The homeodomain: An ancient evolutionary motif in animals and plants

Computers and Chemistry

Volumn 24, Issue 1, 2000, Pages 95-103

  Kappen, Claudia ^a  

^a MAYO CLINIC   (United States)

Author keywords

Evolutionary relationships; Homeodomain; Transcription factors

Indexed keywords

AMINO ACID; HOMEODOMAIN PROTEIN; VEGETABLE PROTEIN;

ANIMAL; ARTICLE; CHEMISTRY; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS;

AMINO ACIDS; ANIMALS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HOMEODOMAIN PROTEINS; MOLECULAR SEQUENCE DATA; PLANT PROTEINS;

EID: 0033627609     PISSN: 00978485     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0097-8485(00)80009-1     Document Type: Article

References (44)

1. Agosti, D., Jacobs, D., DeSalle, R., 1996. On combining protein sequences and nucleic acid sequences in phylogenetic analysis: the homeobox protein case. Cladistics 12, 65-82.
2. Balavoine, G., Telford, M.J., 1995. Identification of planarian homeobox sequences indicates the antiquity of most Hox/ homeotic gene subclasses. Proc. Natl. Acad. Sci. USA 92, 7227-7231.
3. Bharathan, G., Janssen, B.J., Kellogg, E.A., Sinha, N., 1997. Did homeodomain proteins duplicate before the origin of angiosperms, fungi, and metazoa? Proc. Natl. Acad. Sci. USA 94, 13749-13753.
4. Bürglin, T.R., 1998. The PBC domain contains a MEINOX domain: coevolution of Hox and TALE homeobox genes? Develop. Genes Evol. 208, 113-116.
5. Bürglin, T.R., 1997. Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois TGIF) reveals a novel domain conserved between plants and animals. Nucl. Acids Res. 25, 4173-4180.
6. Bürglin, T.R., 1995. The evolution of homeobox genes. In: Arai, R., K.M., Doi, Y. (Eds.), Biodiversity and Evolution, The National Science Museum Foundation, Tokyo, pp. 291-336.
7. Bürglin, T.R., 1994. A comprehensive classification of homeobox genes. In: Duboule, D. (Ed.), Guidebook to the Homeobox Genes. Sambrook and Tooze Publishing Partnership at Oxford University Press, Oxford, UK, pp. 25-71.
8. Bürglin, T.R., 1988. The yeast regulatory gene PHO2 encodes a homeo box. Cell 53, 339-340.
9. Callaerts, P., Halder, G., Gehring, W., 1997. Pax-6 in development and evolution. Ann. Rev. Neurosci. 20, 483-532.
10. Dayhoff, M.O., Barker, W.C., Hunt, L.T., 1983. Establishing homologies in protein sequences. Methods Enzymol. 91, 524-545.
11. Duboule, D., 1995. Vertebrate Hox-genes and proliferation: an alternative pathway to homeosis? Curr. Op. Genet. Develop. 5, 525-528.
12. Feng, D.F., Johnson, M.S., Doolittle, R.F., 1984. Aligning amino acid sequences: comparison of commonly used methods. J. Mol. Evol. 21, 112-125.
13. Field, K.G., Olsen, G.J., Lane, D.J., Giovanni, S.J., Ghiselin, M.T., Raff, E.C., Pace, N.R., Raff, R.A., 1988. Molecular phylogeny of the animal kingdom. Science 239, 748-753.
14. Gehring, W.J., Qian, Y.Q., Billeter, M., Furukubo-Tokunaga, K., Schier, A.F., Resendez-Perez, D., Affolter, M., Otting, G., Wüthrich, K., 1994. Homeodomain-DNA recognition. Cell 78, 211-223.
15. Gillissen, B., Bergemann, J., Sandmann, C., Schroeer, B., Bolker, M., Kahmann, R., 1992. A two-component regulatory system for self/non-self recognition in Ustilago maydis. Cell 68, 647-657.
16. Gonzales, D.H., Valle, E.M., Chan, G.G.R.L., 1997. Interactions between proteins containing homeodomains associated to leucine zippers from sunflower. Biochim. Biophys. Acta 1351, 137-149.
17. Hake, S., Char, B.R., Chuck, G., Foster, T., Long, J., Jackson, D., (1995). Homeobox genes in the functioning of plant meristems. Phil. Trans. R. Soc. Lond. B 350.
18. Hall, M.N., Johnson, A.D., 1987. Homeo domain of the yeast repressor alpha 2 is a sequence-specific DNA-binding domain but is not sufficient for repression. Science 237, 1007-1012.
