Biotechnology Bulletin ›› 2015, Vol. 31 ›› Issue (4): 134-148.doi: 10.13560/j.cnki.biotech.bull.1985.2015.03.017
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Lü Yongkun Du Guocheng Chen Jian Zhou Jingwen
Received:
2015-03-30
Online:
2015-04-22
Published:
2015-04-22
Lü Yongkun, Du Guocheng, Chen Jian, Zhou Jingwen. Advances in Synthetic Biology[J]. Biotechnology Bulletin, 2015, 31(4): 134-148.
[1] Zhang L, Chang S, Wang J. Synthetic biology:From the first synthetic cell to see its current situation and future development[J]. Chinese Science Bulletin, 2011, 56(3):229-237. [2] Mitchell W. Natural products from synthetic biology[J]. Current Opinion in Chemical Biology, 2011, 15(4):505-515. [3] Gibson DG, Glass JI, Lartigue C, et al. Creation of a bacterial cell controlled by a chemically synthesized genome[J]. Science, 2010, 329(5987):52-56. [4] Bailey JE. Toward a science of metabolic engineering[J]. Science, 1991, 252(5013):1668-1675. [5] Stephanopoulos G, Vallino JJ. Network rigidity and metabolic engineering in metabolite overproduction[J]. Science, 1991, 252(5013):1675-1681. [6] Xie LZ, Wang DIC. High cell density and high monoclonal antibody production through medium design and rational control in a bioreactor[J]. Biotechnology and Bioengineering, 1996, 51(6):725-729. [7] Hamilton SR, Bobrowicz P, Bobrowicz B, et al. Production of complex human glycoproteins in yeast[J]. Science, 2003, 301(5637):1244-1246. [8] Stephanopoulos G. Challenges in engineering microbes for biofuels production[J]. Science, 2007, 315(5813):801-804. [9] Kitney R, Freemont P. Synthetic biology-the state of play[J]. Febs Letters, 2012, 586(15):2029-2036. [10] Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators[J]. Nature, 2002, 403(6767):335-338. [11] Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli[J]. Nature, 2000, 403(6767):339-342. [12] Smith HO, Hutchison CA, Pfannkoch C, Venter JC. Generating a synthetic genome by whole genome assembly:phi X174 bacteriophage from synthetic oligonucleotides[J]. Proceedings of the National Academy of Sciences of the United States of America, 2003, 100(26):15440-15445. [13] Good MC, Zalatan JG, Lim WA. Scaffold proteins:Hubs for controlling the flow of cellular information[J]. Science, 2011, 332(6030):680-686. [14] Weber W, Fussenegger M. The impact of synthetic biology on drug discovery[J]. Drug Discovery Today, 2009, 14(19-20):956-963. [15] Rebatchouk D, Daraselia N, Narita JO. NOMAD:A versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design[J]. Proceedings of the National Academy of Sciences of the United States of America, 1996, 93(20):10891-10896. [16] Kwok R. Five hard truths for synthetic biology[J]. Nature, 2010, 463(7279):288-290. [17] Hodgman CE, Jewett MC. Cell-free synthetic biology:Thinking outside the cell[J]. Metabolic Engineering, 2012, 14(3):261-269. [18] Smith MT, Wilding KM, Hunt JM, et al. The emerging age of cell-free synthetic biology[J]. Febs Letters, 2014, 588(17):2755-2761. [19] Swartz JR. Transforming biochemical engineering with cell-free biology[J]. Aiche Journal, 2012, 58(1):5-13. [20] Harris DC, Jewett MC. Cell-free biology:Exploiting the interface between synthetic biology and synthetic chemistry[J]. Current Opinion in Biotechnology, 2012, 23(5):672-678. [21] Forster AC, Church GM. Synthetic biology projects in vitro[J]. Genome Research, 2007, 17(1):1-6. [22] Lopez-Gallego F, Schmidt-Dannert C. Multi-enzymatic synthesis[J]. Current Opinion in Chemical Biology, 2010, 14(2):174-183. [23] Zawada