An RNA-protein Contact Determined by 5-bromouridine Substitution, Photocrosslinking and Sequencing

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1994 Nov 25

PMID 7800485

Citations 12

Authors

M C Willis

K A LeCuyer

K M Meisenheimer

O C Uhlenbeck

T H Koch

Affiliations

Soon will be listed here.

Abstract

An analogue of the replicase translational operator of bacteriophage R17, that contains a 5-bromouridine at position -5 (RNA 1), complexes with a dimer of the coat protein and photocrosslinks to the coat protein in high yield upon excitation at 308 nm with a xenon chloride excimer laser. Tryptic digestion of the crosslinked nucleoprotein complex followed by Edman degradation of the tryptic fragment bearing the RNA indicates crosslinking to tyrosine 85 of the coat protein. A control experiment with a Tyr 85 to Ser 85 variant coat protein showed binding but no photocrosslinking at saturating protein concentration. This is consistent with the observation from model compound studies of preferential photocrosslinking of BrU to the electron rich aromatic amino acids tryptophan, tyrosine, and histidine with 308 nm excitation.

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References

Khalili K, Rappaport J, Khoury G . Nuclear factors in human brain cells bind specifically to the JCV regulatory region. EMBO J. 1988; 7(4):1205-10. PMC: 454457. DOI: 10.1002/j.1460-2075.1988.tb02932.x. View

Dietz T, Koch T . Photochemical coupling of 5-bromouracil to tryptophan, tyrosine and histidine, peptide-like derivatives in aqueous fluid solution. Photochem Photobiol. 1987; 46(6):971-8. DOI: 10.1111/j.1751-1097.1987.tb04879.x. View

Tanner N, Hanna M, Abelson J . Binding interactions between yeast tRNA ligase and a precursor transfer ribonucleic acid containing two photoreactive uridine analogues. Biochemistry. 1988; 27(24):8852-61. DOI: 10.1021/bi00424a025. View

Dietz T, Koch T . Photochemical reduction of 5-bromouracil by cysteine derivatives and coupling of 5-bromouracil to cystine derivatives. Photochem Photobiol. 1989; 49(2):121-9. DOI: 10.1111/j.1751-1097.1989.tb04085.x. View

Valegard K, Liljas L, Fridborg K, Unge T . The three-dimensional structure of the bacterial virus MS2. Nature. 1990; 345(6270):36-41. DOI: 10.1038/345036a0. 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

Gott J, Willis M, Koch T, Uhlenbeck O . A specific, UV-induced RNA-protein cross-link using 5-bromouridine-substituted RNA. Biochemistry. 1991; 30(25):6290-5. DOI: 10.1021/bi00239a030. View

Katouzian-Safadi M, Blazy B, Charlier M . Photochemical cross-linking of the cyclic adenosine 3',5' monophosphate receptor protein to Escherichia coli 5-bromouracil-substituted DNA. Role of the effectors. Photochem Photobiol. 1991; 53(5):611-6. DOI: 10.1111/j.1751-1097.1991.tb08487.x. View

Katouzian-Safadi M, LAINE B, Chartier F, Cremet J, Belaiche D, Sautiere P . Determination of the DNA-interacting region of the archaebacterial chromosomal protein MC1. Photocrosslinks with 5-bromouracil-substituted DNA. Nucleic Acids Res. 1991; 19(18):4937-41. PMC: 328793. DOI: 10.1093/nar/19.18.4937. View

10.

Blatter E, Ebright Y, Ebright R . Identification of an amino acid-base contact in the GCN4-DNA complex by bromouracil-mediated photocrosslinking. Nature. 1992; 359(6396):650-2. DOI: 10.1038/359650a0. View

11.

Liu J, Sodeoka M, Lane W, Verdine G . Evidence for a non-alpha-helical DNA-binding motif in the Rel homology region. Proc Natl Acad Sci U S A. 1994; 91(3):908-12. PMC: 521422. DOI: 10.1073/pnas.91.3.908. View

12.

Hicke B, Willis M, Koch T, Cech T . Telomeric protein-DNA point contacts identified by photo-cross-linking using 5-bromodeoxyuridine. Biochemistry. 1994; 33(11):3364-73. DOI: 10.1021/bi00177a030. View

13.

Eggen K, Nathans D . Regulation of protein synthesis directed by coliphage MS2 RNA. II. In vitro repression by phage coat protein. J Mol Biol. 1969; 39(2):293-305. DOI: 10.1016/0022-2836(69)90318-0. View

14.

Ling C, HUNG P, Overby L . Independent assembly of Qbeta and MS2 phages in doubly infected Escherichia coli. Virology. 1970; 40(4):920-9. DOI: 10.1016/0042-6822(70)90138-8. View

15.

Lin S, Riggs A . Photochemical attachment of lac repressor to bromodeoxyuridine-substituted lac operator by ultraviolet radiation. Proc Natl Acad Sci U S A. 1974; 71(3):947-51. PMC: 388134. DOI: 10.1073/pnas.71.3.947. View

16.

Weintraub H . The assembly of newly replicated DNA into chromatin. Cold Spring Harb Symp Quant Biol. 1974; 38:247-56. DOI: 10.1101/sqb.1974.038.01.028. View

17.

Ogata R, Gilbert W . Contacts between the lac repressor and the thymines in the lac operator. Proc Natl Acad Sci U S A. 1977; 74(11):4973-6. PMC: 432080. DOI: 10.1073/pnas.74.11.4973. View

18.

Barbier B, Charlier M, Maurizot J . Photochemical cross-linking of lac repressor to nonoperator 5-bromouracil-substituted DNA. Biochemistry. 1984; 23(13):2933-9. DOI: 10.1021/bi00308a013. View

19.

Wolfes H, Fliess A, Winkler F, Pingoud A . Cross-linking of bromodeoxyuridine-substituted oligonucleotides to the EcoRI and EcoRV restriction endonucleases. Eur J Biochem. 1986; 159(2):267-73. DOI: 10.1111/j.1432-1033.1986.tb09863.x. View

20.

Studier F, Moffatt B . Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol. 1986; 189(1):113-30. DOI: 10.1016/0022-2836(86)90385-2. View