19. Kappen, C., 1995. Ancient evolutionary origin of homeodomains: studies on yeasts, plants, and animals. In: Nei, M., Takahata, N. (Eds.), Current Topics on Molecular Evolution, Pennsylvania State University, pp. 199-212.
20. Kappen, C., 1996. Theoretical approaches to homeobox gene evolution. Comput. Chem. 20, 49-59.
21. Kappen, C., Ruddle, F.H., 1993. Evolution of a regulatory gene family: HOM/HOX genes. Curr. Op. Genet. Develop. 3, 931-938.
22. Kappen, C., Schughart, K., Ruddle, F.H., 1993. Early evolutionary origin of major homeodomain sequence classes. Genomics 18, 54-70.
23. Kaufmann, E., 1993. In vitro binding to the leucine tRNA gene identifies a novel yeast homeobox gene. Chromosoma 102, 174-179.
24. Kenyon, C., 1994. If birds can fly, why can't we? Homeotic genes and evolution. Cell 78, 175-180.
25. Kerstetter, R., Vollbrecht, E., Lowe, B., Veit, B., Yamaguchi, J., Hake, S., 1994. Sequence analysis and expression patterns divide the maize knotted1-like homeobox genes into two classes. Plant Cell 6, 1877-1887.
26. Knight, S.A., Tamai, K.T., Kosman, D.J., Thiele, D.J., 1994. Identification and analysis of a Saccharomyces cerevisiae copper homeostasis gene encoding a homeodomain protein. Mol. Cell. Biol. 14, 7792-7804.
27. Langdale, J.A., 1994. Plant morphogenesis. More knots untied. Curr. Biol. 4, 529-531.
28. Manak, J.R., Scott, M.P., (1994). A class act: conservation of homeodomain protein functions. Development-Suppl., 61-77.
29. Mavilio, F., Simeone, A., Giampaolo, A., Faiella, A., Zappavigna, V., Acampora, D., Poiana, G., Russo, G., Peschle, C., Boncinelli, E., 1986. Differential and stage-related expression in embryonic tissues of a new human homoeobox gene. Nature 324, 664-668.
30. McGinnis, W., Garber, R.L., Wirz, J., Kuroiwa, A., Gehring, W.J., 1984. A homologous protein-coding sequence in Drosophila homeotic genes and its conservation in other metazoans. Cell 37, 403-408.
31. McGinnis, W., Krumlauf, R., 1992. Homeobox genes and axial patterning. Cell 68, 283-302.
32. Ohta, T., 1990. How gene families evolve. Theor. Popul. Biol. 37, 213-219.
33. Schena, M., Davis, R.W., 1992. HD-Zip proteins: Members of an Arabidopsis homeodomain superfamily. Proc. Natl. Acad. Sci. USA 89, 3894-3898.
34. Schubert, F.R., Nieselt, S.K., Gruss, P., 1993. The Antennapedia-type homeobox genes have evolved from three precursors separated early in metazoan evolution. Proc. Natl. Acad. Sci. USA 90, 143-147.
35. Scott, M.P., 1992. Vertebrate homeobox gene nomenclature. Cell 71, 551-553.
36. Scott, M.P., Weiner, A.J., 1984. Structural relationships among genes that control development: Sequence homology between the Antennapedia, Ultrabithorax and fushi tarazu loci of Drosophila. Proc. Natl. Acad. Sci. USA 81, 4115-4119.
37. Shepherd, J.C., McGinnis, W., Carrasco, A.E., E.M., D.R., Gehring, W.J., (1984). Fly and frog homeodomains show homologies with yeast mating type regulatory proteins. Nature 310, 70-71.
38. Sutton, K.A., Wilkinson, M.F., 1997. Rapid evolution of a homeodomain: evidence for positive selection. Mol. Biol. Evol. 45, 579-588.
39. Swofford, D.L., PAUP Version 3.0., Illinois Natural History Survey, 1991.
40. Treacy, M.N., He, X., Rosenfeld, M.G., 1991. I-POU: a POU-domain protein that inhibits neuron-specific gene activation. Nature 350, 577-584.
41. Tsuchida, T., Ensini, M., Morton, S.B., Baldassare, M., Edlund, T., Jessell, T.M., Pfaff, S.L., 1994. Topographic organization of embryonic motor neurons defined by expression of LIM homeobox genes. Cell 79, 957-970.
42. Wainright, P.O., Hinkle, G., Sogin, M.L., Stickel, S.K., 1993. Monophyletic origin of the metazoa: an evolutionary link with fungi. Science 260, 340-342.
43. Williams, R.W., 1998. Plant homeobox genes: many functions stem from a common motif. Bioessays 20, 280-282.
44. Zhang, J., Nei, M., 1996. Evolution of Antennapedia-class homeobox genes. Genetics 142, 295-303.