The art of reporter proteins in science: Past, present and future applications

BMB Reports

Volumn 43, Issue 7, 2010, Pages 451-460

  Ghim, Cheol Min ^a   Lee, Sung Kuk ^a   Takayama, Shuichi ^a,b   Mitchell, Robert J ^a  

^a Ulsan National Institute of Science and Technology   (South Korea)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Gene fusion; Gfp; LacZ; Luciferase; Reporter

Indexed keywords

BETA GALACTOSIDASE; LUCIFERASE; PHOTOPROTEIN;

GENETICS; MICROFLUIDICS; REPORTER GENE; REVIEW;

BETA-GALACTOSIDASE; GENES, REPORTER; LUCIFERASES; LUMINESCENT PROTEINS; MICROFLUIDICS;

EID: 77956535595     PISSN: 19766696     EISSN: 1976670X     Source Type: Journal    
DOI: 10.3858/BMBRep.2010.43.7.451     Document Type: Review

References (90)

1. http://www.ncbi.nlm.nih.gov.
2. Wood, K. V. (1995) Marker proteins for gene expression. Curr. Opin. Biotechnol. 6, 50-58.
3. Berman, M. L. and Beckwith, J. (1979) Fusions of the lac operon to the transfer RNA gene tyrT of Escherichia coli. J. Mol. Biol. 130, 285-301.
4. Casadaban, M. J., Chou, J. and Cohen, S. N. (1980) In vitro gene fusions that join an enzymatically active beta-galactosidase segment to amino-terminal fragments of exogenous proteins: Escherichia coli plasmid vectors for the detection and cloning of translational initiation signals. J. Bacteriol. 143, 971-980.
5. Lis, J. T., Simon, J. A. and Sutton, C. A. (1983) New heat shock puffs and (-galactosidase activity resulting from transformation of Drosophila with an hsp70-lacZ hybrid gene. Cell 35, 403-410.
6. James, A. L., Perry, J. D., Ford, M., Armstrong, L. and Gould, F. K. (1996) Evaluation of cyclohexenoesculetinbeta-D-galactoside and 8-hydroxyquinoline-beta-D-galactoside as substrates for the detection of beta-galactosidase. Appl. Environ. Microbiol. 62, 3868-3870.
7. Imagawa, M., Yoshitake, S., Ishikawa, E., Endo, Y., Ohtaki, S., Kano, E. and Tsunetoshi, Y. (1981) Highly sensitive sandwich enzyme immunoassay of human IgE with beta-D-galactosidase from Escherichia coli. Clin. Chim. Acta 117, 199-207.
8. Craig, D., Arriaga, E. A., Banks, P., Zhang, Y., Renborg, A., Palcic, M. M. and Dovichi, N. J. (1995) Fluorescencebased enzymatic assay by capillary electrophoresis laser-induced fluorescence detection for the determination of a few beta-galactosidase molecules. Anal. Biochem. 226, 147-153.
9. Bronstein, I., Martin, C. S., Fortin, J. J., Olesen, C. E. and Voyta, J. C. (1996) Chemiluminescence: sensitive detection technology for reporter gene assays. Clin. Chem. 42, 1542-1546.
10. de Wet, J. R., Wood, K. V., Helinski, D. R. and DeLuca, M. (1985) Cloning of firefly luciferase cDNA and the expression of active luciferase in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 82, 7870-7873.
11. de Wet, J. R., Wood, K. V., DeLuca, M., Helinski, D. R. and Subramani, S. (1987) Firefly luciferase gene: structure and expression in mammalian cells. Mol. Cell. Biol. 7, 725-737.
12. Ow, D. W., de Wet, J. R., Helinski, D. R., Howell, S. H., Wood, K. V. and Deluca, M. (1986) Transient and stable expression of the firefly luciferase gene in plant cells and transgenic plants. Science 234, 856-859
13. Keller, G. A., Gould, S., Deluca, M. and Subramani, S. (1987) Firefly luciferase is targeted to peroxisomes in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 84, 3264-3268.
