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Yang Z, Li B, Bu R, Wang Z, Xin Z, Li Z, Zhang L, Wang W. A highly efficient method for genomic deletion across diverse lengths in thermophilic Parageobacillus thermoglucosidasius. Synth Syst Biotechnol 2024; 9:658-666. [PMID: 38817825 PMCID: PMC11137367 DOI: 10.1016/j.synbio.2024.05.009] [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: 04/02/2024] [Revised: 05/07/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024] Open
Abstract
Parageobacillus thermoglucosidasius is emerging as a highly promising thermophilic organism for metabolic engineering. The utilization of CRISPR-Cas technologies has facilitated programmable genetic manipulation in P. thermoglucosidasius. However, the absence of thermostable NHEJ enzymes limited the capability of the endogenous type I CRISPR-Cas system to generate a variety of extensive genomic deletions. Here, two thermophilic NHEJ enzymes were identified and combined with the endogenous type I CRISPR-Cas system to develop a genetic manipulation tool that can achieve long-range genomic deletion across various lengths. By optimizing this tool-through adjusting the expression level of NHEJ enzymes and leveraging our discovery of a negative correlation between GC content of the guide RNA (gRNA) and deletion efficacy-we streamlined a comprehensive gRNA selection manual for whole-genome editing, achieving a 100 % success rate in randomly selecting gRNAs. Notably, using just one gRNA, we achieved genomic deletions spanning diverse length, exceeding 200 kilobases. This tool will facilitate the genomic manipulation of P. thermoglucosidasius for both fundamental research and applied engineering studies, further unlocking its potential as a thermophilic cell factory.
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Affiliation(s)
- Zhiheng Yang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Bixiao Li
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Cluster Science, Ministry of Education, Frontiers Science Center for High Energy Material, Advanced Research Institute of Multidisciplinary Science, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Ruihong Bu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhengduo Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Zhenguo Xin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Ma S, Su T, Lu X, Qi Q. Bacterial genome reduction for optimal chassis of synthetic biology: a review. Crit Rev Biotechnol 2024; 44:660-673. [PMID: 37380345 DOI: 10.1080/07388551.2023.2208285] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/13/2022] [Accepted: 02/20/2023] [Indexed: 06/30/2023]
Abstract
Bacteria with streamlined genomes, that harbor full functional genes for essential metabolic networks, are able to synthesize the desired products more effectively and thus have advantages as production platforms in industrial applications. To obtain streamlined chassis genomes, a large amount of effort has been made to reduce existing bacterial genomes. This work falls into two categories: rational and random reduction. The identification of essential gene sets and the emergence of various genome-deletion techniques have greatly promoted genome reduction in many bacteria over the past few decades. Some of the constructed genomes possessed desirable properties for industrial applications, such as: increased genome stability, transformation capacity, cell growth, and biomaterial productivity. The decreased growth and perturbations in physiological phenotype of some genome-reduced strains may limit their applications as optimized cell factories. This review presents an assessment of the advancements made to date in bacterial genome reduction to construct optimal chassis for synthetic biology, including: the identification of essential gene sets, the genome-deletion techniques, the properties and industrial applications of artificially streamlined genomes, the obstacles encountered in constructing reduced genomes, and the future perspectives.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
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Raman SK, Siva Reddy DV, Jain V, Bajpai U, Misra A, Singh AK. Mycobacteriophages: therapeutic approach for mycobacterial infections. Drug Discov Today 2024; 29:104049. [PMID: 38830505 DOI: 10.1016/j.drudis.2024.104049] [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: 01/28/2024] [Revised: 05/07/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
Tuberculosis (TB) is a significant global health threat, and cases of infection with non-tuberculous mycobacteria (NTM) causing lung disease (NTM-LD) are rising. Bacteriophages and their gene products have garnered interest as potential therapeutic options for bacterial infections. Here, we have compiled information on bacteriophages and their products that can kill Mycobacterium tuberculosis or NTM. We summarize the mechanisms whereby viable phages can access macrophage-resident bacteria and not elicit immune responses, review methodologies of pharmaceutical product development containing mycobacteriophages and their gene products, mainly lysins, in the context of drug regulatory requirements and we discuss industrially relevant methods for producing pharmaceutical products comprising mycobacteriophages, emphasizing delivery of mycobacteriophages to the lungs. We conclude with an outline of some recent case studies on mycobacteriophage therapy.
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Affiliation(s)
- Sunil Kumar Raman
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - D V Siva Reddy
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji , New Delhi 110019, India
| | - Amit Misra
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Amit Kumar Singh
- Experimental Animal Facility, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra 282004, Uttar Pradesh, India.
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Akter S, Kamal E, Schwarz C, Lewin A. Gene knock-out in Mycobacterium abscessus using Streptococcus thermophilus CRISPR/Cas. J Microbiol Methods 2024; 220:106924. [PMID: 38548070 DOI: 10.1016/j.mimet.2024.106924] [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: 02/05/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
The CRISPRi system using dCas9Sth1 from Streptococcus thermophilus developed for Mycobacterium tuberculosis and M. smegmatis was modified to allow gene knock-out in M. abscessus. Efficacy of the knock-out system was evaluated by applying deletions and insertions to the mps1 gene. A comparative genomic analysis of mutants and wild type validated the target specificity.
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Affiliation(s)
- Suriya Akter
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Elisabeth Kamal
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany.
| | - Carsten Schwarz
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany.
| | - Astrid Lewin
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany.
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He P, Zhao B, He W, Song Z, Pei S, Liu D, Xia H, Wang S, Ou X, Zheng Y, Zhou Y, Song Y, Wang Y, Cao X, Xing R, Zhao Y. Impact of MSMEG5257 Deletion on Mycolicibacterium smegmatis Growth. Microorganisms 2024; 12:770. [PMID: 38674714 PMCID: PMC11052289 DOI: 10.3390/microorganisms12040770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacterial membrane proteins play a pivotal role in the bacterial invasion of host cells; however, the precise mechanisms underlying certain membrane proteins remain elusive. Mycolicibacterium smegmatis (Ms) msmeg5257 is a hemolysin III family protein that is homologous to Mycobacterium tuberculosis (Mtb) Rv1085c, but it has an unclear function in growth. To address this issue, we utilized the CRISPR/Cas9 gene editor to construct Δmsmeg5257 strains and combined RNA transcription and LC-MS/MS protein profiling to determine the functional role of msmeg5257 in Ms growth. The correlative analysis showed that the deletion of msmeg5257 inhibits ABC transporters in the cytomembrane and inhibits the biosynthesis of amino acids in the cell wall. Corresponding to these results, we confirmed that MSMEG5257 localizes in the cytomembrane via subcellular fractionation and also plays a role in facilitating the transport of iron ions in environments with low iron levels. Our data provide insights that msmeg5257 plays a role in maintaining Ms metabolic homeostasis, and the deletion of msmeg5257 significantly impacts the growth rate of Ms. Furthermore, msmeg5257, a promising drug target, offers a direction for the development of novel therapeutic strategies against mycobacterial diseases.
