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PLENARY PAPER
From the Purine Research Unit, Guy's Hospital; the
Department of Haematology, King's College Hospital, London; the
Department of Haematology, Royal Hallamshire Hospital, Sheffield,
United Kingdom; the Istituto di Biochimica, Facolta di Medicina,
Universita di Ancona, Italy; the Department of Pediatrics, The National
Hospital, Oslo, Norway; the Institute of Hematology, Chaim Sheba
Medical Center, Tel Hashomer, Israel; and the Department of Chemical
Pathology, University of Cape Town, South Africa.
Pyrimidine 5' nucleotidase (P5'N-1) deficiency is an autosomal
recessive condition causing hemolytic anemia characterized by marked
basophilic stippling and the accumulation of high concentrations of
pyrimidine nucleotides within the erythrocyte. It is implicated in the
anemia of lead poisoning and is possibly associated with learning
difficulties. Recently, a protein with P5'N-1 activity was analyzed and
a provisional complementary DNA (cDNA) sequence published. This
sequence was used to study 3 families with P5'N-1 deficiency. This
approach generated a genomic DNA sequence that was used to search
GenBank and identify the gene for P5'N-1. It is found on chromosome 7, consists of 10 exons with alternative splicing of exon 2, and produces
proteins 286 and 297 amino acids long. Three homozygous mutations were
identified in this gene in 4 subjects with P5'N-1 deficiency: codon 98 GAT Pyrimidine 5' nucleotidase (P5'N-1, also known as
uridine-5'-monophosphate hydrolase-1) catalyzes the dephosphorylation
of the pyrimidine 5' monophosphates UMP and CMP to the corresponding nucleosides. A deficiency of this enzymatic activity was first identified by Valentine et al1,2 in erythrocyte stroma
while investigating patients with hemolytic anemia characterized by marked basophilic stippling. Initial studies showed very high concentrations of what were assumed to be adenine nucleotides in the
erythrocytes, but these were later found to be pyrimidine nucleotides;
the red blood cells (RBCs) also contained high levels of glutathione
and reduced activity of ribose-phosphate pyrophosphokinase. Studies on
3 additional kindreds with hemolytic anemia and basophilic stippling
demonstrated absent or markedly reduced pyrimidine 5' nucleotidase
activity in their RBCs.3 Reports of 40 patients with this
condition have been published, with presumably large numbers
undetected. However, because of the lack of a simple and reliable test
for carriers, the exact prevalence of the condition is unknown.
Reported numbers of homozygotes suggest that it is the third most
common RBC enzymopathy Additional studies have suggested that there are 2 isozymes of
P5'N in RBCs, one with a preference for UMP and CMP, referred to as
P5'N-1, and one able to hydrolyze deoxy-pyrimidine nucleotide monophosphates (P5'N-2).6,7 These are not separable by
electrophoresis in humans but have distinct kinetic properties and
genetics. P5'N-2 has been assigned to the long arm of chromosome 17 by
studying human-mouse somatic cell hybrids.8 The most
convincing evidence for the existence of 2 isozymes arises from studies
of patients with hemolytic anemia, in whom P5'N-1 activity is greatly
reduced but P5'N-2 is normal.7 Purification and partial
protein sequencing of P5'N-1 from RBCs led to the identification and
cloning of the complementary DNA (cDNA) and the expression of the
recombinant enzyme in Escherichia coli.9,10 The
protein consists of 286 amino acids and is identical to a previously
identified lupus inclusion protein, p36, though the significance of
this is unclear. A mammalian 5'(3')-deoxyribonucleotidase with similar
properties to P5'N-2, though lacking its apparent phosphotransferase
activity, has also been cloned.11,12 Although P5'N-1 and
P5'N-2 are not separable by electrophoresis in humans, the 2 proteins
show no homology. We used the putative cDNA sequence for P5'N-1 to
screen families known to have hemolytic anemia caused by pyrimidine 5' nucleotidase deficiency for causative mutations.
Case histories
Norwegian family.
In the early 1980s, a brother and sister from Norway were found to have
P5'N deficiency with typical hemolytic anemia and basophilic
stippling.13 It was unusual that both siblings had intravascular hemolysis, urinary iron loss, iron deposition in the
kidneys, and iron deficiency. This has not been noted in other published reports of P5'N deficiency. Their parents were
hematologically normal and had a common ancestor 5 generations earlier.
Three other children were found to be unaffected. Both affected
siblings are now in their late twenties and maintain hemoglobin levels of approximately 10 g/dL with no significant complications from their
chronic hemolysis.
South African 1.
A South African girl was examined in early childhood for failure to
thrive and typical hemolytic anemia with basophilic stippling, and she
was found to have P5'N-1 deficiency. She was adopted, and it is unknown
whether her parents were related in any way. She appeared to be of
mixed-race origin. After diagnosis, she was lost to follow-up.
South African 2.
A 55-year-old white farmer was referred with anemia, which was found to
be of hemolytic origin and associated with low P5'N levels and
intra-erythrocytic accumulation of pyrimidine nucleotides. He was most
recently seen in his sixties and continues well without any significant
problems related to P5'N-1 deficiency.
