Reporter-based screening and selection of enzymes

FEBS Journal

Volumn 280, Issue 13, 2013, Pages 2979-2996

  Van Rossum, Teunke ^a   Kengen, Servé W M ^a   Van Der Oost, John ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

enzyme; high throughput; in vivo; library; post translational modification; reporter; riboswitch; screening; selection; transcriptional regulator

Indexed keywords

ANTIBIOTIC AGENT; REGULATOR PROTEIN; RIBOZYME;

ANTIBIOTIC RESISTANCE; CONFERENCE PAPER; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME BINDING; ENZYME MECHANISM; ENZYME MODIFICATION; FLUORESCENCE ACTIVATED CELL SORTING; FLUORESCENCE ANALYSIS; HIGH THROUGHPUT SCREENING; IN VIVO STUDY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN PROCESSING; REPORTER GENE; RIBOSWITCH; TRANSCRIPTION INITIATION;

ANIMALS; BIOCATALYSIS; BIOMEDICAL RESEARCH; BIOTECHNOLOGY; GENES, REPORTER; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; PROTEIN ENGINEERING; RECOMBINANT PROTEINS;

EID: 84879223038     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/febs.12281     Document Type: Conference Paper

References (77)

1. Schmid A, Dordick JS, Hauer B, Kiener A, Wubbolts M, &, Witholt B, (2001) Industrial biocatalysis today and tomorrow. Nature 409, 258-268. (Pubitemid 32144296)
2. Sanchez S, &, Demain AL, (2011) Enzymes and bioconversions of industrial, pharmaceutical, and biotechnological significance. Org Process Res Dev 15, 224-230.
3. Leemhuis H, Kelly RM, &, Dijkhuizen L, (2009) Directed evolution of enzymes: library screening strategies. IUBMB Life 61, 222-228.
4. Kaul P, &, Asano Y, (2012) Strategies for discovery and improvement of enzyme function: state of the art and opportunities. Microb Biotechnol 5, 18-33.
5. Liszka MJ, Clark ME, Schneider E, &, Clark DS, (2012) Nature versus nurture: developing enzymes that function under extreme conditions. Annu Rev Chem Biomol Eng 3, 77-102.
6. Illanes A, Cauerhff A, Wilson L, &, Castro GR, (2012) Recent trends in biocatalysis engineering. Bioresour Technol 115, 48-57.
7. Davids T, Schmidt M, Böttcher D, &, Bornscheuer UT, (2013) Strategies for the discovery and engineering of enzymes for biocatalysis. Curr Opin Chem Biol, in press.
8. Huang XF, Santhanam N, Badri DV, Hunter WJ, Manter DK, Decker SR, Vivanco JM, &, Reardon KF, (2013) Isolation and characterization of lignin-degrading bacteria from rainforest soils. Biotechnol Bioeng, in press.
9. Kennedy J, O'Leary ND, Kiran GS, Morrissey JP, O'Gara F, Selvin J, &, Dobson ADW, (2011) Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems. J Appl Microbiol 111, 787-799.
10. Uchiyama T, &, Miyazaki K, (2009) Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 20, 616-622.
11. Timmis K, Carreño CA, &, de Lorenzo V, (2010) Genetic traps for surveying new catalysts in (meta) genomic DNA. In Handbook of Hydrocarbon and Lipid Microbiology, pp. 4563-4579. Springer, Berlin.
12. Fernández-Arrojo L, Guazzaroni ME, López-Cortés N, Beloqui A, &, Ferrer M, (2010) Metagenomic era for biocatalyst identification. Curr Opin Biotechnol 21, 725-733.
13. Boersma YL, Dröge MJ, &, Quax WJ, (2007) Selection strategies for improved biocatalysts. FEBS J 274, 2181-2195. (Pubitemid 46633470)
14. Goldsmith M, &, Tawfik DS, (2012) Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 22, 406-412.
15. Brouns SJJ, Wu H, Akerboom J, Turnbull AP, de Vos WM, &, van der Oost J, (2005) Engineering a selectable marker for hyperthermophiles. J Biol Chem 280, 11422-11431. (Pubitemid 40418451)
