Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour

Nature Communications

Volumn 5, Issue , 2014, Pages

  Lentini, Roberta ^a   Santero, Silvia Perez ^a,b   Chizzolini, Fabio ^a   Cecchi, Dario ^a   Fontana, Jason ^a   Marchioretto, Marta ^c   Del Bianco, Cristina ^a   Terrell, Jessica L ^d,e   Spencer, Amy C ^a   Martini, Laura ^a   Forlin, Michele ^a   Assfalg, Michael ^b   Serra, Mauro Dalla ^c   Bentley, William E ^d,e   Mansy, Sheref S ^a  

^a UNIVERSITY OF TRENTO   (Italy)

^b UNIVERSITY OF VERONA   (Italy)

^c FONDAZIONE BRUNO KESSLER   (Italy)

^d UNIVERSITY OF MARYLAND   (United States)

^e UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA HEMOLYSIN; MESSENGER RNA; RNA POLYMERASE; THEOPHYLLINE; ADENOSINE RECEPTOR BLOCKING AGENT; ESCHERICHIA COLI PROTEIN; HEMOLYSIN; ISOPROPYL THIOGALACTOSIDE; RIBOSWITCH;

COLIFORM BACTERIUM; CYTOLOGY; GENETIC ENGINEERING; GENETICALLY MODIFIED ORGANISM;

ARTICLE; ARTIFICIAL CELL; BACTERIAL CELL; CELL COMMUNICATION; CELL EXPANSION; CELL FUNCTION; CONTROLLED STUDY; ERYTHROCYTE; ESCHERICHIA COLI; FLOW CYTOMETRY; GENE EXPRESSION; GENETIC ENGINEERING; GENETIC MANIPULATION; HEMOLYSIS; IN VITRO STUDY; MEMBRANE VESICLE; NONHUMAN; PROTEIN EXPRESSION; RIBOSWITCH; SIGNAL TRANSDUCTION; STAPHYLOCOCCUS AUREUS; START CODON; CELL ENGINEERING; CYTOPLASM VESICLE; DRUG EFFECTS; GENETICS; METABOLISM; PROCEDURES;

ARTIFICIAL CELLS; CELL ENGINEERING; CYTOPLASMIC VESICLES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HEMOLYSIN PROTEINS; ISOPROPYL THIOGALACTOSIDE; PURINERGIC P1 RECEPTOR ANTAGONISTS; RIBOSWITCH; THEOPHYLLINE;

EID: 84901778640     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms5012     Document Type: Article

References (39)

