Plant synthetic biology

Trends in Plant Science

Volumn 20, Issue 5, 2015, Pages 309-317

  Liu, Wusheng ^a   Stewart, C Neal ^a,b  

^a UNIVERSITY OF TENNESSEE   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Design cycle; Enabling tools; Engineering principles; Pioneering applications; Plant synthetic biology

Indexed keywords

GENETIC ENGINEERING; METABOLISM; PLANT; PROCEDURES; SYNTHETIC BIOLOGY;

GENETIC ENGINEERING; PLANTS; SYNTHETIC BIOLOGY;

EID: 84928828879     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2015.02.004     Document Type: Review

References (92)

1. Slusarczyk A.L., et al. Foundations for the design and implementation of synthetic genetic circuits. Nat. Rev. Genet. 2012, 13:406-420.
2. Gardner T.S., et al. Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403:339-342.
3. Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335-338.
4. Purnick P.E.M., Weiss R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 2009, 10:410-422.
5. Guet C.C., et al. Combinatorial synthesis of genetic networks. Science 2002, 296:1466-1470.
6. Kobayashi H., et al. Programmable cells: interfacing natural and engineered gene networks. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:8414-8419.
7. You L., et al. Programmed population control by cell-cell communication and regulated killing. Nature 2004, 428:868-871.
8. Anderson J.C., et al. Environmentally controlled invasion of cancer cells by engineering bacteria. J. Mol. Biol. 2006, 335:619-627.
9. Lu T.K., Collins J.J. Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:11197-11202.
10. Lu T.K., Collins J.J. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:4629-4634.
11. Smith H.O., et al. Generating a synthetic genome by whole genome assembly: ΦX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:15440-15445.
12. Chan L.Y., et al. Refactoring bacteriophage T7. Mol. Syst. Biol. 2005, 1. 2005.0018.
13. Gibson D.G., et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010, 329:52-56.
14. James J.R., Vale R.D. Biophysical mechanism of T-cell receptor triggering in a reconstituted system. Nature 2012, 487:64-69.
15. Dormitzer P.R., et al. Synthetic generation of influenza vaccine viruses for rapid response to pandemics. Sci. Transl. Med. 2013, 5:185ra68.
16. Ulmer J.B., et al. RNA-based vaccines. Vaccine 2012, 30:4414-4418.
17. Weber W., Fussenegger M. Synthetic gene networks in mammalian cells. Curr. Opin. Biotechnol. 2012, 21:690-696.
18. Kristensen C., et al. Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:1779-1784.
19. Ro D.K., et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 2006, 440:940-943.
20. Diretto G., et al. Metabolic engineering of potato carotenoid content through tuber-specific overexpression of a bacterial mini-pathway. PLoS ONE 2007, 2:e350.
21. Antunes M.S., et al. Engineering key components in a synthetic eukaryotic signal transduction pathway. Mol. Syst. Biol. 2009, 5:270.
22. Antunes M.S., et al. Programmable ligand detection system in plants through a synthetic signal transduction pathway. PLoS ONE 2011, 6:e16292.
23. Schwille P. Bottom-up synthetic biology: engineering in a tinkerer's world. Science 2011, 333:1252-1254.
24. Scharff L.B., Bock R. Synthetic biology in plastids. Plant J. 2014, 78:783-798.
25. Cook C., et al. Opportunities in plant synthetic biology. J. Exp. Bot. 2014, Published online February 6, 2014. 10.1093/jxb/eru013.
26. Chen Y.Y., et al. Synthetic biology: advancing biological frontiers by building synthetic systems. Genome Biol. 2012, 13:240.
27. Andrianantoandro E., et al. Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol. 2006, 2. 2006.0028.
28. Barrett C.L., et al. Systems biology as a foundation for genome-scale synthetic biology. Curr. Opin. Biotechnol. 2006, 17:1-5.
29. Church G.M., et al. Realizing the potential of synthetic biology. Nat. Rev. Mol. Cell Biol. 2014, 15:289-294.
