Abstract
Synthetic biology approaches for rewiring of bacterial constructs to express particular intracellular factors upon induction with the target analyte are emerging as sensing paradigms for applications in environmental and in vivo monitoring. To aid in the design and optimization of bacterial constructs for sensing analytes, there is a need for lysis-free intracellular detection modalities that monitor the signal level and kinetics of expressed factors within different modified bacteria in a multiplexed manner, without requiring cumbersome surface immobilization. Herein, an electrochemical detection system on nanoporous gold that is electrofabricated with a biomaterial redox capacitor is presented for quantifying β-galactosidase expressed inside modified Escherichia coli constructs upon induction with dopamine. This nanostructure-mediated redox amplification approach on a microfluidic platform allows for multiplexed assessment of the expressed intracellular factors from different bacterial constructs suspended in distinct microchannels, with no need for cell lysis or immobilization. Since redox mediators present over the entire depth of the microchannel can interact with the electrode and with the E. coli construct in each channel, the platform exhibits high sensitivity and enables multiplexing. We envision its application in assessing synthetic biology-based approaches for comparing specificity, sensitivity, and signal response time upon induction with target analytes of interest.
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Stephanopoulos G (2012) Synthetic biology and metabolic engineering. ACS Synth Biol 1:514–525. https://doi.org/10.1021/sb300094q
Li JY, Liu Y, Kim E, March JC, Bentley WE, Payne GF (2017) Electrochemical reverse engineering: a systems-level tool to probe the redox-based molecular communication of biology. Free Radic Biol Med 105:110–131. https://doi.org/10.1016/j.freeradbiomed.2016.12.029
Honrado C, McGrath JS, Reale R, Bisegna P, Swami NS, Caselli F (2020) A neural network approach for real-time particle/cell characterization in microfluidic impedance cytometry. Anal Bioanal Chem 412:3835–3845. https://doi.org/10.1007/s00216-020-02497-9
Farmehini V, Varhue W, Salahi A, Hyler AR, Čemažar J, Davalos RV, Swami NS (2020) On-chip impedance for quantifying parasitic voltages during AC electrokinetic trapping. IEEE Trans Biomed Eng 67:1664–1671. https://doi.org/10.1109/TBME.2019.2942572
Kaya T, Nagamine K, Matsui N, Yasukawa T, Shiku H, Matsue T (2004) On-chip electrochemical measurement of beta-galactosidase expression using a microbial chip. Chem Commun 2:248–249. https://doi.org/10.1039/b312462b
Yagi K (2007) Applications of whole-cell bacterial sensors in biotechnology and environmental science. Appl Microbiol Biotechnol 73:1251–1258. https://doi.org/10.1007/s00253-006-0718-6
Ferapontova EE (2020) Electrochemical assays for microbial analysis: how far they are from solving microbiota and microbiome challenges. Curr Opin Electrochem 19:153–161. https://doi.org/10.1016/j.coelec.2019.12.005
Ino K, Nashimoto Y, Taira N, Azcon JR, Shiku H (2018) Intracellular electrochemical sensing. Electroanalysis 30:2195–2209. https://doi.org/10.1002/elan.201800410
Goluch ED (2017) Microbial identification using electrochemical detection of metabolites. Trends Biotechnol 35:1125–1128. https://doi.org/10.1016/j.tibtech.2017.08.001
Liu Y, Moore JH, Kolling GL, McGrath JS, Papin JA, Swami NS (2020) Minimum bactericidal concentration of ciprofloxacin to Pseudomonas aeruginosa determined rapidly based on pyocyanin secretion. Sens. Actuator B-Chem. 312:127936. https://doi.org/10.1016/j.snb.2020.127936
Kim E, Gordonov T, Liu Y, Bentley WE, Payne GF (2013) Reverse engineering to suggest biologically relevant redox activities of phenolic materials. ACS Chem Biol 8:716–724. https://doi.org/10.1021/cb300605s
Tschirhart T, Zhou XYY, Ueda H, Tsao CY, Kim E, Payne GF, Bentley WE (2016) Electrochemical measurement of the beta-galactosidase reporter from live cells: a comparison to the Miller assay. ACS Synth Biol 5:28–35. https://doi.org/10.1021/acssynbio.5b00073
VanArsdale E, Tsao CY, Liu Y, Chen CY, Payne GF, Bentley WE (2019) Redox-based synthetic biology enables electrochemical detection of the herbicides dicamba and roundup via rewired Escherichia coli. ACS Sens. 4:1180–1184. https://doi.org/10.1021/acssensors.9b00085
Liu Y, Tsao CY, Kim E, Tschirhart T, Terrell JL, Bentley WE, Payne GF (2017) Using a redox modality to connect synthetic biology to electronics: hydrogel-based chemo-electro signal transduction for molecular communication. Adv. Healthc. Mater. 6:1600908. https://doi.org/10.1002/adhm.201600908
