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Luan J, Song C, Liu Y, He R, Guo R, Cui Q, Jiang C, Li X, Hao K, Stewart AF, Fu J, Zhang Y, Wang H. Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method. Nat Protoc 2024:10.1038/s41596-024-01016-9. [PMID: 39009664 DOI: 10.1038/s41596-024-01016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/01/2024] [Indexed: 07/17/2024]
Abstract
Seamless site-directed mutagenesis is an important technique for studying protein functions, tuning enzyme catalytic activities and modifying genetic elements in multiple rounds because it can insert, delete or substitute nucleotides, DNA segments or even entire genes at the target site without introducing any unwanted change. To facilitate seamless site-directed mutagenesis in large plasmids and bacterial artificial chromosomes (BACs) with repetitive sequences, we recently developed the RedEx strategy. Compared with previous methods, our approach achieves the recovery of correct recombinants with high accuracy by circumventing unwanted recombination between repetitive sequences. RedEx readily yields more than 80% accuracy in seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters, which are among the most difficult targets due to the large number of repetitive DNA sequences in modules encoding almost identical enzymes. Here we present the RedEx method by describing in detail the seamless site-directed mutagenesis in a BAC vector. Overall, the process includes three parts: (1) insertion of the RedEx cassette containing the desired mutation together with selection-counterselection markers flanked by unique restriction sites and 20-bp overlapping sequences into the target site by recombineering, (2) removal of the selection-counterselection markers in the BAC by restriction digestion and (3) circularization of the linear BAC by exonuclease-mediated in vitro DNA annealing. This protocol can be performed within 3 weeks and will enable researchers with DNA cloning experience to master seamless site-directed mutagenesis to accelerate their research.
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Affiliation(s)
- Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Yan Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruoting He
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruofei Guo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Kexin Hao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China.
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Finkel Y, Nachshon A, Aharon E, Arazi T, Simonovsky E, Dobešová M, Saud Z, Gluck A, Fisher T, Stanton RJ, Schwartz M, Stern-Ginossar N. A virally encoded high-resolution screen of cytomegalovirus dependencies. Nature 2024; 630:712-719. [PMID: 38839957 DOI: 10.1038/s41586-024-07503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Genetic screens have transformed our ability to interrogate cellular factor requirements for viral infections1,2, but most current approaches are limited in their sensitivity, biased towards early stages of infection and provide only simplistic phenotypic information that is often based on survival of infected cells2-4. Here, by engineering human cytomegalovirus to express single guide RNA libraries directly from the viral genome, we developed virus-encoded CRISPR-based direct readout screening (VECOS), a sensitive, versatile, viral-centric approach that enables profiling of different stages of viral infection in a pooled format. Using this approach, we identified hundreds of host dependency and restriction factors and quantified their direct effects on viral genome replication, viral particle secretion and infectiousness of secreted particles, providing a multi-dimensional perspective on virus-host interactions. These high-resolution measurements reveal that perturbations altering late stages in the life cycle of human cytomegalovirus (HCMV) mostly regulate viral particle quality rather than quantity, establishing correct virion assembly as a critical stage that is heavily reliant on virus-host interactions. Overall, VECOS facilitates systematic high-resolution dissection of the role of human proteins during the infection cycle, providing a roadmap for in-depth study of host-herpesvirus interactions.
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Affiliation(s)
- Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Einav Aharon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Arazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elena Simonovsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Martina Dobešová
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Zack Saud
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Avi Gluck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Fisher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Richard J Stanton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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Duan Y, Fang F, Mu X, Wang H, Shen Z, Deng Z, Liu T, Wang Z, Liu R. Exploration of Streptomyces fradiae J1-021 as a Potential Host for the Heterologous Production of Spinosad. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38597928 DOI: 10.1021/acs.jafc.3c08884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Spinosad is a potent insecticide produced by Saccharopolyspora spinosa. However, it harbors certain limitations of a low growing rate and unfeasible genetic manipulation that can be overcome by adopting a superior platform, such as Streptomyces. Herein, we exploited the industrial tylosin-producing Streptomyces fradiae J1-021 for the heterologous production of spinosad. An engineered strain (HW01) with deletion of the tylosin biosynthetic gene cluster (BGC) was constructed and then transformed with the natural spinosad BGC. The distribution and expression levels of the tylosin BGC operons were assessed to construct a natural promoter library. The rate-limiting steps of spinosad biosynthesis were identified by analyzing the transcriptional expression of the spinosad biosynthetic genes. The stepwise engineering work involved the overexpression of the biosynthetic genes participating in rate-limiting pathways using strong promoters, affording an increase in spinosad production to 112.4 μg/L. These results demonstrate that strain HW01 has the potential to be used as a chassis for the heterologous production of polyketides.
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Affiliation(s)
- Yuhua Duan
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fang Fang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin Mu
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China
| | - Hui Wang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiyong Shen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tiangang Liu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhangqian Wang
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Ran Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Gudeta DD, Foley SL. Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation. Microbiol Spectr 2024; 12:e0338723. [PMID: 37991378 PMCID: PMC10782977 DOI: 10.1128/spectrum.03387-23] [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: 10/04/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens including in vivo studies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.
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Affiliation(s)
- Dereje D. Gudeta
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
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Duan J, Yuan B, Jia F, Li X, Chen C, Li G. Development of an Efficient and Seamless Genetic Manipulation Method for Xenorhabdus and Its Application for Enhancing the Production of Fabclavines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:274-283. [PMID: 38109418 DOI: 10.1021/acs.jafc.3c04136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Xenorhabdus can produce numerous natural products, but their development has been hampered by the lack of a seamless genetic manipulation method. In this study, we compared several lethal genes and determined the sacB gene as the most effective counter-selection marker and then established a dual selection/counter-selection system by integrating neo and sacB genes into one cassette. This provides an efficient and seamless genetic manipulation method for Xenorhabdus. Using this method, DNA fragments ranging from 205 to 47,788 bp in length were seamlessly knocked out or replaced with impressively high positive rates of 80 to 100% in Xenorhabdus budapestensis XBD8. In addition, the method was successfully applied with good efficiency (45-100%) in Xenorhabdus nematophila CB6. To further validate the method, different constitutive promoters were used to replace the native fclC promoter in a batch experiment. The positivity rate remained consistently high, at 46.3%. In comparison to WT XBD8, the recombinant strain MX14 demonstrated a significant increase in the production of fabclavine 7 and fabclavine 8 by 4.97-fold and 3.22-fold, respectively, while the overall production of fabclavines was enhanced by 3.52-fold.
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Affiliation(s)
- Jiaqi Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Baoming Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fenglian Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chang Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Green Agricultural Science and Technology Group Co., Ltd, Beijing 100193, China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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de Jong LA, van Oosten L, Pijlman GP. Scarless Baculovirus Genome Editing Using Lambda-Red Recombineering in E. coli. Methods Mol Biol 2024; 2829:109-126. [PMID: 38951330 DOI: 10.1007/978-1-0716-3961-0_8] [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] [Indexed: 07/03/2024]
Abstract
Baculoviruses are widely used for their potential as biological pesticide and as platform for the production of recombinant proteins and gene therapy vectors. The Baculovirus Expression Vector System (BEVS) is used for high level of expression of (multiple) proteins in insect cells. Baculovirus recombinants can be quickly constructed by transposition of the gene(s) of interest into a so-called bacmid, which is a baculovirus infectious clone maintained as single-copy, bacterial artificial chromosome in Escherichia coli. A two-step homologous recombineering technique using the lambda-red system in E. coli allows for scarless editing of the bacmid with PCR products based on sequence homology. In the first step, a selection cassette with 50 bp homology arms, typically generated by PCR, is inserted into the designated locus. In the second step, the selection cassette is removed based on a negative selection marker, such as SacB or rpsL. This lambda-red recombineering technique can be used for multiple gene editing purposes, including (large) deletions, insertions, and even single point mutations. Moreover, since there are no remnants of the editing process, successive modifications of the same bacmid are possible. This chapter provides detailed instructions to design and perform two-step homologous recombineering of baculovirus bacmid DNA in E. coli. We present two case studies demonstrating the utility of this technique for creating a deletion mutant of the chitinase and cathepsin genes and for introducing a single point mutation in the baculovirus gene gp41. This scarless genome editing approach can facilitate functional studies of baculovirus genes and improve the production of recombinant proteins using the BEVS.
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Affiliation(s)
- Linda A de Jong
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Linda van Oosten
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands.
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Yu G, Duan Q, Cui T, Jiang C, Li X, Li Y, Fu J, Zhang Y, Wang H, Luan J. Development of a bacterial gene transcription activating strategy based on transcriptional activator positive feedback. J Adv Res 2023:S2090-1232(23)00400-9. [PMID: 38123018 DOI: 10.1016/j.jare.2023.12.015] [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: 10/01/2023] [Revised: 11/26/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
INTRODUCTION Transcription of biological nitrogen fixation (nif) genes is activated by the NifA protein which recognizes specific activating sequences upstream of σ54-dependent nif promoters. The large quantities of nitrogenase which can make up 20% of the total proteins in the cell indicates high transcription activating efficiency of NifA and high transcription level of nifHDK nitrogenase genes. OBJECTIVES Development of an efficient gene transcription activating strategy in bacteria based on positive transcription regulatory proteins and their regulating DNA sequences. METHODS We designed a highly efficient gene transcription activating strategy in which the nifA gene was placed directly downstream of its regulating sequences. The NifA protein binds its regulating sequences and stimulates transcription of itself and downstream genes. Overexpressed NifA causes transcription activation by positive reinforcement. RESULTS When this gene transcription activating strategy was used to overexpress NifA in Pseudomonas stutzeri DSM4166 containing the nif gene cluster, the nitrogenase activity was increased by 368 folds which was 16 times higher than that obtained by nifA driven by the strongest endogenous constitutive promoter. When this strategy was used to activate transcription of exogenous biosynthetic genes for the plant auxin indole-3-acetic acid and the antitumor alkaloid pigment prodigiosin in DSM4166, both of them resulted in better performance than the strongest endogenous constitutive promoter and the highest reported productions in heterologous hosts to date. Finally, we demonstrated the universality of this strategy using the positive transcriptional regulator of the psp operon, PspF, in E. coli and the pathway-specific positive transcription regulator of the polyene antibiotic salinomycin biosynthesis, SlnR, in Streptomyces albus. CONCLUSION Many positive transcription regulatory proteins and their regulating DNA sequences have been identified in bacteria. The gene transcription activating strategy developed in this study will have broad applications in molecular biology and biotechnology.
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Affiliation(s)
- Guangle Yu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Qiuyue Duan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Tianqi Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Yutong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China.
| | - Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China.