1. Mutalik, V. K. et al. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat. Methods 10, 354-360 (2013).
2. Chen, Y. J. et al. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat. Methods 10, 659-664 (2013).
3. Kosuri, S. et al. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc. Natl Acad. Sci. USA 110, 14024-14029 (2013).
4. Smolke, C. D. & Silver, P. A. Informing biological design by integration of systems and synthetic biology. Cell 144, 855-859 (2011).
5. Albert, R., Collins, J. J. & Glass, L. Introduction to focus issue: quantitative approaches to genetic networks. Chaos 23, 025001 (2013).
6. Regot, S. et al. Distributed biological computation with multicellular engineered networks. Nature 469, 207-211 (2011).
7. Isaacs, F. J. et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348-353 (2011).
8. Gibson, D. G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52-56 (2010).
9. Maurer, L. M., Yohannes, E., Bondurant, S. S., Radmacher, M. & Slonczewski, J. L. pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12. J. Bacteriol. 187, 304-319 (2005). (Pubitemid 40024207)
10. Lynch, S. A. & Gallivan, J. P. A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res. 37, 184-192 (2009).
11. Martini, L. & Mansy, S. S. Cell-like systems with riboswitch controlled gene expression. Chem. Commun. 47, 10734-10736 (2011).
12. Lentini, R. et al. Fluorescent proteins and in vitro genetic organization for cellfree synthetic biology. ACS Synth. Biol. 2, 482-489 (2013).
13. Cassidy, P. & Harshman, S. Studies on the binding of staphylococcal 125Ilabeled alpha-toxin to rabbit erythrocytes. Biochemistry 15, 2348-2355 (1976).
14. Mantri, S., Sapra, K. T., Cheley, S., Sharp, T. H. & Bayley, H. An engineered dimeric protein pore that spans adjacent lipid bilayers. Nat. Commun. 4, 1725 (2013).
15. Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356 (1961).
16. Prindle, A. et al. A sensing array of radically coupled genetic 'biopixels'. Nature 481, 39-44 (2012).
17. Weber, W. & Fussenegger, M. Emerging biomedical applications of synthetic biology. Nat. Rev. Genet. 13, 21-35 (2012).
18. Kostka, J. E. et al. Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the deepwater horizon oil spill. Appl. Environ. Microbiol. 77, 7962-7974 (2011).
19. Xiang, S., Fruehauf, J. & Li, C. J. Short hairpin RNA-expressing bacteria elicit RNA interference in mammals. Nat. Biotechnol. 24, 697-702 (2006). (Pubitemid 43882121)
20. Anderson, J. C., Clarke, E. J., Arkin, A. P. & Voigt, C. A. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355, 619-627 (2006). (Pubitemid 41817623)
21. Gupta, S., Bram, E. E. & Weiss, R. Genetically programmable pathogen sense and destroy. ACS Synth. Biol. 12, 715-723 (2013).
22. Saeidi, N. et al. Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Mol. Syst. Biol. 7, 521 (2011).
23. Kolodkin-Gal, I. et al. D-amino acids trigger biofilm disassembly. Science 328, 627-629 (2010).
24. Kotula, J. W. et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl Acad. Sci. USA 111, 4838-4843 (2014).
25. Duan, F. & March, J. C. Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. Proc. Natl Acad. Sci. USA 107, 11260-11264 (2010).
26. Goh, Y. L., He, H. & March, J. C. Engineering commensal bacteria for prophylaxis against infection. Curr. Opin. Biotechnol. 23, 924-930 (2012).
27. Weitz, M. et al. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. Nat. Chem. 6, 295-302 (2014).
28. Fernandes, R., Roy, V., Wu, H. C. & Bentley, W. E. Engineered biological nanofactories trigger quorum sensing response in targeted bacteria. Nat. Nanotechnol. 5, 213-217 (2010).
29. Li, M., Harbron, R. L., Weaver, J. V., Binks, B. P. & Mann, S. Electrostatically gated membrane permeability in inorganic protocells. Nat. Chem. 5, 529-536 (2013).
30. Huang, X. et al. Interfacial assembly of protein-polymer nano-conjugates into stimulus-responsive biomimetic protocells. Nat. Commun. 4, 2239 (2013).
31. Gardner, P. M., Winzer, K. & Davis, B. G. Sugar synthesis in a protocellular model leads to a cell signalling response in bacteria. Nat. Chem. 1, 377-383 (2009).
32. Gupta, A. et al. Encapsulated fusion protein confers 'sense and respond' activity to chitosan-alginate capsules to manipulate bacterial quorum sensing. Biotechnol. Bioeng. 110, 552-562 (2013).
33. Cronin, L. et al. The imitation game - a computational chemical approach to recognizing life. Nat. Biotechnol. 24, 1203-1206 (2006). (Pubitemid 44564758)
34. Forlin, M., Lentini, R. & Mansy, S. S. Cellular imitations. Curr. Opin. Chem. Biol. 16, 586-592 (2012).
35. Laventie, B. J. et al. p-Sulfonato-calix[n]arenes inhibit staphylococcal bicomponent leukotoxins by supramolecular interactions. Biochem. J. 450, 559-571 (2013).
36. Yu, W. et al. Synthesis of functional protein in liposome. J. Biosci. Bioeng. 92, 590-593 (2001). (Pubitemid 34107181)
37. Spencer, A. C., Torre, P. & Mansy, S. S. The encapsulation of cell-free transcription and translation machinery in vesicles for the construction of cellular mimics. J. Vis. Exp. 80, e51304 (2013).
38. Zhu, T. F. & Szostak, J. W. Preparation of large monodisperse vesicles. PLoS ONE 4, e5009 (2009).
39. Zhou, K. et al. Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR. BMC Mol. Biol. 12, 18 (2011).