Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d

Nature Structural and Molecular Biology

Volumn 11, Issue 3, 2004, Pages 257-264

  Hudson, Brian P ^a   Martinez Yamout, Maria A ^a   Dyson, H Jane ^a   Wright, Peter E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D; MESSENGER RNA; PROTEIN; PROTEIN TIS11D; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

3' UNTRANSLATED REGION; ADENYLATION; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; HUMAN; HUMAN CELL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; RNA SEQUENCE; ZINC FINGER MOTIF;

3' UNTRANSLATED REGIONS; ADENINE; BASE COMPOSITION; BINDING SITES; DNA-BINDING PROTEINS; ELECTROSTATICS; HUMANS; HYDROGEN BONDING; IMMEDIATE-EARLY PROTEINS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; RNA, MESSENGER; TRISTETRAPROLIN; URACIL; ZINC FINGERS;

EID: 1442311533     PISSN: 15459993     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsmb738     Document Type: Article

References (52)

1. Blackshear, P.J. Tristetraprolin and other CCCH tandem zinc-finger proteins in the regulation of mRNA turnover. Biochem. Soc. Trans. 30, 945-952 (2002).
2. Ming, X.F., Stoecklin, G., Lu, M., Looser, R. & Moroni, C. Parallel and independent regulation of interleukin-3 mRNA turnover by phosphatidylinositol 3-kinase and p38 mitogen-activated protein kinase. Mol. Cell. Biol. 21, 5778-5789 (2001).
3. Varnum, B.C., Ma, Q.F., Chi, T.H., Fletcher, B. & Herschman, H.R. The TIS11 primary response gene is a member of a gene family that encodes proteins with a highly conserved sequence containing an unusual Cys-His repeat. Mol. Cell. Biol. 11, 1754-1758 (1991).
4. Lai, W.S., Stumpo, D.J. & Blackshear, P.J. Rapid insulin-stimulated accumulation of an mRNA encoding a proline-rich protein. J. Biol. Chem. 265, 16556-16563 (1990).
5. DuBois, R.N., McLane, M.W., Ryder, K., Lau, L.F. & Nathans, D. A growth factor-inducible nuclear protein with a novel cysteine/histidine repetitive sequence. J. Biol. Chem. 265, 19185-19191 (1990).
6. Lai, W.S., Carballo, E., Thorn, J.M., Kennington, E.A. & Blackshear, P.J. Interactions of CCCH zinc finger proteins with mRNA-binding of tristetraprolin-related zinc finger proteins to Au-rich elements and destabilization of mRNA. J. Biol. Chem. 275, 17827-17837 (2000).
7. Carballo, E., Lai, W.S. & Blackshear, P.J. Feedback inhibition of macrophage tumor necrosis factor-α production by tristetraprolin. Science 281, 1001-1005 (1998).
8. Taylor, G.A. et al. A pathogenetic role for TNF alpha in the syndrome of cachexia, arthritis, and autoimmunity resulting from tristetraprolin (TTP) deficiency. Immunity 4, 445-454 (1996).
9. Chen, C.Y. et al. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107, 451-464 (2001).
10. Lai, W.S., Kennington, E.A. & Blackshear, P.J. Interactions of CCCH zinc finger proteins with mRNA. Non-binding tristetraprolin mutants exert an inhibitory effect on degradation of AU-rich element-containing mRNAs. J. Biol. Chem. 277, 9606-9613 (2002).
11. Worthington, M.T., Amann, B.T., Nathans, D. & Berg, J.M. Metal binding properties and secondary structure of the zinc-binding domain of Nup475. Proc. Natl. Acad. Sci. USA 93, 13754-13759 (1996).
12. Lai, W.S. et al. Evidence that tristetraprolin binds to AU-rich elements and promotes the deadenylation and destabilization of tumor necrosis factor α mRNA. Mol. Cell. Biol. 19, 4311-4323 (1999).
13. Worthington, M.T. et al. RNA binding properties of the AU-rich element-binding recombinant Nup475/TIS11/tristetraprolin protein. J. Biol. Chem. 277, 48558-48564 (2002).
14. Blackshear, P.J. et al. Characteristics of the interaction of a synthetic human tristetraprolin tandem zinc finger peptide with AU-rich element-containing RNA substrates. J. Biol. Chem. 278, 19947 (2003).
15. De Guzman, R.N. et al. Structure of the HIV-1 nucleocapsid protein bound to the SL3 Psi-RNA recognition element. Science 279, 384-388 (1998).
16. Holm, L. & Sander, C. Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20, 478-480 (1995).
17. Amann, B.T., Worthington, M.T. & Berg, J.M. A Cys3His zinc-binding domain from Nup475/tristetraprolin: a novel fold with a disklike structure. Biochemistry 42, 217-221 (2003).
18. Chen, C.Y. & Shyu, A.B. AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem. Sci 20, 465-470 (1995).
