中国化学工程学报 ›› 2023, Vol. 56 ›› Issue (4): 141-151.DOI: 10.1016/j.cjche.2022.07.019
Xueying Zhu, Zhaoyang Zhang, Bin Jia, Yingjin Yuan
收稿日期:
2022-03-22
修回日期:
2022-07-19
出版日期:
2023-04-28
发布日期:
2023-06-13
通讯作者:
Bin Jia,E-mail:bin.jia@tju.edu.cn
基金资助:
Xueying Zhu, Zhaoyang Zhang, Bin Jia, Yingjin Yuan
Received:
2022-03-22
Revised:
2022-07-19
Online:
2023-04-28
Published:
2023-06-13
Contact:
Bin Jia,E-mail:bin.jia@tju.edu.cn
Supported by:
摘要: Synthetic biotechnology has led to the widespread application of genetically modified organisms (GMOs) in biochemistry, bioenergy, and therapy. However, the uncontrolled spread of GMOs may lead to genetic contamination by horizontal gene transfer, resulting in unpredictable biosafety risks. To deal with these challenges, many effective methods have been developed for biocontainment. In this article, we summarize and discuss recent advances in biocontainment strategies from three aspects: DNA replication, transcriptional regulation, and protein translation. We also briefly introduce the efforts in the biocontainment convention, such as the recent publication of the Tianjin Biosecurity Guidelines for the Code of Conduct for Scientists.
Xueying Zhu, Zhaoyang Zhang, Bin Jia, Yingjin Yuan. Current advances of biocontainment strategy in synthetic biology[J]. 中国化学工程学报, 2023, 56(4): 141-151.
Xueying Zhu, Zhaoyang Zhang, Bin Jia, Yingjin Yuan. Current advances of biocontainment strategy in synthetic biology[J]. Chinese Journal of Chemical Engineering, 2023, 56(4): 141-151.
[1] L. Clarke, R. Kitney, Developing synthetic biology for industrial biotechnology applications, Biochem. Soc. Trans. 48 (1) (2020) 113–122. [2] X. Tan, J.H. Letendre, J.J. Collins, W.W. Wong, Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics, Cell 184 (4) (2021) 881–898. [3] M.J. Capeness, L.E. Horsfall, Synthetic biology approaches towards the recycling of metals from the environment, Biochem. Soc. Trans. 48 (4) (2020) 1367–1378. [4] D. Gupta, G. Sharma, P. Saraswat, R. Ranjan, Synthetic biology in plants, a boon for coming decades, Mol. Biotechnol. 63 (12) (2021) 1138–1154. [5] J.W. Lee, C. Chan, S. Slomovic, J.J. Collins, Next-generation biocontainment systems for engineered organisms, Nat. Chem. Biol. 14 (6) (2018) 530–537. [6] S.A. Benner, A.M. Sismour, Synthetic biology, Nat. Rev. Genet. 6 (7) (2005) 533–543. [7] G.H. Moe-Behrens, R. Davis, K.A. Haynes, Preparing synthetic biology for the world, Front Microbiol 4 (2013) 5. [8] D.J. Wilson, NIH guidelines for research involving recombinant DNA molecules, Account. Res. 3 (2–3) (1993) 177–185. [9] G. Lopez, J.C. Anderson, Synthetic auxotrophs with ligand-dependent essential genes for a BL21(DE3) biosafety strain, ACS Synth. Biol. 4 (12) (2015) 1279–1286. [10] R. Hirota, K. Abe, Z.I. Katsuura, R. Noguchi, S. Moribe, K. Motomura, T. Ishida, M. Alexandrov, H. Funabashi, T. Ikeda, A. Kuroda, A novel biocontainment strategy makes bacterial growth and survival dependent on phosphite, Sci. Rep. 7 (2017) 44748. [11] A.J. Rovner, A.D. Haimovich, S.R. Katz, Z. Li, M.W. Grome, B.M. Gassaway, M. Amiram, J.R. Patel, R.R. Gallagher, J. Rinehart, F.J. Isaacs, Recoded organisms engineered to depend on synthetic amino acids, Nature 518 (7537) (2015) 89–93. [12] F. Stirling, A. Naydich, J. Bramante, R. Barocio, M. Certo, H. Wellington, E. Redfield, S. O'Keefe, S. Gao, A. Cusolito, J. Way, P. Silver, Synthetic cassettes for pH-mediated sensing, counting, and containment, Cell Rep 30 (2020) 3139-3148. [13] J.I. Yoo, S. Seppälä, M.A. O’Malley, Engineered fluoride sensitivity enables biocontainment and selection of genetically-modified yeasts, Nat. Commun. 