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Bai X, Chen H, Ren X, Zhong L, Wang X, Ji X, Zhang Y, Wang Y, Bian X. Heterologous Biosynthesis of Complex Bacterial Natural Products in Burkholderia gladioli. ACS Synth Biol 2023; 12:3072-3081. [PMID: 37708405 DOI: 10.1021/acssynbio.3c00389] [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] [Indexed: 09/16/2023]
Abstract
Bacterial natural products (NPs) are an indispensable source of drugs and biopesticides. Heterologous expression is an essential method for discovering bacterial NPs and the efficient biosynthesis of valuable NPs, but the chassis for Gram-negative bacterial NPs remains inadequate. In this study, we built a Burkholderiales mutant Burkholderia gladioli Δgbn::attB by introducing an integrated site (attB) to inactivate the native gladiolin (gbn) biosynthetic gene cluster, which stabilizes large foreign gene clusters and reduces the native metabolite profile. The growth and successful heterologous production of high-value NPs such as phylogenetically close Burkholderiales-derived antitumor polyketides (PKs) rhizoxins, phylogenetically distant Gammaproteobacteria-derived anti-MRSA (methicillin-resistant Staphylococcus aureus) antibiotics WAP-8294As, and Deltaproteobacteria-derived antitumor PKs disorazols demonstrate that this strain is a potential chassis for Gram-negative bacterial NPs. We further improved the yields of WAP-8294As through promoter insertions and precursor pathway overexpression based on heterologous expression in this strain. This study provides a robust bacterial chassis for genome mining, efficient production, and molecular engineering of bacterial NPs.
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Affiliation(s)
- Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiangmei Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lin Zhong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoqi Ji
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266100, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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Yi J, Zhang M, Zhu L, Xu C, Li B, Wu P, Wu H, Zhang B. High-efficiency genetic engineering toolkit for virus based on lambda red-mediated recombination. Biotechnol Lett 2023; 45:1327-1337. [PMID: 37526868 DOI: 10.1007/s10529-023-03412-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
PURPOSE Viruses, such as Ebola virus (EBOV), evolve rapidly and threaten the human health. There is a great demand to exploit efficient gene-editing techniques for the identification of virus to probe virulence mechanism for drug development. METHODS Based on lambda Red recombination in Escherichia coli (E. coli), counter-selection, and in vitro annealing, a high-efficiency genetic method was utilized here for precisely engineering viruses. EBOV trVLPs assay and dual luciferase reporter assay were used to further test the effect of mutations on virus replication. RESULTS Considering the significance of matrix protein VP24 in EBOV replication, the types of mutations within vp24, including several single-base substitutions, one double-base substitution, two seamless deletions, and one targeted insertion, were generated on the multi-copy plasmid of E. coli. Further, the length of the homology arms for recombination and in vitro annealing, and the amount of DNA cassettes and linear plasmids were optimized to create a more elaborate and cost-efficient protocol than original approach. The effects of VP24 mutations on the expression of a reporter gene (luciferase) from the EBOV minigenome were determined, and results indicated that mutations of key sites within VP24 have significant impacts on EBOV replication. CONCLUSION This precise mutagenesis method will facilitate effective and simple editing of viral genes in E. coli.
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Affiliation(s)
- Jing Yi
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Maifei Zhang
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Lin Zhu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Changzhi Xu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Binglin Li
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Panpan Wu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Hang Wu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China.
| | - Buchang Zhang
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
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10
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Abstract
The ability to manipulate the bacterial genome is an obligatory premise for the study of gene function and regulation in bacterial cells. The λ red recombineering technique allows modification of chromosomal sequences with base-pair precision without the need of intermediate molecular cloning steps. Initially conceived to construct insertion mutants, the technique lends itself to a wide variety of applications including the creation of point mutants, seamless deletions, reporter, and epitope tag fusions and chromosomal rearrangements. Here, we introduce some of the most common implementations of the method.
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Affiliation(s)
- Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), 91190 Gif-sur-Yvette, France
| | - Roberto Balbontín
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41080 Sevilla, Spain
| | - Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), 91190 Gif-sur-Yvette, France
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11
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Yoshikawa T, Misu M, Kurosu T, Takamatsu Y, Sugimoto S, Shimojima M, Ebihara H, Saijo M. Markerless bacterial artificial chromosome manipulation method by red proteins of phage λ mediated homologous recombination utilizing fluorescent proteins for both positive and counter selection. Heliyon 2023; 9:e18983. [PMID: 37600421 PMCID: PMC10432722 DOI: 10.1016/j.heliyon.2023.e18983] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
Manipulating viral genomes is an essential technique in reverse genetics and recombinant vaccine development. A strategy for manipulating large viral genomes involves introducing their entire genome into bacterial artificial chromosomes and employing Escherichia coli genetic tools. For sequence manipulation on bacterial artificial chromosomes (bacterial artificial chromosomes recombineering), a well-established method that relies on the Escherichia coli strain GS1783, and the template plasmid, pEPKan-S, is often used. This method, known as markerless DNA manipulation, allows for the generation of a recombinant bacterial artificial chromosome that does not retain the selection markers used during recombination. Although this method is highly innovative, there remains room for improvement as the plasmid is currently only available for positive selection. Additionally, differentiating true recombinants from false negatives often proves time-consuming. Consequently, an improved method for bacterial artificial chromosomes recombineering, which utilizes fluorescent proteins, has been developed. This method's core comprises three plasmids containing the I-SceI recognition site, antibiotic resistance genes (ampicillin, kanamycin, and zeocin), and fluorescent genes (YPet, mOrange, and mScarlet). The success or failure of Red recombination can be confirmed via fluorescent signals. To validate this method, the Lassa virus genes were introduced into the bacterial artificial chromosomes, containing the entire genome of the vaccinia virus strain LC16m8. Consequently, the expression of fluorescent protein genes contributed to positive selection, such as blue-white screening and counter-selection during the first and second Red recombination.
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Affiliation(s)
- Tomoki Yoshikawa
- Department of Virology 1, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Masayasu Misu
- Department of Virology 1, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Takeshi Kurosu
- Department of Virology 1, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Yuki Takamatsu
- Department of Virology 1, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Satoko Sugimoto
- Department of Virology 1, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Masayuki Shimojima
- Department of Virology 1, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Hideki Ebihara
- Department of Virology 1, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Masayuki Saijo
- Department of Virology 1, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama-shi, Tokyo, 208-0011, Japan
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12
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Zhang S, Zhang L, Greule A, Tailhades J, Marschall E, Prasongpholchai P, Leng DJ, Zhang J, Zhu J, Kaczmarski JA, Schittenhelm RB, Einsle O, Jackson CJ, Alberti F, Bechthold A, Zhang Y, Tosin M, Si T, Cryle MJ. P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate. Acta Pharm Sin B 2023; 13:3561-3574. [PMID: 37655329 PMCID: PMC10465960 DOI: 10.1016/j.apsb.2023.03.021] [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: 02/06/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
WS9326A is a peptide antibiotic containing a highly unusual N-methyl-E-2-3-dehydrotyrosine (NMet-Dht) residue that is incorporated during peptide assembly on a non-ribosomal peptide synthetase (NRPS). The cytochrome P450 encoded by sas16 (P450Sas) has been shown to be essential for the formation of the alkene moiety in NMet-Dht, but the timing and mechanism of the P450Sas-mediated α,β-dehydrogenation of Dht remained unclear. Here, we show that the substrate of P450Sas is the NRPS-associated peptidyl carrier protein (PCP)-bound dipeptide intermediate (Z)-2-pent-1'-enyl-cinnamoyl-Thr-N-Me-Tyr. We demonstrate that P450Sas-mediated incorporation of the double bond follows N-methylation of the Tyr by the N-methyl transferase domain found within the NRPS, and further that P450Sas appears to be specific for substrates containing the (Z)-2-pent-1'-enyl-cinnamoyl group. A crystal structure of P450Sas reveals differences between P450Sas and other P450s involved in the modification of NRPS-associated substrates, including the substitution of the canonical active site alcohol residue with a phenylalanine (F250), which in turn is critical to P450Sas activity and WS9326A biosynthesis. Together, our results suggest that P450Sas catalyses the direct dehydrogenation of the NRPS-bound dipeptide substrate, thus expanding the repertoire of P450 enzymes that can be used to produce biologically active peptides.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg 79104, Germany
| | - Anja Greule
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- EMBL Australia, Monash University, Clayton 3800, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
| | - Edward Marschall
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- EMBL Australia, Monash University, Clayton 3800, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
| | | | - Daniel J. Leng
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jingfan Zhang
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Joe A. Kaczmarski
- Research School of Chemistry, the Australian National University, Acton 2601, ACT, Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton 3800, VIC, Australia
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg 79104, Germany
| | - Colin J. Jackson
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
- Research School of Chemistry, the Australian National University, Acton 2601, ACT, Australia
| | - Fabrizio Alberti
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Andreas Bechthold
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg 79104, Germany
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- EMBL Australia, Monash University, Clayton 3800, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
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13
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Wang X, Zhou N, Wang B. Bacterial synthetic biology: tools for novel drug discovery. Expert Opin Drug Discov 2023; 18:1087-1097. [PMID: 37482696 DOI: 10.1080/17460441.2023.2239704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
INTRODUCTION Bacterial synthetic biology has provided powerful tools to revolutionize the drug discovery process. These tools can be harnessed to generate bacterial novel pharmaceutical compounds with enhanced bioactivity and selectivity or to create genetically modified microorganisms as living drugs. AREAS COVERED This review provides a current overview of the state-of-the-art in bacterial synthetic biology tools for novel drug discovery. The authors discuss the application of these tools including bioinformatic tools, CRISPR tools, engineered bacterial transcriptional regulators, and synthetic biosensors for novel drug discovery. Additionally, the authors present the recent progress on reprogramming bacteriophages as living drugs to fight against antibiotic-resistant pathogens. EXPERT OPINION The field of using bacterial synthetic biology tools for drug discovery is rapidly advancing. However, challenges remain in developing reliable and robust methods to engineer bacteria. Further advancements in synthetic biology hold promise to speed up drug discovery, facilitating the development of novel therapeutics against various diseases.
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Affiliation(s)
- Xiyan Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Nan Zhou
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Research Center of Biological Computation, Zhejiang Laboratory, Hangzhou, China
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14
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An Inactivated Novel Trivalent Vaccine Provides Complete Protection against FAdV-4 Causing Hepatitis-Hydropericardium Syndrome and FAdV-8b/-11 Causing Inclusion Body Hepatitis. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/5122382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Outbreaks of hepatitis-hydropericardium syndrome (HHS) caused by fowl adenovirus serotype 4 (FAdV-4) and inclusion body hepatitis (IBH) related to FAdV-8b and FAdV-11 have been increased in chickens in China since 2015. Clinical concurrent infections of FAdV-4, FAdV-8b, and FAdV-11 are quite common, yet there are no commercially available trivalent vaccines against infection by these three serotypes. In our previous study, a bivalent vaccine based on a recombinant FAdV-4, of which fiber-1 was replaced with the fiber of FAdV-8b, has been developed. In this study, a novel recombinant rFAdV-4-fiber/8b + 11 was constructed by inserting FAdV-11 fiber gene into the 1966-bp deletion region of rFAdV-4-fiber/8b genome. The in vitro replication ability of the rFAdV-4-fiber/8b + 11 was similar to the parental FAdV-4. One dose immunization with the inactivated rFAdV-4-fiber/8b + 11 vaccine generated robust immune responses against FAdV-4, FAdV-8b, and FAdV-11, and provided efficient clinical protection against FAdV-4, FAdV-8b, and FAdV-11 challenge. This study provides a novel strategy for developing potential trivalent vaccines for the prevention and control of HHS and IBH.
