From gene switches to mammalian designer cells: Present and future prospects

Trends in Biotechnology

Volumn 31, Issue 3, 2013, Pages 155-168

  Ausländer, Simon ^a   Fussenegger, Martin ^a,b  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF BASEL   (Switzerland)

Author keywords

Biocomputer; Cell implants; Gene circuits; Mammalian gene regulation; Synthetic biology

Indexed keywords

GENES; MAMMALS;

BIOCOMPUTER; CELL IMPLANTS; GENE CIRCUITS; MAMMALIAN GENES; SYNTHETIC BIOLOGY;

CYTOLOGY;

DNA; HYBRID PROTEIN; INSULIN; KRUPPEL LIKE FACTOR; LUCIFERASE; MELANOPSIN; ONCOLYTIC VIRUS; PROTEIN VP16; RNA; TRANSCRIPTION FACTOR YY1;

5' UNTRANSLATED REGION; APOPTOSIS; ASPERGILLUS NIDULANS; BIOTECHNOLOGY; CAULOBACTER CRESCENTUS; CELL THERAPY; CHLAMYDIA TRACHOMATIS; CHLAMYDOPHILA PNEUMONIAE; DEINOCOCCUS RADIODURANS; DNA BINDING; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENE SWITCHING; GOUT; MAMMAL CELL; MAMMALIAN GENETICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PSEUDOMONAS PUTIDA; REVIEW; RHIZOBIUM; RNA DEGRADATION; RNA SPLICING; SACCHAROMYCES CEREVISIAE; YEAST;

MAMMALIA;

EID: 84875268975     PISSN: 01677799     EISSN: 18793096     Source Type: Journal    
DOI: 10.1016/j.tibtech.2012.11.006     Document Type: Review

References (95)