14. Nordeen, S. K. (1988) Luciferase reporter gene vectors for analysis of promoters and enhancers. Biotechniques 6, 454-458.
15. Brasier, A. R., Tate, J. E. and Habener, J. F. (1989) Optimized use of the firefly luciferase assay as a reporter gene in mammalian cell lines. Biotechniques 7, 1116-1122.
16. Mitchell, R. J. and Gu, M. B. (2005) Construction and evaluation of nagR-nagAa::lux fusion strains in the biosensing for salicylic acid derivatives. Appl. Biochem. Biotechnol. 120, 183-198.
17. Mitchell, R. J., Ahn, J. M. and Gu, M. B. (2005) Comparison of Photorhabdus luminescens and Vibrio fischeri lux fusions to study gene expression patterns. J. Microbiol. Biotechnol. 15, 48-54.
18. Mitchell, R. J. and Gu M. B. (2004) Construction and characterization of novel dual-stress-responsive bacterial biosensors. Biosens. Bioelectron. 19, 977-985.
19. Mitchell, R. J. and Gu M. B. (2004) An Escherichia coli biosensor capable of detecting both genotoxic and oxidative damage. Appl. Microbiol. Biotechnol. 64, 46-52.
20. Gupta, R. K., Patterson, S. S., Ripp, S., Simpson, M. L. and Sayler, G. S. (2003) Expression of the Photorhabdus luminescens lux genes (luxA, B, C, D, and E) in Saccharomyces cerevisiae. FEMS Yeast Res. 4, 305-313.
21. Morin, J. G. and Hastings, J. W. (1971) Biochemistry of the bioluminescence of colonial hydroids and other coelenterates. J. Cell Physiol. 77, 305-312.
22. Morin, J. G. and Hastings, J. W. (1971) Energy transfer in a bioluminescent system. J. Cell Physiol. 77, 313-318.
23. Chalfie, M., Tu, Y., Euskirchen, G., Ward, W. W. and Prasher, D. C. (1994) Green fluorescent protein as a marker for gene expression. Science 263, 802-805.
24. Casper, S. J. and Holt, C. A. (1996) Expression of the green fluorescent protein-encoding gene from a tobacco mosaic virus-based vector. Gene 173, 69-73.
25. Amsterdam, A., Lin, S., Moss, L. G. and Hopkins, N. (1996) Requirements for green fluorescent protein detection in transgenic zebrafish embryos. Gene 173, 99-103.
26. http://www.clontech.com/upload/images/WP9X2790_FP.html.
27. Heim, R., Cubitt, A. B. and Tsien, R. Y. (1995) Improved green fluorescence. Nature 373, 663-664.
28. Katranidis, A., Atta, D., Schlesinger, R., Nierhaus, K. H, Choli-Papadopoulou, T., Gregor, I., Gerrits, M., Büldt, G. and Fitter, J. (2009) Fast biosynthesis of GFP molecules: a single-molecule fluorescence study. Angew. Chem. Int. Ed Engl. 48, 1758-1761.
29. Karin, M. (1994) Signal-transduction from the cell-surface to the nucleus through the phosphorylation of transcription factors. Curr. Opin. Cell Biol. 6, 415-424.
30. Treisman, R. (1994) Ternary complex factors: growth factor regulated transcriptional activators. Curr. Opin. Genet. Dev. 4, 96-101.
31. Elowitz, M. B. and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338.
32. Hasty, J., McMillen, D. and Collins, J. J. (2002) Engineered gene circuits. Nature 420, 224-230.
33. Gardner, T. S., Cantor, C. R. and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342.
34. Van Dyk, T. K., DeRose, E. J. and Gonye, G. E. (2001) LuxArray, a high-density, genome wide transcription analysis of Escherichia coli using bioluminescent reporter strains. J. Bacteriol. 183, 5496-5505.
