Transposon-directed base-exchange mutagenesis (TDEM): A novel method for multiple-nucleotide substitutions within a target gene

BioTechniques

Volumn 46, Issue 7, 2009, Pages 534-542

  Kim, Yun Cheol ^a   Lee, Hui Sun ^b   Yoon, Sukjoon ^b   Morrison, Sherie L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Sookmyung Women's University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GALACTOSIDASE; DNA BASE; NUCLEOTIDE;

ALPHA RHYTHM; ARTICLE; BACTERIAL GENE; BASE PAIRING; CODON; DNA SEQUENCE; FRAMESHIFT MUTATION; GENE DELETION; GENE INSERTION; GENE MUTATION; GENE TARGETING; LIBRARY; MUTAGENESIS; MUTANT; MUTATION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; REVERTANT; TRANSPOSON; AMINO ACID SEQUENCE; CHEMISTRY; GENETICS; LACTOSE OPERON; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POLYMERASE CHAIN REACTION; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; BASE PAIRING; BASE SEQUENCE; BETA-GALACTOSIDASE; DNA TRANSPOSABLE ELEMENTS; LAC OPERON; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; MUTATION; NUCLEOTIDES; OPEN READING FRAMES; POLYMERASE CHAIN REACTION;

EID: 70349264444     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/000113152     Document Type: Article

References (45)

