Layering genetic circuits to build a single cell, bacterial half adder

BMC Biology

Volumn 13, Issue 1, 2015, Pages

  Wong, Adison ^a,b,c   Wang, Huijuan ^a   Poh, Chueh Loo ^a   Kitney, Richard I ^b  

^a Nanyang Technological University   (Singapore)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); PROKARYOTA;

5' UNTRANSLATED REGION;

5' UNTRANSLATED REGION; ESCHERICHIA COLI; GENE REGULATORY NETWORK; GENETICS; MOLECULAR COMPUTER; PROCEDURES; PROMOTER REGION; SYNTHETIC BIOLOGY;

5' UNTRANSLATED REGIONS; COMPUTERS, MOLECULAR; ESCHERICHIA COLI; GENE REGULATORY NETWORKS; PROMOTER REGIONS, GENETIC; SYNTHETIC BIOLOGY;

EID: 84936134628     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/s12915-015-0146-0     Document Type: Article

References (50)

1. Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U. Plasticity of the cis-regulatory input function of a gene. PLoS Biol. 2006;4:e45.
2. Peter IS, Faure E, Davidson EH. Predictive computation of genomic logic processing functions in embryonic development. Proc Natl Acad Sci U S A. 2012;109:16434-42.
3. Thomas R. Boolean formalization of genetic control circuits. J Theor Biol. 1973;42:563-85.
4. Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, et al. A synthetic biology framework for programming eukaryotic transcription functions. Cell. 2012;150:647-58.
5. Lou C, Stanton B, Chen Y-J, Munsky B, Voigt CA. Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat Biotechnol. 2012;30:1137-42.
6. Mutalik VK, Guimaraes JC, Cambray G, Lam C, Christoffersen MJ, Mai Q-A, et al. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods. 2013;10:354-60.
7. Cardinale S, Joachimiak Marcin P, Arkin Adam P. Effects of genetic variation on the E. coli host-circuit interface. Cell Reports. 2013;4:231-7.
8. Cardinale S, Arkin AP. Contextualizing context for synthetic biology - identifying causes of failure of synthetic biological systems. Biotechnol J. 2012;7:856-66.
9. Rackham O, Chin JW. A network of orthogonal ribosome-mRNA pairs. Nat Chem Biol. 2005;1:159-66.
10. Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA. Genetic programs constructed from layered logic gates in single cells. Nature. 2012;491:249-53.
11. Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci U S A. 2011;108:8617-22.
12. Wang B, Kitney RI, Joly N, Buck M. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat Commun. 2011;2:508.
13. An W, Chin JW. Synthesis of orthogonal transcription-translation networks. Proc Natl Acad Sci U S A. 2009;106:8477-82.
14. Auslander S, Auslander D, Muller M, Wieland M, Fussenegger M. Programmable single-cell mammalian biocomputers. Nature. 2012;487:123-7.
15. Siuti P, Yazbek J, Lu TK. Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol. 2013;31:448-52.
16. Bonnet J, Yin P, Ortiz ME, Subsoontorn P, Endy D. Amplifying genetic logic gates. Science. 2013;340:599-603.
17. Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature. 2000;403:339-42.
18. Friedland A, Lu T, Wang X, Shi D, Church G, Collins J. Synthetic gene networks that count. Science. 2009;324:1199-202.
19. Bonnet J, Subsoontorn P, Endy D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci U S A. 2012;109:8884-9.
20. Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin AP. RNA processing enables predictable programming of gene expression. Nat Biotechnol. 2012;30:1002-6.
21. Nikel PI, Martinez-Garcia E, de Lorenzo V. Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol. 2014;12:368-79.
22. Chen ZY, Guo LL, Zhang YQ, Walzem RL, Pendergast JS, Printz RL, et al. Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity. J Clin Invest. 2014;124:3391-406.
23. Xiang S, Fruehauf J, Li CJ. Short hairpin RNA-expressing bacteria elicit RNA interference in mammals. Nat Biotechnol. 2006;24:697-702.
