Protein and RNA engineering to customize microbial molecular reporting

Biotechnology Journal

Volumn 7, Issue 4, 2012, Pages 477-499

  Gredell, Joseph A ^a   Frei, Christopher S ^a   Cirino, Patrick C ^a  

^a UNIVERSITY OF HOUSTON   (United States)

Author keywords

Aptamer; Directed evolution; Molecular recognition; Regulatory protein; Riboswitch

Indexed keywords

ALLOSTERIC ACTIVATION; APTAMERS; DIRECTED EVOLUTION; ENVIRONMENTAL MONITORING; HIGH-THROUGHPUT SCREENING; IN-VIVO; LIGAND BINDING; MICROBIAL SCREENING; REGULATORY PROTEIN; REPORTER-GENE EXPRESSION; REPORTING SYSTEMS; RIBOSWITCHES; RNA ENGINEERING; RNA MOLECULES; RNA SEQUENCES; SENSING COMPONENTS; SMALL MOLECULES; SYNTHETIC BIOLOGY;

BIOCHEMISTRY; BIOSENSORS; DIAGNOSIS; GENE EXPRESSION; LIGANDS; MOLECULAR RECOGNITION; MOLECULES; RNA;

PROTEINS;

1,2,4 TRICHLOROBENZENE; 2 NITROTOLUENE; 2,4 DICHLOROPHENOL; 2,4 DINITROTOLUENE; 3 CHLOROBENZOIC ACID; ALITRETINOIN; ANHYDROTETRACYCLINE; ARABINOSE; BENZOIC ACID; BETA GALACTOSIDE; CHLORAMPHENICOL ACETYLTRANSFERASE; CORTICOSTERONE; DIETHYLSTILBESTROL; DOXYCYCLINE; ESTRADIOL; GREEN FLUORESCENT PROTEIN; HYDROXYTAMOXIFEN; LEVANSUCRASE; MALTOSE; MEVALONIC ACID; PERIPLASMIC BINDING PROTEIN; PROGESTERONE; PROTEIN; RNA; SALICYLIC ACID; SUCROSE; TESTOSTERONE; TETRACYCLINE; TRICLOSAN; TRINITROTOLUENE;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; BIOSENSOR; COLORIMETRY; FLUORESCENCE; GENE EXPRESSION; GENETIC ENGINEERING; HUMAN; LIGAND BINDING; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN ENGINEERING; REVIEW; RIBOSWITCH;

ANIMALS; APTAMERS, NUCLEOTIDE; BIOSENSING TECHNIQUES; HUMANS; PROTEIN ENGINEERING; PROTEINS; RNA;

EID: 84859245861     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201100266     Document Type: Review

References (149)

