Skip to main content
NCBI home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1989 Sep;9(9):3938–3950. doi: 10.1128/mcb.9.9.3938

The cyclic nucleotide phosphodiesterase gene of Dictyostelium discoideum utilizes alternate promoters and splicing for the synthesis of multiple mRNAs.

G J Podgorski 1, J Franke 1, M Faure 1, R H Kessin 1
PMCID: PMC362456  PMID: 2779573

Abstract

The cyclic nucleotide phosphodiesterase (phosphodiesterase) gene plays essential roles in the development of Dictyostelium discoideum during cellular aggregation and postaggregation morphogenesis. Genomic clones spanning the gene were isolated and used to determine the sequence and structure of the phosphodiesterase gene. We found an unusually complex organization for a gene of D. discoideum. Two transcripts of 2.4 and 1.9 kilobases (kb) were synthesized from start sites separated by 1.1 kb. A developmentally regulated promoter was utilized for the 2.4-kb mRNA, and a constitutive promoter regulated synthesis of the 1.9-kb transcript. The gene was found to be divided into four exons that are alternately spliced to give rise to the two mRNAs. The precursor of the 2.4-kb mRNA contained a 2.3-kb intron, whereas the precursor of the constitutive transcript was synthesized with a 1.7-kb intron. The two transcripts contained identical protein-coding regions and 400-nucleotide 3' untranslated sequences. The 2.4-kb developmentally regulated mRNA was distinguished by a long 5' untranslated leader of 666 nucleotides. The complex structure of the gene may allow multiple levels of control of the expression of the phosphodiesterase during development.