1. Benenson Y. Biomolecular computing systems: principles, progress and potential. Nat. Rev. Genet. 2012, 13:455-468.
2. Davidson E.H. Emerging properties of animal gene regulatory networks. Nature 2010, 468:911-920.
3. Boyle P.M., Silver P.A. Harnessing nature's toolbox: regulatory elements for synthetic biology. J. R. Soc. Interface 2009, 6(Suppl 4):S535-S546.
4. Muller M., et al. A novel reporter system for bacterial and mammalian cells based on the non-ribosomal peptide indigoidine. Metab. Eng. 2012, 14:325-335.
5. Liss M., et al. Embedding permanent watermarks in synthetic genes. PLoS ONE 2012, 7:e42465.
6. Chen Y.Y., et al. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:8531-8536.
7. Xie Z., et al. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 2011, 333:1307-1311.
8. Auslander S., et al. Programmable single-cell mammalian biocomputers. Nature 2012, 487:123-127.
9. Gossen M., Bujard H. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl. Acad. Sci. U.S.A. 1992, 89:5547-5551.
10. Ramos J.L., et al. The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 2005, 69:326-356.
11. Bacchus W., et al. Synthetic two-way communication between mammalian cells. Nat. Biotechnol. 2012, 30:991-996.
12. Cronin C.A., et al. The lac operator-repressor system is functional in the mouse. Genes Dev. 2001, 15:1506-1517.
13. Fussenegger M., et al. Streptogramin-based gene regulation systems for mammalian cells. Nat. Biotechnol. 2000, 18:1203-1208.
14. Gitzinger M., et al. Controlling transgene expression in subcutaneous implants using a skin lotion containing the apple metabolite phloretin. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:10638-10643.
15. Gitzinger M., et al. The food additive vanillic acid controls transgene expression in mammalian cells and mice. Nucleic Acids Res. 2012, 40:e37.
16. Hartenbach S., et al. An engineered L-arginine sensor of Chlamydia pneumoniae enables arginine-adjustable transcription control in mammalian cells and mice. Nucleic Acids Res. 2007, 35:e136.
17. Kemmer C., et al. Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat. Biotechnol. 2010, 28:355-360.
18. Urlinger S., et al. Exploring the sequence space for tetracycline-dependent transcriptional activators: novel mutations yield expanded range and sensitivity. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:7963-7968.
19. Malphettes L., et al. A novel mammalian expression system derived from components coordinating nicotine degradation in arthrobacter nicotinovorans pAO1. Nucleic Acids Res. 2005, 33:e107.
20. Mullick A., et al. The cumate gene-switch: a system for regulated expression in mammalian cells. BMC Biotechnol. 2006, 6:43.
21. Neddermann P., et al. A novel, inducible, eukaryotic gene expression system based on the quorum-sensing transcription factor TraR. EMBO Rep. 2003, 4:159-165.
22. Weber W., et al. Macrolide-based transgene control in mammalian cells and mice. Nat. Biotechnol. 2002, 20:901-907.
23. Weber W., et al. A biotin-triggered genetic switch in mammalian cells and mice. Metab. Eng. 2009, 11:117-124.
24. Weber W., et al. A genetic redox sensor for mammalian cells. Metab. Eng. 2006, 8:273-280.
25. Weber W., et al. Conditional human VEGF-mediated vascularization in chicken embryos using a novel temperature-inducible gene regulation (TIGR) system. Nucleic Acids Res. 2003, 31:e69.
26. Weber W., et al. Gas-inducible transgene expression in mammalian cells and mice. Nat. Biotechnol. 2004, 22:1440-1444.
27. Weber W., et al. Streptomyces-derived quorum-sensing systems engineered for adjustable transgene expression in mammalian cells and mice. Nucleic Acids Res. 2003, 31:e71.
28. Zhao H.F., et al. A coumermycin/novobiocin-regulated gene expression system. Hum. Gene Ther. 2003, 14:1619-1629.
29. Braselmann S., et al. A selective transcriptional induction system for mammalian cells based on Gal4-estrogen receptor fusion proteins. Proc. Natl. Acad. Sci. U.S.A. 1993, 90:1657-1661.
30. Pengue G., et al. Repression of transcriptional activity at a distance by the evolutionarily conserved KRAB domain present in a subfamily of zinc finger proteins. Nucleic Acids Res. 1994, 22:2908-2914.
31. Luo Y., et al. Mammalian two-hybrid system: a complementary approach to the yeast two-hybrid system. Biotechniques 1997, 22:350-352.
32. Nissim L., Bar-Ziv R.H. A tunable dual-promoter integrator for targeting of cancer cells. Mol. Syst. Biol. 2010, 6:444.
33. Collingwood T.N., et al. Thyroid hormone-mediated enhancement of heterodimer formation between thyroid hormone receptor beta and retinoid X receptor. J. Biol. Chem. 1997, 272:13060-13065.
34. Wang Y., et al. Positive and negative regulation of gene expression in eukaryotic cells with an inducible transcriptional regulator. Gene Ther. 1997, 4:432-441.
35. Ho S.N., et al. Dimeric ligands define a role for transcriptional activation domains in reinitiation. Nature 1996, 382:822-826.
36. Liberles S.D., et al. Inducible gene expression and protein translocation using nontoxic ligands identified by a mammalian three-hybrid screen. Proc. Natl. Acad. Sci. U.S.A. 1997, 94:7825-7830.
37. Liang F.S., et al. Engineering the ABA plant stress pathway for regulation of induced proximity. Sci. Signal. 2011, 4:rs2.
38. Kennedy M.J., et al. Rapid blue-light-mediated induction of protein interactions in living cells. Nat. Methods 2010, 7:973-975.
39. Wang X., et al. Spatiotemporal control of gene expression by a light-switchable transgene system. Nat. Methods 2012, 9:266-269.
40. Yazawa M., et al. Induction of protein-protein interactions in live cells using light. Nat. Biotechnol. 2009, 27:941-945.
41. No D., et al. Ecdysone-inducible gene expression in mammalian cells and transgenic mice. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:3346-3351.
42. Weber W., et al. A synthetic time-delay circuit in mammalian cells and mice. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:2643-2648.
43. Bae K.H., et al. Human zinc fingers as building blocks in the construction of artificial transcription factors. Nat. Biotechnol. 2003, 21:275-280.
44. Boch J. TALEs of genome targeting. Nat. Biotechnol. 2011, 29:135-136.
45. Miller J.C., et al. A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol. 2011, 29:143-148.