35. Xiong, Y. Q., Willard, J., Kadurugamuwa, J. L., Yu, J., Francis, K. P. and Bayer, A. S. (2005) Real-time in vivo bioluminescent imaging for evaluating the efficacy of anti biotics in a rat Staphylococcus aureus endocarditis model. Antimicrob. Agents Chemother. 49, 380-387.
36. Doyle, T. C., Burns, S. M. and Contag, C. H. (2004) In vivo bioluminescence imaging for integrated studies of infection. Cell. Microbiol. 6, 303-317.
37. Lee, S. K., Chou, H. H., Pfleger, B. F., Newman, J. D., Yoshikuni, Y. and Keasling, J. D. (2007) Directed evolution of AraC for improved compatibility of arabinose- and lactose-inducible promoters. Appl. Environ. Microbiol. 73, 5711-5715.
38. Canton, B., Labno, A. and Endy, D. (2008) Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 26, 787-793.
39. Tabor, J. J., Salis, H. M., Simpson, Z. B., Chevalier, A. A., Levskaya, A., Marcotte, E. M., Voigt, C. A. and Ellington, A. D. (2009) A synthetic genetic edge detection program. Cell 137, 1272-1281
40. Bennett, M. R. and Hasty, J. (2009) Microfluidic devices for measuring gene network dynamics in single cells. Nat. Rev. Genet. 10, 628-638.
41. Andersen, J. B., Sternberg, C., Poulsen, L. K., Bjorn, S. P., Givskov, M. and Molin, S. (1998) New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64, 2240-2246.
42. Simpson, M. L. (2007) A destabilized bacterial luciferase for dynamic gene expression studies. Syst. Synth. Biol. 1, 3-9.
43. Kuiper, I., Lagendijk, E. L., Pickford, R., Derrick, J. P., Lamers, G. E., Thomas-Oates, J. E., Lugtenberg, B. J. and Bloemberg, G. V. (2004) Characterization of two Pseudomonas putida lipopeptide biosurfactants, putisolvin I and II, which inhibit biofilm formation and break down existing biofilms. Mol. Microbiol. 51, 97-113.
44. Sabev, H. A., Robson, G. D. and Handley, P. S. (2006) Influence of starvation, surface attachment and biofilm growth on the biocide susceptibility of the biodeteriogenic yeast Aureobasidium pullulans. J. Appl. Microbiol. 101, 319-330.
45. Kim, J., Hahn, J. S., Franklin, M. J., Stewart, P. S. and Yoon, J. (2009) Tolerance of dormant and active cells in Pseudomonas aeruginosa PA01 biofilm to antimicrobial agents. J. Antimicrob. Chemother. 63, 129-135.
46. Marti, M., Trotonda, M. P., Tormo-Mas, M. A., Vergara-Irigaray, M., Cheung, A. L., Lasa, I. and Penades, J. R. (2010) Extracellular proteases inhibit protein-dependent biofilm formation in Staphylococcus aureus. Microbes Infect. 12, 55-64.
47. Wood, T. K, Gonzalez Barrios A. F., Herzberg, M. and Lee, J. (2006) Motility influences biofilm architecture in Escherichia coli. Appl. Microbiol. Biotechnol. 72, 361-367.
48. Yang, X., Ma, Q. and Wood, T. K. (2008) The R1 conjugative plasmid increases Escherichia coli biofilm formation through an envelope stress response. Appl. Environ. Microbiol. 74, 2690-2699.
49. http://www.che.tamu.edu/groups/Wood/biofilm%20 architecture.htm
50. Cowan, S. E., Gilbert, E., Liepmann, D. and Keasling, J. D. (2000) Commensal interactions in a dual-species biofilm exposed to mixed organic compounds. Appl. Environ. Microbiol. 66, 4481-4485.
