Directed evolution of a small-molecule-triggered intein with improved splicing properties in mammalian cells

Chemistry and Biology

Volumn 18, Issue 5, 2011, Pages 619-630

  Peck, Sun H ^a   Chen, Irwin ^a   Liu, David R ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4-HYDROXYTAMOXIFEN; AFIMOXIFENE; DRUG DERIVATIVE; HYBRID PROTEIN; INTEIN; TAMOXIFEN;

ARTICLE; CELL LINE; CHEMISTRY; DIRECTED MOLECULAR EVOLUTION; DRUG EFFECT; GENETICS; HUMAN; KINETICS; METABOLISM; MUTATION; PROTEIN PROCESSING; PROTEIN TERTIARY STRUCTURE; SACCHAROMYCES CEREVISIAE; TEMPERATURE;

CELL LINE; DIRECTED MOLECULAR EVOLUTION; HUMANS; INTEINS; KINETICS; MUTATION; PROTEIN SPLICING; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT FUSION PROTEINS; SACCHAROMYCES CEREVISIAE; TAMOXIFEN; TEMPERATURE;

MAMMALIA; SACCHAROMYCES CEREVISIAE;

EID: 79957473350     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2011.02.014     Document Type: Article

References (44)

1. M. Acar, B.F. Pando, F.H. Arnold, M.B. Elowitz, and A. van Oudenaarden A general mechanism for network-dosage compensation in gene circuits Science 329 2010 1656 1660
2. C.B. Bai, D. Stephen, and A.L. Joyner All mouse ventral spinal cord patterning by hedgehog is Gli dependent and involves an activator function of Gli3 Dev. Cell 6 2004 103 115 (Pubitemid 38089209)
3. L.A. Banaszynski, and T.J. Wandless Conditional control of protein function Chem. Biol. 13 2006 11 21 (Pubitemid 43099920)
4. L.A. Banaszynski, L.C. Chen, L.A. Maynard-Smith, A.G. Ooi, and T.J. Wandless A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules Cell 126 2006 995 1004 (Pubitemid 44310772)
5. M. Barna, P.P. Pandolfi, and L. Niswander Gli3 and Plzf cooperate in proximal limb patterning at early stages of limb development Nature 436 2005 277 281 (Pubitemid 41021280)
6. J.H. Bayle, J.S. Grimley, K. Stankunas, J.E. Gestwicki, T.J. Wandless, and G.R. Crabtree Rapamycin analogs with differential binding specificity permit orthogonal control of protein activity Chem. Biol. 13 2006 99 107 (Pubitemid 43099928)
7. A.R. Buskirk, and D.R. Liu Creating small-molecule-dependent switches to modulate biological functions Chem. Biol. 12 2005 151 161 (Pubitemid 40281323)
8. A.R. Buskirk, Y.C. Ong, Z.J. Gartner, and D.R. Liu Directed evolution of ligand dependence: small-molecule-activated protein splicing Proc. Natl. Acad. Sci. USA 101 2004 10505 10510 (Pubitemid 38955771)
9. P.S. Danielian, D. Muccino, D.H. Rowitch, S.K. Michael, and A.P. McMahon Modification of gene activity in mouse embryos in utero by a tamoxifen-inducible form of Cre recombinase Curr. Biol. 8 1998 1323 1326 (Pubitemid 29006707)
10. R. Feil, J. Brocard, B. Mascrez, M. LeMeur, D. Metzger, and P. Chambon Ligand-activated site-specific recombination in mice Proc. Natl. Acad. Sci. USA 93 1996 10887 10890 (Pubitemid 26333086)
11. A. Fire, S. Xu, M.K. Montgomery, S.A. Kostas, S.E. Driver, and C.C. Mello Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Nature 391 1998 806 811 (Pubitemid 28099681)
12. D.G. Gibson, L. Young, R.Y. Chuang, J.C. Venter, C.A. Hutchison 3rd, and H.O. Smith Enzymatic assembly of DNA molecules up to several hundred kilobases Nat. Methods 6 2009 343 345
13. M. Gossen, and H. Bujard Tight control of gene expression in mammalian cells by tetracycline-responsive promoters Proc. Natl. Acad. Sci. USA 89 1992 5547 5551
14. P.D. Hartley, and H.D. Madhani Mechanisms that specify promoter nucleosome location and identity Cell 137 2009 445 458
15. J. Huang, A. Koide, K.W. Nettle, G.L. Greene, and S. Koide Conformation-specific affinity purification of proteins using engineered binding proteins: application to the estrogen receptor Protein Expr. Purif. 47 2006 348 354 (Pubitemid 43729031)
16. C. Kellendonk, F. Tronche, A.P. Monaghan, P.O. Angrand, F. Stewart, and G. Schutz Regulation of Cre recombinase activity by the synthetic steroid RU 486 Nucleic Acids Res. 24 1996 1404 1411 (Pubitemid 26118971)
17. K. Koebernick, and T. Pieler Gli-type zinc finger proteins as bipotential transducers of Hedgehog signaling Differentiation 70 2002 69 76 (Pubitemid 38230556)
18. B.M. Lew, and H. Paulus An in vivo screening system against protein splicing useful for the isolation of non-splicing mutants or inhibitors of the RecA intein of Mycobacterium tuberculosis Gene 282 2002 169 177 (Pubitemid 34117573)
19. P. Marschang, J. Brich, E.J. Weeber, J.D. Sweatt, J.M. Shelton, J.A. Richardson, R.E. Hammer, and J. Herz Normal development and fertility of knockout mice lacking the tumor suppressor gene LRP1b suggest functional compensation by LRP1 Mol. Cell. Biol. 24 2004 3782 3793 (Pubitemid 38496157)
20. H.D. Mootz, and T.W. Muir Protein splicing triggered by a small molecule J. Am. Chem. Soc. 124 2002 9044 9045 (Pubitemid 34847653)
