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Human Molecular Genetics Pages 743-749  

Mutation of a putative mitochondrial iron transporter gene (ABC7) in X-linked sideroblastic anemia and ataxia (XLSA/A)
Introduction
Results
Discussion
Materials And Methods
   XLSA/A kindred
   Sequencing and sequence analysis
   cDNA cloning
   Northern hybridization
   Mutation detection
   Cloning and mutagenesis in yeast
   Saccharomyces cerevisiae and Escherichia coli strains and manipulations
Acknowledgements
Note Added In Proof
References

Mutation of a putative mitochondrial iron transporter gene (ABC7) in X-linked sideroblastic anemia and ataxia (XLSA/A)

Mutation of a putative mitochondrial iron transporter gene (ABC7) in X-linked sideroblastic anemia and ataxia (XLSA/A)

Rando Allikmets1,2,+,§, Wendy H. Raskind3,+, Amy Hutchinson1,2,§, Nichole D. Schueck4, Michael Dean2,* and David M. Koeller4,5

1Intramural Research Support Program, SAIC-Frederick and 2Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 21-18, Frederick Cancer Research and Development Center, Frederick, MD 21702-1201, USA, 3Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA and 4Department of Pediatrics and 5Department of Cell and Structural Biology, University of Colorado Health Sciences Center, Denver, CO 80262, USA

Received January 6, 1999; Revised and Accepted February 21, 1999

DDBJ/EMBL/GenBank accession no. AF133659

X-linked sideroblastic anemia and ataxia (XLSA/A) is a recessive disorder characterized by an infantile to early childhood onset of non-progressive cerebellar ataxia and mild anemia with hypochromia and microcytosis. A gene encoding an ATP-binding cassette (ABC) transporter was mapped to Xq13, a region previously shown by linkage analysis to harbor the XLSA/A gene. This gene, ABC7, is an ortholog of the yeast ATM1 gene whose product localizes to the mitochondrial inner membrane and is involved in iron homeostasis. The full-length ABC7 cDNA was cloned and the entire coding region screened for mutations in a kindred in which five male members manifested XLSA/A. An I400M variant was identified in a predicted transmembrane segment of the ABC7 gene in patients with XLSA/A. The mutation was shown to segregate with the disease in the family and was not detected in at least 600 chromosomes of general population controls. Introduction of the corresponding mutation into the Saccharomyces cerevisiae ATM1 gene resulted in a partial loss of function of the yeast Atm1 protein. In addition, the human wild-type ABC7 protein was able to complement ATM1 deletion in yeast. These data indicate that ABC7 is the causal gene of XLSA/A and that XLSA/A is a mitochondrial disease caused by a mutation in the nuclear genome.

INTRODUCTION

Sideroblastic anemias are a heterogeneous group of disorders, characterized by hypochromic microcytic erythrocytes and iron accumulation in the mitochondria of bone marrow erythrocyte precursors (1,2). The disorder can be either acquired or inherited and the mode of transmission may be mitochondrial, autosomal or X-linked. The most common inherited form is X-linked. Mutations in the [delta]-aminolevulinate synthase-2 (ALAS2) gene (Xp11.21; MIM 301300) have been found in some X-linked cases (3-5). The anemia is often responsive to supplemental pyridoxine but, irrespective of response, patients may develop secondary iron overload. A distinct form of X-linked sideroblastic anemia with ataxia, XLSA/A (MIM 301310), has been described previously (6) and the putative gene involved was mapped by linkage analysis to the long arm of the X chromosome (Xq13) (7). In contrast to ALAS2-related disease, the XLSA/A syndrome is characterized by non-progressive ataxia that is apparent during early childhood, mild anemia not requiring transfusion, elevated free erythrocyte protoporphyrin levels and lack of excessive parenchymal iron deposition. Some heterozygous females in the XLSA/A family express mild hematologic manifestations, but none exhibits ataxia (6,7). Locus heterogeneity of X-linked forms of sideroblastic anemia was shown by exclusion of the ALAS2 locus from the minimal region containing the XLSA/A gene (3).

