CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS

CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS CHAPTER 24 – PEROXISOMAL ABC TRANSPORTERS

497 24 CHAPTER PEROXISOMAL ABC TRANSPORTERS SHLOMO ALMASHANU AND DAVID VALLE INTRODUCTION The set of proteins found in the membranes of mammalian peroxisomes includes four half ABC transporters (ALDP, ALDR, PMP70, P70R) comprising a distinct subset of the superfamily of ABC transporters designated subfamily D Each has an N-terminal hydrophobic transmembrane domain with multiple transmembrane segments (TMS) and a hydrophilic C-terminal half containing a nucleotide-binding domain (NBD) with Walker A and B motifs Limited topology studies indicate that the C-terminal hydrophilic halves of ALDP and PMP70 extend into the cytosol (Contreras et al., 1996; Kamijo et al., 1990) To provide context in what follows, we first briefly review peroxisome function, genetic diseases and biogenesis; we then focus on the molecular, cellular and evolutionary biology of the mammalian peroxisomal ABC transporters OVERVIEW OF PEROXISOME BIOLOGY Peroxisomes are typically spherical (0.1–1 ␮m diameter), single-membrane-bound organelles present in numbers ranging from a few hundred to a few thousand in most mammalian cells (Figure 24.1) (Gould et al., 2001; Purdue and Lazarow, 2001; Tabak et al., 1999) The pH of the mammalian peroxisome matrix has variously been estimated to be more basic (Dansen et al., ABC Proteins: From Bacteria to Man ISBN 0-12-352551-9 2000) or similar to (Jankowksi et al., 2001) that of cytosol The dense, proteinaceous peroxisome matrix contains 50 or more enzymes, which participate in a variety of metabolic pathways including ␤-oxidation of straight and branched, very long (уC24) and long (C14–22) chain fatty acids (VLCFA and LCFA, respectively), synthesis of cholesterol and ether-lipids (e.g plasmalogens) and oxidation of polyamines, D-amino acids and, in non-primates, uric acid (Gould et al., 2001; Sacksteder and Gould, 2000; Wanders et al., 2001) Many of the peroxisomal oxidation reactions liberate H2O2, which is detoxified by peroxisomal catalase The peroxisome membrane contains a characteristic set of peroxisomal membrane proteins (PMPs) that, in addition to the peroxisomal ABC transporters, includes other small molecule transporters, enzymes and proteins required for import of peroxisomal matrix proteins and peroxisomal membrane biogenesis, plus many whose function is uncertain (Schäfer et al., 2001) PEROXISOMES AND GENETIC DISEASE The rapid growth of our understanding of peroxisome biogenesis and function over the last decade has depended in part on careful analysis of cells from patients with inherited defects in these processes Two categories of peroxisomal genetic disorders are recognized, both with profound phenotypic consequences The first includes the peroxisomal biogenesis disorders (PBDs), a genetically heterogeneous group of Copyright 2003 Elsevier Science Ltd All rights of reproduction in any form reserved 498 ABC PROTEINS: FROM BACTERIA TO MAN A B C Figure 24.1 Peroxisome morphology A, Electron micrograph of peroxisomes in human liver visualized by diaminobenzidine staining for catalase activity (image kindly supplied by M Espeel and F Roels, University of Gent, Belgium); scale bar is 0.5 ␮m Px, peroxisome; M, mitochondrion; ER, endoplasmic reticulum B, Immunofluorescence of human fibroblasts stained with anti-PMP70 antibody Note the punctate appearance of normal peroxisomes C, Confocal image of S cerevisiae, grown on oleic acid to induce peroxisomes and expressing C-terminal PTS1 tagged GFP, which localizes to peroxisomes autosomal recessive disorders characterized by deficiency of multiple peroxisomal functions (Gould and Valle, 2000b; Gould et al., 2001) Zellweger syndrome (MIM#214100), a lethal developmental and metabolic disorder, is the phenotypic paradigm for the PBD Cell fusion and molecular studies have identified at least 12 genes responsible for these disorders, none of which encode peroxisomal ABC transporters (Gould and Valle, 2000b; Gould et al., 2001) The second category includes disorders in which a single peroxisomal function is deficient (Wanders et al., 2001) More than a dozen have been recognized The exemplar is X-linked adrenoleukodystrophy (X-ALD)(MIM#300100), a progressive neurological disorder caused by mutations in ABCD1, the gene that encodes ALDP, a peroxisomal ABC transporter (see below) (Moser et al., 2001) The principal biochemical abnormality of X-ALD, accumulation of VLCFA in plasma and tissues, together with the existence of a VLCFA ␤-oxidation pathway in the peroxisome, has implicated ALDP in the transport of VLCFA or VLCF acyl-CoAs into the peroxisome Tissues and cultured cells from X-ALD patients have a 60–80% reduction in ␤-oxidation of VLCFA PEROXISOME BIOGENESIS Over the last decade at least 23 genes (designated PEX genes) have been identified that encode proteins (peroxins) necessary for peroxisome biogenesis (Gould and Valle, 2000b; Gould et al., 2001; Purdue and Lazarow, 2001) The nomenclature convention is that orthologous PEX genes in different species are indicated by the same number (Distel et al., 1996) Thus, Saccharomyces cerevisiae PEX1 is orthologous to human PEX1 Regulation The number of peroxisomes per cell is dynamic and varies with the metabolic state (Chang et al., 1999; Gould et al., 