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中国生物工程杂志

China Biotechnology
China Biotechnology  2023, Vol. 43 Issue (9): 120-130    DOI: 10.13523/j.cb.2302051
    
Biosafety Risks and Countermeasures of Pathogen Related Synthetic Biology
ZUO Kun-lan1,ZOU Shi-shi2,WU Zong-zhen1,GUO Yuan-yuan3,XU Yan-long4,LIU Huan1,5,**()
1 School of Humanities and Social Science, University of Science and Technology of China, Hefei 230026, China
2 Renmin Hospital of Wuhan University, Wuhan 430060, China
3 Office of Laboratory Management, Chinese Center for Disease Control and Prevention, Beijing 102206, China
4 College of Humanities, University of Chinese Academy of Sciences, Beijing 100049, China
5 Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Abstract  

Synthetic biology, which involves the design and engineering of microorganisms to make them capable of performing novel functions for scientific research, medicine, industry and other fields, has promoted the development of economy and society. With the rapid development of synthetic biotechnology, highly harmful pathogens existing in nature may become objects to be synthesized. The transformation of known pathogens through biotechnology will have an unpredictable impact on human hosts, which is more dangerous than natural pathogens. These circumstances add to the biosecurity elements that need our attention when we adhere to the overall concept of national security. By reviewing the biosafety risks and key points in the areas of known viral synthetic biology, known bacterial synthetic biology, known viral enabling safety risks, known bacterial enabling safety risks, and unknown pathogen synthetic biology in recent years, and focusing both the international cutting-edge scientific and technological (S&T) achievements and advanced S&T development concepts, some biosafety response strategies and scientific suggestions were put forward, which would provide advisory suggestions for the healthy development of synthetic biology and think tank references for decision-makers of national biosafety policies.



Key wordsPathogen      Synthetic biology      Biosafety     
Received: 28 February 2023      Published: 08 October 2023
ZTFLH:  Q819  
Cite this article:

ZUO Kun-lan, ZOU Shi-shi, WU Zong-zhen, GUO Yuan-yuan, XU Yan-long, LIU Huan. Biosafety Risks and Countermeasures of Pathogen Related Synthetic Biology. China Biotechnology, 2023, 43(9): 120-130.

URL:

https://manu60.magtech.com.cn/biotech/10.13523/j.cb.2302051     OR     https://manu60.magtech.com.cn/biotech/Y2023/V43/I9/120

[1]   赵赤鸿, 苏丹丹, 厉春, 等. 总体国家安全观下合成生物学风险和应对策略研究. 中国生物工程杂志, 2022, 42(12): 120-128.
[1]   Zhao C H, Su D D, Li C, et al. Synthetic biology risks and biosafety strategies in the view of overall national security concept. China Biotechnology, 2022, 42(12): 120-128.
[2]   Marsian J, Fox H, Bahar M W, et al. Plant-made polio type 3 stabilized VLPs: a candidate synthetic polio vaccine. Nature Communications, 2017, 8(1): 1-9.
doi: 10.1038/s41467-016-0009-6
[3]   Watanabe T, Watanabe S, Neumann G, et al. Immunogenicity and protective efficacy of replication-incompetent influenza virus-like particles. Journal of Virology, 2002, 76(2): 767-773.
pmid: 11752166
[4]   Si L L, Xu H, Zhou X Y, et al. Generation of influenza A viruses as live but replication-incompetent virus vaccines. Science, 2016, 354(6316): 1170-1173.
pmid: 27934767
[5]   Wang T Y, Sang G J, Wang Q, et al. Generation of premature termination codon (PTC)-harboring pseudorabies virus (PRV) via genetic code expansion technology. Viruses, 2022, 14(3): 572.
doi: 10.3390/v14030572
[6]   Milone M C, O’Doherty U. Clinical use of lentiviral vectors. Leukemia, 2018, 32(7): 1529-1541.
