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Terminal Octanucleotide Sequence in 18S Ribosomal

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Terminal Octanucleotide Sequence in 18S Ribosomal Biochem. J. (1974) 141, 609-615 609 Printed in Great Britain Identical 3'-Terminal Octanucleotide Sequence in 18S Ribosomal Ribonucleic Acid from Different Eukaryotes A PROPOSED ROLE FOR THIS SEQUENCE IN THE RECOGNITION OF TERMINATOR CODONS By JOHN SHINE and LYNN DALGARNO Department ofBiochemistry, School ofGeneral Studies, Australian National University, Canberra, A.C.T. 2600, Australia (Received 7 January 1974) The 3'-terminal sequence of 18S ribosomal RNA from Drosophila melanogaster and Saccharomyces cerevisiae was determined by stepwise degradation from the 3'-terminus and labelling with [3H]isoniazid. The sequence G-A-U-C-A-U-U-AoH was found at the 3'-terminus of both 18S rRNA species. Less extensive data for 18S RNA from a number of other eukaryotes are consistent with the same 3'-terminal sequence, and an identical sequence has previously been reported for the 3'-end of rabbit reticulocyte 18S rRNA (Hunt, 1970). These results suggest that the base sequence in this region is strongly conserved and may be identical in all eukaryotes. As the 3'-terminal hexanucleo- tide is complementary to eukaryotic terminator codons we discuss the possibility that the 3'-end of 18S rRNA may have a direct base-pairing role in the termination ofprotein synthesis. Termination of protein synthesis in prokaryotes A preliminary account of this work has been pub- occurs in response to the presence of one of the lished (Dalgarno & Shine, 1973). terminator codons (UAA, UAG or UGA) in the ribosomal 'A' site (Haselkorn & Rothman-Denes, Experimental 1973). The terminator triplet is specifically recognized since certain other triplet sequences which do not Media and materials code for any amino acid do not lead to polypeptide cerevisiae were grown release (Bretscher et al., 1965). There is good evidence Saccharomyces aerobicaily that tRNA does not recognize terminator codons in the medium described by Gordon & Stewart (Capecchi, 1967; Bretscher, 1968; Fox & Ganoza, (1971). A clone of Antheraea eucalypti (emperor 1968) and this function has been to two gum moth) cells was supplied by Dr. T. D. C. Grace assigned and proteins, or release factors (Scolnick & Caskey, 1969), (Commonwealth Scientific Industrial Research Organisation, grown which are necessary for the release of nascent poly- Canberra, Australia) and in Grace's at peptides in response to terminator codons (Capecchi, (1962) medium 25°C. Propagation of 1967; Scolnick et al., 1968). However, attempts to African green-monkey kidney (Vero) and baby- demonstrate specific binding of terminator codons hamster kidney (BHK) cells was as described by by release factors have been inconclusive (Capecchi & Raghow et al. (1973). Galleria mellonella (wax moth) larvae were reared on Klein, 1969). Although not as well understood, the honeycomb at 25°C. Drosophila process of polypeptide chain termination in melanogaster (larvae and adults) were obtained from eukary- Dr. A. J. otes appears to be fundamentally similar to that in Howells (Australian National University, prokaryotes. Thus UAA, UAG and UGA have been Canberra, Australia). implicated as terminator codons (Hawthorne, 1969; [G-3H]Isonicotinic acid hydrazide (iNzd*) (1 Ci/ Beaudet & mmol) and [carbonyl-'4C]iNzd (11.1 mCi/mmol) were Caskey, 1971; Stewart & Sherman, 1972) from The and a single release factor has been isolated with Radiochemical Centre (Amersham, Bucks., similar activity to the two prokaryotic factors U.K.). Unlabelled iNzd was from Calbiochem (Beaudet & Caskey, 1971). (Los Angeles, Calif., U.S.A.). DEAE-Sephadex A-25 was from Pharmacia was In the present paper we provide sequence data (Uppsala, Sweden). Sucrose which the that ribonuclease-free(Schwarz/Mann, Orangeburg,N.Y., suggest possibility the 3'-terminus of U.S.A.). Aniline (May and eukaryotic 18S rRNA plays a direct base-pairing role Baker Ltd., Dagenham, in the termination of protein synthesis in eukaryotes * Abbreviations: iNzd, isonicotinic acid hydrazide through specific recognition ofthe terminator codons. (isoniazid); iNicHz, isonicotinoylhydrazone. Vol. 141 u 610 J. SHINE AND L. DALGARNO U.K.) was redistilled before use. All other chemicals the 3'-terminal phosphate, RNA (2mg/ml) was were reagent grade. Ribonuclease T1 (grade III, from dissolved in 20mM-ammonium acetate (pH6.9), Aspergillus oryzae) and pancreatic ribonuclease were made 1 mm in MgCl2 and 20cg of alkaline phospha- from Sigma Chemical Co. (St. Louis, Mo., U.S.A.). tase added/ml. The mixture was incubated for Bacterial alkaline phosphatase (BAPF), ribonuclease- 45min at 37°C. After addition of3vol. of0.1 M-NaCl- free, was from Worthington Biochemical Corp. O.OlM-sodium acetate (pH5) the RNA was precipi- (Freehold, N.J., U.S.A.). Nucleosides and dinucleo- tated with ethanol and stored at -20°C. The whole side monophosphates were from Sigma Chemical Co. procedure was repeated five times; after each cycle PPO (2,5-diphenyloxazole) and POPOP [1,4-bis- approx. 