噬菌体合成生物学研究进展和应用

doi:10.12211/2096-8280.2020-027

合成生物学 ›› 2020, Vol. 1 ›› Issue (6): 635-655.DOI: 10.12211/2096-8280.2020-027

噬菌体合成生物学研究进展和应用

袁盛建^1,², 马迎飞¹

^1.中国科学院深圳先进技术研究院，深圳合成生物学创新研究院，中国科学院定量工程生物学重点实验室，广东省合成基因组学重点实验室，深圳市合成基因组学重点实验室，广东　深圳　518055
^2.中国科学院大学，北京　100049

收稿日期:2020-03-16 修回日期:2020-11-27 出版日期:2020-12-31 发布日期:2021-01-15
通讯作者: 马迎飞
作者简介:袁盛建（1988—），男，博士研究生。研究方向为噬菌体人工合成。E-mail：sj.yuan@siat.ac.cn|马迎飞（1978—），男，研究员，博士生导师。主要研究方向：①噬菌体组学，应用生物信息用手段，鉴定各生态系统中噬菌体宏基因组及噬菌体在各生态位中的功能等；②人工噬菌体，对噬菌体进行必需基因功能鉴定，模块化设计与合成；③噬菌体的应用，噬菌体防治耐药菌感染。E-mail：yingfei.ma@siat.ac.cn
基金资助:
广东省合成基因组学重点实验室(2019B030301006);深圳市合成基因组学重点实验室(ZDSYS201802061806209);深圳市海外高层次人才创新团队(KQTD2016112915000294)

Advances and applications of phage synthetic biology

Shengjian YUAN^1,², Yingfei MA¹

^1.Shenzhen Key Laboratory of Synthetic Genomics，Guangdong Provincial Key Laboratory of Synthetic Genomics，CAS Key Laboratory of Quantitative Engineering Biology，Shenzhen Institute of Synthetic Biology，Shenzhen Institutes of Advanced Technology，Chinese Academy of Sciences，Shenzhen 518055，Guangdong，China
^2.University of Chinese Academy of Sciences，Beijing 100049，China

Received:2020-03-16 Revised:2020-11-27 Online:2020-12-31 Published:2021-01-15
Contact: Yingfei MA

摘要/Abstract

摘要：

噬菌体是地球上多样性最高和最丰富的生物体，也是合成生物学研究中重要的模式生物。噬菌体基因组相对较小，结构简单，是研究基本生命过程最简单的生物系统。通过对噬菌体基因组进行编辑，乃至重新设计、合成噬菌体基因组，获得具有新的功能的噬菌体，是当前噬菌体合成生物学研究的重要内容。本文综述了当前合成生物学在解决天然噬菌体的基础研究和应用研究中的主要进展，如通过人工改造的噬菌体已成功用于提高噬菌体的侵染效率，调节噬菌体宿主范围，降低噬菌体毒性和免疫原性，提高给药后噬菌体存活周期，提高噬菌体对生物膜的降解等；此外，噬菌体展示、噬菌体辅助的持续进化和噬菌体介导的DNA转导等也成为合成生物学研究中强大的工具。总之，合成生物学的发展将为模块化设计噬菌体作为多功能生物制剂、控制多重耐药细菌、病原体检测、药物开发、菌群的调控、药物递送，甚至噬菌体纳米材料等铺平道路。

关键词: 噬菌体, 合成生物学, 人工合成基因组, 噬菌体展示, 诊断, 噬菌体治疗

Abstract:

Bacteriophage (phage) are viruses that specifically infect bacterial and archaea. Phage is the most diverse and abundant biological entity on the planet. For more than a century, phage is one of the most important model organisms in the molecular biological research. Many important discoveries upon phage research have enabled us to understand the mechanisms of genetic materials in biological activities, and many phage-derived enzymes are greatly useful in the molecular biological research. Phage has also been recognized as natural antimicrobial agents for treating the bacterial infections. In particular, nowadays, the concern related to the emergence of bacteria resistance to multiple antibiotics is increasing. However, the challenges in phage therapy, such as narrow host range and bacterial resistance, limited the application of phage therapy in treating the diseases of antibiotic-resistant bacterial infections. Novel strategies are needed to be developed to overcome the hurdles associated with phage therapy. Synthetic biology aims to design and reprogram new biological systems according to the known principles. Because of their relatively small genome size (5—735 kb), fast growth rate, ease of genetic manipulation, and simple structure, phages have become the most important biological system for synthetic biology research. In this review, we discuss the advances of synthetic biology facing the major challenges of natural phages in basic and application research. For example, synthetic biology has been applied to enhance the infection efficiency of phages, improve the phage biosafety, alter the phage host ranges, adjust the bacterial communities, and knock out the specific bacterial genes. We also present some examples to show the methods that were widely used for phage engineering to obtain phages with new functions. In addition, phage display and phage-assisted continuous evolution have also become powerful tools in synthetic biology. In short, the development of synthetic biology will inspire scientists to design modular phages as multifunctional biological agents for clearance of multi-drug resistant bacteria, detection of the pathogen, regulation of bacterial diversity, and drug delivery.

