Molecular Biology Reports

, Volume 38, Issue 4, pp 2827–2848 | Cite as

Transcriptional profiling and in silico analysis of Dof transcription factor gene family for understanding their regulation during seed development of rice Oryza sativa L.

Article
First Online:
Received:
Accepted:

Abstract

Seed development is a complex process controlled by temporal and spatial expression of many transcription factors (TF) inside the developing seed. In the present study, transcript profiles of all the 30 members of rice DofTFs from flowering to seed development stages were analyzed. It was found that 16 Dof genes besides a previously characterized Dof gene ‘RPBF’ are differentially expressed during the seed development and unlike RPBF are not seed specific. Based on the expression patterns, these rice DofTFs were categorized into four groups-6 genes were constitutive while 4 genes were up-regulated and 3 genes were down regulated and four genes were maximally expressed at specific stages of seed development viz. one gene at flowering, two genes at watery ripe and one gene at milky stage. The involvement of more than one gene at different stages of seed development is suggestive of combinatorial regulation of their downstream genes involved in seed development. In silico expression analysis of wheat and Arabidopsis Dof Tfs also revealed that more than 50% of the Dof genes are expressed during the seed development process. Further in silico study of regulatory elements present in the promoters of these genes revealed the presence of some unique and common motifs in the promoters of rice and wheat Dof genes which indicate that Dof genes are possibly involved in ethylene and jasmonate signaling pathways affecting grain filling and grain quality. These Dof genes containing ethylene responsive motifs in their promoter region could possibly be the targets of recently identified Sub1 gene which codes for a ethylene responsive factor.

Keywords

Dof transcription factors RT-PCR Expression profiling 

Abbreviations

DAA

Days after anthesis

Dof

DNA binding with one finger

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

Notes

Acknowledgments

The present investigation was a part of the DBT (Department of Biotechnology), Govt. of India supported JRF programme. Financial assistance provided by DBT to Vikram Singh Gaur is duly acknowledged.

