From www.bloodjournal.org by guest on December 22, 2014. For personal use only. Molecular Defect of a Phosphoglycerate Kinase Variant (PGK-Matsue) Associated With Hemolytic Anemia: Leu +. Pro Substitution Caused by T/A -+ C/G Transition in Exon 3 By Masato Maeda and Akira Yoshida We have identified the mutation in a phosphoglycerate kinase variant (PGK-Matsue) associated with severe enzyme deficiency, congenital nonspherocytichemolytic anemia, and mental disorders. The mRNA coding for PGK was reverse transcribed and amplified by the polymerase chain reaction. Nucleotide sequencing of the variant cDNA showed a point mutation, a TIA + CIG transition in exon 3 of the variant gene. No other mutation was found in all coding regions of PGK-Matsue. The nucleotide change created an additional NcA cleavage site in the variant gene; thus, the Ncil fragment types detected by Southern blot hybridization differ in the variant DNA and normal DNA. The mutation should cause Leu + Pro substitution at the 88th position from the NH,terminal Ser of PGK. Because the Leu + Pro substitution is expected to induce serious perturbationand instability in the protein structure, the severe enzyme deficiency is mainly caused by more rapid in vivo denaturation and degradation of the variant enzyme. o 1991 by TheAmerican Society of Hematology. P Amplification of mRNA. About 5 x lo7 fibroblast cells of passages 17 and 26 were harvested from GM00743 and 9024, respectively. Total cellular RNA samples were prepared from the cells by extraction with guanidine thiocyanate followed by density gradient centrifugation in cesium chloride.” The entire coding sequences of mRNA were reverse transcripted and amplified in six overlapped segments, using six sets of sense (A-1, B-1, . . . F-1) and antisense (A-2, B-2, . . . F-2) oligonucleotide primers (Table 1).To create adequate restriction sites, linker sequences were attached to the 5‘ end of these primers (Table 1). The first-strand cDNA copies of mRNA were produced by incubating total RNA (8 to 10 Fg) with one of the antisense primers (A-2, B-2,. . . F-2; 10 pmol) and 20 U of reverse transcriptase from avian myeloblastosis virus (Life Science, St Petersburg, FL) in the reaction mixture (20 FL) as described previously.” The reaction products were amplified by the polymerase chain reaction (PCR)’* using a corresponding set of sense and antisense primers (50 pmol each) in the reaction mixture (100 pL) containing 20 m m o K Tris-HC1 (pH 8.3), 3.1 mmol/L MgCI,, 80 pmoUL D l T , 58 mmoUL KCI, 0.01% gelatin, dNTP (200 pmoVL each), and 5 U of Taq polymerase (Perkin-Elmer Cetus, Norwalk, CT). The reaction was performed with a programmable thermal controller (MJ Research, Inc, Watertown, MA). The cycle, which consisted of 1 minute of denaturation at 94T, 2 minutes of annealing at 50”C, and 3 minutes of elongation at 72”C, was repeated for 40 times and followed by another 12 minutes of elongation at 72°C. To verify the amplification products, 1/20 of each reaction mixture was separated by agarose gel electrophoresis, transferred onto nitrocellulose filters, and hybridized with a ’*P-labeled fulllength human PGK cDNA (1.8 Kb BamHIIXho I insert of PGK 825 clone)” in 50% formamide (vol/vol), 5X Denhardt’s solution, 0.5% sodium dodecyl sulfate, and 100 pg/mL salmon sperm DNA at 42°C. Subcloning and sequencing of amplified DNA. The amplified DNAs were digested with appropriate restriction enzymes, whose recognition sites were created by PCR, and purified by electrophoresis in polyacrylamide gel followed by electro-elution. The purified DNAs were subcloned into the M13 vector as described.” DNA