Key words: phage, synthetic biology, synthetic genome, phage display, diagnostics, phage therapy

中图分类号:

袁盛建, 马迎飞. 噬菌体合成生物学研究进展和应用[J]. 合成生物学, 2020, 1(6): 635-655.

Shengjian YUAN, Yingfei MA. Advances and applications of phage synthetic biology[J]. Synthetic Biology Journal, 2020, 1(6): 635-655.

图/表 3

参考文献 170

1	TWORT F W. An investigation on the nature of ultra-microscopic viruses [J]. The Lancet, 1915, 186(4814): 1241-1243.
2	HENDRIX R W. Bacteriophage genomics [J]. Current Opinion in Microbiology, 2003, 6(5): 506-511.
3	MA Yingfei, YOU Xiaoyan, Guoqin MAI, et al. A human gut phage catalog correlates the gut phageome with type 2 diabetes [J]. Microbiome, 2018, 6(1): 24.
4	HERSHEY A D, CHASE M. Independent functions of viral protein and nucleic acid in growth of bacteriophage [J]. Journal of General Physiology, 1952, 36(1): 39-56.
5	CRICK F H C, BARNETT L, BRENNER S, et al. General nature of the genetic code for proteins [J]. Nature, 1961, 192(4809): 1227-1232.
6	CHAMBERLIN M, RING J. Characterization of T7-specific ribonucleic acid polymerase (I): general properties of the enzymatic reaction and the template specificity of the enzyme [J]. The Journal of Biological Chemistry, 1973, 248(6): 2235-2244.
7	SMITH H O, C A 3rd HUTCHISON, PFANNKOCH C, et al. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides [J]. Proceedings of the National Academy of Sciences of the United States of America, 2003, 100(26): 15440-15445.
8	BARRANGOU R, FREMAUX C, DEVEAU H, et al. CRISPR provides acquired resistance against viruses in prokaryotes [J]. Science, 2007, 315(5819): 1709-1712.
9	DONOHOUE P D, BARRANGOU R, MAY A P. Advances in industrial biotechnology using CRISPR-Cas systems [J]. Trends in Biotechnology, 2018, 36(2): 134-146.
10	POTERA C. Phage renaissance: new hope against antibiotic resistance [J]. Environmental Health Perspectives, 2013, 121(2): a48-53.
11	BARBU E M, CADY K C, HUBBY B. Phage therapy in the era of synthetic biology [J]. Cold Spring Harbor Perspectives in Biology, 2016, 8(10): a023879.
12	LU T K, KOERIS M S. The next generation of bacteriophage therapy [J]. Current Opinion in Microbiology, 2011, 14(5): 524-531.
13	BORN Y, FIESELER L, THONY V, et al. Engineering of bacteriophages Y2:: dpoL1-C and Y2:: luxAB for efficient control and rapid detection of the fire blight pathogen, Erwinia amylovora [J]. Applied and Environmental Microbiology, 2017, 83(12): e00341.
14	ROSTOL J T, MARRAFFINI L. (Ph)ighting phages: how bacteria resist their parasites [J]. Cell Host and Microbe, 2019, 25(2): 184-194.
15	ANDO H, LEMIRE S, PIRES D P, et al. Engineering modular viral scaffolds for targeted bacterial population editing [J]. Cell Systems, 2015, 1(3): 187-196.
16	C A 3rd HUTCHISON, CHUANG Ray-Yuan, NOSKOV V N, et al. Design and synthesis of a minimal bacterial genome [J]. Science, 2016, 351(6280): aad6253.
17	BHATTARAI S R, So Young YOO, Seung-Wuk LEE, et al. Engineered phage-based therapeutic materials inhibit Chlamydia trachomatis intracellular infection [J]. Biomaterials, 2012, 33(20): 5166-5174.
18	LU T K, COLLINS J J. Dispersing biofilms with engineered enzymatic bacteriophage [J]. Proceedings of the National Academy of Sciences of the United States of America, 2007, 104(27): 11197-11202.
19	LIN Han, PAFF M L, MOLINEUX I J, et al. Therapeutic application of phage capsule depolymerases against K1, K5, and K30 capsulated E. coli in mice [J]. Frontiers in Microbiology, 2017, 8: 2257.
20	FLEMING D, RUMBAUGH K P. Approaches to dispersing medical biofilms [J]. Microorganisms, 2017, 5(2): 5020015.
21	CHUNG Yeon-Bo, HINKLE D C. Bacteriophage T7 DNA packaging (I): plasmids containing a T7 replication origin and the T7 concatemer junction are packaged into transducing particles during phage infection [J]. Journal of Molecular Biology, 1990, 216(4): 911-926.
22	HASHIMOTO C, FUJISAWA H. Packaging and transduction of non-T3 DNA by bacteriophage T3 [J]. Virology, 1988, 166(2): 432-439.
23	KROM RJ, BHARGAVA P, LOBRITZ M A, et al. Engineered phagemids for nonlytic, targeted antibacterial therapies [J]. Nano Letters, 2015, 15(7): 4808-4813.
24	BERTOZZI SILVA J, STORMS Z, SAUVAGEAU D. Host receptors for bacteriophage adsorption [J]. FEMS Microbiology Letters, 2016, 363(4): fnw002.
