Knots in the family tree: Evolutionary relationships and functions of knox homeobox genes

Plant Molecular Biology

Volumn 42, Issue 1, 2000, Pages 151-166

  Reiser, Leonore ^a   Sánchez Baracaldo, Patricia ^b   Hake, Sarah ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Evolution; Homeodomain protein; Knox gene; Meristem

Indexed keywords

EVOLUTION; GENE DUPLICATION; GENE EXPRESSION; GENE MUTATION; GENETIC DIVERSITY; GENETIC TRAIT; HOMEOBOX;

EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; GENES, HOMEOBOX; GENES, PLANT; HOMEODOMAIN PROTEINS; PHYLOGENY;

EMBRYOPHYTA; LYCOPERSICON ESCULENTUM; METAZOA;

EID: 0343593689     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1006384122567     Document Type: Article

References (91)

1. Abouheif E: Developmental genetics and homology: a heirarchical approach. Trends Evol Ecol 12: 405-408 (1997).
2. Abouheif E, Akam M, Dickinson W, Holland PWH, Meyer A, Patel N, Raff R, Roth VL, Wray GA: Homology and developmental genes. Trends Genet 13: 432-433 (1997).
3. Ahn S, Tanksley SD: Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90: 7980-7984 (1993).
4. Averof M, Akam M: Hox genes and the diversification of insect and crustacean body plans. Nature 376: 420-423 (1995).
5. Averof M, Dawes R, Ferrier D: Diversification of arthropod HOX genes as a paradigm for the evolution of gene functions. Cell Dev Biol 7: 539-551 (1996).
6. Barton MK, Poethig RS: Formation of the shoot apical meristem in Arabidopsis thaliana: an analysis of development in the wild type and in the shoot meristemless mutant. Development 119: 823-831 (1993).
7. Baum DA: The evolution of development. Curr Opin Plant Biol 1: 79-86 (1998).
8. Becraft PW, Freeling M: Genetic analysis of Rough sheath1 developmental mutants of maize. Genetics 136: 295-311 (1994).
9. Bharathan G, Janssen B-J, Kellogg EA, Sinha N: Did home-odomain proteins duplicate before the origin of angiosperms, fungi and metazoa? Proc Natl Acad Sci USA 94: 13749-13753 (1997).
10. Bharathan G, Janssen B-J, Kellogg EA, Sinha N: Phylogenetic relationships and evolution of the KNOTTED class of plant homeodomain proteins. Mol Biol Evol, in press (1999).
11. Boivin R, Hamel F, Beauseigle D, Bellemare G: Stage-specific transcription of the homeobox gene Bnhd1 in young tissues and flowers of Brassica napus. Biochim Biophys Acta 1219: 201-204 (1994).
12. Brooks D, McLennan: Phylogeny, Ecology and Behavior. University of Chicago Press, Chicago (1991).
13. Bürglin TR: Analysis of TALE superclass homeobox genes (MEIS, PBC, Iriquois, TGIF) reveals a novel domain conserved between plants and animals. Nucl Acids Res 25: 4173-4180 (1997).
14. Burglin TR: The PBC domain contains a MEINOX domain: coevolution of Hox and TALE homeobox genes. Dev Genes Evol 208: 113-116 (1998).
15. Chen J-J, Janssen B-J, Williams A, Sinha N: A gene fusion at a homeobox locus: alterations in leaf shape and implications for morphological evolution. Plant Cell 9: 1289-1304 (1997).
16. Chuck G, Lincoln C, Hake S: KNAT1 induces lobed leaves with ectopic meristems when overexpressed in Arabidopsis. Plant Cell 8: 1277-1289 (1996).
17. Dockx J, Quaedvlieg N, Keultjes G, Kock P, Weisbeek P, Smeekens S: The homeobox gene ATK1 of Arabidopsis thaliana is expressed in the shoot apex of the seedling and in flowers and inflorescence stems of mature plants. Plant Mol Biol 28: 723-737 (1995).
18. Doebley J, Lukens L: Transcriptional regulators and the evolution of plants. Plant Cell 10: 1075-1082 (1998).
19. Doyle J: Evolution of a plant homeotic multigene family: toward connecting molecular systematics and molecular developmental genetics. Syst Biol 43: 307-328 (1994).
20. Endrizzi K, Moussian B, Haecker A, Levin JZ, Laux T: The SHOOT MERISTEMLESS gene is required for maintenance of undifferentiated cells in Arabidopsis shoot and floral meristems and acts at a different regulatory level than the meristem genes WUSCHEL and ZWILLE. Plant J 10: 101-113 (1996).
