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  • Review Article
  • Published:

Where microbiology meets microengineering: design and applications of reporter bacteria

Nature Reviews Microbiology volume 8, pages 511–522 (2010)Cite this article

Subjects

Key Points

  • A range of genetic-circuit designs have emerged for the construction of reporter bacteria that can be used in the monitoring and quantification of toxic compounds in environmental samples, food stuffs and body fluids.

  • Synthetic biology allows further rational engineering and assembly of genetic components to achieve enhanced detection properties of reporter bacteria, including the ability to sense new chemical targets.

  • Bacterial bioreporters have become the preferable biological elements for incorporation into microengineered and microfluidic formats, thereby generating miniaturized assays or cell array platforms for high-throughput screening.

  • Many examples of successful bacterial bioreporter assays have been reported, demonstrating their applicability, flexibility and accuracy.

  • Widespread commercial implementation of bacterial bioreporter assays is currently hampered by the hesitation of potential business partners, by restrictive legislation on the use of genetically modified organisms and by currently unresolved technical hurdles concerning the scaling up of the assays and the long-term preservation of reporter cells.

Abstract

Bacteria have long been the targets for genetic manipulation, but more recently they have been synthetically designed to carry out specific tasks. Among the simplest of these tasks is chemical compound and toxicity detection coupled to the production of a quantifiable reporter signal. In this Review, we describe the current design of bacterial bioreporters and their use in a range of assays to measure the presence of harmful chemicals in water, air, soil, food or biological specimens. New trends for integrating synthetic biology and microengineering into the design of bacterial bioreporter platforms are also highlighted.

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Figure 1: Bacterial bioreporter designs.
Figure 2: Types of bacterial bioreporter assays.
Figure 3: Whole-cell bacterial biosensor devices.

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References

  1. Daunert, S. et al. Genetically engineered whole-cell sensing systems: coupling biological recognition with reporter genes. Chem. Rev. 100, 2705–2738 (2000). An excellent introduction to the concept of bioreporting and the different reporter systems.

    Article  CAS  PubMed  Google Scholar 

  2. Leveau, J. H. J. & Lindow, S. E. Bioreporters in microbial ecology. Curr. Opin. Microbiol. 5, 259–265 (2002).

    Article  PubMed  Google Scholar 

  3. Harms, H., Wells, M. C. & van der Meer, J. R. Whole-cell living biosensors — are they ready for environmental application? Appl. Microbiol. Biotechnol. 70, 273–280 (2006).

    Article  CAS  PubMed  Google Scholar 

  4. Magrisso, S., Erel, Y. & Belkin, S. Microbial reporters of metal bioavailability. Microb. Biotechnol. 1, 320–330 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Tecon, R. & van der Meer, J. R. Information from single-cell bacterial biosensors: what is it good for? Curr. Opin. Biotechnol. 17, 4–10 (2006).

    Article  CAS  PubMed  Google Scholar 

  6. van der Meer, J. R., Tropel, D. & Jaspers, M. C. M. Illuminating the detection chain of bacterial bioreporters. Environ. Microbiol. 6, 1005–1020 (2004). This article takes a detailed look at the chain of events occurring during target detection in bacterial bioreporters.

    Article  CAS  PubMed  Google Scholar 

  7. D'Souza, S. F. Microbial biosensors. Biosens. Bioelectron. 16, 337–353 (2001).

    Article  CAS  PubMed  Google Scholar 

  8. Baumann, B. & van der Meer, J. R. Analysis of bioavailable arsenic in rice with whole cell living bioreporter bacteria. J. Agric. Food Chem. 55, 2115–2120 (2007).

    Article  CAS  PubMed  Google Scholar 

  9. Trang, P. T., Berg, M., Viet, P. H., Van Mui, N. & van der Meer, J. R. Bacterial bioassay for rapid and accurate analysis of arsenic in highly variable groundwater samples. Environ. Sci. Technol. 39, 7625–7630 (2005). This article was awarded a prize for its presentation of the first wide-scale comparative screen using bioreporter assays to test arsenic pollution in Vietnam's potable water sources.

    Article  CAS  PubMed  Google Scholar 

  10. Ames, B. N., Durston, W. E., Yamasaki, E. & Lee, F. D. Carcinogens are mutagens: a simple test system combining liver homogenates for activation and bacteria for detection. Proc. Natl Acad. Sci. USA 70, 2281–2285 (1973).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Quillardet, P., Huisman, O., D'Ari, R. & Hofnung, M. SOS chromotest, a direct assay of induction of an SOS function in Escherichia coli K-12 to measure genotoxicity. Proc. Natl Acad. Sci. USA 79, 5971–5975 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Fry, R. C., Begley, T. J. & Samson, L. D. Genome-wide responses to DNA-damaging agents. Annu. Rev. Microbiol. 59, 357–377 (2005).

    Article  CAS  PubMed  Google Scholar 

  13. Oda, Y., Nakamura, S., Oki, I., Kato, T. & Shinagawa, H. Evaluation of the new system (umu-test) for the detection of environmental mutagens and carcinogens. Mutat. Res. 147, 219–229 (1985).

    Article  CAS  PubMed  Google Scholar 

  14. Quillardet, P. & Hofnung, M. The SOS chromotest: a review. Mutat. Res. 297, 235–279 (1993).

    Article  CAS  PubMed  Google Scholar 

  15. Reifferscheid, G. & Hell, J. Validation of the SOS/umu test using test results of 486 chemicals and comparison with the Ames test and carcinogenicity data. Mutat. Res 369, 129–145 (1996).

    Article  CAS  PubMed  Google Scholar 

  16. International Organization for Standardization. ISO 13829: Water quality – determination of genotoxicity of water and waste water using the umu-test (ISO, Geneva, 1999).

  17. Bulich, A. A. & Isenberg, D. L. Use of the luminescent bacterial system for the rapid assessment of aquatic toxicity. ISA Trans. 20, 29–33 (1981).

    CAS  PubMed  Google Scholar 

  18. International Organization for Standardization. ISO 11348: Water quality – determination of the inhibitory effect of water samples on the light emission of Vibrio fischeri (Luminescent bacteria test) (ISO, Geneva, 2007).

  19. King, J. M. H. et al. Rapid, sensitive bioluminescent reporter technology for naphthalene exposure and biodegradation. Science 249, 778–781 (1990).

    Article  CAS  PubMed  Google Scholar 

  20. Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000). A fascinating account of the effect of serial genetic circuits on reporter output.

    Article  CAS  PubMed  Google Scholar 

  21. Friedland, A. E. et al. Synthetic gene networks that count. Science 324, 1199–1202 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Norman, A., Hestbjerg Hansen, L. & Sørensen, S. J. Construction of a ColD cda promoter-based SOS-green fluorescent protein whole-cell biosensor with higher sensitivity toward genotoxic compounds than constructs based on recA, umuDC, or sulA promoters. Appl. Environ. Microbiol. 71, 2338–2346 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Choi, S. H. & Gu, M. B. A portable toxicity biosensor using freeze-dried recombinant bioluminescent bacteria. Biosens. Bioelectron. 17, 433–440 (2002).

    Article  CAS  PubMed  Google Scholar 

  24. Van Dyk, T. K. et al. Rapid and sensitive pollutant detection by induction of heat shock gene-bioluminescence gene fusions. Appl. Environ. Microbiol. 60, 1414–1420 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Belkin, S., Smulski, D. R., Vollmer, A. C., Van Dyk, T. K. & LaRossa, R. A. Oxidative stress detection with Escherichia coli harboring a katG′::lux fusion. Appl. Environ. Microbiol. 62, 2252–2256 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Van Dyk, T. K. et al. A genomic approach to gene fusion technology. Proc. Natl Acad. Sci. USA 98, 2555–2560 (2001). The first genome-wide search using reporter fusion libraries to find stress-responsive promoters.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kim, B. C., Youn, C. H., Ahn, J.-M. & Gu, M. B. Screening of target-specific stress-responsive genes for the development of cell-based biosensors using a DNA microarray. Anal. Chem. 77, 8020–8026 (2005).

    Article  CAS  PubMed  Google Scholar 

  28. Selifonova, O., Burlage, R. & Barkay, T. Bioluminescent sensors for detection of bioavailable Hg(II) in the environment. Appl. Environ. Microbiol. 59, 3083–3090 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Virta, M., Lampinen, J. & Karp, M. A luminescence-based mercury biosensor. Anal. Chem. 67, 667–669 (1995). An excellent account of the extremely sensitive response of the mercury bioreporter system.

    Article  CAS  Google Scholar 

  30. Park, S. J., Wireman, J. & Summers, A. O. Genetic analysis of the Tn21 mer operator-promoter. J. Bacteriol. 174, 2160–2171 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Ramanathan, S., Shi, W., Rosen, B. P. & Daunert, S. Sensing antimonite and arsenite at the subattomole level with genetically engineered bioluminescent bacteria. Anal. Chem. 69, 3380–3384 (1997).

    Article  CAS  PubMed  Google Scholar 

  32. Tauriainen, S., Karp, M., Chang, W. & Virta, M. Recombinant luminescent bacteria for measuring bioavailable arsenite and antimonite. Appl. Environ. Microbiol. 63, 4456–4461 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Corbisier, P., Ji, G., Nuyts, G., Mergeay, M. & Silver, S. luxAB gene fusions with the arsenic and cadmium resistance operons of Staphylococcus aureus plasmid pI258. FEMS Microbiol. Lett. 110, 231–238 (1993).

    Article  CAS  PubMed  Google Scholar 

  34. Wu, J. & Rosen, B. P. Metalloregulated expression of the ars operon. J. Biol. Chem. 268, 52–58 (1993).

    CAS  PubMed  Google Scholar 

  35. Stocker, J. et al. Development of a set of simple bacterial biosensors for quantitative and rapid field measurements of arsenite and arsenate in potable water. Environ. Sci. Technol. 37, 4743–4750 (2003).

    Article  CAS  PubMed  Google Scholar 

  36. Wackwitz, A. et al. Internal arsenite bioassay calibration using multiple reporter cell lines. Microb. Biotechnol. 1, 149–157 (2008). Some interesting concepts for producing stepwise concentration range-dependent responses from arsenic bioreporters.

    Article  CAS  PubMed  Google Scholar 

  37. Tropel, D., Bähler, A., Globig, K. & van der Meer, J. R. Design of new promoters and of a dual-bioreporter based on cross-activation by the two regulatory proteins XylR and HbpR. Environ. Microbiol. 6, 1186–1196 (2004).

    Article  CAS  PubMed  Google Scholar 

  38. Galvao, T. C., Mencia, M. & de Lorenzo, V. Emergence of novel functions in transcriptional regulators by regression to stem protein types. Mol. Microbiol. 65, 907–919 (2007). A fascinating introduction to the concept of shaping bacterial catabolic regulatory proteins to accommodate new effector proteins.

    Article  CAS  PubMed  Google Scholar 

  39. Wise, A. A. & Kuske, C. R. Generation of novel bacterial regulatory proteins that detect priority pollutant phenols. Appl. Environ. Microbiol. 66, 163–169 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Beggah, S., Vogne, C., Zenaro, E. & van der Meer, J. R. Mutant transcription activator isolation via green fluorescent protein based flow cytometry and cell sorting. Microb. Biotechnol. 1, 68–78 (2008).

    CAS  PubMed  Google Scholar 

  41. Lonneborg, R., Smirnova, I., Dian, C., Leonard, G. A. & Brzezinski, P. In vivo and in vitro investigation of transcriptional regulation by DntR. J. Mol. Biol. 372, 571–582 (2007).

    Article  CAS  PubMed  Google Scholar 

  42. Carmona, M., Fernandez, S., Rodriguez, M. J. & de Lorenzo, V. m-Xylene-responsive Pu-PnifH hybrid σ54 promoters that overcome physiological control in Pseudomonas putida KT2442. J. Bacteriol. 187, 125–134 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Turner, K. et al. Hydroxylated polychlorinated biphenyl detection based on a genetically engineered bioluminescent whole-cell sensing system. Anal. Chem. 79, 5740–5745 (2007). An discussion of possible applications for bioreporter assay detection of trace toxicants in human serum.

    Article  CAS  PubMed  Google Scholar 

  44. Lewis, C. et al. Novel use of a whole cell E. coli bioreporter as a urinary exposure biomarker. Environ. Sci. Technol. 43, 423–428 (2009).

    Article  CAS  PubMed  Google Scholar 

  45. Hansen, L. H., Aarestrup, F. & Sørensen, S. J. Quantification of bioavailable chlortetracycline in pig feces using a bacterial whole-cell biosensor. Vet. Microbiol. 87, 51–57 (2002).

    Article  CAS  PubMed  Google Scholar 

  46. Kurittu, J., Lonnberg, S., Virta, M. & Karp, M. Qualitative detection of tetracycline residues in milk with a luminescence-based microbial method: the effect of milk composition and assay performance in relation to an immunoassay and a microbial inhibition assay. J. Food Prot. 63, 953–957 (2000).

    Article  CAS  PubMed  Google Scholar 

  47. Semple, K. T. et al. Defining bioavailability and bioaccessibility of contaminated soil and sediment is complicated. Environ. Sci. Technol. 38, 228A–231A (2004). An excellent article for anyone wishing to understand the concepts of bioavailability and bioaccessibility.

    Article  CAS  PubMed  Google Scholar 

  48. Patterson, C. J., Semple, K. T. & Paton, G. I. Non-exhaustive extraction techniques (NEETs) for the prediction of naphthalene mineralisation in soil. FEMS Microbiol. Lett. 241, 215–220 (2004).

    Article  CAS  PubMed  Google Scholar 

  49. Tecon, R. & van der Meer, J. R. Effect of two types of biosurfactants on phenanthrene availability to the bacterial bioreporter Burkholderia sartisoli strain RP037. Appl. Microbiol. Biotechnol. 85, 1131–1139 (2009).

    Article  CAS  Google Scholar 

  50. Paton, G. I., Reid, B. J. & Semple, K. T. Application of a luminescence-based biosensor for assessing naphthalene biodegradation in soils from a manufactured gas plant. Environ. Pollut. 157, 1643–1648 (2009). A real-life account of bioreporter assays used with field samples.

    Article  CAS  PubMed  Google Scholar 

  51. Diplock, E. E., Mardlin, D. P., Killham, K. S. & Paton, G. I. Predicting bioremediation of hydrocarbons: laboratory to field scale. Environ. Pollut. 157, 1831–1840 (2009).

    Article  CAS  PubMed  Google Scholar 

  52. Diplock, E. E., Alhadrami, H. A. & Paton, G. I. Application of microbial bioreporters in environmental microbiology and bioremediation. Adv. Biochem. Eng. Biotechnol. 21 May 2009 (doi:10.1007/10_2009_03).

  53. Tecon, R., Binggeli, O. & van der Meer, J. R. Double-tagged fluorescent bacterial bioreporter for the study of polycyclic aromatic hydrocarbon diffusion and bioavailability. Environ. Microbiol. 11, 2271–2283 (2009).

    Article  CAS  PubMed  Google Scholar 

  54. Werlen, C., Jaspers, M. C. M. & van der Meer, J. R. Measurement of biologically available naphthalene in gas and aqueous phases by use of a Pseudomonas putida biosensor. Appl. Environ. Microbiol. 70, 43–51 (2004). The article describes the concept and demonstrates the use of the bacterial reporter 'nose'.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Deepthike, H. U. et al. Unlike PAHs from Exxon Valdez crude oil, PAHs from Gulf of Alaska coals are not readily bioavailable. Environ. Sci. Technol. 43, 5864–5870 (2009). A recent article using bacterial bioreporters and causing renewed uproar about polycyclic aromatic hydrocarbon bioavailability as a result of ancient oil spill disasters.

    Article  CAS  PubMed  Google Scholar 

  56. Kohlmeier, S. et al. Comparison of naphthalene bioavailability determined by whole-cell biosensing and availability determined by extraction with Tenax. Environ. Pollut. 156, 803–808 (2008).

    Article  CAS  PubMed  Google Scholar 

  57. 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. 10, 3305–3316 (2008). An excellent example of the power of scarless cloning of bioreporter circuits.

    Article  CAS  PubMed  Google Scholar 

  58. Simpson, M. L. et al. Bioluminescent-bioreporter integrated circuits form novel whole-cell biosensors. Trends Biotechnol. 16, 332–338 (1998). Probably the first successful integration of bioreporter bacteria onto microdevices.

    Article  CAS  Google Scholar 

  59. Nivens, D. E. et al. Bioluminescent bioreporter integrated circuits: potentially small, rugged and inexpensive whole-cell biosensors for remote environmental monitoring. J. Appl. Microbiol. 96, 33–46 (2004).

    Article  CAS  PubMed  Google Scholar 

  60. Bhattacharya, S., Jang, J. S., Yang, L. J., Akin, D. & Bashir, R. Biomems and nanotechnology-based approaches for rapid detection of biological entities. J. Rapid Methods Autom. Microbiol. 15, 1–32 (2007).

    Article  CAS  Google Scholar 

  61. Bolton, E. K. et al. Integrated CMOS photodetectors and signal processing for very low-level chemical sensing with the bioluminescent bioreporter integrated circuit. Sens. Actuators B Chem. 85, 179–185 (2002).

    Article  CAS  PubMed  Google Scholar 

  62. Inoue, I., Wakamoto, Y., Moriguchi, H., Okano, K. & Yasuda, K. On-chip culture system for observation of isolated individual cells. Lab Chip 1, 50–55 (2001).

    Article  CAS  PubMed  Google Scholar 

  63. Fukuda, J. et al. Micropatterned cell co-cultures using layer-by-layer deposition of extracellular matrix components. Biomaterials 27, 1479–1486 (2006).

    Article  CAS  PubMed  Google Scholar 

  64. Ruckenstein, E. & Li, Z. F. Surface modification and functionalization through the self-assembled monolayer and graft polymerization. Adv. Colloid Interface Sci. 113, 43–63 (2005).

    Article  CAS  PubMed  Google Scholar 

  65. Tani, H., Maehana, K. & Kamidate, T. Chip-based bioassay using bacterial sensor strains immobilized in three-dimensional microfluidic network. Anal. Chem. 76, 6693–6697 (2004). An exceptional article describing multilayered approaches to structuring bioreporter cells in microfluidic networks.

    Article  CAS  PubMed  Google Scholar 

  66. Bjerketorp, J., Hakansson, S., Belkin, S. & Jansson, J. K. Advances in preservation methods: keeping biosensor microorganisms alive and active. Curr. Opin. Biotechnol. 17, 43–49 (2006).

    Article  CAS  PubMed  Google Scholar 

  67. Fesenko, D. O. et al. Alginate gel biochip for real-time monitoring of intracellular processes in bacterial and yeast cells. Mol. Biol. 39, 84–89 (2005).

    Article  CAS  Google Scholar 

  68. Polyak, B., Bassis, E., Novodvorets, A., Belkin, S. & Marks, R. S. Bioluminescent whole cell optical fiber sensor to genotoxicants: system optimization. Sens. Actuators B Chem. 74, 18–26 (2001).

    Article  CAS  Google Scholar 

  69. Premkumar, J. R., Rosen, R., Belkin, S. & Lev, O. Sol-gel luminescence biosensors: encapsulation of recombinant E. coli reporters in thick silicate films. Anal. Chim. Acta 462, 11–23 (2002).

    Article  Google Scholar 

  70. Lee, J. H., Mitchell, R. J., Kim, B. C., Cullen, D. C. & Gu, M. B. A cell array biosensor for environmental toxicity analysis. Biosens. Bioelectron. 21, 500–507 (2005). This paper demonstrates the use of arrays containing bioreporters with different specificities.

    Article  CAS  PubMed  Google Scholar 

  71. Akselrod, G. M. et al. Laser-guided assembly of heterotypic three-dimensional living cell microarrays. Biophys. J. 91, 3465–3473 (2006). The first account of the assembly of complex living-cell arrays in hydrogels without loss of viability.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Balagadde, F. K., You, L. C., Hansen, C. L., Arnold, F. H. & Quake, S. R. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 309, 137–140 (2005).

    Article  CAS  PubMed  Google Scholar 

  73. Belkin, S. A panel of stress-responsive luminous bacteria for monitoring wastewater toxicity. Methods Mol. Biol. 102, 247–258 (1998). A proof-of-principlepaper outlining the idea of bioreporter arrays.

    CAS  PubMed  Google Scholar 

  74. Ahn, J. M., Mitchell, R. J. & Gu, M. B. Detection and classification of oxidative damaging stresses using recombinant bioluminescent bacteria harboring sodA::, pqi::, and katG:: luxCDABE fusions. Enz. Microb. Technol. 35, 540–544 (2004).

    Article  CAS  Google Scholar 

  75. Galluzzi, L. & Karp, M. Whole cell strategies based on lux genes for high throughput applications toward new antimicrobials. Comb. Chem. High Throughput Screen. 9, 501–514 (2006).

    Article  CAS  PubMed  Google Scholar 

  76. Ron, E. Z. Biosensing environmental pollution. Curr. Opin. Biotechnol. 18, 252–256 (2007).

    Article  CAS  PubMed  Google Scholar 

  77. Thaler, E. R. & Hanson, C. W. Medical applications of electronic nose technology. Expert Rev. Med. Devices 2, 559–566 (2005).

    Article  PubMed  Google Scholar 

  78. Vlasov, Y., Legin, A. & Rudnitskaya, A. Electronic tongues and their analytical application. Anal. Bioanal. Chem. 373, 136–146 (2002).

    Article  CAS  PubMed  Google Scholar 

  79. Tani, H., Maehana, K. & Kamidate, T. On-chip bioassay using immobilized sensing bacteria in three-dimensional microfluidic network. Methods Mol. Biol. 385, 37–52 (2007).

    Article  CAS  PubMed  Google Scholar 

  80. Lee, J. H., Youn, C. H., Kim, B. C. & Gu, M. B. An oxidative stress-specific bacterial cell array chip for toxicity analysis. Biosens. Bioelectron. 22, 2223–2229 (2007).

    Article  CAS  PubMed  Google Scholar 

  81. Popovtzer, R. et al. Novel integrated electrochemical nano-biochip for toxicity detection in water. Nano Lett. 5, 1023–1027 (2005).

    Article  CAS  PubMed  Google Scholar 

  82. Van Dyk, T. K., DeRose, E. J. & Gonye, G. E. LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains. J. Bacteriol. 183, 5496–5505 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Freed, N. E. et al. A simple screen to identify promoters conferring high levels of phenotypic noise. PLoS Genet. 4, e1000307 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Pedraza, J. M. & van Oudenaarden, A. Noise propagation in gene networks. Science 307, 1965–1969 (2005). A classic article about the occurrence of noise in transcriptional circuits.

    Article  CAS  PubMed  Google Scholar 

  85. Raser, J. M. & O'Shea, E. K. Noise in gene expression: origins, consequences, and control. Science 309, 2010–2013 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Cebolla, A., Sousa, C. & De Lorenzo, V. Rational design of a bacterial transcriptional cascade for amplifying gene expression capacity. Nucleic Acids Res. 29, 759–766 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Alper, H., Fischer, C., Nevoigt, E. & Stephanopoulos, G. Tuning genetic control through promoter engineering. Proc. Natl Acad. Sci. USA 102, 12678–12683 (2005). A first-class account of the power of directed evolution and the selection of promoter strength.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. De Mey, M., Maertens, J., Lequeux, G. J., Soetaert, W. K. & Vandamme, E. J. Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering. BMC Biotechnol. 7, 34 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Kudla, G., Murray, A. W., Tollervey, D. & Plotkin, J. B. Coding-sequence determinants of gene expression in Escherichia coli. Science 324, 255–258 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Looger, L. L., Dwyer, M. A., Smith, J. J. & Hellinga, H. W. Computational design of receptor and sensor proteins with novel functions. Nature 423, 185–189 (2003).

    Article  CAS  PubMed  Google Scholar 

  91. Galvao, T. C. & de Lorenzo, V. Transcriptional regulators a la carte: engineering new effector specificities in bacterial regulatory proteins. Curr. Opin. Biotechnol. 17, 34–42 (2006).

    Article  CAS  PubMed  Google Scholar 

  92. Kuppardt, A., Chatzinotas, A., Breuer, U., van der Meer, J. R. & Harms, H. Optimization of preservation conditions of As (III) bioreporter bacteria. Appl. Microbiol. Biotechnol. 82, 785–792 (2009).

    Article  CAS  PubMed  Google Scholar 

  93. Diesel, E., Schreiber, M. & van der Meer, J. R. Development of bacteria-based bioassays for arsenic detection in natural waters. Anal. Bioanal. Chem. 394, 687–693 (2009).

    Article  CAS  PubMed  Google Scholar 

  94. Engebrecht, J., Simon, M. & Silverman, M. Measuring gene expression with light. Science 227, 1345–1347 (1985).

    Article  CAS  PubMed  Google Scholar 

  95. Meighen, E. A. Molecular biology of bacterial bioluminescence. Microbiol. Rev. 55, 123–142 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Devine, J. H., Kutuzova, G. D., Green, V. A., Ugarova, N. N. & Baldwin, T. O. Luciferase from the east European firefly Luciola mingrelica: cloning and nucleotide sequence of the cDNA, overexpression in Escherichia coli and purification of the enzyme. Biochim. Biophys. Acta 1173, 121–132 (1993).

    Article  CAS  PubMed  Google Scholar 

  97. Wood, K. V., Amy Lam, Y., Seliger, H. H. & McElroy, W. D. Complementary DNA coding click beetle luciferases can elicit bioluminescence of different colors. Science 244, 700–702 (1989).

    Article  CAS  PubMed  Google Scholar 

  98. Loening, A. M., Wu, A. M. & Gambhir, S. S. Red-shifted Renilla reniformis luciferase variants for imaging in living subjects. Nature Methods 4, 641–643 (2007).

    Article  CAS  PubMed  Google Scholar 

  99. Prasher, D. C. Using GFP to see the light. Trends Genet. 11, 320–323 (1995).

    Article  CAS  PubMed  Google Scholar 

  100. Shaner, N. C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nature Biotech. 22, 1567–1572 (2004). The astonishing demonstration that fluorescent proteins can be engineered to produce spectral colour variants.

    Article  CAS  Google Scholar 

  101. Shaner, N. C. et al. Improving the photostability of bright monomeric orange and red fluorescent proteins. Nature Methods 5, 545–551 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Yagi, K. Applications of whole-cell bacterial sensors in biotechnology and environmental science. Appl. Microbiol. Biotechnol. 73, 1251–1258 (2007).

    Article  CAS  PubMed  Google Scholar 

  103. Shu, X. et al. Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science 324, 804–807 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  104. Drepper, T. et al. Reporter proteins for in vivo fluorescence without oxygen. Nature Biotech. 25, 443–445 (2007).

    Article  CAS  Google Scholar 

  105. Willardson, B. M. et al. Development and testing of a bacterial biosensor for toluene-based environmental contaminants. Appl. Environ. Microbiol. 64, 1006–1012 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Shingler, V. & Moore, T. Sensing or aromatic compounds by the DmpR transcriptional activator of phenol-catabolizing Pseudomonas sp. strain CF600. J. Bacteriol. 176, 1555–1560 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Tecon, R. et al. Development of a multistrain bacterial bioreporter platform for the monitoring of hydrocarbon contaminants in marine environments. Environ. Sci. Technol. 144, 1049–1055 (2010).

    Article  CAS  Google Scholar 

  108. Selifonova, O. V. & Eaton, R. W. Use of an ipb-lux fusion to study regulation of the isopropylbenzene catabolism operon of Pseudomonas putida RE204 and to detect hydrophobic pollutants in the environment. Appl. Environ. Microbiol. 62, 778–783 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Sticher, P., Jaspers, M., Harms, H., Zehnder, A. J. B. & van der Meer, J. R. Development and characterization of a whole cell bioluminescent sensor for bioavailable middle-chain alkanes in contaminated groundwater samples. Appl. Environ. Microbiol. 63, 4053–4060 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Applegate, B. M., Kehrmeyer, S. R. & Sayler, G. S. A chromosomally based tod-luxCDABE whole-cell reporter for benzene, toluene, ethybenzene, and xylene (BTEX) sensing. Appl. Environ. Microbiol. 64, 2730–2735 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  111. Phoenix, P. et al. Characterization of a new solvent-responsive gene locus in Pseudomonas putida F1 and its functionalization as a versatile biosensor. Environ. Microbiol. 5, 1309–1327 (2003).

    Article  CAS  PubMed  Google Scholar 

  112. Leveau, J. H. J. & Lindow, S. E. Appetite of an epiphyte: Quantitative monitoring of bacterial sugar consumption in the phyllosphere. Proc. Natl Acad. Sci. USA 98, 3446–3453 (2001). This article demonstrates the use of bacterial reporters to study sugar availability and heterogeneity on plant leaves.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Shetty, R. S., Ramanathan, S., Badr, I. H., Wolford, J. L. & Daunert, S. Green fluorescent protein in the design of a living biosensing system for L-arabinose. Anal. Chem. 71, 763–768 (1999).

    Article  CAS  PubMed  Google Scholar 

  114. Rasmussen, L. D., Sørensen, S. J., Turner, R. R. & Barkay, T. Application of a mer-lux biosensor for estimating bioavailable mercury in soil. Soil Biol. Biochem. 32, 639–646 (2000).

    Article  CAS  Google Scholar 

  115. Tauriainen, S., Karp, M., Chang, W. & Virta, M. Luminescent bacterial sensor for cadmium and lead. Biosens. Bioelectron. 13, 931–938 (1998).

    Article  CAS  PubMed  Google Scholar 

  116. Ivask, A., Rolova, T. & Kahru, A. A suite of recombinant luminescent bacterial strains for the quantification of bioavailable heavy metals and toxicity testing. BMC Biotechnol. 9, 41 (2009). The latest results in the re-engineering of a concise suite of reporter strains for detecting heavy metals.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Korpela, M. T., Kurittu, J. S., Karvinen, J. T. & Karp, M. T. A recombinant Escherichia coli sensor strain for the detection of tetracyclines. Anal. Chem. 70, 4457–4462 (1998).

    Article  CAS  PubMed  Google Scholar 

  118. Zheng, J. et al. Structure and function of the macrolide biosensor protein, MphR(A), with and without erythromycin. J. Mol. Biol. 387, 1250–1260 (2009).

    Article  CAS  PubMed  Google Scholar 

  119. Urban, A. et al. Novel whole-cell antibiotic biosensors for compound discovery. Appl. Environ. Microbiol. 73, 6436–6443 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Hakovirta, J., Reunanen, J. & Saris, P. E. Bioassay for nisin in milk, processed cheese, salad dressings, canned tomatoes, and liquid egg products. Appl. Environ. Microbiol. 72, 1001–1005 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Wu, H. et al. Detection of N-acylhomoserine lactones in lung tissues of mice infected with Pseudomonas aeruginosa. Microbiology 146, 2481–2493 (2000).

    Article  CAS  PubMed  Google Scholar 

  122. Vollmer, A. C., Belkin, S., Smulski, D. R., Van Dyk, T. K. & LaRossa, R. A. Detection of DNA damage by use of Escherichia coli carrying recA′::lux, uvrA′::lux, or alkA′::lux reporter plasmids. Appl. Environ. Microbiol. 63, 2566–2571 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. Ben-Israel, O., Ben-Israel, H. & Ulitzur, S. Identification and quantification of toxic chemicals by use of Escherichia coli carrying lux genes fused to stress promoters. Appl. Environ. Microbiol. 64, 4346–4352 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. Norman, A., Hansen, L. H. & Sørensen, S. J. A flow cytometry-optimized assay using an SOS–green fluorescent protein (SOS–GFP) whole-cell biosensor for the detection of genotoxins in complex environments. Mutat. Res. 603, 164–172 (2006). A good example of the combined use of bacterial bioreporters and flow cytometry to analyse reporter responses after recovery from complex environments.

    Article  CAS  PubMed  Google Scholar 

  125. van der Lelie, D., Regniers, L., Borremans, B., Provoost, A. & Verschaeve, L. The VITOTOX test, an SOS bioluminescence Salmonella typhimurium test to measure genotoxicity kinetics. Mutat. Res. 389, 279–290 (1997).

    Article  CAS  PubMed  Google Scholar 

  126. Nakamura, S. I., Oda, Y., Shimada, T., Oki, I. & Sugimoto, K. SOS-inducing activity of chemical carcinogens and mutagens in Salmonella typhimurium TA1535/pSK1002: examination with 151 chemicals. Mutat. Res. 192, 239–246 (1987).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

J.R.v.d.M. acknowledges support from the European Commission Framework Programmes (FP6 grant 018361 FACEiT and FP7 grant KBBE-211684, as part of the BACSIN project) and the Swiss National Science Foundation (Sinergia grant CRSI20-122689/1). S.B. acknowledges support from the FP6 project 'Toxichip'. W. Weigel, L. Ceriotti and P. Colpo are gratefully acknowledged for their input.

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Authors and Affiliations

  1. Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland

    Jan Roelof van der Meer

  2. Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel

    Shimshon Belkin

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Correspondence to Jan Roelof van der Meer.

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DATABASES

Entrez Genome Project

Aliivibrio fischeri

Escherichia coli

Photorhabdus luminescens

Pseudomonas fluorescens

Pseudomonas putida

Salmonella enterica subsp. enterica serovar Typhimurium str. L2

Staphylococcus aureus

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Registry of Standard Biological Parts

Glossary

Bioreporter

A microorganism, cell culture or cell line, often genetically engineered, with an activity that reflects changes in environmental conditions in a dose-dependent manner.

Genetic circuit

A genetic construction involving a sensory function, a molecular switch and an output (for example, a reporter protein).

Reporter protein

A protein, ideally non-native, that is synthesized by the cell in response to a pre-determined external stimulus and that can be measured (for activity or amount) non-invasively.

Auxotrophic mutation

A mutation that results in the carrier strain requiring one or more essential substances (that the parental strain is able to synthesize for itself) for growth.

SOS response

A coordinated error-prone DNA repair system that allows DNA replication to continue in spite of lesions or errors; the response is triggered by exposure of the bacterial cell to agents or conditions causing DNA damage and is controlled by LexA and RecA.

ISO standardization

International standards for a range of subjects in numerous disciplines, including test systems.

Effector

A compound that triggers the activator or repressor function of a regulator protein.

Oxidative stress response

The coordinated reaction of the cell to combat the effects of chemicals producing reactive oxygen species (for example, oxygen radicals, peroxides or superoxides) in the cell.

Bioavailable fraction

The molar fraction of a chemical compound that is available to the reporter cell in the time span of the assay.

Non-exhaustive extraction technique

The extraction of complex samples (for example, soil) with mild chemical solvents in order to obtain the bioavailable and bioaccessible compound fractions.

Bioaccessible fraction

The molar fraction of a chemical compound that can potentially become bioavailable to a cell over time.

Biosensor

A device that combines a biological entity (that is, an enzyme, antibody, tissue, organelle, nucleic acid or whole cell) and a suitable hardware platform for the detection of a chemical, a group of chemicals or a biological effect.

Ecotoxicological-safety endpoint

The amount of a pollutant in an environmental matrix that is considered non-harmful for animal and plant life or to human activities and that is thus used as a target in bioremediation strategies.

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van der Meer, J., Belkin, S. Where microbiology meets microengineering: design and applications of reporter bacteria. Nat Rev Microbiol 8, 511–522 (2010). https://doi.org/10.1038/nrmicro2392

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