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Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced species

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Abstract

B3 domain-containing proteins constitute a large transcription factor superfamily. The plant-specific B3 superfamily consists of four family members, i.e., LAV (LEC2 [LEAFY COTYLEDON 2]/ABI3 [ABSCISIC ACID INSENSITIVE 3] − VAL [VP1/ABI3-LIKE]), RAV (RELATED to ABI3/VP1), ARF (AUXIN RESPONSE FACTOR) and REM (REPRODUCTIVE MERISTEM) families. The B3 superfamily plays a central role in plant life, from embryogenesis to seed maturation and dormancy. In previous research, we have characterized ARF family, member of the B3 superfamily in silico (Wang et al., Mol Biol Rep, 2011, doi:10.1007/s11033-011-0991-z). In this study, we systematically analyzed the diversity, phylogeny and evolution of B3 domain-containing proteins based on genomic resources of 11 sequenced species. A total of 865 B3 domain-containing genes were identified from 11 sequenced species through an iterative strategy. The number of B3 domain-containing genes varies not only between species but between gene families. B3 domain-containing genes are unevenly distributed in chromosomes and tend to cluster in the genome. Numerous combinations of B3 domains and their partner domains contribute to the sequences and structural diversification of the B3 superfamiy. Phylogenetic results showed that moss VAL proteins are related to LEC2/ABI3 instead of VAL proteins from higher plants. Lineage-specific expansion of ARF and REM proteins was observed. The REM family is the most diversified member among the B3 superfamily and experiences a rapid divergence during selective sweep. Based on structural and phylogenetic analysis results, two possible evolutional modes of the B3 superfamily were presented. Results presented here provide a resource for further characterization of the B3 superfamily.

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References

  1. Suzuki M, Kao CY, McCarty DR (1997) The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. Plant Cell 9:799–807

    Article  PubMed  CAS  Google Scholar 

  2. Swaminathan K, Peterson K, Jack T (2008) The plant B3 superfamily. Trends Plant Sci 13:647–655

    Article  PubMed  CAS  Google Scholar 

  3. Stone SL, Braybrook SA, Paula SL, Kwong LW, Meuser J, Pelletier J, Hsieh TF, Fischer RL, Goldberg RB, Harada JJ (2008) Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: implications for somatic embryogenesis. Proc Natl Acad Sci USA 105:3151–3156

    Article  PubMed  CAS  Google Scholar 

  4. Stone SL, Kwong LW, Yee KM, Pelletier J, Lepiniec L, Fischer RL, Goldberg RB, Harada JJ (2001) LEAFY COTYLEDON2 encodes a B3 domain transcription factor that induces embryo development. Proc Natl Acad Sci USA 98:11806–11811

    Article  PubMed  CAS  Google Scholar 

  5. Luerssen H, Kirik V, Herrmann P, Miséra S (1998) FUSCA3 encodes a protein with a conserved VP1/AB13-like B3 domain which is of functional importance for the regulation of seed maturation in Arabidopsis thaliana. Plant J 15:755–764

    Article  PubMed  CAS  Google Scholar 

  6. Brady SM, Sarkar SF, Bonetta D, McCourt P (2003) The ABSCISIC ACID INSENSITIVE 3 (ABI3) gene is modulated by farnesylation and is involved in auxin signaling and lateral root development in Arabidopsis. Plant J 34:67–75

    Article  PubMed  CAS  Google Scholar 

  7. McCarty DR (1995) Genetic control and integration of maturation and germination pathways in seed development. Annu Rev Plant Biol 46:71–93

    Article  CAS  Google Scholar 

  8. Rohde A, De Rycke R, Beeckman T, Engler G, Van Montagu M, Boerjan W (2000) ABI3 affects plastid differentiation in dark-grown Arabidopsis seedlings. Plant Cell 12:35–52

    Article  PubMed  CAS  Google Scholar 

  9. Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R, Horvath S, Drews GN, Fischer RL, Okamuro JK, Harada JJ, Goldberg RB (2010) Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci USA 107:8063–8070

