Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects

Nucleic Acids Research

Volumn 44, Issue 4, 2015, Pages

  Lennen, Rebecca M ^a   Nilsson Wallin, Annika I ^a   Pedersen, Margit ^a   Bonde, Mads ^a   Luo, Hao ^a   Herrgård, Markus J ^a   Sommer, Morten O A ^a  

^a Chalmers University of Technology   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DNA ADENINE METHYLTRANSFERASE; GENOMIC DNA; OLIGONUCLEOTIDE; SINGLE STRANDED DNA; SITE SPECIFIC DNA METHYLTRANSFERASE (ADENINE SPECIFIC);

ALLELE; AMPLICON; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; CONTROLLED STUDY; ESCHERICHIA COLI; GENETIC ENGINEERING; GROWTH RATE; HOMOLOGOUS RECOMBINATION; MISMATCH REPAIR; NONHUMAN; PHENOTYPE; PLASMID; PRIORITY JOURNAL; PROTEIN EXPRESSION; TEMPERATURE; BIOSYNTHESIS; GENETICS; MUTATION; PROCEDURES;

DNA MISMATCH REPAIR; DNA, SINGLE-STRANDED; ESCHERICHIA COLI; GENETIC ENGINEERING; GENOME, BACTERIAL; HOMOLOGOUS RECOMBINATION; MUTATION; OLIGONUCLEOTIDES; PLASMIDS; SITE-SPECIFIC DNA-METHYLTRANSFERASE (ADENINE-SPECIFIC);

EID: 84952697170     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1090     Document Type: Article

References (28)

1. Thomason, L., Court, D.L., Bubunenko, M., Constantino, N., Wilson, H., Datta, S. and Oppenheim, A. (2007) Recombineering: genetic engineering in bacteria using homologous recombination. Curr. Protoc. Mol. Biol. Unit1.16.
2. Datsenko, K.A. and Wanner, B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli using PCR products. Proc. Natl. Acad. Sci U.S.A., 97, 6640-6645.
3. Ellis, H.M., Yu, D., DiTizio, T. and Court, D.L. (2001) High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl. Acad. Sci U.S.A., 98, 6742-6746.
4. Sawitzke, J.A., Thomason, L.C., Bubunenko, M., Li, X., Constantino, N. and Court, D.L. (2013) Recombineering: highly efficient in vivo genetic engineering using single-strand oligos. Methods Enzymol., 533, 157-177.
5. Wang, H.H., Isaacs, F.J., Carr, P.A., Sun, Z.Z., Xu, G., Forest, C.R. and Church, G.M. (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460, 894-898.
6. Bonde, M.T., Kosuri, S., Genee, H.J., Sarup-Lytzen, K., Church, G.M., Sommer, M.O. and Wang, H.H. (2015) Direct mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides. ACS Synth. Biol., 4, 17-22.
7. Ng, C.Y., Farasat, I., Maranas, C.D. and Salis, H.M. (2015) Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metab. Eng., 29, 86-96.
8. LaJoie, M.J., Rovner, A.J., Goodman, D.B., Aerni, H.R., Haimovich, A.D., Kuznetsov, G., Mercer, J.A., Wang, H.H., Carr, P.A., Mosberg, J.A. et al. (2013) Genomically recoded organisms expand biological functions. Science, 342, 357-360.
9. LaJoie, M.J., Kosuri, S., Mosberg, J.A., Gregg, C.J., Zhang, D. and Church, G.M. (2013) Probing the limits of genetic recoding in essential genes. Science, 342, 361-363.
10. Sandberg, T.E., Pedersen, M., LaCroix, R.A., Ebrahim, A., Bonde, M., Herrgard, M.J., Palsson, B.O., Sommer, M. and Feist, A.M. (2014) Evolution of Escherichia coli to 42°C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Mol. Biol. Evol., 31, 2647-2662.
11. Munck, C., Gumpert, H.K., Wallin, A.I.N., Wang, H.H. and Sommer, M.O. (2014) Prediction of resistance development against drug combinations by collateral responses to component drugs. Sci. Transl. Med., 6, doi:10.1126/scitranslmed.3009940.
12. Horst, J.P., Wu, T.H. and Marinus, M.G. (1999) Escherichia coli mutator genes. Trends Microbiol., 7, 29-36.
13. Glickman, B.W. and Radman, M. (1980) Escherichia coli mutants deficient in methylation-instructed DNA mismatch correction. Proc. Natl. Acad. Sci. U.S.A., 77, 1063-1067.
14. Wang, H.H., Xu, G., Vonner, A.J. and Church, G. (2011) Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion. Nucleic Acids Res., 39, 7336-7347.
15. Nyerges, Á., Csörgo, B., Nagy, I., Latinovics, D., Szamecz, B., Pósfai, Gy. and Pál, C. (2014) Conditional DNA repair mutants enable highly precise genome engineering. Nucleic Acids Res., 42, e62.
16. Hong, E.S., Yeung, A., Funchain, P., Slupska, M.M. and Miller, J.H. (2005) Mutants with temperature-sensitive defects in the Escherichia coli mismatch repair system: sensitivity to mispairs generated in vivo. J. Bacteriol., 187, 840-846.
17. Yang, H., Wolff, E., Kim, M., Diep, A. and Miller, J.H. (2004) Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach. Mol. Microbiol., 53, 283-295.
18. Winkler, J.D., Garcia, C., Olson, M., Callaway, E. and Kao, K.C. (2014) Evolved osmotolerant Escherichia coli mutants frequently exhibit defective N-acetylglucosamine metabolism and point mutations in cell shape-regulating protein MreB. Appl. Environ. Microbiol., 80, 3729-3740.
19. Bonde, M.T., Klausen, M.S., Anderson, M.V., Wallin, A.I., Wang, H.H. and Sommer, M.O. (2014) MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Res., 42, W408-W415.
20. Freddolino, P.L., Amini, S. and Tavazoie, S. (2012) Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. J. Bacteriol., 194, 303-306.
21. Guzman, L.M., Belin, D., Carson, M.J. and Beckwith, J. (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacteriol., 177, 4121-4130.
22. Geu-Flores, F., Nour-Eldin, H.H., Nielsen, M.T. and Halkier, B.A. (2007) USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res., 35, e55.
23. Lee, J.S., Kallehauge, T.B., Pedersen, L.E. and Kildegaard, H.F. (2015) Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway. Sci. Rep., 5, 8572.
24. Lennen, R.M. and Herrgård, M.J. (2014) Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains. Appl. Environ. Microbiol., 80, 6223-6242.
25. Deatherage, D.E. and Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generations sequencing data using breseq. Methods Mol. Biol., 1151, 165-188.
26. Isaacs, F.J., Carr, P.A., Wang, H.H., Lajoie, M.J., Sterling, B., Kraal, L., Tolonen, A.C., Gianoulis, T.A., Goodman, D.B., Reppas, N.B. et al. (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science, 333, 348-353.
27. Jensen, K.F. (1993) The Escherichia coli K-12 'wild-types' W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J. Bacteriol. 175, 3401-3407.
28. Pukkila, P.J., Peterson, J., Herman, G., Modrich, P. and Meselson, M. (1983) Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli. Genetics, 104, 571-582.