Advantages of mRNA display selections over other selection techniques for investigation of protein-protein interactions

Expert Review of Proteomics

Volumn 8, Issue 3, 2011, Pages 335-346

  Wang, Hui ^a   Liu, Rihe ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

directed evolution; high throughput screening; in vitro selection; mRNA display; protein domain library; proteinprotein interaction; proteome library; random peptide library

Indexed keywords

MESSENGER RNA; POLYPEPTIDE;

AMINO ACID SEQUENCE; CELL COMPARTMENTALIZATION; CELL SURFACE; DNA LIBRARY; IMMUNOPRECIPITATION; MASS SPECTROMETRY; MUTAGENESIS; PHAGE DISPLAY; PROTEIN PROTEIN INTERACTION; REVIEW; RIBOSOME; TWO HYBRID SYSTEM;

ANIMALS; HUMANS; PEPTIDE LIBRARY; PROTEIN BINDING; RNA, MESSENGER;

EID: 79959397966     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/epr.11.15     Document Type: Review

References (81)

1. Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature 340(6230), 245-246 (1989). (Pubitemid 19171591)
2. Smith GP. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228(4705), 1315-1317 (1985). (Pubitemid 15000355)
3. Mattheakis LC, Bhatt RR, Dower WJ. An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc. Natl Acad. Sci. USA 91(19), 9022-9026 (1994).
4. Hanes J, Plückthun A. In vitro selection and evolution of functional proteins by using ribosome display. Proc. Natl Acad. Sci. USA 94(10), 4937-4942 (1997). (Pubitemid 27214714)
5. Roberts RW, Szostak JW. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl Acad. Sci. USA 94(23), 12297-12302 (1997). (Pubitemid 27492522)
6. Nemoto N, Miyamoto-Sato E, Husimi Y Yanagawa H. In vitro virus: bonding of mRNA bearing puromycin at the 3′-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro. FEBS Lett. 414(2), 405-408 (1997). (Pubitemid 27389405)
7. Liu R, Barrick JE, Szostak JW, Roberts RW. Optimized synthesis of RNA-protein fusions for in vitro protein selection. Methods Enzymol. 318, 268-293 (2000). (Pubitemid 30421654)
8. Tawfik DS, Griffiths AD. Man-made cell-like compartments for molecular evolution. Nat. Biotechnol. 16(7), 652-656 (1998). (Pubitemid 28334323)
9. Doi N, Yanagawa H. STABLE: protein- DNA fusion system for screening of combinatorial protein libraries in vitro. FEBS Lett. 457(2), 227-230 (1999). (Pubitemid 29401933)
10. Boder ET, Wittrup KD. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15(6), 553-557 (1997). (Pubitemid 27251573)
11. Francisco JA, Campbell R, Iverson BL, Georgiou G. Production and fluorescence-activated cell sorting of Escherichia coli expressing a functional antibody fragment on the external surface. Proc. Natl Acad. Sci. USA 90(22), 10444-10448 (1993). (Pubitemid 23347058)
12. Levin AM, Weiss GA. Optimizing the affinity and specificity of proteins with molecular display. Mol. Biosyst. 2, 49-57 (2006).
13. Roberts RW. Totally in vitro protein selection using mRNA-protein fusions and ribosome display. Curr. Opin. Chem. Biol. 3(3), 268-273(1999). (Pubitemid 29248622)
14. Hammond PW, Alpin J, Rise CE, Wright M, Kreider BL. In vitro selection and characterization of Bcl-X(L)-binding proteins from a mix of tissue-specific mRNA display libraries. J. Biol. Chem. 276(24), 20898-20906 (2001).
15. Cujec TP, Medeiros PF, Hammond P, Rise C, Kreider BL. Selection of v-abl tyrosine kinase substrate sequences from randomized peptide and cellular proteomic libraries using mRNA display. Chem. Biol. 9(2), 253-264 (2002). (Pubitemid 34196663)
16. McPherson M, Yang Y, Hammond PW, Kreider BL. Drug receptor identification from multiple tissues using cellular-derived mRNA display libraries. Chem. Biol. 9(6), 691-698 (2002). (Pubitemid 34653063)
