Bulletin of Chinese Academy of Sciences (Chinese Version)
crossdisciplinarity; life science; engineering; molecular biology; societal governance
It is their distinct spatial and temporal scales for natural substances defined various kinds of disciplines of natural sciences, as well as their connections. Based on the disruptive advances attributable to the revolutions of Molecular Biology and Genomics in the 20th century, by introducing the principles of engineering science into life science and biotechnology, the third revolution of Convergence has been emerged and rapidly developed into the cutting-edge frontier of academic research since the beginning of this century. The serial review articles of this issue illustrated both the history and the connotations of synthetic biology via highlighting main fields of research for synthetic biology, especially their scientific and technological fundamentals and social governance issues, thus it may cause attentions from the academic, the public and governments.
Bulletin of Chinese Academy of Sciences
Leduc S. The Mechanism of Life. Whitefish: Kessinger Legacy Reprint, 1911.
Way J C, Collins J J, Keasling J D, et al. Integrating biological redesign:Where synthetic biology came from and where it needs to go. Cell, 2014, 157(1):151-161.
Benner S A, Sismour A M. Synthetic biology. Nature Reviews Genetics, 2005, 6(7):533-543.
Cameron D E, Bashor C J, Collins J J. A brief history of synthetic biology. Nature Reviews Microbiology, 2014, 12:381-389.
National Research Council. Convergence:Facilitating Transdisciplinary Integration of Life Science, Physical Science, Engineering, and Beyond. Washington DC:The National Academies Press, 2014.
Purnick P E, Weiss R. The second wave of synthetic biology:from modules to systems. Nature Reviews Molecular Cell Biology, 2009, 10 (6):410-422.
Hezari M, Ketchum R E, Gibson D M, et al. Taxol production and taxadiene synthase activity in Taxus canadensis cell suspension cultures. Archives of Biochemistry and Biophysics, 1997, 337:185-190.
Ajikumar P K, Xiao W H, Tyo K E, et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science, 2010, 330:70-74.
Alper H, Fischer C, Nevoigt E, et al. Tuning genetic control through promoter engineering. Proceedings of the National Academy of Sciences of USA, 2005, 102 (36):12678-12683.
Nevoigt E, Kohnke J, Fischer C R, et al. Engineering of promoter replacement cassettes for fine-tuning of gene expression in Saccharomyces cerevisiae. Applied and Environmental Microbiology, 2006, 72 (8):5266-5273.
Orelle C, Carlson E D, Szal T, et al. Protein synthesis by ribosomes with tethered subunits. Nature, 2015, 524:119-124.
Taylor A I, Pinheiro V B, Smola M J, et al. Catalysts from synthetic genetic polymers. Nature, 2015, 518(7539):427-430.
Kiss G, Çelebi N, Moretti R, et al. Computational enzyme design. Angewandte Chemie International Edition, 2013, 52:5700-5725.
Privett H K, Kiss G, Lee T M, et al. Iterative approach to computational enzyme design. Proceedings of the National Academy of Sciences of USA, 2012, 109:3790-3795.
Liu XH, Kang FY, Hu C, et al. A genetically encoded photosensitizer protein facilitates the rational design of a miniature photocatalytic CO2-reducing enzyme. Nature Chemistry, 2018. doi:10.1038/s41557-018-0150-4.
Gardner T S, Cantor C R, Collins J J. Construction of a genetic toggle switch i n Escherichia coli. Nature, 2000, 403:339-342.
Elowitz M B, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature, 2000, 403:335-338.
Weiss R, Basu S. The device physics of cellular logic gates. First Workshop on Non-Silicon Computing.[2002-01-01]. http://www.hpcaconf.org/hpca8/nsc.pdf.
Endy D. Foundations for engineering biology. Nature, 2005, 438:449-453.
Isaacs F J, Dwyer D J, Ding C, et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology, 2004, 22:841-847.
Levskaya A, Chevalier A A, Tabor J J, et al. Synthetic biology:engineering Escherichia coli to see light. Nature, 2005, 438:441-442.
Stricker J, Cookson S, Bennett M R, et al. A fast, robust and tunable synthetic gene oscillator. Nature, 2008, 456:516-U39.
Tigges M, Marquez-Lago T T, Stelling J, et al. A tunable synthetic mammalian oscillator. Nature, 2009, 457:309-312.
Friedland A E, Lu T K, Wang X, et al. Synthetic gene networks that count. Science, 2009, 324:1199-1202.
Budin I, Devaraj N K. Membrane assembly driven by a biomimetic coupling reaction. Journal of the American Chemical Society, 2012, 134:751-753.