The mitochondrion serves a central role in cellular iron metabolism. It is the site of the final step of heme biosynthesis, addition of Fe2+ to protoporphyrin, and contains a large amount of non-heme iron in the iron-sulfur centers of the electron transport chain. In spite of its importance for normal mitochondrial function, very few human disorders have been described that result from abnormalities in mitochondrial iron homeostasis.

The ATP-binding cassette (ABC) superfamily of transporters contains evolutionarily conserved proteins involved in energy-dependent transport of a wide variety of substrates across cell membranes (8), including those of organelles such as mitochondria, peroxisomes and endoplasmatic reticulum (9-11). Many ABC genes have been implicated in different inherited diseases, including cystic fibrosis (12), adrenoleukodystrophy (13) and a number of retinal dystrophies (14-17). The vital function of ABC proteins makes them reasonable candidates for involvement in diseases caused by potential transport defects.

A yeast mitochondrial ABC protein encoded by the ATM1 gene is required for normal cell growth and maintenance of mitochondrial DNA (9). Yeast strains deficient for the ATM1 gene have been shown to accumulate high levels of iron in mitochondria (18). A similar phenotype has been observed in yeast with a disruption of the YFH1 gene, a homolog of frataxin, the gene involved in Friedreich's ataxia (19-21). Previously, we characterized the human and mouse orthologs of the Saccharomyces cerevisiae ATM1 gene, termed ABC7, and mapped them to the X chromosome in both organisms (22,23). It is interesting to note that patients with XLSA/A manifest both anemia and ataxia (6,7). Together, these data led us to investigate the ABC7 gene as a potential mitochondrial iron transporter involved in XLSA/A.

RESULTS

To isolate the full-length human ABC7 gene, 5[prime] rapid amplification of cDNA ends was performed, together with a search of the expressed sequence tags database (dbEST). The open reading frame (ORF) of the human ABC7 gene contains 2256 bp (752 amino acids) and consists of six potential membrane-spanning hydrophobic segments and an ATP-binding domain (Fig. 1). The human and mouse ABC7 proteins are most closely related to two yeast ABC transporters, S.cerevisiae Atm1p and Schizosaccharomyces pombe Hmt1p. Human ABC7 and yeast Atm1p have >50% identity over 200 amino acids within their ATP-binding domains (Fig. 1). The transmembrane domains of ABC7, predicted by a hydropathy plot (data not shown), align perfectly with the corresponding segments of the yeast Atm1p transporter (9) (GenBank accession no. 1352002), with nearly 50% amino acid identity in these regions. The striking conservation of these proteins led us to hypothesize that the human ABC7 transporter is an ortholog of the yeast ATM1 protein.

Figure 1. Amino acid sequence of the ABC7 protein and alignment with yeast Atm1p. The predicted protein sequence is shown in the one-letter amino acid code. Transmembrane domains predicted by hydropathy plot are underlined, designated TM and numbered; the Walker A and B motifs and the Signature motif C are in bold; and the termination codon is indicated with an asterisk. The basic, positively charged residues of the putative mitochondrial targeting signal are marked by +. The location of the I400M missense mutation is shown above the sequence.

To test the ability of ABC7 to complement an ATM1 deletion, we cloned the ABC7 cDNA into a yeast expression vector (pYES2) adjacent to the galactose-inducible GAL1 promoter. Disruption of the yeast ATM1 gene results in a 20-fold decrease in catalase activity and increased sensitivity to oxidative stress (18). We have also observed an increased sensitivity to copper toxicity in a [Delta]atm1 strain, consistent with the ability of copper to react with molecular oxygen and form free radicals (24). As seen in Figure 2, [Delta]atm1 cells grow more slowly and form smaller colonies than wild-type cells in the presence of 1.2 mM CuSO4. Cells carrying a plasmid-borne copy of either ATM1 or ABC7 have growth characteristics similar to those of the wild-type. Based on the ability of ABC7 to complement the [Delta]atm1 cells, we conclude that ABC7 is an ortholog of ATM1 and that the two ABC transporters share a common substrate(s).


