Abstract
In the ribosome, the aminoacyl–transfer RNA (tRNA) analog 4-thio-dT-p-C-p-puromycin crosslinks photochemically with G2553 of 23 S ribosomal RNA (rRNA). This covalently linked substrate reacts with a peptidyl-tRNA analog to form a peptide bond in a peptidyl transferase–catalyzed reaction. This result places the conserved 2555 loop of 23 S rRNA at the peptidyl transferase A site and suggests that peptide bond formation can occur uncoupled from movement of the A-site tRNA. Crosslink formation depends on occupancy of the P site by a tRNA carrying an intact CCA acceptor end, indicating that peptidyl-tRNA, directly or indirectly, helps to create the peptidyl transferase A site.
References
31
Referenced
68
10.1126/science.1604315
10.1073/pnas.81.12.3607
10.1038/377309a0
- 5′-Dimethoxytrityl- N α -trifluoroacetyl puromycin was attached to alkylamine-derivatized controlled pore glass via a 2′-succinate linkage by standard methods (25). s 4 TCPm was prepared by standard phosphoramidite chemistry with the solid-phase version of puromycin and riboC and 4-thio-dT phosphoramidites (Glen Research). Deprotection was performed by treatment with 3:1 NH 4 OH/MeOH containing 50 mM NaSH overnight at 55°C. Subsequently 40 equivalents of 1 M tetrabutylammonium fluoride in tetrahydrofuran were added to the dried product and incubated overnight at room temperature. Finally 20 mM triethylamine acetate (pH 7.0) was added to the reaction mixture and it was loaded directly on a C 18 high-performance liquid chromatography column and eluted with increasing concentrations of acetonitrile (CH 3 CN). Products were collected and their purity was analyzed on a 20% polyacrylamide 7 M urea gel after 5′ 32 P-end-labeling with polynucleotide kinase.
- Kinetic characterization of s 4 TCPm was done with the tRNA fragment N -Ac-Met-ACCACC used as a P-site substrate under fragment reaction conditions (18) and with analysis of the resulting product s 4 TCPm- N -Ac-Met by paper electrophoresis. The apparent K m of this compound for the ribosome was 10 μM although at high concentrations peptidyl transferase activity was inhibited (8). This is consistent with binding competition by s 4 TCPm at the P site attributable to wobble pairing between 4-thio-dT (which mimics C74 of tRNA) and G2252 of 23 S rRNA (3); no alternative crosslink associated with P-site occupation by s 4 TCPm was observed.
-
Hartz D., McPheeters D. S., Gold L., Methods Enzymol.164, 419 (1988).
(
10.1016/S0076-6879(88)64058-4
) / Methods Enzymol. by Hartz D. (1988) - Tight-couple E. coli 70 S ribosomes (2 μM) were incubated with 1.2 equivalents (2.4 μM) of gene 32 mRNA (6) and deacylated tRNA Phe (26) in 20 mM tris (pH 7.5) 30 mM MgCl 2 50 mM NH 4 Cl 6 mM 2-mercaptoethanol and 10% MeOH. Saturating s 4 TCPm (20 μM) (or [ 32 P]s 4 TCPm) was then added and the mixture was incubated at 37°C for 10 min. s 4 TCPm was crosslinked to B. stearothermophilus 70 S ribosomes under similar conditions except 30 mM tris (pH 7.5) containing 10 mM MgCl 2 and 330 mM KCl was used. Complexes were exposed for various lengths of time to a hand-held UV light source (366 nm) (UVL-56 Blak-Ray Lamp UVP) at a distance of 3 cm (27). The intact rRNAs were then extracted with phenol and resolved on 3.8% polyacrylamide gels containing 7 M urea.
- R. Green and H. F. Noller unpublished data.
-
Picking W. D., Odom O. W., Hardesty B., Biochemistry31, 12565 (1992).
(
10.1021/bi00165a004
) / Biochemistry by Picking W. D. (1992) -
Rodriguez-Fonseca C., Amils R., Garrett R. A., J. Mol. Biol.247, 224 (1995).
(
10.1006/jmbi.1994.0135
) / J. Mol. Biol. by Rodriguez-Fonseca C. (1995) - The 32 P-radiolabeled crosslinked 23 S rRNA species was digested with RNase T1 in 0.2 M NaOAc (pH 5.5) containing 2.5 mM EDTA at 37°C for 20 min and the products were resolved on 24% polyacrylamide gels containing 6 M urea.