2001; Purdue and Lazarow, 2001; Subramani, 1998) In rodents, certain hypolipidemic drugs, plasticizers and naturally occurring lipids induce higher peroxisome numbers and the expression of genes encoding many matrix proteins and peroxisome membrane proteins (PMPs) including the ABC transporters (Reddy et al., 1986; Zomer et al., 2000) This coordinated induction is mediated primarily by activation of peroxisome proliferatoractivated receptor ␣ (PPAR␣), a member of the nuclear hormone receptor superfamily (Kersten et al., 2000; Wahli et al., 1999) Activated PPAR␣ heterodimerizes with a second nuclear hormone receptor, retinoid X-responsive receptor ␣, to form an active transcript factor that recognizes cis-acting sequences, peroxisome proliferator responsive elements (PPRE, consensus two direct AGGA/ TCA separated by a single base pair), in the promoters of its target genes (JugeAubry et al., 1997; Kersten et al., 2000) PEROXISOMAL ABC TRANSPORTERS In normal cells, an increase in peroxisome number results mainly from maturation and enlargement of existing peroxisomes with uptake of both membrane and matrix components followed by fission into daughter organelles (Gould and Valle, 2000a; Purdue and Lazarow, 2001) De novo synthesis of peroxisomes is also possible (South and Gould, 1999) Matrix proteins Peroxisomal matrix proteins are synthesized on free cytosolic ribosomes and targeted post-translationally to the organelle by specific cytosolic receptors that recognize cis-acting sequences (peroxisomal targeting signals or PTSs) in the primary peptide sequence (Gould and Valle, 2000b; Gould et al., 2001; Purdue and Lazarow, 2001) Most matrix proteins are targeted by PTS1, a C-terminal -SKL or conservative variant thereof A few matrix proteins are targeted by PTS2, a degenerate sequence (-R/ KX5Q/HL-) located near the N-terminus A few matrix proteins appear to be targeted by as yet unrecognized PTSs (Purdue and Lazarow, 2001) The PTS1 and receptors have been cloned and characterized The former, PEX5, is a tetratricopeptide repeat protein (Dodt et al., 1995; Fransen et al., 1995; Wiemer et al., 1995); the latter, PEX7, is a WD40 repeat protein (Braverman et al., 1997; Motley et al., 1997; Purdue et al., 1997) The structure of the PEX5 tetratricopeptide repeat domain complexed with a PTS1 peptide has been mapped in S cerevisiae (Klein et al., 2001) and solved for human PEX5 (Gatto et al., 2000a, 2000b) Both PEX5 and PEX7 bind their cargo proteins in the cytosol and transport them to the peroxisome, where they interact with specific docking proteins in the peroxisomal membrane, release their cargo and recycle to the cytosol (Dodt and Gould, 1996) In mammalian cells, the long isoform of PEX5 interacts with PEX7 and is necessary for its function (Braverman et al., 1998; Otera et al., 1998, 2000) Membrane proteins Like peroxisomal matrix proteins, PMPs are synthesized on free cytosolic ribosomes and targeted to the organelle by cis-acting targeting sequences (membrane peroxisome targeting signals or mPTS) In contrast to the discrete, well-defined, single targeting sequences found in matrix proteins, the model emerging for several PMPs includes two non-overlapping targeting segments for each peptide, either of which is sufficient for localization and insertion into the peroxisome membrane In most cases these targeting segments are relatively long and include one or two TM segments This model derives from recent work on several integral PMPs including: human PMP34 (Jones et al., 2001) and its fungal orthologue PMP47 (Dyer et al., 1996; Wang et al., 2001), a peroxisomal member of the mitochondrial carrier family that probably functions as an ATP/ADP transporter (van Roermund et al., 2001); human PMP22, an abundant PMP of unknown function (Brosius et al., 2002; Pause et al., 2000); and PEX13, the docking protein for matrix protein receptors (Jones et al., 2001) Attempts to define specific and necessary sequence motifs in these targeting segments have not been successful A fiveresidue sequence of basic residues implicated in initial studies of PMP47 is not a consistent feature and some targeting persists when these residues are entirely replaced by alanines (Biery and Valle, unpublished; Wang et al., 2001) Work on PMP70 by ourselves (Almashanu and Valle, unpublished) and others (Sacksteder and Gould, 2000) indicates that the peroxisomal membrane ABC transporters also use this two targeting segment mechanism A related question is how the newly synthesized, hydrophobic PMPs traverse the aqueous cytosol to acquire their proper location in the peroxisomal membrane Recent studies with cells from patients with a peroxisome biogenesis disorder (PBD) have implicated PEX19, a farnesylated, mainly cytosolic protein, as a possible receptor for PMPs analogous to the role of PEX5 and PEX7 in the targeting of matrix proteins (Gotte et al., 1998; James et al., 1994; Sacksteder et al., 2000; Snyder et al., 2000) Binding studies show that the multiple PMP targeting segments described above are recognized by PEX19 (Brosius et al., 2002; Jones et al., 2001; Sacksteder et al., 2000) Additionally, two integral PMPs, PEX3 and PEX16, are probably involved in this process (Honsho et al., 1998; Muntau et al., 2000; Snyder et al., 1999; South and Gould, 1999; South et al., 2000) Mutations in any of these three genes not only cause a PBD phenotype but