Hematologic analysis
Enzyme and nucleotide studies Pyrimidine 5' nucleotidase in hemolysates was determined as P5'N-1 and P5'N-2 activities14 by a method using high-performance liquid chromatography with UMP and deoxy-UMP as respective substrates15 or as P5'N-1 by measuring inorganic phosphate release by a colorimetric method after incubation with CMP.16 RBC nucleotides were quantitated spectrophotometrically.17DNA analysis Epstein-Barr virus-transformed lymphoblastoid cell lines were established from fresh EDTA blood of all patients and from the 2 parents and 3 siblings of the Norwegian family. Genomic DNA was extracted from EDTA-anticoagulated blood or cultured lymphoblasts of patients, family members, and 100 anonymous healthy white controls (QIAamp, DNA blood kit; Qiagen, Crawley, United Kingdom). Control cell lines were set up from controls without hemolytic anemia. Messenger RNA (mRNA) was extracted from the cell lines using standard techniques, and first-strand cDNA was synthesized using oligo dT priming and MMLV reverse transcriptase (Gibco-BRL Life Technologies, Paisley, United Kingdom). The coding region of P5'N-1 cDNA was amplified using nested primers in 2 rounds of amplification (Table 1). Polymerase chain reaction (PCR) products were gel purified (Qiaex II Gel Extraction Kit; Qiagen) and directly sequenced (dRhodamine Terminator cycle sequencing kit; PE Applied Biosystems, Warrington, United Kingdom) on an ABI377 automated fluorescent DNA sequencer (PE Applied Biosystems). Reticulocyte mRNA was extracted from control erythrocytes using standard methods and subjected to an identical nested PCR protocol.18 Reticulocyte mRNA was unavailable from the affected families. To define partially the genomic structure of the P5'N-1 gene, combinations of cDNA-specific primers were used to amplify genomic DNA across introns. Gel-purified PCR products were sequenced, and primers were designed to amplify identified exons from genomic DNA (Table 1). When mutations were identified, they were screened for in 100 normal controls using restriction endonuclease digestion of PCR-amplified exons (enzymes from New England Biolabs, Hitchin, United Kingdom). The silent codon 92 TAC TAT mutation was screened for by PCR amplification with a mismatched primer that creates a DdeI site in the presence
of the TAC allele.
Hematologic analysis Basic clinical and hematologic data are summarized in Table 2. Results of P5'N assays for the Norwegian family are shown in Figure 1 and Table 3. Both affected siblings had very low levels of P5'N-1 levels with normal P5'N-2 levels. The parents and 3 healthy siblings had P5'N-1 levels varying upward from the lower end of the normal range, making it difficult to accurately identify carriers of the condition. P5'N-2 levels were all normal, and we have previously found that the P5'N-1/P5'N-2 ratio is a better way of detecting reduced P5'N-1 levels; a ratio of 0.7 or less is significant.19 This ratio shows that both parents are carriers and that the 3 healthy siblings have normal P5'N-1 activity. Analysis of a child of one of the healthy siblings also suggests that he is not a carrier. Both affected siblings were found to have a massive accumulation of intra-erythrocytic pyrimidine nucleotides at the time of diagnosis.13
Fresh blood was unavailable from both South African patients, but assays at the time of diagnosis showed P5'N activities of 1.8 and 0.4 µmol/h per g Hb, respectively (normal range, 6.9-10.7). These assays measured the generation of inorganic phosphate. DNA analysis Sequencing of P5'N-1 nested PCR product from controls and patients showed multiple heterozygous nucleotide substitutions and a 1-bp insertion compared to the published sequence. Most of the sequence changes are predicted to produce nonconservative amino acid changes, and the insertion produces a frame shift and a premature termination of the predicted protein. The presence of these enzyme-inactivating mutations in patients and controls is consistent with the coamplification of a processed P5'N-1 pseudogene from genomic DNA contaminating the RNA preparations. Pseudogene-specific primers were used to amplify and sequence the pseudogene in 2 overlapping segments from genomic DNA. A similarity search of the GenBank databases showed a match between the pseudogene and 169 bp of a contig derived from chromosome 7p14-p15 (NT_002053, locus AC007312, clone RP11-349E11), corresponding to the 5' end of the P5'N-1 cDNA and consistent with partial genomic duplication of the P5'N-1 gene. The cDNA sequence showed extensive homology to elements of a working draft sequence of the chromosome 4 clone, RP11-778G8, and the absence of intervening sequences is characteristic of a processed pseudogene. Amplification of genomic DNA using cDNA primers yielded a single homozygous sequence corresponding to the chromosome 4 pseudogene. It is, therefore, likely that the complex sequence produced by the nested reverse transcription-PCR is produced by amplification of both the P5'N-1 mRNA and contaminating DNA from the processed pseudogene. The chromosome 4 pseudogene sequence contained 2 restriction sites not present in the P5'N-1 cDNA sequence, a PvuII site at nucleotide 353 and an HpaII site at nucleotide 606. Digestion of the nested PCR product with one of these before sequencing the pseudogene and produced a homozygous sequence corresponding to the published sequence for P5'N-1.Two PCR products of slightly different sizes were amplified from
control cell lines and reticulocytes. The smaller transcript was
identical to the P5'N-1 cDNA published sequence,9 but the larger transcript contained a 55-bp insertion near the 5' end. A
selection of primers was used to generate intronic sequence from the 3'
end of the gene, and this information was used to search GenBank.
