Mutational definition of binding requirements of an hnRNP-like protein in Arabidopsis using fluorescence correlation spectroscopy

Biochemical and Biophysical Research Communications

Volumn 453, Issue 1, 2014, Pages 69-74

  Leder, Verena ^a   Lummer, Martina ^a   Tegeler, Kathrin ^a   Humpert, Fabian ^a   Lewinski, Martin ^a   Schüttpelz, Mark ^a   Staiger, Dorothee ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

Fluorescence correlation spectroscopy; RNA binding protein; RNA protein interaction

Indexed keywords

GLUTATHIONE TRANSFERASE; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; NUCLEOTIDE; PHOSPHATE BUFFERED SALINE; ARABIDOPSIS PROTEIN; ATGRP7 PROTEIN, ARABIDOPSIS; PLANT DNA; PROTEIN BINDING; RNA BINDING PROTEIN;

ALGORITHM; ALTERNATIVE RNA SPLICING; ARABIDOPSIS THALIANA; ARTICLE; BINDING SITE; CURVE FITTING; DISSOCIATION CONSTANT; FLUORESCENCE CORRELATION SPECTROSCOPY; GEL MOBILITY SHIFT ASSAY; MUTATIONAL ANALYSIS; NEGATIVE FEEDBACK; NONHUMAN; POINT MUTATION; RNA BINDING; STEADY STATE; ARABIDOPSIS; CHEMISTRY; GENETICS; INTRON; METABOLISM; MUTATION; NUCLEOTIDE SEQUENCE; PLANT GENE; SITE DIRECTED MUTAGENESIS; SPECTROFLUOROMETRY;

ALTERNATIVE SPLICING; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; DNA, PLANT; GENES, PLANT; HETEROGENEOUS-NUCLEAR RIBONUCLEOPROTEINS; INTRONS; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTEIN BINDING; RNA-BINDING PROTEINS; SPECTROMETRY, FLUORESCENCE;

EID: 84908347242     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2014.09.056     Document Type: Article

References (30)

