Mass-spectrometric analysis of proteins cross-linked to 4-thio-uracil- and 5-bromo-uracil-substituted RNA

International Journal of Mass Spectrometry

Volumn 304, Issue 2-3, 2011, Pages 184-194

  Kramer, Katharina ^a   Hummel, Petra ^a   Hsiao, He Hsuan ^a   Luo, Xiao ^b   Wahl, Markus ^b   Urlaub, Henning ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

4 Thio uracil; 5 Bromo uracil; Cross linking; Mass spectrometry; Protein; RNA

Indexed keywords

EID: 79959756726     PISSN: 13873806     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijms.2010.10.009     Document Type: Article

References (34)

1. M.D. Shetlar, J. Christensen, and K. Hom Photochemical addition of amino acids and peptides to DNA Photochem. Photobiol. 39 1984 125 133
2. E.I. Budowsky, M.S. Axentyeva, G.G. Abdurashidova, N.A. Simukova, and L.B. Rubin Induction of polynucleotide-protein cross-linkages by ultraviolet irradiation. Peculiarities of the high-intensity laser pulse irradiation Eur. J. Biochem. 159 1986 95 101 (Pubitemid 16049723)
3. W. Tate, B. Greuer, and R. Brimacombe Codon recognition in polypeptide chain termination: site directed crosslinking of termination codon to Escherichia coli release factor 2 Nucleic Acids Res. 18 1990 6537 6544
4. H. Urlaub, B. Thiede, E.C. Muller, R. Brimacombe, and B. Wittmann-Liebold Identification sequence analysis of contact sites between ribosomal proteins and rRNA in Escherichia coli 30 S subunits by a new approach using matrix-assisted laser desorption/ionization-mass spectrometry combined with N-terminal microsequencing J. Biol. Chem. 272 1997 14547 14555 (Pubitemid 27251714)
5. E. Kuhn-Holsken, C. Lenz, B. Sander, R. Luhrmann, and H. Urlaub Complete MALDI-ToF MS analysis of cross-linked peptide-RNA oligonucleotides derived from nonlabeled UV-irradiated ribonucleoprotein particles RNA 11 2005 1915 1930 (Pubitemid 41720040)
6. E. Kuhn-Holsken, O. Dybkov, B. Sander, R. Luhrmann, and H. Urlaub Improved identification of enriched peptide RNA cross-links from ribonucleoprotein particles (RNPs) by mass spectrometry Nucleic Acids Res. 35 2007 e95
7. C. Lenz, E. Kuhn-Holsken, and H. Urlaub Detection of protein-RNA crosslinks by NanoLC-ESI-MS/MS using precursor ion scanning and multiple reaction monitoring (MRM) experiments J. Am. Soc. Mass Spectrom. 18 2007 869 881 (Pubitemid 46617283)
8. F. Martin Richter, H.H. Hsiao, U. Plessmann, and H. Urlaub Enrichment of protein-RNA crosslinks from crude UV-irradiated mixtures for MS analysis by on-line chromatography using titanium dioxide columns Biopolymers 91 2009 297 309
9. X. Luo, H.H. Hsiao, M. Bubunenko, G. Weber, D.L. Court, M.E. Gottesman, H. Urlaub, and M.C. Wahl Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex Mol. Cell 32 2008 791 802
10. H. Steen, J. Petersen, M. Mann, and O.N. Jensen Mass spectrometric analysis of a UV-cross-linked protein-DNA complex: tryptophans 54 and 88 of E. coli SSB cross-link to DNA Protein Sci. 10 2001 1989 2001 (Pubitemid 32911218)
11. V. Pingoud, H. Geyer, R. Geyer, E. Kubareva, J.M. Bujnicki, and A. Pingoud Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII Mol. Biosyst. 1 2005 135 141 (Pubitemid 43362239)
12. E. Kuhn-Holsken, C. Lenz, A. Dickmanns, H.H. Hsiao, F.M. Richter, B. Kastner, R. Ficner, and H. Urlaub Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry Nucleic Acids Res. 2010
13. K.M. Meisenheimer, and T.H. Koch Photocross-linking of nucleic acids to associated proteins Crit. Rev. Biochem. Mol. Biol. 32 1997 101 140 (Pubitemid 27209328)
14. E.E. Blatter, Y.W. Ebright, and R.H. Ebright Identification of an amino acid-base contact in the GCN4-DNA complex by bromouracil-mediated photocrosslinking Nature 359 1992 650 652
15. B.J. Hicke, M.C. Willis, T.H. Koch, and T.R. Cech Telomeric protein-DNA point contacts identified by photo-cross-linking using 5-bromodeoxyuridine Biochemistry 33 1994 3364 3373 (Pubitemid 24112651)