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15
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Zhang G, Zhang Q, Wang J, Zhang J, Shang G. Characterization of a novel Escherichia coli recombineering selection/counterselection cassette. Biotechnol Lett 2023; 45:191-197. [PMID: 36495358 DOI: 10.1007/s10529-022-03333-z] [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: 09/13/2022] [Revised: 10/31/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
Recombineering is a highly efficient DNA cloning and modification technique by using the recombinase-mediated homologous recombination. Selection/counterselection cassette is often used in chromosomal DNA or large episomal DNA manipulation, in which the selection marker is used for the first step cassette selection while deleting the target gene via allelic exchange, and the counterselection marker is used for the second step replacement of the cassette by the foreign DNA fragment. A variety of selection/counterselection cassettes are reported, however, the cassettes suffer from the shortcomings of the requirement of pre-engineered strain or specific culture medium. Herein, we report a novel S-tetR- PtetA-ccdB-aacC1-S selection/counterselection cassette that sidesteps the disadvantages. As a proof-of-concept, one-step gene cloning (0.7, 1.7, and 4.2 kb) and two-step Escherichia coli chromosomal gene knock-in (0.7 and 4.2 kb) were performed. The gene cloning and gene knock-in efficiencies are high up to 90%. The novel selection/counterselection cassette adds a powerful tool to the recombineering repertoire.
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Affiliation(s)
- Guoyi Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No.1 Wenyuan Rd Xixia District, Nanjing, 210023, Jiangsu Province, People's Republic of China
| | - Qiong Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No.1 Wenyuan Rd Xixia District, Nanjing, 210023, Jiangsu Province, People's Republic of China
| | - Junyu Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No.1 Wenyuan Rd Xixia District, Nanjing, 210023, Jiangsu Province, People's Republic of China
| | - Jiao Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No.1 Wenyuan Rd Xixia District, Nanjing, 210023, Jiangsu Province, People's Republic of China
| | - Guangdong Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No.1 Wenyuan Rd Xixia District, Nanjing, 210023, Jiangsu Province, People's Republic of China.
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16
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Mengiste AA, Wilson RH, Weissman RF, Papa Iii LJ, Hendel SJ, Moore CL, Butty VL, Shoulders MD. Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria. Nucleic Acids Res 2023; 51:e31. [PMID: 36715334 PMCID: PMC10085711 DOI: 10.1093/nar/gkad003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/31/2023] Open
Abstract
Targeted mutagenesis mediated by nucleotide base deaminase-T7 RNA polymerase fusions has recently emerged as a novel and broadly useful strategy to power genetic diversification in the context of in vivo directed evolution campaigns. Here, we expand the utility of this approach by introducing a highly active adenosine deaminase-T7 RNA polymerase fusion protein (eMutaT7A→G), resulting in higher mutation frequencies to enable more rapid directed evolution. We also assess the benefits and potential downsides of using this more active mutator. We go on to show in Escherichia coli that adenosine deaminase-bearing mutators (MutaT7A→G or eMutaT7A→G) can be employed in tandem with a cytidine deaminase-bearing mutator (MutaT7C→T) to introduce all possible transition mutations simultaneously. We illustrate the efficacy of this in vivo mutagenesis approach by exploring mutational routes to antibacterial drug resistance. This work sets the stage for general application of optimized MutaT7 tools able to induce all types of transition mutations during in vivo directed evolution campaigns across diverse organisms.
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Affiliation(s)
- Amanuella A Mengiste
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert H Wilson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel F Weissman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Louis J Papa Iii
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel J Hendel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher L Moore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vincent L Butty
- BioMicroCenter, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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17
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Gong K, Wang M, Duan Q, Li G, Yong D, Ren C, Li Y, Zhang Q, Wang Z, Sun T, Zhang H, Tu Q, Wu C, Fu J, Li A, Song C, Zhang Y, Li R. High-yield production of FK228 and new derivatives in a Burkholderia chassis. Metab Eng 2023; 75:131-142. [PMID: 36528227 DOI: 10.1016/j.ymben.2022.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/30/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
FK228 (romidepsin) is the only natural histone deacetylases (HDACs) inhibitor approved by FDA to treat cutaneous and peripheral T-cell lymphoma. However, the limited supply and severe cardiotoxicity of FK228 underscore the importance to develop an effective synthetic biology platform for the manufacturing and fine-tuning of this drug lead. In this work, we constructed a Burkholderia chassis for the high-yield production of FK228-family (unnatural) natural products. By virtue of the optimized Burkholderia-specific recombineering system, the biosynthetic gene cluster (BGC) encoding the FK228-like skeleton thailandepsins (tdp) in Burkholderia thailandensis E264 was replaced with an attB integration site to afford the basal chassis KOGC1. The tdp BGC directly captured from E264 was hybridized with the FK228-encoding BGC (dep) using the versatile Red/ET technology. The hybrid BGC (tdp-dep) was integrated into the attB site of KOGC1, resulting in the heterologous expression of FK228. Remarkably, the titer reached 581 mg/L, which is 30-fold higher than that of native producer Chromobacterium violaceum No. 968. This success encouraged us to further engineer the NRPS modules 4 or 6 of hybrid tdp-dep BGC by domain units swapping strategy, and eight new FK228 derivatives (1-8) varying in the composition of amino acids were generated. Especially, the titers of 2 and 3 in KOGC1 were up to 985 mg/L and 453 mg/L, respectively. 2 and 3 displayed stronger cytotoxic activity than FK228. All in all, this work established a robust platform to produce FK228 and its new derivatives in sufficient quantities for anticancer drug development.
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Affiliation(s)
- Kai Gong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Maoqin Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiong Duan
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Gang Li
- Department of Natural Medicinal Chemistry and Pharmacognosy, Qingdao University, Qingdao, Shandong, China
| | - Daojing Yong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Cailing Ren
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Yue Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qijun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Zongjie Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Tao Sun
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Huanyun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiang Tu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Changsheng Wu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Ruijuan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
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18
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HEHR: Homing Endonuclease-Mediated Homologous Recombination for Efficient Adenovirus Genome Engineering. Genes (Basel) 2022; 13:genes13112129. [DOI: 10.3390/genes13112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
Adenoviruses are non-enveloped linear double-stranded DNA viruses with over 100 types in humans. Adenovirus vectors have gained tremendous attention as gene delivery vehicles, as vaccine vectors and as oncolytic viruses. Although various methods have been used to generate adenoviral vectors, the vector-producing process remains technically challenging regarding efficacious genome modification. Based on our previously reported adenoviral genome modification streamline via linear–circular homologous recombination, we further develop an HEHR (combining Homing Endonucleases and Homologous Recombination) method to engineer adenoviral genomes more efficiently. I-PpoI, a rare endonuclease encoded by a group I intron, was introduced into the previously described ccdB counter-selection marker. We found that the I-PpoI pre-treatment of counter-selection containing parental plasmid increased the homologous recombination efficiency up to 100%. The flanking of the counter-selection marker with either single or double I-PpoI sites showed enhanced efficacy. In addition, we constructed a third counter-selection marker flanked by an alternative restriction enzyme: AbsI, which could be applied in case the I-PpoI site already existed in the transgene cassette that was previously inserted in the adenovirus genome. Together, HEHR can be applied for seamless sequence replacements, deletions and insertions. The advantages of HEHR in seamless mutagenesis will facilitate rational design of adenoviral vectors for diverse purposes.
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19
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Blanch-Asensio A, Grandela C, Brandão KO, de Korte T, Mei H, Ariyurek Y, Yiangou L, Mol MP, van Meer BJ, Kloet SL, Mummery CL, Davis RP. STRAIGHT-IN enables high-throughput targeting of large DNA payloads in human pluripotent stem cells. CELL REPORTS METHODS 2022; 2:100300. [PMID: 36313798 PMCID: PMC9606106 DOI: 10.1016/j.crmeth.2022.100300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 07/12/2022] [Accepted: 08/31/2022] [Indexed: 04/20/2023]
Abstract
Inserting large DNA payloads (>10 kb) into specific genomic sites of mammalian cells remains challenging. Applications ranging from synthetic biology to evaluating the pathogenicity of disease-associated variants for precision medicine initiatives would greatly benefit from tools that facilitate this process. Here, we merge the strengths of different classes of site-specific recombinases and combine these with CRISPR-Cas9-mediated homologous recombination to develop a strategy for stringent site-specific replacement of genomic fragments at least 50 kb in size in human induced pluripotent stem cells (hiPSCs). We demonstrate the versatility of STRAIGHT-IN (serine and tyrosine recombinase-assisted integration of genes for high-throughput investigation) by (1) inserting various combinations of fluorescent reporters into hiPSCs to assess the excitation-contraction coupling cascade in derivative cardiomyocytes and (2) simultaneously targeting multiple variants associated with inherited cardiac arrhythmic disorders into a pool of hiPSCs. STRAIGHT-IN offers a precise approach to generate genetically matched panels of hiPSC lines efficiently and cost effectively.
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Affiliation(s)
- Albert Blanch-Asensio
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Catarina Grandela
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Karina O. Brandão
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Tessa de Korte
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Yavuz Ariyurek
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Loukia Yiangou
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Mervyn P.H. Mol
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Berend J. van Meer
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Susan L. Kloet
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Christine L. Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
- Department of Applied Stem Cell Technologies, University of Twente, 7500AE Enschede, the Netherlands
| | - Richard P. Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
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20
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Wang B, Song M, Song C, Zhao S, Yang P, Qiao Q, Cong Y, Wang Y, Wang Z, Zhao J. An inactivated novel chimeric FAdV-4 containing fiber of FAdV-8b provides full protection against hepatitis-hydropericardium syndrome and inclusion body hepatitis. Vet Res 2022; 53:75. [PMID: 36175926 PMCID: PMC9523898 DOI: 10.1186/s13567-022-01093-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023] Open
Abstract
Fowl adenovirus serotype 4 (FAdV-4) and FAdV-8b are causative agents of hepatitis-hydropericardium syndrome (HHS) and inclusion body hepatitis (IBH), respectively. HHS and IBH co-infections were often reported in clinical, yet there are no commercially available bivalent vaccines for prevention and control of both FAdV-4 and -8b. In the present study, a chimeric FAdV-4 was firstly generated by substituting fiber-1 of FAdV-4 with fiber of FAdV-8b. The chimeric virus, rFAdV-4-fiber/8b, exhibited similar replication ability in vitro and pathogenicity in vivo to the parental wild type FAdV-4. A single dosage of vaccination with the inactivated rFAdV-4-fiber/8b induced high antibody titers against fiber-2 of FAdV-4 and fiber of FAdV-8b and provided full protection against FAdV-4 and -8b challenge. These results demonstrated that fiber of FAdV-8b could replace the role of fiber-1 of FAdV-4 in the process of viral infection, and rFAdV-4-fiber/8b could be used to make a potential bivalent vaccine for the control and prevention of HHS and IBH.
