Cell-free biosensors for rapid detection of water contaminants.
Journal
Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648
Informations de publication
Date de publication:
12 2020
12 2020
Historique:
received:
25
04
2019
accepted:
19
05
2020
pubmed:
8
7
2020
medline:
21
1
2021
entrez:
8
7
2020
Statut:
ppublish
Résumé
Lack of access to safe drinking water is a global problem, and methods to reliably and easily detect contaminants could be transformative. We report the development of a cell-free in vitro transcription system that uses RNA Output Sensors Activated by Ligand Induction (ROSALIND) to detect contaminants in water. A combination of highly processive RNA polymerases, allosteric protein transcription factors and synthetic DNA transcription templates regulates the synthesis of a fluorescence-activating RNA aptamer. The presence of a target contaminant induces the transcription of the aptamer, and a fluorescent signal is produced. We apply ROSALIND to detect a range of water contaminants, including antibiotics, small molecules and metals. We also show that adding RNA circuitry can invert responses, reduce crosstalk and improve sensitivity without protein engineering. The ROSALIND system can be freeze-dried for easy storage and distribution, and we apply it in the field to test municipal water supplies, demonstrating its potential use for monitoring water quality.
Identifiants
pubmed: 32632301
doi: 10.1038/s41587-020-0571-7
pii: 10.1038/s41587-020-0571-7
pmc: PMC7718425
mid: NIHMS1596286
doi:
Substances chimiques
Aptamers, Nucleotide
0
Ligands
0
Metals
0
Small Molecule Libraries
0
Transcription Factors
0
Water Pollutants, Chemical
0
RNA
63231-63-0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1451-1459Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM118157
Pays : United States
Références
French, K. E. Harnessing synthetic biology for sustainable development. Nat. Sustain. 2, 250–252 (2019).
Slomovic, S., Pardee, K. & Collins, J. J. Synthetic biology devices for in vitro and in vivo diagnostics. Proc. Natl Acad. Sci. USA 112, 14429–14435 (2015).
pubmed: 26598662
Pardee, K. et al. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165, 1255–1266 (2016).
pubmed: 27160350
Gootenberg, J. S. et al. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360, 439–444 (2018).
pubmed: 29449508
pmcid: 5961727
Chen, J. S. et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360, 436–439 (2018).
pubmed: 29449511
pmcid: 6628903
Takahashi, M. K. et al. A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Nat. Commun. 9, 3347 (2018).
pubmed: 30131493
pmcid: 6104080
Vorosmarty, C. J. et al. Global threats to human water security and river biodiversity. Nature 467, 555–561 (2010).
pubmed: 20882010
van der Meer, J. R. & Belkin, S. Where microbiology meets microengineering: design and applications of reporter bacteria. Nat. Rev. Microbiol. 8, 511–522 (2010).
pubmed: 20514043
McNerney, M. P. et al. Active analyte import improves the dynamic range and sensitivity of a vitamin B
pubmed: 31977200
Belkin, S. et al. Remote detection of buried landmines using a bacterial sensor. Nat. Biotechnol. 35, 308–310 (2017).
pubmed: 28398330
Siegal-Gaskins, D. et al. Gene circuit performance characterization and resource usage in a cell-free ‘breadboard’. ACS Synth. Biol. 3, 416–425 (2014).
pubmed: 24670245
Alam, K. K. et al. A fluorescent split aptamer for visualizing RNA–RNA assembly in vivo. ACS Synth. Biol. 6, 1710–1721 (2017).
pubmed: 28548488
pmcid: 5603824
Zhang, Z. et al. Single-molecule tracking of the transcription cycle by sub-second RNA detection. eLife 3, e01775 (2014).
pubmed: 24473079
pmcid: 3901038
Pedelacq, J. D. et al. Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol. 24, 79–88 (2006).
pubmed: 16369541
Shimizu, Y. et al. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751–755 (2001).
pubmed: 11479568
Cuthbertson, L. & Nodwell, J. R. The TetR family of regulators. Microbiol. Mol. Biol. Rev. 77, 440–475 (2013).
pubmed: 24006471
pmcid: 3811609
Dunn, J. J. & Studier, F. W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166, 477–535 (1983).
pubmed: 6864790
Fernandez-Lopez, R. et al. Transcription factor-based biosensors enlightened by the analyte. Front. Microbiol. 6, 648 (2015).
pubmed: 26191047
pmcid: 4486848
Baquero, F., Martinez, J. L. & Canton, R. Antibiotics and antibiotic resistance in water environments. Curr. Opin. Biotechnol. 19, 260–265 (2008).
pubmed: 18534838
Zhang, W. et al. Engineered biosynthesis of a novel amidated polyketide, using the malonamyl-specific initiation module from the oxytetracycline polyketide synthase. Appl. Environ. Microbiol. 72, 2573–2580 (2006).
pubmed: 16597959
pmcid: 1449064
Deochand, D. K. & Grove, A. MarR family transcription factors: dynamic variations on a common scaffold. Crit. Rev. Biochem. Mol. Biol. 52, 595–613 (2017).
pubmed: 28670937
Zhu, T. et al. Deciphering and engineering of the final step halogenase for improved chlortetracycline biosynthesis in industrial Streptomyces aureofaciens. Metab. Eng. 19, 69–78 (2013).
pubmed: 23800859
Noguchi, N. et al. Regulation of transcription of the mph(A) gene for macrolide 2′-phosphotransferase I in Escherichia coli: characterization of the regulatory gene mphR(A). J. Bacteriol. 182, 5052–5058 (2000).
