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Nucleic Acids Res. Nov 1, 1997; 25(21): 4173–4180.
PMCID: PMC147054

Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals.

Abstract

A new Caenorhabditis elegans homeobox gene, ceh-25, is described that belongs to the TALE superclass of atypical homeodomains, which are characterized by three extra residues between helix 1 and helix 2. ORF and PCR analysis revealed a novel type of alternative splicing within the homeobox. The alternative splicing occurs such that two different homeodomains can be generated, which differ in their first 25 amino acids. ceh-25 is an orthologue of the vertebrate Meis genes and it shares a new conserved domain of 130 amino acids with them. A thorough analysis of all TALE homeobox genes was performed and a new classification is presented. Four TALE classes are identified in animals: PBC, MEIS, TGIF and IRO (Iroquois); two types in fungi: the mating type genes (M-ATYP) and the CUP genes; and two types in plants: KNOX and BEL. The IRO class has a new conserved motif downstream of the homeodomain. For the KNOX class, a conserved domain, the KNOX domain, was defined upstream of the homeodomain. Comparison of the KNOX domain and the MEIS domain shows significant sequence similarity revealing the existence of an archetypal group of homeobox genes that encode two associated conserved domains. Thus TALE homeobox genes were already present in the common ancestor of plants, fungi and animals and represent a branch distinct from the typical homeobox genes.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Gehring WJ, Qian YQ, Billeter M, Furukubo-Tokunaga K, Schier AF, Resendez-Perez D, Affolter M, Otting G, Wüthrich K. Homeodomain-DNA recognition. Cell. 1994 Jul 29;78(2):211–223. [PubMed]
  • Wolberger C, Vershon AK, Liu B, Johnson AD, Pabo CO. Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell. 1991 Nov 1;67(3):517–528. [PubMed]
  • Ceska TA, Lamers M, Monaci P, Nicosia A, Cortese R, Suck D. The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding. EMBO J. 1993 May;12(5):1805–1810. [PMC free article] [PubMed]
  • Leiting B, De Francesco R, Tomei L, Cortese R, Otting G, Wüthrich K. The three-dimensional NMR-solution structure of the polypeptide fragment 195-286 of the LFB1/HNF1 transcription factor from rat liver comprises a nonclassical homeodomain. EMBO J. 1993 May;12(5):1797–1803. [PMC free article] [PubMed]
  • Bertolino E, Reimund B, Wildt-Perinic D, Clerc RG. A novel homeobox protein which recognizes a TGT core and functionally interferes with a retinoid-responsive motif. J Biol Chem. 1995 Dec 29;270(52):31178–31188. [PubMed]
  • Astell CR, Ahlstrom-Jonasson L, Smith M, Tatchell K, Nasmyth KA, Hall BD. The sequence of the DNAs coding for the mating-type loci of Saccharomyces cerevisiae. Cell. 1981 Nov;27(1 Pt 2):15–23. [PubMed]
  • Vollbrecht E, Veit B, Sinha N, Hake S. The developmental gene Knotted-1 is a member of a maize homeobox gene family. Nature. 1991 Mar 21;350(6315):241–243. [PubMed]
  • Kamps MP, Murre C, Sun XH, Baltimore D. A new homeobox gene contributes the DNA binding domain of the t(1;19) translocation protein in pre-B ALL. Cell. 1990 Feb 23;60(4):547–555. [PubMed]
  • Nourse J, Mellentin JD, Galili N, Wilkinson J, Stanbridge E, Smith SD, Cleary ML. Chromosomal translocation t(1;19) results in synthesis of a homeobox fusion mRNA that codes for a potential chimeric transcription factor. Cell. 1990 Feb 23;60(4):535–545. [PubMed]
  • Moskow JJ, Bullrich F, Huebner K, Daar IO, Buchberg AM. Meis1, a PBX1-related homeobox gene involved in myeloid leukemia in BXH-2 mice. Mol Cell Biol. 1995 Oct;15(10):5434–5443. [PMC free article] [PubMed]
  • Gomez-Skarmeta JL, Diez del Corral R, de la Calle-Mustienes E, Ferré-Marcó D, Modolell J. Araucan and caupolican, two members of the novel iroquois complex, encode homeoproteins that control proneural and vein-forming genes. Cell. 1996 Apr 5;85(1):95–105. [PubMed]
