Quorum sensing-modulated and-Gate promoters control gene expression in response to a combination of endogenous and exogenous signals

ACS Synthetic Biology

Volumn 3, Issue 4, 2014, Pages 238-246

  Shong, Jasmine ^a,b   Collins, Cynthia H ^a,b  

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

^b RENSSELAER POLYTECHNIC INSTITUTE   (United States)

Author keywords

AND gate; autoinduction; cell cell communication; EsaR; logic gate; Quorum sensing

Indexed keywords

AGAR; N ACYLHOMOSERINE LACTONE; BACTERIAL PROTEIN; ESAR PROTEIN, PANTOEA STEWARTII; GAMMA BUTYROLACTONE; GAMMA BUTYROLACTONE DERIVATIVE; ISOPROPYL THIOGALACTOSIDE; N-(3-OXOHEXANOYL)-3-AMINODIHYDRO-2(3H)-FURANONE; RECOMBINANT PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BACTERIAL STRAIN; BINDING SITE; CELL COMMUNICATION; CELL DENSITY; CELL FUNCTION; DNA SEQUENCE; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE INDUCTION; GENE TARGETING; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; QUORUM SENSING; REPRESSOR GENE; WILD TYPE; ANALOGS AND DERIVATIVES; DRUG EFFECTS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

4-BUTYROLACTONE; ACYL-BUTYROLACTONES; BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; ISOPROPYL THIOGALACTOSIDE; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; QUORUM SENSING; RECOMBINANT PROTEINS; TRANSCRIPTION FACTORS;

EID: 84898954540     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb4000965     Document Type: Article

References (41)