11 (1) (2020) 5459. [14] Y.Z. Cai, N. Agmon, W.J. Choi, A. Ubide, G. Stracquadanio, K. Caravelli, H.P. Hao, J.S. Bader, J.D. Boeke, Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes, PNAS 112 (6) (2015) 1803–1808. [15] K. Motomura, K. Sano, S. Watanabe, A. Kanbara, A.H. Gamal Nasser, T. Ikeda, T. Ishida, H. Funabashi, A. Kuroda, R. Hirota, Synthetic phosphorus metabolic pathway for biosafety and contamination management of cyanobacterial cultivation, ACS Synth. Biol. 7 (9) (2018) 2189–2198. [16] R.L. Clark, G.C. Gordon, N.R. Bennett, H.X. Lyu, T.W. Root, B.F. Pfleger, High-CO 2 requirement as a mechanism for the containment of genetically modified cyanobacteria, ACS Synth. Biol. 7 (2) (2018) 384–391. [17] Y. Zhou, T. Sun, Z. Chen, X. Song, L. Chen, W. Zhang, Development of a new biocontainment strategy in model Cyanobacterium Synechococcus strains, ACS Synth Biol, 8 (2019) 2576-2584. [18] L.L. Si, H. Xu, X.Y. Zhou, Z.W. Zhang, Z.Y. Tian, Y. Wang, Y.M. Wu, B. Zhang, Z.L. Niu, C.L. Zhang, G. Fu, S.L. Xiao, Q. Xia, L.H. Zhang, D.M. Zhou, Generation of influenza A viruses as live but replication-incompetent virus vaccines, Science 354 (6316) (2016) 1170–1173. [19] J. Gressel, Dealing with transgene flow of crop protection traits from crops to their relatives, Pest Manag. Sci. 71 (5) (2015) 658–667. [20] T.M. Chang, S. Prakash, Procedures for microencapsulation of enzymes, cells and genetically engineered microorganisms, Mol. Biotechnol. 17 (3) (2001) 249–260. [21] R.M. Papi, S.A. Chaitidou, F.A. Trikka, D.A. Kyriakidis, Encapsulated Escherichia coli in alginate beads capable of secreting a heterologous pectin lyase, Microb. Cell Fact. 4 (2005) 35. [22] C.J. Kearney, D.J. Mooney, Macroscale delivery systems for molecular and cellular payloads, Nat. Mater. 12 (11) (2013) 1004–1017. [23] T.C. Tang, E. Tham, X.Y. Liu, K. Yehl, A.J. Rovner, H. Yuk, C. de la Fuente-Nunez, F.J. Isaacs, X.H. Zhao, T.K. Lu, Hydrogel-based biocontainment of bacteria for continuous sensing and computation, Nat. Chem. Biol. 17 (6) (2021) 724–731. [24] R.O.Y. Curtiss, M. Inoue, D. Pereira, J.C. Hsu, L. Alexander, L. Rock, Construction and Use of Safer Bacterial Host Strains for Recombinant and Research, in: W.A. Scott, R. Werner (Eds.) Molecular of Cloning of Recombinant DNA, Academic Press, Beijing, (1977) 99-114. [25] H. Zhou, X.C. Li, Z.Y. Wang, J.Y. Yin, H.C. Tan, L. Wang, X.Y. Qiao, Y.P. Jiang, W. Cui, M. Liu, Y.J. Li, Y.G. Xu, L.J. Tang, Construction and characterization of thymidine auxotrophic (ΔthyA) recombinant lactobacillus casei expressing bovine lactoferricin, BMC Vet. Res. 14 (2018) 206. [26] S. Hosseini, A. Curilovs, S.M. Cutting, Biological containment of genetically modified bacillus subtilis, Appl. Environ. Microbiol. 84 (3) (2018) e02334–e02317. [27] L. Steidler, S. Neirynck, N. Huyghebaert, V. Snoeck, A. Vermeire, B. Goddeeris, E. Cox, J.P. Remon, E. Remaut, Biological containment of genetically modified Lactococcus lactis for intestinal delivery of human interleukin 10, Nat Biotechnol, 21 (2003) 785-789. [28] Z. Yang, D. Hutter, P. Sheng, A.M. Sismour, S.A. Benner, Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern, Nucleic Acids Res. 34 (21) (2006) 6095–6101. [29] Z. Yang, F. Chen, J.B. Alvarado, S.A. Benner, Amplification, mutation, and sequencing of a six-letter synthetic genetic system, J. Am. Chem. Soc. 133 (38) (2011) 15105–15112. [30] H.J. Kim, N.A. Leal, S. Hoshika, S.A. Benner, Ribonucleosides for an artificially expanded genetic information system, J. Org. Chem. 79 (7) (2014) 3194–3199. [31] A.M. Leconte, G.T. Hwang, S. Matsuda, P. Capek, Y. Hari, F.E. Romesberg, Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet, J. Am. Chem. Soc. 130 (7) (2008) 2336–2343. [32] Y.J. Seo, G.T. Hwang, P. Ordoukhanian, F.E. Romesberg, Optimization of an unnatural base pair toward natural-like replication, J. Am. Chem. Soc. 131 (9) (2009) 3246–3252. [33] D.A. Malyshev, K. Dhami, T. Lavergne, T.J. Chen, N. Dai, J.M. Foster, I.R. Corrêa Jr, F.E. Romesberg, A semi-synthetic organism with an expanded genetic alphabet, Nature 509 (7500) (2014) 