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Affiliation(s)
- Ping He
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Bing Zhao
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Wencong He
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Zexuan Song
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Shaojun Pei
- School of Public Health, Peking University, Haidian District, Beijing 100871, China;
| | - Dongxin Liu
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Hui Xia
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Shengfen Wang
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Xichao Ou
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yang Zheng
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yang Zhou
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yuanyuan Song
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yiting Wang
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Xiaolong Cao
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Ruida Xing
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yanlin Zhao
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
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Neo DM, Clatworthy AE, Hung DT. A dual-plasmid CRISPR/Cas9-based method for rapid and efficient genetic disruption in Mycobacterium abscessus. J Bacteriol 2024; 206:e0033523. [PMID: 38319218 PMCID: PMC10955840 DOI: 10.1128/jb.00335-23] [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: 10/15/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Mycobacterium abscessus is increasingly recognized for causing infections that are notoriously difficult to treat, owing to its large arsenal of intrinsic antibiotic resistance mechanisms. Tools for the genetic manipulation of the pathogen are critical for enabling a better understanding of M. abscessus biology, pathogenesis, and antibiotic resistance mechanisms. However, existing methods are largely recombination-based, which are relatively inefficient. Meanwhile, CRISPR/Cas9 has revolutionized the field of genome editing including its recent adaptation for use in mycobacteria. In this study, we report a streamlined and efficient method for rapid genetic disruptions in M. abscessus. Harnessing the CRISPR1 loci from Streptococcus thermophilus, we have developed a dual-plasmid workflow that introduces Cas9 and sgRNA cassettes in separate steps but requires no other additional factors to engineer mutations in single genes or multiple genes simultaneously or sequentially using multiple targeting sgRNAs. Importantly, the efficiency of mutant generation is several orders of magnitude higher than reported for homologous recombination-based methods. This work, thus, reports the first application of CRISPR/Cas9 for gene editing in M. abscessus and is an important tool in the arsenal for the genetic manipulation of this human pathogen. IMPORTANCE Mycobacterium abscessus is an opportunistic pathogen of increasing clinical importance due to its poor clinical outcomes and limited treatment options. Drug discovery and development in this highly antibiotic-resistant species will require further understanding of M. abscessus biology, pathogenesis, and antibiotic resistance mechanisms. However, existing methods for facile genetic engineering are relatively inefficient. This study reports on the first application of CRISPR/Cas9 for gene editing in M. abscessus using a dual-plasmid workflow. We establish that our method is easily programmable, efficient, and versatile for genetic disruptions in M. abscessus. This is a critical advancement to facilitating targeted gene function studies in this emerging pathogen.
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Affiliation(s)
- Donavan Marcus Neo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Anne E. Clatworthy
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Deborah T. Hung
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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Wang Z, Qiu H, Chen Y, Chen X, Fu C, Yu L. Microbial metabolism of diosgenin by a novel isolated Mycolicibacterium sp. HK-90: A promising biosynthetic platform to produce 19-carbon and 21-carbon steroids. Microb Biotechnol 2024; 17:e14415. [PMID: 38381074 PMCID: PMC10880577 DOI: 10.1111/1751-7915.14415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/13/2023] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Green manufacture of steroid precursors from diosgenin by microbial replacing multistep chemical synthesis has been elusive. It is currently limited by the lack of strain and degradation mechanisms. Here, we demonstrated the feasibility of this process using a novel strain Mycolicibacterium sp. HK-90 with efficiency in diosgenin degradation. Diosgenin degradation by strain HK-90 involves the selective removal of 5,6-spiroketal structure, followed by the oxygenolytic cleavage of steroid nuclei. Bioinformatic analyses revealed the presence of two complete steroid catabolic gene clusters, SCG-1 and SCG-2, in the genome of strain HK-90. SCG-1 cluster was found to be involved in classic phytosterols or cholesterol catabolic pathway through the deletion of key kstD1 gene, which promoted the mutant m-∆kstD1 converting phytosterols to intermediate 9α-hydroxyandrostenedione (9-OHAD). Most impressively, global transcriptomics and characterization of key genes suggested SCG-2 as a potential gene cluster encoding diosgenin degradation. The gene inactivation of kstD2 in SCG-2 resulted in the conversion of diosgenin to 9-OHAD and 9,16-dihydroxy-pregn-4-ene-3,20-dione (9,16-(OH)2 -PG) in mutant m-ΔkstD2. Moreover, the engineered strain mHust-ΔkstD1,2,3 with a triple deletion of kstDs was constructed, which can stably accumulate 9-OHAD by metabolizing phytosterols, and accumulate 9-OHAD and 9,16-(OH)2 -PG from diosgenin. Diosgenin catabolism in strain mHust-ΔkstD1,2,3 was revealed as a progression through diosgenone, 9,16-(OH)2 -PG, and 9-OHAD to 9α-hydroxytestosterone (9-OHTS). So far, this work is the first report on genetically engineered strain metabolizing diosgenin to produce 21-carbon and 19-carbon steroids. This study presents a promising biosynthetic platform for the green production of steroid precursors, and provide insights into the complex biochemical mechanism of diosgenin catabolism.
