RNA CODEFORDS AA'0 PROTELV SYATTHESIS> II. NTIJCLEOT_7-DE SEQVENCE OF A VALIh-E R-VA CODEWORD BY PFIILIP LEDER A4m M.~F~FL~LL ?~IREKBERG NATIONAL FIEABT INSTIXTE, KATIOXAL INSTITPTES OF HEALTB, BETaESDA, MABPLAND Communicded by R. B. Roberts. June 30. 19.64 Recent studies demonstrate that synthetic @lynucleotides. such as poiy I-. in- duce with specificit,y the binding of C14-amino-ac~l-sR--4 to ribosomes.: -4 Char- acteristics of binding in the ab,wnce of poly II also have been reported." C14- Phe-sRX-4 binding induced by poly Y is thought to represent an early step in pro- tein synthesis before peptide bond format.ion: however. the precise nature of the interaction has not been ckified. To establish the sequence of nucleotides in RX-4 codewords. we devised a rapid, sensitive method for measuring C'"-a~~-~~o-ac~l-sR~~4 binding to ribosomes. and have investigated both characterist.ics of biding and the minimum oligonucleotidr chain length required to direct such binding." pUpI:pC, p-4p.4~~4, and pCpCpC directed the binding of Phe-. Lys--. and Pro-sRXA, respectively, where&s dinucleotides had no effect. Trinucleotides with 5'-t.erminaI phosphate were more active than those with no terminal phosphate, whereas trinucleotides with 2'-(3')~terminal phosphate were inactive.6 In this report, trinucleotides of knoun sequence were used to direct sR!iA bind- ing. GpUpU, but not its sequence isomers, UpGpU and UpUpG, was shown to induce Va.l-sRKA binding to ribosomes. These data indicate that the nucleotide sequence of an RX\`,4 codeword for valine is GpUpU. Mai&& and Melhods.-Andyses of poZy- and digonuckotidcs: (a) Paper elertrophoresti was performed on Whatman 54 or 3 MM paper in 0.05 M NR&OOH buffer, pH 2.i, at 80 vicm for 0.5 hr with authentic reference markers. If a marker wa not available, the expected mobiit! ws calcultLti.' ib,! Descending paper rhromatoephv wac performed at room temperature with Whatman 3 MM paper and the following solvents: (-4 I cont. ~H,0H-N-prc~panc~l-H20, 10/55/35, v/v; (B) 40 gm (h&)8& dissolved in 100 ml 0.1 M sodium phosphate, pH 7.0.& Bands were visualized under C?; light. (cj Ultraviolet absorption measurements were made in a Zeies spectrophotometer, and spectra were obtained in a cam recording spectrophotomnleter The absorbancy of eluates from paper was read against blank paper eluats (d) The base ra.tio of the poly UG preparation (D-132j was O.i4/0.26 (T/G). The base ratio of GpTpG, GpGpr, and GpUpU preparations was determined bJ- incubating 2.0 -4"" uniti with 3.5 x 10e3 units of T1 RNaee* in 0.02 ml of 0.5 M ammonium acetate, pH 4.5, for 2.5 hr at 45". The digestion products were separated by paper electrophoreeis, eluted, and the absorbancy of each at appr<+ Pritlte Lax was determined. Preparation and separation of oZigom&otidcs: I-pT was chararterized BE described 6 UpVpG and UPG were obtained by incubating 3 X 10' A*@' units of poly UG with 1.3 X 10" units of T:- RPuase (Sankpo Co., Ltd., Tokyo) in 4.i ml of 0.1 IV NH+BC& at 37" for 6 hr.