also are associated with the distinct cellular phenotype of absence of peroxisome membranes (Ghaedi et al., 2000; Hettema et al., 2000; Honsho et al., 1998; Matsuzono et al., 1999; Muntau et al., 2000; South and Gould, 1999) 499 500 ABC PROTEINS: FROM BACTERIA TO MAN non-processed pseudogenes with 92–96% nucleotide identity located elsewhere in the genome complicate the molecular diagnosis of X-ALD (Table 24.1) An online X-ALD database (www.x-ald.nl) contains useful information for patients and professionals and is maintained in a collaborative effort between the Peroxisomal Diseases Laboratory at the Kennedy Krieger Institute, Baltimore, MD, USA and the Laboratory of Genetic Metabolic Diseases at the Academic Medical Center, Amsterdam, the Netherlands ALDR is encoded by ABCD2 comprising 10 exons distributed over 33 kb on chromosome 12q12 (Table 24.1) The genomic organization of ABCD2 closely resembles that of ABCD1 consistent with the conclusion, based on sequence similarity (64% identity), that these two members of the peroxisome ABC transporter subfamily diverged recently from a common ancestor (see Figure 24.4) Moreover, this high sequence similarity suggests that the function between ALDP and ALDR may be partially redundant Thus, ALDR may have the potential to modify the phenotype of X-ALD (Holzinger et al., 1997a) Induction of the ABCD2/Abcd2 gene in PEROXISOME ABC TRANSPORTERS The peroxisome ABC transporters are all half ABC transporters and, as a group, are the most thoroughly studied integral PMPs One, PMP70, is routinely used as the standard marker protein for peroxisomal membranes (Figure 24.1) Despite this wealth of information, much remains to be learned about these molecules In what follows, we review the current state of knowledge of these interesting proteins GENES ALDP is encoded by ABCD1, the gene responsible for X-ALD ABCD1 spans ϳ21 kb, contains 10 exons (Sarde et al., 1994) and maps to Xq28 (Table 24.1) (Mosser et al., 1994) ABCD1 mutations, including frameshifting insertions and deletions and nonsense mutations identified in X-ALD patients, provide compelling evidence that it is the gene responsible for this neurodegenerative disorder Four autosomal ABCD1 TABLE 24.1 MAMMALIAN PEROXISOMAL ABC TRANSPORTERS The nomenclature is based on the guidelines for the human and the mouse ABC transporter gene nomenclature (http://www.gene.ucl.ac.uk/nomenclature/genefamily/abc.html) The information on the localization, nucleotide sequence, locus and PubMed IDs was derived from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov) Symbol Previous symbol, ABC # Alias Map location Number of exons Genomic NT mRNA NM Locus ID OMIM PMID Hs ABCD1 ALD ABC42 ALDp ALD AMA Pseudogene Pseudogene Pseudogene Pseudogene ALDR ALDRp PMP70 PXMP1 P70R PMP69 ALD ALDR PMP70 P70R Xq28 10 025965 000033 215 300100 8441467 10 – – 024779 – – – – – – 005164 23785 26983 26982 26957 225 601081 8829626 9215666 9215666 9215666 8577752 1p21–p22 23 029227 002858 5825 170995 1536884 – 005050 5826 603214 9266848 – – – – 007435 011994 008991 008992 11666 26874 19299 19300 Hs ABCD1P1 Hs ABCD1P2 Hs ABCD1P3 Hs ABCD1P4 Hs ABCD2 Hs ABCD3 Hs ABCD4 Mm Abcd1 Mm Abcd2 Mm Abcd3 Mm Abcd4 ALDL1 ABC39 PXMP1 ABC43 PXMP1L ABC41 2p11 10p11 16p11.2 22q11 12q11 14q24.3 X 29.5 cM 15 E–F 56.6cM 12 39.0 cM 19 OMIM, Online Mendelian Inheritance in Man PMID, Pubmed entry or Pubmed indexed for MEDLINE 11076861 10504404 11076861 10708515 PEROXISOMAL ABC TRANSPORTERS cells from X-ALD patients or in the Abcd1 knockout mice by exposure to 4-phenylbutyrate temporarily corrected the deficiency of VLCFA ␤-oxidation (Kemp et al., 1998) If this response could be maintained, it would be a promising therapeutic strategy for X-ALD Expression of ABCD2 is induced by fibrates and other xenobiotics as well as certain endogenous lipids in a response that depends on PPAR␣ (Fourcade et al., 2001) Survey of kb of 5Ј flanking sequence of rat Abcd2 identified several candidate PPREs (see above) but none of these were functional in transient transfection assays with chimeric promoter/reporter constructs Thus, either the responsible PPRE is located more remotely or the PPAR␣-dependent regulation of the Abcd2 involves a different mechanism (Fourcade et al., 2001) An earlier study showed that the human and murine ABCD2 genes share more than 500 bp of conserved 5Ј flanking sequence with potential Sp1- and AP-2-binding sites but no TATAA box Moreover, in transient transfection assays with chimeric promoter/ reporter constructs, 1.3 kb of the 5Ј-flanking region of human and murine ABCD2 genes was shown to be necessary for upregulation by 9-cis-retinoic acid and forskolin, while no effect of PPAR␣ could be detected (Pujol et al., 2000) PMP70, encoded by ABCD3, is abundantly and widely expressed and, like ABCD2, is induced in mammalian liver following the administration of fibrates (Kamijo et al., 1990) A rat Abcd3 cDNA was initially identified by screening an expression library (Kamijo et al., 1990) and the sequence of the rat cDNA was used, in turn, to clone the human PMP70 cDNA and structural gene (Gärtner et al., 1992, 1998) Human ABCD3 maps to chromosome 1p21–p22 (Gärtner et al., 1993) and comprises 23 exons distributed over 65 kb of genomic DNA (Table 24.1) The proximal promoter region of human and murine ABCD3 genes have a high GC content and multiple consensus Sp1-binding