17. Horisawa K, Tateyama S, Ishizaka M et al. In vitro selection of Jun-associated proteins using mRNA display. Nucleic Acids Res. 32(21), e169 (2004).
18. Shen X, Valencia CA, Szostak JW, Dong B, Liu R. Scanning the human proteome for calmodulin-binding proteins. Proc. Natl Acad. Sci. USA 102 (17), 5969-5974 (2005 (Pubitemid 40594239)
19. Shen X, Valencia CA, Gao W et al. Ca2+/calmodulin-binding proteins from the C. elegans proteome. Cell Calcium 43(5), 444-456 (2008).
20. Tateyama S, Horisawa K, Takashima H, Miyamoto-Sato E, Doi N, Yanagawa H. Affinity selection of DNA-binding protein complexes using mRNA display. Nucleic Acids Res. 34(3), e27 (2006).
21. Ju W, Valencia CA, Pang H et al. Proteome-wide identification of family member-specific natural substrate repertoire of caspases. Proc. Natl Acad. Sci. USA 104 (36), 14294-14299 (2007 (Pubitemid 350003256)
22. Fukuda I, Kojoh K, Tabata N et al. In vitro evolution of single-chain antibodies using mRNA display. Nucleic Acids Res. 34(19), e127 (2006).
23. Josephson K, Hartman MC, Szostak JW. Ribosomal synthesis of unnatural peptides. J. Am. Chem. Soc. 127, 11727-11735 (2005). (Pubitemid 41208758)
24. Seelig B, Szostak JW. Selection and evolution of enzymes from a partially randomized non-catalytic scaffold. Nature 448, 828-831 (2007). (Pubitemid 47266338)
25. Phizicky EM, Fields S. Protein-protein interactions: methods for detection and analysis. Microbiol. Rev. 59, 94-123 (1995).
26. Berggard T, Linse S, James P. Methods for the detection and analysis of protein- protein interactions. Proteomics 7, 2833-2842 (2007). (Pubitemid 47359924)
27. Luban J, Goff SP. The yeast two-hybrid system for studying protein-protein interactions. Curr. Opin. Biotechnol. 6(1), 59-64 (1995).
28. Miller J, Stagljar I. Using the yeast two-hybrid system to identify interacting proteins. Methods Mol. Biol. 261, 247-262 (2004).
29. Lin H, Cornish VW. Screening and selection methods for large-scale analysis of protein function. Angew. Chem. Int. Ed. 41, 4402-4425 (2002). (Pubitemid 35462383)
30. Huang H, Jedynak BM, Bader JS. Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput. Biol. 3(11), e214 (2007).
31. Parmley SF, Smith GP. Antibody-selectable filamentous fd phage vectors: affinity purification of target genes. Gene 73(2), 305-318 (1988). (Pubitemid 19043263)
32. Smith GP, Scott JK. Libraries of peptides and proteins displayed on filamentous phage. Methods Enzymol. 217, 228-257 (1993).
33. Conrad U, Scheller J. Considerations on antibody-phage display methodology. Comb. Chem. High Throughput Screen. 8(2), 117-126 (2005). (Pubitemid 40392511)
34. Adey NB, Kay BK. Identification of calmodulin-binding peptide consensus sequences from a phage-displayed random peptide library. Gene 169, 133-134 (1996). (Pubitemid 26075706)
35. Rhyner C, Weichel M, Fluckiger S, Hemmann S, Kleber-Janke T, Crameri R. Cloning allergens via phage display. Methods 32, 212-218 (2004 (Pubitemid 38201274)
36. Weaver-Feldhaus JM, Miller KD, Feldhaus MJ, Siegel RW. Directed evolution for the development of conformation-specific affinity reagents using yeast display. Protein Eng. Des. Sel. 18(11), 527-536 (2005). (Pubitemid 41547152)
37. Fukuda N, Ishii J, Shibasaki S, Ueda M, Fukuda H, Kondo A. High-efficiency recovery of target cells using improved yeast display system for detection of protein-protein interactions. Appl. Microbiol. Biotechnol. 76(1), 151-158 (2007). (Pubitemid 47194672)
38. Jung ST, Jeong KJ, Iverson BL, Georgiou G. Binding and enrichment of Escherichia coli spheroplasts expressing inner membrane tethered scFv antibodies on surface immobilized antigens. Biotechnol. Bioeng. 98(1), 39-47 (2007). (Pubitemid 47325821)