Figure 2. Complementation of an atm1 deletion by ABC7. Wild-type or [Delta]atm1::LEU2 cells were transformed with plasmids as described below and selected on minimal medium lacking uracil (to maintain the plasmids). Equal numbers of cells from the transformants were then plated on galactose-containing minimal medium lacking uracil with 1.2 mM CuSO4. ATM1, wild-type plus pYES2 vector alone; atm1 + ABC7, [Delta]atm1::LEU2 plus ABC7 in pYES2; atm1, [Delta]atm1::LEU2 plus pYES2 vector alone; atm1 + ATM1, [Delta]atm1::LEU2 plus ATM1 in pYES2. Poor growth of the [Delta]atm1::LEU2 cells (atm1) is demonstrated by the smaller colony size, indicative of slower growth.

Mutational analysis of the ABC7 gene was pursued in the previously ascertained XSLA/A kindred (6). A sequence variant was detected (T1200G) that changes the amino acid sequence from Ile (ATT) to Met (ATG) at position 400 (I400M). This residue is within the predicted fifth transmembrane domain of the ABC7 protein (TM5, Fig. 1). Specific PCR primers were designed for this variant and the DNA of all available family members were screened by the single-strand conformation polymorphism (SSCP) technique. The I400M substitution was found to segregate in the family and was detected in all affected individuals and, in the heterozygous state, in female obligate carriers (Fig. 3). The I400M allele was also found in individuals III-4, II-3 and II-4. Although we cannot completely rule out the possibility that this is a rare neutral variant, the I400M mutation was not detected in any of the 600 chromosomes from racially matched (European American) general population controls.


Figure 3. Segregation of SSCP variants of the I400M mutation in the ABC7 gene in kindred with XLSA/A. Sequence analysis of SSCP bands (shown below the pedigree) revealed the existence of wild-type sequence (band 2) and mutant sequence (band 1). DNA sequencing revealed a T1200G (I400M) substitution in band 2. Female carriers are heterozygous for the T1200G (I400M) substitution (reveal both bands 1 and 2), while the affected male offspring (individuals II-1, III-3, III-8 and III-9) harbor the mutant ABC7 allele only.

To evaluate the functional consequences of the observed I400M substitution in the ABC7 protein, the corresponding V365M mutation was made in the yeast ATM1 gene. The yeast gene was chosen for mutagenesis, rather than the human, to ensure proper import, assembly and regulation of the protein. A phenotype of cells with an ATM1 deletion is an increased sensitivity to iron starvation (unpublished data). We interpret this observation to indicate that the [Delta]atm1 cells have a higher iron requirement for growth due to mitochondrial iron deposition. Cells with a disruption of ATM1 were transfected with a plasmid containing either the wild-type or V365M allele of the ATM1 gene and grown under iron limiting conditions. When no iron was added to the medium, neither wild-type nor V365M cells grew (Fig. 4). Addition of 10 µM FeCl3 restored growth, but consistently revealed a difference in the growth rate between cells with the wild-type and V365M alleles of ATM1 (Fig. 4). In four independent experiments, 2- to 8-fold reductions in growth were observed in the cells with the mutant construct. In higher levels of iron (100-1000 µM) no growth difference was observed (data not shown). The detection of a difference between the wild-type and V365M alleles only under very stringent conditions suggests that this mutation results in a partial loss of function. The observation that the XLSA/A patients have only a mild anemia is also consistent with this interpretation.