1. Gilardi, G., Zhou, L. Q., Hibbert, L., Cass, A. E. G., Engineering the maltose-binding protein for reagentless fluorescence sensing. Anal. Chem. 1994, 66, 3840-3847.
2. Soukup, G. A., Breaker, R. R., Allosteric nucleic acid catalysts. Curr. Opin. Struc. Biol. 2000, 10, 318-325.
3. East, A. K., Mauchline, T. H., Poole, P. S., Biosensors for ligand detection, Advances in Applied Microbiology, Vol 64, Elsevier Academic Press Inc, San Diego 2008, pp. 137-166.
4. Marchisio, M. A., Rudolf, F., Synthetic biosensing systems. Int. J. Biochem. Cell Biol. 2011, 43, 310-319.
5. van der Meer, J. R., Belkin, S., Where microbiology meets microengineering: design and applications of reporter bacteria. Nat. Rev. Micro 2010, 8, 511-522.
6. Su, L. A., Jia, W. Z., Hou, C. J., Lei, Y., Microbial biosensors: A review. Biosens. Bioelectron. 2011, 26, 1788-1799.
7. Farre, M., Kantiani, L., Perez, S., Barcelo, D., Sensors and biosensors in support of EU Directives. Trac-Trends Anal. Chem. 2009, 28, 170-185.
8. Wang, J., Katz, E., Digital biosensors with built-in logic for biomedical applications-biosensors based on a biocomputing concept. Anal. Bioanal. Chem. 2010, 398, 1591-1603.
9. Rapp, B. E., Gruhl, F. J., Lange, K., Biosensors with label-free detection designed for diagnostic applications. Anal. Bioanal. Chem. 2010, 398, 2403-2412.
10. Jacob, F., The Birth of the Operon. Science 2011, 332, 767.
11. Jacob, F., Monod, J., Genetic regulatory mechanisms in synthesis of proteins. J. Mol. Biol. 1961, 3, 318-356.
12. De Las Heras, A., Carreño, C. A., Martínez-García, E., De Lorenzo, V., Engineering input/output nodes in prokaryotic regulatory circuits. Fems Microbiol. Rev. 2010, 34, 842-865.
13. Schell, M. A., Poser, E. F., Demonstration, characterization, and mutational analysis of NahR protein-binding to nah and sal promoters. J. Bacteriol. 1989, 171, 837-846.
14. Cebolla, A., Sousa, C., deLorenzo, V., Effector specificity mutants of the transcriptional activator NahR of naphthalene degrading Pseudomonas define protein sites involved in binding of aromatic inducers. J. Biol. Chem. 1997, 272, 3986-3992.
15. Cirino, P. C., Mayer, K. M., Umeno, D., Generating Mutant Libraries Using Error-Prone PCR, in: Arnold, F. H., Georgiou, G. (Eds.), Directed Evolution Library Creation, Humana Press 2003, pp. 3-9.
16. Yanischperron, C., Vieira, J., Messing, J., Improved M13 phage cloning vectors and host strains: nucleotide-sequences of the M13mp18 and pUC19 vectors. Gene 1985, 33, 103-119.
17. Fiet, S. v. S., Beilen, J. B. v., Witholt, B., Selection of biocatalysts for chemical synthesis. Proc. Natl. Acad. Sci. USA 2006, 103, 1693-1698.
18. Skarfstad, E., O'Neill, E., Garmendia, J., Shingler, V., Identification of an effector specificity subregion within the aromatic-responsive regulators DmpR and XylR by DNA shuffling. J. Bacteriol 2000, 182, 3008-3016.
19. Garmendia, J., Devos, D., Valencia, A., de Lorenzo, V., A la carte transcriptional regulators: unlocking responses of the prokaryotic enhancer-binding protein XyIR to non-natural effectors. Mol. Microbiol. 2001, 42, 47-59.
20. Stemmer, W. P. C., Rapid evolution of a protein in vitro by DNA shuffling. Nature 1994, 370, 389-391.
21. Stemmer, W. P. C., DNA shuffling by random fragmentation and reassembly: In-vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 1994, 91, 10747-10751.
22. Wegener, G., Brandt, M., Duda, L., Hofmann, J. et al., Trends in industrial catalysis in the polyurethane industry. Applied Catalysis A: General 2001, 221, 303-335.
23. Galvao, T. C., Mencia, M., de Lorenzo, V., Emergence of novel functions in transcriptional regulators by regression to stem protein types. Mol. Microbiol. 2007, 65, 907-919.
24. de las Heras, A., de Lorenzo, V., Cooperative amino acid changes shift the response of the sigma 54-dependent regulator XylR from natural m-xylene towards xenobiotic 2, 4-dinitrotoluene. Mol. Microbiol. 2011, 79, 1248-1259.