sites, features consistent with its broad tissue expression (Gärtner et al., 1998) Several PPRE-like sequences with the correct spacing are present in the 5Ј flanking sequence of ABCD3 (Berger et al., 1999; Fourcade et al., 2001) The organization of ABCD3 differs from ABCD1 and ABCD2 genes with only of 22 introns falling in positions corresponding to ABCD1 introns This observation plus the fact that the first exon of ABCD1 is exceptionally large (у1286 bp) lead to the speculation that the modern ABCD1 gene may have arisen from an ancient retrotransposition of a cDNA derived from a ABCD3-like gene followed by intron acquisition in the 3Ј half of the gene (Gärtner et al., 1998) P70R, also known as PMP69, is encoded by ABCD4 This gene maps to chromosome 14q24.3, covers 16 kb and has 19 exons (Holzinger et al., 1998; Shani et al., 1997) The position of several ABCD4 introns corresponds to those in ABCD3, consistent with the suggestion, based on sequence similarity, that these two genes are more closely related to each other than to ABCD1 and Also, as in ABCD3, the 5Ј flanking sequence of ABCD4 has a high GC content, contains several consensus Sp1binding sites and lacks a TATAA box No PPREs were identified in the 5Ј 1.8 kb Variant ABCD4 transcripts result from the use of alternative polyadenylation sites and alternative exon splicing events including one that confers an alternative C-terminus (Holzinger et al., 1997b, 1998; Shani et al., 1997) EXPRESSION PATTERNS Northern blot studies of RNA harvested from adult mice have shown different expression patterns for the four peroxisomal ABC transporters (Albet et al., 1997; Berger et al., 1999) Abcd1 is mainly expressed in heart, lung, intestine and spleen; Abcd2 in skeletal muscle and brain; Abcd3 in all tissues studied with greatest abundance in liver and kidney; while Abcd4 mRNA is 10-fold more abundant in kidney than in other tissues analyzed The expression of the four peroxisomal ABC transporter genes is also regulated differentially during mouse brain development Abcd1 mRNA is most abundant in embryonic brain and gradually decreases during maturation; Abcd2 and Abcd4 mRNA accumulates in the early postnatal period; and Abcd3 transcripts increase during the second and third postnatal weeks (Albet et al., 1997; Berger et al., 1999) Similarly, in situ hybridization studies in rat brain showed different spatial and temporal expression patterns of Abcd1 and Abcd3 during postnatal development (Pollard et al., 1995) Abcd3 expression was low at birth and increased to a peak between the second and third week in hippocampus and cerebellum By contrast, Abcd1 expression was maximal at birth in all areas of the brain and decreased thereafter (Pollard et al., 1995) Administration of fenofibrate strongly increased the expression of the Abcd2 and Abcd3 in rat intestine and liver, respectively, but not the expression of 501 502 ABC PROTEINS: FROM BACTERIA TO MAN Abcd1 (Albet et al., 1997) These observations suggest that transcriptional regulation is an important variable in the expression of the peroxisomal half ABC transporters and must be taken into account when considering possible in vivo heterodimerization partners ASSEMBLY OF THE FOUR HALF ABC TRANSPORTERS All known peroxisomal ABC transporters are half transporters that must dimerize to be functional The partially overlapping patterns of developmental and tissue expression suggest that both hetero- and homodimerization are possible Using a yeast two-hybrid system, Liu et al found hetero- and homodimerization of the C-terminal halves of ALDP, ALDR and PMP70 (Liu et al., 1999) P70R was not tested Two mutations in ALDP (P484R and R591Q) known to cause X-ALD impaired both heteroand homodimerization These results were supported by co-immunoprecipitation experiments showing homodimerization of ALDP and heterodimerization of ALDP with either ALDR or PMP70 ALDR also heterodimerized with PMP70 Formation of ALDP homodimers and ALDP/PMP70 heterodimers was also demonstrated by co-immunoprecipitation of in vitro synthesized proteins (Smith et al., 1999) Considering the protein interaction and expression studies, it seems likely that both homodimerization and heterodimerization of certain peroxisomal half ABC transporters takes place and that this may vary from tissue to tissue The functional consequences of the choice of partners are not known TARGETING TO PEROXISOMAL MEMBRANE As discussed above, our understanding of how PMPs achieve their proper and specific location in the peroxisomal membrane is not well understood Nevertheless, recent work suggests that PEX19, a farnesylated protein located primarily in the cytosol, appears to have a major role in PMP import PEX19 interacts in vitro with numerous PMPs including ALDP, PMP70 and ALDR (Gloeckner et al., 2000; Sacksteder et al., 2000; Snyder et al., 2000) More specifically, a region of ALDP located towards the N-terminus (between amino acids 67–186) has been shown to be important for proper peroxisomal targeting and an overlapping fragment (residues 1–203) interacts in a two-hybrid system with PEX19 (Gloeckner et al., 2000) Similarly, expressing a series of N-terminal and C-terminal deletions of PMP70 tagged with a C-terminal green fluorescent protein (GFP) in Chinese hamster ovary (CHO) cells, we localized a peroxisomal membrane targeting signal to the N-terminal 80 amino acids of PMP70 as