16. M.C. Golden, K.A. Resing, B.D. Collins, M.C. Willis, and T.H. Koch Mass spectral characterization of a protein-nucleic acid photocrosslink Protein Sci. 8 1999 2806 2812 (Pubitemid 30007644)
17. H. Geyer, R. Geyer, and V. Pingoud A novel strategy for the identification of protein-DNA contacts by photocrosslinking and mass spectrometry Nucleic Acids Res. 32 2004 e132
18. I. Dix, C.S. Russell, R.T. O'Keefe, A.J. Newman, and J.D. Beggs Protein-RNA interactions in the U5 snRNP of Saccharomyces cerevisiae RNA 4 1998 1239 1250 (Pubitemid 28457854)
19. A. Favre, R. Bezerra, E. Hajnsdorf, Y. Lemaigre Dubreuil, and A. Expert-Bezancon Substitution of uridine in vivo by the intrinsic photoactivable probe 4-thiouridine in Escherichia coli RNA. Its use for E. coli ribosome structural analysis Eur. J. Biochem. 160 1986 441 449 (Pubitemid 17044414)
20. R. Bezerra, and A. Favre In vivo incorporation of the intrinsic photolabel 4-thiouridine into Escherichia coli RNAs Biochem. Biophys. Res. Commun. 166 1990 29 37 (Pubitemid 20040148)
21. A. Favre, G. Moreno, M.O. Blondel, J. Kliber, F. Vinzens, and C. Salet 4-Thiouridine photosensitized RNA-protein crosslinking in mammalian cells Biochem. Biophys. Res. Commun. 141 1986 847 854 (Pubitemid 17001934)
22. M. Hafner, M. Landthaler, L. Burger, M. Khorshid, J. Hausser, P. Berninger, A. Rothballer, M. Ascano Jr., A.C. Jungkamp, M. Munschauer, A. Ulrich, G.S. Wardle, S. Dewell, M. Zavolan, and T. Tuschl Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP Cell 141 2010 129 141
23. D.N. Perkins, D.J. Pappin, D.M. Creasy, and J.S. Cottrell Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 1999 3551 3567 (Pubitemid 30007252)
24. F.W. Studier Protein production by auto-induction in high density shaking cultures Protein Expr. Purif. 41 2005 207 234
25. M.R. Larsen, T.E. Thingholm, O.N. Jensen, P. Roepstorff, and T.J. Jorgensen Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns Mol. Cell. Proteomics 4 2005 873 886 (Pubitemid 41309146)
26. J.V. Olsen, B. Macek, O. Lange, A. Makarov, S. Horning, and M. Mann Higher-energy C-trap dissociation for peptide modification analysis Nat. Methods 4 2007 709 712 (Pubitemid 47338163)
27. K.L. Krivos, and P.A. Limbach Sequence analysis of peptide: oligonucleotide heteroconjugates by electron capture dissociation and electron transfer dissociation J. Am. Soc. Mass Spectrom. 21 2010 1387 1397
28. D. Fabris, and E.T. Yu Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D J. Mass Spectrom. 45 2010 841 860
29. E.T. Yu, A. Hawkins, I.D. Kuntz, L.A. Rahn, A. Rothfuss, K. Sale, M.M. Young, C.L. Yang, C.M. Pancerella, and D. Fabris The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches J. Proteome Res. 7 2008 4848 4857
30. S. Pourshahian, and P.A. Limbach Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry J. Mass Spectrom. 43 2008 1081 1088
31. H. Urlaub, K. Hartmuth, S. Kostka, G. Grelle, and R. Luhrmann A general approach for identification of RNA-protein cross-linking sites within native human spliceosomal small nuclear ribonucleoproteins (snRNPs). Analysis of RNA-protein contacts in native U1 and U4/U6.U5 snRNPs J. Biol. Chem. 275 2000 41458 41468 (Pubitemid 32054982)
32. H. Urlaub, K. Hartmuth, and R. Luhrmann A two-tracked approach to analyze RNA-protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles Methods 26 2002 170 181 (Pubitemid 34969579)
33. H Urlaub, E. Kuhn-Holsken, and R. Luhrmann Analyzing RNA-protein crosslinking sites in unlabeled ribonucleoprotein complexes by mass spectrometry Methods Mol. Biol. 488 2008 221 245
34. H. Urlaub, V.A. Raker, S. Kostka, and R. Luhrmann Sm protein-Sm site RNA interactions within the inner ring of the spliceosomal snRNP core structure EMBO J. 20 2001 187 196 (Pubitemid 32099115)