Recent advances and opportunities in synthetic logic gates engineering in living cells

Alper H, Fischer C, Nevoigt E, Stephanopoulos G (2005) Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA 102(36):12678–12683 Anderson JC, Voigt CA, Arkin AP (2007) Environmental signal integration by a modular AND gate. Mol Syst Biol 3:133 Atkinson MR, Savageau MA, Myers JT, Ninfa AJ (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113(5):597–607 Ausländer S, Ausländer D, Müller M, Wieland M, Fussenegger M (2012) Programmable single-cell mammalian biocomputers. Nature 487(7405):123–127 Bagh S, Mandal M, McMillen DR (2010) Minimal genetic device with multiple tunable functions. Phys Rev E 82(2):021911 Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R (2005) A synthetic multicellular system for programmed pattern formation. Nature 434(7037):1130–1134 Blount KF, Breaker RR (2006) Riboswitches as antibacterial drug targets. Nat Biotechnol 24(12):1558–1564 Bonnet J, Yin P, Ortiz ME, Subsoontorn P, Endy D (2013) Amplifying genetic logic gates. Science 340(6132):599–603 Brophy JA, Voigt CA (2014) Principles of genetic circuit design. Nat Methods 11(5):508–520 Danino T, Mondragón-Palomino O, Tsimring L, Hasty J (2010) A synchronized quorum of genetic clocks. Nature 463(7279):326–330 Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, Keasling JD (2009) Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 27(8):753–759 Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335–338 Endy D (2005) Foundations for engineering biology. Nature 438(7067):449–453 Frezza BM, Cockroft SL, Ghadiri MR (2007) Modular multi-level circuits from immobilized DNA-based logic gates. J Am Chem Soc 129(48):14875–14879 Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ (2009) Synthetic gene networks that count. Science 324(5931):1199–1202 Gaber R, Lebar T, Majerle A, Šter B, Dobnikar A, Benčina M, Jerala R (2014) Designable DNA-binding domains enable construction of logic circuits in mammalian cells. Nat Chem Biol 10(3):203–208 Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767):339–342 Gerasimova YV, Kolpashchikov DM (2012) Connectable DNA logic gates: OR and XOR logics. Chem Asian J 7(3):534–540 Giot L, DeMattei C, Konopka JB (1999) Combining mutations in the incoming and outgoing pheromone signal pathways causes a synergistic mating defect in Saccharomyces cerevisiae. Yeast 15(9):765–780 Goñi-Moreno A, Amos M (2012) A reconfigurable NAND/NOR genetic logic gate. BMC Syst Biol 6:126 Goñi-Moreno A, Amos M, de la Cruz F (2013) Multicellular computing using conjugation for wiring. PLoS ONE 8(6):e65986 Guet CC, Elowitz MB, Hsing W, Leibler S (2002) Combinatorial synthesis of genetic networks. Science 296(5572):1466–1470 Hoffman-Sommer M, Supady A, Klipp E (2012) Cell-to-cell communication circuits: quantitative analysis of synthetic logic gates. Front Physiol 3:287 Huang H, Liu H, Gan YR (2010) Genetic modification of critical enzymes and involved genes in butanol biosynthesis from biomass. Biotechnol Adv 28(5):651–657 Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ (2004) Engineered riboregulators enable posttranscriptional control of gene expression. Nat Biotechnol 22(7):841–847 Jaeger (1997) Microelectronic circuit design, McGraw-Hill, ISBN 0-07-032482-4, pp 226–233 Kramer BP, Fischer C, Fussenegger M (2004) BioLogic gates enable logical transcription control in mammalian cells. Biotechnol Bioeng 87(4):478–484 Krivoruchko A, Siewers V, Nielsen J (2011) Opportunities for yeast metabolic engineering: lessons from synthetic biology. Biotechnol J 6(3):262–276 Lutz R, Bujard H (1997) Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res 25(6):1203–1210 Macia J, Sole R (2014) How to make a synthetic multicellular computer. PLoS ONE 9(2):e81248 Miyamoto T, Razavi S, DeRose R, Inoue T (2013) Synthesizing biomolecule-based Boolean logic gates. ACS Synth Biol 2(2):72–82 Moe-Behrens GH (2013) The biological microprocessor, or how to build a computer with biological parts. Comput Struct Biotechnol J 7:e201304003 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 Moser F, Broers NJ, Hartmans S, Tamsir A, Kerkman R, Roubos JA, Bovenberg R, Voigt CA (2012) Genetic circuit performance under conditions relevant for industrial bioreactors. ACS Synth Biol 1(11):555–564 Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY (2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol 31(2):170–174 Nevoigt E (2008) Progress in metabolic engineering of Saccharomyces cerevisiae. Microbiol Mol Biol Rev 72(3):379–412 Nissim L, Bar-Ziv RH (2010) A tunable dual-promoter integrator for targeting of cancer cells. Mol Syst Biol 6:444 Park SH, Zarrinpar A, Lim WA (2003) Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 299(5609):1061–1064 Park KS, Seo MW, Jung C, Lee JY, Park HG (2012) Simple and universal platform for logic gate operations based on molecular beacon probes. Small 8(14):2203–2212 Pfleger BF, Pitera DJ, Smolke CD, Keasling JD (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 24(8):1027–1032 Prindle A, Selimkhanov J, Li H, Razinkov I, Tsimring LS, Hasty J (2014) Rapid and tunable post-translational coupling of genetic circuits. Nature 508(7496):387–391 Purcell O, Lu TK (2014) Synthetic analog and digital circuits for cellular computation and memory. Curr Opin Biotechnol 29C:146–155 Regot S, Macia J, Conde N, Furukawa K, Kjellén J, Peeters T, Hohmann S, de Nadal E, Posas F, Solé R (2011) Distributed biological computation with multicellular engineered networks. Nature 469(7329):207–211 Rodrigo G, Landrain TE, Jaramillo A (2012) De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc Natl Acad Sci USA 109(38):15271–15276 Rodrigo G, Landrain TE, Shen S, Jaramillo A (2013) A new frontier in synthetic biology: automated design of small RNA devices in bacteria. Trends Genet 29(9):529–536 Sayut DJ, Niu Y, Sun L (2009) Construction and enhancement of a minimal genetic and logic gate. Appl Environ Microbiol 75(3):637–642 Sayut DJ, Niu Y, Sun L (2011) Engineering the logical properties of a genetic AND gate. Methods Mol Biol 743:175–184 Seelig G, Soloveichik D, Zhang DY, Winfree E (2006) Enzyme-free nucleic acid logic circuits. Science 314(5805):1585–1588 Shis DL, Bennett MR (2013) Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants. Proc Natl Acad Sci USA 110(13):5028–5033 Silva-Rocha R, de Lorenzo V (2014) Engineering multicellular logic in bacteria with metabolic wires. ACS Synth Biol 3(4):204–209 Singh V (2014) Recent advancements in synthetic biology: current status and challenges. Gene 535(1):1–11 Singh V, Mani I, Chaudhary DK, Dhar PK (2014) Metabolic engineering of biosynthetic pathway for production of renewable biofuels. Appl Biochem Biotechnol 172(3):1158–1171 Siuti P, Yazbek J, Lu TK (2013) Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol 31(5):448–452 Soma Y, Tsuruno K, Wada M, Yokota A, Hanai T (2014) Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch. Metab Eng 23:175–184 Sowa SW, Baldea M, Contreras LM (2014) Optimizing metabolite production using periodic oscillations. PLoS Comput Biol 10(6):e1003658 Stanton BC, Nielsen AA, Tamsir A, Clancy K, Peterson T, Voigt CA (2014) Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat Chem Biol 10(2):99–105 Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456(7221):516–519 Tamsir A, Tabor JJ, Voigt CA (2011) Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature 469:212–215 Temme K, Hill R, Segall-Shapiro TH, Moser F, Voigt CA (2012) Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Res 40(17):8773–8781 Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M (2009) A tunable synthetic mammalian oscillator. Nature 457:309–312 Tinder RF (2000) Engineering digital design. Revised second edition. ISBN 0-12-691295-5, pp 317–319 Tucker BJ, Breaker RR (2005) Riboswitches as versatile gene control elements. Curr Opin Struct Biol 15(3):342–348 Wang B, Kitney RI, Joly N, Buck M (2011) Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat Commun 2:508 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 Weber W, Fussenegger M (2011) Molecular diversity-the toolbox for synthetic gene switches and networks. Curr Opin Chem Biol 15:414–420 Win MN, Smolke CD (2008) Higher-order cellular information processing with synthetic RNA devices. Science 322(5900):456–460 Winkler W, Nahvi A, Breaker RR (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419(6910):952–956 Xu P, Li L, Zhang F, Stephanopoulos G, Koffas M (2014) Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc Natl Acad Sci USA 111(31):11299–11304 Zhan J, Ding B, Ma R, Ma X, Su X, Zhao Y, Liu Z, Wu J, Liu H (2010) Develop reusable and combinable designs for transcriptional logic gates. Mol Syst Biol 6:388