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Cell-Free Biosensors and AI Integration

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Cell-Free Gene Expression

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2433))

Abstract

Cell-free biosensors hold a great potential as alternatives for traditional analytical chemistry methods providing low-cost low-resource measurement of specific chemicals. However, their large-scale use is limited by the complexity of their development.

In this chapter, we present a standard methodology based on computer-aided design (CAD ) tools that enables fast development of new cell-free biosensors based on target molecule information transduction and reporting through metabolic and genetic layers, respectively. Such systems can then be repurposed to represent complex computational problems, allowing defined multiplex sensing of various inputs and integration of artificial intelligence in synthetic biological systems.

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Change history

  • 05 January 2022

    The chapter authors name was incorrectly published and it has been updated as “Manish Kushwaha” now.

References

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

    Article  CAS  PubMed  Google Scholar 

  2. Chang H-J, Voyvodic PL, Zúñiga A, Bonnet J (2017) Microbially derived biosensors for diagnosis, monitoring and epidemiology. Microb Biotechnol 10:1031–1035. https://doi.org/10.1111/1751-7915.12791

    Article  PubMed  PubMed Central  Google Scholar 

  3. Rodriguez-Mozaz S, de Alda MJL, Marco M-P, Barceló D (2005) Biosensors for environmental monitoring: a global perspective. Talanta 65:291–297. https://doi.org/10.1016/j.talanta.2004.07.006

    Article  CAS  PubMed  Google Scholar 

  4. Koch M, Pandi A, Borkowski O et al (2019) Custom-made transcriptional biosensors for metabolic engineering. Curr Opin Biotechnol 59:78–84. https://doi.org/10.1016/j.copbio.2019.02.016

    Article  CAS  PubMed  Google Scholar 

  5. Zhang L, Guo W, Lu Y (2020) Advances in cell-free biosensors: principle, mechanism, and applications. Biotechnol J 15:2000187. https://doi.org/10.1002/biot.202000187

    Article  CAS  Google Scholar 

  6. Voyvodic PL, Pandi A, Koch M et al (2019) Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors. Nat Commun 10:1697. https://doi.org/10.1038/s41467-019-09722-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Pardee K (2018) Perspective: solidifying the impact of cell-free synthetic biology through lyophilization. Biochem Eng J 138:91–97. https://doi.org/10.1016/j.bej.2018.07.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Sun ZZ, Yeung E, Hayes CA et al (2014) Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system. ACS Synth Biol 3:387–397. https://doi.org/10.1021/sb400131a

    Article  CAS  PubMed  Google Scholar 

  9. Huerta AM, Salgado H, Thieffry D, Collado-Vides J (1998) RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res 26:55–59. https://doi.org/10.1093/nar/26.1.55

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Cipriano MJ, Novichkov PN, Kazakov AE et al (2013) RegTransBase—a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics 14:213. https://doi.org/10.1186/1471-2164-14-213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Koch M, Pandi A, Delépine B, Faulon J-L (2018) A dataset of small molecules triggering transcriptional and translational cellular responses. Data Brief 17:1374–1378. https://doi.org/10.1016/j.dib.2018.02.061

    Article  PubMed  PubMed Central  Google Scholar 

  12. Xue H, Shi H, Yu Z et al (2014) Design, construction, and characterization of a set of biosensors for aromatic compounds. ACS Synth Biol 3:1011–1014. https://doi.org/10.1021/sb500023f

    Article  CAS  PubMed  Google Scholar 

  13. Libis V, Delépine B, Faulon J-L (2016) Expanding biosensing abilities through computer-aided design of metabolic pathways. ACS Synth Biol 5:1076–1085. https://doi.org/10.1021/acssynbio.5b00225

    Article  CAS  PubMed  Google Scholar 

  14. Delépine B, Duigou T, Carbonell P, Faulon J-L (2018) RetroPath2.0: a retrosynthesis workflow for metabolic engineers. Metab Eng 45:158–170. https://doi.org/10.1016/j.ymben.2017.12.002

    Article  CAS  PubMed  Google Scholar 

  15. Delépine B, Libis V, Carbonell P, Faulon J-L (2016) SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic Acids Res 44:W226–W231. https://doi.org/10.1093/nar/gkw305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Pandi A, Koch M, Voyvodic PL et al (2019) Metabolic perceptrons for neural computing in biological systems. Nat Commun 10:3880. https://doi.org/10.1038/s41467-019-11889-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Rosenblatt F (1957) The perceptron, a perceiving and recognizing automaton project para. Cornell Aeronautical Laboratory

    Google Scholar 

  18. Sun ZZ, Hayes CA, Shin J et al (2013) Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. JoVE J Vis Exp:e50762. https://doi.org/10.3791/50762

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Acknowledgments

PS and JLF are supported by the ANR SynBioDiag grant number ANR-18-CE33-0015. LF is supported by the French National Research Institute for Agriculture, Food, and Environment (INRAE), through the “Métaprogramme BIOLPREDICT”. MK acknowledges funding support from Ile-de-France region’s DIM-RFSI, INRAE’s MICA department and the University of Paris-Saclay.

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Correspondence to Jean-Loup Faulon .

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Soudier, P., Faure, L., Kushwaha, M., Faulon, JL. (2022). Cell-Free Biosensors and AI Integration. In: Karim, A.S., Jewett, M.C. (eds) Cell-Free Gene Expression. Methods in Molecular Biology, vol 2433. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1998-8_19

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  • DOI: https://doi.org/10.1007/978-1-0716-1998-8_19

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1997-1

  • Online ISBN: 978-1-0716-1998-8

  • eBook Packages: Springer Protocols

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