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Eukaryotic Cell, August 2007, p. 1439-1449, Vol. 6, No. 8
1535-9778/07/$08.00+0     doi:10.1128/EC.00084-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Conservation of PEX19-Binding Motifs Required for Protein Targeting to Mammalian Peroxisomal and Trypanosome Glycosomal Membranes ^,

Tracy Saveria,^1,2 André Halbach,³ Ralf Erdmann,³ Rudolf Volkmer-Engert,⁴ Christiane Landgraf,⁴ Hanspeter Rottensteiner,^3, and Marilyn Parsons^1,2,*

Seattle Biomedical Research Institute, Seattle, Washington 98109,¹ University of Washington, Seattle, Washington 98105,² Institut für Physiologische Chemie, Abteilung für Systembiochemie, Ruhr-Universität Bochum, 44801 Bochum, Germany,³ Institut für Medizinische Immunologie, Universitätsklinikum Charité, 10115 Berlin, Germany⁴

Received 15 March 2007/ Accepted 5 June 2007

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Glycosomes are divergent peroxisomes found in trypanosomatid protozoa, including those that cause severe human diseases throughout much of the world. While peroxisomes are dispensable for both yeast (Saccharomyces cerevisiae and others) and mammalian cells in vitro, glycosomes are essential for trypanosomes and hence are viewed as a potential drug target. The import of proteins into the matrix of peroxisomes utilizes multiple peroxisomal membrane proteins which require the peroxin PEX19 for insertion into the peroxisomal membrane. In this report, we show that the specificity of peroxisomal membrane protein binding for Trypanosoma brucei PEX19 is very similar to those previously identified for human and yeast PEX19. Our studies show that trafficking is conserved across these distant phyla and that both a PEX19 binding site and a transmembrane domain are required for the insertion of two test proteins into the glycosomal membrane. However, in contrast to T. brucei PEX10 and PEX12, T. brucei PEX14 does not traffic to human peroxisomes, indicating that it is not recognized by the human PEX14 import mechanism.

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Trypanosomatid parasites are responsible for several debilitating, and often lethal, human diseases, including African sleeping sickness, leishmaniasis, and Chagas' disease, caused by Trypanosoma brucei, Leishmania spp., and Trypanosoma cruzi, respectively. In addition to the human scourges caused by this group of organisms, trypanosomatid diseases in livestock add to health and economic burdens in many developing countries. At present, there are no vaccines available and current drug treatments are complicated by emerging resistance or high toxicity, including sometimes lethal side effects (6, 53). Studies delineating the unique biology of trypanosomatids may hold promise for future treatments that are effective yet have minimal side effects.

The single-celled trypanosomatids contain divergent peroxisomes called glycosomes, so named because these organelles house the glycolytic pathway (36). The sequestering of glycolysis within a membrane-bound organelle is unique to trypanosomatids. Previously it was shown that glycosomes, unlike peroxisomes, are essential to cell survival (19, 23). Since trypanosomatid glycolytic enzymes have lost the typical feedback regulation seen in other organisms, loss of compartmentation likely leads to runaway ATP consumption and overproduction of phosphorylated intermediates, resulting in cell death (1, 4, 19). Despite this major difference, glycosomes and peroxisomes have maintained many similarities over the course of evolution (34, 39). For example, both house ether-lipid biosynthesis and utilize similar trafficking routes for the import of matrix proteins. However, the evolutionary divergence between mammals and trypanosomatids is great and differences in glycosomal biogenesis and function may prove useful in discovering drugs that target the parasite organelle while leaving the host unharmed.

The processes of peroxisome biogenesis and matrix protein import both involve a large set of proteins known as peroxins (PEX). The trafficking of proteins destined to the peroxisome matrix has been well studied (11). These proteins contain peroxisomal targeting sequences that mediate association with their respective cytosolic receptors, which then transport the cargo to the organelle (22, 52). Completion of the matrix protein import process involves several peroxisomal membrane proteins (PMPs), including the RING peroxin PEX10 (3, 33, 42). Several peroxin orthologues have been identified in trypanosomatids, including peroxins 2, 5, 6, 7, 10, 11, 12, 14, and 19 (5, 10, 13, 19, 23, 29, 30), generally showing 20 to 25% sequence identity to the human peroxins. Others, such as PEX3, which are essential for the formation and/or function of peroxisomes in mammals and most yeast species (20, 25, 28, 54), have not been identified in the completed genomes.

PMPs are targeted to the peroxisome via a process entirely different from that for matrix proteins. The mechanistic details are still being sorted out, but it is already clear that the integral membrane protein PEX3 and the largely cytosolic protein PEX19 are important in this process. Trafficking of most PMPs appears to be PEX19 dependent. PEX3 is a notable exception (27). The broad binding specificity of PEX19 for multiple PMPs (17, 43, 44, 48), combined with its ability to prevent the aggregation of these proteins in cell-free translation systems (27, 31, 46), has led to the working hypothesis that PEX19 acts as a PMP chaperone and import receptor (27). In this model, PEX19 binds its PMP cargo in the cytosol and carries it to the peroxisome membrane, where PEX19 binds PEX3 for subsequent insertion of the cargo into the membrane. This model is supported by recent work which has shown that PEX19 loaded with PMP cargo has a higher affinity for PEX3 than does unloaded PEX19 and that the import competence of PMPs is determined by a step prior to docking at the peroxisomal membrane (41). However, the finding that for some PMPs, the peroxisome targeting region is separate from the PEX19-binding site suggests that PEX19 may not be a general receptor for all PMPs (17, 48, 55). Rather, it has been postulated that PEX19 may promote assembly or disassembly of some PMP complexes at the peroxisome membrane itself (15, 48). Regardless of current disagreements as to the exact function of PEX19, which may vary in detail between different species, there is little doubt that this protein plays a pivotal role in the life of PMPs.