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Affiliation(s)
- Baiyu Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Mingzhen Song
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Congcong Song
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Shiyi Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Panpan Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qilong Qiao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yanfang Cong
- National Animal Health Products for Engineering Technology Research Center, Qingdao, 266111, China
| | - Yanling Wang
- National Animal Health Products for Engineering Technology Research Center, Qingdao, 266111, China
| | - Zeng Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jun Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
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21
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Bahlmann NA, Tsoukas RL, Erkens S, Wang H, Jönsson F, Aydin M, Naumova EA, Lieber A, Ehrhardt A, Zhang W. Properties of Adenovirus Vectors with Increased Affinity to DSG2 and the Potential Benefits of Oncolytic Approaches and Gene Therapy. Viruses 2022; 14:v14081835. [PMID: 36016457 PMCID: PMC9412290 DOI: 10.3390/v14081835] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 12/14/2022] Open
Abstract
Carcinomas are characterized by a widespread upregulation of intercellular junctions that create a barrier to immune response and drug therapy. Desmoglein 2 (DSG2) represents such a junction protein and serves as one adenovirus receptor. Importantly, the interaction between human adenovirus type 3 (Ad3) and DSG2 leads to the shedding of the binding domain followed by a decrease in the junction protein expression and transient tight junction opening. Junction opener 4 (JO-4), a small recombinant protein derived from the Ad3 fiber knob, was previously developed with a higher affinity to DSG2. JO-4 protein has been proven to enhance the effects of antibody therapy and chemotherapy and is now considered for clinical trials. However, the effect of the JO4 mutation in the context of a virus remains insufficiently studied. Therefore, we introduced the JO4 mutation to various adenoviral vectors to explore their infection properties. In the current experimental settings and investigated cell lines, the JO4-containing vectors showed no enhanced transduction compared with their parental vectors in DSG2-high cell lines. Moreover, in DSG2-low cell lines, the JO4 vectors presented a rather weakened effect. Interestingly, DSG2-negative cell line MIA PaCa-2 even showed resistance to JO4 vector infection, possibly due to the negative effect of JO4 mutation on the usage of another Ad3 receptor: CD46. Together, our observations suggest that the JO4 vectors may have an advantage to prevent CD46-mediated sequestration, thereby achieving DSG2-specific transduction.
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Affiliation(s)
- Nora A. Bahlmann
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Raphael L. Tsoukas
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
- Department of Anesthesiology and Intensive Care Medicine, Medical Faculty, University Hospital Cologne, University of Cologne, 50923 Cologne, Germany
| | - Sebastian Erkens
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Hongjie Wang
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195, USA
| | - Franziska Jönsson
- Institute of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Malik Aydin
- Laboratory of Experimental Pediatric Pneumology and Allergology, Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 42283 Wuppertal, Germany
| | - Ella A. Naumova
- Department of Biological and Material Sciences in Dentistry, Faculty of Health, Witten/Herdecke University, 58455 Witten, Germany
| | - André Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195, USA
| | - Anja Ehrhardt
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
- Correspondence: (A.E.); (W.Z.)
| | - Wenli Zhang
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
- Correspondence: (A.E.); (W.Z.)
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22
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Bubnov DM, Yuzbashev TV, Khozov AA, Melkina OE, Vybornaya TV, Stan GB, Sineoky SP. Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs. Nucleic Acids Res 2022; 50:8947-8960. [PMID: 35920321 PMCID: PMC9410887 DOI: 10.1093/nar/gkac649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Despite advances in bacterial genome engineering, delivery of large synthetic constructs remains challenging in practice. In this study, we propose a straightforward and robust approach for the markerless integration of DNA fragments encoding whole metabolic pathways into the genome. This approach relies on the replacement of a counterselection marker with cargo DNA cassettes via λRed recombineering. We employed a counterselection strategy involving a genetic circuit based on the CI repressor of λ phage. Our design ensures elimination of most spontaneous mutants, and thus provides a counterselection stringency close to the maximum possible. We improved the efficiency of integrating long PCR-generated cassettes by exploiting the Ocr antirestriction function of T7 phage, which completely prevents degradation of unmethylated DNA by restriction endonucleases in wild-type bacteria. The employment of highly restrictive counterselection and ocr-assisted λRed recombineering allowed markerless integration of operon-sized cassettes into arbitrary genomic loci of four enterobacterial species with an efficiency of 50–100%. In the case of Escherichia coli, our strategy ensures simple combination of markerless mutations in a single strain via P1 transduction. Overall, the proposed approach can serve as a general tool for synthetic biology and metabolic engineering in a range of bacterial hosts.
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Affiliation(s)
- Dmitrii M Bubnov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
| | - Tigran V Yuzbashev
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Andrey A Khozov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Lenin's Hills 1-12, Moscow 119234, Russia
| | - Olga E Melkina
- Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Laboratory of Bacterial Genetics, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Tatiana V Vybornaya
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Genomic Center, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Guy-Bart Stan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Sergey P Sineoky
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
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23
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Medina-Ruiz L, Bartolini R, Wilson GJ, Dyer DP, Vidler F, Hughes CE, Schuette F, Love S, Pingen M, Hayes AJ, Fu J, Stewart AF, Graham GJ. Analysis of combinatorial chemokine receptor expression dynamics using multi-receptor reporter mice. eLife 2022; 11:72418. [PMID: 35699420 PMCID: PMC9236609 DOI: 10.7554/elife.72418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 05/23/2022] [Indexed: 12/17/2022] Open
Abstract
Inflammatory chemokines and their receptors are central to the development of inflammatory/immune pathologies. The apparent complexity of this system, coupled with lack of appropriate in vivo models, has limited our understanding of how chemokines orchestrate inflammatory responses and has hampered attempts at targeting this system in inflammatory disease. Novel approaches are therefore needed to provide crucial biological, and therapeutic, insights into the chemokine-chemokine receptor family. Here, we report the generation of transgenic multi-chemokine receptor reporter mice in which spectrally distinct fluorescent reporters mark expression of CCRs 1, 2, 3, and 5, key receptors for myeloid cell recruitment in inflammation. Analysis of these animals has allowed us to define, for the first time, individual and combinatorial receptor expression patterns on myeloid cells in resting and inflamed conditions. Our results demonstrate that chemokine receptor expression is highly specific, and more selective than previously anticipated.
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Affiliation(s)
- Laura Medina-Ruiz
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Robin Bartolini
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gillian J Wilson
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Douglas P Dyer
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Francesca Vidler
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Catherine E Hughes
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Fabian Schuette
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Samantha Love
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Marieke Pingen
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Alan James Hayes
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jun Fu
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany.,Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shandong, China
| | - Adrian Francis Stewart
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany.,Max-Planck-Institute for Cell Biology and Genetics, Dresden, Germany
| | - Gerard J Graham
- Chemokine Research Group, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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24
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Baas-Thomas MS, Oehm SB, Ostrov N, Church GM. Characterization of ColE1 Production for Robust tolC Plate Dual-Selection in E. coli. ACS Synth Biol 2022; 11:2009-2014. [PMID: 35666547 PMCID: PMC9208019 DOI: 10.1021/acssynbio.2c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Bacterial selection
is an indispensable tool for E. coli genetic
engineering. Marker genes allow for mutant isolation even
at low editing efficiencies. TolC is an especially
useful E. coli marker: its presence can be selected
for with sodium dodecyl sulfate, while its absence can be selected
for with the bactericidal protein ColE1. However, utilization of this
selection system is greatly limited by the lack of commercially available
ColE1 protein. Here, we provide a simple, plate-based, ColE1 negative-selection
protocol that does not require purification of ColE1. Using agar plates
containing a nonpurified lysate from a ColE1-production strain, we
achieved a stringent negative selection with an escape rate of 10–7. Using this powerful negative-selection assay, we
then performed the scarless deletion of multiple, large genomic loci
(>10 kb), screening only 12 colonies each. We hope this accessible
protocol for ColE1 production will lower the barrier of entry for
any lab that wishes to harness tolC’s dual
selection for genetic engineering.
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Affiliation(s)
| | - Sebastian B Oehm
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nili Ostrov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
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25
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The Role of Hexon Amino Acid 188 Varies in Fowl Adenovirus Serotype 4 Strains with Different Virulence. Microbiol Spectr 2022; 10:e0149322. [PMID: 35587634 PMCID: PMC9241812 DOI: 10.1128/spectrum.01493-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hepatitis-hydropericardium syndrome (HHS) induced by fowl adenovirus serotype 4 (FAdV-4) has caused huge economic losses to poultry industries. The key genes responsible for different virulence of FAdV-4 strains are not fully elucidated. Previous studies indicated that hexon of pathogenic FAdV-4 has a conserved arginine (R) at position 188, and a conserved isoleucine (I) is present at this position in reported nonpathogenic FAdV-4. Recently, it was reported that R188 of hexon is the determinant site for pathogenicity of the emerging Chinese FAdV-4 strain. However, the role of hexon amino acid 188 (aa188) has not been examined in the nonpathogenic FAdV-4 strain. In this study, three recombinant FAdV-4 viruses, H/H/R188I, O/O/I188R, and H/O/I188R, were constructed by mutating hexon aa188 of FAdV-4 pathogenic strain CH/HNJZ/2015 (H) and nonpathogenic strain ON1 (O), and pathogenicity was assessed in specific-pathogen-free (SPF) chickens. Consistent with previous findings, H/O/I188R exhibited pathogenicity similar to that of CH/HNJZ/2015, yet H/H/R188I induced no mortality. Unexpectedly, all chickens infected with O/O/I188R survived. Postmortem examination of O/O/I188R-infected chickens showed typical lesions of inclusion body hepatitis rather than HHS. Expression of proinflammatory cytokines in CH/HNJZ/2015- and H/O/I188R-infected chickens was significantly higher than that in H/H/R188I-, ON1-, and O/O/I188R-infected chickens. Analysis of predicted hexon protein structures indicated that aa188 mutation leads to conformational changes in the L1 loop of HNJZ-hexon but not in ON1-hexon. In summary, the present study demonstrated that the role of hexon aa188 in the virulence of FAdV-4 varies between different strains. Induction of HHS requires factors aside from hexon aa188 in the emerging Chinese FAdV-4 strain. IMPORTANCE HHS induced by FAdV-4 has caused huge economic losses to the poultry industry. The key determinants for the different virulence of FAdV-4 have not been fully elucidated. Here, we investigated the role of hexon aa188 in FAdV-4 strains with different virulence and showed that the role of hexon aa188 varies in FAdV-4 strains with different genetic contents. The hexon R188 may be the key amino acid for causing inclusion body hepatitis by the pathogenic FAdV-4 strain, and induction of HHS by FAdV-4 may need other viral cofactors. Moreover, the hexon R188I mutation greatly affected the expression of proinflammatory cytokines induced by the pathogenic strain CH/HNJZ/2015, but no significant difference was observed between the nonpathogenic strain ON1 and ON1 with hexon I188R mutation. We found that hexon aa188 mutation induced conformational changes to hexon protein in CH/HNJZ/2015 but not in ON1, which might be the underlying reason for the changing virulence.