21. Fitch WM: Distinguishing homologous from analogous proteins. Syst Zool 19: 99-113 (1970).
22. Foster T, Hake S: It's a Gnarley one! (Gn1). Maize Genet Coop Newsl 68: 2 (1994).
23. Foster T, Veit B, Hake S: Mosaic analysis of the dominant mutant Gnarley1-R reveals distinct lateral and transverse signaling pathways during maize leaf development. Development 126: 305-313 (1999).
24. Foster T, Yamaguchi J, Wong B, Veit B, Hake S: Gnarley1 is a dominant mutation in the knox4 homeobox gene that affects cell identity and cell shape. Plant Cell, in press (1999).
25. Fowler JE, Freeling M: Genetic analysis of mutations that alter cell fates in maize leaves: dominant Liguleless mutations. Dev Genet 18: 198-222 (1996).
26. Fowler JE, Meuhlbauer GJ, Freeling M: Mosaic analysis of the Liguleless3 mutant phenotype in maize by coordinate suppression of mutator insertion alleles. Genetics 143: 489-503 (1996).
27. Freeling M, Hake S: Developmental genetics of mutants that specify Knotted leaves in maize. Genetics 111: 617-634 (1985).
28. Gaut BS, F. DJ: DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94: 6809-6814 (1997).
29. Greene B, Walko R, Hake S: Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations. Genetics 138: 1275-1285 (1994).
30. Hake S, Char BR, Chuck G, Foster T, Long J, Jackson D: Homeobox genes in the functioning of plant meristems. Phil Trans R Soc Lond 350: 45-51 (1995).
31. Hall BK: Homology: The Hierarchical Basis of Comparative Morphology. Academic Press, San Diego (1994).
32. Hareven D, Gutfinger T, Parnis A, Eshed Y, Lifschitz E: The making of a compound leaf: genetic manipulation of leaf architecture in tomato. Cell 84: 735-744 (1996).
33. Helentjaris T, Weber D, Wright S: Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118: 353-363 (1988).
34. Hillis DM: Homology in molecular biology. In: Hall BK (ed), Homology, the Hierarchical Basis of Comparative Morphology, pp. 339-368. Academic Press, San Diego (1994).
35. Hofer J, Turner L, Hellens R, Ambrose M, Matthews P, Michael A, Ellis N: UNIFOLIATA regulates leaf and flower morphogenesis in pea. Curr Biol 7: 581-587 (1997).
36. Holland P: Homeobox genes and vertebrate evolution. BioEssays 14: 267-273 (1992).
37. Holland PW, Garcia-Fernandez J: Hox genes and chordate evolution. Dev Biol 173: 382-395 (1996).
38. Holland PW, Garcia-Fernandez J, Williams NA, Sidow A: Gene duplications and the origins of vertebrate development. Development (Suppl): 125-133 (1994).
39. Jackson D, Veit B, Hake S: Expression of maize KNOTTED1 related homeobox genes in the shoot apical meristem predicts patterns of morphogenesis in the vegetative shoot. Development 120: 405-413 (1994).
40. Janssen B-J, Lund L, Sinha N: Overexpression of a homeobox gene, Let6, reveals indeterminate features of the tomato compound leaf. Plant Physiol 117: 771-786 (1998).
41. Janssen B-J, Williams A, Chen J-J, Mathern J, Hake S, Sinha N: Isolation and characterization of two knotted-like homeobox genes from tomato. Plant Mol Biol 36: 417-25 (1998).
42. Kenyon C: If birds can fly, why can't we? Homeotic genes and evolution. Cell 78: 175-180 (1994).
43. Kerstetter R, Vollbrecht E, Löwe B, Veit B, Yamaguchi J, Hake S: Sequence analysis and expression patterns divide the maize knotted1-like homeobox genes into two classes. Plant Cell 6: 1877-1887 (1994).
44. Kerstetter RA, Laudencia-Chingcuanco D, Smith LG, Hake S: Loss of function mutations in the maize homeobox gene, knotted1, are defective in shoot meristem maintenance. Development 124: 3045-3054 (1997).
45. Krumlauf R: Hox genes in vertebrate development. Cell 78: 191-201 (1994).
46. Lane B, Freeling M: The maize leaf. In: Freeling M, Walbot V (eds), The Maize Handbook, Springer-Verlag, New York (1994).