1. Clarke, N.D., D.C. Lien, and P. Schimmel. 1988. Evidence from cassette mutagenesis for a structure-function motif in a protein of unknown structure. Science 240:521-523.
2. Zhang, Z., J. Akutsu, M. Tsujimura, and Y. Kawarabayasi. 2007. Increasing in archaeal GlcNAc-1-P uridyltransferase activity by targeted mutagenesis while retaining its extreme thermostability. J. Biochem. 141:553-562.
3. Bridges, B.A. 1969. Mechanisms of radiation mutagenesis in cellular and subcellular systems. Annu. Rev. Nucl. Sci. 19:139-178.
4. Witkin, E.M. 1976. Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli. Bacteriol. Rev. 40:869-907.
5. Mattern, I.E., J.M. van Noort, P. van den Berg, D.B. Archer, I.N. Roberts, and C.A. van den Hondel. 1992. Isolation and characterization of mutants of Aspergillus niger deficient in extracellular proteases. Mol. Gen. Genet. 234:332-336.
6. Kano, H., S. Taguchi, and H. Momose. 1997. Cold adaptation of a mesophilic serine protease, subtilisin, by in vitro random mutagenesis. Appl. Microbiol. Biotechnol. 47:46-51.
7. Kadonaga, J.T. and J.R. Knowles. 1985. A simple and efficient method for chemical mutagenesis of DNA. Nucleic Acids Res. 13:1733-1745.
8. Hutchison, C.A., 3rd, S. Phillips, M.H. Edgell, S. Gillam, P. Jahnke, and M. Smith. 1978. Mutagenesis at a specific position in a DNA sequence. J. Biol. Chem. 253:6551-6560.
9. Sen, S., V. Venkata Dasu, and B. Mandal. 2007. Developments in directed evolution for improving enzyme functions. Appl. Biochem. Biotechnol. 143:212-223.
10. Ho, S.N., H.D. Hunt, R.M. Horton, J.K. Pullen, and L.R. Pease. 1989. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59.
11. Sarkar, G. and S.S. Sommer. 1990. The "megaprimer" method of site-directed mutagenesis. BioTechniques 8:404-407.
12. Cunningham, B.C. and J.A. Wells. 1989. High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science 244:1081-1085.
13. Bass, S.H., M.G. Mulkerrin, and J.A. Wells. 1991. A systematic mutational analysis of hormone-binding determinants in the human growth hormone receptor. Proc. Natl. Acad. Sci. USA 88:4498-4502.
14. Childers, B.M., G.G. Weber, M.G. Prouty, M.M. Castaneda, F. Peng, and K.E. Klose. 2007. Identification of residues critical for the function of the Vibrio cholerae virulence regulator ToxT by scanning alanine mutagenesis. J. Mol. Biol. 367:1413-1430.
15. Sorensen, H. , L. Whit taker, J. Hinrichsen, A. Groth, and J. Whittaker. 2004. Mapping of the insulin-like growth factor II binding site of the Type I insulin-like growth factor receptor by alanine scanning mutagenesis. FEBS Lett. 565:19-22.
16. Miyamoto, M., G.D. Han, T. Kimura, Y. Furuichi, and T. Komiyama. 2005. Alanine-scanning mutagenesis of HM-1 killer toxin and the essential residues for killing activity. J. Biochem. 137:517-522.
17. Sahin-Toth, M. and H.R. Kaback. 1993. Cysteine scanning mutagenesis of putative transmembrane helices IX and X in the lactose permease of Escherichia coli. Protein Sci. 2:1024-1033. (Pubitemid 23152094)
18. Fri l l ingos, S., M. Sahin-Toth, J. Wu, and H.R. Kaback. 1998. Cys-scanning mutagenesis: a novel approach to structure function relationships in polytopic membrane proteins. FASEB J. 12:1281-1299.
19. Kuwabara, N., H. Inoue, Y. Tsuboi, N. Nakamura, and H. Kanazawa. 2004. The fourth transmembrane domain of the Helicobacter pylori Na+/H+ antiporter NhaA faces a water-filled channel required for ion transport. J. Biol. Chem. 279:40567-40575.
20. Low, N.M., P.H. Holliger, and G. Winter. 1996. Mimicking somatic hypermutation: affinity maturation of antibodies displayed on bacteriophage using a bacterial mutator strain. J. Mol. Biol. 260:359-368.
21. Boder, E.T. and K.D. Wittrup. 1997. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15:553-557.
22. Liao, H., T. McKenzie, and R. Hageman. 1986. Isolation of a thermostable enzyme variant by cloning and selection in a thermophile. Proc. Natl. Acad. Sci. USA 83:576-580.
23. Bornscheuer, U.T., J. Altenbuchner, and H.H. Meyer. 1998. Directed evolution of an esterase for the stereoselective resolution of a key intermediate in the synthesis of epothilones. Biotechnol. Bioeng. 58:554-559.
24. Stemmer, W.P. 1994. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370:389-391.
25. Cadwell, R.C. and G.F. Joyce. 1992. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2:28-33.
26. Sheryl, B. Rubin-Pitel, C.M.-H.C., Wilfred Chen, Huimin Zhao. 2006. Directed evolution tools in bioproduct and bioprocess development, p. 49-72. In S.-T. Yang (Ed.) Bioprocessing for Value-Added Products from Renewable Resources: New Technologies and Applications, Elsevier Science, New York.
27. Murakami, H., T. Hohsaka, and M. Sisido. 2002. Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nat. Biotechnol. 20:76-81.
28. Poussu, E., M. Vihinen, L. Paulin, and H. Savilahti. 2004. Probing the alpha-complementing domain of E. coli beta-galactosidase with use of an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition. Proteins 54:681-691.
29. Anton, B.P. and E.A. Raleigh. 2004. Transposon-mediated linker insertion scanning mutagenesis of the Escherichia coli McrA endonuclease. J. Bacteriol. 186:5699-5707.
30. Haapa, S., S. Taira, E. Heikkinen, and H. Savilahti. 1999. An efficient and accurate integration of mini-Mu transposons in vitro: a general methodology for functional genetic analysis and molecular biology applications. Nucleic Acids Res. 27:2777-2784.
31. Biery, M.C., F.J. Stewart, A.E. Stellwagen, E.A. Raleigh, and N.L. Craig. 2000. A simple in vitro Tn7-based transposition system with low target site selectivity for genome and gene analysis. Nucleic Acids Res. 28:1067-1077.
32. Kim, Y.C. and S.L. Morrison. 2008. N-terminal domain-deleted Mu transposase exhibits increased transposition activity with low target site preference in modified buffers. J. Mol. Microbiol. Biotechnol. Nov 25. [Epub ahead of print]
33. Craig, N.L. 1995. Unity in transposition reactions. Science 270:253-254.
34. Wong, T.S., K.L. Tee, B. Hauer, and U. Schwaneberg. 2004. Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution. Nucleic Acids Res. 32:e26.
35. Boeke, J.D. and P. Model. 1982. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. Proc. Natl. Acad. Sci. USA 79:5200-5204.
36. Wang, L. and P.G. Schultz. 2001. A general approach for the generation of orthogonal tRNAs. Chem. Biol. 8:883-890.
37. Wang L, T.J. Magliery, D.R. Liu, and P.G. Schultz. 2000. A new functional suppressor tRNA/aminoacyl-tRNA synthetase pair for the in vivo incorporation of unnatural amino acids into proteins. J. Am. Chem. Soc. 122:5010-5011.
38. Bernard, P. and M. Couturier. 1992. Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. J. Mol. Biol. 226:735-745.
39. Haapa-Paananen, S., H. Rita, and H. Savilahti. 2002. DNA transposition of bacteriophage Mu. A quantitative analysis of target site selection in vitro. J. Biol. Chem. 277:2843-2851.
40. Baldwin, A.J., K. Busse, A.M. Simm, and D.D. Jones. 2008. Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx). Nucleic Acids Res. 36:e77.
41. Juers, D.H., R.H. Jacobson, D. Wigley, X.J. Zhang, R.E. Huber, D.E. Tronrud, and B.W. Matthews. 2000. High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation. Protein Sci. 9:1685-1699.
42. Gallagher, C.N. and R.E. Huber. 1999. Stabilities of uncomplemented and complemented M15 beta-galactosidase (Escherichia coli) and the relationship to alpha-complementation. Biochem. Cell Biol. 77:109-118.
43. Bajaj, K., P. Chakrabarti, and R. Varadarajan. 2005. Mutagenesis-based definitions and probes of residue burial in proteins. Proc. Natl. Acad. Sci. USA 102:16221-16226.
44. Noren, C.J., S.J. Anthony-Cahill, M.C. Griffith, and P.G. Schultz. 1989. A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244:182-188.
45. Bain, J.D., E.S. Diala, C.G. Glabe, D.A. Wacker, M.H. Lyttle, T.A. Dix, and A.R. Chamberlin. 1991. Site-specific incorporation of nonnatural residues during in vitro protein biosynthesis with semisynthetic aminoacyl-tRNAs. Biochemistry 30:5411-5421.