250,ug of oxidized RNA was removed and (5-phenyloxazol-2-yl)benzene] (scintillation grade) incubated with 50,ul of [3H]iNzd (5OuCi) in 1 ml of were from Packard Instrument Co., Downers Grove, 0.1M-NaCl-0.01M-sodium acetate (pH5) at 20°C Ill., U.S.A. BBS3 solubilizer was from Beckman for 20h. Residual iNzd and the small amounts of Instruments Inc., Fullerton, Calif., U.S.A., and contaminating polysaccharide were removed by Triton X-100 from Ajax Chemicals Ltd., Sydney, DEAE-cellulose chromatography (Shine &Dalgamo, Australia. 1974). Labelled RNA was precipitated with 2vol. of ethanol and stored at -20°C. The completeness of Methods both the stepwise degradation procedure and the condensation ofiNzd with periodate-oxidized rRNA Preparation of rRNA. Ribosomal RNA was have been previously demonstrated (Hunt, 1965, extracted from Drosophila melanogaster and Galleria 1970; Shine & Dalgarno, 1973). mellonella by homogenization of larvae or adult Enzymic digestion. Digestion of carrier RNA was insects in 20vol. of phenol-cresol-sodium amino- at 370Cfor2h in 0.01M-sodium-potassium phosphate salicylate (Shine & Dalgarno, 1973) at 4°C in a buffer (pH7.4) with lO1ug of ribonuclease Ti/mg of Teflon-glass homogenizer. The same method was RNA. [3H]iNzd-labelled RNA (0.5-1mg/ml) in used for Saccharomyces cerevisiae except that disrup- 0.01 M-phosphate (pH7.4) was digested with lOug tion was in a Braun homogenizer for 30s. Pellets ofribonuclease T1 or 50,ug ofpancreaticribonuclease/ of cultured cells were disrupted by mixing directly mg of RNA at 20°C for 3h. with phenol-cresol-aminosalicylate (Shine & Column chromatography. Chromatography on Dalgarno, 1973). The RNA was precipitated with columns ( cmx 25cm) of DEAE-Sephadex A-25 2vol. of ethanol at -20°C and extracted twice with was used to determine the chain length of oligo- 3M-sodium acetate (pH6) to remove DNA and low- nucleotide hydrazones released by digestion of molecular-weight RNA species. Polysaccharide was [3H]iNzd-labelled RNA. Elution was with a 1-litre removed by centrifugation at 40000g for 30min in linear gradient of 0-0.5 M-NaCl in 7M-urea-0.O1M- O0.M-NaCl-O.OlM-sodium acetate (pH5). Individual phosphate, pH7.4. Under these conditions oligo- rRNA species were separated on gradients (34ml) of nucleotide hydrazones containing from one to eight 5-20% (w/v) sucrose in 0.1M-NaCl-0.01M-sodium nucleoside residues exhibit a characteristic and acetate (pH5) in the SW 27 rotor of a Spinco ultra- reproducible elution profile which bears a fixed centrifuge for 16h at 25000rev./min at 4°C. The 18S relationship to that of the corresponding unmodified rRNA was isolated by pooling peak fractions and oligonucleotides (Hunt, 1973; J. Shine, unpublished precipitating with 2vol. of ethanol at -20°C. Less work). For the determination of radioactivity, lml than 2% contamination of 18S rRNA with other of each column fraction (5ml) was added to lOml of rRNA species (26S, 5S and 4S RNA) was found scintillator solution containing 0.5 % PPO and on resedimentation. The sedimentation profile 0.05 % POPOP dissolved in BBS3 solubilizer (I vol.) showed no evidence ofany degradation ofthe RNA. and toluene (Svol.). Fractions containing both 3H- Stepwise degradation and reaction of iNzd with and 14C-labelled oligonucleotides were counted for periodate-oxidized rRNA. Periodate oxidation of radioactivity on the restricted channels of a Packard rRNAwasaspreviouslydescribed (Shine &Dalgarno, liquid-scintillation spectrometer model 3375 and 1973). Stepwise removal of the 3'-nucleotides from corrected for a 30% spill-over of 14C into the 3H rRNA was essentially as described by Hunt (1970). channel. Periodate-oxidized RNA was dissolved at 4mg/ml Identification of nwnonucleoside hydrazones and in 0.1M-NaCI-0.01M-sodium acetate, pH5. After dinucleoside monophosphatehydrazones. Ribonuclease addition of 3vol. of 0.4M-aniline (adjusted to pH5 digests of terminally labelled RNA were electro- with conc. HCI), the RNA was incubated at 20°C for phoresed on Whatman 3MM paper in 0.1 M-sodium 4h to remove the terminal nucleoside. Then 0.1 vol. formate buffer (pH3). Electrophoresis was at 40V/cm of lM-NaCl-0.lM-sodium acetate, pH5, was added for 2h. Under these conditions the two mono- and the RNA was precipitated with 2vol. of ethanol, nucleoside derivatives with most similar migration resuspended in 0.1M-NaCl-0.01M-sodium acetate rates (G-iNicHz and U-iNicHz) are separated by (pH5) and reprecipitated with ethanol. To remove about 1 cm. Marker mononucleoside hydrazones 1974 CONSERVED 3'-TERMINAL SEQUENCE IN EUKARYOTIC 18S rRNA 611 and dinucleoside monophosphate hydrazones were are markedly different phylogenetically both from prepared as described by Hunt (1965) and mixed with each other and from rabbits. the digest of labelled RNA before electrophoresis. Saccharomyces cerevisiae 18S rRNA was labelled Their positions were determined under u.v. light; with [14C]iNzd and Drosophila melanogaster 18S the electrophoretogram was cut into approx. 1.5cm rRNA with [3H]iNzd. The two preparations were strips, each strip wetted with 0.4ml of water and the combined and digested with T1-ribonuclease.
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