19. Wang, X. & Tanaka Hall, TM. Structural basis for recognition of AU-rich element RNA by the HuD protein. Nat. Struct. Biol. 8, 141-145 (2001).
20. Handa, N. et al. Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature 398, 579-585 (1999).
21. Deo, R.C., Bonanno, J.B., Sonenberg, N. & Burley, S.K. Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell 98, 835-845 (1999).
22. Guedes, S. & Priess, J.R. The C. elegans MEX-1 protein is present in germline blastomeres and is a P granule component. Development 124, 731-739 (1997).
23. Tabara, H., Hill, R.J., Mello, C.C., Priess, J.R. & Kohara, Y. pos-1 encodes a cytoplasmic zinc-finger protein essential for germline specification in C. elegans. Development 126, 1-11 (1999).
24. Reese, K.J., Dunn, M.A., Waddle, J.A. & Seydoux, G. Asymmetric segregation of PIE-1 in C. elegans is mediated by two complementary mechanisms that act through separate PIE-1 protein domains. Mol. Cell 6, 445-455 (2000).
25. Bai, C.Y. & Tolias, P.P. Cleavage of RNA hairpins mediated by a developmentally regulated CCCH zinc finger protein. Mol. Cell. Biol. 16, 6661-6667 (1996).
26. Hendriks, E.F., Robinson, D.R., Hinkins, M. & Matthews. K.R. A novel CCCH protein which modulates differentiation of Trypanosoma brucei to its procyclic form. EMBO J. 20, 6700-6711 (2001).
27. 15N chemical shift referencing in biomolecular NMR. J. Biomol. NMR6, 135-140 (1995).
28. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293 (1995).
29. Johnson, B.A. & Blevins, R.A. NMRView: a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 604-613 (1994).
30. Wittekind, M. & Mueller, L. HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the α- and β-carbon resonances in proteins. J. Magn. Reson. 101, 201-205 (1993).
31. Grzesiek, S. & Bax, A. Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR. J. Am. Chem. Soc. 114, 6291-6293 (1992).
32. Grzesiek, S. & Bax, A. Improved 3D triple-resonance NMR techniques applied to a 31 kDa protein. J. Magn. Reson. 96, 432-440 (1992).
33. 13C magnetization. J. Magn. Reson. B 101, 114-119 (1993).
34. 13C-enriched proteins. J. Magn. Reson. 88, 425-431 (1990).
35. 13C-labeled proteins via scalar couplings. J. Am. Chem. Soc. 115, 11054-11055 (1993).
36. α coupling constants as a probe for protein backbone conformation. J. Biomol. NMR 3, 67-80 (1993).
37. 15N with side chain Hβ resonances in larger proteins. J. Magn. Reson. 95, 636-641 (1991).
38. Zwahlen, C. et al. Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: Application to a bacteriophage λ N-peptide/boxB RNA complex. J. Am. Chem. Soc. 119, 6711-6721 (1997).
39. Grzesiek, S., Kuboniwa, H., Hinck, A.P. & Bax, A. Multiple-quantum line narrowing for measurement of Hα-Hβ J coupling in isotopically enriched proteins. J. Am. Chem. Soc. 117, 5312-5315 (1995).
40. cc couplings between backbone carbonyl and methyl carbons in isotopically enriched proteins. J. Biomol. NMR 3, 487-493 (1993).
41. 13C. J. Am. Chem. Soc. 115, 5334-5335 (1993).
42. Hansen, M.R., Mueller, L. & Pardi, A. Tunable alignment of macromolecules by fi amentous phage yields dipolar coupling interactions. Nat. Struct. Biol. 5, 1065-1074 (1998).
43. 13C' dipolar couplings in a perdeuterated 30 kDa protein dissolved in a dilute liquid crystalline phase. J. Am. Chem. Soc. 120, 7385-7386 (1998).
44. 13C labeled proteins. J. Biomol. NMR 12, 325-332 (1998).
45. Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298 (1997).
46. Duggan, B.M., Legge, G.B., Dyson, H.J. & Wright, P.E. SANE (structure assisted NOE evaluation): an automated model-based approach for NOE assignment. J. Biomol. NMR 19, 321-329 (2001).
47. Cornilescu, G., Delaglio, F. & Bax, A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289-302 (1999).
48. Tsui, V. & Case, D.A. Molecular simulations of nucleic acids using a generalized Born solvation model. J. Am. Chem. Soc. 122, 2489-2498 (2000).
49. Dosset, P., Hus, J.C., Marion, D. & Blackledge, M. A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings. J. Biomol. NMR 20, 223-231 (2001).
50. Koradi, R., Billeter, M. & Wüthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graphics 14, 51-55 (1996).
51. Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296 (1991).
52. Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R. & Thornton, J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR8, 477-486 (1996).