JF, Yin G, Steiner AR, et al. Microscale to manufacturing scale-up of cell-free cytokine production-A new approach for shortening protein production development timelines[J]. Biotechnology and Bioengineering, 2011, 108(7):1570-1578. [24] Kanter G, Yang J, Voloshin A, et al. Cell-free production of scFv fusion proteins:an efficient approach for personalized lymphoma vaccines[J]. Blood, 2007, 109(8):3393-3399. [25] Bundy BC, Franciszkowicz MJ, Swartz JR. Escherichia coli-based cell-free synthesis of virus-like particles[J]. Biotechnology and Bioengineering, 2008, 100(1):28-37. [26] Boyer ME, Stapleton JA, Kuchenreuther JM, et al. Cell-free synthesis and maturation of[FeFe]hydrogenases[J]. Biotechnology and Bioengineering, 2008, 99(1):59-67. [27] Bujara M, Schuemperli M, Billerbeek S, et al. Exploiting cell-free systems:Implementation and debugging of a system of biotransformations[J]. Biotechnology and Bioengineering, 2010, 106(3):376-389. [28] Zhang YHP. Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations:Challenges and opportunities[J]. Biotechnology and Bioengineering, 2010, 105(4):663-677. [29] Wang Y, Huang W, Sathitsuksanoh N, et al. Biohydrogenation from biomass sugar mediated by in vitro synthetic enzymatic pathways[J]. Chemistry & Biology, 2011, 18(3):372-380. [30] Sun ZZ, Yeung E, Hayes CA, et al. Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system[J]. Acs Synthetic Biology, 2014, 3(6):387-397. [31] Singh-Blom A, Hughes RA, Ellington AR. Residue-specific incorpora-tion of unnatural amino acids into proteins in vitro and in vivo[M/OL]//Samuelson JC. Enzyme Engineering, Methods in Molecular Biology. Humana Press, 2013, 978: 93-114. [32] Liu CC, Schultz PG. Adding new chemistries to the genetic code[J]. Annual Review of Biochemistry, 2010, 79(1):413-444. [33] Zimmerman ES, Heibeck TH, Gill A, et al. Production of site-specific antibody-drug conjugates using optimized non-natural amino acids in a cell-free expression system[J]. Bioconjugate Chemistry, 2014, 25(2):351-361. [34] Smith MT, Wu JC, Varner CT, Bundy BC. Enhanced protein stability through minimally invasive, direct, covalent, and site-specific immobilization[J]. Biotechnology Progress, 2013, 29(1):247-254. [35] Smith MT, Hawes AK, Bundy BC. Reengineering viruses and virus-like particles through chemical functionalization strategies[J]. Current Opinion in Biotechnology, 2013, 24(4):620-626. [36] Loscha KV, Herlt AJ, Qi R, et al. Multiple-site labeling of proteins with unnatural amino acids[J]. Angewandte Chemie-Internatio-nal Edition, 2013, 51(9):2243-2246. [37] Yang Z, Hutter D, Sheng P, et al. Artificially expanded genetic information system:a new base pair with an alternative hydrogen bonding pattern[J]. Nucleic Acids Research, 2006, 34(21):6095-6101. [38] Yang Z, Chen F, Alvarado JB, Benner SA. Amplification, mutation, and sequencing of a six-letter synthetic genetic system[J]. Journal of the American Chemical Society, 2011, 133(38):15105-15112. [39] Acevedo-Rocha CG, Fang G, Schmidt M, et al. From essential to persistent genes:a functional approach to constructing synthetic life[J]. Trends in Genetics, 2013, 29(5):273-279. [40] Juhas M, Eberl L, Glass JI. Essence of life:essential genes of minimal genomes[J]. Trends in Cell Biology, 2011, 21(10):562-568. [41] Lagesen K, Ussery DW, Wassenaar TM. Genome update:the 1000th genome - a cautionary tale[J]. Microbiology-Sgm, 2010, 156:603-608. [42] McCutcheon JP. The bacterial essence of tiny symbiont genomes [J]. Current