    Article  PubMed  CAS  Google Scholar 

  10. Nambara E, Hayama R, Tsuchiya Y, Nishimura M, Kawaide H, Kamiya Y, Naito S (2000) The role of ABI3 and FUS3 loci in Arabidopsis thaliana on phase transition from late embryo development to germination. Dev Biol 220:412–423

    Article  PubMed  CAS  Google Scholar 

  11. Parcy F, Valon C, Kohara A, Miséra S, Giraudat J (1997) The ABSCISIC ACID-INSENSITIVE3, FUSCA3, and LEAFY COTYLEDON1 loci act in concert to control multiple aspects of Arabidopsis seed development. Plant Cell 9:1265–1277

    Article  PubMed  CAS  Google Scholar 

  12. Santos-Mendoza M, Dubreucq B, Baud S, Parcy F, Caboche M, Lepiniec L (2008) Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. Plant J 54:608–620

    Article  PubMed  CAS  Google Scholar 

  13. Suzuki M, Wang HH, McCarty DR (2007) Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes. Plant Physiol 143:902–911

    Article  PubMed  CAS  Google Scholar 

  14. Tsukagoshi H, Morikami A, Nakamura K (2007) Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings. Proc Natl Acad Sci USA 104:2543–2547

    Article  PubMed  CAS  Google Scholar 

  15. Tsukagoshi H, Saijo T, Shibata D, Morikami A, Nakamura K (2005) Analysis of a sugar response mutant of Arabidopsis identified a novel B3 domain protein that functions as an active transcriptional repressor. Plant Physiol 138:675–685

    Article  PubMed  CAS  Google Scholar 

  16. Braybrook SA, Harada JJ (2008) LECs go crazy in embryo development. Trends Plant Sci 13:624–630

    Article  PubMed  CAS  Google Scholar 

  17. Che N, Yang Y, Li Y, Wang L, Huang P, Gao Y, An C (2009) Efficient LEC2 activation of OLEOSIN expression requires two neighboring RY elements on its promoter. Sci China C Life Sci 52:854–863

    Article  PubMed  CAS  Google Scholar 

  18. Curaba J, Moritz T, Blervaque R, Parcy F, Raz V, Herzog M, Vachon G (2004) AtGA3ox2, a key gene responsible for bioactive gibberellin biosynthesis, is regulated during embryogenesis by LEAFY COTYLEDON2 and FUSCA3 in Arabidopsis. Plant Physiol 136:3660–3669

    Article  PubMed  CAS  Google Scholar 

  19. Mönke G, Altschmied L, Tewes A, Reidt W, Mock HP, Bäumlein H, Conrad U (2004) Seed-specific transcription factors ABI3 and FUS3: molecular interaction with DNA. Planta 219:158–166

    Article  PubMed  Google Scholar 

  20. Suzuki M, McCarty DR (2008) Functional symmetry of the B3 network controlling seed development. Curr Opin Plant Biol 11:548–553

    Article  PubMed  CAS  Google Scholar 

  21. Kagaya Y, Ohmiya K, Hattori T (1999) RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res 27:470–478

    Article  PubMed  CAS  Google Scholar 

  22. Hu YX, Wang YX, Liu XF, Li JY (2004) Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development. Cell Res 14:8–15

    Article  PubMed  CAS  Google Scholar 

  23. Woo HR, Kim JH, Kim J, Kim J, Lee U, Song IJ, Kim JH, Lee HY, Nam HG, Lim PO (2010) The RAV1 transcription factor positively regulates leaf senescence in Arabidopsis. J Exp Bot 61:3947–3957

    Article  PubMed  CAS  Google Scholar 

  24. Castillejo C, Pelaz S (2008) The balance between CONSTANS and TEMPRANILLO activities determines FT expression to trigger flowering. Curr Biol 18:1338–1343