24. Duan F, March JC. Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. Proc Natl Acad Sci U S A. 2010;107:11260-4.
25. Saeidi N, Wong CK, Lo TM, Nguyen HX, Ling H, Leong SSJ, et al. Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Mol Syst Biol. 2011;7:521.
26. Callura J, Dwyer D, Isaacs F, Cantor C, Collins J. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc Natl Acad Sci U S A. 2010;107:15898-903.
27. Callura JM, Cantor CR, Collins JJ. Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci U S A. 2012;109:5850-5.
28. Temme K, Hill R, Segall-Shapiro TH, Moser F, Voigt CA. Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Res. 2012;40:8773-81.
29. Collins CH, Leadbetter JR, Arnold FH. Dual selection enhances the signaling specificity of a variant of the quorum-sensing transcriptional activator LuxR. Nat Biotechnol. 2006;24:708-12.
30. Canton B, Labno A, Endy D. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol. 2008;26:787-93.
31. Lee SK, Chou HH, Pfleger BF, Newman JD, Yoshikuni Y, Keasling JD. Directed evolution of AraC for improved compatibility of arabinose- and lactose-inducible promoters. Appl Environ Microb. 2007;73:5711-5.
32. Laub MT, Goulian M. Specificity in two-component signal transduction pathways. Annu Rev Genet. 2007;41:121-45.
33. Yu BJ, Kang KH, Lee JH, Sung BH, Kim MS, Kim SC. Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Res. 2008;36:e84.
34. Bloodworth RAM, Gislason AS, Cardona ST. Burkholderia cenocepacia conditional growth mutant library created by random promoter replacement of essential genes. Microbiology Open. 2013;2:243-58.
35. Cardona ST, Mueller CL, Valvano MA. Identification of essential operons with a rhamnose-inducible promoter in Burkholderia cenocepacia. Appl Environ Microb. 2006;72:2547-55.
36. Shis DL, Bennett MR. Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants. Proc Natl Acad Sci U S A. 2013;110:5028-33.
37. Anderson JC, Voigt CA, Arkin AP. Environmental signal integration by a modular AND gate. Mol Syst Biol. 2007;3:133.
38. Tamsir A, Tabor JJ, Voigt CA. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature. 2011;469:212-5.
39. Glick BR. Metabolic load and heterologous gene expression. Biotechnol Adv. 1995;13:247-61.
40. Benson N, Sugiono P, Youderian P. DNA sequence determinants of lambda repressor binding in vivo. Genetics. 1988;118:21-9.
41. Andersen JB, Sternberg C, Poulsen LK, Bjørn SP, Givskov M, Molin S. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ Microb. 1998;64:2240-6.
42. Daniel R, Rubens JR, Sarpeshkar R, Lu TK. Synthetic analog computation in living cells. Nature. 2013;497:619-23.
43. Kitney R, Freemont P. Synthetic biology - the state of play. FEBS Lett. 2012;586:2029-36.
44. Tabor J, Salis H, Simpson Z, Chevalier A, Levskaya A, Marcotte E, et al. A synthetic genetic edge detection program. Cell. 2009;137:1272-81.
45. Zhang H, Lin M, Shi H, Ji W, Huang L, Zhang X, et al. Programming a Pavlovian-like conditioning circuit in Escherichia coli. Nat Commun. 2014;5:3102.
46. Wang JT, Syed A, Gralla JD. Multiple pathways to bypass the enhancer requirement of sigma 54 RNA polymerase: roles for DNA and protein determinants. Proc Natl Acad Sci U S A. 1997;94:9538-43.
47. Wang JT, Syed A, Hsieh M, Gralla JD. Converting Escherichia coli RNA polymerase into an enhancer-responsive enzyme: role of an NH2-terminal leucine patch in sigma 54. Science. 1995;270:992-4.
48. Brophy JAN, Voigt CA. Principles of genetic circuit design. Nat Methods. 2014;11:508-20.
49. Slusarczyk AL, Lin A, Weiss R. Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet. 2012;13:406-20.
50. Rhodius VA, Segall-Shapiro TH, Sharon BD, Ghodasara A, Orlova E, Tabakh H, et al. Design of orthogonal genetic switches based on a crosstalk map of rs, anti-rs, and promoters. Mol Syst Biol. 2013;9:702.