Opinion in Microbiology, 2010, 13(1):73-78. [43] Liu MF, Cescau S, Mechold U, et al. Identification of a novel nanoRNase in Bartonella[J]. Microbiology-Sgm, 2012, 158:886-895. [44] Ouzounis CA, Kunin V, Darzentas N, Goldovsky L. A minimal estimate for the gene content of the last universal common ancestor - exobiology from a terrestrial perspective[J]. Research in Microbiology, 2006, 157(1):57-68. [45] Kim KM, Caetano-Anolles G. The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms[J]. Bmc Evolutionary Biology, 2012, 12:13. [46] Lukjancenko O, Wassenaar TM, Ussery DW. Comparison of 61 sequenced Escherichia coli genomes[J]. Microbial Ecology, 2010, 60(4):708-720. [47] Anthony JR, Anthony LC, Nowroozi F, et al. Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4, 11-diene[J]. Metabolic Engineering, 2009, 11(1):13-19. [48] Yadav VG, De Mey M, Lim CG, et al. The future of metabolic engineering and synthetic biology:Towards a systematic practice[J]. Metabolic Engineering, 2012, 14(3):233-241. [49] Perez-Pinera P, Ousterout DG, Gersbach CA. Advances in targeted genome editing[J]. Current Opinion in Chemical Biology, 2012, 16(3-4):268-277. [50] Kim S, Lee MJ, Kim H, et al. Preassembled zinc-finger arrays for rapid construction of ZFNs[J]. Nature Methods, 2011, 8(1):7. [51] Bhakta MS, Henry IM, Ousterout DG, et al. Highly active zinc-finger nucleases by extended modular assembly[J]. Genome Research, 2013, 23(3):530-538. [52] Miller JC, Tan S, Qiao G, et al. A TALE nuclease architecture for efficient genome editing[J]. Nature Biotechnology, 2011, 29(2):143-148. [53] Gaj T, Gersbach CA, Barbas CF III. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering[J]. Trends in Biotechnology, 2013, 31(7):397-405. [54] Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea:versatile small RNAs for adaptive defense and regulation[J]. Annual Review of Genetics, 2011, 45:273-297. [55] Gasiunas G, Siksnys V. RNA-dependent DNA endonuclease Cas9 of the CRISPR system:Holy Grail of genome editing?[J]. Trends in Microbiology, 2013, 21(11):562-567. [56] Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337(6096):816-821. [57] Ran FA, Hsu PD, Wright J, et al. Genome engineering using the CRISPR-Cas9 system[J]. Nature Protocols, 2013, 8(11):2281-2308. [58] Jiang W, Bikard D, Cox D, et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems[J]. Nature Biotechnology, 2013, 31(3):233-239. [59] Yu Z, Ren M, Wang Z, et al. Highly Efficient genome modifications mediated by CRISPR/Cas9 in Drosophila[J]. Genetics, 2013, 195(1):289-291. [60] Gilbert LA, Larson MH, Morsut L, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes[J]. Cell, 2013, 154(2):442-451. [61] Cobb RE, Sun N, Zhao H. Directed evolution as a powerful synthetic biology tool[J]. Methods, 2013, 60(1):81-90. [62] Cobb RE, Si T, Zhao H. Directed evolution:an evolving and enabling synthetic biology tool[J]. Current Opinion in Chemical Biology, 2012, 16(3-4):285-291. [63] Zha W, Rubin-Pitel SB, Zhao H. Exploiting genetic diversity by directed evolution:molecular breeding of type III polyketide synthases improves productivity[J]. Molecular BioSystems, 2008, 4(3):246-248. [64] Atsumi S, Liao JC. Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli[J]. Applied and Environmental Microbiology, 2008, 74(24):7802-7808. [65] Filipovska A, Rackham O. Building a parallel metabolism within the cell[J]. Acs Chemical Biology, 2008, 3(1):51-63. [66] Liu CC, Mack AV, Brustad EM, et al. Evolution of proteins with genetically encoded “Chemical warheads”[J]. Journal of the American Chemical Society, 2009, 131(28):9616-9617. [67] Pfleger BF, Pitera DJ, Smolke CD, Keasling JD. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes[J]. Nat Biotech, 2006, 24(8):1027-1032. [68] Chen F, Gaucher EA, Leal NA, et al. Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(5):1948-1953. [69] Wang Q, Wu H, Wang A, et al. Prospecting metagenomic enzyme subfamily genes for DNA family shuffling by a novel PCR-based approach[J]. Journal of Biological Chemistry, 2010, 285(53):41509-41516. [70] Dickinson BC, Packer MS, Badran AH, Liu DR. A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations[J]. Nat Commun, 2014, 5:5352. [71] Luan G, Cai Z, Li Y, Ma Y. Genome replication engineering assisted continuous evolution(GREACE)to improve microbial tolerance for biofuels production[J]. Biotechnology for Biofuels, 2013, 6(1):137. [72] Connor MR, Atsumi S. Synthetic biology guides biofuel production[J]. Journal of Biomedicine and Biotechnology, 2010, doi:10. 1155/2010/541698. [73] Wang B, Wang J, Zhang W, Meldrum DR. Application of synthetic biology in cyanobacteria and algae[J]. Frontiers in Microbiology, 2012, 3:344. [74] Jin H, Chen L, Wang J, Zhang W. Engineering biofuel tolerance in non-native producing microorganisms[J]. Biotechnology Advances, 2014, 32(2):541-548. [75] Ramos JL, Duque E, Gallegos MT, et al. Mechanisms of solvent tolerance in gram-negative bacteria[J]. Annual Review of Microbiology, 2002, 56:743-768. [76] Lo TM, Teo WS, Ling H, et al. Microbial engineering strategies to improve cell viability for biochemical production[J]. Biotechnology Advances, 2013, 31(6):903-914. [77] Shao X, Raman B, Zhu M, et al. Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum[J]. Applied Microbiology and Biotechnology, 2011, 92(3):641-652. [78] Kim HJ, Turner TL, Jin YS. Combinatorial genetic perturbation to refine metabolic circuits for producing biofuels and biochemicals [J]. Biotechnology Advances, 2013, 31(6):976-985. [79] Lee SJ, Lee SJ, Lee DW. Design and development of synthetic microbial platform cells for bioenergy[J]. Frontiers in Microbiology, 2013, 4:92. [80] Martin VJJ, Pitera DJ, Withers ST, et al. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids[J]. Nature Biotechnology, 2013, 21(7):796-802. [81] Ro DK, Paradise EM, Ouellet M, et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast[J]. Nature, 2006, 440(7086):940-943. [82] Zhu S, Wu J, Du G, et al. Efficient synthesis of eriodictyol from L-tyrosine in Escherichia coli[J]. Applied and Environmental Microbiology, 2014, 80(10):3072-3080. [83] Neumann H, Neumann-Staubitz P. Synthetic biology approaches in drug discovery and pharmaceutical biotechnology[J]. Applied Microbiology and Biotechnology, 2010, 87(1):75-86. [84] Nguyen VH, Kim HS, Ha JM, et al. Genetically engineered Salmonella typhimurium as an imageable therapeutic probe for cancer[J]. Cancer Research, 2010, 70(1):18-23. [85] Neumann H, Hancock SM, Buning R, et al. A Method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation[J]. Molecular Cell, 2009, 36(1):153-163. [86] Caschera F, Noireaux V. Integration of biological parts toward the synthesis of a minimal cell[J]. Current Opinion in Chemical Biology, 2014, 22:85-91. [87] Noireaux V, Maeda YT, Libchaber A. Development of an artificial cell, from self-organization to computation and self-reproduction[J]. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(9):3473-3480. |
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