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Affiliation(s)
- Zhikuan Wang
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Hailiang Qiu
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Yulong Chen
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Xuemin Chen
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Chunhua Fu
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
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Liu C, Yue Y, Xue Y, Zhou C, Ma Y. CRISPR-Cas9 assisted non-homologous end joining genome editing system of Halomonas bluephagenesis for large DNA fragment deletion. Microb Cell Fact 2023; 22:211. [PMID: 37838676 PMCID: PMC10576340 DOI: 10.1186/s12934-023-02214-y] [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: 04/20/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Halophiles possess several unique properties and have broad biotechnological applications including industrial biotechnology production. Halomonas spp., especially Halomonas bluephagenesis, have been engineered to produce various biopolyesters such as polyhydroxyalkanoates (PHA), some proteins, small molecular compounds, organic acids, and has the potential to become a chassis cell for the next-generation of industrial biotechnology (NGIB) owing to its simple culture, fast growth, contamination-resistant, low production cost, and high production value. An efficient genome editing system is the key for its engineering and application. However, the efficiency of the established CRISPR-Cas-homologous recombination (HR) gene editing tool for large DNA fragments was still relatively low. In this study, we firstly report a CRISPR-Cas9 gene editing system combined with a non-homologous end joining (NHEJ) repair system for efficient large DNA fragment deletion in Halomonas bluephagenesis. RESULTS Three different NHEJ repair systems were selected and functionally identified in Halomonas bluephagenesis TD01. The NHEJ system from M. tuberculosis H37Rv (Mt-NHEJ) can functionally work in H. bluephagenesis TD01, resulting in base deletion of different lengths for different genes and some random base insertions. Factors affecting knockout efficiencies, such as the number and position of sgRNAs on the DNA double-strands, the Cas9 protein promoter, and the interaction between the HR and the NHEJ repair system, were further investigated. Finally, the optimized CRISPR-Cas9-NHEJ editing system was able to delete DNA fragments up to 50 kb rapidly with high efficiency of 31.3%, when three sgRNAs on the Crick/Watson/Watson DNA double-strands and the arabinose-induced promoter Para for Cas9 were used, along with the background expression of the HR repair system. CONCLUSIONS This was the first report of CRISPR-Cas9 gene editing system combined with a non-homologous end joining (NHEJ) repair system for efficient large DNA fragment deletion in Halomonas spp. These results not only suggest that this editing system is a powerful genome engineering tool for constructing chassis cells in Halomonas, but also extend the application of the NHEJ repair system.
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Affiliation(s)
- Chunyan Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaxin Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cheng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China.
- Beijing Key Laboratory for Utilization of Biomass Wastes, Beijing, 100023, China.
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Zhang G, Liu J, He Y, Du Y, Xu L, Chen T, Guo Y, Fu H, Li A, Tian Y, Hu Y, Yang C, Lu M, Deng X, Wang J, Lu N. Modifying Escherichia coli to mimic Shigella for medical microbiology laboratory teaching: a new strategy to improve biosafety in class. Front Cell Infect Microbiol 2023; 13:1257361. [PMID: 37780843 PMCID: PMC10533986 DOI: 10.3389/fcimb.2023.1257361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Laboratory teaching of medical microbiology involves highly pathogenic microorganisms, thus posing potential biosafety risks to the students and the teacher. To address these risks, non/low-pathogenic microorganisms were modified to mimic highly pathogenic ones or highly pathogenic microorganisms were attenuated directly using the CRISPR/Cas9 technology. This study describes the modification of Escherichia coli DH5α to mimic Shigella and its evaluation as a safe alternative for medical laboratory teaching. Methods To generate E. coli DH5α△FliC△tnaA2a, the tnaA and FliC genes in E. coli DH5α were knocked out using CRISPR/Cas9 technology; a plasmid bearing the O-antigen determinant of S. flexneri 2a was then constructed and transformed. Acid tolerance assays and guinea pig eye tests were used to assess the viability and pathogenicity, respectively. Questionnaires were used to analyze teaching effectiveness and the opinions of teachers and students. Results The survey revealed that most teachers and students were inclined towards real-time laboratory classes than virtual classes or observation of plastic specimens. However, many students did not abide by the safety regulations, and most encountered potential biosafety hazards in the laboratory. E. coli DH5α△FliC△tnaA2a was biochemically and antigenically analogous to S. flexneri 2a and had lower resistance to acid than E. coli. There was no toxicity observed in guinea pigs. Most of teachers and students were unable to distinguish E. coli DH5α△FliC△tnaA2a from pure S. flexneri 2a in class. Students who used E. coli DH5α△FliC△tnaA2a in their practice had similar performance in simulated examinations compared to students who used real S. flexneri 2a, but significantly higher than the virtual experimental group. Discussion This approach can be applied to other high-risk pathogenic microorganisms to reduce the potential biosafety risks in medical laboratory-based teaching and provide a new strategy for the development of experimental materials.
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Affiliation(s)
- Guangyuan Zhang
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Jia Liu
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Yonglin He
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Yuheng Du
- Department for Rehabilitation Medicine, The Second College of Clinical Medicine of Chongqing Medical University, Chongqing, China
| | - Lei Xu
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Tingting Chen
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Yanan Guo
- Chongqing Medical University, International Medical College, Chongqing, China
| | - Huichao Fu
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Anlong Li
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Yunbo Tian
- Chongqing Blood Center, Quality Management Section, Chongqing, China
| | - Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Chun Yang
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Mingqi Lu
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Xichuan Deng
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Jingsong Wang
- R&D Department, Chongqing Kebilong Biotechnology Co., Ltd., Chongqing, China
| | - Nan Lu
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
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10
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Zein-Eddine R, Refrégier G, Cervantes J, Yokobori NK. The future of CRISPR in Mycobacterium tuberculosis infection. J Biomed Sci 2023; 30:34. [PMID: 37245014 DOI: 10.1186/s12929-023-00932-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic repeats (CRISPR)-Cas systems rapidly raised from a bacterial genetic curiosity to the most popular tool for genetic modifications which revolutionized the study of microbial physiology. Due to the highly conserved nature of the CRISPR locus in Mycobacterium tuberculosis, the etiological agent of one of the deadliest infectious diseases globally, initially, little attention was paid to its CRISPR locus, other than as a phylogenetic marker. Recent research shows that M. tuberculosis has a partially functional Type III CRISPR, which provides a defense mechanism against foreign genetic elements mediated by the ancillary RNAse Csm6. With the advent of CRISPR-Cas based gene edition technologies, our possibilities to explore the biology of M. tuberculosis and its interaction with the host immune system are boosted. CRISPR-based diagnostic methods can lower the detection threshold to femtomolar levels, which could contribute to the diagnosis of the still elusive paucibacillary and extrapulmonary tuberculosis cases. In addition, one-pot and point-of-care tests are under development, and future challenges are discussed. We present in this literature review the potential and actual impact of CRISPR-Cas research on human tuberculosis understanding and management. Altogether, the CRISPR-revolution will revitalize the fight against tuberculosis with more research and technological developments.
