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. 1997 Oct 15;100(8):1907–1918. doi: 10.1172/JCI119721

A p47-phox pseudogene carries the most common mutation causing p47-phox- deficient chronic granulomatous disease.

A Görlach 1, P L Lee 1, J Roesler 1, P J Hopkins 1, B Christensen 1, E D Green 1, S J Chanock 1, J T Curnutte 1
PMCID: PMC508379  PMID: 9329953

Abstract

The predominant genetic defect causing p47-phox-deficient chronic granulomatous disease (A47 degrees CGD) is a GT deletion (DeltaGT) at the beginning of exon 2. No explanation exists to account for the high incidence of this single mutation causing a rare disease in an unrelated, racially diverse population. In each of 34 consecutive unrelated normal individuals, both the normal and mutant DeltaGT sequences were present in genomic DNA, suggesting that a p47-phox related sequence carrying DeltaGT exists in the normal population. Screening of genomic bacteriophage and YAC libraries identified 13 p47-phox bacteriophage and 19 YAC clones. The GT deletion was found in 11 bacteriophage and 15 YAC clones. Only 5 exonic and 33 intronic differences distinguished all DeltaGT clones from all wild-type clones. The most striking differences were a 30-bp deletion in intron 1 and a 20-bp duplication in intron 2. These results provide good evidence for the existence of at least one highly homologous p47-phox pseudogene containing the DeltaGT mutation. The p47-phox gene and pseudogene(s) colocalize to chromosome 7q11.23. This close linkage, together with the presence within each gene of multiple recombination hot spots, suggests that the predominance of the DeltaGT mutation in A47 degrees CGD is caused by recombination events between the wild-type gene and the pseudogene(s).

