue of PEX12 from yeast tragenic suppression in the CG3 cells that were transfected to humans (always a serine or threonine), missense muta- with the PEX10 or PEX5 expression vectors (data not tions may be silent. We engineered the S320F mutation shown). into the PEX12 expression vector and used a functional Our previous work has established that PEX10 is the complementation assay (Chang et al., 1997; Chang and gene defective in two patients from complementation Gould, 1998) to assess the effects of this mutation. PEX12- group 7 (CG7), PBD052, and PBD100 (Warren et al., deficient cells were transfected with pcDNA3, pcDNA3- 1998). Although we have yet to identify the PEX10 muta- PEX12, or pcDNA3-PEX12/S320F, and 2 d after transfec- tions in four other CG7 patients, we used fibroblasts from tion the percentage of cells importing matrix proteins into

Figure 4. Peroxisomal protein import in PBD054 cells is re- stored by expression of PEX10 or PEX12. PBD054 cells were transfected with pcDNA3 (A and D), pcDNA3-PEX10 (B and E), or pcDNA3-PEX12 (C and F). 2 d after transfection, the cells were fixed, permeabilized with Triton X-100, and pro- cessed for double indirect immu- nofluorescence using anticata- lase antibodies (A–C) and anti–PMP70 antibodies (D–F). Bar, 25 ␮m.

Chang et al. PEX12 Participates in Peroxisomal Matrix Protein Import 767 peroxisomes was determined by immunofluorescence us- ing antibodies to the peroxisomal matrix protein catalase. In each of two trials the PEX12/S320F cDNA displayed 10–15% of the rescue activity of the wild-type PEX12 cDNA (data not shown). The fact that the S320F mutation reduced but did not eliminate PEX12 function was consis- tent with the relatively mild cellular and clinical pheno- types of this patient (PBD054 was diagnosed with neo- natal adrenoleukodystrophy, and a previous study has demonstrated that PBD054 cells are able to import small amounts of some peroxisomal matrix proteins [Dodt and Gould, 1996]). The ability of PEX10 and PEX5 to suppress the PEX12/ S320F mutation was a clear example of allele-specific sup- pression rather than bypass suppression since neither PEX10 nor PEX5 were capable of rescuing peroxisomal protein import in any cells with severe mutations in PEX12. This finding, together with the fact that the PEX12-S320F mutation lies within the zinc-binding do- main of PEX12, suggested that this mutation might reduce the interaction between the zinc ring domain of PEX12 and either PEX10 or PEX5. Using the two-hybrid assay and the blot overlay assay, we observed that the S320F Downloaded from mutation led to a marked reduction in the PEX12–PEX10 interaction (Fig. 5 B). Similarly, the PEX12/S320F muta- tion appeared to reduce the interaction between PEX12 and PEX5 in the yeast two-hybrid assay (Fig. 5 C). It is in- teresting to note that the placement of PBD054 cells into

CG7 of the PBDs was based upon its noncomplementa- jcb.rupress.org tion with PBD052 cells. PBD052 cells are mutated in PEX10 and express one allele with a missense mutation (H290Q) in the PEX10 zinc-binding domain (Warren et al., 1998). These results indicate that the combination of the PEX12/S320F and PEX10/H290Q alleles may have a dele- terious effect on peroxisomal matrix protein import even on November 7, 2017 in the presence of normal alleles of each gene.

