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. 1988 Jun;85(11):3903–3907. doi: 10.1073/pnas.85.11.3903

Structural organization of the human alpha-galactosidase A gene: further evidence for the absence of a 3' untranslated region.

D F Bishop 1, R Kornreich 1, R J Desnick 1
PMCID: PMC280328  PMID: 2836863

Abstract

Human alpha-galactosidase A (alpha-D-galactoside galactohydrolase; EC 3.2.1.22) is a lysosomal hydrolase encoded by a gene localized to the chromosomal region Xq22. The deficient activity of this enzyme results in Fabry disease, an X chromosome-linked recessive disorder that leads to premature death in affected males. For studies of the structure and function of alpha-galactosidase A and for characterization of the genetic lesions in families with Fabry disease, the full-length cDNA was isolated, sequenced, and used to screen human genomic libraries. The 1393-base-pair full-length cDNA had a 60-nucleotide 5' untranslated region and encoded a precursor peptide of 429 amino acids including a signal peptide of 31 residues. Three overlapping lambda clones spanning 32 kilobases were identified that contained the entire approximately equal to 12-kilobase chromosomal gene as well as approximately equal to 9 and approximately equal to 11 kilobases of 5' and 3' flanking sequence, respectively. The gene had seven exons. The genomic exonic and full-length cDNA sequences were identical. All intron-exon splice junctions conformed to the GT/AT consensus sequence. The 5' flanking region of this lysosomal housekeeping gene contained Sp1 and CCAAT box promoter elements as well as sequences corresponding to the activator protein 1 (AP1), octanucleotide ("OCTA"), and "core" enhancer elements. There was an upstream "HTF" island (Hpa II tiny fragments) followed by four direct repeats of the "chorion box" enhancer. The unique lack of a 3' untranslated sequence in the alpha-galactosidase A cDNA was confirmed by sequencing additional cDNA clones and the genomic 3' region.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aldridge J., Kunkel L., Bruns G., Tantravahi U., Lalande M., Brewster T., Moreau E., Wilson M., Bromley W., Roderick T. A strategy to reveal high-frequency RFLPs along the human X chromosome. Am J Hum Genet. 1984 May;36(3):546–564. [PMC free article] [PubMed] [Google Scholar]
  2. Bach G., Rosenmann E., Karni A., Cohen T. Pseudodeficiency of alpha-galactosidase A. Clin Genet. 1982 Jan;21(1):59–64. [PubMed] [Google Scholar]
  3. Benoist C., Chambon P. In vivo sequence requirements of the SV40 early promotor region. Nature. 1981 Mar 26;290(5804):304–310. doi: 10.1038/290304a0. [DOI] [PubMed] [Google Scholar]
  4. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  5. Beutler E., Kuhl W. Absence of cross-reactive antigen in Fabry's disease. N Engl J Med. 1973 Sep 27;289(13):694–695. doi: 10.1056/NEJM197309272891314. [DOI] [PubMed] [Google Scholar]
  6. Beutler E., Kuhl W. Purification and properties of human alpha-galactosidases. J Biol Chem. 1972 Nov 25;247(22):7195–7200. [PubMed] [Google Scholar]
  7. Bird A. P. CpG-rich islands and the function of DNA methylation. Nature. 1986 May 15;321(6067):209–213. doi: 10.1038/321209a0. [DOI] [PubMed] [Google Scholar]
  8. Birnstiel M. L., Busslinger M., Strub K. Transcription termination and 3' processing: the end is in site! Cell. 1985 Jun;41(2):349–359. doi: 10.1016/s0092-8674(85)80007-6. [DOI] [PubMed] [Google Scholar]
  9. Bishop D. F., Calhoun D. H., Bernstein H. S., Hantzopoulos P., Quinn M., Desnick R. J. Human alpha-galactosidase A: nucleotide sequence of a cDNA clone encoding the mature enzyme. Proc Natl Acad Sci U S A. 1986 Jul;83(13):4859–4863. doi: 10.1073/pnas.83.13.4859. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Bishop D. F., Desnick R. J. Affinity purification of alpha-galactosidase A from human spleen, placenta, and plasma with elimination of pyrogen contamination. Properties of the purified splenic enzyme compared to other forms. J Biol Chem. 1981 Feb 10;256(3):1307–1316. [PubMed] [Google Scholar]
