Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenases

PLoS ONE

Volumn 5, Issue 12, 2010, Pages

  Stapleton, James A ^a   Swartz, James R ^a  

^a Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGENASE; IRON IRON HYDROGENASE; OXYGEN; UNCLASSIFIED DRUG; BAYSILON; DIMETICONE; DNA; HYDROGEN; IRON;

ARTICLE; BIOCATALYST; CONTROLLED STUDY; DNA LIBRARY; EMULSION; ENZYME ACTIVATION; ENZYME ACTIVITY; ENZYME SUBSTRATE; FLUORESCENCE ACTIVATED CELL SORTING; GENE AMPLIFICATION; GENE EXPRESSION; HIGH THROUGHPUT SCREENING; IN VITRO COMPARTMENTALIZATION; MOLECULAR EVOLUTION; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; SCREENING; SIGNAL TRANSDUCTION; BIOLOGICAL MODEL; CATALYSIS; CELL FREE SYSTEM; CHEMISTRY; DIRECTED MOLECULAR EVOLUTION; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; IN VITRO STUDY; METHODOLOGY; MICROFLUIDICS; MUTATION; POLYMERASE CHAIN REACTION; SPECTROFLUOROMETRY;

CATALYSIS; CELL-FREE SYSTEM; DIMETHYLPOLYSILOXANES; DIRECTED MOLECULAR EVOLUTION; DNA; ESCHERICHIA COLI; HYDROGEN; HYDROGENASE; IRON; MICROFLUIDICS; MODELS, GENETIC; MUTATION; OXYGEN; POLYMERASE CHAIN REACTION; SPECTROMETRY, FLUORESCENCE;

EID: 78650121749     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0015275     Document Type: Article

References (43)

