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Ashwath P, Somanath D, Sannejal AD. CRISPR and Antisense RNA Technology: Exploiting Nature's Tool to Restrain Virulence in Tenacious Pathogens. Mol Biotechnol 2023; 65:17-27. [PMID: 35980592 DOI: 10.1007/s12033-022-00539-4] [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: 04/11/2022] [Accepted: 07/25/2022] [Indexed: 01/11/2023]
Abstract
Pathogenic bacteria constitute a significant threat to mankind and at the same time represent a huge reservoir of abeyant therapeutics to prevent and treat various diseases. The concept of virulence determinants has been a compelling tool in driving research in the field of bacterial pathogenesis and infectious diseases. In this review, we highlight a few virulence elements forged by the pathogens from the viewpoint of the damage-response scaffold, vandalizing the susceptible host. Seeking an alternative to target the virulence determinants heads a road map toward the exemplary molecular approach. Hence, here we explore some of the exceptional applications of the clustered regulatory interspaced short palindromic repeat (CRISPR)- based therapy and antisense RNA (asRNA) approach, which could be exploited to selectively dismantle adamant components of the pathogen's virulence machinery. To the best of our knowledge, this is the first review paper involving both CRISPR and antisense RNA technology, as an alternative strategy to evade virulence mechanisms in bacterial pathogens.
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Affiliation(s)
- Priyanka Ashwath
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Deralakatte, Mangaluru, 575018, India
| | - Disha Somanath
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Deralakatte, Mangaluru, 575018, India
| | - Akhila Dharnappa Sannejal
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Deralakatte, Mangaluru, 575018, India.
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Tarverdizadeh Y, Khalili M, Esmaeili S, Ahmadian G, Golchin M, Hajizade A. Targeted gene inactivation in Salmonella Typhi by CRISPR/Cas9-assisted homologous recombination. World J Microbiol Biotechnol 2022; 39:58. [PMID: 36572753 DOI: 10.1007/s11274-022-03504-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Targeted gene inactivation (TGI) is a widely used technique for the study of genes' functions. There are many different methods for TGI, however, most of them are so complicated and time-consuming. New promising genetic engineering tools are developing for this purpose. In the present study, for the first time we disrupted a virulence gene from Salmonella enterica serovar Typhi (S. Typhi), located in the bacterial chromosome using CRISPR/Cas9 system and homology directed repair (HDR). METHODS For this aim, pCas9 plasmid containing Cas9 enzyme and required proteins for homology directed recombination was transferred to S. Typhi by electroporation. On the other hand, a specific guide RNA (gRNA) was designed using CRISPOR online tool. Synthetic gRNA was cloned into pTargetF plasmid. Also, a DNA fragment (HDR fragment) was designed to incorporate into the bacterial chromosome following the cleavage of the bacterial genome by Cas9 enzyme. pTargetF containing gRNA and HDR fragment were co-transferred to S. Typhi containing pcas9 plasmid. The transformed bacteria were screened for recombination using PCR, restriction digestion and sequencing. RESULTS The results of PCR, restriction digestion and sequencing showed the successful recombination of S. Typhi, in which the gidA gene is disrupted. CONCLUSION In the present study we aimed to develop a rapid and robust method for targeted gene inactivation in a bacterial species, S. Typhi. This procedure can be exploited for disruption of other Salmonella as well as other bacteria's genes.
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Affiliation(s)
- Yousof Tarverdizadeh
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Khalili
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Saber Esmaeili
- Department of Epidemiology and Biostatics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mehdi Golchin
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Abbas Hajizade
- Biology Research Center, Faculty of Basic Sciences, Imam Hossein University, Tehran, Iran.
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Whole Genome Sequencing and CRISPR/Cas9 Gene Editing of Enterotoxigenic Escherichia coli BE311 for Fluorescence Labeling and Enterotoxin Analyses. Int J Mol Sci 2022; 23:ijms23147502. [PMID: 35886856 PMCID: PMC9321511 DOI: 10.3390/ijms23147502] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/07/2023] Open
Abstract
Some prevention strategies, including vaccines and antibiotic alternatives, have been developed to reduce enterotoxigenic Escherichia coli proliferation in animal production. In this study, a wild-type strain of BE311 with a virulent heat-stable enterotoxin gene identical to E. coli K99 was isolated for its high potential for gene expression ability. The whole genome of E. coli BE311 was sequenced for gene analyses and editing. Subsequently, the fluorescent gene mCherry was successfully knocked into the genome of E. coli BE311 by CRISPR/Cas9. The E. coli BE311−mCherry strain was precisely quantified through the fluorescence intensity and red colony counting. The inflammatory factors in different intestinal tissues all increased significantly after an E. coli BE311−mCherry challenge in Sprague−Dawley rats (p < 0.05). The heat-stable enterotoxin gene of E. coli BE311 was knocked out, and an attenuated vaccine host E. coli BE311-STKO was constructed. Flow cytometry showed apoptotic cell numbers were lower following a challenge of IPEC-J2 cells with E. coli BE311-STKO than with E. coli BE311. Therefore, the E. coli BE311−mCherry and E. coli BE311-STKO strains that were successfully constructed based on the gene knock-in and knock-out technology could be used as ideal candidates in ETEC challenge models and for the development of attenuated vaccines.
