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RNA Sequences

  • T. A. Dyer
Part of the Encyclopedia of Plant Physiology book series (PLANT, volume 14 / B)

Abstract

All RNA molecules have a primary structure which consists of a backbone of alternating ribose and phosphate residues with a purine (guanine or adenine) or pyrimidine (uracil or cytosine) base attached to each ribose (Fig. 1). Although these four bases (abbreviated as G, A, U and C respectively) predominate, some bases may be modified in the formation of the mature molecule. Also there is 2’-O-methylation of a few ribose residues. A comprehensive list of the structures of these modified residues and of the symbols used to denote them has been published (Dunn and Hall 1975).

Keywords

Euglena Gracilis Initiator tRNA Yeast tRNAPhe Prokaryotic Nature Cytosolic mRNA 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Abbreviations

tRNAiMet

initiator tRNA

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References

  1. Almalric F, Merkel C, Gefland R, Attardi G (1978) Fractionation of mitochondrial RNA from HeLa cells by high-resolution electrophoresis under strongly denaturing conditions. J Mol Biol 118: 1–25CrossRefGoogle Scholar
  2. Bartolf M, Price CA (1979) Synthesis of poly(A)-containing RNA by isolated spinach chloroplasts. Biochemistry 18: 1677–1680PubMedCrossRefGoogle Scholar
  3. Bedbrook JR, Smith SM, Ellis RJ (1980) Molecular cloning and sequencing of cDNA encoding the precursor to the small subunit of the chloroplast enzyme ribulose-1,5-bisphosphate carboxylase. Nature (London) 287: 692–697CrossRefGoogle Scholar
  4. Blobel G, Dobberstein B (1975) Transfer of proteins across membranes 1. Presence of proteolytically processed and unprocessed nascent Immunoglobulin light chains on membrane-bound ribosomes of murine myeloma. J Cell Biol 67: 835–851Google Scholar
  5. Bönen L, Doolittle WF (1975) On the prokaryotic nature of red algal chloroplasts. Proc Natl Acad Sci USA 72: 2310–2314PubMedCrossRefGoogle Scholar
  6. Bönen L, Doolittle WF (1976) Partial sequences of 16S RNA and the phylogeny of blue-green algae and chloroplasts. Nature (London) 261: 669–673CrossRefGoogle Scholar
  7. Bönen L, Cunningham RS, Gray MW, Doolittle WF (1977) Wheat embryo mitochondrial 18S ribosomal RNA: evidence for its prokaryotic nature. Nucl Acids Res 4: 663–671PubMedCrossRefGoogle Scholar
  8. Brosius J, Palmer ML, Kennedy PJ, Noller HF (1978) Complete nucleotide sequence of a 16S ribosomal gene from Escherichia coli. Proc Natl Acad Sci USA 75: 4801–4805PubMedCrossRefGoogle Scholar
  9. Burr B, Burr FA, Rubenstein I, Simon MN (1978) Puriflcation and translation of zein messenger RNA from maize endosperm protein bodies. Proc Natl Acad Sci USA 75: 696–700PubMedCrossRefGoogle Scholar
  10. Burrows WJ (1975) Mechanisms of action of cytokinins. Curr Adv Plant Sci 7: 837–847Google Scholar
  11. Calagan JL, Pirtle RM, Pirtle IL, Kashdan MA, Vreman HJ, Dudock BS (1980) Homology between chloroplast and prokaryotic initiator tRNA. Nucleotide sequence of spinach chloroplast methionine initiator tRNA. J Biol Chem 255: 9981–9984Google Scholar
  12. Canaday J, Guillemaut P, Gloeckler R, Weil JH (1981) The nucleotide sequence of spinach chloroplast tryptophan transfer RNA. Nucl Acids Res 9: 47–53PubMedCrossRefGoogle Scholar