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Selected References

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  1. Abo A., Pick E., Hall A., Totty N., Teahan C. G., Segal A. W. Activation of the NADPH oxidase involves the small GTP-binding protein p21rac1. Nature. 1991 Oct 17;353(6345):668–670. doi: 10.1038/353668a0. [DOI] [PubMed] [Google Scholar]
  2. Amor M., Parker K. L., Globerman H., New M. I., White P. C. Mutation in the CYP21B gene (Ile-172----Asn) causes steroid 21-hydroxylase deficiency. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1600–1604. doi: 10.1073/pnas.85.5.1600. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Babior B. M., Kipnes R. S., Curnutte J. T. Biological defense mechanisms. The production by leukocytes of superoxide, a potential bactericidal agent. J Clin Invest. 1973 Mar;52(3):741–744. doi: 10.1172/JCI107236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Breathnach R., Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem. 1981;50:349–383. doi: 10.1146/annurev.bi.50.070181.002025. [DOI] [PubMed] [Google Scholar]
  5. Britten R. J., Baron W. F., Stout D. B., Davidson E. H. Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4770–4774. doi: 10.1073/pnas.85.13.4770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Casimir C. M., Bu-Ghanim H. N., Rodaway A. R., Bentley D. L., Rowe P., Segal A. W. Autosomal recessive chronic granulomatous disease caused by deletion at a dinucleotide repeat. Proc Natl Acad Sci U S A. 1991 Apr 1;88(7):2753–2757. doi: 10.1073/pnas.88.7.2753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cerban F. M., Gea S., Menso E., Vottero-Cima E. Chagas' disease: IgG isotypes against Trypanosoma cruzi cytosol acidic antigens in patients with different degrees of heart damage. Clin Immunol Immunopathol. 1993 Apr;67(1):25–30. doi: 10.1006/clin.1993.1041. [DOI] [PubMed] [Google Scholar]
  8. Chan E. K., Takano S., Andrade L. E., Hamel J. C., Matera A. G. Structure, expression and chromosomal localization of human p80-coilin gene. Nucleic Acids Res. 1994 Oct 25;22(21):4462–4469. doi: 10.1093/nar/22.21.4462. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cheng K. C., Smith G. R. Cutting of chi-like sequences by the RecBCD enzyme of Escherichia coli. J Mol Biol. 1987 Apr 20;194(4):747–750. doi: 10.1016/0022-2836(87)90252-x. [DOI] [PubMed] [Google Scholar]
  10. Clark R. A., Volpp B. D., Leidal K. G., Nauseef W. M. Two cytosolic components of the human neutrophil respiratory burst oxidase translocate to the plasma membrane during cell activation. J Clin Invest. 1990 Mar;85(3):714–721. doi: 10.1172/JCI114496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Collier S., Tassabehji M., Sinnott P., Strachan T. A de novo pathological point mutation at the 21-hydroxylase locus: implications for gene conversion in the human genome. Nat Genet. 1993 Mar;3(3):260–265. doi: 10.1038/ng0393-260. [DOI] [PubMed] [Google Scholar]
  12. Cross A. R., Curnutte J. T. The cytosolic activating factors p47phox and p67phox have distinct roles in the regulation of electron flow in NADPH oxidase. J Biol Chem. 1995 Mar 24;270(12):6543–6548. doi: 10.1074/jbc.270.12.6543. [DOI] [PubMed] [Google Scholar]
  13. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dinauer M. C., Pierce E. A., Bruns G. A., Curnutte J. T., Orkin S. H. Human neutrophil cytochrome b light chain (p22-phox). Gene structure, chromosomal location, and mutations in cytochrome-negative autosomal recessive chronic granulomatous disease. J Clin Invest. 1990 Nov;86(5):1729–1737. doi: 10.1172/JCI114898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Doussiere J., Brandolin G., Derrien V., Vignais P. V. Critical assessment of the presence of an NADPH binding site on neutrophil cytochrome b558 by photoaffinity and immunochemical labeling. Biochemistry. 1993 Aug 31;32(34):8880–8887. doi: 10.1021/bi00085a020. [DOI] [PubMed] [Google Scholar]
  16. Eikenboom J. C., Vink T., Briët E., Sixma J. J., Reitsma P. H. Multiple substitutions in the von Willebrand factor gene that mimic the pseudogene sequence. Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2221–2224. doi: 10.1073/pnas.91.6.2221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Francke U., Hsieh C. L., Foellmer B. E., Lomax K. J., Malech H. L., Leto T. L. Genes for two autosomal recessive forms of chronic granulomatous disease assigned to 1q25 (NCF2) and 7q11.23 (NCF1). Am J Hum Genet. 1990 Sep;47(3):483–492. [PMC free article] [PubMed] [Google Scholar]
  18. Goeddel D. V., Leung D. W., Dull T. J., Gross M., Lawn R. M., McCandliss R., Seeburg P. H., Ullrich A., Yelverton E., Gray P. W. The structure of eight distinct cloned human leukocyte interferon cDNAs. Nature. 1981 Mar 5;290(5801):20–26. doi: 10.1038/290020a0. [DOI] [PubMed] [Google Scholar]