51. Tomlin, K. L., Clark, S. R. and Ceri, H. (2004) Green and red fluorescent protein vectors for use in biofilm studies of the intrinsically resistant Burkholderia cepacia complex. J. Microbiol. Methods 57, 95-106
52. Lee, J., Jayaraman, A. and Wood, T. K. (2007) Indole is an inter-species biofilm signal mediated by SdiA. BMC Microbiol. 7, 42-56.
53. Lederberg, J. and Lederberg, E. M. (1952) Replica plating and indirect selection of bacterial mutants. J. Bacteriol. 63, 399-406.
54. Lee, J. H., Mitchell, R. J., Kim, B. C., Cullen, D. C. and Gu, M. B. (2005) A cell array biosensor for environmental toxicity analysis. Biosens. Bioelectron. 21, 500-507.
55. Mitchell, R. J. and Gu, M. B. (2006) Characterization and optimization of two methods in the immobilization of 12 bioluminescent strains. Biosens. Bioelectron. 22, 192-199.
56. Xu, C. W. (2002) High-density cell microarrays for parallel functional determinations. Genome Res. 12, 482-486.
57. Ingham, C., Bomer, J., Sprenkels, A., van den Berg, A., de Vos, W. and van Hylckama Vlieg, J. (2010) High-resolution microcontact printing and transfer of massive arrays of microorganisms on planar and compartmentalized nanoporous aluminium oxide. Lab Chip 10, 1410-1416.
58. Bearinger, J. P., Dugan, L. C., Wu, L. G., Hill, H., Christian, A. T. and Hubbell, J. A. (2009) Chemical tethering of motile bacteria to silicon surfaces. Biotechniques 46, 209-216.
59. Eun, Y. J. and Weibel, D. B. (2009) Fabrication of microbial biofilm arrays by geometric control of cell adhesion. Langmuir 25, 4643-4654.
60. Tavana, H., Jovic, A., Mosadegh, B., Yi, L. Q., Liu, X., Luker, K. E., Luker, G. D., Weiss, S. J. and Takayama, S. (2009) Nanolitre liquid patterning in aqueous environments for spatially defined reagent delivery to mammalian cells. Nat. Mater. 8, 736-741.
61. Tavana, H., Mosadegh, B. and Takayama, S. (2010) Polymeric aqueous biphasic systems for non-contact cell printing on cells: Engineering heterocellular embryonic stem cell niches. Adv. Mater. online. DOI: 10.1002/adma.200904271.
62. Kuang, Y., Biran, I. and Walt, D. R. (2004) Living bacterial cell array for genotoxin monitoring. Anal. Chem. 76, 2902-2909.
63. Jovic, A., Howell, B. and Takayama, S. (2009) Timing is everything: using fluidics to understand the role of temporal dynamics in cellular systems. Microfluid. Nanofluid. 6, 717-729.
64. Gachon, F., Nagoshi, E., Brown, S. A., Ripperger, J. and Schibler, U. (2004) The mammalian circadian timing system: from gene expression to physiology. Chromosoma 113, 103-112.
65. Iwasaki, H., Williams, S. B., Kitayama, Y., Ishiura, M., Golden, S. S. and Kondo, T. (2000) A KaiC-interacting sensory histidine kinase, SasA, necessary to sustain robust circadian oscillation in cyanobacteria. Cell 101, 223-233.
66. Tsuchiya, M. and Ross, J. (2002) Advantages of external periodic events to the evolution of biochemical oscillatory reactions. Proc. Natl. Acad. Sci. U.S.A. 100, 9691-9695.
67. Bennett, M. R., Pang, W. L., Ostroff, N. A., Baumgartner, B. L., Nayak, S., Tsimring, L. S. and Hasty, J. (2008) Metabolic gene regulation in a dynamically changing environment. Nature 454, 1119-1122.
68. Hersen, P., McClean, M. N., Mahadevan, L. and Ramanathan, S. (2008) Signal processing by the HOG MAP kinase pathway. Proc. Natl. Acad. Sci. U.S.A. 105, 7165-7170.