doi: 10.1038/s41375-018-0106-0 pmid: 29654266
[7]   Hongeng S, Anurathapan U, Songdej D, et al. Wild-type HIV infection after treatment with lentiviral gene therapy for β-thalassemia. Blood Advances, 2021, 5(13): 2701-2706.
doi: 10.1182/bloodadvances.2020003680 pmid: 34196676
[8]   Ferrua F, Aiuti A. Twenty-five years of gene therapy for ADA-SCID: From Bubble babies to an approved drug. Human Gene Therapy, 2017, 28(11): 972-981.
doi: 10.1089/hum.2017.175
[9]   Kaiser J. Gene therapy trials for sickle cell disease halted after two patients develop cancer. Science, 2021, eabh1106. DOI:org/10.1126/science.abh1106.
doi: org/10.1126/science.abh1106
[10]   Çuburu N, Khan S, Thompson C D, et al. Adenovirus vector-based prime-boost vaccination via heterologous routes induces cervicovaginal CD8+ T cell responses against HPV16 oncoproteins. International Journal of Cancer, 2018, 142(7): 1467-1479.
doi: 10.1002/ijc.v142.7
[11]   Bommareddy P K, Shettigar M, Kaufman H L. Integrating oncolytic viruses in combination cancer immunotherapy. Nature Reviews Immunology, 2018, 18(8): 498-513.
doi: 10.1038/s41577-018-0014-6 pmid: 29743717
[12]   Huang H Y, Liu Y Q, Liao W X, et al. Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy. Nature Communications, 2019, 10(1): 1-15.
doi: 10.1038/s41467-018-07882-8
[13]   Stolberg S G. The biotech death of Jesse gelsinger. The New York Times Magazine, 1999, 28: 136-140.
[14]   Mastrangelo M J, Eisenlohr L C, Gomella L, et al. Poxvirus vectors: orphaned and underappreciated. Journal of Clinical Investigation, 2000, 105(8): 1031-1034.
pmid: 10772644
[15]   Pastoret P P, Vanderplasschen A. Poxviruses as vaccine vectors. Comparative Immunology, Microbiology and Infectious Diseases, 2003, 26(5-6): 343-355.
pmid: 12818621
[16]   Noyce R S, Lederman S, Evans D H. Construction of an infectious horsepox virus vaccine from chemically synthesized DNA fragments. PLoS One, 2018, 13(1): e0188453.
doi: 10.1371/journal.pone.0188453
[17]   Yang Z L, Gray M, Winter L. Why do poxviruses still matter? Cell & Bioscience, 2021, 11(1): 96.
[18]   Giotis E S, Skinner M A. Spotlight on avian pathology: fowlpox virus. Avian Pathology: Journal of the W V P A, 2019, 48(2): 87-90.
doi: 10.1080/03079457.2018.1554893
[19]   丁明珠, 李炳志, 王颖, 等. 合成生物学重要研究方向进展. 合成生物学, 2020, 1(1): 7-28.
doi: 10.12211/2096-8280.2020-057
[19]   Ding M Z, Li B Z, Wang Y, et al. Significant research progress in synthetic biology. Synthetic Biology Journal, 2020, 1(1):7-28.
doi: 10.12211/2096-8280.2020-057
[20]   Rosano G L, Morales E S, Ceccarelli E A. New tools for recombinant protein production in Escherichia coli: a 5-year update. Protein Science, 2019, 28(8): 1412-1422.
doi: 10.1002/pro.v28.8
[21]   Smolskaya S, Logashina Y A, Andreev Y A. Escherichia coli extract-based cell-free expression system as an alternative for difficult-to-obtain protein biosynthesis. International Journal of Molecular Sciences, 2020, 21(3): 928.
doi: 10.3390/ijms21030928
[22]   Johns N I, Blazejewski T, Gomes A L, et al. Principles for designing synthetic microbial communities. Current Opinion in Microbiology, 2016, 31: 146-153.
doi: S1369-5274(16)30025-X pmid: 27084981
[23]   Che S, Men Y J. Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges. Journal of Industrial Microbiology & Biotechnology, 2019, 46(9-10): 1343-1358.