  13. Carbon P, Ehresmann C, Ehresmann B, Ebel JP (1978) The sequence of Escherichiacoli ribosomal 16S RNA determined by new rapid gel sequencing methods. FEBS Lett 94: 152–156PubMedCrossRefGoogle Scholar
  14. Chang SH, Hecker M, Silberklang M, Brum CK, Barnett WE, RajBhandary UL (1976) The first nucleotide sequence of an organeile transfer RNA: Chloroplastic tRNAphe. Cell 9: 717–724PubMedCrossRefGoogle Scholar
  15. Chang SH, Brum CK, Schnabel JJ, Heckman JH, RajBhandary UL (1978) Similarities in nucleotide sequence between Euglena gracilis and mammalian cytoplasmic Phenylalanine tRNAs. Fed Proc 37: 1768Google Scholar
  16. Cunningham RS, Bönen L, Doolittle WF, Gray MW (1976) Unique species of 5S, 18S and 26S ribosomal RNA in wheat mitochondria. FEBS Lett 69: 116–122PubMedCrossRefGoogle Scholar
  17. Darzynkiewicz E, Nakashima K, Shatkin AJ (1980) Base pairing in the conserved 3’end of 18S rRNA as determined by psoralen photoreaction and RNase sensitivity. J Biol Chem 255: 4973–4975PubMedGoogle Scholar
  18. Delihas N, Andersen J, Sprouse HM, Kashdan M, Dudock BS (1981) The nucleotide sequence of spinach cytoplasmic 5S RNA. J Biol Chem 256: 7515–7517PubMedGoogle Scholar
  19. Driesel AJ, Crouse EJ, Gordon K, Bohnert HJ, Herrmann RG, Steinmetz A, Mubumbila M, Keller M, Burkard G, Weil JH (1979) Fractionation and identification of spinach chloroplast transfer RNAs and mapping of their genes on the restriction map of chloroplast DNA. Gene 6: 285–306PubMedCrossRefGoogle Scholar
  20. Dudock BS, Katz G (1969) Large oligonucleotide sequences in wheat germ Phenylalanine transfer ribonucleic acid. Derivation of total primary structure. J Biol Chem 244: 3069–3074Google Scholar
  21. Dunn DB, Hall RH (1975) Purines, pyrimidines, nucleosides and nucleotides: physical constants and spectral properties. In: Fasman GD (ed) Handbook of biochemistry and molecular biology Vol I. CRC Press, Cleveland, pp 65–215Google Scholar
  22. Dyer TA, Bowman CM (1979) Nucleotide sequences of chloroplast 5S ribosomal ribonucleic acid in flowering plants. Biochem J 183: 595–604PubMedGoogle Scholar
  23. Dyer TA, Leech RM (1968) Chloroplast and cytoplasmic low-molecular-weight ribonucleic acid components of the leaf of Vicia faba L. Biochem J 106: 689–698PubMedGoogle Scholar
  24. Dyer TA, Zalik S (1979) Analysis of a 5S RNA-protein complex isolated from ribosomes of rye embryos. Can J Biochem 57: 1400–1406PubMedCrossRefGoogle Scholar
  25. Dyer TA, Bowman CM, Payne PI (1977) The low-molecular-weight RNAs of plant ribosomes: their structure, funetion and evolution. In: Bogorad L, Weil JH (eds) Nucleic acids and protein synthesis in plants. Plenum, New York, pp 121–133Google Scholar
  26. Eperon IC, Anderson S, Nierlich DP (1980) Distinctive sequence of human mitochondrial ribosomal RNA genes. Nature (London) 286: 460–466CrossRefGoogle Scholar
  27. Erdmann VA (1981) Collection of published 5S and 5.8S RNA sequences and their precursors. Nucl Acids Res 9: r25–r42PubMedCrossRefGoogle Scholar
  28. Everett GA, Madison JT (1976) Nucleotide sequence of Phenylalanine transfer ribonucleic acid from pea (Pisum sativum, Alaska ). Biochemistry 15: 1016–1021Google Scholar
  29. Filipowitz W (1978) Function of the S’-terminal m7G cap in eukaryotic mRNA. FEBS Lett 96: 1–11CrossRefGoogle Scholar
  30. Gauss DH, Sprinzl M (1981) Compilation of tRNA sequences. Nucl Acids Res 9:rl–r23Google Scholar
