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Isolation and Sequence Analysis of Wheat Tissue-Specific cDNAs by Differential Display

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Abstract

The differential display technology was used to study and isolate tissue-specific cDNA from wheat (Triticum aestivum). cDNA was synthesized by reverse transcription from total RNA from wheat leaves, anthers, and ovaries to search for and isolate tissue-specific cDNAs and use them to screen wheat genomic library to get the corresponding genomic DNA clone. Here, we report the isolation, cloning, and sequencing of various tissue-specific cDNA fragments. Further, we report the isolation of a wheat genomic clone, 18-3. The clone has an unknown open reading frame (ORF238) that is similar to related grain EST sequences, 1,673 bp 5′ flanking region from the ATG and 1321 3′ flanking region. A PlantCARE database search using the 5′ flanking region revealed that there are many cis-acting elements in this region. About 109 cis-acting elements from different plant gene promoters in 24 groups were detected. For example, 26 CAAT elements, a common cis-acting element in promoter and enhancer regions, were detected overall the 5′ flanking region. Multiple TATA-boxes concentrated in three spots and a putative transcription start site also were detected. In addition, MeJA, DRE, GC-motif, ABRE, GCN4_motif, Skn_1-motif, HSE, A-box, ACE, G-box, I-box, TCCC-motif, P-box, TATC-box, and WUN-motif were detected. The putative function of the reported ORF238 and its promoter is unknown.

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References

  • Acevedo-Hernandez GJ, Leon P, Herrera-Estrella L (2005) Sugar and ABA responsiveness of a minimal RBCS light-responsive unit is mediated by direct binding of ABI4. Plant J 43:506–519

    Article  CAS  PubMed  Google Scholar 

  • Altschul FS, Madden LT, Schaaffer 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 25:3389–3402

    Article  CAS  PubMed  Google Scholar 

  • An C, Ichinose Y, Yamada T, Tanaka Y, Shiraishi T, Oku H (1993) Organization of the genes encoding chalcone synthase in Pisum sativum. Plant Mol Biol 21(5):789–803

    Article  CAS  PubMed  Google Scholar 

  • Arguello-Astorga GR, Herrera-Estrella LR (1996) Ancestral multipartite units in light-responsive plant promoters have structural features correlating with specific phototransduction pathways. Plant Physiol 112(3):1151–1166

    Article  CAS  PubMed  Google Scholar 

  • Aryan A, An G, Okita T (1991) Structural and functional analysis of promoter from gliadin, an endosperm-specific storage protein gene of Triticum aestivum. Mol Gen Genet 225:65–71

    Article  CAS  PubMed  Google Scholar 

  • Baker SS, Wilhelm KS, Thomashow MF (1994) The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought-, and ABA-regulated gene expression. Plant Mol Biol 24(5):701–713

    Article  CAS  PubMed  Google Scholar 

  • 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 37:859–869

    Article  CAS  PubMed  Google Scholar 

  • Bodeau JP, Walbot V (1996) Structure and regulation of the maize Bronze2 promoter. Plant Mol Biol 32(4):599–609

    Article  CAS  PubMed  Google Scholar 

  • Bustos MM, Begum D, Kalkan FA, Battraw MJ, Hall TC (1991) Positive and negative cis-acting DNA domains are required for spatial and temporal regulation of gene expression by seed storage protein promoter. EMBO J 10:1460–1479

    Google Scholar 

  • Cao X, Costa LM, Biderre-Petit C, Kbhaya B, Dey N, Perez P, McCarty DR, Gutierrez-Marcos JF, Becraft PW (2007) Abscisic acid and stress signals induce viviparous1 (Vp1) expression in seed and vegetative tissues of maize. Plant Physiol 143:720–731

    Article  CAS  PubMed  Google Scholar 

  • Carranco R, Almoguera C, Jordano J (1997) A plant small heat shock protein gene expressed during zygotic embryogenesis but noninducible by heat stress. J Biol Chem 272(43):27470–27475