  19. Green E. D., Braden V. V., Fulton R. S., Lim R., Ueltzen M. S., Peluso D. C., Mohr-Tidwell R. M., Idol J. R., Smith L. M., Chumakov I. A human chromosome 7 yeast artificial chromosome (YAC) resource: construction, characterization, and screening. Genomics. 1995 Jan 1;25(1):170–183. doi: 10.1016/0888-7543(95)80123-4. [DOI] [PubMed] [Google Scholar]
  20. Helmberg A. Twin genes and endocrine disease: CYP21 and CYP11B genes. Acta Endocrinol (Copenh) 1993 Aug;129(2):97–108. doi: 10.1530/acta.0.1290097. [DOI] [PubMed] [Google Scholar]
  21. Heyworth P. G., Curnutte J. T., Nauseef W. M., Volpp B. D., Pearson D. W., Rosen H., Clark R. A. Neutrophil nicotinamide adenine dinucleotide phosphate oxidase assembly. Translocation of p47-phox and p67-phox requires interaction between p47-phox and cytochrome b558. J Clin Invest. 1991 Jan;87(1):352–356. doi: 10.1172/JCI114993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Higashi Y., Yoshioka H., Yamane M., Gotoh O., Fujii-Kuriyama Y. Complete nucleotide sequence of two steroid 21-hydroxylase genes tandemly arranged in human chromosome: a pseudogene and a genuine gene. Proc Natl Acad Sci U S A. 1986 May;83(9):2841–2845. doi: 10.1073/pnas.83.9.2841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Hirt H., Kimelman J., Birnbaum M. J., Chen E. Y., Seeburg P. H., Eberhardt N. L., Barta A. The human growth hormone gene locus: structure, evolution, and allelic variations. DNA. 1987 Feb;6(1):59–70. doi: 10.1089/dna.1987.6.59. [DOI] [PubMed] [Google Scholar]
  24. Horowitz M., Wilder S., Horowitz Z., Reiner O., Gelbart T., Beutler E. The human glucocerebrosidase gene and pseudogene: structure and evolution. Genomics. 1989 Jan;4(1):87–96. doi: 10.1016/0888-7543(89)90319-4. [DOI] [PubMed] [Google Scholar]
  25. Iwata M., Nunoi H., Yamazaki H., Nakano T., Niwa H., Tsuruta S., Ohga S., Ohmi S., Kanegasaki S., Matsuda I. Homologous dinucleotide (GT or TG) deletion in Japanese patients with chronic granulomatous disease with p47-phox deficiency. Biochem Biophys Res Commun. 1994 Mar 30;199(3):1372–1377. doi: 10.1006/bbrc.1994.1382. [DOI] [PubMed] [Google Scholar]
  26. Jeffreys A. J., Wilson V., Thein S. L. Hypervariable 'minisatellite' regions in human DNA. Nature. 1985 Mar 7;314(6006):67–73. doi: 10.1038/314067a0. [DOI] [PubMed] [Google Scholar]
  27. Knaus U. G., Heyworth P. G., Evans T., Curnutte J. T., Bokoch G. M. Regulation of phagocyte oxygen radical production by the GTP-binding protein Rac 2. Science. 1991 Dec 6;254(5037):1512–1515. doi: 10.1126/science.1660188. [DOI] [PubMed] [Google Scholar]
  28. Krawinkel U., Zoebelein G., Bothwell A. L. Palindromic sequences are associated with sites of DNA breakage during gene conversion. Nucleic Acids Res. 1986 May 12;14(9):3871–3882. doi: 10.1093/nar/14.9.3871. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Lehrman M. A., Russell D. W., Goldstein J. L., Brown M. S. Alu-Alu recombination deletes splice acceptor sites and produces secreted low density lipoprotein receptor in a subject with familial hypercholesterolemia. J Biol Chem. 1987 Mar 5;262(7):3354–3361. [PubMed] [Google Scholar]
  30. Leto T. L., Adams A. G., de Mendez I. Assembly of the phagocyte NADPH oxidase: binding of Src homology 3 domains to proline-rich targets. Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10650–10654. doi: 10.1073/pnas.91.22.10650. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Leto T. L., Lomax K. J., Volpp B. D., Nunoi H., Sechler J. M., Nauseef W. M., Clark R. A., Gallin J. I., Malech H. L. Cloning of a 67-kD neutrophil oxidase factor with similarity to a noncatalytic region of p60c-src. Science. 1990 May 11;248(4956):727–730. doi: 10.1126/science.1692159. [DOI] [PubMed] [Google Scholar]
  32. Liskay R. M., Letsou A., Stachelek J. L. Homology requirement for efficient gene conversion between duplicated chromosomal sequences in mammalian cells. Genetics. 1987 Jan;115(1):161–167. doi: 10.1093/genetics/115.1.161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Lomax K. J., Leto T. L., Nunoi H., Gallin J. I., Malech H. L. Recombinant 47-kilodalton cytosol factor restores NADPH oxidase in chronic granulomatous disease. Science. 1989 Jul 28;245(4916):409–412. doi: 10.1126/science.2547247. [DOI] [PubMed] [Google Scholar]
  34. Maeda N., Smithies O. The evolution of multigene families: human haptoglobin genes. Annu Rev Genet. 1986;20:81–108. doi: 10.1146/annurev.ge.20.120186.000501. [DOI] [PubMed] [Google Scholar]
  35. Mancuso D. J., Tuley E. A., Westfield L. A., Lester-Mancuso T. L., Le Beau M. M., Sorace J. M., Sadler J. E. Human von Willebrand factor gene and pseudogene: structural analysis and differentiation by polymerase chain reaction. Biochemistry. 1991 Jan 8;30(1):253–269. doi: 10.1021/bi00215a036. [DOI] [PubMed] [Google Scholar]
