TTG2-regulated development is related to expression of putative AUXIN RESPONSE FACTOR genes in tobacco

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Zhu, Qian ^a   Li, Baoyan ^a,b   Mu, Shuyuan ^a   Han, Bing ^a   Cui, Runzhi ^a   Xu, Manyu ^a   You, Zhenzhen ^a   Dong, Hansong ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b Yantai Academy of Agricultural Sciences   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANTHOCYANIN; AUXIN; AUXIN RESPONSE FACTOR; TRANSCRIPTOME; TRANSPARENT TESTA GLABRA PROTEIN; UNCLASSIFIED DRUG; VEGETABLE PROTEIN; TRANSCRIPTION FACTOR;

ARF GENE; ARTICLE; FLOWER; FLOWER COLORIZATION; GENE CONTROL; GENE FUNCTION; GENE IDENTIFICATION; GENE OVEREXPRESSION; GENE SILENCING; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC LINKAGE; GROWTH REGULATION; NONHUMAN; NTTTG2 GENE; PLANT DEVELOPMENT; PLANT GENE; PLANT GROWTH; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN SYNTHESIS; QUANTITATIVE ANALYSIS; SEED PRODUCTION; TOBACCO; VEGETATIVE GROWTH; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; PLANT SEED;

FLOWERS; GENE EXPRESSION REGULATION, PLANT; GENE KNOCKDOWN TECHNIQUES; GENE ONTOLOGY; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; PLANT PROTEINS; SEEDS; SEQUENCE ANALYSIS, DNA; TOBACCO; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84887637109     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-806     Document Type: Article

References (76)

1. Bouyer D, Geier F, Kragler F, Schnittger A, Pesch M, Wester K, Balkunde R, Timmer J, Fleck C, Hülskamp M. Two-dimensional patterning by a trapping/depletion mechanism: the role of TTG1 and GL3 in Arabidopsis trichome formation. PLoS Biol 2008, 6:1166-1177.
2. Petroni K, Tonelli C. Recent advances on the regulation of anthocyanin synthesis in reproductive organs. Plant Sci 2011, 181:219-229. 10.1016/j.plantsci.2011.05.009, 21763532.
3. Szymanski DB, Lloyd AM, Marks MD. Progress in the molecular genetic analysis of trichome initiation and morphogenesis in Arabidopsis. Trends Plant Sci 2000, 5:214-219. 10.1016/S1360-1385(00)01597-1, 10785667.
4. Vetten N, Quattrocchio F, Mol J, Koes R. The an11 locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserved in yeast, plants and animals. Gene Dev 1997, 11:1422-1434. 10.1101/gad.11.11.1422, 9192870.
5. Li B, Gao R, Cui R, Lü B, Li X, You Z, Dong H. Tobacco TTG2 suppresses resistance to pathogens by sequestering NPR1 from the nucleus. J Cell Sci 2012, 125:4913-4922. 10.1242/jcs.111922, 22797922.
6. Pang Y, Wenger JP, Saathoff K, Peel GJ, Wen J, Huhman D, Allen SN, Tang Y, Cheng X, Tadege M, Ratet P, Mysore KS, Sumner LW, Marks MD, Dixon RA. A WD40 repeat protein from Medicago truncatula is necessary for tissue-specific anthocyanin and proanthocyanidin biosynthesis but not for trichome development. Plant Physiol 2009, 151:1114-1129. 10.1104/pp.109.144022, 2773055, 19710231.
7. Wang Y, Liu R, Chen L, Wang YC, Liang YC, Wu X, Li B, Wu J, Liang Y, Wang X, Zhang C, Wang Q, Hong X, Dong H. Nicotiana tabacum TTG1 contributes to ParA1-induced signalling and cell death in leaf trichomes. J Cell Sci 2009, 122:2673-2685. 10.1242/jcs.049023, 19596794.