    Article  PubMed  CAS  Google Scholar 

  25. Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14:1675–1690

    Article  PubMed  CAS  Google Scholar 

  26. Kagaya Y, Hattori T (2009) Arabidopsis transcription factors, RAV1 and RAV2, are regulated by touch-related stimuli in a dose-dependent and biphasic manner. Genes Genet Syst 84:95–99

    Article  PubMed  CAS  Google Scholar 

  27. Alvarez JP, Goldshmidt A, Efroni I, Bowman JL, Eshed Y (2009) The NGATHA distal organ development genes are essential for style specification in Arabidopsis. Plant Cell 21:1373–1393

    Article  PubMed  CAS  Google Scholar 

  28. Trigueros M, Navarrete-Gómez M, Sato S, Christensen SK, Pelaz S, Weigel D, Yanofsky MF, Ferrándiz C (2009) The NGATHA genes direct style development in the Arabidopsis gynoecium. Plant Cell 21:1394–1409

    Article  PubMed  CAS  Google Scholar 

  29. Scacchi E, Osmont KS, Beuchat J, Salinas P, Navarrete-Gómez M, Trigueros M, Ferrándiz C, Hardtke CS (2009) Dynamic, auxin-responsive plasma membrane-to-nucleus movement of Arabidopsis BRX. Development 136:2059–2067

    Article  PubMed  CAS  Google Scholar 

  30. Je BI, Piao HL, Park SJ, Park SH, Kim CM, Xuan YH, Park SH, Huang J, Do Choi Y, An G, Wong HL, Fujioka S, Kim MC, Shimamoto K, Han CD (2010) RAV-Like1 maintains Brassinosteroid homeostasis via the coordinated activation of BRI1 and biosynthetic genes in rice. Plant Cell 22:1777–1791

    Article  PubMed  CAS  Google Scholar 

  31. Zhao L, Luo Q, Yang C, Han Y, Li W (2008) A RAV-like transcription factor controls photosynthesis and senescence in soybean. Planta 227:1389–1399

    Article  PubMed  CAS  Google Scholar 

  32. Kwon SH, Lee BH, Kim EY, Seo YS, Lee S, Kim WT, Song JT, Kim JH (2009) Overexpression of a Brassica rapa NGATHA gene in Arabidopsis thaliana negatively affects cell proliferation during lateral organ and root growth. Plant Cell Physiol 50:2162–2173

    Article  PubMed  CAS  Google Scholar 

  33. Ulmasov T, Hagen G, Guilfoyle TJ (1997) ARF1, a transcription factor that binds to auxin response elements. Science 276:1865–1868

    Article  PubMed  CAS  Google Scholar 

  34. Guilfoyle TJ, Hagen G (2001) Auxin response factors. J Plant Growth Reg 20:281–291

    Article  CAS  Google Scholar 

  35. Kalluri UC, Difazio SP, Brunner AM, Tuskan GA (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol 7:59

    Article  PubMed  Google Scholar 

  36. Wang D, Pei K, Fu Y, Sun Z, Li S, Liu H, Tang K, Han B, Tao Y (2007) Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). Gene 394:13–24

    Article  PubMed  CAS  Google Scholar 

  37. Wang Y, Deng D, Shi Y, Miao N, Bian Y, Yin Z (2011) Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes. Mol Biol Rep. doi:10.1007/s11033-011-0991-z

  38. Guilfoyle TJ, Hagen G (2007) Auxin response factors. Curr Opin Plant Biol 10:453–460

    Article  PubMed  CAS  Google Scholar 

  39. Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15:533–543

    Article  PubMed  CAS  Google Scholar 

  40. Liscum E, Reed JW (2002) Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol 49:387–400

    Article  PubMed  CAS  Google Scholar 

  41. Li H, Johnson P, Stepanova A, Alonso JM, Ecker JR (2004) Convergence of signaling pathways in the control of differential cell growth in Arabidopsis. Dev Cell 7:193–204