  31. Guillemaut P, Keith G (1977) Primary structure on bean chloroplastic tRNAPhe. Comparison with Euglena chloroplastic tRNAphe. FEBS Lett 84: 351–356PubMedCrossRefGoogle Scholar
  32. Hagenbüchle O, Santer M, Steitz JA, Mans RJ (1978) Conservation of the primary structure at the 3’ end of 18S rRNA from eukaryotic cells. Cell 13: 551–563PubMedCrossRefGoogle Scholar
  33. Hall BD (1979) Mitochondria spring surprises. Nature (London) 282: 129–130CrossRefGoogle Scholar
  34. Hartley MR (1979) The synthesis and origin of chloroplast low molecular weight ribosomal ribonucleic acid in spinach. Eur J Biochem 96: 311–320PubMedCrossRefGoogle Scholar
  35. Haugland RA, Cline MG (1978) Capping structures at the 5/-terminus of polyadenylated ribonucleic acid in Avena coleoptiles. Plant Physiol 62: 838–840PubMedCrossRefGoogle Scholar
  36. Heckman JE, Alzner-Deweerd B, RajBhandary UL (1979) Interesting and unusual features in the sequence of Neurospora crassa mitochondrial tyrosine transfer RNA. Proc Natl Acad Sci USA 76: 717–721PubMedCrossRefGoogle Scholar
  37. Higgins TJV, Spencer D (1980) Biosynthesis of pea seed proteins: evidence for precursor forms from in vivo and in vitro studies. In: Leaver CJ ( 1980 ) Genome Organization and expression in plants. Plenum, New York, pp 245–258Google Scholar
  38. Janowicz Z, Wower JM, Augustyniak J (1979) Primary structure of barley embryo tRNAPhe and its identity with wheat germ tRNAPhe. Plant Sei Lett 14: 177–183CrossRefGoogle Scholar
  39. Jordan BR, Galling G, Jourdan R (1974) Sequence and conformation of 5S RNA from Chlorella cytoplasmic ribosomes: comparison with other 5S RNA molecules. J Mol Biol 87: 205–225PubMedCrossRefGoogle Scholar
  40. Jukes TH (1977) How many anticodons? Science 198: 319–320PubMedCrossRefGoogle Scholar
  41. Kashdan MA, Pirtle RM, Pirtle IL, Calagan JL, Vreman HJ, Dudock BS (1980) Nucleotide sequence of a spinach chloroplast threonine tRNA. J Biol Chem 255: 8831–8835Google Scholar
  42. Kurland CG (1960) Molecular characterization of ribonucleic acid from Escherichia coli ribosomes. I. Isolation and molecular weight. J Mol Biol 2: 83–91CrossRefGoogle Scholar
  43. Lagerkvist U (1978) “Two out of three”: an alternative method for codon reading. Proc Natl Acad Sci USA 75:1759–1762Google Scholar
  44. Larkins BA, Hurkman WJ (1978) Synthesis and deposition of zein in protein bodies of maize endosperm. Plant Physiol 62: 256–263PubMedCrossRefGoogle Scholar
  45. Leaver CJ (1975) The biogenesis of plant mitochondria, In: Harborne JB, van Sumere CF (eds) The chemistry and biochemistry of plant proteins. Academic Press, London New York, pp 137–166Google Scholar
  46. Leaver CJ, Harmey MA (1976) Higher-plant mitochondria contain a 5S ribosomal ribonucleic acid component. Biochem J 157: 275–277PubMedGoogle Scholar
  47. Loening UE (1968) Molecular weight of ribosomal RNA in relation to evolution. J Mol Biol 38: 355–365PubMedCrossRefGoogle Scholar
  48. Loening UE, Ingle J (1967) Diversity of RNA components in green plant tissues. Nature (London) 215: 363–367CrossRefGoogle Scholar
  49. Luoma GA, Marshall AG (1978) Laser Raman evidence for new cloverleaf secondary structures for eukaryotic 5.8S RNA and prokaryotic 5S RNA. Proc Natl Acad Sci USA 75: 4901–4905PubMedCrossRefGoogle Scholar
