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Nucleic Acids Res. Aug 25, 1987; 15(16): 6643–6653.
PMCID: PMC306128

An inspection of the domain between putative TATA box and translation start site in 79 plant genes.

Abstract

Over 75 published genomic DNA sequences from several higher plants have been collected and flanking regions of the leader sequences have been analysed. In a majority of the plants, the first AUG codon on processed mRNA acted as a translation initiation site. The consensus sequence for the context was TAAACAATGGCT (on plus strand of DNA). This differed from the earlier suggestion for eukaryotic mRNAs based mainly on data from animals. Leader sequences were generally 40-80 nucleotides in length and were A+T rich. Adenine was present in a majority of the cases at the transcription start site which was flanked by pyrimidine bases. The putative TATA box was present 32 +/- 7 nucleotides upstream from the transcription initiation site. The consensus sequence for TATA box and surrounding region was TCACTATATATAG.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Herrera-Estrella L, Van den Broeck G, Maenhaut R, Van Montagu M, Schell J, Timko M, Cashmore A. Light-inducible and chloroplast-associated expression of a chimaeric gene introduced into Nicotiana tabacum using a Ti plasmid vector. Nature. 1984 Jul 12;310(5973):115–120. [PubMed]
  • Fluhr Robert, Moses Phyllis, Morelli Giorgio, Coruzzi Gloria, Chua Nam-Hai. Expression dynamics of the pea rbcS multigene family and organ distribution of the transcripts. EMBO J. 1986 Sep;5(9):2063–2071. [PMC free article] [PubMed]
  • Coruzzi G, Broglie R, Edwards C, Chua NH. Tissue-specific and light-regulated expression of a pea nuclear gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase. EMBO J. 1984 Aug;3(8):1671–1679. [PMC free article] [PubMed]
  • Berry-Lowe SL, Mc Knight TD, Shah DM, Meagher RB. The nucleotide sequence, expression, and evolution of one member of a multigene family encoding the small subunit of ribulose-1,5-bisphosphate carboxylase in soybean. J Mol Appl Genet. 1982;1(6):483–498. [PubMed]
  • Mazur BJ, Chui CF. Sequence of a genomic DNA clone for the small subunit of ribulose bis-phosphate carboxylase-oxygenase from tobacco. Nucleic Acids Res. 1985 Apr 11;13(7):2373–2386. [PMC free article] [PubMed]
  • Tumer NE, Clark WG, Tabor GJ, Hironaka CM, Fraley RT, Shah DM. The genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase are expressed differentially in petunia leaves. Nucleic Acids Res. 1986 Apr 25;14(8):3325–3342. [PMC free article] [PubMed]
  • Dean C, Elzen P, Tamaki S, Dunsmuir P, Bedbrook J. Differential expression of the eight genes of the petunia ribulose bisphosphate carboxylase small subunit multi-gene family. EMBO J. 1985 Dec 1;4(12):3055–3061. [PMC free article] [PubMed]
  • Cashmore AR. Structure and expression of a pea nuclear gene encoding a chlorophyll a/b-binding polypeptide. Proc Natl Acad Sci U S A. 1984 May;81(10):2960–2964. [PMC free article] [PubMed]
  • Leutwiler LS, Meyerowitz EM, Tobin EM. Structure and expression of three light-harvesting chlorophyll a/b-binding protein genes in Arabidopsis thaliana. Nucleic Acids Res. 1986 May 27;14(10):4051–4064. [PMC free article] [PubMed]