    Article  PubMed  CAS  Google Scholar 

  42. Lim PO, Lee IC, Kim J, Kim HJ, Ryu JS, Woo HR, Nam HG (2010) Auxin response factor 2 (ARF2) plays a major role in regulating auxin-mediated leaf longevity. J Exp Bot 61:1419–1430

    Article  PubMed  CAS  Google Scholar 

  43. Schruff MC, Spielman M, Tiwari S, Adams S, Fenby N, Scott RJ (2006) The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs. Development 133:251–261

    Article  PubMed  CAS  Google Scholar 

  44. Sessions A, Nemhauser JL, McColl A, Roe JL, Feldmann KA, Zambryski PC (1997) ETTIN patterns the Arabidopsis floral meristem and reproductive organs. Development 124:4481–4491

    PubMed  CAS  Google Scholar 

  45. Hardtke CS, Berleth T (1998) The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J 17:1405–1411

    Article  PubMed  CAS  Google Scholar 

  46. Cole M, Chandler J, Weijers D, Jacobs B, Comelli P, Werr W (2009) DORNROSCHEN is a direct target of the auxin response factor MONOPTEROS in the Arabidopsis embryo. Development 136:1643–1651

    Article  PubMed  CAS  Google Scholar 

  47. Tabata R, Ikezaki M, Fujibe T, Aida M, Tian CE, Ueno Y, Yamamoto KT, Machida Y, Nakamura K, Ishiguro S (2010) Arabidopsis auxin response factor 6 and 8 regulate jasmonic acid biosynthesis and floral organ development via repression of class 1 KNOX genes. Plant Cell Physiol 51:164–175

    Article  PubMed  CAS  Google Scholar 

  48. Harper RM, Stowe-Evans EL, Luesse DR, Muto H, Tatematsu K, Watahiki MK, Yamamoto K, Liscum E (2000) The NPH4 locus encodes the auxin response factor ARF7, a conditional regulator of differential growth in aerial Arabidopsis tissue. Plant Cell 12:757–770

    Article  PubMed  CAS  Google Scholar 

  49. Goetz M, Vivian-Smith A, Johnson SD, Koltunow AM (2006) AUXIN RESPONSE FACTOR8 is a negative regulator of fruit initiation in Arabidopsis. Plant Cell 18:1873–1886

    Article  PubMed  CAS  Google Scholar 

  50. Li J, Dai X, Zhao Y (2006) A role for auxin response factor 19 in auxin and ethylene signaling in Arabidopsis. Plant Physiol 140:899–908

    Article  PubMed  CAS  Google Scholar 

  51. Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D, Onodera C, Quach H, Smith A, Yu G, Theologis A (2005) Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell 17:444–463

    Article  PubMed  CAS  Google Scholar 

  52. Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY (2005) Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17:2204–2216

    Article  PubMed  CAS  Google Scholar 

  53. Franco-Zorrilla JM, Fernández-Calvín B, Madueño F, Cruz-Alvarez M, Salinas J, Martínez-Zapater JM (1999) Identification of genes specifically expressed in cauliflower reproductive meristems Molecular characterization of BoREM1. Plant Mol Biol 39:427–436

    Article  PubMed  CAS  Google Scholar 

  54. Franco-Zorrilla JM, Cubas P, Jarillo JA, Fernández-Calvín B, Salinas J, Martínez-Zapater JM (2002) AtREM1, a member of a new family of B3 domain-containing genes, is preferentially expressed in reproductive meristems. Plant Physiol 128:418–427

    Article  PubMed  CAS  Google Scholar 

  55. Chandler J, Wilson A, Dean C (1996) Arabidopsis mutants showing an altered response to vernalization. Plant J 10:637–644

    Article  PubMed  CAS  Google Scholar 

  56. Levy YY, Mesnage S, Mylne JS, Gendall AR, Dean C (2002) Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297:243–246