Smanski M J, Bhatia S, Zhao D, et al. Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 2014, 32:1241-1249.
Chen Y, Kim J K, Hirning A J, et al. Emergent genetic oscillations in a synthetic microbial consortium. Science, 2015, 349:986-989.
Gao X J, Chong L S, Kim M S, et al. Programmable protein circuits in living cells. Science, 2018, 361(6408):1252-1258.
Andrews L B, Nielsen A A K, Voigt C A. Cellular checkpoint control using programmable sequential logic. Science, 2018, 361(6408):pii:eaap8987.
Martin V J, Pitera D J, Withers S T, et al. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nature Biotechnology, 2003, 21:796-802.
Win M N, Smolke C D. Higher-order cellular information processing with synthetic RNA devices. Science, 2008, 322:456-460.
Paddon C J, Westfall P J, Pitera D J, et al. High-level semisynthetic production of the potent antimalarial artemisinin. Nature, 2013, 496:528-532.
Galanie S, Thodey K, Trenchard I J, et al. Complete biosynthesis of opioids in yeast. Science, 2015, 349:1095-1100.
Atsumi S, Hanai T, Liao J C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature, 2008, 451:86-89.
Huo Y X, Cho K M, Rivera J G L, et al. Conversion of proteins into biofuels by engineering nitrogen flux. Nature Biotechnology, 2011, 29:346-351.
Steen E J, Kang Y, Bokinsky G, et al. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature, 2010, 463:559-562.
Choi Y J, Lee S Y. Microbial production of short-chain alkanes. Nature, 2013, 502:571-574.
Yim H, Haselbeck R, Niu W, et al. Metabolic engineering of Escherichia coli for direct production of 1, 4-butanediol. Nature Chemical Biology, 2011, 7:445-452.
Holtz W J, Keasling J D. Engineering static and dynamic control of synthetic pathways. Cell, 2010, 140:19-23.
Callura J M, Cantor C R, Collins J J. Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences of USA, 2012, 109:5850-5855.
Yan X, Fan Y, Wei W, et al. Production of bioactive ginsenoside compound K in metabolically engineered yeast. Cell Research, 2014, 24:770-773.
Wang P, Wei Y, Fan Y, et al. Production of bioactive ginsenosides Rh2 and Rg3 by metabolically engineered yeasts. Metabolic Engineering, 2015, 29:97-105.
Wei W, Wang P, Wei Y, et al. Characterization of panax ginseng UDP-Glycosyltransferases catalyzing protopanaxatriol and biosyntheses of bioactive ginsenosides F1 and Rh1 in metabolically engineered yeasts. Molecular Plant, 2015, 8:1412-1424.
Yao Y F, Wang C S, Qiao J, et al. Metabolic engineering of Escherichia coli for production of salvianic acid A via an artificial biosynthetic pathway. Metabolic Engineering, 2013, 19(5):79-87.
Cello J, Paul A V, Wimmer E. Chemical synthesis of poliovirus cDNA:Generation of infectious virus in the absence of natural template. Science, 2002, 297:1016-1018.
mith HO1, Hutchison CA 3rd, Pfannkoch C, et al. Generating a synthetic genome by whole genome assembly:phiX174 bacteriophage from synthetic oligonucleotides. Proceedings of the National Academy of Sciences of USA, 2003, 100(26):15440-15445.
Gibson D G, Glass J I, Lartigue C, et al. Creation of a bacterial cellcontrolled by a chemically synthesized genome. Science, 2010, 329:52-56.
Gibson D G, Smith H O, Hutchison C A, et al. Chemical synthesis of the mouse mitochondrial genome. Nature Methods, 2010, 7(11):901-903.
Dymond J S, Richardson S M, Coombes C E, et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 2011, 477:471-476.
Annaluru N, Muller H, Mitchell L A, et al. Total synthesis of a functional designer eukaryotic chromosome. Science, 2014, 343:1426-1429.
Mercy G, Mozziconacci J, Scolari V F, et al. 3D organization of synthetic and scrambled chromosomes. Science, 2017, 355(6329):eaaf4597.
Shao Y Y, Lu N, Wu Z F, et al. Creating a functional singlechromosome yeast. Nature, 2018, 560:331-335.
Palluk S, Arlow D H, de Rond T, et al. De novo DNA synthesis using polymerase-nucleotide conjugates. Nature Biotechnology, 2018, 36:645-650.
Cong L, Ran F A, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science, 2013, 339(6121):819-823.