39. He M, Taussig MJ. Eukaryotic ribosome display with in situ DNA recovery. Nat. Methods 4(3), 281-288 (2007). (Pubitemid 46358880)
40. Zahnd C, Amstutz P, Plückthun A. Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat. Methods 4(3), 269-279 (2007). (Pubitemid 46358879)
41. Leemhuis H, Stein V, Griffiths AD, Hollfelder F. New genotype-phenotype linkages for directed evolution of functional proteins. Curr. Opin. Struct. Biol. 15, 472-478 (2005). (Pubitemid 41073840)
42. Rothe A, Surjadi RN, Power BE. Novel proteins in emulsions using in vitro compartmentalization. Trends Biotechnol. 24(12), 587-592 (2006). (Pubitemid 44751220)
43. Davidson EA, Dlugosz PJ, Levy M, Ellington AD. Directed evolution of proteins in vitro using compartmentalization in emulsions. Curr. Protoc. Mol. Biol. Chapter 24, Unit 24.6 (2009).
44. Lancet D, Sadovsky E, Seidemann E. Probability model for molecular recognition in biological receptor repertoires: significance to the olfactory system. Proc. Natl Acad. Sci. USA 90(8), 3715-3719 (1993). (Pubitemid 23111438)
45. Lander ES, Linton LM, Birren B et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001). (Pubitemid 32165345)
46. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).
47. Baneyx F, Mujacic M. Recombinant protein folding and misfolding in Escherichia coli. Nat. Biotechnol. 22(11), 1399-1408 (2004).
48. Porro D, Sauer M, Branduardi P, Mattanovich D. Recombinant protein production in yeasts. Mol. Biotechnol. 31(3), 245-259 (2005). (Pubitemid 41456758)
49. Endo Y, Sawasaki T. Cell-free expression systems for eukaryotic protein production. Curr. Opin. Biotechnol. 17(4), 373-380 (2006). (Pubitemid 44163458)
50. Bishop JO, Morton JG, Rosbash M, Richardson M. Three abundance classes in HeLa cell messenger RNA. Nature 250(463), 199-204 (1974).
51. Valencia CA, Cotten SW, Dong B, Liu R. mRNA-display-based selections for proteins with desired functions: a protease-substrate case study. Biotechnol. Prog. 24(3), 561-569 (2008). (Pubitemid 351832708)
52. Yuan L, Kurek I, English J, Keenan R. Laboratory-directed protein evolution. Microbiol. Mol. Biol. Rev. 69(3), 373-392 (2005). (Pubitemid 41306743)
53. Stebel SC, Gaida A, Arndt KM, Müller KM. Directed protein evolution. In:Molecular Biomethods Handbook, Second Edition (Part B). Walker JM, Rapley R (Eds). Humana Press, Totowa, NJ, USA, 631-656 (2008).
54. Tsuji T, Onimaru M, Doi N, Miyamoto-Sato E, Takashima H, Yanagawa H. In vitro selection of GTP-binding proteins by block shuffling of estrogen-receptor fragments. Biochem. Biophys. Res. Commun. 390(3), 689-693 (2009).
55. Liu CC, Schultz PG. Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79, 413-444 (2010).
56. Young TS, Schultz PG. Beyond the canonical 20 amino acids: expanding the genetic lexicon. J. Biol. Chem. 285(15), 11039-11044 (2010).
57. Li S, Millward S, Roberts R. In vitro selection of mRNA display libraries containing an unnatural amino acid. J. Am. Chem. Soc. 124(34), 9972-9973 (2002). (Pubitemid 34919718)
58. Sisido M, Ninomiya K, Ohtsuki T, Hohsaka T. Four-base codon/anticodon strategy and non-enzymatic aminoacylation for protein engineering with non-natural amino acids. Methods 36(3), 270-278 (2005). (Pubitemid 41074958)
59. Muranaka N, Hohsaka T, Sisido M. Four-base codon mediated mRNA display to construct peptide libraries that contain multiple non-natural amino acids. Nucleic Acids Res. 34(1), e7 (2006). (Pubitemid 43167923)
60. Hartman MC, Josephson K, Szostak JW. Enzymatic aminoacylation of tRNA with unnatural amino acids. Proc. Natl Acad. Sci. USA 103, 4356-4361 (2006).
