1932

Abstract

Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry—biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-biophys-070816-033903
2018-05-20
2024-06-22
Loading full text...

Full text loading...

/deliver/fulltext/biophys/47/1/annurev-biophys-070816-033903.html?itemId=/content/journals/10.1146/annurev-biophys-070816-033903&mimeType=html&fmt=ahah

Literature Cited

  1. 1.  Alon U. 2003. Biological networks: the tinkerer as an engineer. Science 301:1866–67
    [Google Scholar]
  2. 2.  Appleton E, Madsen C, Roehner N, Densmore D 2017. Design automation in synthetic biology. Cold Spring Harb. Perspect. Biol. 9:a023978
    [Google Scholar]
  3. 3.  Barrett CL, Kim TY, Kim HU, Palsson BO, Lee SY 2006. Systems biology as a foundation for genome-scale synthetic biology. Curr. Opin. Biotechnol. 17:488–92
    [Google Scholar]
  4. 4.  Bashor CJ, Helman NC, Yan S, Lim WA 2008. Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319:1539–43
    [Google Scholar]
  5. 5.  Bashor CJ, Horwitz AA, Peisajovich SG, Lim WA 2010. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annu. Rev. Biophys. 39:515–37
    [Google Scholar]
  6. 6.  Becskei A, Seraphin B, Serrano L 2001. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J 20:2528–35
    [Google Scholar]
  7. 7.  Becskei A, Serrano L 2000. Engineering stability in gene networks by autoregulation. Nature 405:590–93
    [Google Scholar]
  8. 8.  Bintu L, Yong J, Antebi YE, McCue K, Kazuki Y et al. 2016. Dynamics of epigenetic regulation at the single-cell level. Science 351:720–24
    [Google Scholar]
  9. 9.  Blake WJ, Kærn M, Cantor CR, Collins JJ 2003. Noise in eukaryotic gene expression. Nature 422:633–37
    [Google Scholar]
  10. 10.  Bonnet J, Subsoontorn P, Endy D 2012. Rewritable digital data storage in live cells via engineered control of recombination directionality. PNAS 109:8884–89
    [Google Scholar]
  11. 11.  Bonnet J, Yin P, Ortiz ME, Subsoontorn P, Endy D 2013. Amplifying genetic logic gates. Science 340:599–603
    [Google Scholar]
  12. 12.  Brophy JA, Voigt CA 2014. Principles of genetic circuit design. Nat. Methods 11:508–20
    [Google Scholar]
  13. 13.  Çağatay T, Turcotte M, Elowitz MB, Garcia-Ojalvo J, Süel GM 2009. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139:512–22
    [Google Scholar]
  14. 14.  Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR, Collins JJ 2010. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. PNAS 107:15898–903
    [Google Scholar]
  15. 15.  Cameron DE, Bashor CJ, Collins JJ 2014. A brief history of synthetic biology. Nat. Rev. Microbiol. 12:381–90
    [Google Scholar]
  16. 16.  Cameron DE, Collins JJ 2014. Tunable protein degradation in bacteria. Nat. Biotechnol. 32:1276–81
    [Google Scholar]
  17. 17.  Carroll SB. 2008. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134:25–36
    [Google Scholar]
  18. 18.  Ceroni F, Algar R, Stan GB, Ellis T 2015. Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat. Methods 12:415–18
    [Google Scholar]
  19. 19.  Chau AH, Walter JM, Gerardin J, Tang C, Lim WA 2012. Designing synthetic regulatory networks capable of self-organizing cell polarization. Cell 151:320–32
    [Google Scholar]
  20. 20.  Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M et al. 2015. Highly efficient Cas9-mediated transcriptional programming. Nat. Methods 12:326–28
    [Google Scholar]
  21. 21.  Chen Y, Kim JK, Hirning AJ, Josić K, Bennett MR 2015. Emergent genetic oscillations in a synthetic microbial consortium. Science 349:986–89
    [Google Scholar]
  22. 22.  Danino T, Mondragon-Palomino O, Tsimring L, Hasty J 2010. A synchronized quorum of genetic clocks. Nature 463:326–30
    [Google Scholar]
  23. 23.  Del Vecchio D, Dy AJ, Qian Y 2016. Control theory meets synthetic biology. J. R. Soc. Interface 13:20160380
    [Google Scholar]
  24. 24.  Detwiler PB, Ramanathan S, Sengupta A, Shraiman BI 2000. Engineering aspects of enzymatic signal transduction: photoreceptors in the retina. Biophys. J. 79:2801–17
    [Google Scholar]
  25. 25.  Dueber JE, Yeh BJ, Chak K, Lim WA 2003. Reprogramming control of an allosteric signaling switch through modular recombination. Science 301:1904–8
    [Google Scholar]