69. Mettetal, J. M., Muzzey, D., Gomez-Uribe, C. and van Oudenaarden, A. (2008) The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Science 319, 482-484.
70. Dyszel, J. L., Soares, J. A., Swearingen, M. C., Lindsay, A., Smith, J. N. and Ahmer, B. M. M.(2010) E. coli K-12 and EHEC genes regulated by SdiA. PLoS One 5, e8946.
71. Tani, H., Maehana, K. and Kamidate, T. (2004) Chipbased bioassay using bacterial sensor strains immobilized in three-dimensional microfluidic network. Anal. Chem. 76, 6693-6697.
72. Guet, C. C., Elowitz, M. B., Hsing, W. and Leibler, S. (2002) Combinatorial synthesis of genetic networks. Science 296, 1466-1470.
73. Kim, P. M. and Tidor, B. (2003) Limitations of quantitative gene regulation models: a case study. Genome Res. 13, 2391-2395.
74. Keiler, K. C., Waller, P. R. and Sauer, R. T. (1996) Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990-993.
75. Buchler, N. E., Gerland, U. and Hwa, T. (2005) Nonlinear protein degradation and the function of genetic circuits. Proc. Natl. Acad. Sci. U.S.A. 102, 9559-9564.
76. Ghim, C. M. and Almaas, E. (2008) Genetic noise control via protein oligomerization. BMC Sys. Biol. 2, 94.
77. Ghim, C. M. and Almaas, E. (2009) Two-component genetic switch as a synthetic module with tunable stability. Phys. Rev. Lett. 103, 028101.
78. Regaldo, A. (2005) Next dream for Venter: create entire set of genes from scratch. The Wall Street Journal, June 29th, p A1.
79. Hale, V., Keasling, J. D., Renninger, N. and Diagana, T. T. (2007) Microbially derived artemisinin: a biotechnology solution to the global problem of access to affordable antimalarial drugs. Am. J. Trop. Med. Hyg. 77, 198-202.
80. Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R. Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., Merryman, C., Vashee, S., Krishnakumar, R., Assad-Garcia, N., Andrews-Pfannkoch, C., Denisova, E. A., Young, L., Qi, Z. Q., Segall-Shapiro, T. H., Calvey, C. H., Parmar, P. P., Hutchison, III, C. A., Smith, H. O. and Venter, J. C. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science DOI: 10.1126/science.1190719.
81. Khalil, A. S. and Collins, J. J. (2010) Synthetic biology: applications come of age. Nat. Rev. Genet. 11, 367-379.
82. Martin, L., Che, A. and Endy, D. (2009) Gemini, a bifunctional enzymatic and fluorescent reporter of gene expression. PLoS One 4, e7596. Doi:10.1371/journal. pone.0007569.
83. http://www.worldsciencefestival.com/blog/bioart_process.
84. http://www.psfk.com/2009/01/pic-painting-with-fluorescentbacteria.html.
85. http://www.binder-world.com/eu/en/company/binder-news.cfm/binder/83/laborschraenke-umweltsimulation/painting-with-bacteria.cfm.
86. http://www.microbialart.com/contributed-art/.
87. http://faculty.washington.edu/afolch/FolchLabART.html.
88. Levskaya, A., Chevalier, A. A., Tabor, J. J., Simpson, Z. B., Lavery, L. A., Levy, M., Davidson, E. A., Scouras, A., Ellington, A. D., Marcotte, E. M. and Voigt, C. A. (2005) Synthetic biology: engineering Escherichia coli to see light. Nature 438, 441-442.
89. http://www.utexas.edu/features/2005/bacteria/index.html.
90. Levskaya, A., Weiner, O. D., Lim, W. A. and Voigt C. A. (2009) Spatiotemporal control of cell signaling using a light-switchable protein interaction. Nature 461, 997-1001.