25	HAMDI S, ROUSSEAU G M, LABRIE S J, et al. Characterization of two polyvalent phages infecting Enterobacteriaceae [J]. Scientific Reports, 2017, 7: 40349.
26	STEPHEN T. ABEDON R L C. The Bacteriophages [M]. Oxford, UK: Oxford University Press, 2006.
27	YOSEF I, GOREN M G, GLOBUS R, et al. Extending the host range of bacteriophage particles for DNA transduction [J]. Molecular Cell, 2017, 66(5): 721-728.
28	YEHL K, LEMIRE S, YANG A C, et al. Engineering phage host-range and suppressing bacterial resistance through phage tail fiber mutagenesis [J]. Cell, 2019, 179(2): 459-469.
29	BRÜSSOW H. What is needed for phage therapy to become a reality in Western medicine? [J]. Virology, 2012, 434(2): 138-142.
30	HARGREAVES K R, CLOKIE M R. Clostridium difficile phages: still difficult? [J]. Frontiers in Microbiology, 2014, 5: 184.
31	CANCHAYA C, FOURNOUS G, BRÜSSOW H. The impact of prophages on bacterial chromosomes [J]. Molecular Microbiology, 2004, 53(1): 9-18.
32	HOWARD-VARONA C, HARGREAVES K R, ABEDON S T, et al. Lysogeny in nature: mechanisms, impact and ecology of temperate phages [J]. ISME Journal, 2017, 11(7): 1511-1520.
33	KILCHER S, STUDER P, MUESSNER C, et al. Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria [J]. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(3): 567-572.
34	ZHANG Hongming, FOUTS D E, DEPEW J, et al. Genetic modifications to temperate Enterococcus faecalis phage Ef11 that abolish the establishment of lysogeny and sensitivity to repressor, and increase host range and productivity of lytic infection [J]. Microbiology, 2013, 159(Pt 6): 1023-1035.
35	PARK Joo Youn, MOON Bo Youn, PARK Juw Won, et al. Genetic engineering of a temperate phage-based delivery system for CRISPR/Cas9 antimicrobials against Staphylococcus aureus [J]. Scientific Reports, 2017, 7: 44929.
36	YOSEF I, MANOR M, KIRO R, et al. Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria [J]. Proceedings of the National Academy of Sciences of the United States of America,2015, 112(23): 7267-7272.
37	MARINELLI LJ, PIURI M, SWIGONOV Z, et al. BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes [J]. PLoS One, 2008, 3(12): e3957.
38	DEDRICK R M, GUERRERO-BUSTAMANTE C A, GARLENA R A, et al. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus [J]. Nature Medicine, 2019, 25(5): 730-733.
39	FISCHETTI V A. Phage therapy: a practical approach [M]. Cham: Springer, 2019: 317-334.
40	PASTAGIA M, SCHUCH R, FISCHETTI V A, et al. Lysins: the arrival of pathogen-directed anti-infectives [J]. Journal of Medical Microbiology, 2013, 62(10): 1506-1516.
41	LOEFFLER J M, NELSON D, FISCHETTI V A. Rapid killing of Streptococcus pneumoniae with a bacteriophage cell wall hydrolase [J]. Science, 2001, 294(5549): 2170-2172.
42	LETRADO P, CORSINI B, DÍEZ-MARTÍNEZ R, et al. Bactericidal synergism between antibiotics and phage endolysin Cpl-711 to kill multidrug-resistant pneumococcus [J]. Future Microbiology, 2018, 13(11): 1215-1223.
43	SHEN Yang, BARROS M, VENNEMANN T, et al. A bacteriophage endolysin that eliminates intracellular streptococci [J]. eLife, 2016, 5: 13152.
44	SHEN Yang, KÖLLER T, KREIKEMEYER B, et al. Rapid degradation of Streptococcus pyogenes biofilms by PlyC, a bacteriophage-encoded endolysin [J]. Journal of Antimicrobial Chemotherapy, 2013, 68(8): 1818-1824.
45	YANG Hang, ZHANG Huaidong, WANG Jing, et al. A novel chimeric lysin with robust antibacterial activity against planktonic and biofilm methicillin-resistant Staphylococcus aureus [J]. Scientific Reports, 2017, 7: 40182.
46	SCHUCH R, KHAN B K, RAZ A, et al. Bacteriophage lysin CF-301, a potent antistaphylococcal biofilm agent [J]. Antimicrobial Agents and Chemotherapy, 2017, 61(7): e02666.
47	ZHANG Yufeng, CHENG Mengjun, ZHANG Hao, et al. Antibacterial effects of phage lysin LysGH15 on planktonic cells and biofilms of diverse Staphylococci [J]. Applied and Environmental Microbiology, 2018, 84(15): 00886.
48	LAI Meng-Jiun, LIU Chih-Chin, JIANG Shinn-Jong, et al. Antimycobacterial activities of endolysins derived from a mycobacteriophage, BTCU-1 [J]. Molecules, 2015, 20(10): 19277-19290.
49	KIM Shukho, Da-Won LEE, JIN Jong-Sook, et al. Antimicrobial activity of LysSS, a novel phage endolysin, against Acinetobacter baumannii and Pseudomonas aeruginosa [J]. Journal of Global Antimicrobial Resistance, 2020, 22: 32-39.