`" The reaction mixture waa lyophilised, dissolved in 0.1 M (KH& CC&. and terminal phoephati were removed by incubation with E. coEi alkaline phoephataae, free of diesterase, BE described by Heppel d aI I1 Ohgonucleotide fractions were separated by. paper chromatographp with solvent il for 16 hr. rTltraviolel-at~sc,rbinp ban& with mobiii&sofJUpG and Uplip{; were elated with H,( 1. I~ophilyzrd. and purified sepamtsly by elertrophoresis. GpUpV and Gpr were obtained by digesting pal!- U(; with purified pork hver nuc~Ie~se.~ re- moving terminal pht~phates, and mptrratinp frartmns b> p&per chromatography and electrt* phoresis a~ described above. This procedure >-ielded B fra(*t,iou containing TWpc.; and GpV and also one containing GpUpU, UpGpU, and UpUpG. P&per chromatogrtrphy w1t.h solvent B for 420 VOL. 52. 1% BIOCHEMISTRY: LEDER AND JIRENBERG 421 36 hr resolved each dinucleotide. The trinucleotide fraction was separated into two bands by chromatography with solvent B. The band nearest the origin contained GpUpU of high purity. It wsa eluted with HP, absorbed on acid-washed Norite, and eluted with 4.71~~ ethanol 0.5 M ZT&GH. GpCpU was purified agaiu by chromatography with solvent B, eluted, and desalted h derivative of pancreatic RNase A was used by Dr. Merton Bernfield to catalyze the transfer t)f uridim+2',3'-cyclic phosphate to GpU. I* UpGpC was purified from the reaction mixture by paper chromatography and electrophoresis as described for UpUpC. /7haracti~i&ion of triplets: GpUpU, UpGpC, and UpUpG preparations were purified ss de- wnbed. Only one spot was obeerved after each was subjected to paper chromatography with solvents ;L or B and to paper electrophoresis. Base-ratio and sequence analyses established the purity, chain length, and base sequence of each triplet preparation. Base-ratio analyses were as follows: GpUpU, 1.2 U, 1.0 Up, 1.0 Gp; UpGpU, 1.0 U, 1.0 cp, .OQ Gp; CpCpG, 2.1 Up, 1.6 G. Base sequence was determined as follows: 2.0 Am units of each trinucleotide was digested separately with T1-RXrse (as described earlier) and in other reactions, with 2.0 pg of chromato- graphically purified pancreatic RNsse (Sigma) in O.OSS ml of 0.1 Jf (ZIH,)zCO~, at 37' for 6 hr. Reaction products were separated by paper electrophoresis. Dinucleotide products were eluted, lyophilized, and digested with the RNaae to which they were susceptible, and the products again were separated by electrophoreais. Nucleoeides and nucleotidm were identified by their electrc- phoretic mobility ss well as by their spectra. After digestion of GpUpU, UpGpU, and UpUpG with pancreatic RNase, only the following producte were obtained: GpUp + U; Up + GpG; and Up + G, respectively. After digestion t,f GpUp and GpC' with T1-R&se, Gp + Up and Gp + U were obtained, respectively. Ti- RXaae digestion of GpCpU, UpGpU, and UpCpG yielded Gp + UpU, UpGp + U: and UpUpG, respectively. Digestion of UpC, UpGp, and UpUpG with pancreatic R&se yielded Up + U, Up + Gp, and Up + G, respectively. No other L7-absorbing material was found. Since a 2% contaminant could have been detected, the purity of each trinucleotide was estimated to be >98rc. GpUpU and CpCpU have not been purified previously. Ribommes, sR:V.