The long C-terminal domain of PEX19 binds numerous PMPs (16, 32, 46). The C terminus also contains a CAAX box, but trypanosomatid PEX19s lack this farnesylation motif (5). This motif seems to be required for efficient targeting of PMPs in humans and Saccharomyces cerevisiae (21, 31), suggesting that some aspects of PMP targeting might differ in trypanosomes. Previously, based on studies of S. cerevisiae, we developed a mathematical matrix for the prediction of PEX19-binding sites in PMPs (43). These regions generally consist of approximately 11 hydrophobic or positively charged residues and occur adjacent to or in close proximity to transmembrane domains (43). Although not sufficiently restrictive to identify PMPs out of a predicted proteome of an organism (43), this algorithm has proven useful for predicting PEX19 binding sites in both yeast and human PMPs (24). Its applicability to trypanosomatids has not been extensively studied. Here, we examine PMP targeting by PEX19 via comparative analysis of this process in T. brucei and human cells. We have previously shown that cross-species targeting of PEX10 and PEX12 is conserved among trypanosomatids (45), and therefore we focus the work here on T. brucei as the representative organism for this group. We demonstrate here that although many aspects of PMP trafficking have remained conserved over the course of evolution, subtle differences that may prove useful in fighting trypanosomatid diseases exist.

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Cell strains, media, and growth conditions. T. brucei procyclic strain 29-13 (57) was maintained in JRH Biosciences SDM-79 medium supplemented with 10% fetal calf serum. This strain has integrated copies of the tetracycline (Tet) repressor and T7 polymerase, which allows regulated expression of introduced genes expressed via a T7 promoter with adjacent Tet repressor binding sites. G418, hygromycin, and phleomycin were added to final concentrations of 15, 50, and 2.5 µg/ml, respectively. T. brucei single-marker blood form cells (57) were maintained in HMI-9 medium with 10% fetal calf serum. G418 and phleomycin were each added to a final concentration of 2.5 µg/ml. Transfections were performed as previously described (19, 49). After the isolation of stable transfectants, green fluorescent protein (GFP) fusion protein expression or RNA interference (RNAi) was induced by the addition of Tet to a concentration of 2 µg/ml. Growth analysis was performed as described previously, with the Coulter counter set to identify particles of the approximate size of bloodstream form T. brucei cells (19).

The human skin fibroblast cell line GM5756T was cultured at 37°C in Dulbecco modified Eagle's medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100,000 U/liter penicillin, and 100 mg/liter streptomycin at 8% CO₂. Transient transfection was performed with 1 µg of plasmid DNA and 1.5 µl FuGene 6 according to the manufacturer's instructions (Roche Diagnostics, Mannheim, Germany).

Plasmid construction. For a list of all primers used in plasmid construction, see Table S1 in the supplemental material. The TbPEX19 RNAi plasmid was described previously (5), as were the T. brucei expression plasmids encoding N-terminal GFP fusions to TbPEX10 and TbPEX12 (45). For the expression of N-terminal GFP fusion proteins in human fibroblasts, these genes were amplified from their respective plasmids, cloned into pGEM T-Easy, sequenced, and cloned into the pEGFP-C1 plasmid. The primers used for these reactions contained 5' BglII and 3' BamHI sites for cloning into the pEGFP-C1 vector. For cloning into pLEW79(BLE)GFP+3' or enhanced GFP-C1 vectors, TbPEX14 was amplified from pGEM-Teasy (19), and AflII/BglII and XhoI/BamHI sites were added to the 5' and 3' ends, respectively.

Using the plasmids containing GFP-TbPEX10 as the template, mutant versions were created by site-directed mutagenesis (QuikChange site-directed mutagenesis kit). Following PCR cycling, reactions were treated with DpnI and transformed into Escherichia coli JM109 cells. The region encoding the fusion protein was sequenced. Plasmids were transfected into T. brucei 29.13 procyclic cells or human fibroblasts.

Constructs encoding enhanced GFP-HsALDP fusion proteins for expression in mammalian cells were described previously (24). For the expression of these HsALDP gene regions in T. brucei, each was amplified from its parent template by PCR using primers containing 5' AflII or 3' BamHI (see Table S1 in the supplemental material) and inserted into the pLEW79(BLE)GFP+3' expression plasmid.

The vector pGST-TbPEX19 designed to express a glutathione S-transferase (GST) fusion protein of T. brucei PEX19 was generated by cloning PEX19 (amplified from genomic DNA using primers containing a 5' EcoRI and a 3' NotI site) into pGEX-4T-1 (GE Healthcare). The corresponding vector for the bacterial expression of human PEX19 has been described previously by Halbach et al. (24). Expression of the GST-TbPEX19 fusion proteins was carried out in the BL21 (DE3) derivative C41 strain according to the manufacturer's protocol (GE Healthcare).