sequencing was performed by the dideoxy-nucleotide chain termination method of Sanger et al.l4To avert possible errors in the Taq polymerase reaction, DNA fragments isolated from at least two separate amplification reactions were sequenced in both orientations. Restriction-fiagment analysis. Genomic DNAs were prepared from GM00743 and 9024 fibroblast cells as described.” The DNA samples (approximately 1 p,g each) were amplified using a pair of primers, 5’-GCCAAGTCGGTAGTCClTATG-3’ and 5’-CGCCACAAAGTCTACCAGCAC-3‘, by PCR. The primers used corre- HOSPHOGLYCERATE kinase (ATP: 3-phosphoglycerate 1-phosphotransferase, EC 2.7.3.3 [PGKJ) plays a key role for ATP generation in the glycolytic pathway. The PGK, which exists universally in various tissues of various organisms, is encoded by a single structural gene on the X-chromosome q13 in humans.’,*The complete amino acid sequence, cDNA sequence, and genomic organization have been el~cidated.~.’ An inherited deficiency of this enzyme is associated with chronic nonspherocytic hemolytic anemia and mental disordem6 Occasionally, the sole clinical manifestation has been muscle disease.’ The patient with PGK-Matsue also had severe chronic hemolytic anemia and mental disorders: The activities of the enzyme in red blood cells (RBCs), muscles, and fibroblasts of the patient were about 5% of those of normal tissues? However, the content of mRNA in the patient’s fibroblasts was comparable with that of normal fibroblasts.”’ We determined the nucleotide sequence of the variant cDNA to elucidate the molecular abnormality of PGK-Matsue. MATERIALS AND METHODS Cell lines. The fibroblast cell line from the PGK-Matsue male subject (identification GM00743) was obtained from the NIGMS Human Genetic Mutant Cell Repository (Camden, NJ). A normal fibroblast cell line of human newborn foreskin (9024) was obtained from the cytogenetics laboratory, City of Hope National Medical Center (Duarte, CA). The fibroblast cells were cultured in MEM medium supplemented with 20% (volhrol)fetal calf serum (GIBCO, Grand Island, NY), 24 mmol/L sodium bicarbonate, penicillin (50 UlmL), and streptomycin (50 mg/mL) at 37°C in 5% C0,/95% air. From the Department of Biochemical Genetics, Beckman Research Institute of the City of Hope, Duarte, CA. Submitted July 5,1990; accepted November 6,1990. Supported by US Public Health Service Grant HL-29515. Address reprint requests to Akira Yoshida, PhD, Department of Biochemical Genetics, Beckman Research Institute of the City of Hope, 1450 E Duarte Rd, Duarie, CA 91010. The publication costs of this article were defiayed in part by page charge payment. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. section 1734 solely to indicate this fact. 0 1991 by The American Society of Hematology. 0006-4971I91/7706~OO12$3.00/0 1348 Blood, Vol77, No 6 (March 15). 1991: pp 1348-1352 From www.bloodjournal.org by guest on December 22, 2014. For personal use only. PHOSPHOGLYCERATEKINASE VARIANT (PGK-MATSUE) 1349 Remriction Ses- OliiOnUClaolide A- 1 A-2 B-1 8-2 1.) Site sst1 (-51) 5'-GCgagCTCGlTGACCGAATCACCGA-3'(-27) (287) 5'-AActgCAGAACATCCl-TGCCCAGCAG-3' (262) (224) 5'-AGggaTCClTAGAGCCAGlTGCTGT-3' (248) (557) 5'-CCAmCTGTGGCAGATTGACTCC-3' (532) (450) 5'-CCaAGClTCACllTCCAAGCTAGGG-3' (474) (776) 5'-TCclgCAGAGAAGTGCCAATCTCCA-3'(752) (648)5'-AGcTGCAGACAAGATCCAGCTCAT-3' (671) (1001) 5-ATaaGClTAGCCCGAGTGACAGCC-3' (978) (955) 5'-GAcIGCAGCAAGAAGTATGCTG-3' (976) (1188) (1208) 5'-AGGAGCTCCAAACTGGCACCA-3' (1116) 5'-TGGmACACTGCCAClTGCTGTG-3' (1141) (1374) 5'-GCAaagClTGGCCACTAGCTGAATC-3' (1350) c-1 c-2 D-1 D2 E-1 E-2 F-1 F-2 OligonucleotidesA-1, B-1, . ..F-1correspond to the sense strand of DNA. OligonucleotidesA-2,B-2, DNA. Lowercaseletterswere altered to create corresponding restrictionsites (underlined). 