Synthetic biology: Putting synthesis into biology

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volumn 3, Issue 1, 2011, Pages 7-20

  Liang, Jing ^a   Luo, Yunzi ^a   Zhao, Huimin ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN;

BIOLOGICAL MODEL; BIOSYNTHESIS; CHEMISTRY; GENETIC ENGINEERING; METABOLISM; METABOLOMICS; PROTEIN ENGINEERING; PROTEOMICS; REVIEW;

DNA; GENETIC ENGINEERING; METABOLOMICS; MODELS, BIOLOGICAL; PROTEIN ENGINEERING; PROTEINS; PROTEOMICS;

EID: 79953245664     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.104     Document Type: Review

References (92)

1. What's in a name?. Nat Biotechnol 2009, 27:1071-1073.
2. Keasling JD. Synthetic biology for synthetic chemistry. ACS Chem Biol 2008, 3:64-76.
3. Young E, Alper H. Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol 2010, 12.
4. Mukherji S, van Oudenaarden A. Synthetic biology: understanding biological design from synthetic circuits. Nat Rev Genet 2009, 10:859-871.
5. Yeh BJ, Lim WA. Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol 2007, 3:521-525.
6. Tigges M, Fussenegger M. Recent advances in mammalian synthetic biology-design of synthetic transgene control networks. Curr Opin Biotechnol 2009, 20:449-460.
7. Purnick PEM, Weiss R. The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 2009, 10:410-422.
8. Benner SA, Sismour AM. Synthetic biology. Nat Rev Genet 2005, 6:533-543.
9. Marchisio MA, Stelling J. Computational design tools for synthetic biology. Curr Opin Biotechnol 2009, 20:479-485.
10. Khalil AS, Collins JJ. Synthetic biology: applications come of age. Nat Rev Genet 2010, 11:367-379.
11. Neumann H, Neumann-Staubitz P. Synthetic biology approaches in drug discovery and pharmaceutical biotechnology. Appl Microbiol Biotechnol 2010, DOI: 10.1007/s00253-010-2578-3
12. May M. Engineering a new business. Nat Biotechnol 2009, 27:1112-1120.
13. Mueller S, Coleman JR, Wimmer E. Putting synthesis into biology: a viral view of genetic engineering through de novo gene and genome synthesis. Chem Biol 2009, 16:337-347.
14. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA, Smith HO. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 2008, 319:1215-1220.
15. Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. P Natl Acad Sci USA 2008, 105:20404-20409.
16. Shao Z, Zhao H. Zhao H. DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 2009, 37:e16.
17. Dougherty MJ, Arnold FH. Directed evolution: new parts and optimized function. Curr Opin Biotechnol 2009, 20:486-491.
18. Schmidt-Dannert C. Directed evolution of single proteins, metabolic pathways, and viruses. Biochemistry-US 2001, 40:13125-13136.
19. Rubin-Pitel SB, Zhao HM. Recent advances in biocatalysis by directed enzyme evolution. Comb Chem High Throughput Screen 2006, 9:247-257.
20. Shivange AV, Marienhagen J, Mundhada H, Schenk A, Schwaneberg U. Advances in generating functional diversity for directed protein evolution. Curr Opin Chem Biol 2009, 13:19-25.
21. Arnold FH. Design by directed evolution. Acc Chem Res 1998, 31:125-131.
22. Zhao HM, Chockalingam K, Chen ZL. Directed evolution of enzymes and pathways for industrial biocatalysis. Curr Opin Biotechnol 2002, 13:104-110.
23. Chockalingam K, Chen ZL, Katzenellenbogen JA, Zhao HM. Directed evolution of specific receptorligand pairs for use in the creation of gene switches. Proc Natl Acad Sci USA 2005, 102:5691-5696.
24. Reetz MT, Carballeira JD. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2007, 2:891-903.
25. Herman A, Tawfik DS. Incorporating Synthetic Oligonucleotides via Gene Reassembiv (ISOR): a versatile tool forgenerating targeted libraries. Protein Eng Des Sel 2007, 20:219-226.
26. Hidalgo A, Schliessmann A, Molina R, Hermoso J, Bornscheuer UT. A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution. Protein Eng Des Sel 2008, 21:567-576.
27. Kumar R, Rajagopal K. Single-step overlap-primerwalk polymerase chain reaction for multiple mutagenesis without overlap extension. Anal Biochem 2008, 377:105-107.
28. Deng QW, Luo WS, Donnenberg MS. Rapid site site-directed domain scanning mutagenesis of enteropathogenic Escherichia coli espD. Biol Proced Online 2007, 18-26.
29. Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453:190-195.