References

  1. 1.
    Zhu T et al (2003) Transcriptional control of nutrient partitioning during rice grain filling. Plant Biotechnol J 1:59–70PubMedCrossRefGoogle Scholar
  2. 2.
    Suzuki A et al (1997) Cloning and expression of five Myb-related genes from rice seed. Gene 198:393–398PubMedCrossRefGoogle Scholar
  3. 3.
    Lopez-Dee ZP et al (1999) OsMADS13 a novel rice MADS-box gene expressed during ovule development. Dev Genet 25:237–244PubMedCrossRefGoogle Scholar
  4. 4.
    Sato Y et al (1996) A rice homeobox gene OSH1 is expressed before organ differentiation in a specific region during early embryogenesis. Proc Natl Acad Sci USA 93:8117–8122PubMedCrossRefGoogle Scholar
  5. 5.
    Sato Y et al (1998) Isolation and characterization of a rice homeobox gene OSH15. Plant Mol Biol 38:983–998PubMedCrossRefGoogle Scholar
  6. 6.
    Ito M et al (2002) Position dependent expression of GL2-type homeobox gene Roc1: significance for protodermdifferentiation and radial pattern formation in early rice embryogenesis. Plant J 29:497–507PubMedCrossRefGoogle Scholar
  7. 7.
    Ito Y, Eiguchi M, Kurata N (1999) Expression of novel homeobox genes in early embryogenesis in rice. Biochim Biophys Acta 1444:445–450PubMedGoogle Scholar
  8. 8.
    Sentoku N et al (1999) Regional expression of the rice KN1-type homeobox gene family during embryo shoot and flower development. Plant Cell 11:1651–1664PubMedCrossRefGoogle Scholar
  9. 9.
    Postma-Haarsma AD et al (1999) Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice embryogenesis. Plant Mol Biol 39:257–271PubMedCrossRefGoogle Scholar
  10. 10.
    Duan K et al (2005) New insights into the complex and coordinated transcriptional regulation networks underlying rice seed development through cDNA chip-based analysis. Plant Mol Biol 57:785–804PubMedCrossRefGoogle Scholar
  11. 11.
    Yanagisawa S (2002) The DOF family of plant transcription factors. Trends Plant Sci 7(12):555–560PubMedCrossRefGoogle Scholar
  12. 12.
    Yanagisawa S (2004) DOF domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol 45:386–391PubMedCrossRefGoogle Scholar
  13. 13.
    Mena M et al (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 16:53–62PubMedCrossRefGoogle Scholar
  14. 14.
    Albani D et al (1997) The wheat transcriptional activator SPA: a seedspecific bZIP protein that recognizes the GCN4-like motif in the bifactorial endosperm box of prolamin genes. Plant Cell 9:171–184PubMedCrossRefGoogle Scholar
  15. 15.
    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):130–143Google Scholar
  16. 16.
    Vicente-Carbajosa J et al (1998) Barley BLZ1: a bZIP transcriptional activator that interacts with endospermspecific gene promoters. Plant J 13:629–640PubMedCrossRefGoogle Scholar
  17. 17.
    Conlan RS, Hammond-Kosack M, Bevan M (1999) Transcription activation mediated by the bZIP factor SPA on the endosperm box is modulated by ESBF-1 in vitro. Plant J 19:173–181PubMedCrossRefGoogle Scholar
  18. 18.
    Onate L et al (1999) Barley BLZ2, a seed-specific bZIP protein that interacts with BLZ1 in vivo and activates transcription from the GCN4-like motif of B-hordein promoters in barley endosperm. J Biol Chem 274:9175–9182PubMedCrossRefGoogle Scholar
  19. 19.
    Onodera Y et al (2001) A rice functional transcriptional activator RISBZ1 responsible for endosperm specific expression of storage protein genes through GCN4 motif. J Biol Chem 276:14139–14152PubMedGoogle Scholar
  20. 20.
    Lijavetzky D, Carbonero P, Vicente-Carbajosa J (2003) Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evol Biol 3:17PubMedCrossRefGoogle Scholar
  21. 21.
    Von B et al (1997) Growth stages of mono-and dicotyledonous plants: BBCH monograph. Blackwell, Wess-Verl, pp 20–21, ISBN 3-8263-3152-4Google Scholar
  22. 22.
    Burland TG (2000) DNASTAR’s Lasergene sequence analysis software. Methods Mol Biol 132:71–91PubMedGoogle Scholar
  23. 23.
    Bailey TL, Gribskov M (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14:48–54PubMedCrossRefGoogle Scholar
  24. 24.
    Bailey TL et al (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:W369–W373PubMedCrossRefGoogle Scholar
  25. 25.
    Higo K et al (1999) Plant cis acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27(1):297–300PubMedCrossRefGoogle Scholar
  26. 26.
    Bao JS, Xia YW (1999) Recent advances on molecular biology of starch biosynthesis in rice (Oryza sativa L.). Chin Bull Bot 16:352–358Google Scholar
  27. 27.
    Jiang SM, Xu LL, Wan JM (2002) Advance in the glutelin research on rice. Acta Agricult Universitat Jiangxiensis 24:14–19Google Scholar
  28. 28.
    Nakano M et al (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 34:D731–D735PubMedCrossRefGoogle Scholar
  29. 29.
    Gualberti G et al (2002) Mutations in the Dof zinc finger genes DAG2 and DAG1 influence with opposite effects the germination of Arabidopsis seeds. Plant Cell 14:1253–1263PubMedCrossRefGoogle Scholar
  30. 30.