  11. Blattner F. R., Williams B. G., Blechl A. E., Denniston-Thompson K., Faber H. E., Furlong L., Grunwald D. J., Kiefer D. O., Moore D. D., Schumm J. W. Charon phages: safer derivatives of bacteriophage lambda for DNA cloning. Science. 1977 Apr 8;196(4286):161–169. doi: 10.1126/science.847462. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Calhoun D. H., Bishop D. F., Bernstein H. S., Quinn M., Hantzopoulos P., Desnick R. J. Fabry disease: isolation of a cDNA clone encoding human alpha-galactosidase A. Proc Natl Acad Sci U S A. 1985 Nov;82(21):7364–7368. doi: 10.1073/pnas.82.21.7364. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Clarke J. T., Knaack J., Crawhall J. C., Wolfe L. S. Ceramide trihexosidosis (fabry's disease) without skin lesions. N Engl J Med. 1971 Feb 4;284(5):233–235. doi: 10.1056/NEJM197102042840503. [DOI] [PubMed] [Google Scholar]
  15. Dean K. J., Sweeley C. C. Studies on human liver alpha-galactosidases. I. Purification of alpha-galactosidase A and its enzymatic properties with glycolipid and oligosaccharide substrates. J Biol Chem. 1979 Oct 25;254(20):9994–10000. [PubMed] [Google Scholar]
  16. Dynan W. S., Tjian R. Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. 1985 Aug 29-Sep 4Nature. 316(6031):774–778. doi: 10.1038/316774a0. [DOI] [PubMed] [Google Scholar]
  17. Faust P. L., Kornfeld S., Chirgwin J. M. Cloning and sequence analysis of cDNA for human cathepsin D. Proc Natl Acad Sci U S A. 1985 Aug;82(15):4910–4914. doi: 10.1073/pnas.82.15.4910. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Frischauf A. M., Lehrach H., Poustka A., Murray N. Lambda replacement vectors carrying polylinker sequences. J Mol Biol. 1983 Nov 15;170(4):827–842. doi: 10.1016/s0022-2836(83)80190-9. [DOI] [PubMed] [Google Scholar]
  19. Gil A., Proudfoot N. J. Position-dependent sequence elements downstream of AAUAAA are required for efficient rabbit beta-globin mRNA 3' end formation. Cell. 1987 May 8;49(3):399–406. doi: 10.1016/0092-8674(87)90292-3. [DOI] [PubMed] [Google Scholar]
  20. Gorman C. M., Moffat L. F., Howard B. H. Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol Cell Biol. 1982 Sep;2(9):1044–1051. doi: 10.1128/mcb.2.9.1044. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hanahan D., Meselson M. Plasmid screening at high colony density. Methods Enzymol. 1983;100:333–342. doi: 10.1016/0076-6879(83)00066-x. [DOI] [PubMed] [Google Scholar]
  22. Ish-Horowicz D., Burke J. F. Rapid and efficient cosmid cloning. Nucleic Acids Res. 1981 Jul 10;9(13):2989–2998. doi: 10.1093/nar/9.13.2989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Jenh C. H., Deng T. L., Li D. W., DeWille J., Johnson L. F. Mouse thymidylate synthase messenger RNA lacks a 3' untranslated region. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8482–8486. doi: 10.1073/pnas.83.22.8482. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Keith D. H., Singer-Sam J., Riggs A. D. Active X chromosome DNA is unmethylated at eight CCGG sites clustered in a guanine-plus-cytosine-rich island at the 5' end of the gene for phosphoglycerate kinase. Mol Cell Biol. 1986 Nov;6(11):4122–4125. doi: 10.1128/mcb.6.11.4122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Keller E. B., Noon W. A. Intron splicing: a conserved internal signal in introns of Drosophila pre-mRNAs. Nucleic Acids Res. 1985 Jul 11;13(13):4971–4981. doi: 10.1093/nar/13.13.4971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Kobayashi T., Kira J., Shinnoh N., Goto I., Kuroiwa Y. Fabry's disease with partially deficient hydrolysis of ceramide trihexoside. J Neurol Sci. 1985 Feb;67(2):179–185. doi: 10.1016/0022-510x(85)90114-5. [DOI] [PubMed] [Google Scholar]