RNA analysis. T. brucei bloodstream forms, uninduced or induced (day 2) for RNAi, were collected, washed, and resuspended in TRIzol reagent (Invitrogen). RNA was extracted using the manufacturer's protocol. Northern analysis was carried out as previously described (26).

Immunofluorescence microscopy, cell extraction, and immunoblot analysis. Immunofluorescence microscopy analysis (IFA) of T. brucei cells was performed as described previously (19). Blood form T. brucei cells were fixed in suspension with 4% paraformaldehyde, washed, and applied to poly-L-lysine-coated slides. Procyclic cells were fixed on glass slides with 4% paraformaldehyde. Cells were then permeabilized with 0.1% Triton X-100 and blocked with 8% nonfat milk. Rabbit anti-glycosome antiserum (38), primarily recognizing the glycosomal matrix proteins aldolase, glyceraldehyde phosphate dehydrogenase, and pyruvate phosphate dikinase, was applied and followed with Texas Red-conjugated goat anti-rabbit immunoglobulin G (Southern Biotechnologies). DNA was stained with DAPI (4',6-diamidino-2-phenylindole dihydrochloride; ICN Biomedicals). After Prolong Antifade (Invitrogen) was used as mounting medium, slides were viewed using a Nikon Eclipse E300 microscope equipped with MetaMorph software. Intrinsic fluorescence of GFP was still evident under these conditions.

IFA of human fibroblasts that had been transfected with pEGFP-C1-derived plasmids was carried out essentially as described previously by Halbach et al. (24), with the exception that polyclonal rabbit anti-PMP70 antibodies (Invitrogen, Carlsbad, CA) were used to label peroxisomes in cells expressing GFP-TbPEX14.

For fractionation experiments, cells expressing the proteins of interest were first treated with digitonin at a final concentration of 200 µg/ml for 3 min at 37°C. Following centrifugation, the organellar pellet was treated with 0.2 M sodium carbonate, pH 11, and the integral and peripheral membrane protein fractions were separated by centrifugation as described previously (45). Cell equivalents of the digitonin supernatant, carbonate supernatant (matrix and peripheral membrane proteins), and pellets (integral membrane proteins) were subjected to immunoblot analysis.

Immunoblot analyses were performed using rabbit anti-GFP antisera (Molecular Probes), mouse anti-GFP B2 (Santa Cruz Biotechnology), rabbit anti-phosphoglycerate kinase (38), or, for loading controls in determining expression levels, mouse anti-Nopp44/46 monoclonal antibody 1D2 (40), followed by goat anti-rabbit IRDye 680 (LI-COR Biosciences) and goat anti-mouse IRDye 800CW (LI-COR Biosciences) for simultaneous detection of antibodies. Blots were analyzed using the Odyssey infrared imaging system.

Peptide arrays. Peptide blots were generated as previously described (43). The blots were probed with purified GST-PEX19 fusion proteins (both human and T. brucei PEX19), and specifically bound protein was revealed with a combination of monoclonal anti-GST antibodies and secondary horseradish peroxidase-conjugated antibodies. As a control, GST was added to replicate blots.

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PEX19 is essential in bloodstream stage T. brucei. Previously, we identified the trypanosomatid PEX19 orthologues and demonstrated that partial depletion of the mRNA (70%) resulted in compromised growth of the insect midgut stage (procyclic form) of T. brucei (5). Mammalian infective stages, unlike the procyclic stage, require glycolysis for survival. To assess the importance of PEX19 to the mammalian infective stage, we analyzed the result of RNAi-mediated destruction of PEX19 RNA in bloodstream forms. After the isolation of stable bloodstream form transfectants containing the PEX19 RNAi plasmid, cultures were induced with Tet. As seen in Fig. 1A, by day 2 of this assay, growth of the induced population slowed compared to that of their uninduced counterparts. Although particles were still detected at day 4 using the Coulter Counter, these represented dead cells; no live cells could be found by microscopic visualization. Northern analysis and phosphorimaging showed that PEX19 RNA was reduced by about 70% compared to uninduced controls (Fig. 1A, inset). By day 7, viable parasites were again detected. This result is commonly seen with RNAi of essential genes in T. brucei, where genetic changes in the engineered strain lead to loss of RNAi (8). These results demonstrate that PEX19 is an essential protein in the bloodstream stage of the trypanosome life cycle.

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FIG. 1. PEX19 is essential to blood form T. brucei. (A) Growth analysis of the TbPEX19 RNAi cell line. Bloodstream stage cells containing an RNAi construct targeting PEX19 RNA were induced with Tet in triplicate and counted by Coulter counter daily. The cumulative number of particles (cells plus any dead cells of similar size) is indicated on the y axis. Individual measurements are shown. Because the data were very reproducible, some time points appear to have fewer replicates. The inset shows results from Northern analysis of the RNAi line with (+) or without (–) Tet to induce RNAi. (B) IFA of cells induced (+) for RNAi after 48 h or uninduced controls (–). Cells were stained with anti-glycosome antibody which detects several matrix proteins. The induced cells were heterogeneous (see the text). A cell exhibiting punctate staining and a cell from the same culture exhibiting diffuse staining are shown. Bar, 2 µm.

