Cell-free selection of RNA-binding proteins using in vitro compartmentalization

Nucleic Acids Research

Volumn 36, Issue 19, 2008, Pages

  Chen, Yu ^a   Mandic, Jana ^a   Varani, Gabriele ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HYBRID PROTEIN; RNA BINDING PROTEIN; ZINC FINGER PROTEIN; RNA; SMALL NUCLEAR RIBONUCLEOPROTEIN; U1A PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; CELL COMPARTMENTALIZATION; DNA SEQUENCE; GENE CASSETTE; GENE EXPRESSION; GENOTYPE; IN VITRO STUDY; MOLECULAR EVOLUTION; PHAGE DISPLAY; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN FUNCTION; CHEMICAL STRUCTURE; CHEMISTRY; DIRECTED MOLECULAR EVOLUTION; EVALUATION; GENE LIBRARY; GENETICS; METHODOLOGY; MUTATION; PROTEIN ENGINEERING; PROTEIN TERTIARY STRUCTURE;

DIRECTED MOLECULAR EVOLUTION; GENE LIBRARY; GENOTYPE; MODELS, MOLECULAR; MUTATION; PHENOTYPE; PROTEIN ENGINEERING; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT FUSION PROTEINS; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RNA; RNA-BINDING PROTEINS; ZINC FINGERS;

EID: 56049091246     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn559     Document Type: Article

References (39)