385–388. [34] Y. Zhang, J.L. Ptacin, E.C. Fischer, H.R. Aerni, C.E. Caffaro, K. San Jose, A.W. Feldman, C.R. Turner, F.E. Romesberg, A semi-synthetic organism that stores and retrieves increased genetic information, Nature 551 (7682) (2017) 644–647. [35] Y. Zhang, B.M. Lamb, A.W. Feldman, A.X. Zhou, T. Lavergne, L.J. Li, F.E. Romesberg, A semisynthetic organism engineered for the stable expansion of the genetic alphabet, PNAS 114 (6) (2017) 1317–1322. [36] M.P. Ledbetter, R.J. Karadeema, F.E. Romesberg, Reprograming the replisome of a semisynthetic organism for the expansion of the genetic alphabet, J. Am. Chem. Soc. 140 (2) (2018) 758–765. [37] T. Efthymiou, J. Gavette, M. Stoop, F. De Riccardis, M. Froeyen, P. Herdewijn, R. Krishnamurthy, Chimeric XNA: An unconventional design for orthogonal informational systems, Chemistry, 24 (2018) 12811-12819. [38] A. Ravikumar, A. Arrieta, C.C. Liu, An orthogonal DNA replication system in yeast, Nat. Chem. Biol. 10 (3) (2014) 175–177. [39] G.A. Arzumanyan, K.N. Gabriel, A. Ravikumar, A.A. Javanpour, C.C. Liu, Mutually orthogonal DNA replication systems in vivo, ACS Synth. Biol. 7 (7) (2018) 1722–1729. [40] Y. Sakatani, T. Yomo, N. Ichihashi, Self-replication of circular DNA by a self-encoded DNA polymerase through rolling-circle replication and recombination, Sci Rep 8 (1) (2018) 13089. [41] A.A. Javanpour, C.C. Liu, Genetic compatibility and extensibility of orthogonal replication, ACS Synth. Biol. 8 (6) (2019) 1249–1256. [42] Z. Zhong, B.G. Wong, A. Ravikumar, G.A. Arzumanyan, A.S. Khalil, C.C. Liu, Automated continuous evolution of proteins in vivo, ACS Synth Biol, 9 (2020) 1270-1276. [43] R. Klassen, F. Meinhardt, Linear Protein-Primed Replicating Plasmids in Eukaryotic Microbes, in: F. Meinhardt, R. Klassen (Eds.) Microbial Linear Plasmids, Springer Berlin Heidelberg, Berlin, Heidelberg, (2007) 187-226. [44] H. Heuer, K. Smalla, Horizontal gene transfer between bacteria, Environ. Biosafety Res. 6 (1–2) (2007) 3–13. [45] K.M. Nielsen, P.J. Johnsen, D. Bensasson, D. Daffonchio, Release and persistence of extracellular DNA in the environment, Environ. Biosafety Res. 6 (1–2) (2007) 37–53. [46] K. Gerdes, F.W. Bech, S.T. Jørgensen, A. Løbner-Olesen, P.B. Rasmussen, T. Atlung, L. Boe, O. Karlstrom, S. Molin, K. von Meyenburg, Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon, EMBO J. 5 (8) (1986) 2023–2029. [47] A.K. Bej, M.H. Perlin, R.M. Atlas, Model suicide vector for containment of genetically engineered microorganisms, Appl. Environ. Microbiol. 54 (10) (1988) 2472–2477. [48] Q. Li, Y.J. Wu, A fluorescent, genetically engineered microorganism that degrades organophosphates and commits suicide when required, Appl. Microbiol. Biotechnol. 82 (4) (2009) 749–756. [49] G. Recorbet, C. Robert, A. Givaudan, B. Kudla, P. Normand, G. Faurie, Conditional suicide system of Escherichia coli released into soil that uses the Bacillus subtilis sacB gene, Appl. Environ. Microbiol. 59 (5) (1993) 1361–1366. [50] S. Molin, L. Boe, L.B. Jensen, C.S. Kristensen, M. Givskov, J.L. Ramos, A.K. Bej, Suicidal genetic elements and their use in biological containment of bacteria, Annu. Rev. Microbiol. 47 (1993) 139–166. [51] O. Wright, G.B. Stan, T. Ellis, Building-in biosafety for synthetic biology, Microbiology (Reading) 159 (Pt 7) (2013) 1221–1235. [52] D.C. Pecota, C.S. Kim, K. Wu, K. Gerdes, T.K. Wood, Combining the hok/sok, parDE, and pnd postsegregational killer loci to enhance plasmid stability, Appl. Environ. Microbiol. 