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Non-specificity of transcription factor function in Drosophila melanogaster

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A major problem in developmental genetics is how HOX transcription factors, like Proboscipedia (PB) and Ultrabithorax (UBX), regulate distinct programs of gene expression to result in a proboscis versus a haltere, respectively, when the DNA-binding homeodomain (HD) of HOX transcription factors recognizes similar DNA-binding sequences. Indeed, the lack of DNA-binding specificity is a problem for all transcription factors (TFs), as the DNA-binding domains generally recognize small targets of five to six bases in length. Although not the initial intent of the study, I found extensive non-specificity of TF function. Multiple TFs including HOX and HD-containing and non-HD-containing TFs induced both wingless and eyeless phenotypes. The TFs Labial (LAB), Deformed (DFD), Fushi tarazu (FTZ), and Squeeze (SQZ) induced ectopic larval thoracic (T) 1 beard formation in T2 and T3. The TF Doublesex male (DSXM) rescued the reduced maxillary palp pb phenotype. These examples of non-specificity of TF function across classes of TFs, combined with previous observations, compromise the implicit, initial assumption often made that an intrinsic mechanism of TF specificity is important for function. Interestingly, the functional complementation of the pb phenotype may suggest a larger role for regulation of expression of TFs in restriction of function as opposed to an intrinsic specificity of TF function. These observations have major ramifications for analysis of functional conservation in evolution and development.

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  1. Aplin AC, Kaufman TC (1997) Homeotic transformation of legs to mouthparts by proboscipedia expression in Drosophila imaginal discs. Mech Dev 62:51–60

  2. Argiropoulos B, Ho J, Blachuta BJ, Tayyab I, Percival-Smith A (2003) Low-level ectopic expression of Fushi tarazu in Drosophila melanogaster results in ftzUal/Rpl-like phenotypes and rescues ftz phenotypes. Mech Dev 120:1443–1453

  3. Benassayag C, Plaza S, Callaerts P, Clements J, Romeo Y et al (2003) Evidence for a direct functional antagonism of the selector gene proboscipedia and eyeless in Drosophila head development. Development 130:575–586

  4. Brand AH, Perrimon N (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118:401–415

  5. Carroll SB (1995) Homeotic genes and the evolution of arthopods and chordates. Nature 376:479–485

  6. Carroll SB (2008) Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134:25–36

  7. Carroll SB, Grenier JK, Weatherbee SD (2005) From DNA to diversity: molecular genetics and the evolution of animal design. Blackwell Publishing, Oxford

  8. Chan S-K, Jaffe L, Capovilla M, Botas J, Mann RS (1994) The DNA binding specificity of Ultrabithorax is modulated by cooperative interactions with Extradenticle, another Homeoprotein. Cell 78:803–813

  9. Chen H, Xu Z, Mei C, Yu D, Small S (2012) A system of repressor gradients spatially organizes the boundaries of Bicoid-dependent target genes. Cell 149:618–629

  10. Doe CQ, Hiromi Y, Gehring WJ, Goodman CS (1988) Expression and function of the segmentation gene fushi tarazu during Drosophila neurogenesis. Science 239:170–175

  11. DuBuc TQ, Ryan JF, Shinzato C, Satoh N, Martindale MQ (2012) Coral comparative genomics reveal expanded Hox cluster in the cnidarian-bilaterian ancestor. Integr Comp Biol 52:835–841

  12. Furukubo-Tokunaga K, Flister S, Gehring WJ (1993) Functional specificity of the Antennapedia homeodomain. Proc Natl Acad Sci U S A 90:6360–6364

  13. Galant R, Carroll SB (2002) Evolution of a transcriptional repression domain in an insect Hox protein. Nature 415:910–913

  14. Garcia-Bellido A (1975) Genetic control of wing disc development. CIBA Found Symp:161–182

  15. Greig S, Akam M (1995) The role of homeotic genes in the specification of the drosophila gonad. Curr Biol 5:1057–1062

  16. Guichet A, Copeland JWR, Erdelyi M, Hlousek D, Zavorsky P et al (1997) The nuclear receptor homologue Ftz-F1 and the homeodomain protein Ftz are mutually dependent cofactors. Nature 385:548–552

  17. Hafen E, Levine M, Garber RL, Gehring WJ (1983) An improved in situ hybridization method for the detection of cellular RNAs in Drosophila tissue sections and its application for localizing transcripts of the homeotic Antennapedia gene complex. EMBO J 2:617–623

  18. Halder G, Callaerts P, Gehring WJ (1995) Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. Science 267:1788–1792

  19. Heffer A, Xiang J, Pick L (2013) Variation and constraint in Hox gene evolution. Proc Natl Acad Sci U S A 110:2211–2216

  20. Hirth F, Loop T, Egger B, Miller DFB, Kaufman TC, Reichert H (2001) Functional equivalence of Hox gene products in the specification of the tritocerebrum during embryonic brain development of Drosophila. Development 128:4781–4788