    Article  CAS  PubMed  Google Scholar 

  • Caubet N, Flenet M, Clement B, Brignon P, Gigot C (1996) Identification of cis-elements regulating the expression of an Arabidopsis histone H4 gene. Plant J 10(3):425–435

    Article  Google Scholar 

  • Cazzonelli CI, Velten J (2008) In vivo characterization of plant promoter element interaction using synthetic promoters. Transgenic Res 17:437–457

    Article  CAS  PubMed  Google Scholar 

  • Cinege G, Louis S, Schnitzler RHJ (2009) Regulation of isoperene synthase promoter by environmental and internal factors. Plant Mol Biol 69:593–604

    Article  CAS  PubMed  Google Scholar 

  • Coca MA, Almoguera C, Thomas TL, Jordano J (1996) Differential regulation of small heat-shock genes in plants: analysis of a water-stress-inducible and developmentally activated sunflower promoter. Plant Mol Biol 31:863–876

    Article  CAS  PubMed  Google Scholar 

  • Cocherel S, Perez P, Degroote F, Genestier S, Picard G (1996) A promoter identified in the 3′ end of the Ac transposon can be activated by cis-acting elements in transgenic Arabidopsis lines. Plant Mol Biol 30:539–551

    Article  CAS  PubMed  Google Scholar 

  • Dasgupta S, Dasgupta J, Mandal K (1993) Cloning and sequencing of 5′ flanking sequence from the gene encoding 2 S storage protein, from two Brassica species. Gene 133(2):301–302

    Article  CAS  PubMed  Google Scholar 

  • Donald RG, Cashmore AR (1990) Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter. EMBO J 9:1717–1726

    CAS  PubMed  Google Scholar 

  • Ellerstrom M, Stalberg K, Ezcurra I, Rask L (1996) Functional dissection of a napin gene promoter: identification of promoter elements required for embryo and endosperm-specific transcription. Plant Mol Biol 32:1019–1027

    Article  CAS  PubMed  Google Scholar 

  • Fares S, Loreto F, Kleist E (2008) Stomatal uptake and stomatal deposition of ozone in isoprene monoterpene emitting plants. Plant Biol (Stuttg) 10:44–54

    Article  CAS  Google Scholar 

  • Feldbrugge M, Sprenger M, Dinkelbach M, Yazaki K, Harter K, Weisshaar B (1994) Functional analysis of a light-responsive plant bZIP transcriptional regulator. Plant Cell 6(11):1607–1621

    Article  CAS  PubMed  Google Scholar 

  • Feldbrugge M, Hahlbrock K, Weisshaar B (1996) The transcriptional regulator CPRF1: expression analysis and gene structure. Mol Gen Genet 251(6):619–627

    CAS  PubMed  Google Scholar 

  • Green PJ, Kay SA, Chua NH (1987) Sequence-specific interactions of a pea nuclear factor with light-responsive elements upstream of the rbcS-3a gene. EMBO J 6(9):2543–2549

    CAS  PubMed  Google Scholar 

  • Guerrero FD, Crossland L, Smutzer GS, Hamilton DA, Mascarenhas JP (1990) Promoter sequences from a maize pollen-specific gene direct tissue-specific transcription in tobacco. Mol Gen Genet 224:161–168

    Article  CAS  PubMed  Google Scholar 

  • Hillebrand H, Tiemann B, Hell R, Bartling D, Weiler EW (1996) Structure of the gene encoding nitrilase 1 from Arabidopsis thaliana. Gene 170(2):197–200

    Article  CAS  PubMed  Google Scholar 

  • Ito M, Ichinose Y, Kato H, Shiraishi T, Yamada T (1997) Molecular evolution and functional relevance of the chalcone synthase genes of pea. Mol Gen Genet 255(1):28–37