It can be difficult to detect bloodstream form cells showing mislocalization of glycosomal proteins via IFA, since the parasites become fragile and die rapidly (23). Nonetheless, we attempted to assess glycosomal protein localization to functionally tie the PEX19 phenotype to glycosome biogenesis. IFA was carried out 48 h after induction by using an anti-glycosome antibody that detects three glycosomal matrix enzymes (Fig. 1B). Uninduced cells showed the characteristic punctate glycosomal staining with this antiserum. In the induced population, 25% showed diffuse cytosolic staining. The remaining cells exhibited a punctate staining pattern, although some of these contained enlarged glycosomes, a phenotype we observed when PEX19 abundance was reduced in procyclic cells (5). It is likely that this phenotype represents an intermediate state with residual PEX19.

PEX19 binding site-dependent targeting of human ALDP in T. brucei. Since the RNAi knockdown indicated that PEX19 is essential for peroxisome/glycosome biogenesis in trypanosomes, as it is in humans and yeast, we asked how closely the function of TbPEX19 resembles those of the corresponding human and yeast orthologues. To this end, the targeting of fragments of the human adrenoleukodystrophy protein (ALDP) was inspected in trypanosomes. ALDP is a PMP of the ATP-binding cassette (ABC) transporter protein family that is believed to be involved in the transport of very-long-chain fatty acids into the peroxisome for degradation (56). Peroxisomal targeting of ALDP in human cells and in S. cerevisiae was previously shown to require the presence of both a transmembrane domain (TMD) and a PEX19-binding site (24). The same regions of ALDP were assessed here for their ability to route GFP to the glycosomes of T. brucei. Amino acids (aa) 66 to 87, containing the PEX19-binding site of ALDP, aa 87 to 164, containing two TMDs, and aa 66 to 164, containing both the PEX19-binding site and the TMDs, were each cloned into a T. brucei GFP expression vector for the creation of fusion proteins containing an N-terminal GFP. These constructs were transfected into procyclic form T. brucei for the generation of stable cell lines. After induction with Tet, each cell line expressed an appropriately sized GFP fusion protein (Fig. 2A). An IFA using an antiserum directed against glycosomal matrix proteins was carried out for each of these cell lines; intrinsic GFP fluorescence marked the localization of the fusion proteins. Of these GFP fusion proteins, only the one containing both the PEX19-binding site and the TMDs, ALDP(66-164), showed specific glycosomal localization (Fig. 2B, left panels). The cells expressing GFP fused to the PEX19-binding site, ALDP(66-87), showed diffuse fluorescence, indicating likely cytosolic and nuclear localization of the fusion protein. Cells expressing GFP fused to the TMDs, HsALDP(87-164), showed diffuse, reticular, and punctate patterns, with some colocalization to glycosomes but significant localization elsewhere in the cell, including a variety of intracellular membranes and perhaps the cytosol.

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FIG. 2. Targeting of HsALDP domain fusions in T. brucei. GFP-HsALDP fusion proteins containing the TMDs (aa 87 to 164), the PEX19 binding site (aa 66 to 87), or both (aa 66 to 164) were expressed in T. brucei procyclic cells. (A) Immunoblot analysis of GFP fusion proteins showing migration appropriate to the predicted sizes of 37 kDa for GFP-HsALDP(87-164), 31 kDa for GFP-HsALDP(66-87), and 40 kDa for GFP-HsALDP(66-164). The migration of molecular mass markers is indicated. Tet induces the expression of the fusion proteins (+Tet). (B) Localization of fusion proteins expressed in T. brucei by fluorescence microscopy and cellular fractionation. GFP was visualized by intrinsic fluorescence, while glycosomes were revealed with rabbit anti-glycosome antibody followed by anti-rabbit immunoglobulin G coupled to Texas Red. Bar, 2 µm. For immunoblots, the fractions were analyzed using anti-GFP antibody to detect the fusion protein and anti-phosphoglycerate kinase (PGK) antibody, which detects both a cytosolic (C) and a glycosomal (G) isoform. Lanes are loaded by cell equivalents. T, total lysate; DS, digitonin supernatant containing cytosolic proteins; CS, carbonate supernatant containing organellar matrix and peripheral membrane proteins; CP, carbonate pellet containing integral membrane proteins.

To further characterize the subcellular distribution of these GFP fusion proteins in T. brucei, we analyzed cell fractions by immunoblot analysis. Digitonin treatment and centrifugation yielded the cytosolic supernatant and organellar pellet. The latter was extracted with sodium carbonate to release matrix and peripheral membrane proteins (18). Integral membrane proteins remain membrane associated and partition to the pellet fraction upon ultracentrifugation. The samples were subjected to immunoblot analysis using anti-GFP and anti-phosphoglycerate kinase. The latter antiserum detects both the 45-kDa cytosolic isozyme and the 56-kDa glycosomal matrix isozyme. The cytosolic phosphoglycerate kinase was found in the digitonin supernatant, whereas the glycosomal form partitioned to the digitonin pellet. From there, it associated predominantly to the carbonate supernatant fraction, although some fractionated with the carbonate pellet as observed previously (45). As shown in Fig. 2B (right panels), the GFP-HsALDP(66-164) fusion protein was exclusively present in the integral membrane protein fraction. In contrast, GFP-HsALDP(66-87) was predominantly in the digitonin soluble fraction, although a small amount was associated with the integral membrane fraction. GFP-HsALDP(87-164) was predominantly in the integral membrane fraction, although some was seen in the cytosolic fraction.