25. de las Heras, A., Carreno, C. A., de Lorenzo, V., Stable implantation of orthogonal sensor circuits in Gram-negative bacteria for environmental release. Environ. Microbiol. 2008, 10, 3305-3316.
26. de las Heras, A., de Lorenzo, V., In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules. Anal. Bioanal. Chem. 2011, 400, 1093-1104.
27. Beggah, S., Vogne, C., Zenaro, E., Meer, J. R. v. d., Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting. Microb. Biotechnol. 2008, 1, 68-78.
28. Whitehead, N. A., Barnard, A. M. L., Slater, H., Simpson, N. J. L., Salmond, G. P. C., Quorum-sensing in gram-negative bacteria. Fems Microbiol. Rev. 2001, 25, 365-404.
29. Taga, M. E., Bassler, B. L., Chemical communication among bacteria. Proc. Natl. Acad. Sci. USA 2003, 100, 14549-14554.
30. Eberhard, A., Widrig, C. A., McBath, P., Schineller, J. B., Analogs of the autoinducer of bioluminescence in Vibrio Fischeri. Arch. Microbiol. 1986, 146, 35-40.
31. Stevens, A. M., Greenberg, E. P., Quorum sensing in Vibrio fischeri: Essential elements for activation of the luminescence genes. J. Bacteriol. 1997, 179, 557-562.
32. Collins, C. H., Arnold, F. H., Leadbetter, J. R., Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones. Mol. Microbiol. 2005, 55, 712-723.
33. Hawkins, A. C., Arnold, F. H., Stuermer, R., Hauer, B., Leadbetter, J. R., Directed evolution of Vibrio fischeri LuxR for improved response to butanoyl-homoserine lactone. Appl. Environ. Microb. 2007, 73, 5775-5781.
34. Collins, C. H., Leadbetter, J. R., Arnold, F. H., Dual selection enhances the signaling specificity of a variant of the quorum-sensing transcriptional activator LuxR. Nat. Biotechnol. 2006, 24, 708-712.
35. Yokobayashi, Y., Arnold, F. H., A dual selection module for directed evolution of genetic circuits. Natural Computing 2005, 4, 245-254.
36. Bertram, R., Hillen, W., The application of Tet repressor in prokaryotic gene regulation and expression. Microb. Biotechnol. 2008, 1, 2-16.
37. Scholz, O., Kostner, M., Reich, M., Gastiger, S., Hillen, W., Teaching TetR to recognize a new inducer. J. Mol. Biol. 2003, 329, 217-227.
38. Schnappinger, D., Schubert, P., Pfleiderer, K., Hillen, W., Determinants of protein-protein recognition by four helix bundles: changing the dimerization specificity of Tet repressor. Embo J. 1998, 17, 535-543.
39. Hinrichs, W., Kisker, C., Duvel, M., Muller, A. et al., Structure of the Tet repressor tetracycline-complex and regulation of antibiotic resistance. Science 1994, 264, 418-420.
40. 2+ reveals mechanism of antibiotic resistance. J. Mol. Biol. 1995, 247, 260-280.
41. Orth, P., Cordes, F., Schnappinger, D., Hillen, W. et al., Conformational changes of the Tet repressor induced by tetracycline trapping. J. Mol. Biol. 1998, 279, 439-447.
42. Orth, P., Schnappinger, D., Hillen, W., Saenger, W., Hinrichs, W., Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat. Struct. Biol. 2000, 7, 215-219.
43. Henssler, E. M., Scholz, O., Lochner, S., Gmeiner, P., Hillen, W., Structure-based design of Tet repressor to optimize a new inducer specificity. Biochemistry 2004, 43, 9512-9518.
44. Scholz, O., Henssler, E. M., Bail, J., Schubert, P. et al., Activity reversal of Tet repressor caused by single amino acid exchanges. Mol. Microbiol. 2004, 53, 777-789.
45. Kamionka, A., Bogdanska-Urbaniak, J., Scholz, O., Hillen, W., Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor. Nucleic Acids Res. 2004, 32, 842-847.
46. Kamionka, A., Sehnal, M., Scholz, O., Hillen, W., Independent regulation of two genes in Escherichia coli by tetracyclines and Tet repressor variants. J. Bacteriol. 2004, 186, 4399-4401.
47. Krueger, M., Scholz, O., Wisshak, S., Hillen, W., Engineered Tet repressors with recognition specificity for the tetO-4C5G operator variant. Gene 2007, 404, 93-100.
48. Schleif, R., AraC protein, regulation of the l-arabinose operon in Escherichia coli, and the light switch mechanism of AraC action. Fems Microbiol. Rev. 2010, 34, 779-796.