well as a second site influencing targeting in the C-terminal 100 amino acids (Almashanu and Valle, unpublished observations) Additionally, we made a chimeric protein with the 183 N-terminal residues of PMP70 followed by the 428 C-terminal residues of its Escherichia coli homologue (YDDA) tagged with GFP When expressed in CHO cells, the chimeric PMP70/YDDA-GFP localized to peroxisomes while YDDA-GFP alone showed a nonperoxisomal pattern Mutagenesis studies of conserved residues in the N-terminal 80 amino acids of PMP70 failed to detect a discrete targeting sequence This suggests that recognition of PMP70 by the targeting apparatus depends on more general secondary structure features rather than on specific residues TOPOLOGY By analogy to other ABC transporters, the N-terminal hydrophobic half of the peroxisomal ABC transporters is expected to have six TM segments However, the location and number of these hydrophobic segments has been difficult to establish with certainty (see also Chapter 2) Analyses with multiple protein motif prediction algorithms failed to identify six unequivocal TM segments (TMS) in any of the peroxisomal half ABC transporters (Figure 24.2) Moreover, there was some variation in the location of the predicted TMS In Figure 24.2, we present the TMSs predicted by several algorithms for 11 PMP70 homologues, from bacteria to mammals The location of five TMSs is clear; the position of the sixth is less certain The initial description of rat PMP70 by Kamijo et al included a protease sensitivity study indicating that the C-terminal hydrophobic half of PMP70 faces the cytosol (Kamijo et al., 1990) Similarly, immunohistochemical studies with antibodies directed at specific segments of ALDP indicated that the C-terminal half of the protein projects into the cytosol (Contreras et al., 1996) Additionally, protease treatment followed by immunoblot analysis showed that the C-terminal segment of ALDP could be released from the surface of intact rat liver PEROXISOMAL ABC TRANSPORTERS Figure 24.2 Alignment of the human peroxisomal ABC transporters Amino acid sequences were aligned using the MegAlign program (DNASTAR Inc.) Identical residues in two or more polypeptides are boxed in black The indicated transmembrane segments were predicted using the transmembrane region detection programs available at http://www.us.expasy.org The labeled solid overlines designate the EAA-like motif and the NPDQ motif (see text) The heavy solid overline designates an N-terminal helical hydrophobic region of unknown function present in ALDP, ALDR and PMP70 peroxisomes and retain its ability to bind ATP in vitro (Contreras et al., 1996) We are unaware of any topology studies of ALDR or P70R NON-MAMMALIAN HOMOLOGUES OF THE PEROXISOMAL MEMBRANE ABC TRANSPORTER Homologues from several non-mammalian species have been identified (Smith et al., 1999); those from S cerevisiae have been well characterized PXA1/PAL1/PAT2 (Hettema et al., 1996; Shani et al., 1995; Swartzman et al., 1996) and PXA2/PAT1 (Hettema et al., 1996; Shani and Valle, 1996) are the two yeast homologues of the mammalian half ABC transporters Taking advantage of the induction of PMPs and peroxisomal matrix proteins by growth on oleic acid as a sole carbon source, Shani et al used degenerate PCR primers corresponding to the conserved Walker A and Walker B sequences of ABCD1 and ABCD3 to clone PXA1 The conceptual protein product Pxa1p has 758 amino acids, a predicted molecular mass of 87 kDa and is slightly more similar to ALDP than to PMP70 (Shani et al., 1995) Swartzman et al used an alternate strategy to clone a cDNA identical with PXA1 503 504 ABC PROTEINS: FROM BACTERIA TO MAN over the 758 C-terminal amino acids but with an additional 112 N-terminus codons with a predicted protein mass of 100 kDa (Swartzman et al., 1996) The shorter Pxa1p is clearly functional in that it rescues growth on oleic acid in mutant yeast lacking PXA1 (Shani et al., 1995) Functional studies with Pal1p were not reported and the N-terminal extension of Pal1p is not homologous with the peroxisomal ABC transporters of other species Thus, the significance of this N-terminal extension is uncertain PXA2/PAT1, originally identified as YKL741, encodes a half ABC transporter with highest similarity to mammalian PMP70 and ALDP Shani et al showed that the combined disruption of PXA1 and PXA2 gave a growth phenotype identical to that of either single disruption (Shani and Valle, 1996) and that the stability of Pxa1p was reduced in yeast with a PXA2 deletion Finally, in co-immunoprecipitation studies with either Pxa1p or Pxa2p, they showed direct physical evidence for the heterodimerization of the two proteins to assemble a full peroxisomal half ABC transporter Thus, the functional transporter in yeast is a heterodimer of Pxa1p/Pxa2p CONSERVED SEQUENCE MOTIFS Availability of sequence information of peroxisomal ABC transporters from yeast and mammals provides the opportunity to look for conserved sequence motifs of possible functional significance In addition to the TM segments and the Walker A and B and C segments of the NBD, at least two additional conserved motifs can be identified in the peroxisomal ABC transporters The first, the EAA-like motif, is a 15 amino acid sequence (- N S E E I A F Y X G X K X E X where, in a comparison of Pxa1p, Pxa2p, PMP70 and ALDP, the designated residues are present