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Affiliation(s)
- Rima Zein-Eddine
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, Route de Saclay 91120, Palaiseau, France
| | - Guislaine Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-Sur-Yvette, France
| | - Jorge Cervantes
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, 79905, USA
| | - Noemí Kaoru Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS and CONICET, C1282AFF, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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11
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Mipeshwaree Devi A, Khedashwori Devi K, Premi Devi P, Lakshmipriyari Devi M, Das S. Metabolic engineering of plant secondary metabolites: prospects and its technological challenges. FRONTIERS IN PLANT SCIENCE 2023; 14:1171154. [PMID: 37251773 PMCID: PMC10214965 DOI: 10.3389/fpls.2023.1171154] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023]
Abstract
Plants produce a wide range of secondary metabolites that play vital roles for their primary functions such as growth, defence, adaptations or reproduction. Some of the plant secondary metabolites are beneficial to mankind as nutraceuticals and pharmaceuticals. Metabolic pathways and their regulatory mechanism are crucial for targeting metabolite engineering. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated system has been widely applied in genome editing with high accuracy, efficiency, and multiplex targeting ability. Besides its vast application in genetic improvement, the technique also facilitates a comprehensive profiling approach to functional genomics related to gene discovery involved in various plant secondary metabolic pathways. Despite these wide applications, several challenges limit CRISPR/Cas system applicability in genome editing in plants. This review highlights updated applications of CRISPR/Cas system-mediated metabolic engineering of plants and its challenges.
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Affiliation(s)
| | | | | | | | - Sudripta Das
- Plant Bioresources Division, Institute of Bioresources and Sustainable Development, Imphal, Manipur, India
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12
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Harnessing CRISRP-Cas9 as an anti-mycobacterial system. Microbiol Res 2023; 270:127319. [PMID: 36780784 DOI: 10.1016/j.micres.2023.127319] [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: 08/11/2022] [Revised: 12/31/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Rapid emergence of drug resistance has posed new challenges to the treatment of mycobacterial infections. As the pace of development of new drugs is slow, alternate treatment approaches are required. Recently, CRISPR-Cas systems have emerged as potential antimicrobials. These sequence-specific nucleases introduce double strand cuts in the target DNA, which if left unrepaired, prove fatal to the host. For most bacteria, homologous recombination repair (HRR) is the only pathway for repair and survival. Mycobacteria is one of the few bacteria which possesses the non-homologous end joining (NHEJ) system in addition to HRR for double strand break repair. To assess the antimicrobial potential of CRISPR-system, Cas9-induced breaks were introduced in the genome of Mycobacterium smegmatis and the survival was studied. While the single strand breaks were efficiently repaired, the organism was unable to repair the double strand breaks efficiently. In a mixed population of antibiotic-resistant and sensitive mycobacterial cells, selectively targeting a factor that confers hygromycin resistance, turned the entire population sensitive to the drug. Further, we demonstrate that the sequence-specific targeting could also be used for curing plasmids from mycobacterium cells. Considering the growing interest in nucleic acid-based therapy to curtail infections and combat antimicrobial resistance, our data shows that CRISPR-systems hold promise for future use as an antimicrobial against drug-resistant mycobacterial infections.
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13
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Kumaran A, Jude Serpes N, Gupta T, James A, Sharma A, Kumar D, Nagraik R, Kumar V, Pandey S. Advancements in CRISPR-Based Biosensing for Next-Gen Point of Care Diagnostic Application. BIOSENSORS 2023; 13:202. [PMID: 36831968 PMCID: PMC9953454 DOI: 10.3390/bios13020202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 05/25/2023]
Abstract
With the move of molecular tests from diagnostic labs to on-site testing becoming more common, there is a sudden rise in demand for nucleic acid-based diagnostic tools that are selective, sensitive, flexible to terrain changes, and cost-effective to assist in point-of-care systems for large-scale screening and to be used in remote locations in cases of outbreaks and pandemics. CRISPR-based biosensors comprise a promising new approach to nucleic acid detection, which uses Cas effector proteins (Cas9, Cas12, and Cas13) as extremely specialized identification components that may be used in conjunction with a variety of readout approaches (such as fluorescence, colorimetry, potentiometry, lateral flow assay, etc.) for onsite analysis. In this review, we cover some technical aspects of integrating the CRISPR Cas system with traditional biosensing readout methods and amplification technologies such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA) and continue to elaborate on the prospects of the developed biosensor in the detection of some major viral and bacterial diseases. Within the scope of this article, we also discuss the recent COVID pandemic and the numerous CRISPR biosensors that have undergone development since its advent. Finally, we discuss some challenges and future prospects of CRISPR Cas systems in point-of-care testing.
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Affiliation(s)
- Akash Kumaran
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Nathan Jude Serpes
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Tisha Gupta
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Abija James
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Avinash Sharma
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Rupak Nagraik
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Vaneet Kumar
- Department of Natural Science, CT University, Ludhiana 142024, Punjab, India
| | - Sadanand Pandey
- Department of Chemistry, College of Natural Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea
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14
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Yan MY, Zheng D, Li SS, Ding XY, Wang CL, Guo XP, Zhan L, Jin Q, Yang J, Sun YC. Application of combined CRISPR screening for genetic and chemical-genetic interaction profiling in Mycobacterium tuberculosis. SCIENCE ADVANCES 2022; 8:eadd5907. [PMID: 36417506 PMCID: PMC9683719 DOI: 10.1126/sciadv.add5907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/05/2022] [Indexed: 05/30/2023]
Abstract
CRISPR screening, including CRISPR interference (CRISPRi) and CRISPR-knockout (CRISPR-KO) screening, has become a powerful technology in the genetic screening of eukaryotes. In contrast with eukaryotes, CRISPR-KO screening has not yet been applied to functional genomics studies in bacteria. Here, we constructed genome-scale CRISPR-KO and also CRISPRi libraries in Mycobacterium tuberculosis (Mtb). We first examined these libraries to identify genes essential for Mtb viability. Subsequent screening identified dozens of genes associated with resistance/susceptibility to the antitubercular drug bedaquiline (BDQ). Genetic and chemical validation of the screening results suggested that it provided a valuable resource to investigate mechanisms of action underlying the effects of BDQ and to identify chemical-genetic synergies that can be used to optimize tuberculosis therapy. In summary, our results demonstrate the potential for efficient genome-wide CRISPR-KO screening in bacteria and establish a combined CRISPR screening approach for high-throughput investigation of genetic and chemical-genetic interactions in Mtb.
