Abstract
The capacity of transposable elements to insert into the genomes has been harnessed during the past decades to various in vitro and in vivo applications. This chapter describes in detail the general protocols and principles applicable for the Mu in vitro transposition reaction as well as the assembly of DNA transposition complexes that can be electroporated into bacterial cells to accomplish efficient gene delivery. These techniques with their modifications potentiate various gene and genome modification applications, which are discussed briefly here, and the reader is referred to the original publications for further details.
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References
Mizuuchi K (1983) In vitro transposition of bacteriophage Mu: a biochemical approach to a novel replication reaction. Cell 35:785–794
Haapa S, Taira S, Heikkinen E, Savilahti H (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
Savilahti H, Rice PA, Mizuuchi K (1995) The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J 14:4893–4903
Haapa S, Suomalainen S, Eerikäinen S, Airaksinen M, Paulin L, Savilahti H (1999) An efficient DNA sequencing strategy based on the bacteriophage Mu in vitro DNA transposition reaction. Genome Res 9:308–315
Poussu E, Vihinen M, Paulin L, Savilahti H (2004) Probing the a-complementing domain of E. coli b-galactosidase with use of an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition. Proteins 54:681–692
Poussu E, Jäntti J, Savilahti H (2005) A gene truncation strategy generating N- and C-terminal deletion variants of proteins for functional studies: mapping of the Sec1p binding domain in yeast Mso1p by a Mu in vitro transposition-based approach. Nucleic Acids Res 33:e104
Jones DD (2005) Triplet nucleotide removal at random positions in a target gene: the tolerance of TEM-1 b-lactamase to an amino acid deletion. Nucleic Acids Res 33:e80
Baldwin AJ, Busse K, Simm AM, Jones DD (2008) Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx). Nucleic Acids Res 36:e77
Edwards WR, Busse K, Allemann RK, Jones DD (2008) Linking the functions of unrelated proteins using a novel directed evolution domain insertion method. Nucleic Acids Res 36:e78
Hoeller BM, Reiter B, Abad S, Graze I, Glieder A (2008) Random tag insertions by Transposon Integration mediated Mutagenesis (TIM). J Microbiol Methods 75:251–257
Orsini L, Pajunen M, Hanski I, Savilahti H (2007) SNP discovery by mismatch-targeting of Mu transposition. Nucleic Acids Res 35:e44
Yanagihara K, Mizuuchi K (2002) Mismatch-targeted transposition of Mu: a new strategy to map genetic polymorphism. Proc Natl Acad Sci U S A 99:11317–11321
Vilen H, Eerikäinen S, Tornberg J, Airaksinen MS, Savilahti H (2001) Construction of gene-targeting vectors: a rapid Mu in vitro DNA transposition-based strategy generating null, potentially hypomorphic, and conditional alleles. Transgenic Res 10:69–80
Zhang C, Kitsberg D, Chy H, Zhou Q, Morrison JR (2005) Transposon-mediated generation of targeting vectors for the production of gene knockouts. Nucleic Acids Res 33:e24
Jukkola T, Trokovic R, Maj P, Lamberg A, Mankoo B, Pachnis V, Savilahti H, Partanen J (2005) Meox1Cre: a mouse line expressing Cre recombinase in somitic mesoderm. Genesis 43:148–153
Turakainen H, Saarimaki-Vire J, Sinjushina N, Partanen J, Savilahti H (2009) Transposition-based method for the rapid generation of gene-targeting vectors to produce Cre/Flp-modifiable conditional knock-out mice. PLoS One 4:e4341
Kiljunen S, Pajunen MI, Dilks K, Storf S, Pohlschroder M, Savilahti H (2014) Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii , and its use for gene discovery. BMC Biol 12:103