PEX12 Appears to Act Downstream of Receptor Docking Figure 5. PBD054 is mutated in PEX12. (A) Sequence chro- A variety of earlier studies have established that loss of matographs of PEX12 genomic DNA showing the wild-type se- quence (top) and PBD054 sequence (bottom) in the region cor- PEX12 or PEX10 results in a severe defect in peroxisomal responding to nucleotides 950–968 of the PEX12 ORF. Note the matrix protein import (Kalish et al., 1995; Liu et al., 1995; C to T transition mutation, S320F, which changes the serine Slawecki et al., 1995; Kalish et al., 1996; Chang et al., 1997; codon TCT to the phenylalanine codon TTT (underlined). (B) Okumoto et al., 1998a,b; Warren et al., 1998). It is also The S320F mutation attenuates the interaction between PEX12 known that PEX12 and PEX10 are not required for syn- and PEX10. Two-hybrid reporter strains expressing the indicated thesis of peroxisome membranes or import of peroxisomal fusion proteins were assayed for ␤-galactosidase activity (top). membrane proteins (Kalish et al., 1995, 1996; Chang et al., To assess the effects of this mutation by blot overlay assay, puri- 1997, 1999; Chang and Gould, 1998; Warren et al., 1998). fied MBP-LacZ␣, MBP-PEX12C/S320F, and MBP-PEX12C Furthermore, the morphological abnormalities that have were separated by SDS-PAGE, transferred to membranes, and been reported for peroxisomes in cells lacking PEX12 or probed with 35S-labeled PEX10 (upper half of lower panel). These proteins were also separated by SDS-PAGE and stained PEX10 are indistinguishable from those of peroxisomes in with Coomassie blue (lower half of lower panel). (C) The S320F PEX5-deficient cells and appear to be a secondary effect mutation attenuates the PEX12-PEX5 interaction in the yeast of the metabolic deficiencies that are caused by the matrix two-hybrid assay. Two-hybrid reporter strains expressing the protein import defects in these cells (Baes et al., 1997; listed proteins were assayed for ␤-galactosidase activity (top). Chang et al., 1999). These results, together with our obser- The three strains expressing AD-5S were also lysed and assayed vation that PEX12 interacts with both PEX5 and PEX10, for BD-PEX12 levels by immunoblot with anti–PEX12 antibodies. suggest that PEX12 and PEX10 participate in peroxisomal matrix protein import. Current models suggest that there may be several steps of peroxisomal matrix protein import that are limited to the peroxisome membrane and could, therefore, involve

The Journal of Cell Biology, Volume 147, 1999 768 and pex10 mutants than in wild-type cells (Fig. 6, B–G). These results argue against roles for PEX12 and PEX10 in PEX5 docking and suggest that they participate in a downstream step of peroxisomal matrix protein im- port.

A Missense Mutation in PEX12 Results in PEX5 Import Taken together, the properties of PEX12 indicate that it may participate in peroxisomal matrix protein transloca- tion rather than receptor docking or recycling (as de- scribed in Discussion, the phenotypes of PEX12-deficient cells are not consistent with a role for PEX12 in receptor recycling). One prediction of this hypothesis is that mild mutations in PEX12 might alter the properties of the per- oxisomal matrix protein translocation apparatus without eliminating translocation altogether. Before our discovery that PBD054 cells are mutated in PEX12, we reported that PBD054 cells import PEX5 into the peroxisome lumen and also import small amounts of some peroxisomal ma- trix proteins into peroxisomes (Dodt and Gould, 1996). We revisited the issue of PEX5 distribution in PBD054 Downloaded from cells and also compared it to the distribution of PEX5 in PBD006 cells. By immunofluorescence studies in which all cellular membranes are permeabilized, both PBD006 and PBD054 cells contain detectable levels of peroxisome- associated PEX5 (Fig. 7, A–D). However, differential per-

