Negative selection and stringency modulation in phage-assisted continuous evolution

Nature Chemical Biology

Volumn 10, Issue 3, 2014, Pages 216-222

  Carlson, Jacob C ^a,b   Badran, Ahmed H ^a,b   Guggiana Nilo, Drago A ^c   Liu, David R ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGES; BIOLOGICAL EVOLUTION; DNA-DIRECTED RNA POLYMERASES; EVOLUTION, MOLECULAR; GENETIC VARIATION; MUTATION; PROMOTER REGIONS, GENETIC; SUBSTRATE SPECIFICITY; VIRAL PROTEINS;

EID: 84894101033     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.1453     Document Type: Article

References (22)

1. Esvelt K.M. Carlson J.C. & Liu D.R. A system for the continuous directed evolution of biomolecules. Nature 472 499-503 (2011).
2. Nelson F.K. Friedman S.M. & Smith G.P. Filamentous phage DNA cloning vectors: A noninfective mutant with a nonpolar deletion in gene III. Virology 108 338-350 (1981). (Pubitemid 11188840)
3. Calendar R. The Bacteriophages 1st edn. 376-455 (Oxford Univ. Press 2006).
4. Sergeeva A. Kolonin M.G. Molldrem J.J. Pasqualini R. & Arap W. Display technologies: Application for the discovery of drug and gene delivery agents. Adv. Drug Deliv. Rev. 58 1622-1654 (2006).
5. Yuan L. Kurek I. English J. & Keenan R. Laboratory-directed protein evolution. Microbiol. Mol. Biol. Rev. 69 373-392 (2005). (Pubitemid 41306743)
6. Leconte A.M. et al. A population-based experimental model for protein evolution: effects of mutation rate and selection stringency on evolutionary outcomes. Biochemistry 52 1490-1499 (2013).
7. Dickinson B.C. Leconte A.M. Allen B. Esvelt K.M. & Liu D.R. Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-Assisted continuous evolution. Proc. Natl. Acad. Sci. USA 110 9007-9012 (2013).
8. Doyon J.B. Pattanayak V. Meyer C.B. & Liu D.R. Directed evolution and substrate specificity profile of homing endonuclease I-SceI. J. Am. Chem. Soc. 128 2477-2484 (2006).
9. Tracewell C.A. & Arnold F.H. Directed enzyme evolution: climbing fitness peaks one amino acid at a time. Curr. Opin. Chem. Biol. 13 3-9 (2009).
10. Boeke J.D. Model P. & Zinder N.D. Effects of bacteriophage f1 gene III protein on the host cell membrane. Mol. Gen. Genet. 186 185-192 (1982).
11. Brissette J.L. Weiner L. Ripmaster T.L. & Model P. Characterization and sequence of the Escherichia coli stress-induced psp operon. J. Mol. Biol. 220 35-48 (1991). (Pubitemid 121004541)
12. Brissette J.L. Russel M. Weiner L. & Model P. Phage shock protein a stress protein of Escherichia coli. Proc. Natl. Acad. Sci. USA 87 862-866 (1990).
13. Rakonjac J. Jovanovic G. & Model P. Filamentous phage infection-mediated gene expression: construction and propagation of the gIII deletion mutant helper phage R408d3. Gene 198 99-103 (1997).
14. Bonner G. Lafer E.M. & Sousa R. Characterization of a set of T7 RNA polymerase active site mutants. J. Biol. Chem. 269 25120-25128 (1994). (Pubitemid 24311783)
15. Rakonjac J. Feng J. & Model P. Filamentous phage are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of pIII. J. Mol. Biol. 289 1253-1265 (1999).
16. Bennett N.J. & Rakonjac J. Unlocking of the filamentous bacteriophage virion during infection is mediated by the C domain of pIII. J. Mol. Biol. 356 266-273 (2006). (Pubitemid 43102584)
17. Grant R.A. Lin T.C. Konigsberg W. & Webster R.E. Structure of the filamentous bacteriophage fl. Location of the A C and D minor coat proteins. J. Biol. Chem. 256 539-546 (1981). (Pubitemid 11102369)
18. Lopez J. & Webster R.E. Minor coat protein composition and location of the A protein in bacteriophage f1 spheroids and I-forms. J. Virol. 42 1099-1107 (1982).
19. Lynch S.A. & Gallivan J.P. A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res. 37 184-192 (2009).
20. Raskin C.A. Diaz G. Joho K. & McAllister W.T. Substitution of a single bacteriophage T3 residue in bacteriophage T7 RNA polymerase at position 748 results in a switch in promoter specificity. J. Mol. Biol. 228 506-515 (1992). (Pubitemid 23007572)
21. Cheetham G.M. Jeruzalmi D. & Steitz T.A. Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 399 80-83 (1999).
22. Imburgio D. Rong M. Ma K. & McAllister W.T. Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants. Biochemistry 39 10419-10430 (2000).