50	BRIERS Y, WALMAGH M, PUYENBROECK V VAN, et al. Engineered endolysin-based "Artilysins" to combat multidrug-resistant gram-negative pathogens [J]. mBio, 2014, 5(4): e01379.
51	DEFRAINE V, SCHUERMANS J, GRYMONPREZ B, et al. Efficacy of Artilysin Art-175 against resistant and persistent Acinetobacter baumannii [J]. Antimicrobial Agents and Chemotherapy, 2016, 60(6): 3480-3488.
52	FERNÁNDEZ-RUIZ I, COUTINHO F H, RODRIGUEZ-VALERA F. Thousands of novel endolysins discovered in uncultured phage genomes [J]. Frontiers in Microbiology, 2018, 9: 1033.
53	SMITH G P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface [J]. Science, 1985, 228(4705): 1315-1317.
54	LIU I-Ju, HSUEH Po-Ren, LIN Chin-Tarng, et al. Disease-specific B cell epitopes for serum antibodies from patients with severe acute respiratory syndrome (SARS) and serologic detection of SARS antibodies by epitope-based peptide antigens [J]. The Journal of Infectious Diseases, 2004, 190(4): 797-809.
55	SANTAMARIA H, MANOUTCHARIAN K, ROCHA L, et al. Identification of peptide sequences specific for serum antibodies from human papillomavirus-infected patients using phage display libraries [J]. Clinical Immunology, 2001, 101(3): 296-302.
56	KHURANA S, SUGUITAN A L JR, RIVERA Y, et al. Antigenic fingerprinting of H5N1 avian influenza using convalescent sera and monoclonal antibodies reveals potential vaccine and diagnostic targets [J]. PLoS Medicine, 2009, 6(4): e1000049.
57	WU Chien-Hsun, LIU I-Ju, LU Ruei-Min, et al. Advancement and applications of peptide phage display technology in biomedical science [J]. Journal of Biomedical Science, 2016, 23: 8.
58	HESS K L, JEWELL C M. Phage display as a tool for vaccine and immunotherapy development [J]. Bioengineering & Translational Medicine, 2020, 5(1): e10142.
59	FRENZEL A, SCHIRRMANN T, HUST M. Phage display-derived human antibodies in clinical development and therapy [J]. MAbs, 2016, 8(7): 1177-1194.
60	ESVELT KM, CARLSON JC, LIU D R. A system for the continuous directed evolution of biomolecules [J]. Nature, 2011, 472(7344): 499-503.
61	CARLSON J C, BADRAN A H, GUGGIANA-NILO D A, et al. Negative selection and stringency modulation in phage-assisted continuous evolution [J]. Nature Chemical Biology, 2014, 10(3): 216-222.
62	BRYSON D I, FAN Chenguang. Continuous directed evolution of aminoacyl-tRNA synthetases [J]. Nature Chemical Biology, 2017, 13(12): 1253-1260.
63	PACKER M S, REES H A, LIU D R. Phage-assisted continuous evolution of proteases with altered substrate specificity [J]. Nature Communications, 2017, 8(1): 956.
64	HUBBARD B P, BADRAN A H. Continuous directed evolution of DNA-binding proteins to improve TALEN specificity [J]. Nature Methods, 2015, 12(10): 939-942.
65	BADRAN A H, GUZOV V M, HUAI Qing, et al. Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance [J]. Nature, 2016, 533(7601): 58-63.
66	JOHNSTON C W, BADRAN A H, COLLINS J J. Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway [J]. Nature Communications, 2020, 11(1): 4202.
67	SOUSA R, MUKHERJEE S. T7 RNA polymerase [J] Progress in Nucleic Acid Research and Molecular Biology, 2003, 73: 1-41.
68	LENNEMAN B R, ROTHMAN-DENES L B. Structural and biochemical investigation of bacteriophage N4-encoded RNA polymerases [J]. Biomolecules, 2015, 5(2): 647-667.
69	TEMME K, HILL R, SEGALL-SHAPIRO T H, et al. Modular control of multiple pathways using engineered orthogonal T7 polymerases [J]. Nucleic Acids Research, 2012, 40(17): 8773-8781.
70	MEYER A J, ELLEFSON J W, ELLINGTON A D. Directed evolution of a panel of orthogonal T7 RNA polymerase variants for in vivo or in vitro synthetic circuitry [J]. ACS Synthetic Biology, 2015, 4(10): 1070-1076.
71	ELOWITZ M B, LEIBLER S. A synthetic oscillatory network of transcriptional regulators [J]. Nature, 2000, 403(6767): 335-338.
72	STIRLING F, BITZAN L, O'KEEFE S, et al. Rational design of evolutionarily stable microbial kill switches [J]. Molecular Cell, 2017, 68(4): 686-697.
73	NOMAN N, INNISS M, IBA H, et al. Pulse detecting genetic circuit - a new design approach [J]. PLoS One, 2016, 11(12): e0167162.
74	TAO Pan, WU Xiaorong, TANG Weichun, et al. Engineering of bacteriophage T4 genome using CRISPR-Cas9 [J]. ACS Synthetic Biology, 2017, 6(10): 1952-1961.
75	PAEZ-ESPINO D, ELOE-FADROSH E A, PAVLOPOULOS G A, et al. Uncovering Earth's virome [J]. Nature, 2016, 536(7617): 425-430.
