Tobacco transcription factors: Novel insights into transcriptional regulation in the Solanaceae

Plant Physiology

Volumn 147, Issue 1, 2008, Pages 280-295

  Rushton, Paul J ^a   Bokowiec, Marta T ^a   Han, Shengcheng ^a   Zhang, Hongbo ^a   Brannock, Jennifer F ^a   Chen, Xianfeng ^b   Laudeman, Thomas W ^a   Timko, Michael P ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b UNIVERSITY OF VIRGINIA HEALTH SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSICUM ANNUUM; LYCOPERSICON ESCULENTUM; MAGNOLIOPHYTA; NICOTIANA TABACUM; SOLANACEAE; SOLANUM; SOLANUM TUBEROSUM; TRACHEOPHYTA;

BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; CYCLOPENTANE DERIVATIVE; HOMEODOMAIN PROTEIN; JASMONIC ACID; MADS DOMAIN PROTEIN; OXYLIPIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; GENOME; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; TOBACCO;

AMINO ACID SEQUENCE; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; CYCLOPENTANES; DATABASES, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HOMEODOMAIN PROTEINS; MADS DOMAIN PROTEINS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; OXYLIPINS; TOBACCO; TRANSCRIPTION FACTORS;

EID: 46249099719     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.107.114041     Document Type: Article

References (63)