'Counting from the adenine residue of the initiation codon. - spond to a 5' part of exon 3 (nucleotides 163 183, counting from the adenine residue of the initiation codon of cDNA) and a 5' part of intron 3 (nucleotides 18 + 38. counting from the intron-exon junction). Therefore, the amplified product of 148 bp should contain the mutation site. Half of the amplified products produced from the control and variant DNAs were digested by Ncil (IO U, Stratagene, La Jolla, CA). The digested and undigested samples were electrophoresed on 4% agarose gel in the Tris-Acetate-EDTA buffer system, blotted onto nylon membranes, and hybridized with a PGK cDNA probe ("P-laheled cDNA fragment produced by oligonucleotide primers R-l and R-2). RESULTS Flg 1. Partial nud.atid. soquem of n o m 1 and vahnt PGK-Matsue. The coding sequence h shown aligned with the sequence ladders. Astdslts indicate the substitution she of the PGK-Matsue gene. The encoded amino acid residues are shown. Numerals correspond t o the residue number, counted from the NH,-terrnlnal of the enzyme protein. LeU Leu Set PstI Hindlll PstI sst I Xb8 I Hindlll . . .F-2correspond to the antisense strand of T -c -G a T C G A I I, t ] Lys LYS GlY PSf I Nucleotide sequence analysis of these amplification products originating from PGK-Matsuc RNA showed only one nucleotidc differcnce bctwccn thc variant PGK and the rcportcd sequcncc of normal PGK.' A part of the nuclcotidc scqucncc ladders of PGK-Matsuc and thc normal PGK is shown in Fig 1. A thymidinc rcsiduc at position 266 (counting from thc adeninc rcsiduc of thc initiation codon of mRNA) in thc normal PGK was found to be substitutcd by a cytidine rcsiduc in PGK-Matsue. Based on thc information of the genomic structure of thc PGK locus,' the mutation site is located in exon 3. Thc nuclcotidc substitution is expected to gcncratc a new NciI (and isoschismatic Ahol, Rcnl. Hpoll, Msp I) cleavage site, CCGGG, in thc PGK-Matsuc gcnc. Thc 148-bp mutation region originating from thc variant gcnc was in fact clcavcd by M i l , hut thc corresponding region originating from thc normal gene was not clcaved (Fig 2). Thc transition T/A + C/G in thc gcnc should result in Amplification of total cellular RNA by PCR using six sets of sense and antisense oligonuclcotide primers (Table 1) produccd six overlapping cDNA fragments, which were hybridizablc with thc PGK cDNA prohc and m c r c d entire coding scqucnccs. (3') PstI 88mHl EcoRl Hindlll c!* - G Gly PI Leu T Set \ :j (5') From www.bloodjournal.org by guest on December 22, 2014. For personal use only. MAEDA AND YOSHIDA 1350 A B the amino acid substitution Leu (codon CTG in the normal PGK) + Pro (codon CCG in PGK-Matsuc) at the 88th position from thc NH,-terminal Scr residuc. DISCUSSION 309217- 110- 1 1 2 2 Fig2 ~ b b t h y b r M i t r t k n o f P c R p r o d u c t r o f t h . n o m u l and WK-Motsw DNAs. The 148-bp g ” k region, whkh includes the mutation site, was ampllf’ied by the use of a pair of 5 and 3’ primers. Hall of the ampllf’ied product was dlgostd by NcA. Undigested and digested PCR products wow subjected to agarose gel electrophomsis, and Southem blot hybridization using cDNA as a hybridiratlon probe. (A) Undigested PCR product. Lane 1. product from normal DNA; lane 2. product from PGK-Matsue DNA. (E) PCR product digested by Ncil. Lane 1, normal DNA; lane 2. P G K - M m e DNA. The left-hand column indicates the position of sire markers. Note that a small fragment (44 bp), generated from PGK-Matsue