61. Hartman MC, Josephson K, Lin CW, Szostak JW. An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides. PLoS One 2, e972 (2007).
62. Subtelny AO, Hartman MC, Szostak JW. Ribosomal synthesis of N-methyl peptides. J. Am. Chem. Soc. 130, 6131-6136 (2008). (Pubitemid 351657289)
63. Doi N, Takashima H, Wada A, Oishi Y, Nagano T, Yanagawa H. Photocleavable linkage between genotype and phenotype for rapid and efficient recovery of nucleic acids encoding affinity-selected proteins. J. Biotechnol. 131(3), 231-239 (2007). (Pubitemid 47362430)
64. Tabata N, Sakuma Y, Honda Y et al. Rapid antibody selection by mRNA display on a microfluidic chip. Nucleic Acids Res. 37(8), e64 (2009
65. Lamboy JA, Tam PY, Lee LS et al. Chemical and genetic wrappers for improved phage and RNA display. ChemBioChem 9(17), 2846-2852 (2008).
66. Kurz M, Gu K, Al-Gawari A, Lohse PA. cDNA-protein fusions: covalent protein- gene conjugates for the in vitro selection of peptides and proteins. ChemBioChem 2(9), 666-672 (2001). (Pubitemid 33722618)
67. Tabuchi I, Soramoto S, Nemoto N, Husimi Y. An in vitro DNA virus for in vitro protein evolution. FEBS Lett. 508(3), 309-312 (2001). (Pubitemid 33135460)
68. Yamaguchi J, Naimuddin M, Biyani M et al. cDNA display: a novel screening method for functional disulfide-rich peptides by solid-phase synthesis and stabilization of mRNA-protein fusions. Nucleic Acids Res. 37(16), e108 (2009
69. Huang BC, Liu R. Comparison of mRNA-display-based selections using synthetic peptide and natural protein libraries. Biochemistry 46, 10102-10112 (2007). (Pubitemid 47378602)
70. Wilson DS, Keefe AD, Szostak JW. The use of mRNA display to select high-affinity protein-binding peptides. Proc. Natl Acad. Sci. USA 98, 3750-3755 (2001 (Pubitemid 32249843)
71. Xu L, Aha P, Gu K et al. Directed evolution of high-affinity antibody mimics using mRNA display. Chem. Biol. 9, 933-942 (2002 (Pubitemid 35240913)
72. Ja WW, Olsen BN, Roberts RW. Epitope mapping using mRNA display and a unidirectional nested deletion library. Protein Eng. Des. Sel. 18, 309-319 (2005). (Pubitemid 41399425)
73. Olson CA, Liao HI, Sun R, Roberts RW. mRNA display selection of a high-affinity, modification-specific phospho-IkBa-binding fibronectin. ACS Chem. Biol. 3(8), 480-485 (2008
74. Liao HI, Olson CA, Hwang S et al. mRNA display design of fibronectin-based intrabodies that detect and inhibit severe acute respiratory syndrome coronavirus nucleocapsid protein. J. Biol. Chem. 284(26), 17512-17520 (2009).
75. Matsumura N, Tsuji T, Sumida T et al. mRNA display selection of a high-affinity, Bcl-X(L)-specific binding peptide. FASEB J. 24(7), 2201-2210 (2010).
76. Kosugi S, Hasebe M, Matsumura et al. Six classes of nuclear localization signals specific to different binding grooves of importin alpha. J. Biol. Chem. 284, 478-485 (2009).
77. Austin RJ, Ja WW, Roberts RW. Evolution of class-specific peptides targeting a hot spot of the Gas subunit. J. Mol. Biol. 377, 1406-1418 (2008).
78. Shen X, Xi G, Radhakrishnan Y, Clemmons DR. Identification of novel SHPS-1-associated proteins and their roles in regulation of insulin-like growth factor-dependent responses in vascular smooth muscle cells. Mol. Cell Proteomics 8(7), 1539-1551 (2009).
79. Miyamoto-Sato E, Fujimori S, Ishizaka M et al. A comprehensive resource of interacting protein regions for refining human transcription factor networks. PLoS One. 5(2), e9289 (2010).
80. Shibui T, Kobayashi T, Shiratori M. Isolation of cross-reacting antigen candidates by mRNA-display using a mixed cDNA library. Biotechnol. Lett. 30(12), 2037-2043 (2008
81. Adnexus Therapeutics. PROfusion Discovery Engine www.adnexustx.com/ science-profusion. html