Summary
The gene of a cytoplasmic 18 S ribosomal RNA (18 S rDNA) of the dicotyledonous plant tomato (ycopersicon esculentum) cv. Rentita has been cloned, and its complete primary structure has been determined. The tomato 18 S rDNA is 1805 by long with a G+C content of 49.6%. Its sequence exhibits 94%–96% positional identity when it is colinearly aligned with the previously reported sequences of the 17–18 S rDNAs of the dicot soybean and the monocots maize and rice. A model of the secondary structure of the 18 S rRNA of angiosperms is presented and its genera-specific structural features are compared with a current eukaryotic 18 S rRNA consensus model.
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Appels R, Moran LB, Gustafson JP (1986) The structure of DNA from the rye (Secale cereale) NOR R1 locus and its behaviour in wheat backgrounds. Can J Genet Cytol 28:673–685
Barker RF, Harberd NP, Jarvis MG, Flavell RB (1988) Structure and evolution of the intergenic region in a ribosomal DNA repeat unit of wheat. J Mol Biol 201:1–17
Brimacombe R, Maly P, Zwieb C (1983) The structure of ribosomal RNA and its organisation relative to ribosomal protein. Prog Nucleic Acid Res Mol Biol 28:1–48
Chen EY, Seeburg PH (1985) Supercoil sequencing: A fast and simple method for sequencing plasmid DNA. DNA 4:165–170
Connaughton JF, Rairkar A, Lockard RE, Kumar A (1984) Primary structure of rabbit 18 S ribosomal RNA determined by direct RNA sequence analysis. Nucleic Acids Res 12:4731–4745
Dams E, Hendriks L, Van de Peer Y, Neefs J-M, Smits G, Vandenbempt I, De Wachter R (1988) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 16:r87-r173
Delcasso-Tremousaygue D, Grellet F, Panabieres F, Ananiev ED (1988) Structural and transcriptional characterization of the external spacer of a ribosomal RNA nuclear gene from higher plant. Eur J Biochem 172:767–776
Devereux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387–395
Eckenrode VK, Arnold J, Meagher RB (1985) Comparison of the nucleotide sequence of soybean 18 S rRNA with the sequence of other small subunit rRNAs. J Mol Evol 21:259–269
Ganal MW, Lapitan NLV, Tanksley SD (1988) A molecular and cytogenetic survey of major repeated DNA sequences in tomato (Lycopersicon esculentum). Mol Gen Genet 213:262–268
Graham DE (1978) The isolation of high molecular weight DNA from whole organisms or large tissue masses. Anal Biochem 85:609–613
Gutell RR, Weiser B, Woese CR, Noller HF (1985) Comparative anatomy of 16 S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol 32:155–216
Hemleben V, Ganal M, Gerstner J, Schiebel K, Torres RA (1988) Organization and length heterogeneity of plant ribosomal RNA. In: Kahl G (ed) Architecture of eukaryotic genes. VCh, Weinheim, pp 371–383
Hendriks L, Van Broeckhoven C, Vandenberghe A, Van De Peer Y, De Wachter R (1988) Primary and secondary structure of the 18 S ribosomal RNA of the bird spider Eurypelma californica and evolutionary relationships among eukaryotic phyla. Eur J Biochem 177:15–20
Jacobson AB, Good L, Simonetti J, Zuker M (1984) Some simple computational methods to improve the folding of large RNAs. Nucleic Acids Res 12:45–52
McCarroll R, Olsen GJ, Stahl JD, Woese CR, Sogin ML (1983) Nucleotide sequence of the Dictyostelium discoideum small-subunit ribosomal ribonucleic acid inferred from the gene sequence: evolutionary implications. Biochemistry 22:5858–5868
McMullen M, Hunter B, Phillips RL, Rubenstein I (1986) The structure of the maize ribosomal DNA spacer region. Nucleic Acids Res 14:4953–4968
Messing J, Carlson J, Hagen G, Rubenstein I, Oleson A (1984) Cloning and sequencing of the ribosomal RNA genes in maize: The 17 S region. DNA 3:31–40