DNA by Ncil digestion, cannot be hybridizedwith the cDNA probe because the fragment consists mostly of an Intron sequence and contrlns a coding sequence of only 6 bp. Chronic hcmolytic ancmia associated with RBC PGK deficiency was first obscrvcd by Kraus et all5 in a fcmalc paticnt. Subsequently, in their study of an unrelated large family, Valcntinc et all found that the cnzyme dcficicncy and clinical symptoms wcrc more sevcrc in malc than fcmalc mcmbcrs. and suggcstcd thc Xchromosomc linkcd inhcritancc of P G K dcficicncy. In addition to hcmolytic ancmia, behavioral and ncurologic abnormalitics wcrc obscrvcd in ccrtain affcctcd mcmbcrs of this family. At this timc, 14 rare P G K variants associatcd with cnzyme dcficicncy have becn found in unrclatcd familics (Table 2). The RBC enzyme activity in affcctcd malcs ranged from 3% to 20% of thc normal lcvcl. Thc dcficicncy was obscrvcd also in nucleated tissucs, such as thc lcukocytcs and muscles of the subjccts. Exccpt for PGK-Mhnchcn, which cxhibits rclativcly mild dcficicncy (about 20% of the normal Icvcl), all dcficicnt variants arc associated with chronic nonsphcrocytic hcmolytic ancmia, mcntal disorders, or rhabdomyolysis. In addition to thcsc rare deficient variants, sevcral electrophoretic variants with normal cnzymc activity have bccn found in certain populations.’.” The molecular abnormalitics of three deficient variants, ic, PGK-Munchen,” PGK-Uppsala,” and PGK-Tokyo,” and an clcctrophoretic variant, PGK-II,’D which is common among Southcrn Pacific populations, were prcviously clucidatcd by thc pcptidc mapping analysis (Tablc 2). The impact of thcsc structural abnormalitics on P G K function has becn p r c d i ~ t c d ” . ’bascd ~ ~ ~ on thc thrcc-dimcnsional structurc of horsc PGK,= which is highly analogous (about 97% scqucncc identity) to thc human cnzymc. Clinicel Manifatstions EruymsRopartier invatwwms(-e Kraus et al.” Valentine et a.i‘ Hjelm et al.’Lnn A r m et al.” Canier et aI.= Miwa et al.Konrad et al.” Akatsub et a1.IBoivin et 0 1 . ~ Krietsch et al.”” Rosa et el.’ DiMauro et (11.Sugie et ai.= Guis et at.” Name of Variant Matsue Activity in RBC sex (Kofnamsl) F F,M M F M M 75 5 inM 10 42 20 5 10 15 10 21 M Tokyo M M MGnchen Creteil M M M M SanFrancisco M 3 17 8.2 12 Ebcbophastii Mobility ND ND Faster ND ND Slower ND Slower Normal Slower Slower Slower NO Normal Hen Hmlylii SCebili Anemia ND ND Low ND Normal Low ND Low ND Low Low LOW Normal Normal + + + + + + + + + - + Neurologic Abnomlities Muacb Disease + + - - + + + 2 - + - In addition to the 14 deficient variants listed above, several electrophoretic variants with normal activity were reported. Abbreviations: F, female; M, male; ND, not described. ’The positionof amino acid substitution is counted from the NH,-terminal Ser. - h i m , AcM Subniiution* - Arg+PrOat205 - Leu+PrOat88 + + + - Val-Metat265 Asp-Asnot267 From www.bloodjournal.org by guest on December 22, 2014. For personal use only. 1351 PHOSPHOGLYCERATE KINASE VARIANT (PGK-MATSUE) PGK-Matsue is associated with a very severe enzyme deficiency (about 5% of the normal level) in RBCs as well as in nucleated ~ells.8.~ The patient suffered from chronic hemolytic anemia and mental disorders, and died at age 9 from complications of pneumonia. The content of mRNA in the patient's fibroblasts, estimated by the conventional Northern blot hybridization and by the more accurate quantitative liquid hybridization, was comparable with that of normal fibroblasts." The specific enzyme activity of PGK-Matsue was estimated to be about 35% to 40% of that of normal PGK from the quantitative immunoneutralization test? Because the PGK activity in the patient's RBCs is only 5% of that of normal cells, the molecular concentration of PGK-Matsue in the variant cells should be about 10% to 15% of that of normal cells. PGK-Matsue exhibited higher Km values for all substrates, particularly for ATP and 1,3-diphosphogly~erates.