16. Heselpoth RD, &, Nelson DC, (2012) A new screening method for the directed evolution of thermostable bacteriolytic enzymes. J Vis Exp, 69, e4216.
17. Acharya P, Rajakumara E, Sankaranarayanan R, &, Rao NM, (2004) Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase. J Mol Biol 341, 1271-1281. (Pubitemid 39092314)
18. Barrozo A, Borstnar R, Marloie G, &, Kamerlin SCL, (2012) Computational protein engineering: bridging the gap between rational design and laboratory evolution. Int J Mol Sci 13, 12428-12460.
19. Dietrich JA, McKee AE, &, Keasling JD, (2010) High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu Rev Biochem 79, 563-590.
20. Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, &, Houk KN, (2013) Computational enzyme design. Angew Chem Int Ed Engl, in press.
21. Kipnis Y, &, Baker D, (2012) Comparison of designed and randomly generated catalysts for simple chemical reactions. Protein Sci 21, 1388-1395.
22. Khare SD, &, Fleishman SJ, (2012) Emerging themes in the computational design of novel enzymes and protein-protein interfaces. FEBS Lett 587, 1147-1154.
23. Hediger MR, De Vico L, Svendsen A, Besenmatter W, &, Jensen JH, (2012) A computational methodology to screen activities of enzyme variants. PLoS One 7, e49849.
24. Michener JK, &, Smolke CD, (2012) High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab Eng 14, 306-316.
25. Gredell JA, Frei CS, &, Cirino PC, (2012) Protein and RNA engineering to customize microbial molecular reporting. Biotechnol J 7, 477-499.
26. Yang G, &, Withers SG, (2009) Ultrahigh-throughput FACS-based screening for directed enzyme evolution. ChemBioChem 10, 2704-2715.
27. Konarzycka-Bessler M, &, Jaeger KE, (2006) Select the best: novel biocatalysts for industrial applications. Trends Biotechnol 24, 248-250. (Pubitemid 43831240)
28. Otten LG, Sio CF, Vrielink J, Cool RH, &, Quax WJ, (2002) Altering the substrate specificity of cephalosporin acylase by directed evolution of the β-subunit. J Biol Chem 277, 42121-42127. (Pubitemid 35257528)
29. Fernández-Álvaro E, Snajdrova R, Jochens H, Davids T, Böttcher D, &, Bornscheuer UT, (2011) A combination of in vivo selection and cell sorting for the identification of enantioselective biocatalysts. Angew Chem Int Ed Engl 50, 8584-8587.
30. Böttcher D, Schmidt M, &, Bornscheuer UT, (2010) Screens for active and stereoselective hydrolytic enzymes. Methods Mol Biol 668, 169-176.
31. Willies SC, White JL, &, Turner NJ, (2012) Development of a high-throughput screening method for racemase activity and its application to the identification of alanine racemase variants with activity towards l -arginine. Tetrahedron 68, 7564-7567.
32. Ingham CJ, Sprenkels A, Bomer J, Molenaar D, van den Berg A, van Hylckama Vlieg JET, &, de Vos WM, (2007) The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc Natl Acad Sci USA 104, 18217-18222. (Pubitemid 350210847)
33. Wagschal K, &, Lee CC, (2012) Microplate-based active/inactive 1 degrees screen for biomass degrading enzyme library purification and gene discovery. J Microbiol Methods 89, 83-85.
34. Schmidt-Dannert C, &, Arnold FH, (1999) Directed evolution of industrial enzymes. Trends Biotechnol 17, 135-136. (Pubitemid 29273942)
35. Kintses B, Hein C, Mohamed MF, Fischlechner M, Courtois F, Lainé C, &, Hollfelder F, (2012) Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution. Chem Biol 19, 1001-1009.
36. Ostafe R, Prodanovic R, Commandeur U, &, Fischer R, (2013) Flow cytometry-based ultra-high-throughput screening assay for cellulase activity. Anal Biochem 435, 93-98.