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Ping L, Ruxian J, Mengping Z, Pei J, Zhuoya L, Guosheng L, Zhenyu W, Hailei W. Whole-cell biosynthesis of cytarabine by an unnecessary protein-reduced Escherichia coli that coexpresses purine and uracil phosphorylase. Biotechnol Bioeng 2022; 119:1768-1780. [PMID: 35383880 DOI: 10.1002/bit.28098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 11/10/2022]
Abstract
Currently, whole-cell catalysts face challenges due to the complexity of reaction systems, although they have a cost advantage over pure enzymes. In this work, cytarabine was synthesized by purified purine phosphorylase 1 (PNP1) and uracil phosphorylase (UP), and the conversion of cytarabine from adenine arabinoside reached 72.3±4.3%. However, the synthesis was unsuccessful by whole-cell catalysis due to interference from unnecessary proteins (UNPs) in cells. Thus, we carried out a large-scale gene editing involving 377 genes in the genome of Escherichia coli to reduce the negative effect of UNPs on substrate conversion and cytarabine production. Finally, the PNP1 and UP activities of the obtained mutant were increased significantly compared with the parental strain, and more importantly, the conversion rate of cytarabine by whole-cell catalysis reached 67.4±2.5%. The lack of 148 proteins and down-regulation of 783 proteins caused by gene editing were equivalent to partial purification of the enzymes within cells, and thus, we provided inspiration to solve the problem caused by UNP interference, which is ubiquitous in the field of whole-cell catalysis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Li Ping
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Jing Ruxian
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Zhou Mengping
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Jia Pei
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Li Zhuoya
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Liu Guosheng
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Wang Zhenyu
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Wang Hailei
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China.,Advanced Environmental Biotechnology Center, Nanyang Technological University, Singapore, 637141, Singapore
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Zhang B, Wang H, Zhao W, Shan C, Liu C, Gao L, Zhao R, Ao P, Xiao P, Lv L, Gao H. New insights into the construction of wild-type Saba pig-derived Escherichia coli irp2 gene deletion strains. 3 Biotech 2021; 11:408. [PMID: 34466347 PMCID: PMC8363713 DOI: 10.1007/s13205-021-02951-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/27/2021] [Indexed: 01/24/2023] Open
Abstract
To construct wild-type E. coli irp2 gene deletion strains, CRISPR/Cas9 gene editing technology was used, and the difficulty and key points of gene editing of wild-type strains were analyzed. Based on the resistance of the CRISPR/Cas9 system expression vector, 4 strains of 41 E. coli strains isolated from Saba pigs were selected as the target strains for the deletion of the irp2 gene, which were sensitive to both ampicillin and kanamycin. Then, CRISPR/Cas9 technology was combined with homologous recombination technology to construct recombinant vectors containing Cas9, sgRNA and donor sequences to knock out the irp2 gene. Finally, the absence of the irp2 gene in E. coli was further verified by iron uptake assays, iron carrier production assays and growth curve measurements. The results showed that three of the selected strains showed single base mutations and deletions (Δirp2-1, Δirp2-2 and Δirp2-3). The deletion of the irp2 gene reduced the ability of E. coli to take up iron ions and produce iron carriers, but not affect the growth characteristics of E. coli. It is shown that the CRISPR/Cas9 knock-out system constructed in this study can successfully knock out the irp2 gene of the wild-type E. coli. Our results providing new insights into genome editing in wild-type strains, which enable further functional studies of the irp2 gene in wild-type E. coli.
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Affiliation(s)
- Bo Zhang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Hongdan Wang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Weiwei Zhao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Chunlan Shan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Chaoying Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Libo Gao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Ru Zhao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Pingxing Ao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Peng Xiao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Longbao Lv
- Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| | - Hong Gao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
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