49. Tang, S. Y., Fazelinia, H., Cirino, P. C., AraC regulatory protein mutants with altered effector specificity. J. Am. Chem. Soc. 2008, 130, 5267-5271.
50. Ross, J. J., Gryczynski, U., Schleif, R., Mutational analysis of residue roles in AraC function. J. Mol. Biol. 2003, 328, 85-93.
51. Soisson, S. M., MacDougallShackleton, B., Schleif, R., Wolberger, C., Structural basis for ligand-regulated oligomerization of AraC. Science 1997, 276, 421-425.
52. Kirby, J., Keasling, J. D., Biosynthesis of plant isoprenoids: Perspectives for microbial engineering. Annu. Rev. Plant Biol. 2009, 60, 335-355.
53. Martin, V. J. J., Pitera, D. J., Withers, S. T., Newman, J. D., Keasling, J. D., Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotech. 2003, 21, 796-802.
54. Tang, S.-Y., Cirino, P. C., Design and application of a mevalonate-responsive regulatory protein. Angew. Chem. Int. Edit. 2011, 50, 1084-1086.
55. Martin, V. J. J., Pitera, D. J., Withers, S. T., Newman, J. D., Keasling, J. D., Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 2003, 21, 796-802.
56. Pfleger, B. F., Pitera, D. J., D Smolke, C., Keasling, J. D., Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 2006, 24, 1027-1032.
57. Hansen, C. A., Frost, J. W., Deoxygenation of polyhydroxybenzenes: An alternative strategy for the benzene-free synthesis of aromatic chemicals. J. Am. Chem. Soc. 2002, 124, 5926-5927.
58. Agrawal, J. P., Recent trends in high-energy materials. Prog. Energy Combust. Sci. 1998, 24, 1-30.
59. Eckermann, S., Schroder, G., Schmidt, J., Strack, D. et al., New pathway to polyketides in plants. Nature 1998, 396, 387-390.
60. Gillies, A. R., Skretas, G., Wood, D. W., Engineered systems for detection and discovery of nuclear hormone-like compounds. Biotechnol. Prog. 2008, 1, 8-16.
61. Peet, D. J., Doyle, D. F., Corey, D. R., Mangelsdorf, D. J., Engineering novel specificities for ligand-activated transcription in the nuclear hormone receptor RXR. Chem. Biol. 1998, 5, 13-21.
62. Doyle, D. F., Braasch, D. A., Jackson, L. K., Weiss, H. E. et al., Engineering orthogonal ligand-receptor pairs from "near drugs". J. Am. Chem. Soc. 2001, 123, 11367-11371.
63. Azizi, B., Chang, E. I., Doyle, D. F., Chemical complementation: small-molecule-based genetic selection in yeast. Biochem. Biophys. Res. Commun. 2003, 306, 774-780.
64. Schwimmer, L. J., Rohatgi, P., Azizi, B., Seley, K. L., Doyle, D. F., Creation and discovery of ligand-receptor pairs for small molecule control of transcription. Proc. Nat. Acad. Sci. USA 2004, 101, 14707-14712.
65. Chen, Z. L., Katzenellenbogen, B. S., Katzenellenbogen, J. A., Zhao, H. M., Directed evolution of human estrogen receptor variants with significantly enhanced androgen specificity and affinity. J. Biol. Chem. 2004, 279, 33855-33864.
66. Young, K. H., Yeast two-hybrid: So many interactions, (in) so little time. Biol. Reprod. 1998, 58, 302-311.
67. Katzenellenbogen, J. A., Katzenellenbogen, B. S., Nuclear hormone receptors: Ligand-activated regulators of transcription and diverse cell responses. Chem. Biol. 1996, 3, 529-536.
68. Chockalingam, K., Chen, Z. L., Katzenellenbogen, J. A., Zhao, H. M., Directed evolution of specific receptor-ligand pairs for use in the creation of gene switches. Proc. Natl. Acad. Sci. USA 2005, 102, 5691-5696.
69. Tanenbaum, D. M., Wang, Y., Williams, S. P., Sigler, P. B., Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains. Proc. Natl. Acad. Sci. USA 1998, 95, 5998-6003.
70. Chen, Z. L., Zhao, H. M., Rapid creation of a novel protein function by in vitro coevolution. J. Mol. Biol. 2005, 348, 1273-1282.
71. Marvin, J. S., Corcoran, E. E., Hattangadi, N. A., Zhang, J. V. et al., The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors. Proc. Natl. Acad. Sci. USA 1997, 94, 4366-4371.
72. Looger, L. L., Dwyer, M. A., Smith, J. J., Hellinga, H. W., Computational design of receptor and sensor proteins with novel functions. Nature 2003, 423, 185-190.