  • Dunsmuir P. The petunia chlorophyll a/b binding protein genes: a comparison of Cab genes from different gene families. Nucleic Acids Res. 1985 Apr 11;13(7):2503–2518. [PMC free article] [PubMed]
  • Stayton MM, Black M, Bedbrook J, Dunsmuir P. A novel chlorophyll a/b binding (Cab) protein gene from petunia which encodes the lower molecular weight Cab precursor protein. Nucleic Acids Res. 1986 Dec 22;14(24):9781–9796. [PMC free article] [PubMed]
  • Rafalski JA, Scheets K, Metzler M, Peterson DM, Hedgcoth C, Söll DG. Developmentally regulated plant genes: the nucleotide sequence of a wheat gliadin genomic clone. EMBO J. 1984 Jun;3(6):1409–1415. [PMC free article] [PubMed]
  • Sumner-Smith M, Rafalski JA, Sugiyama T, Stoll M, Söll D. Conservation and variability of wheat alpha/beta-gliadin genes. Nucleic Acids Res. 1985 Jun 11;13(11):3905–3916. [PMC free article] [PubMed]
  • Anderson OD, Litts JC, Gautier MF, Greene FC. Nucleic acid sequence and chromosome assignment of a wheat storage protein gene. Nucleic Acids Res. 1984 Nov 12;12(21):8129–8144. [PMC free article] [PubMed]
  • Forde J, Malpica JM, Halford NG, Shewry PR, Anderson OD, Greene FC, Miflin BJ. The nucleotide sequence of a HMW glutenin subunit gene located on chromosome 1A of wheat (Triticum aestivum L.). Nucleic Acids Res. 1985 Oct 11;13(19):6817–6832. [PMC free article] [PubMed]
  • Thompson RD, Bartels D, Harberd NP. Nucleotide sequence of a gene from chromosome 1D of wheat encoding a HMW-glutenin subunit. Nucleic Acids Res. 1985 Oct 11;13(19):6833–6846. [PMC free article] [PubMed]
  • Forde BG, Heyworth A, Pywell J, Kreis M. Nucleotide sequence of a B1 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat and maize. Nucleic Acids Res. 1985 Oct 25;13(20):7327–7339. [PMC free article] [PubMed]
  • Hu NT, Peifer MA, Heidecker G, Messing J, Rubenstein I. Primary structure of a genomic zein sequence of maize. EMBO J. 1982;1(11):1337–1342. [PMC free article] [PubMed]
  • Pedersen K, Devereux J, Wilson DR, Sheldon E, Larkins BA. Cloning and sequence analysis reveal structural variation among related zein genes in maize. Cell. 1982 Jul;29(3):1015–1026. [PubMed]
  • Spena A, Viotti A, Pirrotta V. A homologous repetitive block structure underlies the heterogeneity of heavy and light chain zein genes. EMBO J. 1982;1(12):1589–1594. [PMC free article] [PubMed]
  • Langridge P, Feix G. A zein gene of maize is transcribed from two widely separated promoter regions. Cell. 1983 Oct;34(3):1015–1022. [PubMed]
  • Slightom JL, Sun SM, Hall TC. Complete nucleotide sequence of a French bean storage protein gene: Phaseolin. Proc Natl Acad Sci U S A. 1983 Apr;80(7):1897–1901. [PMC free article] [PubMed]
  • Lycett GW, Croy RR, Shirsat AH, Richards DM, Boulter D. The 5'-flanking regions of three pea legumin genes: comparison of the DNA sequences. Nucleic Acids Res. 1985 Sep 25;13(18):6733–6743. [PMC free article] [PubMed]
  • Bäumlein H, Wobus U, Pustell J, Kafatos FC. The legumin gene family: structure of a B type gene of Vicia faba and a possible legumin gene specific regulatory element. Nucleic Acids Res. 1986 Mar 25;14(6):2707–2720. [PMC free article] [PubMed]
  • Bevan M, Barker R, Goldsbrough A, Jarvis M, Kavanagh T, Iturriaga G. The structure and transcription start site of a major potato tuber protein gene. Nucleic Acids Res. 1986 Jun 11;14(11):4625–4638. [PMC free article] [PubMed]