8. Neer EJ, Schmidt CJ, Nambudripad R, Smith TF. The ancient regulatory-protein family of WD-repeat proteins. Nature 1994, 371:297-300. 10.1038/371297a0, 8090199.
9. Biedermann S, Hellmann H. WD40 and CUL4-based E3 ligases: lubricating all aspects of life. Trends Plant Sci 2011, 16:38-46. 10.1016/j.tplants.2010.09.007, 20965772.
10. Stirnimann CU, Petsalaki E, Russell RB, Müller CW. WD40 proteins propel cellular networks. Trends Biochem Sci 2010, 35:565-574. 10.1016/j.tibs.2010.04.003, 20451393.
11. Xu C, Min J. Structure and function of WD40 domain proteins. Protein Cell 2011, 2:202-214. 10.1007/s13238-011-1018-1, 21468892.
12. Johnson CS, Kolevski B, Smyth DR. TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. Plant Cell 2002, 14:1359-1375. 10.1105/tpc.001404, 150785, 12084832.
13. Morohashi K, Zhao M, Yang M, Read B, Lloyd A, Lamb R, Grotewold E. Participation of the Arabidopsis bHLH factor GL3 in trichome initiation regulatory events. Plant Physiol 2007, 145:736-746. 10.1104/pp.107.104521, 2048771, 17885086.
14. Ghanashyam C, Jain M. Role of auxin-responsive genes in biotic stress responses. Plant Signal Behav 2009, 4:846-848. 10.4161/psb.4.9.9376, 2802801, 19847104.
15. Truman WM, Bennett MH, Turnbull CGN, Grant MR. Arabidopsis auxin mutants are compromised in systemic acquired resistance and exhibit aberrant accumulation of various indolic compounds. Plant Physiol 2010, 152:1562-1573. 10.1104/pp.109.152173, 2832264, 20081042.
16. Walker AR, Davison PA, Bolognesi-Winfield AC, James CM, Srinivasan N, Blundell TL, Esch JJ, Marks MD, Gray JC. The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein. Plant Cell 1999, 11:1337-1350. 144274, 10402433.
17. Zhao M, Morohashi K, Hatlestad G, Grotewold E, Lloyd A. The TTG1-bHLH-MYB complex controls trichome cell fate and patterning through direct targeting of regulatory loci. Development 2008, 135:1991-1999. 10.1242/dev.016873, 18434419.
18. Kamoun S, Klucher KM, Coffey MD, Tyler BM. A gene encoding a host-specific elicitor protein of Phytophthora parasitica. Mol Plant Microbe Interact 1993, 6:15-25.
19. Wang YC, Li B, Wang Y, Dong H. Cloning of full-length NtTTG1-like cDNA in Nicotiana tabacum, and the analysis of its expression and subcellular localization. Jiangsu Agric Sci 2010, 1:23-26.
20. Cao H, Glazebrook J, Clarke JD, Volko S, Dong X. The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats. Cell 1997, 88:57-63. 10.1016/S0092-8674(00)81858-9, 9019406.
21. Mukhtar MS, Nishimura MT, Dangl J. NPR1 in plant defense: It's not over 'til it's turned over. Cell 2009, 137:805-806.
22. Spoel SH, Mou Z, Tada Y, Spivey NW, Genschik P, Dong X. Proteasome-mediated turnover of the transcription coactivator NPR1 plays dual roles in regulating plant immunity. Cell 2009, 137:860-872. 10.1016/j.cell.2009.03.038, 2704463, 19490895.
23. Quint M, Gray WG. Auxin signaling. Curr Opin Plant Biol 2006, 9:448-453. 10.1016/j.pbi.2006.07.006, 2424235, 16877027.
24. Vanneste S, Friml J. Auxin: A trigger for change in plant development. Cell 2009, 136:1005-1016. 10.1016/j.cell.2009.03.001, 19303845.