meabilization experiments (in which antibodies only have jcb.rupress.org access to cytoplasmically exposed antigens) revealed that cytoplasmically exposed PEX5 could still be detected in Figure 6. PEX12 and PEX10 are not required for PEX5 docking. (A) Postnuclear supernatants were separated into cytosolic su- PBD006 cells but not in PBD054 cells (Fig. 7, E–H). Simi- pernatants (S) and organelle pellets (P). Equal proportions of the lar results were observed in each of three trials. two fractions from each cell line were assayed for PEX5 levels by These differential permeabilization experiments indi- immunoblot. Immunofluorescence experiments were performed cated that PBD006 cells contained more cytoplasmic- on November 7, 2017 with wild-type (B and C), PEX12-deficient PBD006 (D and E), ally exposed PEX5 than PBD054 cells and that PBD054 and PEX10-deficient PBD100 (F and G) cells using anti–PEX5 cells imported PEX5 into the peroxisome lumen. How- antibodies (B, D, and F) and anti–PMP70 antibodies (C, E, and ever, there are two potential caveats to these experiments. G). Bar, 25 ␮m. First, immunofluorescence experiments can be influenced greatly by conformational changes in the antigen, in this case PEX5. Second, they do not address the question of whether some of the peroxisomal PEX5 in PBD006 cells PEX12 or PEX10. These include docking of receptor– may also be protected from antibodies in the differential ligand (matrix protein) complexes to the peroxisome, ma- permeabilization experiments. Therefore, we performed trix protein translocation across the peroxisome mem- protease protection experiments on organelle prepara- brane, and receptor recycling (Braverman et al., 1995; tions from PBD006 and PBD054 cells. Postnuclear super- Rachubinski and Subramani, 1995). To distinguish be- natants were prepared from each cell line, and peroxi- tween these different possibilities, we first tested whether somes and other large organelles were recovered by PEX12 or PEX10 were required for docking of the PTS1 differential centrifugation. These organelle pellets were receptor, PEX5, to peroxisomes. Postnuclear supernatants resuspended and incubated with various amounts of pro- were prepared from normal human fibroblasts and from a tease in the presence or absence of detergent, the reac- fibroblast cell line which appears to lack PEX12 activity tions were quenched, and each sample was assayed for lev- altogether (PBD006 [Chang and Gould, 1998]). Peroxi- els of PEX5 by immunoblot (Fig. 8, A and B). PBD054 somes were pelleted from each postnuclear supernatant by cells appeared to contain more protease-resistant PEX5 centrifugation, and the relative amount of PEX5 in the cy- than PBD006 cells, which may reflect import of PEX5 into tosolic supernatant and organelle pellet was determined the peroxisome lumen of these cells. Similar results were by immunoblot. Levels of peroxisome-associated PEX5 obtained in each of three trials. were not reduced in the absence of PEX12 or PEX10 and If PBD054 cells actually do import PEX5 into the perox- actually appeared to be slightly elevated in the pex10 and isome lumen, we might expect that peroxisomes of these pex12 mutants (Fig. 6 A). This was also evident in immu- cells would contain more PEX5 than those of PBD006 nofluorescence experiments in which the staining for per- cells. We tested this hypothesis by cell fractionation stud- oxisome-associated PEX5 appeared to be greater in the ies. Postnuclear supernatants were prepared from wild-

Chang et al. PEX12 Participates in Peroxisomal Matrix Protein Import 769 Figure 8. Protease protection analysis of peroxisomal PEX5 in PBD006 and PBD054 cells. Organelle fractions were prepared from PBD006 (A) and PBD054 (B) cells and incubated with pro- tease in the absence or presence of detergent, and then assayed for PEX5 by immunoblot binding. (C) Postnuclear supernatants from PBD006 and PBD054 cells were separated into cytosolic su- pernatants (S) and organelle pellets (P). Equal proportions of each were assayed for PEX5 levels by immunoblot. Downloaded from

tion between PEX12 and PEX5, the receptor for newly synthesized peroxisomal matrix proteins. We detected in- teractions between PEX12 and PEX5 using the yeast two- hybrid system, by filter binding assay, in coimmunoprecip- jcb.rupress.org itation experiments, and by genetic suppression studies.