30. Pitera DJ, Paddon CJ, Newman JD, Keasling JD. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab Eng 2007, 9:193-207.
31. Bennett MR, Hasty J. Overpowering the component problem. Nat Biotechnol 2009, 27:450-451.
32. Ellis T, Wang X, Collins JJ. Diversity-based, modelguided construction of synthetic gene networks with predicted functions. Nat Biotechnol 2009, 27:465-471.
33. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KLJ, Keasling JD. Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 2009, 27:753-759.
34. Landrain TE, Carrera J, Kirov B, Rodrigo G, Jaramillo A. Modular model-based design for heterologous bioproduction in bacteria. Curr Opin Biotechnol 2009, 20:272-279.
35. Pósfai G, Plunkett G, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR. Emergent properties of reduced-genome Escherichia coli. Science 2006, 312:1044-1046.
36. Itaya M, Tsuge K, Koizumi M, Fujita K. Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci USA 2005, 102:15971-15976.
37. Chan LY, Kosuri S, Endy D. Refactoring bacteriophage T7. Mol Syst Biol 2005, 1.
38. Zhang YX, Perry K, Vinci VA, Powell K, Stemmer WPC, del Cardayre SB. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 2002, 415:644-646.
39. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460:894-898.
40. Forêt S, Kassahn KS, Grasso LC, Hayward DC, Iguchi A, Ball EE, Miller DJ. Genomic and microarray approaches to coral reef conservation biology. Coral Reefs 2007, 26:475-486.
41. Weniger M, Engelmann JC, Schultz J. Genome expression pathway analysis tool-analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context. BMC Bioinformatics 2007, 8:179.
42. Grandori C, Mac J, Siebelt F, Ayer DE, Eisenman RN. Myc-Max heterodimers activate a DEAD box gene and interact with multiple E box-related sites in vivo. EMBO J 1996, 15:4344-4357.
43. Collas P. The current state of chromatin immunoprecipitation. Mol Biotechnol 2010, 45:87-100.
44. Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nat Biotechnol 2009, 27:455-457.
45. Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10:605-616.
46. Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10:669-680.
47. Griffiths WJ, Wang Y. Mass spectrometry: from proteomics to metabolomics and lipidomics. Chem Soc Rev 2009, 38:1882-1896.
48. Domon B. Mass spectrometry and protein analysis. Science 2006, 312:212-217.
49. Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 2007, 389:1017-1031.
50. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
51. Mann M. Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 2006, 7:952-958.
52. Simon GM, Cravatt BF. Activity-based proteomics of enzyme superfamilies: serine hydrolases as a case study. J Biol Chem 2010, 285:11051-11055.
53. Cravatt BF, Wright AT, Kozarich JW. Activity-based protein profiling: From enzyme chemistry. Annu Rev Biochem 2008, 77:383-414.
54. Goldsmith P, Fenton H, Morris-Stiff G, Ahmad N, Fisher J, Prasad KR. Metabonomics: a useful tool for the future surgeon. J Surg Res 2008, 160:122-132.
55. Kizer L, Pitera DJ, Pfleger BF, Keasling JD. Application of functional genomics to pathway optimization for increased isoprenoid production. Appl Environ Microbiol 2008, 74:3229-3241.
56. Kaznessis YN. Computational methods in synthetic biology. Biotechnol J 2009, 4:1392-1405.
57. Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 2010, 26:925-931.
58. Chou CH, Chang WC, Chiu CM, Huang CC, Huang HD. FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res 2009, 37:W129-W134.
59. Zhang Z, Buckler ES, Casstevens TM, Bradbury PJ. Software engineering the mixed model for genome-wide association studies on large samples. Brief Bioinform 2009, 10:664-675.
60. Lehner B. Modelling genotype-phenotype relationships and human disease with genetic interaction networks. J Exp Biol 2007, 210:1559-1566.
61. Durot M, Bourguignon PY, Schachter V. Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev 2009, 33:164-190.
62. Mo ML, Palsson BO. Understanding human metabolic physiology: a genome-to-systems approach. Trends Biotechnol 2009, 27:37-44.
63. Appella DH. Non-natural nucleic acids for synthetic biology. Curr Opin Chem Biol 2009, 13:687-696.
64. Wang L, Chen S, Xu T, Taghizadeh K, Wishnok JS, Zhou X, You D, Deng Z, Dedon PC. Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol 2007, 3:709-710.