47. Laufs P, Dockx J, Kronenberger J, Traas J: MGOUN1 and MGOUN2: two genes required for primordium initiation at the shoot apical and floral meristems in Arabidopsis thaliana. Development 125: 1253-1260 (1998).
48. Lincoln C, Long J, Yamaguchi J, Serikawa K, Hake S: A knotted1-like homeobox gene in Arabidopsis is expressed in the vegetative meristem and dramatically alters leaf morphology when overexpressed in transgenic plants. Plant Cell 6: 1859-1876 (1994).
49. Long J, Barton MK: The development of apical embryonic pattern in Arabidopsis. Development 125: 3027-3035 (1998).
50. Long JA, Moan EI, Medford JI, Barton MK: A member of the KNOTTED class of homeodomain proteins encoded by the SHOOTMERISTEMLESS gene of Arabidopsis. Nature 379: 66-69 (1996).
51. Ma H, McMullen MD, Finer JJ: Identification of a homeobox-containing gene with enhanced expression during soybean (Glycine max L.) somatic embryo development. Plant Mol Biol 24: 465-473 (1994).
52. Mann R, Chan S-K: Extra specificty from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins. Trends Genet 12: 258-262 (1996).
53. Mann RS, Affolter M: Hox proteins meet more partners. Curr Opin Genet Dev 8: 423-429 (1998).
54. Mathern J, Hake S: Mu element-generated gene conversions in maize attenuate the dominant Knotted1 phenotype. Genetics 147: 305-314 (1997).
55. Matsuoka M, Ichikawa H, Saito A, Tamda Y, Fujimura T, Kano-Murakami Y: Expression of a rice homeobox gene causes altered morphology of transgenic plants. Plant Cell 5: 1039-1048 (1993).
56. McGinnis W, Krumlauf R: Homeobox genes and axial patterning. Cell 68: 283-302 (1992).
57. Meyer A: The evolution of body plans: HOM/hox cluster evolution, model systems, and the importance of phylogeny. In: Harvey PH (ed), New Uses for New Phylogenies, pp. 99-113. Oxford University Press, London (1996).
58. Moore GK, Devos KM, Z W, Gale MD: Grasses, line up and form a circle. Curr Biol 5: 737-739 (1995).
59. Muehlbaur GJ, Fowler JE, Freeling M: Sectors expressing the homeobox gene liguless3 implicate a time-dependent mechanism for cell fate acquisition along the proximal-distal axis of the maize leaf. Development 124: 5097-5106 (1997).
60. Müller K, Romano N, Gerstner O, Garcia-Maroto F, Pozzi C, Salamini F, Rohde W: The barley Hooded mutation caused by a duplication in a homeobox gene intron. Nature 374: 727-730 (1995).
61. Ohno S: Evolution by Gene Duplication. Springer-Verlag, Heidelberg (1970).
62. Parnis A, Cohen O, Gutfinger T, Hareven D, Zamir D, Lifschitz E: The dominant developmental mutants of tomato, Mouse-Ear and Curl, are associated with distinct modes of abnormal transcriptional regulation of a Knotted gene. Plant Cell 9: 2143-2158 (1997).
63. Postma-Haarsma AD, Verwoert IIGS, Stronk OP, Koster J, Lamer G, EM, Hoge HC, Meijer AH: Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice embryogenesis. Plant Mol Biol 39: 257-271 (1999).
64. Purugganan M, Rounsley S, Schmidt R, Yanofsky M: Molecular evolution of flower development: diversification of a plant MADS-box regulatory gene family. Genetics 140: 345-356 (1995).
65. Ruddle FH, Bartels JL, Bentley KL, Kappen C, Murtha MT, Pendelton JW: Evolution of Hox genes. Annu Rev Genet 28: 423-442 (1994).
66. Sato Y, Sentoku N, Matsuoka M: Analysis of the functions of rice homeobox genes. In: Shimamoto K (ed), Molecular Biology of Rice, pp. 119-135. Springer-Verlag, Tokyo (1999).
67. Sato Y, Sentoku N, Miura Y, Hirochicka H, Kitano H, Matsuoka M: Loss-of-function mutations in the rice homeobox gene, OSH15, cause defects in the development of hypodermal schlerenchyma in internodes resulting in dwarf plants. EMBO J 18: 992-1002 (1999).
68. Sato Y, Sentoku N, Nagato Y, Matsuoka M: Isolation and characterization of a rice homeobox gene OSH15. Plant Mol Biol 38: 983-998 (1998).