76	FEH R T, KARCAGI I, BLATTNER F R, et al. Bacteriophage recombineering in the lytic state using the lambda red recombinases [J]. Microbial Biotechnology, 2012, 5(4): 466-476.
77	SHIN Jonghyeon, JARDINE P, NOIREAUX V. Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction [J]. ACS Synthetic Biology, 2012, 1(9): 408-413.
78	HORVATH P, BARRANGOU R. CRISPR/Cas, the immune system of bacteria and archaea [J]. Science, 2010, 327(5962): 167-170.
79	MAKAROVA K S, HAFT D H, BARRANGOU R, et al. Evolution and classification of the CRISPR-Cas systems [J]. Nature Reviews Microbiology2011, 9(6): 467-477.
80	MARTEL B, MOINEAU S. CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages [J]. Nucleic Acids Research, 2014, 42(14): 9504-9513.
81	KIRO R, SHITRIT D, QIMRON U. Efficient engineering of a bacteriophage genome using the type I-E CRISPR-Cas system [J]. RNA Biology, 2014, 11(1): 42-44.
82	LEMAY M L, TREMBLAY D M, MOINEAU S. Genome engineering of virulent lactococcal phages using CRISPR-Cas9 [J]. ACS Synthetic Biology, 2017, 6(7): 1351-1358.
83	SHEN Juntao, ZHOU Jinjie, CHEN Guoqiang, et al. Efficient genome engineering of a virulent Klebsiella bacteriophage using CRISPR-Cas9 [J]. Journal of Virology, 2018, 92(17): e00534.
84	SCHILLING T, DIETRICH S, HOPPERT M, et al. A CRISPR-Cas9-based toolkit for fast and precise in vivo genetic engineering of Bacillus subtilis phages [J]. Viruses, 2018, 10(5): 241.
85	HUPFELD M, TRASANIDOU D, RAMAZZINI L, et al. A functional type II-A CRISPR-Cas system from Listeria enables efficient genome editing of large non-integrating bacteriophage [J]. Nucleic Acids Research, 2018, 46(13): 6920-6933.
86	YUAN Shengjian, CHEN Ling, LIU Quan, et al. Characterization and genomic analyses of Aeromonas hydrophila phages AhSzq-1 and AhSzw-1, isolates representing new species within the T5virus genus [J]. Archives of Virology, 2018, 163(7): 1985-1988.
87	YANG Zhenlong, YUAN Shengjian, CHEN Ling, et al. Complete genome analysis of bacteriophage AsXd-1, a new member of the genus Hk97virus, family Siphoviridae [J]. Archives of Virology, 2018, 163(11): 3195-3197.
88	LI Erna, YIN Zhe, MA Yanyan, et al. Identification and molecular characterization of bacteriophage phiAxp-2 of Achromobacter xylosoxidans [J]. Scientific Reports, 2016, 6: 34300.
89	POPE W H, BOWMAN C A, RUSSELL D A, et al. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity [J]. eLife, 2015, 4: e06416.
90	CHAN L Y, KOSURI S, ENDY D. Refactoring bacteriophage T7 [J]. Molecular Systems Biology, 2005, 1: 2005.0018.
91	GIBSON D G, YOUNG L, CHUANG Ray-Yuan, et al. Enzymatic assembly of DNA molecules up to several hundred kilobases [J]. Nature Methods, 2009, 6(5): 343-345.
92	LEMIRE S, YEHL K M, LU T K. Phage-based applications in synthetic biology [J]. Annual Review of Virology, 2018, 5(1): 453-476.
93	GIBSON D G. Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides [J]. Nucleic Acids Research, 2009, 37(20): 6984-6990.
94	JASCHKE P R, LIEBERMAN E K, RODRIGUEZ J, et al. A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast [J]. Virology, 2012, 434(2): 278-284.
95	OLDFIELD L M, GRZESIK P, VOORHIES A A, et al. Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods [J]. Proceedings of the National Academy of Sciences of the United States Of America, 2017, 114(42): E8885.
96	ALLAN E J, HOISCHEN C, GUMPERT J. Bacterial L-Forms [J]. Advances in Applied Microbiology, 2009, 68: 1-39.
97	SWARTZ J R. Universal cell-free protein synthesis [J]. Nature Biotechnology, 2009, 27(8): 731-732.
98	CHAPPELL J, JENSEN K, FREEMONT P S. Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology [J]. Nucleic Acids Research, 2013, 41(5): 3471-3481.
99	RUSTAD M, EASTLUND A, MARSHALL R, et al. Synthesis of infectious bacteriophages in an E. coli-based cell-free expression system [J]. Journal of Visualized Experiments, 2017, 126: 56144.
100	RUSTAD M, NOIREAUX V, EASTLUND A, et al. Cell-free TXTL synthesis of infectious bacteriophage T4 in a single test tube reaction [J]. Synthetic Biology, 2018, 3(1): ysy002.
101	MESYANZHINOV V V, LEIMAN P G, KOSTYUCHENKO V A, et al. Molecular architecture of bacteriophage T4 [J]. Biochemistry (Moscow), 2004, 69(11): 1190-1202.
