Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering

ACS Synthetic Biology

Volumn 6, Issue 10, 2017, Pages 1825-1833

  Higgins, Sean A ^a   Ouonkap, Sorel V Y ^a   Savage, David F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

directed evolution; fluorescence thermostability; iLOV; protein mutagenesis; recombineering

Indexed keywords

MUTANT PROTEIN; RECOMBINANT PROTEIN;

ARTICLE; CODON; COMPUTER MODEL; CONTROLLED STUDY; ESCHERICHIA COLI; GENE LIBRARY; IN VITRO STUDY; MUTAGENESIS; PEPTIDE LIBRARY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN EXPRESSION; PROTEIN FUNCTION; STRUCTURE ACTIVITY RELATION; THERMOSTABILITY; GENETICS; MOLECULAR EVOLUTION; PLASMID; PROCEDURES; SITE DIRECTED MUTAGENESIS;

EVOLUTION, MOLECULAR; GENE LIBRARY; MUTAGENESIS, SITE-DIRECTED; PLASMIDS; PROTEIN ENGINEERING;

EID: 85031936326     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.7b00112     Document Type: Article

References (27)

1. Majithia, A. R., Tsuda, B., Agostini, M., Gnanapradeepan, K., Rice, R., Peloso, G., Patel, K. A., Zhang, X., Broekema, M. F., Patterson, N., Duby, M., Sharpe, T., Kalkhoven, E., Rosen, E. D., Barroso, I., Ellard, S., Kathiresan, S., O'Rahilly, S., Chatterjee, K., Florez, J. C., Mikkelsen, T., Savage, D. B., and Altshuler, D. (2016) Prospective functional classification of all possible missense variants in PPARG Nat. Genet. 48, 1570-1575 10.1038/ng.3700
2. Heim, R., Cubitt, a B., and Tsien, R. Y. (1995) Improved green fluorescence Nature 373, 663-664 10.1038/373663b0
3. Firnberg, E. and Ostermeier, M. (2012) PFunkel: Efficient, Expansive, User-Defined Mutagenesis PLoS One 7, e52031 10.1371/journal.pone.0052031
4. Melnikov, A., Rogov, P., Wang, L., Gnirke, A., and Mikkelsen, T. S. (2014) Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes Nucleic Acids Res. 42, e112 10.1093/nar/gku511
5. Belsare, K. D., Andorfer, M. C., Cardenas, F., Chael, J. R., Park, H. J., and Lewis, J. C. (2017) A Simple Combinatorial Codon Mutagenesis Method for Targeted Protein Engineering ACS Synth. Biol. 6, 416-420 10.1021/acssynbio.6b00297
6. Wrenbeck, E. E., Klesmith, J. R., Stapleton, J. A., Adeniran, A., Tyo, K. E. J., and Whitehead, T. A. (2016) Plasmid-based one-pot saturation mutagenesis Nat. Methods 13, 928-930 10.1038/nmeth.4029
7. Copeland, N. G., Jenkins, N. a, and Court, D. L. (2001) Recombineering: a powerful new tool for mouse functional genomics Nat. Rev. Genet. 2, 769-779 10.1038/35093556
8. Mosberg, J. a., Lajoie, M. J., and Church, G. M. (2010) Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate Genetics 186, 791-799 10.1534/genetics.110.120782
9. 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 10.1038/nature08187
10. Warner, J. R., Reeder, P. J., Karimpour-Fard, A., Woodruff, L. B. a, and Gill, R. T. (2010) Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides Nat. Biotechnol. 28, 856-862 10.1038/nbt.1653
11. Garst, A. D., Bassalo, M. C., Pines, G., Lynch, S. a, Halweg-Edwards, A. L., Liu, R., Liang, L., Wang, Z., Zeitoun, R., Alexander, W. G., and Gill, R. T. (2016) Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering Nat. Biotechnol. 35, 48-55 10.1038/nbt.3718
12. Thomason, L. C., Costantino, N., Shaw, D. V., and Court, D. L. (2007) Multicopy plasmid modification with phage λ red recombineering Plasmid 58, 148-158 10.1016/j.plasmid.2007.03.001