$ and E. cola' extra&s: E. cdi W 3100 sRN.4 was prepared from cells grown to late log phase in 0.54 nutrient broth, 1% gluc~~~~ E. cdi B aRNA was obtained from General Biochemicals, Inc. Bach Cl*-amin+acyl-sRX.4 was prepared in the presence of 19 Cl*-amino acids as described elsewhere.' In additional experiments C1*-T.m~RNA also was prepared in the absence of other amino acids. CII-GVal, Cl'-GPhe, and C*`-GLeu, uniformly labeled with radioactivities of ;%I, >ZQ, and 435 cpm/wmole (Packard Corp. scintillation counter), respectively, were obtained from New England Nuclear Corp. Ribosomee for binding studies and E. cdi ex- tracts (DNase-treated, preincubatecl. S36 fraction: for amino acid incorporation into protein studies were prepared as described elsewhere.". `a dssays: Each S&l reaction mixture contained 0.1 M u-is-acetate, pH i.2; 0.02 JI mag- nesium acetate; 0.05 .U KCl: and 1.0 .4m units of nbosomcs unless otherwise specified. Incuba- tions were at 24O for 20 mm unless otherwise `indicated. C'*-amin~acyl-sRN.4 binding to ribo- somes was determined. M reported elsewhere, fi by washing the ribosomes on Millipore cilters. Ribosomes with bound sRNh remained on the &her. C?-amino acid incorporation into protein was determined ss reported previou~ly.~J Resuhk-EJect oj Gplpl- and PI* L-G upmz the binding of C"-valine &V--l tu ribosomes: The data of Figure 1 shoti that the binding of Val-sR,\i-\ to ribosomes is stimulated by the addition of GpCpU or poly UG and is dependent upon the con- centration of either template. JIore Val-sR_\iA is bound to ribosomes in the pres- ence of poly UC than in the presence of an equivalent amount of GpUpU. We have observed similar differences between the 3ctivity of pUpITpI.7 and poly I?." In Figure 2, the rates of binding at 0" and 24O are compared, and the specificity of GpUpC: and poly UG for amino-acyl-sRX-4 is shown. At O", poly UG markedly stimulated Val- and Phe-sRNA4 binding to ribosomes, whereas GpCpG stimulated only Val-sRI\3,\ binding. At 34" the rates of binding directed by poly UC were higher than st 0". Slightly higher binding in control reactions was observed BIOCHEMISTRI-: LEDER A-4-D It-IRE-?-BERG Paoc. X. A. S. 0' ' ' ' ' ' 1 ' I a k 8 M~YOL'~S BAFE RE~DIESM 7.8 32 FIG. l.-The relation between GpTpV (01 and poly I`G (D) concentration and Cl'- Val-eR?;A binding to ribosomes. Each re- action mixture contained 2.0 AM unitE of riboeomea and 18.9 MFrnoles of Cl*-Val attached to 0.44 A"O units of sRl"iA. Poly UG and GpUpU were added as specified. (especially of Leu-~33-4). Under the conditions employed, pal- UG had little activity in directing Leu-sRKA binding to ribosomes, compared with its abiliq- to direct amino acid incorporation into protein. Codgword specificity arbd the eflect r!i Of~-~j cwwcentration: The data of Figure 3 demonstrate that poly UG stim- ulates binding of T'al- and Phr-sEEi- to ribosomes optimally at 0.02-0.03 .a1 C.