-
I. Schwartz, J. Ofengand, Biochemistry 17, 2524 (1978); Prince J. B., Taylor B. H., Thurlow D. L., Ofengand J., Zimmerman R. A., Proc. Natl. Acad. Sci. U.S.A. 79, 5450 (1982).
(
10.1073/pnas.79.18.5450
) / Proc. Natl. Acad. Sci. U.S.A. by Prince J. B. (1982) - O. Dontsova, et al., EMBO J. 11, 3105 (1992); Green R., Noller H. F., RNA 2, 1011 (1996). / RNA by Green R. (1996)
- Primer-extension analysis was performed on ribosomal complexes formed in the presence or absence of unlabeled s 4 TCPm compound using cDNA 2639 (5′-CTAGGAGCAGCCCCCC-3′) (15).
10.1016/0092-8674(89)90128-1
10.1002/j.1460-2075.1996.tb00425.x
-
D. J. Eckermann, R. H. Symons, Eur. J. Biochem. 82, 225 (1978); M. O'Connor and Dahlberg A. E., Proc. Natl. Acad. Sci. U.S.A. 90, 9214 (1993).
(
10.1073/pnas.90.19.9214
) / Proc. Natl. Acad. Sci. U.S.A. by Dahlberg A. E. (1993) - Crosslinked 50 S subunits were separated from 30 S subunits gene 32 mRNA and deacylated tRNA Phe on 5 to 20% sucrose gradients in 10 mM tris-HCl (pH 7.5) 30 mM NH 4 Cl and 1 mM MgCl 2 spun in an SW41 rotor at 19 000 rpm for 16 hours. Excess sucrose was removed and the buffer was exchanged to 20 mM tris (pH 7.5) 100 mM NH 4 Cl and 5 mM MgCl 2 using Centricon 100 tubes spun at 2600 revolutions per minute in an SS34 rotor. Peptidyl transferase assays were done as follows: crosslinked 50 S subunit complexes (0.5 μM) were incubated under fragment reaction conditions [50 mM tris (pH 8.3) 0.4 M KOAc 60 mM MgCl 2 and 33% MeOH] with CACCA-( N -Ac-Phe) (2 μM). Aliquots were removed from the reaction mixture at the indicated times the rRNAs were extracted with phenol and digested with RNase T1 and the fragments were resolved on 24% polyacrylamide gels containing 6 M urea.
- For inhibition analysis antibiotics were added to the reaction mixture described above at the following concentrations: chloramphenicol 0.1 mM; carbomycin 0.1 mM; clindamycin 0.1 mM; erythromycin 0.1 mM; neomycin 0.01 mM; sparsomycin 0.1 mM; and puromycin 1 mM. When incubated with ribosomes at these concentrations the antibiotics protect specific positions in 16 S and 23 S rRNA from chemical modification (28). Antibiotic inhibition of crosslinking was performed with limiting [ 32 P]s 4 TCPm and a single time point (2 min) of exposure to UV light (in the linear range of the reaction) under standard conditions. Antibiotic inhibition of peptidyl transferase activity was performed with the fragment P-site substrate CACCA-( N -Ac-Phe) supplied at a concentration of 0.3 μM; a single linear time point of 4 min was used for analysis.
-
Goldberg I. H., Mitsugi K., Biochemistry6, 383 (1967).
(
10.1021/bi00854a003
) / Biochemistry by Goldberg I. H. (1967) -
Pestka S., Cold Spring Harbor Symp. Quant. Biol.34, 395 (1969).