Figure 7. Distribution of PEX5 in PBD006 and PBD054 cells. A Role for PEX12 in Peroxisomal Matrix PBD006 (A, B, E, and F) and PBD054 (C, D, G, and H) cells Protein Import were fixed, permeabilized with either Triton X-100 (A–D) or dig- on November 7, 2017 itonin (E–H), and processed for double indirect immunofluores- It is generally accepted that PEX5 is the receptor for cence using anti–PEX5 antibodies (A, C, E, and G) and anti– newly synthesized PTS1-containing proteins (McCollum PMP70 antibodies (B, D, F, and H). Bar, 25 ␮m. et al., 1993; Dodt et al., 1995; Fransen et al., 1995; Terlecky et al., 1995; Elgersma et al., 1996) and is a predominantly cytoplasmic protein in mammalian cells (Dodt et al., 1995; Dodt and Gould, 1996) and several fungal species (van der type, PBD006 and PBD054 fibroblasts, peroxisomes were Klei et al., 1995; Elgersma et al., 1996; Gould et al., 1996). separated from cytosol by differential centrifugation, and Studies in human cells have suggested that PEX5 shuttles the levels of PEX5 in the cytosolic supernatant and between the cytoplasm and peroxisome (Dodt and Gould, organelle pellet fractions were determined by immuno- 1996), and several models predict that PEX5 moves blot. PBD054 cells contained more peroxisome-associated through a variety of steps as it catalyzes peroxisomal ma- PEX5, as predicted (Fig. 8 C). trix protein import. The proportion of PEX5 that resides in the cytoplasm at steady state probably reflects the needs Discussion of each cell to efficiently capture newly synthesized perox- isomal matrix proteins (ligands) from the cytoplasm. How- In this paper we investigated the role of PEX12 in peroxi- ever, once these ligands are bound by PEX5 many addi- some biogenesis by examining the phenotypes of PEX12- tional events must occur. These may be grouped into the deficient cells and identifying peroxins that physically and general processes of (1) the transport to and docking of genetically interact with PEX12. Previous studies have es- PEX5–ligand complexes with the peroxisome membrane, tablished that loss of PEX12 results in the absence of de- (2) the translocation of ligands into the peroxisome lumen, tectable peroxisomal matrix protein import, but has virtu- and (3) the recycling of receptors back to the cytoplasm ally no effect on the synthesis of peroxisomes or the (Braverman et al., 1995; Rachubinski and Subramani, import of peroxisomal membrane proteins (Kalish et al., 1995). To distinguish which of these events may involve 1996; Chang et al., 1997, 1999; Chang and Gould, 1998; PEX12, we considered the phenotypes that are expected Okumoto et al., 1998b). Such a phenotype alone points to for a mutant in each process and compared them to the a role for PEX12 in peroxisomal matrix protein import. phenotypes of PEX12-deficient cells. However, the data presented in this report advance this Several studies have implicated the integral peroxisomal hypothesis by demonstrating physical and genetic interac- membrane proteins PEX13 and PEX14 in docking of PTS

The Journal of Cell Biology, Volume 147, 1999 770 receptors to the peroxisome membrane (Elgersma et al., the translocation process. The main function of a matrix 1996; Erdmann and Blobel, 1996; Gould et al., 1996; Al- protein translocon would be to move matrix proteins from bertini et al., 1997; Girzalsky et al., 1999). The defining the cytoplasmic side of the peroxisome membrane to the features of these docking factors are as follows: (1) their lumenal side. Given that most of these proteins arrive at ability to bind PEX5 and PEX7, either directly or indi- the peroxisomes in a complex with PEX5 and that studies rectly, and (2) the fact that loss of PEX13 or PEX14 results of Yarrowia lipolytica PEX5 strongly suggest that PEX5 in a significant reduction in the amount of peroxisome- participates in the matrix protein translocation process associated PEX5. The fact that loss-of-function mutations (Szilard et al., 1995), we favor a model for matrix protein in PEX12 do not result in any detectable reduction in the translocation that includes PEX5. Such a model may in- levels of peroxisome-associated PEX5 argues strongly volve: (1) acceptance of PEX5–ligand complexes from against the hypothesis that PEX12 participates in receptor PEX14, the primary PEX5 docking site; (2) retention of docking. In fact, our data indicate that the loss of PEX12 PEX5 at the translocation apparatus; (3) opening of the may actually increase the levels of peroxisome-associated matrix protein translocation pathway; (4) PEX5–ligand PEX5. This observation, together with the fact that recep- dissociation and ligand translocation; (5) closure of the tor docking is the first peroxisome-localized step of perox- translocation pathway; and (6) release of the unoccupied isomal matrix protein import, demonstrates that PEX12 receptor from the translocation apparatus. The ability of acts downstream of the docking event. Thus, PEX12 ap- PEX12 to bind PEX5 suggests that PEX12 may contribute pears to be the first known PEX5-binding protein that is to retaining PEX5 at the translocation apparatus. Some not required for docking the PTS1 receptor to the peroxi- additional support for this hypothesis comes from the fact some. that PEX5 appears to be imported into the peroxisome as Of the two remaining aspects of peroxisomal matrix a result of the PEX12/S320F mutation, which reduces the protein import, protein translocation and receptor recy- interaction between PEX12 and PEX5. cling, there is no report of a bona fide protein transloca- This model predicts that PEX5 enters the peroxisomal Downloaded from tion factor, but there is one report that proposes a role for compartment during the normal course of peroxisomal PEX4 in receptor recycling (van der Klei et al., 1998). This matrix protein import. However, it also predicts that conclusion was based in part on the phenotypes of pex4 PEX5 should normally be retained at the translocation ap- mutants, which display a very mild defect in peroxisomal paratus rather than being released to move freely through matrix protein import and can be suppressed by overex- the peroxisome lumen. A low rate of PEX5 release from