1. Adams MW (1990) The structure and mechanism of iron-hydrogenases. Biochimica et Biophysica Acta 1020: 115-145.
2. Cohen J, Kim K, Posewitz M, Ghirardi ML, Schulten K, et al. (2005) Molecular dynamics and experimental investigation of H2 and O2 diffusion in [Fe]- hydrogenase. Biochem Soc Transact 33: 80-82.
3. Stapleton JA, Swartz JR (2010) A cell-free microtiter plate screen for improved [FeFe] hydrogenases. PLoS ONE 5(5): e10554. DOI:10.1371/journal. pone.0010554.
4. Tawfik DS, Griffiths AD (1998) Man-made cell-like compartments for molecular evolution. Nature Biotechnology 16: 652-656.
5. Hanes J, Pluckthun A (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci U S A 94: 4937-4942.
6. Roberts RW, Szostak JW (1997) RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci U S A 94: 12297-12302.
7. Agresti JJ, Kelly BT, Jäschke A, Griffiths AD (2005) Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization. Proc Natl Acad Sci U S A 102: 16170-16175.
8. Griffiths AD, Tawfik DS (2003) Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization. The EMBO Journal 22: 24-35.
9. Aharoni A, Amitai G, Bernath K, Magdassi S, Tawfik DS (2005) Highthroughput screening of enzyme libraries: thiolactonases evolved by fluorescence- activated sorting of single cells in emulsion compartments. Chemistry & Biology 12: 1281-1289.
10. Brouzes E, Medkova M, Savenelli N, Marran D, Twardowski M, et al. (2009) Droplet microfluidic technology for single-cell high-throughput screening. Proc Natl Acad Sci U S A 106: 14195-14200.
11. Kelly BT, Baret J, Taly V, Griffiths AD (2007) Miniaturizing chemistry and biology in microdroplets. Chemical Communications DOI: 10.1039/b616252e.
12. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
13. Shah RK, Shum HC, Rowat AC, Lee D, Agresti JJ, et al. (2008) Designer emulsions using microfluidics. Materials Today 11: 18-27.
14. Leamon JH, Link DR, Egholm M, Rothberg JM (2006) Overview: methods and applications for droplet compartmentalization of biology. Nature Methods 3: 541-543.
15. Link D, Anna S,Weitz D, Stone H (2004) Geometrically mediated breakup of drops in microfluidic devices. Physical Review Letters DOI: 10.1103/PhysRevLett.92.054503.
16. Schaerli Y, Wootton RC, Robinson T, Stein V, Dunsby C, et al. (2009) Continuous-flow polymerase chain reaction of single-copy DNA in microfluidic microdroplets. Analytical Chemistry 81: 302-306.
17. Frenz L, Blouwolff J, Griffiths AD, Baret J (2008) Microfluidic production of droplet pairs. Langmuir 24: 12073-12076.
18. Agresti JJ, Antipov E, Abate AR, Ahn K, Rowat AC, et al. (2010) Ultrahighthroughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci U S A DOI: 10.1073/pnas.0910781107.
19. Sepp A, Tawfik DS, Griffiths AD (2002) Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry. FEBS letters 532: 455-458.
20. Mastrobattista E, Taly V, Chanudet E, Treacy P, Kelly BT, et al. (2005) Highthroughput screening of enzyme libraries: in vitro evolution of a betagalactosidase by fluorescence-activated sorting of double emulsions. Chemistry & Biology 12: 1291-1300.
21. Bernath K, Hai M, Mastrobattista E, Griffiths AD, Magdassi S, et al. (2004) In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting. Analytical Biochemistry 325: 151-157.
22. Boder ET, Wittrup KD (2000) Yeast surface display for directed evolution of protein expression, affinity, and stability. Methods in Enzymology 328: 430-444.
23. Georgiou G, Stathopoulos C, Daugherty PS, Nayak AR, Iverson BL, et al. (1997) Display of heterologous proteins on the surface of microorganisms: From the screening of combinatorial libraries to live recombinant vaccines. Nature Biotechnology 15: 29-34.
24. Pirrung MC, Huang CY (1996) A general method for the spatially defined immobilization of biomolecules on glass surfaces using "caged" biotin. Bioconjugate Chemistry 7: 317-321.
25. Boyer M, Stapleton JA, Kuchenreuther JM, Wang C, Swartz JR (2008) Cell-free synthesis and maturation of hydrogenases. Biotechnology and Bioengineering 99: 59-67.
26. Kuchenreuther JM, Stapleton JA, Swartz JR (2009) Tyrosine, cysteine, and Sadenosyl methionine stimulate in vitro [FeFe] hydrogenase activation. PLoS ONE 4(10): e7565. DOI:10.1371/journal.pone.0007565.
27. Peters JW, Lanzilotta WN, Lemon BJ, Seefeldt LC (1998) X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution. Science 282: 1853-1858.
28. Davidson EA, Dlugosz PJ, Levy M, Ellington AD (2009) Directed evolution of proteins in vitro using compartmentalization in emulsions. Current Protocols in Molecular Biology DOI: 10.1002/0471142727.mb2406s87.
29. Posewitz MC, King PW, Smolinski SL, Zhang L, Seibert M, et al. (2004) Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase. The Journal of Biological Chemistry 279: 25711-20.
30. Peck H, Gest H (1956) A new procedure for assay of bacterial hydrogenases. Journal of Bacteriology 71: 70-80.
31. Bernath K, Magdassi S, Tawfik DS (2005) Directed evolution of protein inhibitors of DNA-nucleases by in vitro compartmentalization (IVC) and nanodroplet delivery. Journal of Molecular Biology 345: 1015-1026.
32. Anna SL, Bontoux N, Stone HA (2003) Formation of dispersions using "flow focusing" in microchannels. Applied Physics Letters 82: 364-366.
33. Shendure J, Porreca G, Reppas N, Lin X, McCutcheon J, et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728-1732.
34. Pushkarev D, Neff NF, Quake SR (2009) Single-molecule sequencing of an individual human genome. Nature Biotechnology DOI: 10.1038/nbt.1561.
35. Pohl G, Shih I (2004) Principle and applications of digital PCR. Expert Review of Molecular Diagnostics 4: 41-47.
36. Gan R, Yamanaka Y, Kojima T, Nakano H (2008) Microbeads display of proteins using emulsion PCR and cell-free protein synthesis. Biotechnology Progress 24: 3-10.
37. Diehl F, Li M, He Y, Kinzler K, Vogelstein B (2006) BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions. Nature Methods 3: 551-559.
38. Kumaresan P, Yang CJ, Cronier SA, Blazej RG, Mathies RA (2008) Highthroughput single copy DNA amplification and cell analysis in engineered nanoliter droplets. Analytical Chemistry 80: 3522-3529.
39. Brownie J, Shawcross S, Theaker J, Whitcombe D, Ferrie R, et al. (1997) The elimination of primer-dimer accumulation in PCR. Nucleic Acids Research 25: 3235-3241.
40. Rungpragayphan S, Kawarasaki Y, Imaeda T, Kohda K, Nakano H, et al. (2002) High-throughput, cloning-independent protein library construction by combining single-molecule DNA amplification with in vitro expression. Journal of Molecular Biology 318: 395-405.
41. Edd JF, Di Carlo D, Humphry KJ, Köster S, Weitz DA, et al. (2008) Controlled encapsulation of single-cells into monodisperse picolitre drops. Lab on a Chip 8: 1262-1264.
42. Holtze C, Rowat AC, Agresti JJ, Hutchison JB, Angilè FE, et al. (2008) Biocompatible surfactants for water-in-fluorocarbon emulsions. Lab on a Chip 8: 1632-1639.
43. Ghadessy FJ, Holliger P (2004) A novel emulsion mixture for in vitro compartmentalization of transcription and translation in the rabbit reticulocyte system. Protein Engineering, Design, and Selection 17: 201-204.