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Zhang F, Wang JY, Li CL, Zhang WG. HyCas9-12aGEP: an efficient genome editing platform for Corynebacterium glutamicum. Front Bioeng Biotechnol 2024; 12:1327172. [PMID: 38532881 PMCID: PMC10963414 DOI: 10.3389/fbioe.2024.1327172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
Corynebacterium glutamicum plays a crucial role as a significant industrial producer of metabolites. Despite the successful development of CRISPR-Cas9 and CRISPR-Cas12a-assisted genome editing technologies in C. glutamicum, their editing resolution and efficiency are hampered by the diverse on-target activities of guide RNAs (gRNAs). To address this problem, a hybrid CRISPR-Cas9-Cas12a genome editing platform (HyCas9-12aGEP) was developed in C. glutamicum in this study to co-express sgRNA (corresponding to SpCas9 guide RNA), crRNA (corresponding to FnCas12a guide RNA), or hfgRNA (formed by the fusion of sgRNA and crRNA). HyCas9-12aGEP improves the efficiency of mapping active gRNAs and outperforms both CRISPR-Cas9 and CRISPR-Cas12a in genome editing resolution and efficiency. In the experiment involving the deletion of the cg0697-0740 gene segment, an unexpected phenotype was observed, and HyCas9-12aGEP efficiently identified the responsible genotype from more than 40 genes. Here, HyCas9-12aGEP greatly improve our capability in terms of genome reprogramming in C. glutamicum.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | | | | | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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2
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Chen C, Zhang N, Li M, Guo A, Zheng Y, Humak F, Qian P, Tao P. Recombinant bacteriophage T4 displaying key epitopes of the foot-and-mouth disease virus as a novel nanoparticle vaccine. Int J Biol Macromol 2024; 258:128837. [PMID: 38128800 DOI: 10.1016/j.ijbiomac.2023.128837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Foot-and-mouth disease virus (FMDV) is a highly contagious pathogen that has caused significant economic losses in the livestock industry. Peptide vaccines engineered with the protective epitopes of FMDV have provided a safer alternative for disease prevention than the traditional inactivated vaccines. However, the immunogenicity of the peptide is usually poor and therefore an adjuvant is required. Here, we showed that recombinant T4 phages displaying the B-cell epitope of the FMDV VP1 protein (VP1130-158), without additional adjuvants, induced similar levels of antigen-specific IgG1 but higher levels of IgG2a compared to the peptide vaccine. Incorporation of a CD4+ T cell epitope, either 3A21-35 of FMDV 3A protein or P2830-844 of tetanus toxoid, further enhanced the immunogenicity of VP1-T4 phage nanoparticles. Interestingly, the extrinsic adjuvant cannot enhance the immunogenicity of the nanoparticles, indicating the intrinsic adjuvant activities of T4 phage. Furthermore, the recombinant T4 phage can be produced on a large scale within a short period of time at a relatively low-cost using Escherichia coli, heralding its potential in the development of a safe and effective FMDV vaccine.
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Affiliation(s)
- Cen Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Lab, Wuhan, Hubei 430070, China
| | - Nan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Lab, Wuhan, Hubei 430070, China
| | - Mengling Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Lab, Wuhan, Hubei 430070, China
| | - Aili Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Lab, Wuhan, Hubei 430070, China
| | - Yifei Zheng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Lab, Wuhan, Hubei 430070, China
| | - Farwa Humak
- Antimicrobial Resistance Research Lab, Institute of Microbiology, University of Agriculture Faisalabad, 38000, Pakistan
| | - Ping Qian
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Lab, Wuhan, Hubei 430070, China.
| | - Pan Tao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Lab, Wuhan, Hubei 430070, China.
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3
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Carmody CM, Nugen SR. Monomeric streptavidin phage display allows efficient immobilization of bacteriophages on magnetic particles for the capture, separation, and detection of bacteria. Sci Rep 2023; 13:16207. [PMID: 37758721 PMCID: PMC10533843 DOI: 10.1038/s41598-023-42626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Immobilization of bacteriophages onto solid supports such as magnetic particles has demonstrated ultralow detection limits as biosensors for the separation and detection of their host bacteria. While the potential impact of magnetized phages is high, the current methods of immobilization are either weak, costly, inefficient, or laborious making them less viable for commercialization. In order to bridge this gap, we have developed a highly efficient, site-specific, and low-cost method to immobilize bacteriophages onto solid supports. While streptavidin-biotin represents an ideal conjugation method, the functionalization of magnetic particles with streptavidin requires square meters of coverage and therefore is not amenable to a low-cost assay. Here, we genetically engineered bacteriophages to allow synthesis of a monomeric streptavidin during infection of the bacterial host. The monomeric streptavidin was fused to a capsid protein (Hoc) to allow site-specific self-assembly of up to 155 fusion proteins per capsid. Biotin coated magnetic nanoparticles were functionalized with mSA-Hoc T4 phage demonstrated in an E. coli detection assay with a limit of detection of < 10 CFU in 100 mLs of water. This work highlights the creation of genetically modified bacteriophages with a novel capsid modification, expanding the potential for bacteriophage functionalized biotechnologies.