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26
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Chen W, Chen R, He L, Wu X. Development and optimization of Lysis gene E as a counter-selection marker with high stringency. Biotechnol J 2022; 17:e2100423. [PMID: 35373931 DOI: 10.1002/biot.202100423] [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: 08/10/2021] [Revised: 03/19/2022] [Accepted: 04/01/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Seamless modification of bacterial chromosomes is widely performed in both theoretical and practical research. For this purpose, excellent counter-selection marker genes with high stringency are needed. MAIN METHODS AND MAJOR RESULTS The lysis gene E was first constructed under the control of the PL promoter and the cI857 repressor. At 42°C, it could effectively kill Escherichia coli and seamless modification in this bacterium using E as a counter-selection marker was successfully conducted. It also works in another gram-negative strain, Serratia marcescens, under the control of the Arac/PBAD regulatory system. By combining lysis gene E and kil, the counter-selection frequencies of the PL -kil-sd-E cassette in E. coli reached 4.9 × 10-8 and 3.2 × 10-8 at two test loci, which are very close to frequencies observed with the best counter-selection systems reported, the inducible toxin systems. Under the control of the Arac/PBAD , the counter-selection frequency of PBAD -kil-sd-E in S. marcescens reached the level of 10-7 at four test loci. By expressing the araC gene from plasmid pKDsg-ack, 5- to 17-fold improvements in counter-selection stringency were observed at these loci. A surprisingly low counter-selection frequency of 4.9 × 10-9 was obtained at the marR-1 locus, which reflects the highest stringency for a counter-selection cassette reported thus far. Similarly, at the araB locus of E. coli, the counter-selection frequency of PBAD -kil-sd-E was 3 × 10-9 after introducing plasmid pKDsg-ack. CONCLUSIONS AND IMPLICATIONS We have developed and optimized a new universal counter-selection marker based on lysis gene E. The best counter-selection stringency of this new marker exceeds the inducible toxin system several fold. Our work can also provide inspiration for improving counter-selection stringency based on existing markers. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China.,Guangdong Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Ruyi Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Ling He
- Guangdong Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaotong Wu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
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27
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Doerner J, Sallard E, Zhang W, Solanki M, Liu J, Ehrke-Schulz E, Zirngibl H, Lieber A, Ehrhardt A. Novel Group C Oncolytic Adenoviruses Carrying a miRNA Inhibitor Demonstrate Enhanced Oncolytic Activity In Vitro and In Vivo. Mol Cancer Ther 2022; 21:460-470. [PMID: 35027480 PMCID: PMC9377726 DOI: 10.1158/1535-7163.mct-21-0240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/10/2021] [Accepted: 01/03/2022] [Indexed: 01/07/2023]
Abstract
Oncolytic adenoviruses (OAd) represent an attractive treatment option for cancer. Clinical efficacy of commonly utilized human adenovirus type 5 (Ad5)-based oncolytic viruses is limited by variable expression levels of the coxsackie- and adenovirus receptor (CAR) in tumor cells and high prevalence of neutralizing antibodies against human Ad5. However, previous studies have highlighted alternative human Ad types as promising candidates for oncolytic therapy. In this study, we generated novel OAds based on Ad1, -2, -5, and -6 derived from species C Ads. These OAds contain a 24-bp deletion in the early gene E1A for tumor selective replication and express the RNAi inhibitor P19. We examined these OAds for in vitro anticancer activity on various cancer cell lines derived from lung, colon, gynecologic, bone, and pancreatic carcinoma. In most surveyed cell lines, OAds based on Ad1, -2, and -6 demonstrated higher cell lysis capability compared with Ad5, suggesting enhanced oncolytic potential. Moreover, enhanced oncolytic activity was associated with P19 expression in a cell type-dependent manner. We further explored a A549 tumor xenograft mouse model to compare the novel OAds directly with Ad5 and H101, an oncolytic adenovirus used in clinical trials. These P19-containing OAds based on Ad1, -2, and -6 showed significantly decelerated tumor progression compared with H101, indicating better antitumor potency in vivo. Our studies provide a novel path for OAd development based on alternative Ad types with improved effectiveness by RNA interference suppression.
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Affiliation(s)
- Johannes Doerner
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany.,Chair for Surgery II, Helios University Hospital Wuppertal, Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Erwan Sallard
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Wenli Zhang
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Manish Solanki
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Jing Liu
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Eric Ehrke-Schulz
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Hubert Zirngibl
- Chair for Surgery II, Helios University Hospital Wuppertal, Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - André Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - Anja Ehrhardt
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany.,Corresponding Author: Anja Ehrhardt, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Stockumer Strasse 10, Witten 58453, Germany. Phone: +49 23902 926 273; Fax: +49 2302 926 44278; E-mail:
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28
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Yuan H, Zheng Y, Yan X, Wang H, Zhang Y, Ma J, Fu J. Direct cloning of a herpesvirus genome for rapid generation of infectious BAC clones. J Adv Res 2022; 43:97-107. [PMID: 36585118 PMCID: PMC9811322 DOI: 10.1016/j.jare.2022.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION The herpesviridae are DNA viruses with large and complicated genomes. The herpesvirus bacterial artificial chromosomes (BACs) have been useful for generating recombinant viruses to study the biology and pathogenesis. However, the conventional method using homologous recombination is not only time consuming but also prone to accumulate attenuating mutations during serial passage of the virus in cells. Elimination of the BAC vector from the recombinant viral genome requires additional step for phenotypically consistence with the original strain. OBJECTIVES To generate a streamlined approach for generating infectious BAC clones of herpesvirus. METHODS The 142-kb pseudorabies virus genome was directly cloned into a bacterial artificial chromosome (BAC) in Escherichia coli by Exonuclease Combined with RecET recombination (ExoCET). Placement of the BAC vector at the terminus of the linear virus genome enabled excision of the BAC backbone from the viral genome by restriction endonuclease for delivery into mammalian cells, with the subsequent rapid rescue of virus that was genetically identical to the original strain. RESULTS This new approach for molecular cloning of the genome from a large DNA virus and isolation of pure virus lacking the BAC vector from transfected mammalian cells bypass the tedious and time-consuming method of multiple rounds of plaque purification. The viral BAC was stable in E. coli, allowing further mutagenesis mediated by the Red system or various site-specific recombination methods. CONCLUSION An efficient method for construction of infectious clones of herpesvirus was established. It is expected to be potentially useful for other viruses with large double-stranded DNA genomes.
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Affiliation(s)
- Hengxing Yuan
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yaoyao Zheng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoling Yan
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hailong Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China,Corresponding authors.
| | - Jingyun Ma
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China,Corresponding authors.
| | - Jun Fu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China,Corresponding authors.
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Development of a new recombineering system for Agrobacterium species. Appl Environ Microbiol 2022; 88:e0249921. [PMID: 35044833 DOI: 10.1128/aem.02499-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discovery of new and efficient genetic engineering technologies for Agrobacterium will broaden the capacity for fundamental research on this genus and for its utilization as a transgenic vehicle. In this study, we aim to develop an efficient recombineering system for Agrobacterium species. We examined isolates of Agrobacterium and the closely related genus Rhizobium to identify pairs of ET-like recombinases that would aid in the recombineering of Agrobacterium species. Four pairs of ET-like recombinases, named RecETh1h2h3h4AGROB6, RecETh1h2P3RHI597, RecETRHI145, and RecEThRHI483, were identified in Agrobacterium tumefaciens str. B6, Rhizobium leguminosarum bv. trifolii WSM597, Rhizobium sp. LC145, and Rhizobium sp. Root483D2, respectively. Eight more candidate recombineering systems were generated by combining the new ET-like recombinases with Redγ or Pluγ. The PluγETRHI145 system, RecETh1h2h3h4AGROB6 system, and PluγEThRHI483 system were determined to be the most efficient recombineering system for the type strains A. tumefaciens C58, A. tumefaciens EHA105, and R. rhizogenes NBCR13257, respectively. The utility of these systems was demonstrated by knocking out the istB and istA fusion gene in C58, the celI gene in EHA105, and the 3'-5' exonuclease gene and endoglucanase gene in NBCR13257. Our work provides an effective genetic manipulation strategy for Agrobacterium species. IMPORTANCE Agrobacterium is a powerful transgenic vehicle for the genetic manipulation of numerous plant and fungal species and even animal cells. In addition to improving the utility of Agrobacterium as a transgenic vehicle, genetic engineering tools are important for revealing crucial components that are functionally involved in T-DNA translocation events. This work developed an efficient and versatile recombineering system for Agrobacterium. Successful genome modification of Agrobacterium strains revealed that this new recombineering system could be used for the genetic engineering of Agrobacterium.
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Näsvall J. Dup-In and DIRex: Techniques for Single-Step, Scar-Free Mutagenesis with Marker Recycling. Methods Mol Biol 2022; 2479:85-104. [PMID: 35583734 DOI: 10.1007/978-1-0716-2233-9_7] [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] [Indexed: 06/15/2023]
Abstract
This chapter describes two related recombineering-based techniques: "Duplication Insertion" (Dup-In) and "Direct- and Inverted Repeat stimulated excision" (DIRex). Dup-In is used for transferring existing mutations between strains, and DIRex for generating almost any type of mutation. Both techniques use intermediate insertions with counter-selectable cassettes, flanked by directly repeated sequences that enable exact and spontaneous excision of the cassettes. These constructs can be transferred to other strains using generalized transductions, and the final intended mutation is obtained following selection for spontaneous loss of the counter-selectable cassette, which leaves only the intended mutation behind in the final strain. The techniques have been used in several strains of Escherichia coli and Salmonella enterica, and should be readily adaptable to other organisms where λ Red recombineering or similar methods are available.
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Affiliation(s)
- Joakim Näsvall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
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31
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Backes N, Phillips GJ. Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales. EcoSal Plus 2021; 9:eESP00062020. [PMID: 34125584 PMCID: PMC11163844 DOI: 10.1128/ecosalplus.esp-0006-2020] [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: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/20/2022]
Abstract
Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the Enterobacteriales. While many of the applications covered have been initially developed in Escherichia coli, we also highlight the potential, along with the limitations, of this technology for expanding the availability of genetic tools in less-well-characterized non-model species, including bacterial pathogens.
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Affiliation(s)
- Nicholas Backes
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
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32
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Pfitzner S, Bosse JB, Hofmann-Sieber H, Flomm F, Reimer R, Dobner T, Grünewald K, Franken LE. Human Adenovirus Type 5 Infection Leads to Nuclear Envelope Destabilization and Membrane Permeability Independently of Adenovirus Death Protein. Int J Mol Sci 2021; 22:13034. [PMID: 34884837 PMCID: PMC8657697 DOI: 10.3390/ijms222313034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
The human adenovirus type 5 (HAdV5) infects epithelial cells of the upper and lower respiratory tract. The virus causes lysis of infected cells and thus enables spread of progeny virions to neighboring cells for the next round of infection. The mechanism of adenovirus virion egress across the nuclear barrier is not known. The human adenovirus death protein (ADP) facilitates the release of virions from infected cells and has been hypothesized to cause membrane damage. Here, we set out to answer whether ADP does indeed increase nuclear membrane damage. We analyzed the nuclear envelope morphology using a combination of fluorescence and state-of-the-art electron microscopy techniques, including serial block-face scanning electron microscopy and electron cryo-tomography of focused ion beam-milled cells. We report multiple destabilization phenotypes of the nuclear envelope in HAdV5 infection. These include reduction of lamin A/C at the nuclear envelope, large-scale membrane invaginations, alterations in double membrane separation distance and small-scale membrane protrusions. Additionally, we measured increased nuclear membrane permeability and detected nuclear envelope lesions under cryoconditions. Unexpectedly, and in contrast to previous hypotheses, ADP did not have an effect on lamin A/C reduction or nuclear permeability.
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Affiliation(s)
- Søren Pfitzner
- Leibniz Institute for Experimental Virology (HPI), Martinistraße 52, 20251 Hamburg, Germany; (S.P.); (J.B.B.); (H.H.-S.); (F.F.); (R.R.); (T.D.)
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
| | - Jens B. Bosse
- Leibniz Institute for Experimental Virology (HPI), Martinistraße 52, 20251 Hamburg, Germany; (S.P.); (J.B.B.); (H.H.-S.); (F.F.); (R.R.); (T.D.)