  • Shah DM, Hightower RC, Meagher RB. Genes encoding actin in higher plants: intron positions are highly conserved but the coding sequences are not. J Mol Appl Genet. 1983;2(1):111–126. [PubMed]
  • Shah DM, Hightower RC, Meagher RB. Complete nucleotide sequence of a soybean actin gene. Proc Natl Acad Sci U S A. 1982 Feb;79(4):1022–1026. [PMC free article] [PubMed]
  • Vodkin LO, Rhodes PR, Goldberg RB. cA lectin gene insertion has the structural features of a transposable element. Cell. 1983 Oct;34(3):1023–1031. [PubMed]
  • King EB, Vanderlaan M, Jensen RH, Kromhout LK, Hoffman JW. Morphologic changes in rat urothelial cells during carcinogenesis: I. Histologic and cytologic changes. Cytometry. 1984 Sep;5(5):447–453. [PubMed]
  • Halling KC, Halling AC, Murray EE, Ladin BF, Houston LL, Weaver RF. Genomic cloning and characterization of a ricin gene from Ricinus communis. Nucleic Acids Res. 1985 Nov 25;13(22):8019–8033. [PMC free article] [PubMed]
  • Hoffman LM, Donaldson DD. Characterization of two Phaseolus vulgaris phytohemagglutinin genes closely linked on the chromosome. EMBO J. 1985 Apr;4(4):883–889. [PMC free article] [PubMed]
  • Hyldig-Nielsen JJ, Jensen EO, Paludan K, Wiborg O, Garrett R, Jørgensen P, Marcker KA. The primary structures of two leghemoglobin genes from soybean. Nucleic Acids Res. 1982 Jan 22;10(2):689–701. [PMC free article] [PubMed]
  • Wiborg O, Hyldig-Nielsen JJ, Jensen EO, Paludan K, Marcker KA. The nucleotide sequences of two leghemoglobin genes from soybean. Nucleic Acids Res. 1982 Jun 11;10(11):3487–3494. [PMC free article] [PubMed]
  • Brisson N, Verma DP. Soybean leghemoglobin gene family: normal, pseudo, and truncated genes. Proc Natl Acad Sci U S A. 1982 Jul;79(13):4055–4059. [PMC free article] [PubMed]
  • Lee JS, Verma DP. Structure and chromosomal arrangement of leghemoglobin genes in kidney bean suggest divergence in soybean leghemoglobin gene loci following tetraploidization. EMBO J. 1984 Dec 1;3(12):2745–2752. [PMC free article] [PubMed]
  • Mauro VP, Nguyen T, Katinakis P, Verma DP. Primary structure of the soybean nodulin-23 gene and potential regulatory elements in the 5'-flanking regions of nodulin and leghemoglobin genes. Nucleic Acids Res. 1985 Jan 11;13(1):239–249. [PMC free article] [PubMed]
  • Katinakis P, Verma DP. Nodulin-24 gene of soybean codes for a peptide of the peribacteroid membrane and was generated by tandem duplication of a sequence resembling an insertion element. Proc Natl Acad Sci U S A. 1985 Jun;82(12):4157–4161. [PMC free article] [PubMed]
  • Nguyen T, Zelechowska M, Foster V, Bergmann H, Verma DP. Primary structure of the soybean nodulin-35 gene encoding uricase II localized in the peroxisomes of uninfected cells of nodules. Proc Natl Acad Sci U S A. 1985 Aug;82(15):5040–5044. [PMC free article] [PubMed]
  • Schöffl F, Raschke E, Nagao RT. The DNA sequence analysis of soybean heat-shock genes and identification of possible regulatory promoter elements. EMBO J. 1984 Nov;3(11):2491–2497. [PMC free article] [PubMed]
  • Czarnecka E, Gurley WB, Nagao RT, Mosquera LA, Key JL. DNA sequence and transcript mapping of a soybean gene encoding a small heat shock protein. Proc Natl Acad Sci U S A. 1985 Jun;82(11):3726–3730. [PMC free article] [PubMed]