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Affiliation(s)
- Mei-Yi Yan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Dandan Zheng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Si-Shang Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Xin-Yuan Ding
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Chun-Liang Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Xiao-Peng Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Lingjun Zhan
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Yi-Cheng Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
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15
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Feng S, Liang L, Shen C, Lin D, Li J, Lyu L, Liang W, Zhong LL, Cook GM, Doi Y, Chen C, Tian GB. A CRISPR-guided mutagenic DNA polymerase strategy for the detection of antibiotic-resistant mutations in M. tuberculosis. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:354-367. [PMID: 35950213 PMCID: PMC9358013 DOI: 10.1016/j.omtn.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
A sharp increase in multidrug-resistant tuberculosis (MDR-TB) threatens human health. Spontaneous mutation in essential gene confers an ability of Mycobacterium tuberculosis resistance to anti-TB drugs. However, conventional laboratory strategies for identification and prediction of the mutations in this slowly growing species remain challenging. Here, by combining XCas9 nickase and the error-prone DNA polymerase A from M. tuberculosis, we constructed a CRISPR-guided DNA polymerase system, CAMPER, for effective site-directed mutagenesis of drug-target genes in mycobacteria. CAMPER was able to generate mutagenesis of all nucleotides at user-defined loci, and its bidirectional mutagenesis at nick sites allowed editing windows with lengths up to 80 nucleotides. Mutagenesis of drug-targeted genes in Mycobacterium smegmatis and M. tuberculosis with this system significantly increased the fraction of the antibiotic-resistant bacterial population to a level approximately 60- to 120-fold higher than that in unedited cells. Moreover, this strategy could facilitate the discovery of the mutation conferring antibiotic resistance and enable a rapid verification of the growth phenotype-mutation genotype association. Our data demonstrate that CAMPER facilitates targeted mutagenesis of genomic loci and thus may be useful for broad functions such as resistance prediction and development of novel TB therapies.
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16
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Sharaev N, Chacon-Machado L, Musharova O, Savitskaya E, Severinov K. Repair of Double-Stranded DNA Breaks Generated by CRISPR–Cas9 in Pseudomonas putida KT2440. Mol Biol 2022. [DOI: 10.1134/s0026893322060152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Pseudomonas putida KT2440 is a metabolically versatile bacterium with considerable promise as a chassis strain for production and degradation of complex organic compounds. Unlike most bacteria, P. putida KT2440 encodes the Ku and LigD proteins involved in Non-Homologous End Joining (NHEJ). This pathway of repair of double-strand breaks (DSBs) in DNA has an intrinsic mutagenic potential that could be exploited in combination with currently available genome editing tools that generate programmable DSBs. Here, we investigated the effect of removal or overproduction of NHEJ-associated P. putida KT2440 enzymes on mutations generated upon repair of Cas9-mediated DSBs with the double purpose of characterizing the NHEJ pathway and investigating how it functionally interacts with the current gold standard tool for gene editing. The results of our work shed light on non-templated mechanisms of DSB repair in P. putida KT2440, an information that will serve as foundation to expand the gene engineering toolbox for this important microorganism.
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17
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Li W, Huang C, Chen J. The application of CRISPR /Cas mediated gene editing in synthetic biology: Challenges and optimizations. Front Bioeng Biotechnol 2022; 10:890155. [PMID: 36091445 PMCID: PMC9452635 DOI: 10.3389/fbioe.2022.890155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated enzymes (Cas) is a simple and convenient genome editing tool that has been used in various cell factories and emerging synthetic biology in the recent past. However, several problems, including off-target effects, cytotoxicity, and low efficiency of multi-gene editing, are associated with the CRISPR/Cas system, which have limited its application in new species. In this review, we briefly describe the mechanisms of CRISPR/Cas engineering and propose strategies to optimize the system based on its defects, including, but not limited to, enhancing targeted specificity, reducing toxicity related to Cas protein, and improving multi-point editing efficiency. In addition, some examples of improvements in synthetic biology are also highlighted. Finally, future perspectives of system optimization are discussed, providing a reference for developing safe genome-editing tools for new species.
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Affiliation(s)
- Wenqian Li
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Can Huang
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Jingyu Chen
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
- *Correspondence: Jingyu Chen,
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18
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Liu K, Lin GH, Liu K, Liu YJ, Tao XY, Gao B, Zhao M, Wei DZ, Wang FQ. Multiplexed site-specific genome engineering in Mycolicibacterium neoaurum by Att/Int system. Synth Syst Biotechnol 2022; 7:1002-1011. [PMID: 35782483 PMCID: PMC9213222 DOI: 10.1016/j.synbio.2022.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/04/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
Genomic integration of genes and pathway-sized DNA cassettes is often an indispensable way to construct robust and productive microbial cell factories. For some uncommon microbial hosts, such as Mycolicibacterium and Mycobacterium species, however, it is a challenge. Here, we present a multiplexed integrase-assisted site-specific recombination (miSSR) method to precisely and iteratively integrate genes/pathways with controllable copies in the chromosomes of Mycolicibacteria for the purpose of developing cell factories. First, a single-step multi-copy integration method was established in M. neoaurum by a combination application of mycobacteriophage L5 integrase and two-step allelic exchange strategy, the efficiencies of which were ∼100% for no more than three-copy integration events and decreased sharply to ∼20% for five-copy integration events. Second, the R4, Bxb1 and ΦC31 bacteriophage Att/Int systems were selected to extend the available integration toolbox for multiplexed gene integration events. Third, a reconstructed mycolicibacterial Xer recombinases (Xer-cise) system was employed to recycle the selection marker of gene recombination to facilitate the iterative gene manipulation. As a proof of concept, the biosynthetic pathway of ergothioneine (EGT) in Mycolicibacterium neoaurum ATCC 25795 was achieved by remodeling its metabolic pathway with a miSSR system. With six copies of the biosynthetic gene clusters (BGCs) of EGT and pentose phosphate isomerase (PRT), the titer of EGT in the resulting strain in a 30 mL shake flask within 5 days was enhanced to 66 mg/L, which was 3.77 times of that in the wild strain. The improvements indicated that the miSSR system was an effective, flexible, and convenient tool to engineer the genomes of Mycolicibacteria as well as other strains in the Mycobacteriaceae due to their proximate evolutionary relationships.