Complete homology was found to a working draft of chromosome 7 clone
RP11-162O1 (AC083863). Analysis of this revealed 10 exons with
intron-exon boundaries adhering to the canonical AG-GT rule (Figure
2). The 55-bp insertion noted in some
transcripts corresponded to the second exon of the genomic DNA and was
predicted to result in a protein with an additional 11 amino acids at
the N-terminal (Figure 3).
Sequencing of the P5'N-1 transcript from the affected Norwegian
siblings showed 2 homozygous mutations, codon 92 TAC The cDNA from South African patient 1 with P5'N-1 deficiency was found
to be homozygous for a mutation in codon 177 CAA A single PCR product of reduced size was amplified from cDNA of South
African patient 2. Sequencing showed a 201-bp deletion corresponding to
exon 9 of the genomic sequence, removing 67 amino acids from the
predicted protein. Genomic sequencing of a region including exon 9 showed a normal-sized product but a homozygous T
In this study we report 2 novel findings. First, we identified a genomic DNA sequence corresponding to the previously published cDNA for P5'N-1. Second, we identified significant mutations of this genomic sequence in 3 families with P5'N-1 deficiency. This gene for P5'N-1 is found on chromosome 7 and consists of 10 exons. Two alternatively spliced cDNAs were identified and sequenced, predicting the synthesis of proteins 286 and 297 amino acids long. The shorter protein has been shown to have characteristics of P5'N-1,9 but the longer form is yet to be characterized. Both forms are expressed in reticulocytes and lymphocytes. The presence of 2 P5'N-1 cDNAs in lymphoblastoid cell lines and reticulocytes is a consequence of alternative splicing of exon 2. The poly-pyrimidine tract of the intron 1 splice acceptor site is displaced from the conserved AG dinucleotide, and no branch site with homology to the consensus branch site sequence YNYTRAY could be identified within 100 bases of this splice site. This is characteristic of splice acceptors flanking alternatively spliced exons.20 It is interesting that 2 electrophoretic forms of P5'N-1 have been demonstrated in nucleated cells and RBCs,14 which is consistent with our finding that alternative splicing predicts 2 P5'N-1 isoforms. The effect of the addition of 11 amino acids on catalytic activity requires further investigation. It is possible that the isozymes are differentially expressed in various tissues, as has been shown for pyruvate kinase, in which differentially spliced forms of the enzyme are expressed in liver and RBCs.21 We identified 3 different homozygous mutations in unrelated patients with the clinical and biochemical features of P5'N-1 deficiency. Two of the mutations resulted in large deletions of the protein and would be expected to result in severe disruption of enzyme structure and function. The point mutation in the Norwegian siblings involved a nonconservative amino acid change, segregated with P5'N-1 activity in this family, and was not found in 100 healthy controls. Our findings thus establish a direct causal relation between mutation of the P5'N-1 gene and hemolytic anemia with basophilic stippling from RBC P5'N-1 deficiency. The 286-amino acid form of the P5'N-1 enzyme has a predicted mass of
32.7 kd. It contains 5 cysteine residues, some of which may be
implicated in the acquired P5'N-1 deficiency associated with lead
poisoning22 and the oxidative stress of
Similarity searches of the GenBank EST database revealed matches with a
number of partial mouse cDNA sequences. A consensus Mus
musculus polypeptide derived from these sequences shows 95% homology with the human P5'N-1. Searches identified 3 other homologous proteins of unknown function (Figure 4).
Interestingly, the Asp98, mutated in the Norwegian siblings, is
conserved in the CG3362 gene product of Drosophila
melanogaster.
The hematologic phenotype of P5'N-1 deficiency is well
defined
We thank Professor Sir David Weatherall, Professor John Clegg, and Dr J. T. Reilly for advice and Sue Butler for establishing some of the cell lines. We also thank Professor Sverre O. Lie for helping to prepare the manuscript.
Submitted December 1, 2000; accepted January 31, 2001.
Supported in part by CNR Target Project on Biotechnology and by EC grant BMH4-CT98-3079 (A.M.M.).
Martin Seip died during the preparation of this manuscript.
The publication costs of this article were defrayed in part by page charge payment. Therefore, and solely to indicate this fact, this article is hereby marked "advertisement" in accordance with 18 U.S.C. section 1734.
Reprints: David C. Rees, Department of Haematology, Royal Hallamshire Hospital, Glossop Rd, Sheffield, S10 2JF, United Kingdom; e-mail: david.rees{at}csuh.nhs.uk.
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