63 (5) (1997) 1917–1924. [53] I. Martincorena, A.S.N. Seshasayee, N.M. Luscombe, Evidence of non-random mutation rates suggests an evolutionary risk management strategy, Nature 485 (7396) (2012) 95–98. [54] K. Gerdes, E.G. Wagner, RNA antitoxins, Curr Opin Microbiol, 10 (2007) 117-124. [55] S. Brantl, Bacterial type I toxin-antitoxin systems, RNA Biol. 9 (12) (2012) 1488–1490. [56] E. Diago-Navarro, A.M. Hernandez-Arriaga, J. López-Villarejo, A.J. Muñoz-Gómez, M.B. Kamphuis, R. Boelens, M. Lemonnier, R. Díaz-Orejas, parD toxin-antitoxin system of plasmid R1 - basic contributions, biotechnological applications and relationships with closely-related toxin-antitoxin systems, FEBS J. 277 (15) (2010) 3097–3117. [57] E.M. Halvorsen, J.J. Williams, A.J. Bhimani, E.A. Billings, P.J. Hergenrother, Txe, an endoribonuclease of the enterococcal Axe–Txe toxin–antitoxin system, cleaves mRNA and inhibits protein synthesis, Microbiology 157 (2) (2011) 387–397. [58] K. Pedersen, A.V. Zavialov, M.Y. Pavlov, J. Elf, K. Gerdes, M. Ehrenberg, The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site, Cell 112 (1) (2003) 131–140. [59] T.R. Blower, F.L. Short, F. Rao, K. Mizuguchi, X.Y. Pei, P.C. Fineran, B.F. Luisi, G.P. Salmond, Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes, Nucleic Acids Res, 40 (2012) 6158-6173. [60] R.J. Roberts, How restriction enzymes became the workhorses of molecular biology, Proc. Natl. Acad. Sci. USA 102 (17) (2005) 5905–5908. [61] E. Cascales, S.K. Buchanan, D. Duché, C. Kleanthous, R. Lloubès, K. Postle, M. Riley, S. Slatin, D. Cavard, Colicin biology, Microbiology and Molecular Biology Reviews, 71 (2007) 158-229. [62] M.J. Catalão, F. Gil, J. Moniz-Pereira, C. São-José, M. Pimentel, Diversity in bacterial lysis systems: bacteriophages show the way, FEMS Microbiol Rev 37 (4) (2013) 554–571. [63] T. Blazejewski, H.I. Ho, H.H. Wang, Synthetic sequence entanglement augments stability and containment of genetic information in cells, Science 365 (6453) (2019) 595–598. [64] N. Fraikin, F. Goormaghtigh, L. van Melderen, Type II toxin-antitoxin systems: evolution and revolutions, J. Bacteriol. 202 (7) (2020) e00763–e00719. [65] S.M. Knudsen, O.H. Karlström, Development of efficient suicide mechanisms for biological containment of bacteria, Appl. Environ. Microbiol. 57 (1) (1991) 85–92. [66] O. Wright, M. Delmans, G.B. Stan, T. Ellis, GeneGuard: a modular plasmid system designed for biosafety, ACS Synth. Biol. 4 (3) (2015) 307–316. [67] H.M. Salis, E.A. Mirsky, C.A. Voigt, Automated design of synthetic ribosome binding sites to control protein expression, Nat. Biotechnol. 27 (10) (2009) 946–950. [68] D.G. Gibson, J.I. Glass, C. Lartigue, V.N. Noskov, R.Y. Chuang, M.A. Algire, G.A. Benders, M.G. Montague, L. Ma, M.M. Moodie, C. Merryman, S. Vashee, R. Krishnakumar, N. Assad-Garcia, C. Andrews-Pfannkoch, E.A. Denisova, L. Young, Z.Q. Qi, T.H. Segall-Shapiro, C.H. Calvey, P.P. Parmar, C.A. Hutchison III, H.O. Smith, J.C. Venter, Creation of a bacterial cell controlled by a chemically synthesized genome, Science 329 (5987) (2010) 52–56. [69] C.A. Hutchison III, R.Y. Chuang, V.N. Noskov, N. Assad-Garcia, T.J. Deerinck, M.H. Ellisman, J. Gill, K. Kannan, B.J. Karas, L. Ma, J.F. Pelletier, Z.Q. Qi, R.A. Richter, E.A. Strychalski, L.J. Sun, Y. Suzuki, B. Tsvetanova, K.S. Wise, H.O. Smith, J.I. Glass, C. Merryman, D.G. Gibson, J.C. Venter, Design and synthesis of a minimal bacterial genome, Science 351 (6280) (2016) aad6253. [70] C.M. Fraser, J.D. Gocayne, O. White, M.D. Adams, R.A. Clayton, R.D. Fleischmann, C.J. Bult, A.R. Kerlavage, G. Sutton, J.M. Kelley, R.D. Fritchman, J.F. Weidman, K.V. Small, M. Sandusky, J. Fuhrmann, D. Nguyen, T.R. Utterback, D.M. Saudek, C.A. Phillips, J.M. Merrick, J.F. Tomb, B.A. Dougherty, K.F. Bott, P.C. Hu, T.S. Lucier, S.N. Peterson, H.O. Smith, C.A. Hutchison, 3rd, J.C. Venter, The minimal gene complement of Mycoplasma genitalium, Science, 270 (1995) 397-403. [71] R.A.J. Nicholas, R.D. Ayling, L. McAuliffe, Vaccines for Mycoplasma diseases in animals and man, J. Comp. Pathol. 