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19
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Moraes L, Trentini MM, Fousteris D, Eto SF, Chudzinski-Tavassi AM, Leite LCDC, Kanno AI. CRISPR/Cas9 Approach to Generate an Auxotrophic BCG Strain for Unmarked Expression of LTAK63 Adjuvant: A Tuberculosis Vaccine Candidate. Front Immunol 2022; 13:867195. [PMID: 35432328 PMCID: PMC9005855 DOI: 10.3389/fimmu.2022.867195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/09/2022] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis is one of the deadliest infectious diseases and a huge healthcare burden in many countries. New vaccines, including recombinant BCG-based candidates, are currently under evaluation in clinical trials. Our group previously showed that a recombinant BCG expressing LTAK63 (rBCG-LTAK63), a genetically detoxified subunit A of heat-labile toxin (LT) from Escherichia coli, induces improved protection against Mycobacterium tuberculosis (Mtb) in mouse models. This construct uses a traditional antibiotic resistance marker to enable heterologous expression. In order to avoid the use of these markers, not appropriate for human vaccines, we used CRISPR/Cas9 to generate unmarked mutations in the lysA gene, thus obtaining a lysine auxotrophic BCG strain. A mycobacterial vector carrying lysA and ltak63 gene was used to complement the auxotrophic BCG which co-expressed the LTAK63 antigen (rBCGΔ-LTAK63) at comparable levels to the original construct. The intranasal challenge with Mtb confirmed the superior protection induced by rBCGΔ-LTAK63 compared to wild-type BCG. Furthermore, mice immunized with rBCGΔ-LTAK63 showed improved lung function. In this work we showed the practical application of CRISPR/Cas9 in the tuberculosis vaccine development field.
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Affiliation(s)
- Luana Moraes
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Biotecnologia Universidade de São Paulo - Instituto de Pesquisas Tecnológicas - Instituto Butantan (USP-IPT-IB), São Paulo, Brazil
| | | | - Dimitrios Fousteris
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil.,UnivLyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Silas Fernandes Eto
- Development and Innovation Laboratory, Instituto Butantan, São Paulo, Brazil
| | - Ana Marisa Chudzinski-Tavassi
- Development and Innovation Laboratory, Instituto Butantan, São Paulo, Brazil.,Center of Excellence in New Target Discovery (CENTD) Special Laboratory, Instituto Butantan, São Paulo, Brazil
| | | | - Alex Issamu Kanno
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
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20
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Ma S, Su T, Liu J, Lu X, Qi Q. Reduction of the Bacterial Genome by Transposon-Mediated Random Deletion. ACS Synth Biol 2022; 11:668-677. [PMID: 35104106 DOI: 10.1021/acssynbio.1c00353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genome reduction is an important strategy in synthetic biology for constructing functional chassis cells or minimal genomes. However, the limited knowledge of complex gene functions and interactions makes genome reduction by rational design encounter a bottleneck. Here, we present an iterative and random genome reduction method for Escherichia coli, named "transposon-mediated random deletion (TMRD)". TMRD generates random double-strand breaks (DSBs) in the genome by combining Tn5 transposition with the CRISPR/Cas9 system and allows genomic deletions of various sizes at random positions during DSB repair through the intracellular alternative end-joining mechanism. Using E. coli MG1655 as the original strain, a pool of cells with multiple random genomic deletions were obtained after five reduction cycles. The growth rates of the obtained cells were comparable to that of MG1655, while the electroporation efficiency increased by at least 2 magnitudes. TMRD can generate a small E. coli library carrying multiple and random genomic deletions while enriching the cells with environmental fitness in the population. TMRD has the potential to be widely applied in the construction of minimal genomes or chassis cells for metabolic engineering.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Jinming Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
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21
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Ding XY, Li SS, Geng YM, Yan MY, Li GB, Zhang GL, Sun YC. Programmable Base Editing in Mycobacterium tuberculosis Using an Engineered CRISPR RNA-Guided Cytidine Deaminase. Front Genome Ed 2021; 3:734436. [PMID: 34957465 PMCID: PMC8692370 DOI: 10.3389/fgeed.2021.734436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Multidrug-resistant Mycobacterium tuberculosis (Mtb) infection seriously endangers global human health, creating an urgent need for new treatment strategies. Efficient genome editing tools can facilitate identification of key genes and pathways involved in bacterial physiology, pathogenesis, and drug resistance mechanisms, and thus contribute to the development of novel treatments for drug-resistant tuberculosis. Here, we report a two-plasmid system, MtbCBE, used to inactivate genes and introduce point mutations in Mtb. In this system, the assistant plasmid pRecX-NucSE107A expresses RecX and NucSE107A to repress RecA-dependent and NucS-dependent DNA repair systems, and the base editor plasmid pCBE expresses a fusion protein combining cytidine deaminase APOBEC1, Cas9 nickase (nCas9), and uracil DNA glycosylase inhibitor (UGI). Together, the two plasmids enabled efficient G:C to A:T base pair conversion at desired sites in the Mtb genome. The successful development of a base editing system will facilitate elucidation of the molecular mechanisms underlying Mtb pathogenesis and drug resistance and provide critical inspiration for the development of base editing tools in other microbes.
