Real-time bioelectronic sensing of environmental contaminants – Nature

  • Schwarzenbach, R. P. et al. The challenge of micropollutants in aquatic systems. Science 313, 1072–1077 (2006).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Jung, J. K. et al. Cell-free biosensors for rapid detection of water contaminants. Nat. Biotechnol. 38, 1451–1459 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bereza-Malcolm, L. T., Mann, G. & Franks, A. E. Environmental sensing of heavy metals through whole cell microbial biosensors: a synthetic biology approach. ACS Synth. Biol. 4, 535–546 (2015).

    CAS 
    PubMed 

    Google Scholar 

  • Del Valle, I. et al. Translating new synthetic biology advances for biosensing into the earth and environmental sciences. Front. Microbiol. 11, 618373 (2020).

    PubMed 

    Google Scholar 

  • Golitsch, F., Bücking, C. & Gescher, J. Proof of principle for an engineered microbial biosensor based on Shewanella oneidensis outer membrane protein complexes. Biosens. Bioelectron. 47, 285–291 (2013).

    CAS 
    PubMed 

    Google Scholar 

  • Webster, D. P. et al. An arsenic-specific biosensor with genetically engineered Shewanella oneidensis in a bioelectrochemical system. Biosens. Bioelectron. 62, 320–324 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • Ueki, T., Nevin, K. P., Woodard, T. L. & Lovley, D. R. Genetic switches and related tools for controlling gene expression and electrical outputs of Geobacter sulfurreducens. J. Ind. Microbiol. Biotechnol. 43, 1561–1575 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • West, E. A., Jain, A. & Gralnick, J. A. Engineering a native inducible expression system in Shewanella oneidensis to control extracellular electron transfer. ACS Synth. Biol. 6, 1627–1634 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • Ryon, M. G., Stewart, A. J., Kszos, L. A. & Phipps, T. L. Impacts on streams from the use of sulfur-based compounds for dechlorinating industrial effluents. Water Air Soil Pollut. 136, 255–268 (2002).

    ADS 
    CAS 

    Google Scholar 

  • Kidd, K. A. et al. Collapse of a fish population after exposure to a synthetic estrogen. Proc. Natl Acad. Sci. USA 104, 8897–8901 (2007).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rice, J. & Westerhoff, P. High levels of endocrine pollutants in US streams during low flow due to insufficient wastewater dilution. Nat. Geosci. 10, 587–591 (2017).

    ADS 
    CAS 

    Google Scholar 

  • Zhou, A. Y., Baruch, M., Ajo-Franklin, C. M. & Maharbiz, M. M. A portable bioelectronic sensing system (BESSY) for environmental deployment incorporating differential microbial sensing in miniaturized reactors. PLoS ONE 12, e0184994 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Brooks, S. M. & Alper, H. S. Applications, challenges, and needs for employing synthetic biology beyond the lab. Nat. Commun. 12, 1390 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kabessa, Y. et al. Standoff detection of explosives and buried landmines using fluorescent bacterial sensor cells. Biosens. Bioelectron. 79, 784–788 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Tang, T.-C. et al. Hydrogel-based biocontainment of bacteria for continuous sensing and computation. Nat. Chem. Biol. 17, 724–731 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhao, S. et al. A new design for living cell-based biosensors: microgels with a selectively permeable shell that can harbor bacterial species. Sens. Actuators B Chem. 334, 129648 (2021).

    CAS 

    Google Scholar 

  • Liu, X. et al. Stretchable living materials and devices with hydrogel-elastomer hybrids hosting programmed cells. Proc. Natl Acad. Sci. USA 114, 2200–2205 (2017).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bretschger, O. et al. Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl. Environ. Microbiol. 73, 7003–7012 (2007).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jensen, H. M., TerAvest, M. A., Kokish, M. G. & Ajo-Franklin, C. M. CymA and exogenous flavins improve extracellular electron transfer and couple it to cell growth in Mtr-expressing Escherichia coli. ACS Synth. Biol. 5, 679–688 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Goldbeck, C. P. et al. Tuning promoter strengths for improved synthesis and function of electron conduits in Escherichia coli. ACS Synth. Biol. 2, 150–159 (2013).

    CAS 
    PubMed 

    Google Scholar 

  • Atkinson, J. T. et al. Metalloprotein switches that display chemical-dependent electron transfer in cells. Nat. Chem. Biol. 15, 189–195 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • Barstow, B. et al. A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism. J. Biol. Eng. 5, 7 (2011).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yuan, S.-J. et al. A photometric high-throughput method for identification of electrochemically active bacteria using a WO3 nanocluster probe. Sci. Rep. 3, 1315 (2013).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Su, L. et al. Modifying cytochrome c maturation can increase the bioelectronic performance of engineered Escherichia coli. ACS Synth. Biol. 9, 115–124 (2020).

    CAS 
    PubMed 

    Google Scholar 

  • Shibata, H. & Kobayashi, S. Sulfide oxidation in gram-negative bacteria by expression of the sulfide-quinone reductase gene of Rhodobacter capsulatus and by electron transport to ubiquinone. Can. J. Microbiol. 47, 855–860 (2001).