25. Guilfoyle TJ, Ulmasov T, Hagen G. The ARF family of transcription factors and their role in plant hormone-responsive transcription. Cell Mol Life Sci 1998, 54:619-627. 10.1007/s000180050190, 9711229.
26. Kumar R, Agarwal P, Tyagi AK, Sharma AK. Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum). Mol Genet Genomics 2012, 287:221-235. 10.1007/s00438-011-0672-6, 22228229.
27. Liscum E, Reed JW. Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol 2002, 49:387-400. 10.1023/A:1015255030047, 12036262.
28. Walcher CL, Nemhauser JL. Bipartite promoter element required for auxin response. Plant Physiol 2012, 158:273-282. 10.1104/pp.111.187559, 3252081, 22100645.
29. Tiwari SB, Hagen G, Guilfoyle T. The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 2003, 15:533-543. 10.1105/tpc.008417, 141219, 12566590.
30. Ulmasov T, Hagen G, Guilfoyle TJ. Activation and repression of transcription by auxin-response factors. Proc Natl Acad Sci USA 1999, 96:5844-5849. 10.1073/pnas.96.10.5844, 21948, 10318972.
31. Guilfoyle TJ, Hagen G. Auxin response factors. Curr Opin Plant Biol 2007, 10:453-460. 10.1016/j.pbi.2007.08.014, 17900969.
32. Hagen G, Guilfoyle T. Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol Biol 2002, 49:373-385. 10.1023/A:1015207114117, 12036261.
33. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 2011, 332:960-963. 10.1126/science.1203810, 3166216, 21551031.
34. Ha CV, Le DT, Nishiyama R, Watanabe Y, Sulieman S, Tran UT, Mochida K, Dong NV, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS. The auxin response factor transcription factor family in soybean: Genome-wide identification and expression analyses during development and water stress. DNA Res 2013, doi:10.1093/dnares/dst027.
35. Kalluri UC, Difazio SP, Brunner AM, Tuskan GA. Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol 2007, 7:59. 10.1186/1471-2229-7-59, 2174922, 17986329.
36. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 2008, 319:64-69. 10.1126/science.1150646, 18079367.
37. Tromas A, Perrot-Rechenmann C. Recent progress in auxin biology. CR Biol 2010, 333:297-306.
38. Heinekamp T, Strathmann A, Kuhlmann M, Froissard M, Müller A, Catherine PR, Wolfgang DL. The tobacco bZIP transcription factor BZI-1 binds the GH3 promoter in vivo and modulates auxin-induced transcription. Plant J 2004, 38:298-309. 10.1111/j.1365-313X.2004.02043.x, 15078332.
39. Liu ZB, Ulmasov T, Shi X, Hagen G, Guilfoyle TJ. The soybean GH3 promoter contains multiple auxin-inducible elements. Plant Cell 1994, 6:645-657. 160465, 8038604.
40. Ulmasov T, Liu ZB, Hagen G, Guilfoyle TJ. Composite structure of auxin response elements. Plant Cell 1995, 7:1611-1623. 161020, 7580254.
41. Wu J, Liu SY, He YJ, Guan XY, Zhu XF, Cheng L, Wang J, Lu G. Genome-wide analysis of SAUR gene family in Solanaceae species. Gene 2012, 509:38-50. 10.1016/j.gene.2012.08.002, 22903030.
42. Yuan HZ, Zhao K, Lei HJ, Shen XJ, Liu Y, Liao X, Li TH. Genome-wide analysis of the GH3 family in apple (Malus × domestica). BMC Genomics 2013, 14:297. doi:10.1186/1471-2164-14-297, 10.1186/1471-2164-14-297, 3653799, 23638690.
43. Todd AT, Liu E, Polvi SL, Pammett RT, Page JE. A functional genomics screen identifies diverse transcription factors that regulate alkaloid biosynthesis in Nicotiana benthamiana. Plant J 2010, 62:589-600. 10.1111/j.1365-313X.2010.04186.x, 20202168.