1. Kaplan, S., Bren, A., Zaslaver, A., Dekel, E., and Alon, U. (2008) Diverse two-dimensional input functions control bacterial sugar genes Mol. Cell 29, 786-792 (Pubitemid 351400930)
2. Komili, S. and Silver, P. A. (2008) Coupling and coordination in gene expression processes: A systems biology view Nat. Rev. Genet. 9, 38-48 (Pubitemid 350277299)
3. Mehta, P., Goyal, S., Long, T., Bassler, B. L., and Wingreen, N. S. (2009) Information processing and signal integration in bacterial quorum sensing Mol. Sys. Biol. 5, 325-325
4. Teng, S.-W., Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S. (2011) Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi Mol. Sys. Biol. 7, 491-491
5. Espinar, L., Dies, M., Cagatay, T., Süel, G. M., and Garcia-Ojalvo, J. (2013) Circuit-level input integration in bacterial gene regulation Proc. Natl. Acad. Sci. U.S.A. 110, 7091-7096
6. Setty, Y., Mayo, A. E., Surette, M. G., and Alon, U. (2003) Detailed map of a cis-regulatory input function Proc. Natl. Acad. Sci. U.S.A. 100, 7702-7707 (Pubitemid 36760033)
7. Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli Nature 403, 339-342 (Pubitemid 30062394)
8. Elowitz, M. B. and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators Nature 403, 335-338 (Pubitemid 30062393)
9. Ramalingam, K. L., Tomshine, J. R., Maynard, J. A., and Kaznessis, Y. N. (2009) Forward engineering of synthetic bio-logical AND gates Biochem. Eng. J. 47, 38-47
10. Cox, R. S., Surette, M. G., and Elowitz, M. B. (2007) Programming gene expression with combinatorial promoters Mol. Syst. Biol. 3, 145-145
11. Miyamoto, T., Razavi, S., DeRose, R., and Inoue, T. (2013) Synthesizing biomolecule-based boolean logic gates ACS Syn. Biol. 2, 72-82
12. Collado-Vides, J., Magasanik, B., and Gralla, J. D. (1991) Control site location and transcriptional regulation in Escherichia coli Microbiol. Rev. 55, 371-394
13. Murphy, K. F., Balázsi, G., and Collins, J. J. (2007) Combinatorial promoter design for engineering noisy gene expression Proc. Natl. Acad. Sci. U.S.A. 104, 12726-12731 (Pubitemid 47255222)
14. Bagh, S., Mandal, M., and McMillen, D. (2010) Minimal genetic device with multiple tunable functions Phys. Rev. E 82, 1-8
15. Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., Yamamura, M., and Kiga, D. (2010) Construction of a genetic AND gate under a new standard for assembly of genetic parts BMC Genomics 11, S16
16. Sayut, D. J., Niu, Y., and Sun, L. (2009) Construction and enhancement of a minimal genetic AND logic gate Appl. Environ. Microbiol. 75, 637-642
17. Stevens, A. M., Schuster, M., and Rumbaugh, K. P. (2012) Working together for the common good: Cell-cell communication in bacteria J. Bacteriol. 194, 2131-2141
18. Ng, W.-L. and Bassler, B. L. (2009) Bacterial quorum-sensing network architectures Annu. Rev. Genet. 43, 197-222
19. Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H., and Weiss, R. (2005) A synthetic multicellular system for programmed pattern formation Nature 434, 1130-1134 (Pubitemid 40663491)
20. Balagaddé, F. K., Song, H., Ozaki, J., Collins, C. H., Barnet, M., Arnold, F. H., Quake, S. R., and You, L. (2008) A synthetic Escherichia coli predator-prey ecosystem Mol. Syst. Biol. 4, 187
21. Danino, T., Mondragón-Palomino, O., Tsimring, L., and Hasty, J. (2010) A synchronized quorum of genetic clocks Nature 463, 326-330
22. Tamsir, A., Tabor, J. J., and Voigt, C. A. (2011) Robust multicellular computing using genetically encoded NOR gates and chemical 'wires' Nature 469, 212-215
23. Pai, A., Tanouchi, Y., Collins, C. H., and You, L. (2009) Engineering multicellular systems by cell-cell communication Curr. Opin. Biotechnol. 20, 461-470
24. Engebrecht, J. and Silverman, M. (1984) Identification of genes and gene products necessary for bacterial bioluminescence Proc. Natl. Acad. Sci. U.S.A. 81, 4154-4158 (Pubitemid 14054539)
25. Schaefer, A. L., Val, D. L., Hanzelka, B. L., Cronan, J. E., and Greenberg, E. P. (1996) Generation of cell-to-cell signals in quorum sensing: Acyl-homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein Proc. Natl. Acad. Sci. U.S.A. 93, 9505-9509 (Pubitemid 26296638)
26. Fuqua, C., Parsek, M. R., and Greenberg, E. P. (2001) Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing Annu. Rev. Genet. 35, 439-468 (Pubitemid 34032983)
27. Stevens, A. M., Fujita, N., Ishihama, A., and Greenberg, E. P. (1999) Involvement of the RNA polymerase α-subunit C-terminal domain in LuxR-dependent activation of the Vibrio fischeri luminescence genes J. Bacteriol. 181, 4704-4707 (Pubitemid 29357960)
28. Ptashne, M. (2007) Repressors Curr. Biol. 17, R740-R741 (Pubitemid 47333145)
29. Rojo, F. (2001) Mechanisms of transcriptional repression Curr. Opin. Microbiol. 4, 145-151 (Pubitemid 32294415)
30. Egland, K. A. and Greenberg, E. P. (2000) Conversion of the Vibrio fischeri transcriptional activator, LuxR, to a repressor J. Bacteriol. 182, 805-811 (Pubitemid 30054014)
31. von Bodman, S. B., Majerczak, D. R., and Coplin, D. L. (1998) A negative regulator mediates quorum-sensing control of exopolysaccharide production in Pantoea stewartii subsp. stewartii Proc. Natl. Acad. Sci. U.S.A. 95, 7687-7692 (Pubitemid 28293314)
32. Minogue, T. D., Wehland-von Trebra, M., Bernhard, F., and von Bodman, S. B. (2002) The autoregulatory role of EsaR, a quorum-sensing regulator in Pantoea stewartii ssp. stewartii: Evidence for a repressor function Mol. Microbiol. 44, 1625-1635 (Pubitemid 34639438)
33. von Bodman, S. B., Ball, J. K., Faini, M. A., Herrera, C. M., Minogue, T. D., Urbanowski, M. L., and Stevens, A. M. (2003) The quorum sensing negative regulators EsaR and ExpR Ecc, homologues within the LuxR family, retain the ability to function as activators of transcription J. Bacteriol. 185, 7001-7007 (Pubitemid 37444503)
34. Schu, D. J., Carlier, A. L., Jamison, K. P., von Bodman, S., and Stevens, A. M. (2009) Structure/function analysis of the Pantoea stewartii quorum-sensing regulator EsaR as an activator of transcription J. Bacteriol. 191, 7402-7409
35. Shong, J. and Collins, C. H. (2013) Engineering the esaR promoter for tunable quorum sensing-dependent gene expression ACS Syn. Biol. 10.1021/sb4000433
36. Shong, J., Huang, Y.-M., Bystroff, C., and Collins, C. H. (2013) Directed evolution of the quorum-sensing regulator EsaR for increased signal sensitivity ACS Chem. Biol. 8, 789-795
37. Lederer, T., Takahashi, M., and Hillen, W. (1995) Thermodynamic analysis of tetracycline-mediated induction of Tet repressor by a quantitative methylation protection assay Anal. Biochem. 232, 190-196 (Pubitemid 26010258)
38. Tsao, C.-Y., Hooshangi, S., Wu, H.-C., Valdes, J. J., and Bentley, W. E. (2010) Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli Metab. Eng. 12, 291-297
39. Nocadello, S. and Swennen, E. F. (2012) The new pLAI (lux regulon based auto-inducible) expression system for recombinant protein production in Escherichia coli Microbial Cell Fact. 11, 3
40. Studier, F. W. (2005) Protein production by auto-induction in high-density shaking cultures Protein Express. Purif. 41, 207-234
41. Moon, T. S., Lou, C., Tamsir, A., Stanton, B. C., and Voigt, C. A. (2012) Genetic programs constructed from layered logic gates in single cells Nature 491, 249-253