21. H.D. Mootz, E.S. Blum, A.B. Tyszkiewicz, and T.W. Muir Conditional protein splicing: a new tool to control protein structure and function in vitro and in vivo J. Am. Chem. Soc. 125 2003 10561 10569 (Pubitemid 37055907)
22. H.D. Mootz, E.S. Blum, and T.W. Muir Activation of an autoregulated protein kinase by conditional protein splicing Angew. Chem. Int. Ed. Engl. 43 2004 5189 5192 (Pubitemid 39382538)
23. F.B. Nygaard, and K.W. Harlow Heterologous expression of soluble, active proteins in Escherichia coli: the human estrogen receptor hormone-binding domain as paradigm Protein Expr. Purif. 21 2001 500 509 (Pubitemid 34179424)
24. M. Ormo, A.B. Cubitt, K. Kallio, L.A. Gross, R.Y. Tsien, and S.J. Remington Crystal structure of the Aequorea victoria green fluorescent protein Science 273 1996 1392 1395 (Pubitemid 26296528)
25. H. Paulus Protein splicing and related forms of protein autoprocessing Annu. Rev. Biochem. 69 2000 447 496
26. D. Picard Posttranslational regulation of proteins by fusions to steroid-binding domains Methods Enzymol. 327 2000 385 401 (Pubitemid 34193322)
27. M.R. Pratt, E.C. Schwartz, and T.W. Muir Small-molecule-mediated rescue of protein function by an inducible proteolytic shunt Proc. Natl. Acad. Sci. USA 104 2007 11209 11214 (Pubitemid 47175120)
28. C.K. Raymond, T.A. Pownder, and S.L. Sexson General method for plasmid construction using homologous recombination Biotechniques 26 1999 134 138 140-141
29. B. Sauer, and N. Henderson Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1 Proc. Natl. Acad. Sci. USA 85 1988 5166 5170
30. J.S. Schneekloth Jr., F.N. Fonseca, M. Koldobskiy, A. Mandal, R. Deshaies, K. Sakamoto, and C.M. Crews Chemical genetic control of protein levels: selective in vivo targeted degradation J. Am. Chem. Soc. 126 2004 3748 3754 (Pubitemid 38391867)
31. S.L. Schreiber The small-molecule approach to biology: chemical genetics and diversity-oriented organic synthesis make possible the systematic exploration of biology Chem. Eng. News 81 2003 51 61
32. E.C. Schwartz, L. Saez, M.W. Young, and T.W. Muir Post-translational enzyme activation in an animal via optimized conditional protein splicing Nat. Chem. Biol. 3 2007 50 54 (Pubitemid 46005698)
33. J. Shi, and T.W. Muir Development of a tandem protein trans-splicing system based on native and engineered split inteins J. Am. Chem. Soc. 127 2005 6198 6206 (Pubitemid 40627742)
34. M.A. Shogren-Knaak, P.J. Alaimo, and K.M. Shokat Recent advances in chemical approaches to the study of biological systems Annu. Rev. Cell Dev. Biol. 17 2001 405 433 (Pubitemid 33096182)
35. K.M. Specht, and K.M. Shokat The emerging power of chemical genetics Curr. Opin. Cell Biol. 14 2002 155 159 (Pubitemid 34219503)
36. K. Stankunas, J.H. Bayle, J.E. Gestwicki, Y.M. Lin, T.J. Wandless, and G.R. Crabtree Conditional protein alleles using knockin mice and a chemical inducer of dimerization Mol. Cell 12 2003 1615 1624 (Pubitemid 38037028)
37. B. Wang, J.F. Fallon, and P.A. Beachy Hedgehog-regulated processing of Gli3 produces an anterior/posterior repressor gradient in the developing vertebrate limb Cell 100 2000 423 434
38. H. Wang, E. Shimizu, Y.P. Tang, M. Cho, M. Kyin, W. Zuo, D.A. Robinson, P.J. Alaimo, C. Zhang, and H. Morimoto Inducible protein knockout reveals temporal requirement of CaMKII reactivation for memory consolidation in the brain Proc. Natl. Acad. Sci. USA 100 2003 4287 4292 (Pubitemid 36418195)
39. S.L. Wong, and F.P. Roth Transcriptional compensation for gene loss plays a minor role in maintaining genetic robustness in Saccharomyces cerevisiae Genetics 171 2005 829 833 (Pubitemid 43156468)
40. M.Q. Xu, M.W. Southworth, F.B. Mersha, L.J. Hornstra, and F.B. Perler In vitro protein splicing of purified precursor and the identification of a branched intermediate Cell 75 1993 1371 1377 (Pubitemid 24021911)
41. C.M. Yuen, S.J. Rodda, S.A. Vokes, A.P. McMahon, and D.R. Liu Control of transcription factor activity and osteoblast differentiation in mammalian cells using an evolved small-molecule-dependent intein J. Am. Chem. Soc. 128 2006 8939 8946 (Pubitemid 44061552)
42. M. Zaccolo, D.M. Williams, D.M. Brown, and E. Gherardi An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues J. Mol. Biol. 255 1996 589 603 (Pubitemid 26107188)
43. Y. Zhang, C. Riesterer, A.M. Ayrall, F. Sablitzky, T.D. Littlewood, and M. Reth Inducible site-directed recombination in mouse embryonic stem cells Nucleic Acids Res. 24 1996 543 548 (Pubitemid 26085826)
44. H. Zhao, and W. Zha In vitro 'sexual' evolution through the PCR-based staggered extension process (StEP) Nat. Protoc. 1 2006 1865 1871 (Pubitemid 46773307)