  26. 26.  Dunlap JC. 1999. Molecular bases for circadian clocks. Cell 96:271–90
    [Google Scholar]
  27. 27.  Ellis T, Adie T, Baldwin GS 2011. DNA assembly for synthetic biology: from parts to pathways and beyond. Integr. Biol. 3:109–18
    [Google Scholar]
  28. 28.  Elowitz MB, Leibler S 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403:335–38
    [Google Scholar]
  29. 29.  Elowitz MB, Levine AJ, Siggia ED, Swain PS 2002. Stochastic gene expression in a single cell. Science 297:1183–86
    [Google Scholar]
  30. 30.  Elowitz MB, Lim WA 2010. Build life to understand it. Nature 468:889–90
    [Google Scholar]
  31. 31.  Endy D. 2005. Foundations for engineering biology. Nature 438:449–53
    [Google Scholar]
  32. 32.  Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD et al. 2011. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473:43–49
    [Google Scholar]
  33. 33.  Erwin DH, Davidson EH 2009. The evolution of hierarchical gene regulatory networks. Nat. Rev. Genet. 10:141–48
    [Google Scholar]
  34. 34.  Farzadfard F, Lu TK 2014. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science 346:1256272
    [Google Scholar]
  35. 35.  Fischbach MA, Bluestone JA, Lim WA 2013. Cell-based therapeutics: the next pillar of medicine. Sci. Transl. Med. 5:179ps7
    [Google Scholar]
  36. 36.  Fischbach MA, Voigt CA 2010. Prokaryotic gene clusters: a rich toolbox for synthetic biology. Biotechnol. J. 5:1277–96
    [Google Scholar]
  37. 37.  Frieda KL, Linton JM, Hormoz S, Choi J, Chow KK et al. 2017. Synthetic recording and in situ readout of lineage information in single cells. Nature 541:107–11
    [Google Scholar]
  38. 38.  Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ 2009. Synthetic gene networks that count. Science 324:1199–202
    [Google Scholar]
  39. 39.  Gardner TS, Cantor CR, Collins JJ 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403:339–42
    [Google Scholar]
  40. 40.  Gordley RM, Bugaj LJ, Lim WA 2016. Modular engineering of cellular signaling proteins and networks. Curr. Opin. Struct. Biol. 39:106–14
    [Google Scholar]
  41. 41.  Gordley RM, Williams RE, Bashor CJ, Toettcher JE, Yan S, Lim WA 2016. Engineering dynamical control of cell fate switching using synthetic phospho-regulons. PNAS 113:13528–33
    [Google Scholar]
  42. 42.  Green AA, Silver PA, Collins JJ, Yin P 2014. Toehold switches: de-novo-designed regulators of gene expression. Cell 159:925–39
    [Google Scholar]
  43. 43.  Guido NJ, Lee P, Wang X, Elston TC, Collins JJ 2007. A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophys. J. 93:L55–57
    [Google Scholar]
  44. 44.  Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J et al. 2006. A bottom-up approach to gene regulation. Nature 439:856–60
    [Google Scholar]
  45. 45.  Hannon GJ, Rossi JJ 2004. Unlocking the potential of the human genome with RNA interference. Nature 431:371–78
    [Google Scholar]
  46. 46.  Hartwell LH, Hopfield JJ, Leibler S, Murray AW 1999. From molecular to modular cell biology. Nature 402:C47–52
    [Google Scholar]
  47. 47.  Hasty J, Dolnik M, Rottschafer V, Collins JJ 2002. Synthetic gene network for entraining and amplifying cellular oscillations. Phys. Rev. Lett. 88:148101
    [Google Scholar]
  48. 48.  Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE et al. 2015. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33:510–17
    [Google Scholar]
  49. 49.  Hodgkin AL, Huxley AF 1952. A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. 117:500–44
    [Google Scholar]
  50. 50.  Howard PL, Chia MC, Del Rizzo S, Liu FF, Pawson T 2003. Redirecting tyrosine kinase signaling to an apoptotic caspase pathway through chimeric adaptor proteins. PNAS 100:11267–72
    [Google Scholar]
  51. 51.  Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ 2004. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22:841–47
    [Google Scholar]
  52. 52.  Isaacs FJ, Hasty J, Cantor CR, Collins JJ 2003. Prediction and measurement of an autoregulatory genetic module. PNAS 100:7714–19
    [Google Scholar]
  53. 53.  Isalan M, Lemerle C, Michalodimitrakis K, Horn C, Beltrao P et al. 2008. Evolvability and hierarchy in rewired bacterial gene networks. Nature 452:840–45