30. Kitney R., Freemont P. Synthetic biology - the state of play. FEBS Lett. 2012, 586:2029-2036.
31. Alterovitz G., et al. The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. Brief. Bioimform. 2009, 11:80-95.
32. Rollie S., et al. Designing biological systems: systems engineering meets synthetic biology. Chem. Eng. Sci. 2011, 69:1-29.
33. Way J.C., et al. Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 2014, 157:151-161.
34. Liu W., et al. Advanced genetics tools for plant biotechnology. Nat. Rev. Genet. 2013, 14:781-793.
35. Endy D. Foundations for engineering biology. Nature 2005, 438:449-453.
36. Haseltine E.L., Arnold F.H. Synthetic gene circuits: design with directed evolution. Annu. Rev. Biophys. Biomol. Struct. 2007, 36:1-19.
37. Heinemann M., Panke S. Synthetic biology - putting engineering into biology. Bioinformatics 2006, 22:2790-2799.
38. de Lorenzo V., Danchin A. Synthetic biology: discovering new worlds and new words. EMBO Rep. 2008, 9:822-827.
39. Bashor C.J., et al. Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 2008, 319:1539-1543.
40. Lim W.A. Designing customized cell signaling circuits. Nat. Rev. Mol. Cell Biol. 2010, 11:393-403.
41. Mukherji S., van Oudenaarden A. Synthetic biology: understanding biological design from synthetic circuits. Nat. Rev. Genet. 2009, 10:859-871.
42. Nandagopal N., Elowitz M.B. Synthetic biology: integrated gene circuits. Science 2011, 333:1244-1248.
43. Venter M. Synthetic promoters: genetic control through cis engineering. Trends Plant Sci. 2007, 12:118-124.
44. Liu W., et al. Computational discovery of soybean promoter cis-regulatory elements for the construction of soybean cyst nematode inducible synthetic promoters. Plant Biotechnol. J. 2014, 12:1015-1026.
45. Smolke C.D. Building outside of the box: iGEM and the BioBricks Foundation. Nat. Biotechnol. 2009, 27:1099-1102.
46. Yancey A., Stewart C.N. Are university researchers at risk for patent infringement?. Nat. Biotechnol. 2007, 25:1225-1228.
47. Lux M.W., et al. Genetic design automation: engineering fantasy or scientific renewal?. Trends Biotechnol. 2011, 30:120-126.
48. Marchisio M., Stelling J. Computational design tools for synthetic biology. Curr. Opin. Biotechnol. 2009, 20:479-485.
49. Medema M.H., et al. Computational tools for the synthetic design of biochemical pathways. Nat. Rev. Microbiol. 2012, 10:191-202.
50. Richardson S.M., et al. GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome Res. 2006, 16:550-556.
51. Villalobos A., et al. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinform. 2006, 7:285.
52. Czar M.J., et al. Writing DNA with GenoCAD™. Nucleic Acids Res. 2009, 37:W40-W47.
53. Dasika M.S., Maranas C.D. OptCircuit: an optimization based method for computational design of genetic circuits. BMC Syst. Biol. 2008, 2:24.
54. Hill A.D., et al. Synthetic BiologySS: the synthetic biology modeling suite. Bioinformatics 2008, 24:2551-2553.
55. Weeding E., et al. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. Brief. Bioinform. 2010, 11:394-402.
56. Funahashi A. CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proc. IEEE 2008, 96:1254-1265.
57. Funahashi A., et al. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. Biosilico 2003, 1:159-162.
58. Ishii N., et al. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 2007, 316:593-597.
59. Tomita M., et al. E-CELL: software environment for whole-cell simulation. Bioinformatics 1999, 15:72-84.
60. Hoops S. COPASI - a COmplex PAthway SImulator. Bioinformatics 2006, 22:3067-3074.
61. Mendes P., et al. Computational modeling of biochemical networks using COPASI. Systems Biology 2009, 17-59. Springer. I.V. Maly (Ed.).
62. Chaturvedi R., et al. Multi-model simulations of chicken limb morphogenesis. Lect. Notes Comput. Sci. 2003, 2659:39-49.