73. Derbyshire, V., Wood, D. W., Wu, W., Dansereau, J. T. et al., Genetic definition of a protein-splicing domain: Functional mini-inteins support structure predictions and a model for intein evolution. Proc. Natl. Acad. Sci. USA 1997, 94, 11466-11471.
74. Buskirk, A. R., Ong, Y. C., Gartner, Z. J., Liu, D. R., Directed evolution of ligand dependence: Small-molecule-activated protein splicing. Proc. Natl. Acad. Sci. USA 2004, 101, 10505-10510.
75. Skretas, G., Wood, D. W., A Bacterial biosensor of endocrine modulators. J. Mol. Biol. 2005, 349, 464-474.
76. Skretas, G., Wood, D. W., Rapid detection of subtype-selective nuclear hormone receptor binding with bacterial genetic selection. Appl. Environ. Microb. 2005, 71, 8995-8997.
77. Skretas, G., Meligova, A. K., Villalonga-Barber, C., Mitsiou, D. J. et al., Engineered chimeric enzymes as tools for drug discovery: Generating reliable bacterial screens for the detection, discovery, and assessment of estrogen receptor modulators. J. Am. Chem. Soc. 2007, 129, 8443-8457.
78. Gawrys, M. D., Hartman, I., Landweber, L. F., Wood, D. W., Use of engineered Escherichia coli cells to detect estrogenicity in everyday consumer products. J. Chem. Technol. Biotechnol. 2009, 84, 1834-1840.
79. Liang, R. B., Zhou, J., Liu, J. H., Construction of a bacterial assay for estrogen detection based on an estrogen-sensitive intein. Appl. Environ. Microb. 2011, 77, 2488-2495.
80. Guntas, G., Ostermeier, M., Creation of an allosteric enzyme by domain insertion. J. Mol. Biol. 2004, 336, 263-273.
81. Graf, R., Schachman, H. K., Random circular permutation of genes and expressed polypeptide chains: Application of the method to the catalytic chains of aspartate transcarbamoylase. Proc. Natl. Acad. Sci. USA 1996, 93, 11591-11596.
82. Ostermeier, M., Benkovic, S. J., Construction of hybrid gene libraries involving the circular permutation of DNA. Biotechnol. Lett. 2001, 23, 303-310.
83. Guntas, G., Mitchell, S. F., Ostermeier, M., A molecular switch created by in vitro recombination of nonhomologous genes. Chem. Biol. 2004, 11, 1483-1487.
84. Guntas, G., Mansell, T. J., Kim, J. R., Ostermeier, M., Directed evolution of protein switches and their application to the creation of ligand-binding proteins. Proc. Natl. Acad. Sci. USA 2005, 102, 11224-11229.
85. Quiocho, F. A., Spurlino, J. C., Rodseth, L. E., Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport chemosensory receptor. Structure 1997, 5, 997-1015.
86. Ellington, A. D., Szostak, J. W., In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346, 818-822.
87. Zhang, J., Lau, M. W., Ferre-D'Amare, A. R., Ribozymes and riboswitches: Modulation of RNA function by small molecules. Biochemistry 2010, 49, 9123-9131.
88. Tuerk, C., Gold, L., Systematic evolution of ligands by exponential enrichment - RNA ligands to bacteriophage-T4 DNA-polymerase. Science 1990, 249, 505-510.
89. Lee, J. F., Hesselberth, J. R., Meyers, L. A., Ellington, A. D., Aptamer database. Nucleic Acids Res. 2004, 32, D95-D100.
90. Liu, J. W., Cao, Z. H., Lu, Y., Functional Nucleic Acid Sensors. Chem. Rev. 2009, 109, 1948-1998.
91. Werstuck, G., Green, M. R., Controlling gene expression in living cells through small molecule-RNA interactions. Science 1998, 282, 296-298.
92. Nahvi, A., Sudarsan, N., Ebert, M. S., Zou, X. et al., Genetic control by a metabolite binding mRNA. Chem. Biol. 2002, 9, 1043-1049.
93. Winkler, W., Nahvi, A., Breaker, R. R., Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 2002, 419, 952-956.
94. Mironov, A. S., Gusarov, I., Rafikov, R., Lopez, L. E. et al., Sensing small molecules by nascent RNA: A mechanism to control transcription in bacteria. Cell 2002, 111, 747-756.
95. Famulok, M., Hartig, J. S., Mayer, G., Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem. Rev. 2007, 107, 3715-3743.