140 (2–3) (2009) 85–96. [72] M. Ishfaq, W.Y. Hu, M.Z. Khan, I. Ahmad, W.X. Guo, J.C. Li, Current status of vaccine research, development, and challenges of vaccines for Mycoplasma gallisepticum, Poult. Sci. 99 (9) (2020) 4195–4202. [73] D. Maes, F. Boyen, B. Devriendt, P. Kuhnert, A. Summerfield, F. Haesebrouck, Perspectives for improvement of Mycoplasma hyopneumoniae vaccines in pigs, Vet Res 52 (1) (2021) 67. [74] A. Broto, E. Gaspari, S. Miravet-Verde, V.A.P.M. dos Santos, M. Isalan, A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications, Nature communications, 13 (2022) 1910. [75] G.G. Corrêa, M.R. da Costa Ribeiro Lins, B.F. Silva, G.B. de Paiva, V.F.B. Zocca, N.V. Ribeiro, F.P. Picheli, M. Mack, D.B. Pedrolli, A modular autoinduction device for control of gene expression in Bacillus subtilis, Metab. Eng. 61 (2020) 326–334. [76] E. Denkovskienė, Š. Paškevičius, S. Werner, Y. Gleba, A. Ražanskienė, Inducible Expression of agrobacterium virulence gene VirE2 for stringent regulation of T-DNA transfer in plant transient expression systems, Molecular plant-microbe interactions, 28 (2015) 1247-1255. [77] M. Gossen, S. Freundlieb, G. Bender, G. Müller, W. Hillen, H. Bujard, Transcriptional activation by tetracyclines in mammalian cells, Science 268 (5218) (1995) 1766–1769. [78] N. Agmon, Z.J. Tang, K. Yang, B. Sutter, S. Ikushima, Y.Z. Cai, K. Caravelli, J.A. Martin, X.J. Sun, W.J. Choi, A. Zhang, G. Stracquadanio, H.P. Hao, B.P. Tu, D. Fenyo, J.S. Bader, J.D. Boeke, Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae, PNAS 114 (8) (2017) e1470-e1479. [79] S. Ikushima, J.D. Boeke, New orthogonal transcriptional switches derived from Tet repressor homologues for saccharomyces cerevisiae regulated by 2, 4-diacetylphloroglucinol and other ligands, ACS Synth. Biol. 6 (3) (2017) 497–506. [80] S. Ikushima, Y. Zhao, J.D. Boeke, Development of a tightly controlled off switch for saccharomyces cerevisiae regulated by camphor, a low-cost natural product, G3 (Bethesda) 5 (10) (2015) 1983–1990. [81] M. Tominaga, K. Nozaki, D. Umeno, J. Ishii, A. Kondo, Robust and flexible platform for directed evolution of yeast genetic switches, Nat Commun 12 (1) (2021) 1846. [82] M.J. Oliver, J.E. Quisenberry, N. Trolinder, D.L. Keim, Control of plant gene expression, US Pat., EP0775212A2 (1998). [83] S. Hoshika, N.A. Leal, M.J. Kim, M.S. Kim, N.B. Karalkar, H.J. Kim, A.M. Bates, N.E. Watkins Jr, H.A. SantaLucia, A.J. Meyer, S. DasGupta, J.A. Piccirilli, A.D. Ellington, J. SantaLucia Jr, M.M. Georgiadis, S.A. Benner, Hachimoji DNA and RNA: a genetic system with eight building blocks, Science 363 (6429) (2019) 884–887. [84] M.L. Gleghorn, E.K. Davydova, L.B. Rothman-Denes, K.S. Murakami, Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase, Mol. Cell 32 (5) (2008) 707–717. [85] D.S. Leventhal, A. Sokolovska, N. Li, C. Plescia, S.A. Kolodziej, C.W. Gallant, R. Christmas, J.R. Gao, M.J. James, A. Abin-Fuentes, M. Momin, C. Bergeron, A. Fisher, P.F. Miller, K.A. West, J.M. Lora, Immunotherapy with engineered bacteria by targeting the STING pathway for anti-tumor immunity, Nat. Commun. 11 (2020) 2739. [86] H. Čelešnik, A. Tanšek, A. Tahirović, A. Vižintin, J. Mustar, V. Vidmar, M. Dolinar, Biosafety of biotechnologically important microalgae: intrinsic suicide switch implementation in cyanobacterium Synechocystis sp. PCC 6803, Biol. Open 5 (4) (2016) 519–528. [87] C.T. Chan, J.W. Lee, D.E. Cameron, C.J. Bashor, J.J. Collins, ‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment, Nat. Chem. Biol. 12 (2) (2016) 82–86. [88] R.R. Gallagher, J.R. Patel, A.L. Interiano, A.J. Rovner, F.J. Isaacs, Multilayered genetic safeguards limit growth of microorganisms to defined environments, Nucleic Acids Res. 43 (3) (2015) 1945–1954. [89] L. Vidal, J. Pinsach, G. Striedner, G. Caminal, P. Ferrer, Development of an antibiotic-free plasmid selection system based on glycine auxotrophy for recombinant protein overproduction in Escherichia coli, J. Biotechnol. 134 (1–2) (2008) 127–136. [90] T. Mukai, M.J. Lajoie, M. Englert, D. Söll, Rewriting the genetic code, Annu. Rev. Microbiol. 