    Article  CAS  PubMed  Google Scholar 

  • John ME, Petersen MW (1994) Cotton (Gossypium hirsutum L.) pollen-specific polygalacturonase mRNA: tissue and temporal specificity of its promoter in transgenic tobacco. Plant Mol Biol 26:1989–1993

    Article  CAS  PubMed  Google Scholar 

  • Keddie JS, Hubner G, Slocombe SP, Jarvis RP, Cummins EW, Shaw CH, Murphy DJ (1992) Cloning and characterization of an oleosin gene from Brassica napus. Plant Mol Biol 19(3):443–453

    Article  CAS  PubMed  Google Scholar 

  • Kim JK, Cao J, Wu R (1992) Regulation and interaction of multiple protein factors with the proximal promoter regions of a rice high pI alpha-amylase gene. Mol Gen Genet 232(3):383–393

    Article  CAS  PubMed  Google Scholar 

  • Kim SY, Wu R (1990) Multiple protein factors bind to a rice glutelin promoter region. Nucleic Acids Res 18(23):6845–6852

    Article  CAS  PubMed  Google Scholar 

  • Klotz KL, Lagrimini LM (1996) Phytohormone control of the tobacco anionic peroxidase promoter. Plant Mol Biol 31(3):565–573

    Article  CAS  PubMed  Google Scholar 

  • Lamacchia C, Shewry PR, Di Fonzo N, Forsyth JL, Harris N, Lazzeri PA, Napier JA, Halford NG, Barcelo P (2001) Endosperm-specific activity of a storage protein gene promoter in transgenic wheat seed. J Exp Bot 52:243–250

    Article  CAS  PubMed  Google Scholar 

  • Lexcot M, Dehais P, Thijs G, Marchal K, Moreau Y, de Peer YV, Rouze 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

    Article  Google Scholar 

  • Li F, Barnathan ES, Kariko K (1994) Rapid method for screening and cloning cDNAs generated in differential mRNA display: application of Northern blot for affinity capturing of cDNAs. Nucleic Acids Res 22:1764–1765

    Article  CAS  PubMed  Google Scholar 

  • Li ZT, Jayasankar S, Gray DJ (2004) Bi-directional duplex promoters with duplicated enhancers significantly increases transgene expression in grape and tobacco. Transgenic Res 13:143–154

    Article  CAS  PubMed  Google Scholar 

  • Liang P, Pardee AB (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:967–971

    Article  CAS  PubMed  Google Scholar 

  • Litts JC, Erdman MB, Huang N, Karrer EE, Noueiry A, Quatrano RS, Rodriguez RL (1992) Nucleotide sequence of the rice (Oryza sativa) Em protein gene (Emp1). Plant Mol Biol 19(2):335–337

    Article  CAS  PubMed  Google Scholar 

  • Liu Z, Ulmasov T, Xiangyang S, Hagen G, Guilfoyle T (1994) Soybean GH3 promoter contains multiple auxin-inducible elements. Plant Cell 6:645–657

    Article  CAS  PubMed  Google Scholar 

  • Logemann E, Parniske M, Hahlbrock K (1995) Modes of expression and common structural features of the complete phenylalanine amonia-lyase gene family in parsley. Proc Natl Acad Sci USA 92(13):5905–5909

    Article  CAS  PubMed  Google Scholar 

  • Loivamaki M, Louis S, Cinege G et al (2007) Circadian rhythms of isoperene biosynthesis in grey poplar leaves. Plant Physiol 143:540–551

    Article  PubMed  Google Scholar 

  • Lu CA, Lim EK, Yu SM (1998) Sugar response sequence in the promoter of a rice amylase gene serves as a transcriptional enhancer. J Biol Chem 273:10120–10131

    Article  CAS  PubMed  Google Scholar 

  • Manjunath S, Sachs MM (1997) Molecular characterization and promoter analysis of the maize cytosolic glyceraldehyde-3-phosphate dehydrogenase gene family and its expression during anoxia. Plant Mol Biol 33(1):97–112