96. Suess, B., Hanson, S., Berens, C., Fink, B. et al., Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res. 2003, 31, 1853-1858.
97. Hanson, S., Berthelot, K., Fink, B., McCarthy, J. E. G., Suess, B., Tetracycline-aptamer-mediated translational regulation in yeast. Mol. Microbiol. 2003, 49, 1627-1637.
98. Hanson, S., Bauer, G., Fink, B., Suess, B., Molecular analysis of a synthetic tetracycline-binding riboswitch. RNA 2005, 11, 503-511.
99. Muller, M., Weigand, J. E., Weichenrieder, O., Suess, B., Thermodynamic characterization of an engineered tetracycline-binding riboswitch. Nucleic Acids Res. 2006, 34, 2607-2617.
100. Weigand, J. E., Suess, B., Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast. Nucleic Acids Res. 2007, 35, 4179-4185.
101. Suess, B., Fink, B., Berens, C., Stentz, R., Hillen, W., A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res. 2004, 32, 1610-1614.
102. Soukup, G. A., Breaker, R. R., Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA. 1999, 96, 3584-3589.
103. Famulok, M., Molecular recognition of amino acids by RNA-aptamers: An L-citrulline binding RNA motif and its evolution into an L-arginine binder. J. Am. Chem. Soc. 1994, 116, 1698-1706.
104. Wallis, M. G., Vonahsen, U., Schroeder, R., Famulok, M., A novel RNA motif for neomycin recognition. Chem. Biol. 1995, 2, 543-552.
105. Weigand, J. E., Sanchez, M., Gunnesch, E. B., Zeiher, S. et al., Screening for engineered neomycin riboswitches that control translation initiation. RNA 2008, 14, 89-97.
106. Jenison, R. D., Gill, S. C., Pardi, A., Polisky, B., High-resolution molecular discrimination by RNA. Science 1994, 263, 1425-1429.
107. Desai, S. K., Gallivan, J. P., Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J. Am. Chem. Soc. 2004, 126, 13247-13254.
108. Lynch, S. A., Desai, S. K., Sajja, H. K., Gallivan, J. P., A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem. Biol. 2007, 14, 173-184.
109. Topp, S., Gallivan, J. P., Guiding bacteria with small molecules and RNA. J. Am. Chem. Soc. 2007, 129, 6807-6811.
110. Topp, S., Gallivan, J. P., Random walks to synthetic riboswitches - A high-throughput selection based on cell motility. ChemBioChem 2008, 9, 210-213.
111. Lynch, S. A., Gallivan, J. P., A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res. 2009, 37, 184-192.
112. Sinha, J., Reyes, S. J., Gallivan, J. P., Reprogramming bacteria to seek and destroy an herbicide. Nat. Chem. Biol. 2010, 6, 464-470.
113. Fowler, C. C., Brown, E. D., Li, Y. F., A FACS-based approach to engineering artificial riboswitches. ChemBioChem 2008, 9, 1906-1911.
114. Nomura, Y., Yokobayashi, Y., Reengineering a natural riboswitch by dual genetic selection. J. Am. Chem. Soc. 2007, 129, 13814-13815.
115. + antiporter: three independent groups of phenotypes are conferred by TetA (C). Mol. Membr. Biol. 1994, 11, 271-277.
116. Podolsky, T., Fong, S. T., Lee, B. T. O., Direct selection of tetracycline-sensitive Escherichia coli cells using nickel salts. Plasmid 1996, 36, 112-115.
117. Sharma, V., Nomura, Y., Yokobayashi, Y., Engineering Complex Riboswitch Regulation by Dual Genetic Selection. J. Am. Chem. Soc. 2008, 130, 16310-16315.
118. Welz, R., Breaker, R. R., Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA 2007, 13, 573-582.
119. Muranaka, N., Sharma, V., Nomura, Y., Yokobayashi, Y., Efficient design strategy for whole-cell and cell-free biosensors based on engineered riboswitches. Anal. Lett. 2009, 42, 108-122.
120. Muranaka, N., Sharma, V., Nomura, Y., Yokobayashi, Y., An efficient platform for genetic selection and screening of gene switches in Escherichia coli. Nucleic Acids Re. 2009, 37, 9.
121. Muranaka, N., Yokobayashi, Y., Posttranscriptional signal integration of ENGINEERED riboswitches yields band-pass output. Angew. Chem.-Int. Edit. 2010, 49, 4653-4655.
122. Muranaka, N., Yokobayashi, Y., A synthetic riboswitch with chemical band-pass response. Chem. Commun. 2010, 46, 6825-6827.
123. Bayer, T. S., Smolke, C. D., Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 2005, 23, 337-343.