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Affiliation(s)
- Xin-Yuan Ding
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Si-Shang Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi-Man Geng
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Mei-Yi Yan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guo-Bao Li
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Guo-Liang Zhang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Yi-Cheng Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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22
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Liu K, Gao Y, Li ZH, Liu M, Wang FQ, Wei DZ. CRISPR-Cas12a assisted precise genome editing of Mycolicibacterium neoaurum. N Biotechnol 2021; 66:61-69. [PMID: 34653700 DOI: 10.1016/j.nbt.2021.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/09/2021] [Accepted: 10/10/2021] [Indexed: 12/27/2022]
Abstract
Efficient and convenient genetic manipulation of mycobacteria, important microorganisms in human healthcare and the pharmaceutical industry, is limited. In this study, using a model strain Mycolicibacterium neoaurum ATCC 25795, the classical bacterium for the production of valuable steroidal pharmaceuticals, a genome editing system employing CRISPR-Cas12a to achieve efficient and precise genetic manipulation has been developed. Targeted genome mutations could be easily achieved by the CRISPR-Cas12a system without exogenous donor templates, assisted by innate non-homologous end-joining (NHEJ). CRISPR-Cas12a enabled rapid one-step genomic DNA fragment deletions of 1 kb, 5 kb, 10 kb, 15 kb, 20 kb and 24 kb with efficiencies of 70 %, 30 %, 30 %, 20 %, 20 % and 10 %, respectively. Combined with the pNIL/pGOAL system, CRISPR-Cas12a successfully integrated the gene of interest into the targeted genomic site by single crossover and double crossovers with efficiencies of 100 % and 9 %, respectively, using a two-plasmid system. The robust CRISPR systems developed demonstrated strong potential for precise genome editing in M. neoaurum, including targeted deletion of DNA sequences of various lengths and integration of targeted genes into desired sites in the genome.
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Affiliation(s)
- Ke Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yang Gao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Zhen-Hai Li
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
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23
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Engineering a new vaccine platform for heterologous antigen delivery in live-attenuated Mycobacterium tuberculosis. Comput Struct Biotechnol J 2021; 19:4273-4283. [PMID: 34429847 PMCID: PMC8355830 DOI: 10.1016/j.csbj.2021.07.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022] Open
Abstract
Live vaccines are attractive vehicles for antigen delivery as a strategy to immunize against heterologous pathogens. The live vaccine MTBVAC is based on rational attenuation of Mycobacterium tuberculosis with the objective of improving BCG protection against pulmonary tuberculosis. However, the development of recombinant mycobacteria as antigen-presenting microorganisms has been hindered due to their fastidious genetic manipulation. In this study, we used MTBVAC as a genetic platform to deliver diphtheria, tetanus, or pertussis toxoids, which are the immunogenic constituents of the DTP vaccine. When using nonoptimal genetic conditions, the expression of these immunogens was barely detectable. Accordingly, we pursued a rational, step-by-step optimization of the genetic components to achieve the expression and secretion of these toxoids. We explored variants of the L5 mycobacteriophage promoter to ensure balanced antigen expression and plasmid stability. Optimal signal sequences were identified by comparative proteomics of MTBVAC and its parental strain. It was determined that proteins secreted by the Twin Arginine Translocation pathway displayed higher secretion in MTBVAC, and the Ag85A secretion sequence was selected as the best candidate. Because the coding regions of diphtheria, tetanus, and pertussis toxoids significantly differ in G + C content relative to mycobacterial genes, their codon usage was optimized. We also placed a 3xFLAG epitope in frame with the C-terminus of these toxoids to facilitate protein detection. Altogether, these optimizations resulted in the secretion of DTP antigens by MTBVAC, as demonstrated by western blot and MRM-MS. Finally, we examined specific antibody responses in mice vaccinated with recombinant MTBVAC expressing DTP antigens.
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24
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Sioson VA, Kim M, Joo J. Challenges in delivery systems for CRISPR-based genome editing and opportunities of nanomedicine. Biomed Eng Lett 2021; 11:217-233. [PMID: 34350049 PMCID: PMC8316527 DOI: 10.1007/s13534-021-00199-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/19/2021] [Accepted: 07/04/2021] [Indexed: 12/29/2022] Open
Abstract
The CRISPR-based genome editing technology has opened extremely useful strategies in biological research and clinical therapeutics, thus attracting great attention with tremendous progress in the past decade. Despite its robust potential in personalized and precision medicine, the CRISPR-based gene editing has been limited by inefficient in vivo delivery to the target cells and by safety concerns of viral vectors for clinical setting. In this review, recent advances in tailored nanoparticles as a means of non-viral delivery vector for CRISPR/Cas systems are thoroughly discussed. Unique characteristics of the nanoparticles including controllable size, surface tunability, and low immune response lead considerable potential of CRISPR-based gene editing as a translational medicine. We will present an overall view on essential elements in CRISPR/Cas systems and the nanoparticle-based delivery carriers including advantages and challenges. Perspectives to advance the current limitations are also discussed toward bench-to-bedside translation in engineering aspects.
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Affiliation(s)
- Victor Aaron Sioson
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919 Republic of Korea
| | - Minjong Kim
- Department of Biological Science, Ulsan National Institute of Science and Technology, Ulsan, 44919 Republic of Korea
| | - Jinmyoung Joo
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919 Republic of Korea
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25
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Wu J, Xin Y, Kong J, Guo T. Genetic tools for the development of recombinant lactic acid bacteria. Microb Cell Fact 2021; 20:118. [PMID: 34147119 PMCID: PMC8214781 DOI: 10.1186/s12934-021-01607-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
Lactic acid bacteria (LAB) are a phylogenetically diverse group with the ability to convert soluble carbohydrates into lactic acid. Many LAB have a long history of safe use in fermented foods and are recognized as food-grade microorganisms. LAB are also natural inhabitants of the human intestinal tract and have beneficial effects on health. Considering these properties, LAB have potential applications as biotherapeutic vehicles to delivery cytokines, antigens and other medicinal molecules. In this review, we summarize the development of, and advances in, genome manipulation techniques for engineering LAB and the expected future development of such genetic tools. These methods are crucial for us to maximize the value of LAB. We also discuss applications of the genome-editing tools in enhancing probiotic characteristics and therapeutic functionalities of LAB.
