Skip to main content
SpringerLink
Log in

Genome-wide identification and characterization of the Dof gene family in moso bamboo (Phyllostachys heterocycla var. pubescens)

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

The Dof (DNA binding with One Finger) family of single zinc finger proteins is a family of plant-specific transcription factors. These transcription factors have a variety of important functions in different biological processes in plants. In the current study, we identified 26 Dof family genes in moso bamboo (Phyllostachys heterocycla var. pubescens). A complete overview of PhDof genes in moso bamboo is presented, including the gene structures, phylogeny, protein motifs and expression patterns. Phylogenetic analysis of the 26 PhDof proteins identified four classes constituting seven clusters (A, B1, C1, C2, D1, D2 and D3). In addition, a comparative analysis between the Dof genes in moso bamboo, Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.) was also performed, and several putative paralogous and orthologous genes were identified. The exon numbers in Dof genes ranged from one to three in many plants; however, the exon number in PhDofs ranged from one to four. The PhDof genes displayed differential expression in different parts of the shoot and at different flower development stages. This study represents the first step towards a genome-wide analysis of the Dof genes in moso bamboo. Our study provides a useful reference for cloning and functional analysis of members of the Dof gene family in moso bamboo and other species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • 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 11:323–333

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cai X, Zhang Y, Zhang C, Zhang T, Hu T, Ye J, Zhang J, Wang T, Li H, Ye Z (2013) Genome-wide analysis of plant-specific Dof transcription factor family in tomato. J Integr Plant Biol 6:552–566

    Article  Google Scholar 

  • Chen X, Wang D, Liu C, Wang M, Wang T, Zhao Q, Yu J (2012) Maize transcription factor Zmdof1 involves in the regulation of Zm401 gene. Plant Growth Regul 66:271–284

    Article  CAS  Google Scholar 

  • Cominelli E, Galbiati M, Albertini A, Fornara F, Conti L, Coupland G, Tonelli C (2011) DOF-binding sites additively contribute to guard cell-specificity of AtMYB60 promoter. BMC Plant Biol 11:162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Dios Barajas-López J, Tezycka J, Travaglia CN, Serrato AJ, Chueca A, Thormählen I, Geigenberger P, Sahrawy M (2012) Expression of the chloroplast thioredoxins f and m is linked to shortterm changes in the sugar and thiol status in leaves of Pisum sativum. J Exp Bot 13:4887–4990

    Article  Google Scholar 

  • Deng W, Wang Y, Liu Z, Cheng H, Xue Y (2014) HemI: a toolkit for illustrating heatmaps. PLoS one 11:e111988

    Article  Google Scholar 

  • Diaz I, Vicente-Carbajosa J, Abraham Z, Martinez M, Moneda II, Carbonero P (2002) The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development. Plant J 4:453–464

    Article  Google Scholar 

  • Dong G, Ni Z, Yao Y, Sun XN, Qi X (2007) Wheat Dof transcription factor WPBF interacts with TaQM and activates transcription of an alpha-gliadin gene during wheat seed development. Plant Mol Biol 63:73–84

    Article  CAS  PubMed  Google Scholar 

  • Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:29–37

    Article  Google Scholar 

  • Fornara F, Panigrahi KCS, 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 17:75–86

    Article  CAS  PubMed  Google Scholar 

  • Gabriele S, Rizza A, Martone J, Circelli P, Costantino P, Vittorioso P (2010) The Dof protein DAG1 mediates PIL5 activity on seed germination by negatively regulating GA biosynthetic gene AtGA3ox1. Plant J 61:312–323

    Article  CAS  PubMed  Google Scholar 

  • Gao X (2011) Study on the components and biological activity of bamboo shoot shell extractions. Dissertation, Beijing Forestry University

  • Gao J, Zhang Y, Zhang CL, Qi FY, Li XP, Mu SH, Peng ZH (2014) Characterization of the floral transcriptome of moso bamboo (Phyllostachys edulis) at different flowering developmental stages by transcriptome sequencing and RNA-Seq analysis. PLoS one 9:e98910

    Article  PubMed  PubMed Central  Google Scholar 

  • Gardiner J, Sherr I, Scarpella E (2010) Expression of DOF genes identifies early stages of vascular development in Arabidopsis leaves. Int J Dev Biol 54:1389–1396

    Article  CAS  PubMed  Google Scholar 

  • Gaur VS, Singh US, Kumar A (2011) Transcriptional profiling and in silico analysis of Dof transcription factor gene family for understanding their regulation during seed development of rice (Oryza sativa L.). Mol Biol Rep 38:2827–2848