65. Shaw BR, Dobrikov M, Wang X, Wan J, He K, Lin JL, Li P, Rait V, Sergueeva ZA, Sergueev D. Reading, writing, and modulating genetic information with boranophosphate mimics of nucleotides, DNA, and RNA. Ann NY Acad Sci 2003, 1002:12-29.
66. Renders M, Lievrouw R, Krecmerová M, Holý A, Herdewijn P. Enzymatic polymerization of phosphonate nucleosides. Chembiochem 2008, 9:2883-2888.
67. Benner SA. Understanding nucleic acids using synthetic chemistry. Acc Chem Res 2004, 37:784-797.
68. Yang Z, Hutter D, Sheng P, Sismour AM, Benner SA. Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Res 2006, 34:6095-6101.
69. Wang L, Brock A, Herberich B, Schultz PG. Expanding the genetic code of Escherichia coli. Science 2001, 292:498-500.
70. Hirao I, Ohtsuki T, Fujiwara T, Mitsui T, Yokogawa T, Okuni T, Nakayama H, Takio K, Yabuki T, Kigawa T, Kodama K, Yokogawa T, Nishikawa K, Yokoyama S. An unnatural base pair for incorporating amino acid analogs into proteins. Nat Biotechnol 2002, 20:177-182.
71. Ibba M, Hennecke H. Towards engineering proteins by site-directed incorporation in vivo of non-natural amino acids. Biotechnology (NY) 1994, 12:678-682.
72. Liu W, Brock A, Chen S, Chen S, Schultz PG. Genetic incorporation of unnatural amino acids into proteins in mammalian cells. Nat Methods 2007, 4:239-244.
73. Wang Q, Parrish AR, Wang L. Expanding the genetic code for biological studies. Chem Biol 2009, 16:323-336.
74. Rowe L, Ensor M, Mehl R, Daunert S. Modulating the bioluminescence emission of photoproteins by in vivo site-directed incorporation of non-natural amino acids. ACS Chem Biol 2010, DOI: 10.1021/cb9002909
75. Taira H, Fukushima M, Hohsaka T, Sisido M. Fourbase codon-mediated incorporation of non-natural amino acids into proteins in a eukaryotic cell-free translation system. J Biosci Bioeng 2005, 99:473-476.
76. Leloup JC, Goldbeter A. A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins. J Biol Rhythms 1998, 13:70-87.
77. Hasty J, McMillen D, Collins JJ. Engineered gene circuits. Nature 2002, 420:224-230.
78. Lu TK, Khalil AS, Collins JJ. Next-generation synthetic gene networks. Nat Biotechnol 2009, 27:1139-1150.
79. Cadatay T, Turcotte M, Elowitz MB, Garcia-Ojalvo J, Süel GM. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 2009, 139:512-522.
80. Tsuruta H, Paddon CJ, Eng D, Lenihan JR, Horning T, Anthony LC, Regentin R, Keasling JD, Renninger NS, Newman JD. High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS ONE 2009, 4:e4489.
81. van Zyl WH, Lynd LR, Den Haan R, McBride JE. Consolidated bioprocessing for bioethanol production using Saccharomyces cerevisiae. Adv Biochem Eng Biotechnol 2007, 108:205-235.
82. Carere CR, Sparling R, Cicek N, Levin DB. Third generation biofuels via direct cellulose fermentation. Int J Mol Sci 2008, 9:1342-1360.
83. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA 3rd, Smith HO, Venter JC. Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 2006, 103:425-430.
84. Marshall A. The sorcerer of synthetic genomes. Nat Biotechnol 2009, 27:1121-1124.
85. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang R-Y, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC. Creation of a bacterial cell controlled by a chemically synthesized genome. Science, DOI: 2010:10.1126/science.1190719
86. Wimmer E, Mueller S, Tumpey TM, Taubenberger JK. Synthetic viruses: a new opportunity to understand and prevent viral disease. Nat Biotechnol 2009, 27:1163-1172.
87. Budin I, Szostak JW. Expanding roles for diverse physical phenomena during the origin of life. Annu Rev Biophys 2010, 39:245-263.
88. Balagaddé FK, Song H, Ozaki J, Collins CH, BarnetM, Arnold FH, Quake SR, You L. A synthetic Escherichia coli predator-prey ecosystem. Mol Syst Biol 2008, 4:187.
89. Brenner K, You L, Arnold FH. Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol 2008, 26:483-489.
90. Alper H, Stephanopoulos G. Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential? Nat Rev Microbiol 2009, 7:715-723.
91. Morrison M, Pope PB, Denman SE, McSweeney CS. Plant biomass degradation by gut microbiomes: more of the same or something new? Curr Opin Biotechnol 2009, 20:358-363.
92. Eiteman MA, Lee SA, Altman E. A co-fermentation strategy to consume sugar mixtures effectively. J Biol Eng 2008, 2:3.