  • Dennis ES, Sachs MM, Gerlach WL, Finnegan EJ, Peacock WJ. Molecular analysis of the alcohol dehydrogenase 2 (Adh2) gene of maize. Nucleic Acids Res. 1985 Feb 11;13(3):727–743. [PMC free article] [PubMed]
  • Chang C, Meyerowitz EM. Molecular cloning and DNA sequence of the Arabidopsis thaliana alcohol dehydrogenase gene. Proc Natl Acad Sci U S A. 1986 Mar;83(5):1408–1412. [PMC free article] [PubMed]
  • Werr W, Frommer WB, Maas C, Starlinger P. Structure of the sucrose synthase gene on chromosome 9 of Zea mays L. EMBO J. 1985 Jun;4(6):1373–1380. [PMC free article] [PubMed]
  • Marchionni M, Gilbert W. The triosephosphate isomerase gene from maize: introns antedate the plant-animal divergence. Cell. 1986 Jul 4;46(1):133–141. [PubMed]
  • Boutry M, Chua NH. A nuclear gene encoding the beta subunit of the mitochondrial ATP synthase in Nicotiana plumbaginifolia. EMBO J. 1985 Sep;4(9):2159–2165. [PMC free article] [PubMed]
  • Keil M, Sanchez-Serrano J, Schell J, Willmitzer L. Primary structure of a proteinase inhibitor II gene from potato (Solanum tuberosum). Nucleic Acids Res. 1986 Jul 25;14(14):5641–5650. [PMC free article] [PubMed]
  • Chen J, Varner JE. An extracellular matrix protein in plants: characterization of a genomic clone for carrot extensin. EMBO J. 1985 Sep;4(9):2145–2151. [PMC free article] [PubMed]
  • Kozak M. Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs. Nucleic Acids Res. 1984 Jan 25;12(2):857–872. [PMC free article] [PubMed]
  • Kozak M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell. 1986 Jan 31;44(2):283–292. [PubMed]
  • Kozak M. Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in vivo. Nature. 1984 Mar 15;308(5956):241–246. [PubMed]
  • Breathnach R, Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem. 1981;50:349–383. [PubMed]
  • Lütcke HA, Chow KC, Mickel FS, Moss KA, Kern HF, Scheele GA. Selection of AUG initiation codons differs in plants and animals. EMBO J. 1987 Jan;6(1):43–48. [PMC free article] [PubMed]
  • Kozak M. Influences of mRNA secondary structure on initiation by eukaryotic ribosomes. Proc Natl Acad Sci U S A. 1986 May;83(9):2850–2854. [PMC free article] [PubMed]
  • Timko MP, Kausch AP, Castresana C, Fassler J, Herrera-Estrella L, Van den Broeck G, Van Montagu M, Schell J, Cashmore AR. Light regulation of plant gene expression by an upstream enhancer-like element. Nature. 1985 Dec 12;318(6046):579–582. [PubMed]
  • Chen ZL, Schuler MA, Beachy RN. Functional analysis of regulatory elements in a plant embryo-specific gene. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8560–8564. [PMC free article] [PubMed]
  • Chen MJ, Shimada T, Moulton AD, Cline A, Humphries RK, Maizel J, Nienhuis AW. The functional human dihydrofolate reductase gene. J Biol Chem. 1984 Mar 25;259(6):3933–3943. [PubMed]
  • Kwoh TJ, Engler JA. The nucleotide sequence of the chicken thymidine kinase gene and the relationship of its predicted polypeptide to that of the vaccinia virus thymidine kinase. Nucleic Acids Res. 1984 May 11;12(9):3959–3971. [PMC free article] [PubMed]
  • Keith B, Chua NH. Monocot and dicot pre-mRNAs are processed with different efficiencies in transgenic tobacco. EMBO J. 1986 Oct;5(10):2419–2425. [PMC free article] [PubMed]

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