44. Kumar R, Tyagi AK, Sharma AK. Genome-wide analysis of auxin response factor (ARF) gene family from tomato and analysis of their role in flower and fruit development. Mol Genet Genomics 2011, 285:245-260. 10.1007/s00438-011-0602-7, 21290147.
45. Sanchez MA, Mateos I, Labrador E, Dopico B. Brassinolides and IAA induce the transcription of four α-expansin genes related to development in Cicer arietinum. Plant Physiol Biochem 2004, 42:709-716. 10.1016/j.plaphy.2004.07.004, 15474376.
46. Yi L, Jones L, McQueen-Mason S. Expansins and cell growth. Curr Opin Plant Biol 2003, 6:603-610. 10.1016/j.pbi.2003.09.003, 14611960.
47. Asen S, Stewart RN, Norris KH. Co-pigmentation of anthocyanins in plant tissues and its effect on color. Phytochemistry 1972, 11:1139-114.
48. Hichri I, Barrieu F, Bogs J, Kappel C, Delrot S, Lauvergeat V. Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. J Exp Bot 2011, 62:2465-2483. 10.1093/jxb/erq442, 21278228.
49. Saito K, Yamazaki M. Biochemistry and molecular biology of the late-stage of biosynthesis of anthocyanin: lessons from Perilla frutescens as a model plant. New Phytol 2002, 155:9-23.
50. Tanaka Y, Brugliera F, Kalc G, Senior M, Dyson B, Nakamura N, Katsumoto Y, Chandler S. Flower color modification by engineering of the flavonoid biosynthetic pathway: practical perspectives. Biosci Biotech Biochem 2010, 74:1760-1769.
51. Góngora-Castillo E, Buell CR. Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence. Nat Prod Rep 2013, 30:490-500. 10.1039/c3np20099j, 23377493.
52. Van Belleghem SM, Roelofs D, Van Houdt J, Hendrickx F. De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae). PLoS One 2012, 7:e42605. 10.1371/journal.pone.0042605, 3411629, 22870338.
53. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda SH, Robles M, Talón M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008, 36:3420-3435. 10.1093/nar/gkn176, 2425479, 18445632.
54. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006, 34:W293-297. 10.1093/nar/gkl031, 1538768, 16845012.
55. Moon EK, Chung DI, Hong YC, Ahn TI, Kong HH. Acanthamoeba castellanii: Gene profile of encystation by ESTs analysis and KOG assignment. Exp Parasitol 2008, 119:111-116. 10.1016/j.exppara.2008.01.001, 18280471.
56. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
57. Sloan J, Backhaus A, Malinowski R, McQueen-Mason S, Fleming AJ. Phased control of expansin activity during leaf development identifies a sensitivity window for expansin-mediated induction of leaf growth. Plant Physiol 2009, 151:1844-1854. 10.1104/pp.109.144683, 2786001, 19789287.
58. Wang G, Gao Y, Wang J, Yang L, Song R, Li X, Shi J. Overexpression of two cambium-abundant Chinese fir (Cunninghamia lanceolata) α-expansin genes ClEXPA1 and ClEXPA2 affect growth and development in transgenic tobacco and increase the amount of cellulose in stem cell walls. Plant Biotechnol J 2011, 9:486-502. 10.1111/j.1467-7652.2010.00569.x, 20955182.
59. Cosgrove DJ. Loosening of plant cell walls by expansins. Nature 2000, 407:321-326. 10.1038/35030000, 11014181.
60. Lee Y, Kende H. Expression of β-expansins is correlated with internodal elongation in deepwater rice. Plant Physiol 2001, 127:645-654. 10.1104/pp.010345, 125099, 11598238.
61. Nieuwland J, Feron R, Huisman BA, Fasolino A, Hilbers CW, Derksena J, Mariani C. Lipid transfer proteins enhance cell wall extension in tobacco. Plant Cell 2005, 17:2009-2019. 10.1105/tpc.105.032094, 1167548, 15937228.