    Article  CAS  PubMed  Google Scholar 

  • Gualberti G, Papi M, Bellucci L, Ricci I, Bouche D, Camilleri C, Costantino P, Vittorioso P (2002) Mutations in the Dof zinc finger genes DAG2 and DAG1 influence with opposite effects the germination of Arabidopsis seeds. Plant Cell 14:1253–1263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo Y, Qiu L (2013) Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics. PLoS one 9:e76809

    Article  Google Scholar 

  • Guo Y, Qin G, Gu H, Qu L (2009) Dof5.6/HCA2, a Dof transcription factor gene, regulates interfascicular cambium formation and vascular tissue development in Arabidopsis. Plant Cell 21:3518–3534

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • He L, Su C, Wang Y, Wei Z (2015) ATDOF5.8 protein is the upstream regulator of ANAC069 and is responsive to abiotic stress. Biochimie 110:17–24

    Article  CAS  PubMed  Google Scholar 

  • Hernando-Amado S, González-Calle V, Carbonero P, Barrero-Sicilia C (2012) The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling. BMC Plant Biol 12:202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 309:293

    Article  CAS  PubMed  Google Scholar 

  • Iwamoto M, Higo K, Takano M (2009) Circadian clock- and phytochrome-regulated Dof-like gene, Rdd1, is associated with grain size in rice. Plant Cell Environ 32:592–603

    Article  CAS  PubMed  Google Scholar 

  • Jiang Y, Zeng B, Zhao H, Zhang M, Xie S, Lai J (2012) Genome-wide transcription factor gene prediction and their expressional tissue-specificities in maize. J Integr Plant Biol 9:616–630

    Article  Google Scholar 

  • Jin J, Zhang H, Kong L, Gao G, Luo J (2014a) PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res 42:D1182–D1187

    Article  CAS  PubMed  Google Scholar 

  • Jin Z, Chandrasekaran U, Liu A (2014b) Genome-wide analysis of the Dof transcription factors in castor bean (Ricinus communis L.). Genes Genom 36:527–537

    Article  CAS  Google Scholar 

  • Kang H, Singh KB (2000) Characterization of salicylic acid-responsive, Arabidopsis Dof domain proteins: overexpression of OBP3 leads to growth defects. Plant J 4:329–339

    Article  Google Scholar 

  • Kang H, Foley RC, Onate-Sanchez L, Lin C, Singh KB (2003) Target genes for OBP3, a Dof transcription factor, include novel basic helix-loop-helix domain proteins inducible by salicylic acid. Plant J 35:362–372

    Article  CAS  PubMed  Google Scholar 

  • Kawakatsu T, Takaiwa F (2010) Differences in transcriptional regulatory mechanisms functioning for free lysine content and seed storage protein accumulation in rice grain. Plant Cell Physiol 12:1964–1974

    Article  Google Scholar 

  • 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 10:1054–1064

    Article  Google Scholar 

  • Konishi M, Yanagisawa S (2007) Sequential activation of two Dof transcription factor gene promoters during vascular development in Arabidopsis thaliana. Plant Physiol and Biochem 45:623–629

    Article  CAS  Google Scholar 

  • Kumar R, Taware R, Gaur VS, Guru SK, Kumar A (2009) Influence of nitrogen on the expression of TaDof1 transcription factor in wheat and its relationship with photo synthetic and ammonium assimilating efficiency. Mol Biol Rep 36:2209–2220

    Article  CAS  PubMed  Google Scholar 

  • Kurai T, Wakayama M, Abiko T, Yanagisawa S, Aoki N, Ohsugi R (2011) Introduction of the ZmDof1 gene into rice enhances carbon and nitrogen assimilation under low-nitrogen conditions. Plant Biotechnol J 9:826–837

    Article  CAS  PubMed  Google Scholar 

  • Kushwaha H, Gupta S, Singh VK, Rastogi S, Yadav D (2011) 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

    Article  CAS  PubMed  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics. Bioinformatics 21:2947–2948

    Article  Google Scholar 

  • Latchman DS (1997) Transcription factors: an overview. Int J Biochem Cell Biol 29:1305–1312

    Article  CAS  PubMed  Google Scholar 

  • Li D, Yang C, Li X, Gan Q, Zhao X, Zhu L (2009) Functional characterization of rice OsDof12. Planta 229:1159–1169