Interestingly, the expression of glycosomally targeted GFP-ALDP(66-164) was toxic, as these cells rounded up and began to die within 24 h of induction, indicating that the correctly targeted fragment may adversely affect the structure or metabolic function of the glycosome. Despite this effect, matrix proteins continued to be properly localized, as shown both by the IFA and by digitonin fractionation (Fig. 2B). Immunoblot analysis showed that this toxic fusion protein was not overexpressed relative to the other HsALDP fusion proteins (Fig. 2A). This interference notwithstanding, the data are clear in that the HsALDP fragments showed a subcellular distribution in T. brucei similar to that observed in human fibroblasts and S. cerevisiae and that targeting to the glycosome requires both the regions containing the TMDs and the previously described PEX19-binding site.

The apparent requirement for the human PEX19-binding site further suggested that TbPEX19 is able to recognize this site, even though the two PEX19 orthologues exhibit only 21% amino acid sequence identity. To experimentally address this possibility, peptide arrays were synthesized to contain the 13-aa sequence of the HsALDP PEX19-binding site (FLQRLLWLLRLLF), along with single amino acid substitutions for each residue. Peptide blots were then incubated with GST-tagged versions of human or T. brucei PEX19, and bound PEX19 was revealed by using anti-GST antibody. A comparison of the array results of HsPEX19 and TbPEX19 revealed not only that TbPEX19 bound the human ALDP PEX19-binding site but also that the binding specificities of both proteins are very similar, although not identical, in this assay (Fig. 3). No binding was detected to GST alone. As indicated in previous studies, the central leucines (but not the tryptophan) appear to be important features for binding. Thus, TbPEX19 does recognize sequences similar to those detected by human PEX19.

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FIG. 3. Substitution analysis of the PEX19 binding site in ALDP. Replicate peptide arrays harboring the 13-amino-acid PEX19 binding peptide of HsALDP (FLQRLLWLLRLLF) as well as peptides with single amino acid substitutions thereof were tested for interaction with GST fused to human PEX19 (upper panel) or T. brucei PEX19 (middle panel) or with GST alone (bottom panel). The first column has replicate peptides with no substitutions. Subsequent columns have peptides in which each residue is replaced individually by the amino acid indicated at the top of the column (e.g., column 2 has peptides with Ala substitutions). Bound PEX19 was visualized by monoclonal anti-GST antibodies in combination with the enhanced chemiluminescence reaction system. Spots of reduced intensity reflect peptides with a decreased binding affinity for PEX19. Similar binding patterns were observed for both PEX19 proteins.

Prediction and identification of PEX19-binding sites in T. brucei PMPs. To identify potential PEX19-binding sites in trypanosomatid PMPs, we used an algorithm that had been developed for the prediction of PEX19-binding sites in S. cerevisiae PMPs (43) and which had proven valuable for the prediction of such sites in human PMPs (24). This in silico method generates predictions in 15-residue segments, with the central 9 aa representing the primary sequence-specific entity. We submitted known PMPs from three trypanosomatid species (T. brucei, T. cruzi, and Leishmania major) to the algorithm, resulting in predictions of binding for most proteins (Table 1). However, for a few proteins, namely PEX14 from all three species and T. cruzi Gim5a, no high-scoring peptide (>3,000) was identified. To determine whether this algorithm is able to correctly predict PEX19-binding sites in trypanosomatid PMPs, proteins with at least one site that scored above 3,000 were further analyzed using peptide arrays. All peptides spanning the high-scoring regions and some additional minor scoring regions were synthesized on arrays, which were then probed with GST-TbPEX19. Each tested region was represented by nine 15-mer peptides covering 31 aa in total, with the central residue on the array representing the peak scoring peptide. The results of this PEX19 binding assay are shown in Fig. 4A (left panel). Many trypanosomatid PMPs bound TbPEX19 in the regions predicted by the pattern search. More precisely, of the 32 binding sites analyzed, 21 exhibited significant binding. Of these, 16 showed little or no binding to GST and five showed some binding to GST, albeit at a lower level (Fig. 4A, right panel). These results compare well with those of a study of predicted sites in yeast PMPs, where 38% of the predicted peptides bound to GST-ScPEX19 (43). The results are summarized in Table 1. In some cases, the peptides which bound GST-PEX19 were in homologous positions in multiple proteins, while in other cases they were unique to a given protein. For all of these PMPs, except TbPEX12 and LmGIM5a, peptides corresponding to at least one predicted site bound to GST-TbPEX19. As an example, Fig. 4B shows the prediction scores for the RING finger peroxin TbPEX10, with a peak at aa 175 to 189. Several peptides centered around aa 175 to 189 bound to GST-TbPEX19 (Fig. 4A and C), although a second predicted region (aa 101 to 115) failed to do so (Fig. 4A).