    Article  PubMed  CAS  Google Scholar 

  57. Matias-Hernandez L, Battaglia R, Galbiati F, Rubes M, Eichenberger C, Grossniklaus U, Kater MM, Colombo L (2010) VERDANDI is a direct target of the MADS domain ovule identity complex and affects embryo sac differentiation in Arabidopsis. Plant Cell 22:1702–1715

    Article  PubMed  CAS  Google Scholar 

  58. Romanel EA, Schrago CG, Couñago RM, Russo CA, Alves-Ferreira M (2009) Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification. PLoS One 4:e5791

    Article  PubMed  Google Scholar 

  59. Wang Y, Deng D, Bian Y, Lv Y, Xie Q (2010) Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays L.). Mol Biol Rep 37:3991–4001

    Article  PubMed  CAS  Google Scholar 

  60. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38:D211–D222

    Article  PubMed  CAS  Google Scholar 

  61. Eddy SR (2008) A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol 4:e1000069

    Article  PubMed  Google Scholar 

  62. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37:D211–D215

    Article  PubMed  CAS  Google Scholar 

  63. Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi Chuan 29:1023–1026

    Article  PubMed  CAS  Google Scholar 

  64. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  PubMed  CAS  Google Scholar 

  65. 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

    Article  PubMed  CAS  Google Scholar 

  66. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 37:D205–D210

    Article  PubMed  CAS  Google Scholar 

  67. Wang Y, Deng D, Bian Y, Xie Q, Lv Y (2010) Cloning and characterization of DNA topoisomerase I gene Top1 from maize (Zea mays L.). Plant Sci 178:47–54

    Article  CAS  Google Scholar 

  68. Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009) The SWISS-MODEL repository and associated resources. Nucleic Acids Res 37:D387–D392

    Article  PubMed  CAS  Google Scholar 

  69. Maiti R, Van Domselaar GH, Zhang H, Wishart DS (2004) SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res 32:W590–W594

    Article  PubMed  CAS  Google Scholar 

  70. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667–1678

    Article  PubMed  CAS  Google Scholar 

  71. Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 93:10274–10279

    Article  PubMed  CAS  Google Scholar 

  72. Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17:1483–1498

    PubMed  CAS  Google Scholar 

  73. Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34:W609–W612

    Article  PubMed  CAS  Google Scholar 

  74. Comeron JM (1999) K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinformatics 15:763–764

    Article  PubMed  CAS  Google Scholar 

  75. Devos KM (2010) Grass genome organization and evolution. Curr Opin Plant Biol 13:139–145

    Article  PubMed  CAS  Google Scholar 

  76. Waltner JK, Peterson FC, Lytle BL, Volkman BF (2005) Structure of the B3 domain from Arabidopsis thaliana protein At1g16640. Protein Sci 14:2478–2483

    Article  PubMed  CAS  Google Scholar 

  77. Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S (2004) Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. Plant Cell 16:3448–3459

    Article  PubMed  CAS  Google Scholar 

  78. Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V (2009) Structural mechanisms for the 5’-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Nucleic Acids Res 37:6613–6624

    Article  PubMed  CAS  Google Scholar 

  79. Hu R, Qi G, Kong Y, Kong D, Gao Q, Zhou G (2010) Comprehensive analysis of NAC domain transcription factor gene family in Populus trichocarpa. BMC Plant Biol 10:145

    Article  PubMed  Google Scholar 

  80. Lee MH, Kim B, Song SK, Heo JO, Yu NI, Lee SA, Kim M, Kim DG, Sohn SO, Lim CE, Chang KS, Lee MM, Lim J (2008) Large-scale analysis of the GRAS gene family in Arabidopsis thaliana. Plant Mol Biol 67:659–670

    Article  PubMed  CAS  Google Scholar 

  81. Xu H, Li Y, Yan Y, Wang K, Gao Y, Hu Y (2010) Genome-scale identification of soybean BURP domain-containing genes and their expression under stress treatments. BMC Plant Biol 10:197