pression of PEX5. However, we observed that cells lack- the translocation apparatus into the lumen could explain the jcb.rupress.org ing human PEX12 display a severe defect in peroxisomal detection of intraperoxisomal PEX5 in Hansenula poly- matrix protein import that cannot be suppressed by over- morpha (van der Klei et al., 1995). Y. lipolytica PEX5, expression of PEX5. Thus, PEX12 does not have the prop- which is detected only on or in the peroxisome, could also erties we might expect of a factor that is required for re- function within such a model, provided that it participates ceptor recycling. in just the peroxisome-limited steps of matrix protein im- The remaining aspect of peroxisomal matrix protein im- port (Szilard et al., 1995). on November 7, 2017 port to consider is the protein translocation process. Actu- We thank James Morrell for excellent technical assistance in plasmid con- ally, a role for PEX12 in peroxisomal matrix protein trans- struction. We also thank Dr. Gabrielle Dodt (Ruhr-Universitat, Bochum, location would fit well with the known properties of this Germany) for providing polyclonal anti–PEX5 antibodies that were used protein. First, PEX12 has the appropriate physical charac- in some of the experiments. teristics for such a role: it is an integral peroxisomal mem- This work was supported by grants from the National Institutes of brane protein that spans the membrane twice and extends Health to S.J. Gould (DK45787 and HD10987). its NH2 and COOH termini toward the cytoplasm where Submitted: 23 August 1999 they may interact with other protein import factors (Ka- Revised: 8 October 1999 lish et al., 1996; Chang et al., 1997; Okumoto and Fujiki, Accepted: 12 October 1999 1997). Second, it utilizes its COOH-terminal zinc-binding domain to interact with PEX5, the PTS1 receptor. Third, cells with inactivating mutations in PEX12 are unable to References import peroxisomal matrix proteins but do synthesize per- Adams, A., D.E. Gottschling, C.A. Kaiser, and T. Stearns. 1997. Methods in oxisomes and import integral peroxisomal membrane pro- Yeast Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor. teins (Kalish et al., 1996; Chang et al., 1997, 1999; Chang 115–116. Albertini, M., P. Rehling, R. Erdmann, W. Girzalsky, J.A. Kiel, M. Veenhuis, and Gould, 1998). Fourth, PEX12 interacts with PEX10, and W.-H. Kunau. 1997. Pex14p, a peroxisomal membrane protein binding another integral peroxisomal membrane protein that dis- both receptors of the two PTS-dependent import pathways. Cell. 89:83–92. Baes, M., P. Gressens, E. Baumgart, P. Carmeliet, M. Casteels, M. Fransen, P. plays a specific defect in the import of peroxisomal matrix Evrard, D. Fahimi, P.E. Declercq, D. Collen, P.P. van Veldhoven, and G.P. proteins (Kalish et al., 1995; Warren et al., 1998) and yet Mannaerts. 1997. A mouse model for Zellweger syndrome. Nat. Genet. 17: does not appear to participate in receptor docking or recy- 49–57. Borden, K.L. 1998. RING fingers and B-boxes: zinc-binding protein-protein in- cling. Fifth, a missense mutation in PEX12, S320F, ap- teraction domains. Biochem. Cell Biol. 76:351–358. pears to affect the specificity of the translocation appara- Braverman, N., G. Dodt, S.J. Gould, and D. Valle. 1995. Disorders of peroxi- tus, resulting in the import of PEX5 into the peroxisome some biogenesis. Hum. Mol. Genet. 4:1791–1798. Braverman, N., G. Steel, C. Obie, A. Moser, H. Moser, S.J. Gould, and D. lumen. Valle. 1997. Human PEX7 encodes the peroxisomal PTS2 receptor and is re- Although there is no established in vitro protein translo- sponsible for rhizomelic chondrodysplasia punctata. Nat. Genet. 15:369–376. Braverman, N., G. Dodt, S.J. Gould, and D. Valle. 1998. An isoform of Pex5p, cation assay that can be used to test this hypothesis di- the human PTS1 receptor, is required for the import of PTS2 proteins into rectly, it is useful to consider possible roles for PEX12 in peroxisomes. Hum. Mol. Genet. 7:1195–1205.

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