Engineering multicellular logic in bacteria with metabolic wires

ACS Synthetic Biology

Volumn 3, Issue 4, 2014, Pages 204-209

  Silva Rocha, Rafael ^a,b   De Lorenzo, Victor ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

biodegradation; logic gates; Pseudomonas; regulator inducer specificity; regulatory networks; TOL system

Indexed keywords

BACTERIAL ENZYME; BENZOIC ACID; TOLUENE; BENZOIC ACID DERIVATIVE;

ARTICLE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL STRAIN; BIODEGRADATION; BIOLUMINESCENCE; BIOMEDICAL ENGINEERING; CELL COMMUNICATION; CITRIC ACID CYCLE; CONTROLLED STUDY; KINETICS; LIQUID CULTURE; METABOLISM; MICROPLATE READER; MULTICELLULAR LOGIC; NONHUMAN; OPERON; PRIORITY JOURNAL; PROMOTER REGION; PSEUDOMONAS PUTIDA; BIOREMEDIATION; GENETIC ENGINEERING; GENETICS; PROCEDURES;

BENZOATES; BIODEGRADATION, ENVIRONMENTAL; CELL COMMUNICATION; GENETIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; PROMOTER REGIONS, GENETIC; PSEUDOMONAS PUTIDA; TOLUENE;

EID: 84896735601     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb400064y     Document Type: Article

References (38)