102	BROWN R, LENGELING A, WANG Baojun. Phage engineering: how advances in molecular biology and synthetic biology are being utilized to enhance the therapeutic potential of bacteriophages [J]. Quantitative Biology, 2017, 5(1): 42-54.
103	PASIN F, MENZEL W, DAR S J A. Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses [J]. Plant Biotechnology Journal, 2019, 17(6): 1010-1026.
104	HEMMINGA M A, VOS W L, NAZAROV P V, et al. Viruses: incredible nanomachines. New advances with filamentous phages [J]. European Biophysics Journal, 2010, 39(4): 541-550.
105	KUPFERSCHMIDT K. Resistance fighters [J]. Science, 2016, 352(6287): 758-761.
106	REARDON S. Phage therapy gets revitalized [J]. Nature, 2014, 510(7503): 15-16.
107	SUMMERS W C. The strange history of phage therapy [J]. Bacteriophage, 2012, 2(2): 130-133.
108	KUTTER E, DE VOS D, GVASALIA G, et al. Phage therapy in clinical practice: treatment of human infections [J]. Current Pharmaceutical Biotechnology2010, 11(1): 69-86.
109	ROHWER F, SEGALL A M. In retrospect: a century of phage lessons [J]. Nature, 2015, 528(7580): 46-48.
110	LUONG T, SALABARRIA AC, ROACH DR. Phage therapy in the resistance era: where do we stand and where are we going? [J]. Clinical Therapeutics, 2020, 42(9): 1659-1680.
111	BAO Juan, WU Nannan, ZENG Yigang, et al. Non-active antibiotic and bacteriophage synergism to successfully treat recurrent urinary tract infection caused by extensively drug-resistant Klebsiellapneumoniae [J]. Emerging Microbes & Infections, 2020, 9(1): 771-774.
112	MIĘDZYBRODZKI R, BORYSOWSKI J, WEBER-DĄBROWSKA B, et al. Clinical aspects of phage therapy [J] Advances in Virus Research, 2012, 83: 73-121.
113	HEILMANN S, SNEPPEN K, KRISHNA S. Sustainability of virulence in a phage-bacterial ecosystem [J]. Journal of Virology, 2010, 84(6): 3016-22.
114	CHEN Ling, YUAN Shengjian, LIU Quan, et al. In vitro design and evaluation of phage cocktails against Aeromonas salmonicida [J]. Frontiers in Microbiology, 2018, 9: 1476.
115	CANCHAYA C, PROUX C, FOURNOUS G, et al. Prophage genomics [J]. Microbiology and Molecular Biology Reviews, 2003, 67(2): 238-276.
116	GÓRSKI A, MIĘDZYBRODZKI R, BORYSOWSKI J, et al. Phage as a modulator of immune responses: practical implications for phage therapy[J]. Advances in Virus Research, 2012, 83: 41-71.
117	COOPER C J, MIRZAEI M K, NILSSON A S. Adapting drug approval pathways for bacteriophage-based therapeutics[J]. Frontiers in Microbiology, 2016, 7: 1209.
118	SAMSON J E, MAGADAN A H, SABRI M, et al. Revenge of the phages: defeating bacterial defences [J]. Nature Reviews Microbiology, 2013, 11(10): 675-687.
119	LABRIE S J, SAMSON J E, MOINEAU S. Bacteriophage resistance mechanisms [J]. Nature Reviews Microbiology, 2010, 8(5): 317-327.
120	OJALA V, LAITALAINEN J, JALASVUORI M. Fight evolution with evolution: plasmid-dependent phages with a wide host range prevent the spread of antibiotic resistance [J]. Evolutionary Applications, 2013, 6(6): 925-932.
121	MATSUDA T, FREEMAN T A, HILBERT D W, et al. Lysis-deficient bacteriophage therapy decreases endotoxin and inflammatory mediator release and improves survival in a murine peritonitis model [J]. Surgery, 2005, 137(6): 639-646.
122	MUROOKA Y, TAKIZAWA N, HARADA T. Introduction of bacteriophage Mu into bacteria of various genera and intergeneric gene transfer by RP4:: Mu [J]. Journal of Bacteriology, 1981, 145(1): 358-368.
123	MUROOKA Y, HARADA T. Expansion of the host range of coliphage P1 and gene transfer from enteric bacteria to other gram-negative bacteria [J]. Applied and Environmental Microbiology, 1979, 38(4): 754-757.
124	NAMURA M, HIJIKATA T, MIYANAGA K, et al. Detection of Escherichia coli with fluorescent labeled phages that have a broad host range to E. coli in sewage water [J]. Biotechnology Progress, 2008, 24(2): 481-486.
125	EDGAR R, MCKINSTRY M, HWANG Jeeseong, et al. High-sensitivity bacterial detection using biotin-tagged phage and quantum-dot nanocomplexes [J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(13): 4841-4845.
126	SCHOFIELD D A, WESTWATER C. Phage-mediated bioluminescent detection of Bacillus anthracis [J]. Journal of Applied Microbiology, 2009, 107(5): 1468-1478.
127	O'DONNELL M R, PYM A, JAIN P, et al. A novel reporter phage to detect tuberculosis and rifampin resistance in a high-HIV-burden population [J]. Journal of Clinical Microbiology, 2015, 53(7): 2188-2194.