    Article  PubMed  Google Scholar 

  82. Shen C, Wang S, Bai Y, Wu Y, Zhang S, Chen M, Guilfoyle TJ, Wu P, Qi Y (2010) Functional analysis of the structural domain of ARF proteins in rice (Oryza sativa L.). J Exp Bot 61:3971–3981

    Article  PubMed  CAS  Google Scholar 

  83. Charoensawan V, Wilson D, Teichmann SA (2010) Lineage-specific expansion of DNA-binding transcription factor families. Trends Genet 26:388–393

    Article  PubMed  CAS  Google Scholar 

  84. Perry J, Zhao Y (2003) The CW domain, a structural module shared amongst vertebrates, vertebrate-infecting parasites and higher plants. Trends Biochem Sci 28:576–580

    Article  PubMed  CAS  Google Scholar 

  85. Weigel D (1995) The APETALA2 domain is related to a novel type of DNA binding domain. Plant Cell 7:388–389

    Article  PubMed  CAS  Google Scholar 

  86. Demuth JP, Hahn MW (2009) The life and death of gene families. Bioessays 31:29–39

    Article  PubMed  Google Scholar 

  87. Braybrook SA, Stone SL, Park S, Bui AQ, Le BH, Fischer RL, Goldberg RB, Harada JJ (2006) Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis. Proc Natl Acad Sci USA 103:3468–3473

    Article  PubMed  CAS  Google Scholar 

  88. Gazzarrini S, Tsuchiya Y, Lumba S, Okamoto M, McCourt P (2004) The transcription factor FUSCA3 controls developmental timing in Arabidopsis through the hormones gibberellin and abscisic acid. Dev Cell 7:373–385

    Article  PubMed  CAS  Google Scholar 

  89. Ledwoń A, Gaj MD (2009) LEAFY COTYLEDON2 gene expression and auxin treatment in relation to embryogenic capacity of Arabidopsis somatic cells. Plant Cell Rep 28:1677–1688

    Article  PubMed  Google Scholar 

  90. Vert G, Walcher CL, Chory J, Nemhauser JL (2008) Integration of auxin and brassinosteroid pathways by Auxin Response Factor 2. Proc Natl Acad Sci USA 105:9829–9834

    Article  PubMed  CAS  Google Scholar 

  91. Wang S, Bai Y, Shen C, Wu Y, Zhang S, Jiang D, Guilfoyle TJ, Chen M, Qi Y (2010) Auxin-related gene families in abiotic stress response in Sorghum bicolor. Funct Integr Genomics 10:533–546

    Article  PubMed  CAS  Google Scholar 

  92. Marin E, Jouannet V, Herz A, Lokerse AS, Weijers D, Vaucheret H, Nussaume L, Crespi MD, Maizel A (2010) miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 22:1104–1117

    Article  PubMed  CAS  Google Scholar 

  93. Gutierrez L, Bussell JD, Pacurar DI, Schwambach J, Pacurar M, Bellini C (2009) Phenotypic plasticity of adventitious rooting in Arabidopsis is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance. Plant Cell 21:3119–3132

    Article  PubMed  CAS  Google Scholar 

  94. Wu MF, Tian Q, Reed JW (2006) Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133:4211–4218

    Article  PubMed  CAS  Google Scholar 

  95. Remington DL, Vision TJ, Guilfoyle TJ, Reed JW (2004) Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiol 135:1738–1752

    Article  PubMed  CAS  Google Scholar 

  96. Chaw SM, Chang CC, Chen HL, Li WH (2004) Dating the monocot–dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol 58:424–441

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We are grateful to editors and reviewers for their helpful comments. This work is supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions, the Innovative Foundation of Yangzhou University (2011CXJ046, 2010CXJ035) and the Nature Science Foundation of Universities in Jiangsu Province (No. 09KJB180010).