[24]   Alerasol M, Mousavi Gargari S L, Nazarian S, et al. Immunogenicity of a fusion protein comprising coli surface antigen 3 and labile B subunit of enterotoxigenic Escherichia coli. Iranian Biomedical Journal, 2014, 18(4): 212-218.
doi: 10.6091/ibj.1344.2014 pmid: 25326019
[25]   Oloketuyi S F, Khan F. Strategies for biofilm inhibition and virulence attenuation of foodborne pathogen-Escherichia coli O157: H7. Current Microbiology, 2017, 74(12): 1477-1489.
doi: 10.1007/s00284-017-1314-y pmid: 28744570
[26]   Pang Y R, Zhao Y K, Li S L, et al. Engineering the oleaginous yeast Yarrowia lipolytica to produce limonene from waste cooking oil. Biotechnology for Biofuels, 2019, 12: 241.
doi: 10.1186/s13068-019-1580-y
[27]   Shao Y Y, Lu N, Wu Z F, et al. Creating a functional single-chromosome yeast. Nature, 2018, 560(7718): 331-335.
doi: 10.1038/s41586-018-0382-x
[28]   Nielsen J. Yeast systems biology: model organism and cell factory. Biotechnology Journal, 2019, 14(9): 1800421.
doi: 10.1002/biot.v14.9
[29]   Duman-Scheel M. Saccharomyces cerevisiae (Baker’s yeast) as an interfering RNA expression and delivery system. Current Drug Targets, 2019, 20(9): 942-952.
doi: 10.2174/1389450120666181126123538 pmid: 30474529
[30]   Anoop V, Rotaru S, Shwed P S, et al. Review of current methods for characterizing virulence and pathogenicity potential of industrial Saccharomyces cerevisiae strains towards humans. FEMS Yeast Research, 2015, 15(6): fov057.
doi: 10.1093/femsyr/fov057
[31]   Gibson D G, Glass J I, Lartigue C, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 2010, 329(5987): 52-56.
doi: 10.1126/science.1190719 pmid: 20488990
[32]   Hutchison C A 3rd, Chuang R Y, Noskov V N, et al. Design and synthesis of a minimal bacterial genome. Science, 2016, 351(6280): aad6253.
doi: 10.1126/science.aad6253
[33]   Reyes-Prieto M, Gil R, Llabrés M, et al. The metabolic building blocks of a minimal cell. Biology, 2020, 10(1): 5.
doi: 10.3390/biology10010005
[34]   Kamminga T, Koehorst J J, Vermeij P, et al. Persistence of functional protein domains in Mycoplasma species and their role in host specificity and synthetic minimal life. Frontiers in Cellular and Infection Microbiology, 2017, 7: 31.
doi: 10.3389/fcimb.2017.00031 pmid: 28224116
[35]   Wasik B R, de Wit E, Munster V, et al. Onward transmission of viruses: how do viruses emerge to cause epidemics after spillover? Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 2019, 374(1782): 20190017.
[36]   Kuchipudi S V, Nelli R K, Gontu A, et al. Sialic acid receptors: the key to solving the Enigma of zoonotic virus spillover. Viruses, 2021, 13(2): 262.
doi: 10.3390/v13020262
[37]   Herfst S, Schrauwen E J A, Linster M, et al. Airborne transmission of influenza A/H5N1 virus between ferrets. Science, 2012, 336(6088): 1534-1541.
doi: 10.1126/science.1213362 pmid: 22723413
[38]   Sigal L J. The pathogenesis and immunobiology of mousepox. Advances in Immunology, 2016, 129: 251-276.
doi: 10.1016/bs.ai.2015.10.001 pmid: 26791861
[39]   Wang J, Liu X P, Zhu Q, et al. Identification, isolation, and characterization of an ectromelia virus new strain from an experimental mouse. Virologica Sinica, 2021, 36(1): 155-158.
doi: 10.1007/s12250-020-00263-w
[40]   付萌萌, 苏丹丹, 左锟澜, 等. 人体免疫相关的合成生物学生物安全风险和应对策略研究. 中国生物工程杂志, 2023, 43(6):125-132.