128	PIURI M, JACOBS W R JR, HATFULL G F. Fluoromycobacteriophages for rapid, specific, and sensitive antibiotic susceptibility testing of Mycobacterium tuberculosis [J]. PLoS One, 2009, 4(3): e4870.
129	KUMAR V, LOGANATHAN P, SIVARAMAKRISHNAN G, et al. Characterization of temperate phage Che12 and construction of a new tool for diagnosis of tuberculosis [J]. Tuberculosis, 2008, 88(6): 616-623.
130	DUSTHACKEER A, KUMAR V, SUBBIAN S, et al. Construction and evaluation of luciferase reporter phages for the detection of active and non-replicating tubercle bacilli [J]. Journal of Microbiological Methods, 2008, 73(1): 18-25.
131	PENG Yong, JIN Yanqiu, LIN Hong, et al. Application of the VPp1 bacteriophage combined with a coupled enzyme system in the rapid detection of Vibrio parahaemolyticus [J]. Journal of Microbiological Methods, 2014, 98: 99-104.
132	KIM Seongmi, KIM Minsik, Sangryeol RYU. Development of an engineered bioluminescent reporter phage for the sensitive detection of viable Salmonella typhimurium [J]. Analytical Chemistry, 2014, 86(12): 5858-5864.
133	VANDAMM JP, RAJANNA C, SHARP N J, et al. Rapid detection and simultaneous antibiotic susceptibility analysis of Yersinia pestis directly from clinical specimens by use of reporter phage [J]. Journal of Clinical Microbiology, 2014, 52(8): 2998-3003.
134	SCHOFIELD DA, MOLINEUX I J, WESTWATER C. Diagnostic bioluminescent phage for detection of Yersinia pestis [J]. Journal of Clinical Microbiology, 2009, 47(12): 3887-3894.
135	SCHOFIELD D A, WRAY D J, MOLINEUX I J. Isolation and development of bioluminescent reporter phages for bacterial dysentery [J]. European Journal of Clinical Microbiology and Infectious Diseases, 2015, 34(2): 395-403.
136	SHARP N J, VANDAMM J P, MOLINEUX I J, et al. Rapid detection of Bacillus anthracis in complex food matrices using phage-mediated bioluminescence [J]. Journal of Food Protection, 2015, 78(5): 963-968.
137	SHARP N J, MOLINEUX I J, PAGE M A, et al. Rapid detection of viable Bacillus anthracis spores in environmental samples by using engineered reporter phages [J]. Applied and Environmental Microbiology, 2016, 82(8): 2380-2387.
138	KIM Jinwoo, KIM Minsik, KIM Seongmi, et al. Sensitive detection of viable Escherichia coli O157: H7 from foods using a luciferase-reporter phage phiV10lux [J]. International Journal of Food Microbiology, 2017, 254: 11-17.
139	KANNAN P, YONG Ho Yao, REIMAN L, et al. Bacteriophage-based rapid and sensitive detection of Escherichia coli O157: H7 isolates from ground beef [J]. Foodborne Pathogens and Disease, 2010, 7(12): 1551-1558.
140	SCHOFIELD D A, SHARP N J, WESTWATER C. Phage-based platforms for the clinical detection of human bacterial pathogens [J]. Bacteriophage, 2012, 2(2): 105-283.
141	SCHMIDT A, RABSCH W, BROEKER N K, et al. Bacteriophage tailspike protein based assay to monitor phase variable glucosylations in Salmonella O-antigens [J]. BMC Microbiology, 2016, 16(1): 207.
142	GÓMEZ-TORRES N, DUNNE M, GARDE S, et al. Development of a specific fluorescent phage endolysin for in situ detection of Clostridium species associated with cheese spoilage [J]. Microbial Biotechnology, 2018, 11(2): 332-345.
143	BENEŠÍK M, NOVÁČEK J, JANDA L, et al. Role of SH3b binding domain in a natural deletion mutant of Kayvirus endolysin LysF1 with a broad range of lytic activity [J]. Virus Genes, 2018, 54(1): 130-139.
144	FEDERICI S, NOBS SP, ELINAV E. Phages and their potential to modulate the microbiome and immunity [J]. Cellular & Molecular Immunology, 2020. DOI: 10.1038/s41423-020-00532-4. DOI URL
145	WANG Xiaofang, WEI Zhong, YANG Keming, et al. Phage combination therapies for bacterial wilt disease in tomato [J]. Nature Biotechnology, 2019, 37(12): 1513-1520.
146	HSU B B, GIBSON TE, YELISEYEV V, et al. Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model [J]. Cell Host and Microbe, 2019, 25(6): 803-814.
147	CITORIK R J, MIMEE M, LU T K. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases [J]. Nature Biotechnology, 2014, 32(11): 1141-1145.
148	KATO T, YUI M, DEO V K, et al. Development of Rous sarcoma Virus-like particles displaying hCC49 scFv for specific targeted drug delivery to human colon carcinoma cells [J]. Pharmaceutical Research, 2015, 32(11): 3699-3707.