71 (2017) 557–577. [91] R. Rubini, C. Mayer, Addicting escherichia coli to new-to-nature reactions, ACS Chem. Biol. 15 (12) (2020) 3093–3098. [92] C. Mayer, Selection, addiction and catalysis: emerging trends for the incorporation of noncanonical amino acids into peptides and proteins in vivo, Chembiochem 20 (11) (2019) 1357–1364. [93] J. Kuo, F. Stirling, Y.H. Lau, Y. Shulgina, J.C. Way, P.A. Silver, Synthetic genome recoding: new genetic codes for new features, Curr. Genet. 64 (2) (2018) 327–333. [94] F.J. Isaacs, P.A. Carr, H.H. Wang, M.J. Lajoie, B. Sterling, L. Kraal, A.C. Tolonen, T.A. Gianoulis, D.B. Goodman, N.B. Reppas, C.J. Emig, D. Bang, S.J. Hwang, M.C. Jewett, J.M. Jacobson, G.M. Church, Precise manipulation of chromosomes in vivo enables genome-wide codon replacement, Science, 333 (2011) 348-353. [95] C.M. Scheidler, M. Vrabel, S. Schneider, Genetic code expansion, protein expression, and protein functionalization in bacillus subtilis, ACS Synth. Biol. 9 (3) (2020) 486–493. [96] D.A. Stork, G.R. Squyres, E. Kuru, K.A. Gromek, J. Rittichier, A. Jog, B.M. Burton, G.M. Church, E.C. Garner, A.M. Kunjapur, Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights, Nat. Commun. 12 (1) (2021) 5429. [97] S. Changko, P.D. Rajakumar, R.E.B. Young, S. Purton, The phosphite oxidoreductase gene, ptxD as a bio-contained chloroplast marker and crop-protection tool for algal biotechnology using Chlamydomonas, Appl. Microbiol. Biotechnol. 104 (2) (2020) 675–686. [98] R.E.B. Young, S. Purton, Codon reassignment to facilitate genetic engineering and biocontainment in the chloroplast of Chlamydomonas reinhardtii, Plant Biotechnol. J. 14 (5) (2016) 1251–1260. [99] N.X. Wang, Y. Li, W. Niu, M. Sun, R. Cerny, Q.S. Li, J.T. Guo, Construction of a live-attenuated HIV-1 vaccine through genetic code expansion, Angew. Chem. Int. Ed Engl. 53 (19) (2014) 4867–4871. [100] W.E. Robertson, L. Funke, D. de la Torre, J. Fredens, T.S. Elliott, M. Spinck, Y. Christova, D. Cervettini, F.L. Böge, K.C. Liu, S. Buse, S. Maslen, G. Salmond, J.W. Chin, Sense codon reassignment enables viral resistance and encoded polymer synthesis, Science 372 (6546) (2021) 1057–1062. [101] Y.H. Lau, F. Stirling, J. Kuo, M.A.P. Karrenbelt, Y.A. Chan, A. Riesselman, C.A. Horton, E. Schäfer, D. Lips, M.T. Weinstock, D.G. Gibson, J.C. Way, P.A. Silver, Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA, Nucleic Acids Res, 45 (2017) 6971-6980. [102] M.J. Lajoie, A.J. Rovner, D.B. Goodman, H.R. Aerni, A.D. Haimovich, G. Kuznetsov, J.A. Mercer, H.H. Wang, P.A. Carr, J.A. Mosberg, N. Rohland, P.G. Schultz, J.M. Jacobson, J. Rinehart, G.M. Church, F.J. Isaacs, Genomically recoded organisms expand biological functions, Science 342 (6156) (2013) 357–360. [103] Z.-Y. Zhang, D.-N. Liao, Y.-X. Ma, B. Jia, Y.-J. Yuan, Orthogonality of redesigned tRNA molecules with three stop codons, Chinese Journal of Chemistry, 40 (2022) 825-831. [104] N. Ostrov, M. Landon, M. Guell, G. Kuznetsov, J. Teramoto, N. Cervantes, M. Zhou, K. Singh, M.G. Napolitano, M. Moosburner, E. Shrock, B.W. Pruitt, N. Conway, D.B. Goodman, C.L. Gardner, G. Tyree, A. Gonzales, B.L. Wanner, J.E. Norville, M.J. Lajoie, G.M. Church, Design, synthesis, and testing toward a 57-codon genome, Science 353 (6301) (2016) 819–822. [105] S.M. Richardson, L.A. Mitchell, G. Stracquadanio, K. Yang, J.S. Dymond, J.E. DiCarlo, D. Lee, C.L.V. Huang, S. Chandrasegaran, Y.Z. Cai, J.D. Boeke, J.S. Bader, Design of a synthetic yeast genome, Science 355 (6329) (2017) 1040–1044. [106] L.A. Mitchell, A. Wang, G. Stracquadanio, Z. Kuang, X.Y. Wang, K. Yang, S. Richardson, J.A. Martin, Y. Zhao, R. Walker, Y.S. Luo, H.J. Dai, K. Dong, Z.J. Tang, Y.L. Yang, Y.Z. Cai, A. Heguy, B. Ueberheide, D. Fenyö, J.B. Dai, J.S. Bader, J.D. Boeke, Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond, Science 