Nairn CJ, Ferl RJ (1988) The complete nucleotide sequence of the small-subunit ribosomal RNA coding region for the cycad Zamia pumila: phylogenetic implications. J Mol Evol 27:133–141
Nelles L, Fang B-L, Volkaert G, Vandenberghe A, De Wachter R (1984) Nucleotide sequence of a crustacean 18 S ribosomal RNA gene and the secondary structure of eukaryotic small subunit RNAs. Nucleic Acids Res 12:8749–8768
Noller HF (1984) Structure of ribosomal RNA. Annu Rev Biochem 53:119–162
Noller HF, Woese CR (1981) Secondary structure of 16 S ribosomal RNA. Science 212:403–411
Olsen GJ, McCarroll R, Sogin ML (1983) Secondary structure of the Dictyostelium discoideum small subunit ribosomal RNA. Nucleic Acids Res 11:8037–8049
Raué HA, Klootwijk J, Musters W (1988) Evolutionary conservation of structure and function of high molecular weight ribosomal RNA. Prog Biophys Mol Biol 51:77–129
Raynal F, Michot B, Bachellerie JP (1984) Complete nucleotide sequence of mouse 18 S rRNA gene: comparison with other available homologs. FEBS Lett 167:263–268
Reeck GR, de Haen C, Teller DC, Doolittle RF, Fitch WM, Dickerson RE, Chambon P, McLachlan AD, Margoliash E, Jukes TH, Zuckerkandl E (1987) “Homology” in proteins and nucleic acids: A terminology muddle and a way out of it. Cell 50:667
Rogers SO, Bendich AJ (1987) Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol Biol 9:509–520
Rubtsov PM, Musakhanov MM, Zakharyev VM, Krayec AS, Skryabin KG, Bayev AA (1980) The structure of the yeast ribosomal RNA genes: I. The complete nucleotide sequence of the 18 S ribosomal RNA gene in Saccharomyces cerevisiae. Nucleic Acids Res 8:5779–5794
Salim M, Maden BEH (1981) Nucleotide sequence of Xenopus laevis 18 S ribosomal RNA inferred from gene sequence. Nature 291:205–208
Takaiwa F, Oono K, Sugiura M (1984) The complete nucleotide sequence of a rice 17 S rRNA gene. Nucleic Acids Res 12:5441–5448
Toloczyki C, Feix G (1986) Occurrence of 9 homologous repeat units in the external spacer region of a nuclear maize rRNA gene unit. Nucleic Acids Res 14:4969–4986
Torczynski RM, Bollon AP, Fuke M (1983) The complete nucleotide sequence of the rat 18 S ribosomal RNA gene and comparison with the respective yeast and frog genes. Nucleic Acids Res 11:4879–4890
Torczynski RM, Fuke M, Bollon AP (1985) Cloning and sequencing of the human 18 S ribosomal RNA gene. DNA 4:283–291
Turner DH, Sugimoto N, Jaeger JA, Longfellow CE, Freier SM, Kierzek R (1987) Improved parameters for prediction of RNA structure. Cold Spring Harbor Symp Quant Biol 52:123–133
Vallejos CE, Tanksley SD, Bernatzky R (1986) Localization in the tomato genome of DNA restriction fragments containing sequences homologous to the rRNA (45S), the major chlorophyll a/b binding polypeptide and the ribulose bisphosphate carboxylase genes. Genetics 112:93–105
Woese CR, Magrum LJ, Gupta R, Siegel RB, Stahl DA, Kop J, Crawford N, Brosius J, Gutell R, Hogan JJ, Noller HIT (1980) Secondary structure model for bacterial 16 S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res 8:2275–2293
Woese CR, Gutell RR, Gupta R, Noller HF (1983) Detailed analysis of the higher-order structure of 16 S-like ribosomal ribonucleic acids. Microbiol Rev 47:621–669
Zwieb C, Glotz C, Brimacombe R (1981) Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species. Nucleic Acids Res 3621–3640
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Schmidt-Puchta, W., Kütemeier, G., Günther, I. et al. Cloning and sequence analysis of the 18 S ribosomal RNA gene of tomato and a secondary structure model for the 18 S rRNA of angiosperms. Molec. Gen. Genet. 219, 17–25 (1989). https://doi.org/10.1007/BF00261152
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DOI: https://doi.org/10.1007/BF00261152