Recognition of Correct Reading Frame by the Ribosome

Overview

Journal Biochimie

Specialty Biochemistry

Date 1992 Apr 1

PMID 1637861

Citations 4

Authors

E N Trifonov

Affiliations

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Abstract

The translation frame-monitoring mechanism has been suggested earlier, based on transient complementary contacts, between mRNA and rRNA. Recent studies related to the frame-monitoring mechanism are reviewed. The mechanism is well supported by both new experimental and sequence analysis data. Experiments are suggested for further elucidation of the structural details of the mRNA-rRNA interaction in the ribosome.

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References

Atkins J, GESTELAND R, Reid B, Anderson C . Normal tRNAs promote ribosomal frameshifting. Cell. 1979; 18(4):1119-31. DOI: 10.1016/0092-8674(79)90225-3. View

Gornicki P, Nurse K, Hellmann W, Boublik M, OFENGAND J . High resolution localization of the tRNA anticodon interaction site on the Escherichia coli 30 S ribosomal subunit. J Biol Chem. 1984; 259(16):10493-8. View

Trifonov E . Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences. J Mol Biol. 1987; 194(4):643-52. DOI: 10.1016/0022-2836(87)90241-5. View

Lasater L, Cann P, Glitz D . Localization of an oligodeoxynucleotide complementing 16S ribosomal RNA residues 520-531 on the small subunit of Escherichia coli ribosomes: electron microscopy of ribosome-cDNA-antibody complexes. Nucleic Acids Res. 1990; 18(3):477-85. PMC: 333451. DOI: 10.1093/nar/18.3.477. View

Jacks T, Madhani H, Masiarz F, Varmus H . Signals for ribosomal frameshifting in the Rous sarcoma virus gag-pol region. Cell. 1988; 55(3):447-58. PMC: 7133365. DOI: 10.1016/0092-8674(88)90031-1. View

Wollenzien P, Favre A . Sites of contact of mRNA with 16S rRNA and 23S rRNA in the Escherichia coli ribosome. Biochemistry. 1991; 30(7):1788-95. DOI: 10.1021/bi00221a009. View

Powers T, Noller H . A functional pseudoknot in 16S ribosomal RNA. EMBO J. 1991; 10(8):2203-14. PMC: 452909. DOI: 10.1002/j.1460-2075.1991.tb07756.x. View

Kang C, Cantor C . Structure of ribosome-bound messenger RNA as revealed by enzymatic accessibility studies. J Mol Biol. 1985; 181(2):241-51. DOI: 10.1016/0022-2836(85)90088-9. View

Ciesiolka J, Nurse K, Klein J, OFENGAND J . Conservation of RNA sequence and cross-linking ability in ribosomes from a higher eukaryote: photochemical cross-linking of the anticodon of P site bound tRNA to the penultimate cytidine of the UACACACG sequence in Artemia salina 18S rRNA. Biochemistry. 1985; 24(13):3233-9. DOI: 10.1021/bi00334a024. View

10.

Sedlacek J, Fabry M, Rychlik I, Volny D, Vitek A . The arrangement of nucleotides in the coding regions of natural templates. Mol Gen Genet. 1979; 172(1):31-6. DOI: 10.1007/BF00276212. View

11.

Evstafieva A, Shatsky I, Bogdanov A, Semenkov Y, Vasiliev V . Localization of 5' and 3' ends of the ribosome-bound segment of template polynucleotides by immune electron microscopy. EMBO J. 1983; 2(5):799-804. PMC: 555188. DOI: 10.1002/j.1460-2075.1983.tb01503.x. View

12.

Kant J, Lord S, Crabtree G . Partial mRNA sequences for human A alpha, B beta, and gamma fibrinogen chains: evolutionary and functional implications. Proc Natl Acad Sci U S A. 1983; 80(13):3953-7. PMC: 394177. DOI: 10.1073/pnas.80.13.3953. View

13.

Weiss R, Dunn D, Dahlberg A, Atkins J, GESTELAND R . Reading frame switch caused by base-pair formation between the 3' end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli. EMBO J. 1988; 7(5):1503-7. PMC: 458402. DOI: 10.1002/j.1460-2075.1988.tb02969.x. View

14.

Oakes M, Lake J . DNA-hybridization electron microscopy. Localization of five regions of 16 S rRNA on the surface of 30 S ribosomal subunits. J Mol Biol. 1990; 211(4):897-906. DOI: 10.1016/0022-2836(90)90082-W. View

15.

Weiss R, Dunn D, Atkins J, GESTELAND R . Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting. Cold Spring Harb Symp Quant Biol. 1987; 52:687-93. DOI: 10.1101/sqb.1987.052.01.078. View

16.

Gold L, Pribnow D, Schneider T, Shinedling S, Singer B, Stormo G . Translational initiation in prokaryotes. Annu Rev Microbiol. 1981; 35:365-403. DOI: 10.1146/annurev.mi.35.100181.002053. View

17.

Dontsova O, Kopylov A, Brimacombe R . The location of mRNA in the ribosomal 30S initiation complex; site-directed cross-linking of mRNA analogues carrying several photo-reactive labels simultaneously on either side of the AUG start codon. EMBO J. 1991; 10(9):2613-20. PMC: 452960. DOI: 10.1002/j.1460-2075.1991.tb07803.x. View

18.

Trifonov E . Sequence-dependent variations of B-DNA structure and protein-DNA recognition. Cold Spring Harb Symp Quant Biol. 1983; 47 Pt 1:271-8. DOI: 10.1101/sqb.1983.047.01.032. View

19.

Moazed D, Noller H . Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell. 1986; 47(6):985-94. DOI: 10.1016/0092-8674(86)90813-5. View

20.

Oakes M, Kahan L, Lake J . DNA-hybridization electron microscopy tertiary structure of 16 S rRNA. J Mol Biol. 1990; 211(4):907-18. DOI: 10.1016/0022-2836(90)90083-X. View