Figure 4. Effect of a V365M mutation on Atm1p. Haploid [Delta]atm1::LEU2 cells were transfected with either the wild-type or V365M allele of ATM1 in YCplac33, in which expression of each gene is controlled by the ATM1 promoter. Cells were grown in minimal medium containing either 0 (open symbols) or 10 µM FeCl3 (closed symbols) and monitored for growth by measurement of OD600 at the indicated times. In medium containing 10 µM FeCl3, the cells expressing the wild-type allele (closed circles), consistently in four independent experiments, showed a faster growth rate than cells with the V365M allele (closed squares). The data shown in the figure are derived from two representative experiments.

Our results strongly suggest that a mutation in the ABC7 gene results in XLSA/A. Therefore, we sought to correlate the symptoms with the pattern of gene expression. Northern blot analysis revealed that the ABC7 mRNA is present, at various levels, in most human tissues examined. Significantly higher expression was detected in heart, muscle and pancreas, tissues with a high rate of metabolism and rich in mitochondria (Fig. 5). This observation is consistent with the predicted mitochondrial localization of ABC7. It is to be noted, however, that the expression of ABC7 was not detected in brain. XLSA/A has its onset during infancy, is non-progressive and is characterized by cerebellar ataxia without other neurologic dysfunction. The combination of this clinical phenotype and the lack of expression of ABC7 in the whole adult brain may indicate a restricted role in the developing cerebellum.


Figure 5. Expression of ABC7 in human tissues. A fragment of the ABC7 cDNA clone was hybridized to a blot containing mRNA from heart (H), whole brain (B), placenta (Pl), lung (Lu), liver (Li), skeletal muscle (M), kidney (K) and pancreas (Pa).


DISCUSSION

The functions of ABC7 and Atm1p are not known. To date all characterized eukaryotic energy-dependent ABC transporters move substrates from the side of the lipid bilayer where their ATP-binding domains are located to the opposite side. Analysis of Atm1p has shown that it is located in the mitochondrial inner membrane with its C-terminus in the matrix (9). Based on this orientation it is predicted to export substrate from the matrix to the intermembrane space. Previous studies have eliminated heme export (9) and iron import (18) as possible functions of Atm1p. Two observations support the hypothesis that these proteins function to export iron. The first is the accumulation of mitochondrial iron in the bone marrow cells of patients with the I400M mutation in ABC7 and in the [Delta]atm1 yeast strain (6,7,18). Secondly, both Atm1p and ABC7 show a high degree of sequence similarity to Hmt1p, a heavy metal transporter from the fission yeast S.pombe (23). Definitive identification of the substrates for ABC7 and Atm1p must await further biochemical studies.

Friedreich's ataxia (MIM 229300) is another disorder associated with abnormal iron homeostasis (25). This rare autosomal recessive, progressive spinocerebellar degeneration is caused by mutations in the frataxin gene (21), whose product is associated with the mitochondrial inner membrane (26). Deletion of the yeast homolog of frataxin (YFH1) results in mitochondrial iron overload, oxidative stress and instability of the mitochondrial DNA (20,27), a phenotype that is very similar to that caused by an ATM1 deletion. It has been proposed that Yfh1p regulates iron homeostasis, possibly through an iron transporter on the mitochondrial inner membrane (20). It is possible that Atm1p is the transporter that is regulated by Yfh1p and, by homology, that frataxin regulates the activity of ABC7.

To date, all characterized ABC half-transporters function as heterodimers. It is not known whether Atm1p and ABC7 form homo- or heterodimers, though candidate dimerization partners have been identified. Sequence analysis of the yeast genome predicts 29 ABC transporter genes (28). Five of these genes, including ATM1, are predicted to encode half-transporters. One of these proteins, Mdl1p (29), is predicted to be mitochondrial and thus is a potential dimerization partner for Atm1p. In the human genome there is an ABC gene located on chromosome 2 (HUEST45597) which is closely related to ABC7 (22). Further studies will be required to identify the dimerization partners for Atm1p and ABC7.

In summary, we have demonstrated that a mutation in the human ABC7 gene is responsible for XLSA/A. The combination of such disparate clinical symptoms, ataxia and anemia, resulting from a single gene mutation reflects the pleiotropic nature of mutations that effect the function of the mitochondrion.