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Affiliation(s)
- Caitlin M Carmody
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sam R Nugen
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
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4
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Li M, Chen C, Wang X, Guo P, Feng H, Zhang X, Zhang W, Gu C, Zhu J, Wen G, Feng Y, Xiao L, Peng G, Rao VB, Tao P. T4 bacteriophage nanoparticles engineered through CRISPR provide a versatile platform for rapid development of flu mucosal vaccines. Antiviral Res 2023; 217:105688. [PMID: 37516153 DOI: 10.1016/j.antiviral.2023.105688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 07/31/2023]
Abstract
Vaccines that trigger mucosal immune responses at the entry portals of pathogens are highly desired. Here, we showed that antigen-decorated nanoparticle generated through CRISPR engineering of T4 bacteriophage can serve as a universal platform for the rapid development of mucosal vaccines. Insertion of Flu viral M2e into phage T4 genome through fusion to Soc (Small Outer Capsid protein) generated a recombinant phage, and the Soc-M2e proteins self-assembled onto phage capsids to form 3M2e-T4 nanoparticles during propagation of T4 in E. coli. Intranasal administration of 3M2e-T4 nanoparticles maintains antigen persistence in the lungs, resulting in increased uptake and presentation by antigen-presenting cells. M2e-specific secretory IgA, effector (TEM), central (TCM), and tissue-resident memory CD4+ T cells (TRM) were efficiently induced in the local mucosal sites, which mediated protections against divergent influenza viruses. Our studies demonstrated the mechanisms of immune protection following 3M2e-T4 nanoparticles vaccination and provide a versatile T4 platform that can be customized to rapidly develop mucosal vaccines against future emerging epidemics.
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Affiliation(s)
- Mengling Li
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
| | - Cen Chen
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
| | - Xialin Wang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
| | - Pengju Guo
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
| | - Helong Feng
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430070, China
| | - Xueqi Zhang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
| | - Wanpo Zhang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Changqin Gu
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jingen Zhu
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Guoyuan Wen
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430070, China
| | - Yaoyu Feng
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Lihua Xiao
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
| | - Venigalla B Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Pan Tao
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Hubei Hongshan Lab, Wuhan, Hubei, 430070, China.
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5
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Wang S, Sun E, Liu Y, Yin B, Zhang X, Li M, Huang Q, Tan C, Qian P, Rao VB, Tao P. Landscape of New Nuclease-Containing Antiphage Systems in Escherichia coli and the Counterdefense Roles of Bacteriophage T4 Genome Modifications. J Virol 2023; 97:e0059923. [PMID: 37306585 PMCID: PMC10308915 DOI: 10.1128/jvi.00599-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 05/19/2023] [Indexed: 06/13/2023] Open
Abstract
Many phages, such as T4, protect their genomes against the nucleases of bacterial restriction-modification (R-M) and CRISPR-Cas systems through covalent modification of their genomes. Recent studies have revealed many novel nuclease-containing antiphage systems, raising the question of the role of phage genome modifications in countering these systems. Here, by focusing on phage T4 and its host Escherichia coli, we depicted the landscape of the new nuclease-containing systems in E. coli and demonstrated the roles of T4 genome modifications in countering these systems. Our analysis identified at least 17 nuclease-containing defense systems in E. coli, with type III Druantia being the most abundant system, followed by Zorya, Septu, Gabija, AVAST type 4, and qatABCD. Of these, 8 nuclease-containing systems were found to be active against phage T4 infection. During T4 replication in E. coli, 5-hydroxymethyl dCTP is incorporated into the newly synthesized DNA instead of dCTP. The 5-hydroxymethylcytosines (hmCs) are further modified by glycosylation to form glucosyl-5-hydroxymethylcytosine (ghmC). Our data showed that the ghmC modification of the T4 genome abolished the defense activities of Gabija, Shedu, Restriction-like, type III Druantia, and qatABCD systems. The anti-phage T4 activities of the last two systems can also be counteracted by hmC modification. Interestingly, the Restriction-like system specifically restricts phage T4 containing an hmC-modified genome. The ghmC modification cannot abolish the anti-phage T4 activities of Septu, SspBCDE, and mzaABCDE, although it reduces their efficiency. Our study reveals the multidimensional defense strategies of E. coli nuclease-containing systems and the complex roles of T4 genomic modification in countering these defense systems. IMPORTANCE Cleavage of foreign DNA is a well-known mechanism used by bacteria to protect themselves from phage infections. Two well-known bacterial defense systems, R-M and CRISPR-Cas, both contain nucleases that cleave the phage genomes through specific mechanisms. However, phages have evolved different strategies to modify their genomes to prevent cleavage. Recent studies have revealed many novel nuclease-containing antiphage systems from various bacteria and archaea. However, no studies have systematically investigated the nuclease-containing antiphage systems of a specific bacterial species. In addition, the role of phage genome modifications in countering these systems remains unknown. Here, by focusing on phage T4 and its host Escherichia coli, we depicted the landscape of the new nuclease-containing systems in E. coli using all 2,289 genomes available in NCBI. Our studies reveal the multidimensional defense strategies of E. coli nuclease-containing systems and the complex roles of genomic modification of phage T4 in countering these defense systems.