1. Auweter,S.D., Obestrass,F.C. and Allain,F.H.T. (2006) Sequence-specific binding of single-stranded RNA: Is there a code for recognition? Nucleic Acids Res., 34, 4943-4959.
2. Lunde,B.M., Moore,C. and Varani,G. (2007) RNA-binding proteins: Modular design for efficient function. Nature Rev. Mol. Cell. Biol., 8 479-490.
3. Chen,Y. and Varani,G. (2005) Protein families and RNA recognition. FEBS J., 272, 2088-2097.
4. Pabo,C.O., Peisach,E. and Grant,R.A. (2001) Design and selection of novel Cys(2)His(2) zinc finger proteins. Annual Rev. Biochem., 70, 313-340.
5. Cheong,C.G. and Hall,T.M.T. (2006) Engineering RNA sequence specificity of Pumilio repeats. Proc. Natl Acad. Sci., 103, 13635-13639.
6. Wang,X., McLachlan,J., Zamore,P.D. and Hall,T.M.T. (2002) Modular recognition of RNA by a human pumilio-homology domain. Cell., 110, 501-512.
7. McColl,D.J., Honchell,C.D. and Frankel,A.D. (1999) Structure-based design of an RNA-binding zinc finger. Proc. Natl Acad. Sci., 96 9521-9526.
8. Friesen,W.J. and Darby,M.K. (1998) Specific RNA binding proteins constructed from zinc fingers. Nat. Stru. Biol., 5, 543-546.
9. Hudson,B.P., Martinez-Yamout,M.A., Dyson,H.J. and Wright,P.E. (2004) Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d. Nat. Stru. Mol. Biol., 111, 257-264.
10. Lu,D., Searles,M.A. and Klug,A. (2003) Crystal structure of a zinc finger - RNA complex reveals two modes of molecular recognition. Nature., 426, 96-100.
11. Chen,Y., Kortemme,T., Robertson,T. and Varani,G. (2004) A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contact and discriminate decoys. Nucleic Acids Res. 32, 5147-5162.
12. Zheng,S., Robertson,T.A. and Varani,G. (2007) An knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins. FEBS J., 274, 6378-6391.
13. Röthlisberger,D., Khersonsky,O., Wollacott,A.M., Jiang,L., DeChancie,J., Betker,J., Gallaher,J.L., Althoff,E.A., Zanghellini,A. et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature., 453, 190-195.
14. Kehoe,J.W. and Kay,B.K. (2005) Filamentous phage display in the new millennium. Chem. Rev., 105, 4056-4072.
15. Laird-Offringa,I.A. and Belasco,J.G. (1995) Analysis of RNAbinding proteins by in vitro genetic selection: Identification of an amino acid residue important for locking U1A onto its RNA target. Proc. Natl Acad. Sci., 92, 11859-11863.
16. Danner,S. and Belasco,J.G. (2001) T7 phage display: A novel genetic selection system for cloning RNA-binding proteins from cDNA libraries. Proc. Natl Acad. Sci., 98, 12954-12959.
17. Tawfik,D.S. and Griffiths,A.D. (1998) Man-made cell-like compartments for molecular evolution. Nature Biotech., 16, 652-656.
18. Miller,O.J., Bernath,K., Agresti,J.J., Amitai,G., Kelly,B.T., Mastrobattista,E., Taly,V., Magdassi,S., Tawfik,D.S. et al. (2006) Directed evolution by in vitro compartmentalization. Nature Methods 7, 561-570.
19. Griffiths,A.D. and Tawfik,D.S. (2006) Miniaturizing the laboratory in emulsion droplets. Trends in Biotech., 24, 395-402.
20. Sepp,A. and Choo,Y. (2005) Cell-free selection of zinc finger DNA-binding proteins using in vitro compartmentalization. J. Mol. Biol., 354, 212-219.
21. Ghadessy,F.J. and Holliger,P. (2004) A novel emulsion mixture for in vitro compartmentalization of transcription and translation in the rabbit reticulocyte system. Protein Eng. Des. Sel., 17, 201-204.
22. Kim,J.S. and Pabo,C.O. (1998) Getting a handhold on DNA: Design of poly-zinc finger proteins with femtomolar dissociation constants. Proc. Natl Acad. Sci., 95, 2812-2817.
23. Moore,M., Klug,A. and Choo,Y. (2001) Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units. Proc. Natl Acad. Sci., 98, 1437-1441.
24. Moore,M., Choo,Y. and Klug,A. (2001) Design of polyzinc finger peptides with structured linkers. Proc. Natl Acad. Sci., 98, 1432-1436.
25. Jessen,T.-H., Oubridge,C., Teo,C.H., Pritchard,C. and Nagai,K. (1991) Identification of molecule contacts between the U1A small ribonucleoprotein and U1 RNA. EMBO J., 10, 3447-3456.
26. Kranz,J.K. and Hall,K.B. (1999) RNA recognition by the human U1A protein is mediated by a network of local cooperative interactions that create the optimal binding surface. J. Mol. Biol., 285, 315-231.
27. George,R.A. and Heringa,J. (2003) An analysis of protein domain linkers: their classification and role in protein folding. Protein Eng., 15, 871-879.
28. Liu,Q., Segal,D.J., Ghiara,J.B. and Barbas,C.F. III (1997) Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. Proc. Natl Acad. Sci., 94, 5525-5530.
29. Park-Lee,S., Kim,S. and Laird-Offringa,I.A. (2003) Characterization of the interaction between neuronal RNA-binding protein HuD and AU-rich RNA. J. Biol. Chem., 278, 39801-39808.
30. Oubridge,C., Ito,N., Evans,P.R., Teo,C.H. and Nagai,K. (1994) Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature., 372, 432-438.
31. Allain,F.H.T., Howe,P.A., Neuhaus,D. and Varani,G. (1997) Structural basis of the RNA-binding specificity of human U1A protein. EMBO J. 16, 5764-5772.
32. Avis,J.M., Allain,F.H., Howe,P.W., Varani,G., Nagai,K. and Neuhaus,D. (1996) Solution structure of the N-terminal RNP domain of U1A protein: the role of C-terminal residues in structure stability and RNA binding. J. Mol. Biol., 257, 398-411.
33. Law,M.J., Chambers,E.J., Katsamba,P.S., Haworth,I.S. and Laird-Offringa, I.A. (2005) Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction. Nucleic Acid Res., 33, 2917-2928.
34. Shiels,J.C., Tuite,J.B., Nolan,S.J. and Baranger,A.M. (2002) Investigation of a conserved stacking interaction in target site recognition by the U1A protein. Nucleic Acids Res., 30, 550-558.
35. Birney,E., Kumar,S. and Krainer,A.R. (1993) Analysis of the RNA-recognition motif and RS and RGG domains: Conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res., 21, 5803-5816.
36. Simpson,G.G., Clark,G.P., Rothnie,H.M., Boelens,W., Van Venrooij,W. and Brown,J.W.S. (1995) Molecular characterization of the spliceosomal proteins U1A and U2B00 from higher plants. EMBO J., 14, 4540-4550.
37. Kranz,J.K., Lu,J. and Hall,K.B. (1996) Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain. Protein Sci., 5, 1567-1583.
38. Nolte,R.T., Conlin,R.M., Harrison,S.C. and Brown,R.S. (1998) Di.ering roles for zinc fingers in DNA recognition: Structure of a six-finger transcription factor IIIA complex. Proc. Natl Acad. Sci., 95 2938-2943.
39. Pavletich,N.P. and Pabo,C.O. (1991) Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.8Å. Science, 252, 809-817.