[40]   Fu M M, Su D D, Zuo K L, et al. Study on biosafety risks and countermeasures of synthetic biology related to human immunity. China Biotechnology, 2023, 43(6):125-132.
[41]   Oliveira E R A, Bouvier M. Immune evasion by adenoviruses: a window into host-virus adaptation. FEBS Letters, 2019, 593(24): 3496-3503.
doi: 10.1002/1873-3468.13682 pmid: 31736048
[42]   Venkatesan S, Rosenthal R, Kanu N, et al. Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution. Annals of Oncology, 2018, 29(3): 563-572.
doi: S0923-7534(19)35515-2 pmid: 29324969
[43]   Schnupf P, Sansonetti P J. Shigella pathogenesis: new insights through advanced methodologies. Microbiology Spectrum, 2019, 7(2). DOI: 10.1128/microbiolspec.BAI-0023-2019.
doi: 10.1128/microbiolspec.BAI-0023-2019
[44]   Mattock E, Blocker A J. How do the virulence factors of Shigella work together to cause disease? Frontiers in Cellular and Infection Microbiology, 2017, 7: 64.
doi: 10.3389/fcimb.2017.00064 pmid: 28393050
[45]   Jiang J S, Pentelute B L, Collier R J, et al. Atomic structure of anthrax protective antigen pore elucidates toxin translocation. Nature, 2015, 521(7553): 545-549.
doi: 10.1038/nature14247
[46]   宁峻涛, 邹诗施, 左锟澜, 等. 合成生物活性物质的生物安全风险和应对策略研究. 中国生物工程杂志, 2023, 43(2): 180-189.
[46]   Ning J T, Zou S S, Zuo K L, et al. Biosafety risks and countermeasures of active substance in synthesis biology. China Biotechnology, 2023, 43(2): 180-189.
[47]   Hauke C A, Taylor R K. Production of putative enhanced oral cholera vaccine strains that express toxin-coregulated pilus. PLoS One, 2017, 12(4): e0175170.
doi: 10.1371/journal.pone.0175170
[48]   Garrigues L, Do T D, Bideaux C, et al. Insights into Clostridium tetani: from genome to bioreactors. Biotechnology Advances, 2022, 54: 107781.
doi: 10.1016/j.biotechadv.2021.107781
[49]   Keller M D, Ching K L, Liang F X, et al. Decoy exosomes provide protection against bacterial toxins. Nature, 2020, 579(7798): 260-264.
doi: 10.1038/s41586-020-2066-6
[50]   Walther B, Klein K S, Barton A K, et al. Equine methicillin-resistant sequence type 398 Staphylococcus aureus (MRSA) harbor mobile genetic elements promoting host adaptation. Frontiers in Microbiology, 2018, 9: 2516.
doi: 10.3389/fmicb.2018.02516 pmid: 30405574
[51]   Wei J W, Lu N, Li Z Y, et al. The Mycobacterium tuberculosis CRISPR-associated Cas1 involves persistence and tolerance to anti-tubercular drugs. BioMed Research International, 2019, 2019: 1-9.
[52]   Steinmetz M, Richter R. Plasmids designed to alter the antibiotic resistance expressed by insertion mutations in Bacillus subtilis, through in vivo recombination. Gene, 1994, 142(1): 79-83.
pmid: 8181761
[53]   Karpov D S, Osipova P G, Domashin A I, et al. Hyper-resistance of the Bacillus licheniformis 24 strain to oxidative stress is associated with overexpression of enzymatic antioxidant system genes. Molecular Biology, 2020, 54(5): 757-768.
doi: 10.1134/S0026893320050040
[54]   Lemire S, Yehl K M, Lu T K. Phage-based applications in synthetic biology. Annual Review of Virology, 2018, 5: 453-476.
