Probing Sequence-specific RNA Recognition by the Bacteriophage MS2 Coat Protein

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1995 Jul 11

PMID 7543200

Citations 38

Authors

P G Stockley

N J Stonehouse

J B Murray

S T Goodman

S J Talbot

C J Adams

L Liljas

K Valegard

Affiliations

Soon will be listed here.

Abstract

We present the results of in vitro binding studies aimed at defining the key recognition elements on the MS2 RNA translational operator (TR) essential for complex formation with coat protein. We have used chemically synthesized operators carrying modified functional groups at defined nucleotide positions, which are essential for recognition by the phage coat protein. These experiments have been complemented with modification-binding interference assays. The results confirm that the complexes which form between TR and RNA-free phage capsids, the X-ray structure of which has recently been reported at 3.0 A, are identical to those which form in solution between TR and a single coat protein dimer. There are also effects on operator affinity which cannot be explained simply by the alteration of direct RNA-protein contacts and may reflect changes in the conformational equilibrium of the unliganded operator. The results also provide support for the approach of using modified oligoribonucleotides to investigate the details of RNA-ligand interactions.

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References

Beckett D, Uhlenbeck O . Ribonucleoprotein complexes of R17 coat protein and a translational operator analog. J Mol Biol. 1988; 204(4):927-38. DOI: 10.1016/0022-2836(88)90052-6. View

Ehresmann C, Baudin F, Mougel M, Romby P, Ebel J, Ehresmann B . Probing the structure of RNAs in solution. Nucleic Acids Res. 1987; 15(22):9109-28. PMC: 306456. DOI: 10.1093/nar/15.22.9109. View

Uhlenbeck O, Carey J, Romaniuk P, Lowary P, Beckett D . Interaction of R17 coat protein with its RNA binding site for translational repression. J Biomol Struct Dyn. 1983; 1(2):539-52. DOI: 10.1080/07391102.1983.10507460. View

Peabody D . Translational repression by bacteriophage MS2 coat protein expressed from a plasmid. A system for genetic analysis of a protein-RNA interaction. J Biol Chem. 1990; 265(10):5684-9. View

Haneef I, Talbot S, Stockley P . Modeling loop structures in proteins and nucleic acids: an RNA stem-loop. J Mol Graph. 1989; 7(4):186-95. DOI: 10.1016/0263-7855(89)80001-3. View

Witherell G, Gott J, Uhlenbeck O . Specific interaction between RNA phage coat proteins and RNA. Prog Nucleic Acid Res Mol Biol. 1991; 40:185-220. DOI: 10.1016/s0079-6603(08)60842-9. View

Talbot S, Medina G, Fishwick C, Haneef I, Stockley P . Hyperreactivity of adenines and conformational flexibility of a translational repression site. FEBS Lett. 1991; 283(1):159-64. DOI: 10.1016/0014-5793(91)80576-o. View

Peabody D, Ely K . Control of translational repression by protein-protein interactions. Nucleic Acids Res. 1992; 20(7):1649-55. PMC: 312251. DOI: 10.1093/nar/20.7.1649. View

Mastico R, Talbot S, Stockley P . Multiple presentation of foreign peptides on the surface of an RNA-free spherical bacteriophage capsid. J Gen Virol. 1993; 74 ( Pt 4):541-8. DOI: 10.1099/0022-1317-74-4-541. View

10.

Stockley P, Stonehouse N, Walton C, Walters D, Medina G, Macedo J . Molecular mechanism of RNA-phage morphogenesis. Biochem Soc Trans. 1993; 21 ( Pt 3)(3):627-33. DOI: 10.1042/bst0210627. View

11.

Murray J, Collier A, Arnold J . A general purification procedure for chemically synthesized oligoribonucleotides. Anal Biochem. 1994; 218(1):177-84. DOI: 10.1006/abio.1994.1157. View

12.

Valegard K, Murray J, Stockley P, Stonehouse N, Liljas L . Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature. 1994; 371(6498):623-6. DOI: 10.1038/371623a0. View

13.

Sugiyama T, Hebert R, Hartman K . Ribonucleoprotein complexes formed between bacteriophage MS2 RNA and MS2 protein in vitro. J Mol Biol. 1967; 25(3):455-63. DOI: 10.1016/0022-2836(67)90198-2. View

14.

Donis-Keller H, Maxam A, Gilbert W . Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977; 4(8):2527-38. PMC: 342589. DOI: 10.1093/nar/4.8.2527. View

15.

SANGER F, Nicklen S, Coulson A . DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977; 74(12):5463-7. PMC: 431765. DOI: 10.1073/pnas.74.12.5463. View

16.

SANGER F, Coulson A . The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978; 87(1):107-10. DOI: 10.1016/0014-5793(78)80145-8. View

17.

Carey J, Uhlenbeck O . Kinetic and thermodynamic characterization of the R17 coat protein-ribonucleic acid interaction. Biochemistry. 1983; 22(11):2610-5. DOI: 10.1021/bi00280a003. View

18.

Melton D, Krieg P, Rebagliati M, Maniatis T, Zinn K, Green M . Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 1984; 12(18):7035-56. PMC: 320141. DOI: 10.1093/nar/12.18.7035. View

19.

Romaniuk P, Uhlenbeck O . Nucleoside and nucleotide inactivation of R17 coat protein: evidence for a transient covalent RNA-protein bond. Biochemistry. 1985; 24(15):4239-44. DOI: 10.1021/bi00336a064. View

20.

Sorger P, Stockley P, Harrison S . Structure and assembly of turnip crinkle virus. II. Mechanism of reassembly in vitro. J Mol Biol. 1986; 191(4):639-58. DOI: 10.1016/0022-2836(86)90451-1. View