  50. Mackay RM (1981) The origin of plant chloroplast 4.5S ribsosomal RNA. FEBS Lett 123: 17–18CrossRefGoogle Scholar
  51. Mackay RM, Spencer DF, Doolittle WF, Gray WM (1980) Nucleotide sequences of wheat embryo cytosol 5S and 5.8S ribosomal ribonucleic acids. Eur J Biochem 112: 561–576PubMedCrossRefGoogle Scholar
  52. Marcu KB, Mignery RE, Dudock B (1977) Complete nucleotide sequence and properties of the major species of glycine transfer RNA from wheat germ. Biochemistry 16: 797–806PubMedCrossRefGoogle Scholar
  53. Marcu K, Marcu D, Dudock B (1978) Wheat germ rRNAs containing uridine in place of ribothymidine: a characterization of an unusual class of eukaryotic tRNAs. Nucl Acids Res 5: 1075–1092PubMedCrossRefGoogle Scholar
  54. Moorman AFM, Van Ommen GJB, Grivell LA (1978) Transcription in yeast mitochondria: isolation and physical mapping of messenger RNAs for subunits of cytochrome C oxidase and ATPase. Mol Gen Genet 160: 13–24PubMedGoogle Scholar
  55. Nichols JL (1979) N6-methyladenosine in maize poly(A)-containing RNA. Plant Sci Lett 15: 357–361CrossRefGoogle Scholar
  56. Olins PO, Jones DS (1980) Nucleotide sequence of Scenedesmus obliquus cytoplasmic initiator tRNA. Nucl Acids Res 8: 715–729PubMedGoogle Scholar
  57. Osorio-Almeida ML, Guillemaut P, Keith G, Canaday J, Weil JH (1980) Primary structure of three leucine transfer RNAs from bean chloroplast. Biochem Biophys Res Commun 92: 102–108PubMedCrossRefGoogle Scholar
  58. Payne PI, Dyer TA (1971) Characterization of cytoplasmic and chloroplast 5S ribosomal ribonucleic acid from broad-bean leaves. Biochem J 124: 83–89PubMedGoogle Scholar
  59. Payne PI, Dyer TA (1972) Plant 5.8S RNA is a components of 80S but not 70S ribosomes. Nature New Biology 235: 145–147PubMedGoogle Scholar
  60. Payne PI, Dyer TA (1976) Evidence for the sequence of 5-S rRNA from the flowering plant Seeale eereale ( Rye ). Eur J Biochem 71: 33–38Google Scholar
  61. Phillips DO, Carr NG (1977) Nucleic acid analysis and the endosymbiont hypothesis. Taxon 26: 3–42CrossRefGoogle Scholar
  62. Pirtle RM, Pirtle IL, Kashdan MA, Vreman HJ, Dudock BS (1981) The nucleotide sequence of spinach chloroplast methionine elongator tRNA. Nucl Acids Res 9: 183–188PubMedCrossRefGoogle Scholar
  63. Pring DR (1974) Maize mitochondria: puriflcation and characterization of ribosomes and ribosomal ribonucleic acid. Plant Physiol 53: 677–683PubMedCrossRefGoogle Scholar
  64. Rafalski AJ, Barciszewski J, Gulewicz K, Twardowski T, Keith G (1977) Nucleotide sequence of tRNAphe from the seeds of lupin (Lupinus luteus). Comparison of the major species with wheat germ tRNA Phe. Acta Biochem Pol 24: 301–318Google Scholar
  65. Rieh A, Kim SH (1978) The three dimensional structure of transfer RNA. Sci Am 238: 52–62Google Scholar
  66. Rochaix JD, Malnoe P (1978) Anatomy of the chloroplast ribosomal DNA of Chlamydomonasreinhardii. Cell 15: 661–670PubMedCrossRefGoogle Scholar
  67. Rosenberg M, Patterson BM (1979) Efficient cap-dependent translation of polycistronic prokaryotic mRNAs is restricted to the first gene of the operon. Nature (London) 279: 696–701CrossRefGoogle Scholar
  68. Saini MS, Lane BG (1977) Wheat embryo ribonucleates VIII The presence of 7-methylguanosine ’cap structures’ in the RNA of imbibing wheat embryos. Can J Biochem 55: 819–824PubMedCrossRefGoogle Scholar