  27. Kozak M. Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs. Nucleic Acids Res. 1984 Jan 25;12(2):857–872. doi: 10.1093/nar/12.2.857. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kusiak J. W., Quirk J. M., Brady R. O. Purification and properties of the two major isozymes of alpha-galactosidase from human placenta. J Biol Chem. 1978 Jan 10;253(1):184–190. [PubMed] [Google Scholar]
  29. Lee W., Mitchell P., Tjian R. Purified transcription factor AP-1 interacts with TPA-inducible enhancer elements. Cell. 1987 Jun 19;49(6):741–752. doi: 10.1016/0092-8674(87)90612-x. [DOI] [PubMed] [Google Scholar]
  30. Lemansky P., Bishop D. F., Desnick R. J., Hasilik A., von Figura K. Synthesis and processing of alpha-galactosidase A in human fibroblasts. Evidence for different mutations in Fabry disease. J Biol Chem. 1987 Feb 15;262(5):2062–2065. [PubMed] [Google Scholar]
  31. Lenardo M., Pierce J. W., Baltimore D. Protein-binding sites in Ig gene enhancers determine transcriptional activity and inducibility. Science. 1987 Jun 19;236(4808):1573–1577. doi: 10.1126/science.3109035. [DOI] [PubMed] [Google Scholar]
  32. Lindsay S., Bird A. P. Use of restriction enzymes to detect potential gene sequences in mammalian DNA. 1987 May 28-Jun 3Nature. 327(6120):336–338. doi: 10.1038/327336a0. [DOI] [PubMed] [Google Scholar]
  33. Mayes J. S., Beutler E. alpha-galactosidase A from human placenta. Stability and subunit size. Biochim Biophys Acta. 1977 Oct 13;484(2):408–416. doi: 10.1016/0005-2744(77)90096-1. [DOI] [PubMed] [Google Scholar]
  34. McDevitt M. A., Hart R. P., Wong W. W., Nevins J. R. Sequences capable of restoring poly(A) site function define two distinct downstream elements. EMBO J. 1986 Nov;5(11):2907–2913. doi: 10.1002/j.1460-2075.1986.tb04586.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. McLauchlan J., Gaffney D., Whitton J. L., Clements J. B. The consensus sequence YGTGTTYY located downstream from the AATAAA signal is required for efficient formation of mRNA 3' termini. Nucleic Acids Res. 1985 Feb 25;13(4):1347–1368. doi: 10.1093/nar/13.4.1347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. doi: 10.1016/0076-6879(83)01005-8. [DOI] [PubMed] [Google Scholar]
  37. Mohandas T., Sparkes R. S., Bishop D. F., Desnick R. J., Shapiro L. J. Frequency of reactivation and variability in expression of X-linked enzyme loci. Am J Hum Genet. 1984 Jul;36(4):916–925. [PMC free article] [PubMed] [Google Scholar]
  38. Mount S. M. A catalogue of splice junction sequences. Nucleic Acids Res. 1982 Jan 22;10(2):459–472. doi: 10.1093/nar/10.2.459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Myerowitz R., Piekarz R., Neufeld E. F., Shows T. B., Suzuki K. Human beta-hexosaminidase alpha chain: coding sequence and homology with the beta chain. Proc Natl Acad Sci U S A. 1985 Dec;82(23):7830–7834. doi: 10.1073/pnas.82.23.7830. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Okayama H., Berg P. A cDNA cloning vector that permits expression of cDNA inserts in mammalian cells. Mol Cell Biol. 1983 Feb;3(2):280–289. doi: 10.1128/mcb.3.2.280. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Okayama H., Berg P. High-efficiency cloning of full-length cDNA. Mol Cell Biol. 1982 Feb;2(2):161–170. doi: 10.1128/mcb.2.2.161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Perlman D., Halvorson H. O. A putative signal peptidase recognition site and sequence in eukaryotic and prokaryotic signal peptides. J Mol Biol. 1983 Jun 25;167(2):391–409. doi: 10.1016/s0022-2836(83)80341-6. [DOI] [PubMed] [Google Scholar]