doi: 10.1146/annurev-virology-092917-043544 pmid: 30001182
[55]   袁盛建, 马迎飞. 噬菌体合成生物学研究进展和应用. 合成生物学, 2020(6): 635-655.
doi: 10.12211/2096-8280.2020-027
[55]   Yuan S J, Ma Y F. Advances and applications of phage synthetic biology. Synthetic Biology Journal, 2020(6): 635-655.
doi: 10.12211/2096-8280.2020-027
[56]   Yu L F, Marchisio M A. Types I and V anti-CRISPR proteins: from phage defense to eukaryotic synthetic gene circuits. Frontiers in Bioengineering and Biotechnology, 2020, 8: 575393.
doi: 10.3389/fbioe.2020.575393
[57]   Nakamura M, Srinivasan P, Chavez M, et al. Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nature Communications, 2019, 10(1): 1-11.
doi: 10.1038/s41467-018-07882-8
[58]   Kim B O, Kim E S, Yoo Y J, et al. Phage-derived antibacterials: harnessing the simplicity, plasticity, and diversity of phages. Viruses, 2019, 11(3): 268.
doi: 10.3390/v11030268
[59]   Anosova I, Kowal E A, Dunn M R, et al. The structural diversity of artificial genetic polymers. Nucleic Acids Research, 2016, 44(3): 1007-1021.
doi: 10.1093/nar/gkv1472 pmid: 26673703
[60]   Eremeeva E, Herdewijn P. Reprint of: non canonical genetic material. Current Opinion in Biotechnology, 2019, 60: 259-267.
doi: S0958-1669(19)30119-3 pmid: 31759815
[61]   Medina E, Yik E J, Herdewijn P, et al. Functional comparison of laboratory-evolved XNA polymerases for synthetic biology. ACS Synthetic Biology, 2021, 10(6): 1429-1437.
doi: 10.1021/acssynbio.1c00048
[62]   Cozens C, Pinheiro V B. XNA synthesis and reverse transcription by engineered thermophilic polymerases. Current Protocols in Chemical Biology, 2018, 10(3): e47.
doi: 10.1002/cpch.v10.3
[63]   Melnikov S V, Söll D. Aminoacyl-tRNA synthetases and tRNAs for an expanded genetic code: what makes them orthogonal? International Journal of Molecular Sciences, 2019, 20(8): 1929.
doi: 10.3390/ijms20081929
[64]   Italia J S, Addy P S, Erickson S B, et al. Mutually orthogonal nonsense-suppression systems and conjugation chemistries for precise protein labeling at up to three distinct sites. Journal of the American Chemical Society, 2019, 141(15): 6204-6212.
doi: 10.1021/jacs.8b12954 pmid: 30909694
[65]   Schmidt M, Pei L, Budisa N. Xenobiology:state-of-the-art, ethics, and philosophy of new-to-nature organisms. Synthetic Biology - Metabolic Engineering. Cham: Springer International Publishing, 2017: 301-315.
[66]   刘旭霞, 秦宇. 欧美合成生物学应用的风险治理经验及启示. 华中农业大学学报(社会科学版), 2022, 158(2):177-184.
[66]   Liu X X, Qin Y. Risk Governance experience and enlightenment of synthetic biology application in Europe and the US. Journal of Huazhong Agricultural University(Social Sciences Edition), 2022, 158(2):177-184.
[67]   彭耀进. 合成生物学时代: 生物安全、生物安保与治理. 国际安全研究, 2020, 38(5): 29-57, 157-158.
[67]   Peng Y J. The era of synthetic biology: biosafety, biosecurity and governance. Journal of International Security Studies, 2020, 38(5): 29-57, 157-158.
[68]   Purwar S, Srivastava S. Development of modern tools for environmental monitoring of pathogens and toxicant. environmental microbiology and biotechnology. Singapore: Springer, 2021: 185-210.
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