149	DEO V K, KATO T, PARK E Y. Virus-like particles displaying recombinant short-chain fragment region and interleukin 2 for targeting colon cancer tumors and attracting macrophages [J]. Journal of Pharmaceutical Sciences, 2016, 105(5): 1614-1622.
150	LINO C A, CALDEIRA J C, PEABODY D S. Display of single-chain variable fragments on bacteriophage MS2 virus-like particles [J]. Journal of Nanobiotechnology, 2017, 15(1): 13.
151	VAKS L, BENHAR I. Antibacterial application of engineered bacteriophage nanomedicines: antibody-targeted, chloramphenicol prodrug loaded bacteriophages for inhibiting the growth of Staphylococcus aureus bacteria [J]. Methods in Molecular Biology, 2011, 726: 187-206.
152	ANAND P, O'NEIL A, LIN E, et al. Tailored delivery of analgesic ziconotide across a blood brain barrier model using viral nanocontainers [J]. Scientific Reports, 2015, 5: 12497.
153	QAZI S, MIETTINEN H M, WILKINSON R A, et al. Programmed self-assembly of an active P22-Cas9 nanocarrier system [J]. Molecular Pharmaceutics, 2016, 13(3): 1191-1196.
154	HUME H K C, VIDIGAL J. Synthetic biology for bioengineering virus-like particle vaccines [J]. Cellular & Molecular Immunology, 2019, 116(4): 919-35.
155	LUA L H, CONNORS N K, SAINSBURY F, et al. Bioengineering virus-like particles as vaccines [J]. Biotechnology and Bioengineering, 2014, 111(3): 425-40.
156	DENG L, ROOSE K, JOB E R, et al. Oral delivery of Escherichia coli persistently infected with M2e-displaying bacteriophages partially protects against influenza A virus [J]. Journal of Controlled Release, 2017, 264: 55-65.
157	XU Hai, BAO Xi, LU Yu, et al. Immunogenicity of T7 bacteriophage nanoparticles displaying G-H loop of foot-and-mouth disease virus (FMDV) [J]. Vet Microbiol, 2017, 205: 46-52.
158	BAHADIR A O, BALCIOGLU B K, UZYOL K S, et al. Phage displayed HBV core antigen with immunogenic activity [J]. Applied Biochemistry and Biotechnology, 2011, 165(7/8): 1437-1447.
159	GAO Jianming, LIU Z, HUANG M, et al. T7 phage displaying latent membrane protein 1 of Epstein-Barr virus elicits humoral and cellular immune responses in rats [J]. Acta Virologica, 2011, 55(2): 117-121.
160	BUTTERFIELD G L, LAJOIE M J, GUSTAFSON H H, et al. Evolution of a designed protein assembly encapsulating its own RNA genome [J]. Nature, 2017, 552(7685): 415-420.
161	HAN Lei, SHAO Changxu, LIANG Bo, et al. Genetically engineered phage-templated MnO₂ nanowires: synthesis and their application in electrochemical glucose biosensor operated at neutral pH condition [J]. ACS Applied Materials & Interfaces, 2016, 8(22): 13768-13776.
162	MANIVANNAN S, KANG Inhak, Yeji SEO, et al. M13 virus-incorporated biotemplates on electrode surfaces to nucleate metal nanostructures by electrodeposition [J]. ACS Applied Materials & Interfaces, 2017, 9(38): 32965-32976.
163	Dahyun OH, QI Jifa, HAN Binghong, et al. M13 virus-directed synthesis of nanostructured metal oxides for lithium-oxygen batteries [J]. Nano Letters, 2014, 14(8): 4837-4845.
164	YI Hyunjung, GHOSH D, Moon Ho HAM, et al. M13 phage-functionalized single-walled carbon nanotubes as nanoprobes for second near-infrared window fluorescence imaging of targeted tumors [J]. Nano Letters, 2012, 12(3): 1176-1183.
165	SZOT-KARPIŃSKA K, GOLEC P, LEŚNIEWSKI A, et al. Modified filamentous bacteriophage as a scaffold for carbon nanofiber [J]. Bioconjugate Chemistry, 2016, 27(12): 2900-2910.
166	Hwa Kyoung LEE, Yujean LEE, KIM Hyori, et al. Screening of Pro-Asp sequences exposed on bacteriophage M13 as an ideal anchor for gold nanocubes [J]. ACS Synthetic Biology, 2017, 6(9): 1635-1641.
167	GIESSEN T W, SILVER P A. A catalytic nanoreactor based on in vivo encapsulation of multiple enzymes in an engineered protein nanocompartment [J]. ChemBioChem, 2016, 17(20): 1931-1935.
168	MYHRVOLD C, POLKA J K, SILVER P A. Synthetic lipid-containing scaffolds enhance production by colocalizing enzymes [J]. ACS Synthetic Biology, 2016, 5(12): 1396-4103.
169	DION M B, OECHSLIN F, MOINEAU S. Phage diversity, genomics and phylogeny [J]. Nature Reviews Microbiology, 2020, 18(3): 125-138.
170	SHARMA U, PAUL V D. Bacteriophage lysins as antibacterials [J]. Critical Care, 2017, 21(1): 99.

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噬菌体合成生物学研究进展和应用

Advances and applications of phage synthetic biology

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