    Article  CAS  PubMed  Google Scholar 

  • Li CH, Cai B, Lou XM, Tang R (2013) Genome-wide analysis of the Dof transcription factor gene family in grape. J Yangzhou Univ (Agric Life Sci Ed) 4:99–103

    Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Lin XC, Chow TY, Chen HH, Liu CC, Chou SJ, Huang BL, Kuo CI, Wen CK, Huang LC, Fang W (2010) Understanding bamboo flowering based on large-scale analysis of expressed sequence tags. Genet Mol Res 9:1085–1093

    Article  CAS  PubMed  Google Scholar 

  • Marzabal P, Gas E, Fontanet P, Vicente-Carbajosa J, Torrent M, Ludevid MD (2008) The maize Dof protein PBF activates transcription of γ-zein during maize seed development. Plant Mol Biol 67:441–454

    Article  CAS  PubMed  Google Scholar 

  • 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 1:53–62

    Article  Google Scholar 

  • Mena M, Cejudo FJ, Isabel-Lamoneda I, Carbonero P (2002) A role for the DOF transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone. Plant Physiol 130:111–119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moreno-Risueno MA, Dıaz I, Carrillo L, Fuentes R, Carbonero P (2007a) The HvDOF19 transcription factor mediates the abscisic acid-dependent repression of hydrolase genes in germinating barley aleurone. Plant J 51:352–365

    Article  CAS  PubMed  Google Scholar 

  • Moreno-Risueno MÁ, Martínez M, Vicente-Carbajosa J, Carbonero P (2007b) The family of DOF transcription factors: from green unicellular algae to vascular plants. Mol Genet Genom 277:379–390

    Article  CAS  Google Scholar 

  • Papi M, Sabatini S, Bouchez D, Camilleri C, Costantino P, Vittorioso P (2000) Identification and disruption of an Arabidopsis zinc finger gene controlling seed germination. Gene Dev 14:28–33

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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 34:161–171

    Article  CAS  PubMed  Google Scholar 

  • Peng ZH, Lu TT, Li LB, Liu X, Gao ZM, Hu T, Yang X, Feng Q, Guan J, Weng QJ et al (2010) Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences. BMC Plant Biol 10:116

    Article  PubMed  PubMed Central  Google Scholar 

  • Peng Z, Lu Y, Li L, Zhao Q, Feng Q, Gao ZM, Lu HY, Hu T, Yao N, Liu KY et al (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nature Genet 4:456–463

    Article  Google Scholar 

  • 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 4:455–464

    Google Scholar 

  • Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda Ratcliffe J, Samaha RR et al (2000) Arabidopsis transcription factors genome-wide comparative analysis among eukaryotes. Science 290:2105–2110

    Article  CAS  PubMed  Google Scholar 

  • Rizza A, Boccaccini A, Lopez-Vidriero I, Costantino P, Vittorioso P (2011) Inactivation of the ELIP1 and ELIP2 genes affects Arabidopsis seed germination. New Phytol 190:896–905

    Article  CAS  PubMed  Google Scholar 

  • Rueda-Lopez M, Crespillo R, Canovas FM, Avila C (2008) Differential regulation of two glutamine synthetase genes by a single Dof transcription factor. Plant J 56:73–85

    Article  CAS  PubMed  Google Scholar 

  • Rueda-Romero P, Barrero-Sicilia C, Gomez-Cadenas A, Carbonero P, Onate-Sanchez L (2012) Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14. J Exp Bot 5:1937–1949

    Article  Google Scholar 

  • Sawa M, Nusinow DA, Kay SA, Imaizumi T (2007) FKF1 and GIGANTEA complex formation is required for day-length measurement in Arabidopsis. Science 318:261–265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183

    Article  CAS  PubMed  Google Scholar 

  • Shaw LM, McIntyre CL, Gresshoff PM, Xue G (2009) Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation. Funct Integr Genom 9:485–498

    Article  CAS  Google Scholar 

  • Shigyo M, Tabei N, Yoneyama T, Yanagisawa S (2007) Evolutionary processes during the formation of the plant-specific Dof transcription factor family. Plant Cell Physiol 1:179–185

    Google Scholar 

  • Skirycz A, Reichelt M, Burow M, Birkemeyer C, Rolcik J, Kopka J, Zanor MI, Gershenzon J, Strnad M, Szopa J et al (2006) DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. Plant J 47:10–24

    Article  CAS  PubMed  Google Scholar 

  • Skirycz A, Jozefczuk S, Stobiecki M, Muth D, Zanor MI, Witt I, Mueller-Roeber B (2007) Transcription factor AtDOF4.2 affects phenylpropanoid metabolism in Arabidopsis thaliana. New Phytol 175:425–438