    Article  CAS  PubMed  Google Scholar 

  • Martin-Laurent F, Franken P, Gianinazzi S (1995) Screening of cDNA fragments generated by differential RNA display. Anal Biochem 228:182–184

    Article  CAS  PubMed  Google Scholar 

  • Martinez-Hernandez A, Lopez-Ochoa L, Arguello-Astorga GR, Herrera-Estrella L (2002) Functional properties and regulatory complexity of a minimal RBCS light responsive unit activated by phytochrome, cryptochrome, and plastid signals. Plant Physiol 128:1223–1233

    Article  CAS  PubMed  Google Scholar 

  • Ni M, Cui D, Einstein J, Narasimhulu S, Vergara Q, Gelvin S (1995) Strength and tissue specificity of chimeric promoters derived from octopine and mannopine synthase genes. Plant J 7:661–676

    Article  CAS  Google Scholar 

  • Odell JT, Nagy F, Chua NH (1985) Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter. Nature 313:810–812

    Article  CAS  PubMed  Google Scholar 

  • Pasquali G, Erven AS, Ouwerkerk PB, Menke FL, Memelink J (1999) The promoter of the strictosidine synthase gene from periwinkle confers elicitoe-inducible expression in transgenic tobacco and binds nuclear factors GT-1 and GBF. Plant Mol Biol 39(6):1299–1310

    Article  CAS  PubMed  Google Scholar 

  • Pastuglia M, Roby D, Dumas C, Cock JM (1997) Rapid induction by wounding and bacterial infection of an S gene family receptor-like kinase gene in Brassica oleracea. Plant Cell 9(1):49–60

    Article  CAS  PubMed  Google Scholar 

  • Prieto-Dapena P, Almoguera C, Rojas A, Jordano J (1999) Seed-specific expression patterns and regulation by ABI3 of an unusual late embryogenesis-abundant gene in sunflower. Plant Mol Biol 39(3):615–627

    Article  CAS  PubMed  Google Scholar 

  • Puente P, Wei N, Deng XW (1996) Combinatorial interplay of promoter elements constitutes the minimal determinants for light and developmental control of gene expression in Arabidopsis. EMBO J 15:3732–3743

    CAS  PubMed  Google Scholar 

  • Robert LS, Thompson RD, Flavell RB (1989) Tissue specific expression of a wheat high molecular weight glutenin gene in transgenic tobacco. Plant Cell 1:569–578

    Article  CAS  PubMed  Google Scholar 

  • Rouster J, Leach R, Mundy J, Cameron-Mills V (1997) Identification of a methyl jasmonate-responsive region in the promoter of a lipoxygenase 1 gene expressed in barley grain. Plant J 11(3):513–523

    Article  CAS  PubMed  Google Scholar 

  • Sambrook J et al (1989) Molecular cloning—a laboratory manual—2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Google Scholar 

  • Sasaki K, Ohare K, Yazazki K (2005) Gene expression characterization of isoperene synthase from Populus alba. FEBS Lett 579:2514–2518

    Article  CAS  PubMed  Google Scholar 

  • Shen Q, TH HO (1995) Functional dissection of an abscisic acid (ABA)-induced gene reveals two independent ABA-responsive complexes each containing a G-box and a novel cis-acting element. Plant Cell 7(3):295–307

    Article  CAS  PubMed  Google Scholar 

  • Shirsat A, Wilford N, Croy R, Boulter D (1989) Sequences responsible for the tissue specific promoter activity of a pea legumin gene in tobacco. Mol Gen Genet 215:326–331

    Article  CAS  PubMed  Google Scholar 

  • Solano R, Nieto C, Avila J, Canas L, Diaz I, Paz-Ares J (1995) Dual DNA binding specificity of a petal epidermis-specific MYB transcription factor (MYB.Ph3) from Petunia hybrida. EMBO J 14(8):1773–1784

    CAS  PubMed  Google Scholar 

  • Stockinger EJ, Gilmour SJ, Thomashow MF (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci USA 94(3):1035–1040