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TABLE 1. Prediction of PEX19-binding sitesa

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FIG. 4. Identification of PEX19 binding sites in PMPs from trypanosomes. (A) Peptide scans for predicted PEX19 binding sites. The regions predicted to contain PEX19 binding sites were synthesized as stretches of nine overlapping 15-mer peptides with two amino acid shifts between neighboring peptides and tested for interaction with a GST fusion of TbPEX19. The central peptide represents the actual peak scoring peptide as listed in Table 1. (B) Binding site prediction for TbPEX10. The hits obtained with the PEX19 binding site prediction matrix for TbPEX10 are presented as dotted vertical lines. Two sites with a high probability score (in arbitrary units [a.u.]) are visible, with the more C-terminal site showing a cluster of hits around a peak scoring peptide, the position and amino acid sequence of which is indicated. (C) Peptide scan for TbPEX10. Peptides (15-mers) with three amino acid shifts between neighboring peptides (rather than the two amino acid shifts for Fig. 4A) and covering the entire protein were synthesized on a nitrocellulose membrane and tested for interaction with GST fusions of PEX19 from T. brucei (upper panel) and Homo sapiens (lower panel). For TbPEX19, two binding sites were identified (indicated by the arrows), one of which was also recognized by HsPEX19. Grid intersections mark the center region for each separate peptide on the array.

To otherwise test whether TbPEX19 recognizes sites in TbPEX10 that are not foreseen by the algorithm, full-length TbPEX10 was subjected to peptide array scanning (Fig. 4C). GST-TbPEX19 bound to the highest scoring region (aa 172 to 196), named hereafter as BS2, which was consistent with the result of the binding-site screen (Fig. 4), but also to a second region in PEX10 (BS1; aa 82 to 102) that was not classified as a PEX19-binding site by the prediction program. To see whether the latter site is trypanosome specific, a replicate blot was incubated with purified GST-HsPEX19. Human PEX19 bound strongly to the predicted BS2 but only marginally to BS1 in this assay. This result suggests that the latter site significantly deviates from the typical conserved PEX19-binding site.

PEX10 targeting in humans and T. brucei. The presence of two apparently nonequivalent PEX19 binding sites in TbPEX10 prompted us to test for their individual roles in targeting this PMP in vivo. We generated constructs encoding TbPEX10 deletion mutants fused to GFP (as well as a full-length GFP-TbPEX10 fusion) for expression in both T. brucei and human cells. Immunoblot analysis of lysates from induced T. brucei transfectants showed that all proteins were expressed and that each migrated at its expected molecular mass (Fig. 5). Figure 5 shows the targeting of each construct in human cells (left panels) or in T. brucei (right panels). Full-length TbPEX10 fused to GFP was localized to glycosomes in T. brucei and to peroxisomes in human fibroblasts, demonstrating that this trypanosomatid PMP is able to target to the human organelle. The necessity of the individual PEX19-binding sites for appropriate targeting was then analyzed by splitting the protein in two parts, one fragment containing aa 1 to 124, including the first predicted TMD and BS1, and a second fragment containing aa 113 to 299, including TMD2 and BS2. The N-terminal fragment was cytosolic in both T. brucei and human cells, indicating that BS1 and TMD1 are not sufficient for targeting to either the glycosome or the peroxisome (Fig. 5). In contrast, the C-terminal TbPEX10 fragment gave rise to a peroxisomal staining pattern when expressed in human fibroblasts, although some cytosolic staining was also noted. Expression of the same construct in T. brucei resulted in a punctate, glycosomal pattern for the GFP fluorescence. Surprisingly, the IFA showed that in these cells, glycosomal matrix proteins were mislocalized [see anti-glycosome antibody staining for TbPEX10(113-299) in Fig. 5], indicating that the truncated protein, while able to target to the glycosome, caused a dominant-negative defect in matrix protein import. Within 2 days after induction, many of the parasites were swollen or dead. This fusion protein contains the only motif known to be essential for function, the C-terminal RING domain (35). Although not the focus of the current study, this result indicates that the N-terminal half of PEX10 may also play a critical although yet undetermined role. Indeed, a roughly corresponding N-terminal deletion of S. cerevisiae PEX10 is not able to complement a pex10 mutant (S. Daubert and R. Erdmann, unpublished data).

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FIG. 5. Evolutionarily conserved PEX19 binding site-dependent targeting of TbPEX10. Full-length GFP-TbPEX10 and various truncations (cartooned at left of panels) were expressed in human or T. brucei procyclic cells to assess the function of the TbPEX10 targeting signal. Immunoblot analysis of the T. brucei transfectants are shown for each construct, either uninduced (–) or induced (+) for expression of the fusion protein. These blots demonstrate migration to the expected molecular masses of 59 kDa for GFP-TbPEX10(173-190), 42 kDa for GFP-TbPEX10(1-124), 48 kDa for GFP-TbPEX10(113-299), and 45 kDa for GFP-TbPEX10(140-299). The full-length construct in T. brucei was previously verified (45). (Left three panels) GFP fusion proteins were expressed in human fibroblasts by transient transfection with appropriate expression plasmids. Cells were processed for the IFA using polyclonal anti-PEX14 antibodies. Merged images reveal predominant colocalization of the GFP fusion proteins with peroxisomal PEX14 (Px). Bar, 10 µm. (Right three panels) GFP fusion constructs were transfected into T. brucei procyclic cells to create stable cell lines. Induction with Tet was followed by the IFA at 24 h, as described for Fig. 2. Bar, 2 µm.

To test for the importance of BS2 in the context of the full-length protein, a fusion protein missing just BS2 (aa 173 to 190) was also expressed in these two cell lines (Fig. 5). In both human fibroblasts and T. brucei, this fusion protein was cytosolic, indicating that BS2 is indeed necessary for targeting. The importance of TMDs for trypanosomatid PMP targeting was analyzed with a final GFP fusion protein containing aa 140 to 299, which includes BS2 but lacks either TMD. This truncated protein did not localize to T. brucei glycosomes or to human peroxisomes. Taken together, these results show that the predicted binding site BS2 and a transmembrane domain are required for targeting to either glycosomes or peroxisomes. Overall, these data show that the targeting patterns for TbPEX10 are similar in both human and T. brucei cells and that the nonconserved BS1 plays no role or only an ancillary role in PMP targeting.