    [Google Scholar]
  54. 54.  Jacob F, Monod J 1961. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3:318–56
    [Google Scholar]
  55. 55.  Jenuwein T, Allis CD 2001. Translating the histone code. Science 293:1074–80
    [Google Scholar]
  56. 56.  Jones DL, Brewster RC, Phillips R 2014. Promoter architecture dictates cell-to-cell variability in gene expression. Science 346:1533–36
    [Google Scholar]
  57. 57.  Jusiak B, Cleto S, Perez-Pinera P, Lu TK 2016. Engineering synthetic gene circuits in living cells with CRISPR technology. Trends Biotechnol 34:535–47
    [Google Scholar]
  58. 58.  Kærn M, Blake WJ, Collins JJ 2003. The engineering of gene regulatory networks. Annu. Rev. Biomed. Eng. 5:179–206
    [Google Scholar]
  59. 59.  Keung AJ, Bashor CJ, Kiriakov S, Collins JJ, Khalil AS 2014. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell 158:110–20
    [Google Scholar]
  60. 60.  Khalil AS, Collins JJ 2010. Synthetic biology: applications come of age. Nat. Rev. Genet. 11:367–79
    [Google Scholar]
  61. 61.  Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC et al. 2012. A synthetic biology framework for programming eukaryotic transcription functions. Cell 150:647–58
    [Google Scholar]
  62. 62.  Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN et al. 2014. CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nat. Methods 11:723–26
    [Google Scholar]
  63. 63.  Kirschner M, Gerhart J 1998. Evolvability. PNAS 95:8420–27
    [Google Scholar]
  64. 64.  Kornberg A. 1960. Biologic synthesis of deoxyribonucleic acid. Science 131:1503–8
    [Google Scholar]
  65. 65.  Lee JW, Gyorgy A, Cameron DE, Pyenson N, Choi KR et al. 2016. Creating single-copy genetic circuits. Mol. Cell 63:329–36
    [Google Scholar]
  66. 66.  Liu AP, Fletcher DA 2009. Biology under construction: in vitro reconstitution of cellular function. Nat. Rev. Mol. Cell Biol. 10:644–50
    [Google Scholar]
  67. 67.  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 25:1203–10
    [Google Scholar]
  68. 68.  McAdams HH, Arkin A 1997. Stochastic mechanisms in gene expression. PNAS 94:814–19
    [Google Scholar]
  69. 69.  Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U 2002. Network motifs: simple building blocks of complex networks. Science 298:824–27
    [Google Scholar]
  70. 70.  Nielsen AA, Der BS, Shin J, Vaidyanathan P, Paralanov V et al. 2016. Genetic circuit design automation. Science 352:aac7341
    [Google Scholar]
  71. 71.  Nielsen J, Keasling JD 2016. Engineering cellular metabolism. Cell 164:1185–97
    [Google Scholar]
  72. 72.  Nocedal I, Johnson AD 2015. How transcription networks evolve and produce biological novelty. Cold Spring Harb. Symp. Quant. Biol. 80:265–74
    [Google Scholar]
  73. 73.  O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA 2011. Tunable signal processing in synthetic MAP kinase cascades. Cell 144:119–31
    [Google Scholar]
  74. 74.  Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A 2002. Regulation of noise in the expression of a single gene. Nat. Genet. 31:69–73
    [Google Scholar]
  75. 75.  Panne D. 2008. The enhanceosome. Curr. Opin. Struct. Biol. 18:236–42
    [Google Scholar]
  76. 76.  Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A et al. 2014. Paper-based synthetic gene networks. Cell 159:940–54
    [Google Scholar]
  77. 77.  Pardee K, Green AA, Takahashi MK, Braff D, Lambert G et al. 2016. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165:1255–66
    [Google Scholar]
  78. 78.  Pardee K, Slomovic S, Nguyen PQ, Lee JW, Donghia N et al. 2016. Portable, on-demand biomolecular manufacturing. Cell 167:248–59.e12
    [Google Scholar]
  79. 79.  Park SH, Zarrinpar A, Lim WA 2003. Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 299:1061–64
    [Google Scholar]
  80. 80.  Pawson T. 1995. Protein modules and signalling networks. Nature 373:573–80
    [Google Scholar]
  81. 81.  Pedraza JM, van Oudenaarden A 2005. Noise propagation in gene networks. Science 307:1965–69
    [Google Scholar]
  82. 82.  Potvin-Trottier L, Lord ND, Vinnicombe G, Paulsson J 2017. Synchronous long-term oscillations in a synthetic gene circuit. Nature 538:514–17
    [Google Scholar]