46. Beerli R.R., et al. Chemically regulated zinc finger transcription factors. J. Biol. Chem. 2000, 275:32617-32627.
47. Rivera V.M., et al. A humanized system for pharmacologic control of gene expression. Nat. Med. 1996, 2:1028-1032.
48. Miller C.P., Blau C.A. Using gene transfer to circumvent off-target effects. Gene Ther. 2008, 15:759-764.
49. Okazuka K., et al. Long-term regulation of genetically modified primary hematopoietic cells in dogs. Mol. Ther. 2011, 19:1287-1294.
50. Ye H., et al. A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 2011, 332:1565-1568.
51. Kemmer C., et al. A designer network coordinating bovine artificial insemination by ovulation-triggered release of implanted sperms. J. Control. Release 2011, 150:23-29.
52. Stanley S.A., et al. Radio-wave heating of iron oxide nanoparticles can regulate plasma glucose in mice. Science 2012, 336:604-608.
53. Mittal V. Improving the efficiency of RNA interference in mammals. Nat. Rev. Genet. 2004, 5:355-365.
54. Szulc J., et al. A versatile tool for conditional gene expression and knockdown. Nat. Methods 2006, 3:109-116.
55. Famulok M., et al. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem. Rev. 2007, 107:3715-3743.
56. An C.I., et al. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA 2006, 12:710-716.
57. Beisel C.L., et al. Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing. Nucleic Acids Res. 2011, 39:2981-2994.
58. Kumar D., et al. Conditional RNA interference mediated by allosteric ribozyme. J. Am. Chem. Soc. 2009, 131:13906-13907.
59. Auslander D., et al. Rational design of a small molecule-responsive intramer controlling transgene expression in mammalian cells. Nucleic Acids Res. 2011, 39:e155.
60. Kim D.S., et al. Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing. BMC Mol. Biol. 2008, 9:23.
61. Culler S.J., et al. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 2010, 330:1251-1255.
62. Wang Y., et al. Engineering splicing factors with designed specificities. Nat. Methods 2009, 6:825-830.
63. Saito H., et al. Synthetic translational regulation by an L7Ae-kink-turn RNP switch. Nat. Chem. Biol. 2010, 6:71-78.
64. Stripecke R., et al. Proteins binding to 5' untranslated region sites: a general mechanism for translational regulation of mRNAs in human and yeast cells. Mol. Cell. Biol. 1994, 14:5898-5909.
65. Werstuck G., Green M.R. Controlling gene expression in living cells through small molecule-RNA interactions. Science 1998, 282:296-298.
66. Wieland M., Hartig J.S. RNA quadruplex-based modulation of gene expression. Chem. Biol. 2007, 14:757-763.
67. Auslander S., et al. A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol. Biosyst. 2010, 6:807-814.
68. Ketzer P., et al. Synthetic riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses. Nucleic Acids Res. 2012, 40:e167.
69. Nishimura K., et al. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat. Methods 2009, 6:917-922.
70. Banaszynski L.A., et al. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules. Cell 2006, 126:995-1004.
71. Bonger K.M., et al. Small-molecule displacement of a cryptic degron causes conditional protein degradation. Nat. Chem. Biol. 2011, 7:531-537.
72. Iwamoto M., et al. A general chemical method to regulate protein stability in the mammalian central nervous system. Chem. Biol. 2010, 17:981-988.
73. Miyazaki Y., et al. Destabilizing domains derived from the human estrogen receptor. J. Am. Chem. Soc. 2012, 134:3942-3945.
74. Schneekloth J.S., et al. Chemical genetic control of protein levels: selective in vivo targeted degradation. J. Am. Chem. Soc. 2004, 126:3748-3754.
75. Los G.V., et al. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem. Biol. 2008, 3:373-382.
76. Neklesa T.K., et al. Small-molecule hydrophobic tagging-induced degradation of HaloTag fusion proteins. Nat. Chem. Biol. 2011, 7:538-543.
77. Rivera V.M., et al. Regulation of protein secretion through controlled aggregation in the endoplasmic reticulum. Science 2000, 287:826-830.
78. Deans T.L., et al. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 2007, 130:363-372.
79. Auslander S., et al. Smart medication through combination of synthetic biology and cell microencapsulation. Metab. Eng. 2011, 14:252-260.
80. Weber W., et al. A synthetic mammalian gene circuit reveals antituberculosis compounds. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:9994-9998.
81. Leisner M., et al. Rationally designed logic integration of regulatory signals in mammalian cells. Nat. Nanotechnol. 2010, 5:666-670.
82. Lohmueller J.J., et al. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Res. 2012, 40:5180-5187.
83. Burrill D.R., et al. Synthetic memory circuits for tracking human cell fate. Genes Dev. 2012, 26:1486-1497.
84. Greber D., Fussenegger M. An engineered mammalian band-pass network. Nucleic Acids Res. 2010, 38:e174.
85. Kramer B.P., et al. BioLogic gates enable logical transcription control in mammalian cells. Biotechnol. Bioeng. 2004, 87:478-484.
86. Kramer B.P., Fussenegger M. Hysteresis in a synthetic mammalian gene network. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:9517-9522.
87. Miyamoto T., et al. Rapid and orthogonal logic gating with a gibberellin-induced dimerization system. Nat. Chem. Biol. 2012, 8:465-470.
88. Rinaudo K., et al. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol. 2007, 25:795-801.
89. Saito H., et al. Synthetic human cell fate regulation by protein-driven RNA switches. Nat. Commun. 2011, 2:160.
90. Tigges M., et al. A synthetic low-frequency mammalian oscillator. Nucleic Acids Res. 2010, 38:2702-2711.
91. Tigges M., et al. A tunable synthetic mammalian oscillator. Nature 2009, 457:309-312.
92. Weber W., et al. A synthetic metabolite-based mammalian inter-cell signaling system. Mol. Biosyst. 2009, 5:757-763.
93. Weber W., et al. Synthetic ecosystems based on airborne inter- and intrakingdom communication. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:10435-10440.
94. Boorsma M., et al. A temperature-regulated replicon-based DNA expression system. Nat. Biotechnol. 2000, 18:429-432.
95. Tascou S., et al. Stringent rosiglitazone-dependent gene switch in muscle cells without effect on myogenic differentiation. Mol. Ther. 2004, 9:637-649.