    Article  CAS  PubMed  Google Scholar 

  • Song YH, Smith RW, To BJ, Millar AJ, Imaizumi T (2012) FKF1 conveys crucial timing information for CONSTANS stabilization in the photoperiodic flowering. Science 6084:1045–1049

    Article  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Abiko T, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony. Mol Biol Evol 10:2731–2739

    Article  Google Scholar 

  • Tanaka M, Takahata Y, Nakayama H, Nakatan M, Tahara M (2009) Altered carbohydrate metabolism in the storage roots of sweetpotato plants overexpressing the SRF1 gene, which encodes a Dof zinc finger transcription factor. Planta 230:737–746

    Article  CAS  PubMed  Google Scholar 

  • Vicente-Carbajosa J, Moose SP, Parsons RL, 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 94:7685–7690

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang H, Zhang B, Hao Y, Huang J, Tian A, Liao Y, Zhang J, Chen S (2007) The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. Plant J 52:716–729

    Article  CAS  PubMed  Google Scholar 

  • Ward JM, Cufr CA, Denzel MA, Neff MM (2005) The Dof transcription factor OBP3 modulates phytochrome and cryptochrome signaling in Arabidopsis. Plant Cell 17:475–485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 133:850–863

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei P, Tan F, Gao X, Zhang X, Wang G, Xu H, Li L, Chen J, Wang X (2010) Over-expression of AtDOF4.7, an Arabidopsis DOF family transcription factor, induces floral organ abscission deficiency in Arabidopsis. Plant Physiol 153:1031–1045

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yanagisawa S (1995) A novel DNA-binding domain that may form a single zinc finger motif. Nucleic Acids Res 17:3403–3410

    Article  Google Scholar 

  • Yanagisawa S (2000) Dof1 and Dof2 transcription factors are associated with expression of multiple genes involved in carbon metabolism in maize. Plant J 3:281–288

    Article  Google Scholar 

  • Yanagisawa S, Sheen J (1998) Involvement of maize Dof zinc finger proteins in tissue-specific and light-regulated gene expression. Plant Cell 10:75–89

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang XH, Tuskan GA, Cheng ZM (2006a) Divergence of the dof gene families in poplar, Arabidopsis and rice suggests multiple modes of gene evolution after duplication. Plant Physiol 142:820–830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang X, Tuskan GA, Cheng Z (2006b) Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant Physiol 142:820–830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang J, Yang M, Wang D, Chen F, Shen S (2010) JcDof1 a Dof transcription factor gene, is associated with the light-mediated circadian clock in Jatropha curcas. Physiol Plantarum 139:324–334

    CAS  Google Scholar 

  • Yang J, Yang M, Zhang W, Chen F, Shen S (2011) A putative flowering-time-related Dof transcription factor gene, JcDof3, is controlled by the circadian clock in Jatropha curcas. Plant Sci 181:667–674

    Article  CAS  PubMed  Google Scholar 

  • Zhang B, Chen W, Foley RC, Büttner M, Singh KB (1995) Interactions between distinct types of DNA binding proteins enhance binding to ocs element promoter. Plant Cell 7:2241–2252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by the Forestry Project of the Ministry of Science and Technology of the People’s Republic of China (Grant 200704001 to Z. J.), and the Chinese Academy of Sciences (KSCX2-YW-G-034 to B. H.).

Author information

Author notes

    Authors and Affiliations

    1. State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China

      Tao Wang, Xue-Ji Wang, Lu Xu & Lu-Bin Li

    2. Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400, China

      Jin-Jun Yue & Xiao-Ping Gu

    Authors
    1. Tao Wang
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Jin-Jun Yue
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Xue-Ji Wang
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Lu Xu
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Lu-Bin Li
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. Xiao-Ping Gu
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding authors

    Correspondence to Lu-Bin Li or Xiao-Ping Gu.

    Ethics declarations

    Conflict of interest

    We declare that no competing interests exist.

    Additional information

    Tao Wang and Jin-Jun Yue have contributed equally to this paper.

    Electronic supplementary material

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Wang, T., Yue, JJ., Wang, XJ. et al. Genome-wide identification and characterization of the Dof gene family in moso bamboo (Phyllostachys heterocycla var. pubescens). Genes Genom 38, 733–745 (2016). https://doi.org/10.1007/s13258-016-0418-2

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s13258-016-0418-2

    Keywords

    Search

    Navigation