(
10.1101/SQB.1969.034.01.046
) / Cold Spring Harbor Symp. Quant. Biol. by Pestka S. (1969) - Templates for transcription of mutant tRNA Phe were generated by polymerase chain reaction amplification of CF23 plasmid (26) with the following primers; T7 top 5′-TAA TAC GAC TCA CTA TAG-3′; ΔA 5′-GGT GCC CGG ACT CGG AAT CGA-3′; ΔCA 5′-GTG CCC GGA CTC GGA ATC GAA-3′; C74A 5′-TGT TGC CCG GAC TCG GAA TCG-3′; C75A 5′-TTG TGC CCG GAC TCG GAA TCG-3′; and A76C 5′-GGG TGC CCG GAC TCG GAA TCG-3′. Amplified DNA was extracted once with phenol and once with chloroform precipitated with ethanol and transcribed in vitro with T7 RNA polymerase under standard conditions with the following alterations; 2 mM each nucleoside triphosphate 10 mM guanosine 5′-monophosphate and 14 mM MgCl 2 . Crude transcription reaction mixtures were purified on 12% acrylamide gels (55 cm long 1 mm thick) containing 7 M urea and with the xylene cyanol dye marker run to the bottom (26). Transcripts were passively eluted into 0.3 M NaOAc extracted with phenol and chloroform and precipitated. RNAs were then labeled with [ 32 P]Cp and T4 RNA ligase and digested to completion with 1 unit of RNase T2 in 100 mM NH 4 OAc (pH 5.4) at 37°C for 120 min. Np (Ap Cp Gp and Up) products were resolved by paper electrophoresis at pH 3.5 (pyridine acetate) (30 min at 3000 V). The integrity of the 3' termini of the mutant tRNAs was at least 75% correct (8).
- T. Hishizawa, S. Pestka, Arch. Biochem. Biophys. 147, 624 (1971); Ulbrich B., Mertens G., Nierhaus K. H., ibid 190, 149 (1978). / ibid by Ulbrich B. (1978)
10.1038/342142a0
- T. Atkinson and M. Smith in Oligonucleotide Synthesis: A Practical Approach M. Gait Ed. (IRL Press Oxford 1985) pp. 35–81.
-
Sampson J. R., Uhlenbeck O. C., Proc. Natl. Acad. Sci. U.S.A.85, 1033 (1988).
(
10.1073/pnas.85.4.1033
) / Proc. Natl. Acad. Sci. U.S.A. by Sampson J. R. (1988) -
Tate W., Greuer B., Brimacombe R., Nucleic Acids Res.18, 6537 (1990).
(
10.1093/nar/18.22.6537
) / Nucleic Acids Res. by Tate W. (1990) 10.1038/327389a0
-
J. Wower, S. S. Hixson, R. A. Zimmerman, Proc. Natl. Acad. Sci. U.S.A. 86, 5232 (1989); P. Mitchell, K. Stade, M. Osswald, R. Brimacombe, Nucleic Acids Res. 15, 8783 (1993); C. C. Hall, D. Johnson, B. S. Cooperman, Biochemistry 27, 3983 (1988); Steiner G., Kuechler E., Barta A., EMBO J. 7, 3949 (1988).
(
10.1002/j.1460-2075.1988.tb03281.x
) / EMBO J. by Steiner G. (1988) -
Puglisi E. V., Green R., Noller H. F., Puglisi J. D., Nature Struct. Biol.4, 775 (1997).
(
10.1038/nsb1097-775
) / Nature Struct. Biol. by Puglisi E. V. (1997) - We thank B. Cormack G. Culver L. Holmberg K. Fredrick K. Lieberman and E. Strauss for helpful comments on the manuscript and S. Joseph and C. Merryman for helpful discussions. Supported by grants from the National Institutes of Health the National Science Foundation the Lucille P. Markey Charitable Trust to the Center for Molecular Biology of RNA and a Burroughs-Wellcome Career Award to R.G.
Dates
Type | When |
---|---|
Created | 23 years ago (July 27, 2002, 5:42 a.m.) |
Deposited | 1 year, 7 months ago (Jan. 13, 2024, 12:13 a.m.) |
Indexed | 1 year, 2 months ago (June 3, 2024, 1:55 a.m.) |
Issued | 27 years, 4 months ago (April 10, 1998) |
Published | 27 years, 4 months ago (April 10, 1998) |
Published Print | 27 years, 4 months ago (April 10, 1998) |
@article{Green_1998, title={Ribosome-Catalyzed Peptide-Bond Formation with an A-Site Substrate Covalently Linked to 23 S Ribosomal RNA}, volume={280}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.280.5361.286}, DOI={10.1126/science.280.5361.286}, number={5361}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Green, Rachel and Switzer, Christopher and Noller, Harry F.}, year={1998}, month=apr, pages={286–289} }