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Affiliation(s)
- Shuangshuang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Erchao Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Yuepeng Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Baoqi Yin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Xueqi Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Mengling Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Ping Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Pan Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
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6
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Jia HJ, Jia PP, Yin S, Bu LK, Yang G, Pei DS. Engineering bacteriophages for enhanced host range and efficacy: insights from bacteriophage-bacteria interactions. Front Microbiol 2023; 14:1172635. [PMID: 37323893 PMCID: PMC10264812 DOI: 10.3389/fmicb.2023.1172635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Bacteriophages, the most abundant organisms on earth, have the potential to address the rise of multidrug-resistant bacteria resulting from the overuse of antibiotics. However, their high specificity and limited host range can hinder their effectiveness. Phage engineering, through the use of gene editing techniques, offers a means to enhance the host range of bacteria, improve phage efficacy, and facilitate efficient cell-free production of phage drugs. To engineer phages effectively, it is necessary to understand the interaction between phages and host bacteria. Understanding the interaction between the receptor recognition protein of bacteriophages and host receptors can serve as a valuable guide for modifying or replacing these proteins, thereby altering the receptor range of the bacteriophage. Research and development focused on the CRISPR-Cas bacterial immune system against bacteriophage nucleic acids can provide the necessary tools to promote recombination and counter-selection in engineered bacteriophage programs. Additionally, studying the transcription and assembly functions of bacteriophages in host bacteria can facilitate the engineered assembly of bacteriophage genomes in non-host environments. This review highlights a comprehensive summary of phage engineering methods, including in-host and out-of-host engineering, and the use of high-throughput methods to understand their role. The main aim of these techniques is to harness the intricate interactions between bacteriophages and hosts to inform and guide the engineering of bacteriophages, particularly in the context of studying and manipulating the host range of bacteriophages. By employing advanced high-throughput methods to identify specific bacteriophage receptor recognition genes, and subsequently introducing modifications or performing gene swapping through in-host recombination or out-of-host synthesis, it becomes possible to strategically alter the host range of bacteriophages. This capability holds immense significance for leveraging bacteriophages as a promising therapeutic approach against antibiotic-resistant bacteria.
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Affiliation(s)
- Huang-Jie Jia
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Supei Yin
- Urinary Nephropathy Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ling-Kang Bu
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Guan Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, China
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7
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Hussain W, Yang X, Ullah M, Wang H, Aziz A, Xu F, Asif M, Ullah MW, Wang S. Genetic engineering of bacteriophages: Key concepts, strategies, and applications. Biotechnol Adv 2023; 64:108116. [PMID: 36773707 DOI: 10.1016/j.biotechadv.2023.108116] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Bacteriophages are the most abundant biological entity in the world and hold a tremendous amount of unexplored genetic information. Since their discovery, phages have drawn a great deal of attention from researchers despite their small size. The development of advanced strategies to modify their genomes and produce engineered phages with desired traits has opened new avenues for their applications. This review presents advanced strategies for developing engineered phages and their potential antibacterial applications in phage therapy, disruption of biofilm, delivery of antimicrobials, use of endolysin as an antibacterial agent, and altering the phage host range. Similarly, engineered phages find applications in eukaryotes as a shuttle for delivering genes and drugs to the targeted cells, and are used in the development of vaccines and facilitating tissue engineering. The use of phage display-based specific peptides for vaccine development, diagnostic tools, and targeted drug delivery is also discussed in this review. The engineered phage-mediated industrial food processing and biocontrol, advanced wastewater treatment, phage-based nano-medicines, and their use as a bio-recognition element for the detection of bacterial pathogens are also part of this review. The genetic engineering approaches hold great potential to accelerate translational phages and research. Overall, this review provides a deep understanding of the ingenious knowledge of phage engineering to move them beyond their innate ability for potential applications.