    Article  CAS  PubMed  Google Scholar 

  • Straub PF, Shen Q, Ho TD (1994) Structure and promoter analysis of an ABA- and stress-regulated barley gene, HVA1. Plant Mol Biol 26(2):617–630

    Article  CAS  PubMed  Google Scholar 

  • Thomas MS, Flavell RB (1990) Identification of an enhancer element for the endosperm-specific expression of high molecular weight glutenin. Plant Cell 2:1171–1180

    Article  CAS  PubMed  Google Scholar 

  • Vauterin M, Frankard V, Jacobs M (1999) The Arabidopsis thaliana dhdps gene encoding dihydrodipicolinate synthase, key enzyme of lysine biosynthesis, is expressed in a cell-specific manner. Plant Mol Biol 39(4):695–708

    Article  CAS  PubMed  Google Scholar 

  • Venter M (2007) Synthetic promoters: genetic control through cis engineering. Trends Plant Sci 12:118–124

    Article  CAS  PubMed  Google Scholar 

  • Washida H, Wu CY, Suzuki A, Yamanouchi U, Alkihama T, Harada K, Takaiwa F (1999) Identification of cis-regulatory elements required for endosperm expression of the rice storage protein glutelin gene GluB-1. Plant Mol Biol 40(1):1–12

    Article  CAS  PubMed  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (1994) A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6(2):251–264

    Article  CAS  PubMed  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (2005) Organization of cis-acting regulatory elements in osmotic- and cold-stress responsive promoters. Trends Plant Sci 10:88–94

    Article  CAS  PubMed  Google Scholar 

  • Yin S, Mei L, Newman J et al (1997) Regulation of sesquiterpene cyclase gene expression. Characterization of an elicitor-pathogen-inducible promoter. Plant Physiol 115:437–451

    Article  CAS  PubMed  Google Scholar 

  • Yoshihara T, Washida H, Takaiwa F (1996) A 45-bp proximal region containing AACA and GCN4 motif is sufficient to confer endosperm-specific expression of the rice storage protein glutelin gene, GluA-3. FEBS Lett 383:213–218

    Article  CAS  PubMed  Google Scholar 

  • Zegzouti H, Marty C, Jones B, Bouquin T, Latche A, Pech JC, Bouzayen M (1997) Improved screening of cDNAs generated by mRNA differential display enables the selection of true positives and isolation of weakly expressed messages. Plant Mol Biol Report 15:236–245

    Article  CAS  Google Scholar 

  • Zhang H, Zhang R, Liang P (1996) Differential screening of gene expression difference enriched by differential display. Nucleic Acids Res 24:2454

    Article  CAS  PubMed  Google Scholar 

  • Zhou MY, Xue D, Gomez-Sanchez EP, Gomez-Sanchez CE (1994) Improved downward capillary transfer for blotting of DNA and RNA. Biotechniques 16:58–60

    CAS  Google Scholar 

  • Zhu JK (2002) Salt and drought stress signals transduction in plants. Annu Rev Plant Bio 53:247–273

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Biotechnology, Faculty of Science, Taif University, Taif, Kingdom of Saudi Arabia

    Ahmed M. El-Shehawi

  2. Department of Genetics, Faculty of Agriculture, Alexandria University, Alexandria, Egypt

    Mona M. Elseehy

  3. Department of Biochemistry, Kansas State University, Manhattan, KS, 66506, USA

    Charles Hedgcoth

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  1. Ahmed M. El-Shehawi
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  2. Mona M. Elseehy
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Correspondence to Ahmed M. El-Shehawi.

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El-Shehawi, A.M., Elseehy, M.M. & Hedgcoth, C. Isolation and Sequence Analysis of Wheat Tissue-Specific cDNAs by Differential Display. Plant Mol Biol Rep 29, 135–148 (2011). https://doi.org/10.1007/s11105-010-0213-1

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