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Affiliation(s)
- Jiapeng Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yongping Xin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
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26
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Chimukuche NM, Williams MJ. Genetic Manipulation of Non-tuberculosis Mycobacteria. Front Microbiol 2021; 12:633510. [PMID: 33679662 PMCID: PMC7925387 DOI: 10.3389/fmicb.2021.633510] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/27/2021] [Indexed: 11/25/2022] Open
Abstract
Non-tuberculosis mycobacteria (NTMs) comprise a large group of organisms that are phenotypically diverse. Analysis of the growing number of completed NTM genomes has revealed both significant intra-genus genetic diversity, and a high percentage of predicted genes that appear to be unique to this group. Most NTMs have not been studied, however, the rise in NTM infections in several countries has prompted increasing interest in these organisms. Mycobacterial research has recently benefitted from the development of new genetic tools and a growing number of studies describing the genetic manipulation of NTMs have now been reported. In this review, we discuss the use of both site-specific and random mutagenesis tools in NTMs, highlighting the challenges that exist in applying these techniques to this diverse group of organisms.
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Affiliation(s)
| | - Monique J Williams
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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27
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Wong AI, Rock JM. CRISPR Interference (CRISPRi) for Targeted Gene Silencing in Mycobacteria. Methods Mol Biol 2021; 2314:343-364. [PMID: 34235662 DOI: 10.1007/978-1-0716-1460-0_16] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The genetic basis for Mycobacterium tuberculosis pathogenesis is incompletely understood. One reason for this knowledge gap is the relative difficulty of genetic manipulation of M. tuberculosis. To close this gap, we recently developed a robust CRISPR interference (CRISPRi) platform for programmable gene silencing in mycobacteria. In this chapter, we: (1) discuss some of the advantages and disadvantages of CRISPRi relative to more traditional genetic approaches; and (2) provide a protocol for the application of CRISPRi to reduce transcription of target genes in mycobacteria.
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Affiliation(s)
- Andrew I Wong
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
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28
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Borgers K, Vandewalle K, Van Hecke A, Michielsen G, Plets E, van Schie L, Vanmarcke S, Schindfessel L, Festjens N, Callewaert N. Development of a Counterselectable Transposon To Create Markerless Knockouts from an 18,432-Clone Ordered Mycobacterium bovis Bacillus Calmette-Guérin Mutant Resource. mSystems 2020; 5:e00180-20. [PMID: 32788404 PMCID: PMC7426150 DOI: 10.1128/msystems.00180-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/20/2020] [Indexed: 12/02/2022] Open
Abstract
Mutant resources are essential to improve our understanding of the biology of slow-growing mycobacteria, which include the causative agents of tuberculosis in various species, including humans. The generation of deletion mutants in slow-growing mycobacteria in a gene-by-gene approach in order to make genome-wide ordered mutant resources is still a laborious and costly approach, despite the recent development of improved methods. On the other hand, transposon mutagenesis in combination with Cartesian pooling-coordinate sequencing (CP-CSeq) allows the creation of large archived Mycobacterium transposon insertion libraries. However, such mutants contain selection marker genes with a risk of polar gene effects, which are undesired both for research and for use of these mutants as live attenuated vaccines. In this paper, a derivative of the Himar1 transposon is described which allows the generation of clean, markerless knockouts from archived transposon libraries. By incorporating FRT sites for FlpE/FRT-mediated recombination and I-SceI sites for ISceIM-based transposon removal, we enable two thoroughly experimentally validated possibilities to create unmarked mutants from such marked transposon mutants. The FRT approach is highly efficient but leaves an FRT scar in the genome, whereas the I-SceI-mediated approach can create mutants without any heterologous DNA in the genome. The combined use of CP-CSeq and this optimized transposon was applied in the BCG Danish 1331 vaccine strain (WHO reference 07/270), creating the largest ordered, characterized resource of mutants in a member of the Mycobacterium tuberculosis complex (18,432 clones, mutating 83% of the nonessential M. tuberculosis homologues), from which markerless knockouts can be easily generated.IMPORTANCE While speeding up research for many fields of biology (e.g., yeast, plant, and Caenorhabditis elegans), genome-wide ordered mutant collections are still elusive in mycobacterial research. We developed methods to generate such resources in a time- and cost-effective manner and developed a newly engineered transposon from which unmarked mutants can be efficiently generated. Our library in the WHO reference vaccine strain of Mycobacterium bovis BCG Danish targets 83% of all nonessential genes and was made publicly available via the BCCM/ITM Mycobacteria Collection. This resource will speed up Mycobacterium research (e.g., drug resistance research and vaccine development) and paves the way to similar genome-wide mutant collections in other strains of the Mycobacterium tuberculosis complex. The stretch to a full collection of mutants in all nonessential genes is now much shorter, with just 17% remaining genes to be targeted using gene-by-gene approaches, for which highly effective methods have recently also been described.
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Affiliation(s)
- Katlyn Borgers
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kristof Vandewalle
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Annelies Van Hecke
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Gitte Michielsen
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Evelyn Plets
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Loes van Schie
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sandrine Vanmarcke
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Nele Festjens
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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29
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Xu Z, Li Y, Li M, Xiang H, Yan A. Harnessing the type I CRISPR-Cas systems for genome editing in prokaryotes. Environ Microbiol 2020; 23:542-558. [PMID: 32510745 DOI: 10.1111/1462-2920.15116] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/26/2022]
Abstract
Genetic analysis is crucial to the understanding, exploitation, and control of microorganisms. The advent of CRISPR-Cas-based genome-editing techniques, particularly those mediated by the single-effector (Cas9 and Cas12a) class 2 CRISPR-Cas systems, has revolutionized the genetics in model eukaryotic organisms. However, their applications in prokaryotes are rather limited, largely owing to the exceptional diversity of DNA homeostasis in microorganisms and severe cytotoxicity of overexpressing these nuclease proteins in certain genotypes. Remarkably, CRISPR-Cas systems belonging to different classes and types are continuously identified in prokaryotic genomes and serve as a deep reservoir for expansion of the CRISPR-based genetic toolkits. ~90% of the CRISPR-Cas systems identified so far belong to the class 1 system which hinges on multi-protein effector complexes for DNA interference. Harnessing these widespread native CRISPR-Cas systems for 'built-in' genome editing represents an emerging and powerful genetic tool in prokaryotes, especially in the genetically recalcitrant non-model species and strains. In this progress review, we introduce the general workflow of this emerging editing platform and summarize its establishment in a growing number of prokaryotes by harnessing the most widespread, diverse type I CRISPR-Cas systems present in their genomes. We also discuss the various factors affecting the success and efficiency of this editing platform and the corresponding solutions.
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Affiliation(s)
- Zeling Xu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yanran Li
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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