13. Turrientes, M. C., Baquero, F., Levin, B. R., Martinez, J. L., Ripoll, A., Gonzalez-Alba, J. M., Tobes, R., Manrique, M., Baquero, M. R., Rodriguez-Dominguez, M. J., Canton, R., and Galan, J. C. (2013) Normal Mutation Rate Variants Arise in a Mutator (Mut S) Escherichia coli Population PLoS One 8, e72963 10.1371/journal.pone.0072963
14. Nyerges, á., Csörgö, B., Nagy, I., Bálint, B., Bihari, P., Lázár, V., Apjok, G., Umenhoffer, K., Bogos, B., Pósfai, G., and Pál, C. (2016) A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species Proc. Natl. Acad. Sci. U. S. A. 113, 2502-2507 10.1073/pnas.1520040113
15. Chapman, S., Faulkner, C., Kaiserli, E., Garcia-Mata, C., Savenkov, E. I., Roberts, A. G., Oparka, K. J., and Christie, J. M. (2008) The photoreversible fluorescent protein iLOV outperforms GFP as a reporter of plant virus infection Proc. Natl. Acad. Sci. U. S. A. 105, 20038-20043 10.1073/pnas.0807551105
16. Christie, J. M., Hitomi, K., Arvai, A. S., Hartfield, K. a., Mettlen, M., Pratt, A. J., Tainer, J. a., and Getzoff, E. D. (2012) Structural tuning of the fluorescent protein iLOV for improved photostability J. Biol. Chem. 287, 22295-22304 10.1074/jbc.M111.318881
17. Lim, S. I., Min, B. E., and Jung, G. Y. (2008) Lagging Strand-Biased Initiation of Red Recombination by Linear Double-Stranded DNAs J. Mol. Biol. 384, 1098-1105 10.1016/j.jmb.2008.10.047
18. Callis, P. R. and Liu, T. (2006) Short range photoinduced electron transfer in proteins: QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins Chem. Phys. 326, 230-239 10.1016/j.chemphys.2006.01.039
19. Mukherjee, A., Weyant, K. B., Agrawal, U., Walker, J., Cann, I. K. O., and Schroeder, C. M. (2015) Engineering and characterization of new LOV-based fluorescent proteins from chlamydomonas reinhardtii and vaucheria frigida ACS Synth. Biol. 4, 371-377 10.1021/sb500237x
20. Tokuriki, N. and Tawfik, D. S. (2009) Stability effects of mutations and protein evolvability Curr. Opin. Struct. Biol. 19, 596-604 10.1016/j.sbi.2009.08.003
21. Firnberg, E., Labonte, J. W., Gray, J. J., and Ostermeier, M. (2014) A comprehensive, high-resolution map of a Gene's fitness landscape Mol. Biol. Evol. 31, 1581-1592 10.1093/molbev/msu081
22. Steinberg, B. and Ostermeier, M. (2016) Environmental changes bridge evolutionary valleys Sci. Adv. 2, e1500921-e1500921 10.1126/sciadv.1500921
23. Heinzelman, P., Snow, C. D., Wu, I., Nguyen, C., Villalobos, A., Govindarajan, S., Minshull, J., and Arnold, F. H. (2009) A family of thermostable fungal cellulases created by structure-guided recombination Proc. Natl. Acad. Sci. U. S. A. 106, 5610-5615 10.1073/pnas.0901417106
24. Olson, C. A., Wu, N. C., and Sun, R. (2014) A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain Curr. Biol. 24, 2643-2651 10.1016/j.cub.2014.09.072
25. Nadler, D. C., Morgan, S.-A., Flamholz, A., Kortright, K. E., and Savage, D. F. (2016) Rapid construction of metabolite biosensors using domain-insertion profiling Nat. Commun. 7, 12266 10.1038/ncomms12266
26. Engler, C., Kandzia, R., and Marillonnet, S. (2008) A one pot, one step, precision cloning method with high throughput capability PLoS One 3, e3647 10.1371/journal.pone.0003647
27. Wang, H. and Church, G. (2011) Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering Methods Enzymol. 498, 409-426 10.1016/B978-0-12-385120-8.00018-8