\lg+-;j. whereas GpUpV directs bind- ing of Val-sRX4 optimally at higher concentrations. ilt higher (big++) con- centrations, a small and apparently non- specific increase in Yak. Leu-! and Phe- sRX*4 binding was observed in control reaction mix-tures (no addition). Tri- and polynucleotides induce specific sRKA binding. GpUpU directed only Val-sRKA binding, whereas UpGpU and UpUpG had no effect upon either Val-, Leu-, or Phe-sRXA. The addition of tri- or polynucleotides did not. appreciably increase Leu-sRXA binding over that of control reactions within the range of (Mg++) concentrations tested. The specifxity of di-, tri-, and polynucleotides in directing amino-acyl-sRX4 binding is shown in Table 1. Poly UG directed Val- and Phe-sRK.4 binding. whereas poly U directed the binding only of Phe-sRKA. UpU, GpC, and UpG did not, stimulate Val-, Phe-, or Leu-sRKA binding. The effect of GpUpU was tested upon the binding of I 7 other sRS-4 preparations, each with a different C"-amino accepted (CWasparagine and C"-glutamine-sRK-4 not. tested). GpUpC was found to direct the binding only of T'al-sR?;A. Amino acid incorporation into protein: Since poly UG had little effect upon Leu-sRX-4 binding to ribosomes, w-e investigated the ability of poly UG to direct TABLE 1 CODEWORD SPECIFICITY Addition. Expt. mrmolee base residues ClcAminc-AcyLsRKA Bound to Ribmomes, ~~molee C"-Bal-nRE;A CW%HIRIGA C'LLeu-sRNA 1 ?; one 0.38 0.22 0.3i 4.; Poiy r 0.23 4 73 0.22 4 i Poly LrG 2.65 1.93 0.24 2 None 0.40 0.22 0.62 4 i GpFpl` 1.11 0.2i 0.56 4 7 UpGpI- 0.40 0.25 0.55 4 7 UpUpG 0.33 0 25 0 .44 3 None 0.1s 0.22 0.69 4.i GpT 0.20 0.22 0 .69 4.7 UpG 0 19 0.21 0.71 4.i UpI: 0.11 0 20 0.6T Obgonucleot~dc spwificrt?- m directing sRKA C-`-\-al attached to G.3 Am unita of aRN.4 17.0 bindma to ribmomes Where indicated. 0.10 @m&E ,wnoler C'cPbc attached to 0.; -4' unita of sRNA. or 21.0 wmoias C'CLeu attached to 1.6 A= +ta of r,RK-4 welt added to reactmn nuxtu~-~. i.OL. x2. I!w BIOCHEJIISTRY: LEDER d.VD .VIRE.VBERG 423 Fro. %.-Effect of GpcpU and poly c:G u 1 on sRNA to riboaomea at 0" and 24". The sym the rates of binding of Val-, Leu-, and Phe- mrmoles of base residues; (0) GpUpU, ols represent the addition of: ( ~1 poly UC, 4.70 2.35 mfimolea of base residues; (0) no addition. Where indicated, li mpmoles of Cl'-Vai attached to 0.44 A" units of eRN-4, 8.5 gfirnoles C"-Phe at- tached to 1.5 A?"0 units sRNA, or Sl.O.~gnolea of C*4-Leu attached to 1.5 A' units of sRXA were added. Samples were incubated at the temperatures and for the timea indicated. amino acid incorporation into protein in E. coli extracts at 0' and 24O (also at 137~ to make these data comparable to previously reported studiesI 15). -1s shown in Table 2. poly CG directed Phe, Val, and Leu into protein at 37" and 34', and as re- ported previousiy,`4, l5 Leu incorporation almost equaled that of Val. Amino acid incorporation into protein was not detected at 0". D~c~cussiun:-Previously we have shown that LpUpcI, -4pAp.\, and pCpCpC specifically induce the binding to ribosomes of Phe-. Lys-, and Pro-sRX.4. respec- tively The present study demonstrates that the trinucleotide, GpUpU. can induce the binding of Val-sR_\;;I to ribosomes. whereas sequence isomers such as UpGpU and L-pUpG. and dimucleotides have no activity. When the specificity of poly CG was compared with that of GpIYpL-, the polynucleotide was found to direct both Ammo .irid Incorporated into Prorem. rurmoles C' 4- rvli ne C'+heoylahn~ne C'~Ie1mne the trinucleotide, GpTpT. and by poly UG. but not by TpGpc, I`pVpG, or di- nucleotides. GpUpT: had no effect upon the