    CAS 
    PubMed 

    Google Scholar 

  • Shibata, H., Suzuki, K. & Kobayashi, S. Menaquinone reduction by an HMT2-like sulfide dehydrogenase from Bacillus stearothermophilus. Can. J. Microbiol. 53, 1091–1100 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • Liu, H. et al. Synthetic gene circuits enable Escherichia coli to use endogenous H2S as a signaling molecule for quorum sensing. ACS Synth. Biol. 8, 2113–2120 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • Cosnefroy, A. et al. A stable fish reporter cell line to study estrogen receptor transactivation by environmental (xeno)estrogens. Toxicol. in Vitro 23, 1450–1454 (2009).

    CAS 
    PubMed 

    Google Scholar 

  • Wu, B., Atkinson, J. T., Kahanda, D., Bennett, G. N. & Silberg, J. J. Combinatorial design of chemical‐dependent protein switches for controlling intracellular electron transfer. AIChE J. 66, e16796 (2020).

    CAS 

    Google Scholar 

  • Mimee, M. et al. An ingestible bacterial–electronic system to monitor gastrointestinal health. Science 360, 915–918 (2018).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • VanArsdale, E. et al. Redox-based synthetic biology enables electrochemical detection of the herbicides dicamba and Roundup via rewired Escherichia coli. ACS Sens. 4, 1180–1184 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • VanArsdale, E. et al. A coculture based tyrosine-tyrosinase electrochemical gene circuit for connecting cellular communication with electronic networks. ACS Synth. Biol. 9, 1117–1128 (2020).

    CAS 
    PubMed 

    Google Scholar 

  • Su, L., Yin, T., Du, H., Zhang, W. & Fu, D. Synergistic improvement of Shewanella loihica PV-4 extracellular electron transfer using a TiO2@TiN nanocomposite. Bioelectrochemistry 134, 107519 (2020).

    CAS 
    PubMed 

    Google Scholar 

  • Terrell, J. L. et al. Bioelectronic control of a microbial community using surface-assembled electrogenetic cells to route signals. Nat. Nanotechnol. 16, 688–697 (2021).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Gordley, R. M. et al. Engineering dynamical control of cell fate switching using synthetic phospho-regulons. Proc. Natl Acad. Sci. USA 113, 13528–13533 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gao, X. J., Chong, L. S., Kim, M. S. & Elowitz, M. B. Programmable protein circuits in living cells. Science 361, 1252–1258 (2018).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Smith, D. A., Sessions, A. L., Dawson, K. S., Dalleska, N. & Orphan, V. J. Rapid quantification and isotopic analysis of dissolved sulfur species. Rapid Commun. Mass Spectrom. 31, 791–803 (2017).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Bobin-Dubigeon, C. et al. New UPLC–MS/MS assay for the determination of tamoxifen and its metabolites in human plasma, application to patients. Future Sci. OA 5, FSO374 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Monteiro, T. & Almeida, M. G. Electrochemical enzyme biosensors revisited: old solutions for new problems. Crit. Rev. Anal. Chem. 49, 44–66 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • Reimers, C. E., Tender, L. M., Fertig, S. & Wang, W. Harvesting energy from the marine sediment−water interface. Environ. Sci. Technol. 35, 192–195 (2001).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Esri. Community Map https://www.arcgis.com/home/item.html?id=e64f06e8d912465a96f9ea9bfdb72676 (accessed 21 April 2021).

  • Pinske, C., Bönn, M., Krüger, S., Lindenstrauss, U. & Sawers, R. G. Metabolic deficiences revealed in the biotechnologically important model bacterium Escherichia coli BL21(DE3). PLoS ONE 6, e22830 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Spiro, S. & Guest, J. R. Adaptive responses to oxygen limitation in Escherichia coli. Trends Biochem. Sci. 16, 310–314 (1991).

    CAS 
    PubMed 

    Google Scholar 

  • Monk, J. M. et al. Multi-omics quantification of species variation of Escherichia coli links molecular features with strain phenotypes. Cell Syst. 3, 238–251.e12 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kim, H., Kim, S. & Yoon, S. H. Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3). PLoS ONE 13, e0204375 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Sauer, U., Canonaco, F., Heri, S., Perrenoud, A. & Fischer, E. The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J. Biol. Chem. 279, 6613–6619 (2004).

    CAS 
    PubMed 

    Google Scholar 

  • Fan, J. et al. Quantitative flux analysis reveals folate-dependent NADPH production. Nature 510, 298–302 (2014).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).

    CAS 
    PubMed 

    Google Scholar 

  • Torella, J. P. et al. Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications. Nat. Protoc. 9, 2075–2089 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bassalo, M. C. et al. Rapid and efficient one-step metabolic pathway integration in E. coli. ACS Synth. Biol. 5, 561–568 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Datta, S., Costantino, N. & Court, D. L. A set of recombineering plasmids for gram-negative bacteria. Gene 379, 109–115 (2006).

    CAS 
    PubMed 

    Google Scholar 

  • Zhang, Y. & Weiner, J. H. A simple semi-quantitative in vivo method using H2S detection to monitor sulfide metabolizing enzymes. Biotechniques 57, 208–210 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • Fatin-Rouge, N., Starchev, K. & Buffle, J. Size effects on diffusion processes within agarose gels. Biophys. J. 86, 2710–2719 (2004).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

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