Enabling complex genetic circuits to respond to extrinsic environmental signals

Biotechnology and Bioengineering

Volumn 114, Issue 7, 2017, Pages 1626-1631

  Hoynes O'Connor, Allison ^a   Shopera, Tatenda ^a   Hinman, Kristina ^a   Creamer, John Philip ^b   Moon, Tae Seok ^a,b  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^b WASHINGTON UNIVERSITY   (United States)

Author keywords

AND gate; genetic circuit; genetic sensor; NAND gate; synthetic biology

Indexed keywords

ESCHERICHIA COLI; METABOLIC ENGINEERING; NAND CIRCUITS; RNA; SALMONELLA; TIMING CIRCUITS;

AND GATE; ENVIRONMENTAL CHALLENGES; GENETIC CIRCUITS; NAND GATE; PH- AND TEMPERATURE-RESPONSIVE; SALMONELLA TYPHIMURIUM; SYNTHETIC BIOLOGY; TYPE III SECRETION SYSTEM;

HYDROGELS;

COMPLEMENTARY RNA; TYPE III SECRETION SYSTEM;

ARTICLE; BACTERIAL GENOME; ESCHERICHIA COLI; GENETICS; NONHUMAN; PH; PROMOTER REGION; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; TEMPERATURE; TYPE III SECRETION SYSTEM; GENE REGULATORY NETWORK; MOLECULAR COMPUTER; PROCEDURES; SIGNAL PROCESSING; SIGNAL TRANSDUCTION; SYNTHETIC BIOLOGY;

COMPUTERS, MOLECULAR; ESCHERICHIA COLI; GENE REGULATORY NETWORKS; SALMONELLA TYPHIMURIUM; SIGNAL PROCESSING, COMPUTER-ASSISTED; SIGNAL TRANSDUCTION; SYNTHETIC BIOLOGY; TYPE III SECRETION SYSTEMS;

EID: 85019650173     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.26279     Document Type: Article

References (26)

1. Bacchus W, Aubel D, Fussenegger M. 2013. Biomedically relevant circuit-design strategies in mammalian synthetic biology. Mol Syst Biol 9:1–12.
2. Bradley RW, Buck M, Wang B. 2016. Tools and principles for microbial gene circuit engineering. J Mol Biol 428(5):862–888.
3. Brandi A, Spurio R, Gualerzi CO, Pon CL. 1999. Massive presence of the Escherichia coli “major cold-shock protein” CspA under non-stress conditions. EMBO J 18(6):1653–1659.
4. Brophy JAN, Voigt CA. 2014. Principles of genetic circuit design. Nat Methods 11(5):508–520.
5. Cress BF, Trantas EA, Ververidis F, Linhardt RJ, Koffas MA. 2015. Sensitive cells: Enabling tools for static and dynamic control of microbial metabolic pathways. Curr Opin Biotechnol 36:205–214.
6. Darwin KH, Miller VL. 2001. Type III secretion chaperone-dependent regulation: Activation of virulence genes by SicA and InvF in Salmonella typhimurium. Embo J 20(8):1850–1862.
7. Ding M, Li R, He R, Wang X, Yi Q, Wang W. 2015. P53 activated by AND gate genetic circuit under radiation and hypoxia for targeted cancer gene therapy. Cancer Sci 106(9):1163–1173.
8. Engler C, Kandzia R, Marillonnet S. 2008. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3(11):e3647.
9. Giuliodori AM, Di Pietro F, Marzi S, Masquida B, Wagner R, Romby P, Gualerzi CO, Pon CL. 2010. The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA. Mol Cell 37(1):21–33.
10. Glick BR. 1995. Metabolic load and heterologous gene expression. Biotechnol Adv 13(2):247–261.
11. Gualerzi CO, Giuliodori AM, Pon CL. 2003. Transcriptional and post-transcriptional control of cold-shock genes. J Mol Biol 331(3):527–539.
12. Hoynes-O'Connor A, Hinman K, Kirchner L, Moon TS. 2015. De novo design of heat-repressible RNA thermosensors in E. coli. Nucleic Acids Res 43(12):6166–6179.
13. Hoynes-O'Connor A, Moon TS. 2015. Programmable genetic circuits for pathway engineering. Curr Opin Biotechnol 36:115–121.
14. Hoynes-O'Connor A, Moon TS. 2016. Development of design rules for reliable antisense RNA behavior in E. coli. ACS Synth Biol 5(12):1441–1454.
15. Immethun CM, Ng KM, DeLorenzo DM, Waldron-Feinstein B, Lee YC, Moon TS. 2016. Oxygen-responsive genetic circuits constructed in Synechocystis sp. PCC 6803. Biotechnol Bioeng 113(2):433–442.
16. Lu P, Vogel C, Wang R, Yao X, Marcotte EM. 2007. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25(1):117–124.
17. Ma KC, Perli SD, Lu TK. 2016. Foundations and emerging paradigms for computing in living cells. J Mol Biol 428(5):893–915.
18. Ogasawara H, Hasegawa A, Kanda E, Miki T, Yamamoto K, Ishihama A. 2007. Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade. J Bacteriol 189(13):4791–4799.
19. Polizzi KM, Kontoravdi C. 2015. Genetically-encoded biosensors for monitoring cellular stress in bioprocessing. Curr Opin Biotechnol 31:50–56.
20. Raman S, Rogers JK, Taylor ND, Church GM. 2014. Evolution-guided optimization of biosynthetic pathways. Proc Natl Acad Sci USA 111(50):17803–17808.
21. Rogers JK, Church GM. 2016. Genetically encoded sensors enable real-time observation of metabolite production. Proc Natl Acad Sci USA 113(9):2388–2393.
22. Schukur L, Fussenegger M. 2016. Engineering of synthetic gene circuits for (re-)balancing physiological processes in chronic diseases. Wiley Interdiscip Rev Syst Biol Med 8(5):402–422.
23. Wang B, Barahona M, Buck M. 2013. A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals. Biosens Bioelectron 40(1):368–376.
24. Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y. 2011. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333(6047):1307–1311.
25. Yamanaka K, Mitta M, Inouye M. 1999. Mutation analysis of the 5′ untranslated region of the cold shock cspA mRNA of Escherichia coli. J Bacteriol 181(20):6284–6291.
26. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406–3415.