in three out of four and the underlined residues are present in all four proteins) The EAA-like motif is present between TMS and and resembles the central core of a 30-residue sequence (the EAA motif) found in a similar location in many prokaryotic ABC transporters (Saurin et al., 1994; Shani et al., 1996b) Mutagenesis studies in Pxa1 showed that conservative missense mutations at E294 and G301 reduce the function of Pxa1p but not alter stability or targeting (Shani et al., 1996a) Recent mutagenesis and crosslinking studies of the prokaryotic EAA motif suggest that this sequence may interact with certain regions of the ATP-binding cassette (Hunke et al., 2000; Mourez et al., 1997) Photoaffinity labeling and mass spectrometry study of the human P-glycoprotein (Pgp, ABCB1) showed that its EAA-like motif (cytoplasmic loop 2) was one of nine tryptic peptides that bind to photoaffinitylabeled substrate analogues (Ecker et al., 2002) These results suggest that the EAA-like motif participates in substrate binding/translocation or in the interaction of these processes with ATP binding/hydrolysis The second conserved motif, which we designate the NPDQ motif (see Figure 24.3 for sequence consensus), is located between TMS and Preliminary studies replacing one, two or four of the residues in the conserved NPDQ core with alanines did not affect targeting (Almashanu and Valle, unpublished) We could not identify this motif in other categories of ABC transporters including other mammalian half ABC transporters like the TAP proteins Therefore, we considered that it might be specific for the peroxisomal ABC transporters and used it to search for the subset of ABC transporters with homology to the known peroxisome members of the superfamily Interestingly, our results suggest that the NPDQ motif is a specific signature for peroxisomal transporters among eukaryotes but that it is also present in a small subset of prokaryotic transporters (see section on evolution, below) FUNCTION OF THE PEROXISOME ABC TRANSPORTERS The spectrum of physiological ligands and the direction of transport is not known with certainty for any of the mammalian peroxisomal half ABC transporters A variety of studies suggest, however, that one or more of the peroxisomal ABC transporters transport straight or branched LCFA or VLCFA or their acyl-CoA derivatives into the peroxisome Two important variables in the transport of fatty acids across membranes are the chain length and the site of activation of the fatty acid to its acylCoA derivative The latter is accomplished by acyl-CoA synthetases that differ in chain length specificity and subcellular location In general, the longer the chain length, the more difficult it becomes for fatty acids to move across the peroxisomal membrane; medium-chain fatty acids not require transporters while LCFAs Activation of fatty acids makes them more polar and impairs movement across the peroxisomal membrane (Hettema and Tabak, 2000) PEROXISOMAL ABC TRANSPORTERS The most detailed studies of the functions of the peroxisomal ABC transporters have utilized S cerevisiae as a model system In this regard, yeast offer several advantages over mammalian cells for the study of peroxisome biogenesis and function (Kunau et al., 1993) In contrast to mammalian peroxisomes, the peroxisomes of yeast are more easily isolated and their components more easily induced Moreover, fatty acid ␤-oxidation in yeast is limited to peroxisomes, while in mammalian cells, ␤-oxidation of fatty acids occurs in both peroxisomes and mitochondria In S cerevisiae, Pxa1p and Pxa2p heterodimerize to form the functional peroxisome ABC transporter that is essential for growth on LCFAs, especially oleic acid, C18:1, as a sole carbon source (Hettema et al., 1996; Shani and Valle, 1996) ␤-Oxidation of LCFA in intact cells deleted for either the PXA1 or PXA2 gene is reduced to approximately 20% of the wild-type level In detergent lysates of these same mutant yeasts, ␤-oxidation of LCFA is unaffected, indicating that the peroxisome membrane is a barrier in the intact mutant yeast (Hettema and Tabak, 2000; Hettema et al., 1996) Using protoplasts in which the plasma membrane has been selectively permeabilized by digitonin, it was shown that C18:1-CoA, but not C8:0-CoA, enters peroxisomes in a Pxa1p/Pxa2p and ATPdependent process (Hettema and Tabak, 2000; Verleur et al., 1997) This result is consistent with the observation that the acyl-CoA synthetase with activity towards long-chain fats is extraperoxisomal in yeast (Hettema et al., 1996) Thus, the available evidence indicates that the yeast PXA transporter is necessary for the transport of LCF acyl-CoAs into the peroxisome Our understanding of peroxisomal ABC transporter function in mammalian cells derives largely from observations made in cells or tissues with mutations in one or more of the transporters Mutations in ABCD1 cause X-ALD, a neurodegenerative disorder with a highly variable clinical phenotype (Moser et al., 2001) Biochemically, X-ALD patients accumulate VLCFA in plasma and tissues and exhibit deficient VLCFA ␤-oxidation with decreased activity of the peroxisomal VLCFA acyl-CoA synthetase (VLCS) that activates VLCFAs to their CoA thioesters (Moser et al., 2001) The latter is thought to be localized on the matrix side of the peroxisome membrane (Lazo et al., 1990; Steinberg et al., 1999b) Functional interaction