Full text

PDF
3938

Images in this article

3941Image
on p.3941
3945Image
on p.3945
3946Image
on p.3946

Selected References

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

  1. Barklis E., Pontius B., Barfield K., Lodish H. F. Structure of the promoter of the Dictyostelium discoideum prespore EB4 gene. Mol Cell Biol. 1985 Jun;5(6):1465–1472. doi: 10.1128/mcb.5.6.1465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Barklis E., Pontius B., Lodish H. F. Structure of the Dictyostelium discoideum prestalk D11 gene and protein. Mol Cell Biol. 1985 Jun;5(6):1473–1479. doi: 10.1128/mcb.5.6.1473. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Barra J., Barrand P., Blondelet M. H., Brachet P. pdsA, a gene involved in the production of active phosphodiesterase during starvation of Dictyostelium discoideum amoebae. Mol Gen Genet. 1980;177(4):607–613. doi: 10.1007/BF00272671. [DOI] [PubMed] [Google Scholar]
  4. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Brewer G., Ross J. Poly(A) shortening and degradation of the 3' A+U-rich sequences of human c-myc mRNA in a cell-free system. Mol Cell Biol. 1988 Apr;8(4):1697–1708. doi: 10.1128/mcb.8.4.1697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Ceccarelli A., McRobbie S. J., Jermyn K. A., Duffy K., Early A., Williams J. G. Structural and functional characterization of a Dictyostelium gene encoding a DIF inducible, prestalk-enriched mRNA sequence. Nucleic Acids Res. 1987 Sep 25;15(18):7463–7476. doi: 10.1093/nar/15.18.7463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chisholm R. L. Isolation of developmentally regulated genes. Methods Cell Biol. 1987;28:461–470. doi: 10.1016/s0091-679x(08)61663-5. [DOI] [PubMed] [Google Scholar]
  8. Chisholm R. L., Rushforth A. M., Pollenz R. S., Kuczmarski E. R., Tafuri S. R. Dictyostelium discoideum myosin: isolation and characterization of cDNAs encoding the essential light chain. Mol Cell Biol. 1988 Feb;8(2):794–801. doi: 10.1128/mcb.8.2.794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dale R. M., McClure B. A., Houchins J. P. A rapid single-stranded cloning strategy for producing a sequential series of overlapping clones for use in DNA sequencing: application to sequencing the corn mitochondrial 18 S rDNA. Plasmid. 1985 Jan;13(1):31–40. doi: 10.1016/0147-619x(85)90053-8. [DOI] [PubMed] [Google Scholar]
  10. Datta S., Firtel R. A. An 80-bp cis-acting regulatory region controls cAMP and development regulation of a prestalk gene in Dictyostelium. Genes Dev. 1988 Mar;2(3):294–304. doi: 10.1101/gad.2.3.294. [DOI] [PubMed] [Google Scholar]
  11. Dinauer M. C., Steck T. L., Devreotes P. N. Cyclic 3',5'-AMP relay in Dictyostelium discoideum IV. Recovery of the cAMP signaling response after adaptation to cAMP. J Cell Biol. 1980 Aug;86(2):545–553. doi: 10.1083/jcb.86.2.545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Driscoll D. M., Williams J. G. Two divergently transcribed genes of Dictyostelium discoideum are cyclic AMP-inducible and coregulated during development. Mol Cell Biol. 1987 Dec;7(12):4482–4489. doi: 10.1128/mcb.7.12.4482. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Early A. E., Williams J. G., Meyer H. E., Por S. B., Smith E., Williams K. L., Gooley A. A. Structural characterization of Dictyostelium discoideum prespore-specific gene D19 and of its product, cell surface glycoprotein PsA. Mol Cell Biol. 1988 Aug;8(8):3458–3466. doi: 10.1128/mcb.8.8.3458. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fagan J. B., Pastan I., de Crombrugghe B. Sequence rearrangement and duplication of double stranded fibronectin cDNA probably occurring during cDNA synthesis by AMV reverse transcriptase and Escherichia coli DNA polymerase I. Nucleic Acids Res. 1980 Jul 11;8(13):3055–3064. doi: 10.1093/nar/8.13.3055. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Faure M., Camonis J. H., Jacquet M. Molecular characterization of a Dictyostelium discoideum gene encoding a multifunctional enzyme of the pyrimidine pathway. Eur J Biochem. 1989 Feb 1;179(2):345–358. doi: 10.1111/j.1432-1033.1989.tb14560.x. [DOI] [PubMed] [Google Scholar]
  16. Faure M., Podgorski G. J., Franke J., Kessin R. H. Disruption of Dictyostelium discoideum morphogenesis by overproduction of cAMP phosphodiesterase. Proc Natl Acad Sci U S A. 1988 Nov;85(21):8076–8080. doi: 10.1073/pnas.85.21.8076. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Faure M., Podgorski G. J., Franke J., Kessin R. H. Rescue of a Dictyostelium discoideum mutant defective in cyclic nucleotide phosphodiesterase. Dev Biol. 1989 Feb;131(2):366–372. doi: 10.1016/s0012-1606(89)80010-7. [DOI] [PubMed] [Google Scholar]
  18. Feinberg A. P., Vogelstein B. "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity". Addendum. Anal Biochem. 1984 Feb;137(1):266–267. doi: 10.1016/0003-2697(84)90381-6. [DOI] [PubMed] [Google Scholar]
  19. Fields S., Winter G. Nucleotide-sequence heterogeneity and sequence rearrangements in influenza virus cDNA. Gene. 1981 Nov;15(2-3):207–214. doi: 10.1016/0378-1119(81)90130-x. [DOI] [PubMed] [Google Scholar]
