Long-range interactions in nonsense-mediated mRNA decay are mediated by intrinsically disordered protein regions

Journal of Molecular Biology

Volumn 424, Issue 3-4, 2012, Pages 125-131

  Kalmar, Lajos ^a   Acs, Veronika ^a   Silhavy, Daniel ^b   Tompa, Peter ^a,c,d  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^b SZENT ISTVÁN UNIVERSITY   (Hungary)

^c DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^d VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

Author keywords

fly casting; long range interaction; nonsense mediated decay; protein disorder

Indexed keywords

ERF1 PROTEIN; ERF3 PROTEIN; INITIATION FACTOR 4A; MAGOH PROTEIN; MESSENGER RNA; MLN51 PROTEIN; NCBP1 PROTEIN; NCBP2 PROTEIN; PABP1 PROTEIN; PABP2 PROTEIN; PNRC2 PROTEIN; PROTEIN; RNPS1 PROTEIN; SMG5 PROTEIN; SMG6 PROTEIN; SMG7 PROTEIN; SMG8 PROTEIN; SMG9 PROTEIN; UNCLASSIFIED DRUG; UPF1 PROTEIN; UPF2 PROTEIN; UPF3B PROTEIN; WIBG PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CODON; MOLECULAR BIOLOGY; NONSENSE MEDIATED MESSENGER RNA DECAY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RNA DEGRADATION; RNA STRUCTURE;

EID: 84869084749     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2012.09.002     Document Type: Article

References (28)

1. L.E. Maquat, W.Y. Tarn, and O. Isken The pioneer round of translation: features and functions Cell 142 2010 368 374
2. S. Durand, and J. Lykke-Andersen SnapShot: nonsense-mediated mRNA decay Cell 145 2011 324 324.e2
3. A.B. Eberle, L. Stalder, H. Mathys, R.Z. Orozco, and O. Muhlemann Posttranscriptional gene regulation by spatial rearrangement of the 3′ untranslated region PLoS Biol. 6 2008 e92
4. J. Hwang, H. Sato, Y. Tang, D. Matsuda, and L.E. Maquat UPF1 association with the cap-binding protein, CBP80, promotes nonsense-mediated mRNA decay at two distinct steps Mol. Cell 39 2010 396 409
5. K.D. Pruitt, T. Tatusova, G.R. Brown, and D.R. Maglott NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy Nucleic Acids Res. 40 2010 D130 D135
6. B.A. Shoemaker, J.J. Portman, and P.G. Wolynes Speeding molecular recognition by using the folding funnel: the fly-casting mechanism Proc. Natl Acad. Sci. USA 97 2000 8868 8873 (Pubitemid 30626639)
7. P. Tompa Structure and Function of Intrinsically Disordered Proteins 2009 CRC Press (Taylor and Francis Group) Boca Raton, FL
8. Z. Dosztanyi, V. Csizmok, P. Tompa, and I. Simon The pairwise energy content estimated from amino acid composition discriminates between folded and instrinsically unstructured proteins J. Mol. Biol. 347 2005 827 839 (Pubitemid 40357923)
9. Z. Dosztanyi, V. Csizmok, P. Tompa, and I. Simon IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content Bioinformatics 21 2005 3433 3434 (Pubitemid 41222453)
10. A. Lupas, M. Van Dyke, and J. Stock Predicting coiled coils from protein sequences Science 252 1991 1162 1164 (Pubitemid 21917026)
11. Z. Dosztanyi, B. Meszaros, and I. Simon ANCHOR: web server for predicting protein binding regions in disordered proteins Bioinformatics 25 2009 2745 2746
12. P.V. Ivanov, N.H. Gehring, J.B. Kunz, M.W. Hentze, and A.E. Kulozik Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways EMBO J. 27 2008 736 747 (Pubitemid 351506680)
13. I. Rebbapragada, and J. Lykke-Andersen Execution of nonsense-mediated mRNA decay: what defines a substrate? Curr. Opin. Cell Biol. 21 2009 394 402
14. G. Singh, I. Rebbapragada, and J. Lykke-Andersen A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay PLoS Biol. 6 2008 e111
15. D. Suveges, Z. Gaspari, G. Toth, and L. Nyitray Charged single alpha-helix: a versatile protein structural motif Proteins 74 2009 905 916
16. N.H. Gehring, S. Lamprinaki, M.W. Hentze, and A.E. Kulozik The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay PLoS Biol. 7 2009 e1000120
17. H. Cho, K.M. Kim, and Y.K. Kim Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex Mol. Cell 33 2009 75 86
18. Y. Okada-Katsuhata, A. Yamashita, K. Kutsuzawa, N. Izumi, F. Hirahara, and S. Ohno N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD Nucleic Acids Res. 40 2011 1251 1266
19. A.H. Benkovics, T. Nyiko, Z. Merai, D. Silhavy, and G.D. Bisztray Functional analysis of the grapevine paralogs of the SMG7 NMD factor using a heterolog VIGS-based gene depletion-complementation system Plant Mol. Biol. 75 2011 277 290
20. N. Fukuhara, J. Ebert, L. Unterholzner, D. Lindner, E. Izaurralde, and E. Conti SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway Mol. Cell 17 2005 537 547 (Pubitemid 40269118)
21. I. Kashima, S. Jonas, U. Jayachandran, G. Buchwald, E. Conti, A.N. Lupas, and E. Izaurralde SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay Genes Dev. 24 2010 2440 2450
22. P. Romero, Z. Obradovic, X. Li, E.C. Garner, C.J. Brown, and A.K. Dunker Sequence complexity of disordered protein Proteins 42 2001 38 48
23. Y. Huang, and Z. Liu Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the fly-casting mechanism J. Mol. Biol. 393 2009 1143 1159
24. D. Vuzman, A. Azia, and Y. Levy Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails J. Mol. Biol. 396 2010 674 684
25. T.R. Dafforn, and C.J. Smith Natively unfolded domains in endocytosis: hooks, lines and linkers EMBO Rep. 5 2004 1046 1052 (Pubitemid 39600202)
26. M. Clerici, A. Mourao, I. Gutsche, N.H. Gehring, M.W. Hentze, A. Kulozik, J. Kadlec, M. Sattler, and S. Cusack Unusual bipartite mode of interaction between the nonsense-mediated decay factors, UPF1 and UPF2 EMBO J. 28 2009 2293 2306
27. G. Buchwald, J. Ebert, C. Basquin, J. Sauliere, U. Jayachandran, and F. Bono Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex Proc. Natl Acad. Sci. USA 107 2010 10050 10055
28. Y. Ishigaki, X. Li, G. Serin, and L.E. Maquat Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20 Cell 106 2001 607 617 (Pubitemid 32879322)