Abstract
The Dof (DNA binding with One Finger) family represents a classic zinc-finger transcription factors involved with multifarious roles exclusively in plants. There exists great diversity in terms of number of Dof genes observed in different crops. In current study, a total of 28 putative Dof genes have been predicted in silico from the recently available whole genome shotgun sequence of Sorghum bicolor (L.) Moench (with assigned accession numbers TPA:BK006983–BK007006 and TPA:BK007079–BK007082). The predicted SbDof genes are distributed on nine out of ten chromosomes of sorghum and most of these genes lack introns based on canonical intron/exon structure. Phylogenetic analysis of 28 SbDof proteins resulted in four subgroups constituting six clusters. The comparative phylogenetic analysis of these Dof proteins along with 30 rice and 36 Arabidopsis Dof proteins revealed six major groups similar to what has been observed earlier for rice and Arabidopsis. Motif analysis revealed the presence of conserved 50–52 amino acids Dof domain uniformly distributed across all the 28 Dof proteins of sorghum. The in silico cis-regulatory elements analysis of these SbDof genes suggested its diverse functions associated with light responsiveness, endosperm specific gene expression, hormone responsiveness, meristem specific expression and stress responsiveness.
Similar content being viewed by others
References
Yanagisawa S (2004) Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol 45(4):386–391
Takatsuji H (1998) Zinc-finger transcription factors in plants. Cell Mol Life Sci 54(6):582–596
Liu L, White MJ, MacRae TH (1999) Transcription factors and their genes in higher plants: functional domains, evolution and regulation. Eur J Biochem 262(2):247–257
Riechmann JL, Ratcliffe OJ (2000) A genomic perspective on plant transcription factors. Curr Opin Plant Biol 3(5):423–434
Yanagisawa S (2002) The Dof family of plant transcription factors. Trends Plant Sci 7(12):555–560
Lijavetzky D, Carbonero P, Vicente-Carbajosa J (2003) Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evol Biol 3:17
Kushwaha H, Yadav D (2010) Biochemical, molecular and in silico characterization of DNA-binding with one finger (DOF) transcription factor and investigating its diverse function in plants. In: Rao V (ed) Current topics on bioprocesses in food industry, vol III. Asiatech, New Delhi, pp 150–168
Yanagisawa S, Schmidt RJ (1999) Diversity and similarity among recognition sequences of Dof transcription factors. Plant J 17(2):209–214
Umemura Y, Ishiduka T, Yamamoto R, Esaka M (2004) The Dof domain, a zinc finger DNA-binding domain conserved only in higher plants, truly functions as a Cys2/Cys2 Zn finger domain. Plant J 37(5):741–749
Yanagisawa S (1997) Dof DNA binding domains of plant transcription factors contribute to multiple protein–protein interactions. Eur J Biochem 250(2):403–410
Krohn NM, Yanagisawa S, Grasser KD (2002) Specificity of the stimulatory interaction between chromosomal HMBG proteins and the transcription factor Dof2 and its negative regulation by protein kinase CK2 mediated phosphorylation. J Biol Chem 277(36):32438–32444
Moreno-Risueno MA, Martinez M, Vicente-Carbajosa J, Carbonero P (2007) The family of DOF transcription factors: from green unicellular algae to vascular plants. Mol Gen Genomics 277(4):379–390
Shaw LM, McIntyre CL, Gresshoff PM, Xue GP (2009) Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation. Funct Integr Genomics 9(4):485–498
Libault M, Joshi T, Benedito VA, Xu D, Udvardi MK, Stacey G (2009) Legume transcription factor genes: what makes legumes so special? Plant Physiol 151:991–1001
Eulgem T, Rushton PJ, Robatzek S, Somssich IE (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci 5(5):199–206
Martin C, Paz-Ares J (1997) MYB transcription factors in plants. Trends Genet 13(2):67–73
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(3):106–111
Parenicova L, de Folter S, Kieffer M, Horner DS, Favalli C, Busscher J, Cook HE, Ingram RM, Kater MM, Davies B, Angenent GC, Colombo L (2003) Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell 15(7):1538–1551
Reyes JC, Muro-Pastor MI, Florencio FJ (2004) The GATA family of transcription factors in Arabidopsis and rice. Plant Physiol 134(4):1718–1732