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. [PubMed]
  • 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. [PMC free article] [PubMed]
  • Kuhner MK, Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol. 1994 May;11(3):459–468. [PubMed]
  • Kerstetter R, Vollbrecht E, Lowe B, Veit B, Yamaguchi J, Hake S. Sequence analysis and expression patterns divide the maize knotted1-like homeobox genes into two classes. Plant Cell. 1994 Dec;6(12):1877–1887. [PMC free article] [PubMed]
  • Bürglin TR, Ruvkun G. New motif in PBX genes. Nat Genet. 1992 Aug;1(5):319–320. [PubMed]
  • Nakamura T, Jenkins NA, Copeland NG. Identification of a new family of Pbx-related homeobox genes. Oncogene. 1996 Nov 21;13(10):2235–2242. [PubMed]
  • Steelman S, Moskow JJ, Muzynski K, North C, Druck T, Montgomery JC, Huebner K, Daar IO, Buchberg AM. Identification of a conserved family of Meis1-related homeobox genes. Genome Res. 1997 Feb;7(2):142–156. [PubMed]
  • McNeill H, Yang CH, Brodsky M, Ungos J, Simon MA. mirror encodes a novel PBX-class homeoprotein that functions in the definition of the dorsal-ventral border in the Drosophila eye. Genes Dev. 1997 Apr 15;11(8):1073–1082. [PubMed]
  • Ryan AK, Tejada ML, May DL, Dubaova M, Deeley RG. Isolation and characterization of the chicken homeodomain protein AKR. Nucleic Acids Res. 1995 Aug 25;23(16):3252–3259. [PMC free article] [PubMed]
  • Reiser L, Modrusan Z, Margossian L, Samach A, Ohad N, Haughn GW, Fischer RL. The BELL1 gene encodes a homeodomain protein involved in pattern formation in the Arabidopsis ovule primordium. Cell. 1995 Dec 1;83(5):735–742. [PubMed]
  • Quaedvlieg N, Dockx J, Rook F, Weisbeek P, Smeekens S. The homeobox gene ATH1 of Arabidopsis is derepressed in the photomorphogenic mutants cop1 and det1. Plant Cell. 1995 Jan;7(1):117–129. [PMC free article] [PubMed]
  • Holland PW, Garcia-Fernàndez J, Williams NA, Sidow A. Gene duplications and the origins of vertebrate development. Dev Suppl. 1994:125–133. [PubMed]
  • Hanes SD, Brent R. DNA specificity of the bicoid activator protein is determined by homeodomain recognition helix residue 9. Cell. 1989 Jun 30;57(7):1275–1283. [PubMed]
  • Treacy MN, Neilson LI, Turner EE, He X, Rosenfeld MG. Twin of I-POU: a two amino acid difference in the I-POU homeodomain distinguishes an activator from an inhibitor of transcription. Cell. 1992 Feb 7;68(3):491–505. [PubMed]
  • Simeone A, Pannese M, Acampora D, D'Esposito M, Boncinelli E. At least three human homeoboxes on chromosome 12 belong to the same transcription unit. Nucleic Acids Res. 1988 Jun 24;16(12):5379–5390. [PMC free article] [PubMed]
  • Wright CV, Cho KW, Fritz A, Bürglin TR, De Robertis EM. A Xenopus laevis gene encodes both homeobox-containing and homeobox-less transcripts. EMBO J. 1987 Dec 20;6(13):4083–4094. [PMC free article] [PubMed]
  • Monica K, Galili N, Nourse J, Saltman D, Cleary ML. PBX2 and PBX3, new homeobox genes with extensive homology to the human proto-oncogene PBX1. Mol Cell Biol. 1991 Dec;11(12):6149–6157. [PMC free article] [PubMed]
  • Tamaoki M, Tsugawa H, Minami E, Kayano T, Yamamoto N, Kano-Murakami Y, Matsuoka M. Alternative RNA products from a rice homeobox gene. Plant J. 1995 Jun;7(6):927–938. [PubMed]
  • Kahmann R, Bölker M. Self/nonself recognition in fungi: old mysteries and simple solutions. Cell. 1996 Apr 19;85(2):145–148. [PubMed]
  • Mann RS, Chan SK. Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins. Trends Genet. 1996 Jul;12(7):258–262. [PubMed]
  • Treisman R. DNA-binding proteins. Inside the MADS box. Nature. 1995 Aug 10;376(6540):468–469. [PubMed]
  • Nakamura T, Largaespada DA, Shaughnessy JD, Jr, Jenkins NA, Copeland NG. Cooperative activation of Hoxa and Pbx1-related genes in murine myeloid leukaemias. Nat Genet. 1996 Feb;12(2):149–153. [PubMed]

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