37. Yang G, Rich JR, Gilbert M, Wakarchuk WW, Feng Y, &, Withers SG, (2010) Fluorescence activated cell sorting as a general ultra-high-throughput screening method for directed evolution of glycosyltransferases. J Am Chem Soc 132, 10570-10577.
38. Prodanovic R, Ostafe R, Scacioc A, &, Schwaneberg U, (2011) Ultrahigh throughput screening system for directed glucose oxidase evolution in yeast cells. Comb Chem High Throughput Screen 14, 55-60.
39. de Las Heras A, Carreño CA, Martínez-García E, &, de Lorenzo V, (2010) Engineering input/output nodes in prokaryotic regulatory circuits. FEMS Microbiol Rev 34, 842-865.
40. Michener JK, Thodey K, Liang JC, &, Smolke CD, (2012) Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab Eng 14, 212-222.
41. Kelkar M, &, De A, (2012) Bioluminescence based in vivo screening technologies. Curr Opin Pharmacol 12, 592-600.
42. Garmendia J, de las Heras A, Galvão TC, &, de Lorenzo V, (2008) Tracing explosives in soil with transcriptional regulators of Pseudomonas putida evolved for responding to nitrotoluenes. Microb Biotechnol 1, 236-246.
43. de Las Heras A, &, de Lorenzo V, (2012) Engineering whole-cell biosensors with no antibiotic markers for monitoring aromatic compounds in the environment. Methods Mol Biol 834, 261-281.
44. Sinha J, Reyes SJ, &, Gallivan JP, (2010) Reprogramming bacteria to seek and destroy an herbicide. Nat Chem Biol 6, 464-470.
45. Beggah S, Vogne C, Zenaro E, &, Van Der Meer JR, (2008) Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting. Microb Biotechnol 1, 68-78.
46. Uchiyama T, Abe T, Ikemura T, &, Watanabe K, (2005) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23, 88-93. (Pubitemid 41724630)
47. Uchiyama T, &, Watanabe K, (2008) Substrate-induced gene expression (SIGEX) screening of metagenome libraries. Nat Protoc 3, 1202-1212.
48. de Las Heras A, Chavarría M, &, de Lorenzo V, (2011) Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation. Mol Microbiol 82, 287-299.
49. de Lorenzo V, (2005) Problems with metagenomic screening. Nat Biotechnol 23, 1045; author reply, 1045-1046.
50. Uchiyama T, &, Miyazaki K, (2010) Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes. Appl Environ Microbiol 76, 7029-7035.
51. Allert M, Rizk SS, Looger LL, &, Hellinga HW, (2004) Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proc Natl Acad Sci USA 101, 7907-7912. (Pubitemid 38698027)
52. Looger LL, Dwyer MA, Smith JJ, &, Hellinga HW, (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423, 185-190. (Pubitemid 36569543)
53. Schreier B, Stumpp C, Wiesner S, &, Höcker B, (2009) Computational design of ligand binding is not a solved problem. Proc Natl Acad Sci USA 106, 18491-18496.
54. Malisi C, Schumann M, Toussaint NC, Kageyama J, Kohlbacher O, &, Höcker B, (2012) Binding pocket optimization by computational protein design. PLoS One 7, e52505.
55. van Sint Fiet S, van Beilen JB, &, Witholt B, (2006) Selection of biocatalysts for chemical synthesis. Proc Natl Acad Sci USA 103, 1693-1698. (Pubitemid 43228755)
56. Cebolla A, Sousa C, &, de Lorenzo V, (1997) Effector specificity mutants of the transcriptional activator NahR of naphthalene degrading Pseudomonas define protein sites involved in binding of aromatic inducers. J Biol Chem 272, 3986-3992. (Pubitemid 27078458)
57. Mohn WW, Garmendia J, Galvao TC, &, de Lorenzo V, (2006) Surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes. Environ Microbiol 8, 546-555.
58. Tang SY, &, Cirino PC, (2011) Design and application of a mevalonate-responsive regulatory protein. Angew Chem Int Ed Engl 50, 1084-1086.