MATERIALS AND METHODS

XLSA/A kindred

Subjects gave informed consent and were evaluated and sampled under protocols approved by the University of Washington Institutional Review Board. The members of the family are identified by their pedigree positions as shown in Figure 3. Individuals II-1, III-3, III-8 and III-9 are affected males. Individuals I-2, II-2, II-5, II-6, II-7 and III-1 are obligate heterozygotes. A sample was not obtained from the affected son of II-5 (data not shown). Although neither II-3 nor I-4 has affected children and free erythrocyte protoporphyrin levels were normal, marrow examination of both revealed ringed sideroblasts, strongly suggesting that they are also carriers of XLSA/A. II-8 has one unaffected son (data not shown) and was shown to have normal free erythrocyte protoporphyrin levels.

Sequencing and sequence analysis

Primers for the cDNA sequences of ABC7 were designed with the PRIMER program (30). Both ABC7 cDNA clones and genomic clones became templates for sequencing. Sequencing was performed with the Taq Dye Deoxy Terminator Cycle Sequencing kit (PE Applied Biosystems, Foster City, CA), according to the manufacturer's instructions. Sequencing reactions were resolved on an ABI 373A automated sequencer. Searches of the dbEST database were performed with BLAST (31) on the NCBI file server. Amino acid alignments were generated with PILEUP (32). Sequences were analyzed with programs of the Genetics Computer Group package (33) on a VAX computer.

cDNA cloning

cDNA clones containing ABC7 sequences were obtained from Research Genetics (Huntsville, AL) and Genome Systems (St Louis, MO) and sequenced fully. Primers were designed from the compiled contig of the ABC7 cDNA sequence, from the 5[prime] and 3[prime] regions of the gene, and used to amplify the full-length ABC7 gene sequences by PCR with testis QUICK-Clone cDNA (Clontech, Palo Alto, CA) as a template. Amplification was performed with AmpliTaq Gold polymerase in a 25 µl volume in 1× PCR buffer supplied by the manufacturer (PE Applied Biosystems). Samples were heated to 95°C for 10 min and amplified for 35-40 cycles of 96°C for 20 s, 58°C for 30 s and 72°C for 30 s. PCR products were analyzed on 1-1.5% agarose gels and in some cases digested with appropriate restriction enzymes to verify their sequence. PCR products were cloned into pGEM-T vector (Promega, Madison, WI) and verified by direct sequencing. Primer sequences and specific reaction conditions are available upon request. The sequence of the ABC7 cDNA has been deposited with GenBank under accession no. AF133659. While this work was in progress two other groups (34,35) reported sequences for ABC7 (GenBank accession nos AB005289 and AF038950).

Northern hybridization

DNA fragments used as probes were purified on a 1% low melting temperature agarose gel. DNA was labeled directly in agarose with the Random Primed DNA Labeling kit (Boehringer Mannheim, Indianapolis, IN) and hybridized to multiple tissue northern (MTN) blots (Clontech), according to the manufacturer's instructions. Each blot contained 2 µg of poly(A)+ RNA from various human tissues. Hybridization with additional probes demonstrated that the whole brain RNA was intact (data not shown).

Mutation detection

Purified mRNA and DNA were isolated for all available family members from previously established B lymphoblastoid cell lines (36). RT-PCR and direct sequencing methods were utilized on mRNA of affected individuals II-1, III-3, III-8 and III-9 and of the obligate carrier grandmother (I-1). Mutation detection was performed by direct sequencing of PCR products, obtained by RT-PCR (GeneAmp kit; PE Applied Biosystems) using mRNA as a template. Segregation analysis and screening of controls were performed by SSCP (37) analysis under optimized conditions (38). Genomic DNA samples (50 ng) were amplified with AmpliTaq Gold polymerase in 1× PCR buffer supplied by the manufacturer (PE Applied Biosystems) containing [32P]dCTP. Samples were heated to 95°C for 10 min and amplified for 35-40 cycles of 96°C for 20 s, 58°C for 30 s and 72°C for 30 s. Products were diluted in 1:3 stop solution, denatured at 95°C for 5 min, chilled in ice for 5 min and loaded on gels. Gel formulations included: 6% acrylamide:bisacrylamide (2.6% crosslinking), 10% glycerol at room temperature, 12 W; 10% acrylamide:bisacrylamide (1.5% crosslinking) at 4°C, 70 W. Gels were run for 2-16 h (3000 V h/100 bp), dried and exposed to X-ray film for 2-12 h.

