Skip to main content
Genetics logoLink to Genetics
. 1994 Mar;136(3):965–977. doi: 10.1093/genetics/136.3.965

Evolutionary Conservation of the Structure and Expression of Alternatively Spliced Ultrabithorax Isoforms from Drosophila

H M Bomze 1, A J Lopez 1
PMCID: PMC1205900  PMID: 7911773

Abstract

In Drosophila melanogaster, alternatively spliced mRNAs from the homeotic gene Ultrabithorax (Ubx) encode a family of structurally distinct homeoprotein isoforms. The developmentally regulated expression patterns of these isoforms suggest that they have specialized stage- and tissue-specific functions. To evaluate the functional importance of UBX isoform diversity and gain clues to the mechanism that regulates processing of Ubx RNAs, we have investigated whether the Ubx RNAs of other insects undergo similar alternative splicing. We have isolated and characterized Ubx cDNA fragments from D. melanogaster, Drosophila pseudoobscura, Drosophila hydei and Drosophila virilis, species separated by as much as 60 million years of evolution, and have found that three aspects of Ubx RNA processing have been conserved. (1) These four species exhibit identical patterns of optional exon use in a region adjacent to the homeodomain. (2) These four species produce the same family of UBX protein isoforms with identical amino acid sequences in the optional exons, even though the common amino-proximal region has undergone substantial divergence. The nucleotide sequences of the optional exons, including third positions of rare codons, have also been conserved strongly, suggesting functional constraints that are not limited to coding potential. (3) The tissue- and stage-specific patterns of expression of different UBX isoforms are identical among these Drosophila species, indicating that the developmental regulation of the alternative splicing events has also been conserved. These findings argue for an important role of alternative splicing in Ubx function. We discuss the implications of these results for models of UBX protein function and the mechanism of alternative splicing.

Full Text

The Full Text of this article is available as a PDF (13.0 MB).