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  1. Key Laboratory of Jiangsu Province for Crop Genetics and Physiology, Key Laboratory of Ministry of Education for Plant Functional Genomics, Yangzhou University, Yangzhou, 225009, China

    Yijun Wang, Dexiang Deng, Rong Zhang, Suxin Wang, Yunlong Bian & Zhitong Yin

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  1. Yijun Wang
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  2. Dexiang Deng
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  3. Rong Zhang
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  4. Suxin Wang
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Correspondence to Yijun Wang.

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Supplementary Fig. 1

Strategy for identification of B3 genes. An iterative strategy was employed to isolate and validate B3 genes in this study. The core of this technique lies in the iteration of data mining and HMM profiles construction. Details of this method were described in the text (TIFF 75 kb)

Supplementary Fig. 2

Schematic organization of B3 proteins. Possible DNA-binding domains B3, zf-CW and AP2 are marked in glaucous, purple and golden, respectively. Other characterized regions auxin response factor domain Auxin_resp and heterodimerization domain AUX_IAA are colored in kelly and nattierblue, respectively. Accession numbers of representative genes are showed below single lines (TIFF 143 kb)

Supplementary Fig. 3

Phylogeny and residues constitution of consensus sequences from B3 domains. a Phylogenesis of consensus sequences of B3 domains. Symbols LEC2/ABI3, VAL, RAV and ARF represent consensus sequences of B3 domains from LEC2/ABI3, VAL, RAV and ARF proteins, respectively. REM-1B3, REM-2B3 and REM-3B3 denote consensus sequences from the first, second and third B3 domains of REM proteins, respectively. Signs 1wid and 1yel figure consensus sequences of B3 domains from Arabidopsis RAV1 and At1g16640 proteins, respectively. Nine consensus sequences of B3 domains are classified into four groups. b Multiple alignment of consensus sequences of B3 domains. Consensus sequences are generated from B3 domains of RAV1, At1g16640, 38 LEC2/ABI3, 32 VAL, 115 RAV, 279 ARF, 401 REM-1B3, 178 REM-2B3 and 45 REM-3B3, respectively. Characterized regions β sheets and α helixes are showed above. Residues in RAV1 which contact with DNA directly are emphasized by arrows (TIFF 633 kb)

Supplementary Fig. 4

Phylogenesis and gene structure of proliferated ARF genes. The left is the phylogenetic tree of proliferated ARF proteins. The right is schematic structures of proliferated ARF genes. Exons and introns are showed by filled boxes and single lines, respectively. Domains B3, ARF and Aux/IAA are marked in red, blue and yellow, respectively (TIFF 139 kb)

Supplementary Fig. 5

Phylogenesis of the REM family based on whole sequences. REM proteins are primarily divided into monocot-specific, eudicot-specific and mixed groups. Divergent subgroups are in groups. The eudicot-specific proliferation of REM genes was observed (emphasized as rosids REM genes expansion group in figure) (TIFF 110 kb)

Supplementary Fig. 6

Ka/Ks ratios of sister pairs of B3 genes containing two B3 domains. The sliding window analysis method was used to estimate selective pressures on B3 genes. The first and second B3 domains are displayed by red and green boxes, respectively (TIFF 139 kb)

Supplementary Table 1

B3 genes in 11 species. Details of 865 B3 genes, including locus name, gene nomenclature, chromosomal location, deduced protein length, the number, position and E-value of B3 domains are presented (XLS 234 kb)

Supplementary Table 2

B3 genes cluster. B3 genes, especially REM genes tend to cluster in genomic regions of higher plants. The largest cluster of B3 genes is in a 140 kb genomic region on sorghum chromosome 1 which contains 12 REM genes (DOC 45 kb)

Supplementary Table 3

Duplication dates of sister pairs of B3 genes. Duplication time of sister pairs was approximately estimated by calculating the d S value in this study (DOC 28 kb)

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Wang, Y., Deng, D., Zhang, R. et al. Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced species. Mol Biol Rep 39, 6267–6282 (2012). https://doi.org/10.1007/s11033-012-1448-8

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  • DOI: https://doi.org/10.1007/s11033-012-1448-8

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