    Yamamoto MP et al (2006) Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes. Plant Physiol 141:1694–1707PubMedCrossRefGoogle Scholar
  31. 31.
    Doebley J, Lukens L (1998) Transcriptional regulators and the evolution of plant form. Plant Cell 10:1075–1082PubMedCrossRefGoogle Scholar
  32. 32.
    Yang T, Poovaiah BW (2002) A Calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants. J Biol Chem 277(47):45049–45058PubMedCrossRefGoogle Scholar
  33. 33.
    Morgan PW, Drew MC (1997) Ethylene and plant responses to stress. Physiol Plant 100:620–630CrossRefGoogle Scholar
  34. 34.
    Davies PJ (2004) The plant hormones: their nature, occurrence and function. In: Davies PJ (ed) Plant hormones, biosynthesis, signal transduction, action! Kluwer, Dordrecht, pp 1–15Google Scholar
  35. 35.
    Yang J, Zhang J, Liu K, Wang Z, Liu L (2007) Abscisic acid and ethylene interact in rice spikelets in response to water stress during meiosis. J Plant Growth Regul 26:318–328CrossRefGoogle Scholar
  36. 36.
    Cheng CY, Lur HS (1996) Ethylene may be involved in abortion of the maize caryopsis. Physiol Plant 98:245–252CrossRefGoogle Scholar
  37. 37.
    Beltrano J, Carbone A, Montaldi ER, Guiamet JJ (1994) Ethylene as promoter of wheat grain maturation and ear senescence. Plant Growth Regul 15:107–112CrossRefGoogle Scholar
  38. 38.
    Yang J, Zhang J, Liu K, Wang Z, Liu L (2006) Abscisic acid and ethylene interact in wheat grains in response to soil drying during grain filling. New Phytol 271:293–303CrossRefGoogle Scholar
  39. 39.
    Yang J, Zhang J, Wang Z, Liu K, Wang P (2006) Postanthesis development of inferior and superior spikelets in rice in relation to abscisic acid and ethylene. J Exp Bot 57:149–160PubMedCrossRefGoogle Scholar
  40. 40.
    Mohapatra PK, Naik PK, Patel R (2000) Ethylene inhibitors improve dry matter partitioning and development of late flowering spikelets on rice panicles. Aust J Plant Physiol 27:311–323CrossRefGoogle Scholar
  41. 41.
    Kim EH et al (2009) Methyl jasmonate reduces grain yield by mediating stress signals to alter spikelet development in rice. Plant Physiol 149:1751–1760PubMedCrossRefGoogle Scholar
  42. 42.
    Yang J et al (2006) Post-anthesis development of inferior and superior spikelets in rice in relation to abscisic acid and ethylene. J Exp Bot 57(1):149–160PubMedCrossRefGoogle Scholar
  43. 43.
    Zhang H, Tan G, Wan Z, Yang J, Zhang J (2009) Ethylene and ACC levels in developing grains are related to the poor appearance and milling quality of rice. Plant Growth Regul 58:85–96CrossRefGoogle Scholar
  44. 44.
    Panda BB, Kariali E, Panigrahi R, Mohapatra PK (2009) High ethylene production slackens seed filling in compact panicled rice cultivar. Plant Growth Regul 58:141–151CrossRefGoogle Scholar
  45. 45.
    Xu K, Xu X, Fukao T, Canlas P, Rodriguez RM, Heuer S, Ismail AM, Serres JB, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708PubMedCrossRefGoogle Scholar
  46. 46.
    Fukao T, Harris T, Serres JB (2009) Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice. Ann Bot 103(2):143–150PubMedCrossRefGoogle Scholar
  47. 47.
    Dehesh K, Bruce WB, Quail PH (1990) A trans-acting factor that binds to a GT-motif in a phytochrome gene promoter. Science 250:1397–1399PubMedCrossRefGoogle Scholar
  48. 48.
    Buchel AS et al (1999) Mutation of GT-1 binding sites in the Pr-1A promoter influences the level of inducible gene expression in vivo. Plant Mol Biol 40:387–396PubMedCrossRefGoogle Scholar
  49. 49.
    Bate N, Twell D (1998) Functional architecture of a late pollen promoter: pollen-specific transcription is developmentally regulated by multiple stage-specific and co-dependent activator elements. Plant Mol Biol 37(5):859–869PubMedCrossRefGoogle Scholar
  50. 50.
    Filichkin SA et al (2004) A novel endo-mannanase gene in tomato LeMAN5 is associated with anther and pollen development. Plant Physiol 134:1080–1087PubMedCrossRefGoogle Scholar
  51. 51.
    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 photosynthetic and ammonium assimilating efficiency. Mol Biol Rep 36(8):2209–2220PubMedCrossRefGoogle Scholar
  52. 52.
    Chen RM, Ni ZF, Qin YX, Nie XL, Lin Z, Dong GQ, Sun QX (2005) Isolation and characterization of TaDof1 transcription factor in wheat (Triticum aestivum L.). DNA Sequence 16:358–363PubMedGoogle Scholar
  53. 53.
    Dong GQ, Ni ZF, Yao YY, Nie XL, Sun QX (2007) Wheat Dof transcription factor WPBF interacts with TaQM and activates transcription of an alpha-gliadin gene during wheat seed development. Plant Mol Biol 63:73–84PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Department of Molecular Biology and Genetic EngineeringCollege of Basic Sciences and Humanities, G.B. Pant University of Agriculture and TechnologyPantnagarIndia
  2. 2.Department of Plant PathologyCollege of Agriculture, G.B. Pant University of Agriculture and TechnologyPantnagarIndia
  3. 3.International Rice Research InstituteNew DelhiIndia

Personalised recommendations