Zhou YS, Ino K, Shiku H, Matsue T (2015) Evaluation of senescence in individual MCF-7 spheroids based on electrochemical measurement of senescence-associated beta-galactosidase activity. Electrochim Acta 186:449–454. https://doi.org/10.1016/j.electacta.2015.10.115
Truong NC, Bui KH, Van Pham P (2018). Characterization of senescence of human adipose-derived stem cells after long-term expansion. Tissue Eng Regen Med. 109–128. Springer, Cham. https://link.springer.com/chapter/10.1007/5584_2018_235
Sanghavi BJ, Wolfbeis OS, Hirsch T, Swami NS (2015) Nanomaterial-based electrochemical sensing of neurological drugs and neurotransmitters. Microchim Acta 182:1–41. https://doi.org/10.1007/s00604-014-1308-4
Hiramoto K, Ino K, Nashimoto Y, Ito K, Shiku H (2019) Electric and electrochemical microfluidic devices for cell analysis. Front Chem 7:396. https://doi.org/10.3389/fchem.2019.00396
Fernandez RE, Sanghavi BJ, Farmehini V, Chávez JL, Hagen J, Kelley-Loughnane N, Chou CF, Swami NS (2016) Aptamer-functionalized graphene-gold nanocomposites for label-free detection of dielectrophoretic-enriched neuropeptide Y. Electrochem Commun 72:144–147. https://doi.org/10.1016/j.elecom.2016.09.017
Kim E, Liu Z, Liu Y, Bentley WE, Payne GF (2017) Catechol-based hydrogel for chemical information processing. Biomimetics 2:11. https://doi.org/10.3390/biomimetics2030011
Yan K, Liu Y, Guan YG, Bhokisham N, Tsao CY, Kim E, Shi XW, Wang Q, Bentley WE, Payne GF (2018) Catechol-chitosan redox capacitor for added amplification in electrochemical immunoanalysis. Colloid Surf. B-Biointerfaces 169:470–477. https://doi.org/10.1016/j.colsurfb.2018.05.048
Liu Y, McGrath JS, Moore JH, Kolling GL, Papin JA, Swami NS (2019) Electrofabricated biomaterial-based capacitor on nanoporous gold for enhanced redox amplification. Electrochim Acta 318:828–836. https://doi.org/10.1016/j.electacta.2019.06.127
Shang W, Liu Y, Kim E, Tsao CY, Payne GF, Bentley WE (2018) Selective assembly and functionalization of miniaturized redox capacitor inside microdevices for microbial toxin and mammalian cell cytotoxicity analyses. Lab Chip 18:3578–3587. https://doi.org/10.1039/c8lc00583d
Zeng J, Spiro S (2013) Finely tuned regulation of the aromatic amine degradation pathway in Escherichia coli. J Bacteriol 195:5141–5150. https://doi.org/10.1128/JB.00837-13
Lin YK, Yeh YC (2017) Dual-signal microbial biosensor for the detection of dopamine without inference from other catecholamine neurotransmitters. Anal Chem 89:11178–11182. https://doi.org/10.1021/acs.analchem.7b02498
Ceres P, Trausch JJ, Batey RT (2013) Engineering modular ‘ON’ RNA switches using biological components. Nucleic Acids Res 41:10449–10461. https://doi.org/10.1093/nar/gkt787
Strulson CA, Boyer JA, Whitman EE, Bevilacqua PC (2014) Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions. RNA 20:331–347. https://doi.org/10.1261/rna.042747.113
Mahen EM, Harger JW, Calderon EM, Fedor MJ (2005) Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast. Mol Cell 19:27–37. https://doi.org/10.1016/j.molcel.2005.05.025
Noh S, Choe Y, Tamilavan V, Hyun MH, Kang HY, Yang H (2015) Facile electrochemical detection of Escherichia coli using redox cycling of the product generated by the intracellular beta-D-galactosidase. Sens. Actuator B-Chem. 209:951–956. https://doi.org/10.1016/j.snb.2014.12.073
Seker E, Shih WC, Stine KJ (2018) Nanoporous metals by alloy corrosion: bioanalytical and biomedical applications. MRS Bull 43:49–56. https://doi.org/10.1557/mrs.2017.298
Liu Y, Kim E, White IM, Bentley WE, Payne GF (2014) Information processing through a bio-based redox capacitor: signatures for redox-cycling. Bioelectrochemistry 98:94–102. https://doi.org/10.1016/j.bioelechem.2014.03.012
Kim E, Gordonov T, Bentley WE, Payne GF (2013) Amplified and in situ detection of redox-active metabolite using a biobased redox capacitor. Anal Chem 85:2102–2108. https://doi.org/10.1021/ac302703y
Marcano-Velázquez JG, Batey RT (2015) Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context. J Biol Chem 290:4464–4475. https://doi.org/10.1074/jbc.M114.613497
Tyrrell J, McGinnis JL, Weeks KM, Pielak GJ (2013) The cellular environment stabilizes adenine riboswitch RNA structure. Biochemistry 52:8777–8785. https://doi.org/10.1021/bi401207q
Acknowledgements
Support from University of Virginia’s Global Infectious Diseases Institute, from MOST (Taiwan) grant #107-2923-M-001-011-MY3 and from AFOSR grants FA2386-18-1-4100 and FA2386-21-1-4070 are acknowledged.
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Liu, Y., Moore, J.H., Harbaugh, S. et al. Multiplexed assessment of engineered bacterial constructs for intracellular β-galactosidase expression by redox amplification on catechol-chitosan modified nanoporous gold. Microchim Acta 189, 4 (2022). https://doi.org/10.1007/s00604-021-05109-0
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DOI: https://doi.org/10.1007/s00604-021-05109-0