1. C. Maris, C. Dominguez, and F.H. Allain The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression FEBS J. 272 2005 2118 2131
2. G. Sachetto-Martins, L.O. Franco, and D.E. de Oliveira Plant glycine-rich proteins: a family or just proteins with a common motif? Biochim. Biophys. Acta 1492 2000 1 14
3. A. Ziemienowicz, D. Haasen, D. Staiger, and T. Merkle Arabidopsis transportin1 is the nuclear import receptor for the circadian clock-regulated RNA-binding protein AtGRP7 Plant Mol. Biol. 53 2003 201 212
4. M. Lummer, F. Humpert, C. Steuwe, M. Schüttpelz, M. Sauer, and D. Staiger Reversible photoswitchable DRONPA-s monitors nucleocytoplasmic transport of an RNA-binding protein in transgenic plants Traffic 12 2011 693 702
5. H. Siomi, and G. Dreyfuss A nuclear localization domain in the hnRNP A1 protein J. Cell Biol. 129 1995 551 560
6. C. Streitner, T. Köster, C.G. Simpson, P. Shaw, S. Danisman, J.W.S. Brown, and D. Staiger An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with target transcripts in Arabidopsis thaliana Nucleic Acids Res. 40 2012 11240 11255
7. T. Köster, K. Meyer, C. Weinholdt, L.M. Smith, M. Lummer, C. Speth, I. Grosse, D. Weigel, and D. Staiger Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis Nucleic Acids Res. 24 2014
8. D. Staiger, L. Zecca, D.A. Wieczorek Kirk, K. Apel, and L. Eckstein The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA Plant J. 33 2003 361 371
9. J.C. Schöning, C. Streitner, I.M. Meyer, Y. Gao, and D. Staiger Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis Nucleic Acids Res. 36 2008 6977 6987
10. C. Schmal, P. Reimann, and D. Staiger A circadian clock-regulated toggle switch explains AtGRP7 and AtGRP8 oscillations in Arabidopsis thaliana PLoS Comput. Biol. 2013
11. M. Schüttpelz, J.C. Schöning, S. Doose, H. Neuweiler, E. Peters, D. Staiger, and M. Sauer Changes of conformational dynamics of mRNA upon AtGRP7 binding studied by fluorescence correlation spectroscopy J. Am. Chem. Soc. 130 2008 9507 9513
12. H. Neuweiler, M. Lollmann, S. Doose, and M. Sauer Dynamics of unfolded polypeptide chains in crowded environment studied by fluorescence correlation spectroscopy J. Mol. Biol. 365 2007 856 869
13. E. Haustein, and P. Schwille Fluorescence correlation spectroscopy: novel variations of an established technique Annu. Rev. Biophys. Biomol. Struct. 36 2007 151 169
14. F. Khan, M.A. Daniëls, G.E. Folkers, R. Boelens, S.M. Saqlan Naqvi, and H.V. Ingen Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function Nucleic Acids Res. 42 2014 8705 8718
15. J.C. Schöning, C. Streitner, D.R. Page, S. Hennig, K. Uchida, E. Wolf, M. Furuya, and D. Staiger Autoregulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation Plant J. 52 2007 1119 1130
16. A. Fuhrmann, J.C. Schoening, D. Anselmetti, D. Staiger, and R. Ros Quantitative analysis of single-molecule RNA-protein interaction Biophys. J. 96 2009 5030 5039
17. J. Kim, S.R. Doose, H. Neuweiler, and M. Sauer The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy Nucleic Acids Res. 34 2006 2516 2527
18. S. Doose, H. Neuweiler, and M. Sauer A close look at fluorescence quenching of organic dyes by tryptophan ChemPhysChem 6 2005 2277 2285
19. S. Doose, H. Barsch, and M. Sauer Polymer properties of polythymine as revealed by translational diffusion Biophys. J. 93 2007 1224 1234
20. K. Nagai, C. Oubridge, T.H. Jessen, J. Li, and P.R. Evans Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A Nature 348 1990 515 520
21. Z.Q. Fu, M. Guo, B.R. Jeong, F. Tian, T.E. Elthon, R.L. Cerny, D. Staiger, and J.R. Alfano A type III effector ADP-ribosylates RNA-binding proteins and quells plant immunity Nature 447 2007 284 288
22. C. Streitner, S. Danisman, F. Wehrle, J.C. Schöning, J.R. Alfano, and D. Staiger The small glycine-rich RNA-binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana Plant J. 56 2008 239 250
23. B.-R. Jeong, Y. Lin, A. Joe, M. Guo, C. Korneli, H. Yang, P. Wang, M. Yu, R.L. Cerny, D. Staiger, J.R. Alfano, and Y. Xu Structure function analysis of an ADP-ribosyltransferase type III effector and its RNA-binding target in plant immunity J. Biol. Chem. 286 2011 43272 43281
24. V. Nicaise, A. Joe, B. Jeong, C. Korneli, F. Boutrot, I. Wested, D. Staiger, J.R. Alfano, and C. Zipfel Pseudomonas HopU1 affects interaction of plant immune receptor mRNAs to the RNA-binding protein GRP7 EMBO J. 32 2013 701 712
25. J.S. Kim, S.J. Park, K.J. Kwak, Y.O. Kim, J.Y. Kim, J. Song, B. Jang, C.H. Jung, and H. Kang Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli Nucleic Acids Res. 35 2006 506 516
26. F. Cobianchi, C. Calvio, M. Stoppini, M. Buvoli, and S. Riva Phosphorylation of human hnRNP protein A1 abrogates in vitro strand annealing activity Nucleic Acids Res. 21 1993 949 955
27. C. Streitner, L. Hennig, C. Korneli, and D. Staiger Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7 BMC Plant Biol. 10 2010 221
28. A. Werner, P.V. Konarev, D.I. Svergun, and U. Hahn Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering Anal. Biochem. 389 2009 52 62
29. A. Werner, V. Skakun, C. Meyer, and U. Hahn RNA dimerization monitored by fluorescence correlation spectroscopy Eur. Biophys. J. 40 2011 907 921
30. C.K. Nandi, P.P. Parui, B. Brutschy, U. Scheffer, and M. Göbel Fluorescence correlation spectroscopy at single molecule level on the Tat-TAR complex and its inhibitors Biopolymers 89 2008 17 25