63. Hester S.D., et al. A multi-cell, multi-scale model of vertebrate segmentation and somite formation. PLoS Comput. Biol. 2011, 7:e1002155.
64. Dupuy L., et al. A system for modelling cell-cell interactions during plant morphogenesis. Ann. Bot. 2008, 101:1255-1265.
65. Federici F., et al. Integrated genetic and computation methods for in planta cytometry. Nat. Methods 2012, 9:483-485.
66. Depuy L., et al. Coordination of plant cell division and expansion in a simple morphogenetic system. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:2711-2716.
67. Havens K.A., et al. A synthetic approach reveals extensive tunability of auxin signaling. Plant Physiol. 2012, 160:135-142.
68. Weed S., et al. A quantitative ratiometric sensor for time-resolved analysis of auxin dynamics. Sci. Rep. 2013, 3:1-7.
69. Zurcher E., et al. A robust and sensitive synthetic sensor to monitor the transcriptional output of the cytokinin signaling network in planta. Plant Physiol. 2013, 161:106-107.
70. Muller K., et al. A red light-controlled synthetic gene expression switch for plant system. Mol. Plant 2014, 10:1679-1688.
71. Liu W., et al. Rapid in vivo analysis of synthetic promoters for plant pathogen phytosensing. BMC Biotechnol. 2011, 11:108.
72. Liu W., et al. Bacterial pathogen phytosensing in transgenic tobacco and Arabidopsis. Plant Biotechnol. J. 2013, 11:43-52.
73. Fethe M.H., et al. The performance of pathogenic bacterial phytosensing transgenic tobacco in the field. Plant Biotechnol. J. 2014, 12:755-764.
74. Koschmann J., et al. Intergration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis. Plant Physiol. 2012, 160:178-191.
75. DePaoli H.C., et al. Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. J. Exp. Bot. 2014, Published online February 24, 2014. 10.1093/jxb/eru038.
76. Fesenko E., Edwards R. Plant synthetic biology: a new platform for industrial biotechnology. J. Exp. Bot. 2014, 65:1927-1937.
77. Rogers C., Oldroyd G.E.D. Synthetic biology approaches to engineering the nitrogen symbiosis in cereals. J. Exp. Bot. 2014, 65:1939-1946.
78. Farre G., et al. Engineering complex metabolic pathways in plants. Annu. Rev. Plant Biol. 2014, 65:187-223.
79. Yang F., et al. Engineering secondary cell wall deposition in plants. Plant Biotechnol. J. 2013, 11:325-335.
80. Nielsen A.Z., et al. Redirecting photosynthetic reducing power toward bioactive natural product synthesis. ACS Synth. Biol. 2014, 2:308-315.
81. Paddon C.J., et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 2013, 496:528-532.
82. Fossati E., et al. Reconstitution of a 10-gene pathway for synthesis of the plant alkaloid dihydrosanguinarine in Saccharomyces cerevisiae. Nat. Commun. 2014, 5:3283.
83. Dymond J.S., et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 2011, 477:471-476.
84. Juhas M., et al. Essence of life: essential genes of minimal genomes. Trends Cell Biol. 2011, 21:562-568.
85. Baker M. The next step for the synthetic genome. Nature 2011, 473:403-408.
86. Agapakis C.M., et al. Towards a synthetic chloroplast. PLoS ONE 2011, 6:e18877.
87. Kumar S., et al. Remodeling the isoprenoid pathway in tobacco by expressing the cytoplasmic mevalonate pathway in chloroplasts. Metab. Eng. 2012, 14:19-28.
88. Verhounig A., et al. Inducible gene expression from the plastid genome by a synthetic riboswitch. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:6204-6209.
89. Gallage N.J., Moller B.L. Vanillin - bioconversion and bioengineering of the most popular plant flavor and its de novo biosynthesis in the vanilla orchid. Mol. Plant 2014, 8:40-57.
90. Lu T.K., et al. Next-generation synthetic gene networks. Nat. Biotechnol. 2009, 27:1139-1150.
91. Borak B., et al. Energy and carbon accounting to compare bioenergy crops. Curr. Opin. Biotechnol. 2013, 24:369-375.
92. Jones H.D. Regulatory uncertainty over genome editing. Nat. Plants 2015, Published online January 8, 2015. 10.1038/nplants.2014.11.