  21. Hittinger CT, Stern DL, Carroll SB (2005) Pleiotropic functions of a conserved insect-specific Hox peptide motif. Development 132:5261–5270

  22. Hudry B, Viala S, Graba Y, Merabet S (2011) Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay. BMC Biol 9:5. doi:10.1186/1741-7007-9-5

  23. Hueber SD, Bezdan D, Henz SR, Blank M, Wu H, Lohmann I (2007) Comparative analysis of Hox downstream genes in Drosophila. Development 134:381–392

  24. Hunter C, Keynon C (1995) Specification of anteroposterior cell fates in Caenorabditis elegans by Drosophila Hox proteins. Nature 377:229–232

  25. Ish-Horowicz D, Pinchin SM, Ingham PW, Gyurkovics HG (1989) Autocatalytic ftz activation and metameric instability induced by ectopic ftz expression. Cell 57:223–232

  26. Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A et al (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131:530–543

  27. Joshi R, Sun L, Mann RS (2010) Dissecting the functional specificities of two Hox proteins. Genes Dev 24:1533–1545

  28. Joulia L, Deutsch J, Bourbon H, Cribbs DL (2006) The specification of a highly derived arthropod appendage, the Drosophila labial palps, requires the joint action of selectors and signaling pathways. Dev Genes Evol 216:431–442

  29. Kramer JM, Staveley BE (2003) GAL4 causes developmental defects and apoptosis when expressed in the developing eye of Drosophila melanogaster. Genet Mol Res 2:43–47

  30. Krause H, Klemenz R, Gehring WJ (1988) Expression, modification, and localization of the fushi tarazu protein in Drosophila embryos. Genes Dev 2:1021–1036

  31. Lelli KM, Noro B, Mann RS (2011) Variable motif utilization in homeotic selector (Hox)-cofactor complex formation controls specificity. Proc Natl Acad Sci U S A 108:21122–21127

  32. Lewis EB (1978) A gene complex controlling segmentation in Drosophila. Nature 276:565–570

  33. Lohr U, Pick L (2005) Cofactor-interaction motifs and the cooption of a homeotic Hox protein into the segmentation pathway of Drosophila melanogaster. Curr Biol 15:643–649

  34. Lutz B, Lu H-C, Eichele G, Millar D, Kaufman TC (1996) Rescue of Drosophila labial null mutant by chicken ortholog Hoxb-1 demonstrates that the function of Hox gene is phylogenetically conserved. Genes Dev 10:176–184

  35. Malicki J, Schughart K, McGinnis W (1990) Mouse Hox-2.2 specifies thoracic segmental identity in Drosophila embryos and larvae. Cell 63:961–967

  36. Merabet S, Litim-Mecheri I, Karlsson D, Dixit R, Saadaoui M et al (2011) Insights into Hox protein function from a large scale combinatorial analysis of protein domains. PLoS Genet 7:e1002302

  37. Negre NCD, Brown L, Ma CA, Bristow SW, Miller et al (2011) A cis-regulatory map of the Drosophila genome. Nature 471:527–531

  38. Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal AK (1999) Structure of a DNA bound Ultrabithorax-Extradenticle homeodomain complex. Nature 397:714–719

  39. Pattatucci AM, Otteson DC, Kaufman TC (1991) A functional and structural analysis of the sex combs reduced locus of Drosophila melanogaster. Genetics 129:423–441

  40. Peifer M, Wieschaus E (1990) Mutations in the Drosophila gene extradenticle affect the way specific homeodomain proteins regulate segmental identity. Genes Dev 4:1209–1223

  41. Percival-Smith A, Hayden DJ (1998) Analysis in Drosophila melanogaster of the interaction between Sex combs reduced and extradenticle activity in the determination of tarsus and arista identity. Genetics 150:189–198

  42. Percival-Smith A, Laing Bondy JA (1999) Analysis of murine HOXA-2 activity in Drosophila melanogaster. Dev Genet 24:336–344

  43. Percival-Smith A, Muller M, Affolter M, Gehring WJ (1990) The interaction with DNA of wild-type and mutant fushi tarazu homeodomains. EMBO J 9:3967–3674

  44. Percival-Smith A, Sivanantharajah L, Pelling JJ, Teft WA (2013) Developmental competence and the induction of ectopic proboscises in Drosophila melanogaster. Dev Genes Evol 223:375–387

  45. Percival-Smith A, Teft WA, Barta JL (2005) Tarsus determination in Drosophila melanogaster. Genome 48:712–721

  46. Percival-Smith A, Weber J, Gilfoyle E, Wilson P (1997) Genetic characterization of the role of the two HOX proteins, Proboscipedia and Sex combs reduced, in determination of adult antennal, tarsal, maxillary palp and proboscis identities in Drosophila melanogaster. Development 124:5049–5062

  47. Plaza S, Prince F, Adachi Y, Punzo C, Cribbs D, Gehring WJ (2008) Cross-regulatory protein-protein interactions between Hox and Pax transcription factors. Proc Natl Acad Sci U S A 105:13439–13444