69. Sato Y, Tamaoki M, Murakami T, Yamamoto N, Kano-Murakami Y, Matsuoka M: Abnormal cell divisions in leaf primordia caused by the expression of the rice homeobox gene OSH1 lead to altered morphology of leaves in transgenic tobacco. Mol Gen Genet 251: 13-22 (1996).
70. Scanlon MJ, Schneeberger RG, Freeling M: The maize mutant narrow sheath fails to establish leaf margin identity in a meristematic domain. Development 122: 1683-1691 (1996).
71. Schneeberger R, Tsantis M, Freeling M, Langdale JA: The rough sheath2 gene negatively regulates homeobox gene expression during maize leaf development. Development 125: 2857-2865 (1998).
72. Schneeberger RG, Becraft PW, Hake S, Freeling M: Ectopic expression of the knox homeobox gene rough sheath1 alters cell fate in the maize leaf. Genes Dev 9: 2292-2304 (1995).
73. Serikawa KA, Martinez-Laborda A, Kim H-S, Zambryski P: Localization of expression of KNAT3, a class 2 knotted1-like gene. Plant J 11: 853-861 (1997).
74. Serikawa KA, Martinez-Laborda A, Zambryski P: Three knotted1-like homeobox genes in Arabidopsis. Plant Mol Biol 32: 673-683 (1996).
75. Sinha N: Simple or compound leaves: reduction or multiplication? Trends Plant Sci 2: 396-402 (1997).
76. Sinha NR, Williams RE, Hake S: Overexpression of the maize homeo box gene, KNOTTED-1, causes a switch from determinate to indeterminate cell fates. Genes Dev 7: 787-795 (1993).
77. Smith LG, Greene B, Veit B, Hake S: A dominant mutation in the maize homeobox gene, Knotted-1, causes its ectopic expression in leaf cells with altered fates. Development 116: 21-30 (1992).
78. Smith LG, Jackson D, Hake S: The expression of Knotted1 marks shoot meristem formation during maize embryogenesis. Dev Genet 16: 344-348 (1995).
79. Såndas-Larsson A, Svenson M, Liao H, Engstrom P: A homeobox gene with potential developmental control function in the meristem of the conifer Picea abies. Proc Natl Acad Sci USA 95: 15118-15122 (1998).
80. Swofford DL: Phylogenetic Analysis Using Parsimony. Illinois Natural History Survey, Champaign, IL (1991).
81. Tamaoki M, Kusuba S, Kano-Murakami Y, Matsuoka M: Ectopic expression of a tobacco homeobox gene, NTH15, dramatically alters leaf morphology and hormone levels in transgenic tobacco. Plant Cell Physiol 38: 917-927 (1997).
82. Theiben G, Kim J, Saedler H: Classification and phylogeny of the MADs box multigene family suggest defined roles of MADS box gene subfamilies in the morphological evolution of eukaryotes. J Mol Evol 43: 484-516 (1996).
83. Timmermans MCP, Schutes NP, Jankovsky JP, Nelson T: Leaf-bladeless1 is required for dorsiventrality of lateral organs in maize. Development 125: 2813-2823 (1998).
84. Veit B, Vollbrecht E, Mathern J, Hake S: A tandem duplication causes the Kn1-O allele of Knotted, a dominant morphological mutant of maize. Genetics 125: 623-631 (1990).
85. Vollbrecht E, Veit B, Sinha N, Hake S: The developmental gene Knotted-1 is a member of a maize homeobox gene family. Nature 350: 241-243 (1991).
86. Waites R, Hudson A: phantastica, a gene required for dorsiventrality in leaves of Antirrhinum majus. Development 121: 2143-2154 (1995).
87. Waites R, Selvadurai HRN, Oliver IR, Hudson A: The PHANTASTICA gene encodes a MYB transcription factor involved in growth and dorsiventrality of lateral organs in Antirrhinum. Cell 93: 779-789 (1998).
88. Watillon B, Kettmann R, Boxus P, Burney A: Knotted1-like. homeobox genes are expressed during apple tree (Malus domestica L. Borkh) growth and development. Plant Mol Biol 33: 757-763 (1997).
89. Weatherwax P: Position of the scutellum and homology of the coleoptile in maize. Bot Gaz 69: 179-182 (1920).
90. Williams RW: Plant homeobox genes: many functions stem from a common motif. BioEssays 20: 280-282 (1998).
91. Williams-Carrier RE, Lie YS, Hake S, Lemaux PG: Ectopic expression of the maize kn1 gene phenocopies the Hooded mutant of barley. Development 124: 3737-3745 (1997).