1. Aida M, Ishida T, Fukaki H, Fujisawa H, Tasaka M (1997) Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 9: 841-857
2. Bailey PC, Martin C, Toledo-Ortiz G, Quail PH, Huq E, Heim MA, Jakoby M, Werber M, Weisshaar B (2003) Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell 15: 2497-2501
3. Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rohlfing T, Fries J, Bradford K, et al (2005) Sorghum genome sequencing by methylation filtration. PLoS Biol 3: 103-115
4. Bennetzen JL, Schrick K, Springer PS, Brown WE, Sanmiguel P (1994) Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37: 565-576
5. Byzova MV, Franken J, Aarts MGM, de Almeida-Engler J, Engler G, Mariani C, Van Lookeren Campagne MM, Angenent GC (1999) Arabidopsis STERILE APETALA, a multifunctional gene regulating inflorescence, flower, and ovule development. Genes Dev 13: 1002-1014
6. Chan RL, Gago GM, Palena CM, Gonzalez DH (1998) Homeoboxes in plant development. Biochim Biophys Acta 1442: 1-19
7. Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP (2007) CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics 8: 129
8. Chini A, Fonseca S, Fernandez G, Adie B, Chico JM, Lorenzo O, Garcia-Casado G, Lopez-Vidriero I, Lozano FM, Ponce MR, et al (2007) The JAZ family of repressors is the missing link in jasmonate signalling. Nature 448: 666-671
9. Choi JH, Jung HY, Kim HS, Cho HG (2000) PhyloDraw: a phylogenetic tree drawing system. Bioinformatics 16: 1056-1058
10. De Sutter V, Vanderhaeghen R, Tilleman S, Lammertyn F, Vanhoutte I, Karimi M, Inze D, Goossens A, Hilson P (2005) Exploration of jasmonate signalling via automated and standardized transient expression assays in tobacco cells. Plant J 44: 1065-1076
11. Ernst HA, Olsen AN, Skriver K, Larsen S, Lo Leggio L (2004) Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors. EMBO Rep 5: 297-303
12. Eulgem T, Rushton PJ, Robatzek S, Somssich IE (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci 5: 199-206
13. Gadani F, Hayes A, Opperman CH, Lommel SA, Sosinski BR, Burke M, Hi L, Brierly R, Salstead A, Heer J (2003) Large scale genome sequencing and analysis of Nicotiana tabacum: the tobacco genome initiative. In 5émes Journées Scientifiques du Tabac de Bergerac. Institut du Tabac-Bergerac, Dordogne, France, pp 117-130
14. Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J (2006) DRTF: a database of rice transcription factors. Bioinformatics 22: 1286-1287
15. Geelen DNV, Inze DG (2001) A bright future for the Bright Yellow-2 cell culture. Plant Physiol 127: 1375-1379
16. Gehring WJ (1987) Homeotic genes, the homeobox, and the spatial-organization of the embryo. Harvey Lect 81: 153-172
17. Goodspeed TH (1954) The Genus Nicotiana. Chronica Botanica, Waltham, MA
18. Goossens A, Hakkinen ST, Laakso I, Seppanen-Laakso T, Biondi S, De Sutter V, Lammertyn F, Nuutila AM, Soderlund H, Zabeau M, et al (2003) A functional genomics approach toward the understanding of secondary metabolism in plant cells. Proc Natl Acad Sci USA 100: 8595-8600
19. Guo AY, He K, Liu D, Bai SN, Gu XC, Wei LP, Luo JC (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics 21: 2568-2569
20. Haecker A, Gross-Hardt R, Geiges B, Sarkar A, Breuninger H, Herrmann M, Laux T (2004) Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana. Development 131: 657-668
21. Hake S, Smith HMS, Holtan H, Magnani E, Mele G, Ramirez J (2004) The role of knox genes in plant development. Annu Rev Cell Dev Biol 20: 125-151
22. Hanna-Rose W, Licht JD, Hansen U (1997) Two evolutionarily conserved repression domains in the Drosophila Kruppel protein differ in activator specificity. Mol Cell Biol 17: 4820-4829
23. Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC (2003) The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol Biol Evol 20: 735-747
24. Jakoby M, Weisshaar B, Droge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7: 106-111
25. Kranz HD, Denekamp M, Greco R, Jin H, Leyva A, Meissner RC, Petroni K, Urzainqui A, Bevan M, Martin C, et al (1998) Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana. Plant J 16: 263-276
26. McGrath KC, Dombrecht B, Manners JM, Schenk PM, Edgar CI, Maclean DJ, Scheible WR, Udvardi MK, Kazan K (2005) Repressor-and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiol 139: 949-959
27. Mueller LA, Tanksley SD, Giovannoni JJ, van Eck J, Stack S, Choi D, Kim BD, Chen MS, Cheng ZK, Li CY, et al (2005) The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL). Comp Funct Genomics 6: 153-158
28. Mullins E, Milbourne D, Petti C, Doyle-Prestwich BM, Meade C (2006) Potato in the age of biotechnology. Trends Plant Sci 11: 254-260
29. Murad L, Lim KY, Christopodulou V, Matyasek R, Lichtenstein CP, Kovarik A, Leitch AR (2002) The origin of tobacco's T genome is traced to a particular lineage within Nicotiana tomentosiformis (Solanaceae). Am J Bot 89: 921-928
30. Nagata T, Nemoto Y, Hasezawa S (1992) Tobacco BY-2 cell line as the HeLa cell in the cell biology of higher plants. Int Rev Cytol 132: 1-30
31. Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol 140: 411-432
32. Ogata K, Hojo H, Aimoto S, Nakai T, Nakamura H, Sarai A, Ishii S, Nishimura Y (1992) Solution structure of a DNA-binding unit of Myb: a helix turn helix-related motif with conserved tryptophans forming a hydrophobic core. Proc Natl Acad Sci USA 89: 6428-6432
33. Ohme-Takagi M, Shinshi H (1995) Ethylene-inducible DNA-binding proteins that interact with an ethylene-responsive element. Plant Cell 7: 173-182
34. Oksman-Caldentey KM (2007) Tropane and nicotine alkaloid biosynthesis: novel approaches towards biotechnological production of plant-derived pharmaceuticals. Curr Pharm Biotechnol 8: 203-210
35. Olsen AN, Ernst HA, Lo Leggio L, Skriver K (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci 10: 79-87
36. Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, Matsubara K, Osato N, Kawai J, Carninci P, et al (2003) Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res 10: 239-247
37. Palmer LE, Rabinowicz PD, O'Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR (2003) Maize genome sequencing by methylation filtrations. Science 302: 2115-2117
38. Parenicova L, de Folter S, Kieffer M, Horner DS, Favalli C, Busscher J, Cook HE, Ingram RM, Kater MM, Davies B, et al (2003) Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell 15: 1538-1551
39. Prigge MJ, Otsuga D, Alonso JM, Ecker JR, Drews GN, Clark SE (2005) Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. Plant Cell 17: 61-76
40. Qu LJ, Zhu YX (2006) Transcription factor families in Arabidopsis: major progress and outstanding issues for future research. Commentary. Curr Opin Plant Biol 9: 544-549
41. Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Parnell LD, Stein L, McCombie WR, Martienssen RA (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat Genet 23: 305-308
42. Richardt S, Lang D, Reski R, Frank W, Rensing SA (2007) PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol 143: 1452-1466
43. Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, et al (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290: 2105-2110
44. Rijpkema AS, Gerats T, Vandenbussche M (2007) Evolutionary complexity of MADS complexes. Curr Opin Plant Biol 10: 32-38
45. Rushton PJ, Bokowiec MT, Laudeman TW, Brannock JF, Chen X, Timko MP (2008) TOBFAC: the database of tobacco transcription factors. BMC Bioinformatics 9: 53
46. Rushton PJ, Macdonald H, Huttly AK, Lazarus CM, Hooley R (1995) Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes. Plant Mol Biol 29: 691-702
47. Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K, Somssich IE (1996) Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. EMBO J 15: 5690-5700
48. Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 4: 447-456
49. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599
50. Thines B, Katsir L, Melotto M, Niu Y, Mandaokar A, Liu G, Nomura K, He SY, Howe GA, Browse J (2007) JAZ repressor proteins are targets of the SCFCOI1 complex during jasmonate signalling. Nature 448: 661-665
51. Timko MP, Rushton PJ, Laudeman TW, Bokowiec MT, Chipumuro E, Cheung F, Town CD, Chen X (2008) Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 9: 103
52. Toledo-Ortiz G, Huq E, Quail PH (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15: 1749-1770
53. Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, Zhang JY, Benedito V, Hofer JMI, Chueng F, et al (2007) Legume transcription factors: global regulators of plant development and response to the environment. Plant Physiol 144: 538-549
54. Ulker B, Somssich IE (2004) WRKY transcription factors: from DNA binding towards biological function. Curr Opin Plant Biol 7: 491-498
55. van der Fits L, Memelink J (2000) ORCA3, a jasmonate-responsive transcriptional regulator of plant primary and secondary metabolism. Science 289: 295-297
56. van der Fits L, Memelink J (2001) The jasmonate-inducible AP2/ERF-domain transcription factor ORCA3 activates gene expression via interaction with a jasmonate-responsive promoter element. Plant J 25: 43-53
57. Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, et al (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120
58. Xiong YQ, Liu TY, Tian CG, Sun SH, Li JY, Chen MS (2005) Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots. Plant Mol Biol 59: 191-203
59. Yin Y, Vafeados D, Tao Y, Yoshida S, Asami T, Chory J (2005) A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis. Cell 120: 249-259
60. Yin Y, Wang ZY, Mora-Garcia S, Li J, Yoshida S, Asami T, Chory J (2002) BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell 109: 181-191
61. Zhang YJ, Wang LJ (2005) The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol 5: 1
62. Zhu QH, Guo AY, Gao G, Zhong YF, Xu M, Huang M, Luo J (2007) DPTF: a database of poplar transcription factors. Bioinformatics 23: 1307-1308
63. Zonneveld BJM, Leitch IJ, Bennett MD (2005) First nuclear DNA amounts in more than 300 angiosperms. Ann Bot (Lond) 96: 229-244