  83. 83.  Prindle A, Selimkhanov J, Li H, Razinkov I, Tsimring LS, Hasty J 2014. Rapid and tunable post-translational coupling of genetic circuits. Nature 508:387–91
    [Google Scholar]
  84. 8484.  Ptashne M, Johnson AD, Pabo CO 1982. A genetic switch in a bacterial virus. Sci. Am. 247:128–40
    [Google Scholar]
  85. 85.  Purnick PE, Weiss R 2009. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10:410–22
    [Google Scholar]
  86. 86.  Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS et al. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–83
    [Google Scholar]
  87. 87.  Razooky BS, Pai A, Aull K, Rouzine IM, Weinberger LS 2015. A hardwired HIV latency program. Cell 160:990–1001
    [Google Scholar]
  88. 88.  Rice MK, Ruder WC 2014. Creating biological nanomaterials using synthetic biology. Sci. Technol. Adv. Mater. 15:014401
    [Google Scholar]
  89. 89.  Roquet N, Soleimany AP, Ferris AC, Aaronson S, Lu TK 2016. Synthetic recombinase-based state machines in living cells. Science 353:aad8559
    [Google Scholar]
  90. 90.  Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB 2005. Gene regulation at the single-cell level. Science 307:1962–65
    [Google Scholar]
  91. 91.  Ruder WC, Lu T, Collins JJ 2011. Synthetic biology moving into the clinic. Science 333:1248–52
    [Google Scholar]
  92. 92.  Siuti P, Yazbek J, Lu TK 2013. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31:448–52
    [Google Scholar]
  93. 93.  Slomovic S, Collins JJ 2015. DNA sense-and-respond protein modules for mammalian cells. Nat. Methods 12:1085–90
    [Google Scholar]
  94. 94.  Slomovic S, Pardee K, Collins JJ 2015. Synthetic biology devices for in vitro and in vivo diagnostics. PNAS 112:14429–35
    [Google Scholar]
  95. 95.  Smanski MJ, Bhatia S, Zhao D, Park Y, Woodruff LBA et al. 2014. Functional optimization of gene clusters by combinatorial design and assembly. Nat. Biotechnol. 32:1241–49
    [Google Scholar]
  96. 96.  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. 10:99–105
    [Google Scholar]
  97. 97.  Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J 2008. A fast, robust and tunable synthetic gene oscillator. Nature 456:516–19
    [Google Scholar]
  98. 98.  Süel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB 2006. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440:545–50
    [Google Scholar]
  99. 99.  Süel GM, Kulkarni RP, Dworkin J, Garcia-Ojalvo J, Elowitz MB 2007. Tunability and noise dependence in differentiation dynamics. Science 315:1716–19
    [Google Scholar]
  100. 100.  Tigges M, Fussenegger M 2009. Recent advances in mammalian synthetic biology—design of synthetic transgene control networks. Curr. Opin. Biotechnol. 20:449–60
    [Google Scholar]
  101. 101.  Toprak E, Veres A, Yildiz S, Pedraza JM, Chait R et al. 2013. Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition. Nat. Protoc. 8:555–67
    [Google Scholar]
  102. 102.  Ubersax JA, Ferrell JE Jr. 2007. Mechanisms of specificity in protein phosphorylation. Nat. Rev. Mol. Cell Biol. 8:530–41
    [Google Scholar]
  103. 103.  Weinberg BH, Pham NTH, Caraballo LD, Lozanoski T, Engel A et al. 2017. Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nat. Biotechnol. 35:453–62
    [Google Scholar]
  104. 104.  Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV 2005. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122:169–82
    [Google Scholar]
  105. 105.  Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y 2011. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333:1307–11
    [Google Scholar]
  106. 106.  Yeh BJ, Rutigliano RJ, Deb A, Bar-Sagi D, Lim WA 2007. Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors. Nature 447:596–600
    [Google Scholar]
  107. 107.  Yeung E, Dy AJ, Martin KB, Ng AH, Del Vecchio D et al. 2017. Biophysical constraints arising from compositional context in synthetic gene networks. Cell Syst 5:11–24.e12
    [Google Scholar]
  108. 108.  Young RA. 2011. Control of the embryonic stem cell state. Cell 144:940–54
    [Google Scholar]
/content/journals/10.1146/annurev-biophys-070816-033903
Loading
/content/journals/10.1146/annurev-biophys-070816-033903
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error