~ In the present study, a single T/A + C/G base transition and a consequent amino acid substitution Leu -+ Pro at position 88 from the NH,-terminal were found in PGKMatsue. The substitution position is in a random coil between a-helices I1 (residues 77 through 87) and a p-strand C (residues 91 through 94) of PGK Because the pyrrolidine ring of the Pro residue causes a substantial change in backbone torsional angle in a peptide chain,'.2a structural instability and functional retardation are expected to be induced in PGK-Matsue by the mutation. Indeed, all human hemoglobin and other protein variants with the Leu + Pro substitution are The major cause of a diminished concentration (10% to 15% of the normal level) of PGK-Matsue in RBCs and other tissues is most likely a more rapid denaturation and degradation of the variant enzyme originating from the Leu + Pro substitution. REFERENCES 1. Chen SH, Malcolm LA, Yoshida A, Giblett E Phosphoglycerate kinase: An X-linked polymorphism in man. Am J Hum Genet 23:87,1971 2. Willard HF, Goss SJ, Holmes MT, Munrose D L Regional localization of the phosphoglycerate kinase gene and pseudogene on the human X chromosome and assignment of a related DNA sequence on chromosome 19. Hum Genet 71:138,1985 3. Huang I-Y, Welch CD, Yoshida A Complete amino acid sequence of human phosphoglycerate kinase: Cyanogen bromide peptides and complete amino acid sequence. J Biol Chem 255: 6412,1980 4. 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Krietsch WK, Krietsch H, Kaiser W, Dunnwald M, Kuntz GWK, Duhm J, Biicher T: Hereditary deficiency of phosphoglycerate kinase: A new variant in erythrocytes and leukocytes, not associated with hemolytic anemia. Eur J Clin Invest 7:427, 1977 35. DiMauro S, Dalakas M, Miranda AF: Phosphoglycerate kinase deficiency: Another cause of recurrent myoglobinuria. Ann Neurol 13:11,1983 36. Sugie H, Sugie Y, Ichimura M, Tsurui S, Itoh M, Shimizu K, Nishida H, Igarashi Y, Yonekawa 0, Kanno T: Phosphoglycerate kinase deficiency with recurrent myoglobinuria. No To Hattatsu 18:36,1986 37. Guis MS, Karadsheh N, Mentzer WC: Phosphoglycerate kinase San Francisco: A new variant associated with hemolytic anemia but not with neuromuscular manifestations. Am J Hematol 25:175, 1987 From www.bloodjournal.org by guest on December 22, 2014. For personal use only. 1991 77: 1348-1352 Molecular defect of a phosphoglycerate kinase variant (PGK-Matsue) associated with hemolytic anemia: Leu----Pro substitution caused by T/A- ---C/G transition in exon 3 M Maeda and A Yoshida Updated information and services can be found at: http://www.bloodjournal.org/content/77/6/1348.full.html Articles on similar topics can be found in the following Blood collections Information about reproducing this article in parts or in its entirety may be found online at: http://www.bloodjournal.org/site/misc/rights.xhtml#repub_requests Information about ordering reprints may be found online at: http://www.bloodjournal.org/site/misc/rights.xhtml#reprints Information about subscriptions and ASH membership may be found online at: http://www.bloodjournal.org/site/subscriptions/index.xhtml Blood (print ISSN 0006-4971, online ISSN 1528-0020), is published weekly by the American Society of Hematology, 2021 L St, NW, Suite 900, Washington DC 20036. 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