Targeting of TbPEX12 and TbPEXP14 in human fibroblasts. The results for TbPEX10 localization in both human and T. brucei indicate that PEX19-dependent targeting is conserved for at least one trypanosomatid PMP. That this conservation is valid on a more general basis is suggested by the number of correctly predicted PEX19-binding sites shown in Fig. 4A. However, another PMP, the RING finger protein TbPEX12 (29, 45), does not seem to follow this prediction pattern, as it did not show binding of its highest scoring regions to GST-TbPEX19. We therefore assessed whether this protein would target to human peroxisomes. Despite the fact that our algorithm was unable to predict a PEX19-binding site for this protein, TbPEX12 clearly localized to human peroxisomes (Fig. 6A, left panels), as indicated by its punctate staining pattern and colocalization with the peroxisomal marker protein HsPEX14.

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FIG. 6. Targeting of TbPEX12 and TbPEX14 in human fibroblasts. (A) Conserved targeting of TbPEX12. Human fibroblasts were transiently transfected with a plasmid designed to express a GFP fusion of TbPEX12. Thereafter, cells were processed for indirect immunofluorescence using polyclonal anti-PEX14 antibodies. The merged image reveals colocalization of the GFP-TbPEX12 with endogenous peroxisomal PEX14 (Px). Bar, 10 µm. The three panels on the right show T. brucei procyclic forms expressing the same GFP fusion protein, analyzed as in Fig. 2, at 24 h postinduction. Bar, 2 µm. (B) Localization of GFP-TbPEX14 was similarly analyzed in human and trypanosome cells, except that peroxisomes were visualized with anti-PMP70 antibodies. No colocalization of GFP-TbPEX14 and PMP70 is observed in the merged image, although the fusion protein is glycosomal in T. brucei.

PEX14, another PMP, is involved in the docking of PEX5 to the peroxisome membrane (2, 14). Previous studies indicate that HsPEX14 binds to a different region of HsPEX19 than do other human PMPs (16). Unlike in PEX12, for which we did identify a PEX19-binding site in the L. major and T. cruzi orthologues, the prediction algorithm did not detect a significant PEX19-binding site in any of the trypanosomatid PEX14 proteins (Fig. 4A). We therefore expressed GFP-TbPEX14 in human fibroblasts to determine whether it would target appropriately to peroxisomes. Interestingly, TbPEX14 was localized to the cytosol in human peroxisomes (Fig. 6B, left panels), although this same fusion protein clearly targets to glycosomes when expressed in trypanosomes (Fig. 6B, right panels). These results indicate that targeting of PEX14 represents an exception to conserved PEX19-dependent targeting of PMPs.

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Molecular taxonomy indicates that trypanosomatids are highly divergent organisms related to relatively obscure groups, such as diplonemids, and more well-studied organisms, such as euglenids, that branch distinctly from organisms, such as fungi, metazoans, and Apicomplexa (47). The ancient divergence of these organisms is reflected in novel processes, such as mitochondrial RNA editing (51) and polycistronic transcription coupled with obligatory trans splicing (37). Trypanosomatids are the most divergent organisms known to possess peroxisomes, and therefore it is perhaps not surprising that the metabolic capabilities of the modified organelle, the glycosome, have adapted considerably compared to those of other organisms (9). Nonetheless, early studies showed that the import signals on matrix proteins are closely related and predominantly cross-functional with those seen in traditional yeast and human systems (7, 50). Furthermore, several of the peroxins required for peroxisomal matrix protein import are conserved in trypanosomatids, implying conservation of the mechanisms and processes involved.

The mechanisms by which membrane proteins are targeted to and inserted in peroxisomal membranes have come under scrutiny recently. A key player in this process is PEX19, a predominantly cytosolic protein that interacts with multiple PMPs (17, 27, 43, 44, 48) and prevents their aggregation in cell-free translation systems (41, 46). PEX19 is required for the biogenesis of functional peroxisomes in all organisms analyzed so far. Previously, we showed that a modest knockdown of PEX19 in T. brucei procyclic cells leads to the generation of enlarged glycosomes and delayed growth (5). Here, we demonstrated by RNAi that PEX19 knockdown in the bloodstream stage is lethal, further validating the essentiality of the glycosome to the mammalian infective stages.