  69. Sano H, Spaeth E, Burton WG (1979) Messenger RNA of the large subunit of ribulose-1,5-bisphosphate carboxylase from Chlamydomonas reinhardii. Eur J Biochem 93: 173–180PubMedCrossRefGoogle Scholar
  70. Schwarz Zs, Kössel H (1980) The primary structure of 16S rDNA from Zea mays chloroplasts is homologous to E coli 16S rRNA. Nature (London) 283: 739–742CrossRefGoogle Scholar
  71. Shatkin AJ (1976) Capping of eukaryotic mRNAs. Cell 9: 645–653PubMedCrossRefGoogle Scholar
  72. Shine J, Dalgarno L (1974) The 3/-terminal sequence of Escherichia coli 16S ribosomal RNA: complementary to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 71: 1342–1346PubMedCrossRefGoogle Scholar
  73. Smith SM, Ellis RJ (1979) Processing of small subunit precursor of ribulose bisphosphate carboxylase and its assembly into whole enzyme are stromal events. Nature (London) 278: 662–664CrossRefGoogle Scholar
  74. Steiner DF (1979) Processing of protein precursors. Nature (London) 279: 674–675CrossRefGoogle Scholar
  75. Sun SM, Slightom JL, Hall TC (1981) Intervening sequences in a plant gene–comparison of the partial sequence of cDNA and genomic DNA of French bean phaseolin. Nature (London) 289: 37–41CrossRefGoogle Scholar
  76. Tanaka Y, Dyer TA, Brownlee GG (1980) An improved direct RNA sequence method; its application to Vicia faba 5.8S ribosomal RNA. Nucl Acids Res 86: 1259–1272CrossRefGoogle Scholar
  77. Van Holde KE, Hill WE (1974) General physical properties of ribosomes. In: Nomura M, Tissieres A, Lengyel P (eds) Ribosomes. Cold Spring Harbor Lab, New York, pp 53–91Google Scholar
  78. Verdier G (1979 a) Poly(adenylic acid)-containing RNA of Euglena gracilis during chloroplast development. I Analysis of their complexity by hybridisation to complementary DNA. Eur J Biochem 93:573–580Google Scholar
  79. Verdier G (1979 b) Poly(adenylic acid)-containing RNA of Euglena gracilis during chloroplast development. 2 Transcriptional origin of the different RNA. Eur J Biochem 93:581–586Google Scholar
  80. Weil JH (1979) Cytoplasmic and organellar tRNAs in plants. In: Hall TC, Davies J (eds) Nucleic acids in plants Vol I. CRC Press, Boca Raton, pp 143–192Google Scholar
  81. Weinand U, Feix G (1978) Electrophoretic fractionation and translation in vitro of poly(rA)-containing RNA from maize endosperm. Eur J Biochem 92: 605–611CrossRefGoogle Scholar
  82. Wheeler AM, Hartley MR (1975) Spinach chloroplast messenger RNA does not contain poly(A). Nature (London) 257: 66–67CrossRefGoogle Scholar
  83. Whitfeld PR, Leaver CJ, Bottomley W, Atchison BA (1978) Low-molecular-weight (4.5S) ribonucleic acid in higher plant-chloroplast ribosomes. Biochem J 175: 1103–1112PubMedGoogle Scholar
  84. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sei USA 74: 5088–5090CrossRefGoogle Scholar
  85. Wollenzein P, Hearst JE, Thammana P, Cantor CR (1979) Base-pairing between distant regions of the Escherichia coli 16S ribosomal RNA in Solution. J Mol Biol 135: 255–269CrossRefGoogle Scholar
  86. Zahlen LB, Kissil MS, Woese CR, Buetow DE (1975) The phylogenetic origin of the chloroplasts and prokaryotic nature of its ribosomal RNA. Proc Natl Acad Sci USA 72: 2418–2422CrossRefGoogle Scholar

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© Springer-Verlag Berlin-Heidelberg 1982

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  • T. A. Dyer

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