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Affiliation(s)
- Wajid Hussain
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaohan Yang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mati Ullah
- Department of Biotechnology, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huan Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ayesha Aziz
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fang Xu
- Huazhong University of Science and Technology Hospital, Wuhan 430074, China
| | - Muhammad Asif
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Shenqi Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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8
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Sun Q, Shen L, Zhang BL, Yu J, Wei F, Sun Y, Chen W, Wang S. Advance on Engineering of Bacteriophages by Synthetic Biology. Infect Drug Resist 2023; 16:1941-1953. [PMID: 37025193 PMCID: PMC10072152 DOI: 10.2147/idr.s402962] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Since bacteriophages (phages) were firstly reported at the beginning of the 20th century, the study on them experiences booming-fading-emerging with discovery and overuse of antibiotics. Although they are the hotspots for therapy of antibiotic-resistant strains nowadays, natural phage applications encounter some challenges such as limited host range and bacterial resistance to phages. Synthetic biology, one of the most dramatic directions in the recent 20-years study of microbiology, has generated numerous methods and tools and has contributed a lot to understanding phage evolution, engineering modification, and controlling phage-bacteria interactions. In order to better modify and apply phages by using synthetic biology techniques in the future, in this review, we comprehensively introduce various strategies on engineering or modification of phage genome and rebooting of recombinant phages, summarize the recent researches and potential directions of phage synthetic biology, and outline the current application of engineered phages in practice.
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Affiliation(s)
- Qingqing Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Lixin Shen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Bai-Ling Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People’s Republic of China
| | - Jiaoyang Yu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, People’s Republic of China
| | - Fu Wei
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Wei Chen
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, People’s Republic of China
- The Clinical Infectious Disease Center of Nanjing, Nanjing, 210003, People’s Republic of China
- Correspondence: Wei Chen; Shiwei Wang, Email ;
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
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9
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Mahler M, Costa AR, van Beljouw SPB, Fineran PC, Brouns SJJ. Approaches for bacteriophage genome engineering. Trends Biotechnol 2022; 41:669-685. [PMID: 36117025 DOI: 10.1016/j.tibtech.2022.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 12/26/2022]
Abstract
In recent years, bacteriophage research has been boosted by a rising interest in using phage therapy to treat antibiotic-resistant bacterial infections. In addition, there is a desire to use phages and their unique proteins for specific biocontrol applications and diagnostics. However, the ability to manipulate phage genomes to understand and control gene functions, or alter phage properties such as host range, has remained challenging due to a lack of universal selectable markers. Here, we discuss the state-of-the-art techniques to engineer and select desired phage genomes using advances in cell-free methodologies and clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR-Cas) counter-selection approaches.
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Affiliation(s)
- Marina Mahler
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Sam P B van Beljouw
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand; Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands.
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10
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Lee C, Kim H, Ryu S. Bacteriophage and endolysin engineering for biocontrol of food pathogens/pathogens in the food: recent advances and future trends. Crit Rev Food Sci Nutr 2022; 63:8919-8938. [PMID: 35400249 DOI: 10.1080/10408398.2022.2059442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite advances in modern technologies, various foodborne outbreaks have continuously threatened the food safety. The overuse of and abuse/misuse of antibiotics have escalated this threat due to the prevalence of multidrug-resistant (MDR) pathogens. Therefore, the development of new methodologies for controlling microbial contamination is extremely important to ensure the food safety. As an alternative to antibiotics, bacteriophages(phages) and derived endolysins have been proposed as novel, effective, and safe antimicrobial agents and applied for the prevention and/or eradication of bacterial contaminants even in foods and food processing facilities. In this review, we describe recent genetic and protein engineering tools for phages and endolysins. The major aim of engineering is to overcome limitations such as a narrow host range, low antimicrobial activity, and low stability of phages and endolysins. Phage engineering also aims to deter the emergence of phage resistance. In the case of endolysin engineering, enhanced antibacterial ability against Gram-negative and Gram-positive bacteria is another important goal. Here, we summarize the successful studies of phages and endolysins treatment in different types of food. Moreover, this review highlights the recent advances in engineering techniques for phages and endolysins, discusses existing challenges, and suggests technical opportunities for further development, especially in terms of antimicrobial agents in the food industry.
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Affiliation(s)
- Chanyoung Lee
- Department of Food and Animal Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Hyeongsoon Kim
- Department of Food and Animal Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
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