pubmed: 10960087
pmcid: 94651
Richardson, S. D. & Ternes, T. A. Water analysis: emerging contaminants and current issues. Anal. Chem. 90, 398–428 (2018).
pubmed: 29112806
Kasey, C. M. et al. Development of transcription factor-based designer macrolide biosensors for metabolic engineering and synthetic biology. ACS Synth. Biol. 7, 227–239 (2018).
pubmed: 28950701
Carballa, M. et al. Behavior of pharmaceuticals, cosmetics and hormones in a sewage treatment plant. Water Res. 38, 2918–2926 (2004).
pubmed: 15223286
Hiromoto, T. et al. Characterization of MobR, the 3-hydroxybenzoate-responsive transcriptional regulator for the 3-hydroxybenzoate hydroxylase gene of Comamonas testosteroni KH122-3s. J. Mol. Biol. 364, 863–877 (2006).
pubmed: 17046018
Kim, M. et al. Widely used benzalkonium chloride disinfectants can promote antibiotic resistance. Appl. Microbiol. 84, e01201-18. (2018).
Grkovic, S. et al. QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA. J. Biol. Chem. 273, 18665–18673 (1998).
pubmed: 9660841
Lu, W. J. et al. Enantiomers of naringenin as pleiotropic, stereoselective inhibitors of cytochrome P450 isoforms. Chirality 23, 891–896 (2011).
pubmed: 21953762
pmcid: 3252466
Rogers, J. K. et al. Synthetic biosensors for precise gene control and real-time monitoring of metabolites. Nucleic Acids Res. 43, 7648–7660 (2015).
pubmed: 26152303
pmcid: 4551912
Liu, X. et al. De novo design of programmable inducible promoters. Nucleic Acids Res. 47, 10452–10463 (2019).
pubmed: 31552424
pmcid: 6821364
Juraschek, S. P. et al. Gout, urate-lowering therapy, and uric acid levels among adults in the United States. Arthrit. Care Res. 67, 588–592 (2015).
Wilkinson, S. & Grove, A. HucR, a novel uric acid-responsive member of the MarR family of transcriptional regulators from Deinococcus radiodurans. J. Biol. Chem. 279, 51442–51450 (2004).
pubmed: 15448166
Abraham, J., Dowling, K. & Florentine, S. Risk of post-fire metal mobilization into surface water resources: a review. Sci. Total Environ. 599, 1740–1755 (2017).
pubmed: 28535601
Hanna-Attisha, M. et al. Elevated blood lead levels in children associated with the Flint drinking water crisis: a spatial analysis of risk and public health response. Am. J. Public Health 106, 283–290 (2016).
pubmed: 26691115
pmcid: 4985856
Calle, G. R. et al. Enhanced copper release from pipes by alternating stagnation and flow events. Environ. Sci. Technol. 41, 7430–7436 (2007).
pubmed: 18044522
VanZile, M. L., Chen, X. & Giedroc, D. P. Allosteric negative regulation of smt O/P binding of the zinc sensor, SmtB, by metal ions: a coupled equilibrium analysis. Biochemistry 41, 9776–9786 (2002).
pubmed: 12146943
Chang, F. M. et al. Cu(I)-mediated allosteric switching in a copper-sensing operon repressor (CsoR). J. Biol. Chem. 289, 19204–19217 (2014).
pubmed: 24831014
pmcid: 4081955
Busenlehner, L. S. et al. Spectroscopic properties of the metalloregulatory Cd(II) and Pb(II) sites of S. aureus pI258 CadC. Biochemistry 40, 4426–4436 (2001).
pubmed: 11284699
Lloyd, J. et al. Dynamic control of aptamer–ligand activity using strand displacement reactions. ACS Synth. Biol. 7, 30–37 (2018).
pubmed: 29028334
Reyes-Caballero, H. et al. The metalloregulatory zinc site in Streptococcus pneumoniae AdcR, a zinc-activated MarR family repressor. J. Mol. Biol. 403, 197–216 (2010).
pubmed: 20804771
pmcid: 2949468
Danner, M. C. et al. Antibiotic pollution in surface fresh waters: occurrence and effects. Sci. Total Environ. 664, 793–804 (2019).
pubmed: 30763859
Steber, M. et al. Mechanistic basis for RNA aptamer-based induction of TetR. ChemBioChem 12, 2608–2614 (2011).
pubmed: 22021209
Pardee, K. et al. Paper-based synthetic gene networks. Cell 159, 940–954 (2014).
pubmed: 25417167
pmcid: 4243060
Haklay, M. A. W. P. Openstreetmap: UserGenerated street maps. IEEE Pervas. Comput. 7, 12–18 (2008).
Vega, A. S., Lizama, K. & Pastén, P. A. in Water Policy in Chile (ed. Donoso, G.) 25–51 (Springer International Publishing, 2018).
Chen, X. et al. Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs. Nat. Biotechnol. 37, 1287–1293 (2019).
pubmed: 31548726
Ellefson, J. W., Ledbetter, M. P. & Ellington, A. D. Directed evolution of a synthetic phylogeny of programmable Trp repressors. Nat. Chem. Biol. 14, 361–367 (2018).
pubmed: 29483643
McNerney, M. P. et al. Point-of-care biomarker quantification enabled by sample-specific calibration. Sci. Adv. 5, eaax4473 (2019).
pubmed: 31579825
pmcid: 6760921
Capdevila, D. A. et al. Tuning site-specific dynamics to drive allosteric activation in a pneumococcal zinc uptake regulator. eLife 7, e37268 (2018).