355 (6329) (2017) eaaf4831 [107] G. Mercy, J. Mozziconacci, V.F. Scolari, K. Yang, G. Zhao, A. Thierry, Y. Luo, L.A. Mitchell, M. Shen, Y. Shen, R. Walker, W. Zhang, Y. Wu, Z.X. Xie, Z. Luo, Y. Cai, J. Dai, H. Yang, Y.J. Yuan, J.D. Boeke, J.S. Bader, H. Muller, R. Koszul, 3D organization of synthetic and scrambled chromosomes, Science, 355.6329 (2017) eaaf4597. [108] Y. Shen, Y. Wang, T. Chen, F. Gao, J.H. Gong, D. Abramczyk, R. Walker, H.C. Zhao, S.H. Chen, W. Liu, Y.S. Luo, C.A. Müller, A. Paul-Dubois-Taine, B. Alver, G. Stracquadanio, L.A. Mitchell, Z.Q. Luo, Y.Q. Fan, B.J. Zhou, B. Wen, F.J. Tan, Y.J. Wang, J. Zi, Z.X. Xie, B.Z. Li, K. Yang, S.M. Richardson, H. Jiang, C.E. French, C.A. Nieduszynski, R. Koszul, A.L. Marston, Y.J. Yuan, J. Wang, J.S. Bader, J.B. Dai, J.D. Boeke, X. Xu, Y.Z. Cai, H.M. Yang, Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome, Science 355 (6329) (2017) eaaf4791. [109] Y. Wu, B.Z. Li, M. Zhao, L.A. Mitchell, Z.X. Xie, Q.H. Lin, X. Wang, W.H. Xiao, Y. Wang, X. Zhou, H. Liu, X. Li, M.Z. Ding, D. Liu, L. Zhang, B.L. Liu, X.L. Wu, F.F. Li, X.T. Dong, B. Jia, W.Z. Zhang, G.Z. Jiang, Y. Liu, X. Bai, T.Q. Song, Y. Chen, S.J. Zhou, R.Y. Zhu, F. Gao, Z. Kuang, X.Y. Wang, M. Shen, K. Yang, G. Stracquadanio, S.M. Richardson, Y.C. Lin, L.H. Wang, R. Walker, Y.S. Luo, P.S. Ma, H.M. Yang, Y.Z. Cai, J.B. Dai, J.S. Bader, J.D. Boeke, Y.J. Yuan, Bug mapping and fitness testing of chemically synthesized chromosome X, Science 355 (6329) (2017) eaaf4706. [110] Z.X. Xie, B.Z. Li, L.A. Mitchell, Y. Wu, X. Qi, Z. Jin, B. Jia, X. Wang, B.X. Zeng, H.M. Liu, X.L. Wu, Q. Feng, W.Z. Zhang, W. Liu, M.Z. Ding, X. Li, G.R. Zhao, J.J. Qiao, J.S. Cheng, M. Zhao, Z. Kuang, X.Y. Wang, J.A. Martin, G. Stracquadanio, K. Yang, X. Bai, J. Zhao, M.L. Hu, Q.H. Lin, W.Q. Zhang, M.H. Shen, S. Chen, W. Su, E.X. Wang, R. Guo, F. Zhai, X.J. Guo, H.X. Du, J.Q. Zhu, T.Q. Song, J.J. Dai, F.F. Li, G.Z. Jiang, S.L. Han, S.Y. Liu, Z.C. Yu, X.N. Yang, K. Chen, C. Hu, D.S. Li, N. Jia, Y. Liu, L.T. Wang, S. Wang, X.T. Wei, M.Q. Fu, L.M. Qu, S.Y. Xin, T. Liu, K.R. Tian, X.N. Li, J.H. Zhang, L.X. Song, J.G. Liu, J.F. Lv, H. Xu, R. Tao, Y. Wang, T.T. Zhang, Y.X. Deng, Y.R. Wang, T. Li, G.X. Ye, X.R. Xu, Z.B. Xia, W. Zhang, S.L. Yang, Y.L. Liu, W.Q. Ding, Z.N. Liu, J.Q. Zhu, N.Z. Liu, R. Walker, Y.S. Luo, Y. Wang, Y. Shen, H.M. Yang, Y.Z. Cai, P.S. Ma, C.T. Zhang, J.S. Bader, J.D. Boeke, Y.J. Yuan, “Perfect” designer chromosome V and behavior of a ring derivative, Science 355 (6329) (2017) eaaf4704. [111] W.M. Zhang, G.H. Zhao, Z.Q. Luo, Y.C. Lin, L.H. Wang, Y.K. Guo, A. Wang, S.Y. Jiang, Q.W. Jiang, J.H. Gong, Y. Wang, S. Hou, J. Huang, T.Y. Li, Y.R. Qin, J.K. Dong, Q. Qin, J.Y. Zhang, X.Z. Zou, X. He, L. Zhao, Y.B. Xiao, M. Xu, E.C. Cheng, N. Huang, T. Zhou, Y. Shen, R. Walker, Y.S. Luo, Z. Kuang, L.A. Mitchell, K. Yang, S.M. Richardson, Y. Wu, B.Z. Li, Y.J. Yuan, H.M. Yang, J.W. Lin, G.Q. Chen, Q.Y. Wu, J.S. Bader, Y.Z. Cai, J.D. Boeke, J.B. Dai, Engineering the ribosomal DNA in a megabase synthetic chromosome, Science 355 (6329) (2017) eaaf3981. [112] D.S. Tack, J.W. Ellefson, R. Thyer, B. Wang, J. Gollihar, M.T. Forster, A.D. Ellington, Addicting diverse bacteria to a noncanonical amino acid, Nat. Chem. Biol. 12 (3) (2016) 138–140. [113] A. Kuthning, P. Durkin, S. Oehm, M.G. Hoesl, N. Budisa, R.D. Süssmuth, Towards biocontained cell factories: an evolutionarily adapted escherichia coli strain produces a new-to-nature bioactive lantibiotic containing thienopyrrole-alanine, Sci. Rep. 6 (2016) 33447. [114] D.J. Mandell, M.J. Lajoie, M.T. Mee, R. Takeuchi, G. Kuznetsov, J.E. Norville, C.J. Gregg, B.L. Stoddard, G.M. Church, Biocontainment of genetically modified organisms by synthetic protein design, Nature 518 (7537) (2015) 55–60. [115] T. Thi Nhu