Several previous studies have shown that many PMPs can target appropriately when introduced into heterologous species. Several yeast PMPs target to peroxisomes in mammals (12), human PMPs target to yeast peroxisomes (24), and recently, it was shown that glycosomal ABC transporter GAT2 fragments are able to target to human peroxisomes (58). Molecular analyses have revealed much of the basis for this cross-targeting. The rigid C-terminal domain of PEX19 binds specifically to PMPs in regions that have been previously analyzed by two-hybrid (17) and mutational (16) studies and verified by in vivo testing (27, 31). Such work enabled the generation of an algorithm that predicts potential PEX19 binding sites on yeast and human PMPs (24, 43). Here we extend the studies to the most divergent case, the trypanosome. When fragments of the human ALDP protein were expressed in T. brucei, targeting to glycosomes required the presence of regions containing both the previously identified HsPEX19-binding site and a TMD, similar to the minimal requirements for proper targeting in yeast and human cells. These findings indicate that TbPEX19 can recognize a human PEX19-binding site. Likewise, the HsALDP binding sites for human and T. brucei PEX19 were found to be nearly identical when tested by substitution blot. The fact that both HsPEX19 and TbPEX19 can recognize the same region of this human PMP is especially interesting in light of the relatively low homology between the two PEX19 proteins and the lack of the farnesylation motif on the trypanosomatid orthologue (5). We have gathered evidence that farnesylation is required to increase the binding affinity of human PEX19 towards PMPs without changing its binding site specificity (data not shown).

The above results encouraged us to employ the algorithm to search for PEX19-binding sites in all known trypanosomatid PMPs and then to test these sites experimentally for their abilities to bind TbPEX19. Almost all PMPs contained one or more predicted sites, and typically at least one of these bound to TbPEX19. We studied one protein, PEX10, in detail. The algorithm predicted two sites, and peptide scanning confirmed one of these sites. In view of the predictions for the entire TbPEX10, the appearance of the true binding site is striking, with a number of hits clustering around the peak scoring peptide (FVLMLELLIRLWRAV) (Fig. 4B), whereas the erroneously predicted site is represented by a single peak only. Additionally, a PEX19 binding site was predicted in all three trypanosomatid orthologues in this position. In vivo studies then confirmed that this specific binding site is required for the targeting of TbPEX10 to glycosomes and peroxisomes. In studies of the PMP70-like protein GAT1, other researchers have shown that residues 1 to 169 are sufficient to confer glycosomal targeting in GFP fusions, whereas aa 1 to 141 are not (58). Interestingly, the PEX19 binding site identified in our study maps in silico to aa 98 to 112 (Table 1) and in vitro to aa 92 to 120 (Fig. 4A) (TbGAT1). The 1-141 fusion may traffic improperly because it is truncated within the transmembrane domain adjacent to the binding site identified in the current studies. On the other hand, the algorithm fails to correctly predict a PEX19-binding site for TbPEX12, even though this protein clearly is able to target to both trypanosome and human peroxisomes. It is interesting to note that while TbPEX12 is an integral membrane protein, it does not possess strongly predicted transmembrane domains and could be targeted via a distinct interaction, which could either map to a different region of PEX19 or possibly be PEX19 independent. Hence, the algorithm is a useful but imperfect tool for guiding in vivo experiments assessing potential targeting sequences of trypanosomatid PMPs.

PEX3 and PEX14 are the only PMPs known to bind to the N-terminal portion of PEX19. PEX3 binds with high affinity to a 31-aa region at the N terminus of human PEX19 and with much lower affinity to a region slightly overlapping the PMP binding region, while PEX14 binds just downstream of the PEX3 high-affinity binding region (16, 32, 46). The C-terminal region of PEX19 binds to all other PMPs analyzed thus far, and this interaction is the focus of the prediction matrix. Thus, the inability to detect a PEX19-binding site in TbPEX14 is not unexpected, particularly given that the predicted PEX19-binding site in HsPEX14 did not bind HsPEX19 (24). It is interesting to compare the sequence similarity of human and T. brucei PEX19 across these domains. The alpha helix known to convey high-affinity binding to PEX3 is most highly conserved (45% similar or identical residues), and the helices involved in PMP binding are also relatively well conserved (41%). In contrast, the PEX14 binding helix is only 21% conserved. The high level of similarity in the PEX3 binding region is intriguing given that it has not been possible to identify a PEX3 orthologue in trypanosomatids on the basis of sequence analysis. Given its essential role in PMP insertion and peroxisome biogenesis, a functional PEX3 orthologue likely exists, although the sequence has considerably diverged. The low similarity in the PEX14 binding region of PEX19 ties well with our findings that TbPEX14 did not target to human peroxisomes. A precedent exists for a higher level of species specificity within this region. Previous work using a chimera of human and yeast PEX19 containing the N-terminal two-thirds of the yeast protein and the C-terminal one-third of the human protein showed that it could complement a yeast PEX19 mutant (21). All other combinations failed to complement. Only the C-terminal domain of PEX19 (the PMP interactor) is exchangeable. The potential of specifically interrupting glycosomal biogenesis as opposed to peroxisome biogenesis could lie in the PEX14-PEX19 interaction or in the as yet unidentified PEX3.

 
We thank Peter Kessler and Bryan Jensen for helpful discussions.

This work was supported in part by grant NIH R01 AI22635 (M.P.), Deutsche Forschungsgemeinschaft grants SFB480 (H.R.), SFB449 (R.V.-E.), and SFB642 (R.E.), and the FP6 European Union Project "Peroxisome" (LHSG-CT-2004-512018).

 
* Corresponding author. Mailing address: Seattle Biomedical Research Institute, 307 Westlake Ave. N., Seattle, WA 98109. Phone: (206) 256-7315. Fax: (206) 256-7229. E-mail: marilyn.parsons{at}sbri.org

Published ahead of print on 22 June 2007.

Supplemental material for this article may be found at http://ec.asm.org/.

These authors contributed equally to the manuscript.

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Eukaryotic Cell, August 2007, p. 1439-1449, Vol. 6, No. 8
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