124. Cochrane, J. C., Strobel, S. A., Catalytic strategies of self-cleaving ribozymes. Accounts Chem. Res. 2008, 41, 1027-1035.
125. Fedor, M. J., Comparative enzymology and structural biology of RNA self-cleavage. Annu. Rev. Biophysics 2009, 38, 271-299.
126. Win, M. N., Smolke, C. D., A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc. Natl. Acad. Sci. USA 2007, 104, 14283-14288.
127. Win, M. N., Smolke, C. D., Higher-order cellular information processing with synthetic RNA devices. Science 2008, 322, 456-460.
128. Ogawa, A., Maeda, M., An artificial aptazyme-based riboswitch and its cascading system in E. coli. ChemBioChem 2008, 9, 206-209.
129. Wieland, M., Hartig, J. S., Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew. Chem. Int. Edit. 2008, 47, 2604-2607.
130. Wieland, M., Benz, A., Klauser, B., Hartig, J. S., Artificial ribozyme switches containing natural riboswitch aptamer domains. Angew. Chem.-Int. Edit. 2009, 48, 2715-2718.
131. Berschneider, B., Wieland, M., Rubini, M., Hartig, J. S., Small-molecule-DEPENDENT regulation of transfer RNA in bacteria. Angew. Chem. Int. Edit. 2009, 48, 7564-7567.
132. Ogawa, A., Maeda, M., A novel label-free biosensor using an aptazyme-suppressor-tRNA conjugate and an amber mutated reporter gene. Chembiochem 2008, 9, 2204-2208.
133. Wieland, M., Berschneider, B., Erlacher, M. D., Hartig, J. S., Aptazyme-mediated regulation of 16S ribosomal RNA. Chem. Biol. 2010, 17, 236-242.
134. Bernstein, D. S., Buter, N., Stumpf, C., Wickens, M., Analyzing mRNA-protein complexes using a yeast three-hybrid system. Methods 2002, 26, 123-141.
135. Buskirk, A. R., Kehayova, P. D., Landrigan, A., Liu, D. R., In vivo evolution of an RNA-based transcriptional activator. Chem. Biol. 2003, 10, 533-540.
136. Buskirk, A. R., Landrigan, A., Liu, D. R., Engineering a ligand-dependent RNA transcriptional activator. Chem. Biol. 2004, 11, 1157-1163.
137. Yoo, E. H., Lee, S. Y., Glucose biosensors: An overview of use in clinical practice. Sensors 2010, 10, 4558-4576.
138. Sadik, O. A., Aluoch, A. O., Zhou, A. L., Status of biomolecular recognition using electrochemical techniques. Biosens. Bioelectron. 2009, 24, 2749-2765.
139. Krueger, C., Schmidt, A., Danke, C., Hillen, W., Berens, C., Transactivator mutants with altered effector specificity allow selective regulation of two genes by tetracycline variants. Gene 2004, 331, 125-131.
140. Chen, Y. Y., Jensen, M. C., Smolke, C. D., Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc. Natl. Acad. Sci. USA 2010, 107, 8531-8536.
141. Beisel, C. L., Chen, Y. Y., Culler, S. J., Hoff, K. G., Smolke, C. D., Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing. Nucleic Acids Res. 2010.
142. Culler, S. J., Hoff, K. G., Smolke, C. D., Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 2010, 330, 1251-1255.
143. Auslander, S., Ketzer, P., Hartig, J. S., A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol. Biosyst. 2010, 6, 807-814.
144. An, C. I., Trinh, V. B., Yokobayashi, Y., Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA 2006, 12, 710-716.
145. Yen, L., Svendsen, J., Lee, J. S., Gray, J. T. et al., Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 2004, 431, 471-476.
146. Taylor, J. L., Rohatgi, P., Spencer, H. T.., Doyle, D. F., Azizi, B. et al., Characterization of a molecular switch system that regulates gene expression in mammalian cells through a small molecule. BMC Biotechnol. 2010, 10.
147. Miller, O. J., Bernath, K., Agresti, J. J., Amitai, G. et al., Directed evolution by in vitro compartmentalization. Nat. Methods 2006, 3, 561-570.
148. Griffiths, A. D., Tawfik, D. S., Miniaturising the laboratory in emulsion droplets. Trends Biotechnol. 2006, 24, 395-402.
149. Stapleton, J. A., Swartz, J. R., Development of an in vitro compartmentalization screen for high-throughput directed evolution of FeFe hydrogenases. Plos One 2010, 5.