Ran F A, Hsu P D, Lin C Y, et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 2013, 154(6):1380-1389.
Komor A C, Kim Y B, Packer M S, et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature, 2016, 533:420-424.
Wang H, Russa M L, Qi L S. CRISPR/Cas9 in genome editing and beyond. Annual Review of Biochemistry, 2016, 85:227-264.
Li S Y, Cheng Q X, Wang J M, et al. CRISPR-Cas12a-assisted nucleic acid detection. Cell Discovery, 2018, 4:20.
Li S Y, Cheng Q X, Liu J K, et al., CRISPR-Cas12a has both cis-and trans-cleavage activities on single-stranded DNA. Cell Research, 2018, 28(4):491-493.
Harrington L B, Burstein D, Chen J S, et al. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science, 2018, eaav4294.
Chen J S, Ma E, Harrington L B, et al., CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science, 2018, 360(6387):436-439.
Gootenberg J S, Abudayyeh O O, Lee J W, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science, 2017, 356(6336):438-442.
June C H, O'Connor R S, Kawalekar O U, et al. CAR T cell immunotherapy for human cancer. Science, 2018, 359(6382):1361-1365.
Singh N, Shi J, June C H, et al. Genome-editing technologies in adoptive T cell immunotherapy for cancer. Current Hematologic Malignancy Reports, 2017, 12(6):522-529.
Anderson J C, Clarke E J, Arkin A P, et al. Environmentally controlled invasion of cancer cells by engineered bacteria. Journal of Molecular Biology, 2006, 355:619-627.
Gupta S, Bram E E, Weiss R. Genetically programmable pathogen sense and destroy. ACS Synthetic Biology, 2013, 2:715-723.
Duan F, March J C. Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. Proceedings of the National Academy of Sciences of USA, 2010, 107:11260-11264.
Jiang H, Wang Y Y, Fan W M, et al. Improvement of natamycin production by engineering of phosphopanteth transferases in streptomyces chattanoogensis L10. Applied and Environmental Microbiology, 2013, 79(11):3346-3354.
Mao X M, Luo S, Zhou R C, et al. Transcriptional regulation of the daptomycin gene cluster in streptomyces roseosporusby an autoregulator, AtrA *. Journal of Biological Chemistry, 2015, 290:7992-8001.
Zhang X S, Lou H D, Tao Y, et al. FkbN and Tcs7 are pathwayspecific regulators of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis L19. Journal of Industrial Microbiology & Biotechnology, 2016, 43:1693-1703.
Anesiadis N, Cluett W R, Mahadevan R. Dynamic metabolic engineering for increasing bioprocess productivity. Metabolic Engineering, 2008, 10:255-266.
Steen E J, Kang Y, Bokinsky G, et al. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature, 2010, 463:559.
Yu X Y, Liu T G, Zhu F Y, et al. In vitro reconstitution and steadystate analysis of the fatty acid synthase from Escherichia coli. Proceedings of the National Academy of Sciences of USA, 2011, 108(46):18643-18648.
Zhu X N, Tan Z G, Xu H T, et al. Metabolic evolution of two reducing equivalent-conserving pathways for high-yield succinate production in Escherichia coli. Metabolic Engineering, 2014, 24:87-96.
Jin H, Chen L, Zhang W. Engineering biofuel tolerance in nonnative producing microorganisms. Biotechnology Advances, 2014, 32(2):541-548.
Zhou J, Zhang H F, Zhang Y P, et al. Designing and creating a modularized synthetic pathway in cyanobacterium Synechocystis enables production of acetone from carbon dioxide. Metabolic Engineering, 2012, 14(4):394-400.
Wang B, Pugh S, Nielsen D R, et al. Engineering cyanobacteria for photosynthetic production of 3-hydroxybutyrate directly from CO 2. Metabolic Engineering, 2013, 16:68-77.
National Research Council. Convergence:Facilitating Transdisciplinary Integration of Life Sciences, Physical Sciences, Engineering, and Beyond.Washinton DC:National Academies Press, 2014.
Farny N G. A vision for teaching the values of synthetic biology. Trends Biotechnol, 2018, 36(11):1097-1100.
谭静, 胡启文, 肖文刚, 等.国际基因工程机器大赛对本科生创新能力培养的启示.卫生职业教育, 2018, (1):1-3.
"Synthetic Biology: Unsealing the Convergence Era of Life Science Research,"
Bulletin of Chinese Academy of Sciences (Chinese Version): Vol. 33
, Article 1.
Available at: https://bulletinofcas.researchcommons.org/journal/vol33/iss11/1