Krupovic M, Vilen H, Bamford JK, Kivelä HM, Aalto JM, Savilahti H, Bamford DH (2006) Genome characterization of lipid-containing marine bacteriophage PM2 by transposon insertion mutagenesis. J Virol 80:9270–9278
Vilen H, Aalto JM, Kassinen A, Paulin L, Savilahti H (2003) A direct transposon insertion tool for modification and functional analysis of viral genomes. J Virol 77:123–134
Kekarainen T, Savilahti H, Valkonen JP (2002) Functional genomics on potato virus A: virus genome-wide map of sites essential for virus propagation. Genome Res 12:584–594
Laurent LC, Olsen MN, Crowley RA, Savilahti H, Brown PO (2000) Functional characterization of the human immunodeficiency virus type 1 genome by genetic footprinting. J Virol 74:2760–2769
Pajunen M, Turakainen H, Poussu E, Peränen J, Vihinen M, Savilahti H (2007) High-precision mapping of protein–protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform. Nucleic Acids Res 35:e103
Weber M, Chernov K, Turakainen H, Wohlfahrt G, Pajunen M, Savilahti H, Jantti J (2010) Mso1p regulates membrane fusion through interactions with the putative N-peptide-binding area in Sec1p domain 1. Mol Biol Cell 21:1362–1374
Lamberg A, Nieminen S, Qiao M, Savilahti H (2002) Efficient insertion mutagenesis strategy for bacterial genomes involving electroporation of in vitro-assembled DNA transposition complexes of bacteriophage Mu. Appl Environ Microbiol 68:705–712
Pajunen MI, Pulliainen AT, Finne J, Savilahti H (2005) Generation of transposon insertion mutant libraries for Gram-positive bacteria by electroporation of phage Mu DNA transposition complexes. Microbiology 151:1209–1218
Paatero AO, Turakainen H, Happonen LJ, Olsson C, Palomäki T, Pajunen MI, Meng X, Otonkoski T, Tuuri T, Berry C, Malani N, Frilander MJ, Bushman FD, Savilahti H (2008) Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Res 36:e148
Tu Quoc PH, Genevaux P, Pajunen M, Savilahti H, Georgopoulos C, Schrenzel J, Kelley WL (2007) Isolation and characterization of biofilm formation-defective mutants of Staphylococcus aureus. Infect Immun 75:1079–1088
Wu Z, Xuanyuan Z, Li R, Jiang D, Li C, Xu H, Bai Y, Zhang X, Turakainen H, Saris PE, Savilahti H, Qiao M (2009) Mu transposition complex mutagenesis in Lactococcus lactis--identification of genes affecting nisin production. J Appl Microbiol 106:41–48
Butterfield YSN, Marra MA, Asano JK, Chan SY, Guin R, Krzywinski MI, Lee SS, MacDonald KWK, Mathewson CA, Olson TE, Pandoh PK, Prabhu A-L, Schnerch A, Skalska U, Smailus DE, Stott JM, Tsai MI, Yang GS, Zuyderduyn SD, Schein JE, Jones SJM (2002) An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. Nucleic Acids Res 30:2460–2468
Haapa-Paananen S, Rita H, Savilahti H (2002) DNA transposition of bacteriophage Mu. A quantitative analysis of target site selection in vitro. J Biol Chem 277:2843–2851
Mizuuchi M, Mizuuchi K (1993) Target site selection in transposition of phage Mu. Cold Spring Harb Symp Quant Biol 58:515–523
Baker TA, Mizuuchi M, Savilahti H, Mizuuchi K (1993) Division of labor among monomers within the Mu transposase tetramer. Cell 74:723–733
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This work was supported by the Academy of Finland (Grant 251168).
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Haapa-Paananen, S., Savilahti, H. (2018). Applications of the Bacteriophage Mu In Vitro Transposition Reaction and Genome Manipulation via Electroporation of DNA Transposition Complexes. In: Clokie, M., Kropinski, A., Lavigne, R. (eds) Bacteriophages. Methods in Molecular Biology, vol 1681. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7343-9_20
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DOI: https://doi.org/10.1007/978-1-4939-7343-9_20
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