  20. Franke J., Kessin R. A defined minimal medium for axenic strains of Dictyostelium discoideum. Proc Natl Acad Sci U S A. 1977 May;74(5):2157–2161. doi: 10.1073/pnas.74.5.2157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Franke J., Podgorski G. J., Kessin R. H. The expression of two transcripts of the phosphodiesterase gene during the development of Dictyostelium discoideum. Dev Biol. 1987 Dec;124(2):504–511. doi: 10.1016/0012-1606(87)90503-3. [DOI] [PubMed] [Google Scholar]
  22. Frohman M. A., Dush M. K., Martin G. R. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8998–9002. doi: 10.1073/pnas.85.23.8998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Gerisch G. Cyclic AMP and other signals controlling cell development and differentiation in Dictyostelium. Annu Rev Biochem. 1987;56:853–879. doi: 10.1146/annurev.bi.56.070187.004225. [DOI] [PubMed] [Google Scholar]
  24. Gerisch G., Fromm H., Huesgen A., Wick U. Control of cell-contact sites by cyclic AMP pulses in differentiating Dictyostelium cells. Nature. 1975 Jun 12;255(5509):547–549. doi: 10.1038/255547a0. [DOI] [PubMed] [Google Scholar]
  25. Giorda R., Ennis H. L. Structure of two developmentally regulated Dictyostelium discoideum ubiquitin genes. Mol Cell Biol. 1987 Jun;7(6):2097–2103. doi: 10.1128/mcb.7.6.2097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Giorda R., Ohmachi T., Ennis H. L. Organization of a gene family developmentally regulated during Dictyostelium discoideum spore germination. J Mol Biol. 1989 Jan 5;205(1):63–69. doi: 10.1016/0022-2836(89)90364-1. [DOI] [PubMed] [Google Scholar]
  27. Hu M. C., Sharp S. B., Davidson N. The complete sequence of the mouse skeletal alpha-actin gene reveals several conserved and inverted repeat sequences outside of the protein-coding region. Mol Cell Biol. 1986 Jan;6(1):15–25. doi: 10.1128/mcb.6.1.15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Jacquet M., Guilbaud R., Garreau H. Sequence analysis of the DdPYR5-6 gene coding for UMP synthase in Dictyostelium discoideum and comparison with orotate phosphoribosyl transferases and OMP decarboxylases. Mol Gen Genet. 1988 Mar;211(3):441–445. doi: 10.1007/BF00425698. [DOI] [PubMed] [Google Scholar]
  29. Jacquet M., Kalekine M., Boy-Marcotte E. Sequence analysis of a Dictyostelium discoideum gene coding for an active dihydroorotate dehydrogenase in yeast. Biochimie. 1985 Jun;67(6):583–588. doi: 10.1016/s0300-9084(85)80197-8. [DOI] [PubMed] [Google Scholar]
  30. Janssens P. M., Van Haastert P. J. Molecular basis of transmembrane signal transduction in Dictyostelium discoideum. Microbiol Rev. 1987 Dec;51(4):396–418. doi: 10.1128/mr.51.4.396-418.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Kessin R. H. Genetics of early Dictyostelium discoideum development. Microbiol Rev. 1988 Mar;52(1):29–49. doi: 10.1128/mr.52.1.29-49.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Kimmel A. R., Firtel R. A. Sequence organization in Dictyostelium: unique structure at the 5'-ends of protein coding genes. Nucleic Acids Res. 1983 Jan 25;11(2):541–552. doi: 10.1093/nar/11.2.541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Klein C., Juliani M. H. cAMP,-induced changes in cAMP-binding sites on D; discoideum amebae. Cell. 1977 Feb;10(2):329–335. doi: 10.1016/0092-8674(77)90227-6. [DOI] [PubMed] [Google Scholar]
  34. Kozak M. An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 1987 Oct 26;15(20):8125–8148. doi: 10.1093/nar/15.20.8125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Kozak M. Leader length and secondary structure modulate mRNA function under conditions of stress. Mol Cell Biol. 1988 Jul;8(7):2737–2744. doi: 10.1128/mcb.8.7.2737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Kumagai A., Pupillo M., Gundersen R., Miake-Lye R., Devreotes P. N., Firtel R. A. Regulation and function of G alpha protein subunits in Dictyostelium. Cell. 1989 Apr 21;57(2):265–275. doi: 10.1016/0092-8674(89)90964-1. [DOI] [PubMed] [Google Scholar]
  37. Lacombe M. L., Podgorski G. J., Franke J., Kessin R. H. Molecular cloning and developmental expression of the cyclic nucleotide phosphodiesterase gene of Dictyostelium discoideum. J Biol Chem. 1986 Dec 25;261(36):16811–16817. [PubMed] [Google Scholar]
  38. Maniak M., Nellen W. A developmentally regulated membrane protein gene in Dictyostelium discoideum is also induced by heat shock and cold shock. Mol Cell Biol. 1988 Jan;8(1):153–159. doi: 10.1128/mcb.8.1.153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Mann S. K., Firtel R. A. Cyclic AMP regulation of early gene expression in Dictyostelium discoideum: mediation via the cell surface cyclic AMP receptor. Mol Cell Biol. 1987 Jan;7(1):458–469. doi: 10.1128/mcb.7.1.458. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Mann S. K., Firtel R. A. Two-phase regulatory pathway controls cAMP receptor-mediated expression of early genes in Dictyostelium. Proc Natl Acad Sci U S A. 1989 Mar;86(6):1924–1928. doi: 10.1073/pnas.86.6.1924. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. 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]