  36. McPhail L. C. SH3-dependent assembly of the phagocyte NADPH oxidase. J Exp Med. 1994 Dec 1;180(6):2011–2015. doi: 10.1084/jem.180.6.2011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Metzenberg A. B., Wurzer G., Huisman T. H., Smithies O. Homology requirements for unequal crossing over in humans. Genetics. 1991 May;128(1):143–161. doi: 10.1093/genetics/128.1.143. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Parkos C. A., Dinauer M. C., Walker L. E., Allen R. A., Jesaitis A. J., Orkin S. H. Primary structure and unique expression of the 22-kilodalton light chain of human neutrophil cytochrome b. Proc Natl Acad Sci U S A. 1988 May;85(10):3319–3323. doi: 10.1073/pnas.85.10.3319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Rodaway A. R., Teahan C. G., Casimir C. M., Segal A. W., Bentley D. L. Characterization of the 47-kilodalton autosomal chronic granulomatous disease protein: tissue-specific expression and transcriptional control by retinoic acid. Mol Cell Biol. 1990 Oct;10(10):5388–5396. doi: 10.1128/mcb.10.10.5388. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Roos D., de Boer M., Kuribayashi F., Meischl C., Weening R. S., Segal A. W., Ahlin A., Nemet K., Hossle J. P., Bernatowska-Matuszkiewicz E. Mutations in the X-linked and autosomal recessive forms of chronic granulomatous disease. Blood. 1996 Mar 1;87(5):1663–1681. [PubMed] [Google Scholar]
  42. Rotrosen D., Yeung C. L., Leto T. L., Malech H. L., Kwong C. H. Cytochrome b558: the flavin-binding component of the phagocyte NADPH oxidase. Science. 1992 Jun 5;256(5062):1459–1462. doi: 10.1126/science.1318579. [DOI] [PubMed] [Google Scholar]
  43. Royer-Pokora B., Kunkel L. M., Monaco A. P., Goff S. C., Newburger P. E., Baehner R. L., Cole F. S., Curnutte J. T., Orkin S. H. Cloning the gene for an inherited human disorder--chronic granulomatous disease--on the basis of its chromosomal location. Nature. 1986 Jul 3;322(6074):32–38. doi: 10.1038/322032a0. [DOI] [PubMed] [Google Scholar]
  44. Safaya S., Rieder R. F. Dysfunctional alpha-globin gene in hemoglobin H disease in blacks. A dinucleotide deletion produces a frameshift and a termination codon. J Biol Chem. 1988 Mar 25;263(9):4328–4332. [PubMed] [Google Scholar]
  45. Segal A. W., West I., Wientjes F., Nugent J. H., Chavan A. J., Haley B., Garcia R. C., Rosen H., Scrace G. Cytochrome b-245 is a flavocytochrome containing FAD and the NADPH-binding site of the microbicidal oxidase of phagocytes. Biochem J. 1992 Jun 15;284(Pt 3):781–788. doi: 10.1042/bj2840781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Slightom J. L., Blechl A. E., Smithies O. Human fetal G gamma- and A gamma-globin genes: complete nucleotide sequences suggest that DNA can be exchanged between these duplicated genes. Cell. 1980 Oct;21(3):627–638. doi: 10.1016/0092-8674(80)90426-2. [DOI] [PubMed] [Google Scholar]
  47. Stoppa-Lyonnet D., Carter P. E., Meo T., Tosi M. Clusters of intragenic Alu repeats predispose the human C1 inhibitor locus to deleterious rearrangements. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1551–1555. doi: 10.1073/pnas.87.4.1551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Thrasher A. J., Keep N. H., Wientjes F., Segal A. W. Chronic granulomatous disease. Biochim Biophys Acta. 1994 Oct 21;1227(1-2):1–24. doi: 10.1016/0925-4439(94)90100-7. [DOI] [PubMed] [Google Scholar]
  49. Tsunawaki S., Mizunari H., Nagata M., Tatsuzawa O., Kuratsuji T. A novel cytosolic component, p40phox, of respiratory burst oxidase associates with p67phox and is absent in patients with chronic granulomatous disease who lack p67phox. Biochem Biophys Res Commun. 1994 Mar 30;199(3):1378–1387. doi: 10.1006/bbrc.1994.1383. [DOI] [PubMed] [Google Scholar]
  50. Urabe K., Kimura A., Harada F., Iwanaga T., Sasazuki T. Gene conversion in steroid 21-hydroxylase genes. Am J Hum Genet. 1990 Jun;46(6):1178–1186. [PMC free article] [PubMed] [Google Scholar]
  51. Volpp B. D., Lin Y. In vitro molecular reconstitution of the respiratory burst in B lymphoblasts from p47-phox-deficient chronic granulomatous disease. J Clin Invest. 1993 Jan;91(1):201–207. doi: 10.1172/JCI116171. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Volpp B. D., Nauseef W. M., Donelson J. E., Moser D. R., Clark R. A. Cloning of the cDNA and functional expression of the 47-kilodalton cytosolic component of human neutrophil respiratory burst oxidase. Proc Natl Acad Sci U S A. 1989 Sep;86(18):7195–7199. doi: 10.1073/pnas.86.18.7195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Wientjes F. B., Hsuan J. J., Totty N. F., Segal A. W. p40phox, a third cytosolic component of the activation complex of the NADPH oxidase to contain src homology 3 domains. Biochem J. 1993 Dec 15;296(Pt 3):557–561. doi: 10.1042/bj2960557. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Wilde C. D. Pseudogenes. CRC Crit Rev Biochem. 1986;19(4):323–352. [PubMed] [Google Scholar]

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