Papi M, Sabatini S, Bouchez D, Camilleri C, Constantino P, Vittorioso P (2000) Identification and disruption of an Arabidopsis zinc finger gene controlling seed germination. Genes Dev 14(1):28–33
Papi M, Sabatini S, Altamura MM, Hennig L, Schafer E, Costantino P, Vittorioso (2002) Inactivation of the phloem-specific Dof zinc finger gene DAG1 affects response to light and integrity of the testa of Arabidopsis seeds. Plant Physiol 128(2):411–417
Gualberti G, Papi M, Bellucci L, Ricci I, Bouchez D, Camilleri C, Costantino P, Vittorioso P (2002) Mutation in the Dof zinc finger genes DAG2 and DAG1 influence with opposite effects the germination of Arabidopsis seeds. Plant Cell 14(6):1253–1263
Imaizumi T, Schultz TF, Harmon FG, Ho LA, Kay SA (2005) FKF1 F-BOX protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Science 309(5732):293–297
Imaizumi T, Kay SA (2006) Photoperiodic control of flowering: not only by coincidence. Trends Plant Sci 11(11):550–558
Park DH, Lim PO, Kim JS, Cho DS, Hong SH, Nam HG (2003) The Arabidopsis COG1 gene encodes a Dof domain transcription factor and negatively regulates phytochrome signaling. Plant J 34(2):161–171
Ward JM, Cufr CA, Denzel MA, Neff MM (2005) The Dof transcription factor OBP3 modulates phytochrome and cryptochrome signaling in Arabidopsis. Plant Cell 17(2):475–485
Skirycz A, Radziejwoski A, Busch W, Hannah MA, Czeszejko J, Kwaśniewski M, Zanor MI, Lohmann JU, De Veylder L, Witt I, Mueller-Roeber B (2008) The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana. Plant J 56(5):779–792
Washio K (2001) Identification of DOF proteins with implication in the gibberellin-regulated expression of a peptidase gene following the germination of rice grains. Biochim Biophys Acta 1520(1):54–62
Washio K (2003) Functional dissections between GAMYB and Dof transcription factors suggest a role for protein–protein associations in the gibberellin-mediated expression of the RAmy1A gene in the rice aleurone. Plant Physiol 133(2):850–863
Yangisawa S (2000) Dof1 & Dof2 protein are associated with expression of multiple gene involved in carbon metabolism in maize. Plant J 21(3):281–288
Yanagisawa S, Akiyama A, Kisaka H, Uchimiya H, Miwa T (2004) Metabolic engineering with Dof1 transcription factor in plants: improved nitrogen assimilation and growth under low-nitrogen conditions. Proc Natl Acad Sci USA 101(20):7833–7838
Yanagisawa S, Sheen J (1998) Involvement of maize Dof zinc finger proteins in tissue specific and light regulated gene expression. Plant Cell 10(1):75–89
Chen R, Ni Z, Qin Y, Nie X, Lin Z, Dong G, Sun Q (2005) Isolation and characterization of TaDof1 transcription factor in wheat (Triticum aestivum L.). DNA Seq 16(5):358–363
Vicente-Carbajosa J, Moose SP, Parsons R, Schmidt RJ (1997) A maize zinc-finger protein binds the prolamin box in zein gene promoters and interacts with the basic leucine zipper transcriptional activator Opaque2. Proc Natl Acad Sci USA 94(14):7685–7690
Mena M, Vicente-Carbajosa J, Schmidt RJ, Carbonero P (1998) An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm. Plant J 16(1):53–62
Mena M, Cejudo FJ, Isabel-Lamoneda I, Carbonero P (2002) A role for the DOF transcription factor BPBF in the regulation of gibberellins responsive genes in barley aleurone. Plant Physiol 130(1):111–119
Dong G, Ni Z, Yao Y, Nie X, Sun Q (2007) Wheat Dof transcription factor WPBF interacts with TaQM and activates transcription of an alpha-gliadin gene during wheat seed development. Plant Mol Biol 63(1):73–84
Yamamoto MP, Onodera Y, Touno SM, Takaiwa F (2006) Synergism between RPBF DOF and RISBZ1 bZIP activators in regulation of rice seed expression genes. Plant Physiol 141(4):1694–1707
Kushwaha H, Gupta N, Singh VK, Kumar A, Yadav D (2008) In silico analysis of PCR amplified DOF (DNA binding with one finger) transcription factor domain and cloned genes from cereals and millets. Online J Bioinform 9(2):130–143
De Paolis A, Sabatini S, De Pascalis L, Costantino P, Capone I (1996) A rolB regulatory factor belongs to a new class of a single zinc finger plant proteins. Plant J 10(2):215–223
Kisu Y, Ono T, Shimofurutani N, Suzuki M, Esaka M (1998) Characterization and expression of a new class of zinc finger protein that binds to silencer region of ascorbate oxidase gene. Plant Cell Physiol 39(10):1054–1064