  42. Nellen W., Silan C., Saur U., Firtel R. A. Regulatory sequences in the promoter of the Dictyostelium Actin 6 gene. EMBO J. 1986 Dec 1;5(12):3367–3372. doi: 10.1002/j.1460-2075.1986.tb04652.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Pears C. J., Mahbubani H. M., Williams J. G. Characterization of two highly diverged but developmentally co-regulated cysteine proteinase genes in Dictyostelium discoideum. Nucleic Acids Res. 1985 Dec 20;13(24):8853–8866. doi: 10.1093/nar/13.24.8853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Pears C. J., Williams J. G. Identification of a DNA sequence element required for efficient expression of a developmentally regulated and cAMP-inducible gene of Dictyostelium discoideum. EMBO J. 1987 Jan;6(1):195–200. doi: 10.1002/j.1460-2075.1987.tb04738.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Pears C. J., Williams J. G. Multiple copies of a G-rich element upstream of a cAMP-inducible Dictyostelium gene are necessary but not sufficient for efficient gene expression. Nucleic Acids Res. 1988 Sep 12;16(17):8467–8486. doi: 10.1093/nar/16.17.8467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Podgorski G. J., Franke J., Kessin R. H. Isolation of a cDNA encoding a portion of the cyclic nucleotide phosphodiesterase of Dictyostelium discoideum. J Gen Microbiol. 1986 Apr;132(4):1043–1050. doi: 10.1099/00221287-132-4-1043. [DOI] [PubMed] [Google Scholar]
  47. Poole S. J., Firtel R. A. Conserved structural features are found upstream from the three co-ordinately regulated discoidin I genes of Dictyostelium discoideum. J Mol Biol. 1984 Jan 15;172(2):203–220. doi: 10.1016/s0022-2836(84)80038-8. [DOI] [PubMed] [Google Scholar]
  48. Proudfoot N. J., Brownlee G. G. 3' non-coding region sequences in eukaryotic messenger RNA. Nature. 1976 Sep 16;263(5574):211–214. doi: 10.1038/263211a0. [DOI] [PubMed] [Google Scholar]
  49. Ragheb J. A., Dottin R. P. Structure and sequence of a UDP glucose pyrophosphorylase gene of Dictyostelium discoideum. Nucleic Acids Res. 1987 May 11;15(9):3891–3906. doi: 10.1093/nar/15.9.3891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Reymond C. D., Gomer R. H., Mehdy M. C., Firtel R. A. Developmental regulation of a Dictyostelium gene encoding a protein homologous to mammalian ras protein. Cell. 1984 Nov;39(1):141–148. doi: 10.1016/0092-8674(84)90199-5. [DOI] [PubMed] [Google Scholar]
  51. Romans P., Firtel R. A. Organization of the Dictyostelium discoideum actin multigene family. Flanking sequences show subfamily homologies and unusual dyad symmetries. J Mol Biol. 1985 Jun 5;183(3):311–326. doi: 10.1016/0022-2836(85)90003-8. [DOI] [PubMed] [Google Scholar]
  52. Schaap P., Wang M. Interactions between adenosine and oscillatory cAMP signaling regulate size and pattern in Dictyostelium. Cell. 1986 Apr 11;45(1):137–144. doi: 10.1016/0092-8674(86)90545-3. [DOI] [PubMed] [Google Scholar]
  53. Sogin M. L., Gunderson J. H., Elwood H. J., Alonso R. A., Peattie D. A. Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science. 1989 Jan 6;243(4887):75–77. doi: 10.1126/science.2911720. [DOI] [PubMed] [Google Scholar]
  54. Steel L. F., Smyth A., Jacobson A. Nucleotide sequence and characterization of the transcript of a Dictyostelium ribosomal protein gene. Nucleic Acids Res. 1987 Dec 23;15(24):10285–10298. doi: 10.1093/nar/15.24.10285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Volckaert G., Tavernier J., Derynck R., Devos R., Fiers W. Molecular mechanisms of nucleotide-sequence rearrangements in cDNA clones of human fibroblast interferon mRNA. Gene. 1981 Nov;15(2-3):215–223. doi: 10.1016/0378-1119(81)90131-1. [DOI] [PubMed] [Google Scholar]
  56. Welker D. L., Hirth K. P., Williams K. L. Inheritance of extrachromosomal ribosomal DNA during the asexual life cycle of Dictyostelium discoideum: examination by use of DNA polymorphisms. Mol Cell Biol. 1985 Feb;5(2):273–280. doi: 10.1128/mcb.5.2.273. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Williams J. G., North M. J., Mahbubani H. A developmentally regulated cysteine proteinase in Dictyostelium discoideum. EMBO J. 1985 Apr;4(4):999–1006. doi: 10.1002/j.1460-2075.1985.tb03730.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Williams J. G. The role of diffusible molecules in regulating the cellular differentiation of Dictyostelium discoideum. Development. 1988 May;103(1):1–16. [PubMed] [Google Scholar]
  59. Wilson T., Treisman R. Removal of poly(A) and consequent degradation of c-fos mRNA facilitated by 3' AU-rich sequences. Nature. 1988 Nov 24;336(6197):396–399. doi: 10.1038/336396a0. [DOI] [PubMed] [Google Scholar]
  60. Witke W., Schleicher M., Lottspeich F., Noegel A. Studies on the transcription, translation, and structure of alpha-actinin in Dictyostelium discoideum. J Cell Biol. 1986 Sep;103(3):969–975. doi: 10.1083/jcb.103.3.969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Yeh R. P., Chan F. K., Coukell M. B. Independent regulation of the extracellular cyclic AMP phosphodiesterase-inhibitor system and membrane differentiation by exogenous cyclic AMP in Dictyostelium discoideum. Dev Biol. 1978 Oct;66(2):361–374. doi: 10.1016/0012-1606(78)90245-2. [DOI] [PubMed] [Google Scholar]
  62. van Ormondt H., Galibert F. Nucleotide sequences of adenovirus DNAs. Curr Top Microbiol Immunol. 1984;110:73–142. doi: 10.1007/978-3-642-46494-2_4. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES