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Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks

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Hybrid Systems Biology (HSB 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7699))

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Abstract

The understanding of the regulatory networks controlling the adaptation of bacteria to changes in their environment is critically dependent on the ability to monitor the dynamics of gene expression. Here, we review the use of fluorescent reporter genes for dynamically quantifying promoter activity and other quantities characterizing gene expression. We discuss critical physical and biological parameters in the design, development, and use of fluorescent reporter strains. Moreover, we review measurement models that have been proposed to interpret primary fluorescence data and inference methods for estimating gene expression profiles from these data. As an illustration of the use of fluorescent reporter strains for analyzing bacterial regulatory networks, we consider two applications in the model bacterium Escherichia coli in some detail: the joint control of gene expression by global physiological effects and specific regulatory interactions, and the importance of protein stability for the inference and analysis of transcriptional regulatory networks. We conclude by discussing some current trends in the use of fluorescent reporter genes.

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References

  1. Aïchaoui, L., Jules, M., Le Chat, L., Aymerich, S., Fromion, V., Goelzer, A.: BasyLiCA: a tool for automatic processing of a Bacterial Live Cell Array. Bioinf. 28(20), 2705–2706 (2012)

    Article  Google Scholar 

  2. Alon, U.: An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC, Boca Raton (2007)

    MATH  Google Scholar 

  3. Bansal, L., Chu, Y., Laird, C., Hahn, J.: Determining transcription factor profiles from fluorescent reporter systems involving regularization of inverse problems. In: Proceedings of the 2012 American Control Conference (ACC 2012), pp. 2725–30 (2012)

    Google Scholar 

  4. Barembruch, C., Hengge, R.: Cellular levels and activity of the flagellar sigma factor FliA of Escherichia coli are controlled by FlgM-modulated proteolysis. Mol. Microbiol. 65(1), 76–89 (2007)

    Article  Google Scholar 

  5. Bernstein, J., Khodursky, A., Lin, P.H., Lin-Chao, S., Cohen, S.: Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. USA 99(15), 9697–9702 (2002)

    Article  Google Scholar 

  6. Berthoumieux, S., de Jong, H., Baptist, G., Pinel, C., Ranquet, C., Ropers, D., Geiselmann, J.: Shared control of gene expression in bacteria by transcription factors and global physiology of the cell. Mol. Syst. Biol. 9(634), 634 (2013)

    Google Scholar 

  7. Boyer, F., Besson, B., Baptist, G., Izard, J., Pinel, C., Ropers, D., Geiselmann, J., de Jong, H.: WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data. Bioinf. 26(9), 1262–1263 (2010)

    Article  Google Scholar 

  8. Browning, D.F., Busby, S.J.W.: The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2(1), 57–65 (2004)

    Article  Google Scholar 

  9. Chevance, F., Hughes, K.: Coordinating assembly of a bacterial macromolecular machine. Nat. Rev. Microbiol. 6, 455–465 (2008)

    Article  Google Scholar 

  10. Chudakov, D., Matz, M., Lukyanov, S., Lukyanov, K.: Fluorescent proteins and their applications in imaging living cells and tissues. Physiol. Rev. 90(3), 1103–1163 (2010)

    Article  Google Scholar 

  11. Cox, J., Mann, M.: Quantitative, high-resolution proteomics for data-driven systems biology. Curr. Opin. Biotechnol. 80, 273–299 (2011)

    Google Scholar 

  12. de Jong, H., Ranquet, C., Ropers, D., Pinel, C., Geiselmann, J.: Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. BMC Syst. Biol. 4(1), 55 (2010)

    Article  Google Scholar 

  13. Dharmadi, Y., Gonzalez, R.: DNA microarrays: experimental issues, data analysis, and application to bacterial systems. Biotechnol. Prog. 20(5), 1309–1324 (2004)

    Article  Google Scholar 

  14. Dudin, O., Geiselmann, J., Oqasawara, H., Ishihama, A., Lacour, S.: Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation. J. Bacteriol. 196(3), 707–715 (2014)

    Article  Google Scholar 

  15. Finkenstädt, B., Heron, E., Komorowski, M., Edwards, K., Tang, S., Harper, C., Davis, J., White, M., Millar, A., Rand, D.: Reconstruction of transcriptional dynamics from gene reporter data using differential equations. Bioinf. 24(24), 2901–2907 (2008)

    Article  Google Scholar 

  16. Gerosa, L., Kochanowski, K., Heinemann, M., Sauer, U.: Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol. Syst. Biol. 9, 658 (2013)

    Article  Google Scholar 

  17. Giepmans, B., Adams, S., Ellisman, M., Tsien, R.: The fluorescent toolbox for assessing protein location and function. Sci. 312(5771), 217–224 (2006)

    Article  Google Scholar 

  18. Hebisch, E., Knebel, J., Landsberg, J., Frey, E., Leisner, M.: High variation of fluorescence protein maturation times in closely related Escherichia coli strains. PLoS ONE 8(10), e75991 (2013)

    Article  Google Scholar 

  19. Huang, Z., Senocak, F., Jayaraman, A., Hahn, J.: Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data. BMC Syst. Biol. 2, 64 (2008)

    Article  Google Scholar 

  20. Ingolia, N.: Ribosome profiling: new views of translation, from single codons to genome scale. Nat. Rev. Genet. 15(3), 205–213 (2014)

    Article  Google Scholar 

  21. Kalir, S., McClure, J., Pabbaraju, K., Southward, C., Ronen, M., et al.: Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Sci. 292(5524), 2080–2083 (2001)

    Article  Google Scholar 

  22. Keren, L., Zackay, O., Lotan-Pompan, M., Barenholz, U., Dekel, E., et al.: Promoters maintain their relative activity levels under different growth conditions. Mol. Syst. Biol. 9, 701 (2013)

    Article  Google Scholar 

  23. Keseler, I., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gi, M., Gama-Castro, S., et al.: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 39, D583–D590 (2011)

    Article  Google Scholar 

  24. Klumpp, S., Zhang, Z., Hwa, T.: Growth rate-dependent global effects on gene expression in bacteria. Cell 139(7), 1366–1375 (2009)

    Article  Google Scholar 

  25. Koga, K., Harada, T., Shimizu, H., Tanaka, K.: Bacterial luciferase activity and the intracellular redox pool in Escherichia coli. Mol. Genet. Genom. 274(2), 180–188 (2005)

    Article  Google Scholar 

  26. Leveau, J., Lindow, S.: Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria. J. Bacteriol. 183(23), 6752–6762 (2001)

    Article  Google Scholar 

  27. Liang, S., Bipatnath, M., Xu, Y., Chen, S., Dennis, P., Ehrenberg, M., Bremer, H.: Activities of constitutive promoters in Escherichia coli. J. Mol. Biol. 292(1), 19–37 (1999)

    Article  Google Scholar 

  28. Lichten, C., White, R., Clark, I., Swain, P.: Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers. BMC Biotechnol. 14, 11 (2014)

    Article  Google Scholar 

  29. Longo, D., Hasty, J.: Dynamics of single-cell gene expression. Mol. Syst. Biol. 2, 64 (2006)

    Article  Google Scholar 

  30. Lu, P., Vogel, C., Wang, R., Yao, X., Marcotte, E.: Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25(1), 117–124 (2007)

    Article  Google Scholar 

  31. Macnab, R.: Flagella and motility. In: Neidhardt, F., Curtiss III, R., Ingraham, J., Lin, E., Low, K., Magasanik, B., Reznikoff, W., Riley, M., Schaechter, M., Umbarger, H. (eds.) Escherichia coli and Salmonella: Cellular and Molecular Biology, pp. 123–45. ASM Press, Washington, DC, 2nd edn. (1996)

    Google Scholar 

  32. Mäder, U., Nicolas, P., Richard, H., Bessières, P., Aymerich, S.: Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods. Curr. Opin. Biotechnol. 22(1), 32–41 (2011)

    Article  Google Scholar 

  33. Manen, D., Pougeon, M., Damay, P., Geiselmann, J.: A sensitive reporter gene system using bacterial luciferase based on a series of plasmid cloning vectors compatible with derivatives of pBR322. Gene 186(2), 197–200 (1997)

    Article  Google Scholar 

  34. Van Dyk, T., Wei, Y., Hanafey, M., Dolan, M., Reeve, M., Rafalski, J., Rothman-Denes, L., LaRossa, R.: A genomic approach to gene fusion technology. Proc. Natl. Acad. Sci. USA 98(5), 2555–2560 (2001)

    Article  Google Scholar 

  35. Meighen, E.A.: Bacterial bioluminescence: organization, regulation, and application of the lux genes. FASEB J. 7(11), 1016–1022 (1993)

    Google Scholar 

  36. Muzzey, D., van Oudenaarden, A.: Quantitative time-lapse fluorescence microscopy in single cells. Annu. Rev. Cell. Dev. Biol. 25, 301–327 (2009)

    Article  Google Scholar 

  37. Porreca, R., Cinquemani, E., Lygeros, J., Ferrari-Trecate, G.: Structural identification of unate-like genetic network models from time-lapse protein concentration measurements. In: Proceedings of 49th IEEE Conference on Decision and Control (CDC 2010), pp. 2529–2534 (2010)

    Google Scholar 

  38. Ronen, M., Rosenberg, R., Shraiman, B., Alon, U.: Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. USA 99(16), 10555–10560 (2002)

    Article  Google Scholar 

  39. Rowe, L., Dikici, E., Daunert, S.: Engineering bioluminescent proteins: Expanding their analytical potential. Anal. Chem. 81(21), 8662–8668 (2009)

    Article  Google Scholar 

  40. Schaechter, M., Ingraham, J., Neidhardt, F.: Microbe. ASM Press, Washington DC (2006)

    Book  Google Scholar 

  41. Sharan, S.K., Thomason, L.C., Kuznetsov, S.G., Court, D.L.: Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 4(2), 206–223 (2009)

    Article  Google Scholar 

  42. Silhavy, T.: Gene fusions. J. Bacteriol. 182(21), 5935–5938 (2000)

    Article  Google Scholar 

  43. Stefan, D., Pinel, C., Pinhal, S., Cinquemani, E., Geiselmann, J., de Jong, H.: Inference of quantitative models of bacterial promoters from time-series reporter gene data. PLoS Comput. Biol. 11(1), e1004028 (2015)

    Article  Google Scholar 

  44. Süel, G.: Use of fluorescence microscopy to analyze genetic circuit dynamics. Methods Enzymol. 497, 275–293 (2011)

    Article  Google Scholar 

  45. Taniguchi, Y., Choi, P., Li, G.W., Chen, H., Babu, M., Hearn, J., Emili, A., Xie, X.: Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Sci. 329(5991), 533–539 (2010)

    Article  Google Scholar 

  46. Pédelacq, J.D., Cabantous, S., Tran, T., Terwilliger, T.C., Waldo, G.S.: Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol. 24(1), 79–88 (2006)

    Article  Google Scholar 

  47. Tsien, R.Y.: The green fluorescent protein. Annu. Rev. Biochem. 67, 509–544 (1998)

    Article  Google Scholar 

  48. Wang, X., Errede, B., Elston, T.: Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters. Biophys. J. 94(6), 2017–2026 (2008)

    Article  Google Scholar 

  49. Young, J., Locke, J., Altinok, A., Rosenfeld, N., Bacarian, T., Swain, P., Mjolsness, E., Elowitz, M.: Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nat. Protoc. 7(1), 80–88 (2011)

    Article  Google Scholar 

  50. Zaslaver, A., Bren, A., Ronen, M., Itzkovitz, S., Kikoin, I., Shavit, S., Liebermeister, W., Surette, M., Alon, U.: A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3(8), 623–628 (2006)

    Article  Google Scholar 

  51. Zulkower, V., Page, M., Ropers, D., Geiselmann, J., de Jong, H.: Robust reconstruction of gene expression profiles from reporter gene data using linear inversion. Bioinf. 31(12), i71–i79 (2015)

    Article  Google Scholar 

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Acknowledgements

This work was supported by the Investissements d’avenir Bio-informatique programme under project Reset (ANR-11-BINF-0005).

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Authors and Affiliations

  1. INRIA, Grenoble - Rhône-Alpes Research Centre, 655 avenue de l’Europe, Montbonnot, 38334, Saint-Ismier Cedex, France

    Hidde de Jong & Johannes Geiselmann

  2. Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Université Grenoble Alpes, 140 Avenue de la Physique - BP 87, 38402, Saint Martin d’Hères, France

    Johannes Geiselmann

Authors
  1. Hidde de Jong
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Correspondence to Hidde de Jong .

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Editors and Affiliations

  1. "CNRS-VERIMAG, University of Grenoble-Alpes (UGA), Grenoble, France

    Oded Maler

  2. West Virginia University, Morgantown, West Virginia, USA

    Ádám Halász

  3. VERIMAG, Gieres, France

    Thao Dang

  4. University of Udine, Udine, Italy

    Carla Piazza

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de Jong, H., Geiselmann, J. (2015). Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks. In: Maler, O., Halász, Á., Dang, T., Piazza, C. (eds) Hybrid Systems Biology. HSB 2014. Lecture Notes in Computer Science(), vol 7699. Springer, Cham. https://doi.org/10.1007/978-3-319-27656-4_2

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  • DOI: https://doi.org/10.1007/978-3-319-27656-4_2

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