62. Liu F, Liu H, Jia Q, Wu X, Guo X, Guo X, Zhang S, Song F, Dong H. The internal glycinea-rich motif and cysteine suppress several effects of the HpaGXooc protein in plants. Phytopathology 2006, 10:1052-1059.
63. Ren H, Gu G, Long J, Yin Q, Wu T, Song T, Zhang S, Chen Z, Dong H. Combinative effects of a bacterial type-III effector and a biocontrol bacterium on rice growth and disease resistance. J Biosci 2006, 31:617-627. 10.1007/BF02708414, 17301500.
64. Catala C, Rose JK, Bennett AB. Auxin-regulated genes encoding cell wall-modifying proteins are expressed during early tomato fruit growth. Plant Physiol 2000, 122:527-534. 10.1104/pp.122.2.527, 58889, 10677445.
65. Cox MC, Benschop JJ, Vreeburg RA, Wagemaker CA, Moritz T, Peeters AJ, Voesenek LA. The roles of ethylene, auxin, abscisic acid, and gibberellin in the hyponastic growth of submerged Rumex palustris petioles. Plant Physiol 2004, 136:2948-2960. 10.1104/pp.104.049197, 523357, 15466223.
66. Breuer C, Ishida T, Sugimoto K. Developmental control of endocycles and cell growth in plants. Curr Opin Plant Biol 2010, 13:654-660. 10.1016/j.pbi.2010.10.006, 21094078.
67. Li F, Xing S, Guo Q, Zhao M, Zhang J, Gao Q, Wang G, Wang W. Drought tolerance through over-expression of the expansin gene TaEXPB23 in transgenic tobacco. J Plant Physiol 2011, 168:960-966. 10.1016/j.jplph.2010.11.023, 21316798.
68. Goldsbrough A, Belzile F, Yoder JI. Complementation of the tomato anthocyanin without (aw) mutant using the dihydroflavonol 4-reductase gene. Plant Physiol 1994, 105:491-496. 159386, 12232217.
69. Xie D, Sharma SB, Paiva NL, Ferreira D, Dixon RA. Role of anthocyanidin reductase, encoded by BANYULS in plant flavonoid biosynthesis. Science 2003, 299:396-399. 10.1126/science.1078540, 12532018.
70. Bombarely A, Rosli HG, Vrebalov J, Moffett P, Mueller LA, Martin GB. A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant Microbe Interact 2012, 25:1523-1530. 10.1094/MPMI-06-12-0148-TA, 22876960.
71. Chen L, Qian J, Qu S, Long J, Yin Q, Zhang C, Wu X, Sun F, Wu T, Beer SV, Dong H. Identification of specific fragments of HpaGXooc, a harpin protein from Xanthomonas oryzae pv. oryzicola, that induce disease resistance and enhanced growth in rice. Phytopathology 2008, 98:781-791. 10.1094/PHYTO-98-7-0781, 18943254.
72. Liu R, Chen L, Jia Z, Lü B, Dong H. Transcription factor AtMYB44 regulates induced expression of the ETHYLENE INSENSITIVE2 gene in Arabidopsis responding to a harpin protein. Mol Plant Microbe Interact 2010, 24:377-389.
73. Peng J, Bao Z, Ren H, Wang J, Dong H. Expression of harpinXoo in transgenic tobacco induces pathogen defense in the absence of hypersensitive response. Phytopathology 2004, 94:1048-1055. 10.1094/PHYTO.2004.94.10.1048, 18943792.
74. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29:644-652. 10.1038/nbt.1883, 3571712, 21572440.
75. Kim H, Schmidt CJ, Decker KS, Emara MG. A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data. Anim Genet 2003, 34:249-54. 10.1046/j.1365-2052.2003.01003.x, 12873212.
76. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676. 10.1093/bioinformatics/bti610, 16081474.