Thao, F. Labroussaa, N. Ebert, P. V'Kovski, H. Stalder, J. Portmann, J. Kelly, S. Steiner, M. Holwerda, A. Kratzel, M. Gultom, K. Schmied, L. Laloli, L. Hüsser, M. Wider, S. Pfaender, D. Hirt, V. Cippà, S. Crespo-Pomar, S. Schröder, D. Muth, D. Niemeyer, V.M. Corman, M.A. Müller, C. Drosten, R. Dijkman, J. Jores, V. Thiel, Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform, Nature, 582 (2020) 561-565. [116] Z. Yuan, N.X. Wang, G.B. Kang, W. Niu, Q.S. Li, J.T. Guo, Controlling multicycle replication of live-attenuated HIV-1 using an unnatural genetic switch, ACS Synth. Biol. 6 (4) (2017) 721–731. [117] R.A. Langlois, R.A. Albrecht, B. Kimble, T. Sutton, J.S. Shapiro, C. Finch, M. Angel, M.A. Chua, A.S. Gonzalez-Reiche, K.M. Xu, D. Perez, A. García-Sastre, B.R. TenOever, microRNA-based strategy to mitigate the risk of gain-of-function influenza studies, Nat. Biotechnol. 31 (9) (2013) 844–847. [118] Y. Wang, Y. Zhang, J. Chen, M. Wang, T. Zhang, W. Luo, Y. Li, Y. Wu, B. Zeng, K. Zhang, R. Deng, W. Li, Detection of SARS-CoV-2 and its mutated variants via CRISPR-Cas13-based transcription amplification, Analytical chemistry, 93 (2021) 3393-3402. [119] Z. Cao, Y. Ma, B. Jia, Y.J. Yuan, Mobile CRISPR-Cas9 based anti-phage system in E. coli, Front. Chem. Sci. Eng. 16 ( 2022 ) 1281 – 1289. [120] A. Hui, H.A. de Boer, Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli, Proc. Natl. Acad. Sci. USA 84 (14) (1987) 4762–4766. [121] A.S. Hui, D.H. Eaton, H.A. de Boer, Mutagenesis at the mRNA decoding site in the 16S ribosomal RNA using the specialized ribosome system in Escherichia coli, EMBO J. 7 (13) (1988) 4383–4388. [122] K. Lee, C.A. Holland-Staley, P.R. Cunningham, Genetic analysis of the Shine-Dalgarno interaction: selection of alternative functional mRNA-rRNA combinations, Rna, 2 (1996) 1270-1285. [123] J.M. Callura, D.J. Dwyer, F.J. Isaacs, C.R. Cantor, J.J. Collins, Tracking, tuning, and terminating microbial physiology using synthetic riboregulators, Proc. Natl. Acad. Sci. USA 107 (36) (2010) 15898–15903. [124] C. Orelle, E.D. Carlson, T. Szal, T. Florin, M.C. Jewett, A.S. Mankin, Protein synthesis by ribosomes with tethered subunits, Nature 524 (7563) (2015) 119–124. [125] O. Rackham, J.W. Chin, A network of orthogonal ribosome x mRNA pairs, Nat. Chem. Biol. 1 (3) (2005) 159–166. [126] L.M. Chubiz, C.V. Rao, Computational design of orthogonal ribosomes, Nucleic Acids Res 36 (12) (2008) 4038–4046. [127] B. Jia, H. Qi, B.Z. Li, S. Pan, D. Liu, H. Liu, Y.Z. Cai, Y.J. Yuan, Orthogonal ribosome biofirewall, ACS Synth. Biol. 6 (11) (2017) 2108–2117. [128] T.A. Novossiolova, S. Whitby, M. Dando, G.S. Pearson, The vital importance of a web of prevention for effective biosafety and biosecurity in the twenty-first century, One Health Outlook 3 (1) (2021) 17. [129] L. Pei, M. Garfinkel, M. Schmidt, Bottlenecks and opportunities for synthetic biology biosafety standards, Nat. Commun. 13 (1) (2022) 2175. [130] K.L. Arnolds, L.R. Dahlin, L. Ding, C. Wu, J.P. Yu, W. Xiong, C. Zuniga, Y. Suzuki, K. Zengler, J.G. Linger, M.T. Guarnieri, Biotechnology for secure biocontainment designs in an emerging bioeconomy, Curr. Opin. Biotechnol. 71 (2021) 25–31. [131] C. Wu, H.G. Jiang, I. Kalra, X. Wang, M. Cano, P. Maness, J.P. Yu, W. Xiong, A generalized computational framework to streamline thermodynamics and kinetics analysis of metabolic pathways, Metab. Eng. 57 (2020) 140–150. [132] B.J. Caliando, C.A. Voigt, Targeted DNA degradation using a CRISPR device stably carried in the host genome, Nat. Commun. 6 (2015) 6989. [133] A.J. Simon, A.D. Ellington, Recent advances in synthetic biosafety, F1000Research 5 (2016) F1000FacultyRev–F1000Faculty2118. [134] W.H. Schmied, Z. Tnimov, C. Uttamapinant, C.D. Rae, S.D. Fried, J.W. Chin, Controlling orthogonal ribosome subunit interactions enables evolution of new function, Nature 564 (7736) (2018) 444–448. |
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