Applying neutral drift to the directed molecular evolution of a -glucuronidase into a -galactosidase: Two different evolutionary pathways lead to the same variant

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  Smith, Wendy S ^a   Hale, Jennifer R ^a   Neylon, Cameron ^b  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b RUTHERFORD APPLETON LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI;

EID: 79955648827     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-138     Document Type: Article

References (29)

1. An efficient method for generating proteins with altered enzymatic properties: application to beta-lactamase. AR Oliphant K Struhl, Proc Natl Acad Sci USA 1989 86 9094 8 10.1073/pnas.86.23.9094 2687873 (Pubitemid 20010371)
2. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. K Chen FH Arnold, Proc Natl Acad Sci USA 1993 90 5618 22 10.1073/pnas.90.12.5618 8516309 (Pubitemid 23176212)
3. Advances in generating functional diversity for directed protein evolution. AV Shivange J Marienhagen H Mundhanda A Schenk U Schwaneberg, Current Opinion in Chemical Biology 2009 13 1 7 10.1016/j.cbpa.2009.02.022 19272831
4. Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx). AJ Baldwin K Busse AM Simm DD Jones, Nucleic Acids Res 2008 36 77 10.1093/nar/gkn358 18559360
5. Transversion enriched sequence saturation mutagenesis (SeSaM-TV+): a random mutagenesis method with consecutive nucleotide exchanges that complements the bias of error prone PCR. TS Wong D Roccatano D Loakes KL Te A Schenk B Hauer U Schwaneberg, Biotechnol J 2008 3 74 82 10.1002/biot.200700193 18022859 (Pubitemid 351200933)
6. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. MT Reetz JD Carballeira, Nat Protoc 2007 2 891 903 10.1038/nprot.2007.72 17446890 (Pubitemid 46758808)
7. Latent evolutionary potentials under the neutral mutational drift of an enzyme. G Amitai RD Gupta DS Tawfik, HFSP Journal 2007 1 67 78 10.2976/1.2739115 19404461
8. Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. JD Bloom PA Romero Z Lu FH Arnold, Biology Direct 2007 2 17 10.1186/1745-6150-2-17 17598905
9. Intense Neutral Drifts Yield Robust and Evolvable Consensus Proteins. S Bershtein K Goldin DS Tawfik, J Mol Biol 2008 379 1029 1044 10.1016/j.jmb.2008. 04.024 18495157
10. In the light of directed evolution: Pathways of adaptive protein evolution. JD Bloom FH Arnold, Proc Natl Acad Sci USA 2009 9995 10000
11. Directed enzyme evolution: climbing fitness peaks one amino acid at a time. CA Tracewell FH Arnold, Curr Opin Chem Biol 2009 13 3 9 10.1016/j.cbpa.2009.01.017 19249235
12. The subtle benefits of being promiscuous: adaptive evolution potentiated by enzyme promiscuity. MA DePristo, HFSP Journal 2007 1 94 98 10.2976/1.2754665 19404414
13. In vitro evolution of a beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. I Matsumura AD Ellington, J Mol Biol 2001 305 331 339 10.1006/jmbi.2000.4259 11124909 (Pubitemid 32099464)
14. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. KA Datsenko BL Wanner, Proc Natl Acad Sci USA 2000 97 6640 5 10.1073/pnas.120163297 10829079 (Pubitemid 30412767)
15. A comparison of directed evolution approaches using the beta-glucuronidase model system. LA Rowe ML Geddie OB Alexander I Matsumura, J Mol Biol 2003 332 851 60 10.1016/S0022-2836(03)00972-0 12972256 (Pubitemid 37101372)
16. Increasing the thermal stability of an oligomeric protein, beta glucuronidase. H Flores AD Ellington, J Mol Biol 2002 315 325 337 10.1006/jmbi.2001.5223 11786015 (Pubitemid 34729343)
17. DNA shuffling by random fragmentation and reassembly. WPC Stemmer, vitro recombination for molecular evolution Proc Natl Acad Sci USA 1993 91 10747 10751
18. Rapid evolution of a protein in vitro by DNA shuffling. WPC Stemmer, Nature 1994 370 389 391 10.1038/370389a0 8047147 (Pubitemid 24259765)
19. Rapid evolution of beta-glucuronidase specificity by saturation mutagenesis of an active site loop. ML Geddie I Matsumura, J Biol Chem 2004 279 26462 8 10.1074/jbc.M401447200 15069062 (Pubitemid 38798799)
20. Directed enzyme evolution via small and effective neutral drift libraries. RD Gupta DS Tawfik, Nature Methods 2008 5 939 941 10.1038/nmeth.1262 18931667
21. Directed evolution of mammalian paraoxonases PON1 and PON3 for bacterial expression and catalytic specialization. A Aharoni L Gaidukov S Yagur L Toker I Silman DS Tawfik, Proc Natl Acad Sci USA 2004 101 2 482 487 10.1073/pnas. 2536901100 14695884 (Pubitemid 38084662)
22. High-Throughput Screening of Enzyme Libraries: Thiolactonases Evolved by Fluorescence-Activated Sorting of Single Cells in Emulsion Compartments. A Aharoni G Amitai K Bernath S Magdassi DS Tawfik, Chemistry & Biology 2005 12 1281 1289 10.1016/j.chembiol.2005.09.012 21574252 (Pubitemid 41779468)
23. Structural perturbation and compensation at physiological temperature leads to thermo-stabilization of beta-lactamase. J Hecky KM Muller, Biochemistry 2005 44 12640 12654 10.1021/bi0501885 16171379 (Pubitemid 41377305)
24. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. S Bershtein M Segal R Bekerman N Tokuriki DS Tawfik, Nature 2006 444 929 932 10.1038/nature05385 17122770 (Pubitemid 46025005)
25. Degenerate oligonucleotide gene shuffling (DOGS) and random drift mutagenesis (RNDM): Two complementary techniques for enzyme evolution. PL Bergquist RA Reeves MD Gibbs, Biomol Eng 2005 22 63 72 10.1016/j.bioeng.2004.10. 002 15857785 (Pubitemid 40602595)
26. Structure of human beta-glucuronidase reveals candidate lysosomal targeting and active-site motifs. S Jain WB Drendel ZW Chen FS Mathews WS Sly JH Grubb, Nat Struct Biol 1996 3 375 81 10.1038/nsb0496-375 8599764 (Pubitemid 26112636)
27. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. N Guex MC Peitsch, Electrophoresis 1997 18 2714 23 10.1002/elps.1150181505 9504803 (Pubitemid 28059943)
28. SWISS-MODEL: An automated protein homology-modelling server. T Schwede J Kopp N Guex MC Peitsch, Nucleic Acids Res 2003 31 3381 5 10.1093/nar/gkg520 12824332 (Pubitemid 37442164)
29. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. MM Bradford, Anal Biochem 1976 72 248 54 10.1016/0003-2697(76)90527-3 942051