binding to ribosomes of sRP\`A cor- responding to li other amino acids. The nucleotide sequence GpVpT was pro- posed for a valine RX-4 codeword. The implications of these findings and pre- dictions based on amino acid replacement data are discussed briefly. We are grateful to Drs. Leon Heppel and George Rushizky for rheil advice on oligonuc*ieotlde separations. It is also a pleasure to thank Norma Zabrlskie and Theresa Caryk for their ex- tremely skillful technical assistance. The following abbreviations are used: Val, valine; Phe, phenylalanine, Leu. leucinr : p oiy Ty, polyuridylir acid; poly C, polycytidglic acid; ~011 A, pal:-adenylie acid: pal>- UG, copolymer of uridylic and guanylic acids: TCA, trichloroacetic acid; sRK.4. transfer RI\`A: mRKA, messenger RK.4. For mono- and oligonucleotides of specific BtrUCtUre; the "p" to the left of a terminal nucleoside initial indicates a 5'-terminal phosphate: the "p" to the right, a 2'-(3' j-terminal phosphate. Internal phosphates of oligonucleotides are (3',5',+linkagea. 1 Arlinghaus, R., G. Favelukes, and R. Schweet, Biochem. Bwphys. Res. Pommun., 11, 92 (1963J. * Kakamoto, T., T. W. Conway, J. E. Allende, G. J. Spyides. and F. Lipmann, in Synthrsu and Strudurr of Macrem&cuks, Cold Spring Harbor Symposia on Quantitatk Biology, vol. 25 cl963j, p. 227. 3 Kaji, A., and H. Iiaji. Biochem. Res. CowLmun., 13, 186 (19G): Federation Proc. ( .4 bstv.,, 23, 4% j1964;. 4 Sp:+des, G. J., Federation Proc. 1 rl bstr. j, 23, 31s cl964 j. 6 Cannon, M., R. Brug, and W. Gilbert, J. Mol. Biol., 7, 360 !. 1963). 6 Kirenberg, M. W., and P. Leder, Sctirz~, in press. 7 Markham, R., and J. D. Smith, Biochem. J., 52, 5% ;1953 I. 6 Rushizky, G. K., and H. -4. Sober, J. Biol. Cheer., 237, "SK9 1,1962 I. Pfiid., 238, 371 (1963). w Ibid.., 237, 834 (1962 j. 11 Heppel, L. A., D. R. Harkneas, and R. J. Hilmoe, J. Biol. Chem., 237, 841 (1962`1. I* Bemfield, M. R., and M. W. Krenberg, Abstracti, 148th Xational Meeting, American Chemical Society. Chicago, Illinois, August 1964. I1 ?jirenberg. M. W., in Methods 211 Enqw~&gy, ed. S. P. Colonick and I\`. 0. Kaplan (Xea York: Academir Press, IWX;, vol. 6, p. 17. 14 Nirenberg. hl. W.? J. H. Matthaei, 0. K. Jones, R. G. Nartin, and P. H. Barondes. Frdvatzon Pm.. 22, 55 (1963). a Sii~ger, >I. F., 0. W. Jones, and M. W. Sl'irenberg, these PROCEEDINGS, 49, 3% i,l%S,. If Tanofsky, C.. m Synthms and Structure of Macromokc~ks. Cold spring Harbor Symposia on Quantitative &olog~, vol. 28 (1963 J, p. 551. Ii Wlttmann, H. G., and B. Wibtmarm-Liebold, in S.yntheszs and Structure qf Manomokcu1ch. Coid Spring Harbor Symposia on Quantitativr Biolog\-. vol. 2b 1963 J, p. 5R9. B Tsugita. .4.. personal communiwtion. I* Crick, F. H C.; L. Bamett. 5. Brenner, and R. J. WatsTobm, -qVaturrj 192, 1227 11961 :. 1o Nirenberg, M., 0. Jones, P. Leder. B. Clark, W. Sly. and 3. Pestka, SynthPszs and Strw-ture of YacsomoEe~~~lt~, Cold Spring Harbor Symposia on Quantitative Biology, vol. 2% I 1963 8, p. .?A!). !I Wahba, A. J., C. BaYilio, J. F. Speper, P. Lengyel, R. S. Miller, and 8. Ochoa, these PILOCEEW INGS, 48, t683 (l%a). 22 Xrenberg, hf. W., and 0. W. Jonps. in Infow~~&wl .lil~omoler&.u, ed. H. I-ngel rt