  48. Plaza S, Prince F, Jaeger J, Kloter U, Flister S et al (2001) Molecular basis for the inhibition of Drosophila eye development by Antennapedia. EMBO J 20:802–811

  49. Prince F, Katsuyama T, Oshima Y, Plaza S, Resendez-Perez D, Berry M et al (2008) The YPWM motif links Antennapedia to the basal transcriptional machinery. Development 135:1669–1679

  50. Prud’homme B, Minervino C, Hocine M, Cande JD, Aouane A, Dufour HD, Kassner VA, Gompel N (2011) Body plan innovation in treehoppers through the evolution of an extra wing-like appendage. Nature 473:83–86

  51. Ptashne M (1992). A genetic switch 2nd edn. Cell Press and Blackwell Scientific publications

  52. Rideout EJ, Dornan AJ, Neville MC, Eadie S, Goodwin SF (2010) Control of sexual differentiation and behavior by the doublesex gene in Drosophila melanogaster. Nat Neurosci 13:458–466

  53. Rubin GM, Spradling AC (1982) Genetic transformation of Drosophila with transposable element vectors. Science 218:348–353

  54. Ryan JF, Pang K, Comparative Sequencing Program NISC, Mullikin JC, Martindale MQ, Baxevanis AD (2010) The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa. EvoDevo 1:9

  55. Ryoo HD, Mann RS (1999) The control of trunk Hox specificity and activity by Extradenticle. Genes Dev 13:1704–1716

  56. Scott EK, Mason L, Arrenberg AB, Ziv L, Gosse N et al (2007) Targeting neural circuitry in zebrafish using GAL4 enhancer trapping. Nat Meth 4:323–326

  57. Scott MP, Weiner AJ, Hazelrigg TI, Polisky BA, Pirrotta V et al (1983) The molecular organization of the Antennapedia locus of Drosophila. Cell 35:763–776

  58. Sivanantharajah L, Percival-Smith A (2009) Analysis of the sequence and phenotype of Drosophila Sex combs reduced alleles reveals potential functions of conserved protein motifs of the Sex combs reduced protein. Genetics 182:191–203

  59. Sivanantharajah L, Percival-Smith A (2014). Acquisition of a leucine zipper motif as a mechanism of antimorphy for an allele of the Drosophila Hox gene Sex combs reduced. G3 4: 829–838

  60. Sivanantharajah L, Percival-Smith A (2015) Differential pleiotrophy and HOX functional organization. Dev Biol 398:1–10

  61. Staehling-Hampton K, Jackson PD, Clark MJ, Brand AH, Hoffman FM (1994) Specificity of bone morphogenetic protein-related factors: cell fate and gene expression changes in Drosophila embryos induced by decapentaplegic but not 60A. Cell Growth Differ 5:585–593

  62. Stathopoulos A, Levine M (2005) Localized repressor delinate the neurogenic ectoderm in the early Drosophila embryo. Dev Biol 280:482–493

  63. Tour E, Hittinger CT, McGinnis W (2005) Evolutionarily conserved domains required for activation and repression functions of the Drosophila Hox protein Ultrabithorax. Development 132:5271–5281

  64. Wieschaus E, Nusslien-Volhard C (1986) Looking at embryos. In: Roberts DB (ed) Drosophila: a practical approach. IRL Press, Oxford, U. K., pp. 199–228

  65. Yagi R, Mayer F, Basler K (2010) Refined LexA transactivators and their use in combination with the Drosophila Gal4 system. Proc Natl Acad Sci U S A 107:16166–16171

  66. Yu Y, Li W, Su K, Han W, Yussa M, Perrimon N, Pick L (1997) The nuclear hormone receptor FTZ-F1 is a cofactor for the Drosophila homeodomain protein ftz. Nature 385:552–555

  67. Zeng W, Andrews DJ, Mathies LD, Horner MA, Scott MP (1993) Ectopic expression and function of the Antp and Scr homeotic genes: the N terminus of the homeodomain is critical to functional specificity. Development 118:339–352

  68. Zhao JJ, Lazzarini RA, Pick L (1993) The mouse Hox-1.3 gene is functionally equivalent to the Drosophila Sex combs reduced gene. Genes Dev 7:343–454

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I thank the Bloomington Stock Center, Jim Jayne, and Richard Mann for sending fly stocks. I thank Leslie Pick for discussions at Walter Gehring’s 75th birthday conference. I would like to thank two anonymous reviewers for their suggestions for improvement of the manuscript. Imaging was performed in the imaging module of the Biotron at the University of Western Ontario. This work was supported by a National Science and Engineering Research Council of Canada Discovery Grant awarded to A.P.-S.

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Correspondence to Anthony Percival-Smith.

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Communicated by Claude Desplan

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Percival-Smith, A. Non-specificity of transcription factor function in Drosophila melanogaster . Dev Genes Evol 227, 25–39 (2017). https://doi.org/10.1007/s00427-016-0566-z

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  • Homeotic selector genes
  • Body plan
  • Eyeless
  • Doublesex
  • Transcription regulation
  • Fushi tarazu
  • Extradenticle