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
- Hannover Medical School, Institute of Virology, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Helga Hofmann-Sieber
- Leibniz Institute for Experimental Virology (HPI), Martinistraße 52, 20251 Hamburg, Germany; (S.P.); (J.B.B.); (H.H.-S.); (F.F.); (R.R.); (T.D.)
| | - Felix Flomm
- Leibniz Institute for Experimental Virology (HPI), Martinistraße 52, 20251 Hamburg, Germany; (S.P.); (J.B.B.); (H.H.-S.); (F.F.); (R.R.); (T.D.)
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
- Hannover Medical School, Institute of Virology, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Rudolph Reimer
- Leibniz Institute for Experimental Virology (HPI), Martinistraße 52, 20251 Hamburg, Germany; (S.P.); (J.B.B.); (H.H.-S.); (F.F.); (R.R.); (T.D.)
| | - Thomas Dobner
- Leibniz Institute for Experimental Virology (HPI), Martinistraße 52, 20251 Hamburg, Germany; (S.P.); (J.B.B.); (H.H.-S.); (F.F.); (R.R.); (T.D.)
| | - Kay Grünewald
- Leibniz Institute for Experimental Virology (HPI), Martinistraße 52, 20251 Hamburg, Germany; (S.P.); (J.B.B.); (H.H.-S.); (F.F.); (R.R.); (T.D.)
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Universität Hamburg, Institute for Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Linda E. Franken
- Leibniz Institute for Experimental Virology (HPI), Martinistraße 52, 20251 Hamburg, Germany; (S.P.); (J.B.B.); (H.H.-S.); (F.F.); (R.R.); (T.D.)
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
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Soeriyadi AH, Ongley SE, Kehr JC, Pickford R, Dittmann E, Neilan BA. Tailoring Enzyme Stringency Masks the Multispecificity of a Lyngbyatoxin (Indolactam Alkaloid) Nonribosomal Peptide Synthetase. Chembiochem 2021; 23:e202100574. [PMID: 34850512 DOI: 10.1002/cbic.202100574] [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: 10/24/2021] [Revised: 11/30/2021] [Indexed: 11/11/2022]
Abstract
Indolactam alkaloids are activators of protein kinase C (PKC) and are of pharmacological interest for the treatment of pathologies involving PKC dysregulation. The marine cyanobacterial nonribosomal peptide synthetase (NRPS) pathway for lyngbyatoxin biosynthesis, which we previously expressed in E. coli, was studied for its amenability towards the biosynthesis of indolactam variants. Modification of culture conditions for our E. coli heterologous expression host and analysis of pathway products suggested the native lyngbyatoxin pathway NRPS does possess a degree of relaxed specificity. Site-directed mutagenesis of two positions within the adenylation domain (A-domain) substrate-binding pocket was performed, resulting in an alteration of substrate preference between valine, isoleucine, and leucine. We observed relative congruence of in vitro substrate activation by the LtxA NRPS to in vivo product formation. While there was a preference for isoleucine over leucine, the substitution of alternative tailoring domains may unveil the true in vivo effects of the mutations introduced herein.
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Affiliation(s)
- Angela H Soeriyadi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Sarah E Ongley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.,School of Environmental and Life Sciences, University of Newcastle, Callaghan, 2308, Australia
| | - Jan-Christoph Kehr
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Russel Pickford
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, 2052, Australia
| | - Elke Dittmann
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.,School of Environmental and Life Sciences, University of Newcastle, Callaghan, 2308, Australia
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Hidalgo P, Pimentel A, Mojica-Santamaría D, von Stromberg K, Hofmann-Sieber H, Lona-Arrona C, Dobner T, González RA. Evidence That the Adenovirus Single-Stranded DNA Binding Protein Mediates the Assembly of Biomolecular Condensates to Form Viral Replication Compartments. Viruses 2021; 13:1778. [PMID: 34578359 PMCID: PMC8473285 DOI: 10.3390/v13091778] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022] Open
Abstract
A common viral replication strategy is characterized by the assembly of intracellular compartments that concentrate factors needed for viral replication and simultaneously conceal the viral genome from host-defense mechanisms. Recently, various membrane-less virus-induced compartments and cellular organelles have been shown to represent biomolecular condensates (BMCs) that assemble through liquid-liquid phase separation (LLPS). In the present work, we analyze biophysical properties of intranuclear replication compartments (RCs) induced during human adenovirus (HAdV) infection. The viral ssDNA-binding protein (DBP) is a major component of RCs that contains intrinsically disordered and low complexity proline-rich regions, features shared with proteins that drive phase transitions. Using fluorescence recovery after photobleaching (FRAP) and time-lapse studies in living HAdV-infected cells, we show that DBP-positive RCs display properties of liquid BMCs, which can fuse and divide, and eventually form an intranuclear mesh with less fluid-like features. Moreover, the transient expression of DBP recapitulates the assembly and liquid-like properties of RCs in HAdV-infected cells. These results are of relevance as they indicate that DBP may be a scaffold protein for the assembly of HAdV-RCs and should contribute to future studies on the role of BMCs in virus-host cell interactions.
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Affiliation(s)
- Paloma Hidalgo
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.M.-S.); (C.L.-A.)
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (K.v.S.); (H.H.-S.); (T.D.)
| | - Arturo Pimentel
- Laboratorio Nacional de Microscopía Avanzada (LNMA), Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca 62210, Mexico;
| | - Diana Mojica-Santamaría
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.M.-S.); (C.L.-A.)
| | - Konstantin von Stromberg
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (K.v.S.); (H.H.-S.); (T.D.)
| | - Helga Hofmann-Sieber
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (K.v.S.); (H.H.-S.); (T.D.)
| | - Christian Lona-Arrona
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.M.-S.); (C.L.-A.)
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Thomas Dobner
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (K.v.S.); (H.H.-S.); (T.D.)
| | - Ramón A. González
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.M.-S.); (C.L.-A.)
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Li R, Shi H, Zhao X, Liu X, Duan Q, Song C, Chen H, Zheng W, Shen Q, Wang M, Wang X, Gong K, Yin J, Zhang Y, Li A, Fu J. Development and application of an efficient recombineering system for Burkholderia glumae and Burkholderia plantarii. Microb Biotechnol 2021; 14:1809-1826. [PMID: 34191386 PMCID: PMC8313284 DOI: 10.1111/1751-7915.13840] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 02/07/2023] Open
Abstract
The lambda phage Red proteins Redα/Redβ/Redγ and Rac prophage RecE/RecT proteins are powerful tools for precise and efficient genetic manipulation but have been limited to only a few prokaryotes. Here, we report the development and application of a new recombineering system for Burkholderia glumae and Burkholderia plantarii based on three Rac bacteriophage RecET-like operons, RecETheBDU8 , RecEThTJI49 and RecETh1h2eYI23 , which were obtained from three different Burkholderia species. Recombineering experiments indicated that RecEThTJI49 and RecETh1h2eYI23 showed higher recombination efficiency compared to RecETheBDU8 in Burkholderia glumae PG1. Furthermore, all of the proteins currently categorized as hypothetical proteins in RecETh1h2eYI23, RecEThTJI49 and RecETheBDU8 may have a positive effect on recombination in B. glumae PG1 except for the h2 protein in RecETh1h2eYI23 . Additionally, RecETYI23 combined with exonuclease inhibitors Pluγ or Redγ exhibited equivalent recombination efficiency compared to Redγβα in Escherichia coli, providing potential opportunity of recombineering in other Gram-negative bacteria for its loose host specificity. Using recombinase-assisted in situ insertion of promoters, we successfully activated three cryptic non-ribosomal peptide synthetase biosynthetic gene clusters in Burkholderia strains, resulting in the generation of a series of lipopeptides that were further purified and characterized. Compound 7 exhibited significant potential anti-inflammatory activity by inhibiting lipopolysaccharide-stimulated nitric oxide production in RAW 264.7 macrophages. This recombineering system may greatly enhance functional genome research and the mining of novel natural products in the other species of the genus Burkholderia after optimization of a protocol.
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Affiliation(s)
- Ruijuan Li
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Hongbo Shi
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Xiaoyu Zhao
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Xianqi Liu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Qiong Duan
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Chaoyi Song
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Hanna Chen
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Wentao Zheng
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Qiyao Shen
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Maoqin Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Xue Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Kai Gong
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Jia Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationCollege of Life SciencesHunan Normal UniversityChangshaHunan410081China
| | - Youming Zhang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Aiying Li
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Jun Fu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
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Base editing-coupled survival screening enabled high-sensitive analysis of PAM compatibility and finding of the new possible off-target. iScience 2021; 24:102769. [PMID: 34337358 PMCID: PMC8324807 DOI: 10.1016/j.isci.2021.102769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/20/2021] [Accepted: 06/21/2021] [Indexed: 11/21/2022] Open
Abstract
Base editing (BE) is a promising genome engineering tool for modifying DNA or RNA and has been widely used in various microorganisms as well as eukaryotic cells. Despite the proximal protospacer adjacent motif (PAM) is critical to the targeting range and off-target effect of BE, there is still lack of a specific approach to analyze the PAM pattern in BE systems. Here, we developed a base editing-coupled survival screening method. Using dCas9 from Streptococcus pyogenes (SpdCas9) and its variants xdCas9 3.7 and dCas9 NG as example, their PAM patterns in BE systems were extensively characterized using the NNNN PAM library with high sensitivity. In addition to the typical PAM recognition features, we observed more unique PAMs exhibiting BE activity. These PAM patterns will boost the finding of potential off-target editing event arising from non-canonical PAMs and provide the guidelines for PAM usage in the BE system.
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Zhang Y, Yun K, Huang H, Tu R, Hua E, Wang M. Antisense RNA Interference-Enhanced CRISPR/Cas9 Base Editing Method for Improving Base Editing Efficiency in Streptomyces lividans 66. ACS Synth Biol 2021; 10:1053-1063. [PMID: 33720688 DOI: 10.1021/acssynbio.0c00563] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
CRISPR/Cas9-mediated base editors, based on cytidine deaminase or adenosine deaminase, are emerging genetic technologies that facilitate genomic manipulation in many organisms. Since base editing is free from DNA double-strand breaks (DSBs), it has certain advantages, such as a lower toxicity, compared to the traditional DSB-based genome engineering technologies. In terms of Streptomyces, a base editing method has been successfully applied in several model and non-model species, such as Streptomyces coelicolor and Streptomyces griseofuscus. In this study, we first proved that BE2 (rAPOBEC1-dCas9-UGI) and BE3 (rAPOBEC1-nCas9-UGI) were functional base editing tools in Streptomyces lividans 66, albeit with a much lower editing efficiency compared to that of S. coelicolor. Uracil generated in deamination is a key intermediate in the base editing process, and it can be hydrolyzed by uracil DNA glycosidase (UDG) involved in the intracellular base excision repair, resulting in a low base editing efficiency. By knocking out two endogenous UDGs (UDG1 and UDG2), we managed to improve the base editing efficiency by 3.4-67.4-fold among different loci. However, the inactivation of UDG is detrimental to the genome stability and future application of engineered strains. Therefore, we finally developed antisense RNA interference-enhanced CRISPR/Cas9 Base Editing method (asRNA-BE) to transiently disrupt the expression of uracil DNA glycosidases during base editing, leading to a 2.8-65.8-fold enhanced editing efficiency and better genome stability. Our results demonstrate that asRNA-BE is a much better editing tool for base editing in S. lividans 66 and might be beneficial for improving the base editing efficiency and genome stability in other Streptomyces strains.