Selected References

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

  1. Akam M. E., Martinez-Arias A. The distribution of Ultrabithorax transcripts in Drosophila embryos. EMBO J. 1985 Jul;4(7):1689–1700. doi: 10.1002/j.1460-2075.1985.tb03838.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Akam M. Hox and HOM: homologous gene clusters in insects and vertebrates. Cell. 1989 May 5;57(3):347–349. doi: 10.1016/0092-8674(89)90909-4. [DOI] [PubMed] [Google Scholar]
  3. Artero R. D., Akam M., Pérez-Alonso M. Oligonucleotide probes detect splicing variants in situ in Drosophila embryos. Nucleic Acids Res. 1992 Nov 11;20(21):5687–5690. doi: 10.1093/nar/20.21.5687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beachy P. A., Helfand S. L., Hogness D. S. Segmental distribution of bithorax complex proteins during Drosophila development. Nature. 1985 Feb 14;313(6003):545–551. doi: 10.1038/313545a0. [DOI] [PubMed] [Google Scholar]
  5. Berleth T., Burri M., Thoma G., Bopp D., Richstein S., Frigerio G., Noll M., Nüsslein-Volhard C. The role of localization of bicoid RNA in organizing the anterior pattern of the Drosophila embryo. EMBO J. 1988 Jun;7(6):1749–1756. doi: 10.1002/j.1460-2075.1988.tb03004.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bienz M., Tremml G. Domain of Ultrabithorax expression in Drosophila visceral mesoderm from autoregulation and exclusion. Nature. 1988 Jun 9;333(6173):576–578. doi: 10.1038/333576a0. [DOI] [PubMed] [Google Scholar]
  7. Brower D. L. Ultrabithorax gene expression in Drosophila imaginal discs and larval nervous system. Development. 1987 Sep;101(1):83–92. doi: 10.1242/dev.101.1.83. [DOI] [PubMed] [Google Scholar]
  8. Busturia A., Vernos I., Macias A., Casanova J., Morata G. Different forms of Ultrabithorax proteins generated by alternative splicing are functionally equivalent. EMBO J. 1990 Nov;9(11):3551–3555. doi: 10.1002/j.1460-2075.1990.tb07565.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Caccone A., Amato G. D., Powell J. R. Rates and patterns of scnDNA and mtDNA divergence within the Drosophila melanogaster subgroup. Genetics. 1988 Apr;118(4):671–683. doi: 10.1093/genetics/118.4.671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Canal I., Ferrús A. The expression of Ultrabithorax (Ubx) during development of the nervous system of Drosophila. J Neurogenet. 1987 Jun;4(4):161–177. [PubMed] [Google Scholar]
  11. Crowe J. S., Cooper H. J., Smith M. A., Sims M. J., Parker D., Gewert D. Improved cloning efficiency of polymerase chain reaction (PCR) products after proteinase K digestion. Nucleic Acids Res. 1991 Jan 11;19(1):184–184. doi: 10.1093/nar/19.1.184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dietz H. C., Valle D., Francomano C. A., Kendzior R. J., Jr, Pyeritz R. E., Cutting G. R. The skipping of constitutive exons in vivo induced by nonsense mutations. Science. 1993 Jan 29;259(5095):680–683. doi: 10.1126/science.8430317. [DOI] [PubMed] [Google Scholar]
  13. Driever W., Nüsslein-Volhard C. A gradient of bicoid protein in Drosophila embryos. Cell. 1988 Jul 1;54(1):83–93. doi: 10.1016/0092-8674(88)90182-1. [DOI] [PubMed] [Google Scholar]
  14. Driever W., Siegel V., Nüsslein-Volhard C. Autonomous determination of anterior structures in the early Drosophila embryo by the bicoid morphogen. Development. 1990 Aug;109(4):811–820. doi: 10.1242/dev.109.4.811. [DOI] [PubMed] [Google Scholar]
  15. Duncan I. The bithorax complex. Annu Rev Genet. 1987;21:285–319. doi: 10.1146/annurev.ge.21.120187.001441. [DOI] [PubMed] [Google Scholar]
  16. Gavis E. R., Hogness D. S. Phosphorylation, expression and function of the Ultrabithorax protein family in Drosophila melanogaster. Development. 1991 Aug;112(4):1077–1093. doi: 10.1242/dev.112.4.1077. [DOI] [PubMed] [Google Scholar]
  17. Hafen E., Levine M., Gehring W. J. Regulation of Antennapedia transcript distribution by the bithorax complex in Drosophila. Nature. 1984 Jan 19;307(5948):287–289. doi: 10.1038/307287a0. [DOI] [PubMed] [Google Scholar]
  18. Hayes P. H., Sato T., Denell R. E. Homoeosis in Drosophila: the ultrabithorax larval syndrome. Proc Natl Acad Sci U S A. 1984 Jan;81(2):545–549. doi: 10.1073/pnas.81.2.545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Heuer J. G., Kaufman T. C. Homeotic genes have specific functional roles in the establishment of the Drosophila embryonic peripheral nervous system. Development. 1992 May;115(1):35–47. doi: 10.1242/dev.115.1.35. [DOI] [PubMed] [Google Scholar]
  20. Hooper J. E., Pérez-Alonso M., Bermingham J. R., Prout M., Rocklein B. A., Wagenbach M., Edstrom J. E., de Frutos R., Scott M. P. Comparative studies of Drosophila Antennapedia genes. Genetics. 1992 Oct;132(2):453–469. doi: 10.1093/genetics/132.2.453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hooper Joan E. Homeotic gene function in the muscles of Drosophila larvae. EMBO J. 1986 Sep;5(9):2321–2329. doi: 10.1002/j.1460-2075.1986.tb04500.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Johnson F. B., Krasnow M. A. Stimulation of transcription by an Ultrabithorax protein in vitro. Genes Dev. 1990 Jun;4(6):1044–1052. doi: 10.1101/gad.4.6.1044. [DOI] [PubMed] [Google Scholar]
  23. Karch F., Bender W., Weiffenbach B. abdA expression in Drosophila embryos. Genes Dev. 1990 Sep;4(9):1573–1587. doi: 10.1101/gad.4.9.1573. [DOI] [PubMed] [Google Scholar]
  24. Kaufman T. C., Seeger M. A., Olsen G. Molecular and genetic organization of the antennapedia gene complex of Drosophila melanogaster. Adv Genet. 1990;27:309–362. doi: 10.1016/s0065-2660(08)60029-2. [DOI] [PubMed] [Google Scholar]