Baumann K, De Paolis A, Costantino P, Gualberti G (1999) The DNA binding site of the Dof protein NtBBF1 is essential for tissue specific and auxin-regulated expression of the rolB oncogene in plants. Plant Cell 11(3):323–333
Kang HG, Singh KB (2000) Characterization of salicylic acid responsive, Arabidopsis Dof domain proteins: over expression of OBP3 leads to growth defects. Plant J 21(4):329–339
Zhang B, Chen W, Foley RC, Büttner M, Singh KB (1995) Interaction between distinct types of DNA binding proteins enhance binding to ocs element promoter sequences. Plant Cell 7(12):2241–2252
Chen W, Chao G, Singh K (1996) The promoter of an H2O2 inducible Arabidopsis glutathione S-transferase gene contains closely linked OSF & OBP1 binding sites. Plant J 10(6):955–966
Skirycz A, Reichelt M, Burow M, Birkemeyer C, Rolcik J, Kopka J, Zanor MI, Gershenzon J, Strnad M, Szopa J, Mueller-Roeber B, Witt I (2006) DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. Plant J 47(1):10–24
Plesch G, Ehrhardt T, Mueller-Roeber B (2001) Involvement of TAAAG elements suggests a role for Dof transcription factors in guard cell specific gene expression. Plant J 28(4):455–464
Varshney RK, Hoisington AD, Tyagi KA (2006) Advances in cereal genomics and applications in crop breeding. Trends Biotechnol 24(11):490–499
Kellogg EA, Birchler JA (1993) Linking phylogeny and genetics: Zea mays as a tool for phylogenetic studies. Syst Biol 42:415–439
Kellogg EA (1998) Relationships of cereal crops and other grasses. Proc Natl Acad Sci USA 95(5):2005–2010
Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12(5):637–646
Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101(26):9903–9908
Paterson AH, Freeling M, Sasaki T (2005) Grains of knowledge: genomics of model cereals. Genome Res 15(12):1643–1650
Caetano-Anolles (2005) Evolution of genome size in the grasses. Crop Sci 45:1809–1816
Grenier C, Bramel-Cox PJ, Hamon P (2001) Core collection of sorghum: I. Stratification based on eco-geographical data. Crop Sci 41:234–240
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556
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(10):1286–1287
Guo A, He K, Liu D, Bai S, Gu S, Wei L, Luo J (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics 21(10):2568–2569
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402
Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated nonredundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:D61–D65
Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7(1):S10.1–S10.12
Stormo GD (2000) Gene-finding approaches for eukaryotes. Genome Res 10(4):394–397
Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer ELL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247–D251
de Castro E, Sigrist CJA, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 34:W362–W365
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:W116–W120
Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJ, Hofmann K, Bairoch A (2002) The PROSITE database, its status in 2002. Nucleic Acids Res 30(1):235–238
Brameier M, Krings A, Maccallum RM (2007) NucPred—predicting nuclear localization of proteins. Bioinformatics 23(9):1159–1160
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25(24):4876–4882
Saitou N, Nei M (1987) The neighbor-joining method—a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425
Bailey TL, Gribskov M (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14(1):48–54
Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:W369–W373
Lescot M, Hais PD, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouz P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30(1):325–327
Fornara F, Panigrahi KC, Gissot L, Sauerbrunn N, Ruhl M, Jarillo JA, Coupland G (2009) Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response. Dev Cell 17(1):75–86
Acknowledgments
The authors wish to acknowledge Head, Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur for providing the infrastructural facilities. The facilities provided by DBT-funded SUB-DIC, Bioinformatics Centre, School of Biotechnology, BHU, Varanasi is also thankfully acknowledged.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Kushwaha, H., Gupta, S., Singh, V.K. et al. Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis. Mol Biol Rep 38, 5037–5053 (2011). https://doi.org/10.1007/s11033-010-0650-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11033-010-0650-9