1. Andrianantoandro, E., Basu, S., Karig, D. K., and Weiss, R. (2006) Synthetic biology: new engineering rules for an emerging discipline Mol. Syst. Biol. 2, 0028
2. Purnick, P. E. and Weiss, R. (2009) The second wave of synthetic biology: from modules to systems Nat. Rev. Mol. Cell Biol. 10, 410-422
3. Hermsen, R., Tans, S., and ten Wolde, P. R. (2006) Transcriptional regulation by competing transcription factor modules PLoS Comput. Biol. 2, e164
4. Silva-Rocha, R. and de Lorenzo, V. (2008) Mining logic gates in prokaryotic transcriptional regulation networks FEBS Lett. 582, 1237-1244
5. Zhan, J., Ding, B., Ma, R., Ma, X., Su, X., Zhao, Y., Liu, Z., Wu, J., and Liu, H. (2010) Develop reusable and combinable designs for transcriptional logic gates Mol. Syst. Biol. 6, 388
6. Hunziker, A., Tuboly, C., Horvath, P., Krishna, S., and Semsey, S. (2010) Genetic flexibility of regulatory networks Proc. Natl. Acad. Sci. U. S. A. 107, 12998-13003
7. 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
8. Siuti, P., Yazbek, J., and Lu, T. K. (2013) Synthetic circuits integrating logic and memory in living cells Nat. Biotechnol. 31, 448-452
9. Ghosh, B., Karmakar, R., and Bose, I. (2005) Noise characteristics of feed forward loops Phys. Biol. 2, 36-45 (Pubitemid 41238216)
10. Pedraza, J. M. and van Oudenaarden, A. (2005) Noise propagation in gene networks Science 307, 1965-1969
11. Sprinzak, D. and Elowitz, M. B. (2005) Reconstruction of genetic circuits Nature 438, 443-448 (Pubitemid 41742009)
12. Voigt, C. A. (2006) Genetic parts to program bacteria Curr. Opin. Biotechnol. 17, 548-557 (Pubitemid 44442933)
13. Mutalik, V. K., Guimaraes, J. C., Cambray, G., Mai, Q. A., Christoffersen, M. J., Martin, L., Yu, A., Lam, C., Rodriguez, C., Bennett, G., Keasling, J. D., Endy, D., and Arkin, A. P. (2013) Quantitative estimation of activity and quality for collections of functional genetic elements Nat. Methods 10, 347-353
14. Bonnet, J., Yin, P., Ortiz, M. E., Subsoontorn, P., and Endy, D. (2013) Amplifying genetic logic gates Science 340, 599-603
15. Regot, S., Macia, J., Conde, N., Furukawa, K., Kjellen, J., Peeters, T., Hohmann, S., de Nadal, E., Posas, F., and Sole, R. (2011) Distributed biological computation with multicellular engineered networks Nature 469, 207-211
16. Waters, C. M. and Bassler, B. L. (2005) Quorum sensing: cell-to-cell communication in bacteria Annu. Rev. Cell Dev. Biol. 21, 319-346 (Pubitemid 41740638)
17. van der Meer, J. R. and Sentchilo, V. (2003) Genomic islands and the evolution of catabolic pathways in bacteria Curr. Opin. Biotechnol. 14, 248-254 (Pubitemid 36782652)
18. Tropel, D. and van der Meer, J. R. (2004) Bacterial transcriptional regulators for degradation pathways of aromatic compounds Microbiol. Mol. Biol. Rev. 68, 474-500 (Pubitemid 39238279)
19. Galvao, T. C., Mohn, W. W., and de Lorenzo, V. (2005) Exploring the microbial biodegradation and biotransformation gene pool Trends Biotechnol. 23, 497-506 (Pubitemid 41317913)
20. Diaz, E., Jimenez, J. I., and Nogales, J. (2012) Aerobic degradation of aromatic compounds Curr. Opin. Biotechnol. 24, 431-442
21. Diaz, E. and Prieto, M. A. (2000) Bacterial promoters triggering biodegradation of aromatic pollutants Curr. Opin. Biotechnol. 11, 467-475
22. Carbajosa, G., Trigo, A., Valencia, A., and Cases, I. (2009) Bionemo: molecular information on biodegradation metabolism Nucleic Acids Res. 37, D598-602
23. Katsuyama, C., Nakaoka, S., Takeuchi, Y., Tago, K., Hayatsu, M., and Kato, K. (2009) Complementary cooperation between two syntrophic bacteria in pesticide degradation J. Theor. Biol. 256, 644-654
24. Ramos, J. L., Marques, S., and Timmis, K. N. (1997) Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators Annu. Rev. Microbiol. 51, 341-373 (Pubitemid 27433053)
25. Jimenez, J. I., Minambres, B., Garcia, J. L., and Diaz, E. (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440 Environ. Microbiol. 4, 824-841 (Pubitemid 36064174)
26. Williams, P. A. and Murray, K. (1974) Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid J. Bacteriol. 120, 416-423
27. Spooner, R. A., Lindsay, K., and Franklin, F. C. (1986) Genetic, functional and sequence analysis of the xylR and xylS regulatory genes of the TOL plasmid pWW0 J. Gen. Microbiol. 132, 1347-1358 (Pubitemid 16115643)
28. Inouye, S., Nakazawa, A., and Nakazawa, T. (1987) Expression of the regulatory gene xylS on the TOL plasmid is positively controlled by the xylR gene product Proc. Natl. Acad. Sci. U. S. A. 84, 5182-5186
29. Harwood, C. S. and Parales, R. E. (1996) The beta-ketoadipate pathway and the biology of self-identity Annu. Rev. Microbiol. 50, 553-590
30. Bagdasarian, M., Lurz, R., Ruckert, B., Franklin, F. C., Bagdasarian, M. M., Frey, J., and Timmis, K. N. (1981) Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas Gene 16, 237-247 (Pubitemid 12132054)
31. Silva-Rocha, R. and de Lorenzo, V. (2013) The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space Environ. Microbiol. 15, 271-286
32. Cowles, C. E., Nichols, N. N., and Harwood, C. S. (2000) BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida J. Bacteriol. 182, 6339-6346
33. Diaz, E. (2004) Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility Int. Microbiol. 7, 173-180 (Pubitemid 40515129)
34. Silva-Rocha, R., Martinez-Garcia, E., Calles, B., Chavarria, M., Arce-Rodriguez, A., de Las Heras, A., Paez-Espino, A. D., Durante-Rodriguez, G., Kim, J., Nikel, P. I., Platero, R., and de Lorenzo, V. (2013) The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes Nucleic Acids Res. 41, D666-675
35. Shetty, R. P., Endy, D., and Knight, T. F., Jr. (2008) Engineering BioBrick vectors from BioBrick parts J. Biol. Eng. 2, 5
36. de Lorenzo, V. and Timmis, K. N. (1994) Analysis and construction of stable phenotypes in gram-negative bacteria with Tn 5-and Tn 10 -derived minitransposons Methods Enzymol. 235, 386-405
37. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, New York.
38. Choi, K. H., Gaynor, J. B., White, K. G., Lopez, C., Bosio, C. M., Karkhoff-Schweizer, R. R., and Schweizer, H. P. (2005) A Tn 7 -based broad-range bacterial cloning and expression system Nat. Methods 2, 443-448 (Pubitemid 40916563)