between ALDP and peroxisomal VLCS is also implied by the observation of a synergistic effect on VLCFA ␤-oxidation when both VLCS and ALDP were overexpressed in humans and mouse fibroblasts (Steinberg et al., 1999a; Yamada et al., 1999) Several hypotheses regarding the functional relationship between VLCS and ALDP and their role in the pathogenesis of X-ALD have been proposed but the mechanism remains obscure A relationship between fatty acid ␤-oxidation and PMP70 has also been suggested Imanaka et al (1999) demonstrated a two- to threefold increase in ␤-oxidation of palmitic acid (C16:0) in CHO cell line overexpressing PMP70, whereas the oxidation of lignoceric acid (C24:0) decreased about 30–40% In summary, current data suggest that ALDP and PMP70 are involved in the transport of LCFA and VLCFA or their CoA derivatives across the peroxisomal membrane Creation of mouse models, each lacking one of the four peroxisomal half ABC transporters, also has the promise of providing functional insight Targeted knockouts for the genes encoding ALDP, ALDR and PMP70 have been produced (Forss-Petter et al., 1997; Lu et al., 1997; Yamada et al., 2000) The X-ALD mouse model has some of the human biochemical features including high levels of VLCFA in brain and adrenal gland However, the mice appear to lack the neurological phenotype of humans as they not develop symptoms or evidence of cerebral or spinal cord demyelination by up to years of age The phenotypes of both the ALDR and the PMP70 knockout mice not correspond to a recognizable human disease Mice lacking PMP70 have impaired metabolism of very long branched-chain fatty acids including pristanic acid, phytanic acid and bile acid precursors (Jimenez-Sanchez et al., 2000) Biochemical studies of purified peroxisomal ABC transporters in reconstituted lipid vesicles should help to clarify our understanding of their function but have not yet been described EVOLUTION OF THE PEROXISOMAL HALF ABC TRANSPORTERS The superfamily of ABC proteins is large and diverse The availability of whole genome sequences from an increasing number of organisms has led to the identification of many new members and to a better understanding of the set of ABC transporters characteristic of each species Taking advantage of this sequence information, we searched for a specific signature sequence for the ABCD subfamily that would identify all known peroxisomal ABC 505 506 ABC PROTEINS: FROM BACTERIA TO MAN Figure 24.3 Sequence alignment of the NPDQ motif from 30 homologues of human ALDP We used ClustalX 1.81 to align the protein sequences listed in Table 24.2 Color code for residues: G, brown; P, yellow; conserved K, R, red; conserved D, E, purple; conserved neutrals, green, blue, teal Residue number is indicated on the right transporters in different species We used a short segment of a highly conserved motif located at the second predicted loop of the mammalian peroxisomal half ABC transporters (the NPDQ motif; Figure 24.3) and used it to perform BLAST searches of different NCBI databases This specifically identified all the known peroxisomal half ABC transporters as well as their apparent orthologues whose subcellular localization is yet to be determined in other eukaryotes Additionally this search identified a subset of prokaryotic half ABC transporters Interestingly, these prokaryotic transporters are all half ABC transporters, each is encoded by a single gene without subdivision into an operon We used more than 30 of the hits (Table 24.2) to run the ClustalX algorithm, producing a multiple sequence alignment, and we analyzed this comparison to generate a phylogenetic relationship by maximum parsimony (Figure 24.4) This analysis indicates that among the four mammalian peroxisomal half ABC proteins P70R represents the ancestral gene, more closely related to the bacterial and the plant homologues Pxa1p and Pxa2p, the two S cerevisiae homologues, are more divergent from the ancestral gene and closer to the PMP70/ALDP branch Interestingly, two of the Caenorhabiditis elegans homologues are closely related to P70R, two to PMP70 and only one to ALDP/ALDR This supports the hypothesis that genes encoding these two transporters diverged relatively recently, a hypothesis that is also supported by the genomic organization of these two genes (see section on genes, above) In addition, the genomic organization of ABCD3 gene, when compared to that of ABCD1 and ABCD2, suggests that the modern ABCD1 gene may have arisen from an ancient retrotransposition event followed by intron acquisition (Gärtner et al., 1998) The prokaryotic homologues identified in this search number one per species but Haemophilus influenzae Rd and possibly E coli have two A separate and additional aspect of the evolutionary history of the human ABCD1 gene is the presence of four autosomal ABCD1 pseudogenes PEROXISOMAL ABC TRANSPORTERS TABLE 24.2 HOMOLOGUES FOR THE HUMAN PEROXISOMAL ABC TRANSPORTERS The human ALDP NPDQ motif (Figure 24.3) was used as the query for the PSI- and PHI-blast algorithms, National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/ BLAST/) and for the CMR-blast at TIGR (The Institute for Genomic Research) website (http://tigrblast.tigr.org/cmr-blast) Species Gene/Protein name Number of amino acids Protein accession # PID Homo sapiensa Homo sapiensa Homo sapiensa Homo sapiensa Mus musculusa Mus musculusa Mus