  43. Proia R. L., Soravia E. Organization of the gene encoding the human beta-hexosaminidase alpha-chain. J Biol Chem. 1987 Apr 25;262(12):5677–5681. [PubMed] [Google Scholar]
  44. Prywes R., Roeder R. G. Inducible binding of a factor to the c-fos enhancer. Cell. 1986 Dec 5;47(5):777–784. doi: 10.1016/0092-8674(86)90520-9. [DOI] [PubMed] [Google Scholar]
  45. Quinn M., Hantzopoulos P., Fidanza V., Calhoun D. H. A genomic clone containing the promoter for the gene encoding the human lysosomal enzyme, alpha-galactosidase A. Gene. 1987;58(2-3):177–188. doi: 10.1016/0378-1119(87)90374-x. [DOI] [PubMed] [Google Scholar]
  46. Rietra P. J., Molenaar J. L., Hamers M. N., Tager J. M., Borst P. Investigation of the alpha-galactosidase deficiency in Fabry's disease using antibodies against the purified enzyme. Eur J Biochem. 1974 Jul 1;46(1):89–98. doi: 10.1111/j.1432-1033.1974.tb03600.x. [DOI] [PubMed] [Google Scholar]
  47. Romeo G., D'Urso M., Pisacane A., Blum E., De Falco A., Ruffilli A. Residual activity of alpha-galactosidase A in Fabry's disease. Biochem Genet. 1975 Oct;13(9-10):615–628. doi: 10.1007/BF00484919. [DOI] [PubMed] [Google Scholar]
  48. Ruskin B., Krainer A. R., Maniatis T., Green M. R. Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell. 1984 Aug;38(1):317–331. doi: 10.1016/0092-8674(84)90553-1. [DOI] [PubMed] [Google Scholar]
  49. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Sorge J., West C., Westwood B., Beutler E. Molecular cloning and nucleotide sequence of human glucocerebrosidase cDNA. Proc Natl Acad Sci U S A. 1985 Nov;82(21):7289–7293. doi: 10.1073/pnas.82.21.7289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  52. Spoerel N., Nguyen H. T., Kafatos F. C. Gene regulation and evolution in the chorion locus of Bombyx mori. Structural and developmental characterization of four eggshell genes and their flanking DNA regions. J Mol Biol. 1986 Jul 5;190(1):23–35. doi: 10.1016/0022-2836(86)90072-0. [DOI] [PubMed] [Google Scholar]
  53. Spradling A. C., de Cicco D. V., Wakimoto B. T., Levine J. F., Kalfayan L. J., Cooley L. Amplification of the X-linked Drosophila chorion gene cluster requires a region upstream from the s38 chorion gene. EMBO J. 1987 Apr;6(4):1045–1053. doi: 10.1002/j.1460-2075.1987.tb04857.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Tsuji S., Martin B. M., Kaslow D. C., Migeon B. R., Choudary P. V., Stubbleflied B. K., Mayor J. A., Murray G. J., Barranger J. A., Ginns E. I. Signal sequence and DNA-mediated expression of human lysosomal alpha-galactosidase A. Eur J Biochem. 1987 Jun 1;165(2):275–280. doi: 10.1111/j.1432-1033.1987.tb11438.x. [DOI] [PubMed] [Google Scholar]
  55. Watson M. E. Compilation of published signal sequences. Nucleic Acids Res. 1984 Jul 11;12(13):5145–5164. doi: 10.1093/nar/12.13.5145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Wood W. I., Capon D. J., Simonsen C. C., Eaton D. L., Gitschier J., Keyt B., Seeburg P. H., Smith D. H., Hollingshead P., Wion K. L. Expression of active human factor VIII from recombinant DNA clones. Nature. 1984 Nov 22;312(5992):330–337. doi: 10.1038/312330a0. [DOI] [PubMed] [Google Scholar]
  57. Yang T. P., Caskey C. T. Nuclease sensitivity of the mouse HPRT gene promoter region: differential sensitivity on the active and inactive X chromosomes. Mol Cell Biol. 1987 Aug;7(8):2994–2998. doi: 10.1128/mcb.7.8.2994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. von Heijne G. A new method for predicting signal sequence cleavage sites. Nucleic Acids Res. 1986 Jun 11;14(11):4683–4690. doi: 10.1093/nar/14.11.4683. [DOI] [PMC free article] [PubMed] [Google Scholar]

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