Programmable bacteria detect and record an environmental signal in the mammalian gut

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 13, 2014, Pages 4838-4843

  Kotula, Jonathan W ^a,b   Kerns, S Jordan ^a,b   Shaket, Lev A ^b   Siraj, Layla ^b   Collins, James J ^b,c,d   Way, Jeffrey C ^b   Silver, Pamela A ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b HARVARD UNIVERSITY   (United States)

^c BOSTON UNIVERSITY   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Genetic switch; Synthetic biology

Indexed keywords

ANHYDROTETRACYCLINE;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIAL SURVIVAL; BACTERIOPHAGE LAMBDA; BACTERIUM ISOLATION; BIOMEDICAL ENGINEERING; CELL DIVISION; CONTROLLED STUDY; CRO GENE; DRUG EXPOSURE; ENVIRONMENTAL MONITORING; ESCHERICHIA COLI; FEMALE; GENE STRUCTURE; GENE SWITCHING; IN VITRO STUDY; INTESTINE; LABORATORY DEVICE; MEMORY ELEMENT; MEMORY SYSTEM; MOLECULAR STABILITY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SIGNAL DETECTION;

GENETIC SWITCH; SYNTHETIC BIOLOGY;

ANIMALS; ESCHERICHIA COLI; GASTROINTESTINAL TRACT; GENETIC ENGINEERING; HUMANS; MAMMALS; MICE; MICROBIOTA; TETRACYCLINES;

EID: 84897482912     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1321321111     Document Type: Article

References (46)

1. Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI (2011) Human nutrition, the gut microbiome and the immune system. Nature 474(7351):327-336.
2. Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA (2012) The application of ecological theory toward an understanding of the human microbiome. Science 336(6086):1255-1262.
3. Modi SR, Lee HH, Spina CS, Collins JJ (2013) Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499(7457):219-222.
4. Burrill DR, Inniss MC, Boyle PM, Silver PA (2012) Synthetic memory circuits for tracking human cell fate. Genes Dev 26(13):1486-1497.
5. Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA (2012) Genetic programs constructed from layered logic gates in single cells. Nature 491(7423):249-253.
6. Bonnet J, Yin P, Ortiz ME, Subsoontorn P, Endy D (2013) Amplifying genetic logic gates. Science 340(6132):599-603.
7. Siuti P, Yazbek J, Lu TK (2013) Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol 31(5):448-452.
8. Friedland AE, et al. (2009) Synthetic gene networks that count. Science 324(5931): 1199-1202.
9. Kobayashi H, et al. (2004) Programmable cells: Interfacing natural and engineered gene networks. Proc Natl Acad Sci USA 101(22):8414-8419.
10. Litcofsky KD, Afeyan RB, Krom RJ, Khalil AS, Collins JJ (2012) Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nat Methods 9(11):1077-1080.
11. Garcia JR, Cha HJ, Rao G, Marten MR, BentleyWE (2009) Microbial nar-GFP cell sensors reveal oxygen limitations in highly agitated and aerated laboratory-scale fermentors. Microb Cell Fact 8:6.
12. Neubauer Z, Calef E (1970) Immunity phase-shift in defective lysogens: Non-mutational hereditary change of early regulation of lambda prophage. J Mol Biol 51(1):1-13.
13. Toman Z, Dambly-Chaudière C, Tenenbaum L, Radman M (1985) A system for detection of genetic and epigenetic alterations in Escherichia coli induced by DNAdamaging agents. J Mol Biol 186(1):97-105.
14. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767):339-342.
15. Wittrup KD, Bailey JE (1990) Mathematical modeling of a single-cell enzyme assay. Biotechnol Bioeng 35(5):525-532.
16. Wittrup KD, Bailey JE, Ratzkin B, Patel A (1990) Propagation of an amplifiable recombinant plasmid in Saccharomyces cerevisiae: Flow cytometry studies and segregated modeling. Biotechnol Bioeng 35(6):565-577.
17. O'Gorman SF, Fox DT, Wahl GM (1991) Recombinase-mediated gene activation and site-specific integration in mammalian cells. Science 251(4999):1351-1355.
18. Dymecki SMT, Tomasiewicz H (1998) Using Flp-recombinase to characterize expansion of Wnt1-expressing neural progenitors in the mouse. Dev Biol 201(1):57-65.
19. Zinyk DLM, Mercer EH, Harris E, Anderson DJ, Joyner AL (1998) Fate mapping of the mouse midbrain-hindbrain constriction using a site-specific recombination system. Curr Biol 8(11):665-668.
20. Bonnet J, Subsoontorn P, Endy D (2012) Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci USA 109(23): 8884-8889.
21. Ajo-Franklin CM, et al. (2007) Rational design of memory in eukaryotic cells. Genes Dev 21(18):2271-2276.
22. Ptashne M, et al. (1980) How the lambda repressor and cro work. Cell 19(1):1-11.
23. Shea MA, Ackers GK (1985) The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J Mol Biol 181(2):211-230.
24. Arkin A, Ross J, McAdams HH (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149(4): 1633-1648.
25. Gimble FS, Sauer RT (1985) Mutations in bacteriophage lambda repressor that prevent RecA-mediated cleavage. J Bacteriol 162(1):147-154.
26. Reichardt L, Kaiser AD (1971) Control of lambda repressor synthesis. Proc Natl Acad Sci USA 68(9):2185-2189.
27. Bentley WE, Mirjalili N, Andersen DC, Davis RH, Kompala DS (1990) Plasmid-encoded protein: The principal factor in the "metabolic burden" associated with recombinant bacteria. Biotechnol Bioeng 35(7):668-681.
28. Moyed HSB, Bertrand KP (1983) Mutations in multicopy Tn10 tet plasmids that confer resistance to inhibitory effects of inducers of tet gene expression. J Bacteriol 155(2): 557-564.
29. Dodd IB, Perkins AJ, Tsemitsidis D, Egan JB (2001) Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. Genes Dev 15(22):3013-3022.
30. Bailone A, Levine A, Devoret R (1979) Inactivation of prophage lambda repressor in vivo. J Mol Biol 131(3):553-572.
31. Morelli MJ, Ten Wolde PR, Allen RJ (2009) DNA looping provides stability and robustness to the bacteriophage lambda switch. Proc Natl Acad Sci USA 106(20): 8101-8106.
32. Thomason L, et al. (2007) Recombineering: genetic engineering in bacteria using homologous recombination. Curr Protoc Mol Biol Chapter 1:16.
33. Novick A, Szilard L (1950) Experiments with the Chemostat on spontaneous mutations of bacteria. Proc Natl Acad Sci USA 36(12):708-719.
34. Foucault ML, Thomas L, Goussard S, Branchini BR, Grillot-Courvalin C (2010) In vivo bioluminescence imaging for the study of intestinal colonization by Escherichia coli in mice. Appl Environ Microbiol 76(1):264-274.
35. Böcker R, Warnke L, Estler CJ (1984) Blood and organ concentrations of tetracycline and doxycycline in female mice. Comparison to males. Arzneimittelforschung 34(4): 446-448.
36. Gupta S, Bram EE, Weiss R (2013) Genetically programmable pathogen sense and destroy. ACS Synth Biol 2(12):715-723.
37. Hwang IY, et al. (2013) Reprogramming microbes to be pathogen-seeking killers. ACS Synth Biol, 10.1021/sb400077j.
38. Duan F, March JC (2010) Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. Proc Natl Acad Sci USA 107(25):11260-11264.
39. Higuchi R, Krummel B, Saiki RK (1988) A general method of in vitro preparation and specific mutagenesis of DNA fragments: Study of protein and DNA interactions. Nucleic Acids Res 16(15):7351-7367.
40. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97(12):6640-6645.
41. Timms AR, Steingrimsdottir H, Lehmann AR, Bridges BA (1992) Mutant sequences in the rpsL gene of Escherichia coli B/r: Mechanistic implications for spontaneous and ultraviolet light mutagenesis. Mol Gen Genet 232(1):89-96.
42. Springer B, et al. (2001) Mechanisms of streptomycin resistance: Selection of mutations in the 16S rRNA gene conferring resistance. Antimicrob Agents Chemother 45(10):2877-2884.
43. Miller JH (1972) Experiments in Molecular Genetics (Cold Spring Harbor Lab Press, Cold Spring Harbor, N.Y.), pp xvi, 466 pp.
44. Sanger F, Coulson AR, Hong GF, Hill DF, Petersen GB (1982) Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol 162(4):729-773.
45. Blattner FR, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277(5331):1453-1462.
46. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173(2):697-703.