Cloning and mutagenesis in yeast

The ATM1 ORF along with 500 bp of flanking DNA, which includes its promoter, was amplified from yeast genomic DNA by PCR (forward primer, 5[prime]-GCAGTCATTACCAAATGTGAAGAAG; reverse primer, 5[prime]-TGCTAATACAATACCTAAAATACCACAC) and cloned into pCR2.1-TOPO (Invitrogen, Carlsbad, CA). Subsequently, this fragment was subcloned into yCPlac3354 and designated pMW114. Mutagenesis was done with the Quik Change site-directed mutagenesis kit (Stratagene, La Jolla, CA) using pMW114 as a template. The sequence of the forward primer was 5[prime]-GTTGCACCGGCATGATTGGTGGCAACTTGAC, of the reverse primer 5[prime]-TCAAGTTGCCACCAATCATGCCGGTGCAAC. The entire ATM1 ORF was sequenced to confirm the presence of the mutation and to ensure that no additional mutations had been acquired during PCR amplification and subsequent manipulations. The human ABC7 cDNA and the ATM1p open reading frame were expressed with the GAL1 promoter by subcloning into pYES2 (Invitrogen). Dideoxy sequencing was done with the ALFexpress autoread sequencing kit using ALFexpress dATP labeling mix and read on an ALFexpress automated DNA sequencer (Amersham Pharmacia Biotech, Piscataway, NJ).

Saccharomyces cerevisiae and Escherichia coli strains and manipulations

The following S.cerevisiae strains were used in this paper: JDL5 (MATa, ura3, his4-519, leu2-3,112) and JDL4 (MATa, ura3, his4-519, leu2-3,112, atm1::LEU2), from J. Leighton (University of Basel, Switzerland). Growth and manipulations of yeast cultures were done using standard methods (39). For selection for copper resistance cells were plated on minimal medium without uracil containing 2% glucose and 1.2 mM CuSO4. Iron-limited medium was made with yeast nitrogen base supplemented with amino acids but lacking uracil, containing 2% glucose, 1 mM EDTA, 20 mM Na3-citrate and variable amounts of FeCl3 (40). DNA manipulations were done using standard techniques (41) in E.coli strain DH5[alpha].

ACKNOWLEDGEMENTS

We appreciate the participation of the XLSA/A family, without whose cooperation this work would not have been possible. We thank J. Wolff for expert technical assistance and S. Cevario for oligonucleotide synthesis and DNA sequencing, J. Leighton and G. Schatz for helpful discussions and sharing reagents and M. Woontner for helpful discussions. DNA sequence analysis was performed using the Frederick Biomedical Supercomputing Center. This work was supported in part by NIH grant R01 CA16448 and research funds from the Department of Veteran Affairs (W.H.R.) and in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract no. NO1-CO-56000 (R.A.). The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services nor does mention of trade names, commercial products or organizations imply endorsement by the US Government.

NOTE ADDED IN PROOF

While this manuscript was in preparation, complementation of the ATM1 deletion by ABC7 was independently demonstrated by Csere et al. (42).

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*To whom correspondence should be addressed. Tel: +1 301 846 5931; Fax: +1 301 846 1909; Email: dean@mail.ncifcrf.gov
§Present address: Departments of Ophthalmology and Pathology, Columbia University, New York, NY 10032, USA
+These authors contributed equally to this work

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