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Affiliation(s)
- Yue Zhang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Kaiyue Yun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Huamei Huang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ran Tu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Erbing Hua
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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38
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Baishya S, Deshamukhya C, Wangkheimayum J, Das BJ, Anbarasu A, Talukdar AD, Bhattacharjee A, Choudhury MD. Transcriptional expression of secondary resistance genes ccdB and repA2 is enhanced in presence of cephalosporin and carbapenem in Escherichia coli. BMC Microbiol 2021; 21:79. [PMID: 33750290 PMCID: PMC7941987 DOI: 10.1186/s12866-021-02136-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/26/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The issue of carbapenem resistance in E.coli is very concerning and it is speculated that cumulative effect of both primary resistance genes and secondary resistance genes that act as helper to the primary resistance genes are the reason behind their aggravation. Therefore, here we attempted to find the role of two secondary resistance genes (SRG) ccdB and repA2 in carbapenem resistance in E. coli (CRE). In this context influential genes belonging to secondary resistome that act as helper to the primary resistance genes like blaNDM and blaCTX-M in aggravating β-lactam resistance were selected from an earlier reported in silico study. Transcriptional expression of the selected genes in clinical isolates of E.coli that were discretely harboring blaNDM-1, blaNDM-4, blaNDM-5, blaNDM-7 and blaCTX-M-15 with and without carbapenem and cephalosporin stress (2 μg/ml) was determined by real time PCR. Cured mutants sets that were lacking (i) primary resistance genes, (ii) secondary resistance genes and (iii) both primary and secondary resistance genes were prepared by SDS treatment. These sets were then subjected to antibiotic susceptibility testing by Kirby Bauer disc diffusion method. RESULTS Out of the 21 genes reported in the in silico study, 2 genes viz. repA2 and ccdB were selected for transcriptional expression analysis. repA2, coding replication regulatory protein, was downregulated in response to carbapenems and cephalosporins. ccdB, coding for plasmid maintenance protein, was also downregulated in response to carbapenems except imipenem and cephalosporins. Following plasmid elimination assay increase in diameter of zone of inhibition under stress of both antibiotics was observed as compared to uncured control hinting at the reversion of antibiotic susceptibility by the-then resistant bacteria. CONCLUSION SRGs repA2 and ccdB help sustenance of blaNDM and blaCTX-M under carbapenem and cephalosporin stress.
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Affiliation(s)
- Somorita Baishya
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | | | | | | | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences & Technology, VIT University, Vellore, India
| | - Anupam Das Talukdar
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
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39
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Song C, Luan J, Li R, Jiang C, Hou Y, Cui Q, Cui T, Tan L, Ma Z, Tang YJ, Stewart AF, Fu J, Zhang Y, Wang H. RedEx: a method for seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters. Nucleic Acids Res 2021; 48:e130. [PMID: 33119745 PMCID: PMC7736807 DOI: 10.1093/nar/gkaa956] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/08/2020] [Accepted: 10/08/2020] [Indexed: 11/23/2022] Open
Abstract
Biosynthesis reprograming is an important way to diversify chemical structures. The large repetitive DNA sequences existing in polyketide synthase genes make seamless DNA manipulation of the polyketide biosynthetic gene clusters extremely challenging. In this study, to replace the ethyl group attached to the C-21 of the macrolide insecticide spinosad with a butenyl group by refactoring the 79-kb gene cluster, we developed a RedEx method by combining Redαβ mediated linear-circular homologous recombination, ccdB counterselection and exonuclease mediated in vitro annealing to insert an exogenous extension module in the polyketide synthase gene without any extra sequence. RedEx was also applied for seamless deletion of the rhamnose 3′-O-methyltransferase gene in the spinosad gene cluster to produce rhamnosyl-3′-desmethyl derivatives. The advantages of RedEx in seamless mutagenesis will facilitate rational design of complex DNA sequences for diverse purposes.
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Affiliation(s)
- Chaoyi Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ruijuan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Yu Hou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Tianqi Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Long Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Zaichao Ma
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
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40
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Zhong L, Diao X, Zhang N, Li F, Zhou H, Chen H, Bai X, Ren X, Zhang Y, Wu D, Bian X. Engineering and elucidation of the lipoinitiation process in nonribosomal peptide biosynthesis. Nat Commun 2021; 12:296. [PMID: 33436600 PMCID: PMC7804268 DOI: 10.1038/s41467-020-20548-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/02/2020] [Indexed: 12/18/2022] Open
Abstract
Nonribosomal peptide synthetases containing starter condensation domains direct the biosynthesis of nonribosomal lipopeptides, which generally exhibit wide bioactivities. The acyl chain has strong impacts on bioactivity and toxicity, but the lack of an in-depth understanding of starter condensation domain-mediated lipoinitiation limits the bioengineering of NRPSs to obtain novel derivatives with desired acyl chains. Here, we show that the acyl chains of the lipopeptides rhizomide, holrhizin, and glidobactin were modified by engineering the starter condensation domain, suggesting a workable approach to change the acyl chain. Based on the structure of the mutated starter condensation domain of rhizomide biosynthetic enzyme RzmA in complex with octanoyl-CoA and related point mutation experiments, we identify a set of residues responsible for the selectivity of substrate acyl chains and extend the acyl chains from acetyl to palmitoyl. Furthermore, we illustrate three possible conformational states of starter condensation domains during the reaction cycle of the lipoinitiation process. Our studies provide further insights into the mechanism of lipoinitiation and the engineering of nonribosomal peptide synthetases.
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Affiliation(s)
- Lin Zhong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xiaotong Diao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Na Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Fengwei Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xintong Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
| | - Dalei Wu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
- Suzhou Research Institute, Shandong University, Suzhou, Jiangsu, 215123, China.
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
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41
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Rondelet A, Pozniakovsky A, Namboodiri D, Cardoso da Silva R, Singh D, Leuschner M, Poser I, Ssykor A, Berlitz J, Schmidt N, Röhder L, Vader G, Hyman AA, Bird AW. ESI mutagenesis: a one-step method for introducing mutations into bacterial artificial chromosomes. Life Sci Alliance 2020; 4:4/2/e202000836. [PMID: 33293335 PMCID: PMC7756954 DOI: 10.26508/lsa.202000836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 01/23/2023] Open
Abstract
A simple and efficient recombineering-based method for introducing point mutations into bacterial artificial chromosomes using an artificial intron cassette. Bacterial artificial chromosome (BAC)–based transgenes have emerged as a powerful tool for controlled and conditional interrogation of protein function in higher eukaryotes. Although homologous recombination-based recombineering methods have streamlined the efficient integration of protein tags onto BAC transgenes, generating precise point mutations has remained less efficient and time-consuming. Here, we present a simplified method for inserting point mutations into BAC transgenes requiring a single recombineering step followed by antibiotic selection. This technique, which we call exogenous/synthetic intronization (ESI) mutagenesis, relies on co-integration of a mutation of interest along with a selectable marker gene, the latter of which is harboured in an artificial intron adjacent to the mutation site. Cell lines generated from ESI-mutated BACs express the transgenes equivalently to the endogenous gene, and all cells efficiently splice out the synthetic intron. Thus, ESI mutagenesis provides a robust and effective single-step method with high precision and high efficiency for mutating BAC transgenes.
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Affiliation(s)
- Arnaud Rondelet
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Andrei Pozniakovsky
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Divya Singh
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Marit Leuschner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrea Ssykor
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Julian Berlitz
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Nadine Schmidt
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lea Röhder
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Gerben Vader
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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42
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Fels U, Gevaert K, Van Damme P. Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics. Front Microbiol 2020; 11:548410. [PMID: 33013782 PMCID: PMC7516269 DOI: 10.3389/fmicb.2020.548410] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Serving a robust platform for reverse genetics enabling the in vivo study of gene functions primarily in enterobacteriaceae, recombineering -or recombination-mediated genetic engineering-represents a powerful and relative straightforward genetic engineering tool. Catalyzed by components of bacteriophage-encoded homologous recombination systems and only requiring short ∼40–50 base homologies, the targeted and precise introduction of modifications (e.g., deletions, knockouts, insertions and point mutations) into the chromosome and other episomal replicons is empowered. Furthermore, by its ability to make use of both double- and single-stranded linear DNA editing substrates (e.g., PCR products or oligonucleotides, respectively), lengthy subcloning of specific DNA sequences is circumvented. Further, the more recent implementation of CRISPR-associated endonucleases has allowed for more efficient screening of successful recombinants by the selective purging of non-edited cells, as well as the creation of markerless and scarless mutants. In this review we discuss various recombineering strategies to promote different types of gene modifications, how they are best applied, and their possible pitfalls.
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Affiliation(s)
- Ursula Fels
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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43
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Csörgő B, Nyerges A, Pál C. Targeted mutagenesis of multiple chromosomal regions in microbes. Curr Opin Microbiol 2020; 57:22-30. [PMID: 32599531 PMCID: PMC7613694 DOI: 10.1016/j.mib.2020.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/20/2022]
Abstract
Directed evolution allows the effective engineering of proteins, biosynthetic pathways, and cellular functions. Traditional plasmid-based methods generally subject one or occasionally multiple genes-of-interest to mutagenesis, require time-consuming manual interventions, and the genes that are subjected to mutagenesis are outside of their native genomic context. Other methods mutagenize the whole genome unselectively which may distort the outcome. Recent recombineering- and CRISPR-based technologies radically change this field by allowing exceedingly high mutation rates at multiple, predefined loci in their native genomic context. In this review, we focus on recent technologies that potentially allow accelerated tunable mutagenesis at multiple genomic loci in the native genomic context of these target sequences. These technologies will be compared by four main criteria, including the scale of mutagenesis, portability to multiple microbial species, off-target mutagenesis, and cost-effectiveness. Finally, we discuss how these technical advances open new avenues in basic research and biotechnology.
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Affiliation(s)
- Bálint Csörgő
- Department of Microbiology and Immunology, University of California, San Francisco, 94143, San Francisco, CA, USA; Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Akos Nyerges
- Synthetic and Systems Biology Unit, Biological Research Centre, 6726, Szeged, Hungary; Department of Genetics, Harvard Medical School, 02115, Boston, MA, USA
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Biological Research Centre, 6726, Szeged, Hungary.
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44
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Pfitzner S, Hofmann-Sieber H, Bosse JB, Franken LE, Grünewald K, Dobner T. Fluorescent protein tagging of adenoviral proteins pV and pIX reveals 'late virion accumulation compartment'. PLoS Pathog 2020; 16:e1008588. [PMID: 32584886 PMCID: PMC7343190 DOI: 10.1371/journal.ppat.1008588] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/08/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022] Open
Abstract
The human adenovirus type 5 (HAdV5) causes disease of the upper and lower respiratory tract. The early steps of HAdV5 entry up to genome replication in the host nucleus have been extensively studied. However, late stages of infection remain poorly understood. Here, we set out to elucidate the spatiotemporal orchestration of late adenovirus nuclear remodeling in living cells. We generated virus mutants expressing fluorescently tagged protein IX (pIX) and protein V (pV), a capsid and viral genome associated protein, respectively. We found that during progeny virion production both proteins localize to a membrane-less, nuclear compartment, which is highly impermeable such that in immunofluorescence microscopy antibodies can hardly penetrate it. We termed this compartment ‘late virion accumulation compartment’ (LVAC). Correlation between light- and electron microscopy revealed that the LVAC contains paracrystalline arrays of viral capsids that arrange tightly packed within a honeycomb-like organization of viral DNA. Live-cell microscopy as well as FRAP measurements showed that the LVAC is rigid and restricts diffusion of larger molecules, indicating that capsids are trapped inside. Understanding the regulation of adenovirus morphogenesis is not only of interest to cell biologists but is also key to define novel drug targets as well as to optimize adenoviruses as tools for gene therapy. While early steps of the adenovirus ‘life cycle’ are well understood, it is currently debated how, when and where capsid components associate with viral DNA. Here we used a combination of imaging methods to detail virus-induced spatiotemporal changes at late stages of infection. We found that HAdV5 induces a structured, membrane-less nuclear compartment. In this compartment capsids are closely packed within a honeycomb-like organization of replicated DNA, such that the newly formed particles appear to be trapped and show very little motility. Interestingly, we found a clear discrepancy between immunostaining and fluorescent fusion tagging, indicating a limited penetration of immunostains into this compartment. Since other pathogens induce similar compartments during replication, interpretation of immunostaining data requires careful evaluation.
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Affiliation(s)
- Søren Pfitzner
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Center for Structural Systems Biology, Hamburg, Germany
| | - Helga Hofmann-Sieber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Jens B. Bosse
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Center for Structural Systems Biology, Hamburg, Germany
- RESIST Cluster of Excellence, Hannover Medical School, Germany
| | - Linda E. Franken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Center for Structural Systems Biology, Hamburg, Germany
| | - Kay Grünewald
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Center for Structural Systems Biology, Hamburg, Germany
- Universität Hamburg, Institute for Biochemistry and Molecular Biology, Hamburg, Germany
| | - Thomas Dobner
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail:
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45
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Xu J, Xia K, Li P, Qian C, Li Y, Liang X. Functional investigation of the chromosomal ccdAB and hipAB operon in Escherichia coli Nissle 1917. Appl Microbiol Biotechnol 2020; 104:6731-6747. [PMID: 32535695 PMCID: PMC7293176 DOI: 10.1007/s00253-020-10733-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/23/2020] [Accepted: 06/07/2020] [Indexed: 12/31/2022]
Abstract
Toxin-antitoxin systems (TASs) have attracted much attention due to their important physiological functions. These small genetic factors have been widely studied mostly in commensal Escherichia coli strains, whereas the role of TASs in the probiotic E. coli Nissle 1917 (EcN) is still elusive. Here, the physiological role of chromosomally encoded type II TASs in EcN was examined. We showed that gene pair ECOLIN_00240-ECOLIN_00245 and ECOLIN_08365-ECOLIN_08370 were two functional TASs encoding CcdAB and HipAB, respectively. The homologs of CcdAB and HipAB were more conserved in E. coli species belonging to pathogenic groups, suggesting their important roles in EcN. CRISPRi-mediated repression of ccdAB and hipAB significantly reduced the biofilm formation of EcN in the stationary phase. Moreover, ccdAB and hipAB were shown to be responsible for the persister formation in EcN. Biofilm and persister formation of EcN controlled by the ccdAB and hipAB were associated with the expression of genes involved in DNA synthesis, SOS response, and stringent response. Besides, CRISPRi was proposed to be an efficient tool in annotating multiple TASs simultaneously. Collectively, our results advance knowledge and understanding of the role of TASs in EcN, which will enhance the utility of EcN in probiotic therapy. Key points • Two TASs in EcN were identified as hipAB and ccdAB. • Knockdown of HipAB and CcdAB resulted in decreased biofilm formation of EcN. • Transcriptional silencing of hipAB and ccdAB affected the persister formation of EcN. • An attractive link between TASs and stress response was unraveled in EcN. • CRISPRi afforded a fast and in situ annotation of multiple TASs simultaneously.
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Affiliation(s)
- Jun Xu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Kai Xia
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Pinyi Li
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Chenggong Qian
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Yudong Li
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Xinle Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
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46
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Li M, Chen J, Wang Y, Liu J, Huang J, Chen N, Zheng P, Sun J. Efficient Multiplex Gene Repression by CRISPR-dCpf1 in Corynebacterium glutamicum. Front Bioeng Biotechnol 2020; 8:357. [PMID: 32391351 PMCID: PMC7193084 DOI: 10.3389/fbioe.2020.00357] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/31/2020] [Indexed: 01/14/2023] Open
Abstract
Corynebacterium glutamicum is an important workhorse for industrial production of diversiform bioproducts. Multiplex control of metabolic pathway genes is crucial for maximizing biosynthesis of desired products. However, few tools for simultaneously regulating multiple genes in C. glutamicum have been reported. Here, a CRISPR-dCpf1-based multiplex gene repression system was developed for C. glutamicum. This system successfully repressed two fluorescent reporter genes simultaneously by expressing a dCpf1 (E1006A, D917A) and a designed single crRNA array. To demonstrate applications of this CRISPR-dCpf1 system in metabolic engineering, we applied this system to repress four genes involved in lysine biosynthesis (gltA, pck, pgi, and hom) with a single array, which increased the lysine titer and yield for over 4.0-fold. Quantitative PCR demonstrated that transcription of all the four endogenous target genes were repressed by over 90%. Thus, the CRISPR-dCpf1 system is a simple and effective technique for multiplex gene repression in C. glutamicum and holds promise for metabolic engineering of C. glutamicum to produce valuable chemicals and fuels.
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Affiliation(s)
- Mingyue Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingwen Huang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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47
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Improvement of the dP-nucleoside-mediated herpes simplex virus thymidine kinase negative-selection system by manipulating dP metabolism genes. J Biosci Bioeng 2020; 130:121-127. [PMID: 32229092 DOI: 10.1016/j.jbiosc.2020.03.002] [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: 01/07/2020] [Revised: 02/14/2020] [Accepted: 03/03/2020] [Indexed: 11/21/2022]
Abstract
A variety of positive/negative selection systems have been exploited as genome engineering tools and screening platforms for genetic switches. While numerous positive-selection systems are available, only a handful of negative-selection systems are useful for such applications. We previously reported a powerful negative-selection system using herpes simplex virus thymidine kinase (HsvTK) and the mutagenic nucleoside analog 6-(β-d-2-deoxyribofuranosyl)-3,4-dihydro-8H-pyrimido [4,5-c][1,2] oxazin-7-one (dP). Upon addition of 1000 nM dP, cells expressing HsvTK quickly die, with unprecedented efficacy. However, this selection procedure elevates the spontaneous mutation rate of the host cells by 10-fold due to the mutagenic nature of dP. To decrease the operative concentration of dP required for negative selection, we systematically created the strains of Escherichia coli either by removing or overexpressing genes involved in DNA/RNA metabolism. We found that over-expression of NupC and NupG (nucleoside uptake-related inner membrane transporters), Tsx (outer membrane transporter), NdK (nucleotide kinase) sensitized E. coli cells to dP. Simultaneous overexpression of these three genes (ndk-nupC-tsx) significantly improved the dP-sensitivity of E. coli, lowering the necessary operative concentration of dP for negative selection by 10-fold. This enabled robust and selective elimination of strains harboring chromosomally-encoded hsvtk simply by adding as low as 100 nM dP, which causes only a modest increase in the spontaneous mutation frequency as compared to the cells without hsvtk.
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SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly. Nat Struct Mol Biol 2020; 27:260-273. [PMID: 32123389 PMCID: PMC7096898 DOI: 10.1038/s41594-020-0385-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/23/2020] [Indexed: 02/08/2023]
Abstract
SRSF7 is an essential RNA-binding protein whose misexpression promotes cancer. Here, we describe how SRSF7 maintains its protein homeostasis in murine P19 cells using an intricate negative feedback mechanism. SRSF7 binding to its premessenger RNA promotes inclusion of a poison cassette exon and transcript degradation via nonsense-mediated decay (NMD). However, elevated SRSF7 levels inhibit NMD and promote translation of two protein halves, termed Split-ORFs, from the bicistronic SRSF7-PCE transcript. The first half acts as dominant-negative isoform suppressing poison cassette exon inclusion and instead promoting the retention of flanking introns containing repeated SRSF7 binding sites. Massive SRSF7 binding to these sites and its oligomerization promote the assembly of large nuclear bodies, which sequester SRSF7 transcripts at their transcription site, preventing their export and restoring normal SRSF7 protein levels. We further show that hundreds of human and mouse NMD targets, especially RNA-binding proteins, encode potential Split-ORFs, some of which are expressed under specific cellular conditions.
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Huang C, Ding T, Wang J, Wang X, Guo L, Wang J, Zhu L, Bi C, Zhang X, Ma X, Huo YX. CRISPR-Cas9-assisted native end-joining editing offers a simple strategy for efficient genetic engineering in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:8497-8509. [PMID: 31501938 DOI: 10.1007/s00253-019-10104-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/07/2019] [Accepted: 08/26/2019] [Indexed: 12/17/2022]
Abstract
Unlike eukaryotes, prokaryotes are less proficient in homologous recombination (HR) and non-homologous end-joining (NHEJ). All existing genomic editing methods for Escherichia coli (E. coli) rely on exogenous HR or NHEJ systems to repair DNA double-strand breaks (DSBs). Although an E. coli native end-joining (ENEJ) system has been reported, its potential in genetic engineering has not yet been explored. Here, we present a CRISPR-Cas9-assisted native end-joining editing and show that ENEJ-dependent DNA repair can be used to conduct rapid and efficient deletion of chromosome fragments up to 83 kb or gene inactivation. Moreover, the positive rate and editing efficiency are independent of high-efficiency competent cells. The method requires neither exogenous DNA repair systems nor introduced editing template. The Cas9-sgRNA complex is the only foreign element in this method. This study is the first successful engineering effort to utilize ENEJ mechanism in genomic editing and provides an effective strategy for genetic engineering in bacteria that are inefficient in HR and NHEJ.
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Affiliation(s)
- Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Tingting Ding
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China.,UCLA (Suzhou) Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, People's Republic of China
| | - Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Xueqin Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Jialei Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Lin Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China. .,UCLA (Suzhou) Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, People's Republic of China.
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Abstract
Recombineering inserts PCR products into DNA using homologous recombination. A pair of short homology arms (50 base pairs) on the ends of a PCR cassette target the cassette to its intended location. These homology arms can be easily introduced as 5' primer overhangs during the PCR reaction. The flexibility to choose almost any pair of homology arms enables the precise modification of virtually any DNA for purposes of sequence deletion, replacement, insertion, or point mutation. Recombineering often offers significant advantages relative to previous homologous recombination methods that require the construction of cassettes with large homology arms, and relative to traditional cloning methods that become intractable for large plasmids or DNA sequences. However, the tremendous number of variables, options, and pitfalls that can be encountered when designing and performing a recombineering protocol for the first time introduce barriers that can make recombineering a challenging technique for new users to adopt. This article focuses on three recombineering protocols we have found to be particularly robust, providing a detailed guide for choosing the simplest recombineering method for a given application and for performing and troubleshooting experiments. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Louis J Papa
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts
| | - Matthew D Shoulders
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts
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