59. Firestine SM, Salinas F, Nixon AE, Baker SJ, &, Benkovic SJ, (2000) Using an AraC-based three-hybrid system to detect biocatalysts in vivo. Nat Biotechnol 18, 544-547. (Pubitemid 30313960)
60. Baker K, Bleczinski C, Lin H, Salazar-Jimenez G, Sengupta D, Krane S, &, Cornish VW, (2002) Chemical complementation: a reaction-independent genetic assay for enzyme catalysis. Proc Natl Acad Sci USA 99, 16537-16542. (Pubitemid 36034008)
61. Lin H, Tao HY, &, Cornish VW, (2004) Directed evolution of a glycosynthase via chemical complementation. J Am Chem Soc 126, 15051-15059. (Pubitemid 39557264)
62. Peralta-Yahya P, Carter BT, Lin H, Tao H, &, Cornish VW, (2008) High-throughput selection for cellulase catalysts using chemical complementation. J Am Chem Soc 130, 17446-17452.
63. Verhoeven KD, Altstadt OC, &, Savinov SN, (2012) Intracellular detection and evolution of site-specific proteases using a genetic selection system. Appl Biochem Biotechnol 166, 1340-1354.
64. Ruigrok VJ, Levisson M, Eppink MHM, Smidt H, &, van der Oost J, (2011) Alternative affinity tools: more attractive than antibodies? Biochem J 436, 1-13.
65. Ruigrok VJ, van Duijn E, Barendregt A, Dyer K, Tainer JA, Stoltenburg R, Strehlitz B, Levisson M, Smidt H, &, van der Oost J, (2012) Kinetic and stoichiometric characterisation of streptavidin-binding aptamers. ChemBioChem 13, 829-836.
66. Desai SK, &, Gallivan JP, (2004) Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J Am Chem Soc 126, 13247-13254. (Pubitemid 39382751)
67. Kostallas G, Löfdahl PA, &, Samuelson P, (2011) Substrate profiling of tobacco etch virus protease using a novel fluorescence-assisted whole-cell assay. PLoS One 6, e16136.
68. O'Loughlin TL, Greene DN, &, Matsumura I, (2006) Diversification and specialization of HIV protease function during in vitro evolution. Mol Biol Evol 23, 764-778.
69. Owen JG, Robins KJ, Parachin NS, &, Ackerley DF, (2012) A functional screen for recovery of 4′-phosphopantetheinyl transferase and associated natural product biosynthesis genes from metagenome libraries. Environ Microbiol 14, 1198-1209.
70. Gupta RD, &, Tawfik DS, (2008) Directed enzyme evolution via small and effective neutral drift libraries. Nat Methods 5, 939-942.
71. Japrung D, Chusacultanachai S, Yuvaniyama J, Wilairat P, &, Yuthavong Y, (2005) A simple dual selection for functionally active mutants of Plasmodium falciparum dihydrofolate reductase with improved solubility. Protein Eng Des Sel 18, 457-464. (Pubitemid 41433102)
72. García-Fruitós E, González-Montalbán N, Morell M, Vera A, Ferraz RM, Arís A, Ventura S, &, Villaverde A, (2005) Aggregation as bacterial inclusion bodies does not imply inactivation of enzymes and fluorescent proteins. Microb Cell Fact 4, 27.
73. Pourmir A, &, Johannes TW, (2012) Directed evolution: selection of the host organism. Comput Struct Biotechnol J 2, e201209012.
74. Hu JC, Kornacker MG, &, Hochschild A, (2000) Escherichia coli one- and two-hybrid systems for the analysis and identification of protein-protein interactions. Methods 20, 80-94. (Pubitemid 30119603)
75. Joung JK, Ramm EI, &, Pabo CO, (2000) A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci USA 97, 7382-7387. (Pubitemid 30431472)
76. Marvin JS, Schreiter ER, Echevarría IM, &, Looger LL, (2011) A genetically encoded, high-signal-to-noise maltose sensor. Proteins 79, 3025-3036.
77. Xiong AS, Peng RH, Zhuang J, Davies J, Zhang J, &, Yao QH, (2012) Advances in directed molecular evolution of reporter genes. Crit Rev Biotechnol 32, 133-142.