Contrasting modes of diversification in the Aux/IAA and ARF gene families

Plant Physiology

Volumn 135, Issue 3, 2004, Pages 1738-1752

  Remington, David L ^a   Vision, Todd J ^b   Guilfoyle, Thomas J ^c   Reed, Jason W ^b  

^a UNIVERSITY OF NORTH CAROLINA AT GREENSBORO   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c University of Missouri   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; MORPHOLOGY; PLANTS (BOTANY); PROTEINS;

GENE FAMILIES; GENOMIC SEGMENTS; GENOMIC SEQUENCES;

PHYSIOLOGY;

ARABIDOPSIS; EMBRYOPHYTA;

EID: 3543024524     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.039669     Document Type: Article

References (49)

1. Abel S, Nguyen MD, Theologis A (1995) The PS-IAA4/5-like family of early auxin-inducible mRNAs in Arabidopsis thaliana. J Mol Biol 251: 533-549
2. Allen KD (2002) Assaying gene content in Arabidopsis. Proc Natl Acad Sci USA 99: 9568-9572
3. Barakat A, Szick-Miranda K, Chang I-F, Guyot R, Blanc G, Cooke R, Delseny M, Bailey-Serres J (2001) The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. Plant Physiol 127: 398-415
4. Basu S, Sun H, Brian L, Quatrano RL, Muday GK (2002) Early embryo development in Fucus distichus is auxin sensitive. Plant Physiol 130: 292-302
5. Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000) Extensive duplication and reshuffling in the arabidopsis genome. Plant Cell 12: 1093-1101
6. Blanc G, Hokamp K, Wolfe KH (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13: 137-144
7. Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438
8. Cannon SB, Young ND (2003) OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies. BMC Bioinformatics 4: 35
9. Cooke TJ, Poli DB, Sztein AE, Cohen JD (2002) Evolutionary patterns in auxin action. Plant Mol Biol 49: 319-338
10. Dayhoff MO (1979) Atlas of Protein Sequence and Structure, Vol 5, Suppl 3, 1978. National Biomedical Research Foundation, Washington, DC
11. Dillon N, Trimborn T, Strouboulis J, Fraser P, Grosveld F (1997) The effect of distance on long-range chromatin interactions. Mol Cell 1: 131-139
12. Force A, Lynch M, Pickett FB, Amores A, Yan Y-L, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545
13. Fukaki H, Tameda S, Masuda H, Tasaka M (2002) Lateral root formation is blocked by a gain-of-function mutation in the SOLITARY-ROOT/IAA14 mutation of Arabidopsis. Plant J 29: 153-168
14. Gottlieb LD, Ford VS (1997) A recently silenced, duplicate PgiC locus in Clarkia. Mol Biol Evol 14: 125-132
15. TIR1-dependent degradation of AUX/IAA proteins. Nature 414: 271-276
16. Gu X, Huang W (2002) Testing the parsimony test of genome duplications: a counterexample. Genome Res 12: 1-2
17. Hagen G, Guilfoyle TJ (2002) Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol Biol 49: 373-385
18. Hedges SB (2002) The origin and evolution of model organisms. Nat Rev Genet 3: 838-849
19. Herault Y, Fraudeau N, Zakany J, Duboule D (1997) Ulnaless (Ul), a regulatory mutation inducing both loss-of-function and gain-of-function of posterior Hoxd genes. Development 124: 3493-3500
20. Hughes MK, Hughes AL (1993) Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol Biol Evol 10: 1360-1369
21. Imaizumi T, Kadota A, Hasebe M, Wada M (2002) Cryptochrome light signals control development to suppress auxin sensitivity in the moss Physcomitrella patens. Plant Cell 14: 373-386
22. Kim J, Harter K, Theologis A (1997) Protein-protein interactions among the Aux/IAA proteins. Proc Natl Acad Sci USA 94: 11786-11791
23. Kmita M, Fraudeau N, Herault Y, Duboule D (2002) Serial deletions and duplications suggest a mechanism for the collinearity of Hoxd genes in limbs. Nature 420: 145-150
24. Knox K, Grierson CS, Leyser O (2003) AXR3 and SHY2 interact to regulate root hair development. Development 130: 5769-5777
25. Ku H-M, Vision T, Liu J, Tanksley SD (2000) Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA 97: 9121-9126
26. Lettice LA, Horikoshi T, Heaney SJ, van Baren MJ, van der Linde HC, Breedveld GJ, Joosse M, Akarsu N, Oostra BA, Endo N, et al (2002) Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proc Natl Acad Sci USA 99: 7548-7553
27. Liscum E, Reed JW (2002) Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol 49: 387-400
28. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155
29. Ohno S (1970) Evolution by Gene Duplication. Springer-Verlag, Berlin
30. Paterson AH, Lan TH, Reischmann KP, Chang C, Lin YR, Liu SC, Burow MD, Kowalski SP, Katsar CS, DelMonte TA, et al (1996) Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nat Genet 14: 380-382
31. Raes J, Vandepoele K, Saeys Y, Simillion C, Van de Peer Y (2003) Investigating ancient duplication events in the Arabidopsis genome. J Struct Funct Genomics 3: 117-129
32. Reed JW (2001) Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci 6: 420-425
33. Rogg LE, Lasswell J, Bartel B (2001) A gain-of-function mutation in IAA28 supresses lateral root development. Plant Cell 13: 465-480
34. Rosenquist M, Alsterfjord M, Larsson C, Sommarin M (2001) Data mining the Arabidopsis genome reveals fifteen 14-3-3 genes: expression is demonstrated for two out of five novel genes. Plant Physiol 127: 142-149
35. Sedgewick R (1990) Algorithms in C. Addison-Wesley, Reading, MA
36. Simillion C, Vandepoele K, Van Montagu MCE, Zabeau M, Van de Peer Y (2002) The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci USA 99: 13627-13632
37. Stam M, Belele C, Ramakrishna W, Dorweiler JE, Bennetzen JL, Chandler VL (2002) The regulatory regions required for B′ paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162: 917-930
38. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
39. Tian Q, Nagpal P, Reed JW (2003) Regulation of Arabidopsis SHY2/IAA3 protein turnover. Plant J 36: 643-651
40. Tian Q, Reed JW (1999) Control of auxin-regulated root development by the Arabidopsis thaliana SHY2/IAA3 gene. Development 126: 711-721
41. Tian Q, Uhlir NJ, Reed JW (2002) Arabidopsis SHY2/IAA3 inhibits auxin-regulated gene expression. Plant Cell 14: 301-319
42. Tiwari SB, Hagen G, Guilfoyle TJ (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15: 533-543
43. Tiwari SB, Wang X-J, Hagen G, Guilfoyle TJ (2001) AUX/IAA proteins are active repressors, and their stability and activity are modulated by auxin. Plant Cell 13: 2809-2822
44. Ulmasov T, Hagen G, Guilfoyle TJ (1999a) Activation and repression of transcription by auxin-response factors. Proc Natl Acad Sci USA 96: 5844-5849
45. Ulmasov T, Hagen G, Guilfoyle TJ (1999b) Dimerization and DNA binding of auxin response factors. Plant J 19: 309-319
46. Vandepoele K, Raes J, De Veylder L, Rouze P, Rombauts S, Inze D (2002) Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell 14: 903-916
47. Vision TJ, Brown DG, Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117
48. Wikstrom N, Savolainen V, Chase MW (2001) Evolution of the angiosperms: calibrating the family tree. Proc R Soc Lond B Biol Sci 268: 2211-2220
49. Wolfe KH (2001) Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2: 333-341