musculusa Mus musculus Drosophila melanogaster Drosophila melanogaster Caenorhabditis elegans Caenorhabditis elegans Caenorhabditis elegans Caenorhabditis elegans Caenorhabditis elegans Neurospora crassa Saccharomyces cerevisiaea Saccharomyces cerevisiaea Oryza sativa Arabidopsis thaliana Arabidopsis thaliana Microcystis aeruginosa Nostoc sp Synechocystis sp Haemophilus influenzae Rd Haemophilus influenzae Rd Mycobacterium leprae Mycobacterium tuberculosis Escherichia coli Sinorhizobium meliloti Pasteurella multocida Pasteurella multocida ALDp ALDRp PMP70p P70Rp ALDp ALDRp PMP70p P70Rp CG2316 CG12703 C54G10.3 T10H9.5 C44B7.8 C44B7.9 T02D1.5 B17C10.260 Pxalp Pxa2p 745 740 659 606 736 741 659 606 730 618 660 598 665 661 734 700 758 853 514 514 1383 538 663 661 592 589 638 639 561 606 585 564 NP_000024 NP_005155 NP_002849 NP_005041 NP_031461 NP_036124 NP_033017 NP_033018 AAF59365 AAF49018 CAA99810 AAC19238 AAA68339 AAA68340 T24357 CAB91246 AAC49009 NP_012733 BAB16495 AAD25615 CAB38898 AAF00956 AAF17285 BAA10424 AAC21714 AAC23116 CAA15479 CAB01460 AAC74569 CAA12533 AAK03156 AAK02125 7262393 9945308 4506341 4826958 6671497 6752942 6680612 6680614 7304333 7293647 3875241 3193212 861307 861308 7506941 7800888 619668 6322660 10800075 4585979 4490736 6007549 6563404 1001688 1572982 1574308 2578388 1483552 1787772 2808503 12721409 12720245 McyH NosG YDDA ExsE PM1072 PM0041 a Experimental evidence for peroxisomal localization identified using the 3Ј exons as a hybridization probe (Sarde et al., 1994) These were mapped to pericentric regions of chromosomes 2, 10, 16 and 22 Sarde et al proposed interchromosomal duplications of a genomic segment containing the ABCD1 locus as the mechanism leading to these pericentromeric pseudogenes The breakpoint sequences and phylogenetic analysis of the duplicated segments predicted a two-step transposition model in which a duplication from Xq28 to pericentromeric 2p11 occurred once followed by a rapid distribution of a large duplication cassette among the other pericentromeric regions, 10p11, 16p11, and 22p11 (Eichler et al., 1997) Fluorescence in situ hybridization (FISH) analysis using cloned genomic fragments of the autosomal pseudogenes identified two additional paralogs on chromosomes and 20, which may represent more divergent sequences arising from an earlier duplication (Smith et al., 507 508 ABC PROTEINS: FROM BACTERIA TO MAN 0.396 S meliloti – ExsE 0.316 0.030 995 P multocida – AAK02125 0.336 E coli – YDDA 0.341 C elegans – AAC19238 0.039 1000 0.038 0.300 0.054 0.232 1000 999 0.035 1000 C elegans – CAA99810 0.051 0.365 S cerevisiae – Pxa1p 0.374 S cerevisiae – Pxa2p 0.033 1000 0.148 0.097 1000 0.009 745 0.025 984 0.067 1000 954 0.150 0.203 0.301 0.287 0.023 942 0.112 1000 0.317 D melanogaster – CG2316 0.236 0.013 860 0.051 1000 0.010 0.165 903 0.027 1000 C elegans – T02D1.5 0.147 1000 0.140 1000 0.177 0.154 997 0.044 1000 0.014 718 Nostoc sp – NosG M aeruginosa – McyH A thaliana – AAD25615 0.174 O sativa – BAB16495 0.123 0.131 0.200 0.084 1000 0.030 M musculus – ALDR 0.030 H sapiens – ALDR 0.041 M musculus – ALDP 0.040 H sapiens – ALDP Synechocystis sp – BAA10424 0.172 0.162 1000 C elegans – AAA68339 N crassa – CAB91246 0.249 0.062 1000 C elegans – AAA68340 D melanogaster – CG12703 0.029 M musculus – PMP70 0.026 H sapiens – PMP70 0.010 781 0.183 1000 0.016 771 M musculus – P70R H sapiens – P70R 0.203 H influenzae Rd – AAC23116 M tuberculosis – Rv1819c M leprae – CAA15479 P multocida – AAK03156 H influenzae Rd – AAC21714 0.1 Figure 24.4 Unrooted phylogenetic tree of ALDP homologues We used the ClustalX 1.81 alignment of the protein sequences listed in Table 24.2 as the input for calculating the tree, and the neighbor-joining method to calculate the distances (percent divergence) indicated above each line and the bootstrap values (1000 replicates) below each line The scale at the bottom relates the length of the branch to the number of substitutions 1999) Southern blot analysis of murine and primate genomic DNA indicated that there might have been two duplication events of the X-ALD locus in higher primates, supporting the twostep transposition model An initial expansion appears to have occurred on the evolutionary line leading to orang utans with a subsequent or independent expansion in the great apes (Braun et al., 1996; Smith et al., 1999) ACKNOWLEDGMENTS We thank Amir Rattner for help with the phylogenetic analysis, and Sandy Muscelli for help with manuscript preparation A portion of this work was supported by a grant from NICHD (2PO1HD 10981) (D.V.) 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(2000) Pristanic acid acid and phytanic acid: Naturally occurring ligands for the nuclear receptor peroxisome proliferatoractivated receptor ␣ J Lipid Res 41, 1801–1807 513 ... 10 – – 0247 79 – – – – – – 005164 23785 26983 26982 26957 225 601081 8829626 9215666 9215666 9215666 8577752 1p21–p22 23 029227 002858 5825 170995 1536884 – 005050 5826 603214 9266848 – – – – 007435... 19300 Hs ABCD1P1 Hs ABCD1P2 Hs ABCD1P3 Hs ABCD1P4 Hs ABCD2 Hs ABCD3 Hs ABCD4 Mm Abcd1 Mm Abcd2 Mm Abcd3 Mm Abcd4 ALDL1 ABC3 9 PXMP1 ABC4 3 PXMP1L ABC4 1 2p11 10p11 16p11.2 22q11 12q11 14q24.3 X 29.5... evolutionary history of the human ABCD1 gene is the presence of four autosomal ABCD1 pseudogenes PEROXISOMAL ABC TRANSPORTERS TABLE 24. 2 HOMOLOGUES FOR THE HUMAN PEROXISOMAL ABC TRANSPORTERS The human ALDP