  25. Kornfeld K., Saint R. B., Beachy P. A., Harte P. J., Peattie D. A., Hogness D. S. Structure and expression of a family of Ultrabithorax mRNAs generated by alternative splicing and polyadenylation in Drosophila. Genes Dev. 1989 Feb;3(2):243–258. doi: 10.1101/gad.3.2.243. [DOI] [PubMed] [Google Scholar]
  26. Krasnow M. A., Saffman E. E., Kornfeld K., Hogness D. S. Transcriptional activation and repression by Ultrabithorax proteins in cultured Drosophila cells. Cell. 1989 Jun 16;57(6):1031–1043. doi: 10.1016/0092-8674(89)90341-3. [DOI] [PubMed] [Google Scholar]
  27. Kuziora M. A., McGinnis W. Autoregulation of a Drosophila homeotic selector gene. Cell. 1988 Nov 4;55(3):477–485. doi: 10.1016/0092-8674(88)90034-7. [DOI] [PubMed] [Google Scholar]
  28. Lewis E. B. A gene complex controlling segmentation in Drosophila. Nature. 1978 Dec 7;276(5688):565–570. doi: 10.1038/276565a0. [DOI] [PubMed] [Google Scholar]
  29. Lopez A. J., Hogness D. S. Immunochemical dissection of the Ultrabithorax homeoprotein family in Drosophila melanogaster. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):9924–9928. doi: 10.1073/pnas.88.22.9924. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Mann R. S., Hogness D. S. Functional dissection of Ultrabithorax proteins in D. melanogaster. Cell. 1990 Feb 23;60(4):597–610. doi: 10.1016/0092-8674(90)90663-y. [DOI] [PubMed] [Google Scholar]
  31. Mavilio F., Simeone A., Giampaolo A., Faiella A., Zappavigna V., Acampora D., Poiana G., Russo G., Peschle C., Boncinelli E. Differential and stage-related expression in embryonic tissues of a new human homoeobox gene. Nature. 1986 Dec 18;324(6098):664–668. doi: 10.1038/324664a0. [DOI] [PubMed] [Google Scholar]
  32. McGinnis W., Krumlauf R. Homeobox genes and axial patterning. Cell. 1992 Jan 24;68(2):283–302. doi: 10.1016/0092-8674(92)90471-n. [DOI] [PubMed] [Google Scholar]
  33. Mlodzik M., Fjose A., Gehring W. J. Molecular structure and spatial expression of a homeobox gene from the labial region of the Antennapedia-complex. EMBO J. 1988 Aug;7(8):2569–2578. doi: 10.1002/j.1460-2075.1988.tb03106.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. O'Connor M. B., Binari R., Perkins L. A., Bender W. Alternative RNA products from the Ultrabithorax domain of the bithorax complex. EMBO J. 1988 Feb;7(2):435–445. doi: 10.1002/j.1460-2075.1988.tb02831.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Peifer M., Wieschaus E. Mutations in the Drosophila gene extradenticle affect the way specific homeo domain proteins regulate segmental identity. Genes Dev. 1990 Jul;4(7):1209–1223. doi: 10.1101/gad.4.7.1209. [DOI] [PubMed] [Google Scholar]
  36. Regulski M., Dessain S., McGinnis N., McGinnis W. High-affinity binding sites for the Deformed protein are required for the function of an autoregulatory enhancer of the Deformed gene. Genes Dev. 1991 Feb;5(2):278–286. doi: 10.1101/gad.5.2.278. [DOI] [PubMed] [Google Scholar]
  37. Reuter R., Panganiban G. E., Hoffmann F. M., Scott M. P. Homeotic genes regulate the spatial expression of putative growth factors in the visceral mesoderm of Drosophila embryos. Development. 1990 Dec;110(4):1031–1040. doi: 10.1242/dev.110.4.1031. [DOI] [PubMed] [Google Scholar]
  38. Scott M. P., Tamkun J. W., Hartzell G. W., 3rd The structure and function of the homeodomain. Biochim Biophys Acta. 1989 Jul 28;989(1):25–48. doi: 10.1016/0304-419x(89)90033-4. [DOI] [PubMed] [Google Scholar]
  39. Seeger M. A., Kaufman T. C. Molecular analysis of the bicoid gene from Drosophila pseudoobscura: identification of conserved domains within coding and noncoding regions of the bicoid mRNA. EMBO J. 1990 Sep;9(9):2977–2987. doi: 10.1002/j.1460-2075.1990.tb07490.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Shapiro M. B., Senapathy P. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res. 1987 Sep 11;15(17):7155–7174. doi: 10.1093/nar/15.17.7155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Stroeher V. L., Jorgensen E. M., Garber R. L. Multiple transcripts from the Antennapedia gene of Drosophila melanogaster. Mol Cell Biol. 1986 Dec;6(12):4667–4675. doi: 10.1128/mcb.6.12.4667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Thali M., Müller M. M., DeLorenzi M., Matthias P., Bienz M. Drosophila homoeotic genes encode transcriptional activators similar to mammalian OTF-2. Nature. 1988 Dec 8;336(6199):598–601. doi: 10.1038/336598a0. [DOI] [PubMed] [Google Scholar]
  43. Vershon A. K., Johnson A. D. A short, disordered protein region mediates interactions between the homeodomain of the yeast alpha 2 protein and the MCM1 protein. Cell. 1993 Jan 15;72(1):105–112. doi: 10.1016/0092-8674(93)90054-t. [DOI] [PubMed] [Google Scholar]
  44. Wada K., Wada Y., Doi H., Ishibashi F., Gojobori T., Ikemura T. Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):1981–1986. doi: 10.1093/nar/19.suppl.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Watakabe A., Tanaka K., Shimura Y. The role of exon sequences in splice site selection. Genes Dev. 1993 Mar;7(3):407–418. doi: 10.1101/gad.7.3.407. [DOI] [PubMed] [Google Scholar]
  46. White R. A., Wilcox M. Distribution of Ultrabithorax proteins in Drosophila. EMBO J. 1985 Aug;4(8):2035–2043. doi: 10.1002/j.1460-2075.1985.tb03889.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. White R. A., Wilcox M. Protein products of the bithorax complex in Drosophila. Cell. 1984 Nov;39(1):163–171. doi: 10.1016/0092-8674(84)90202-2. [DOI] [PubMed] [Google Scholar]
  48. Winslow G. M., Hayashi S., Krasnow M., Hogness D. S., Scott M. P. Transcriptional activation by the Antennapedia and fushi tarazu proteins in cultured Drosophila cells. Cell. 1989 Jun 16;57(6):1017–1030. doi: 10.1016/0092-8674(89)90340-1. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES